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Yang C, Zheng YX, Gu HY, Chen H, Li W, Li F, Bi YW, Chen J, Wang FK, Sun QQ, Meng HB, Wu ZH, Yu S, Gu J, Cheng Y. Genomic characteristics, virulence potential, antimicrobial resistance profiles, and phylogenetic insights into Nocardia cyriacigeorgica. Ann Clin Microbiol Antimicrob 2025; 24:22. [PMID: 40188140 PMCID: PMC11972502 DOI: 10.1186/s12941-025-00791-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2025] [Accepted: 03/27/2025] [Indexed: 04/07/2025] Open
Abstract
BACKGROUND Nocardia cyriacigeorgica, an opportunistic pathogen, is increasingly implicated in human infections. This pathogen predominantly causes pulmonary infections, leading to acute, subacute, or chronic necrotizing suppurative lesions, in severe cases, may progress to disseminated infections. Effective clinical diagnosis, prevention, and treatment strategies require a thorough understanding of its biological characteristics and pathogenic mechanisms. However, despite the rising incidence of nocardial diseases, research on the pathogenicity of N. cyriacigeorgica remains limited, primarily focusing on case reports and epidemiological studies. This study aimed to provide a comprehensive analysis of the genomic features, phylogenetic relationships, antimicrobial resistance profiles, and candidate virulence factors of N. cyriacigeorgica strains to inform future investigations into its pathogenesis. METHODS Whole-genome sequencing was conducted on five N. cyriacigeorgica strains isolated from patients with pulmonary infection at our hospital. This analysis utilized a combination of second-generation Illumina HiSeq and third-generation PacBio sequencing technologies. Additionally, publicly available genomic data from 58 strains in the National Center Biotechnology Information database were integrated, resulting in a dataset of 63 genomes. These genomes were subjected to comparative genomic analyses, including phylogenetic reconstruction, pan-genome evaluation, and gene distribution assessments. RESULTS Phylogenetic analysis identified five major clades within N. cyriacigeorgica. ANI analysis further subdivided clade B into five distinct subgroups. Pan-genome analysis revealed clade-specific orthogroups in the distribution of genes assigned to Clusters of Orthologous Groups, with clade A containing the highest number of clade-specific gene families. Comparative genomic analysis uncovered several potential pathogenic genes implicated in host cell invasion, phagosomal maturation arrest, and intracellular survival within macrophages, which were conserved across all analyzed strains. Notable differences in the distribution of enterobactin-encoding genes were observed among the clades. The mce3C gene also displayed variable distributions across clades; however, no correlation was established between its presence and strain source. Among the 63 strains, 27 were found to harbor both mce3C and mce4F genes, which were categorized into five distinct patterns. Furthermore, antibiotic resistance genes, including VanSO, VanRO, erm(O)-Irm, srmB, ermH, bcl, bla1, and cmIR, demonstrated clade-specific distribution patterns. Notably, the genes erm(O)-Irm, srmB, and ermH were associated with the isolation origin of the strains. CONCLUSIONS This study provides a comprehensive evaluation of the genomic characteristics, potential virulence factors, antimicrobial resistance genes, and phylogenetic relationships of N. cyriacigeorgica. The findings offer valuable insights into the mechanisms underlying intracellular survival, replication within macrophages, and pathogen-host interactions in N. cyriacigeorgica infections. These results establish a foundation for future research into the pathogenesis and clinical management of N. cyriacigeorgica.
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Affiliation(s)
- Chen Yang
- National Engineering Research Center of Immunological ProductsDepartment of Microbiology and Biochemical PharmacyCollege of Pharmacy, Army Medical University, Chongqing, 400038, China
| | - Yue-Xin Zheng
- Department of General Surgery, The Sixth Medical Center of PLA General Hospital, Beijing, 100048, China
| | - Hong-Yi Gu
- Department of Public Affairs Management, Tianjin Medical University, Tianjin, 300203, China
| | - Hong Chen
- Department of Clinical Pharmacy, Bethune International Peace Hospital, Shijiazhuang, 050081, China
| | - Wei Li
- Department of Clinical Laboratory, Bethune International Peace Hospital, Shijiazhuang, 050081, China
| | - Fang Li
- Department of Clinical Laboratory, Bethune International Peace Hospital, Shijiazhuang, 050081, China
| | - Yu-Wang Bi
- Department of Information, Bethune International Peace Hospital, Shijiazhuang, 050081, China
| | - Jing Chen
- Department of Clinical Laboratory, Bethune International Peace Hospital, Shijiazhuang, 050081, China
| | - Fu-Kun Wang
- Department of Clinical Laboratory, Bethune International Peace Hospital, Shijiazhuang, 050081, China
| | - Qing-Qing Sun
- Department of Basic Medical Laboratory, Bethune International Peace Hospital, Shijiazhuang, 050081, China
| | - Han-Bing Meng
- Department of Basic Medical Laboratory, Bethune International Peace Hospital, Shijiazhuang, 050081, China
| | - Zuo-Hao Wu
- Department of Clinical Laboratory, Bethune International Peace Hospital, Shijiazhuang, 050081, China
| | - Shu Yu
- Department of Laboratory Medicine, People's Hospital of Chongqing Hechuan, Chongqing, 401520, China.
| | - Jiang Gu
- National Engineering Research Center of Immunological ProductsDepartment of Microbiology and Biochemical PharmacyCollege of Pharmacy, Army Medical University, Chongqing, 400038, China.
| | - Yan Cheng
- Department of Clinical Laboratory, Bethune International Peace Hospital, Shijiazhuang, 050081, China.
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Karmakar M, Sur S. Unlocking the Mycobacteroides abscessus pan-genome using computational tools: insights into evolutionary dynamics and lifestyle. Antonie Van Leeuwenhoek 2024; 118:30. [PMID: 39579164 DOI: 10.1007/s10482-024-02042-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Accepted: 11/15/2024] [Indexed: 11/25/2024]
Abstract
Mycobacteroides abscessus is a non-tuberculous mycobacteria implicated in causing lung infections. It is difficult to control owing to resistance to antibiotics and disinfectants. This work was aimed at comprehending: the pan-genome architecture, evolutionary dynamics, and functionalities of pan-genome components linked to COGs and KEGG. Around 2802 core genes were present in each strain of the M. abscessus genome. The number of accessory genes ranged from 1615 to 2481. The open pan-genome of M. abscessus was attributed to the accessory genes underlining its adaptability in the host. Phylogenetic analysis revealed cluster-based relationships and highlighted factors shaping variability and adaptive capabilities. Transcription, metabolism, and pathogenic genes were vital for M. abscessus lifestyle. The accessory genes contributed to the diverse metabolic capability. The incidence of a significant portion of secondary metabolite biosynthesis genes provided insights for investigating their biosynthetic gene clusters. Additionally, a high proportion of xenobiotic biodegradation genes highlighted potential metabolic capabilities. In silico screening identified a potential vaccine candidate among hypothetical proteins in COGs. Functional analysis of M. abscessus pan-genome components unveiled factors associated with virulence, pathogenicity, infection establishment, persistence, and resistance. Notable amongst them were: MMPL family transporters, PE-PPE domain-containing proteins, TetR family transcriptional regulators, ABC transporters, Type-I, II, III, VII secretion proteins, DUF domain-containing proteins, cytochrome P450, VapC family toxin, virulence factor Mce family protein, type II toxin-antitoxin system. Overall, these results enhanced understanding of the metabolism, host-pathogen dynamics, pathogenic lifestyle, and adaptations. This will facilitate further investigations for combating infections and designing suitable therapies.
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Affiliation(s)
- Mistu Karmakar
- Department of Botany, Ramananda College, Life Sciences Block, Bishnupur, West Bengal, 722122, India
| | - Saubashya Sur
- Department of Botany, Ramananda College, Life Sciences Block, Bishnupur, West Bengal, 722122, India.
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Blake R, Jensen K, Mabbott N, Hope J, Stevens J. The role of Mce proteins in Mycobacterium avium paratuberculosis infection. Sci Rep 2024; 14:14964. [PMID: 38942800 PMCID: PMC11213854 DOI: 10.1038/s41598-024-65592-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 06/21/2024] [Indexed: 06/30/2024] Open
Abstract
Mycobacterium avium subspecies paratuberculosis (MAP) is the causative agent of Johne's Disease, a chronic granulomatous enteritis of ruminants. MAP establishes an infection in the host via the small intestine. This requires the bacterium to adhere to, and be internalised by, cells of the intestinal tract. The effector molecules expressed by MAP for this purpose remain to be fully identified and understood. Mammalian cell entry (mce) proteins have been shown to enable other Mycobacterial species to attach to and invade host epithelial cells. Here, we have expressed Mce1A, Mce1D, Mce3C and Mce4A proteins derived from MAP on the surface of a non-invasive Escherichia coli to characterise their role in the initial interaction between MAP and the host. To this end, expression of mce1A was found to significantly increase the ability of the E. coli to attach and survive intracellularly in human monocyte-like THP-1 cells, whereas expression of mce1D was found to significantly increase attachment and invasion of E. coli to bovine epithelial cell-like MDBK cells, implying cell-type specificity. Furthermore, expression of Mce1A and Mce1D on the surface of a previously non-invasive E. coli enhanced the ability of the bacterium to infect 3D bovine basal-out enteroids. Together, our data contributes to our understanding of the effector molecules utilised by MAP in the initial interaction with the host, and may provide potential targets for therapeutic intervention.
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Affiliation(s)
- Rosemary Blake
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.
| | - Kirsty Jensen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Neil Mabbott
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Jayne Hope
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Joanne Stevens
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
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Poonawala H, Zhang Y, Kuchibhotla S, Green AG, Cirillo DM, Di Marco F, Spitlaeri A, Miotto P, Farhat MR. Transcriptomic responses to antibiotic exposure in Mycobacterium tuberculosis. Antimicrob Agents Chemother 2024; 68:e0118523. [PMID: 38587412 PMCID: PMC11064486 DOI: 10.1128/aac.01185-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 03/06/2024] [Indexed: 04/09/2024] Open
Abstract
Transcriptional responses in bacteria following antibiotic exposure offer insights into antibiotic mechanism of action, bacterial responses, and characterization of antimicrobial resistance. We aimed to define the transcriptional antibiotic response (TAR) in Mycobacterium tuberculosis (Mtb) isolates for clinically relevant drugs by pooling and analyzing Mtb microarray and RNA-seq data sets. We generated 99 antibiotic transcription profiles across 17 antibiotics, with 76% of profiles generated using 3-24 hours of antibiotic exposure and 49% within one doubling of the WHO antibiotic critical concentration. TAR genes were time-dependent, and largely specific to the antibiotic mechanism of action. TAR signatures performed well at predicting antibiotic exposure, with the area under the receiver operating curve (AUC) ranging from 0.84-1.00 (TAR <6 hours of antibiotic exposure) and 0.76-1.00 (>6 hours of antibiotic exposure) for upregulated genes and 0.57-0.90 and 0.87-1.00, respectfully, for downregulated genes. This work desmonstrates that transcriptomics allows for the assessment of antibiotic activity in Mtb within 6 hours of exposure.
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Affiliation(s)
- Husain Poonawala
- Department of Medicine and Department of Pathology and Laboratory Medicine, Tufts Medical Center, Boston, Massachusetts, USA
- Department of Medicine and Department of Anatomic and Clinical Pathology, Tufts University School of Medicine, Boston, Massachusetts, USA
- Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance, Boston, Massachusetts, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Yu Zhang
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Anna G. Green
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Federico Di Marco
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Andrea Spitlaeri
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milan, Italy
| | - Paolo Miotto
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Maha R. Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
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Dutta A, Kanaujia SP. The Structural Features of MlaD Illuminate its Unique Ligand-Transporting Mechanism and Ancestry. Protein J 2024; 43:298-315. [PMID: 38347327 DOI: 10.1007/s10930-023-10179-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/22/2023] [Indexed: 05/01/2024]
Abstract
The membrane-associated solute-binding protein (SBP) MlaD of the maintenance of lipid asymmetry (Mla) system has been reported to help the transport of phospholipids (PLs) between the outer and inner membranes of Gram-negative bacteria. Despite the availability of structural information, the molecular mechanism underlying the transport of PLs and the ancestry of the protein MlaD remain unclear. In this study, we report the crystal structures of the periplasmic region of MlaD from Escherichia coli (EcMlaD) at a resolution range of 2.3-3.2 Å. The EcMlaD protomer consists of two distinct regions, viz. N-terminal β-barrel fold consisting of seven strands (referred to as MlaD domain) and C-terminal α-helical domain (HD). The protein EcMlaD oligomerizes to give rise to a homo-hexameric ring with a central channel that is hydrophobic and continuous with a variable diameter. Interestingly, the structural analysis revealed that the HD, instead of the MlaD domain, plays a critical role in determining the oligomeric state of the protein. Based on the analysis of available structural information, we propose a working mechanism of PL transport, viz. "asymmetric protomer movement (APM)". Wherein half of the EcMlaD hexamer would rise in the periplasmic side along with an outward movement of pore loops, resulting in the change of the central channel geometry. Furthermore, this study highlights that, unlike typical SBPs, EcMlaD possesses a fold similar to EF/AMT-type beta(6)-barrel and a unique ancestry. Altogether, the findings firmly establish EcMlaD to be a non-canonical SBP with a unique ligand-transport mechanism.
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Affiliation(s)
- Angshu Dutta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Shankar Prasad Kanaujia
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India.
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Sturm A, Sun P, Avila-Pacheco J, Clatworthy AE, Bloom-Ackermann Z, Wuo MG, Gomez JE, Jin S, Clish CB, Kiessling LL, Hung DT. Genetic factors affecting storage and utilization of lipids during dormancy in Mycobacterium tuberculosis. mBio 2024; 15:e0320823. [PMID: 38236034 PMCID: PMC10865790 DOI: 10.1128/mbio.03208-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024] Open
Abstract
Mycobacterium tuberculosis (Mtb) can adopt a non-growing dormant state during infection that may be critical to both active and latent tuberculosis. During dormancy, Mtb is widely tolerant toward antibiotics, a significant obstacle in current anti-tubercular drug regimens, and retains the ability to persist in its environment. We aimed to identify novel mechanisms that permit Mtb to survive dormancy in an in vitro carbon starvation model using transposon insertion sequencing and gene expression analysis. We identified a previously uncharacterized component of the lipid transport machinery, omamC, which was upregulated and required for survival during carbon starvation. We show that OmamC plays a role both in increasing fatty acid stores during growth in rich media and enhancing fatty acid utilization during starvation. Besides its involvement in lipid metabolism, OmamC levels affected the expression of the anti-anti-sigma factor rv0516c and other genes to improve Mtb survival during carbon starvation and increase its tolerance toward rifampicin, a first-line drug effective against non-growing Mtb. Importantly, we show that Mtb can be eradicated during carbon starvation, in an OmamC-dependent manner, by inhibiting lipid metabolism with the lipase inhibitor tetrahydrolipstatin. This work casts new light into the survival processes of non-replicating, drug-tolerant Mtb by identifying new proteins involved in lipid metabolism required for the survival of dormant bacteria and exposing a potential vulnerability that could be exploited for antibiotic discovery.IMPORTANCETuberculosis is a global threat, with ~10 million yearly active cases. Many more people, however, live with "latent" infection, where Mycobacterium tuberculosis survives in a non-replicative form. When latent bacteria activate and regrow, they elicit immune responses and result in significant host damage. Replicating and non-growing bacilli can co-exist; however, non-growing bacteria are considerably less sensitive to antibiotics, thus complicating treatment by necessitating long treatment durations. Here, we sought to identify genes important for bacterial survival in this non-growing state using a carbon starvation model. We found that a previously uncharacterized gene, omamC, is involved in storing and utilizing fatty acids as bacteria transition between these two states. Importantly, inhibiting lipid metabolism using a lipase inhibitor eradicates non-growing bacteria. Thus, targeting lipid metabolism may be a viable strategy for treating the non-growing population in strategies to shorten treatment durations of tuberculosis.
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Affiliation(s)
- Alexander Sturm
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, Massachusetts, USA
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Penny Sun
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, Massachusetts, USA
| | | | - Anne E. Clatworthy
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, Massachusetts, USA
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Zohar Bloom-Ackermann
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, Massachusetts, USA
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael G. Wuo
- Department of Chemistry, MIT, Cambridge, Massachusetts, USA
| | - James E. Gomez
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, Massachusetts, USA
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Soomin Jin
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, Massachusetts, USA
| | - Clary B. Clish
- Metabolomics Platform, Broad Institute, Cambridge, Massachusetts, USA
| | | | - Deborah T. Hung
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, Massachusetts, USA
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
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7
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Alexander LT, Durairaj J, Kryshtafovych A, Abriata LA, Bayo Y, Bhabha G, Breyton C, Caulton SG, Chen J, Degroux S, Ekiert DC, Erlandsen BS, Freddolino PL, Gilzer D, Greening C, Grimes JM, Grinter R, Gurusaran M, Hartmann MD, Hitchman CJ, Keown JR, Kropp A, Kursula P, Lovering AL, Lemaitre B, Lia A, Liu S, Logotheti M, Lu S, Markússon S, Miller MD, Minasov G, Niemann HH, Opazo F, Phillips GN, Davies OR, Rommelaere S, Rosas‐Lemus M, Roversi P, Satchell K, Smith N, Wilson MA, Wu K, Xia X, Xiao H, Zhang W, Zhou ZH, Fidelis K, Topf M, Moult J, Schwede T. Protein target highlights in CASP15: Analysis of models by structure providers. Proteins 2023; 91:1571-1599. [PMID: 37493353 PMCID: PMC10792529 DOI: 10.1002/prot.26545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 06/15/2023] [Indexed: 07/27/2023]
Abstract
We present an in-depth analysis of selected CASP15 targets, focusing on their biological and functional significance. The authors of the structures identify and discuss key protein features and evaluate how effectively these aspects were captured in the submitted predictions. While the overall ability to predict three-dimensional protein structures continues to impress, reproducing uncommon features not previously observed in experimental structures is still a challenge. Furthermore, instances with conformational flexibility and large multimeric complexes highlight the need for novel scoring strategies to better emphasize biologically relevant structural regions. Looking ahead, closer integration of computational and experimental techniques will play a key role in determining the next challenges to be unraveled in the field of structural molecular biology.
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Affiliation(s)
- Leila T. Alexander
- BiozentrumUniversity of BaselBaselSwitzerland
- Computational Structural BiologySIB Swiss Institute of BioinformaticsBaselSwitzerland
| | - Janani Durairaj
- BiozentrumUniversity of BaselBaselSwitzerland
- Computational Structural BiologySIB Swiss Institute of BioinformaticsBaselSwitzerland
| | | | - Luciano A. Abriata
- School of Life SciencesÉcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Yusupha Bayo
- Department of BiosciencesUniversity of MilanoMilanItaly
- IBBA‐CNR Unit of MilanoInstitute of Agricultural Biology and BiotechnologyMilanItaly
| | - Gira Bhabha
- Department of Cell BiologyNew York University School of MedicineNew YorkNew YorkUSA
| | | | | | - James Chen
- Department of Cell BiologyNew York University School of MedicineNew YorkNew YorkUSA
| | | | - Damian C. Ekiert
- Department of Cell BiologyNew York University School of MedicineNew YorkNew YorkUSA
- Department of MicrobiologyNew York University School of MedicineNew YorkNew YorkUSA
| | - Benedikte S. Erlandsen
- Wellcome Centre for Cell BiologyInstitute of Cell Biology, University of EdinburghEdinburghUK
| | - Peter L. Freddolino
- Department of Biological Chemistry, Computational Medicine and BioinformaticsUniversity of MichiganAnn ArborMichiganUSA
| | - Dominic Gilzer
- Department of ChemistryBielefeld UniversityBielefeldGermany
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
- Securing Antarctica's Environmental FutureMonash UniversityClaytonVictoriaAustralia
- Centre to Impact AMRMonash UniversityClaytonVictoriaAustralia
- ARC Research Hub for Carbon Utilisation and RecyclingMonash UniversityClaytonVictoriaAustralia
| | - Jonathan M. Grimes
- Division of Structural Biology, Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Rhys Grinter
- Department of Microbiology, Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
- Centre for Electron Microscopy of Membrane ProteinsMonash Institute of Pharmaceutical SciencesParkvilleVictoriaAustralia
| | - Manickam Gurusaran
- Wellcome Centre for Cell BiologyInstitute of Cell Biology, University of EdinburghEdinburghUK
| | - Marcus D. Hartmann
- Max Planck Institute for BiologyTübingenGermany
- Interfaculty Institute of Biochemistry, University of TübingenTübingenGermany
| | - Charlie J. Hitchman
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLeicesterUK
| | - Jeremy R. Keown
- Division of Structural Biology, Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Ashleigh Kropp
- Department of Microbiology, Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
| | - Petri Kursula
- Department of BiomedicineUniversity of BergenBergenNorway
- Faculty of Biochemistry and Molecular Medicine & Biocenter OuluUniversity of OuluOuluFinland
| | | | - Bruno Lemaitre
- School of Life SciencesÉcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Andrea Lia
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLeicesterUK
- ISPA‐CNR Unit of LecceInstitute of Sciences of Food ProductionLecceItaly
| | - Shiheng Liu
- Department of Microbiology, Immunology, and Molecular GeneticsUniversity of CaliforniaLos AngelesCaliforniaUSA
- California NanoSystems InstituteUniversity of CaliforniaLos AngelesCaliforniaUSA
| | - Maria Logotheti
- Max Planck Institute for BiologyTübingenGermany
- Interfaculty Institute of Biochemistry, University of TübingenTübingenGermany
- Present address:
Institute of BiochemistryUniversity of GreifswaldGreifswaldGermany
| | - Shuze Lu
- Lanzhou University School of Life SciencesLanzhouChina
| | | | | | - George Minasov
- Department of Microbiology‐ImmunologyNorthwestern Feinberg School of MedicineChicagoIllinoisUSA
| | | | - Felipe Opazo
- NanoTag Biotechnologies GmbHGöttingenGermany
- Institute of Neuro‐ and Sensory PhysiologyUniversity of Göttingen Medical CenterGöttingenGermany
- Center for Biostructural Imaging of Neurodegeneration (BIN)University of Göttingen Medical CenterGöttingenGermany
| | - George N. Phillips
- Department of BiosciencesRice UniversityHoustonTexasUSA
- Department of ChemistryRice UniversityHoustonTexasUSA
| | - Owen R. Davies
- Wellcome Centre for Cell BiologyInstitute of Cell Biology, University of EdinburghEdinburghUK
| | - Samuel Rommelaere
- School of Life SciencesÉcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Monica Rosas‐Lemus
- Department of Microbiology‐ImmunologyNorthwestern Feinberg School of MedicineChicagoIllinoisUSA
- Present address:
Department of Molecular Genetics and MicrobiologyUniversity of New MexicoAlbuquerqueNew MexicoUSA
| | - Pietro Roversi
- IBBA‐CNR Unit of MilanoInstitute of Agricultural Biology and BiotechnologyMilanItaly
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLeicesterUK
| | - Karla Satchell
- Department of Microbiology‐ImmunologyNorthwestern Feinberg School of MedicineChicagoIllinoisUSA
| | - Nathan Smith
- Department of Biochemistry and the Redox Biology CenterUniversity of NebraskaLincolnNebraskaUSA
| | - Mark A. Wilson
- Department of Biochemistry and the Redox Biology CenterUniversity of NebraskaLincolnNebraskaUSA
| | - Kuan‐Lin Wu
- Department of ChemistryRice UniversityHoustonTexasUSA
| | - Xian Xia
- Department of Microbiology, Immunology, and Molecular GeneticsUniversity of CaliforniaLos AngelesCaliforniaUSA
- California NanoSystems InstituteUniversity of CaliforniaLos AngelesCaliforniaUSA
| | - Han Xiao
- Department of BiosciencesRice UniversityHoustonTexasUSA
- Department of ChemistryRice UniversityHoustonTexasUSA
- Department of BioengineeringRice UniversityHoustonTexasUSA
| | - Wenhua Zhang
- Lanzhou University School of Life SciencesLanzhouChina
| | - Z. Hong Zhou
- Department of Microbiology, Immunology, and Molecular GeneticsUniversity of CaliforniaLos AngelesCaliforniaUSA
- California NanoSystems InstituteUniversity of CaliforniaLos AngelesCaliforniaUSA
| | | | - Maya Topf
- University Medical Center Hamburg‐Eppendorf (UKE)HamburgGermany
- Centre for Structural Systems BiologyLeibniz‐Institut für Virologie (LIV)HamburgGermany
| | - John Moult
- Department of Cell Biology and Molecular Genetics, Institute for Bioscience and Biotechnology ResearchUniversity of MarylandRockvilleMarylandUSA
| | - Torsten Schwede
- BiozentrumUniversity of BaselBaselSwitzerland
- Computational Structural BiologySIB Swiss Institute of BioinformaticsBaselSwitzerland
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8
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Kumar C, Shrivastava K, Singh A, Chauhan V, Giri A, Gupta S, Sharma NK, Bose M, Sharma S, Varma-Basil M. Expression of mammalian cell entry genes in clinical isolates of M. tuberculosis and the cell entry potential and immunological reactivity of the Rv0590A protein. Med Microbiol Immunol 2023; 212:407-419. [PMID: 37787822 DOI: 10.1007/s00430-023-00781-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/31/2023] [Indexed: 10/04/2023]
Abstract
Mammalian cell entry (mce) operons play a vital role in cell invasion and survival of M. tuberculosis. Of the mce genes, the function of Rv0590A is still unknown. The present study was performed to investigate the function and immunogenic properties of the protein Rv0590A. Human leukemia monocytic cell line (THP-1) derived macrophages were infected with M. tuberculosis H37Rv at 3, 6, and 24 h of infection. The maximum colony forming units (CFU) were observed at 6 h (p < 0.005), followed by 3 h after infection. M. tuberculosis H37Rv and clinical isolates representative of Delhi/CAS, EAI, Beijing, Haarlem and Euro-American-superlineage were included in the study for expression analysis of mce1A, mce2A, mce3A, mce4A, and Rv0590A genes. Maximum upregulation of all mce genes was observed at 3 h of infection. All the five clinical isolates and H37Rv upregulated Rv0590A at various time points. Macrophage infection with M. tuberculosis H37Rv-overexpressing Rv0590A gene showed higher intracellular CFU as compared to that of wild-type H37Rv. Further, purified Rv0590A protein stimulated the production of TNFα, IFNγ, and IL-10 in macrophages. Thus, Rv0590A was found to be involved in cell invasion and showed good immunological response.
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Affiliation(s)
- Chanchal Kumar
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, 110007, India
| | - Kamal Shrivastava
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, 110007, India
| | - Anupriya Singh
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, 110007, India
| | - Varsha Chauhan
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, 110007, India
- Maharshi Dayanand University, Rohtak, Haryana, India
| | - Astha Giri
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, 110007, India
- Deshbandhu College, University of Delhi, Delhi, India
| | - Shraddha Gupta
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, 110007, India
| | - Naresh Kumar Sharma
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, 110007, India
- University of Manitoba, Winnipeg, MB, Canada
| | - Mridula Bose
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, 110007, India
| | - Sadhna Sharma
- Department of Zoology, Miranda House, University of Delhi, Delhi, 110007, India
| | - Mandira Varma-Basil
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, 110007, India.
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9
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Maity D, Singh D, Bandhu A. Mce1R of Mycobacterium tuberculosis prefers long-chain fatty acids as specific ligands: a computational study. Mol Divers 2023; 27:2523-2543. [PMID: 36385433 DOI: 10.1007/s11030-022-10566-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 11/04/2022] [Indexed: 11/17/2022]
Abstract
The mce1 operon of Mycobacterium tuberculosis, which codes the Mce1 transporter, facilitates the transport of fatty acids. Fatty acids are one of the major sources for carbon and energy for the pathogen during its intracellular survival and pathogenicity. The mce1 operon is transcriptionally regulated by Mce1R, a VanR-type regulator, which could bind specific ligands and control the expression of the mce1 operon accordingly. This work reports computational identification of Mce1R-specific ligands. Initially by employing cavity similarity search algorithm by the ProBis server, the cavities of the proteins similar to that of Mce1R and the bound ligands were identified from which fatty acids were selected as the potential ligands. From the earlier-generated monomeric structure, the dimeric structure of Mce1R was then modeled by the GalaxyHomomer server and validated computationally to use in molecular docking and molecular dynamics simulation analysis. The fatty acid ligands were found to dock within the cavity of Mce1R and the docked complexes were subjected to molecular dynamics simulation to explore their stabilities and other dynamic properties. The data suggest that Mce1R preferably binds to long-chain fatty acids and undergoes distinct structural changes upon binding.
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Affiliation(s)
- Dipanwita Maity
- Department of Biotechnology, National Institute of Technology Warangal, Warangal, Telangana, 506004, India
| | - Dheeraj Singh
- Department of Biotechnology, National Institute of Technology Warangal, Warangal, Telangana, 506004, India
| | - Amitava Bandhu
- Department of Biotechnology, National Institute of Technology Warangal, Warangal, Telangana, 506004, India.
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Chen J, Fruhauf A, Fan C, Ponce J, Ueberheide B, Bhabha G, Ekiert DC. Structure of an endogenous mycobacterial MCE lipid transporter. Nature 2023; 620:445-452. [PMID: 37495693 DOI: 10.1038/s41586-023-06366-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 06/22/2023] [Indexed: 07/28/2023]
Abstract
To replicate inside macrophages and cause tuberculosis, Mycobacterium tuberculosis must scavenge a variety of nutrients from the host1,2. The mammalian cell entry (MCE) proteins are important virulence factors in M. tuberculosis1,3, where they are encoded by large gene clusters and have been implicated in the transport of fatty acids4-7 and cholesterol1,4,8 across the impermeable mycobacterial cell envelope. Very little is known about how cargos are transported across this barrier, and it remains unclear how the approximately ten proteins encoded by a mycobacterial mce gene cluster assemble to transport cargo across the cell envelope. Here we report the cryo-electron microscopy (cryo-EM) structure of the endogenous Mce1 lipid-import machine of Mycobacterium smegmatis-a non-pathogenic relative of M. tuberculosis. The structure reveals how the proteins of the Mce1 system assemble to form an elongated ABC transporter complex that is long enough to span the cell envelope. The Mce1 complex is dominated by a curved, needle-like domain that appears to be unrelated to previously described protein structures, and creates a protected hydrophobic pathway for lipid transport across the periplasm. Our structural data revealed the presence of a subunit of the Mce1 complex, which we identified using a combination of cryo-EM and AlphaFold2, and name LucB. Our data lead to a structural model for Mce1-mediated lipid import across the mycobacterial cell envelope.
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Affiliation(s)
- James Chen
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Alice Fruhauf
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Catherine Fan
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Jackeline Ponce
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University School of Medicine, New York, NY, USA
| | - Beatrix Ueberheide
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University School of Medicine, New York, NY, USA
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
- Department of Neurology, New York University School of Medicine, New York, NY, USA
| | - Gira Bhabha
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA.
| | - Damian C Ekiert
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA.
- Department of Microbiology, New York University School of Medicine, New York, NY, USA.
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11
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Structure sheds light on a lipid-transport machine in mycobacteria. Nature 2023:10.1038/d41586-023-02184-6. [PMID: 37495784 DOI: 10.1038/d41586-023-02184-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
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12
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Lima FR, Simões MMR, da Costa Manso GM, Toro DM, Antunes VMG, Felisbino GC, Dias GF, Riley LW, Arruda S, de Paula NA, Lugão HB, Perecin FAMC, Foss NT, Frade MAC. Serological testing for Hansen’s disease diagnosis: Clinical significance and performance of IgA, IgM, and IgG antibodies against Mce1A protein. Front Med (Lausanne) 2023; 10:1048759. [PMID: 37007773 PMCID: PMC10062478 DOI: 10.3389/fmed.2023.1048759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 02/24/2023] [Indexed: 03/18/2023] Open
Abstract
Hansen’s disease (HD) is an infectious, treatable, and chronic disease. It is the main cause of infectious peripheral neuropathy. Due to the current limitations of laboratory tests for the diagnosis of HD, early identification of infected contacts is an important factor that would allow us to control the magnitude of this disease in terms of world public health. Thus, a cross-sectional study was conducted in the Brazilian southeast with the objective of evaluating humoral immunity and describing the accuracy of the immunoassay based on IgA, IgM, and IgG antibodies against surface protein Mce1A of Mycobacterium, the predictive potential of these molecules, the clinical significance of positivity, and the ability to segregate new HD cases (NC; n = 200), contacts (HHC; n = 105), and healthy endemic controls (HEC; n = 100) as compared to α-PGL-I serology. α-Mce1A levels for all tested antibodies were significantly higher in NC and HHC than in HEC (p < 0.0001). The performance of the assay using IgA and IgM antibodies was rated as highly accurate (AUC > 0.85) for screening HD patients. Among HD patients (NC), positivity was 77.5% for IgA α-Mce1A ELISA, 76.5% for IgM, and 61.5% for IgG, while α-PGL-I serology showed only 28.0% positivity. Multivariate PLS-DA showed two defined clusters for the HEC and NC groups [accuracy = 0.95 (SD = 0.008)] and the HEC and HHC groups [accuracy = 0.93 (SD = 0.011)]. IgA was the antibody most responsible for clustering HHC as compared to NC and HEC, evidencing its usefulness for host mucosal immunity and as an immunological marker in laboratory tests. IgM is the key antibody for the clustering of NC patients. Positive results with high antibody levels indicate priority for screening, new clinical and laboratory evaluations, and monitoring of contacts, mainly with antibody indexes ≥2.0. In light of recent developments, the incorporation of new diagnostic technologies permits to eliminate the main gaps in the laboratory diagnosis of HD, with the implementation of tools of greater sensitivity and accuracy while maintaining satisfactory specificity.
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Affiliation(s)
- Filipe Rocha Lima
- Healing and Hansen’s Disease Laboratory, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and Hansen’s Disease, University Hospital, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Mateus Mendonça Ramos Simões
- Healing and Hansen’s Disease Laboratory, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and Hansen’s Disease, University Hospital, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Gabriel Martins da Costa Manso
- Healing and Hansen’s Disease Laboratory, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and Hansen’s Disease, University Hospital, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Diana Mota Toro
- Department of Clinical, Toxicological and, Bromatological Analyses, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Vanderson Mayron Granemann Antunes
- Healing and Hansen’s Disease Laboratory, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and Hansen’s Disease, University Hospital, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Giovani Cesar Felisbino
- Healing and Hansen’s Disease Laboratory, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and Hansen’s Disease, University Hospital, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Gabriela Ferreira Dias
- Healing and Hansen’s Disease Laboratory, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and Hansen’s Disease, University Hospital, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Lee W. Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, United States
| | - Sérgio Arruda
- Advanced Public Health Laboratory, Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Salvador, Brazil
| | - Natália Aparecida de Paula
- Healing and Hansen’s Disease Laboratory, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and Hansen’s Disease, University Hospital, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Helena Barbosa Lugão
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and Hansen’s Disease, University Hospital, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Fernanda André Martins Cruz Perecin
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and Hansen’s Disease, University Hospital, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Norma Tiraboschi Foss
- Healing and Hansen’s Disease Laboratory, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and Hansen’s Disease, University Hospital, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Marco Andrey Cipriani Frade
- Healing and Hansen’s Disease Laboratory, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and Hansen’s Disease, University Hospital, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- *Correspondence: Marco Andrey Cipriani Frade,
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Kavela S, Vyas P, CP J, Kushwaha SK, Majumdar SS, Faisal SM. Use of an Integrated Multi-Omics Approach To Identify Molecular Mechanisms and Critical Factors Involved in the Pathogenesis of Leptospira. Microbiol Spectr 2023; 11:e0313522. [PMID: 36853003 PMCID: PMC10100824 DOI: 10.1128/spectrum.03135-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 02/06/2023] [Indexed: 03/01/2023] Open
Abstract
Leptospirosis, a bacterial zoonosis caused by pathogenic Leptospira spp., is prevalent worldwide and has become a serious threat in recent years. Limited understanding of Leptospira pathogenesis and host response has hampered the development of effective vaccine and diagnostics. Although Leptospira is phagocytosed by innate immune cells, it resists its destruction, and the evading mechanism involved is unclear. In the present study, we used an integrative multi-omics approach to identify the critical molecular factors of Leptospira involved in pathogenesis during interaction with human macrophages. Transcriptomic and proteomic analyses were performed at 24 h postinfection of human macrophages (phorbol-12-myristate-13-acetate differentiated THP-1 cells) with the pathogenic Leptospira interrogans serovar Icterohaemorrhagiae strain RGA (LEPIRGA). Our results identified a total of 1,528 transcripts and 871 proteins that were significantly expressed with an adjusted P value of <0.05. The correlations between the transcriptomic and proteomic data were above average (r = 0.844), suggesting the role of the posttranscriptional processes during host interaction. The conjoint analysis revealed the expression of several virulence-associated proteins such as adhesins, invasins, and secretory and chemotaxis proteins that might be involved in various processes of attachment and invasion and as effectors during pathogenesis in the host. Further, the interaction of bacteria with the host cell (macrophages) was a major factor in the differential expression of these proteins. Finally, eight common differentially expressed RNA-protein pairs, predicted as virulent, outer membrane/extracellular proteins were validated by quantitative PCR. This is the first report using integrated multi-omics approach to identify critical factors involved in Leptospira pathogenesis. Validation of these critical factors may lead to the identification of target antigens for the development of improved diagnostics and vaccines against leptospirosis. IMPORTANCE Leptospirosis is a zoonotic disease of global importance. It is caused by a Gram-negative bacterial spirochete of the genus Leptospira. The current challenge is to detect the infection at early stage for treatment or to develop potent vaccines that can induce cross-protection against various pathogenic serovars. Understanding host-pathogen interactions is important to identify the critical factors involved in pathogenesis and host defense for developing improved vaccines and diagnostics. Utilizing an integrated multi-omics approach, our study provides important insight into the interaction of Leptospira with human macrophages and identifies a few critical factors (such as virulence-associated proteins) involved in pathogenesis. These factors can be exploited for the development of novel tools for the detection, treatment, or prevention of leptospirosis.
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Affiliation(s)
- Sridhar Kavela
- Laboratory of Vaccine Immunology, National Institute of Animal Biotechnology, Hyderabad, India
| | - Pallavi Vyas
- Laboratory of Vaccine Immunology, National Institute of Animal Biotechnology, Hyderabad, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Jusail CP
- Laboratory of Vaccine Immunology, National Institute of Animal Biotechnology, Hyderabad, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Sandeep K. Kushwaha
- Bioinformatics Lab, National Institute of Animal Biotechnology, Hyderabad, India
| | - Subeer S. Majumdar
- Gene and Protein Engineering Lab, National Institute of Animal Biotechnology, Hyderabad, India
| | - Syed M. Faisal
- Laboratory of Vaccine Immunology, National Institute of Animal Biotechnology, Hyderabad, India
- Regional Centre for Biotechnology, Faridabad, India
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14
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Alam MS, Guan P, Zhu Y, Zeng S, Fang X, Wang S, Yusuf B, Zhang J, Tian X, Fang C, Gao Y, Khatun MS, Liu Z, Hameed HMA, Tan Y, Hu J, Liu J, Zhang T. Comparative genome analysis reveals high-level drug resistance markers in a clinical isolate of Mycobacterium fortuitum subsp . fortuitum MF GZ001. Front Cell Infect Microbiol 2023; 12:1056007. [PMID: 36683685 PMCID: PMC9846761 DOI: 10.3389/fcimb.2022.1056007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 12/05/2022] [Indexed: 01/06/2023] Open
Abstract
Introduction Infections caused by non-tuberculosis mycobacteria are significantly worsening across the globe. M. fortuitum complex is a rapidly growing pathogenic species that is of clinical relevance to both humans and animals. This pathogen has the potential to create adverse effects on human healthcare. Methods The MF GZ001 clinical strain was collected from the sputum of a 45-year-old male patient with a pulmonary infection. The morphological studies, comparative genomic analysis, and drug resistance profiles along with variants detection were performed in this study. In addition, comparative analysis of virulence genes led us to understand the pathogenicity of this organism. Results Bacterial growth kinetics and morphology confirmed that MF GZ001 is a rapidly growing species with a rough morphotype. The MF GZ001 contains 6413573 bp genome size with 66.18 % high G+C content. MF GZ001 possesses a larger genome than other related mycobacteria and included 6156 protein-coding genes. Molecular phylogenetic tree, collinearity, and comparative genomic analysis suggested that MF GZ001 is a novel member of the M. fortuitum complex. We carried out the drug resistance profile analysis and found single nucleotide polymorphism (SNP) mutations in key drug resistance genes such as rpoB, katG, AAC(2')-Ib, gyrA, gyrB, embB, pncA, blaF, thyA, embC, embR, and iniA. In addition, the MF GZ001strain contains mutations in iniA, iniC, pncA, and ribD which conferred resistance to isoniazid, ethambutol, pyrazinamide, and para-aminosalicylic acid respectively, which are not frequently observed in rapidly growing mycobacteria. A wide variety of predicted putative potential virulence genes were found in MF GZ001, most of which are shared with well-recognized mycobacterial species with high pathogenic profiles such as M. tuberculosis and M. abscessus. Discussion Our identified novel features of a pathogenic member of the M. fortuitum complex will provide the foundation for further investigation of mycobacterial pathogenicity and effective treatment.
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Affiliation(s)
- Md Shah Alam
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
| | - Ping Guan
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, China
| | - Yuting Zhu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Sanshan Zeng
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
| | - Xiange Fang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
| | - Shuai Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People's Hospital, Shenzhen, China
| | - Buhari Yusuf
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
| | - Jingran Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
| | - Xirong Tian
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
| | - Cuiting Fang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
| | - Yamin Gao
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
| | - Mst Sumaia Khatun
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
| | - Zhiyong Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
| | - H M Adnan Hameed
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
| | - Yaoju Tan
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, China
| | - Jinxing Hu
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, China
| | - Jianxiong Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
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15
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Ifijen IH, Atoe B, Ekun RO, Ighodaro A, Odiachi IJ. Treatments of Mycobacterium tuberculosis and Toxoplasma gondii with Selenium Nanoparticles. BIONANOSCIENCE 2023; 13:249-277. [PMID: 36687337 PMCID: PMC9838309 DOI: 10.1007/s12668-023-01059-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/02/2023] [Indexed: 01/13/2023]
Abstract
Toxoplasma gondii and Mycobacterium tuberculosis are pathogens that are harmful to humans. When these diseases interact in humans, the result is typically fatal to the public health. Several investigations on the relationship between M. tuberculosis and T. gondii infections have found that there is a strong correlation between them with each infection having a reciprocal effect on the other. TB may contribute to the reactivation of innate toxoplasmosis or enhance susceptibility to a new infection, and toxoplasma co-infection may worsen the severity of pulmonary tuberculosis. As a consequence, there is an earnest and urgent necessity to generate novel therapeutics that can subdue these challenges. Selenium nanostructures' compelling properties have been shown to be a successful treatment for Mycobacterium TB and Toxoplasma gondii. Despite the fact that selenium (Se) offers many health advantages for people, it also has a narrow therapeutic window; therefore, consuming too much of either inorganic or organic compounds based on selenium can be hazardous. Compared to both inorganic and organic Se, Se nanoparticles (SeNPs) are less hazardous. They are biocompatible and excellent in selectively targeting specific cells. As a consequence, this review conducted a summary of the efficacy of biogenic Se NPs in the treatment of tuberculosis (TB) and toxoplasmosis. Mycobacterium tuberculosis, Toxoplasma gondii, and their co-infection were all briefly described.
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Affiliation(s)
- Ikhazuagbe H. Ifijen
- Department of Research Outreach, Rubber Research Institute of Nigeria, Iyanomo, P.M.B, 1049, Benin City, Nigeria
| | - Best Atoe
- Department of Daily Need, Worldwide Healthcare, 100, Textile Mill Road, Benin City, Edo State Nigeria
| | - Raphael O. Ekun
- grid.440833.80000 0004 0642 9705Department of Electrical Electronics, Cyprus International University, Haspolat, Lefkosa, North Cyprus Mersin 10 Turkey
| | - Augustine Ighodaro
- Depatment of Aseptic Quality, Quantum Pharmaceuticals, Quantum House, Durham, UK
| | - Ifeanyi J. Odiachi
- grid.461933.a0000 0004 0446 5040Department of Science Laboratory Technology, Delta State Polytechnic Ogwashi-Uku, Ogwashi-Uku, Nigeria
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16
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Giacometti SI, MacRae MR, Dancel-Manning K, Bhabha G, Ekiert DC. Lipid Transport Across Bacterial Membranes. Annu Rev Cell Dev Biol 2022; 38:125-153. [PMID: 35850151 DOI: 10.1146/annurev-cellbio-120420-022914] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The movement of lipids within and between membranes in bacteria is essential for building and maintaining the bacterial cell envelope. Moving lipids to their final destination is often energetically unfavorable and does not readily occur spontaneously. Bacteria have evolved several protein-mediated transport systems that bind specific lipid substrates and catalyze the transport of lipids across membranes and from one membrane to another. Specific protein flippases act in translocating lipids across the plasma membrane, overcoming the obstacle of moving relatively large and chemically diverse lipids between leaflets of the bilayer. Active transporters found in double-membraned bacteria have evolved sophisticated mechanisms to traffic lipids between the two membranes, including assembling to form large, multiprotein complexes that resemble bridges, shuttles, and tunnels, shielding lipids from the hydrophilic environment of the periplasm during transport. In this review, we explore our current understanding of the mechanisms thought to drive bacterial lipid transport.
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Affiliation(s)
- Sabrina I Giacometti
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA; , , ,
| | - Mark R MacRae
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA; , , ,
| | - Kristen Dancel-Manning
- Office of Science and Research, New York University School of Medicine, New York, NY, USA;
| | - Gira Bhabha
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA; , , ,
| | - Damian C Ekiert
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA; , , ,
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
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17
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Lai WY, Wong Z, Chang CH, Samian MR, Watanabe N, Teh AH, Noordin R, Ong EBB. Identifying Leptospira interrogans putative virulence factors with a yeast protein expression screen. Appl Microbiol Biotechnol 2022; 106:6567-6581. [DOI: 10.1007/s00253-022-12160-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/17/2022] [Accepted: 08/30/2022] [Indexed: 11/24/2022]
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18
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Comín J, Madacki J, Rabanaque I, Zúñiga-Antón M, Ibarz D, Cebollada A, Viñuelas J, Torres L, Sahagún J, Klopp C, Gonzalo-Asensio J, Brosch R, Iglesias MJ, Samper S. The MtZ Strain: Molecular Characteristics and Outbreak Investigation of the Most Successful Mycobacterium tuberculosis Strain in Aragon Using Whole-Genome Sequencing. Front Cell Infect Microbiol 2022; 12:887134. [PMID: 35685752 PMCID: PMC9173592 DOI: 10.3389/fcimb.2022.887134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/11/2022] [Indexed: 11/13/2022] Open
Abstract
Since 2004, a tuberculosis surveillance protocol has been carried out in Aragon, thereby managing to detect all tuberculosis outbreaks that take place in the community. The largest outbreak was caused by a strain named Mycobacterium tuberculosis Zaragoza (MtZ), causing 242 cases as of 2020. The main objective of this work was to analyze this outbreak and the molecular characteristics of this successful strain that could be related to its greater transmission. To do this, we first applied whole-genome sequencing to 57 of the isolates. This revealed two principal transmission clusters and six subclusters arising from them. The MtZ strain belongs to L4.8 and had eight specific single nucleotide polymorphisms (SNPs) in genes considered to be virulence factors [ptpA, mc3D, mc3F, VapB41, pks15 (two SNPs), virS, and VapC50]. Second, a transcriptomic study was carried out to better understand the multiple IS6110 copies present in its genome. This allowed us to observe three effects of IS6110: the disruption of the gene in which the IS6110 is inserted (desA3), the overexpression of a gene (ppe38), and the absence of transcription of genes (cut1:Rv1765c) due to the recombination of two IS6110 copies. Finally, because of the disruption of ppe38 and ppe71 genes by an IS6110, a study of PE_PGRS secretion was carried out, showing that MtZ secretes these factors in higher amounts than the reference strain, thereby differing from the hypervirulent phenotype described for the Beijing strains. In conclusion, MtZ consists of several SNPs in genes related to virulence, pathogenesis, and survival, as well as other genomic polymorphisms, which may be implicated in its success among our population.
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Affiliation(s)
- Jessica Comín
- Grupo de Genética de Micobacterias, Instituto Aragonés de Ciencias de la Salud, Zaragoza, Spain
| | - Jan Madacki
- Unit for Integrated Mycobacterial Pathogenomics, Institut Pasteur, Université de Paris, CNRS UMR 3525, Paris, France
| | - Isabel Rabanaque
- Departamento de Geografía y Ordenación del Territorio, Universidad de Zaragoza, Zaragoza, Spain.,Instituto Universitario de Investigación en Ciencias Ambientales de Aragón, Zaragoza, Spain.,Fundación Instituto de Investigación Sanitaria (IIS) Aragón, Zaragoza, Spain
| | - María Zúñiga-Antón
- Departamento de Geografía y Ordenación del Territorio, Universidad de Zaragoza, Zaragoza, Spain.,Instituto Universitario de Investigación en Ciencias Ambientales de Aragón, Zaragoza, Spain.,Fundación Instituto de Investigación Sanitaria (IIS) Aragón, Zaragoza, Spain
| | - Daniel Ibarz
- Grupo de Genética de Micobacterias, Facultad de Medicina, Universidad de Zaragoza, Zaragoza, Spain
| | - Alberto Cebollada
- Unidad de Biocomputación, Instituto Aragonés de Ciencias de la Salud, Zaragoza, Spain
| | - Jesús Viñuelas
- Hospital Universitario Miguel Servet, Zaragoza, Spain.,Grupo de Estudio de Infecciones por Micobacterias (GEIM), Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica, Madrid, Spain
| | | | - Juan Sahagún
- Hospital Clínico Universitario Lozano Blesa, Zaragoza, Spain
| | | | - Jesús Gonzalo-Asensio
- Grupo de Genética de Micobacterias, Facultad de Medicina, Universidad de Zaragoza, Zaragoza, Spain
| | - Roland Brosch
- Unit for Integrated Mycobacterial Pathogenomics, Institut Pasteur, Université de Paris, CNRS UMR 3525, Paris, France
| | - María-José Iglesias
- Fundación Instituto de Investigación Sanitaria (IIS) Aragón, Zaragoza, Spain.,Grupo de Genética de Micobacterias, Facultad de Medicina, Universidad de Zaragoza, Zaragoza, Spain.,Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Respiratorias, Madrid, Spain
| | - Sofía Samper
- Grupo de Genética de Micobacterias, Instituto Aragonés de Ciencias de la Salud, Zaragoza, Spain.,Fundación Instituto de Investigación Sanitaria (IIS) Aragón, Zaragoza, Spain.,Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Respiratorias, Madrid, Spain
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19
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Lima FR, Filho FB, Antunes VMG, Santana JM, de Almeida RCP, Toro DM, Bragagnollo VF, Manso GMDC, de Paula NA, Alves ES, Riley LW, Arruda S, Frade MAC. Serological Immunoassay for Hansen's Disease Diagnosis and Monitoring Treatment: Anti-Mce1A Antibody Response Among Hansen's Disease Patients and Their Household Contacts in Northeastern Brazil. Front Med (Lausanne) 2022; 9:855787. [PMID: 35755036 PMCID: PMC9218539 DOI: 10.3389/fmed.2022.855787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 04/26/2022] [Indexed: 11/25/2022] Open
Abstract
Hansen's disease (HD) is an ancient disease, but more than 200,000 new cases were reported worldwide in 2019. Currently, there are not many satisfactory immunoassay methods for its diagnosis. We evaluated antibodies against Mce1A as a promising new serological biomarker. We collected plasma from new cases, contacts, and endemic controls in the city of Parnaíba and treated patients at Carpina, a former HD colony in Piauí state, northeastern Brazil. Receiver operating characteristic (ROC) curves were used to assess the assay thresholds, specificity and sensitivity of the IgA, IgM, and IgG antibodies against α-Mce1A by indirect ELISA and compared it with IgM anti-PGL-I and molecular diagnosis by quantitative polymerase chain reaction (qPCR). Venn diagrams were generated to represent the overlap in the antibody positivity pattern. Multivariate analysis was performed to assess the potential predictor of antibodies for the outcome of having an HD diagnosis. IgA and IgG were positive in 92.3 and 84% of patients, respectively. IgM was negative for all treated patients. IgG had a sensitivity and specificity of 94.7 and 100%, respectively. IgM-positive individuals had a 3.6 chance of being diagnosed with HD [OR = 3.6 (95% CI = 1.1-11.6); p = 0.028], while IgA-positive individuals had a 2.3 chance [OR = 2.3 (95% CI = 1.2-4.3); p = 0.005] compared to endemic controls. We found that the Mce1A antibody profile can be an excellent diagnostic method of HD. IgA is an ideal biomarker for confirming contact with the bacillus. IgM has potential in the detection of active disease. IgG antibodies confirm the performance of these serological markers in diagnosis and therapeutic follow-up.
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Affiliation(s)
- Filipe Rocha Lima
- Healing and Hansen’s Disease Laboratory, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and HD, Clinical Hospital of the Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Fred Bernardes Filho
- Healing and Hansen’s Disease Laboratory, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and HD, Clinical Hospital of the Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Vanderson Mayron Granemann Antunes
- Healing and Hansen’s Disease Laboratory, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and HD, Clinical Hospital of the Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Jaci Maria Santana
- Healing and Hansen’s Disease Laboratory, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and HD, Clinical Hospital of the Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Regina Coeli Palma de Almeida
- Healing and Hansen’s Disease Laboratory, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and HD, Clinical Hospital of the Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Diana Mota Toro
- Department of Clinical, Toxicological, and Bromatological Analyses, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Vinicius Fozatti Bragagnollo
- Healing and Hansen’s Disease Laboratory, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and HD, Clinical Hospital of the Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Gabriel Martins da Costa Manso
- Healing and Hansen’s Disease Laboratory, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and HD, Clinical Hospital of the Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Natália Aparecida de Paula
- Healing and Hansen’s Disease Laboratory, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and HD, Clinical Hospital of the Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Eliracema Silva Alves
- Directorate of Unit and Health Care Surveillance, HD Control Program, State Department of Health, Piauí, Brazil
- Federal University of Piauí, Piauí, Brazil
| | - Lee W. Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, United States
| | - Sérgio Arruda
- Advanced Public Health Laboratory, Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Salvador, Brazil
| | - Marco Andrey Cipriani Frade
- Healing and Hansen’s Disease Laboratory, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and HD, Clinical Hospital of the Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
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20
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Vieni C, Coudray N, Isom GL, Bhabha G, Ekiert DC. Role of Ring6 in the function of the E. coli MCE protein LetB. J Mol Biol 2022; 434:167463. [PMID: 35077766 PMCID: PMC9112829 DOI: 10.1016/j.jmb.2022.167463] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 01/15/2022] [Accepted: 01/18/2022] [Indexed: 10/19/2022]
Abstract
LetB is a tunnel-forming protein found in the cell envelope of some double-membraned bacteria, and is thought to be important for the transport of lipids between the inner and outer membranes. In Escherichia coli the LetB tunnel is formed from a stack of seven rings (Ring1 - Ring7), in which each ring is composed of a homo-hexameric assembly of MCE domains. The primary sequence of each MCE domain of the LetB protein is substantially divergent from the others, making each MCE ring unique in nature. The role of each MCE domain and how it contributes to the function of LetB is not well understood. Here we probed the importance of each MCE ring for the function of LetB, using a combination of bacterial growth assays and cryo-EM. Surprisingly, we find that ΔRing3 and ΔRing6 mutants, in which Ring3 and Ring6 have been deleted, confer increased resistance to membrane perturbing agents. Specific mutations in the pore-lining loops of Ring6 similarly confer increased resistance. A cryo-EM structure of the ΔRing6 mutant shows that despite the absence of Ring6, which leads to a shorter assembly, the overall architecture is maintained, highlighting the modular nature of MCE proteins. Previous work has shown that Ring6 is dynamic and in its closed state, may restrict the passage of substrate through the tunnel. Our work suggests that removal of Ring6 may relieve this restriction. The deletion of Ring6 combined with mutations in the pore-lining loops leads to a model for the tunnel gating mechanism of LetB. Together, these results provide insight into the functional roles of individual MCE domains and pore-lining loops in the LetB protein.
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21
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Wei Y, Chen T, Yang W, Li H, Fang C, Liu Q, Chen Y, Mei Q. Detection of a novel antigen for Crohn's disease. Scand J Gastroenterol 2021; 56:1427-1433. [PMID: 34487462 DOI: 10.1080/00365521.2021.1973088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
BACKGROUND AND AIMS Accurate serological assays are desirable for the diagnosis of inflammatory bowel disease (IBD). We identify an antigen-like substance called Crohn's disease (CD) antibody binding polypeptide (CABP). As a serological marker, anti-CABP may contribute to the diagnosis of IBD. The present study aims to evaluate the clinical role of anti-CABP as a serological antibody for IBD. METHODS Using enzyme-linked immunosorbent assay (ELISA), serum anti-CABP, anti-Saccharomyces cerevisiae antibody (ASCA) and perinuclear anti-neutrophil cytoplasmic antibody (pANCA), titers were tested in 168 CD patients, 123 ulcerative colitis (UC) patients and 170 controls. The correlation between serum antibody and clinical characteristics was investigated. The diagnostic potential of the anti-CABP was evaluated by receiver operating characteristic (ROC) analysis. RESULTS The titers of anti-CABP (IgA or IgG) and ASCA IgG of CD patients were significantly higher than non-CD group (all p < .01). In the differential diagnosis of CD and non-CD, anti-CABP IgA revealed an area under the curve (AUC) of 0.706 and anti-CABP IgG demonstrated an AUC of 0.788. As an individual antibody, anti-CABP could effectively distinguish CD from non-CD (AUC 0.816), and the diagnostic efficacy was better than that of ASCA (AUC 0.680). The combined use of anti-CABP, ASCA and pANCA significantly improved the diagnostic value (AUC 0.857). Anti-CABP positive rates were associated with perianal lesions and disease location in CD patients (both p < .05). CONCLUSIONS Our results suggested that anti-CABP could be used as a serological marker to assist the diagnosis of CD. CLINICAL TRIAL REGISTRATION This trial is registered with clinical trial registration unique identifier ChiCTR2000037094.
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Affiliation(s)
- Yarong Wei
- Department of Gastroenterology, the Key Laboratory of Digestive Diseases of Anhui Province, the First Affiliated Hospital of Anhui Medical University, Hefei, China
| | | | - Wu Yang
- Shanxi Ruihao Biotechnology Co. LTD, Taiyuan, China
| | - Huihui Li
- Department of Gastroenterology, the Key Laboratory of Digestive Diseases of Anhui Province, the First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Chen Fang
- Department of Gastroenterology, the Key Laboratory of Digestive Diseases of Anhui Province, the First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Qiuyuan Liu
- Department of Gastroenterology, the Key Laboratory of Digestive Diseases of Anhui Province, the First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yonghao Chen
- Department of Gastroenterology, the Key Laboratory of Digestive Diseases of Anhui Province, the First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Qiao Mei
- Department of Gastroenterology, the Key Laboratory of Digestive Diseases of Anhui Province, the First Affiliated Hospital of Anhui Medical University, Hefei, China
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22
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Mycolicibacterium cell factory for the production of steroid-based drug intermediates. Biotechnol Adv 2021; 53:107860. [PMID: 34710554 DOI: 10.1016/j.biotechadv.2021.107860] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 10/19/2021] [Accepted: 10/19/2021] [Indexed: 12/30/2022]
Abstract
Steroid-based drugs have been developed as the second largest medical category in pharmaceutics. The well-established route of steroid industry includes two steps: the conversion of natural products with a steroid framework to steroid-based drug intermediates and the synthesis of varied steroid-based drugs from steroid-based drug intermediates. The biosynthesis of steroid-based drug intermediates from phytosterols by Mycolicibacterium cell factories bypasses the potential undersupply of diosgenin in the traditional steroid chemical industry. Moreover, the biosynthesis route shows advantages on multiple steroid-based drug intermediate products, more ecofriendly processes, and consecutive reactions carried out in one operation step and in one pot. Androsta-4-ene-3,17-dione (AD), androsta-1,4-diene-3,17-dione (ADD) and 9-hydroxyandrostra-4-ene-3,17-dione (9-OH-AD) are the representative steroid-based drug intermediates synthesized by mycolicibacteria. Other steroid metabolites of mycolicibacteria, like 4-androstene-17β-ol-3-one (TS), 22-hydroxy-23,24-bisnorchol-4-ene-3-one (4-HBC), 22-hydroxy-23,24-bisnorchol-1,4-diene-3-one (1,4-HBC), 9,22-dihydroxy-23,24-bisnorchol-4-ene-3-one (9-OH-HBC), 3aα-H-4α-(3'-propionic acid)-7aβ-methylhexahydro-1,5-indanedione (HIP) and 3aα-H-4α-(3'-propionic acid)-5α-hydroxy-7aβ-methylhexahydro-1-indanone-δ-lactone (HIL), also show values as steroid-based drug intermediates. To improve the bio-production efficiency of the steroid-based drug intermediates, mycolicibacterial strains and biotransformation processes have been continuously studied in the past decades. Many mycolicibacteria that accumulate steroid drug intermediates have been isolated, and subsequently optimized by conventional mutagenesis and genetic engineering. Especially, with the clarification of the mycolicibacterial steroid metabolic pathway and the developments on gene editing technologies, rational design is becoming an important measure for the construction and optimization of engineered mycolicibacteria strains that produce steroid-based drug intermediates. Hence, by reviewing researches in the past two decades, this article updates the overall process of steroid metabolism in mycolicibacteria and provides comprehensive schemes for the rational construction of mycolicibacterial strains that accumulate steroid-based drug intermediates. In addition, the special strategies for the bioconversion of highly hydrophobic steroid in aqueous media are discussed as well.
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23
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Asthana P, Singh D, Pedersen JS, Hynönen MJ, Sulu R, Murthy AV, Laitaoja M, Jänis J, Riley LW, Venkatesan R. Structural insights into the substrate-binding proteins Mce1A and Mce4A from Mycobacterium tuberculosis. IUCRJ 2021; 8:757-774. [PMID: 34584737 PMCID: PMC8420772 DOI: 10.1107/s2052252521006199] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 06/15/2021] [Indexed: 05/28/2023]
Abstract
Mycobacterium tuberculosis (Mtb), which is responsible for more than a million deaths annually, uses lipids as the source of carbon and energy for its survival in the latent phase of infection. Mtb cannot synthesize all of the lipid molecules required for its growth and pathogenicity. Therefore, it relies on transporters such as the mammalian cell entry (Mce) complexes to import lipids from the host across the cell wall. Despite their importance for the survival and pathogenicity of Mtb, information on the structural properties of these proteins is not yet available. Each of the four Mce complexes in Mtb (Mce1-4) comprises six substrate-binding proteins (SBPs; MceA-F), each of which contains four conserved domains (N-terminal transmembrane, MCE, helical and C-terminal unstructured tail domains). Here, the properties of the various domains of Mtb Mce1A and Mce4A, which are involved in the import of mycolic/fatty acids and cholesterol, respectively, are reported. In the crystal structure of the MCE domain of Mce4A (MtMce4A39-140) a domain-swapped conformation is observed, whereas solution studies, including small-angle X-ray scattering (SAXS), indicate that all Mce1A and Mce4A domains are predominantly monomeric. Further, structural comparisons show interesting differences from the bacterial homologs MlaD, PqiB and LetB, which form homohexamers when assembled as functional transporter complexes. These data, and the fact that there are six SBPs in each Mtb mce operon, suggest that the MceA-F SBPs from Mce1-4 may form heterohexamers. Also, interestingly, the purification and SAXS analysis showed that the helical domains interact with the detergent micelle, suggesting that when assembled the helical domains of MceA-F may form a hydrophobic pore for lipid transport, as observed in EcPqiB. Overall, these data highlight the unique structural properties of the Mtb Mce SBPs.
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Affiliation(s)
- Pooja Asthana
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Dhirendra Singh
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Jan Skov Pedersen
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
| | - Mikko J. Hynönen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Ramita Sulu
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Abhinandan V. Murthy
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Mikko Laitaoja
- Department of Chemistry, University of Eastern Finland, Joensuu, Finland
| | - Janne Jänis
- Department of Chemistry, University of Eastern Finland, Joensuu, Finland
| | - Lee W. Riley
- School of Public Health, University of California, Berkeley, California, USA
| | - Rajaram Venkatesan
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
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Sundararajan S, Muniyan R. Latent tuberculosis: interaction of virulence factors in Mycobacterium tuberculosis. Mol Biol Rep 2021; 48:6181-6196. [PMID: 34351540 DOI: 10.1007/s11033-021-06611-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/29/2021] [Indexed: 11/28/2022]
Abstract
Tuberculosis (TB) remains a prominent health concern worldwide. Besides extensive research and vaccinations available, attempts to control the pandemic are cumbersome due to the complex physiology of Mycobacterium tuberculosis (Mtb). Alongside the emergence of drug-resistant TB, latent TB has worsened the condition. The tubercle bacilli are unusually behaved and successful with its strategies to modulate genes to evade host immune system and persist within macrophages. Under latent/unfavorable conditions, Mtb conceals itself from immune system and modulates its genes. Among many intracellular modulated genes, important are those involved in cell entry, fatty acid degradation, mycolic acid synthesis, phagosome acidification inhibition, inhibition of phagosome-lysosome complex and chaperon protein modulation. Though the study on these genes date back to early times of TB, an insight on their inter-relation within and to newly evolved genes are still required. This review focuses on the findings and discussions on these genes, possible mechanism, credibility as target for novel drugs and repurposed drugs and their interaction that enables Mtb in survival, pathogenesis, resistance and latency.
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Affiliation(s)
- Sadhana Sundararajan
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Rajiniraja Muniyan
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.
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25
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Perea C, Ciaravino G, Stuber T, Thacker TC, Robbe-Austerman S, Allepuz A, de Val BP. Whole-Genome SNP Analysis Identifies Putative Mycobacterium bovis Transmission Clusters in Livestock and Wildlife in Catalonia, Spain. Microorganisms 2021; 9:microorganisms9081629. [PMID: 34442709 PMCID: PMC8401651 DOI: 10.3390/microorganisms9081629] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/23/2021] [Accepted: 07/28/2021] [Indexed: 12/02/2022] Open
Abstract
The high-resolution WGS analyses of MTBC strains have provided useful insight for determining sources of infection for animal tuberculosis. In Spain, tuberculosis in livestock is caused by Mycobacterium bovis and Mycobacterium caprae, where wildlife reservoirs play an important role. We analyzed a set of 125 M. bovis isolates obtained from livestock and wildlife from Catalonia to investigate strain diversity and identify possible sources and/or causes of infection. Whole-genome SNP profiles were used for phylogenetic reconstruction and pairwise SNP distance analysis. Additionally, SNPs were investigated to identify virulence and antimicrobial resistance factors to investigate clade-specific associations. Putative transmission clusters (≤12 SNPs) were identified, and associated epidemiological metadata were used to determine possible explanatory factors for transmission. M. bovis distribution was heterogeneous, with 7 major clades and 21 putative transmission clusters. In order of importance, the explanatory factors associated were proximity and neighborhood, residual infection, livestock-wildlife interaction, shared pasture, and movement. Genes related to lipid transport and metabolism showed the highest number of SNPs. All isolates were pyrazinamide resistant, and five were additionally resistant to isoniazid, but no clade-specific associations could be determined. Our findings highlight the importance of high-resolution molecular surveillance to monitor bovine tuberculosis dynamics in a low-prevalence setting.
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Affiliation(s)
- Claudia Perea
- National Veterinary Services Laboratories, U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Veterinary Services, Ames, IA 50010, USA; (T.S.); (T.C.T.); (S.R.-A.)
- Correspondence:
| | - Giovanna Ciaravino
- Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; (G.C.); (A.A.)
| | - Tod Stuber
- National Veterinary Services Laboratories, U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Veterinary Services, Ames, IA 50010, USA; (T.S.); (T.C.T.); (S.R.-A.)
| | - Tyler C. Thacker
- National Veterinary Services Laboratories, U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Veterinary Services, Ames, IA 50010, USA; (T.S.); (T.C.T.); (S.R.-A.)
| | - Suelee Robbe-Austerman
- National Veterinary Services Laboratories, U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Veterinary Services, Ames, IA 50010, USA; (T.S.); (T.C.T.); (S.R.-A.)
| | - Alberto Allepuz
- Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; (G.C.); (A.A.)
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), 08197 Bellaterra, Spain;
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), 08193 Bellaterra, Spain
| | - Bernat Pérez de Val
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), 08197 Bellaterra, Spain;
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), 08193 Bellaterra, Spain
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Abstract
The outer membrane of Gram-negative bacteria is essential for their survival in harsh environments and provides intrinsic resistance to many antibiotics. This membrane is remarkable; it is a highly asymmetric lipid bilayer. The inner leaflet of the outer membrane contains phospholipids, whereas the fatty acyl chains attached to lipopolysaccharide (LPS) comprise the hydrophobic portion of the outer leaflet. This lipid asymmetry, and in particular the exclusion of phospholipids from the outer leaflet, is key to creating an almost impenetrable barrier to hydrophobic molecules that can otherwise pass through phospholipid bilayers. It has long been known that these lipids are not made in the outer membrane. It is now believed that conserved multisubunit protein machines extract these lipids after their synthesis is completed at the inner membrane and transport them to the outer membrane. A longstanding question is how the cell builds and maintains this asymmetric lipid bilayer in coordination with the assembly of the other components of the cell envelope. This Review describes the trans-envelope lipid transport systems that have been identified to participate in outer-membrane biogenesis: LPS transport via the Lpt machine, and phospholipid transport via the Mla pathway and several recently proposed transporters.
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Affiliation(s)
| | - Daniel Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
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Evidence for the Mycobacterial Mce4 Transporter Being a Multiprotein Complex. J Bacteriol 2021; 203:JB.00685-20. [PMID: 33649150 DOI: 10.1128/jb.00685-20] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/24/2021] [Indexed: 01/01/2023] Open
Abstract
Mycobacteria possess Mce transporters that import lipids and are thought to function analogously to ATP-binding cassette (ABC) transporters. However, whereas ABC transporters import substrates using a single solute-binding protein (SBP) to deliver a substrate to permease proteins in the membrane, mycobacterial Mce transporters have a potential for six SBPs (MceA to MceF) working with a pair of permeases (YrbEA and YrbEB), a cytoplasmic ATPase (MceG), and multiple Mce-associated membrane (Mam) and orphaned Mam (Omam) proteins to transport lipids. In this study, we used the model mycobacterium Mycobacterium smegmatis to study the requirement for individual Mce, Mam, and Omam proteins in Mce4 transport of cholesterol. All of the Mce4 and Mam4 proteins we investigated were required for cholesterol uptake. However, not all Omam proteins, which are encoded by genes outside mce loci, proved to contribute to cholesterol import. OmamA and OmamB were required for cholesterol import, while OmamC, OmamD, OmamE, and OmamF were not. In the absence of any single Mce4, Mam4, or Omam protein that we tested, the abundance of Mce4A and Mce4E declined. This relationship between the levels of Mce4A and Mce4E and these additional proteins suggests a network of interactions that assemble and/or stabilize a multiprotein Mce4 transporter complex. Further support for Mce transporters being multiprotein complexes was obtained by immunoprecipitation-mass spectrometry, in which we identified every single Mce, YrbE, MceG, Mam, and Omam protein with a role in cholesterol transport as associating with Mce4A. This study represents the first time any of these Mce4 transporter proteins has been shown to associate.IMPORTANCE How lipids travel between membranes of diderm bacteria is a challenging mechanistic question because lipids, which are hydrophobic molecules, must traverse a hydrophilic periplasm. This question is even more complex for mycobacteria, which have a unique cell envelope that is highly impermeable to molecules. A growing body of knowledge identifies Mce transporters as lipid importers for mycobacteria. Here, using protein stability experiments and immunoprecipitation-mass spectrometry, we provide evidence for mycobacterial Mce transporters existing as multiprotein complexes.
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Shin MK, Shin SJ. Genetic Involvement of Mycobacterium avium Complex in the Regulation and Manipulation of Innate Immune Functions of Host Cells. Int J Mol Sci 2021; 22:ijms22063011. [PMID: 33809463 PMCID: PMC8000623 DOI: 10.3390/ijms22063011] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/09/2021] [Accepted: 03/12/2021] [Indexed: 12/12/2022] Open
Abstract
Mycobacterium avium complex (MAC), a collection of mycobacterial species representing nontuberculous mycobacteria, are characterized as ubiquitous and opportunistic pathogens. The incidence and prevalence of infectious diseases caused by MAC have been emerging globally due to complications in the treatment of MAC-pulmonary disease (PD) in humans and the lack of understating individual differences in genetic traits and pathogenesis of MAC species or subspecies. Despite genetically close one to another, mycobacteria species belonging to the MAC cause diseases to different host range along with a distinct spectrum of disease. In addition, unlike Mycobacterium tuberculosis, the underlying mechanisms for the pathogenesis of MAC infection from environmental sources of infection to their survival strategies within host cells have not been fully elucidated. In this review, we highlight unique genetic and genotypic differences in MAC species and the virulence factors conferring the ability to MAC for the tactics evading innate immune attacks of host cells based on the recent advances in genetic analysis by exemplifying M. avium subsp. hominissuis, a major representative pathogen causing MAC-PD in humans. Further understanding of the genetic link between host and MAC may contribute to enhance host anti-MAC immunity, but also provide novel therapeutic approaches targeting the pangenesis-associated genes of MAC.
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Affiliation(s)
- Min-Kyoung Shin
- Department of Microbiology and Convergence Medical Sciences, Institute of Health Sciences, College of Medicine, Gyeongsang National University, Jinju 52727, Korea;
| | - Sung Jae Shin
- Department of Microbiology and Institute for Immunology and Immunological Diseases, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
- Correspondence: ; Tel.: +82-2-2228-1813
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29
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Molecular Cloning, Purification and Characterization of Mce1R of Mycobacterium tuberculosis. Mol Biotechnol 2021; 63:200-220. [PMID: 33423211 DOI: 10.1007/s12033-020-00293-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2020] [Indexed: 10/22/2022]
Abstract
The mce1 operon of Mycobacterium tuberculosis, important for lipid metabolism/transport, host cell invasion, modulation of host immune response and pathogenicity, is under the transcriptional control of Mce1R. Hence characterizing Mce1R is an important step for novel anti-tuberculosis drug discovery. The present study reports functional and in silico characterization of Mce1R. In this work, we have computationally modeled the structure of Mce1R and have validated the structure by computational and experimental methods. Mce1R has been shown to harbor the canonical VanR-like structure with a flexible N-terminal 'arm', carrying conserved positively charged residues, most likely involved in the operator DNA binding. The mce1R gene has been cloned, expressed, purified and its DNA-binding activity has been measured in vitro. The Kd value for Mce1R-operator DNA interaction has been determined to be 0.35 ± 0.02 µM which implies that Mce1R binds to DNA with moderate affinity compared to the other FCD family of regulators. So far, this is the first report for measuring the DNA-binding affinity of any VanR-type protein. Despite significant sequence similarity at the N-terminal domain, the wHTH motif of Mce1R exhibits poor conservancy of amino acid residues, critical for DNA-binding, thus results in moderate DNA-binding affinity. The N-terminal DNA-binding domain is structurally dynamic while the C-terminal domain showed significant stability and such profile of structural dynamics is most likely to be preserved in the structural orthologs of Mce1R. In addition to this, a cavity has been detected in the C-terminal domain of Mce1R which contains a few conserved residues. Comparison with other FCD family of regulators suggests that most of the conserved residues might be critical for binding to specific ligand. The max pKd value and drug score for the cavity are estimated to be 9.04 and 109 respectively suggesting that the cavity represents a suitable target site for novel anti-tuberculosis drug discovery approaches.
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Schniete JK, Selem-Mojica N, Birke AS, Cruz-Morales P, Hunter IS, Barona-Gomez F, Hoskisson PA. ActDES - a curated Actinobacterial Database for Evolutionary Studies. Microb Genom 2021; 7:mgen000498. [PMID: 33433310 PMCID: PMC8115908 DOI: 10.1099/mgen.0.000498] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 12/06/2020] [Indexed: 12/25/2022] Open
Abstract
Actinobacteria is a large and diverse phylum of bacteria that contains medically and ecologically relevant organisms. Many members are valuable sources of bioactive natural products and chemical precursors that are exploited in the clinic and made using the enzyme pathways encoded in their complex genomes. Whilst the number of sequenced genomes has increased rapidly in the last 20 years, the large size, complexity and high G+C content of many actinobacterial genomes means that the sequences remain incomplete and consist of large numbers of contigs with poor annotation, which hinders large-scale comparative genomic and evolutionary studies. To enable greater understanding and exploitation of actinobacterial genomes, specialized genomic databases must be linked to high-quality genome sequences. Here, we provide a curated database of 612 high-quality actinobacterial genomes from 80 genera, chosen to represent a broad phylogenetic group with equivalent genome re-annotation. Utilizing this database will provide researchers with a framework for evolutionary and metabolic studies, to enable a foundation for genome and metabolic engineering, to facilitate discovery of novel bioactive therapeutics and studies on gene family evolution. This article contains data hosted by Microreact.
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Affiliation(s)
- Jana K. Schniete
- Biology Department, Edge Hill University, St Helens Road, Ormskirk, Lancashire L39 4QP, UK
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK
| | - Nelly Selem-Mojica
- Evolution of Metabolic Diversity Laboratory, Langebio, Cinvestav-IPN, Libramiento Norte Carretera Leon Km 9.6, 36821 Irapuato, Guanajuato, México
| | - Anna S. Birke
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK
| | - Pablo Cruz-Morales
- Evolution of Metabolic Diversity Laboratory, Langebio, Cinvestav-IPN, Libramiento Norte Carretera Leon Km 9.6, 36821 Irapuato, Guanajuato, México
| | - Iain S. Hunter
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK
| | - Francisco Barona-Gomez
- Evolution of Metabolic Diversity Laboratory, Langebio, Cinvestav-IPN, Libramiento Norte Carretera Leon Km 9.6, 36821 Irapuato, Guanajuato, México
| | - Paul A. Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK
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31
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Wibberg D, Price-Carter M, Rückert C, Blom J, Möbius P. Complete Genome Sequence of Ovine Mycobacterium avium subsp. paratuberculosis Strain JIII-386 (MAP-S/type III) and Its Comparison to MAP-S/type I, MAP-C, and M. avium Complex Genomes. Microorganisms 2020; 9:microorganisms9010070. [PMID: 33383865 PMCID: PMC7823733 DOI: 10.3390/microorganisms9010070] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/21/2020] [Accepted: 12/24/2020] [Indexed: 02/07/2023] Open
Abstract
Mycobacterium avium (M. a.) subsp. paratuberculosis (MAP) is a worldwide-distributed obligate pathogen in ruminants causing Johne’s disease. Due to a lack of complete subtype III genome sequences, there is not yet conclusive information about genetic differences between strains of cattle (MAP-C, type II) and sheep (MAP-S) type, and especially between MAP-S subtypes I, and III. Here we present the complete, circular genome of MAP-S/type III strain JIII-386 (DE) closed by Nanopore-technology and its comparison with MAP-S/type I closed genome of strain Telford (AUS), MAP-S/type III draft genome of strain S397 (U.S.), twelve closed MAP-C strains, and eight closed M.-a.-complex-strains. Structural comparative alignments revealed clearly the mosaic nature of MAP, emphasized differences between the subtypes and the higher diversity of MAP-S genomes. The comparison of various genomic elements including transposases and genomic islands provide new insights in MAP genomics. MAP type specific phenotypic features may be attributed to genes of known large sequence polymorphisms (LSPSs) regions I–IV and deletions #1 and #2, confirmed here, but could also result from identified frameshifts or interruptions of various virulence-associated genes (e.g., mbtC in MAP-S). Comprehensive core and pan genome analysis uncovered unique genes (e.g., cytochromes) and genes probably acquired by horizontal gene transfer in different MAP-types and subtypes, but also emphasized the highly conserved and close relationship, and the complex evolution of M.-a.-strains.
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Affiliation(s)
- Daniel Wibberg
- Center for Biotechnology (CeBiTec), Bielefeld University, 33501 Bielefeld, Germany; (D.W.); (C.R.)
| | - Marian Price-Carter
- AgResearch, Hopkirk Research Institute, Grasslands Research Centre, Palmerston North 4442, New Zealand;
| | - Christian Rückert
- Center for Biotechnology (CeBiTec), Bielefeld University, 33501 Bielefeld, Germany; (D.W.); (C.R.)
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University Gießen, D-35390 Gießen, Germany;
| | - Petra Möbius
- Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, 07743 Jena, Germany
- Correspondence: ; Tel.: +49-(0)3641-8042280
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32
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Zaychikova MV, Danilenko VN. The Actinobacterial mce Operon: Structure and Functions. BIOLOGY BULLETIN REVIEWS 2020. [PMCID: PMC7709480 DOI: 10.1134/s2079086420060079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- M. V. Zaychikova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 117971 Moscow, Russia
| | - V. N. Danilenko
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 117971 Moscow, Russia
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33
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34
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Yimer SA, Kalayou S, Homberset H, Birhanu AG, Riaz T, Zegeye ED, Lutter T, Abebe M, Holm-Hansen C, Aseffa A, Tønjum T. Lineage-Specific Proteomic Signatures in the Mycobacterium tuberculosis Complex Reveal Differential Abundance of Proteins Involved in Virulence, DNA Repair, CRISPR-Cas, Bioenergetics and Lipid Metabolism. Front Microbiol 2020; 11:550760. [PMID: 33072011 PMCID: PMC7536270 DOI: 10.3389/fmicb.2020.550760] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 08/17/2020] [Indexed: 01/17/2023] Open
Abstract
Despite the discovery of the tubercle bacillus more than 130 years ago, its physiology and the mechanisms of virulence are still not fully understood. A comprehensive analysis of the proteomes of members of the human-adapted Mycobacterium tuberculosis complex (MTBC) lineages 3, 4, 5, and 7 was conducted to better understand the evolution of virulence and other physiological characteristics. Unique and shared proteomic signatures in these modern, pre-modern and ancient MTBC lineages, as deduced from quantitative bioinformatics analyses of high-resolution mass spectrometry data, were delineated. The main proteomic findings were verified by using immunoblotting. In addition, analysis of multiple genome alignment of members of the same lineages was performed. Label-free peptide quantification of whole cells from MTBC lineages 3, 4, 5, and 7 yielded a total of 38,346 unique peptides derived from 3092 proteins, representing 77% coverage of the predicted proteome. MTBC lineage-specific differential expression was observed for 539 proteins. Lineage 7 exhibited a markedly reduced abundance of proteins involved in DNA repair, type VII ESX-3 and ESX-1 secretion systems, lipid metabolism and inorganic phosphate uptake, and an increased abundance of proteins involved in alternative pathways of the TCA cycle and the CRISPR-Cas system as compared to the other lineages. Lineages 3 and 4 exhibited a higher abundance of proteins involved in virulence, DNA repair, drug resistance and other metabolic pathways. The high throughput analysis of the MTBC proteome by super-resolution mass spectrometry provided an insight into the differential expression of proteins between MTBC lineages 3, 4, 5, and 7 that may explain the slow growth and reduced virulence, metabolic flexibility, and the ability to survive under adverse growth conditions of lineage 7.
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Affiliation(s)
- Solomon Abebe Yimer
- Unit for Genome Dynamics, Department of Microbiology, University of Oslo, Oslo, Norway.,Coalition for Epidemic Preparedness Innovations, Oslo, Norway
| | - Shewit Kalayou
- Division of Laboratory Medicine, Department of Microbiology, Oslo University Hospital, Oslo, Norway.,International Centre of Insect Physiology and Ecology, Nairobi, Kenya
| | - Håvard Homberset
- Unit for Genome Dynamics, Department of Microbiology, University of Oslo, Oslo, Norway
| | - Alemayehu Godana Birhanu
- Unit for Genome Dynamics, Department of Microbiology, University of Oslo, Oslo, Norway.,Division of Laboratory Medicine, Department of Microbiology, Oslo University Hospital, Oslo, Norway.,Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Tahira Riaz
- Unit for Genome Dynamics, Department of Microbiology, University of Oslo, Oslo, Norway
| | - Ephrem Debebe Zegeye
- NORCE Norwegian Research Centre AS, Centre for Applied Biotechnology, Bergen, Norway
| | - Timo Lutter
- Unit for Genome Dynamics, Department of Microbiology, University of Oslo, Oslo, Norway
| | - Markos Abebe
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Carol Holm-Hansen
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Abraham Aseffa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Tone Tønjum
- Unit for Genome Dynamics, Department of Microbiology, University of Oslo, Oslo, Norway.,Division of Laboratory Medicine, Department of Microbiology, Oslo University Hospital, Oslo, Norway
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The Sterol Carrier Hydroxypropyl-β-Cyclodextrin Enhances the Metabolism of Phytosterols by Mycobacterium neoaurum. Appl Environ Microbiol 2020; 86:AEM.00441-20. [PMID: 32414803 DOI: 10.1128/aem.00441-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 05/13/2020] [Indexed: 01/23/2023] Open
Abstract
Androst-4-ene-3,17-dione (AD) and androst-1,4-diene-3,17-dione (ADD) are valuable steroid pharmaceutical intermediates obtained by soybean phytosterol biotransformation by Mycobacterium Cyclodextrins (CDs) are generally believed to be carriers for phytosterol delivery and can improve the production of AD and ADD due to their effects on steroid solubilization and alteration in cell wall permeability for steroids. To better understand the mechanisms of CD promotion, we performed proteomic quantification of the effects of hydroxypropyl-β-CD (HP-β-CD) on phytosterol metabolism in Mycobacterium neoaurum TCCC 11978 C2. Perturbations are observed in steroid catabolism and glucose metabolism by adding HP-β-CD in a phytosterol bioconversion system. AD and ADD, as metabolic products of phytosterol, are toxic to cells, with inhibited cell growth and biocatalytic activity. Treatment of mycobacteria with HP-β-CD relieves the inhibitory effect of AD(D) on the electron transfer chain and cell growth. These results demonstrate the positive relationship between HP-β-CD and phytosterol metabolism and give insight into the complex functions of CDs as mediators of the regulation of sterol metabolism.IMPORTANCE Phytosterols from soybean are low-cost by-products of soybean oil production and, owing to their good bioavailability in mycobacteria, are preferred as the substrates for steroid drug production via biotransformation by Mycobacterium However, the low level of production of steroid hormone drugs due to the low aqueous solubility (below 0.1 mmol/liter) of phytosterols limits the commercial use of sterol-transformed strains. To improve the bioconversion of steroids, cyclodextrins (CDs) are generally used as an effective carrier for the delivery of hydrophobic steroids to the bacterium. CDs improve the biotransformation of steroids due to their effects on steroid solubilization and alterations in cell wall permeability for steroids. However, studies have rarely reported the effects of CDs on cell metabolic pathways related to sterols. In this study, the effects of hydroxypropyl-β-CD (HP-β-CD) on the expression of enzymes related to steroid catabolic pathways in Mycobacterium neoaurum were systematically investigated. These findings will improve our understanding of the complex functions of CDs in the regulation of sterol metabolism and guide the application of CDs to sterol production.
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36
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Hemati Z, Derakhshandeh A, Haghkhah M, Chaubey KK, Gupta S, Singh M, Singh SV, Dhama K. Mammalian cell entry operons; novel and major subset candidates for diagnostics with special reference to Mycobacterium avium subspecies paratuberculosis infection. Vet Q 2020; 39:65-75. [PMID: 31282842 PMCID: PMC6830979 DOI: 10.1080/01652176.2019.1641764] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Mammalian cell entry (mce) genes are the components of the mce operon and play a vital role in the entry of Mycobacteria into the mammalian cell and their survival within phagocytes and epithelial cells. Mce operons are present in the DNA of Mycobacteria and translate proteins associated with the invasion and long-term existence of these pathogens in macrophages. The exact mechanism of action of mce genes and their functions are not clear yet. However, with the loss of these genes Mycobacteria lose their pathogenicity. Mycobacterium avium subspecies paratuberculosis (MAP), the etiological agent of Johne’s disease, is the cause of chronic enteritis of animals and significantly affects economic impact on the livestock industry. Since MAP is not inactivated during pasteurization, human population is continuously at the risk of getting exposed to MAP infection through consumption of dairy products. There is need for new candidate genes and/or proteins for developing improved diagnostic assays for the diagnosis of MAP infection and for the control of disease. Increasing evidences showed that expression of mce genes is important for the virulence of MAP. Whole-genome DNA microarray representing MAP revealed that there are 14 large sequence polymorphisms with LSPP12 being the most widely conserved MAP-specific region that included a cluster of six homologs of mce-family involved in lipid metabolism. On the other hand, LSP11 comprising part of mce2 operon was absent in MAP isolates. This review summarizes the advancement of research on mce genes of Mycobacteria with special reference to the MAP infection.
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Affiliation(s)
- Zahra Hemati
- Department of Pathobiology, School of Veterinary Medicine, Shiraz University , Shiraz , Iran
| | - Abdollah Derakhshandeh
- Department of Pathobiology, School of Veterinary Medicine, Shiraz University , Shiraz , Iran
| | - Masoud Haghkhah
- Department of Pathobiology, School of Veterinary Medicine, Shiraz University , Shiraz , Iran
| | - Kundan Kumar Chaubey
- Department of Biotechnology, Institute of Applied Sciences and Humanities, GLA University , Mathura , India
| | - Saurabh Gupta
- Department of Biotechnology, Institute of Applied Sciences and Humanities, GLA University , Mathura , India
| | - Manju Singh
- Department of Biotechnology, Institute of Applied Sciences and Humanities, GLA University , Mathura , India
| | - Shoorvir V Singh
- Department of Biotechnology, Institute of Applied Sciences and Humanities, GLA University , Mathura , India
| | - Kuldeep Dhama
- Department of Pathology, Indian Veterinary Research Institute , Bareilly , India
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Serum anti-Mce1A immunoglobulin detection as a tool for differential diagnosis of tuberculosis and latent tuberculosis infection in children and adolescents. Tuberculosis (Edinb) 2019; 120:101893. [PMID: 32090854 DOI: 10.1016/j.tube.2019.101893] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 11/28/2019] [Accepted: 12/01/2019] [Indexed: 11/21/2022]
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38
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Powers MJ, Trent MS. Intermembrane transport: Glycerophospholipid homeostasis of the Gram-negative cell envelope. Proc Natl Acad Sci U S A 2019; 116:17147-17155. [PMID: 31420510 PMCID: PMC6717313 DOI: 10.1073/pnas.1902026116] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
This perspective addresses recent advances in lipid transport across the Gram-negative inner and outer membranes. While we include a summary of previously existing literature regarding this topic, we focus on the maintenance of lipid asymmetry (Mla) pathway. Discovered in 2009 by the Silhavy group [J. C. Malinverni, T. J. Silhavy, Proc. Natl. Acad. Sci. U.S.A. 106, 8009-8014 (2009)], Mla has become increasingly appreciated for its role in bacterial cell envelope physiology. Through the work of many, we have gained an increasingly mechanistic understanding of the function of Mla via genetic, biochemical, and structural methods. Despite this, there is a degree of controversy surrounding the directionality in which Mla transports lipids. While the initial discovery and subsequent studies have posited that it mediated retrograde lipid transport (removing glycerophospholipids from the outer membrane and returning them to the inner membrane), others have asserted the opposite. This Perspective aims to lay out the evidence in an unbiased, yet critical, manner for Mla-mediated transport in addition to postulation of mechanisms for anterograde lipid transport from the inner to outer membranes.
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Affiliation(s)
- Matthew J Powers
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
- Department of Microbiology, College of Arts and Sciences, University of Georgia, Athens, GA 30602
| | - M Stephen Trent
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602;
- Department of Microbiology, College of Arts and Sciences, University of Georgia, Athens, GA 30602
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
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Idris I, Abdurrahman AH, Fatulrachman, Aftitah VB, Fadlitha VB, Sato N, Fujimura T, Takimoto H. Invasion of human microvascular endothelial cells by Mycobacterium leprae through Mce1A protein. J Dermatol 2019; 46:853-858. [PMID: 31432529 DOI: 10.1111/1346-8138.15047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 07/22/2019] [Indexed: 11/29/2022]
Abstract
In patients with lepromatous leprosy, Mycobacterium leprae is often observed inside the human microvascular endothelial cells (HMVEC) surrounding Schwann cells (SC) at the site of lesions in the peripheral nerves. Based on this observation, it is considered that the nasal mucous may be the invasion pathway for M. leprae and HMVEC serve as an important reservoir for the bacteria before they invade SC. In light of previous research which revealed that Mce1A protein mediates bacterial invasion into nasal epithelial cells and HMVEC, we conducted a study to determine whether the invasion of M. leprae into HMVEC can be suppressed by blocking the Mce1A protein. In this study, we analyzed bacterial invasive activity by adding recombinant Escherichia coli, which express the active region (InvX:72 a.a.) of Mce1A protein on their external membrane, into cultured HMVEC, using the adhesin involved in the diffuse adherence mechanism. The number of bacteria that invaded into the cells was then measured by a colony counting method. The active region of Mce1A was divided into four sections, and hyperimmune antisera was prepared for each section for analyzing the inhibitory effect against invasion. The invasive activity was suppressed by antibodies against InvX regions 1-24 a.a., 25-46 a.a. and 58-72 a.a. This suggests that the InvX regions 1-24 a.a., 25-46 a.a. and 58-72 a.a. of Mce1A protein play an important role in the invasion of M. leprae into HMVEC and that it may be possible to suppress entry of M. leprae in HMVEC with antibodies against these regions.
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Affiliation(s)
- Irfan Idris
- Hasanuddin University Medical Research Center, Makassar, Indonesia.,Departments of, Departments of, Dermatology, Kitasato University Graduate School of Medical Science, Sagamihara, Japan
| | - Ahmad Haykal Abdurrahman
- Hasanuddin University Medical Research Center, Makassar, Indonesia.,Departments of, Departments of, Dermatology, Kitasato University Graduate School of Medical Science, Sagamihara, Japan
| | - Fatulrachman
- Departments of, Departments of, Dermatology, Kitasato University Graduate School of Medical Science, Sagamihara, Japan
| | - Vienza Beby Aftitah
- Cellular Immunology, Kitasato University Graduate School of Medical Science, Sagamihara, Japan
| | - Viesta Beby Fadlitha
- Departments of, Departments of, Dermatology, Kitasato University Graduate School of Medical Science, Sagamihara, Japan
| | - Naoya Sato
- Department of Dermatology, Toshiba Rinkan Hospital, Sagamihara, Japan.,Departments of, Departments of, Dermatology, Kitasato University School of Medicine, Sagamihara, Japan
| | - Takao Fujimura
- Departments of, Departments of, Dermatology, Kitasato University Graduate School of Medical Science, Sagamihara, Japan.,Departments of, Departments of, Dermatology, Kitasato University School of Medicine, Sagamihara, Japan
| | - Hiroaki Takimoto
- Bioscience, Kitasato University School of Science, Sagamihara, Japan
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Screen for fitness and virulence factors of Francisella sp. strain W12-1067 using amoebae. Int J Med Microbiol 2019; 309:151341. [PMID: 31451389 DOI: 10.1016/j.ijmm.2019.151341] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 07/17/2019] [Accepted: 08/18/2019] [Indexed: 11/21/2022] Open
Abstract
Francisella tularensis is the causative agent of the human disease referred to as tularemia. Other Francisella species are known but less is understood about their virulence factors. The role of environmental amoebae in the life-cycle of Francisella is still under discussion. Francisella sp. strain W12-1067 (F-W12) is an environmental Francisella isolate recently identified in Germany which is negative for the Francisella pathogenicity island, but exhibits a putative alternative type VI secretion system. Putative virulence factors have been identified in silico in the genome of F-W12. In this work, we established a "scatter screen", used earlier for pathogenic Legionella, to verify experimentally and identify candidate fitness factors using a transposon mutant bank of F-W12 and Acanthamoeba lenticulata as host organism. In these experiments, we identified 79 scatter clones (amoeba sensitive), which were further analyzed by an infection assay identifying 9 known virulence factors, but also candidate fitness factors of F-W12 not yet described as fitness factors in Francisella. The majority of the identified genes encoded proteins involved in the synthesis or maintenance of the cell envelope (LPS, outer membrane, capsule) or in the metabolism (glycolysis, gluconeogenesis, pentose phosphate pathway). Further 13C-flux analysis of the Tn5 glucokinase mutant strain revealed that the identified gene indeed encodes the sole active glucokinase in F-W12. In conclusion, candidate fitness factors of the new Francisella species F-W12 were identified using the scatter screen method which might also be usable for other Francisella species.
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41
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Fadlitha VB, Yamamoto F, Idris I, Dahlan H, Sato N, Aftitah VB, Febriyanda A, Fujimura T, Takimoto H. The unique tropism of Mycobacterium leprae to the nasal epithelial cells can be explained by the mammalian cell entry protein 1A. PLoS Negl Trop Dis 2019; 13:e0006704. [PMID: 30835734 PMCID: PMC6420055 DOI: 10.1371/journal.pntd.0006704] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 03/15/2019] [Accepted: 01/28/2019] [Indexed: 11/18/2022] Open
Abstract
Leprosy is a chronic infection where the skin and peripheral nervous system is invaded by Mycobacterium leprae. The infection mechanism remains unknown in part because culture methods have not been established yet for M. leprae. Mce1A protein (442 aa) is coded by mce1A (1326 bp) of M. leprae. The Mce1A homolog in Mycobacterium tuberculosis is known to be associated with M. tuberculosis epithelial cell entry, and survival and multiplication within macrophages. Studies using recombinant proteins have indicated that Mce1A of M. leprae is also associated with epithelial cell entry. This study is aimed at identifying particular sequences within Mce1A associated with M. leprae epithelial cell entry. Recombinant proteins having N-terminus and C-terminus truncations of the Mce1A region of M. leprae were created in Escherichia coli. Entry activity of latex beads, coated with these truncated proteins (r-lep37 kDa and r-lep27 kDa), into HeLa cells was observed by electron microscopy. The entry activity was preserved even when 315 bp (105 aa) and 922 bp (308 aa) was truncated from the N-terminus and C-terminus, respectively. This 316-921 bp region was divided into three sub-regions: 316-531 bp (InvX), 532-753 bp (InvY), and 754-921 bp (InvZ). Each sub-region was cloned into an AIDA vector and expressed on the surface of E. coli. Entry of these E. coli into monolayer-cultured HeLa and RPMI2650 cells was observed by electron microscopy. Only E. coli harboring the InvX sub-region exhibited cell entry. InvX was further divided into 4 domains, InvXa-InvXd, containing sequences 1-24 aa, 25-46 aa, 47-57 aa, and 58-72 aa, respectively. Recombinant E. coli, expressing each of InvXa-InvXd on the surface, were treated with antibodies against these domains, then added to monolayer cultured RPMI cells. The effectiveness of these antibodies in preventing cell entry was studied by colony counting. Entry activity was suppressed by antibodies against InvXa, InvXb, and InvXd. This suggests that these three InvX domains of Mce1A are important for M. leprae invasion into nasal epithelial cells.
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Affiliation(s)
- Viesta Beby Fadlitha
- Department of Dermatology, Kitasato University Graduate School of Medical Science, Sagamihara, Kanagawa, Japan
| | - Fuki Yamamoto
- Department of Dermatology, Kitasato University Graduate School of Medical Science, Sagamihara, Kanagawa, Japan
| | - Irfan Idris
- Hasanuddin University Medical Research Centre, Makassar, South Sulawesi, Indonesia
| | - Haslindah Dahlan
- Hasanuddin University Medical Research Centre, Makassar, South Sulawesi, Indonesia
| | - Naoya Sato
- Department of Dermatology, Toshiba Rinkan Hospital, Sagamihara, Kanagawa, Japan
- Department of Dermatology, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Vienza Beby Aftitah
- Department of Cellular Immunology, Kitasato University Graduate School of Medical Science, Sagamihara, Kanagawa, Japan
| | - Andini Febriyanda
- Hasanuddin University Medical Research Centre, Makassar, South Sulawesi, Indonesia
| | - Takao Fujimura
- Department of Dermatology, Kitasato University Graduate School of Medical Science, Sagamihara, Kanagawa, Japan
- Department of Dermatology, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
- * E-mail:
| | - Hiroaki Takimoto
- Department of Bioscience, Kitasato University School of Science, Sagamihara, Kanagawa, Japan
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42
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Cell wall enrichment unveils proteomic changes in the cell wall during treatment of Mycobacterium smegmatis with sub-lethal concentrations of rifampicin. J Proteomics 2019; 191:166-179. [DOI: 10.1016/j.jprot.2018.02.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 02/02/2018] [Accepted: 02/10/2018] [Indexed: 12/21/2022]
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43
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Abhishek S, Saikia UN, Gupta A, Bansal R, Gupta V, Singh N, Laal S, Verma I. Transcriptional Profile of Mycobacterium tuberculosis in an in vitro Model of Intraocular Tuberculosis. Front Cell Infect Microbiol 2018; 8:330. [PMID: 30333960 PMCID: PMC6175983 DOI: 10.3389/fcimb.2018.00330] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 08/28/2018] [Indexed: 12/18/2022] Open
Abstract
Background: Intraocular tuberculosis (IOTB), an extrapulmonary manifestation of tuberculosis of the eye, has unique and varied clinical presentations with poorly understood pathogenesis. As it is a significant cause of inflammation and visual morbidity, particularly in TB endemic countries, it is essential to study the pathogenesis of IOTB. Clinical and histopathologic studies suggest the presence of Mycobacterium tuberculosis in retinal pigment epithelium (RPE) cells. Methods: A human retinal pigment epithelium (ARPE-19) cell line was infected with a virulent strain of M. tuberculosis (H37Rv). Electron microscopy and colony forming units (CFU) assay were performed to monitor the M. tuberculosis adherence, invasion, and intracellular replication, whereas confocal microscopy was done to study its intracellular fate in the RPE cells. To understand the pathogenesis, the transcriptional profile of M. tuberculosis in ARPE-19 cells was studied by whole genome microarray. Three upregulated M. tuberculosis transcripts were also examined in human IOTB vitreous samples. Results: Scanning electron micrographs of the infected ARPE-19 cells indicated adherence of bacilli, which were further observed to be internalized as monitored by transmission electron microscopy. The CFU assay showed that 22.7 and 8.4% of the initial inoculum of bacilli adhered and invaded the ARPE-19 cells, respectively, with an increase in fold CFU from 1 dpi (0.84) to 5dpi (6.58). The intracellular bacilli were co-localized with lysosomal-associated membrane protein-1 (LAMP-1) and LAMP-2 in ARPE-19 cells. The transcriptome study of intracellular bacilli showed that most of the upregulated transcripts correspond to the genes encoding the proteins involved in the processes such as adherence (e.g., Rv1759c and Rv1026), invasion (e.g., Rv1971 and Rv0169), virulence (e.g., Rv2844 and Rv0775), and intracellular survival (e.g., Rv1884c and Rv2450c) as well as regulators of various metabolic pathways. Two of the upregulated transcripts (Rv1971, Rv1230c) were also present in the vitreous samples of the IOTB patients. Conclusions:M. tuberculosis is phagocytosed by RPE cells and utilizes these cells for intracellular multiplication with the involvement of late endosomal/lysosomal compartments and alters its transcriptional profile plausibly for its intracellular adaptation and survival. The findings of the present study could be important to understanding the molecular pathogenesis of IOTB with a potential role in the development of diagnostics and therapeutics for IOTB.
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Affiliation(s)
- Sudhanshu Abhishek
- Department of Biochemistry, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Uma Nahar Saikia
- Department of Histopathology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Amod Gupta
- Department of Ophthalmology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Reema Bansal
- Department of Ophthalmology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Vishali Gupta
- Department of Ophthalmology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Nirbhai Singh
- Department of Ophthalmology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Suman Laal
- Department of Pathology, New York University Langone Medical Center, New York, NY, United States
- Veterans Affairs New York Harbor Healthcare System, New York, NY, United States
| | - Indu Verma
- Department of Biochemistry, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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44
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Han HJ, Kwak MJ, Ha SM, Yang SJ, Kim JD, Cho KH, Kim TW, Cho MY, Kim BY, Jung SH, Chun J. Genomic characterization of Nocardia seriolae strains isolated from diseased fish. Microbiologyopen 2018; 8:e00656. [PMID: 30117297 PMCID: PMC6436429 DOI: 10.1002/mbo3.656] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 04/23/2018] [Accepted: 04/24/2018] [Indexed: 11/24/2022] Open
Abstract
Members of the genus Nocardia are widespread in diverse environments; a wide range of Nocardia species are known to cause nocardiosis in several animals, including cat, dog, fish, and humans. Of the pathogenic Nocardia species, N. seriolae is known to cause disease in cultured fish, resulting in major economic loss. We isolated two N. seriolae strains, CK‐14008 and EM15050, from diseased fish and sequenced their genomes using the PacBio sequencing platform. To identify their genomic features, we compared their genomes with those of other Nocardia species. Phylogenetic analysis showed that N. seriolae shares a common ancestor with a putative human pathogenic Nocardia species. Moreover, N. seriolae strains were phylogenetically divided into four clusters according to host fish families. Through genome comparison, we observed that the putative pathogenic Nocardia strains had additional genes for iron acquisition. Dozens of antibiotic resistance genes were detected in the genomes of N. seriolae strains; most of the antibiotics were involved in the inhibition of the biosynthesis of proteins or cell walls. Our results demonstrated the virulence features and antibiotic resistance of fish pathogenic N. seriolae strains at the genomic level. These results may be useful to develop strategies for the prevention of fish nocardiosis.
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Affiliation(s)
- Hyun-Ja Han
- Pathology Research Division, National Institute of Fisheries Science, Busan, Korea
| | | | - Sung-Min Ha
- ChunLab Inc., Seoul, Korea.,Laboratory of evolutionary bioinformatics, Seoul National University, Seoul, Korea
| | | | - Jin Do Kim
- Pathology Research Division, National Institute of Fisheries Science, Busan, Korea
| | | | | | - Mi Young Cho
- Pathology Research Division, National Institute of Fisheries Science, Busan, Korea
| | | | - Sung-Hee Jung
- Pathology Research Division, National Institute of Fisheries Science, Busan, Korea
| | - Jongsik Chun
- ChunLab Inc., Seoul, Korea.,Laboratory of evolutionary bioinformatics, Seoul National University, Seoul, Korea
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45
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Folkvardsen DB, Norman A, Andersen ÅB, Rasmussen EM, Lillebaek T, Jelsbak L. A Major Mycobacterium tuberculosis outbreak caused by one specific genotype in a low-incidence country: Exploring gene profile virulence explanations. Sci Rep 2018; 8:11869. [PMID: 30089859 PMCID: PMC6082827 DOI: 10.1038/s41598-018-30363-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 07/10/2018] [Indexed: 12/30/2022] Open
Abstract
Denmark, a tuberculosis low burden country, still experiences significant active Mycobacterium tuberculosis (Mtb) transmission, especially with one specific genotype named Cluster 2/1112-15 (C2), the most prevalent lineage in Scandinavia. In addition to environmental factors, antibiotic resistance, and human genetics, there is increasing evidence that Mtb strain variation plays a role for the outcome of infection and disease. In this study, we explore the reasons for the success of the C2 genotype by analysing strain specific polymorphisms identified through whole genome sequencing of all C2 isolates identified in Denmark between 1992 and 2014 (n = 952), and the demographic distribution of C2. Of 234 non-synonymous (NS) monomorphic SNPs found in C2 in comparison with Mtb reference strain H37Rv, 23 were in genes previously reported to be involved in Mtb virulence. Of these 23 SNPs, three were specific for C2 including a NS mutation in a gene associated with hyper-virulence. We show that the genotype is readily transmitted to different ethnicities and is also found outside Denmark. Our data suggest that strain specific virulence factor variations are important for the success of the C2 genotype. These factors, likely in combination with poor TB control, seem to be the main drivers of C2 success.
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Affiliation(s)
- Dorte Bek Folkvardsen
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark.
| | - Anders Norman
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Åse Bengård Andersen
- Department of Infectious Diseases, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Research Unit for Infectious Diseases, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Erik Michael Rasmussen
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
| | - Troels Lillebaek
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
| | - Lars Jelsbak
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
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46
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Das S, Hameed S, Fatima Z. Potential Drug Targets in Mycobacterial Cell Wall: Non-Lipid Perspective. Curr Drug Discov Technol 2018; 17:147-153. [PMID: 29875004 DOI: 10.2174/1570163815666180605113609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Revised: 05/21/2018] [Accepted: 05/22/2018] [Indexed: 11/22/2022]
Abstract
Tuberculosis (TB) caused by Mycobacterium tuberculosis (MTB), still remains a deadly disease worldwide. With prolonged usage of anti-TB drugs, the current therapeutic regimes are becoming ineffective, particularly due to emergence of drug resistance in MTB. Under such compelling circumstances, it is pertinent to look for new drug targets. The cell wall envelope of MTB is composed of unique lipids that are frequently targeted for anti-TB therapy. This is evident from the fact that most of the commonly used front line drugs (Isoniazid and Ethambutol) act on lipid machinery of MTB. Thus, despite the fact that much of the attention is towards understanding the MTB lipid biology, in search for identification of new drug targets, our knowledge of bacterial cell wall non-lipid components remains rudimentary and underappreciated. Better understanding of such components of mycobacterial cell structure will help in the identification of new drug targets that can be utilized on the persistent mycobacterium. This review at a common platform summarizes some of the non-lipid cell wall components in MTB that have potential to be exploited as future drug targets.
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Affiliation(s)
- Shrayanee Das
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram (Manesar)-122413, India
| | - Saif Hameed
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram (Manesar)-122413, India
| | - Zeeshan Fatima
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram (Manesar)-122413, India
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47
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Yano H, Iwamoto T, Nishiuchi Y, Nakajima C, Starkova DA, Mokrousov I, Narvskaya O, Yoshida S, Arikawa K, Nakanishi N, Osaki K, Nakagawa I, Ato M, Suzuki Y, Maruyama F. Population Structure and Local Adaptation of MAC Lung Disease Agent Mycobacterium avium subsp. hominissuis. Genome Biol Evol 2018; 9:2403-2417. [PMID: 28957464 PMCID: PMC5622343 DOI: 10.1093/gbe/evx183] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2017] [Indexed: 12/11/2022] Open
Abstract
Mycobacterium avium subsp. hominissuis (MAH) is one of the most common nontuberculous mycobacterial species responsible for chronic lung disease in humans. Despite increasing worldwide incidence, little is known about the genetic mechanisms behind the population evolution of MAH. To elucidate the local adaptation mechanisms of MAH, we assessed genetic population structure, the mutual homologous recombination, and gene content for 36 global MAH isolates, including 12 Japanese isolates sequenced in the present study. We identified five major MAH lineages and found that extensive mutual homologous recombination occurs among them. Two lineages (MahEastAsia1 and MahEastAsia2) were predominant in the Japanese isolates. We identified alleles unique to these two East Asian lineages in the loci responsible for trehalose biosynthesis (treS and mak) and in one mammalian cell entry operon, which presumably originated from as yet undiscovered mycobacterial lineages. Several genes and alleles unique to East Asian strains were located in the fragments introduced via recombination between East Asian lineages, suggesting implication of recombination in local adaptation. These patterns of MAH genomes are consistent with the signature of distribution conjugative transfer, a mode of sexual reproduction reported for other mycobacterial species.
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Affiliation(s)
- Hirokazu Yano
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan.,Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Tomotada Iwamoto
- Department of Infectious Diseases, Kobe Institute of Health, Kobe, Japan
| | - Yukiko Nishiuchi
- Toneyama Institute for Tuberculosis Research, Osaka City University Medical School, Osaka, Japan
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan.,The Global Station for Zoonosis Control, Hokkaido University Global Institution for Collaborative Research and Education, Sapporo, Japan
| | | | - Igor Mokrousov
- St. Petersburg Pasteur Institute, St. Petersburg, Russia
| | - Olga Narvskaya
- St. Petersburg Pasteur Institute, St. Petersburg, Russia
| | - Shiomi Yoshida
- Clinical Research Center, National Hospital Organization, Kinki-Chuo Chest Medical Center, Osaka, Japan
| | - Kentaro Arikawa
- Department of Infectious Diseases, Kobe Institute of Health, Kobe, Japan
| | - Noriko Nakanishi
- Department of Infectious Diseases, Kobe Institute of Health, Kobe, Japan
| | - Ken Osaki
- TOMY Digital Biology Co. Ltd, Taito-Ku, Tokyo, Japan
| | - Ichiro Nakagawa
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Manabu Ato
- Department of Immunology, National Institute of Infectious Diseases, Shinjuku-Ku, Tokyo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan.,The Global Station for Zoonosis Control, Hokkaido University Global Institution for Collaborative Research and Education, Sapporo, Japan
| | - Fumito Maruyama
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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48
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Chai Q, Zhang Y, Liu CH. Mycobacterium tuberculosis: An Adaptable Pathogen Associated With Multiple Human Diseases. Front Cell Infect Microbiol 2018; 8:158. [PMID: 29868514 PMCID: PMC5962710 DOI: 10.3389/fcimb.2018.00158] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 04/25/2018] [Indexed: 12/15/2022] Open
Abstract
Mycobacterium tuberculosis, the etiological agent of tuberculosis (TB), is an extremely successful pathogen that adapts to survive within the host. During the latency phase of infection, M. tuberculosis employs a range of effector proteins to be cloud the host immune system and shapes its lifestyle to reside in granulomas, sophisticated, and organized structures of immune cells that are established by the host in response to persistent infection. While normally being restrained in immunocompetent hosts, M. tuberculosis within granulomas can cause the recrudescence of TB when host immunity is compromised. Aside from causing TB, accumulating evidence suggests that M. tuberculosis is also associated with multiple other human diseases, such as pulmonary complications, autoimmune diseases, and metabolic syndromes. Furthermore, it has been recently appreciated that M. tuberculosis infection can also reciprocally interact with the human microbiome, which has a strong link to immune balance and health. In this review, we highlight the adaptive survival of M. tuberculosis within the host and provide an overview for regulatory mechanisms underlying interactions between M. tuberculosis infection and multiple important human diseases. A better understanding of how M. tuberculosis regulates the host immune system to cause TB and reciprocally regulates other human diseases is critical for developing rational treatments to better control TB and help alleviate its associated comorbidities.
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Affiliation(s)
- Qiyao Chai
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Yong Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Cui Hua Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
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49
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Cruz JN, Costa JFS, Khayat AS, Kuca K, Barros CAL, Neto AMJC. Molecular dynamics simulation and binding free energy studies of novel leads belonging to the benzofuran class inhibitors of Mycobacterium tuberculosis Polyketide Synthase 13. J Biomol Struct Dyn 2018; 37:1616-1627. [PMID: 29633908 DOI: 10.1080/07391102.2018.1462734] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
In this work, the binding mechanism of new Polyketide Synthase 13 (Pks13) inhibitors has been studied through molecular dynamics simulation and free energy calculations. The drug Tam1 and its analogs, belonging to the benzofuran class, were submitted to 100 ns simulations, and according to the results obtained for root mean square deviation, all the simulations converged from approximately 30 ns. For the analysis of backbone flotation, the root mean square fluctuations were plotted for the Cα atoms; analysis revealed that the greatest fluctuation occurred in the residues that are part of the protein lid domain. The binding free energy value (ΔGbind) obtained for the Tam16 lead molecule was of -51.43 kcal/mol. When comparing this result with the ΔGbind values for the remaining analogs, the drug Tam16 was found to be the highest ranked: this result is in agreement with the experimental results obtained by Aggarwal and collaborators, where it was verified that the IC50 for Tam16 is the smallest necessary to inhibit the Pks13 (IC50 = 0.19 μM). The energy decomposition analysis suggested that the residues which most interact with inhibitors are: Ser1636, Tyr1637, Asn1640, Ala1667, Phe1670, and Tyr1674, from which the greatest energy contribution to Phe1670 was particularly notable. For the lead molecule Tam16, a hydrogen bond with the hydroxyl of the phenol not observed in the other analogs induced a more stable molecular structure. Aggarwal and colleagues reported this hydrogen bonding as being responsible for the stability of the molecule, optimizing its physic-chemical, toxicological, and pharmacokinetic properties.
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Key Words
- CNPq, National Council for Scientific and Technological Development
- CoA, coenzyme A
- FAS, fatty acid synthase
- GAFF, general amber force field
- GB, generalized born
- HB, hydrogen bonds
- INH, isoniazid
- KatG, catalase-peroxidase
- MD, molecular dynamics
- MDR, multi-drug resistant
- MM/GBSA, molecular mechanics/generalized-born surface area
- NAD, nicotinamide adenine dinucleotide
- NS, nanoseconds
- PCA, acyl carrier protein
- Pks13
- Pks13, polyketide synthase 13
- RESP, restrained electrostatic potential
- RMSD, root mean square deviation
- RMSF, root mean square fluctuations
- TB, tuberculosis
- TE, C-terminal thioesterase
- XDR, extensively drug resistant
- benzofuran
- free energy
- inhibitors
- molecular dynamics
- Δ internal energy
- Δ, Van Der Waals contributions
- Δ, electrostatic contribution
- Δ, electrostatic contributions
- Δ, energy of desolvation
- Δ, energy of the molecular mechanics
- Δ, non-polar contributions
- Δ, polar contributions
- Δ, polar solvation contribution
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Affiliation(s)
- Jorddy N Cruz
- a Laboratory of Preparation and Computation of Nanomaterials , Federal University of Pará , CP 479, 66075-110 Belém , PA , Brazil
| | - José F S Costa
- a Laboratory of Preparation and Computation of Nanomaterials , Federal University of Pará , CP 479, 66075-110 Belém , PA , Brazil
| | - André S Khayat
- b Oncology Research Center , Federal University of Pará , CP 479, 6675-105 Belém , PA , Brazil
| | - Kamil Kuca
- c Biomedical Research Center , University Hospital Hradec Kralove , Sokolska 581, 500 05 Hradec Kralove , Czech Republic
| | - Carlos A L Barros
- d Department of Pharmacy , Federal University of Pará , CP 479, 66050-160 Belém , PA , Brazil
| | - A M J C Neto
- a Laboratory of Preparation and Computation of Nanomaterials , Federal University of Pará , CP 479, 66075-110 Belém , PA , Brazil
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Khan S, Khan FI, Mohammad T, Khan P, Hasan GM, Lobb KA, Islam A, Ahmad F, Imtaiyaz Hassan M. Exploring molecular insights into the interaction mechanism of cholesterol derivatives with the Mce4A: A combined spectroscopic and molecular dynamic simulation studies. Int J Biol Macromol 2018; 111:548-560. [DOI: 10.1016/j.ijbiomac.2017.12.160] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 11/16/2017] [Accepted: 12/30/2017] [Indexed: 01/08/2023]
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