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Fang WW, Kong XL, Yang JY, Tao NN, Li YM, Wang TT, Li YY, Han QL, Zhang YZ, Hu JJ, Li HC, Liu Y. PE/PPE mutations in the transmission of Mycobacterium tuberculosis in China revealed by whole genome sequencing. BMC Microbiol 2024; 24:206. [PMID: 38858614 PMCID: PMC11163795 DOI: 10.1186/s12866-024-03352-y] [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: 11/08/2023] [Accepted: 05/26/2024] [Indexed: 06/12/2024] Open
Abstract
OBJECTIVE This study aims to examine the impact of PE/PPE gene mutations on the transmission of Mycobacterium tuberculosis (M. tuberculosis) in China. METHODS We collected the whole genome sequencing (WGS) data of 3202 M. tuberculosis isolates in China from 2007 to 2018 and investigated the clustering of strains from different lineages. To evaluate the potential role of PE/PPE gene mutations in the dissemination of the pathogen, we employed homoplastic analysis to detect homoplastic single nucleotide polymorphisms (SNPs) within these gene regions. Subsequently, logistic regression analysis was conducted to analyze the statistical association. RESULTS Based on nationwide M. tuberculosis WGS data, it has been observed that the majority of the M. tuberculosis burden in China is caused by lineage 2 strains, followed by lineage 4. Lineage 2 exhibited a higher number of transmission clusters, totaling 446 clusters, of which 77 were cross-regional clusters. Conversely, there were only 52 transmission clusters in lineage 4, of which 9 were cross-regional clusters. In the analysis of lineage 2 isolates, regression results showed that 4 specific gene mutations, PE4 (position 190,394; c.46G > A), PE_PGRS10 (839,194; c.744 A > G), PE16 (1,607,005; c.620T > G) and PE_PGRS44 (2,921,883; c.333 C > A), were significantly associated with the transmission of M. tuberculosis. Mutations of PE_PGRS10 (839,334; c.884 A > G), PE_PGRS11 (847,613; c.1455G > C), PE_PGRS47 (3,054,724; c.811 A > G) and PPE66 (4,189,930; c.303G > C) exhibited significant associations with the cross-regional clusters. A total of 13 mutation positions showed a positive correlation with clustering size, indicating a positive association. For lineage 4 strains, no mutations were found to enhance transmission, but 2 mutation sites were identified as risk factors for cross-regional clusters. These included PE_PGRS4 (338,100; c.974 A > G) and PPE13 (976,897; c.1307 A > C). CONCLUSION Our results indicate that some PE/PPE gene mutations can increase the risk of M. tuberculosis transmission, which might provide a basis for controlling the spread of tuberculosis.
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Affiliation(s)
- Wei-Wei Fang
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong First Medical University, Jinan, Shandong, 250021, PR China
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, People's Republic of China
| | - Xiang-Long Kong
- Shandong Artificial Intelligence Institute, Qilu University of Technology & Shandong Academy of Sciences, Jinan, Shandong, PR China
| | - Jie-Yu Yang
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong First Medical University, Jinan, Shandong, 250021, PR China
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, People's Republic of China
| | - Ning-Ning Tao
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong First Medical University, Jinan, Shandong, 250021, PR China
| | - Ya-Meng Li
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong First Medical University, Jinan, Shandong, 250021, PR China
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, PR China
| | - Ting-Ting Wang
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong First Medical University, Jinan, Shandong, 250021, PR China
| | - Ying-Ying Li
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong First Medical University, Jinan, Shandong, 250021, PR China
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, PR China
| | - Qi-Lin Han
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong First Medical University, Jinan, Shandong, 250021, PR China
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, People's Republic of China
| | - Yu-Zhen Zhang
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong First Medical University, Jinan, Shandong, 250021, PR China
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, People's Republic of China
| | - Jin-Jiang Hu
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong First Medical University, Jinan, Shandong, 250021, PR China
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, People's Republic of China
| | - Huai-Chen Li
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong First Medical University, Jinan, Shandong, 250021, PR China
| | - Yao Liu
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong First Medical University, Jinan, Shandong, 250021, PR China.
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Ullah H, Shi X, Taj A, Cheng L, Yan Q, Sha S, Ahmad, Kang J, Haris M, Ma X, Ma Y. Mycobacterium tuberculosis PE_PGRS38 Enhances Intracellular Survival of Mycobacteria by Inhibiting TLR4/NF-κB-Dependent Inflammation and Apoptosis of the Host. BIOLOGY 2024; 13:313. [PMID: 38785795 PMCID: PMC11118070 DOI: 10.3390/biology13050313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/20/2024] [Accepted: 04/27/2024] [Indexed: 05/25/2024]
Abstract
Mycobacterium tuberculosis (Mtb) ranks as the most lethal human pathogen, able to fend off repeated attacks by the immune system or medications. PE_PGRS proteins are hallmarks of the pathogenicity of Mtb and contribute to its antigenic diversity, virulence, and persistence during infection. M. smegmatis is a nonpathogenic mycobacterium that naturally lacks PE_PGRS and is used as a model to express Mtb proteins. PE_PGRS has the capability to evade host immune responses and enhance the intracellular survival of M. smegmatis. Despite the intense investigations into PE_PGRS proteins, their role in tuberculosis remains elusive. We engineered the recombinant M. smegmatis strain Ms-PE_PGRS38. The result shows that PE_PGRS38 is expressed in the cell wall of M. smegmatis. PE_PGRS38 contributes to biofilm formation, confers permeability to the cell wall, and shows variable responses to exogenous stresses. PE_PGRS38 downregulated TLR4/NF-κB signaling in RAW264.7 macrophages and lung tissues of infected mice. In addition, PE_PGRS38 decreased NLRP3-dependent IL-1β release and limited pathogen-mediated inflammasome activity during infection. Moreover, PE_PGRS38 inhibited the apoptosis of RAW264.7 cells by downregulating the expression of apoptotic markers including Bax, cytochrome c, caspase-3, and caspase-9. In a nutshell, our findings demonstrate that PE_PGRS38 is a virulence factor for Mtb that enables recombinant M. smegmatis to survive by resisting and evading the host's immune responses during infection.
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Affiliation(s)
- Hayan Ullah
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, China; (H.U.); (A.T.); (L.C.); (S.S.); (J.K.); (M.H.)
- Department of Microbiology, Dalian Medical University, Dalian 116044, China;
| | - Xiaoxia Shi
- Department of Experimental Teaching Center of Public Health, Dalian Medical University, Dalian 116044, China;
| | - Ayaz Taj
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, China; (H.U.); (A.T.); (L.C.); (S.S.); (J.K.); (M.H.)
| | - Lin Cheng
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, China; (H.U.); (A.T.); (L.C.); (S.S.); (J.K.); (M.H.)
| | - Qiulong Yan
- Department of Microbiology, Dalian Medical University, Dalian 116044, China;
| | - Shanshan Sha
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, China; (H.U.); (A.T.); (L.C.); (S.S.); (J.K.); (M.H.)
| | - Ahmad
- Department of Immunology, Dalian Medical University, Dalian 116044, China;
| | - Jian Kang
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, China; (H.U.); (A.T.); (L.C.); (S.S.); (J.K.); (M.H.)
| | - Muhammad Haris
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, China; (H.U.); (A.T.); (L.C.); (S.S.); (J.K.); (M.H.)
| | - Xiaochi Ma
- Pharmaceutical Research Center, The Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Yufang Ma
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian 116044, China; (H.U.); (A.T.); (L.C.); (S.S.); (J.K.); (M.H.)
- Department of Microbiology, Dalian Medical University, Dalian 116044, China;
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Li F, Guo X, Bi Y, Jia R, Pitt ME, Pan S, Li S, Gasser RB, Coin LJ, Song J. Digerati - A multipath parallel hybrid deep learning framework for the identification of mycobacterial PE/PPE proteins. Comput Biol Med 2023; 163:107155. [PMID: 37356289 DOI: 10.1016/j.compbiomed.2023.107155] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/27/2023]
Abstract
The genome of Mycobacterium tuberculosis contains a relatively high percentage (10%) of genes that are poorly characterised because of their highly repetitive nature and high GC content. Some of these genes encode proteins of the PE/PPE family, which are thought to be involved in host-pathogen interactions, virulence, and disease pathogenicity. Members of this family are genetically divergent and challenging to both identify and classify using conventional computational tools. Thus, advanced in silico methods are needed to identify proteins of this family for subsequent functional annotation efficiently. In this study, we developed the first deep learning-based approach, termed Digerati, for the rapid and accurate identification of PE and PPE family proteins. Digerati was built upon a multipath parallel hybrid deep learning framework, which equips multi-layer convolutional neural networks with bidirectional, long short-term memory, equipped with a self-attention module to effectively learn the higher-order feature representations of PE/PPE proteins. Empirical studies demonstrated that Digerati achieved a significantly better performance (∼18-20%) than alignment-based approaches, including BLASTP, PHMMER, and HHsuite, in both prediction accuracy and speed. Digerati is anticipated to facilitate community-wide efforts to conduct high-throughput identification and analysis of PE/PPE family members. The webserver and source codes of Digerati are publicly available at http://web.unimelb-bioinfortools.cloud.edu.au/Digerati/.
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Affiliation(s)
- Fuyi Li
- College of Information Engineering, Northwest A&F University, Yangling, 712100, China; Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, 792 Elizabeth Street, Melbourne, Victoria, 3000, Australia.
| | - Xudong Guo
- College of Information Engineering, Northwest A&F University, Yangling, 712100, China
| | - Yue Bi
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, 3800, Australia
| | - Runchang Jia
- College of Information Engineering, Northwest A&F University, Yangling, 712100, China
| | - Miranda E Pitt
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, 792 Elizabeth Street, Melbourne, Victoria, 3000, Australia
| | - Shirui Pan
- School of Information and Communication Technology, Griffith University, QLD, 4222, Australia
| | - Shuqin Li
- College of Information Engineering, Northwest A&F University, Yangling, 712100, China
| | - Robin B Gasser
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, VIC, 3010, Australia
| | - Lachlan Jm Coin
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, 792 Elizabeth Street, Melbourne, Victoria, 3000, Australia.
| | - Jiangning Song
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, 3800, Australia.
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Maharajh R, Pillay M, Senzani S. A computational method for the prediction and functional analysis of potential Mycobacterium tuberculosis adhesin-related proteins. Expert Rev Proteomics 2023; 20:483-493. [PMID: 37873953 DOI: 10.1080/14789450.2023.2275678] [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: 08/04/2023] [Accepted: 10/20/2023] [Indexed: 10/25/2023]
Abstract
OBJECTIVES Mycobacterial adherence plays a major role in the establishment of infection within the host. Adhesin-related proteins attach to host receptors and cell-surface components. The current study aimed to utilize in-silico strategies to determine the adhesin potential of conserved hypothetical (CH) proteins. METHODS Computational analysis was performed on the whole Mycobacterium tuberculosis H37Rv proteome using a software program for the prediction of adhesin and adhesin-like proteins using neural networks (SPAAN) to determine the adhesin potential of CH proteins. A robust pipeline of computational analysis tools: Phyre2 and pFam for homology prediction; Mycosub, PsortB, and Loctree3 for subcellular localization; SignalP-5.0 and SecretomeP-2.0 for secretory prediction, were utilized to identify adhesin candidates. RESULTS SPAAN revealed 776 potential adhesins within the whole MTB H37Rv proteome. Comprehensive analysis of the literature was cross-tabulated with SPAAN to verify the adhesin prediction potential of known adhesin (n = 34). However, approximately a third of known adhesins were below the probability of adhesin (Pad) threshold (Pad ≥0.51). Subsequently, 167 CH proteins of interest were categorized using essential in-silico tools. CONCLUSION The use of SPAAN with supporting in-silico tools should be fundamental when identifying novel adhesins. This study provides a pipeline to identify CH proteins as functional adhesin molecules.
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Affiliation(s)
- Rivesh Maharajh
- Discipline of Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Manormoney Pillay
- Discipline of Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Sibusiso Senzani
- Discipline of Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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Ruaro-Moreno M, Monterrubio-López GP, Reyes-Gastellou A, Castelán-Vega JA, Jiménez-Alberto A, Aparicio-Ozores G, Delgadillo-Gutiérrez K, González-Y-Merchand JA, Ribas-Aparicio RM. Design of a Multi-Epitope Vaccine against Tuberculosis from Mycobacterium tuberculosis PE_PGRS49 and PE_PGRS56 Proteins by Reverse Vaccinology. Microorganisms 2023; 11:1647. [PMID: 37512820 PMCID: PMC10385543 DOI: 10.3390/microorganisms11071647] [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: 05/08/2023] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 07/30/2023] Open
Abstract
Tuberculosis is a disease caused by Mycobacterium tuberculosis, representing the second leading cause of death by an infectious agent worldwide. The available vaccine against this disease has insufficient coverage and variable efficacy, accounting for a high number of cases worldwide. In fact, an estimated third of the world's population has a latent infection. Therefore, developing new vaccines is crucial to preventing it. In this study, the highly antigenic PE_PGRS49 and PE_PGRS56 proteins were analyzed. These proteins were used for predicting T- and B-cell epitopes and for human leukocyte antigen (HLA) protein binding efficiency. Epitopes GGAGGNGSLSS, FAGAGGQGGLGG, GIGGGTQSATGLG (PE_PGRS49), and GTGWNGGKGDTG (PE_PGRS56) were selected based on their best physicochemical, antigenic, non-allergenic, and non-toxic properties and coupled to HLA I and HLA II structures for in silico assays. A construct with an adjuvant (RS09) plus each epitope joined by GPGPG linkers was designed, and the stability of the HLA-coupled construct was further evaluated by molecular dynamics simulations. Although experimental and in vivo studies are still necessary to ensure its protective effect against the disease, this study shows that the vaccine construct is dynamically stable and potentially effective against tuberculosis.
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Affiliation(s)
- Maritriny Ruaro-Moreno
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (M.R.-M.); (G.P.M.-L.); (A.R.-G.); (G.A.-O.); (K.D.-G.)
- Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico;
| | - Gloria Paulina Monterrubio-López
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (M.R.-M.); (G.P.M.-L.); (A.R.-G.); (G.A.-O.); (K.D.-G.)
| | - Abraham Reyes-Gastellou
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (M.R.-M.); (G.P.M.-L.); (A.R.-G.); (G.A.-O.); (K.D.-G.)
| | - Juan Arturo Castelán-Vega
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (M.R.-M.); (G.P.M.-L.); (A.R.-G.); (G.A.-O.); (K.D.-G.)
- Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico;
| | - Alicia Jiménez-Alberto
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (M.R.-M.); (G.P.M.-L.); (A.R.-G.); (G.A.-O.); (K.D.-G.)
- Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico;
| | - Gerardo Aparicio-Ozores
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (M.R.-M.); (G.P.M.-L.); (A.R.-G.); (G.A.-O.); (K.D.-G.)
- Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico;
| | - Karen Delgadillo-Gutiérrez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (M.R.-M.); (G.P.M.-L.); (A.R.-G.); (G.A.-O.); (K.D.-G.)
| | - Jorge Alberto González-Y-Merchand
- Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico;
| | - Rosa María Ribas-Aparicio
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (M.R.-M.); (G.P.M.-L.); (A.R.-G.); (G.A.-O.); (K.D.-G.)
- Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico;
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Dong W, Wang G, Bai Y, Li Y, Huo X, Zhao J, Lu W, Lu H, Wang C, Wang X, Chen H, Tan C. Analysis of the noncoding RNA regulatory networks of H37Rv- and H37Rv△1759c-infected macrophages. Front Microbiol 2023; 14:1106643. [PMID: 36992931 PMCID: PMC10042141 DOI: 10.3389/fmicb.2023.1106643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 02/13/2023] [Indexed: 03/31/2023] Open
Abstract
Noncoding RNAs regulate the process of Mycobacterium tuberculosis (M. tb) infecting the host, but there is no simultaneous transcriptional information of long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) and the global regulatory networks of non-coding RNA. Rv1759c, a virulence factor, is a member of protein family containing the proline-glutamic acid (PE) in M. tb, which can increase M. tb survival. To reveal the noncoding RNA regulatory networks and the effect of Rv1759c on non-coding RNA expression during M. tb infection, we collected samples of H37Rv- and H37Rv△1759c-infected macrophages and explored the full transcriptome expression profile. We found 356 mRNAs, 433 lncRNAs, 168 circRNAs, and 12 miRNAs differentially expressed during H37Rv infection, 356 mRNAs, 433 lncRNAs, 168 circRNAs, and 12 miRNAs differentially expressed during H37Rv△1759c infection. We constructed lncRNA/circRNA-miRNA-mRNA regulatory networks during H37Rv and H37Rv△1759c infection. We demonstrated the role of one of the hubs of the networks, hsa-miR-181b-3p, for H37Rv survival in macrophages. We discovered that the expression changes of 68 mRNAs, 92 lncRNAs, 26 circRNAs, and 3 miRNAs were only related to the deletion of Rv1759c by comparing the transcription profiles of H37Rv and H37Rv△1759c. Here, our study comprehensively characterizes the transcriptional profiles in THP1-derived-macrophages infected with H37Rv and H37Rv△1759c, which provides support and new directions for in-depth exploration of noncoding RNA and PE/PPE family functions during the infection process.
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Affiliation(s)
- Wenqi Dong
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, China
| | - Gaoyan Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yajuan Bai
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yuxin Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xinyu Huo
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jing Zhao
- WuHan Animal Disease Control Center, Wuhan, Hubei, China
| | - Wenjia Lu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Hao Lu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Chenchen Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xiangru Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, China
| | - Chen Tan
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, China
- *Correspondence: Chen Tan,
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ppe51 Variants Enable Growth of Mycobacterium tuberculosis at Acidic pH by Selectively Promoting Glycerol Uptake. J Bacteriol 2022; 204:e0021222. [PMID: 36226966 PMCID: PMC9664963 DOI: 10.1128/jb.00212-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In defined media supplemented with single carbon sources, Mycobacterium tuberculosis (Mtb) exhibits carbon source specific growth restriction. When supplied with glycerol as the sole carbon source at pH 5.7, Mtb establishes a metabolically active state of nonreplicating persistence known as acid growth arrest. We hypothesized that acid growth arrest on glycerol is not a metabolic restriction, but rather an adaptive response. To test this hypothesis, we selected for and identified several Mtb mutants that could grow under these restrictive conditions. All mutations were mapped to the ppe51 gene and resulted in variants with 3 different amino acid substitutions- S211R, E215K, and A228D. Expression of the ppe51 variants in Mtb promoted growth at acidic pH showing that the mutant alleles are sufficient to cause the dominant gain-of-function, Enhanced Acid Growth (EAG) phenotype. Testing growth on other single carbon sources showed the PPE51 variants specifically enhanced growth on glycerol, suggesting PPE51 plays a role in glycerol uptake. Using radiolabeled glycerol, enhanced glycerol uptake was observed in Mtb expressing the PPE51 (S211R) variant, with glycerol overaccumulation in triacylglycerol. Notably, the EAG phenotype is deleterious for growth in macrophages, where the mutants have selectively faster replication and reduced survival in activated macrophages compared to resting macrophages. Recombinant PPE51 protein exhibited differential thermostability in the wild type (WT) or S211R variants in the presence of glycerol, supporting the model that EAG substitutions alter PPE51-glycerol interactions. Together, these findings support that PPE51 variants selectively promote glycerol uptake and that slowed growth at acidic pH is an important adaptive mechanism required for macrophage pathogenesis. IMPORTANCE It is puzzling why Mycobacterium tuberculosis (Mtb) cannot grow on glycerol at acidic pH, as it has a carbon source and oxygen, everything it needs to grow. In this study, we found that Mtb limits uptake of glycerol at acidic pH to restrict its growth and that mutations in ppe51 promote uptake of glycerol at acidic pH and enable growth. That is, Mtb can grow well at acidic pH on glycerol, but has adapted instead to stop growth. Notably, ppe51 variants exhibit enhanced replication and reduced survival in activated macrophages, supporting a role for pH-dependent slowed growth during macrophage pathogenesis.
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Berisio R, Delogu G. PGRS domain structures: Doomed to sail the mycomembrane. PLoS Pathog 2022; 18:e1010760. [PMID: 36048802 PMCID: PMC9436101 DOI: 10.1371/journal.ppat.1010760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The impact of artificial intelligence (AI) in understanding biological processes is potentially immense. Structural elucidation of mycobacterial PE_PGRS is sustenance to unveil the role of these enigmatic proteins. We propose a PGRS “sailing” model as a smart tool to diffuse along the mycomembrane, to expose structural motifs for host interactions, and/or to ship functional protein modules at their C-terminus.
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Affiliation(s)
- Rita Berisio
- Institute of Biostructures and Bioimaging, IBB, CNR, Naples, Italy
- * E-mail: (RB); (GD)
| | - Giovanni Delogu
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie–Sezione di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy
- Mater Olbia Hospital, Olbia, Italy
- * E-mail: (RB); (GD)
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Mycobacterial Adhesion: From Hydrophobic to Receptor-Ligand Interactions. Microorganisms 2022; 10:microorganisms10020454. [PMID: 35208908 PMCID: PMC8875947 DOI: 10.3390/microorganisms10020454] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/07/2022] [Accepted: 02/12/2022] [Indexed: 11/24/2022] Open
Abstract
Adhesion is crucial for the infective lifestyles of bacterial pathogens. Adhesion to non-living surfaces, other microbial cells, and components of the biofilm extracellular matrix are crucial for biofilm formation and integrity, plus adherence to host factors constitutes a first step leading to an infection. Adhesion is, therefore, at the core of pathogens’ ability to contaminate, transmit, establish residency within a host, and cause an infection. Several mycobacterial species cause diseases in humans and animals with diverse clinical manifestations. Mycobacterium tuberculosis, which enters through the respiratory tract, first adheres to alveolar macrophages and epithelial cells leading up to transmigration across the alveolar epithelium and containment within granulomas. Later, when dissemination occurs, the bacilli need to adhere to extracellular matrix components to infect extrapulmonary sites. Mycobacteria causing zoonotic infections and emerging nontuberculous mycobacterial pathogens follow divergent routes of infection that probably require adapted adhesion mechanisms. New evidence also points to the occurrence of mycobacterial biofilms during infection, emphasizing a need to better understand the adhesive factors required for their formation. Herein, we review the literature on tuberculous and nontuberculous mycobacterial adhesion to living and non-living surfaces, to themselves, to host cells, and to components of the extracellular matrix.
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10
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Li F, Guo X, Xiang D, Pitt ME, Bainomugisa A, Coin LJ. Computational analysis and prediction of PE_PGRS proteins using machine learning. Comput Struct Biotechnol J 2022; 20:662-674. [PMID: 35140886 PMCID: PMC8804200 DOI: 10.1016/j.csbj.2022.01.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/09/2022] [Accepted: 01/18/2022] [Indexed: 12/18/2022] Open
Abstract
Mycobacterium tuberculosis genome comprises approximately 10% of two families of poorly characterised genes due to their high GC content and highly repetitive nature. The largest sub-group, the proline-glutamic acid polymorphic guanine-cytosine-rich sequence (PE_PGRS) family, is thought to be involved in host response and disease pathogenicity. Due to their high genetic variability and complexity of analysis, they are typically disregarded for further research in genomic studies. There are currently limited online resources and homology computational tools that can identify and analyse PE_PGRS proteins. In addition, they are computational-intensive and time-consuming, and lack sensitivity. Therefore, computational methods that can rapidly and accurately identify PE_PGRS proteins are valuable to facilitate the functional elucidation of the PE_PGRS family proteins. In this study, we developed the first machine learning-based bioinformatics approach, termed PEPPER, to allow users to identify PE_PGRS proteins rapidly and accurately. PEPPER was built upon a comprehensive evaluation of 13 popular machine learning algorithms with various sequence and physicochemical features. Empirical studies demonstrated that PEPPER achieved significantly better performance than alignment-based approaches, BLASTP and PHMMER, in both prediction accuracy and speed. PEPPER is anticipated to facilitate community-wide efforts to conduct high-throughput identification and analysis of PE_PGRS proteins.
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Affiliation(s)
- Fuyi Li
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, 792 Elizabeth Street, Melbourne, VIC 3000, Australia
| | - Xudong Guo
- School of Information Engineering, Ningxia University, Yinchuan, Ningxia 750021, China
| | - Dongxu Xiang
- Faculty of Engineering and Information Technology, The University of Melbourne, VIC 3000, Australia
| | - Miranda E. Pitt
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, 792 Elizabeth Street, Melbourne, VIC 3000, Australia
| | | | - Lachlan J.M. Coin
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, 792 Elizabeth Street, Melbourne, VIC 3000, Australia
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11
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Imidazole-Thiosemicarbazide Derivatives as Potent Anti- Mycobacterium tuberculosis Compounds with Antibiofilm Activity. Cells 2021; 10:cells10123476. [PMID: 34943984 PMCID: PMC8700351 DOI: 10.3390/cells10123476] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 02/06/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) is an intracellular pathogenic bacterium and the causative agent of tuberculosis. This disease is one of the most ancient and deadliest bacterial infections, as it poses major health, social and economic challenges at a global level, primarily in low- and middle-income countries. The lack of an effective vaccine, the long and expensive drug therapy, and the rapid spread of drug-resistant strains of Mtb have led to the re-emergence of tuberculosis as a global pandemic. Here, we assessed the in vitro activity of new imidazole-thiosemicarbazide derivatives (ITDs) against Mtb infection and their effects on mycobacterial biofilm formation. Cytotoxicity studies of the new compounds in cell lines and human monocyte-derived macrophages (MDMs) were performed. The anti-Mtb activity of ITDs was evaluated by determining minimal inhibitory concentrations of resazurin, time-kill curves, bacterial intracellular growth and the effect on biofilm formation. Mutation frequency and whole-genome sequencing of mutants that were resistant to ITDs were performed. The antimycobacterial potential of ITDs with the ability to penetrate Mtb-infected human macrophages and significantly inhibit the intracellular growth of tubercle bacilli and suppress Mtb biofilm formation was observed.
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12
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Beg MA, Hejazi II, Thakur SC, Athar F. Domain-wise differentiation of Mycobacterium tuberculosis H 37 Rv hypothetical proteins: A roadmap to discover bacterial survival potentials. Biotechnol Appl Biochem 2021; 69:296-312. [PMID: 33469971 DOI: 10.1002/bab.2109] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 01/06/2021] [Indexed: 01/08/2023]
Abstract
Proteomic information revealed approximately 3,923 proteins in Mycobacterium tuberculosis H37 Rv genome of which around ∼25% of proteins are hypothetical proteins (HPs). The present work comprises computational approaches to identify and characterize the HPs of M. tuberculosis that symbolize the putative target for rationale development of a drug or antituberculosis strategy. Proteins were primarily classified based on motif and domain information, which were further analyzed for the presence of virulence factors (VFs), determination of localization, and signal peptide/enzymatic cleavage sites. 863 HPs were found, and 599 HPs were finalized based on motifs, that is, GTP (525), Trx (47), SAM (14), PE-PGRS (5), and CBD (8). 80 HPs contain virulence factor (VF), 24 HPs localized in membrane region, and 4 HPs contain signal peptide/enzymatic cleavage sites. The overall parametric study finalizes four HPs Rv0679c, Rv0906, Rv3627c, and Rv3811 that also comprise GTPase domain. Structure prediction, structure-based function prediction, molecular docking and mutation analysis of selected proteins were done. Docking studies revealed that GTP and GTPase inhibitor (mac0182344) were docked with all four proteins with high affinities. In silico point mutation studies showed that substitution of aspartate with glycine within a GTPase motif showed the largest decrease in stability and pH differentiation also affects protein's stability. This analysis thus fixes a roadmap in the direction of finding potential target of this bacterium for drug development and enlightens the efficacy of GTP as a major regulator of Mycobacterial cellular pathways.
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Affiliation(s)
- Md Amjad Beg
- Centre for Interdisciplinary Research in Basic Science, Jamia Millia Islamia, Jamia Nagar, New Delhi, India
| | - Iram Iqbal Hejazi
- Centre for Interdisciplinary Research in Basic Science, Jamia Millia Islamia, Jamia Nagar, New Delhi, India
| | - Sonu Chand Thakur
- Centre for Interdisciplinary Research in Basic Science, Jamia Millia Islamia, Jamia Nagar, New Delhi, India
| | - Fareeda Athar
- Centre for Interdisciplinary Research in Basic Science, Jamia Millia Islamia, Jamia Nagar, New Delhi, India
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13
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PE_PGRS33, an Important Virulence Factor of Mycobacterium tuberculosis and Potential Target of Host Humoral Immune Response. Cells 2021; 10:cells10010161. [PMID: 33467487 PMCID: PMC7830552 DOI: 10.3390/cells10010161] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/04/2021] [Accepted: 01/12/2021] [Indexed: 01/16/2023] Open
Abstract
PE_PGRS proteins are surface antigens of Mycobacterium tuberculosis (Mtb) and a few other pathogenic mycobacteria. The PE_PGRS33 protein is among the most studied PE_PGRSs. It is known that the PE domain of PE_PGRS33 is required for the protein translocation through the mycobacterial cell wall, where the PGRS domain remains available for interaction with host receptors. Interaction with Toll like receptor 2 (TLR2) promotes secretion of inflammatory chemokines and cytokines, which are key in the immunopathogenesis of tuberculosis (TB). In this review, we briefly address some key challenges in the development of a TB vaccine and attempt to provide a rationale for the development of new vaccines aimed at fostering a humoral response against Mtb. Using PE_PGRS33 as a model for a surface-exposed antigen, we exploit the availability of current structural data using homology modeling to gather insights on the PGRS domain features. Our study suggests that the PGRS domain of PE_PGRS33 exposes four PGII sandwiches on the outer surface, which, we propose, are directly involved through their loops in the interactions with the host receptors and, as such, are promising targets for a vaccination strategy aimed at inducing a humoral response.
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14
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Xie Y, Zhou Y, Liu S, Zhang XL. PE_PGRS: Vital proteins in promoting mycobacterial survival and modulating host immunity and metabolism. Cell Microbiol 2020; 23:e13290. [PMID: 33217152 DOI: 10.1111/cmi.13290] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/04/2020] [Accepted: 11/08/2020] [Indexed: 12/20/2022]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (M. tb), is the leading infectious cause of mortality worldwide. One of the key reasons for M. tb pathogenesis is the capability of M. tb to evade immune elimination and survive in macrophage, eventually causing chronic infection. However the pathogenicity mechanism of M. tb is not unclear yet, and thus diagnosis and therapy for TB remains a challenge. The genome of M. tb, encodes a unique protein family known as the PGRS family, with largely unexplored functions. Recently, an increasing number of reports have shown that the PE_PGRS proteins play critical roles in bacterial pathogenesis and immune evasion. The PE_PGRS protein family, characterized by a special N-terminal PE (Pro (P)-Glu (E) motif) domain and a C-terminal PGRS (Polymorphic GC-rich Repetitive Sequences) domain, is restricted mainly to pathogenic mycobacteria. Here we summarize current literature on the PE_PGRS as vital proteins in promoting bacterial survival and modulating host immunity, cell death and metabolism. We also highlight the potential of PE_PGRS as novel targets of anti-mycobacterial interventions for TB control.
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Affiliation(s)
- Yan Xie
- Hubei Province Key Laboratory of Allergy and Immunology, Department of Allergy Zhongnan Hospital, Department of Immunology Wuhan University School of Basic Medical Sciences, Wuhan, China.,State Key Laboratory of Virology, Frontier Science Center for Immunology and Metabolism, Wuhan University School of Medicine, Wuhan, China
| | - Yidan Zhou
- Department of Microbiology, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
| | - Sheng Liu
- Hubei Province Key Laboratory of Allergy and Immunology, Department of Allergy Zhongnan Hospital, Department of Immunology Wuhan University School of Basic Medical Sciences, Wuhan, China
| | - Xiao-Lian Zhang
- Hubei Province Key Laboratory of Allergy and Immunology, Department of Allergy Zhongnan Hospital, Department of Immunology Wuhan University School of Basic Medical Sciences, Wuhan, China.,State Key Laboratory of Virology, Frontier Science Center for Immunology and Metabolism, Wuhan University School of Medicine, Wuhan, China
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15
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Liu S, Xie Y, Luo W, Dou Y, Xiong H, Xiao Z, Zhang XL. PE_PGRS31-S100A9 Interaction Promotes Mycobacterial Survival in Macrophages Through the Regulation of NF-κB-TNF-α Signaling and Arachidonic Acid Metabolism. Front Microbiol 2020; 11:845. [PMID: 32457723 PMCID: PMC7225313 DOI: 10.3389/fmicb.2020.00845] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 04/08/2020] [Indexed: 12/17/2022] Open
Abstract
Mycobacterium tuberculosis (M. tb) evades the surveillance of immune responses for survival in macrophages. However, the precise mechanism and toxins/proteins encoded by M. tb involved in the bacterial escape remain elusive. The function of Rv1768 protein (also referred to as PE_PGRS31, belonging to the PE_PGRS family) encoded by the region of deletion 14 (RD-14) in the virulent M. tb H37Rv strain has not, to the best of our knowledge, been reported previously. Here, we found that Rv1768 remarkably promotes bacterial survival in macrophages. Compared to wild type (WT) H37Rv, the Rv1768 deficient strain (H37RvΔ1768) showed significantly decreased colony-forming units in the lungs, spleen, and liver of the murine M. tb infection model. The bacterial burdens of WT H37Rv in WT macrophages and C57BL/6 mice were significantly higher than those in S100A9 deficiency cells and mice, but there were no significant differences for H37RvΔRv1768. Rv1768 binds S100A9 with the proline-glutamic acid domain (PE domain) and blocks the interaction between S100A9 and Toll-like receptor 4 (TLR4), and suppresses TLR4-myeloid differentiation factor 88-nuclear factor-kappa B (NF-κB)-tumor necrosis factor α (TNF-α) signaling in macrophages. Interestingly, Rv1768 binding to S100A9 also disturbs the metabolism of arachidonic acid by activating 5-lipoxygenase, increasing lipotoxin A4, and down-regulating cyclooxygenase-2 and prostaglandin E2 expression, thus, promoting mycobacterial survival. Our results revealed that M. tb Rv1768 promotes mycobacterial survival in macrophages by regulating NF-κB-TNF-α signaling and arachidonic acid metabolism via S100A9. Disturbing the interaction between Rv1768 and S100A9 may be a potential therapeutic target for tuberculosis.
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Affiliation(s)
- Sheng Liu
- Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, Wuhan University School of Basic Medical Sciences and Department of Allergy, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Yan Xie
- Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, Wuhan University School of Basic Medical Sciences and Department of Allergy, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Wei Luo
- Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, Wuhan University School of Basic Medical Sciences and Department of Allergy, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Yafeng Dou
- Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, Wuhan University School of Basic Medical Sciences and Department of Allergy, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Huan Xiong
- Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, Wuhan University School of Basic Medical Sciences and Department of Allergy, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Zhen Xiao
- Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, Wuhan University School of Basic Medical Sciences and Department of Allergy, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Xiao-Lian Zhang
- Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, Wuhan University School of Basic Medical Sciences and Department of Allergy, Zhongnan Hospital, Wuhan University, Wuhan, China.,State Key Laboratory of Virology, Frontier Science Center for Immunology and Metabolism, Wuhan University School of Medicine, Wuhan, China
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16
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Long Q, Xiang X, Yin Q, Li S, Yang W, Sun H, Liu Q, Xie J, Deng W. PE_PGRS62 promotes the survival of Mycobacterium smegmatis within macrophages via disrupting ER stress-mediated apoptosis. J Cell Physiol 2019; 234:19774-19784. [PMID: 30937925 DOI: 10.1002/jcp.28577] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 02/16/2019] [Accepted: 02/20/2019] [Indexed: 12/16/2022]
Abstract
Mycobacterium tuberculosis, the leading causative agent of tuberculosis, remains one of the most deadly infectious pathogens. PE_PGRS proteins become a new focus as their species specificity in mycobacteria, especially in pathogenic mycobacteria. Despite intensive research, PE_PGRS proteins are still a mysterious aspect of mycobacterial pathogenesis with unknown mechanism. Herein, we focused on a PE_PGRS member from M. tuberculosis, PE_PGRS62, characterized by a surface-exposed protein function in disrupting phagolysosome maturation. Expression of PE_PGRS62 in Mycobacterium smegmatis, a nonpathogenic species naturally deficient in PE_PGRS genes, resulted in enhanced resistance to various in vitro stresses and cellular survival in macrophage. As a consequence, the cytokine profiles of macrophage were disturbed and cell apoptosis were inhibited via decreasing endoplasmic reticulum stress response.
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Affiliation(s)
- Quanxin Long
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, People's Republic of China
| | - Xiaohong Xiang
- School of Pharmacy, Chongqing Medical and Pharmaceutical College, Chongqing, People's Republic of China
| | - Qingqin Yin
- Department of Respiratory Medicine, China National Clinical Research Center for Respiratory Diseases, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, People's Republic of China
| | - Shuangjiang Li
- Department of Physical Examination Center, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, People's Republic of China
| | - Wenmin Yang
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University, People's Republic of China
| | - Hang Sun
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, People's Republic of China
| | - Qi Liu
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, People's Republic of China
| | - Jianping Xie
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University, People's Republic of China
| | - Wanyan Deng
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, People's Republic of China
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17
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Child SA, Rossi VP, Bell SG. Selective ϖ-1 oxidation of fatty acids by CYP147G1 from Mycobacterium marinum. Biochim Biophys Acta Gen Subj 2019; 1863:408-417. [DOI: 10.1016/j.bbagen.2018.11.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 11/17/2018] [Accepted: 11/22/2018] [Indexed: 10/27/2022]
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18
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De Maio F, Battah B, Palmieri V, Petrone L, Corrente F, Salustri A, Palucci I, Bellesi S, Papi M, Rubino S, Sali M, Goletti D, Sanguinetti M, Manganelli R, De Spirito M, Delogu G. PE_PGRS3 of Mycobacterium tuberculosis is specifically expressed at low phosphate concentration, and its arginine-rich C-terminal domain mediates adhesion and persistence in host tissues when expressed in Mycobacterium smegmatis. Cell Microbiol 2018; 20:e12952. [PMID: 30192424 DOI: 10.1111/cmi.12952] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 08/22/2018] [Accepted: 08/28/2018] [Indexed: 12/14/2022]
Abstract
PE_PGRSs of Mycobacterium tuberculosis (Mtb) represent a family of complex and peculiar proteins whose role and function remain elusive. In this study, we investigated PE_PGRS3 and PE_PGRS4, two highly homologous PE_PGRSs encoded by two contiguous genes in the Mtb genome. Using a gene-reporter system in Mycobacterium smegmatis (Ms) and transcriptional analysis in Mtb, we show that PE_PGRS3, but not PE_PGRS4, is specifically expressed under low phosphate concentrations. Interestingly, PE_PGRS3, but not PE_PGRS4, has a unique, arginine-rich C-terminal domain of unknown function. Heterologous expression of PE_PGRS3 in Ms was used to demonstrate cellular localisation of the protein on the mycobacterial surface, where it significantly affects net surface charge. Moreover, expression of full-length PE_PGRS3 enhanced adhesion of Ms to murine macrophages and human epithelial cells and improved bacterial persistence in spleen tissue following infection in mice. Expression of the PE_PGRS3 functional deletion mutant lacking the C-terminal domain in Ms did not enhance adhesion to host cells, showing a phenotype similar to the Ms parental strain. Interestingly, enhanced persistence of Ms expressing PE_PGRS3 did not correlate with increased concentrations of inflammatory cytokines. These results point to a critical role for the ≈ 80 amino acids long, arginine-rich C-terminal domain of PE_PGRS3 in tuberculosis pathogenesis.
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Affiliation(s)
- Flavio De Maio
- Institute of Microbiology, Fondazione Policlinico Universitario A. Gemelli, IRCCS - Università Cattolica del Sacro Cuore, Rome, Italy
| | - Basem Battah
- Institute of Microbiology, Fondazione Policlinico Universitario A. Gemelli, IRCCS - Università Cattolica del Sacro Cuore, Rome, Italy.,Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Valentina Palmieri
- Institute of Physics, Fondazione Policlinico Universitario A. Gemelli, IRCCS - Università Cattolica del Sacro Cuore, Rome, Italy
| | - Linda Petrone
- Translational Research Unit, Department of Epidemiology and Preclinical Research, National Institute for Infectious Diseases, Rome, Italy
| | - Francesco Corrente
- Institute of Haematology, Fondazione Policlinico Universitario A. Gemelli, IRCCS - Università Cattolica del Sacro Cuore, Rome, Italy
| | - Alessandro Salustri
- Institute of Microbiology, Fondazione Policlinico Universitario A. Gemelli, IRCCS - Università Cattolica del Sacro Cuore, Rome, Italy
| | - Ivana Palucci
- Institute of Microbiology, Fondazione Policlinico Universitario A. Gemelli, IRCCS - Università Cattolica del Sacro Cuore, Rome, Italy
| | - Silvia Bellesi
- Institute of Haematology, Fondazione Policlinico Universitario A. Gemelli, IRCCS - Università Cattolica del Sacro Cuore, Rome, Italy
| | - Massimiliano Papi
- Institute of Physics, Fondazione Policlinico Universitario A. Gemelli, IRCCS - Università Cattolica del Sacro Cuore, Rome, Italy
| | - Salvatore Rubino
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Michela Sali
- Institute of Microbiology, Fondazione Policlinico Universitario A. Gemelli, IRCCS - Università Cattolica del Sacro Cuore, Rome, Italy
| | - Delia Goletti
- Translational Research Unit, Department of Epidemiology and Preclinical Research, National Institute for Infectious Diseases, Rome, Italy
| | - Maurizio Sanguinetti
- Institute of Microbiology, Fondazione Policlinico Universitario A. Gemelli, IRCCS - Università Cattolica del Sacro Cuore, Rome, Italy
| | | | - Marco De Spirito
- Institute of Physics, Fondazione Policlinico Universitario A. Gemelli, IRCCS - Università Cattolica del Sacro Cuore, Rome, Italy
| | - Giovanni Delogu
- Institute of Microbiology, Fondazione Policlinico Universitario A. Gemelli, IRCCS - Università Cattolica del Sacro Cuore, Rome, Italy
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19
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Structural and functional characterisation of the cytochrome P450 enzyme CYP268A2 from Mycobacterium marinum. Biochem J 2018; 475:705-722. [DOI: 10.1042/bcj20170946] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 01/10/2018] [Accepted: 01/16/2018] [Indexed: 11/17/2022]
Abstract
Members of the cytochrome P450 monooxygenase family CYP268 are found across a broad range of Mycobacterium species including the pathogens Mycobacterium avium, M. colombiense, M. kansasii, and M. marinum. CYP268A2, from M. marinum, which is the first member of this family to be studied, was purified and characterised. CYP268A2 was found to bind a variety of substrates with high affinity, including branched and straight chain fatty acids (C10–C12), acetate esters, and aromatic compounds. The enzyme was also found to bind phenylimidazole inhibitors but not larger azoles, such as ketoconazole. The monooxygenase activity of CYP268A2 was efficiently reconstituted using heterologous electron transfer partner proteins. CYP268A2 hydroxylated geranyl acetate and trans-pseudoionone at a terminal methyl group to yield (2E,6E)-8-hydroxy-3,7-dimethylocta-2,6-dien-1-yl acetate and (3E,5E,9E)-11-hydroxy-6,10-dimethylundeca-3,5,9-trien-2-one, respectively. The X-ray crystal structure of CYP268A2 was solved to a resolution of 2.0 Å with trans-pseudoionone bound in the active site. The overall structure was similar to that of the related phytanic acid monooxygenase CYP124A1 enzyme from Mycobacterium tuberculosis, which shares 41% sequence identity. The active site is predominantly hydrophobic, but includes the Ser99 and Gln209 residues which form hydrogen bonds with the terminal carbonyl group of the pseudoionone. The structure provided an explanation on why CYP268A2 shows a preference for shorter substrates over the longer chain fatty acids which bind to CYP124A1 and the selective nature of the catalysed monooxygenase activity.
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20
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Immune recognition surface construction of Mycobacterium tuberculosis epitope-specific antibody responses in tuberculosis patients identified by peptide microarrays. Int J Infect Dis 2017; 56:155-166. [DOI: 10.1016/j.ijid.2017.01.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 01/14/2017] [Indexed: 11/17/2022] Open
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21
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Meena PR, Monu, Meena LS. Fibronectin binding protein and Ca 2+ play an access key role to mediate pathogenesis in Mycobacterium tuberculosis: An overview. Biotechnol Appl Biochem 2017; 63:820-826. [PMID: 26275158 DOI: 10.1002/bab.1434] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 08/09/2015] [Indexed: 12/31/2022]
Abstract
The anomalous distribution of adhesive proteins throughout on the cell surface of the Mycobacterium tuberculosis H37 Rv and their contribution in cell surface adhesion and host-pathogen interaction remain elusive. The completion of M. tuberculosis H37 Rv genome sequence analysis gives some interesting information about polymorphic GC-rich repetitive sequence (PGRS) subfamily of M. tuberculosis that encodes fibronectin binding proteins (FnBP), which have been extensively studied, but the function in the pathogenesis of most of these proteins remains unknown and unclear. This review addresses the M. tuberculosis entry mechanism in the host cell. In particular, an effort has been made to focus on several aspects, (a) association of FnBP encodes by PE_PGRS protein family of M. tuberculosis during host-pathogen interactions. (b) Effect of calcium ions in and outside of the host cell is overriding to maintenance of calcium trafficking in phagocytosis. Furthermore, FnBP may be a potential source of antigenic variation that participating in evoking immune response. M. tuberculosis entry mechanism does not have a major influence alone, involvement of calcium ions, perhaps shed light on host-pathogen interaction relationship, and could open up new avenues for development of novel drug by targeting M. tuberculosis FnBP and blockade of selective adhesions could be useful for therapeutics.
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Affiliation(s)
- Prem Raj Meena
- CSIR-Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, Mall Road, Delhi, India
| | - Monu
- CSIR-Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, Mall Road, Delhi, India
| | - Laxman S Meena
- CSIR-Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, Mall Road, Delhi, India
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Abstract
Type VII secretion (T7S) systems of mycobacteria secrete substrates over the unusual diderm cell envelope. Furthermore, T7S gene clusters are present throughout the phylum Actinobacteria, and functional T7S-like systems have been identified in Firmicutes. Most of the T7S substrates can be divided into two families: the Esx proteins, which are found in both Firmicutes and Actinobacteria, and the PE and PPE proteins, which are more mycobacterium-specific. Members of both families have been shown to be secreted as folded heterodimers, suggesting that this is a conserved feature of T7S substrates. Most knowledge of the mechanism of T7S and the roles of T7S systems in virulence comes from studies of pathogenic mycobacteria. These bacteria can contain up to five T7S systems, called ESX-1 to ESX-5, each having its own role in bacterial physiology and virulence. In this article, we discuss the general composition of T7S systems and the role of the individual components in secretion. These conserved components include two membrane proteins with (predicted) enzymatic activities: a predicted ATPase (EccC), likely to be required for energy provision of T7S, and a subtilisin-like protease (MycP) involved in processing of specific substrates. Additionally, we describe the role of a conserved intracellular chaperone in T7S substrate recognition, based on recently published crystal structures and molecular analysis. Finally, we discuss system-specific features of the different T7S systems in mycobacteria and their role in pathogenesis and provide an overview of the role of T7S in virulence of other pathogenic bacteria.
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In-depth analysis of the genome sequence of a clinical, extensively drug-resistant Mycobacterium bovis strain. Tuberculosis (Edinb) 2016; 100:46-52. [DOI: 10.1016/j.tube.2016.06.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 06/22/2016] [Accepted: 06/23/2016] [Indexed: 11/23/2022]
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Abstract
Through thousands of years of reciprocal coevolution, Mycobacterium tuberculosis has become one of humanity's most successful pathogens, acquiring the ability to establish latent or progressive infection and persist even in the presence of a fully functioning immune system. The ability of M. tuberculosis to avoid immune-mediated clearance is likely to reflect a highly evolved and coordinated program of immune evasion strategies that interfere with both innate and adaptive immunity. These include the manipulation of their phagosomal environment within host macrophages, the selective avoidance or engagement of pattern recognition receptors, modulation of host cytokine production, and the manipulation of antigen presentation to prevent or alter the quality of T-cell responses. In this article we review an extensive array of published studies that have begun to unravel the sophisticated program of specific mechanisms that enable M. tuberculosis and other pathogenic mycobacteria to persist and replicate in the face of considerable immunological pressure from their hosts. Unraveling the mechanisms by which M. tuberculosis evades or modulates host immune function is likely to be of major importance for the development of more effective new vaccines and targeted immunotherapy against tuberculosis.
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Comparison of Sample Preparation Methods Used for the Next-Generation Sequencing of Mycobacterium tuberculosis. PLoS One 2016; 11:e0148676. [PMID: 26849565 PMCID: PMC4744016 DOI: 10.1371/journal.pone.0148676] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 01/20/2016] [Indexed: 11/19/2022] Open
Abstract
The advent and widespread application of next-generation sequencing (NGS) technologies to the study of microbial genomes has led to a substantial increase in the number of studies in which whole genome sequencing (WGS) is applied to the analysis of microbial genomic epidemiology. However, microorganisms such as Mycobacterium tuberculosis (MTB) present unique problems for sequencing and downstream analysis based on their unique physiology and the composition of their genomes. In this study, we compare the quality of sequence data generated using the Nextera and TruSeq isolate preparation kits for library construction prior to Illumina sequencing-by-synthesis. Our results confirm that MTB NGS data quality is highly dependent on the purity of the DNA sample submitted for sequencing and its guanine-cytosine content (or GC-content). Our data additionally demonstrate that the choice of library preparation method plays an important role in mitigating downstream sequencing quality issues. Importantly for MTB, the Illumina TruSeq library preparation kit produces more uniform data quality than the Nextera XT method, regardless of the quality of the input DNA. Furthermore, specific genomic sequence motifs are commonly missed by the Nextera XT method, as are regions of especially high GC-content relative to the rest of the MTB genome. As coverage bias is highly undesirable, this study illustrates the importance of appropriate protocol selection when performing NGS studies in order to ensure that sound inferences can be made regarding mycobacterial genomes.
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Hongo JA, de Castro GM, Cintra LC, Zerlotini A, Lobo FP. POTION: an end-to-end pipeline for positive Darwinian selection detection in genome-scale data through phylogenetic comparison of protein-coding genes. BMC Genomics 2015; 16:567. [PMID: 26231214 PMCID: PMC4521464 DOI: 10.1186/s12864-015-1765-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 07/10/2015] [Indexed: 11/29/2022] Open
Abstract
Background Detection of genes evolving under positive Darwinian evolution in genome-scale data is nowadays a prevailing strategy in comparative genomics studies to identify genes potentially involved in adaptation processes. Despite the large number of studies aiming to detect and contextualize such gene sets, there is virtually no software available to perform this task in a general, automatic, large-scale and reliable manner. This certainly occurs due to the computational challenges involved in this task, such as the appropriate modeling of data under analysis, the computation time to perform several of the required steps when dealing with genome-scale data and the highly error-prone nature of the sequence and alignment data structures needed for genome-wide positive selection detection. Results We present POTION, an open source, modular and end-to-end software for genome-scale detection of positive Darwinian selection in groups of homologous coding sequences. Our software represents a key step towards genome-scale, automated detection of positive selection, from predicted coding sequences and their homology relationships to high-quality groups of positively selected genes. POTION reduces false positives through several sophisticated sequence and group filters based on numeric, phylogenetic, quality and conservation criteria to remove spurious data and through multiple hypothesis corrections, and considerably reduces computation time thanks to a parallelized design. Our software achieved a high classification performance when used to evaluate a curated dataset of Trypanosoma brucei paralogs previously surveyed for positive selection. When used to analyze predicted groups of homologous genes of 19 strains of Mycobacterium tuberculosis as a case study we demonstrated the filters implemented in POTION to remove sources of errors that commonly inflate errors in positive selection detection. A thorough literature review found no other software similar to POTION in terms of customization, scale and automation. Conclusion To the best of our knowledge, POTION is the first tool to allow users to construct and check hypotheses regarding the occurrence of site-based evidence of positive selection in non-curated, genome-scale data within a feasible time frame and with no human intervention after initial configuration. POTION is available at http://www.lmb.cnptia.embrapa.br/share/POTION/. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1765-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jorge A Hongo
- Laboratório Multiusuário de Bioinformática, Embrapa Informática Agropecuária, Empresa Brasileira de Pesquisa Agropecuária (Embrapa), Campinas, São Paulo, 13083-886, Brazil.
| | - Giovanni M de Castro
- Laboratório Multiusuário de Bioinformática, Embrapa Informática Agropecuária, Empresa Brasileira de Pesquisa Agropecuária (Embrapa), Campinas, São Paulo, 13083-886, Brazil.
| | - Leandro C Cintra
- Laboratório Multiusuário de Bioinformática, Embrapa Informática Agropecuária, Empresa Brasileira de Pesquisa Agropecuária (Embrapa), Campinas, São Paulo, 13083-886, Brazil.
| | - Adhemar Zerlotini
- Laboratório Multiusuário de Bioinformática, Embrapa Informática Agropecuária, Empresa Brasileira de Pesquisa Agropecuária (Embrapa), Campinas, São Paulo, 13083-886, Brazil.
| | - Francisco P Lobo
- Laboratório Multiusuário de Bioinformática, Embrapa Informática Agropecuária, Empresa Brasileira de Pesquisa Agropecuária (Embrapa), Campinas, São Paulo, 13083-886, Brazil.
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Meena LS, Meena J. Cloning and characterization of a novel PE_PGRS60 protein (Rv3652) of Mycobacterium tuberculosis H37 Rv exhibit fibronectin-binding property. Biotechnol Appl Biochem 2015; 63:525-31. [PMID: 26158346 DOI: 10.1002/bab.1411] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 07/01/2015] [Indexed: 11/08/2022]
Abstract
The binding of pathogenic bacteria to extracellular matrix components enhances adhesion and invasion of host cells. The host receptor proteins such as fibronectin (Fn) targeted to pathogenic ligands that have clinical importance. In the present study, we cloned, expressed, purified, and identified a novel Fn-binding protein from PE_PGRS60 (Rv3652) of Mycobacterium tuberculosis H37 Rv. The protein product of Rv3652 showed optimum binding efficiency to 10 ng Fn at 0.2 µg purified protein of PE_PGRS60 and 20 ng Fn at 0.2 µg concentrations, respectively. PE_PGRS60 protein (primary sequences) of different pathogenic mycobacterium species retrieved from NCBI exhibited complete homology at the 104 residues on multiple sequence alignment. The primary sequence of protein from H37 Rv was further used to predict cleavage signals. The secondary structure prediction method revealed a number of residues responsible for alpha helices formation and percentage of residues participating in the random coils and extended strands. In addition, online prediction tools such as B- and T-cell epitopes showed the surface probability scale and antigenic propensity scale. The current finding opens new opportunity to mycobacterial survival and pathogenesis research of PE-polymorphic GC-rich repetitive sequences (PE-PGRS) family proteins.
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Affiliation(s)
- Laxman S Meena
- CSIR-Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, Delhi, India
| | - Jaishree Meena
- CSIR-Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, Delhi, India
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Deng W, Zeng J, Xiang X, Li P, Xie J. PE11 (Rv1169c) selectively alters fatty acid components of Mycobacterium smegmatis and host cell interleukin-6 level accompanied with cell death. Front Microbiol 2015; 6:613. [PMID: 26157429 PMCID: PMC4477156 DOI: 10.3389/fmicb.2015.00613] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Accepted: 06/02/2015] [Indexed: 11/26/2022] Open
Abstract
PE/PPE family proteins, named after their conserved PE (Pro-Glu) and PPE (Pro-Pro-Glu) domains of N-terminal, are most intriguing aspects of pathologic mycobacterial genome. The roles of most members of this family remain unknown, although selected genes of this family are related to the virulence of Mycobacterium tuberculosis. In order to decipher the role of Rv1169c, the Mycobacterium smegmatis strain heterologous expressed this ORF was constructed and identified that Rv1169c was a cell wall associated protein with a novel function in modifying the cell wall fatty acids. The growth of Rv1169c expressing strain was affected under surface stress, acidic condition and antibiotics treatment. M. smegmatis expressing Rv1169c induced necrotic cell death of macrophage after infection and significantly decreased interlukin-6 production compared to controls. In general, these results underscore a proposing role of Rv1169c in virulence of M. tuberculosis, as it's role in the susceptibility of anti-mycobacteria factors caused by modified cell wall fatty acid, and the induced necrotic cell death by Rv1169c is crucial for M. tuberculosis virulence during infection.
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Affiliation(s)
- Wanyan Deng
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University Chongqing, China
| | - Jie Zeng
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University Chongqing, China
| | - Xiaohong Xiang
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University Chongqing, China
| | - Ping Li
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University Chongqing, China
| | - Jianping Xie
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University Chongqing, China
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Identification of Novel Potential Vaccine Candidates against Tuberculosis Based on Reverse Vaccinology. BIOMED RESEARCH INTERNATIONAL 2015; 2015:483150. [PMID: 25961021 PMCID: PMC4413515 DOI: 10.1155/2015/483150] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Accepted: 01/07/2015] [Indexed: 11/21/2022]
Abstract
Tuberculosis (TB) is a chronic infectious disease, considered as the second leading cause of death worldwide, caused by Mycobacterium tuberculosis. The limited efficacy of the bacillus Calmette-Guérin (BCG) vaccine against pulmonary TB and the emergence of multidrug-resistant TB warrants the need for more efficacious vaccines. Reverse vaccinology uses the entire proteome of a pathogen to select the best vaccine antigens by in silico approaches. M. tuberculosis H37Rv proteome was analyzed with NERVE (New Enhanced Reverse Vaccinology Environment) prediction software to identify potential vaccine targets; these 331 proteins were further analyzed with VaxiJen for the determination
of their antigenicity value. Only candidates with values ≥0.5 of antigenicity and 50% of adhesin probability and without homology with human proteins or transmembrane regions were selected, resulting in 73 antigens. These proteins were grouped by families in seven groups and analyzed by amino acid sequence alignments, selecting 16 representative proteins. For each candidate, a search of the literature and protein analysis with different bioinformatics tools, as well as a simulation of the immune response, was conducted. Finally, we selected six novel vaccine candidates, EsxL, PE26, PPE65, PE_PGRS49, PBP1, and Erp, from M. tuberculosis that can be used to improve or design new TB vaccines.
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Gastelum-Aviña P, Velazquez C, Espitia C, Lares-Villa F, Garibay-Escobar A. A PE_PGRS33 protein ofMycobacterium tuberculosis: an ideal target for future tuberculosis vaccine design. Expert Rev Vaccines 2015; 14:699-711. [DOI: 10.1586/14760584.2015.1015995] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Meena LS. An overview to understand the role of PE_PGRS family proteins in Mycobacterium tuberculosis H37 Rv and their potential as new drug targets. Biotechnol Appl Biochem 2014; 62:145-53. [PMID: 24975480 DOI: 10.1002/bab.1266] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 06/19/2014] [Indexed: 11/12/2022]
Abstract
Tuberculosis has long been the scourge of humanity, claiming millions of lives. The family of PE_PGRS gene has been attributed to the Mycobacterium tuberculosis pathogenesis over the past few decades. The gene of PE_PGRS family proteins are most often clustered in a region of the genome often as overlapping genes and role in cell surface markers, adhesion and invasion of defense cells of the host (macrophage and dendritic cells). The proline-glutamic acid (PE) domain is responsible for the cellular localization of these proteins on bacterial cells. This gene family shows immense genetic variability in terms of multiple insertion-deletions and single-nucleotide polymorphisms as seen in PE_PGRS9, PE_PGRS17, PE_PGRS18, and PE_PGRS33. In spite of variability, there are indications of shared epitopes in these proteins. Few of these gene sequences that have been studied from evolutionary perspective show indication of positive selection and also landmarks of recent evolutionary events. Many of these proteins show calcium-binding motifs and consequently seen to be responsible in inhibition of phagolysosome formation via a calmodulin-kinase-dependent pathway. A number of PE_PGRS genes were tested for its expression with different growth conditions in vitro and in vivo, among which the contrast in expressivity was seen vividly in PE_PGRS16 (upregulated) and PE_PGRS26 (downregulated) in bacteria persisting in macrophages. Similarly, PE_PGRS33 has been indicated in macrophagial necrosis by a tumor necrosis factor-α-induced pathway. These PE_PGRS family genes may be an interesting subject for research and development. Their fibronectin-binding and calcium-binding property may be strongly implicated in immunopathogenesis of virulent M. tuberculosis strain. In this review, an attempt has been made to evaluate and present data for better understanding of in vivo pathogen functions, for understanding the physiological significance of PE_PGRS gene family, and their potential as new drug targets.
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Affiliation(s)
- Laxman S Meena
- CSIR-Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, Delhi, India
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Cohen I, Parada C, Acosta-Gío E, Espitia C. The PGRS Domain from PE_PGRS33 of Mycobacterium tuberculosis is Target of Humoral Immune Response in Mice and Humans. Front Immunol 2014; 5:236. [PMID: 24904584 PMCID: PMC4033847 DOI: 10.3389/fimmu.2014.00236] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Accepted: 05/06/2014] [Indexed: 12/05/2022] Open
Abstract
The PE_PGRS33 protein is a member of the PE family, which encompasses the PE and the PE_PGRS subfamilies. Among PE_PGRS’s, this protein is one of the most studied antigens and its immunomodulatory properties are influence by both PE and PGRS domains. However, the contribution of these domains to the host immune recognition of the PE_PGRS33 protein and their potential role in latent tuberculosis infection in humans is still unknown. In this study, the immunogenic properties of the complete PE_PGRS33 protein and each domain separately were evaluated in BALB/c mice and latent tuberculosis infected (LTBI) humans. In mice, PE_PGRS33 and its domains induced similar antibody production and secretion of IFN-γ. PE_PGRS33 and the PE domain stimulated higher CD4+ and CD8+ T-cell proliferation compared to the PGRS domain. This demonstrated that the principal difference in the immune recognition of the domains is the higher activation of T-cell subpopulations involved in the control of tuberculosis. In humans, the secretion of IFN-γ in response to PE_PGRS33 was detected in both LTBI and in non-infected vaccinated individuals. The same was observed for antibody response, which targets epitopes located in the PGRS domain but not in the PE domain. These observations suggest that T and B cell responses to PE_PGRS33 are induced by BCG vaccination and can be maintained for many years in non-infected individuals. This also indicates that the IFN-γ response detected might not be associated with latent tuberculosis infection. These results contribute to the elucidation of the role of the PE_PGRS33 protein and its PE and PGRS domains in the immune response against Mycobacterium tuberculosis.
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Affiliation(s)
- Ingrid Cohen
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México , Mexico City , Mexico
| | - Cristina Parada
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México , Mexico City , Mexico
| | - Enrique Acosta-Gío
- Facultad de Odontología, Universidad Nacional Autónoma de México , Mexico City , Mexico
| | - Clara Espitia
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México , Mexico City , Mexico
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Houston S, Russell S, Hof R, Roberts AK, Cullen P, Irvine K, Smith DS, Borchers CH, Tonkin ML, Boulanger MJ, Cameron CE. The multifunctional role of the pallilysin-associated Treponema pallidum protein, Tp0750, in promoting fibrinolysis and extracellular matrix component degradation. Mol Microbiol 2014; 91:618-34. [PMID: 24303899 PMCID: PMC3954913 DOI: 10.1111/mmi.12482] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/03/2013] [Indexed: 12/25/2022]
Abstract
The mechanisms that facilitate dissemination of the highly invasive spirochaete, Treponema pallidum, are incompletely understood. Previous studies showed the treponemal metalloprotease pallilysin (Tp0751) possesses fibrin clot degradation capability, suggesting a role in treponemal dissemination. In the current study we report characterization of the functionally linked protein Tp0750. Structural modelling predicts Tp0750 contains a von Willebrand factor type A (vWFA) domain, a protein-protein interaction domain commonly observed in extracellular matrix (ECM)-binding proteins. We report Tp0750 is a serine protease that degrades the major clot components fibrinogen and fibronectin. We also demonstrate Tp0750 cleaves a matrix metalloprotease (MMP) peptide substrate that is targeted by several MMPs, enzymes central to ECM remodelling. Through proteomic analyses we show Tp0750 binds the endothelial fibrinolytic receptor, annexin A2, in a specific and dose-dependent manner. These results suggest Tp0750 constitutes a multifunctional protein that is able to (1) degrade infection-limiting clots by both inhibiting clot formation through degradation of host coagulation cascade proteins and promoting clot dissolution by complexing with host proteins involved in the fibrinolytic cascade and (2) facilitate ECM degradation via MMP-like proteolysis of host components. We propose that through these activities Tp0750 functions in concert with pallilysin to enable T. pallidum dissemination.
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Affiliation(s)
- Simon Houston
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
| | - Shannon Russell
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
| | - Rebecca Hof
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
| | - Alanna K. Roberts
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
| | - Paul Cullen
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
| | - Kyle Irvine
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
| | - Derek S. Smith
- University of Victoria-Genome BC Proteomics Centre, Victoria, British Columbia, Canada, V8Z 7X8
| | - Christoph H. Borchers
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
- University of Victoria-Genome BC Proteomics Centre, Victoria, British Columbia, Canada, V8Z 7X8
| | - Michelle L. Tonkin
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
| | - Martin J. Boulanger
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
| | - Caroline E. Cameron
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
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Cronje L, Warren R, Klumperman B. pH-dependent adhesion of mycobacteria to surface-modified polymer nanofibers. J Mater Chem B 2013; 1:6608-6618. [DOI: 10.1039/c3tb21393e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Moreno-Altamirano MMB, Paredes-González IS, Espitia C, Santiago-Maldonado M, Hernández-Pando R, Sánchez-García FJ. Bioinformatic identification of Mycobacterium tuberculosis proteins likely to target host cell mitochondria: virulence factors? MICROBIAL INFORMATICS AND EXPERIMENTATION 2012; 2:9. [PMID: 23259719 PMCID: PMC3563495 DOI: 10.1186/2042-5783-2-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 12/19/2012] [Indexed: 02/03/2023]
Abstract
Background M. tuberculosis infection either induces or inhibits host cell death, depending on the bacterial strain and the cell microenvironment. There is evidence suggesting a role for mitochondria in these processes. On the other hand, it has been shown that several bacterial proteins are able to target mitochondria, playing a critical role in bacterial pathogenesis and modulation of cell death. However, mycobacteria–derived proteins able to target host cell mitochondria are less studied. Results A bioinformaic analysis based on available genomic sequences of the common laboratory virulent reference strain Mycobacterium tuberculosis H37Rv, the avirulent strain H37Ra, the clinical isolate CDC1551, and M. bovis BCG Pasteur strain 1173P2, as well as of suitable bioinformatic tools (MitoProt II, PSORT II, and SignalP) for the in silico search for proteins likely to be secreted by mycobacteria that could target host cell mitochondria, showed that at least 19 M. tuberculosis proteins could possibly target host cell mitochondria. We experimentally tested this bioinformatic prediction on four M. tuberculosis recombinant proteins chosen from this list of 19 proteins (p27, PE_PGRS1, PE_PGRS33, and MT_1866). Confocal microscopy analyses showed that p27, and PE_PGRS33 proteins colocalize with mitochondria. Conclusions Based on the bioinformatic analysis of whole M. tuberculosis genome sequences, we propose that at least 19 out of 4,246 M. tuberculosis predicted proteins would be able to target host cell mitochondria and, in turn, control mitochondrial physiology. Interestingly, such a list of 19 proteins includes five members of a mycobacteria specific family of proteins (PE/PE_PGRS) thought to be virulence factors, and p27, a well known virulence factor. P27, and PE_PGRS33 proteins experimentally showed to target mitochondria in J774 cells. Our results suggest a link between mitochondrial targeting of M. tuberculosis proteins and virulence.
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Affiliation(s)
- María Maximina Bertha Moreno-Altamirano
- Laboratorio de Inmunorregulación, Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala, Col, Sto, Tomás, México D,F, México.
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Verma-Kumar S, Abraham D, Dendukuri N, Cheeran JV, Sukumar R, Balaji KN. Serodiagnosis of tuberculosis in Asian elephants (Elephas maximus) in Southern India: a latent class analysis. PLoS One 2012; 7:e49548. [PMID: 23166708 PMCID: PMC3500311 DOI: 10.1371/journal.pone.0049548] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 10/10/2012] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Mycobacterium tuberculosis, a causative agent of chronic tuberculosis disease, is widespread among some animal species too. There is paucity of information on the distribution, prevalence and true disease status of tuberculosis in Asian elephants (Elephas maximus). The aim of this study was to estimate the sensitivity and specificity of serological tests to diagnose M. tuberculosis infection in captive elephants in southern India while simultaneously estimating sero-prevalence. METHODOLOGY/PRINCIPAL FINDINGS Health assessment of 600 elephants was carried out and their sera screened with a commercially available rapid serum test. Trunk wash culture of select rapid serum test positive animals yielded no animal positive for M. tuberculosis isolation. Under Indian field conditions where the true disease status is unknown, we used a latent class model to estimate the diagnostic characteristics of an existing (rapid serum test) and new (four in-house ELISA) tests. One hundred and seventy nine sera were randomly selected for screening in the five tests. Diagnostic sensitivities of the four ELISAs were 91.3-97.6% (95% Credible Interval (CI): 74.8-99.9) and diagnostic specificity were 89.6-98.5% (95% CI: 79.4-99.9) based on the model we assumed. We estimate that 53.6% (95% CI: 44.6-62.8) of the samples tested were free from infection with M. tuberculosis and 15.9% (97.5% CI: 9.8 - to 24.0) tested positive on all five tests. CONCLUSIONS/SIGNIFICANCE Our results provide evidence for high prevalence of asymptomatic M. tuberculosis infection in Asian elephants in a captive Indian setting. Further validation of these tests would be important in formulating area-specific effective surveillance and control measures.
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Affiliation(s)
- Shalu Verma-Kumar
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka, India
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore, Karnataka, India
| | - David Abraham
- Asian Nature Conservation Foundation, Bangalore, Karnataka, India
| | - Nandini Dendukuri
- Department of Medicine, McGill University, Montreal, Quebec, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Quebec, Canada
| | | | - Raman Sukumar
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore, Karnataka, India
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Singh SK, Tripathi DK, Singh PK, Sharma S, Srivastava KK. Protective and survival efficacies of Rv0160c protein in murine model of Mycobacterium tuberculosis. Appl Microbiol Biotechnol 2012; 97:5825-37. [PMID: 23104642 DOI: 10.1007/s00253-012-4493-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Revised: 10/01/2012] [Accepted: 10/02/2012] [Indexed: 12/20/2022]
Abstract
The proline-glutamic acid (PE) and proline-proline-glutamic acid (PPE) multi-gene families code for approximately 10% of the Mycobacterium tuberculosis (Mtb) genome. These proteins are thought to be virulence factors that participate in impounding the host immune responses. While some members have been studied, the functions of most PE/PPE proteins are yet to be explored. The studies presented here have specifically characterized the roles of one of the PE proteins of Mtb, Rv0160c (PE4), in mycobacterial persistence and in prophylactic efficacy. We have expressed Rv0160c in a non-pathogenic fast-growing Mycobacterium smegmatis strain and demonstrated that the protein improves the survival of mycobacteria in macrophages and in mice. The protein has also shown its effect under physiological stress of bacteria, as evidenced by elevated expression in acidic and in hypoxic conditions. In mice, the level of Rv0160c was noticeably high during the chronic stage of tuberculosis. The seroreactivity of the protein against different categories of tuberculosis patients revealed a strong B-cell humoral response in freshly infected pulmonary tuberculosis patients. In mice, it exhibited increased IL-2, TNF, and IL-6 production. The antigenic properties of the protein directed towards the protective efficacy against the Mtb challenge. All together, our findings have identified Rv0160c as an in vivo expressed immunodominant antigen which plays a crucial role in the pathogenesis of mycobacterial disease and could prove to be a good preventive antigen for tuberculosis.
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Affiliation(s)
- Susmita K Singh
- Division of Microbiology, CSIR--Central Drug Research Institute, Lucknow 226001, India
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Kohli S, Singh Y, Sharma K, Mittal A, Ehtesham NZ, Hasnain SE. Comparative genomic and proteomic analyses of PE/PPE multigene family of Mycobacterium tuberculosis H₃₇Rv and H₃₇Ra reveal novel and interesting differences with implications in virulence. Nucleic Acids Res 2012; 40:7113-22. [PMID: 22618876 PMCID: PMC3424577 DOI: 10.1093/nar/gks465] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Tuberculosis, caused by Mycobacterium tuberculosis, remains a leading infectious disease taking one human life every 15 s globally. The two well-characterized strains H37Rv and H37Ra, derived from the same parental strain M. tuberculosis H37, show dramatically different pathogenic phenotypes. PE/PPE gene family, comprising of 176 open reading frames and present exclusively in genus Mycobacterium, accounts for ∼10% of the M. tuberculosis genome. Our comprehensive in silico analyses of PE/PPE family of H37Ra and virulent H37Rv strains revealed genetic differences between these strains in terms of several single nucleotide variations and InDels and these manifested in changes in physico-chemical properties, phosphorylation sites, and protein: protein interacting domains of the corresponding proteomes. Similar comparisons using the 13 sigma factor genes, 36 members of the mammalian cell entry family, 13 mycobacterial membrane protein large family members and 11 two-component signal transduction systems along with 5 orphaned response regulators and 2 orphaned sensor kinases failed to reveal very significant difference between H37Rv and H37Ra, reinforcing the importance of PE/PPE genes. Many of these changes between H37Rv and H37Ra can be correlated to differences in pathogenesis and virulence of the two strains.
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Affiliation(s)
- Sakshi Kohli
- Kusuma School of Biological Sciences, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India
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McEvoy CRE, Cloete R, Müller B, Schürch AC, van Helden PD, Gagneux S, Warren RM, Gey van Pittius NC. Comparative analysis of Mycobacterium tuberculosis pe and ppe genes reveals high sequence variation and an apparent absence of selective constraints. PLoS One 2012; 7:e30593. [PMID: 22496726 PMCID: PMC3319526 DOI: 10.1371/journal.pone.0030593] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 12/19/2011] [Indexed: 11/18/2022] Open
Abstract
Mycobacterium tuberculosis complex (MTBC) genomes contain 2 large gene families termed pe and ppe. The function of pe/ppe proteins remains enigmatic but studies suggest that they are secreted or cell surface associated and are involved in bacterial virulence. Previous studies have also shown that some pe/ppe genes are polymorphic, a finding that suggests involvement in antigenic variation. Using comparative sequence analysis of 18 publicly available MTBC whole genome sequences, we have performed alignments of 33 pe (excluding pe_pgrs) and 66 ppe genes in order to detect the frequency and nature of genetic variation. This work has been supplemented by whole gene sequencing of 14 pe/ppe (including 5 pe_pgrs) genes in a cohort of 40 diverse and well defined clinical isolates covering all the main lineages of the M. tuberculosis phylogenetic tree. We show that nsSNP's in pe (excluding pgrs) and ppe genes are 3.0 and 3.3 times higher than in non-pe/ppe genes respectively and that numerous other mutation types are also present at a high frequency. It has previously been shown that non-pe/ppe M. tuberculosis genes display a remarkably low level of purifying selection. Here, we also show that compared to these genes those of the pe/ppe families show a further reduction of selection pressure that suggests neutral evolution. This is inconsistent with the positive selection pressure of "classical" antigenic variation. Finally, by analyzing such a large number of genes we were able to detect large differences in mutation type and frequency between both individual genes and gene sub-families. The high variation rates and absence of selective constraints provides valuable insights into potential pe/ppe function. Since pe/ppe proteins are highly antigenic and have been studied as potential vaccine components these results should also prove informative for aspects of M. tuberculosis vaccine design.
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Affiliation(s)
- Christopher R E McEvoy
- Department of Science and Technology, Medical Research Council Centre for Molecular and Cellular Biology, Stellenbosch University, Tygerberg, Cape Town, South Africa.
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Akhter Y, Ehebauer MT, Mukhopadhyay S, Hasnain SE. The PE/PPE multigene family codes for virulence factors and is a possible source of mycobacterial antigenic variation: Perhaps more? Biochimie 2012; 94:110-6. [DOI: 10.1016/j.biochi.2011.09.026] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Accepted: 09/27/2011] [Indexed: 02/03/2023]
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Integrative analysis of transcriptome and genome indicates two potential genomic islands are associated with pathogenesis of Mycobacterium tuberculosis. Gene 2011; 489:21-9. [PMID: 21924330 DOI: 10.1016/j.gene.2011.08.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Revised: 07/20/2011] [Accepted: 08/26/2011] [Indexed: 11/20/2022]
Abstract
Mycobacterium tuberculosis (M.tb) is a successful human pathogen and widely prevalent throughout the world. Genomic islands (GIs) are thought to be related to pathogenicity. In this study, we predicted two potential genomic islands in M.tb genome, respectively named as GI-1 and GI-2. It is indicated that the genes belong to PE_PGRS family in GI-1 and genes involved in sulfolipid-1 (SL-1) synthesis in GI-2 are strongly associated with M.tb pathogenesis. Sequence analysis revealed that the five PGRS genes are more polymorphic than other PGRS members in full virulence M.tb complex strains at significance level 0.01 but not in attenuated strains. Expression analysis of microarrays collected from literatures displayed that GI-1 genes, especially Rv3508 might be correlated with the response to the inhibition of aerobic respiration. Microarray analysis also showed that SL-1 cluster genes are drastically down-expressed in attenuated strains relative to full virulence strains. We speculated that the effect of SL-1 on M.tb pathogenicity could be associated with long-term survival and persistence establishment during infection. Additionally, the gene Rv3508 in GI-1 was under positive selection. Rv3508 may involve the response of M.tb to the inhibition of aerobic respiration by low oxygen or drug PA-824, and it may be a common feature of genes in GI-1. These findings may provide some novel insights into M.tb physiology and pathogenesis.
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Mukhopadhyay S, Balaji KN. The PE and PPE proteins of Mycobacterium tuberculosis. Tuberculosis (Edinb) 2011; 91:441-7. [DOI: 10.1016/j.tube.2011.04.004] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 04/09/2011] [Accepted: 04/10/2011] [Indexed: 11/30/2022]
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Kanji A, Hasan Z, Tanveer M, Mahboob R, Jafri S, Hasan R. Presence of RD149 deletions in M. tuberculosis Central Asian Strain 1 isolates affect growth and TNFα induction in THP-1 monocytes. PLoS One 2011; 6:e24178. [PMID: 21904612 PMCID: PMC3163664 DOI: 10.1371/journal.pone.0024178] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Accepted: 08/02/2011] [Indexed: 12/17/2022] Open
Abstract
Central Asian Strain 1 (CAS1) is the prevalent Mycobacterium tuberculosis genogroup in South Asia. CAS1 strains carry deletions in RD149 and RD152 regions. Significance of these deletions is as yet unknown. We compared CAS1 strains with RD149 and concurrent RD149-RD152 deletions with CAS1 strains without deletions and with the laboratory reference strain, M. tuberculosis H37Rv for growth and for induction of TNFα, IL6, CCL2 and IL10 in THP-1 cells. Growth of CAS1 strains with deletions was slower in broth (RD149; p = 0.024 and RD149-RD152; p = 0.025) than that of strains without deletions. CAS1 strains with RD149 deletion strains further showed reduced intracellular growth (p = 0.013) in THP-1 cells as compared with strains without deletions, and also as compared with H37Rv (p = 0.007) and with CAS1 RD149-RD152 deletion strains (p = 0.029). All CAS1 strains induced higher levels of TNFα and IL10 secretion in THP-1 cells than H37Rv. Additionally, CAS1 strains with RD149 deletions induced more TNFα secretion than those without deletions (p = 0.013). CAS1 RD149 deletion strains from extrapulmonary sources showed more rapid growth and induced lower levels of TNFα and IL6 secretion in THP-1 cells than isolates from pulmonary sources. This data suggests that presence of RD149 reduces growth and increases the induction of TNFα in host cells by CAS1 strains. Differences observed for extrapulmonary strains may indicate an adaptation which increases potential for dissemination and tropism outside the lung. Overall, we hypothesise that RD149 deletions generate genetic diversity within strains and impact interactions of CAS1 strains with host cells with important clinical consequences.
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Affiliation(s)
- Akbar Kanji
- Department of Pathology and Microbiology, Aga Khan University, Karachi, Pakistan
| | - Zahra Hasan
- Department of Pathology and Microbiology, Aga Khan University, Karachi, Pakistan
| | - Mehnaz Tanveer
- Department of Pathology and Microbiology, Aga Khan University, Karachi, Pakistan
| | - Raunaq Mahboob
- Department of Pathology and Microbiology, Aga Khan University, Karachi, Pakistan
| | - Sana Jafri
- Department of Pathology and Microbiology, Aga Khan University, Karachi, Pakistan
| | - Rumina Hasan
- Department of Pathology and Microbiology, Aga Khan University, Karachi, Pakistan
- * E-mail:
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Henderson B, Nair S, Pallas J, Williams MA. Fibronectin: a multidomain host adhesin targeted by bacterial fibronectin-binding proteins. FEMS Microbiol Rev 2011; 35:147-200. [DOI: 10.1111/j.1574-6976.2010.00243.x] [Citation(s) in RCA: 227] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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Tian C, Jian-ping X. Roles of PE_PGRS family in Mycobacterium tuberculosis pathogenesis and novel measures against tuberculosis. Microb Pathog 2010; 49:311-4. [DOI: 10.1016/j.micpath.2010.07.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2010] [Revised: 07/06/2010] [Accepted: 07/10/2010] [Indexed: 11/27/2022]
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Cadieux N, Parra M, Cohen H, Maric D, Morris SL, Brennan MJ. Induction of cell death after localization to the host cell mitochondria by the Mycobacterium tuberculosis PE_PGRS33 protein. MICROBIOLOGY-SGM 2010; 157:793-804. [PMID: 21081760 DOI: 10.1099/mic.0.041996-0] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
PE_PGRS33 is the most studied member of the unique PE family of mycobacterial proteins. These proteins are composed of a PE domain (Pro-Glu motif), a linker region and a PGRS domain (polymorphic GC-rich-repetitive sequence). Previous studies have shown that PE_PGRS33 is surface-exposed, constitutively expressed during growth and infection, involved in creating antigenic diversity, and able to induce death in transfected or infected eukaryotic cells. In this study, we showed that PE_PGRS33 co-localizes to the mitochondria of transfected cells, a phenomenon dependent on the linker region and the PGRS domain, but not the PE domain. Using different genetic fusions and chimeras, we also demonstrated a direct correlation between localization to the host mitochondria and the induction of cell death. Finally, although all constructs localizing to the mitochondria did induce apoptosis, only the wild-type PE_PGRS33 with its own PE domain also induced primary necrosis, indicating a potentially important role for the PE domain. Considering the importance of primary necrosis in Mycobacterium tuberculosis dissemination during natural infection, the PE_PGRS33 protein may play a crucial role in the pathogenesis of tuberculosis.
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Affiliation(s)
- Nathalie Cadieux
- Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, MD, USA
| | - Marcela Parra
- Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, MD, USA
| | - Hannah Cohen
- Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, MD, USA
| | - Dragan Maric
- National Institute of Neurological Disorders and Stroke, Flow Cytometry Core Facility, NIH, Bethesda, MD, USA
| | - Sheldon L Morris
- Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, MD, USA
| | - Michael J Brennan
- Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, MD, USA
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Singh G, Singh G, Jadeja D, Kaur J. Lipid hydrolizing enzymes in virulence: Mycobacterium tuberculosis as a model system. Crit Rev Microbiol 2010; 36:259-69. [PMID: 20500016 DOI: 10.3109/1040841x.2010.482923] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
This review is focused on the virulent traits of lipolytic enzymes from bacteria with special emphasis on Mycobacterium tuberculosis. In vivo, triacylglycerols in the form of inclusion bodies are present in tubercle bacilli in the lungs. This pathogenic bacterium possesses a lipase gene (Lip) family, which is expressed and differentially regulated under a variety of in vitro conditions. Not much research work has been carried out on these lipolytic enzymes. A better understanding of lipolytic enzymes in mycobacteria would lead to develop new strategies for tuberculosis treatment. The present review highlights the recent work done in the field of mycobacterium lipolytic enzymes and their involvement in the virulence and pathogenicity.
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Affiliation(s)
- Gurdyal Singh
- Department of Biotechnology, Panjab University, Chandigarh-160014, India
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Jang HJ, Nde C, Toghrol F, Bentley WE. Global transcriptome analysis of the Mycobacterium bovis BCG response to sodium hypochlorite. Appl Microbiol Biotechnol 2009; 85:127-40. [PMID: 19756581 DOI: 10.1007/s00253-009-2208-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Revised: 08/12/2009] [Accepted: 08/13/2009] [Indexed: 11/28/2022]
Abstract
Tuberculosis is a common and often deadly infectious disease caused by mycobacteria, mainly Mycobacterium tuberculosis and infrequently by other subspecies of the M. tuberculosis complex, such as M. bovis. Sodium hypochlorite (bleach) is routinely used in hospitals and health care facilities for surface sterilization; however, the modes of action of bleach on M. bovis BCG and how this organism develops resistance to sodium hypochlorite have not been elucidated. In this study, we performed a global toxicogenomic analysis of the M. bovis response to 2.5 mM sodium hypochlorite after 10 and 20 min. M. bovis BCG growth was monitored by measuring the quantity of ATP in picomoles produced over a short exposure time (10-60 min) to sodium hypochlorite. This study revealed significant regulation of oxidative stress response genes of M. bovis BCG, such as oxidoreductase, peroxidase, heat shock proteins and lipid transport, and metabolism genes. We interpreted this response as a potentially more lethal interplay between fatty acid metabolism, sulfur metabolism, and oxidative stress. Our results also suggest that sodium hypochlorite repressed transcription of genes involved in cell wall synthesis of M. bovis. This study shows that the treatment of M. bovis BCG with bleach inhibits the biosynthesis of outer cell wall mycolic acids and also induces oxidative damage.
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Affiliation(s)
- Hyeung-Jin Jang
- Department of Biochemistry, College of Oriental Medicine, Kyung Hee University, Seoul, Republic of Korea
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Jang HJ, Nde C, Toghrol F, Bentley WE. Microarray analysis of Mycobacterium bovis BCG revealed induction of iron acquisition related genes in response to hydrogen peroxide. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2009; 43:9465-9472. [PMID: 19924887 DOI: 10.1021/es902255q] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Mycobacterium bovis BCG strain Pasteur 1173P2 responds with adaptive and protective strategies against oxidative stress. Despite advances in our understanding of the responses to oxidative stress in many specific cases, the connectivity between targeted protective genes and the rest of cell metabolism remains obscure. This study was therefore carried out to investigate the genome-wide response of M. bovis BCG to hydrogen peroxide after 10 and 60 min of treatment. ATP measurements were carried out in order to monitor the changes in M. bovis BCG growth over a 1 h period. The furA gene in Mycobacterium bovis, a pleiotropic regulator that couples iron metabolism to the oxidative stress response was involved in the response to hydrogen peroxide stress. There were also increased levels of catalase/ peroxidase (KatG) and the biosynthesis operon of mycobactin. This study revealed significant upregulation of the oxidative response group of M. bovis, amino acid transport and metabolism, defense mechanisms, DNA replication, recombination and repair, and downregulation of cell cycle control, mitosis, and meiosis, lipid transport and metabolism, and cell wall/membrane biogenesis. This study shows that the treatment of M. bovis BCG with hydrogen peroxide induces iron acquisition related genes and oxidative stress response genes within one hour of treatment.
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Affiliation(s)
- Hyeung-Jin Jang
- Department of Biochemistry, College of Oriental Medicine, Kyung Hee University, Seoul 130-701, Republic of Korea
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McEvoy CRE, van Helden PD, Warren RM, van Pittius NCG. Evidence for a rapid rate of molecular evolution at the hypervariable and immunogenic Mycobacterium tuberculosis PPE38 gene region. BMC Evol Biol 2009; 9:237. [PMID: 19769792 PMCID: PMC2758852 DOI: 10.1186/1471-2148-9-237] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2009] [Accepted: 09/21/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND PPE38 (Rv2352c) is a member of the large PPE gene family of Mycobacterium tuberculosis and related mycobacteria. The function of PPE proteins is unknown but evidence suggests that many are cell-surface associated and recognised by the host immune system. Previous studies targeting other PPE gene members suggest that some display high levels of polymorphism and it is thought that this might represent a means of providing antigenic variation. We have analysed the genetic variability of the PPE38 genomic region on a cohort of M. tuberculosis clinical isolates representing all of the major phylogenetic lineages, along with the ancestral M. tuberculosis complex (MTBC) member M. canettii, and supplemented this with analysis of publicly available whole genome sequences representing additional M. tuberculosis clinical isolates, other MTBC members and non tuberculous mycobacteria (NTM). Where possible we have extended this analysis to include the adjacent plcABC and PPE39/40 genomic regions. RESULTS We show that the ancestral MTBC PPE38 region comprises 2 homologous PPE genes (PPE38 and PPE71), separated by 2 esat-6 (esx)-like genes and that this structure derives from an esx/esx/PPE duplication in the common ancestor of M. tuberculosis and M. marinum. We also demonstrate that this region of the genome is hypervariable due to frequent IS6110 integration, IS6110-associated recombination, and homologous recombination and gene conversion events between PPE38 and PPE71. These mutations result in combinations of gene deletion, gene truncation and gene disruption in the majority of clinical isolates. These mutations were generally found to be IS6110 strain lineage-specific, although examples of additional within-lineage and even within-cluster mutations were observed. Furthermore, we provide evidence that the published M. tuberculosis H37Rv whole genome sequence is inaccurate regarding this region. CONCLUSION Our results show that this antigen-encoding region of the M. tuberculosis genome is hypervariable. The observation that numerous different mutations have become fixed within specific lineages demonstrates that this genomic region is undergoing rapid molecular evolution and that further lineage-specific evolutionary expansion and diversification has occurred subsequent to the lineage-defining mutational events. We predict that functional loss of these genes could aid immune evasion. Finally, we also show that the PPE38 region of the published M. tuberculosis H37Rv whole genome sequence is not representative of the ATCC H37Rv reference strain.
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Affiliation(s)
- Christopher RE McEvoy
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, PO Box 19063, Tygerberg, South Africa
| | - Paul D van Helden
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, PO Box 19063, Tygerberg, South Africa
| | - Robin M Warren
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, PO Box 19063, Tygerberg, South Africa
| | - Nicolaas C Gey van Pittius
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, PO Box 19063, Tygerberg, South Africa
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