301
|
Draft Genome Sequence of Chromobacterium subtsugae MWU12-2387 Isolated from a Wild Cranberry Bog in Truro, Massachusetts. GENOME ANNOUNCEMENTS 2017; 5:5/12/e01633-16. [PMID: 28336605 PMCID: PMC5364230 DOI: 10.1128/genomea.01633-16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Chromobacterium subtsugae MWU12-2387 was isolated from the rhizosphere of cranberry plants. While it is unknown what environmental role these bacteria play in bog soils, they hold potential as biological control agents against nematodes and insect pests. Potential virulence genes were identified, including the violacein synthesis pathway, siderophores, and several chitinases.
Collapse
|
302
|
Jia X, Yang L, Dong M, Chen S, Lv L, Cao D, Fu J, Yang T, Zhang J, Zhang X, Shang Y, Wang G, Sheng Y, Huang H, Chen F. The Bioinformatics Analysis of Comparative Genomics of Mycobacterium tuberculosis Complex (MTBC) Provides Insight into Dissimilarities between Intraspecific Groups Differing in Host Association, Virulence, and Epitope Diversity. Front Cell Infect Microbiol 2017; 7:88. [PMID: 28377903 PMCID: PMC5360109 DOI: 10.3389/fcimb.2017.00088] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 03/06/2017] [Indexed: 12/31/2022] Open
Abstract
Tuberculosis now exceeds HIV as the top infectious disease cause of mortality, and is caused by the Mycobacterium tuberculosis complex (MTBC). MTBC strains have highly conserved genome sequences (similarity >99%) but dramatically different phenotypes. To analyze the relationship between genotype and phenotype, we conducted the comparative genomic analysis on 12 MTBC strains representing different lineages (i.e., Mycobacterium bovis; M. bovis BCG; M. microti; M. africanum; M. tuberculosis H37Rv; M. tuberculosis H37Ra, and six M. tuberculosis clinical isolates). The analysis focused on the three aspects of pathogenicity: host association, virulence, and epitope variations. Host association analysis indicated that eight mce3 genes, two enoyl-CoA hydratases, and five PE/PPE family genes were present only in human isolates; these may have roles in host-pathogen interactions. There were 15 SNPs found on virulence factors (including five SNPs in three ESX secretion proteins) only in the Beijing strains, which might be related to their more virulent phenotype. A comparison between the virulent H37Rv and non-virulent H37Ra strains revealed three SNPs that were likely associated with the virulence attenuation of H37Ra: S219L (PhoP), A219E (MazG) and a newly identified I228M (EspK). Additionally, a comparison of animal-associated MTBC strains showed that the deletion of the first four genes (i.e., pe35, ppe68, esxB, esxA), rather than all eight genes of RD1, might play a central role in the virulence attenuation of animal isolates. Finally, by comparing epitopes among MTBC strains, we found that four epitopes were lost only in the Beijing strains; this may render them better capable of evading the human immune system, leading to enhanced virulence. Overall, our comparative genomic analysis of MTBC strains reveals the relationship between the highly conserved genotypes and the diverse phenotypes of MTBC, provides insight into pathogenic mechanisms, and facilitates the development of potential molecular targets for the prevention and treatment of tuberculosis.
Collapse
Affiliation(s)
- Xinmiao Jia
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of SciencesBeijing, China; College of Life Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Li Yang
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of SciencesBeijing, China; College of Life Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Mengxing Dong
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of SciencesBeijing, China; College of Life Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Suting Chen
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute Beijing, China
| | - Lingna Lv
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute Beijing, China
| | - Dandan Cao
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences Beijing, China
| | - Jing Fu
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of SciencesBeijing, China; College of Life Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Tingting Yang
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of SciencesBeijing, China; College of Life Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Ju Zhang
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences Beijing, China
| | - Xiangli Zhang
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of SciencesBeijing, China; College of Life Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Yuanyuan Shang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute Beijing, China
| | - Guirong Wang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute Beijing, China
| | - Yongjie Sheng
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Jilin University Changchun, China
| | - Hairong Huang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute Beijing, China
| | - Fei Chen
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of SciencesBeijing, China; College of Life Sciences, University of Chinese Academy of SciencesBeijing, China; Sino-Danish College, University of Chinese Academy of SciencesBeijing, China; Collaborative Innovation Center for Genetics and DevelopmentShanghai, China
| |
Collapse
|
303
|
Vidyarthi A, Khan N, Agnihotri T, Siddiqui KF, Nair GR, Arora A, Janmeja AK, Agrewala JN. Antibody response against PhoP efficiently discriminates among healthy individuals, tuberculosis patients and their contacts. PLoS One 2017; 12:e0173769. [PMID: 28319170 PMCID: PMC5358785 DOI: 10.1371/journal.pone.0173769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 02/27/2017] [Indexed: 02/06/2023] Open
Abstract
Tuberculosis continues to be one of the most devastating global health problem. Its diagnosis will benefit in timely initiation of the treatment, cure and therefore reduction in the transmission of the disease. Tests are available, but none can be comprehensively relied on for its diagnosis; especially in TB-endemic zones. PhoP is a key player in Mycobacterium tuberculosis virulence but nothing has been known about its role in the diagnosis of TB. We monitored the presence of anti-PhoP antibodies in the healthy, patients and their contacts. In addition, we also measured antibodies against early secretory antigens ESAT-6 and CFP-10, and latency associated antigen Acr-1 to include proteins that are associated with the different stages of disease progression. Healthy subjects showed high antibody titer against PhoP than patients and their contacts. In addition, a distinct pattern in the ratio of Acr-1/PhoP was observed among all cohorts. This study for the first time demonstrates a novel role of anti-PhoP antibodies, as a possible marker for the diagnosis of TB and therefore will contribute in the appropriate action and management of the disease.
Collapse
Affiliation(s)
| | - Nargis Khan
- CSIR-Institute of Microbial Technology, Chandigarh, India
| | | | | | - Girish R. Nair
- CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Ashish Arora
- CSIR-Central Drug Research Institute, Lucknow, India
| | | | | |
Collapse
|
304
|
Sharma S, Ryndak MB, Aggarwal AN, Yadav R, Sethi S, Masih S, Laal S, Verma I. Transcriptome analysis of mycobacteria in sputum samples of pulmonary tuberculosis patients. PLoS One 2017; 12:e0173508. [PMID: 28282458 PMCID: PMC5345810 DOI: 10.1371/journal.pone.0173508] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 02/21/2017] [Indexed: 11/18/2022] Open
Abstract
Pulmonary tuberculosis, the disease caused by Mycobacterium tuberculosis, still retains a top rank among the deadliest communicable diseases. Sputum expectorated during the disease continues to be a primary diagnostic specimen and also serves as a reservoir of bacteria. The expression pattern of mycobacteria in sputum will lead to an insight into bacterial adaptation at the most highly transmissible stage of infection and can also help in identifying newer diagnostic as well as drug targets. Thus, in the present study, a whole genome microarray of Mycobacterium tuberculosis was used to elucidate the transcriptional profile of mycobacteria in the sputum samples of smear positive pulmonary tuberculosis patients. Overall, the mycobacteria in sputum appeared to be in a low energy and low replicative state as compared to in vitro grown log phase M. tb with downregulation of genes involved in ATP synthesis, aerobic respiration and translational machinery. Simultaneously, downregulation was also seen in the genes involved in secretion machinery of mycobacteria along with the downregulation of genes involved in the synthesis of phthiocerol dimycocerosate and phenol glycolipids. In contrast, the majority of the genes which showed an upregulation in sputum mycobacteria were of unknown function. Further identification of these genes may provide new insights into the mycobacterial behavior during this phase of infection and may help in deciphering candidates for development of better diagnostic and drug candidates.
Collapse
Affiliation(s)
- Sumedha Sharma
- Department of Biochemistry, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Michelle B. Ryndak
- Department of Pathology, New York University Langone Medical Center, New York, New York, United States of America
| | - Ashutosh N. Aggarwal
- Department of Pulmonary Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Rakesh Yadav
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Sunil Sethi
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Shet Masih
- Molecular Diagnostic and Research Laboratory (MDRL) Pvt. Ltd., Chandigarh, India
| | - Suman Laal
- Department of Pathology, New York University Langone Medical Center, New York, New York, United States of America
- Veterans Affairs New York Harbor Healthcare System, New York, New York, United States of America
| | - Indu Verma
- Department of Biochemistry, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| |
Collapse
|
305
|
Yasuike M, Nishiki I, Iwasaki Y, Nakamura Y, Fujiwara A, Shimahara Y, Kamaishi T, Yoshida T, Nagai S, Kobayashi T, Katoh M. Analysis of the complete genome sequence of Nocardia seriolae UTF1, the causative agent of fish nocardiosis: The first reference genome sequence of the fish pathogenic Nocardia species. PLoS One 2017; 12:e0173198. [PMID: 28257489 PMCID: PMC5336288 DOI: 10.1371/journal.pone.0173198] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 02/16/2017] [Indexed: 01/15/2023] Open
Abstract
Nocardiosis caused by Nocardia seriolae is one of the major threats in the aquaculture of Seriola species (yellowtail; S. quinqueradiata, amberjack; S. dumerili and kingfish; S. lalandi) in Japan. Here, we report the complete nucleotide genome sequence of N. seriolae UTF1, isolated from a cultured yellowtail. The genome is a circular chromosome of 8,121,733 bp with a G+C content of 68.1% that encodes 7,697 predicted proteins. In the N. seriolae UTF1 predicted genes, we found orthologs of virulence factors of pathogenic mycobacteria and human clinical Nocardia isolates involved in host cell invasion, modulation of phagocyte function and survival inside the macrophages. The virulence factor candidates provide an essential basis for understanding their pathogenic mechanisms at the molecular level by the fish nocardiosis research community in future studies. We also found many potential antibiotic resistance genes on the N. seriolae UTF1 chromosome. Comparative analysis with the four existing complete genomes, N. farcinica IFM 10152, N. brasiliensis HUJEG-1 and N. cyriacigeorgica GUH-2 and N. nova SH22a, revealed that 2,745 orthologous genes were present in all five Nocardia genomes (core genes) and 1,982 genes were unique to N. seriolae UTF1. In particular, the N. seriolae UTF1 genome contains a greater number of mobile elements and genes of unknown function that comprise the differences in structure and gene content from the other Nocardia genomes. In addition, a lot of the N. seriolae UTF1-specific genes were assigned to the ABC transport system. Because of limited resources in ocean environments, these N. seriolae UTF1 specific ABC transporters might facilitate adaptation strategies essential for marine environment survival. Thus, the availability of the complete N. seriolae UTF1 genome sequence will provide a valuable resource for comparative genomic studies of N. seriolae isolates, as well as provide new insights into the ecological and functional diversity of the genus Nocardia.
Collapse
Affiliation(s)
- Motoshige Yasuike
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
- * E-mail: (AF); (MY)
| | - Issei Nishiki
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Yuki Iwasaki
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Yoji Nakamura
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Atushi Fujiwara
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
- * E-mail: (AF); (MY)
| | - Yoshiko Shimahara
- Research Center of Fish Diseases, National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Saiki, Oita, Japan
| | - Takashi Kamaishi
- Fisheries Agency, Ministry of Agriculture, Forestry and Fisheries, Chiyoda-ku, Tokyo, Japan
| | | | - Satoshi Nagai
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Takanori Kobayashi
- Headquarters, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Masaya Katoh
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| |
Collapse
|
306
|
Peddireddy V, Doddam SN, Ahmed N. Mycobacterial Dormancy Systems and Host Responses in Tuberculosis. Front Immunol 2017; 8:84. [PMID: 28261197 PMCID: PMC5309233 DOI: 10.3389/fimmu.2017.00084] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/18/2017] [Indexed: 12/15/2022] Open
Abstract
Tuberculosis (TB) caused by the intracellular pathogen, Mycobacterium tuberculosis (Mtb), claims more than 1.5 million lives worldwide annually. Despite promulgation of multipronged strategies to prevent and control TB, there is no significant downfall occurring in the number of new cases, and adding to this is the relapse of the disease due to the emergence of antibiotic resistance and the ability of Mtb to remain dormant after primary infection. The pathology of Mtb is complex and largely attributed to immune-evading strategies that this pathogen adopts to establish primary infection, its persistence in the host, and reactivation of pathogenicity under favorable conditions. In this review, we present various biochemical, immunological, and genetic strategies unleashed by Mtb inside the host for its survival. The bacterium enables itself to establish a niche by evading immune recognition via resorting to masking, establishment of dormancy by manipulating immune receptor responses, altering innate immune cell fate, enhancing granuloma formation, and developing antibiotic tolerance. Besides these, the regulatory entities, such as DosR and its regulon, encompassing various putative effector proteins play a vital role in maintaining the dormant nature of this pathogen. Further, reactivation of Mtb allows relapse of the disease and is favored by the genes of the Rtf family and the conditions that suppress the immune system of the host. Identification of target genes and characterizing the function of their respective antigens involved in primary infection, dormancy, and reactivation would likely provide vital clues to design novel drugs and/or vaccines for the control of dormant TB.
Collapse
Affiliation(s)
- Vidyullatha Peddireddy
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad , Hyderabad , India
| | - Sankara Narayana Doddam
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad , Hyderabad , India
| | - Niyaz Ahmed
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, India; Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh
| |
Collapse
|
307
|
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.
Collapse
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
| |
Collapse
|
308
|
Nuru A, Mamo G, Zewude A, Mulat Y, Yitayew G, Admasu A, Medhin G, Pieper R, Ameni G. Preliminary investigation of the transmission of tuberculosis between farmers and their cattle in smallholder farms in northwestern Ethiopia: a cross-sectional study. BMC Res Notes 2017; 10:31. [PMID: 28061860 PMCID: PMC5219749 DOI: 10.1186/s13104-016-2349-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Accepted: 12/16/2016] [Indexed: 11/17/2022] Open
Abstract
Background The feeding habits and close physical contact between Ethiopian farmers and their cattle promote the transmission of tuberculosis (TB) between the farmers and their cattle. This study aimed to investigate the transmission of TB between farmers and their cattle in smallholder farms in northwestern Ethiopia. Results A total of 70 human TB lymphadenitis (TBLN) cases visiting the Felegehiwot Comprehensive Specialized Hospital in Bahir Dar City and 660 cattle were investigated. Half of the cattle were owned by households with TB cases, and the remaining half by TB free households. Among the 70 human TBLN patients interviewed, 65.7% (46 out of 70) of the respondents were not aware of zoonotic TB, and 67.1% (47/70) of them consumed raw milk. Positive cultures of TB were obtained in 40 of the 70 cases where TBLN tests were positive with fine needle aspiration cytology. Spoligotyping resulted in 31 different patterns, of which 25 isolates were Mycobacterium (M.) tuberculosis, and the remaining were M. africanum (4 isolates) and M. bovis (2 isolates). None of the animals showed positive test results for bovine TB by comparative intradermal tuberculin test. Conclusions Based on the identification of M. bovis from two patients diagnosed with TBLN, we obtained preliminary evidence of zoonotic transmission of TB in northwestern Ethiopia. We did not identify a direct route of transmission between cattle and its owners. This is the objective of further investigations.
Collapse
Affiliation(s)
- Anwar Nuru
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia. .,College of Veterinary Medicine and Animal Sciences, University of Gondar, P.O. Box 346, Gondar, Ethiopia.
| | - Gezahegne Mamo
- College of Veterinary Medicine and Agriculture, Addis Ababa University, P.O. Box 34, Debre Zeit, Ethiopia
| | - Aboma Zewude
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia
| | - Yitayal Mulat
- Felegehiwot Comprehensive Specialized Hospital, P. O. Box: 47, Bahir Dar, Ethiopia
| | - Gashaw Yitayew
- Bahir Dar Regional Health Research Laboratory Centre, P.O. Box 641, Bahir Dar, Ethiopia
| | - Aschalew Admasu
- Bahir Dar Regional Health Research Laboratory Centre, P.O. Box 641, Bahir Dar, Ethiopia
| | - Girmay Medhin
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia
| | - Rembert Pieper
- J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD, USA
| | - Gobena Ameni
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia
| |
Collapse
|
309
|
Bigi MM, Lopez B, Blanco FC, Sasiain MDC, De la Barrera S, Marti MA, Sosa EJ, Fernández Do Porto DA, Ritacco V, Bigi F, Soria MA. Single nucleotide polymorphisms may explain the contrasting phenotypes of two variants of a multidrug-resistant Mycobacterium tuberculosis strain. Tuberculosis (Edinb) 2017; 103:28-36. [PMID: 28237031 DOI: 10.1016/j.tube.2016.12.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Revised: 12/27/2016] [Accepted: 12/30/2016] [Indexed: 01/18/2023]
Abstract
Globally, about 4.5% of new tuberculosis (TB) cases are multi-drug-resistant (MDR), i.e. resistant to the two most powerful first-line anti-TB drugs. Indeed, 480,000 people developed MDR-TB in 2015 and 190,000 people died because of MDR-TB. The MDR Mycobacterium tuberculosis M family, which belongs to the Haarlem lineage, is highly prosperous in Argentina and capable of building up further drug resistance without impairing its ability to spread. In this study, we sequenced the whole genomes of a highly prosperous M-family strain (Mp) and its contemporary variant, strain 410, which produced only one recorded tuberculosis case in the last two decades. Previous reports have demonstrated that Mp induced dysfunctional CD8+ cytotoxic T cell activity, suggesting that this strain has the ability to evade the immune response against M. tuberculosis. Comparative analysis of Mp and 410 genomes revealed non-synonymous polymorphisms in eleven genes and five intergenic regions with polymorphisms between both strains. Some of these genes and promoter regions are involved in the metabolism of cell wall components, others in drug resistance and a SNP in Rv1861, a gene encoding a putative transglycosylase that produces a truncated protein in Mp. The mutation in Rv3787c, a putative S-adenosyl-l-methionine-dependent methyltransferase, is conserved in all of the other prosperous M strains here analysed and absent in non-prosperous M strains. Remarkably, three polymorphic promoter regions displayed differential transcriptional activity between Mp and 410. We speculate that the observed mutations/polymorphisms are associated with the reported higher capacity of Mp for modulating the host's immune response.
Collapse
Affiliation(s)
- María Mercedes Bigi
- Universidad de Buenos Aires, Facultad de Agronomía, Cátedra de Microbiología Agrícola.INBA-CONICET, Av. San Martín 4453, C1417DSE, Buenos Aires, Argentina.
| | - Beatriz Lopez
- Instituto Nacional de Enfermedades Infecciosas-ANLIS Carlos Malbrán, Av. Vélez Sarsfield 563, C1282AFF, Buenos Aires, Argentina.
| | - Federico Carlos Blanco
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (INTA), N. Repetto and De los Reseros, Hurlingham, 1686, Buenos Aires, Argentina.
| | - María Del Carmen Sasiain
- IMEX-CONICET, Academia Nacional de Medicina, José Andrés Pacheco de Melo 3081, C1425AUM, Buenos Aires, Argentina.
| | - Silvia De la Barrera
- IMEX-CONICET, Academia Nacional de Medicina, José Andrés Pacheco de Melo 3081, C1425AUM, Buenos Aires, Argentina.
| | - Marcelo A Marti
- Departamento de Química Biológica, e IQUIBICEN-CONICET, FCEyN, UBA, Intendente Güiraldes 2160, C1428EGA, Buenos Aires, Argentina.
| | - Ezequiel Jorge Sosa
- Plataforma de Bioinformática Argentina, Instituto de Cálculo, FCEyN, UBA, Intendente Güiraldes 2160, C1428EGA, Buenos Aires, Argentina.
| | - Darío Augusto Fernández Do Porto
- Plataforma de Bioinformática Argentina, Instituto de Cálculo, FCEyN, UBA, Intendente Güiraldes 2160, C1428EGA, Buenos Aires, Argentina.
| | - Viviana Ritacco
- Instituto Nacional de Enfermedades Infecciosas-ANLIS Carlos Malbrán, Av. Vélez Sarsfield 563, C1282AFF, Buenos Aires, Argentina.
| | - Fabiana Bigi
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (INTA), N. Repetto and De los Reseros, Hurlingham, 1686, Buenos Aires, Argentina.
| | - Marcelo Abel Soria
- Universidad de Buenos Aires, Facultad de Agronomía, Cátedra de Microbiología Agrícola.INBA-CONICET, Av. San Martín 4453, C1417DSE, Buenos Aires, Argentina.
| |
Collapse
|
310
|
Biological and Epidemiological Consequences of MTBC Diversity. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1019:95-116. [PMID: 29116631 DOI: 10.1007/978-3-319-64371-7_5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Tuberculosis is caused by different groups of bacteria belonging to the Mycobacterium tuberculosis complex (MTBC). The combined action of human factors, environmental conditions and bacterial virulence determine the extent and form of human disease. MTBC virulence is a composite of different clinical phenotypes such as transmission rate and disease severity among others. Clinical phenotypes are also influenced by cellular and immunological phenotypes. MTBC phenotypes are determined by the genotype, therefore finding genotypes responsible for clinical phenotypes would allow discovering MTBC virulence factors. Different MTBC strains display different cellular and clinical phenotypes. Strains from Lineage 5 and Lineage 6 are metabolically different, grow slower, and are less virulent. Also, at least certain groups of Lineage 2 and Lineage 4 strains are more virulent in terms of disease severity and human-to-human transmission. Because phenotypic differences are ultimately caused by genotypic differences, different genomic loci have been related to various cellular and clinical phenotypes. However, defining the impact of specific bacterial genomic loci on virulence when other bacterial determinants, human and environmental factors are also impacting the phenotype would contribute to a better knowledge of tuberculosis virulence and ultimately benefit tuberculosis control.
Collapse
|
311
|
Abstract
Intracellular bacterial pathogens have evolved to exploit the protected niche provided within the boundaries of a eukaryotic host cell. Upon entering a host cell, some bacteria can evade the adaptive immune response of its host and replicate in a relatively nutrient-rich environment devoid of competition from other host flora. Growth within a host cell is not without their hazards, however. Many pathogens enter their hosts through receptor-mediated endocytosis or phagocytosis, two intracellular trafficking pathways that terminate in a highly degradative organelle, the phagolysosome. This usually deadly compartment is maintained at a low pH and contains degradative enzymes and reactive oxygen species, resulting in an environment to which few bacterial species are adapted. Some intracellular pathogens, such as Shigella, Listeria, Francisella, and Rickettsia, escape the phagosome to replicate within the cytosol of the host cell. Bacteria that remain within a vacuole either alter the trafficking of their initial phagosomal compartment or adapt to survive within the harsh environment it will soon become. In this chapter, we focus on the mechanisms by which different vacuolar pathogens either evade lysosomal fusion, as in the case of Mycobacterium and Chlamydia, or allow interaction with lysosomes to varying degrees, such as Brucella and Coxiella, and their specific adaptations to inhabit a replicative niche.
Collapse
|
312
|
Tanwar B, Kumar A, Yogeeswari P, Sriram D, Chakraborti AK. Design, development of new synthetic methodology, and biological evaluation of substituted quinolines as new anti-tubercular leads. Bioorg Med Chem Lett 2016; 26:5960-5966. [DOI: 10.1016/j.bmcl.2016.10.082] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 10/25/2016] [Accepted: 10/27/2016] [Indexed: 10/20/2022]
|
313
|
Brown TS, Narechania A, Walker JR, Planet PJ, Bifani PJ, Kolokotronis SO, Kreiswirth BN, Mathema B. Genomic epidemiology of Lineage 4 Mycobacterium tuberculosis subpopulations in New York City and New Jersey, 1999-2009. BMC Genomics 2016; 17:947. [PMID: 27871225 PMCID: PMC5117616 DOI: 10.1186/s12864-016-3298-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 11/15/2016] [Indexed: 12/31/2022] Open
Abstract
Background Whole genome sequencing (WGS) has rapidly become an important research tool in tuberculosis epidemiology and is likely to replace many existing methods in public health microbiology in the near future. WGS-based methods may be particularly useful in areas with less diverse Mycobacterium tuberculosis populations, such as New York City, where conventional genotyping is often uninformative and field epidemiology often difficult. This study applies four candidate strategies for WGS-based identification of emerging M. tuberculosis subpopulations, employing both phylogenomic and population genetics methods. Results M. tuberculosis subpopulations in New York City and New Jersey can be distinguished via phylogenomic reconstruction, evidence of demographic expansion and subpopulation-specific signatures of selection, and by determination of subgroup-defining nucleotide substitutions. These methods identified known historical outbreak clusters and previously unidentified subpopulations within relatively monomorphic M. tuberculosis endemic clone groups. Neutrality statistics based on the site frequency spectrum were less useful for identifying M. tuberculosis subpopulations, likely due to the low levels of informative genetic variation in recently diverged isolate groups. In addition, we observed that isolates from New York City endemic clone groups have acquired multiple non-synonymous SNPs in virulence- and growth-associated pathways, and relatively few mutations in drug resistance-associated genes, suggesting that overall pathoadaptive fitness, rather than the acquisition of drug resistance mutations, has played a central role in the evolutionary history and epidemiology of M. tuberculosis subpopulations in New York City. Conclusions Our results demonstrate that some but not all WGS-based methods are useful for detection of emerging M. tuberculosis clone groups, and support the use of phylogenomic reconstruction in routine tuberculosis laboratory surveillance, particularly in areas with relatively less diverse M. tuberculosis populations. Our study also supports the use of wider-reaching phylogenomic and population genomic methods in tuberculosis public health practice, which can support tuberculosis control activities by identifying genetic polymorphisms contributing to epidemiological success in local M. tuberculosis populations and possibly explain why certain isolate groups are apparently more successful in specific host populations. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3298-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Tyler S Brown
- Department of Medicine, Columbia University, New York, NY, USA
| | - Apurva Narechania
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
| | - John R Walker
- The Genomic Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Paul J Planet
- Department of Pediatrics, Division of Infectious Diseases, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Pablo J Bifani
- Novartis Institute for Tropical Diseases, Singapore, Singapore
| | - Sergios-Orestis Kolokotronis
- Department of Epidemiology and Biostatistics, School of Public Health, SUNY Downstate Medical Center, Brooklyn, NY, USA
| | | | - Barun Mathema
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, USA.
| |
Collapse
|
314
|
Sharma AK, Dhasmana N, Dubey N, Kumar N, Gangwal A, Gupta M, Singh Y. Bacterial Virulence Factors: Secreted for Survival. Indian J Microbiol 2016; 57:1-10. [PMID: 28148975 DOI: 10.1007/s12088-016-0625-1] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 10/03/2016] [Indexed: 12/29/2022] Open
Abstract
Virulence is described as an ability of an organism to infect the host and cause a disease. Virulence factors are the molecules that assist the bacterium colonize the host at the cellular level. These factors are either secretory, membrane associated or cytosolic in nature. The cytosolic factors facilitate the bacterium to undergo quick adaptive-metabolic, physiological and morphological shifts. The membrane associated virulence factors aid the bacterium in adhesion and evasion of the host cell. The secretory factors are important components of bacterial armoury which help the bacterium wade through the innate and adaptive immune response mounted within the host. In extracellular pathogens, the secretory virulence factors act synergistically to kill the host cells. In this review, we revisit the role of some of the secreted virulence factors of two human pathogens: Mycobacterium tuberculosis-an intracellular pathogen and Bacillus anthracis-an extracellular pathogen. The advances in research on the role of secretory factors of these pathogens during infection are discussed.
Collapse
Affiliation(s)
- Aditya Kumar Sharma
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007 India.,Academy of Scientific and Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi, 110001 India
| | - Neha Dhasmana
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007 India.,Academy of Scientific and Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi, 110001 India
| | - Neha Dubey
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Nishant Kumar
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007 India.,Academy of Scientific and Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi, 110001 India
| | - Aakriti Gangwal
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007 India
| | - Meetu Gupta
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007 India
| | - Yogendra Singh
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007 India.,Department of Zoology, University of Delhi, Delhi, 110007 India
| |
Collapse
|
315
|
Aguilar-Ayala DA, Palomino JC, Vandamme P, Martin A, Gonzalez-Y-Merchand JA. "Genetic regulation of Mycobacterium tuberculosis in a lipid-rich environment". INFECTION GENETICS AND EVOLUTION 2016; 55:392-402. [PMID: 27771519 DOI: 10.1016/j.meegid.2016.10.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 10/15/2016] [Accepted: 10/18/2016] [Indexed: 01/19/2023]
Abstract
Tuberculosis (TB) remains as one of the leading causes of morbidity and mortality among infectious diseases worldwide. Although lipids (mainly fatty acids and cholesterol) have been reported to play an important role during active and latent infection of M. tuberculosis, there are other molecular aspects of bacterial response to those substrates that are not fully understood, involving gene regulation background. This review highlights recent insights on pathogen gene expression: regulation during its active growth, during survival in presence of lipids and under variable hostile host microenvironments. We also propose several application options of this knowledge that may contribute for improved TB control.
Collapse
Affiliation(s)
- Diana A Aguilar-Ayala
- Departamento de Microbiologia, Escuela Nacional de Ciencias Biologicas, Instituto Politecnico Nacional, Prolongacion de Carpio y Plan de Ayala S/N, Mexico City, Mexico; Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Juan Carlos Palomino
- Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Peter Vandamme
- Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Anandi Martin
- Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium.
| | - Jorge A Gonzalez-Y-Merchand
- Departamento de Microbiologia, Escuela Nacional de Ciencias Biologicas, Instituto Politecnico Nacional, Prolongacion de Carpio y Plan de Ayala S/N, Mexico City, Mexico; Red Multidisciplinaria de Investigación en Tuberculosis, Mexico.
| |
Collapse
|
316
|
Saw SH, Tan JL, Chan XY, Chan KG, Ngeow YF. Chromosomal rearrangements and protein globularity changes in Mycobacterium tuberculosis isolates from cerebrospinal fluid. PeerJ 2016; 4:e2484. [PMID: 27688977 PMCID: PMC5036109 DOI: 10.7717/peerj.2484] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 08/24/2016] [Indexed: 01/07/2023] Open
Abstract
Background Meningitis is a major cause of mortality in tuberculosis (TB). It is not clear what factors promote central nervous system invasion and pathology but it has been reported that certain strains of Mycobacterium tuberculosis (Mtb) might have genetic traits associated with neurotropism. Methods In this study, we generated whole genome sequences of eight clinical strains of Mtb that were isolated from the cerebrospinal fluid (CSF) of patients presenting with tuberculous meningitis (TBM) in Malaysia, and compared them to the genomes of H37Rv and other respiratory Mtb genomes either downloaded from public databases or extracted from local sputum isolates. We aimed to find genomic features that might be distinctly different between CSF-derived and respiratory Mtb. Results Genome-wide comparisons revealed rearrangements (translocations, inversions, insertions and deletions) and non-synonymous SNPs in our CSF-derived strains that were not observed in the respiratory Mtb genomes used for comparison. These rearranged segments were rich in genes for PE (proline-glutamate)/PPE (proline-proline-glutamate), transcriptional and membrane proteins. Similarly, most of the ns SNPs common in CSF strains were noted in genes encoding PE/PPE proteins. Protein globularity differences were observed among mycobacteria from CSF and respiratory sources and in proteins previously reported to be associated with TB meningitis. Transcription factors and other transcription regulators featured prominently in these proteins. Homologs of proteins associated with Streptococcus pneumoniae meningitis and Neisseria meningitidis virulence were identified in neuropathogenic as well as respiratory mycobacterial spp. examined in this study. Discussion The occurrence of in silico genetic differences in CSF-derived but not respiratory Mtb suggests their possible involvement in the pathogenesis of TBM. However, overall findings in this comparative analysis support the postulation that TB meningeal infection is more likely to be related to the expression of multiple virulence factors on interaction with host defences than to CNS tropism associated with specific genetic traits.
Collapse
Affiliation(s)
- Seow Hoon Saw
- Department of Pre-Clinical Sciences, Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Bandar Sungai Long, Malaysia.,Department of Biomedical Science, Faculty of Science, Universiti Tunku Abdul Rahman, Kampar, Perak, Malaysia
| | - Joon Liang Tan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.,Faculty of Information Science and Technology, Multimedia University, Melaka, Malaysia
| | - Xin Yue Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Kok Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Yun Fong Ngeow
- Department of Pre-Clinical Sciences, Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Bandar Sungai Long, Malaysia.,Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| |
Collapse
|
317
|
EsxA membrane-permeabilizing activity plays a key role in mycobacterial cytosolic translocation and virulence: effects of single-residue mutations at glutamine 5. Sci Rep 2016; 6:32618. [PMID: 27600772 PMCID: PMC5013644 DOI: 10.1038/srep32618] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 08/10/2016] [Indexed: 12/11/2022] Open
Abstract
EsxA is required for virulence of Mycobacterium tuberculosis (Mtb) and plays an essential role in phagosome rupture and translocation to the cytosol of macrophages. Recent biochemical studies have demonstrated that EsxA is a membrane-permeabilizing protein. However, evidence that link EsxA membrane-permeabilizing activity to Mtb cytosolic translocation and virulence is lacking. Here we found that mutations at glutamine 5 (Q5) could up or down regulate EsxA membrane-permeabilizing activity. The mutation Q5K significantly diminished the membrane-permeabilizing activity, while Q5V enhanced the activity. By taking advantage of the single-residue mutations, we tested the effects of EsxA membrane-permeabilizing activity on mycobacterial virulence and cytosolic translocation using the esxA/esxB knockout strains of Mycobacterium marinum (Mm) and Mtb. Compared to wild type (WT), the Q5K mutant exhibited significantly attenuated virulence, evidenced by intracellular survival and cytotoxicity in mouse macrophages as well as infection of zebra fish embryos. The attenuated virulence of the Q5K mutant was correlated to the impaired cytosolic translocation. On the contrary, the Q5V mutant had a significantly increased cytosolic translocation and showed an overall increased virulence. This study provides convincing evidence that EsxA contributes to mycobacterial virulence with its membrane-permeabilizing activity that is required for cytosolic translocation.
Collapse
|
318
|
Leisching G, Pietersen RD, Wiid I, Baker B. Virulence, biochemistry, morphology and host-interacting properties of detergent-free cultured mycobacteria: An update. Tuberculosis (Edinb) 2016; 100:53-60. [DOI: 10.1016/j.tube.2016.07.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 05/26/2016] [Accepted: 07/05/2016] [Indexed: 12/17/2022]
|
319
|
Rahi A, Matta SK, Dhiman A, Garhyan J, Gopalani M, Chandra S, Bhatnagar R. Enolase of Mycobacterium tuberculosis is a surface exposed plasminogen binding protein. Biochim Biophys Acta Gen Subj 2016; 1861:3355-3364. [PMID: 27569900 DOI: 10.1016/j.bbagen.2016.08.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 08/12/2016] [Accepted: 08/24/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND Enolase, a glycolytic enzyme, has long been studied as an anchorless protein present on the surface of many pathogenic bacteria that aids in tissue remodeling and invasion by binding to host plasminogen. METHODS Anti-Mtb enolase antibodies in human sera were detected using ELISA. Immunoelectron microscopy, immunofluorescence microscopy and flow cytometry were used to show surface localization of Mtb enolase. SPR was used to determine the affinity of enolase-plasminogen interaction. Plasmin formation upon plasminogen binding to enolase and Mtb surface was measured by ELISA. Mice challenge and histopathological studies were undertaken to determine the protective efficacy of enolase immunization. RESULTS Enolase of Mtb is present on its surface and binds human plasminogen with high affinity. There was an average of 2-fold increase in antibody mediated recognition of Mtb enolase in human sera from TB patients with an active disease over control individuals. Substitution of C-terminal lysine to alanine in rEno decreased its binding affinity with human plasminogen by >2-folds. Enolase bound plasminogen showed urokinase mediated conversion into plasmin. Binding of plasminogen to the surface of Mtb and its conversion into fibrinolytic plasmin was significantly reduced in the presence of anti-rEno antibodies. Immunization with rEno also led to a significant decrease in lung CFU counts of mice upon infection with Mtb H37Rv. CONCLUSIONS Mtb enolase is a surface exposed plasminogen binding protein which upon immunization confers significant protection against Mtb challenge. GENERAL SIGNIFICANCE Plasminogen binding has been recognized for Mtb, however, proteins involved have not been characterized. We show here that Mtb enolase is a moonlighting plasminogen binding protein.
Collapse
Affiliation(s)
- Amit Rahi
- Laboratory of Molecular Biology and Genetic Engineering, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.
| | - Sumit Kumar Matta
- Laboratory of Molecular Biology and Genetic Engineering, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.
| | - Alisha Dhiman
- Laboratory of Molecular Biology and Genetic Engineering, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.
| | - Jaishree Garhyan
- Laboratory of Molecular Biology and Genetic Engineering, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.
| | - Monisha Gopalani
- Laboratory of Molecular Biology and Genetic Engineering, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.
| | - Subhash Chandra
- Laboratory of Molecular Biology and Genetic Engineering, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.
| | - Rakesh Bhatnagar
- Laboratory of Molecular Biology and Genetic Engineering, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.
| |
Collapse
|
320
|
Ben-Kahla I, Al-Hajoj S. Drug-resistant tuberculosis viewed from bacterial and host genomes. Int J Antimicrob Agents 2016; 48:353-60. [PMID: 27566907 DOI: 10.1016/j.ijantimicag.2016.07.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Revised: 06/26/2016] [Accepted: 07/15/2016] [Indexed: 12/14/2022]
Abstract
The outcome of infection with Mycobacterium tuberculosis (MTB) is largely influenced by the host-pathogen interaction in which both the human host and the MTB genetic backgrounds play an important role. Whether this interaction also influences the selection and expansion of drug-resistant MTB strains is the primary focus of this review. We first outline the main and recent findings regarding MTB determinants implicated in the development of drug resistance. Second, we examine data regarding human genetic factors that may play a role in TB drug resistance. We highlight interesting openings for TB research and therapy.
Collapse
Affiliation(s)
- Imen Ben-Kahla
- Mycobacteriology Section, Department of Infection and Immunity, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Sahal Al-Hajoj
- Mycobacteriology Section, Department of Infection and Immunity, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia.
| |
Collapse
|
321
|
Satta G, Witney AA, Shorten RJ, Karlikowska M, Lipman M, McHugh TD. Genetic variation in Mycobacterium tuberculosis isolates from a London outbreak associated with isoniazid resistance. BMC Med 2016; 14:117. [PMID: 27530812 PMCID: PMC4988016 DOI: 10.1186/s12916-016-0659-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 07/26/2016] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The largest outbreak of isoniazid-resistant (INH-R) Mycobacterium tuberculosis in Western Europe is centred in North London, with over 400 cases diagnosed since 1995. In the current study, we evaluated the genetic variation in a subset of clinical samples from the outbreak with the hypothesis that these isolates have unique biological characteristics that have served to prolong the outbreak. METHODS Fitness assays, mutation rate estimation, and whole-genome sequencing were performed to test for selective advantage and compensatory mutations. RESULTS This detailed analysis of the genetic variation of these INH-R samples suggests that this outbreak consists of successful, closely related, circulating strains with heterogeneous resistance profiles and little or no associated fitness cost or impact on their mutation rate. CONCLUSIONS Specific deletions and SNPs could be a peculiar feature of these INH-R M. tuberculosis isolates, and could potentially explain their persistence over the years.
Collapse
Affiliation(s)
- Giovanni Satta
- Department of Infection, Centre for Clinical Microbiology, University College London, London, UK. .,Imperial College Healthcare NHS Trust, London, UK.
| | - Adam A Witney
- Institute of Infection and Immunity, St George's, University of London, London, UK
| | - Robert J Shorten
- Department of Infection, Centre for Clinical Microbiology, University College London, London, UK.,Public Health Laboratory Manchester, Manchester Royal Infirmary, Manchester, UK
| | - Magdalena Karlikowska
- Department of Infection, Centre for Clinical Microbiology, University College London, London, UK
| | - Marc Lipman
- Royal Free London NHS Foundation Trust, London, UK.,UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Timothy D McHugh
- Department of Infection, Centre for Clinical Microbiology, University College London, London, UK
| |
Collapse
|
322
|
Milewski MC, Broger T, Kirkpatrick J, Filomena A, Komadina D, Schneiderhan-Marra N, Wilmanns M, Parret AHA. A standardized production pipeline for high profile targets from Mycobacterium tuberculosis. Proteomics Clin Appl 2016; 10:1049-1057. [PMID: 27400835 PMCID: PMC5095800 DOI: 10.1002/prca.201600033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 05/23/2016] [Accepted: 07/07/2016] [Indexed: 01/21/2023]
Abstract
Purpose Tuberculosis is still a major threat to global health. New tools and strategies to produce disease‐related proteins are quintessential for the development of novel vaccines and diagnostic markers. Experimental design To obtain recombinant proteins from Mycobacterium tuberculosis (Mtb) for use in clinical applications, a standardized procedure was developed that includes subcloning, protein expression in Mycobacterium smegmatis and protein purification using chromatography. The potential for the different protein targets to serve as diagnostic markers for tuberculosis was established using multiplex immunoassays. Results Twelve soluble proteins from Mtb, including one protein complex, were purified to near‐homogeneity following recombinant expression in M. smegmatis. Protein purity was assessed both by size exclusion chromatography and MS. Multiplex serological testing of the final protein preparations showed that all but one protein displayed a clear antibody response in serum samples from 278 tuberculosis patients. Conclusion and clinical relevance The established workflow comprises a simple, cost‐effective, and scalable pipeline for production of soluble proteins from Mtb and can be used to prioritize immunogenic proteins suitable for use as diagnostic markers.
Collapse
Affiliation(s)
- Morlin C Milewski
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, Hamburg, Germany
| | - Tobias Broger
- Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland
| | - Joanna Kirkpatrick
- European Molecular Biology Laboratory (EMBL), Proteomics Core Facility, Heidelberg, Germany
| | - Angela Filomena
- Natural and Medical Sciences Institute, University of Tübingen, Reutlingen, Germany
| | - Dana Komadina
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, Hamburg, Germany
| | | | - Matthias Wilmanns
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, Hamburg, Germany.,University of Hamburg Clinical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Annabel H A Parret
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, Hamburg, Germany.
| |
Collapse
|
323
|
Functional divergence of HBHA from Mycobacterium tuberculosis and its evolutionary relationship with TadA from Rhodococcus opacus. Biochimie 2016; 127:241-8. [DOI: 10.1016/j.biochi.2016.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 06/06/2016] [Indexed: 12/13/2022]
|
324
|
A hypervariable genomic island identified in clinical and environmental Mycobacterium avium subsp. hominissuis isolates from Germany. Int J Med Microbiol 2016; 306:495-503. [PMID: 27481640 DOI: 10.1016/j.ijmm.2016.07.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 06/06/2016] [Accepted: 07/17/2016] [Indexed: 11/21/2022] Open
Abstract
Mycobacterium avium subsp. hominissuis (MAH) is an opportunistic human pathogen widespread in the environment. Genomic islands (GI)s represent a part of the accessory genome of bacteria and influence virulence, drug-resistance or fitness and trigger bacterial evolution. We previously identified a novel GI in four MAH genomes. Here, we further explored this GI in a larger collection of MAH isolates from Germany (n=41), including 20 clinical and 21 environmental isolates. Based on comparative whole genome analysis, we detected this GI in 39/41 (95.1%) isolates. Although all these GIs integrated in the same insertion hotspot, there is high variability in the genetic structure of this GI: eight different types of GI have been identified, designated A-H (sized 6.2-73.3kb). These GIs were arranged as single GI (23/41, 56.1%), combination of two different GIs (14/41, 34.1%) or combination of three different GIs (2/41, 4.9%) in the insertion hotspot. Moreover, two GI types shared more than 80% sequence identity with sequences of M. canettii, responsible for Tuberculosis. A total of 253 different genes were identified in all GIs, among which the previously documented virulence-related genes mmpL10 and mce. The diversity of the GI and the sequence similarity with other mycobacteria suggests cross-species transfer, involving also highly pathogenic species. Shuffling of potential virulence genes such as mmpL10 via this GI may create new pathogens that can cause future outbreaks.
Collapse
|
325
|
Guo J, Wang C, Han Y, Liu Z, Wu T, Liu Y, Liu Y, Tan Y, Cai X, Cao Y, Wang B, Zhang B, Liu C, Tan S, Zhang T. Identification of Lysine Acetylation in Mycobacterium abscessus Using LC-MS/MS after Immunoprecipitation. J Proteome Res 2016; 15:2567-78. [PMID: 27323652 DOI: 10.1021/acs.jproteome.6b00116] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Mycobacterium abscessus (MAB), which manifests in the pulmonary system, is one of the neglected causes of nontuberculous mycobacteria (NTM) infection. Treatment against MAB is difficult, characterized by its intrinsic antibiotic drug resistance. Lysine acetylation can alter the physiochemical property of proteins in living organisms. This study aimed to determine if this protein post-translational modification (PTM) exists in a clinical isolate M. abscessus GZ002. We used the antiacetyl-lysine immunoprecipitation to enrich the low-abundant PTM proteins, followed by the LC-MS/MS analysis. The lysine acetylome of M. abscessus GZ002 was determined. There were 459 lysine acetylation sites found in 289 acetylated proteins. Lysine acetylation occurred in 5.87% of the M. abscessus GZ002 proteome, and at least 25% of them were growth essential. Aerobic respiration and carbohydrate metabolic pathways of M. abscessus GZ002 were enriched with lysine acetylation. Through bioinformatics analysis, we identified four major acetyl motif logos (K(ac)Y, K(ac)F, K(ac)H, and DK(ac)). Further comparison of the reported M. tuberculosis (MTB) acetylomes and that of MAB GZ002 revealed several common features between these two species. The lysine residues of several antibiotic-resistance, virulence, and persistence-related proteins were acetylated in both MAB GZ002 and MTB. There were 51 identical acetylation sites in 37 proteins found in common between MAB GZ002 and MTB. Overall, we demonstrate a profile of lysine acetylation in MAB GZ002 proteome that shares similarities with MTB. Interventions that target at these conserved sections may be valuable as anti-NTM or anti-TB therapies.
Collapse
Affiliation(s)
- Jintao Guo
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS) , Guangzhou, China
| | - Changwei Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS) , Guangzhou, China
| | - Yi Han
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS) , Guangzhou, China
| | - Zhiyong Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS) , Guangzhou, China
| | - Tian Wu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS) , Guangzhou, China
| | - Yan Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS) , Guangzhou, China
| | - Yang Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS) , Guangzhou, China.,School of Life Sciences, University of Anhui , Hefei, China
| | - Yaoju Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, The Guangzhou Chest Hospital , Guangzhou, China
| | - Xinshan Cai
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, The Guangzhou Chest Hospital , Guangzhou, China
| | - Yuanyuan Cao
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS) , Guangzhou, China.,School of Life Sciences, University of Anhui , Hefei, China
| | - Bangxing Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS) , Guangzhou, China.,School of Life Sciences, University of Anhui , Hefei, China
| | - Buchang Zhang
- School of Life Sciences, University of Anhui , Hefei, China
| | - Chunping Liu
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, The Guangzhou Chest Hospital , Guangzhou, China
| | - Shouyong Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, The Guangzhou Chest Hospital , Guangzhou, China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS) , Guangzhou, China
| |
Collapse
|
326
|
Bespyatykh J, Shitikov E, Butenko I, Altukhov I, Alexeev D, Mokrousov I, Dogonadze M, Zhuravlev V, Yablonsky P, Ilina E, Govorun V. Proteome analysis of the Mycobacterium tuberculosis Beijing B0/W148 cluster. Sci Rep 2016; 6:28985. [PMID: 27356881 PMCID: PMC4928086 DOI: 10.1038/srep28985] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 06/13/2016] [Indexed: 12/18/2022] Open
Abstract
Beijing B0/W148, a "successful" clone of Mycobacterium tuberculosis, is widespread in the Russian Federation and some countries of the former Soviet Union. Here, we used label-free gel-LC-MS/MS shotgun proteomics to discover features of Beijing B0/W148 strains that could explain their success. Qualitative and quantitative proteome analyses of Beijing B0/W148 strains allowed us to identify 1,868 proteins, including 266 that were differentially abundant compared with the control strain H37Rv. To predict the biological effects of the observed differences in protein abundances, we performed Gene Ontology analysis together with analysis of protein-DNA interactions using a gene regulatory network. Our results demonstrate that Beijing B0/W148 strains have increased levels of enzymes responsible for long-chain fatty acid biosynthesis, along with a coincident decrease in the abundance of proteins responsible for their degradation. Together with high levels of HsaA (Rv3570c) protein, involved in steroid degradation, these findings provide a possible explanation for the increased transmissibility of Beijing B0/W148 strains and their survival in host macrophages. Among other, we confirmed a very low level of the SseA (Rv3283) protein in Beijing B0/W148 characteristic for all «modern» Beijing strains, which could lead to increased DNA oxidative damage, accumulation of mutations, and potentially facilitate the development of drug resistance.
Collapse
Affiliation(s)
- Julia Bespyatykh
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Egor Shitikov
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Ivan Butenko
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Ilya Altukhov
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Dmitry Alexeev
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Igor Mokrousov
- St. Petersburg Pasteur Institute, St. Petersburg, Russian Federation
| | - Marine Dogonadze
- Research Institute of Phtisiopulmonology, St. Petersburg, Russian Federation
| | | | - Peter Yablonsky
- Research Institute of Phtisiopulmonology, St. Petersburg, Russian Federation
| | - Elena Ilina
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Vadim Govorun
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| |
Collapse
|
327
|
Khan S, Islam A, Hassan MI, Ahmad F. Purification and structural characterization of Mce4A from Mycobacterium tuberculosis. Int J Biol Macromol 2016; 93:235-241. [PMID: 27355757 DOI: 10.1016/j.ijbiomac.2016.06.059] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 06/17/2016] [Accepted: 06/19/2016] [Indexed: 01/08/2023]
Abstract
The mce4A gene of Mycobacterium tuberculosis encodes a 400 amino acid residues protein of 43kDa, which is a mammalian cell entry protein (Mce4A) and plays important role in host cell invasion. Mce4A helps in long-term survival of M. tuberculosis by cholesterol utilization. Host cholesterol utilization mechanism by Mce4A is not clearly understood. In order to investigate the role of Mce4A in M. tuberculosis pathogenesis, we purified the recombinant protein by affinity chromatography, analyzed by SDS-PAGE and confirmed by western blot. We performed structural studies of Mce4A as function of pH and salt concentration by using different spectroscopic techniques. This protein was found to be stable over the wide range of pH 5.5≤pH≤11.5. An addition of sodium chloride up to the concentration of 150mM, shows no significant change in the secondary structure content of the protein. To confirm its activity, we performed isothermal titration calorimetry measurements of Mce4A in the presence of cholesterol. This is the first report of binding of cholesterol to Mce4A in vitro. Binding of cholesterol to Mce4A is sequential four-step and entropy driven process. The structural studies of this protein will help to understand the mechanism of pathogenesis of M. tuberculosis.
Collapse
Affiliation(s)
- Shagufta Khan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India.
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| |
Collapse
|
328
|
Network analysis identifies Rv0324 and Rv0880 as regulators of bedaquiline tolerance in Mycobacterium tuberculosis. Nat Microbiol 2016; 1:16078. [PMID: 27573104 PMCID: PMC5010021 DOI: 10.1038/nmicrobiol.2016.78] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 04/27/2016] [Indexed: 12/26/2022]
Abstract
Resilience of Mycobacterium tuberculosis (MTB) emerges from its ability to effectively counteract immunological, environmental, and antitubercular challenges. Here, we demonstrate that MTB can tolerate drug treatment by adopting a tolerant state that can be deciphered through systems analysis of its transcriptional responses. Specifically, we demonstrate how treatment with the antitubercular drug bedaquiline activates a regulatory network that coordinates multiple resistance mechanisms to push MTB into a tolerant state. Disruption of this network, by knocking out its predicted transcription factors, Rv0324 and Rv0880, significantly increased bedaquiline killing and enabled the discovery of a second drug pretomanid that potentiated killing by bedaquiline. We demonstrate that the synergistic effect of this combination emerges, in part, through disruption of the tolerance network. We discuss how this network strategy also predicts drug combinations with antagonistic interactions, potentially accelerating the discovery of new effective combination drug regimens for TB.
Collapse
|
329
|
Peters JS, Calder B, Gonnelli G, Degroeve S, Rajaonarifara E, Mulder N, Soares NC, Martens L, Blackburn JM. Identification of Quantitative Proteomic Differences between Mycobacterium tuberculosis Lineages with Altered Virulence. Front Microbiol 2016; 7:813. [PMID: 27303394 PMCID: PMC4885829 DOI: 10.3389/fmicb.2016.00813] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 05/12/2016] [Indexed: 11/22/2022] Open
Abstract
Evidence currently suggests that as a species Mycobacterium tuberculosis exhibits very little genomic sequence diversity. Despite limited genetic variability, members of the M. tuberculosis complex (MTBC) have been shown to exhibit vast discrepancies in phenotypic presentation in terms of virulence, elicited immune response and transmissibility. Here, we used qualitative and quantitative mass spectrometry tools to investigate the proteomes of seven clinically-relevant mycobacterial strains—four M. tuberculosis strains, M. bovis, M. bovis BCG, and M. avium—that show varying degrees of pathogenicity and virulence, in an effort to rationalize the observed phenotypic differences. Following protein preparation, liquid chromatography mass spectrometry (LC MS/MS) and data capture were carried out using an LTQ Orbitrap Velos. Data analysis was carried out using a novel bioinformatics strategy, which yielded high protein coverage and was based on high confidence peptides. Through this approach, we directly identified a total of 3788 unique M. tuberculosis proteins out of a theoretical proteome of 4023 proteins and identified an average of 3290 unique proteins for each of the MTBC organisms (representing 82% of the theoretical proteomes), as well as 4250 unique M. avium proteins (80% of the theoretical proteome). Data analysis showed that all major classes of proteins are represented in every strain, but that there are significant quantitative differences between strains. Targeted selected reaction monitoring (SRM) assays were used to quantify the observed differential expression of a subset of 23 proteins identified by comparison to gene expression data as being of particular relevance to virulence. This analysis revealed differences in relative protein abundance between strains for proteins which may promote bacterial fitness in the more virulent W. Beijing strain. These differences may contribute to this strain's capacity for surviving within the host and resisting treatment, which has contributed to its rapid spread. Through this approach, we have begun to describe the proteomic portrait of a successful mycobacterial pathogen. Data are available via ProteomeXchange with identifier PXD004165.
Collapse
Affiliation(s)
- Julian S Peters
- Centre of Excellence for Biomedical TB Research, Witwatersrand University Johannesburg, South Africa
| | - Bridget Calder
- Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town Cape Town, South Africa
| | | | | | - Elinambinina Rajaonarifara
- Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town Cape Town, South Africa
| | - Nicola Mulder
- Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town Cape Town, South Africa
| | - Nelson C Soares
- Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town Cape Town, South Africa
| | | | - Jonathan M Blackburn
- Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town Cape Town, South Africa
| |
Collapse
|
330
|
Bhagyaraj E, Nanduri R, Saini A, Dkhar HK, Ahuja N, Chandra V, Mahajan S, Kalra R, Tiwari D, Sharma C, Janmeja AK, Gupta P. Human Xenobiotic Nuclear Receptor PXR Augments Mycobacterium tuberculosis Survival. THE JOURNAL OF IMMUNOLOGY 2016; 197:244-55. [PMID: 27233963 DOI: 10.4049/jimmunol.1600203] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 05/03/2016] [Indexed: 01/16/2023]
Abstract
Mycobacterium tuberculosis can evade host defense processes, thereby ensuring its survival and pathogenesis. In this study, we investigated the role of nuclear receptor, pregnane X receptor (PXR), in M. tuberculosis infection in human monocyte-derived macrophages. In this study, we demonstrate that PXR augments M. tuberculosis survival inside the host macrophages by promoting the foamy macrophage formation and abrogating phagolysosomal fusion, inflammation, and apoptosis. Additionally, M. tuberculosis cell wall lipids, particularly mycolic acids, crosstalk with human PXR (hPXR) by interacting with its promiscuous ligand binding domain. To confirm our in vitro findings and to avoid the reported species barrier in PXR function, we adopted an in vivo mouse model expressing hPXR, wherein expression of hPXR in mice promotes M. tuberculosis survival. Therefore, pharmacological intervention and designing antagonists to hPXR may prove to be a promising adjunct therapy for tuberculosis.
Collapse
Affiliation(s)
- Ella Bhagyaraj
- Council for Scientific and Industrial Research, Institute of Microbial Technology, Chandigarh 160036, India; and
| | - Ravikanth Nanduri
- Council for Scientific and Industrial Research, Institute of Microbial Technology, Chandigarh 160036, India; and
| | - Ankita Saini
- Council for Scientific and Industrial Research, Institute of Microbial Technology, Chandigarh 160036, India; and
| | - Hedwin Kitdorlang Dkhar
- Council for Scientific and Industrial Research, Institute of Microbial Technology, Chandigarh 160036, India; and
| | - Nancy Ahuja
- Council for Scientific and Industrial Research, Institute of Microbial Technology, Chandigarh 160036, India; and
| | - Vemika Chandra
- Council for Scientific and Industrial Research, Institute of Microbial Technology, Chandigarh 160036, India; and
| | - Sahil Mahajan
- Council for Scientific and Industrial Research, Institute of Microbial Technology, Chandigarh 160036, India; and
| | - Rashi Kalra
- Council for Scientific and Industrial Research, Institute of Microbial Technology, Chandigarh 160036, India; and
| | - Drishti Tiwari
- Council for Scientific and Industrial Research, Institute of Microbial Technology, Chandigarh 160036, India; and
| | - Charu Sharma
- Council for Scientific and Industrial Research, Institute of Microbial Technology, Chandigarh 160036, India; and
| | | | - Pawan Gupta
- Council for Scientific and Industrial Research, Institute of Microbial Technology, Chandigarh 160036, India; and
| |
Collapse
|
331
|
Santana-Jorge KTO, Santos TM, Tartaglia NR, Aguiar EL, Souza RFS, Mariutti RB, Eberle RJ, Arni RK, Portela RW, Meyer R, Azevedo V. Putative virulence factors of Corynebacterium pseudotuberculosis FRC41: vaccine potential and protein expression. Microb Cell Fact 2016; 15:83. [PMID: 27184574 PMCID: PMC4869379 DOI: 10.1186/s12934-016-0479-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 05/03/2016] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Corynebacterium pseudotuberculosis, a facultative intracellular bacterial pathogen, is the etiological agent of caseous lymphadenitis (CLA), an infectious disease that affects sheep and goats and it is responsible for significant economic losses. The disease is characterized mainly by bacteria-induced caseous necrosis in lymphatic glands. New vaccines are needed for reliable control and management of CLA. Thus, the putative virulence factors SpaC, SodC, NanH, and PknG from C. pseudotuberculosis FRC41 may represent new target proteins for vaccine development and pathogenicity studies. RESULTS SpaC, PknG and NanH presented better vaccine potential than SodC after in silico analyses. A total of 136 B and T cell epitopes were predicted from the four putative virulence factors. A cluster analysis was performed to evaluate the redundancy degree among the sequences of the predicted epitopes; 57 clusters were formed, most of them (34) were single clusters. Two clusters from PknG and one from SpaC grouped epitopes for B and T-cell (MHC I and II). These epitopes can thus potentially stimulate a complete immune response (humoral and cellular) against C. pseudotuberculosis. Several other clusters, including two from NanH, grouped B-cell epitopes with either MHC I or II epitopes. The four target proteins were expressed in Escherichia coli. A purification protocol was developed for PknG expression. CONCLUSIONS In silico analyses show that the putative virulence factors SpaC, PknG and NanH present good potential for CLA vaccine development. Target proteins were successfully expressed in E. coli. A protocol for PknG purification is described.
Collapse
Affiliation(s)
- Karina T. O. Santana-Jorge
- />Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antonio Carlos, 6627, Pampulha, Belo Horizonte, 31270-901 Brazil
| | - Túlio M. Santos
- />Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antonio Carlos, 6627, Pampulha, Belo Horizonte, 31270-901 Brazil
- />Uniclon Biotecnologia, Belo Horizonte, MG Brazil
| | - Natayme R. Tartaglia
- />Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antonio Carlos, 6627, Pampulha, Belo Horizonte, 31270-901 Brazil
| | - Edgar L. Aguiar
- />Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antonio Carlos, 6627, Pampulha, Belo Horizonte, 31270-901 Brazil
| | - Renata F. S. Souza
- />Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antonio Carlos, 6627, Pampulha, Belo Horizonte, 31270-901 Brazil
| | - Ricardo B. Mariutti
- />Multiuser Center for Biomolecular Innovation, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista “Júlio de Mesquita Filho”, São José Do Rio Preto, SP Brazil
| | - Raphael J. Eberle
- />Multiuser Center for Biomolecular Innovation, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista “Júlio de Mesquita Filho”, São José Do Rio Preto, SP Brazil
| | - Raghuvir K. Arni
- />Multiuser Center for Biomolecular Innovation, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista “Júlio de Mesquita Filho”, São José Do Rio Preto, SP Brazil
| | - Ricardo W. Portela
- />Laboratório de Imunologia e Biologia Molecular, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, BA Brazil
| | - Roberto Meyer
- />Laboratório de Imunologia e Biologia Molecular, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, BA Brazil
| | - Vasco Azevedo
- />Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antonio Carlos, 6627, Pampulha, Belo Horizonte, 31270-901 Brazil
| |
Collapse
|
332
|
Dhanda SK, Vir P, Singla D, Gupta S, Kumar S, Raghava GPS. A Web-Based Platform for Designing Vaccines against Existing and Emerging Strains of Mycobacterium tuberculosis. PLoS One 2016; 11:e0153771. [PMID: 27096425 PMCID: PMC4838326 DOI: 10.1371/journal.pone.0153771] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 04/04/2016] [Indexed: 01/08/2023] Open
Abstract
Development of an effective vaccine against drug-resistant Mycobacterium tuberculosis (Mtb) is crucial for saving millions of premature deaths every year due to tuberculosis. This paper describes a web portal developed for assisting researchers in designing vaccines against emerging Mtb strains using traditional and modern approaches. Firstly, we annotated 59 genomes of Mycobacterium species to understand similarity/dissimilarity between tuberculoid, non-tuberculoid and vaccine strains at genome level. Secondly, antigen-based vaccine candidates have been predicted in each Mtb strain. Thirdly, epitopes-based vaccine candidates were predicted/discovered in above antigen-based vaccine candidates that can stimulate all arms of immune system. Finally, a database of predicted vaccine candidates at epitopes as well at antigen level has been developed for above strains. In order to design vaccine against a newly sequenced genome of Mtb strain, server integrates three modules for identification of strain-, antigen-, epitope-specific vaccine candidates. We observed that 103522 unique peptides (9mers) had the potential to induce an antibody response and/or promiscuous binder to MHC alleles and/or have the capability to stimulate T lymphocytes. In summary, this web-portal will be useful for researchers working on designing vaccines against Mtb including drug-resistant strains. Availability: The database is available freely at http://crdd.osdd.net/raghava/mtbveb/.
Collapse
Affiliation(s)
- Sandeep Kumar Dhanda
- Bioinformatics Centre, Institute of Microbial Technology, Chandigarh, 160036, India
| | - Pooja Vir
- Bioinformatics Centre, Institute of Microbial Technology, Chandigarh, 160036, India
| | - Deepak Singla
- Bioinformatics Centre, Institute of Microbial Technology, Chandigarh, 160036, India
| | - Sudheer Gupta
- Bioinformatics Centre, Institute of Microbial Technology, Chandigarh, 160036, India
| | - Shailesh Kumar
- Bioinformatics Centre, Institute of Microbial Technology, Chandigarh, 160036, India
| | - Gajendra P. S. Raghava
- Bioinformatics Centre, Institute of Microbial Technology, Chandigarh, 160036, India
- * E-mail:
| |
Collapse
|
333
|
Peddireddy V, Doddam SN, Qureshi IA, Yerra P, Ahmed N. A putative nitroreductase from the DosR regulon of Mycobacterium tuberculosis induces pro-inflammatory cytokine expression via TLR2 signaling pathway. Sci Rep 2016; 6:24535. [PMID: 27094446 PMCID: PMC4837367 DOI: 10.1038/srep24535] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 03/30/2016] [Indexed: 01/14/2023] Open
Abstract
Tuberculosis caused by Mycobacterium tuberculosis is a global encumbrance and it is estimated that nearly one third population of the world acts as a reservoir for this pathogen without any symptoms. In this study, we attempted to characterise one of the genes of DosR regulon, Rv3131, a FMN binding nitroreductase domain containing protein, for its ability to alter cytokine profile, an essential feature of M. tuberculosis latency. Recombinant Rv3131 stimulated pro-inflammatory cytokines in THP-1 cells and human peripheral blood mononuclear cells in a time and dose dependent manner. In silico analyses using docking and simulations indicated that Rv3131 could strongly interact with TLR2 via a non-covalent bonding which was further confirmed using cell based colorimetric assay. In THP-1 cells treated with Rv3131 protein, a significant upsurge in the surface expression, overall induction and expression of mRNA of TLR2 was observed when analysed by flow cytometry, western blotting and real time PCR, respectively. Activation of TLR2 by Rv3131 resulted in the phosphorylation of NF- κβ. Results of this study indicate a strong immunogenic capability of Rv3131 elicited via the activation of TLR2 signalling pathway. Therefore, it can be surmised that cytokine secretion induced by Rv3131 might contribute to establishment of M. tuberculosis in the granulomas.
Collapse
Affiliation(s)
- Vidyullatha Peddireddy
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad 500046 India
| | - Sankara Narayana Doddam
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad 500046 India
| | - Insaf A. Qureshi
- Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad India
| | - Priyadarshini Yerra
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad 500046 India
| | - Niyaz Ahmed
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad 500046 India
| |
Collapse
|
334
|
Wee WY, Tan TK, Jakubovics NS, Choo SW. Whole-Genome Sequencing and Comparative Analysis of Mycobacterium brisbanense Reveals a Possible Soil Origin and Capability in Fertiliser Synthesis. PLoS One 2016; 11:e0152682. [PMID: 27031249 PMCID: PMC4816395 DOI: 10.1371/journal.pone.0152682] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 03/17/2016] [Indexed: 11/18/2022] Open
Abstract
Mycobacterium brisbanense is a member of Mycobacterium fortuitum third biovariant complex, which includes rapidly growing Mycobacterium spp. that normally inhabit soil, dust and water, and can sometimes cause respiratory tract infections in humans. We present the first whole-genome analysis of M. brisbanense UM_WWY which was isolated from a 70-year-old Malaysian patient. Molecular phylogenetic analyses confirmed the identification of this strain as M. brisbanense and showed that it has an unusually large genome compared with related mycobacteria. The large genome size of M. brisbanense UM_WWY (~7.7Mbp) is consistent with further findings that this strain has a highly variable genome structure that contains many putative horizontally transferred genomic islands and prophage. Comparative analysis showed that M. brisbanense UM_WWY is the only Mycobacterium species that possesses a complete set of genes encoding enzymes involved in the urea cycle, suggesting that this soil bacterium is able to synthesize urea for use as plant fertilizers. It is likely that M. brisbanense UM_WWY is adapted to live in soil as its primary habitat since the genome contains many genes associated with nitrogen metabolism. Nevertheless, a large number of predicted virulence genes were identified in M. brisbanense UM_WWY that are mostly shared with well-studied mycobacterial pathogens such as Mycobacterium tuberculosis and Mycobacterium abscessus. These findings are consistent with the role of M. brisbanense as an opportunistic pathogen of humans. The whole-genome study of UM_WWY has provided the basis for future work of M. brisbanense.
Collapse
Affiliation(s)
- Wei Yee Wee
- Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, Kuala Lumpur, 50603, Malaysia
- Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, 50603, Malaysia
| | - Tze King Tan
- Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, Kuala Lumpur, 50603, Malaysia
- Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, 50603, Malaysia
| | - Nicholas S. Jakubovics
- Center for Oral Health Research, School of Dental Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne, United Kingdom
- Genome Solutions Sdn Bhd, Suite 8, Innovation Incubator UM, Level 5, Research Management & Innovation Complex, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Siew Woh Choo
- Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, Kuala Lumpur, 50603, Malaysia
- Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, 50603, Malaysia
- * E-mail:
| |
Collapse
|
335
|
Guimarães LC, Florczak-Wyspianska J, de Jesus LB, Viana MVC, Silva A, Ramos RTJ, Soares SDC, Soares SDC. Inside the Pan-genome - Methods and Software Overview. Curr Genomics 2016; 16:245-52. [PMID: 27006628 PMCID: PMC4765519 DOI: 10.2174/1389202916666150423002311] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 04/20/2015] [Accepted: 04/21/2015] [Indexed: 12/11/2022] Open
Abstract
The number of genomes that have been deposited in databases has increased exponentially
after the advent of Next-Generation Sequencing (NGS), which produces high-throughput sequence
data; this circumstance has demanded the development of new bioinformatics software and the creation
of new areas, such as comparative genomics. In comparative genomics, the genetic content of an
organism is compared against other organisms, which helps in the prediction of gene function and coding region sequences,
identification of evolutionary events and determination of phylogenetic relationships. However, expanding comparative
genomics to a large number of related bacteria, we can infer their lifestyles, gene repertoires and minimal genome
size. In this context, a powerful approach called Pan-genome has been initiated and developed. This approach involves the
genomic comparison of different strains of the same species, or even genus. Its main goal is to establish the total number
of non-redundant genes that are present in a determined dataset. Pan-genome consists of three parts: core genome; accessory
or dispensable genome; and species-specific or strain-specific genes. Furthermore, pan-genome is considered to be
“open” as long as new genes are added significantly to the total repertoire for each new additional genome and “closed”
when the newly added genomes cannot be inferred to significantly increase the total repertoire of the genes. To perform
all of the required calculations, a substantial amount of software has been developed, based on orthologous and paralogous
gene identification.
Collapse
Affiliation(s)
- Luis Carlos Guimarães
- Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Avenue Antônio Carlos, 6627, Belo Horizonte, Minas Gerais, Brazil;; Department of Genetics, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | | | - Leandro Benevides de Jesus
- Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Avenue Antônio Carlos, 6627, Belo Horizonte, Minas Gerais, Brazil
| | - Marcus Vinícius Canário Viana
- Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Avenue Antônio Carlos, 6627, Belo Horizonte, Minas Gerais, Brazil
| | - Artur Silva
- Department of Genetics, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Rommel Thiago Jucá Ramos
- Department of Genetics, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Siomar de Castro Soares
- Department of Immunology, Microbiology and Parasitology, Institute of Biological Sciences and Natural Sciences Federal University of Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Siomar de Castro Soares
- Department of Immunology, Microbiology and Parasitology, Institute of Biological Sciences and Natural Sciences Federal University of Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| |
Collapse
|
336
|
Lerner TR, de Souza Carvalho-Wodarz C, Repnik U, Russell MR, Borel S, Diedrich CR, Rohde M, Wainwright H, Collinson LM, Wilkinson RJ, Griffiths G, Gutierrez MG. Lymphatic endothelial cells are a replicative niche for Mycobacterium tuberculosis. J Clin Invest 2016; 126:1093-108. [PMID: 26901813 PMCID: PMC4767353 DOI: 10.1172/jci83379] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 01/04/2016] [Indexed: 12/13/2022] Open
Abstract
In extrapulmonary tuberculosis, the most common site of infection is within the lymphatic system, and there is growing recognition that lymphatic endothelial cells (LECs) are involved in immune function. Here, we identified LECs, which line the lymphatic vessels, as a niche for Mycobacterium tuberculosis in the lymph nodes of patients with tuberculosis. In cultured primary human LECs (hLECs), we determined that M. tuberculosis replicates both in the cytosol and within autophagosomes, but the bacteria failed to replicate when the virulence locus RD1 was deleted. Activation by IFN-γ induced a cell-autonomous response in hLECs via autophagy and NO production that restricted M. tuberculosis growth. Thus, depending on the activation status of LECs, autophagy can both promote and restrict replication. Together, these findings reveal a previously unrecognized role for hLECs and autophagy in tuberculosis pathogenesis and suggest that hLECs are a potential niche for M. tuberculosis that allows establishment of persistent infection in lymph nodes.
Collapse
Affiliation(s)
- Thomas R. Lerner
- Host-pathogen interactions in tuberculosis laboratory, The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
| | - Cristiane de Souza Carvalho-Wodarz
- Department of Drug Delivery, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research, Saarland University, Saarbrücken, Germany
| | - Urska Repnik
- Department of Biosciences, University of Oslo, Blindernveien, Oslo, Norway
| | - Matthew R.G. Russell
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, Lincoln’s Inn Fields Laboratory, London, United Kingdom
| | - Sophie Borel
- Host-pathogen interactions in tuberculosis laboratory, The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
| | - Collin R. Diedrich
- Clinical Infectious Diseases Research Initiative, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Helen Wainwright
- Department of Anatomical Pathology, University of Cape Town Faculty of Health Sciences and National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa
| | - Lucy M. Collinson
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, Lincoln’s Inn Fields Laboratory, London, United Kingdom
| | - Robert J. Wilkinson
- Host-pathogen interactions in tuberculosis laboratory, The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
- Clinical Infectious Diseases Research Initiative, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Department of Medicine, Imperial College London, London, United Kingdom
| | - Gareth Griffiths
- Department of Biosciences, University of Oslo, Blindernveien, Oslo, Norway
| | - Maximiliano G. Gutierrez
- Host-pathogen interactions in tuberculosis laboratory, The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
| |
Collapse
|
337
|
Souza de Lima D, Morishi Ogusku M, Porto dos Santos M, de Melo Silva CM, Alves de Almeida V, Assumpção Antunes I, Boechat AL, Ramasawmy R, Sadahiro A. Alleles of HLA-DRB1*04 Associated with Pulmonary Tuberculosis in Amazon Brazilian Population. PLoS One 2016; 11:e0147543. [PMID: 26901036 PMCID: PMC4764689 DOI: 10.1371/journal.pone.0147543] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 01/04/2016] [Indexed: 12/16/2022] Open
Abstract
Immunogenetic host factors are associated with susceptibility or protection to tuberculosis (TB). Strong associations of HLA class II genes with TB are reported. We analyzed the HLA-DRB1*04 alleles to identify subtypes associated with pulmonary TB and their interaction with risk factors such as alcohol, smoking, and gender in 316 pulmonary TB patients and 306 healthy individuals from the Brazilian Amazon. The HLA-DRB1*04 was prevalent in patients with pulmonary TB (p<0.0001; OR = 2.94; 95% CI = 2.12 to 4.08). Direct nucleotide sequencing of DRB1 exon 2 identified nine subtypes of HLA-DRB1*04. The subtype HLA-DRB1*04:11:01 (p = 0.0019; OR = 2.23; 95% CI = 1.34 to 3.70) was associated with susceptibility to pulmonary TB while DRB1*04:07:01 (p<0.0001; OR = 0.02; 95% CI = 0.001 to 0.33) to protection. Notably, the interaction between alcohol and HLA-DRB1*04:11:01 increased the risk for developing pulmonary TB (p = 0.0001; OR = 51.3; 95% CI = 6.81 to 386). Multibacillary pulmonary TB, the clinical presentation of disease transmission, was strongly associated with interaction to alcohol (p = 0.0026; OR = 11.1; 95% CI = 3.99 to 30.9), HLA-DRB1*04:11:01 (p = 0.0442; OR = 2.01; 95% CI = 1.03 to 3.93) and DRB1*04:92 (p = 0.0112; OR = 8.62; 95% CI = 1.63 to 45.5). These results show that HLA-DRB1*04 are associated with pulmonary TB. Interestingly, three subtypes, DRB1*04:07:01, DRB1*04:11:01 and DRB1*04:92 of the HLA-DRB1*04 could be potential immunogenetic markers that may help to explain mechanisms involved in disease development.
Collapse
Affiliation(s)
- Dhêmerson Souza de Lima
- Programa de Pós-Graduação em Imunologia Básica e Aplicada, Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brasil
- * E-mail:
| | - Mauricio Morishi Ogusku
- Laboratório de Micobacteriologia, Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Amazonas, Brasil
| | - Maisa Porto dos Santos
- Laboratório de Micobacteriologia, Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Amazonas, Brasil
| | - Cláudia Maria de Melo Silva
- Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Ciências Farmacêuticas (FCF), Manaus, Amazonas, Brasil
| | - Vanessa Alves de Almeida
- Programa de Pós-Graduação em Imunologia Básica e Aplicada, Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brasil
| | | | - Antonio Luiz Boechat
- Programa de Pós-Graduação em Imunologia Básica e Aplicada, Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brasil
| | - Rajendranath Ramasawmy
- Programa de Pós-Graduação em Imunologia Básica e Aplicada, Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brasil
- Fundação de Medicina Tropical Doutor Heitor Vieira Dourado (FMT/HVD), Manaus, Amazonas, Brasil
- Universidade Nilton Lins, Manaus, Amazonas, Brasil
| | - Aya Sadahiro
- Programa de Pós-Graduação em Imunologia Básica e Aplicada, Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brasil
| |
Collapse
|
338
|
Calder B, Albeldas C, Blackburn JM, Soares NC. Mass Spectrometry Offers Insight into the Role of Ser/Thr/Tyr Phosphorylation in the Mycobacteria. Front Microbiol 2016; 7:141. [PMID: 26904014 PMCID: PMC4751927 DOI: 10.3389/fmicb.2016.00141] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 01/25/2016] [Indexed: 12/23/2022] Open
Abstract
Phosphorylation is a post translational modification which can rapidly regulate biochemical pathways by altering protein function, and has been associated with pathogenicity in bacteria. Once engulfed by host macrophages, pathogenic bacteria are exposed to harsh conditions and must respond rapidly in order to survive. The causative agent of TB, Mycobacterium tuberculosis, is unusual amongst the bacteria because it can survive within the host macrophage for decades in a latent state, demonstrating a remarkable capacity to successfully evade the host immune response. This ability may be mediated in part by regulatory mechanisms such as ser/thr/tyr phosphorylation. Mass spectrometry-based proteomics has afforded us the capacity to identify hundreds of phosphorylation sites in the bacterial proteome, allowing for comparative phosphoproteomic studies in the mycobacteria. There remains an urgent need to validate the reported phosphosites, and to elucidate their biological function in the context of pathogenicity. However, given the sheer number of putative phosphorylation events in the mycobacterial proteome, and the technical difficulty of assigning biological function to a phosphorylation event, it will not be trivial to do so. There are currently six published phosphoproteomic investigations of a member of mycobacteria. Here, we combine the datasets from these studies in order to identify commonly detected phosphopeptides and phosphosites in order to present high confidence candidates for further validation. By applying modern mass spectrometry-based techniques to improve our understanding of phosphorylation and other PTMs in pathogenic bacteria, we may identify candidates for therapeutic intervention.
Collapse
Affiliation(s)
- Bridget Calder
- Applied and Chemical Proteomics Group, Medical Biochemistry Division, Faculty of Health Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town Cape Town, South Africa
| | - Claudia Albeldas
- Applied and Chemical Proteomics Group, Medical Biochemistry Division, Faculty of Health Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town Cape Town, South Africa
| | - Jonathan M Blackburn
- Applied and Chemical Proteomics Group, Medical Biochemistry Division, Faculty of Health Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town Cape Town, South Africa
| | - Nelson C Soares
- Applied and Chemical Proteomics Group, Medical Biochemistry Division, Faculty of Health Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town Cape Town, South Africa
| |
Collapse
|
339
|
Perkowski EF, Miller BK, McCann JR, Sullivan JT, Malik S, Allen IC, Godfrey V, Hayden JD, Braunstein M. An orphaned Mce-associated membrane protein of Mycobacterium tuberculosis is a virulence factor that stabilizes Mce transporters. Mol Microbiol 2016; 100:90-107. [PMID: 26712165 DOI: 10.1111/mmi.13303] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/03/2015] [Indexed: 12/17/2022]
Abstract
Mycobacterium tuberculosis proteins that are exported out of the bacterial cytoplasm are ideally positioned to be virulence factors; however, the functions of individual exported proteins remain largely unknown. Previous studies identified Rv0199 as an exported membrane protein of unknown function. Here, we characterized the role of Rv0199 in M. tuberculosis virulence using an aerosol model of murine infection. Rv0199 appears to be a member of a Mce-associated membrane (Mam) protein family leading us to rename it OmamA, for orphaned Mam protein A. Consistent with a role in Mce transport, we showed OmamA is required for cholesterol import, which is a Mce4-dependent process. We further demonstrated a function for OmamA in stabilizing protein components of the Mce1 transporter complex. These results indicate a function of OmamA in multiple Mce transporters and one that may be analogous to the role of VirB8 in stabilizing Type IV secretion systems, as structural similarities between Mam proteins and VirB8 proteins are predicted by the Phyre 2 program. In this study, we provide functional information about OmamA and shed light on the function of Mam family proteins in Mce transporters.
Collapse
Affiliation(s)
| | - Brittany K Miller
- Department of Microbiology and Immunology, University of North Carolina
| | - Jessica R McCann
- Department of Microbiology and Immunology, University of North Carolina
| | | | - Seidu Malik
- Department of Microbiology and Immunology, University of North Carolina
| | - Irving Coy Allen
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine
| | - Virginia Godfrey
- Department of Pathology and Laboratory Medicine, University of North Carolina
| | - Jennifer D Hayden
- Department of Microbiology and Immunology, University of North Carolina
| | - Miriam Braunstein
- Department of Microbiology and Immunology, University of North Carolina
| |
Collapse
|
340
|
Wachira E, Tran K, Taylor S, Hoger S, Dunn J. Genotyping and Resolution of a Case of Osteomyelitis in a 16-Month-Old Boy of Hispanic/African American Ethnicity. Lab Med 2015; 47:57-62. [PMID: 26715611 DOI: 10.1093/labmed/lmv001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Most cases of osteomyelitis in children are caused by Staphylococcus aureus, although Kingella kingae, various streptococci, and Salmonella species also underlie this condition. Organisms such as Mycobacterium, Histoplasma, and Cryptococcus are much less commonly identified as etiologic agents in osteomyelitis. This case report describes a 16-month-old boy of Hispanic/African American ethnicity who had extensive inflammation of and discharge from his right ankle. Imaging studies supported a diagnosis of osteomyelitis. Acid-fast bacillus (AFB) and routine wound cultures were ordered on the wound discharge. The AFB culture yielded a positive result for Mycobacterium bovis, and molecular diagnostic testing further genotyped the microorganism as Mycobacterium bovis, Bacillus Calmette-Guerin (BCG). Herein, we report a rare case of osteomyelitis that we believe resulted from a BCG vaccine that the patient had received outside the United States.
Collapse
Affiliation(s)
- Eunice Wachira
- Departments of Clinical Laboratory Science, Tarleton State University, Fort Worth, TX
| | - Kayla Tran
- Departments of Clinical Laboratory Science, Tarleton State University, Fort Worth, TX
| | - Sara Taylor
- Departments of Clinical Laboratory Science, Tarleton State University, Fort Worth, TX,
| | - Sally Hoger
- Departments of Clinical Laboratory Science, Tarleton State University, Fort Worth, TX
| | - James Dunn
- Departments of Pathology & Immunology, Baylor College of Medicine, Houston, TX, and Departments of Pathology, Texas Children's Hospital, Houston, TX
| |
Collapse
|
341
|
Lv Y, Guo S, Li XG, Chi JY, Qu YQ, Zhong HL. Sputum and serum microRNA-144 levels in patients with tuberculosis before and after treatment. Int J Infect Dis 2015; 43:68-73. [PMID: 26724775 DOI: 10.1016/j.ijid.2015.12.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 12/17/2015] [Accepted: 12/17/2015] [Indexed: 01/21/2023] Open
Abstract
OBJECTIVE To measure the expression levels of sputum and serum microRNA-144 (miR-144) before and after the treatment of patients with tuberculosis (TB). METHODS Details of the cases of a total of 124 TB patients were collected at Qilu Hospital of Shandong University between April 2014 and April 2015. Fifty-three of these patients had sputum positive for bacteria and a cavity on imaging (group A), 20 patients had sputum negative for bacteria and a cavity on imaging (group B), and 51 patients had sputum negative for bacteria and no cavity on imaging (group C). One hundred seventeen healthy people who attended the hospital for a physical examination were recruited as controls. Quantitative real-time PCR (qRT-PCR) was used to measure the levels of sputum and serum miR-144 before anti-TB treatment and at 1 month after treatment. RESULTS Before treatment, sputum and serum miR-144 expression levels in the TB patients were both higher than those of the controls (both p<0.05). After treatment, sputum and serum miR-144 levels in the TB patients were significantly lower than those measured before treatment (both p<0.05). The levels of sputum and serum miR-144 in the improved TB patients decreased significantly after treatment compared to those measured before treatment (both p<0.001). Significant differences were found in sputum and serum miR-144 levels in the TB patients, with or without improvement, compared with the healthy controls (all p<0.05). CONCLUSION Sputum and serum miR-144 levels were significantly upregulated in the TB patients, but were found to decrease significantly after anti-TB treatment.
Collapse
Affiliation(s)
- Yan Lv
- Department of Respiration, Qilu Hospital of Shandong University, Wenhua West Road, No. 107, Jinan 250012, Shandong, China; Internal Medicine-Tuberculosis, Shandong Chest Hospital, Jinan, Shandong, China
| | - Shuai Guo
- Department of Respiration, Shandong Chest Hospital, Jinan, Shandong, China
| | - Xue-Gang Li
- Internal Medicine-Tuberculosis, Yantai City Hospital for Infectious Disease, Yantai, Shandong, China
| | - Jing-Yu Chi
- Internal Medicine-Tuberculosis, Shandong Chest Hospital, Jinan, Shandong, China
| | - Yi-Qing Qu
- Department of Respiration, Qilu Hospital of Shandong University, Wenhua West Road, No. 107, Jinan 250012, Shandong, China.
| | - Hai-Lai Zhong
- Department of Respiration, Qilu Hospital of Shandong University, Wenhua West Road, No. 107, Jinan 250012, Shandong, China
| |
Collapse
|
342
|
Affiliation(s)
- Marko Pesu
- a Immunoregulation, BioMediTech ; University of Tampere ; Tampere , Finland.,b Department of Dermatology ; Tampere University Hospital ; Tampere , Finland
| |
Collapse
|
343
|
Bhaduri A, Misra R, Dhamija N. The Tussle Between Mycobacteria and Host: To Eat or Not To Eat. Indian J Microbiol 2015; 55:456-9. [PMID: 26543272 DOI: 10.1007/s12088-015-0541-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 07/04/2015] [Indexed: 11/24/2022] Open
Abstract
Autophagy is a catabolic process of cellular homeostasis evolutionarily conserved in eukaryotes. To block infection of intracellular bacterial pathogens, metazoans deploy autophagy for pathogen clearance through phago-lysosome formation and specific bactericidal peptides. Although an array of research have publicized the host regulatory factors, the function of bacterial effectors are yet to be understood in detail. In this article, we focus on the autophagic response to one of the most successful intracellular bacteria Mycobacterium tuberculosis.
Collapse
Affiliation(s)
- Asani Bhaduri
- Cluster Innovation Centre, University of Delhi, Delhi, 110007 India
| | - Richa Misra
- Miranda House, University of Delhi, Delhi, 110007 India
| | - Neeru Dhamija
- Daulat Ram College, University of Delhi, Delhi, 110007 India
| |
Collapse
|
344
|
Comparative Genome and Network Centrality Analysis to Identify Drug Targets of Mycobacterium tuberculosis H37Rv. BIOMED RESEARCH INTERNATIONAL 2015; 2015:212061. [PMID: 26618166 PMCID: PMC4651637 DOI: 10.1155/2015/212061] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 09/09/2015] [Accepted: 09/27/2015] [Indexed: 12/01/2022]
Abstract
Potential drug targets of Mycobacterium tuberculosis H37Rv were identified through systematically integrated comparative genome and network centrality analysis. The comparative analysis of the complete genome of Mycobacterium tuberculosis H37Rv against Database of Essential Genes (DEG) yields a list of proteins which are essential for the growth and survival of the pathogen. Those proteins which are nonhomologous with human were selected. The resulting proteins were then prioritized by using the four network centrality measures: degree, closeness, betweenness, and eigenvector. Proteins whose centrality value is close to the centre of gravity of the interactome network were proposed as a final list of potential drug targets for the pathogen. The use of an integrated approach is believed to increase the success of the drug target identification process. For the purpose of validation, selective comparisons have been made among the proposed targets and previously identified drug targets by various other methods. About half of these proteins have been already reported as potential drug targets. We believe that the identified proteins will be an important input to experimental study which in the way could save considerable amount of time and cost of drug target discovery.
Collapse
|
345
|
Singh AK, Dutta D, Singh V, Srivastava V, Biswas RK, Singh BN. Characterization of Mycobacterium smegmatis sigF mutant and its regulon: overexpression of SigF antagonist (MSMEG_1803) in M. smegmatis mimics sigF mutant phenotype, loss of pigmentation, and sensitivity to oxidative stress. Microbiologyopen 2015; 4:896-916. [PMID: 26434659 PMCID: PMC4694148 DOI: 10.1002/mbo3.288] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 08/15/2015] [Accepted: 08/18/2015] [Indexed: 12/22/2022] Open
Abstract
In Mycobacterium smegmatis, sigF is widely expressed during different growth stages and plays role in adaptation to stationary phase and oxidative stress. Using a sigF deletion mutant of M. smegmatis mc2155, we demonstrate that SigF is not essential for growth of bacterium. Deletion of sigF results in loss of carotenoid pigmentation which rendered increased susceptibility to H2O2 induced oxidative stress in M. smegmatis. SigF modulates the cell surface architecture and lipid biosynthesis extending the repertoire of SigF function in this species. M. smegmatis SigF regulon included variety of genes expressed during exponential and stationary phases of growth and those responsible for oxidative stress, lipid biosynthesis, energy, and central intermediary metabolism. Furthermore, we report the identification of a SigF antagonist, an anti‐sigma factor (RsbW), which upon overexpression in M. smegmatis wild type strain produced a phenotype similar to M. smegmatis mc2155 ΔsigF strain. The SigF‐anti‐SigF interaction is duly validated using bacterial two‐hybrid and pull down assays. In addition, anti‐sigma factor antagonists, RsfA and RsfB were identified and their interactions with anti‐sigma factor were experimentally validated. Identification of these proteins will help decode regulatory circuit of this alternate sigma factor.
Collapse
Affiliation(s)
- Anirudh K Singh
- Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow, 226031, India
| | - Debashis Dutta
- Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow, 226031, India
| | - Vandana Singh
- Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow, 226031, India
| | - Vishal Srivastava
- Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow, 226031, India
| | - Rajesh K Biswas
- Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow, 226031, India
| | - Bhupendra N Singh
- Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow, 226031, India
| |
Collapse
|
346
|
Ng TW, Saavedra-Ávila NA, Kennedy SC, Carreño LJ, Porcelli SA. Current efforts and future prospects in the development of live mycobacteria as vaccines. Expert Rev Vaccines 2015; 14:1493-507. [PMID: 26366616 DOI: 10.1586/14760584.2015.1089175] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The development of more effective vaccines against Mycobacterium tuberculosis (Mtb) remains a major goal in the effort to reduce the enormous global burden of disease caused by this pathogen. Whole-cell vaccines based on live mycobacteria with attenuated virulence represent an appealing approach, providing broad antigen exposure and intrinsic adjuvant properties to prime durable immune responses. However, designing vaccine strains with an optimal balance between attenuation and immunogenicity has proven to be extremely challenging. Recent basic and clinical research efforts have broadened our understanding of Mtb pathogenesis and created numerous new vaccine candidates that have been designed to overcome different aspects of immune evasion by Mtb. In this review, we provide an overview of the current efforts to create improved vaccines against tuberculosis based on modifications of live attenuated mycobacteria. In addition, we discuss the use of such vaccine strains as vectors for stimulating protective immunity against other infectious diseases and cancers.
Collapse
Affiliation(s)
- Tony W Ng
- a 1 Albert Einstein College of Medicine - Microbiology & Immunology, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Noemí A Saavedra-Ávila
- a 1 Albert Einstein College of Medicine - Microbiology & Immunology, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Steven C Kennedy
- a 1 Albert Einstein College of Medicine - Microbiology & Immunology, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Leandro J Carreño
- a 1 Albert Einstein College of Medicine - Microbiology & Immunology, 1300 Morris Park Avenue, Bronx, NY 10461, USA.,b 2 Millennium Institute on Immunology and Immunotherapy, Programa Disciplinario de Inmunologia, Instituto de Ciencias Biomedicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Steven A Porcelli
- a 1 Albert Einstein College of Medicine - Microbiology & Immunology, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| |
Collapse
|
347
|
George R, Cavalcante R, Jr CC, Marques E, Waugh JB, Unlap MT. Use of siRNA molecular beacons to detect and attenuate mycobacterial infection in macrophages. World J Exp Med 2015; 5:164-181. [PMID: 26309818 PMCID: PMC4543811 DOI: 10.5493/wjem.v5.i3.164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 05/05/2015] [Accepted: 06/11/2015] [Indexed: 02/06/2023] Open
Abstract
Tuberculosis is one of the leading infectious diseases plaguing mankind and is mediated by the facultative pathogen, Mycobacterium tuberculosis (MTB). Once the pathogen enters the body, it subverts the host immune defenses and thrives for extended periods of time within the host macrophages in the lung granulomas, a condition called latent tuberculosis (LTB). Persons with LTB are prone to reactivation of the disease when the body’s immunity is compromised. Currently there are no reliable and effective diagnosis and treatment options for LTB, which necessitates new research in this area. The mycobacterial proteins and genes mediating the adaptive responses inside the macrophage is largely yet to be determined. Recently, it has been shown that the mce operon genes are critical for host cell invasion by the mycobacterium and for establishing a persistent infection in both in vitro and in mouse models of tuberculosis. The YrbE and Mce proteins which are encoded by the MTB mce operons display high degrees of homology to the permeases and the surface binding protein of the ABC transports, respectively. Similarities in structure and cell surface location impute a role in cell invasion at cholesterol rich regions and immunomodulation. The mce4 operon is also thought to encode a cholesterol transport system that enables the mycobacterium to derive both energy and carbon from the host membrane lipids and possibly generating virulence mediating metabolites, thus enabling the bacteria in its long term survival within the granuloma. Various deletion mutation studies involving individual or whole mce operon genes have shown to be conferring varying degrees of attenuation of infectivity or at times hypervirulence to the host MTB, with the deletion of mce4A operon gene conferring the greatest degree of attenuation of virulence. Antisense technology using synthetic siRNAs has been used in knocking down genes in bacteria and over the years this has evolved into a powerful tool for elucidating the roles of various genes mediating infectivity and survival in mycobacteria. Molecular beacons are a newer class of antisense RNA tagged with a fluorophore/quencher pair and their use for in vivo detection and knockdown of mRNA is rapidly gaining popularity.
Collapse
|
348
|
Sun J, Siroy A, Lokareddy RK, Speer A, Doornbos KS, Cingolani G, Niederweis M. The tuberculosis necrotizing toxin kills macrophages by hydrolyzing NAD. Nat Struct Mol Biol 2015; 22:672-8. [PMID: 26237511 PMCID: PMC4560639 DOI: 10.1038/nsmb.3064] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 07/06/2015] [Indexed: 12/29/2022]
Abstract
Mycobacterium tuberculosis (Mtb) induces necrosis of infected cells to evade immune responses. Recently, we found that Mtb uses the protein CpnT to kill human macrophages by secreting its C-terminal domain, named tuberculosis necrotizing toxin (TNT), which induces necrosis by an unknown mechanism. Here we show that TNT gains access to the cytosol of Mtb-infected macrophages, where it hydrolyzes the essential coenzyme NAD(+). Expression or injection of a noncatalytic TNT mutant showed no cytotoxicity in macrophages or in zebrafish zygotes, respectively, thus demonstrating that the NAD(+) glycohydrolase activity is required for TNT-induced cell death. To prevent self-poisoning, Mtb produces an immunity factor for TNT (IFT) that binds TNT and inhibits its activity. The crystal structure of the TNT-IFT complex revealed a new NAD(+) glycohydrolase fold of TNT, the founding member of a toxin family widespread in pathogenic microorganisms.
Collapse
Affiliation(s)
- Jim Sun
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Axel Siroy
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Ravi K Lokareddy
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Alexander Speer
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Kathryn S Doornbos
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Gino Cingolani
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Michael Niederweis
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| |
Collapse
|
349
|
Bailo R, Bhatt A, Aínsa JA. Lipid transport in Mycobacterium tuberculosis and its implications in virulence and drug development. Biochem Pharmacol 2015; 96:159-67. [DOI: 10.1016/j.bcp.2015.05.001] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 05/05/2015] [Indexed: 11/26/2022]
|
350
|
Delogu G, Provvedi R, Sali M, Manganelli R. Mycobacterium tuberculosis virulence: insights and impact on vaccine development. Future Microbiol 2015; 10:1177-94. [PMID: 26119086 DOI: 10.2217/fmb.15.26] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The existing TB vaccine, the attenuated Mycobacterium bovis strain BCG, is effective in protecting infants from severe forms of the disease, while its efficacy in protecting adults from pulmonary TB is poor. In the last two decades, a renewed interest in TB resulted in the development of several candidate vaccines that are now entering clinical trials. However, most of these vaccines are based on a common rationale and aim to induce a strong T-cell response against Mycobacterium tuberculosis. Recent advancements in the understanding of M. tuberculosis virulence determinants and associated pathogenic strategies are opening a new and broader view of the complex interaction between this remarkable pathogen and the human host, providing insights at molecular level that could lead to a new rationale for the design of novel antitubercular vaccines. A vaccination strategy that simultaneously targets different steps in TB pathogenesis may result in improved protection and reduced TB transmission.
Collapse
Affiliation(s)
- Giovanni Delogu
- Institute of Microbiology, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168, Rome, Italy
| | - Roberta Provvedi
- Department of Molecular Medicine, University of Padova, Via Aristide Gabelli 63, 35121, Padova, Italy
| | - Michela Sali
- Institute of Microbiology, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168, Rome, Italy
| | - Riccardo Manganelli
- Department of Molecular Medicine, University of Padova, Via Aristide Gabelli 63, 35121, Padova, Italy
| |
Collapse
|