1
|
Levendosky K, Janisch N, Quadri LEN. Comprehensive essentiality analysis of the Mycobacterium kansasii genome by saturation transposon mutagenesis and deep sequencing. mBio 2023; 14:e0057323. [PMID: 37350613 PMCID: PMC10470612 DOI: 10.1128/mbio.00573-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/01/2023] [Indexed: 06/24/2023] Open
Abstract
Mycobacterium kansasii (Mk) is an opportunistic pathogen that is frequently isolated from urban water systems, posing a health risk to susceptible individuals. Despite its ability to cause tuberculosis-like pulmonary disease, very few studies have probed the genetics of this opportunistic pathogen. Here, we report a comprehensive essentiality analysis of the Mk genome. Deep sequencing of a high-density library of Mk Himar1 transposon mutants revealed that 86.8% of the chromosomal thymine-adenine (TA) dinucleotide target sites were permissive to insertion, leaving 13.2% TA sites unoccupied. Our analysis identified 394 of the 5,350 annotated open reading frames (ORFs) as essential. The majority of these essential ORFs (84.8%) share essential mutual orthologs with Mycobacterium tuberculosis (Mtb). A comparative genomics analysis identified 139 Mk essential ORFs that share essential orthologs in four other species of mycobacteria. Thirteen Mk essential ORFs share orthologs in all four species that were identified as being not essential, while only two Mk essential ORFs are absent in all species compared. We used the essentiality data and a comparative genomics analysis reported here to highlight differences in essentiality between candidate Mtb drug targets and the corresponding Mk orthologs. Our findings suggest that the Mk genome encodes redundant or additional pathways that may confound validation of potential Mtb drugs and drug target candidates against the opportunistic pathogen. Additionally, we identified 57 intergenic regions containing four or more consecutive unoccupied TA sites. A disproportionally large number of these regions were located upstream of pe/ppe genes. Finally, we present an essentiality and orthology analysis of the Mk pRAW-like plasmid, pMK1248. IMPORTANCE Mk is one of the most common nontuberculous mycobacterial pathogens associated with tuberculosis-like pulmonary disease. Drug resistance emergence is a threat to the control of Mk infections, which already requires long-term, multidrug courses. A comprehensive understanding of Mk biology is critical to facilitate the development of new and more efficacious therapeutics against Mk. We combined transposon-based mutagenesis with analysis of insertion site identification data to uncover genes and other genomic regions required for Mk growth. We also compared the gene essentiality data set of Mk to those available for several other mycobacteria. This analysis highlighted key similarities and differences in the biology of Mk compared to these other species. Altogether, the genome-wide essentiality information generated and the results of the cross-species comparative genomics analysis represent valuable resources to assist the process of identifying and prioritizing potential Mk drug target candidates and to guide future studies on Mk biology.
Collapse
Affiliation(s)
- Keith Levendosky
- Department of Biology, Brooklyn College, City University of New York, Brooklyn, New York, USA
- Biology Program, Graduate Center, Biology Program, Graduate Center, City University of New York, New York, New York, USA
| | - Niklas Janisch
- Department of Biology, Brooklyn College, City University of New York, Brooklyn, New York, USA
- Biology Program, Graduate Center, Biology Program, Graduate Center, City University of New York, New York, New York, USA
| | - Luis E. N. Quadri
- Department of Biology, Brooklyn College, City University of New York, Brooklyn, New York, USA
- Biology Program, Graduate Center, Biology Program, Graduate Center, City University of New York, New York, New York, USA
- Biochemistry Program, Graduate Center, City University of New York, New York, New York, USA
| |
Collapse
|
2
|
Li W, Yan Z, Zhang N, Zhang Z, Xiang X. Novel role of PE_PGRS47 in the alteration of mycobacterial cell wall integrity and drug resistance. Arch Microbiol 2023; 205:174. [PMID: 37022460 DOI: 10.1007/s00203-023-03515-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 03/11/2023] [Accepted: 03/23/2023] [Indexed: 04/07/2023]
Abstract
The proline-glutamic acid and proline-proline-glutamic acid (PE/PPE) family of proteins is widespread in pathogenic mycobacteria and plays different roles in mycobacterial physiology. While several PE/PPE family proteins have been studied, the exact function of most PE/PPE proteins in the physiology of Mycobacterium tuberculosis (Mtb) remains unknown. PE_PGRS47 belongs to the PE/PPE family of proteins reported to help Mtb evade protective host immune responses. In this study, we demonstrate a novel role of PE_PGRS47. Heterologous expression of the pe_pgrs47 gene in a non-pathogenic Mycobacterium smegmatis, intrinsically deficient of PE_PGRS protein, exhibits modulated colony morphology and cell wall lipid profile leading to a marked susceptibility to multiple antibiotics and environmental stressors. Using ethidium bromide/Nile red uptake assays, Mycobacterium smegmatis expressing PE_PGRS47 showed higher cell wall permeability than the control strain. Overall, these data suggested that PE_PGRS47 is cell surface exposed and influences cell wall integrity and the formation of mycobacterial colonies, ultimately potentiating the efficacy of lethal stresses against mycobacteria.
Collapse
Affiliation(s)
- Wu Li
- Key Laboratory of Regional Characteristic Agricultural Resources, College of Life Sciences, Neijiang Normal University, Neijiang, 641100, Sichuan, People's Republic of China.
| | - Zifei Yan
- Key Laboratory of Regional Characteristic Agricultural Resources, College of Life Sciences, Neijiang Normal University, Neijiang, 641100, Sichuan, People's Republic of China
| | - Nan Zhang
- Key Laboratory of Regional Characteristic Agricultural Resources, College of Life Sciences, Neijiang Normal University, Neijiang, 641100, Sichuan, People's Republic of China
| | - Zhiyong Zhang
- Key Laboratory of Regional Characteristic Agricultural Resources, College of Life Sciences, Neijiang Normal University, Neijiang, 641100, Sichuan, People's Republic of China
| | - Xiaohong Xiang
- School of Pharmacy, Chongqing Medical and Pharmaceutical College, Chongqing, 401331, People's Republic of China.
| |
Collapse
|
3
|
Tang J, Zhao Z, Zhou J, Jiao L, Zhou W, Ying B, Yang Y. Multiple CD59 Polymorphisms in Chinese Patients with Mycobacterium tuberculosis Infection. J Immunol Res 2023; 2023:1216048. [PMID: 37050931 PMCID: PMC10083888 DOI: 10.1155/2023/1216048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/02/2023] [Accepted: 03/19/2023] [Indexed: 04/04/2023] Open
Abstract
Background and Objective. Tuberculosis (TB) is a major threat to human health, especially in developing countries. Its susceptibility and progression depend on interactions between mycobacterium tuberculosis, host immune system, and genetic and environmental factors. Up to now, many studies have presented the association between TB susceptibility and host genetic polymorphisms, but never regarding CD59 gene, which is an essential complement regulator. This study investigated the relationship between multiple CD59 single nucleotide polymorphisms (SNPs) and susceptibility to TB among Chinese patients. Methods. A case–control study was conducted to investigate the SNPs at CD59 rs1047581, rs7046, rs2231460, rs184251026, rs41275164, rs831633, rs704700, rs41275166, and rs10768024 by sequence-specific primer-polymerase chain reaction (SSP-PCR) in 900 tuberculosis patients and 1,534 controls. Results. The minor allele frequencies at rs2231460, rs184251026, rs41275164, and rs41275166 were extremely low both in the Cases (0.00%–0.61%) and in the Controls (0.07%–0.43%), comparatively at rs1047581, rs7046, rs831633, rs704700, and rs10768024 were notably higher both in the Cases (8.23%–48.39%) and in the Controls (8.57%–47.16%). Among the nine SNPs, only homozygous CC genotype at rs10768024 showed a significant protective effect against TB than homozygous TT genotype (OR(95% CI) = 0.59(0.38, 0.91), χ2 = 5.779,
), and homozygous TT and heterozygous CT genotypes showed a significant risk of TB infection in the recessive model (OR(95% CI) = 1.68(1.10, 2.56), χ2 = 5.769,
). Further analysis verified that rs10768024 CC genotype independently related to TB susceptibility (OR(95% CI) = 0.60(0.39, 0.91), Wald χ2 = 5.664,
) in multivariate logistic regression analysis, and its genetic mutation was independent of the other SNPs (r2 = 0.00–0.20) in haplotype analysis. Conclusions. The first investigation of the CD59 gene and susceptibility to TB suggests a significant risk with homozygous TT and heterozygous CT genotypes at rs10768024 loci. The homozygous CC mutation at rs10768024 loci showed a significant protection against TB susceptibility.
Collapse
Affiliation(s)
- Jie Tang
- Department of Laboratory Medicine, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang 621000, China
| | - Zhenzhen Zhao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Juan Zhou
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Lin Jiao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Wenjing Zhou
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yuwei Yang
- Department of Laboratory Medicine, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang 621000, China
| |
Collapse
|
4
|
Yu X, Huang Y, Li Y, Li T, Yan S, Ai X, Lv X, Fan L, Xie J. Mycobacterium tuberculosis PE_PGRS1 promotes mycobacteria intracellular survival via reducing the concentration of intracellular free Ca 2+ and suppressing endoplasmic reticulum stress. Mol Immunol 2023; 154:24-32. [PMID: 36584479 DOI: 10.1016/j.molimm.2022.12.007] [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: 08/19/2022] [Revised: 11/03/2022] [Accepted: 12/13/2022] [Indexed: 12/29/2022]
Abstract
Mycobacterium tuberculosis (M. tuberculosis) is the causative agent of tuberculosis (TB). And the PE_PGRS family members of M. tuberculosis are closely associated with virulence and antigen presentation but with function largely elusive. PE_PGRS1(Rv0109) contained 7 Ca2+ binding domains of GGXGXD/NXUX (X is any amino acid), which can reduce intracellular Ca2+ surge. In addition, PE_PGRS1 can mitigate the activation of PERK branch in endoplasmic reticulum (ER) stress by down-regulating the expression of CHOP, Bip, p-PERK, p-eIF2α, and ATF4. Interestingly, we found that two splicing variations of Bax/Bcl-2, Baxβ, and Bcl-2α, were differentially expressed after infection with Ms_PE_PGRS1, and may be involved in the regulation of apoptosis. Hence, this study identified that PE_PGRS1 is a novel calcium-associated protein that can decrease intracellular Ca2+ levels and the PERK axis. And the weakening of the PERK-eIF2α-ATF4 axis reduces THP-1 macrophages apoptosis, promotes the survival of mycobacteria in macrophages.
Collapse
Affiliation(s)
- Xi Yu
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Yu Huang
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Yuzhu Li
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Tongxin Li
- Chongqing Public Health Medical Center, Southwest University Public Health Hospital, central laboratory, Chongqing 400715, China
| | - Shuangquan Yan
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Xuefeng Ai
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Xi Lv
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Lin Fan
- Shanghai Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai Key Laboratory of Tuberculosis, Shanghai 200433, China.
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400715, China.
| |
Collapse
|
5
|
Evaluating the Performance of PPE44, HSPX, ESAT-6 and CFP-10 Factors in Tuberculosis Subunit Vaccines. Curr Microbiol 2022; 79:260. [PMID: 35852636 PMCID: PMC9295111 DOI: 10.1007/s00284-022-02949-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 06/23/2022] [Indexed: 11/26/2022]
Abstract
Mycobacterium tuberculosis (M. tuberculosis) is an intracellular pathogen causing long-term infection in humans that mainly attacks macrophages and can escape from the immune system with the various mechanisms. The only FDA-approved vaccine against M. tuberculosis (MTB) is Mycobacterium bovis bacillus Calmette-Guérin (BCG). The protection of this vaccine typically lasts 10–15 years. Due to the increasing number of people becoming ill with MTB each year worldwide, the need to develop a new effective treatment against the disease has been increased. During the past two decades, the research budget for TB vaccine has quadrupled to over half a billion dollars. Most of these research projects were based on amplifying and stimulating the response of T-cells and developing the subunit vaccines. Additionally, these studies have demonstrated that secretory and immunogenic proteins of MTB play a key role in the pathogenesis of the bacteria. Therefore, these proteins were used to develop the new subunit vaccines. In this review, based on the use of these proteins in the successful new subunit vaccines, the PPE44, HSPX, CFP-10 and ESAT-6 antigens were selected and the role of these antigens in designing and developing new subunit vaccines against TB and for the prevention of TB were investigated.
Collapse
|
6
|
Zonghai C, Tao L, Pengjiao M, Liang G, Rongchuan Z, Xinyan W, Wenyi N, Wei L, Yi W, Lang B. Mycobacterium tuberculosis ESAT6 modulates host innate immunity by downregulating miR-222-3p target PTEN. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166292. [PMID: 34710568 DOI: 10.1016/j.bbadis.2021.166292] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/18/2021] [Accepted: 10/12/2021] [Indexed: 12/24/2022]
Abstract
Tuberculosis (TB) remains a major cause of mortality and morbidity worldwide, and it is instant to discover novel anti-TB drugs due to the rapidly growing drug-resistance TB. Mycobacterium tuberculosis (Mtb) secreted effector ESAT6 plays a critical role in modulation miRNAs to regulate host defense mechanisms during Mtb infection, it can be a possible target for new tuberculosis drugs. The non-tuberculous mycobacteria Mycobacterium smegmatis (M. smegmatis) and Mtb have high gene homology but no pathogenicity. We used ESAT6 to interfere with macrophages or mice infected by M. smegmatis and determined that it enhanced the survival rate of bacteria and regulated miR-222-3p target PTEN. Expression of miR-222-3p reduced and PTEN enhanced with the progression of macrophages infected by M. smegmatis with ESAT6 co-incubation. MiR-222-3p overexpression diminished M. smegmatis survival and upregulated proinflammatory cytokines. VO-Ohpic trihydrate (PTEN inhibitor) reduced M. smegmatis survival and upregulated proinflammatory cytokines in vivo and in vitro, and VO-Ohpic trihydrate reversed the tissue damage of mouse organs caused by ESAT6. These results uncover an ESAT6 dependent role for miR-222-3p and its target PTEN in regulating host immune responses to bacterial infection and may provide a potential site for the development of anti-tuberculosis drugs that specifically antagonize the virulence of ESAT6.
Collapse
Affiliation(s)
- Chen Zonghai
- Laboratory of Infection and Immunity, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Luo Tao
- Laboratory of Infection and Immunity, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Ma Pengjiao
- Laboratory of Infection and Immunity, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Ge Liang
- Laboratory of Infection and Immunity, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Zhao Rongchuan
- Laboratory of Infection and Immunity, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Wang Xinyan
- Laboratory of Infection and Immunity, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Ni Wenyi
- Laboratory of Infection and Immunity, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Liao Wei
- Laboratory of Infection and Immunity, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Wang Yi
- Laboratory of Infection and Immunity, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Bao Lang
- Laboratory of Infection and Immunity, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
| |
Collapse
|
7
|
Chen Y, Zhai W, Zhang K, Liu H, Zhu T, Su L, Bermudez L, Chen H, Guo A. Small RNA Profiling in Mycobacterium Provides Insights Into Stress Adaptability. Front Microbiol 2021; 12:752537. [PMID: 34803973 PMCID: PMC8600241 DOI: 10.3389/fmicb.2021.752537] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/01/2021] [Indexed: 11/29/2022] Open
Abstract
Mycobacteria encounter a number of environmental changes during infection and respond using different mechanisms. Small RNA (sRNA) is a post-transcriptionally regulatory system for gene functions and has been investigated in many other bacteria. This study used Mycobacterium tuberculosis and Mycobacterium bovis Bacillus Calmette-Guérin (BCG) infection models and sequenced whole bacterial RNAs before and after host cell infection. A comparison of differentially expressed sRNAs using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) and target prediction was carried out. Six pathogenically relevant stress conditions, growth rate, and morphology were used to screen and identify sRNAs. From these data, a subset of sRNAs was differentially expressed in multiple infection groups and stress conditions. Many were found associated with lipid metabolism. Among them, ncBCG427 was significantly downregulated when BCG entered into macrophages and was associated with increased biofilm formation. The reduction of virulence possibility depends on regulating lipid metabolism.
Collapse
Affiliation(s)
- Yingyu Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,National Animal Tuberculosis Para-Reference Laboratory (Wuhan) of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Wenjun Zhai
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,National Animal Tuberculosis Para-Reference Laboratory (Wuhan) of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Kailun Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,National Animal Tuberculosis Para-Reference Laboratory (Wuhan) of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Han Liu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,National Animal Tuberculosis Para-Reference Laboratory (Wuhan) of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Tingting Zhu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,National Animal Tuberculosis Para-Reference Laboratory (Wuhan) of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Li Su
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,National Animal Tuberculosis Para-Reference Laboratory (Wuhan) of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Luiz Bermudez
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,National Animal Tuberculosis Para-Reference Laboratory (Wuhan) of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Aizhen Guo
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,National Animal Tuberculosis Para-Reference Laboratory (Wuhan) of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
8
|
Mizzi R, Timms VJ, Price-Carter ML, Gautam M, Whittington R, Heuer C, Biggs PJ, Plain KM. Comparative Genomics of Mycobacterium avium Subspecies Paratuberculosis Sheep Strains. Front Vet Sci 2021; 8:637637. [PMID: 33659287 PMCID: PMC7917049 DOI: 10.3389/fvets.2021.637637] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/25/2021] [Indexed: 12/15/2022] Open
Abstract
Mycobacterium avium subspecies paratuberculosis (MAP) is the aetiological agent of Johne's disease (JD), a chronic enteritis that causes major losses to the global livestock industry. Further, it has been associated with human Crohn's disease. Several strains of MAP have been identified, the two major groups being sheep strain MAP, which includes the Type I and Type III sub-lineages, and the cattle strain or Type II MAP lineage, of which bison strains are a sub-grouping. Major genotypic, phenotypic and pathogenic variations have been identified in prior comparisons, but the research has predominately focused on cattle strains of MAP. In countries where the sheep industries are more prevalent, however, such as Australia and New Zealand, ovine JD is a substantial burden. An information gap exists regarding the genomic differences between sheep strain sub-lineages and the relevance of Type I and Type III MAP in terms of epidemiology and/or pathogenicity. We therefore investigated sheep MAP isolates from Australia and New Zealand using whole genome sequencing. For additional context, sheep MAP genome datasets were downloaded from the Sequence Read Archive and GenBank. The final dataset contained 18 Type III and 16 Type I isolates and the K10 cattle strain MAP reference genome. Using a pan-genome approach, an updated global phylogeny for sheep MAP from de novo assemblies was produced. When rooted with the K10 cattle reference strain, two distinct clades representing the lineages were apparent. The Australian and New Zealand isolates formed a distinct sub-clade within the type I lineage, while the European type I isolates formed another less closely related group. Within the type III lineage, isolates appeared more genetically diverse and were from a greater number of continents. Querying of the pan-genome and verification using BLAST analysis revealed lineage-specific variations (n = 13) including genes responsible for metabolism and stress responses. The genetic differences identified may represent important epidemiological and virulence traits specific to sheep MAP. This knowledge will potentially contribute to improved vaccine development and control measures for these strains.
Collapse
Affiliation(s)
- Rachel Mizzi
- Farm Animal Health Group, Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW, Australia
| | - Verlaine J Timms
- Centre for Infectious Diseases and Microbiology, Public Health, Westmead Hospital, Westmead, NSW, Australia
| | | | - Milan Gautam
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Richard Whittington
- Farm Animal Health Group, Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW, Australia
| | - Cord Heuer
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Patrick J Biggs
- School of Veterinary Science, Massey University, Palmerston North, New Zealand.,School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Karren M Plain
- Farm Animal Health Group, Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW, Australia
| |
Collapse
|
9
|
Qian J, Chen R, Wang H, Zhang X. Role of the PE/PPE Family in Host-Pathogen Interactions and Prospects for Anti-Tuberculosis Vaccine and Diagnostic Tool Design. Front Cell Infect Microbiol 2020; 10:594288. [PMID: 33324577 PMCID: PMC7726347 DOI: 10.3389/fcimb.2020.594288] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 10/31/2020] [Indexed: 12/13/2022] Open
Abstract
The pe/ppe genes are found in pathogenic, slow-growing Mycobacterium tuberculosis and other M. tuberculosis complex (MTBC) species. These genes are considered key factors in host-pathogen interactions. Although the function of most PE/PPE family proteins remains unclear, accumulating evidence suggests that this family is involved in M. tuberculosis infection. Here, we review the role of PE/PPE proteins, which are believed to be linked to the ESX system function. Further, we highlight the reported functions of PE/PPE proteins, including their roles in host cell interaction, immune response regulation, and cell fate determination during complex host-pathogen processes. Finally, we propose future directions for PE/PPE protein research and consider how the current knowledge might be applied to design more specific diagnostics and effective vaccines for global tuberculosis control.
Collapse
Affiliation(s)
- Jianing Qian
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Run Chen
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Honghai Wang
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Xuelian Zhang
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China.,Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
| |
Collapse
|
10
|
Niskanen M, Myllymäki H, Rämet M. DNA vaccination with the Mycobacterium marinum MMAR_4110 antigen inhibits reactivation of a latent mycobacterial infection in the adult Zebrafish. Vaccine 2020; 38:5685-5694. [PMID: 32624250 DOI: 10.1016/j.vaccine.2020.06.053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 06/03/2020] [Accepted: 06/18/2020] [Indexed: 12/31/2022]
Abstract
BACKGROUND Tuberculosis is a major challenge for health care, as options for its treatment and prevention are limited. Therefore, novel approaches, such as DNA vaccination, to both prevent primary infections and the reactivation of latent infections need to be developed. A Mycobacterium marinum infection in adult zebrafish (Danio rerio) recapitulates features of the human Mycobacterium tuberculosis infection, providing a convenient preclinical animal model for studying tuberculosis. METHODS Hypoxic M. marinum cultures were produced with the Wayne model, and further reaerated to replicate the in vivo reactivation in vitro. Expression levels of M. marinum genes were studied with mRNA sequencing from exponentially growing bacteria, anaerobic cultures and at 2 and 12 h after reaeration. Seven reactivation-associated genes were selected for further studies, where their antigen potentiality as DNA-vaccines to prevent reactivation of a latent mycobacterial infection was investigated in the adult zebrafish model. The Mann-Whitney test was used to evaluate differences in bacterial counts between the groups. RESULTS The mRNA sequencing data showed that, seven M. marinum genes, MMAR_0444, MMAR_0514, MMAR_0552, MMAR_0641, MMAR_1093, MMAR_4110 and MMAR_4524, were upregulated during reactivation when compared to both dormant and logarithmic growing bacteria. Four different MMAR_4110 antigens prevented the reactivation of a latent mycobacterial infection in the adult zebrafish. CONCLUSION This study provides novel information about reactivation-related M. marinum genes. One of the antigens, MMAR_4110, inhibited the reactivation of a latent M. marinum infection in zebrafish, implicating that the characterized genes could be potential targets for further vaccine and drug development against mycobacterial diseases.
Collapse
Affiliation(s)
- Mirja Niskanen
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Henna Myllymäki
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Mika Rämet
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland; PEDEGO Research Unit and Medical Research Centre, University of Oulu, Finland.
| |
Collapse
|
11
|
Ali MK, Zhen G, Nzungize L, Stojkoska A, Duan X, Li C, Duan W, Xu J, Xie J. Mycobacterium tuberculosis PE31 ( Rv3477) Attenuates Host Cell Apoptosis and Promotes Recombinant M. smegmatis Intracellular Survival via Up-regulating GTPase Guanylate Binding Protein-1. Front Cell Infect Microbiol 2020; 10:40. [PMID: 32117813 PMCID: PMC7020884 DOI: 10.3389/fcimb.2020.00040] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 01/21/2020] [Indexed: 12/23/2022] Open
Abstract
The Mycobacterium (M.) tuberculosis comprising proline–glutamic acid (PE) subfamily proteins associate with virulence, pathogenesis, and host-immune modulations. While the functions of most of this family members are not yet explored. Here, we explore the functions of “PE only” subfamily member PE31 (Rv3477) in virulence and host-pathogen interactions. We have expressed the M. tuberculosis PE31 in non-pathogenic Mycobacterium smegmatis strain (Ms_PE31) and demonstrated that PE31 significantly altered the cell facet features including colony morphology and biofilm formation. PE31 expressing M. smegmatis showed more resistant to the low pH, diamide, H2O2 and surface stress. Moreover, Ms_PE31 showed higher intracellular survival in macrophage THP-1 cells. Ms_PE31 significantly down-regulated the production of IL-12p40 and IL-6, while up-regulates the production of IL-10 in macrophages. Ms_PE31 also induced the expression of guanylate-binding protein-1 (GBP-1) in macrophages. Further analysis demonstrates that Ms_PE31 inhibits the caspase-3 activation and reduces the macrophages apoptosis. Besides, the NF-κB signaling pathway involves the interplay between Ms_PE31 and macrophages. Collectively, our finding identified that PE31 act as a functionally relevant virulence factor of M. tuberculosis.
Collapse
Affiliation(s)
- Md Kaisar Ali
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University, Chongqing, China
| | - Gong Zhen
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University, Chongqing, China
| | - Lambert Nzungize
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University, Chongqing, China
| | - Andrea Stojkoska
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University, Chongqing, China
| | - Xiangke Duan
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University, Chongqing, China
| | - Chunyan Li
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University, Chongqing, China
| | - Wei Duan
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University, Chongqing, China
| | - Junqi Xu
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University, Chongqing, China
| | - Jianping Xie
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University, Chongqing, China
| |
Collapse
|
12
|
Tong J, Liu Q, Wu J, Jiang Y, Takiff HE, Gao Q. Mycobacterium tuberculosis strains of the modern Beijing sublineage excessively accumulate triacylglycerols in vitro. Tuberculosis (Edinb) 2019; 120:101892. [PMID: 31783320 DOI: 10.1016/j.tube.2019.101892] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 11/18/2019] [Accepted: 11/21/2019] [Indexed: 11/18/2022]
Abstract
Mycobacterium tuberculosis (Mtb) strains of modern Beijing sublineage appear to be more transmissible and cause more severe disease than strains of other sublineages, but the responsible pathogenic mechanisms remain unclear. We previously identified genetic changes that are specific for the modern Beijing sublineage, and here we characterize the lipidome and transcriptome differences between modern and ancient Beijing sublineages. We report that modern Beijing strains accumulated 2.89 (95%CI: 2.05-3.73) times more triacylglycerol (TAG) than ancient Beijing strains in vitro. We also observed that modern Beijing strains had a 2.64-fold (95%CI: 1.29-4.00) upregulation of tgs2 (annotated as TAG synthetase 2), whose role in TAG accumulation was further confirmed in Mycobacterium marinum (Mm). Because TAG serves as a crucial carbon source and reservoir of free fatty acids, the results suggest that the excessive accumulation of TAG might fuel the growth of modern Beijing strains after infection and lead to rapid development of disease.
Collapse
Affiliation(s)
- Jingfeng Tong
- Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 200032, China; Shenzhen Center for Chronic Disease Control, Shenzhen, 518000, China
| | - Qingyun Liu
- Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 200032, China; Shenzhen Center for Chronic Disease Control, Shenzhen, 518000, China
| | - Jie Wu
- Department of Tuberculosis Control, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, 200336, China
| | - Yuan Jiang
- Department of Tuberculosis Control, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, 200336, China
| | - Howard E Takiff
- Integrated Mycobacterial Pathogenomics Unit, Institut Pasteur, Paris, France; Nanshan Center for Chronic Disease Control, Shenzhen, China
| | - Qian Gao
- Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 200032, China; Shenzhen Center for Chronic Disease Control, Shenzhen, 518000, China.
| |
Collapse
|