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Gómez-González PJ, Grabowska AD, Tientcheu LD, Tsolaki AG, Hibberd ML, Campino S, Phelan JE, Clark TG. Functional genetic variation in pe/ ppe genes contributes to diversity in Mycobacterium tuberculosis lineages and potential interactions with the human host. Front Microbiol 2023; 14:1244319. [PMID: 37876785 PMCID: PMC10591178 DOI: 10.3389/fmicb.2023.1244319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 09/21/2023] [Indexed: 10/26/2023] Open
Abstract
Introduction Around 10% of the coding potential of Mycobacterium tuberculosisis constituted by two poorly understood gene families, the pe and ppe loci, thought to be involved in host-pathogen interactions. Their repetitive nature and high GC content have hindered sequence analysis, leading to exclusion from whole-genome studies. Understanding the genetic diversity of pe/ppe families is essential to facilitate their potential translation into tools for tuberculosis prevention and treatment. Methods To investigate the genetic diversity of the 169 pe/ppe genes, we performed a sequence analysis across 73 long-read assemblies representing seven different lineages of M. tuberculosis and M. bovis BCG. Individual pe/ppe gene alignments were extracted and diversity and conservation across the different lineages studied. Results The pe/ppe genes were classified into three groups based on the level of protein sequence conservation relative to H37Rv, finding that >50% were conserved, with indels in pe_pgrs and ppe_mptr sub-families being major drivers of structural variation. Gene rearrangements, such as duplications and gene fusions, were observed between pe and pe_pgrs genes. Inter-lineage diversity revealed lineage-specific SNPs and indels. Discussion The high level of pe/ppe genes conservation, together with the lineage-specific findings, suggest their phylogenetic informativeness. However, structural variants and gene rearrangements differing from the reference were also identified, with potential implications for pathogenicity. Overall, improving our knowledge of these complex gene families may have insights into pathogenicity and inform the development of much-needed tools for tuberculosis control.
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Affiliation(s)
| | - Anna D. Grabowska
- Department of Biophysics, Physiology and Pathophysiology, Medical University of Warsaw, Warsaw, Poland
| | - Leopold D. Tientcheu
- MRC Unit, The Gambia at the London School of Hygiene and Tropical Medicine, Vaccines and Immunity Theme, Fajara, The Gambia
| | - Anthony G. Tsolaki
- Department of Life Sciences, Brunel University London, Uxbridge, United Kingdom
| | - Martin L. Hibberd
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Jody E. Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Taane G. Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
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Rastogi S, Singh AK, Pant G, Mitra K, Sashidhara KV, Krishnan MY. Down-regulation of PE11, a cell wall associated esterase, enhances the biofilm growth of Mycobacterium tuberculosis and reduces cell wall virulence lipid levels. MICROBIOLOGY-SGM 2017; 163:52-61. [PMID: 28198348 DOI: 10.1099/mic.0.000417] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
PE11 (Rv1169c or LipX) is a cell wall associated esterase/lipase of Mycobacterium tuberculosis (Mtb). Evidences suggest that PE11 is expressed by Mtb both in vitro and in vivo. Previous studies have shown that PE11 leads to modification in cell wall lipid content and enhanced virulence when expressed in the non-pathogenic surrogate Mycobacterium smegmatis. Since cell wall lipids often play different roles in pathogenic and non-pathogenic mycobacteria, we investigated the role of PE11 in its host, Mtb. Mtb with lowered expression of PE11 (PE11 knock-down) displayed significant changes in colony morphology and cell wall lipid profile, confirming the role of PE11 in cell wall architecture. In addition, the levels of phthiocerol dimycocerosates, a cell wall virulence factor, were decreased. Levels of trehalose esters and free mycolic acids were increased. In contrast to M. smegmatis expressing Mtb PE11, a role reversal was observed in Mtb with respect to pellicle/biofilm formation. The PE11 knock-down Mtb strain showed significantly enhanced aggregation and early biofilm growth in detergent-free medium, compared to the wild-type. Knock-down strain also showed nearly 27-fold up-regulation of a fibronectin attachment protein (Rv1759c), linking biofilm growth with over-expression of bacterial proteins that help in aggregation and/or binding to host extracellular matrix. The knock-down also resulted in poor virulence of Mtb in PMA (phorbol 12-myristate 13-acetate) treated and PMA+IFN-γ treated THP-1 macrophages. Therefore, the study not only links PE11 to cell wall virulence lipids but also reveals the involvement of this cell wall associated esterase in down-regulation of biofilm in Mtb.
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Affiliation(s)
- Shivangi Rastogi
- Division of Microbiology, Council of Scientific and Industrial Research, Central Drug Research Institute, Sitapur Road, Lucknow, Uttar Pradesh 226 031, India
| | - Amit Kumar Singh
- Division of Molecular and Structural Biology, Council of Scientific and Industrial Research, Central Drug Research Institute, Sitapur Road, Lucknow, Uttar Pradesh 226 031, India
| | - Garima Pant
- Sophisticated Analytical Instrument Facility, Council of Scientific and Industrial Research, Central Drug Research Institute, Sitapur Road, Lucknow, Uttar Pradesh 226 031, India
| | - Kalyan Mitra
- Sophisticated Analytical Instrument Facility, Council of Scientific and Industrial Research, Central Drug Research Institute, Sitapur Road, Lucknow, Uttar Pradesh 226 031, India
| | - Koneni V Sashidhara
- Medicinal and Process Chemistry Division, Council of Scientific and Industrial Research, Central Drug Research Institute, Sitapur Road, Lucknow, Uttar Pradesh 226 031, India
| | - Manju Y Krishnan
- Division of Microbiology, Council of Scientific and Industrial Research, Central Drug Research Institute, Sitapur Road, Lucknow, Uttar Pradesh 226 031, India
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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.
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Shi X, Lin Y, Qiu Y, Li Y, Jiang M, Chen Q, Jiang Y, Yuan J, Cao H, Hu Q, Huang S. Comparative Screening of Digestion Tract Toxic Genes in Proteus mirabilis. PLoS One 2016; 11:e0151873. [PMID: 27010388 PMCID: PMC4807080 DOI: 10.1371/journal.pone.0151873] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 03/04/2016] [Indexed: 11/18/2022] Open
Abstract
Proteus mirabilis is a common urinary tract pathogen, and may induce various inflammation symptoms. Its notorious ability to resist multiple antibiotics and to form urinary tract stones makes its treatment a long and painful process, which is further challenged by the frequent horizontal gene transferring events in P. mirabilis genomes. Three strains of P. mirabilis C02011/C04010/C04013 were isolated from a local outbreak of a food poisoning event in Shenzhen, China. Our hypothesis is that new genes may have been acquired horizontally to exert the digestion tract infection and toxicity. The functional characterization of these three genomes shows that each of them independently acquired dozens of virulent genes horizontally from the other microbial genomes. The representative strain C02011 induces the symptoms of both vomit and diarrhea, and has recently acquired a complete type IV secretion system and digestion tract toxic genes from the other bacteria.
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Affiliation(s)
- Xiaolu Shi
- School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, 510515, China
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Yiman Lin
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Yaqun Qiu
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Yinghui Li
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Min Jiang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Qiongcheng Chen
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Yixiang Jiang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Jianhui Yuan
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Hong Cao
- School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Qinghua Hu
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
- * E-mail: (QHH); (SHH)
| | - Shenghe Huang
- School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, 510515, China
- * E-mail: (QHH); (SHH)
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Naqvi AAT, Ahmad F, Hassan MI. Identification of functional candidates amongst hypothetical proteins of Mycobacterium leprae Br4923, a causative agent of leprosy. Genome 2015; 58:25-42. [DOI: 10.1139/gen-2014-0178] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Mycobacterium leprae is an intracellular obligate parasite that causes leprosy in humans, and it leads to the destruction of peripheral nerves and skin deformation. Here, we report an extensive analysis of the hypothetical proteins (HPs) from M. leprae strain Br4923, assigning their functions to better understand the mechanism of pathogenesis and to search for potential therapeutic interventions. The genome of M. leprae encodes 1604 proteins, of which the functions of 632 are not known (HPs). In this paper, we predicted the probable functions of 312 HPs. First, we classified all HPs into families and subfamilies on the basis of sequence similarity, followed by domain assignment, which provides many clues for their possible function. However, the functions of 320 proteins were not predicted because of low sequence similarity with proteins of known function. Annotated HPs were categorized into enzymes, binding proteins, transporters, and proteins involved in cellular processes. We found several novel proteins whose functions were unknown for M. leprae. These proteins have a requisite association with bacterial virulence and pathogenicity. Finally, our sequence-based analysis will be helpful for further validation and the search for potential drug targets while developing effective drugs to cure leprosy.
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Affiliation(s)
- Ahmad Abu Turab Naqvi
- Department of Computer Science, Jamia Millia Islamia, Jamia Nagar, New Delhi – 110025, India
| | - Faizan Ahmad
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi – 110025, India
| | - Md. Imtaiyaz Hassan
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi – 110025, India
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