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Sparks IL, Kado T, Prithviraj M, Nijjer J, Yan J, Morita YS. Lipoarabinomannan mediates localized cell wall integrity during division in mycobacteria. Nat Commun 2024; 15:2191. [PMID: 38467648 PMCID: PMC10928101 DOI: 10.1038/s41467-024-46565-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 02/29/2024] [Indexed: 03/13/2024] Open
Abstract
The growth and division of mycobacteria, which include clinically relevant pathogens, deviate from that of canonical bacterial models. Despite their Gram-positive ancestry, mycobacteria synthesize and elongate a diderm envelope asymmetrically from the poles, with the old pole elongating more robustly than the new pole. The phosphatidylinositol-anchored lipoglycans lipomannan (LM) and lipoarabinomannan (LAM) are cell envelope components critical for host-pathogen interactions, but their physiological functions in mycobacteria remained elusive. In this work, using biosynthetic mutants of these lipoglycans, we examine their roles in maintaining cell envelope integrity in Mycobacterium smegmatis and Mycobacterium tuberculosis. We find that mutants defective in producing mature LAM fail to maintain rod cell shape specifically at the new pole and para-septal regions whereas a mutant that produces a larger LAM becomes multi-septated. Therefore, LAM plays critical and distinct roles at subcellular locations associated with division in mycobacteria, including maintenance of local cell wall integrity and septal placement.
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Affiliation(s)
- Ian L Sparks
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA
| | - Takehiro Kado
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA
| | | | - Japinder Nijjer
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
- Quantitative Biology Institute, Yale University, New Haven, CT, USA
| | - Jing Yan
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
- Quantitative Biology Institute, Yale University, New Haven, CT, USA
| | - Yasu S Morita
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA.
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Sparks IL, Nijjer J, Yan J, Morita YS. Lipoarabinomannan regulates septation in Mycobacterium smegmatis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.26.534150. [PMID: 36993273 PMCID: PMC10055410 DOI: 10.1101/2023.03.26.534150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The growth and division of mycobacteria, which include several clinically relevant pathogens, deviate significantly from that of canonical bacterial models. Despite their Gram-positive ancestry, mycobacteria synthesize and elongate a diderm envelope asymmetrically from the poles, with the old pole elongating more robustly than the new pole. In addition to being structurally distinct, the molecular components of the mycobacterial envelope are also evolutionarily unique, including the phosphatidylinositol-anchored lipoglycans lipomannan (LM) and lipoarabinomannan (LAM). LM and LAM modulate host immunity during infection, but their role outside of intracellular survival remains poorly understood, despite their widespread conservation among non-pathogenic and opportunistically pathogenic mycobacteria. Previously, Mycobacterium smegmatis and Mycobacterium tuberculosis mutants producing structurally altered LM and LAM were shown to grow slowly under certain conditions and to be more sensitive to antibiotics, suggesting that mycobacterial lipoglycans may support cellular integrity or growth. To test this, we constructed multiple biosynthetic lipoglycan mutants of M. smegmatis and determined the effect of each mutation on cell wall biosynthesis, envelope integrity, and division. We found that mutants deficient in LAM, but not LM, fail to maintain cell wall integrity in a medium-dependent manner, with envelope deformations specifically associated with septa and new poles. Conversely, a mutant producing abnormally large LAM formed multiseptated cells in way distinct from that observed in a septal hydrolase mutant. These results show that LAM plays critical and distinct roles at subcellular locations associated with division in mycobacteria, including maintenance of local cell envelope integrity and septal placement.
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Affiliation(s)
- Ian L. Sparks
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA
| | - Japinder Nijjer
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven CT, USA
- Quantitative Biology Institute, Yale University, New Haven, CT, USA
| | - Jing Yan
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven CT, USA
- Quantitative Biology Institute, Yale University, New Haven, CT, USA
| | - Yasu S. Morita
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA
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Amiri Moghaddam J, Dávila-Céspedes A, Kehraus S, Crüsemann M, Köse M, Müller CE, König GM. Cyclopropane-Containing Fatty Acids from the Marine Bacterium Labrenzia sp. 011 with Antimicrobial and GPR84 Activity. Mar Drugs 2018; 16:md16100369. [PMID: 30297608 PMCID: PMC6213206 DOI: 10.3390/md16100369] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 10/01/2018] [Accepted: 10/03/2018] [Indexed: 11/23/2022] Open
Abstract
Bacteria of the family Rhodobacteraceae are widespread in marine environments and known to colonize surfaces, such as those of e.g., oysters and shells. The marine bacterium Labrenzia sp. 011 is here investigated and it was found to produce two cyclopropane-containing medium-chain fatty acids (1, 2), which inhibit the growth of a range of bacteria and fungi, most effectively that of a causative agent of Roseovarius oyster disease (ROD), Pseudoroseovarius crassostreae DSM 16950. Additionally, compound 2 acts as a potent partial, β-arrestin-biased agonist at the medium-chain fatty acid-activated orphan G-protein coupled receptor GPR84, which is highly expressed on immune cells. The genome of Labrenzia sp. 011 was sequenced and bioinformatically compared with those of other Labrenzia spp. This analysis revealed several cyclopropane fatty acid synthases (CFAS) conserved in all Labrenzia strains analyzed and a putative gene cluster encoding for two distinct CFASs is proposed as the biosynthetic origin of 1 and 2.
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Affiliation(s)
| | | | - Stefan Kehraus
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany.
| | - Max Crüsemann
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany.
| | - Meryem Köse
- Pharmaceutical Institute, Pharmaceutical Chemistry I, An der Immenburg 4, D-53121 Bonn, Germany.
| | - Christa E Müller
- Pharmaceutical Institute, Pharmaceutical Chemistry I, An der Immenburg 4, D-53121 Bonn, Germany.
| | - Gabriele Maria König
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany.
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4
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Birhanu AG, Yimer SA, Holm-Hansen C, Norheim G, Aseffa A, Abebe M, Tønjum T. N ε- and O-Acetylation in Mycobacterium tuberculosis Lineage 7 and Lineage 4 Strains: Proteins Involved in Bioenergetics, Virulence, and Antimicrobial Resistance Are Acetylated. J Proteome Res 2017; 16:4045-4059. [PMID: 28920697 DOI: 10.1021/acs.jproteome.7b00429] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Increasing evidence demonstrates that lysine acetylation is involved in Mycobacterium tuberculosis (Mtb) virulence and pathogenesis. However, previous investigations in Mtb have only monitored acetylation at lysine residues using selected reference strains. We analyzed the global Nε- and O-acetylation of three Mtb isolates: two lineage 7 clinical isolates and the lineage 4 H37Rv reference strain. Quantitative acetylome analysis resulted in identification of 2490 class-I acetylation sites, 2349 O-acetylation and 141 Nε-acetylation sites, derived from 953 unique proteins. Mtb O-acetylation was thereby significantly more abundant than Nε-acetylation. The acetylated proteins were found to be involved in central metabolism, translation, stress responses, and antimicrobial drug resistance. Notably, 261 acetylation sites on 165 proteins were differentially regulated between lineage 7 and lineage 4 strains. A total of 257 acetylation sites on 161 proteins were hypoacetylated in lineage 7 strains. These proteins are involved in Mtb growth, virulence, bioenergetics, host-pathogen interactions, and stress responses. This study provides the first global analysis of O-acetylated proteins in Mtb. This quantitative acetylome data expand the current understanding regarding the nature and diversity of acetylated proteins in Mtb and open a new avenue of research for exploring the role of protein acetylation in Mtb physiology.
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Affiliation(s)
- Alemayehu Godana Birhanu
- Department of Microbiology, University of Oslo , P.O. Box 4950, Nydalen, NO-0424 Oslo, Norway.,Addis Ababa University , Institute of Biotechnology, P.O. Box 1176, Addis Ababa, Ethiopia
| | - Solomon Abebe Yimer
- Department of Microbiology, University of Oslo , P.O. Box 4950, Nydalen, NO-0424 Oslo, Norway.,Department of Microbiology, Oslo University Hospital , P.O. Box 4950, Nydalen, NO-0424 Oslo, Norway
| | - Carol Holm-Hansen
- Infection Control and Environmental Health, Norwegian Institute of Public Health , P.O. Box 4404, Nydalen, NO-0403 Oslo, Norway
| | - Gunnstein Norheim
- Infection Control and Environmental Health, Norwegian Institute of Public Health , P.O. Box 4404, Nydalen, NO-0403 Oslo, Norway
| | - Abraham Aseffa
- Armauer Hansen Research Institute , Jimma Road, P.O. Box 1005, Addis Ababa, Ethiopia
| | - Markos Abebe
- Armauer Hansen Research Institute , Jimma Road, P.O. Box 1005, Addis Ababa, Ethiopia
| | - Tone Tønjum
- Department of Microbiology, University of Oslo , P.O. Box 4950, Nydalen, NO-0424 Oslo, Norway.,Department of Microbiology, Oslo University Hospital , P.O. Box 4950, Nydalen, NO-0424 Oslo, Norway
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Elghraoui A, Modlin SJ, Valafar F. SMRT genome assembly corrects reference errors, resolving the genetic basis of virulence in Mycobacterium tuberculosis. BMC Genomics 2017; 18:302. [PMID: 28415976 PMCID: PMC5393005 DOI: 10.1186/s12864-017-3687-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Accepted: 04/06/2017] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The genetic basis of virulence in Mycobacterium tuberculosis has been investigated through genome comparisons of virulent (H37Rv) and attenuated (H37Ra) sister strains. Such analysis, however, relies heavily on the accuracy of the sequences. While the H37Rv reference genome has had several corrections to date, that of H37Ra is unmodified since its original publication. RESULTS Here, we report the assembly and finishing of the H37Ra genome from single-molecule, real-time (SMRT) sequencing. Our assembly reveals that the number of H37Ra-specific variants is less than half of what the Sanger-based H37Ra reference sequence indicates, undermining and, in some cases, invalidating the conclusions of several studies. PE_PPE family genes, which are intractable to commonly-used sequencing platforms because of their repetitive and GC-rich nature, are overrepresented in the set of genes in which all reported H37Ra-specific variants are contradicted. Further, one of the sequencing errors in H37Ra masks a true variant in common with the clinical strain CDC1551 which, when considered in the context of previous work, corresponds to a sequencing error in the H37Rv reference genome. CONCLUSIONS Our results constrain the set of genomic differences possibly affecting virulence by more than half, which focuses laboratory investigation on pertinent targets and demonstrates the power of SMRT sequencing for producing high-quality reference genomes.
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Affiliation(s)
- Afif Elghraoui
- Biological and Medical Informatics Research Center, San Diego State University, Campanile Drive, San Diego, 92182, USA
| | - Samuel J Modlin
- Biological and Medical Informatics Research Center, San Diego State University, Campanile Drive, San Diego, 92182, USA
| | - Faramarz Valafar
- Biological and Medical Informatics Research Center, San Diego State University, Campanile Drive, San Diego, 92182, USA.
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Sekizuka T, Kai M, Nakanaga K, Nakata N, Kazumi Y, Maeda S, Makino M, Hoshino Y, Kuroda M. Complete genome sequence and comparative genomic analysis of Mycobacterium massiliense JCM 15300 in the Mycobacterium abscessus group reveal a conserved genomic island MmGI-1 related to putative lipid metabolism. PLoS One 2014; 9:e114848. [PMID: 25503461 PMCID: PMC4263727 DOI: 10.1371/journal.pone.0114848] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 11/14/2014] [Indexed: 12/30/2022] Open
Abstract
Mycobacterium abscessus group subsp., such as M. massiliense, M. abscessus sensu stricto and M. bolletii, are an environmental organism found in soil, water and other ecological niches, and have been isolated from respiratory tract infection, skin and soft tissue infection, postoperative infection of cosmetic surgery. To determine the unique genetic feature of M. massiliense, we sequenced the complete genome of M. massiliense type strain JCM 15300 (corresponding to CCUG 48898). Comparative genomic analysis was performed among Mycobacterium spp. and among M. abscessus group subspp., showing that additional ß-oxidation-related genes and, notably, the mammalian cell entry (mce) operon were located on a genomic island, M. massiliense Genomic Island 1 (MmGI-1), in M. massiliense. In addition, putative anaerobic respiration system-related genes and additional mycolic acid cyclopropane synthetase-related genes were found uniquely in M. massiliense. Japanese isolates of M. massiliense also frequently possess the MmGI-1 (14/44, approximately 32%) and three unique conserved regions (26/44; approximately 60%, 34/44; approximately 77% and 40/44; approximately 91%), as well as isolates of other countries (Malaysia, France, United Kingdom and United States). The well-conserved genomic island MmGI-1 may play an important role in high growth potential with additional lipid metabolism, extra factors for survival in the environment or synthesis of complex membrane-associated lipids. ORFs on MmGI-1 showed similarities to ORFs of phylogenetically distant M. avium complex (MAC), suggesting that horizontal gene transfer or genetic recombination events might have occurred within MmGI-1 among M. massiliense and MAC.
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Affiliation(s)
- Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
- * E-mail: (TS); (YH)
| | - Masanori Kai
- Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kazue Nakanaga
- Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Noboru Nakata
- Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yuko Kazumi
- Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Shinji Maeda
- Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Masahiko Makino
- Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yoshihiko Hoshino
- Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- * E-mail: (TS); (YH)
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
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7
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Liu F, Yang M, Wang X, Yang S, Gu J, Zhou J, Zhang XE, Deng J, Ge F. Acetylome analysis reveals diverse functions of lysine acetylation in Mycobacterium tuberculosis. Mol Cell Proteomics 2014; 13:3352-66. [PMID: 25180227 DOI: 10.1074/mcp.m114.041962] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The lysine acetylation of proteins is a reversible post-translational modification that plays a critical regulatory role in both eukaryotes and prokaryotes. Mycobacterium tuberculosis is a facultative intracellular pathogen and the causative agent of tuberculosis. Increasing evidence shows that lysine acetylation may play an important role in the pathogenesis of M. tuberculosis. However, only a few acetylated proteins of M. tuberculosis are known, presenting a major obstacle to understanding the functional roles of reversible lysine acetylation in this pathogen. We performed a global acetylome analysis of M. tuberculosis H37Ra by combining protein/peptide prefractionation, antibody enrichment, and LC-MS/MS. In total, we identified 226 acetylation sites in 137 proteins of M. tuberculosis H37Ra. The identified acetylated proteins were functionally categorized into an interaction map and shown to be involved in various biological processes. Consistent with previous reports, a large proportion of the acetylation sites were present on proteins involved in glycolysis/gluconeogenesis, the citrate cycle, and fatty acid metabolism. A NAD(+)-dependent deacetylase (MRA_1161) deletion mutant of M. tuberculosis H37Ra was constructed and its characterization showed a different colony morphology, reduced biofilm formation, and increased tolerance of heat stress. Interestingly, lysine acetylation was found, for the first time, to block the immunogenicity of a peptide derived from a known immunogen, HspX, suggesting that lysine acetylation plays a regulatory role in immunogenicity. Our data provide the first global survey of lysine acetylation in M. tuberculosis. The dataset should be an important resource for the functional analysis of lysine acetylation in M. tuberculosis and facilitate the clarification of the entire metabolic networks of this life-threatening pathogen.
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Affiliation(s)
- Fengying Liu
- From the ‡Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Mingkun Yang
- §Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xude Wang
- From the ‡Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Shanshan Yang
- From the ‡Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Jing Gu
- From the ‡Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Jie Zhou
- ¶Foshan Fourth People's Hospital, Foshan, China
| | - Xian-En Zhang
- ‖National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiaoyu Deng
- From the ‡Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China;
| | - Feng Ge
- §Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China;
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8
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Choudhury C, Deva Priyakumar U, Sastry GN. Molecular dynamics investigation of the active site dynamics of mycobacterial cyclopropane synthase during various stages of the cyclopropanation process. J Struct Biol 2014; 187:38-48. [DOI: 10.1016/j.jsb.2014.04.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 04/16/2014] [Accepted: 04/17/2014] [Indexed: 11/28/2022]
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Prasanna AN, Mehra S. Comparative phylogenomics of pathogenic and non-pathogenic mycobacterium. PLoS One 2013; 8:e71248. [PMID: 24015186 PMCID: PMC3756022 DOI: 10.1371/journal.pone.0071248] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 06/26/2013] [Indexed: 11/19/2022] Open
Abstract
Mycobacterium species are the source of a variety of infectious diseases in a range of hosts. Genome based methods are used to understand the adaptation of each pathogenic species to its unique niche. In this work, we report the comparison of pathogenic and non-pathogenic Mycobacterium genomes. Phylogenetic trees were constructed using sequence of core orthologs, gene content and gene order. It is found that the genome based methods can better resolve the inter-species evolutionary distances compared to the conventional 16S based tree. Phylogeny based on gene order highlights distinct evolutionary characteristics as compared to the methods based on sequence, as illustrated by the shift in the relative position of M. abscessus. This difference in gene order among the Mycobacterium species is further investigated using a detailed synteny analysis. It is found that while rearrangements between some Mycobacterium genomes are local within synteny blocks, few possess global rearrangements across the genomes. The study illustrates how a combination of different genome based methods is essential to build a robust phylogenetic relationship between closely related organisms.
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Affiliation(s)
- Arun N. Prasanna
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Sarika Mehra
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
- * E-mail:
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10
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Smith SE, Showers-Corneli P, Dardenne CN, Harpending HH, Martin DP, Beiko RG. Comparative genomic and phylogenetic approaches to characterize the role of genetic recombination in mycobacterial evolution. PLoS One 2012; 7:e50070. [PMID: 23189179 PMCID: PMC3506542 DOI: 10.1371/journal.pone.0050070] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Accepted: 10/19/2012] [Indexed: 02/01/2023] Open
Abstract
The genus Mycobacterium encompasses over one hundred named species of environmental and pathogenic organisms, including the causative agents of devastating human diseases such as tuberculosis and leprosy. The success of these human pathogens is due in part to their ability to rapidly adapt to their changing environment and host. Recombination is the fastest way for bacterial genomes to acquire genetic material, but conflicting results about the extent of recombination in the genus Mycobacterium have been reported. We examined a data set comprising 18 distinct strains from 13 named species for evidence of recombination. Genomic regions common to all strains (accounting for 10% to 22% of the full genomes of all examined species) were aligned and concatenated in the chromosomal order of one mycobacterial reference species. The concatenated sequence was screened for evidence of recombination using a variety of statistical methods, with each proposed event evaluated by comparing maximum-likelihood phylogenies of the recombinant section with the non-recombinant portion of the dataset. Incongruent phylogenies were identified by comparing the site-wise log-likelihoods of each tree using multiple tests. We also used a phylogenomic approach to identify genes that may have been acquired through horizontal transfer from non-mycobacterial sources. The most frequent associated lineages (and potential gene transfer partners) in the Mycobacterium lineage-restricted gene trees are other members of suborder Corynebacterinae, but more-distant partners were identified as well. In two examined cases of potentially frequent and habitat-directed transfer (M. abscessus to Segniliparus and M. smegmatis to Streptomyces), observed sequence distances were small and consistent with a hypothesis of transfer, while in a third case (M. vanbaalenii to Streptomyces) distances were larger. The analyses described here indicate that whereas evidence of recombination in core regions within the genus is relatively sparse, the acquisition of genes from non-mycobacterial lineages is a significant feature of mycobacterial evolution.
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Affiliation(s)
- Silvia E. Smith
- School of Medicine, Department of Ophthalmology and Visual Sciences, University of Utah, Salt Lake City, Utah, United States of America
- Department of Anthropology, University of Utah, Salt Lake City, Utah, United States of America
| | | | - Caitlin N. Dardenne
- School of Medicine, Department of Ophthalmology and Visual Sciences, University of Utah, Salt Lake City, Utah, United States of America
- Department of Anthropology, University of Utah, Salt Lake City, Utah, United States of America
| | - Henry H. Harpending
- Department of Anthropology, University of Utah, Salt Lake City, Utah, United States of America
| | - Darren P. Martin
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, South Africa
| | - Robert G. Beiko
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
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11
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Turnbull WB, Stalford SA. Methylthioxylose--a jewel in the mycobacterial crown? Org Biomol Chem 2012; 10:5698-706. [PMID: 22575989 DOI: 10.1039/c2ob25630d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Ten years ago an unusual sugar was discovered in a cell wall polysaccharide of Mycobacterium tuberculosis. Structural elucidation revealed the presence of the first thiosugar in a bacterial polysaccharide. Synthetic studies have helped to define its relative and absolute configuration as α-D-methylthioxylofuranosyl. While its biosynthetic origins remain the subject of speculation, work has begun to define its possible biological roles.
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Affiliation(s)
- W Bruce Turnbull
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
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12
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Donova MV, Egorova OV. Microbial steroid transformations: current state and prospects. Appl Microbiol Biotechnol 2012; 94:1423-47. [PMID: 22562163 DOI: 10.1007/s00253-012-4078-0] [Citation(s) in RCA: 323] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Revised: 04/03/2012] [Accepted: 04/03/2012] [Indexed: 12/14/2022]
Abstract
Studies of steroid modifications catalyzed by microbial whole cells represent a well-established research area in white biotechnology. Still, advances over the last decade in genetic and metabolic engineering, whole-cell biocatalysis in non-conventional media, and process monitoring raised research in this field to a new level. This review summarizes the data on microbial steroid conversion obtained since 2003. The key reactions of structural steroid functionalization by microorganisms are highlighted including sterol side-chain degradation, hydroxylation at various positions of the steroid core, and redox reactions. We also describe methods for enhancement of bioprocess productivity, selectivity of target reactions, and application of microbial transformations for production of valuable pharmaceutical ingredients and precursors. Challenges and prospects of whole-cell biocatalysis applications in steroid industry are discussed.
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Affiliation(s)
- Marina V Donova
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, pr. Nauki 5, Pushchino, Moscow Region 142290, Russia.
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13
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Ignatov D, Kondratieva E, Azhikina T, Apt A. Mycobacterium avium-triggered diseases: pathogenomics. Cell Microbiol 2012; 14:808-18. [DOI: 10.1111/j.1462-5822.2012.01776.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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14
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Caspi R, Altman T, Dreher K, Fulcher CA, Subhraveti P, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Pujar A, Shearer AG, Travers M, Weerasinghe D, Zhang P, Karp PD. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res 2011; 40:D742-53. [PMID: 22102576 PMCID: PMC3245006 DOI: 10.1093/nar/gkr1014] [Citation(s) in RCA: 430] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The MetaCyc database (http://metacyc.org/) provides a comprehensive and freely accessible resource for metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are experimentally determined, small-molecule metabolic pathways and are curated from the primary scientific literature. MetaCyc contains more than 1800 pathways derived from more than 30 000 publications, and is the largest curated collection of metabolic pathways currently available. Most reactions in MetaCyc pathways are linked to one or more well-characterized enzymes, and both pathways and enzymes are annotated with reviews, evidence codes and literature citations. BioCyc (http://biocyc.org/) is a collection of more than 1700 organism-specific Pathway/Genome Databases (PGDBs). Each BioCyc PGDB contains the full genome and predicted metabolic network of one organism. The network, which is predicted by the Pathway Tools software using MetaCyc as a reference database, consists of metabolites, enzymes, reactions and metabolic pathways. BioCyc PGDBs contain additional features, including predicted operons, transport systems and pathway-hole fillers. The BioCyc website and Pathway Tools software offer many tools for querying and analysis of PGDBs, including Omics Viewers and comparative analysis. New developments include a zoomable web interface for diagrams; flux-balance analysis model generation from PGDBs; web services; and a new tool called Web Groups.
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Affiliation(s)
- Ron Caspi
- SRI International, 333 Ravenswood, Menlo Park, CA 94025, USA, USA
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