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Shu HW, Liu TT, Chan HI, Liu YM, Wu KM, Shu HY, Tsai SF, Hsiao KJ, Hu WS, Ng WV. Complexity of the Mycoplasma fermentans M64 genome and metabolic essentiality and diversity among mycoplasmas. PLoS One 2012; 7:e32940. [PMID: 22509252 PMCID: PMC3317919 DOI: 10.1371/journal.pone.0032940] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 02/02/2012] [Indexed: 11/30/2022] Open
Abstract
Recently, the genomes of two Mycoplasma fermentans strains, namely M64 and JER, have been completely sequenced. Gross comparison indicated that the genome of M64 is significantly bigger than the other strain and the difference is mainly contributed by the repetitive sequences including seven families of simple and complex transposable elements ranging from 973 to 23,778 bps. Analysis of these repeats resulted in the identification of a new distinct family of Integrative Conjugal Elements of M. fermentans, designated as ICEF-III. Using the concept of “reaction connectivity”, the metabolic capabilities in M. fermentans manifested by the complete and partial connected biomodules were revealed. A comparison of the reported M. pulmonis, M. arthritidis, M. genitalium, B. subtilis, and E. coli essential genes and the genes predicted from the M64 genome indicated that more than 73% of the Mycoplasmas essential genes are preserved in M. fermentans. Further examination of the highly and partly connected reactions by a novel combinatorial phylogenetic tree, metabolic network, and essential gene analysis indicated that some of the pathways (e.g. purine and pyrimidine metabolisms) with partial connected reactions may be important for the conversions of intermediate metabolites. Taken together, in light of systems and network analyses, the diversity among the Mycoplasma species was manifested on the variations of their limited metabolic abilities during evolution.
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Affiliation(s)
- Hung-Wei Shu
- Laboratory Science in Medicine, Department of Biotechnology, Institute of Biotechnology in Medicine, National Yang Ming University, Taipei, Taiwan, Republic of China
| | - Tze-Tze Liu
- Genome Research Center, National Yang Ming University, Taipei, Taiwan, Republic of China
| | - Huang-I Chan
- Institute of Biomedical Informatics, National Yang Ming University, Taipei, Taiwan, Republic of China
| | - Yen-Ming Liu
- Institute of Genome Sciences, Department of Life Sciences, National Yang Ming University, Taipei, Taiwan, Republic of China
| | - Keh-Ming Wu
- Genome Research Center, National Yang Ming University, Taipei, Taiwan, Republic of China
| | - Hung-Yu Shu
- Genome Research Center, National Yang Ming University, Taipei, Taiwan, Republic of China
| | - Shih-Feng Tsai
- Genome Research Center, National Yang Ming University, Taipei, Taiwan, Republic of China
- Institute of Genome Sciences, Department of Life Sciences, National Yang Ming University, Taipei, Taiwan, Republic of China
- Division of Molecular and Genome Medicine, National Health Research Institute, Zhunan Town, Miaoli County, Taiwan, Republic of China
| | - Kwang-Jen Hsiao
- Department of Medical Research and Education, Taipei Veterans General Hospital, Taipei, Taiwan, Republic of China
- Department of Education and Research, Taipei City Hospital, Taipei, Taiwan, Republic of China
| | - Wensi S. Hu
- Laboratory Science in Medicine, Department of Biotechnology, Institute of Biotechnology in Medicine, National Yang Ming University, Taipei, Taiwan, Republic of China
- * E-mail: (WSH); (WVN)
| | - Wailap Victor Ng
- Laboratory Science in Medicine, Department of Biotechnology, Institute of Biotechnology in Medicine, National Yang Ming University, Taipei, Taiwan, Republic of China
- Institute of Biomedical Informatics, National Yang Ming University, Taipei, Taiwan, Republic of China
- * E-mail: (WSH); (WVN)
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Genome sequence of the repetitive-sequence-rich Mycoplasma fermentans strain M64. J Bacteriol 2011; 193:4302-3. [PMID: 21642450 DOI: 10.1128/jb.05228-11] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycoplasma fermentans is a microorganism commonly found in the genitourinary and respiratory tracts of healthy individuals and AIDS patients. The complete genome of the repetitive-sequence-rich M. fermentans strain M64 is reported here. Comparative genomics analysis revealed dramatic differences in genome size between this strain and the recently completely sequenced JER strain.
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Afshar B, Pitcher D, Nicholas RAJ, Miles RJ. An evaluation of PCR methods to detect strains of Mycoplasma fermentans. Biologicals 2008; 36:117-21. [PMID: 17892949 DOI: 10.1016/j.biologicals.2007.07.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2007] [Revised: 06/12/2007] [Accepted: 07/11/2007] [Indexed: 10/22/2022] Open
Abstract
A panel of 30 putative Mycoplasma fermentans strains, isolated from various sources including human, ovine and cell lines, were tested by a previously described polymerase chain reaction (PCR) to confirm their identity by amplification of a conserved 206 bp region of the insertion sequence IS1550. In addition, the application of another PCR based on the major part of the IS1550 element showed one or two products of different length (1144 and 1341 bp) enabling M. fermentans strains to be divided into two types designated as Type A and Type B. A PCR, which amplifies the macrophage activating lipopeptide gene (malp), supported the identification of all the strains as M. fermentans. Thirteen other species of Mycoplasma from human sources gave negative results in these tests, with the exception of Mycoplasma orale, which was detected by both IS1550-PCRs based on the major part and the conserved 206 bp region of the IS1550 element. This study suggests that all M. fermentans isolates possess both the IS1550 element and the malp gene. In contrast to the IS1550, the malp gene is shown to be species-specific and the use of a malp PCR described here could prove to be a useful adjunct to IS1550 detection as confirmation of the presence of M. fermentans in clinical material.
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Affiliation(s)
- Baharak Afshar
- Division of Life Sciences, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 8WA, UK.
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Richer E, Courville P, Bergevin I, Cellier MFM. Horizontal gene transfer of "prototype" Nramp in bacteria. J Mol Evol 2004; 57:363-76. [PMID: 14708570 DOI: 10.1007/s00239-003-2472-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Eukaryotic Nramp genes encode divalent metal ion permeases important for nutrition and resistance to microbial infection. Bacterial homologs encode proton-dependent transporters of manganese (MntH), and other divalent metal ions. Bacterial MntH were classified in three homology groups (A, B, C) and MntH C further subdivided in Calpha, Cbeta, Cgamma. The proteins from C. tepidum (MntH B) and E. faecalis (MntH Cbeta1, 2), divergent in sequence and hydropathy profile, conferred increased metal sensitivity when expressed in E. coli, suggesting conservation of divalent metal transport function in MntH B and C. Several genomic evidence suggest horizontal gene transfer (HGT) of mntH C genes: (i) The enterobacteria Wigglesworthia mntH Cbeta gene is linked to an Asn t-RNA, and its sequence most conserved with Gram positive bacteria homologs; (ii) all the Cbeta genes identified in oral streptococcaceae are associated with different potentially mobile DNA elements; (iii) Lactococcus lactis and Burkholderia mallei genomes contain an mntH gene prematurely terminated and a novel full-length mntH C gene; (iv) remarkable sequence relatedness between the unicellular alga C. reinhardtii "prototype" Nramp and some MntH Calpha (e.g., Nostoc spp., Listeria spp.) suggests HGT between Eukarya and Bacteria. Other "prototype" Nramp genes (intronless, encoding proteins strongly conserved with MntH A and B proteins) identified in invertebrates represent a possible source for transfer of Nramp genes toward opportunistic bacteria. This study demonstrates complex evolution of MntH in Bacteria. It is proposed that "prototype" Nramp are ancestors of bacterial MntH C proteins, which could facilitate bacterial infection.
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Affiliation(s)
- Etienne Richer
- INRS-Institut Armand-Frappier, 531, Bd des prairies, Laval, PQ, Canada H7V 1B7
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