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J Bacteriol. Aug 2011; 193(16): 4302–4303.
PMCID: PMC3147699
Genome Sequence of the Repetitive-Sequence-Rich Mycoplasma fermentans Strain M64[down-pointing small open triangle]
Hung-Wei Shu,1 Tze-Tze Liu,2 Huang-I Chan,3 Yen-Ming Liu,4 Keh-Ming Wu,2 Hung-Yu Shu,2 Shih-Feng Tsai,2,4,5§ Kwang-Jen Hsiao,6§ Wensi S. Hu,1,7§* and Wailap Victor Ng1,3,7§*
1Institute of Biotechnology in Medicine, Department of Biotechnology and Laboratory Science in Medicine
2Genome Research Center
3Institute of Biomedical Informatics, National Yang Ming University, Taipei, Taiwan, Republic of China
4Division of Molecular and Genome Medicine, National Health Research Institute, Zhunan Town, Miaoli County, Taiwan, Republic of China
5Institute of Genome Sciences, Department of Life Sciences, National Yang Ming University, Taipei, Taiwan, Republic of China
6Department of Medical Research and Education, Taipei Veterans General Hospital, and Department of Education and Research, Taipei City Hospital, Taipei, Taiwan, Republic of China
7Clinical Biotechnology Research Center, Taipei City Hospital, Taipei, Taiwan, Republic of China
*Corresponding author. Mailing address: Institute of Biotechnology in Medicine, National Yang Ming University, 155 Linong Street, Section 2, Taipei, Taiwan 112, Republic of China. Phone for Wailap Victor Ng: 886-2-2826-7321. Fax: 886-2-2826-4092. E-mail: wvng/at/ym.edu.tw. Phone for Wensi S. Hu: 886-2-2826-7151. Fax: 886-2-2826-4092. E-mail: huws/at/ym.edu.tw.
Hung-Wei Shu and Tze-Tze Liu contributed equally to this study.
Present address: Department of Bioscience Technology, Chang Jung Christian University, Tainan, Taiwan, Republic of China.
§S.-F. Tsai, K.-J. Hsiao, W. S. Hu, and W. V. Ng share senior authorship.
Received May 5, 2011; Accepted May 16, 2011.
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.
Mycoplasma fermentans is a fastidious Gram-negative bacterium commonly isolated from human genitourinary and respiratory tracts. It has been implicated in HIV pathogenesis, sexually transmitted genital tract infections, systemic infections, rheumatic disorders, chronic fatigue syndrome, and other diseases (1, 2, 8, 9, 12, 14, 15, 18, 25, 27, 28). Notwithstanding the clinical significance, the roles it plays and the molecular mechanisms involved in various diseases have yet to be elucidated.
In this study, we have determined the repetitive-sequence-rich genome sequence of M. fermentans strain M64 isolated from a non-AIDS patient (16). Escherichia coli DH5α and pUC18 vector were used in the construction of whole-genome shotgun libraries (2 to 3 kb and 5 to 7 kb) as previously described (7, 30). The whole-genome shotgun sequences (BigDye Terminator 3.1 kit and ABI3730XL DNA analyzer; both from Applied Biosystems, Foster City, CA) were assembled with the Phredphrap software using the “Hide-and-Seek” sequence assembly strategy (4, 10, 11, 13, 22). The assembled genome sequence was validated by restriction mapping and Southern hybridization analyses of BglI, KpnI, MluI, and AhdI fragments resolved by pulsed-field gel electrophoresis (CHEF Mapper XA system; Bio-Rad, Hercules, CA) (26). The gene prediction program GeneMark.hmm (version 2.4; http://exon.gatech.edu/gmhmm2_prok.cgi) was applied to predict the protein-coding genes using Mycoplasma synoviae, the phylogenetically closest species, as the training model. The functions of predicted proteins (translation table 4) were analyzed by Blastp (3) searches against the proteomes of sequenced prokaryotic organisms in the Integr8 database (www.ebi.ac.uk/integr8/). The protein motifs and COG (clusters of orthologous groups) functional categories were assigned by RPSBLAST searches (3) against the NCBI Conserved Domain Database (20, 21). The rRNA and tRNA genes were identified by blastn (3) and tRNAscan-SE (19), respectively.
M. fermentans M64 has a 1,118,751-bp circular chromosome encoding 1,050 putative protein genes, two 16S-23S rRNA operons, one 5S rRNA gene, and 35 tRNA genes. Like Mycoplasma mycoides subsp. mycoides (29), the M. fermentans M64 genome also bears a high density of transposable elements. The genome contained nine copies of two families of large repeat sequences (integrative conjugal elements of M. fermentans [ICEF] and [var phi]MFV1 prophage) and many insertion sequence elements, including IS1550, IS1630, and ISMf1 (5, 6, 17, 24). These sequences and elements accounted for approximately 21.6% of the genome. Among these, a new family of ICEF, designated ICEF-III, was discovered in this study. Perusal of the integrity of the IS elements and ICEFs and their flanking sequences suggested that the current genome architecture of M. fermentans M64 might be partly associated with the transposition and/or recombination of these elements in the past. Interestingly, despite the fact that the organizations of the two genomes are highly similar, the M. fermentans M64 genome is approximately 141 kb bigger than the recently completely sequenced M. fermentans strain JER (977,524 bp) (23). The size difference is mainly attributed to the differences in the copy numbers of ICEF and [var phi]MFV1 prophage which are by and large absent in the JER genomes (6, 24). The transposable-element-rich region in the middle of the genome exhibited chaotic arrangement probably due to transposition events. After all, unveiling this special reduced genome which is rich in transposable elements may help to elucidate the elusive relationships between M. fermentans M64 and the implicated diseases.
Nucleotide sequence accession number.
The genome sequence with annotations of Mycoplasma fermentans strain M64 reported in this paper has been deposited in the GenBank database under accession number NC_014921.
Acknowledgments
This work was supported by grant 96-2628-B-010-003-MY3 from the National Science Council and intramural funding from the Aim for the Top University Grant awarded to National Yang Ming University from the Ministry of Education in Taiwan, Republic of China.
Footnotes
[down-pointing small open triangle]Published ahead of print on 3 June 2011.
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