Abstract
The complete genome of Mycoplasma hyorhinisstrain MCLD has been sequenced and annotated. This genome differs by the inversion of a 14.4-kb and a 3.7-kb fragment and the deletion of a 9.9-kb fragment from M. hyorhinisstrain HUB-1, isolated from swine respiratory tract. The genome revealed 778 coding sequences (CDSs), with a limited number of vlpgenes encoding variable surface lipoproteins.
GENOME ANNOUNCEMENT
Mycoplasma hyorhinisis a swine pathogen causing respiratory diseases and arthritis. Additionally, it is a frequent cell culture contaminant and has recently been detected in human gastric carcinoma tissues (13). M. hyorhinisMCLD has been isolated from a primary human melanoma cell line (5). Although mycoplasmas were considered adherent extracellular microorganisms (10), it has been shown that M. hyorhinisMCLD invades host cells (7). Furthermore, host cells infected with M. hyorhinisMCLD showed elevated expression of a CD99 ligand on melanoma cells (5) and a marked increase in the cellular concentration of the protease inhibitor calpastatin within infected neuroblastoma cells (4).
The M. hyorhinisMCLD genome was sequenced by using GS FLX Titanium technology and annotated using RAST (1) and PGAAP with manual curation. The fully assembled circular chromosome has 829,709 bp and an average G+C content of 25.9%. We predicted 778 coding sequences (CDSs) with a coding density of 89.2%, of which 273 CDSs were hypothetical or conserved hypothetical proteins.
Genome alignment of M. hyorhinisMCLD with the M. hyorhinisHUB-1 sequence (8), starting at the dnaAgene (SRH_2175) in the reverse complement orientation and using MAUVE (3), revealed 18 locally colinear blocks (LCBs). Unlike recent data on M. mycoides(12), no function-specific LCBs were identified. The MAUVE progressive mode utilized to identify conserved large segments revealed that each chromosome was composed of 4 regions and that differences may be explained by 2 inversions (14.4 kb, SRH_02645 to SRH_02545, and 3.7 kb, SRH_2605 to SRH_2635).
Similar to other mycoplasmas, 10 putative transcriptional regulators were detected in the M. hyorhinisMCLD genome, among them two sigma factors and the transcriptional repressor HrcA. Unlike other mycoplasma species, no homologs of the RelA and SpoT families were found.
The bacterial translational system components are conserved and included 30 tRNAs and 21 tRNA synthetases, a single copy of the 16S-23S rRNA operon, and a separate 5S rRNA gene. Three protein initiation factors, 4 elongation factors, and a single peptide release factor (RF-1) were also identified. However, the peptide chain release factor 2 (RF-2) was not detected.
It has been proposed that the variable surface lipoprotein (vlp) locus in M. hyorhiniscontains seven distinct vlpgenes (2). Comparative analysis of the vlplocus among five M. hyorhinisstrains (MCLD, GDL, SK76, HUB-1, and a clonal variant of SK76) revealed that the vlpgenes in M. hyorhinisMCLD are reduced, containing only 4 genes, vlpD(SRH_00185), vlpE(SRH_00180), vlpB(SRH_00175), and vlpC(SRH_00170), with no IS elements within the vlplocus. The vlplocus of M. hyorhinisHUB-1, isolated from pneumonic swine, and the arthritogenic SK76 strain (14) contain seven vlpgenes (vlpAto vlpG), and the cell-culture isolate M. hyorhinisGDL possesses six (vlpAto vlpF) vlpgenes (2, 8, 15). Only three vlpgenes (vlpAto vlpC) were detected in the clonal variant SK76 (derived from the SK76 strain after broth medium passage [14]). Similar to other mycoplasmas with variable surface protein machinery (6, 9, 11), a putative integrase recombinase (SRH_00140) was found 5.3 kb downstream from the vlpCgene.
Nucleotide sequence accession number.
This genome sequence of M. hyorhinis was deposited with annotation at GenBank under accession number CP002669. The version described in this paper is the first version.
Acknowledgments
This work was supported by an intramural grant to Shlomo Rottem at Hebrew University. Additional partial support was obtained from intramural funding to Ran Nir-Paz at the Hadassah-Hebrew University Medical Center.
Footnotes
Published ahead of print on 24 June 2011.
REFERENCES
- 1. Aziz R. K., et al. 2008. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9:75. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2. Citti C., Watson-McKown R., Droesse M., Wise K. S. 2000. Gene families encoding phase- and size-variable surface lipoproteins of Mycoplasma hyorhinis. J. Bacteriol. 182:1356–1363 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3. Darling A. E., Mau B., Perna N. T. 2010. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 5:e11147. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4. Elkind E., et al. 2010. Mycoplasma hyorhinisupregulates calpastatin and inhibits calpain dependent proteolysis in SH-SY5Y neuroblastoma cells. FEMS Microbiol. Lett. 304:62–68 [DOI] [PubMed] [Google Scholar]
- 5. Gazit R., et al. 2004. Recognition of Mycoplasma hyorhinisby CD99-Fc molecule. Eur. J. Immunol. 34:2032–2040 [DOI] [PubMed] [Google Scholar]
- 6. Glew M. D., Marenda M., Rosengarten R., Citti C. 2002. Surface diversity in Mycoplasma agalactiaeis driven by site-specific DNA inversions within the vpmamultigene locus. J. Bacteriol. 184:5987–5998 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7. Kornspan J. D., Tarshis M., Rottem S. 2010. Invasion of melanoma cells by Myoplasma hyorhinis: enhancement by protease treatment. Infect. Immun. 78:611–617 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8. Liu W., et al. 2010. Complete genome sequence of Mycoplasma hyorhinisstrain HUB-1. J. Bacteriol. 192:5844–5845 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9. Ron Y., Flitman-Tene R., Dybvig K., Yogev D. 2002. Identification and characterization of a site-specific tyrosine recombinase within the variable loci of Mycoplasma bovis, Mycoplasma pulmonisand Mycoplasma agalactiae. Gene 292:205–211 [DOI] [PubMed] [Google Scholar]
- 10. Rottem S. 2003. Interaction of mycoplasmas with host cells. Physiol. Rev. 83:417–432 [DOI] [PubMed] [Google Scholar]
- 11. Sitaraman R., Denison A. M., Dybvig K. 2002. A unique, bifunctional site-specific DNA recombinase from Mycoplasma pulmonis. Mol. Microbiol. 46:1033–1040 [DOI] [PubMed] [Google Scholar]
- 12. Thiaucourt F., et al. 2011. Mycoplasma mycoides, from “mycoides Small Colony” to “capri.” A microevolutionary perspective. BMC Genomics 12:114. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13. Yang H., et al. 2010. Mycoplasma hyorhinisinfection in gastric carcinoma and its effects on the malignant phenotypes of gastric cancer cells. BMC Gastroenterol. 10:132. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 14. Yogev D., Rosengarten R., Watson-Mckown R., Wise K. S. 1991. Molecular basis of Mycoplasma surface antigenic variation: a novel set of divergent genes undergo spontaneous mutation of periodic coding regions and 5′ regulatory sequences. EMBO J. 10:4069–4079 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 15. Yogev D., Watson-Mckown R., Rosengarten R., Im J., Wise K. S. 1995. Increased structural and combinatorial diversity in an extended family of genes encoding Vlp surface proteins of Mycoplasma hyorhinis. J. Bacteriol. 177:5636–5643 [DOI] [PMC free article] [PubMed] [Google Scholar]