1887

Abstract

is a pleomorphic facultative anaerobe and the sole species in the class , which has tentatively been placed in the phylum . In the present study, the complete genome sequence of HC45 was obtained and analysed. The genome size was 3.82 Mbp and the DNA G+C content was 69.73 %. Phylogenetic analyses based on the 30S-50S ribosomal proteins and 23S rRNA gene consistently indicated that is phylogenetically isolated from the other members of the phylum . Ultrastructural observation revealed that possesses a Gram-negative-type cell wall and the capacity to form endospores. Accordingly, the genome has characteristics that are specific to Gram-negative bacteria and contains many genes that are involved in sporulation. On the other hand, several sporulation genes were absent from the genome although they have been regarded as essential for the endospore-forming system of members of the phylum . The B gene of possesses an intein sequence. The genome has a high percentage of GTG start codons and lacks several conserved genes related to cell division.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.000881
2016-03-01
2019-10-22
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/66/3/1330.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.000881&mimeType=html&fmt=ahah

References

  1. Abecasis A. B. , Serrano M. , Alves R. , Quintais L. , Pereira-Leal J. B. , Henriques A. O. . ( 2013;). A genomic signature and the identification of new sporulation genes. J Bacteriol 195: 2101–2115 [CrossRef] [PubMed].
    [Google Scholar]
  2. Aizawa S. . ( 2014;). The Flagellar World: Electron Microscopic Images of Bacterial Flagella and Related Surface Structures Waltham, MA: Academic Press, Elsevier;.
    [Google Scholar]
  3. Ajithkumar B. , Ajithkumar V. P. , Iriye R. , Doi Y. , Sakai T. . ( 2003;). Spore-forming Serratia marcescens subsp. sakuensis subsp. nov., isolated from a domestic wastewater treatment tank. Int J Syst Evol Microbiol 53: 253–258 [CrossRef] [PubMed].
    [Google Scholar]
  4. Alauzet C. , Marchandin H. , Courtin P. , Mory F. , Lemée L. , Pons J.-L. , Chapot-Chartier M. P. , Lozniewski A. , Jumas-Bilak E. . ( 2014;). Multilocus analysis reveals diversity in the genus Tissierella: description of Tissierella carlieri sp. nov. in the new class Tissierellia classis nov. Syst Appl Microbiol 37: 23–34 [CrossRef] [PubMed].
    [Google Scholar]
  5. Barák I. . ( 2013;). Open questions about the function and evolution of bacterial Min systems. Front Microbiol 4: 378 [CrossRef] [PubMed].
    [Google Scholar]
  6. Beppu T. , Ueda K. . ( 2009;). Family XVIII incertae sedis . . In Bergey's Manual of Systematic Bacteriology , 2nd edn.., vol. 3, The Firmicutes , pp. 1188–1190. Edited by De Vos P. , Garrity G. M. , Jones D. , Krieg N. R. , Ludwig W. , Rainey F. A. , Schleifer K.-H. , Whitman W. B. . New York: Springer;.
    [Google Scholar]
  7. Bernadac A. , Gavioli M. , Lazzaroni J. C. , Raina S. , Lloubès R. . ( 1998;). Escherichia coli tol-pal mutants form outer membrane vesicles. J Bacteriol 180: 4872–4878 [PubMed].
    [Google Scholar]
  8. Bland C. , Ramsey T. L. , Sabree F. , Lowe M. , Brown K. , Kyrpides N. C. , Hugenholtz P. . ( 2007;). CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics 8: 209 [CrossRef] [PubMed].
    [Google Scholar]
  9. Chase D. G. , Erlandsen S. L. . ( 1976;). Evidence for a complex life cycle and endospore formation in the attached, filamentous, segmented bacterium from murine ileum. J Bacteriol 127: 572–583 [PubMed].
    [Google Scholar]
  10. Chin C. S. , Alexander D. H. , Marks P. , Klammer A. A. , Drake J. , Heiner C. , Clum A. , Copeland A. , Huddleston J. , other authors . ( 2013;). Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 10: 563–569 [CrossRef] [PubMed].
    [Google Scholar]
  11. Ciccarelli F. D. , Doerks T. , von Mering C. , Creevey C. J. , Snel B , Bork P. . ( 2006;). Toward automatic reconstruction of a highly resolved tree of life. Science 311: 1283–1287 [CrossRef] [PubMed].
    [Google Scholar]
  12. da Costa M. S. , Rainey F. A. , Albuquerque L. . ( 2009;). Family XVII incertae sedis. Genus I. Sulfobacillus . . In Bergey's Manual of Systematic Bacteriology , 2nd edn.., vol. 3 The Firmicutes , pp. 1181–1184. Edited by De Vos P. , Garrity G. M. , Jones D. , Krieg N. R. , Ludwig W. , Rainey F. A. , Schleifer K.-H. , Whitman W. B. . New York: Springer;.
    [Google Scholar]
  13. Daniel R. A. , Harry E. J. , Katis V. L. , Wake R. G. , Errington J. . ( 1998;). Characterization of the essential cell division gene ftsL (yIID) of Bacillus subtilis and its role in the assembly of the division apparatus. Mol Microbiol 29: 593–604 [CrossRef] [PubMed].
    [Google Scholar]
  14. Deatherage B. L. , Cookson B. T. . ( 2012;). Membrane vesicle release in bacteria, eukaryotes, and archaea: a conserved yet underappreciated aspect of microbial life. Infect Immun 80: 1948–1957 [CrossRef] [PubMed].
    [Google Scholar]
  15. Egan A. J. F. , Vollmer W. . ( 2013;). The physiology of bacterial cell division. Ann N Y Acad Sci 1277: 8–28 [CrossRef] [PubMed].
    [Google Scholar]
  16. Filippova S. N. , Gorbatiuk E. V. , Poglazova M. N. , Soina V. S. , Kuznetsov V. D. , El'-Registan G. I. . ( 2005;). [Endospore formation by Streptomyces avermitilis in submerged culture]. Mikrobiologiia 74: 204–214 (in Russian).
    [Google Scholar]
  17. Galperin M. Y. . ( 2013;). Genome diversity of spore-forming Firmicutes . Microbiol Spectr 1: TBS-0015-2012 [CrossRef] [PubMed].
    [Google Scholar]
  18. Galperin M. Y. , Mekhedov S. L. , Puigbo P. , Smirnov S. , Wolf Y. I. , Rigden D. J. . ( 2012;). Genomic determinants of sporulation in Bacilli and Clostridia: towards the minimal set of sporulation-specific genes. Environ Microbiol 14: 2870–2890 [CrossRef] [PubMed].
    [Google Scholar]
  19. Garrity G. M. , Bell J. A. , Lilburn T. . ( 2005;). The revised road map of the manual. . In Bergey's Manual of Systematic Bacteriology , 2nd edn.., vol. 2 The Proteobacteria, Part A , pp. 159–187. Edited by Brenner D. J. , Krieg N. R. , Staley J. T. , Garrity G. M. . New York: Springer;.[CrossRef]
    [Google Scholar]
  20. Ghosh J. , Larsson P. , Singh B. , Pettersson B. M. , Islam N. M. , Sarkar S. N. , Dasgupta S. , Kirsebom L. A. . ( 2009;). Sporulation in mycobacteria. Proc Natl Acad Sci U S A 106: 10781–10786 [CrossRef] [PubMed].
    [Google Scholar]
  21. Girija K. R. , Sasikala Ch. , Ramana Ch. V. , Spröer C. , Takaichi S. , Thiel V. , Imhoff J. F. . ( 2010;). Rhodobacter johrii sp. nov., an endospore-producing cryptic species isolated from semi-arid tropical soils. Int J Syst Evol Microbiol 60: 2099–2107 [CrossRef] [PubMed].
    [Google Scholar]
  22. Jolley K. A. , Bliss C. M. , Bennett J. S. , Bratcher H. B. , Brehony C. , Colles F. M. , Wimalarathna H. , Harrison O. B. , Sheppard S. K. , other authors . ( 2012;). Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain. Microbiology 158: 1005–1015 [PubMed].[CrossRef]
    [Google Scholar]
  23. Kiss H. , Nett M. , Domin N. , Martin K. , Maresca J. A. , Copeland A. , Lapidus A. , Lucas S. , Berry K. W. , other authors . ( 2011;). Complete genome sequence of the filamentous gliding predatory bacterium Herpetosiphon aurantiacus type strain (114-95T). Stand Genomic Sci 5: 356–370 [PubMed].[CrossRef]
    [Google Scholar]
  24. Koch A. L. . ( 2003;). Were Gram-positive rods the first bacteria?. Trends Microbiol 11: 166–170 [CrossRef] [PubMed].
    [Google Scholar]
  25. Kuwahara T. , Ogura Y. , Oshima K. , Kurokawa K. , Ooka T. , Hirakawa H. , Itoh T. , Nakayama-Imaohji H. , Ichimura M. , other authors . ( 2011;). The lifestyle of the segmented filamentous bacterium: a non-culturable gut-associated immunostimulating microbe inferred by whole-genome sequencing. DNA Res 18: 291–303 [CrossRef] [PubMed].
    [Google Scholar]
  26. Lagesen K. , Hallin P. , Rødland E. A. , Staerfeldt H. H. , Rognes T. , Ussery D. W. . ( 2007;). RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35: 3100–3108 [CrossRef] [PubMed].
    [Google Scholar]
  27. Lamont E. A. , Bannantine J. P. , Armién A. , Ariyakumar D. S. , Sreevatsan S. . ( 2012;). Identification and characterization of a spore-like morphotype in chronically starved Mycobacterium avium subsp. paratuberculosis cultures. PLoS One 7: e30648 [CrossRef] [PubMed].
    [Google Scholar]
  28. Larkin M. A. , Blackshields G. , Brown N. P. , Chenna R. , McGettigan P. A. , McWilliam H. , Valentin F. , Wallace I. M. , Wilm A. , other authors . ( 2007;). Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947–2948 [CrossRef] [PubMed].
    [Google Scholar]
  29. Lowe T. M. , Eddy S. R. . ( 1997;). tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: 955–964 [CrossRef] [PubMed].
    [Google Scholar]
  30. Ludwig W. , Klenk H. P. . ( 2001;). Overview: a phylogenetic backbone and taxonomic framework for procaryotic systematics. . In Bergey's Manual of Systematic Bacteriology , 2nd edn.., vol. 1 The Archaea and the Deeply Branching and Phototrophic Bacteria , pp. 49–65. Edited by Boone D. R. , Castenholz R. W. , Garrity G. M. . New York: Springer;.[CrossRef]
    [Google Scholar]
  31. Ludwig W. , Schleifer K. H. . ( 1999;). Phylogeny of Bacteria beyond the 16S rRNA standard. ASM News 65: 752–757.
    [Google Scholar]
  32. Ludwig W. , Strunk O. , Klugbauer S. , Klugbauer N. , Weizenegger M. , Neumaier J. , Bachleitner M. , Schleifer K. H. . ( 1998;). Bacterial phylogeny based on comparative sequence analysis. Electrophoresis 19: 554–568 [CrossRef] [PubMed].
    [Google Scholar]
  33. Ludwig W. , Schleifer K. H. , Whitman W. B. . ( 2009;). Revised road map to the phylum Firmicutes . . In Bergey's Manual of Systematic Bacteriology , 2nd edn.., vol. 3 The Firmicutes , pp. 1–14. Edited by De Vos P. , Garrity G. M. , Jones D. , Krieg N. R. , Ludwig W. , Rainey F. A. , Schleifer K.-H. , Whitman W. B. . New York: Springer;.
    [Google Scholar]
  34. MacGregor B. J. , Biddle J. F. , Teske A. . ( 2013;). Mobile elements in a single-filament orange Guaymas Basin Beggiatoa (“Candidatus Maribeggiatoa”) sp. draft genome: evidence for genetic exchange with cyanobacteria. Appl Environ Microbiol 79: 3974–3985 [CrossRef] [PubMed].
    [Google Scholar]
  35. Magee J. G. , Ward A. C. . ( 2012;). Genus I. Mycobacterium . . In Bergey's Manual of Systematic Bacteriology , 2nd edn.., vol. 5 The Actinobacteria, part A , pp. 312–375. Edited by Goodfellow M. , Kämpfer P. , Busse H.-J. , Trujillo M. E. , Suzuki K. , Ludwig W. , Whitman W. B. . New York: Springer;.
    [Google Scholar]
  36. Marchandin H. , Teyssier C. , Campos J. , Jean-Pierre H. , Roger F. , Gay B. , Carlier J.-P. , Jumas-Bilak E. . ( 2010;). Negativicoccus succinicivorans gen. nov., sp. nov., isolated from human clinical samples, emended description of the family Veillonellaceae and description of Negativicutes classis nov., Selenomonadales ord. nov. and Acidaminococcaceae fam. nov. in the bacterial phylum Firmicutes . Int J Syst Evol Microbiol 60: 1271–1279 [CrossRef] [PubMed].
    [Google Scholar]
  37. Nakamura Y. , Kaneko T. , Sato S. , Mimuro M. , Miyashita H. , Tsuchiya T. , Sasamoto S. , Watanabe A. , Kawashima K. , other authors . ( 2003;). Complete genome structure of Gloeobacter violaceus PCC 7421, a cyanobacterium that lacks thylakoids. DNA Res 10: 137–145 [CrossRef] [PubMed].
    [Google Scholar]
  38. Newton-Foot M. , Gey van Pittius N. C. . ( 2013;). The complex architecture of mycobacterial promoters. Tuberculosis (Edinb) 93: 60–74 [CrossRef] [PubMed].
    [Google Scholar]
  39. Noguchi H. , Taniguchi T. , Itoh T. . ( 2008;). MetaGeneAnnotator: detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes. DNA Res 15: 387–396 [CrossRef] [PubMed].
    [Google Scholar]
  40. Opiyo S. O. , Pardy R. L. , Moriyama H. , Moriyama E. N. . ( 2010;). Evolution of the Kdo2-lipid A biosynthesis in bacteria. BMC Evol Biol 10: 362 [CrossRef] [PubMed].
    [Google Scholar]
  41. Schleifer K. H. . ( 2009;). Phylum XIII. Firmicutes Gibbons and Murray 1978, 5 (Firmacutes [sic] Gibbons and Murray 1978, 5). . In Bergey's Manual of Systematic Bacteriology , 2nd edn.., vol. 3 The Firmicutes , p. 19. Edited by De Vos P. , Garrity G. M. , Jones D. , Krieg N. R. , Ludwig W. , Rainey F. A. , Schleifer K.-H. , Whitman W. B. . New York: Springer;.
    [Google Scholar]
  42. Singh B. , Ghosh J. , Islam N. M. , Dasgupta S. , Kirsebom L. A. . ( 2010;). Growth, cell division and sporulation in mycobacteria. Antonie van Leeuwenhoek 98: 165–177 [CrossRef] [PubMed].
    [Google Scholar]
  43. Sokolova T. , Hanel J. , Onyenwoke R. U. , Reysenbach A. L. , Banta A. , Geyer R. , González J. M. , Whitman W. B. , Wiegel J. . ( 2007;). Novel chemolithotrophic, thermophilic, anaerobic bacteria Thermolithobacter ferrireducens gen. nov., sp. nov. and Thermolithobacter carboxydivorans sp. nov. Extremophiles 11: 145–157 [CrossRef] [PubMed].
    [Google Scholar]
  44. Soucy S. M. , Fullmer M. S. , Papke R. T. , Gogarten J. P. . ( 2014;). Inteins as indicators of gene flow in the halobacteria. Front Microbiol 5: 299 [CrossRef] [PubMed].
    [Google Scholar]
  45. Spanevello M. D. , Patel B. K. C. . ( 2009;). Family XVII incertae sedis. Genus II. Thermaerobacter . . In Bergey's Manual of Systematic Bacteriology , 2nd edn.., vol. 3 The Firmicutes , pp. 1184–1187. Edited by De Vos P. , Garrity G. M. , Jones D. , Krieg N. R. , Ludwig W. , Rainey F. A. , Schleifer K.-H. , Whitman W. B. . New York: Springer;.
    [Google Scholar]
  46. Sugawara H. , Ohyama A. , Mori H. , Kurokawa K. . ( 2009;). Microbial GenomeAnnotation Pipeline (MiGAP) for diverse users. In Proceedings of the 20th International Conference on Genome Informatics (GIW 2009) Yokohama, Japan, software demonstrations S001–1-2L.
  47. Tamura K. , Peterson D. , Peterson N. , Stecher G. , Nei M. , Kumar S. . ( 2011;). mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731–2739 [CrossRef] [PubMed].
    [Google Scholar]
  48. Traag B. A. , Driks A. , Stragier P. , Bitter W. , Broussard G. , Hatfull G. , Chu F. , Adams K. N. , Ramakrishnan L. , Losick R. . ( 2010;). Do mycobacteria produce endospores?. Proc Natl Acad Sci U S A 107: 878–881 [CrossRef] [PubMed].
    [Google Scholar]
  49. Veiga H. , Pinho M. G. . ( 2012;). Bacterial cell division: what it takes to divide a prokaryotic cell. Canal BQ 9: 18–26.
    [Google Scholar]
  50. Watanabe M. , Kojima H. , Fukui M. . ( 2015;). Limnochorda pilosa gen. nov., sp. nov., a moderately thermophilic, facultatively anaerobic, pleomorphic bacterium and proposal of Limnochordaceae fam. nov., Limnochordales ord. nov. and Limnochordia classis nov. in the phylum Firmicutes . Int J Syst Evol Microbiol 65: 2378–2384 [CrossRef] [PubMed].
    [Google Scholar]
  51. Yarza P. , Ludwig W. , Euzéby J. , Amann R. , Schleifer K. H. , Glöckner F. O. , Rosselló-Móra R. . ( 2010;). Update of the all-species living tree project based on 16S and 23S rRNA sequence analyses. Syst Appl Microbiol 33: 291–299 [CrossRef] [PubMed].
    [Google Scholar]
  52. Yutin N. , Galperin M. Y. . ( 2013;). A genomic update on clostridial phylogeny: Gram-negative spore formers and other misplaced clostridia. Environ Microbiol 15: 2631–2641 [PubMed].
    [Google Scholar]
  53. Yutin N. , Puigbò P. , Koonin E. V. , Wolf Y. I. . ( 2012;). Phylogenomics of prokaryotic ribosomal proteins. PLoS One 7: e36972 [CrossRef] [PubMed].
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.000881
Loading
/content/journal/ijsem/10.1099/ijsem.0.000881
Loading

Data & Media loading...

Most Cited This Month

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error