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Antonie van Leeuwenhoek

, Volume 103, Issue 2, pp 385–398 | Cite as

Comparative bacterial genomics: defining the minimal core genome

  • C. H. Huang
  • T. Hsiang
  • J. T. Trevors
Original Paper

Abstract

A comparative genomics analysis revealed 702 genes present in the bacterial Gram-negative core gene set (92 species analyzed) and 959 genes in the Gram-positive core gene set (93 species analyzed). Mycoplasma genitalium, which has the smallest known genome (517 genes) of a non-symbiont, was used in a three-way reciprocal analysis with the Gram-negative core genes and the Gram-positive core genes, and 151 common bacterial core genes were found. Of these 151 core genes, 39 were putative genes encoding the 30S and 50S ribosomal subunits, whilst among recognized cell division genes, only one gene, the major ftsZ, was present. In addition, 86 reciprocal matches were identified between the 151 common bacterial genes and a previously determined 2,723 common eukaryotic core gene set. An analysis was also done to optimize the threshold bit score used to declare that genes were homologous, and a bit score cutoff of 40 was selected.

Keywords

Bacteria Bacillus subtilis Bacteria Cell division genes Core minimal genome Evolution Escherichia coli Genes Genome 

Notes

Acknowledgments

Research by J.T.Trevors and T.Hsiang are supported by the NSERC (Canada) Discovery Program.

Supplementary material

10482_2012_9819_MOESM1_ESM.xls (476 kb)
Supplementary material 1 (XLS 477 kb)

References

  1. Adams DW, Errington J (2009) Bacterial cell division: assembly, maintenance and disassembly of the Z ring. Nat Rev Microbiol 7:642–653PubMedCrossRefGoogle Scholar
  2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic Local Alignment Search Tool. J Mol Biol 215:403–410PubMedGoogle Scholar
  3. Charlebois RL, Doolittle WF (2004) Computing prokaryotic gene ubiquity: rescuing the core from extinction. Genome Res 14:2469–2477PubMedCrossRefGoogle Scholar
  4. Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676PubMedCrossRefGoogle Scholar
  5. Delaye L, Moya A (2010) Evolution of reduced prokaryotic genomes and the minimal cell concept: variations on a theme. BioEssays 32:281–287PubMedCrossRefGoogle Scholar
  6. Doolittle RF, Handy J (1998) Evolutionary anomalies among the aminoacyl-tRNA synthetases. Curr Opin Genet Dev 8:630–636PubMedCrossRefGoogle Scholar
  7. Gil R, Silva FJ, Pereto J, Moya A (2004) Determination of the core of a minimal bacterial gene set. Microbiol Mol Biol Rev 68: 518–537Google Scholar
  8. Glass JI, Assad-Garcia N, Alperovich N, Yooseph S, Lewis MR, Maruf M, Hutchison CA, Smith HO, Venter JC (2006) Essential genes of a minimal bacterium. Proc Natl Acad Sci U S A 103:425–430PubMedCrossRefGoogle Scholar
  9. Gotz S, Garcia-Gomez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ, Robles M, Talon M, Dopazo J, Conesa A (2008) High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res 36:3420–3435PubMedCrossRefGoogle Scholar
  10. Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel S, Fisk DG, Hirschman JE, Hong EL, Nash RS, Sethuraman A, Theesfeld CL, Botstein D, Dolinski K, Feierbach B, Berardini T, Mundodi S, Rhee SY, Apweiler R, Barrell D, Camon E, Dimmer E, Lee V, Chisholm R, Gaudet P, Kibbe W, Kishore R, Schwarz EM, Sternberg P, Gwinn M, Hannick L, Wortman J, Berriman M, Wood V, de la Cruz N, Tonellato P, Jaiswal P, Seigfried T, White R, Consortium GO (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 32: D258–D261Google Scholar
  11. Hashimoto M, Ichimura T, Mizoguchi H, Tanaka K, Fujimitsu K, Keyamura K, Ote T, Yamakawa T, Yamazaki Y, Mori H, Katayama T, Kato J (2005) Cell size and nucleoid organization of engineered Escherichia coli cells with a reduced genome. Mol Microbiol 55:137–149PubMedCrossRefGoogle Scholar
  12. Hsiang T, Baillie DL (2005) Comparison of the yeast proteome to other fungal genomes to find core fungal genes. J Mol Evol 60:475–483PubMedCrossRefGoogle Scholar
  13. Hutchison C, Montague M (2002) Mycoplasmas and the minimal genome concept. In: Razin S, Herrmann R (eds) Molecular biology and pathogenicity of mycoplasmas. Kluwer Academic, New York, pp 221–231CrossRefGoogle Scholar
  14. Islas S, Becerra A, Luisi PL, Lazcano A (2004) Comparative genomics and the gene complement of a minimal cell. Orig Life Evol Biosph 34:243–256PubMedCrossRefGoogle Scholar
  15. Itaya M (1995) An estimation of minimal genome size required for life. FEBS Lett 362:257–260PubMedCrossRefGoogle Scholar
  16. Jewett MC, Forster AC (2010) Update on designing and building minimal cells. Curr Opin Biotechnol 21:697–703PubMedCrossRefGoogle Scholar
  17. Juhas M, Eberl L, Glass JI (2011) Essence of life: essential genes of minimal genomes. Trends Cell Biol 21:562–568PubMedCrossRefGoogle Scholar
  18. Kahsay RY, Gao G, Liao L (2005) An improved hidden Markov model for transmembrane protein detection and topology prediction and its applications to complete genomes. Bioinformatics 21:1853–1858PubMedCrossRefGoogle Scholar
  19. Kobayashi K, Ehrlich SD, Albertini A, Amati G, Andersen KK, Arnaud M, Asai K, Ashikaga S, Aymerich S, Bessieres P, Boland F, Brignell SC, Bron S, Bunai K, Chapuis J, Christiansen LC, Danchin A, Debarbouille M, Dervyn E, Deuerling E, Devine K, Devine SK, Dreesen O, Errington J, Fillinger S, Foster SJ, Fujita Y, Galizzi A, Gardan R, Eschevins C, Fukushima T, Haga K, Harwood CR, Hecker M, Hosoya D, Hullo MF, Kakeshita H, Karamata D, Kasahara Y, Kawamura F, Koga K, Koski P, Kuwana R, Imamura D, Ishimaru M, Ishikawa S, Ishio I, Le Coq D, Masson A, Mauel C, Meima R, Mellado RP, Moir A, Moriya S, Nagakawa E, Nanamiya H, Nakai S, Nygaard P, Ogura M, Ohanan T, O’Reilly M, O’Rourke M, Pragai Z, Pooley HM, Rapoport G, Rawlins JP, Rivas LA, Rivolta C, Sadaie A, Sadaie Y, Sarvas M, Sato T, Saxild HH, Scanlan E, Schumann W, Seegers JFML, Sekiguchi J, Sekowska A, Seror SJ, Simon M, Stragier P, Studer R, Takamatsu H, Tanaka T, Takeuchi M, Thomaides HB, Vagner V, van Dijl JM, Watabe K, Wipat A, Yamamoto H, Yamamoto M, Yamamoto Y, Yamane K, Yata K, Yoshida K, Yoshikawa H, Zuber U, Ogasawara N (2003) Essential Bacillus subtilis genes. Proc Natl Acad Sci U S A 100:4678–4683PubMedCrossRefGoogle Scholar
  20. Koonin EV (2000) How many genes can make a cell: the minimal-gene-set concept. Annu Rev Genomics Hum Genet 1:99–116PubMedCrossRefGoogle Scholar
  21. Krogh A, Br Larsson, von Heijne G, Sonnhammer ELL (2001) Predicting transmembrane protein topology with a hidden markov model: application to complete genomes. J Mol Biol 305:567–580PubMedCrossRefGoogle Scholar
  22. Lapierre P, Gogarten JP (2009) Estimating the size of the bacterial pan-genome. Trends Genet 25:107–110PubMedCrossRefGoogle Scholar
  23. Leaver M, Dominguez-Cuevas P, Coxhead JM, Daniel RA, Errington J (2009) Life without a wall or division machine in Bacillus subtilis. Nature 457:849–853PubMedCrossRefGoogle Scholar
  24. Lluch-Senar M, Querol E, Pinol J (2010) Cell division in a minimal bacterium in the absence of ftsZ. Mol Microbiol 78:278–289PubMedCrossRefGoogle Scholar
  25. Moya A, Pereto J, Gil R, Latorre A (2008) Learning how to live together: genomic insights into prokaryote-animal symbioses. Nat Rev Genet 9:218–229PubMedCrossRefGoogle Scholar
  26. Mushegian A (1999) The minimal genome concept. Curr Opin Genet Dev 9:709–714PubMedCrossRefGoogle Scholar
  27. Mushegian AR, Koonin EV (1996) A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc Natl Acad Sci U S A 93:10268–10273PubMedCrossRefGoogle Scholar
  28. Shiba K, Motegi H, Schimmel P (1997) Maintaining genetic code through adaptations of tRNA synthetases to taxonomic domains. Trends Biochem Sci 22:453–457PubMedCrossRefGoogle Scholar
  29. Smalley DJ, Whiteley M, Conway T (2003) In search of the minimal Escherichia coli genome. Trends Microbiol 11:6–8PubMedCrossRefGoogle Scholar
  30. Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JGR, Korf I, Lapp H, Lehvaslaiho H, Matsalla C, Mungall CJ, Osborne BI, Pocock MR, Schattner P, Senger M, Stein LD, Stupka E, Wilkinson MD, Birney E (2002) The bioperl toolkit: Perl modules for the life sciences. Genome Res 12:1611–1618PubMedCrossRefGoogle Scholar
  31. Stano P, Ferri F, Luisi PL (2011) Semi-synthetic minimal living cells, in: Luigi P, Chiarabelli C (Eds), Chemical synthetic biology. John Wiley,New York, pp 247–286Google Scholar
  32. Sutcliffe I, Harrington D, Hutchings M (2012) A phylum level analysis reveals lipoprotein biosynthesis to be a fundamental property of bacteria. Protein Cell 3:163–170PubMedCrossRefGoogle Scholar
  33. Trevors JT (1999) Evolution of gene transfer in bacteria. World J Microbiol Biotechnol 15:1–7CrossRefGoogle Scholar
  34. Trevors JT (2003) Possible origin of a membrane in the subsurface of the Earth. Cell Biol Intern 27:451–457CrossRefGoogle Scholar
  35. Trevors JT (2004) Evolution of cell division in bacteria. Theory Biosciences 123:3–15CrossRefGoogle Scholar
  36. Trevors JT (2010a) Perspective: researching the transition from non-living to the first microorganisms: methods and experiments are major challenges. J Microbiol Methods 81:259–263PubMedCrossRefGoogle Scholar
  37. Trevors JT (2010b) Suitable microscopic entropy for the origin of microbial life: microbiological methods are challenges. J Microbiol Methods 83:341–344PubMedCrossRefGoogle Scholar
  38. Trevors JT (2011) The composition and organization of cytoplasm in prebiotic cells. Intern J Mol Sci 12:1650–1659CrossRefGoogle Scholar
  39. Trevors JT, Masson L (2011a) How much cytoplasm can a bacterial genome control? J Microbiol Methods 84:147–150PubMedCrossRefGoogle Scholar
  40. Trevors JT, Masson L (2011b) Quantum microbiology. Curr Issues Mol Biol 13:43–49PubMedGoogle Scholar
  41. Trevors JT, Pollack GH (2005) Hypothesis: the origin of life in a hydrogel environment. Prog Biophys Mol Biol 89:1–8PubMedCrossRefGoogle Scholar
  42. Trevors JT, Pollack GH (2012) Origin of microbial life hypothesis: a gel cytoplasm lacking a bilayer membrane, with infrared radiation producing exclusion zone (EZ) water, hydrogen as an energy source and thermosynthesis for bioenergetics. Biochimie 94:258–262PubMedCrossRefGoogle Scholar
  43. Trevors JT, Psenner R (2001) From self-assembly of life to present-day bacteria: a possible role for nanocells. FEMS Microbiol Rev 25:573–582PubMedCrossRefGoogle Scholar
  44. Zhang L, Chang S, Wang J (2010) How to make a minimal genome for synthetic minimal cell. Protein Cell 1:427–434PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2012

Authors and Affiliations

  1. 1.School of Environmental Sciences, University of GuelphGuelphCanada

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