A minimal gene set for cellular life derived by comparison of complete bacterial genomes
TLDR
Fraser et al. as mentioned in this paper compared the 468 predicted M. genitalium protein sequences with the 1703 protein sequences encoded by the other completely sequenced small bacterial genome, that of Haemophilus influenzae, and suggested that the remaining 256 genes are close to the minimal gene set that is necessary and sufficient to sustain the existence of a modern type cell.Abstract:
The recently sequenced genome of the parasitic bacterium Mycoplasma genitalium contains only 468 identified protein-coding genes that have been dubbed a minimal gene complement [Fraser, C.M., Gocayne, J.D., White, O., Adams, M.D., Clayton, R.A., et al. (1995) Science 270, 397-403]. Although the M. genitalium gene complement is indeed the smallest among known cellular life forms, there is no evidence that it is the minimal self-sufficient gene set. To derive such a set, we compared the 468 predicted M. genitalium protein sequences with the 1703 protein sequences encoded by the other completely sequenced small bacterial genome, that of Haemophilus influenzae. M. genitalium and H. influenzae belong to two ancient bacterial lineages, i.e., Gram-positive and Gram-negative bacteria, respectively. Therefore, the genes that are conserved in these two bacteria are almost certainly essential for cellular function. It is this category of genes that is most likely to approximate the minimal gene set. We found that 240 M. genitalium genes have orthologs among the genes of H. influenzae. This collection of genes falls short of comprising the minimal set as some enzymes responsible for intermediate steps in essential pathways are missing. The apparent reason for this is the phenomenon that we call nonorthologous gene displacement when the same function is fulfilled by nonorthologous proteins in two organisms. We identified 22 nonorthologous displacements and supplemented the set of orthologs with the respective M. genitalium genes. After examining the resulting list of 262 genes for possible functional redundancy and for the presence of apparently parasite-specific genes, 6 genes were removed. We suggest that the remaining 256 genes are close to the minimal gene set that is necessary and sufficient to sustain the existence of a modern-type cell. Most of the proteins encoded by the genes from the minimal set have eukaryotic or archaeal homologs but seven key proteins of DNA replication do not. We speculate that the last common ancestor of the three primary kingdoms had an RNA genome. Possibilities are explored to further reduce the minimal set to model a primitive cell that might have existed at a very early stage of life evolution.read more
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Kazuto Kobayashi,Stanislav Dusko Ehrlich,Alessandra M. Albertini,G. Amati,Kasper Krogh Andersen,Maryvonne Arnaud,Kei Asai,S. Ashikaga,Stéphane Aymerich,Philippe Bessières,F. Boland,S.C. Brignell,Sierd Bron,Keigo Bunai,J. Chapuis,L.C. Christiansen,Antoine Danchin,Michel Débarbouillé,Etienne Dervyn,E. Deuerling,Kevin M. Devine,Susanne Krogh Devine,Oliver Dreesen,Jeffery Errington,Sabine Fillinger,Simon J. Foster,Yasutaro Fujita,Alessandro Galizzi,Rozenn Gardan,Caroline Eschevins,Tatsuya Fukushima,Kazuko Haga,Colin R. Harwood,Michael Hecker,D. Hosoya,Marie-Françoise Hullo,Hiroshi Kakeshita,Dimitri Karamata,Yasuhiro Kasahara,Fujio Kawamura,K. Koga,P. Koski,Ritsuko Kuwana,Daisuke Imamura,M. Ishimaru,Shu Ishikawa,I. Ishio,D. Le Coq,Anne Masson,Catherine Mauël,Rob Meima,Rafael P. Mellado,Anne Moir,Shigeki Moriya,E. Nagakawa,Hideaki Nanamiya,S. Nakai,Per Nygaard,Mitsuo Ogura,T. Ohanan,Mary O'Reilly,M. O'Rourke,Zoltán Prágai,H.M. Pooley,Georges Rapoport,J.P. Rawlins,L.A. Rivas,Carlo Rivolta,A. Sadaie,Yoshito Sadaie,Matti Sarvas,T. Sato,Hans Henrik Saxild,E. Scanlan,Wolfgang Schumann,J.F.M.L. Seegers,Junichi Sekiguchi,Agnieszka Sekowska,Simone J. Séror,M. Simon,P. Stragier,R. Studer,Hiromu Takamatsu,Teruo Tanaka,M. Takeuchi,H.B. Thomaides,Valerie Vagner,J.M. van Dijl,Kazuhito Watabe,Anil Wipat,Hiroki Yamamoto,M. Yamamoto,Y. Yamamoto,Kunio Yamane,Katsunori Yata,K. Yoshida,Hisashi Yoshikawa,Ulrich Zuber,Naotake Ogasawara +98 more
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Bergey's Manual of Systematic Bacteriology
TL;DR: BCL3 and Sheehy cite Bergey's manual of determinative bacteriology of which systematic bacteriology, first edition, is an expansion.
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