Gene arrangements and branching orders of gram-positive bacteria

Journal of Theoretical Biology

Volumn 222, Issue 4, 2003, Pages 495-503

  Kunisawa, Takashi ^a  

^a TOKYO UNIVERSITY OF SCIENCE   (Japan)

Author keywords

Gene order; Gram positive bacteria; Phylogeny

Indexed keywords

CYTOSINE; DNA DIRECTED DNA POLYMERASE GAMMA; GUANINE; RIBOSOME PROTEIN; UNCLASSIFIED DRUG; URIDINE DIPHOSPHATE; URIDINE DIPHOSPHATE N ACETYLMURAMATE ALANINE LIGASE;

BACTERIUM; GENETICS; PHYLOGENY;

ACTINOBACTERIA; ALPHA CHAIN; ARTICLE; BACILLUS SUBTILIS; BACTERIAL GENE; BACTERIAL GENOME; COMPUTER ANALYSIS; DNA TRANSPOSITION; GENE CONSTRUCT; GENE DELETION; GENE INSERTION; GENE ORDER; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC LINE; GRAM POSITIVE BACTERIUM; INFORMATION PROCESSING; METHODOLOGY; MOLECULAR EVOLUTION; MYCOPLASMA; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SPECIES DIFFERENTIATION; THERMOANAEROBACTER TENGCONGENSIS; THERMOPHILIC BACTERIUM;

ACTINOBACTERIA; BACILLUS SUBTILIS; BACTERIA (MICROORGANISMS); INSERTION SEQUENCES; MYCOPLASMA; MYCOPLASMATALES; POSIBACTERIA; THERMOANAEROBACTER; THERMOANAEROBACTER TENGCONGENSIS;

EID: 0037763690     PISSN: 00225193     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-5193(03)00064-X     Document Type: Article

References (56)

1. Aravind L., Tatusov R.L., Wolf Y.I., Walker D.R., Koonin E.V. Evidence for massive gene exchange between archaeal and bacterial thermophiles. Trends Genet. 25:1998;442-444.
2. Bao Q., Tian Y., Li W., Xu Z., Xuan Z.et al. A complete sequence of T. tengcongensis genome. Genome Res. 12:2002;689-700.
3. Blattner F.R., Plunkett III G., Bloch C.A., Perna N.T., Burland V.et al. The complete genome sequence of Escherichia coli K-12. Science. 277:1997;1453-1474.
4. Boccheta M., Gribaldo S., Sanangelantoni A., Cammarano P. Phylogenetic depth of the bacterial genera Aquifex and Thermotoga inferred from analysis of ribosomal protein, elongation factor, and RNA polymerase subunit sequences. J. Mol. Evol. 50:2000;366-380.
5. Brochier C., Philippe H. A non-hyperthermophilic ancestor for bacteria. Nature. 417:2002;244.
6. Brown J.R., Douady C.J., Italia M.J., Marshall W.E., Stanhope M.J. Universal trees based on large combined protein sequence data sets. Nat. Genet. 28:2001;281-285.
7. Chambaud I., Heilig R., Ferris S., Barbe V., Samson D.et al. The complete genome sequence of the murine respiratory pathogen Mycoplasma pulmonis. Nucleic Acids Res. 29:2001;2145-2153.
8. Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.et al. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature. 393:1998;537-544.
9. Cole S.T., Eiglmeier K., Parkhill J., James K.D., Thomson N.R.et al. Massive gene decay in the leprosy bacillus. Nature. 409:2001;1007-1011.
10. Daubin V., Gouy M., Perrière G. A phylogenetic approach to bacterial phylogeny. evidence of a core of genes sharing a common history Genome Res. 12:2002;1080-1090.
11. Deckert G., Warren P.V., Gaasterland T., Young W.G., Lenox A.L.et al. The complete genome of the hyperthermophilic bacterium Aquifex aeolicus. Nature. 392:1998;353-358.
12. Doolittle W.F. Phylogenetic classification and the universal tree. Science. 284:1999;2129-2141.
13. Eisen J.A. The RecA protein as a model molecule for molecular systematic studies of bacteria. comparison of trees of recas and 16s rrnas from the same species J. Mol. Evol. 41:1995;1105-1123.
14. Felsenstein J. Evolutionary trees from dna sequences. a maximum likelihood approach J. Mol. Evol. 17:1981;368-376.
15. Fitch W.M. Toward defining the course of evolution. minimum change for a specific tree topology Syst. Zool. 20:1971;406-416.
16. Fraser C.M., Gocayne J.D., White O., Adams M.D., Clayton R.A.et al. The minimal gene complement of Mycoplasma genitalium. Science. 270:1995;397-403.
17. Fraser C.M., Casjens S., Huang W.M., Sutton G.G., Clayton R.et al. Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi. Nature. 390:1997;580-586.
18. Fraser C.M., Norris S.J., Weinstock G.M., White O., Sutton G.G.et al. Complete genome sequence of Treponema pallidum, the syphilis spirochete. Science. 281:1998;375-388.
19. Galibert F., Finan T.M., Long S.R., Puhler A., Abola P. The composite genome of the legume symbiont Sinorhizobium meliloti. Science. 293:2001;668-672.
20. Galtier N., Gouy M. Inferring phylogeny from DNA sequences of unequal base compositions. Proc. Natl Acad. Sci. USA. 92:1995;11317-11321.
21. Glaser P., Frangeul L., Buchrieser C., Rusniok C., Amend A.et al. Comparative genomics of Listeria species. Science. 294:2001;849-852.
22. Glass J.I., Lefkowitz E.J., Glass J.S., Heiner C.R., Chen E.Y., Cassell G.H. The complete sequence of mucosal pathogen Ureaplasma urealyticum. Nature. 407:2000;757-762.
23. Gupta R.S. Protein phylogenies and signature sequences. a reappraisal of evolutionary relationships among archaebacteria, eubacteria and eukaryotes Microbiol. Mol. Biol. Rev. 62:1998;1435-1491.
24. Gupta R.S. The phylogeny of proteobacteria. relationships to other eubacterial phyla and eukaryotes FEMS Microbiol. Rev. 24:2000;367-402.
25. Gupta R.S. The branching order and phylogenetic placements of species from completed bacterial genomes based on conserved indels found in various proteins. Int. Microbiol. 4:2001;187-202.
26. Hansmann S., Martin W. Phylogeny of 33 ribosomal and six other proteins encoded in ancient gene cluster that is conserved across prokaryotic genomes. influences of excluding poorly alignable sites from analysis Int. J. Syst. Evol. Microbiol. 50:2000;1655-1663.
27. Himmelreich R., Hilbert H., Plagens H., Pirkl E., Li B.C., Herrmann R. Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae. Nucleic Acid Res. 24:1996;4420-4449.
28. House C.H., Fitz-gibbon S.T. Using homolog groups to create a whole-genomic tree of free-living organisms. an update J. Mol. Biol. 54:2002;539-547.
29. Kalman S., Mitchell W., Marathe R., Lammel C., Fan J.et al. Comparative genomes of Chlamydia pneumoniae and C. trachomatis. Nat. Genet. 21:1999;385-389.
30. Kaneko T., Sato S., Kotani H., Tanaka A., Asamizu E.et al. Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. DNA Res. 3:1996;109-136.
31. Kaneko T., Nakamura Y., Wolk C.P., Kuritz T., Sasamoto S. Complete genomic sequence of the filamentous nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120. DNA Res. 8:2001;205-213.
32. Kapatral V., Anderson I., Ivanova N., Reznik G., Los T.et al. Genome sequence and analysis of the oral bacterium Fusobacterium nucleatum strain ATCC 25586. J. Bacteriol. 184:2002;2005-2018.
33. Kishino H., Hasegawa M. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea. J. Mol. Evol. 29:1989;170-179.
34. Klenk H.-P., Meier T.-D., Durovic P., Schwass V., Lottspeich F., Dennis P.P., Zilling W. RNA polymerase of Aquifex pyrophilus. implications for the evolution of the bacterial rpoBC operon and extremely thermophilic bacteria J. Mol. Evol. 48:1999;528-541.
35. Kunisawa T. Identification and chromosomal distribution of DNA sequence segments conserved since divergence between Escherichia coli and Bacillus subtilis. J. Mol. Evol. 40:1995;585-593.
36. Kunisawa T. Gene arrangements and phylogeny in the class Proteobacteria. J. theor. Biol. 213:2001;9-19.
37. Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G. The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature. 390:1997;249-256.
38. Kuroda M., Ohta T., Uchiyama I., Baba T., Yuzawa H., Kobayashi I., Cui L., Oguchi A., Aoki K., Nagai Y., Lian J., Ito T., Kanamori M., Matsumaru H., Maruyama A., Murakami H., Hosoyama A., Mizutani-Ui Y., Kobayashi N., Sawano T., Imoue R., Kaito C., Sekimizu K., Hirakawa H., Kuhara S., Goto S., Yabuzaki J., Kanehisa M., Yamashita A., Oshima K., Furuya K., Yashino C., Shiba T., Hattori M., Ogasawara N., Hayashi H., Hiramatsu K. Whole genome sequencing of meticillin-resistant Staphylococcus aureus. Lancet. 357:2001;1225-1240.
39. Lake J.A. Reconstructing evolutionary trees from DNA and protein sequences. paralinear distances Proc. Natl Acad. Sci. USA. 91:1994;1455-1459.
40. Lin J., Gerstein M. Whole-genome trees based on the occurrence of folds and orthologs. implications for comparing genomes on different levels Genome Res. 10:2000;808-818.
41. Nelson K.E., Clayton R.A., Gill S.R., Gwinn M.L., Dodson R.J. Evidence for lateral gene transfer between archaea and bacteria from genome sequence of Thermotoga maritima. Nature. 399:1999;323-329.
42. Ochman H., Lawrence J.G., Groisman E.A. Lateral gene transfer and the nature of bacterial innovation. Nature. 405:2000;299-304.
43. Olsen G.J., Woese C.R., Overbeek R. The winds of (evolutionary) change. breathing new life into microbiology J. Bacteriol. 176:1994;1-6.
44. Pearson W.R., & Lipman D.J. Improved tools for biological sequence comparison. Proc. Natl Acad. Sci. USA. 85:1988;2444-2448.
45. Philippe H., Forterre P. The rooting of the universal tree of life is not reliable. J. Mol. Evol. 49:1999;509-523.
46. Philippe H., Germot A. Phylogeny of eukaryotes based on ribosomal RNA. long-branch attraction and models of sequence evolution Mol. Biol. Evol. 17:2000;830-834.
47. Ragan M.A. On surrogate methods for detecting lateral gene transfer. FEMS Microbiol. Lett. 201:2001;187-191.
48. Saitou N., Nei M. The neighbor-joining method. a new method for reconstructing phylogenetic trees Mol. Biol. Evol. 4:1987;406-425.
49. Takami H., Nakasone K., Hirama C., Takaki Y., Masui N.K. Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with Bacillus subtilis. Nucleic Acid Res. 28:2000;4317-4331.
50. Tatusov R.L., Koonin E.V., Lipman D. A genomic perspective on protein families. Science. 278:1997;631-637.
51. Tatusov R.L., Natale D.A., Garkavtsev I.V., Tatusova T.A., Shankavaram U.T., Rao B.S., Kiryutin B., Galperin M.Y., Fedorova N.D., Koonin E.V. The COG database. new developments in phylogenetic classification of proteins from complete genomes Nucleic Acid Res. 29:2001;22-28.
52. Tekaia F., Lazcano A., Dujon B. The genomic tree as revealed from whole proteome comparisons. Genome Res. 9:1999;550-557.
53. Wächtershäuser G. Towards a reconstruction of ancestral genomes by gene cluster alignment. Syst. Appl. Microbiol. 21:1998;473-477.
54. White O., Eisen J.A., Heidelberg J.F., Hickey E.K., Peterson J.D.et al. Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1. Science. 286:1999;1571-1577.
55. Woese C.R. Bacterial evolution. Microbiol. Rev. 51:1987;221-271.
56. Yang Z. Among-site rate variation and its impact on phylogenetic analyses. Trends Ecol. Evol. 11:1996;367-370.