A close relationship between primary nucleotides sequence structure and the composition of functional genes in the genome of prokaryotes

Molecular Phylogenetics and Evolution

Volumn 61, Issue 3, 2011, Pages 650-658

  Garcia, Juan A L ^a   Fernández Guerra, Antoni ^a   Casamayor, Emilio O ^a  

^a CENTRE D ESTUDIS AVANÇATS DE BLANES CEAB CSIC   (Spain)

Author keywords

Comparative genome analyses; Detrended fluctuation analysis (DFA); DNA walk; Large scale genome structure; Long range correlation; Microbial ecology

Indexed keywords

ARCHAEAL DNA; BACTERIAL DNA; NUCLEOTIDE;

ARCHAEAL GENOME; ARTICLE; BACTERIAL GENOME; BIOLOGY; GENETICS; METABOLISM; MULTIGENE FAMILY; NUCLEOTIDE SEQUENCE; PHYLOGENY; PROKARYOTIC CELL;

BASE SEQUENCE; COMPUTATIONAL BIOLOGY; DNA, ARCHAEAL; DNA, BACTERIAL; GENOME, ARCHAEAL; GENOME, BACTERIAL; MULTIGENE FAMILY; NUCLEOTIDES; PHYLOGENY; PROKARYOTIC CELLS;

AQUIFICAE; AQUIFICAE (CLASS); ARCHAEA; BACTERIA (MICROORGANISMS); DICTYOGLOMI; FUSOBACTERIA; NITROSPIRAE; PROKARYOTA; THERMOTOGAE; THERMOTOGAE (CLASS);

EID: 80055105388     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2011.08.011     Document Type: Article

References (55)

1. Afifi A.A., Clark V.A., May S. Discriminant Analysis, Computer-aided Multivariate Analysis 2004, Chapman & Hall/CRC, New York.
2. Akberova, N.I., Yu, A.L., 1996. Symmetrical structure in genetic texts of prokaryotes DNA replication origins. NetSci. Available from: http://www.netsci.org/Science/Bioinform/feature05.html.
3. Aravind L., Tatusov R.L., Wolf Y.I., Walker D.R., Koonin E.V. Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles. Trends Genet. 1998, 14:442-444.
4. Auguet J.C., Barberán A., Casamayor E.O. Global ecological patterns in uncultured Archaea. ISME J. 2010, 4:182-190.
5. Auguet J.C., Nomokonova N., Camarero L., Casamayor E.O. Seasonal changes of freshwater ammonia oxidizing archaeal assemblages and nitrogen species in oligotrophic alpine lakes. Appl. Environ. Microbiol. 2011, 77:1937-1945.
6. Barberán A., Fernández-Guerra A., Auguet J.C., Galand P.E., Casamayor E.O. Phylogenetic ecology of widespread uncultured clades of the Kingdom Euryarchaeota. Mol. Ecol. 2011, 20:1988-1996.
7. Bentley S.D., Parkhill J. Comparative genomic structure of prokaryotes. Annu. Rev. Genet. 2004, 38:771-791.
8. Bernaola-Galván P., Carpena P., Román-Roldán R., Oliver J.L. Study of statistical correlations in DNA sequences. Gene 2002, 300:105-115.
9. Bernaola-Galván P., Oliver J.L., Carpena P., Clay O., Bernardi G. Quantifying intrachromosomal GC heterogeneity in prokaryotic genomes. Gene 2004, 333:121-133.
10. Bernardi G. Structural and Evolutionary Genomics. Natural Selection in Genome Evolution 2004, Elsevier, Amsterdam.
11. Boussau B., Karlberg E.O., Frank A.C., Legault B.A., Andersson S.G.E. Computational inference of scenarios for α-proteobacterial genome evolution. PNAS 2004, 101:9722-9727.
12. Buldyrev S.V., Goldberger A.L., Havlin S., Mantegna R.N., Matsa M.E., Peng C.K., Simons M., Stanley H.E. Long-range correlation properties of coding and noncoding DNA sequences: GenBank analysis. Phys. Rev. E 1995, 51:5084-5091.
13. Cebrat C., Dudek M.R. The effect of DNA phase structure on DNA walks. Eur. Phys. J., B Cond. Matter Phys. 1998, 3:271-276.
14. Chen L.L., Zhang C.T. Seven GC-rich microbial genomes adopt similar codon usage patterns regardless of their phylogenetic lineages. Biochem. Biophys. Res. Commun. 2003, 306:310-317.
15. Doolittle W.F. Lateral genomics. Trends Cell Biol. 1999, 9:M5-M8.
16. Doolittle W.F. Phylogenetic classification and the universal tree. Science 1999, 284:2124-2129.
17. Foerstner K.U., Mering C.V., Hooper S.D., Bork P. Environments shape the nucleotide composition of genomes. EMBO Rep. 2005, 6:1208-1213.
18. Garcia J.A.L., Bartumeus F., Roche D., Giraldo J., Stanley H.E., Casamayor E.O. Ecophysiological significance of scale-dependent patterns in prokaryotic genomes unveiled by a combination of statistic and genometric analyses. Genomics 2008, 91:538-543.
19. Garrity G.M., Boone D.R., Castenholz R.W. Bergey's Manual of Systematic Bacteriology 2001, Springer, Berlin. second ed.
20. Ge F., Wang L.S., Kim J. The cobweb of life revealed by genome-scale estimates of horizontal gene transfer. PLoS Biol. 2005, 3:E316.
21. Grigoriev A. Analyzing genomes with cumulative skew diagrams. Nucleic Acids Res. 1998, 26:2286-2290.
22. Ho J.W.K., Adams C.E., Lew J.B., Matthews T.J., Ng C.C., Shahabi-Sirjani A., Tan L.H., Zhao Y., Easteal S., Wilson S.R., Jermiin L.S. SeqVis: visualization of compositional heterogeneity in large alignments of nucleotides. Bioinformatics 2006, 22:2162-2163.
23. Hotelling H. Relations between two sets of variates. Biometrika 1936, 28:321-377.
24. Jain R., Rivera M.C., Lake J.A. Horizontal gene transfer among genomes: the complexity hypothesis. PNAS 1999, 96:3801-3806.
25. Konstantinidis K.T., James M., Tiedje J.M. Trends between gene content and genome size in prokaryotic species with larger genomes. PNAS 2004, 101:3160-3165.
26. Koonin E.V., Galperin M.Y. Sequence-Evolution-Function. Computational Approaches in Comparative Genomics 2002, Kluwer Acadademic Publication, New York.
27. Koonin E.V., Wolf Y.I. Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucleic Acids Res. 2008, 36:6688-6719.
28. Koonin E.V., Mushegian A.R., Galperin M.Y., Walker D.R. Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea. Mol. Microbiol. 1997, 25:619-637.
29. Koonin E.V., Aravind L., Kondrashov A.S. The impact of comparative genomics on our understanding of evolution. Cell 2000, 101:573-576.
30. Lerat E., Daubin V., Moran N.A. From gene trees to organismal phylogeny in prokaryotes: the case of the gammaproteobacteria. PLoS Biol. 2003, 1:E19.
31. Lerat E., Daubin V., Ochman H., Moran N.A. Evolutionary origins of genomic repertoires in bacteria. PLoS Biol. 2005, 3:E130.
32. Lindahl T. Instability and decay of the primary structure of DNA. Nature 1993, 362:709-715.
33. Lobry J.R. A simple vectorial representation of DNA sequences for the detection of replication origins in bacteria. Biochimie 1996, 78:323-326.
34. Lobry J.R. Genomic landscapes. Microbiol. Today 1999, 26:164-165.
35. Logsdon J.M., Faguy D.M. Evolutionary genomics: Thermotoga heats up lateral gene transfer. Curr. Biol. 1999, 9:747-751.
36. Mackiewicz P., Kowalczuk M., Mackiewicz D., Nowicka A., Dudkiewicz M., Laszkiewicz A., Dudek M., Cebrat S. Replication associated mutational pressure generating long-range correlation in DNA. Physica A 2002, 314:646-654.
37. Makarova K.S., Wolf Y.I., Koonin E.V. Potential genomic determinants of hyperthermophily. Trends Genet. 2003, 19:172-176.
38. Makarova K.S., Sorokin A.V., Novichkov P.S., Wolf Y.I., Koonin E.V. Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea. Biol. Direct 2007, 2:33.
39. McEwan C.E., Gatherer D., McEwan N.R. Nitrogen-fixing aerobic bacteria have higher genomic GC content than non-fixing species within the same genus. Hereditas 1998, 128:173-178.
40. Mrázek J., Karlin S. Strand compositional asymmetry in bacterial and large viral genomes. Proc. Natl. Acad. Sci. 1997, 95:3720-3725.
41. Naya H., Romero H., Zavala A., Alvarez B., Musto H. Aerobiosis increases the genomic guanine plus cytosine content (GC%) in prokaryotes. J. Mol. Evol. 2002, 55:260-264.
42. Nelson K.E., Clayton R.A., Gill S.R., Gwinn M.L., Dodson R.J., et al. Evidence for lateral gene transfer between archaea and bacteria from genome sequence of Thermotoga maritima. Nature 1999, 399:323-329.
43. Novichkov P.S., Omelchenko M.V., Gelfand M.S., Mironov A.A., Wolf Y.I., Koonin E.V. Genome-wide molecular clock and horizontal gene transfer in bacterial evolution. J. Bacteriol. 2004, 186:6575-6585.
44. Ochman H., Jones I.B. Evolutionary dynamics of full genome content in Escherichia coli. EMBO J. 2000, 19:6637-6643.
45. Omelchenko M.V., Wolf Y.I., Gaidamakova E.K., Matrosova V.Y., Vasilenko A., Zhai M., Daly M.J., Koonin E.V., Makarova K.S. Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance. BMC Evol. Biol. 2005, 5:57.
46. Pushker R., Mira A., Rodríguez-Valera F. Comparative genomics of gene-family size in closely related bacteria. Genome Biol. 2004, 5:27.
47. Rao C.R. The use and interpretation of principal component analysis in applied research. Sankhya A 1964, 26:329-358.
48. Rocha E.P.C. Evolutionary patterns in prokaryotic genomes. Curr. Opin. Microbiol. 2008, 11:454-460.
49. Sen A., Sur S., Bothra A.K., Benson D.R., Normand P., Tisa L.S. The implication of life style on codon usage patterns and predicted highly expressed genes for three Frankia genomes. Antonie Van Leeuwenhoek 2008, 93:335-346.
50. Simonato F., Campanaro S., Lauro F.M., Vezzi A., D'Angelo M., Vitulo N., Valle G., Bartlett D.H. Piezophilic adaptation: a genomic point of view. J. Biotechnol. 2006, 126:11-25.
51. Tatusov R.L., Koonin E.V., Lipman D.J. A genomic perspective on protein families. Science 1997, 278:631-637.
52. Tatusov R.L., Fedorova N.D., Jackson J.D., Jacobs A.R., Kiryutin B., Koonin E.V., Krylov D.M., Mazumder R., Mekhedov S.L., Nikolskaya A.N., Rao B.S., Smirnov S., Sverdlov A.V., Vasudevan S., Wolf Y.I., Yin J.J., Natale D.A. The COG database: an updated version includes eukaryotes. BMC Bioinf. 2003, 4:41.
53. Ter Braak, C.J.F., 1988. CANOCO - a FORTRAN Program for Canonical Community Ordination by [Partial] [Detrended] [Canonical] Correspondence Analysis, Principal Component Analysis and Redundancy Analysis (Version 2.1). Wageningen.
54. Toh H., Weiss B.L., Perkin S.A.H., Yamashita A., Oshima K., Hattori M., Aksoy S. Massive genome erosion and functional adaptations provide insights into the symbiotic lifestyle of Sodalis glossinidius in the tsetse host. Genome Res. 2006, 16:149-156.
55. Voss R.F. Evolution of long-range fractal correlations and 1/fα noise in DNA base sequences. Phys. Rev. Lett. 1992, 68:3805-3808.