Quantitative analysis of replication-related mutation and selection pressures in bacterial chromosomes and plasmids using generalised GC skew index

BMC Genomics

Volumn 10, Issue , 2009, Pages

  Arakawa, Kazuharu ^a   Suzuki, Haruo ^b   Tomita, Masaru ^a  

^a KEIO UNIVERSITY   (Japan)

^b Department of Obstetrics Gynecology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; CYTOSINE; GUANINE;

ARCHAEBACTERIUM; ARTICLE; BACTERIAL CHROMOSOME; BACTERIAL GENOME; BACTERIAL STRAIN; CONTROLLED STUDY; DNA REPLICATION; GENE MUTATION; GENETIC CORRELATION; GENETIC SELECTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMID; QUANTITATIVE ANALYSIS; REPLICON; ARCHAEAL GENOME; BACTERIUM; BIOLOGICAL MODEL; BIOLOGY; CHROMOSOME; DNA REPLICATION ORIGIN; GENETICS; MUTATION;

BACTERIA (MICROORGANISMS);

ARCHAEA; BACTERIA; CHROMOSOMES, ARCHAEAL; CHROMOSOMES, BACTERIAL; COMPUTATIONAL BIOLOGY; DNA REPLICATION; DNA, BACTERIAL; GENOME, ARCHAEAL; GENOME, BACTERIAL; MODELS, GENETIC; MUTATION; PLASMIDS; REPLICATION ORIGIN; SELECTION, GENETIC;

EID: 74549117150     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-10-640     Document Type: Article

References (50)

1. Couturier E, Rocha EP. Replication-associated gene dosage effects shape the genomes of fast-growing bacteria but only for transcription and translation genes. Mol Microbiol 2006, 59(5):1506-1518. 10.1111/j.1365-2958.2006.05046.x, 16468991.
2. Rocha EP. The replication-related organization of bacterial genomes. Microbiology 2004, 150(Pt 6):1609-1627. 10.1099/mic.0.26974-0, 15184548.
3. Lobry JR, Louarn JM. Polarisation of prokaryotic chromosomes. Curr Opin Microbiol 2003, 6(2):101-108. 10.1016/S1369-5274(03)00024-9, 12732297.
4. Arakawa K, Uno R, Nakayama Y, Tomita M. Validating the significance of genomic properties of Chi sites from the distribution of all octamers in Escherichia coli. Gene 2007, 392(1-2):239-246. 10.1016/j.gene.2006.12.022, 17270364.
5. Kowalczykowski SC, Dixon DA, Eggleston AK, Lauder SD, Rehrauer WM. Biochemistry of homologous recombination in Escherichia coli. Microbiol Rev 1994, 58(3):401-465. 372975, 7968921.
6. Bigot S, Saleh OA, Lesterlin C, Pages C, El Karoui M, Dennis C, Grigoriev M, Allemand JF, Barre FX, Cornet F. KOPS: DNA motifs that control E. coli chromosome segregation by orienting the FtsK translocase. Embo J 2005, 24(21):3770-3780. 10.1038/sj.emboj.7600835, 1276719, 16211009.
7. Hendrickson H, Lawrence JG. Selection for chromosome architecture in bacteria. J Mol Evol 2006, 62(5):615-629. 10.1007/s00239-005-0192-2, 16612541.
8. Rocha EP. The organization of the bacterial genome. Annu Rev Genet 2008, 42:211-233. 10.1146/annurev.genet.42.110807.091653, 18605898.
9. Lobry JR. Asymmetric substitution patterns in the two DNA strands of bacteria. Mol Biol Evol 1996, 13(5):660-665.
10. Lobry JR, Sueoka N. Asymmetric directional mutation pressures in bacteria. Genome Biol 2002, 3(10):RESEARCH0058. 10.1186/gb-2002-3-10-research0058, 134625, 12372146.
11. Frank AC, Lobry JR. Oriloc: prediction of replication boundaries in unannotated bacterial chromosomes. Bioinformatics 2000, 16(6):560-561. 10.1093/bioinformatics/16.6.560, 10980154.
12. Arakawa K, Tomita M. Selection effects on the positioning of genes and gene structures from the interplay of replication and transcription in bacterial genomes. Evol Bioinform Online 2007, 3:279-286. 2684129, 19461975.
13. Chen C, Chen CW. Quantitative analysis of mutation and selection pressures on base composition skews in bacterial chromosomes. BMC Genomics 2007, 8:286. 10.1186/1471-2164-8-286, 2031905, 17711583.
14. Tillier ER, Collins RA. The contributions of replication orientation, gene direction, and signal sequences to base-composition asymmetries in bacterial genomes. J Mol Evol 2000, 50(3):249-257.
15. Touchon M, Rocha EP. From GC skews to wavelets: a gentle guide to the analysis of compositional asymmetries in genomic data. Biochimie 2008, 90(4):648-659. 10.1016/j.biochi.2007.09.015, 17988781.
16. Zhang CT, Zhang R, Ou HY. The Z curve database: a graphic representation of genome sequences. Bioinformatics 2003, 19(5):593-599. 10.1093/bioinformatics/btg041, 12651717.
17. Kowalczuk M, Mackiewicz P, Mackiewicz D, Nowicka A, Dudkiewicz M, Dudek MR, Cebrat S. DNA asymmetry and the replicational mutational pressure. J Appl Genet 2001, 42(4):553-577.
18. Salzberg SL, Salzberg AJ, Kerlavage AR, Tomb JF. Skewed oligomers and origins of replication. Gene 1998, 217(1-2):57-67. 10.1016/S0378-1119(98)00374-6, 9795135.
19. Worning P, Jensen LJ, Hallin PF, Staerfeldt HH, Ussery DW. Origin of replication in circular prokaryotic chromosomes. Environ Microbiol 2006, 8(2):353-361. 10.1111/j.1462-2920.2005.00917.x, 16423021.
20. Arakawa K, Tomita M. The GC Skew Index: A Measure of Genomic Compositional Asymmetry and the Degree of Replicational Selection. Evol Bioinform Online 2007, 3:159-168. 2684130, 19461976.
21. Arakawa K, Saito R, Tomita M. Noise-reduction filtering for accurate detection of replication termini in bacterial genomes. FEBS Lett 2007, 581(2):253-258. 10.1016/j.febslet.2006.12.021, 17188685.
22. del Solar G, Giraldo R, Ruiz-Echevarria MJ, Espinosa M, Diaz-Orejas R. Replication and control of circular bacterial plasmids. Microbiol Mol Biol Rev 1998, 62(2):434-464. 98921, 9618448.
23. Cevallos MA, Cervantes-Rivera R, Gutierrez-Rios RM. The repABC plasmid family. Plasmid 2008, 60(1):19-37. 10.1016/j.plasmid.2008.03.001, 18433868.
24. Khan SA. Plasmid rolling-circle replication: recent developments. Mol Microbiol 2000, 37(3):477-484. 10.1046/j.1365-2958.2000.02001.x, 10931341.
25. Khan SA. Plasmid rolling-circle replication: highlights of two decades of research. Plasmid 2005, 53(2):126-136. 10.1016/j.plasmid.2004.12.008, 15737400.
26. Lawrence JG, Ochman H. Amelioration of bacterial genomes: rates of change and exchange. J Mol Evol 1997, 44(4):383-397. 10.1007/PL00006158, 9089078.
27. Ochman H, Lawrence JG, Groisman EA. Lateral gene transfer and the nature of bacterial innovation. Nature 2000, 405(6784):299-304. 10.1038/35012500, 10830951.
28. Rocha EP, Danchin A. Base composition bias might result from competition for metabolic resources. Trends Genet 2002, 18(6):291-294. 10.1016/S0168-9525(02)02690-2, 12044357.
29. van Passel MW, Bart A, Luyf AC, van Kampen AH, Ende A. Compositional discordance between prokaryotic plasmids and host chromosomes. BMC Genomics 2006, 7:26. 10.1186/1471-2164-7-26, 1382213, 16480495.
30. Campbell A, Mrazek J, Karlin S. Genome signature comparisons among prokaryote, plasmid, and mitochondrial DNA. Proc Natl Acad Sci USA 1999, 96(16):9184-9189. 10.1073/pnas.96.16.9184, 17754, 10430917.
31. Suzuki H, Sota M, Brown CJ, Top EM. Using Mahalanobis distance to compare genomic signatures between bacterial plasmids and chromosomes. Nucleic Acids Res 2008, 36(22):e147. 10.1093/nar/gkn753, 2602791, 18953039.
32. Grigoriev A. Analyzing genomes with cumulative skew diagrams. Nucleic Acids Res 1998, 26(10):2286-2290. 10.1093/nar/26.10.2286, 147580, 9580676.
33. Fricke WF, Seedorf H, Henne A, Kruer M, Liesegang H, Hedderich R, Gottschalk G, Thauer RK. The genome sequence of Methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and H2 for methane formation and ATP synthesis. J Bacteriol 2006, 188(2):642-658. 10.1128/JB.188.2.642-658.2006, 1347301, 16385054.
34. Kennedy SP, Ng WV, Salzberg SL, Hood L, DasSarma S. Understanding the adaptation of Halobacterium species NRC-1 to its extreme environment through computational analysis of its genome sequence. Genome Res 2001, 11(10):1641-1650. 10.1101/gr.190201, 311145, 11591641.
35. Zhang R, Zhang CT. Multiple replication origins of the archaeon Halobacterium species NRC-1. Biochem Biophys Res Commun 2003, 302(4):728-734. 10.1016/S0006-291X(03)00252-3, 12646230.
36. Berquist BR, DasSarma S. An archaeal chromosomal autonomously replicating sequence element from an extreme halophile, Halobacterium sp. strain NRC-1. J Bacteriol 2003, 185(20):5959-5966. 10.1128/JB.185.20.5959-5966.2003, 225043, 14526006.
37. Bernander R, Skarstad K. Mapping of a chromosome replication origin in an archaeon. Trends Microbiol 2000, 8(12):535-537. 10.1016/S0966-842X(00)01878-3, 11115744.
38. Matsunaga F, Forterre P, Ishino Y, Myllykallio H. In vivo interactions of archaeal Cdc6/Orc1 and minichromosome maintenance proteins with the replication origin. Proc Natl Acad Sci USA 2001, 98(20):11152-11157. 10.1073/pnas.191387498, 58699, 11562464.
39. Matsunaga F, Glatigny A, Mucchielli-Giorgi MH, Agier N, Delacroix H, Marisa L, Durosay P, Ishino Y, Aggerbeck L, Forterre P. Genomewide and biochemical analyses of DNA-binding activity of Cdc6/Orc1 and Mcm proteins in Pyrococcus sp. Nucleic Acids Res 2007, 35(10):3214-3222. 10.1093/nar/gkm212, 1904270, 17452353.
40. Myllykallio H, Forterre P. Mapping of a chromosome replication origin in an archaeon: response. Trends Microbiol 2000, 8(12):537-539. 10.1016/S0966-842X(00)01881-3, 11201257.
41. Myllykallio H, Lopez P, Lopez-Garcia P, Heilig R, Saurin W, Zivanovic Y, Philippe H, Forterre P. Bacterial mode of replication with eukaryotic-like machinery in a hyperthermophilic archaeon. Science 2000, 288(5474):2212-2215. 10.1126/science.288.5474.2212, 10864870.
42. Database of Plasmid Replicon Database of Plasmid Replicon., http://www.essex.ac.uk/bs/staff/osborn/DPR/DPR_database.htm
43. del Solar G, Espinosa M. Plasmid copy number control: an ever-growing story. Mol Microbiol 2000, 37(3):492-500. 10.1046/j.1365-2958.2000.02005.x, 10931343.
44. Freeman JM, Plasterer TN, Smith TF, Mohr SC. Patterns of Genome Organization in Bacteria. Science 1998, 279(5358):1827a.
45. Arakawa K, Mori K, Ikeda K, Matsuzaki T, Kobayashi Y, Tomita M. G-language Genome Analysis Environment: a workbench for nucleotide sequence data mining. Bioinformatics 2003, 19(2):305-306. 10.1093/bioinformatics/19.2.305, 12538262.
46. Arakawa K, Suzuki H, Tomita M. Computational Genome Analysis Using The G-language System. Genes, Genomes and Genomics 2008, 2(1):1-13.
47. Arakawa K, Tomita M. G-language System as a platform for large-scale analysis of high-throughput omics data. Journal of Pesticide Science 2006, 31(3):282-288.
48. G-language REST Web Service G-language REST Web Service., http://rest.g-language.org/
49. NCBI RefSeq FTP Repository NCBI RefSeq FTP Repository., http://www.ncbi.nlm.nih.gov/Ftp/
50. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.