Association of purine asymmetry, strand-biased gene distribution and PolC within Firmicutes and beyond: A new appraisal

BMC Genomics

Volumn 15, Issue 1, 2014, Pages

  Saha, Sanjoy K ^a   Goswami, Aranyak ^a   Dutta, Chitra ^a  

^a INDIAN INSTITUTE OF CHEMICAL BIOLOGY   (India)

Author keywords

Base usage; Codon sites; Cytosine methylation; Fusobacteria; G dominance; Lagging strand; Leading strand; Mutational bias; Tenericutes; Thermotogae

Indexed keywords

PURINE; PYRIMIDINE; BACTERIAL PROTEIN; DNA DIRECTED DNA POLYMERASE; DNA DIRECTED DNA POLYMERASE GAMMA; DNA POLYMERASE III, ALPHA SUBUNIT; POLC PROTEIN, BACTERIA; PURINE DERIVATIVE;

ACIDAMINOCOCCUS; ACIDAMINOCOCCUS INTESTINI; ACIDOBACTERIUM CAPSULATUM; ACINETOBACTER; AQUIFEX AEOLICUS; ARTICLE; BACILLUS ANTHRACIS; BACTERIAL GENE; BACTERIAL STRAIN; BARTONELLA HENSELAE; CANDIDATUS PROTOCHLAMYDIA AMOEBOPHILA; CLOSTRIDIALES; CLOSTRIDIALES GENOMOSP; CLOSTRIDIUM DIFFICILE; CODON USAGE; CONTROLLED STUDY; ENTEROCOCCUS FAECALIS; FIRMICUTES; FUSOBACTERIACEAE; FUSOBACTERIUM NUCLEATUM; GENETIC PARAMETERS; GEOBACILLUS; GEOBACILLUS KAUSTOPHILUS; ILLYOBACTER POLYTROPUS; LARGE SCALE PRODUCTION; LEPTOTRICHIA BUCCALIS; LISTERIA MONOCYTOGENES; MYCOBACTERIUM TUBERCULOSIS; MYCOPLASMA MYCOIDES; MYCOPLASMA SYNOVIAE; NONHUMAN; OENOCOCCUS OENI; ORTHOLOGY; POLC; PURINE ASYMMETRY; RUMINOCOCCUS ALBUS; SPECIES DOMINANCE; STAPHYLOCOCCUS AUREUS; STOP CODON; STRAND BIASED GENE DISTRIBUTION; STREPTOBACILLUS MONILIFORMIS; STREPTOCOCCUS AGALACTIAE; SULFOBACILLUS ACIDOPHILUS; THERMOANAEROBACTER; THERMOANAEROBACTER TENGCONGENSIS; THERMODESULFOBIUM NARUGENSE; THERMOTOGA MARITIMA; VEILLONELLA PARVULA; BACTERIA; BACTERIAL GENOME; DNA REPLICATION; ENZYMOLOGY; GENETICS; METABOLISM;

BACTERIA (MICROORGANISMS); FIRMICUTES; FUSOBACTERIA; MOLLICUTES; THERMOTOGAE; THERMOTOGAE (CLASS);

BACTERIA; BACTERIAL PROTEINS; DNA POLYMERASE III; DNA REPLICATION; DNA-DIRECTED DNA POLYMERASE; GENES, BACTERIAL; GENOME, BACTERIAL; PURINES;

EID: 84902553494     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-430     Document Type: Article

References (52)

1. Hu J, Zhao X, Yu J. Replication-associated purine asymmetry may contribute to strand-biased gene distribution. Genomics 2007, 90(2):186-194. 10.1016/j.ygeno.2007.04.002, 17532183.
2. Qu H, Wu H, Zhang T, Zhang Z, Hu S, Yu J. Nucleotide compositional asymmetry between the leading and lagging strands of eubacterial genomes. Res Microbiol 2010, 161(10):838-846. 10.1016/j.resmic.2010.09.015, 20868744.
3. Rocha E. Is there a role for replication fork asymmetry in the distribution of genes in bacterial genomes?. Trends Microbiol 2002, 10(9):393-395. 10.1016/S0966-842X(02)02420-4, 12217498.
4. Rocha EP, Danchin A. Gene essentiality determines chromosome organisation in bacteria. Nucleic Acids Res 2003, 31(22):6570-6577. 10.1093/nar/gkg859, 275555, 14602916.
5. Rocha EP, Danchin A. Essentiality, not expressiveness, drives gene-strand bias in bacteria. Nat Genet 2003, 34(4):377-378. 10.1038/ng1209, 12847524.
6. Dervyn E, Suski C, Daniel R, Bruand C, Chapuis J, Errington J, Janniere L, Ehrlich SD. Two essential DNA polymerases at the bacterial replication fork. Science 2001, 294(5547):1716-1719. 10.1126/science.1066351, 11721055.
7. Bao Q, Tian Y, Li W, Xu Z, Xuan Z, Hu S, Dong W, Yang J, Chen Y, Xue Y, Xu Y, Lai X, Huang L, Dong X, Ma Y, Ling L, Tan H, Chen R, Wang J, Yu J, Yang H. A complete sequence of the T. tengcongensis genome. Genome Res 2002, 12(5):689-700. 10.1101/gr.219302, 186588, 11997336.
8. Mira A, Pushker R, Legault BA, Moreira D, Rodriguez-Valera F. Evolutionary relationships of Fusobacterium nucleatum based on phylogenetic analysis and comparative genomics. BMC Evol Biol 2004, 4:50. 10.1186/1471-2148-4-50, 535925, 15566569.
9. Lobry JR, Sueoka N. Asymmetric directional mutation pressures in bacteria. Genome Biol 2002, 3(10):1-14.
10. Charneski CA, Honti F, Bryant JM, Hurst LD, Feil EJ. Atypical AT skew in Firmicute genomes results from selection and not from mutation. PLoS Genet 2011, 7(9):e1002283. 10.1371/journal.pgen.1002283, 3174206, 21935355.
11. Paul S, Million-Weaver S, Chattopadhyay S, Sokurenko E, Merrikh H. Accelerated gene evolution through replication-transcription conflicts. Nature 2013, 495(7442):512-515. 10.1038/nature11989, 3807732, 23538833.
12. Wu H, Qu H, Wan N, Zhang Z, Hu S, Yu J. Strand-biased gene distribution in bacteria is related to both horizontal gene transfer and strand-biased nucleotide composition. Genomics Proteomics Bioinformatics 2012, 10(4):186-196. 10.1016/j.gpb.2012.08.001, 23084774.
13. Zhao X, Zhang Z, Yan J, Yu J. GC content variability of eubacteria is governed by the pol III alpha subunit. Biochem Biophys Res Commun 2007, 356(1):20-25. 10.1016/j.bbrc.2007.02.109, 17336933.
14. Francino MP, Ochman H. Strand asymmetries in DNA evolution. Trends Genet 1997, 13(6):240-245. 10.1016/S0168-9525(97)01118-9, 9196330.
15. Freeman JM, Plasterer TN, Smith TF, Mohr SC. Patterns of genome organization in bacteria. Science 1998, 279(5358):1827-1827.
16. McLean MJ, Wolfe KH, Devine KM. Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes. J Mol Evol 1998, 47(6):691-696. 10.1007/PL00006428, 9847411.
17. McInerney JO. Replicational and transcriptional selection on codon usage in Borrelia burgdorferi. Proc Natl Acad Sci USA 1998, 95(18):10698-10703. 10.1073/pnas.95.18.10698, 27958, 9724767.
18. Romero H, Zavala A, Musto H. Codon usage in Chlamydia trachomatis is the result of strand-specific mutational biases and a complex pattern of selective forces. Nucleic Acids Res 2000, 28(10):2084-2090. 10.1093/nar/28.10.2084, 105376, 10773076.
19. Das S, Paul S, Chatterjee S, Dutta C. Codon and amino acid usage in two major human pathogens of genus Bartonella-optimization between replicational-transcriptional selection, translational control and cost minimization. DNA Res 2005, 12(2):91-102. 10.1093/dnares/12.2.91, 16303741.
20. Das S, Paul S, Dutta C. Evolutionary constraints on codon and amino acid usage in two strains of human pathogenic actinobacteria Tropheryma whipplei. J Mol Evol 2006, 62(5):645-658. 10.1007/s00239-005-0164-6, 16557339.
21. Frank A, Lobry J. Asymmetric substitution patterns: a review of possible underlying mutational or selective mechanisms. Gene 1999, 238(1):65-77. 10.1016/S0378-1119(99)00297-8, 10570985.
22. Lao PJ, Forsdyke DR. Thermophilic bacteria strictly obey Szybalski's transcription direction rule and politely purine-load RNAs with both adenine and guanine. Genome Res 2000, 10(2):228-236. 10.1101/gr.10.2.228, 310832, 10673280.
23. Trifonov E. Translation framing code and frame-monitoring mechanism as suggested by the analysis of mRNA and 16 S rRNA nucleotide sequences. J Mol Biol 1987, 194(4):643-652. 10.1016/0022-2836(87)90241-5, 2443708.
24. Engelen S, Vallenet D, Medigue C, Danchin A. Distinct co-evolution patterns of genes associated to DNA polymerase III DnaE and PolC. BMC Genomics 2012, 13(1):69. 10.1186/1471-2164-13-69, 3814617, 22333191.
25. Bohlin J, Hardy S, Ussery D. Stretches of alternating pyrimidine/purines and purines are respectively linked with pathogenicity and growth temperature in prokaryotes. BMC Genomics 2009, 10(1):346. 10.1186/1471-2164-10-346, 2728739, 19646265.
26. Rapoport AE, Trifonov EN. Excessive Clustering of Third Codon Position Pyrimidines in Prokaryotes. J Biomol Struct Dyn 2008, 25(6):647-653. 10.1080/07391102.2008.10507211, 18399698.
27. Svejstrup JQ. Mechanisms of transcription-coupled DNA repair. Nat Rev Mol Cell Biol 2002, 3(1):21-29. 10.1038/nrm703, 11823795.
28. Baran RH, Ko H, Jernigan RW. Methods for comparing sources of strand compositional asymmetry in microbial chromosomes. DNA Res 2003, 10(3):85-95. 10.1093/dnares/10.3.85, 12886951.
29. Necşulea A, Lobry JR. A new method for assessing the effect of replication on DNA base composition asymmetry. Mol Biol Evol 2007, 24(10):2169-2179. 10.1093/molbev/msm148, 17646257.
30. Sohail A, Hayes CS, Divvela P, Setlow P, Bhagwat AS. Protection of DNA by alpha/beta-type small, acid-soluble proteins from Bacillus subtilis spores against cytosine deamination. Biochemistry 2002, 41(38):11325-11330. 10.1021/bi026332t, 12234173.
31. Setlow P. I will survive: DNA protection in bacterial spores. Trends Microbiol 2007, 15(4):172-180. 10.1016/j.tim.2007.02.004, 17336071.
32. Paredes-Sabja D, Setlow P, Sarker MR. Germination of spores of Bacillales and Clostridiales species: mechanisms and proteins involved. Trends Microbiol 2011, 19(2):85-94. 10.1016/j.tim.2010.10.004, 21112786.
33. Nelson KE, Clayton RA, Gill SR, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Nelson WC, Ketchum KA. Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature 1999, 399(6734):323-329. 10.1038/20601, 10360571.
34. Ludwig W, Schleifer K-H, Whitman WB. Revised road map to the phylum Firmicutes. Bergey's Manual® of Systematic Bacteriology 2009, 1-13. Springer New York.
35. Wolf M, Muller T, Dandekar T, Pollack JD. Phylogeny of Firmicutes with special reference to Mycoplasma (Mollicutes) as inferred from phosphoglycerate kinase amino acid sequence data. Int J Syst Evol Microbiol 2004, 54(3):871-875. 10.1099/ijs.0.02868-0, 15143038.
36. Liang Y, Hou X, Wang Y, Cui Z, Zhang Z, Zhu X, Xia L, Shen X, Cai H, Wang J. Genome rearrangements of completely sequenced strains of Yersinia pestis. J Clin Microbiol 2010, 48(5):1619-1623. 10.1128/JCM.01473-09, 2863931, 20200297.
37. Brown JR, Douady CJ, Italia MJ, Marshall WE, Stanhope MJ. Universal trees based on large combined protein sequence data sets. Nat Genet 2001, 28(3):281-285. 10.1038/90129, 11431701.
38. Brochier C, Philippe H. Phylogeny: a non-hyperthermophilic ancestor for bacteria. Nature 2002, 417(6886):244. 10.1038/417244a, 12015592.
39. Daubin V, Gouy M, Perriere G. A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history. Genome Res 2002, 12(7):1080-1090. 10.1101/gr.187002, 186629, 12097345.
40. Pruitt KD, Tatusova T, Maglott DR. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 2007, 35(suppl 1):D61-D65. 1716718, 17130148.
41. Stothard P, Van Domselaar G, Shrivastava S, Guo A, O'Neill B, Cruz J, Ellison M, Wishart DS. BacMap: an interactive picture atlas of annotated bacterial genomes. Nucleic Acids Res 2005, 33(suppl 1):D317-D320. 540029, 15608206.
42. Arakawa K, Suzuki H, Tomita M. Quantitative analysis of replication-related mutation and selection pressures in bacterial chromosomes and plasmids using generalised GC-skew index. BMC Genomics 2009, 10(1):640. 10.1186/1471-2164-10-640, 2804667, 20042086.
43. Grigoriev A. Analyzing genomes with cumulative skew diagrams. Nucleic Acids Res 1998, 26(10):2286-2290. 10.1093/nar/26.10.2286, 147580, 9580676.
44. Lobry JR. Asymmetric substitution patterns in the two DNA strands of bacteria. Mol Biol Evol 1996, 13(5):660-665. 10.1093/oxfordjournals.molbev.a025626, 8676740.
45. Lobry J. A simple vectorial representation of DNA sequences for the detection of replication origins in bacteria. Biochimie 1996, 78(5):323-326. 10.1016/0300-9084(96)84764-X, 8905151.
46. Sernova NV, Gelfand MS. Identification of replication origins in prokaryotic genomes. Brief Bioinform 2008, 9(5):376-391. 10.1093/bib/bbn031, 18660512.
47. Song J, Ware A, Liu S-L. Wavelet to predict bacterial ori and ter: a tendency towards a physical balance. BMC Genomics 2003, 4(1):17. 10.1186/1471-2164-4-17, 156607, 12732098.
48. Zhang R, Zhang C-T. Identification of replication origins in archaeal genomes based on the Z-curve method. Archaea 2005, 1(5):335-346. 10.1155/2005/509646, 2685548, 15876567.
49. Grigoriev A. Graphical genome comparison: rearrangements and replication origin of Helicobacter pylori. Trends Genet 2000, 16(9):376-378. 10.1016/S0168-9525(00)02087-4, 10973064.
50. Mackiewicz P, Zakrzewska-Czerwinska J, Zawilak A, Dudek MR, Cebrat S. Where does bacterial replication start? Rules for predicting the oriC region. Nucleic Acids Res 2004, 32(13):3781-3791. 10.1093/nar/gkh699, 506792, 15258248.
51. Gao F, Luo H, Zhang C-T. DoriC 5.0: an updated database of oriC regions in both bacterial and archaeal genomes. Nucleic Acids Res 2013, 41(D1):D90-D93. 10.1093/nar/gks990, 3531139, 23093601.
52. Mao X, Zhang H, Yin Y, Xu Y. The percentage of bacterial genes on leading versus lagging strands is influenced by multiple balancing forces. Nucleic Acids Res 2012, 40(17):8210-8218. 10.1093/nar/gks605, 3458553, 22735706.