Compositional dynamics of guanine and cytosine content in prokaryotic genomes

Research in Microbiology

Volumn 158, Issue 4, 2007, Pages 363-370

  Hu, Jianfei ^a,b   Zhao, Xiaoqian ^b,d   Zhang, Zhang ^b,c,d   Yu, Jun ^b,c,e  

^a PEKING UNIVERSITY   (China)

^b Chinese Academy of Sciences and China National Center for Bioinformation   (China)

^c INSTITUTE OF COMPUTING TECHNOLOGY   (China)

^d UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^e ZHEJIANG UNIVERSITY   (China)

Author keywords

Codon positions (GC1, GC2 and GC3); GC content gradient (Gd); Genomic GC content (gGC)

Indexed keywords

AMINO ACID; CYTOSINE; GUANINE;

AMINO ACID ANALYSIS; ARCHAEBACTERIUM; ARTICLE; BACILLUS ANTHRACIS; BACTERIAL GENOME; BACTERIUM; CALCULATION; CODON; CORRELATION ANALYSIS; DEINOCOCCUS RADIODURANS; GENOME ANALYSIS; MOLECULAR DYNAMICS; NITROSOMONAS EUROPAEA; NONHUMAN; PRIORITY JOURNAL; PROKARYOTE;

AMINO ACIDS; BASE COMPOSITION; CODON; CYTOSINE; GENES, BACTERIAL; GENOME, BACTERIAL; GUANINE; PROKARYOTIC CELLS;

PROKARYOTA;

EID: 34249341112     PISSN: 09232508     EISSN: 17697123     Source Type: Journal    
DOI: 10.1016/j.resmic.2007.02.007     Document Type: Article

References (33)

1. Akman L., Yamashita A., Watanabe H., Oshima K., Shiba T., Hattori M., and Aksoy S. Genome sequence of the endocellular obligate symbiont of tsetse flies, Wigglesworthia glossinidia. Nat. Genet. 32 (2002) 402-407
2. 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., and Yang H. A complete sequence of the T. tengcongensis genome. Genome Res. 12 (2002) 689-700
3. Bentley S.D., Chater K.F., Cerdeno-Tarraga A.M., Challis G.L., Thomson N.R., James K.D., Harris D.E., Quail M.A., Kieser H., Harper D., Bateman A., Brown S., Chandra G., Chen C.W., Collins M., Cronin A., Fraser A., Goble A., Hidalgo J., Hornsby T., Howarth S., Huang C.H., Kieser T., Larke L., Murphy L., Oliver K., O'Neil S., Rabbinowitsch E., Rajandream M.A., Rutherford K., Rutter S., Seeger K., Saunders D., Sharp S., Squares R., Squares S., Taylor K., Warren T., Wietzorrek A., Woodward J., Barrell B.G., Parkhill J., and Hopwood D.A. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417 (2002) 141-147
4. Bentley S.D., and Parkhill J. Comparative genomic structure of prokaryotes. Annu. Rev. Genet. 38 (2004) 771-792
5. Chargaff E. Structure and function of nucleic acids as cell constituents. Fed. Proc. 10 (1951) 654-659
6. Chargaff E. How genetics got a chemical education. Ann. N.Y. Acad. Sci. 325 (1979) 344-360
7. Foster P.G., Jermiin L.S., and Hickey D.A. Nucleotide composition bias affects amino acid content in proteins coded by animal mitochondria. J. Mol. Evol. 44 (1997) 282-288
8. Galtier N., Tourasse N., and Gouy M. A nonhyperthermophilic common ancestor to extant life forms. Science 283 (1999) 220-221
9. Green P., Ewing B., Miller W., Thomas P.J., and Green E.D. Transcription-associated mutational asymmetry in mammalian evolution. Nat. Genet. 33 (2003) 514-517
10. Grigoriev A. Analyzing genomes with cumulative skew diagrams. Nucleic Acids Res. 26 (1998) 2286-2290
11. Gu X., Hewett-Emmett D., and Li W.H. Directional mutational pressure affects the amino acid composition and hydrophobicity of proteins in bacteria. Genetica 102-103 (1998) 383-391
12. Hagstrom A., Pommier T., Rohwer F., Simu K., Stolte W., Svensson D., and Zweifel U.L. Use of 16S ribosomal DNA for delineation of marine bacterioplankton species. Appl. Environ. Microbiol. 68 (2002) 3628-3633
13. Hooper S.D., and Berg O.G. Gradients in nucleotide and codon usage along Escherichia coli genes. Nucleic Acids Res. 28 (2000) 3517-3523
14. Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.K., Codani J.J., Connerton I.F., Danchin A., et al. The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature 390 (1997) 249-256
15. Li W.H. Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol. 36 (1993) 96-99
16. Lobry J.R. Properties of a general model of DNA evolution under no-strand-bias conditions. J. Mol. Evol. 40 (1995) 326-330
17. Lobry J.R. Asymmetric substitution patterns in the two DNA strands of bacteria. Mol. Biol. Evol. 13 (1996) 660-665
18. Musto R., Bigotti M.G., Travaglini-Allocatelli C., Brunori M., and Cutruzzola F. Folding of Aplysia limacina apomyoglobin involves an intermediate in common with other evolutionarily distant globins. Biochemistry 43 (2004) 230-236
19. NCBI.
20. Nei M., and Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3 (1986) 418-426
21. Nomura M. Engineering of bacterial ribosomes: replacement of all seven Escherichia coli rRNA operons by a single plasmid-encoded operon. Proc. Natl. Acad. Sci. U.S.A. 96 (1999) 1820-1822
22. Rocap G., Larimer F.W., Lamerdin J., Malfatti S., Chain P., Ahlgren N.A., Arellano A., Coleman M., Hauser L., Hess W.R., Johnson Z.I., Land M., Lindell D., Post A.F., Regala W., Shah M., Shaw S.L., Steglich C., Sullivan M.B., Ting C.S., Tolonen A., Webb E.A., Zinser E.R., and Chisholm S.W. Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 424 (2003) 1042-1047
23. Singer G.A., and Hickey D.A. Nucleotide bias causes a genomewide bias in the amino acid composition of proteins. Mol. Biol. Evol. 17 (2000) 1581-1588
24. Sueoka N. Correlation between base composition of deoxyribonucleic acid and amino acid composition of protein. Proc. Natl. Acad. Sci. U.S.A. 47 (1961) 1141-1149
25. Sueoka N. Intrastrand parity rules of DNA base composition and usage biases of synonymous codons. J. Mol. Evol. 40 (1995) 318-325
26. Svejstrup J.Q. Mechanisms of transcription-coupled DNA repair. Nat. Rev. Mol. Cell Biol. 3 (2002) 21-29
27. Sweder K.S., Verhage R.A., Crowley D.J., Crouse G.F., Brouwer J., and Hanawalt P.C. Mismatch repair mutants in yeast are not defective in transcription-coupled DNA repair of UV-induced DNA damage. Genetics 143 (1996) 1127-1135
28. Wada A., Suyama A., and Hanai R. Phenomenological theory of GC/AT pressure on DNA base composition. J. Mol. Evol. 32 (1991) 374-378
29. Wada A., Tachibana H., Gotoh O., and Takanami M. Long range homogeneity of physical stability in double-stranded DNA. Nature 263 (1976) 439-440
30. Wong G.K., Wang J., Tao L., Tan J., Zhang J., Passey D.A., and Yu J. Compositional gradients in Gramineae genes. Genome Res. 12 (2002) 851-856
31. Yang Z., and Nielsen R. Synonymous and nonsynonymous rate variation in nuclear genes of mammals. J. Mol. Evol. 46 (1998) 409-418
32. Yu J., Hu S., Wang J., Wong G.K., Li S., Liu B., Deng Y., Dai L., Zhou Y., Zhang X., Cao M., Liu J., Sun J., Tang J., Chen Y., Huang X., Lin W., Ye C., Tong W., Cong L., Geng J., Han Y., Li L., Li W., Hu G., Huang X., Li W., Li J., Liu Z., Li L., Liu J., Qi Q., Liu J., Li L., Li T., Wang X., Lu H., Wu T., Zhu M., Ni P., Han H., Dong W., Ren X., Feng X., Cui P., Li X., Wang H., Xu X., Zhai W., Xu Z., Zhang J., He S., Zhang J., Xu J., Zhang K., Zheng X., Dong J., Zeng W., Tao L., Ye J., Tan J., Ren X., Chen X., He J., Liu D., Tian W., Tian C., Xia H., Bao Q., Li G., Gao H., Cao T., Wang J., Zhao W., Li P., Chen W., Wang X., Zhang Y., Hu J., Wang J., Liu S., Yang J., Zhang G., Xiong Y., Li Z., Mao L., Zhou C., Zhu Z., Chen R., Hao B., Zheng W., Chen S., Guo W., Li G., Liu S., Tao M., Wang J., Zhu L., Yuan L., and Yang H. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296 (2002) 79-92
33. Zamyatnin A.A. Protein volume in solution. Prog. Biophys. Mol. Biol. 24 (1972) 107-123