[1]
|
Kyte, J. and Doolittle, R.F. (1982) A simple method for displaying the hydropathic character of a protein. Journal of Molecular Biology, 157, 105-132.
doi:10.1016/0022-2836(82)90515-0
|
[2]
|
Klein, P., Ka-nehisa, M. and DeLisi, C. (1985) The detection and classification of membrane-spanning proteins. Biochimica et Biophysica Acta-Biomembranes, 815, 468- 476. doi:10.1016/0005-2736(85)90375-X
|
[3]
|
Hirokawa, T., Boon-Chieng, S. and Mitaku, S. (1998) SOSUI: Classification and secondary structure prediction system for membrane proteins. Bioinformatics, 14, 378- 379. doi:10.1093/bioinformatics/14.4.378
|
[4]
|
Nakashima, H. and Kuroda, Y. (2011) Differences in dinucleotide frequencies of thermophilic genes encoding water soluble and membrane proteins. Journal of Zhejiang University-Science B (Biomedicine & Biotechnology), 12, 419-427.
|
[5]
|
Muto, A. and Osawa, S. (1987) The gua-nine and cytosine content of genomic DNA and bacterial evolution. Proceedings of the National Academy of Sciences of the United States of America, 84, 166-169.
doi:10.1073/pnas.84.1.166
|
[6]
|
Lawrence, J.G. and Ochman, H. (1997) Amelioration of bacterial genomes: rates of change and exchange. Journal of Molecular Evolution, 44, 383-397.
doi:10.1007/PL00006158
|
[7]
|
Karlin, S. and Burge, C. (1995) Dinucleotide relative abundance extremes: A ge-nomic signature. Trends in Genetics, 11, 283-290. doi:10.1016/S0168-9525(00)89076-9
|
[8]
|
Karlin, S., Mrázek, J. and Campbell, A.M. (1997) Compositional biases of bacterial genomes and evolutionary implications. Journal of Bacteriology, 179, 3899-3913.
|
[9]
|
Nakashima, H., Ota, M., Nishikawa, K. and Ooi, T. (1998) Gene from nine genomes are separated into their organisms in the dinucleotide composition space. DNA Research, 5, 251- 259. doi:10.1093/dnares/5.5.251
|
[10]
|
Singer, G.A.C. and Hickey, D.A. (2000) Nucleotide bias causes a genome-wide bias in the amino acid composition of proteins. Molecular Biology and Evolution, 17, 1581-1588. doi:10.1093/oxfordjournals.molbev.a026257
|
[11]
|
Bharanidharan, D., Bhargavi, G.R., Uthanumallian, K. and Gau-tham, N. (2004) Correlations between nucleotide frequencies and amino acid composition in 115 bacterial species. Biochemical and Biophysical Research Communications, 315, 1097-1103.
doi:10.1016/j.bbrc.2004.01.129
|
[12]
|
Hu, J., Zhao, X., Zhang, Z. and Yu, J. (2007) Compositional dynamics of guanine and cytochine content in prokaryotic genomes. Research in Microbiology, 158, 363- 370. doi:10.1016/j.resmic.2007.02.007
|
[13]
|
Lobry, J.R. (1997) Influence of genomic G+C content on average aminoacid composition of proteins from 59 bacterial species. Gene, 205, 309-316.
doi:10.1016/S0378-1119(97)00403-4
|
[14]
|
Kumar, S., Tsai, C.J. and Nussinov, R. (2000) Factors enhancing protein thermostability. Protein Engineering, 13, 179-191. doi:10.1093/protein/13.3.179
|
[15]
|
Kreil, D.P. and Ou-zounis, C.A. (2001) Identification of thermophilic species by the amino acid compositions deduced from their genomes. Nucleic Acids Research, 29, 1608-1615. doi:10.1093/nar/29.7.1608
|
[16]
|
Farias, S.T. and Bonato, M.C.M. (2003) Preferred amino acids and thermostability. Genetics and Molecular Research, 2, 383-393.
|
[17]
|
Yokota, K., Satou, K. and Ohki, S. (2006) Comparative analysis of protein thermostability: Differences in amino acid content and substitution at the surfaces and in the core regions of thermophilic and mesophilic proteins. Science and Technology of Advanced Materials, 7, 255-262. doi:10.1016/j.stam.2006.03.003
|
[18]
|
Zhou, X.-X., Wang, Y.-B., Pan, Y.-J. and Li, W.-F. (2008) Differences in amino acids composition and coupling patterns between mesophilic and thermophilic proteins. Amino Acids, 34, 25-33. doi:10.1007/s00726-007-0589-x
|
[19]
|
Fukuchi, S., Yoshimune, K., Wakayama, M., Moriguchi, M. and Ni-shikawa, K. (2003) Unique amino acid composition of proteins in halophilic bacteria. Journal of Molecular Biology, 327, 347-357.
doi:10.1016/S0022-2836(03)00150-5
|
[20]
|
Kawarabayasi, Y., Hino, Y., Horikawa, H., Jin-no, K., Takahashi, M., Sekine, M., Baba, S., Ankai, A., Kosugi, H., Hosoyama, A., Fukui, S., Nagai, Y., Nishijima, K., Otsuka, R., Nakazawa, H., Takamiya, M., Kato, Y., Yoshizawa, T., Tanaka, T., Kudoh, Y., Yamazaki, J., Kushida, N., Oguchi, A., Aoki, K., Masuda, S., Yanagii, M., Nishimura, M., Yamagishi, A., Oshima, T. and Kikuchi, H. (2001) Complete genome sequence of an aerobic thermoacidophilic crenarchaeon, Sulfolobus tokodaii strain 7. DNA Research, 8, 123-140.
doi:10.1093/dnares/8.4.123
|
[21]
|
Klenk, H.-P., Clayton, R.A., Tomb, J.-F., White, O., Nelson, K.E., Ketchum, K.A., Dodson, R.J., Gwinn, M., Hickey, E.K., Peterson, J.D., Richardson, D.L., Kerlavage, A.R., Graham, D.E., Kyrpides, N.C., Fleischmann, R.D., Quackenbush, J., Lee, N.H., Sutton, G.G., Gill, S., Kirkness, E.F., Dougherty, B.A., McKenney, K., Adams, M.D., Loftus, B., Peterson, S., Reich, C.I., McNeil, L.K., Badger, J.H., Glodek, A., Zhou, L., Overbeek, R., Gocayne, J.D., Weidman, J.F., McDonald, L., Utterback, T., Cotton, M.D., Spriggs, T., Artiach, P., Kaine, B.P., Sykes, S.M., Sadow, P.W., D’Andrea, K.P., Bowman, C., Fujii, C., Garland, S.A., Mason, T.M., Olsen, G.J., Fraser, C.M., Smith, H.O., Woese, C.R. and Venter, J.C. (1997) The complete ge-nome sequence of the hyperthermophilic, sul-phate-reducing archaeon Archaeoglobus fulgidus. Nature, 390, 364-370. doi:10.1038/37052
|
[22]
|
Slesarev, A.I., Mezhevaya, K.V., Makarova, K.S., Polushin, N.N., Sh-cherbinina, O.V., Shakhova, V.V., Belova, G.I., Aravind, L., Natale, D.A., Rogozin, I.B., Tatusov, R.L., Wolf, Y.I., Stetter, K.O., Malykh, A.G., Koonin, E.V. and Kozyavkin, S.A. (2002) The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens. Proceedings of the National Academy of Sciences of the United States of America, 99, 4644-4649.
doi:10.1073/pnas.032671499
|
[23]
|
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. (2002) A complete sequence of the T. tengcongensis ge-nome. Genome Research, 12, 689-700. doi:10.1101/gr.219302
|
[24]
|
Nelson, K.E., Clayton, R.A., Gill, S.R., Gwinn, M.L., Dodson, R.J., Haft, D.H., Hick-ey, E.K., Peterson, J.D., Nelson, W.C., Ketchum, K.A., McDonald, L., Utterback, T.R., Malek, J.A., Linher, K.D., Garrett, M.M., Stewart, A.M., Cotton, M.D., Pratt, M.S., Phillips, C.A., Richardson, D., Heidelberg, J., Sutton, G.G., Fleischmann, R.D., Eisen, J.A., White, O., Salzberg, S.L., Smith, H.O., Venter, J.C. and Fraser, C.M. (1999) Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima. Nature, 399, 323-329.
doi:10.1038/20601
|
[25]
|
Fricke, W.F., Seedorf, H., Henne, A., Krüer, M., Liesegang, H., Hedderich, R., Gottschalk, G. and Thauer, R.K. (2006) The genome sequence of Methanosphaera stad-tmanae reveals why this human intestinal archaeon is restricted to methanol and H2 for methane formation and ATP synthesis. Journal of Bacteriology, 188, 642-658.
doi:10.1128/JB.188.2.642-658.2006
|
[26]
|
Anderson, I., Ulrich, L.E., Lupa, B., Susanti, D., Porat, I., Hooper, S.D., Lykidis, A., Sieprawska-Lupa, M., Dharmarajan, L., Goltsman, E., Lapidus, A., Saunders, E., Han, C., Land, M., Lucas, S., Mukhopadhyay, B., Whitman, W.B., Woese, C., Bristow, J. and Kyrpides, N. (2009) Genomic characterization of methanomicrobiales reveals three classes of methanogens. PLoS One, 4, 1-9.
doi:10.1371/journal.pone.0005797
|
[27]
|
Ng, W.V., Ken-nedy, S.P., Mahairas, G.G., Berquist, B., Pan, M., Shukla, H.D., Lasky, S.R., Baliga, N.S., Thorsson, V., Sbrogna, J., Swartzell, S., Weir, D., Hall, J., Dahl, T.A., Welti, R., Goo, Y.A., Leithauser, B., Keller, K., Cruz, R., Danson, M.J., Hough, D.W., Maddocks, D.G., Jablonski, P.E., Krebs, M.P., Angevine, C.M., Dale, H., Isenbarger, T.A., Peck, R.F., Pohlshroder, M., Spudich, J.L., Jung, K-H., Alam, M., Freitas, T., Hou, S., Daniels, C.J., Dennis, P.P., Omer, A.D., Ebhardt, H., Lowe, T.M., Liang, P., Riley, M., Hood, L. and DasSarma S. (2000) Genome sequence of Halobacterium species NRC-1. Proceedings of the National Academy of Sciences of the United States of America, 97, 12176-12181.
doi:10.1073/pnas.190337797
|
[28]
|
Fleischmann, R.D., Adams, M.D., White, O., Clayton, R.A., Kirkness, E.F., Kerlavage, A.R., Bult, C.J., Tomb, J.-F., Dougherty, B.A., Merrick, J.M., Mckenney, K., Sutton, G., FitzHugh, W., Fields, C., Gocayne, J.D., Scott, J., Shirley, R., Liu, L.-I., Glodek, A., Kelley, J.M., Weidman, J.F., Philips, C.A., Spriggs, T., Hedbolm, E., Cotton, M.D., Utterback, T.R., Hanna, M.C., Nguyen, D.T., Saudek, D.M., Brandon, R.C., Fine, L.D., Fritchman, J.L., Fuhrmann, J.L., Geog-hagen, N.S.M., Gnehm, C.L., McDonald, L.A., Small, K.V., Fraser, C.M., Smith, H.O. and Venter, J.C. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae rd. Science, 269, 496-512. doi:10.1126/science.7542800
|
[29]
|
Blattner, F.R., Plunkett, G.III., Bloch, C.A., Perna, N.T., Burland, V., Riley, M., Collado-Vides, J., Glasner, J.D., Rode, C.K., Mayhew, G.F., Gregor, J., Davis, N.W., Kirkpatrick, H.A., Goeden, M.A., Rose, D.J., Mau, B. and Shao, Y. (1997) The complete genome sequence of Escherichia coli K-12. Science, 277, 1453-1462.
doi:10.1126/science.277.5331.1453
|
[30]
|
Stover, C.K., Pham, X.Q., Erwin, A.L., Mizoguchi, S.D., Warrener, P., Hickey, M.J., Brinkman, F.S.L., Hufnagle, W.O., Kowalik, D.J., Lagrou, M., Garber, R.L., Goltry, L., Tolentino, E., Westbrock-Wadman, S., Yuan, Y., Brody, L.L., Coulter, S.N., Folger, K.R., Kas, A., Larbig, K., Lim, R., Smith, K., Spencer, D., Wong, G.K.-S., Wu, Z., Paulsen, I.T., Reizer, J., Saier, M.H., Hancock, R.E.W., Lory, S. and Olson, M.V. (2000) Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen. Nature, 406, 959-964.
doi:10.1038/35023079
|
[31]
|
Kawabata, T., Fukuchi, S., Homma, K., Ota, M., Araki, J., Ito, T., Ichiyoshi, N. and Nishikawa, K. (2002) GTOP: A database of protein structures predicted from genome sequences. Nucleic Acids Research, 30, 294-298.
doi:10.1093/nar/30.1.294
|
[32]
|
Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) Basic local alignment search tool. Journal of Molecular Biology, 215, 403-410.
|
[33]
|
Wilquet, V. and Van de Casteele, M. (1999) The role of the codon first letter in the relationship between genomic GC content and protein amino acid composition. Research in Microbiology, 150, 21-32.
doi:10.1016/S0923-2508(99)80043-6
|
[34]
|
Nakashima, H., Fukuchi, S. and Nishikawa, K. (2003) Compositional changes in RNA, DNA and proteins for bacterial adaptation to higher and lower temperatures. The Journal of Biochemistry, 133, 507-513.
doi:10.1093/jb/mvg067
|
[35]
|
Jaenicke, R. and B?hm, G. (1998) The stability of proteins in extreme environments. Current Opinion in Structural Biology, 8, 738-748.
doi:10.1016/S0959-440X(98)80094-8
|
[36]
|
Barrel, B.G., Anderson, S., Bankier, A.T., de Bruijn, M.H.L., Chen, E., Coulson, A.R., Drouin, J., Eperon, I.C., Nerlich, D.P., Roe, B.A., Sanger, F., Schreier, P.H., Smith, A.J.H., Sta-den, R. and Young I.G. (1980) Different pattern of codon recognition by mammalian mitochondrial tRNAs. Proceedings of the National Academy of Sciences of the United States of America, 77, 3164- 3166. doi:10.1073/pnas.77.6.3164
|
[37]
|
Nakashima, H., Nishi-kawa, K. and Ooi, T. (1990) Distinct character in hydrophobicity of amino acid compositions of mitochondrial proteins. Proteins, 8, 173-178.
doi:10.1002/prot.340080207
|
[38]
|
Chargaff, E., Lipshitz, R., Green, C. and Hodes, M.E. (1951) The composition of the desoxyribonucleic acid of salmon sperm. The Journal of Biological Chemistry, 192, 223-230.
|
[39]
|
Chargaff, E., Lipshitz, R. and Green, C. (1952) Composition of the desoxypentose nucleic acids of four genera of sea-urchin. The Journal of Biological Chemistry, 195, 155-160.
|
[40]
|
Karkas, J.D., Runder, R. and Chargaff, E. (1968) Separation of B. subtilis DNA into complementary strands, II. Template functions and composition as determined by transcription with RNA polymerase. Proceedings of the National Academy of Sciences of the United States of America, 60, 915-920. doi:10.1073/pnas.60.3.915
|
[41]
|
Runder, R., Karkas, J.D. and Chargaff, E. (1968) Separation of B. subtilis DNA into complementary strands, III. Direct analysis. Proceedings of the National Academy of Sciences of the United States of America, 60, 921-922.
doi:10.1073/pnas.60.3.921
|
[42]
|
Mitchell, D. and Bridge, R. (2006) A test of Chargaff’s second rule. Biochemical and Biophysical Research Com- munications, 340, 90-94. doi:10.1016/j.bbrc.2005.11.160
|
[43]
|
King, J.L. and Jukes, T.H. (1969) Non-Darwinian evolution. Science, 164, 788-798.
doi:10.1126/science.164.3881.788
|
[44]
|
Lutsenko, E. and Bhagwat, A.S. (1999) Principal causes of hot spots for cytosine to thymine mutations at sites of cytosine methy-lation in growing cells: A model, its experimental support and implications. Mutation Research, 437, 11-20. doi:10.1016/S1383-5742(99)00065-4
|