同义密码子重复序列中密码子的使用与比较
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摘要
本论文共分三部分:
第一部分通过对大肠杆菌编码序列中同义密码子重复序列的研究,分析了同义密码子重复序列与全部编码序列中密码子使用的差异:发现部分密码子在同义密码子重复序列中的使用与在全序列中的使用存在很大的差异;同义密码子4重复片段中相同密码子重复有明显的位置偏好,在同义密码子重复序列中,部分密码子的使用与基因表达水平有关。
第二部分以6种模式生物闪烁古生球菌、枯草杆菌、大肠杆菌、酿酒酵母、线虫和拟南芥基因组中编码序列所翻译的氨基酸序列为样本,研究氨基酸重复序列中氨基酸的使用情况。给出了不同长度氨基酸重复片段数目的分布规律以及与生物进化的关系,得到了氨基酸重复序列中氨基酸含量随联体长度的变化趋势,以及氨基酸联体最大长度的分布与氨基酸疏亲水、体积和极性的关系。
第三部分通过上述6种生物基因组中编码序列的分析,得到关于密码子在同义密码子重复序列中的一些基本性质。结果表明一部分密码子在同义密码子重复序列中的使用与其在全编码序列中明显不同。给出了密码子的联体能力,发现密码子的联体能力各不相同,尤其对于同一个碱基构成的密码子,它们的联体能力低。在同义密码子重复序列中相同的密码子重复片段有非常明显的位置偏好。最后讨论了这些性质与基因组进化的关系。
In the first part, based on the synonymous codon repeat sequences of E.coli coding sequences, the difference of codon usage is analyzed between synonymous codon repeat sequences and all coding sequences. Compared with all of the coding sequences, we find that the codon usage has distinct difference for some codons in synonymous codon repeat sequences; the same codon repeats have the position bias in 4 synonymous codon repeat segments; some codons' usage is correlated with the gene expression levels in synonymous codon repeat segments.In the second part: based on the amino acid sequences which translated by coding sequence in six genomes, which are Archaeoglobus fulgidus Bacillus subtilis Escherichia coli Saccharomyces cerevisiae Caenorhabditis elegans and
Arabidopsis thaliana, the amino acid usage in amino acid repeat sequences is discussed. The distribution of amino acid repeat segment numbers with its repeat lengh is given. We find that the distributions are correlated with genome evolution and the amino acid content is changed with the amino acid repeat lengh. Furthermore, we find that the maximum lenghs of amino acid repeat are affected by the hydrophobicity and hydrophilicity and amino acid volume as well as the polarity of amino acid.In the third part, by using the coding sequences of the six genomes (shown above), some basic characters about the codon usage in synonymous codon repeat sequences are analyzed. The results show that some codons' usage in synonymous codon repeat sequences is different from the codon usage in all coding sequences; and the characteristic of codon repeat ability is given. We find that codon repeat ability is different, especially, for same base repeat codons, its repeat ability is low. There is distinct position bias for the same codon repeat segments in synonymous codon repeat sequences. Finally, we discuss the relationship of those characters with genome evolution.
第一部分通过对大肠杆菌编码序列中同义密码子重复序列的研究,分析了同义密码子重复序列与全部编码序列中密码子使用的差异:发现部分密码子在同义密码子重复序列中的使用与在全序列中的使用存在很大的差异;同义密码子4重复片段中相同密码子重复有明显的位置偏好,在同义密码子重复序列中,部分密码子的使用与基因表达水平有关。
第二部分以6种模式生物闪烁古生球菌、枯草杆菌、大肠杆菌、酿酒酵母、线虫和拟南芥基因组中编码序列所翻译的氨基酸序列为样本,研究氨基酸重复序列中氨基酸的使用情况。给出了不同长度氨基酸重复片段数目的分布规律以及与生物进化的关系,得到了氨基酸重复序列中氨基酸含量随联体长度的变化趋势,以及氨基酸联体最大长度的分布与氨基酸疏亲水、体积和极性的关系。
第三部分通过上述6种生物基因组中编码序列的分析,得到关于密码子在同义密码子重复序列中的一些基本性质。结果表明一部分密码子在同义密码子重复序列中的使用与其在全编码序列中明显不同。给出了密码子的联体能力,发现密码子的联体能力各不相同,尤其对于同一个碱基构成的密码子,它们的联体能力低。在同义密码子重复序列中相同的密码子重复片段有非常明显的位置偏好。最后讨论了这些性质与基因组进化的关系。
In the first part, based on the synonymous codon repeat sequences of E.coli coding sequences, the difference of codon usage is analyzed between synonymous codon repeat sequences and all coding sequences. Compared with all of the coding sequences, we find that the codon usage has distinct difference for some codons in synonymous codon repeat sequences; the same codon repeats have the position bias in 4 synonymous codon repeat segments; some codons' usage is correlated with the gene expression levels in synonymous codon repeat segments.In the second part: based on the amino acid sequences which translated by coding sequence in six genomes, which are Archaeoglobus fulgidus Bacillus subtilis Escherichia coli Saccharomyces cerevisiae Caenorhabditis elegans and
Arabidopsis thaliana, the amino acid usage in amino acid repeat sequences is discussed. The distribution of amino acid repeat segment numbers with its repeat lengh is given. We find that the distributions are correlated with genome evolution and the amino acid content is changed with the amino acid repeat lengh. Furthermore, we find that the maximum lenghs of amino acid repeat are affected by the hydrophobicity and hydrophilicity and amino acid volume as well as the polarity of amino acid.In the third part, by using the coding sequences of the six genomes (shown above), some basic characters about the codon usage in synonymous codon repeat sequences are analyzed. The results show that some codons' usage in synonymous codon repeat sequences is different from the codon usage in all coding sequences; and the characteristic of codon repeat ability is given. We find that codon repeat ability is different, especially, for same base repeat codons, its repeat ability is low. There is distinct position bias for the same codon repeat segments in synonymous codon repeat sequences. Finally, we discuss the relationship of those characters with genome evolution.
引文
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[2] 贾弘缇.人类基因超过14万[J].生命的化学,2000,20(2):49.
[3] 李璞.人类基因组计划[J].科学前沿,2000,51(4):11-15.
[4] Rowen L., Mahairas G., Hood L. Sequencing the human genomes [J]. Science, 1997, 278(5338): 605-607.
[5] 罗辽复.生命进化的物理观[M].上海:上海科技出版社,2000:56-127.
[6] Knight R.D., Freeland S. I., Landweber L. F. Selection, history and chemistry: the three faces of the genetic code [J]. Trends Biochem. Sci. 1999, 24: 241-247.
[7] Di GiuIio M. On the origin of the genetic code [J]. J.theo.Biol. 1997, 187: 573-581.
[8] Grocock, Russell J., Sharp, P.M. Synonymous codon usage in Pseudo-monas aeruginosa PA01 [J]. Gene, 2002, 2590-2): 131-139.
[9] Adam, Rodney D. The Giardia lamblia genome [J]. International Journal for Parasitology, 2000, 30(4): 475-484.
[10] Sueoka, Noboru, Kawanishi, Yuichi. DNA G+C content of the third codon position and codon usage biases of human genes [J]. Gene, 2000, 261(1): 33-62.
[11] D'Onfrio G., Mouchiroud D., Aissani B., et al. Correlation betweem the compositional propertied of human genes, codon usage, and amino acid composition of protein [J]. J Mol Evol, 1991, 32(5): 504-510.
[12] Grigoriev, Andrei. Strand-specific compositional asymmetries in double-stranded DNA viruses[J]. Yirus Research, 1999, 60(1): 1-19.
[13] McLean M.J., Wolfe K.H., Devine K.M.. Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes [J]. J. Mol. Evol. 1998, 47: 691-695.
[14] Ghosh T. Studies on codon usage in Entamocba histolytica [J]. International Journal of Parasitology, 2000, 30: 715-722.
[15] Karlin S., Mrazek J. What drives codon choices in human genes [J]. Journal of Molecular Biology, 1995, 252: 459-472.
[16] Gupta S.K., Ghosh T.C. Gene expressivity is the main factor indictating the codon usage variation among the genes in Pseudomonas aeruginso [J]. Gene, 2001, 273: 63-70.
[17] Marais G., Duret L. Synonymous Codon Usage, Accuracy of Translation and Gene Length in Caenorhabditis elegan [J]. J. Mol Evol. 2001, 52: 275-280.
[18] 赵翔,李至,陆身枫,等.酵母Yanowia lipolytica 的密码子用法分析[J].复旦大学学报(自然科学版),1999,10:510-516.
[19] Sharp EM. and Devine K.M.. Codon usage and geng expression level in Dictostelium discoideum: Highly expressed genes do'prefer' optimal eodons [J]. Nucleic Acids Research, 1989, 17(13): 5029-5039.
[20] Grantham R., Gautier C., Gouy M., et al. Codon catalog usage and the genome hypothesis [J]. Nucleic Acids Research, 1980, 8:49r-62r.
[21] Grantham R, Gautier C, Gouy M, et al. Codon catalog usage is a genome strategy modulated for gene expressivity [J]. Nucleic Acids Research, 1981, 9: 43r-74r.
[22] Gouy M., Gautier C. Codon usage in bacteria: correlation with gene expressivity [J]. Nucleic Acids Research, 1982, 10: 7055-7074.
[23] 李宏,罗辽复.基因表达水平与同义密码子使用关系的初步研究[J].生物物理学报,1995,11(2):237-244.
[24] Carlini D.B., Chen Y., Stephan W. The relationship between third-codon position nueleotide content, eodon bias, mRNA secondary structure and gene expression in the drosophild alcohol dehydrogenase genes Adh and Adhr [J]. Genetics, 2001, 159(2): 623-633.
[25] Sajau H., W ashio T., Saito R. et al. Correlation between sequence conservation of the 5' untranslated region and codon usage bias in Musmusculus genes[J]. Gene, 2001,276(1-2):101-105.
[26] Stenstrm C. M., Jin H.N., Major L. L., et al. Codon bias at the 3' -side of the initiation codon is correlated with translation initiation efficiency in Escherichia coli [J]. Gene, 2001, 263(1-2): 273-284.
[27] Fedorov A., Saxonov S., Gilhert W. Regularities of eontex-dependent codon bias in eukaryotie genes [J]. Nucleic Acids Res, 2002, 30(5): 1192-1197.
[28] Ohno S. Universal role for coding sequence construction: TA/GC deficiency- TG/CT excess [J]. Proc Natl Acad SciUSA, 1988, 85(24): 9530-9534.
[29] Karlin S. Campbell A. M., Mrazek J. Comparative DNA analysis across diverse genomes [J]. Annu Rev Genetics, 1998, 32: 185-225.
[30] 石秀凡,黄京飞,柳树群,等.人类基因同义密码子偏好的特征以及与基因GC含量的关系[J].生物化学与生物物理进展,2002,29(3):411-414.
[31] Rodriguez Trelles E, Tarrio R., Ayala F.J. Switch in codon bias and increased rates of Amino Acid substitution in the Drosophila saltans species group [J]. Genetics, 1999, 153(1): 339-350.
[32] Modyama E. N., Powell J. R. Gene length and codon usage bias in Drosophila melanogaster, Saccha romyces cerevisiae and Escherichia coli [J]. Nucleic Acids Res, 1998, 26(13): 3188-3193.
[33] Moriyama E. N., Powell J. R. Codon usage bias and tRNA abundance in Drosophila [J]. J MolEvol, 1997, 45(5): 514-523.
[34] Moszer I., Rocha E. P. C, Danchin A. Codon usage and lateral gene transfer in Bacillvs subtilis [J]. Current Opinion in Microbiology, 1999, 2(5): 524-528.
[35] 顾万君,马建民,周童,等.不同结构的蛋白质编码基因的密码子偏性研究[J].生物物理学报,2002,18(1):81-86.
[36] 石秀凡,黄京飞,梁宠荣,等.人类基因中同义密码子的偏好与密码子—反密码子间的结合强度密切相关吗?[J].科学通报,2000,45(23):2520—2525.
[37] Morton B R. Selection on the codon bias of chloroplast and cyanelle genes in different plant and algal lineages [J]. JMol Evol, 1998, 46(4): 449-459.
[38] Sharp, P.M. & Li, W.H. The codon adaptation index: a measure of directional synonymous codon bias and its potential application [J]. Nucl.Acid Res, 1987, 15: 1281-1295.
[39] Bermetzen, J.L. & Hall, B.D. Codon selection in yeast [J]. The Journal of Biological Chemistry, 1981, 257: 3026-3031.
[40] Warrick H M., Spudich J A. Codon preference in Dictyostelium discoideum [J]. Nucleic Acids Res, 1988, 16(14): 6617-6635.
[41] Wright F. The 'effective number of codons'used in a gene [J]. Gene, 1990, 87: 23-29.
[42] Ikemura T. Correlation between the abundance of Eschefichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E.coli system [J]. Journal of Molecular Biology, 1981,151:389-409
[43] Sharp P. M., Stenico M., Peden J. F. et al. Codon usage: mutational bias, teranslational selection, on both? [J]. Biochem. Soc Trans. 1993,21:835-841.
[44] Ohno, H., Sakai, H., Washio, T., Tomita, M.. Preferential usage of some minor codons in bacteria [J]. Gene, 2001,276(1-2): 107-115.
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