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A. thaliana Protein Abundance Analysis Coresponding with Elongation Efficiency
WANG Xi-guang, WANG Juan, ZHANG Lin
China Biotechnology ›› 2017, Vol. 37 ›› Issue (2) : 40-47.
PDF(651 KB)
PDF(651 KB)
A. thaliana Protein Abundance Analysis Coresponding with Elongation Efficiency
Protein synthesis is a complex dynamic process, its abundance is a final measurement of gene expression level. Functional important proteins are always highly expressed in most of tissues. The protein abundance of A. thaliana from PaxDB database and computed translation elongation index (ITE and CAI) of protein coding genes of A. thaliana by both DAMBE and codon W were compiled, and the correlation between protein abundance and translation elongation efficiency was analysed,especially used logarithm in the analysis. The results showed that ITE is better than orignal CAI to analysis, high expressed genes have similar expression level in different tissues in A. thaliana and there was clear correlation between protein abundance and ITE in A. thaliana.
ITE / Protein abundance / Elongation efficiency / Gene expression / CAI / Correlation analysis / A. thaliana {{custom_keyword}} /
[1] 李定辰, 杨冬, 姜颖, 等. 蛋白质丰度调控及整体分布的规律性认识. 中国科学生命科学, 2013, 43(1):54-62. Li D C, Yang D, Jiang Y, et al. Insights into the regular patterns of protein abundance regulation and distribution. Scientia Sinica Vitae, 2013, 43(1):54-62.
[2] Marquerat S, Schmidt A, Codlin S, et al. Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells. Cell, 2012, 151(3):671-683.
[3] Schwanhausser B, Weiss M, Simonovic M,et al. Global quantification of mammalian gene expression control. Nature, 2011, 473(7347):337-342.
[4] Vogel C, Abreu R S, Ko D, et al. Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line. Mol Syst Biol, 2010, 6(1):400.
[5] Ingvarsson P K. Gene expression and protein length influence codon usage and rates of sequence evolution in Populus tremula. Mol Biol Evol, 2007, 24(3):836-884.
[6] McHardy A C, Puhler A, Kalinowski J, et al. Comparing expression level-dependent features in codon usage with protein abundance:an analysis of ‘predictive proteomics’. Proteomics, 2004, 4(1):46-45.
[7] Ikemura T.Correlation between codon usage and tRNA content in microorganisms. In:Hatfield D L, Lee B J, Pirtle R M. Transfer RNA in Protein Synthesis, Boca Raton:CRC Press,1992:87-111.
[8] Na D, Lee D. RBSDesigner:software for designing synthetic ribosome binding sites that yields a desired level of protein expression. Bioinformatics, 2010,26(20):2633-2634.
[9] Nakamoto T. A unified view of the initiation of protein synthesis. Biochem Biophys Res Commun, 2006,341(3):675-678.
[10] Schattner P, Brooks A N, Lowe T M. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res, 2005,33:686-689.
[11] Seo S W, Yang J S, Kim I, et al. Predictive design of mRNA translation initiation region to control prokaryotic translation efficiency. Metab Eng, 2012,15(1):67-74.
[12] Tuller T, Waldman Y Y, Kupiec M, et al. Translation efficiency is determined by both codon bias and folding energy. Proc Natl Acad Sci U S A, 2010,107(8):3645-3650.
[13] Xia X. Position weight matrix, Gibbs sampler, and the associated significance tests in motif characterization and prediction. Scientifica, 2012:917540.
[14] Sharp P M, Li W H. The codon adaptation index——a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res, 1987,15(3):1281-1295.
[15] Ikemura T. Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs. J Mol Biol, 1982,158(4):573-597.
[16] Comeron J M, Aguade M. An evaluation of measures of synonymous codon usage bias. J Mol Evol, 1998,47(3):268-274.
[17] Xia X. DAMBE5:A comprehensive software package for data analysis in molecular biology and evolution. Mol Biol Evol,2013,30(7):1720-1728.
[18] Xia X. A major controversy in codon-anticodon adaptation resolved by a new codon usage index. Genetics, 2014,199(2):573-579.
[19] Chithambaram S, Prabhakaran R, Xia X. Differential codon adaptation between dsDNA and ssDNA phages in Escherichia coli. Molecular Biology & Evolution,2014,31(6):1606-1617.
[20] Wang M, Weiss M, Simonovic M, et al. PaxDb, a database of protein abundance averages across all three domains of life. Molecular & Cellular Proteomics, 2012,11(8):492-500.
[21] Wang M, Herrmann C J, Simonovic M, et al. Version 4.0 of PaxDb:Protein abundance data, integrated across model organisms, tissues, and cell-lines. Proteomics,2015,15(18):3163-3168.
[22] Schrimpf S P, Weiss M, Reiter L, et al. Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes. PLoS Biology, 2009,7(3):616-627.
[23] Baerenfaller K, Grossmann J, Grobei M A, et al. Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics. Science,2008,320(5878):938-941.
[24] Castellana N E, Payne S H, Shen Z, et al. Discovery and revision of Arabidopsis genes by proteogenomics. Proceedings of the National Academy of Sciences,2008,105(52):21034-21038.
[25] Schneeberger K. Reference-guided assembly of four diverse Arabidopsis thaliana genomes. Proc Natl Acad Sci U S A, 2011,108(25):10249-10254.
[26] Theologis A, Ecker J R, Palm C J, et al.Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana. Nature, 2000,408(6814):816-820.
[27] Salanoubat M, Lemcke K, Rieger M. Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana. Nature, 2000,408(6814):820-822.
[28] Tabata S, Kaneko T, Nakamura Y, et al.Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana. Nature, 2000,408(6814):823-826.
[29] Sato S.Complete structure of the chloroplast genome of Arabidopsis thaliana. DNA Res, 1999,6(5):283-290.
[30] Giegé P.RNA editing in Arabidopsis mitochondria effects 441 C to U changes in ORFs. Proc Natl Acad Sci U S A, 1999,96(26):15324-15329.
[31] Lin X.Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana. Nature, 1999,402(6763):761-768.
[32] Mayer K.Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana. Nature, 1999,402(6763):769-777.
[33] Wright F. The effective number of codons used in a gene. Gene, 1990,87(1):23-29.
[34] Xia X. An improved implementation of codon adaptation index. Evolutionary Bioinformatics, 2007,3(1):53-58.
[35] Nagaraj N, Wisniewski J R, Geiger T, et al. Deep proteome and transcriptome mapping of a human cancer cell line. Mol Syst Biol, 2011, 7(1):548-557.
[36] Hofacker I L. Vienna RNA secondary structure server.Nucleic Acids Res, 2003,31(13):3429-3431.
[37] Lukow O M, Preston K R, Watts B M, et al. Measuring the influence of wheat protein in breadmaking:from damage control to genetic manipulation of protein composition in wheat. In:Wvigleyc W.Wheat Quality Elucidation. The Bushuk Legacy. St-Paul, MN:2002,42(3):50-64.
[38] Mokshina N, Gorshkova T, Deyholos M K. Chitinase-like (CTL) and cellulose synthase (CESA) gene expression in gelatinous-type cellulosic walls of flax (Linum usitatissimum L.) Bast Fibers. Plos One, 2014,9(6):e97949.
[39] Ahmed M M, Ralph Patrick,Timothy L,et al. Predicting the dynamics of protein abundance. Molecular & Cellular Proteomics, 2014,13(5):1330-1340.
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