普通野生稻线粒体蛋白质编码基因密码子使用偏好性的分析
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摘要
以普通野生稻(Oryza rufipogon Griff.)线粒体基因组为对象,分析其蛋白质编码基因的密码子使用特征及与亚洲栽培稻(O. sativa L.)的差异,探讨其密码子偏性形成的影响因素和进化过程。结果显示:普通野生稻线粒体基因组编码序列第1、第2和第3位碱基的GC含量依次为49.18%、42.67%和40.86%;有效密码子数(Nc)分布于45.32～61.00之间,其密码子偏性较弱; Nc值仅与GC_3呈显著相关,密码子第3位的碱基组成对密码子偏性影响较大;第1向量轴上显示9.91%的差异,其与GC_(3s)、Nc、密码子偏好指数(CBI)和最优密码子使用频率(Fop)的相关性均达到显著水平;而GC_3和GC_(12)的相关性未达到显著水平。因此,普通野生稻线粒体基因组密码子的使用偏性主要受自然选择压力影响而形成。本研究确定了21个普通野生稻线粒体基因组的最优密码子,大多以A或T结尾,与叶绿体密码子具有趋同进化,但是与核基因组具有不同的偏好性。同义密码子相对使用度(RSCU)、PR2偏倚分析和中性绘图分析显示,普通野生稻线粒体基因功能和其密码子使用密切相关,且线粒体密码子使用在普通野生稻、粳稻(O. sativa L. subsp. japonica Kato)和籼稻(O. sativa L. subsp.indica Kato)内具有同质性。
The mitochondrial genome of Oryza rufipogon Griff. was used to analyze the codon usage characteristics of protein-coding genes and the differences with Asian cultivated rice( O. sativa L.),and to explore the influencing factors of codon usage bias and codon evolution. Results showed that the effective number of codons( Nc) ranged from 45. 32 to61. 00,indicating that codon bias was weak. GC content at the three codon positions was49. 18%,42. 67%,and 40. 86%. The Nc value was significantly correlated with GC_3 but not with GC_1 or GC_2,suggesting that base composition at the third codon position had a greater effect on codon bias. In the corresponding analysis,the first axis showed 9.91% variation and was significantly correlated with GC_(3s),Nc,CBI,and Fop. Furthermore,GC_(12) showed nonsignificant correlation with GC_3. Codon bias in the mitogenome of O. rufipogon was mainly affected by natural selection. In addition,we identified 21 optimal codons,with most of the preferred synonymous codons ending in A or T. The mitochondrial codons showed convergent evolution with Oryza chloroplast codons,but different preferences with the nuclear genome.Based on neutrality plot analysis, PR2-plot analysis, and RSCU analysis, we found no significant differences among the three Oryza species. Our results also confirmed homogeneity in mitochondrial codon usage among the three Oryza species.
The mitochondrial genome of Oryza rufipogon Griff. was used to analyze the codon usage characteristics of protein-coding genes and the differences with Asian cultivated rice( O. sativa L.),and to explore the influencing factors of codon usage bias and codon evolution. Results showed that the effective number of codons( Nc) ranged from 45. 32 to61. 00,indicating that codon bias was weak. GC content at the three codon positions was49. 18%,42. 67%,and 40. 86%. The Nc value was significantly correlated with GC_3 but not with GC_1 or GC_2,suggesting that base composition at the third codon position had a greater effect on codon bias. In the corresponding analysis,the first axis showed 9.91% variation and was significantly correlated with GC_(3s),Nc,CBI,and Fop. Furthermore,GC_(12) showed nonsignificant correlation with GC_3. Codon bias in the mitogenome of O. rufipogon was mainly affected by natural selection. In addition,we identified 21 optimal codons,with most of the preferred synonymous codons ending in A or T. The mitochondrial codons showed convergent evolution with Oryza chloroplast codons,but different preferences with the nuclear genome.Based on neutrality plot analysis, PR2-plot analysis, and RSCU analysis, we found no significant differences among the three Oryza species. Our results also confirmed homogeneity in mitochondrial codon usage among the three Oryza species.
引文
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[29]Nair RR,Nandhini MB,Sethuraman T,Doss G.Mutational pressure dictates synonymous codon usage in freshwater unicellularα-cyanobacterial descendant Paulinella chromatophora andβ-cyanobacterium Synechococcus elongatus PCC6301[J].Springer Plus,2013,2:492.
[30]Kannaujiya VK,Rastogi RP,Sinha RP.GC constituents and relative codon expressed amino acid composition in cyanobacterial hycobiliproteins[J].Gene,2014,546(2):162-171.
[31]Zhou M,Li X.Analysis of synonymous codon usage patterns in different plant mitochondrial genomes[J].Mol Biol Rep,2009,36(8):2039-2046.
[32]Zhang WJ,Zhou J,Li ZF,Wang L,Gu X,Zhong Y.Comparative analysis of codon usage patterns among mitochondrion,chloroplast and nuclear genes in Triticum aestivum L.[J].J Integr Plant Biol,2007,49(2):246-254.
[2]Qiu S,Zeng K,Slotte T,Wright S,Charlesworth D.Reduced efficacy of natural selection on codon usage bias in selfing Arabidopsis and Capsella species[J].Genome Biol Evol,2011,3:868-880.
[3]Supek F.The code of silence:widespread associations between synonymous codon biases and gene function[J].J Mol Evol,2016,82(1):65-73.
[4]Duret L.Evolution of synonymous codon usage in metazoans[J].Curr Opin Genet Dev,2002,12(6):640-649.
[5]Sharp MP,Li W.Codon usage in regulatory genes in Escherichia coli does not reflect selection for rare codons[J].Nucleic Acids Res,1986,14(19):7737-7749.
[6]Bulmer M.The selection-mutation-drift theory of synonymous codon usage[J].Genetics,1991,129(3):897-907.
[7]Li WH,Gojobori T,Nei M.Pseudogenes as a paradigm of neutral evolution[J].Nature,1981,292(5820):237-239.
[8]Song H,Gao H,Liu J,Tian P,Nan Z.Comprehensive analysis of correlations among codon usage bias,gene expression,and substitution rate in Arachis duranensis and Arachis ipa3nsis orthologs[J].Sci Rep,2017,7(1):14853.
[9]Clément Y,Sarah G,Holtz Y,Homa F,Pointet S,et al.Evolutionary forces affecting synonymous variations in plant genomes[J].PLo S genetics,2017,13(5):e1006799.
[10]Olejniczak M,Uhlenbeck OC.tRNA residues that have coevolved with their anticodon to ensure uniform and accurate codon recognition[J].Biochimie,2006,88(8):943-950.
[11]Gu W,Zhou T,Ma J,Sun X.The relationship between synonymous codon usage and protein structure in Escherichia coli and Homo sapiens[J].Biosystems,2004,73(2):89-97.
[12]Fickett JW.Recognition of protein coding regions in DNAsequences[J].Nucleic Acids Res,1982,10:5303-5318.
[13]Gualberto JM,Newton KJ.Plant mitochondrial genomes:dynamics and mechanisms of mutation[J].Annu Rev Plant Biol,2017,68:225-252.
[14]Liberatore KL,Dukowic-Schulze S,Miller ME,Chen C,Kianian SF.The role of mitochondria in plant development and stress tolerance[J].Free Radic Biol Med,2016,100:238-256.
[15]Curole JP,Kocher TD.Mitogenomics:digging deeper with complete mitochondrial genomes[J].Trends Ecol Evol,1999,14(10):394-398.
[16]Liang X,Tian X,Liu W,Wei T,Wang W,et al.Comparative analysis of the mitochondrial genomes of Colletotrichum gloeosporioides sensu lato:insights into the evolution of a fungal species complex interacting with diverse plants[J].BMC Genomics,2017,18(1):171.
[17]Fujii S,Kazama T,Yamada M,Toriyama K.Discovery of global genomic reorganization based on comparison of two newly sequenced rice mitochondrial genomes with cytoplasmic male sterility-related genes[J].BMC Genomics,2010,11:209.
[18]陈乐天,刘耀光.水稻野败型细胞质雄性不育的发现利用与分子机理[J].科学通报,2016,61(35):3804-3812.Chen LT,Liu YG.Discovery,utilization and molecular mechanisms of CMS-WA in rice[J].Chinese Science Bulletin,2016,61(35):3804-3812.
[19]刘庆坡,谭军,薛庆中.籼稻品种93-11同义密码子的使用偏性[J].遗传学报,2003,30(4):335-340.Liu QB,Tan J,Xue QZ.Synonymous codon usage bias in the rice cultivar 93-11(Oryza sativa L.ssp.indica)[J].Acta Genetica Sinica,2003,30(4):335-340.
[20]刘庆坡,薛庆中.粳稻叶绿体基因组的密码子用法[J].作物学报,2004,30(12):1220-1224.Liu QP,Xue QZ.Codon usage in the chloroplast genome of rice(Oryza sativa L.ssp.japonica)[J].Acta agronomica sinica,2004,30(12):1220-1224.
[21]Tian X,Zheng J,Hu S,Yu J.The rice mitochondrial genomes and their variations[J].Plant Physiol,2006,140(2):401-410.
[22]Notsu Y,Masood S,Nishikawa T,Kubo N,Akiduki G,et al.The complete sequence of the rice(Oryza sativa L.)mitochondrial genome:frequent DNA sequence acquisition and loss during the evolution of flowering plants[J].Mol Genet Genomics,2002,268(4):434-445.
[23]Puigbo P,Bravo IG,Garcia-Vallve S.CAIcal:a combined set of tools to assess codon usage adaptation[J].Biol Direct,2008,3:38.
[24]Sueoka N.Two aspects of DNA base composition:G+Ccontent and translation-coupled deviation from intra-strand rule of A=T and G=C[J].J Mol Evol,1999,49(1):49-62.
[25]Sueoka N.Directional mutation pressure and neutral molecular evolution[J].Proc Natl Acad Sci USA,1988,85(8):2653-2657.
[26]Maria D,Ermolaeva.Synonymous codon usage in bacteria[J].Curr Issues Mol Biol,2001,3(4):91-97.
[27]Wang L,Xing H,Yuan Y,Wang X,Saeed M,et al.Genome-wide analysis of codon usage bias in four sequenced cotton species[J].PLo S One,2018,13(3):e0194372.
[28]Mazumdar P,Binti Othman R,Mebus K,Ramakrishnan N,Ann Harikrishna J.Codon usage and codon pair patterns in non-grass monocot genomes[J].Ann Bot,2017,120(6):893-909.
[29]Nair RR,Nandhini MB,Sethuraman T,Doss G.Mutational pressure dictates synonymous codon usage in freshwater unicellularα-cyanobacterial descendant Paulinella chromatophora andβ-cyanobacterium Synechococcus elongatus PCC6301[J].Springer Plus,2013,2:492.
[30]Kannaujiya VK,Rastogi RP,Sinha RP.GC constituents and relative codon expressed amino acid composition in cyanobacterial hycobiliproteins[J].Gene,2014,546(2):162-171.
[31]Zhou M,Li X.Analysis of synonymous codon usage patterns in different plant mitochondrial genomes[J].Mol Biol Rep,2009,36(8):2039-2046.
[32]Zhang WJ,Zhou J,Li ZF,Wang L,Gu X,Zhong Y.Comparative analysis of codon usage patterns among mitochondrion,chloroplast and nuclear genes in Triticum aestivum L.[J].J Integr Plant Biol,2007,49(2):246-254.