苋菜AmMYB2基因密码子偏好性与进化分析
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摘要
为了解苋菜AmMYB2基因的密码子使用偏好性、与不同物种中调控色素相关的R2R3-MYB基因的同源关系及异源表达受体,利用Codon W与EMBOSS程序及Excel、SPSS、Origin等软件,分析苋菜与其他物种中调控色素代谢的R2R3-MYB基因的密码子使用偏好性,比较苋菜AmMYB2基因与模式生物的密码子使用频率.结果显示:苋菜AmMYB2基因中,所有密码子的GC、GC1、GC2、GC3含量均低于50%,偏好性较强的密码子有17个(RSCU> 1),偏好性最强的有7个(RSCU> 2),其中以A/T结尾的密码子有19个,表明苋菜AmMYB2基因的密码子偏好以A/T结尾,一些氨基酸对密码子的使用具有较强的偏好性;苋菜AmMYB2基因密码子的有效密码子数(Effective number of codons,ENC)值为49.63,苋菜AmMYB2基因的密码子在ENC绘图中的基因位点更接近期望曲线,说明在进化过程中苋菜AmMYB2基因的密码子偏好性受突变压力的影响较大;苋菜基因与甜菜色素代谢相关的R2R3-MYB基因的密码子使用偏好性参数相近,同源关系较近物种密码子使用偏好性具有相似性;从密码子使用频率上分析得出,酵母菌表达系统更适合苋菜AmMYB2基因的异源表达,模式植物拟南芥、烟草、番茄均可作为苋菜AmMYB2基因的遗传转化受体,同苋菜代谢途径相似的甜菜也可以作为苋菜AmMYB2基因的瞬时表达受体.本研究可为苋菜AmMYB2基因功能的进一步研究提供重要参考.(图5表2参31)
This study was done to explore the codon usage bias, homology with the R2 R3-MYB genes associated with pigment regulation in various species, and genetic transformation receptors of the AmMYB2 gene of amaranth(Amaranthus tricolor L.). The Codon W and EMBOSS online programs and Excel, SPSS, and Origin software were used to analyze the codon usage bias of the amaranth AmMYB2 gene. Correlation analysis was conducted to compare the codon usage bias of the amaranth AmMYB2 gene and the R2 R3-MYB genes controlling pigment metabolism in other species with those in model organisms for which relatively mature genetic transformation systems are available. The results showed that the content of GC, GC1, GC2,and GC3 in the amaranth AmMYB2 gene are all lower than 50%. There are seventeen more strongly favored codons(RSCU >1) in this gene, seven of which were aggressively favored over others(RSCU > 2). Among these, there are 19 codons ending in A or T, which showed that the genetic codon bias in the amaranth AmMYB2 gene favors codons with A or T as the third bit in the codon, and thus favors the use these highly favored codons in some amino acids. The effective number of codons(ENC) in the amaranth AmMYB2 gene was 49.63, and the locus of the amaranth AmMYB2 gene in the ENC plot was closer to the desired curve, which showed that the codon bias of the amaranth AmMYB2 gene has mainly been affected by mutation pressure.The codons of the R2 R3-MYB gene related to the metabolism of beet pigment were similar in their preference parameters to amaranth, and the codon bias parameters of the amaranth AmMYB2 gene were also similar to those of the R2 R3-MYB genes of closely related species. Based on the analysis of the frequency of codon usage across species, a yeast expression system was found to be the most suitable for use with the AmMYB2 gene, and the model plants Arabidopsis, tobacco, and tomato could be used as genetic transformation receptors of the AmMYB2 gene. Because of the similarity of its metabolic pathways to those of amaranth, beet can also act as the transient expression receptor of the amaranth AmMYB2 gene. This study provides important reference information for further studies on the function of the AmMYB2 gene in amaranth.
This study was done to explore the codon usage bias, homology with the R2 R3-MYB genes associated with pigment regulation in various species, and genetic transformation receptors of the AmMYB2 gene of amaranth(Amaranthus tricolor L.). The Codon W and EMBOSS online programs and Excel, SPSS, and Origin software were used to analyze the codon usage bias of the amaranth AmMYB2 gene. Correlation analysis was conducted to compare the codon usage bias of the amaranth AmMYB2 gene and the R2 R3-MYB genes controlling pigment metabolism in other species with those in model organisms for which relatively mature genetic transformation systems are available. The results showed that the content of GC, GC1, GC2,and GC3 in the amaranth AmMYB2 gene are all lower than 50%. There are seventeen more strongly favored codons(RSCU >1) in this gene, seven of which were aggressively favored over others(RSCU > 2). Among these, there are 19 codons ending in A or T, which showed that the genetic codon bias in the amaranth AmMYB2 gene favors codons with A or T as the third bit in the codon, and thus favors the use these highly favored codons in some amino acids. The effective number of codons(ENC) in the amaranth AmMYB2 gene was 49.63, and the locus of the amaranth AmMYB2 gene in the ENC plot was closer to the desired curve, which showed that the codon bias of the amaranth AmMYB2 gene has mainly been affected by mutation pressure.The codons of the R2 R3-MYB gene related to the metabolism of beet pigment were similar in their preference parameters to amaranth, and the codon bias parameters of the amaranth AmMYB2 gene were also similar to those of the R2 R3-MYB genes of closely related species. Based on the analysis of the frequency of codon usage across species, a yeast expression system was found to be the most suitable for use with the AmMYB2 gene, and the model plants Arabidopsis, tobacco, and tomato could be used as genetic transformation receptors of the AmMYB2 gene. Because of the similarity of its metabolic pathways to those of amaranth, beet can also act as the transient expression receptor of the amaranth AmMYB2 gene. This study provides important reference information for further studies on the function of the AmMYB2 gene in amaranth.
引文
1 Kumar N,Bera BC,Greenbaum BD.Revelation of influencing factors in overall codon usage bias of equine influenza viruses[J].PLoS ONE,2016,11(4):e0154376
2 Vervoort EB,Ravestein AV,Peij N.Optimizing heterologous expressionin dictyostelium:importance of 5'codon adaptation[J].Nucleic Acids Res,2000,28(10):2069-2074
3 Jiang Y,Deng F,Wang H.An extensive analysis on the global codon usage pattern of baculoviruses[J].Archives Virol,2008,153(12):2273-2282
4 Liu H,He R,Zhang H.Analysis of synonymous codon usage in Zea mays[J].Mol Biol Rep,2010,37(2):677-684
5 Ma QP,Li C,Wang J.Analysis of synonymous codon usage in FAD7genes from different plant species[J].Genetics Mol Res GMR,2015,14(1):1414-1422
6 Liu Q,Hu H,Wang H.Mutational bias is the driving force for shaping the synonymous codon usage pattern of alternatively spliced genes in rice(Oryza sa liva L.)[J].Mol Genetics Gen,2015,290(2):1-12
7 Singha HS,Chakraborty S,Deka H.Stress induced MAPK genes show distinct pattern of codon usage in Arabidopsis thaliana,Glycine max and Oryza sativa[J].Bioinformation,2014,10(7):436-442
8 Murray EE,Lotzer J,Eberle M.Codon usage in plant genes[J].Nucleic Acids Res,1989,17(2):477-498
9 Lu H,Zhao WM,Zheng Y.Analysis of synonymous codon usage bias in chlamydia[J].Acta Biochim Biophys Sin,2010,37(12):1-10
10 Humphreys DP,Sehdev M,Chapman AP.High-level periplasmic expression in escherichiyotic coli using a eukar signal peptide:importance of codon usage at the 5'end of the coding sequence[J].Protein Exp P urif,2000,20(2):252-264a
11 Li L,Yu XF,Thompson A.Arabidopsis MYRB30 is a direct target of BEST and cooperates with BES1 to regulate brassinosteroid-induced gene expression[J].Plant J,2010,58(2):275-286
12 Lee MM,Schiefelbein J.Cell pattern in the Arabidopsis root epiderAmis determined by lateral inhibition with feedback[J].Plant Cell,2002,14(3):611-618
13 Kim JH,Hyun WY,Nguyen HN.AtMyb7,a subgroup 4 R2R3 Myb,negatively regulates ABA-induced inhibition of seed germination by blocking the expression of the bZIP transcription factor ABI5[J].Pla nt Cell Environ,2015,38(3):559-571
14 Wang N,Zhang W,Qin M.Drought tolerance conferred in soybean(Glycine max L.)by GmMYB84,a novel R2R3-MYB transcription factor[J].Plant Cell Physiol,2017,58(10):1764-1776
15 Lee HG,Seo PJ.The MYB96-HHP module iIntegrates cold and ABA signaling to activate the CBF-COR pathway in Arabidopsis[J].Plant J,2015,82(6):962-977
16 Zhu ZR.MiR-140-3p i.s involved in in-stent restenosis by targeting C-Myb and BCL-2 in peripheral artery disease[J].J Atherosclerosis Thrombosis,2018:44624
17 Lin-Wang K,Bolitho K,Grafton K.An R2R3 MYB transcription factor associated with regulation of the anthocyanin biosynthetic pathway in Rosaceae[J].BMC Plant Biol,2010,10(1):50
18 Hatlestad GJ,Akhavan NA,Sunnadeniya RM.The beet Y locus encodesan anthocyanin MYB-like protein that activates the betalain red pigment pathway[J].Nat Genet,2015,47(1):92-106
19谢礼洋,刘生财,白玉.苋菜甜菜红素合成相关基因AmMYB1的克隆及表达分析[J].西北植物学报,2016,36(6):1080-1090[Xie LY,Liu SC,Bai Y.Cloning and expression analysis of betalain-related transcription factor gene AmMYBl in Amaranthus tricolor L.[J].Acta Bot Bor-Occid Sin,2016,36(6):1080-1090]
20 Sharp PM,Tuohy TMF,Mosurski KR.Codon usage in yeast:cluster analysis clearly differentiates highly and lowly expressed genes[J].Nucleic Acids Res,1986,14(13):5125-5143
21 Peden JF.Analysis of codon usage[J].Univ Nottingham,2000,90(1):73-74
22陈哲,胡福初,王祥和.菠萝密码子使用偏好性分析[J].果树学报.2017,8(8):946-955[Chen Z,Fuchu HU,Wang XH.Analysis of codon usage bias of Ananas comosus with genome sequencing data[J].J Fruit Sci,2017,8(8):946-955]
23 Zhao Y,Hao Z,Xu A.Analysis of codon usage bias of envelope glycoprotein genes in nuclear polyhedrosis virus(NPV)and its relation to evolution[J].BMC Genomics,2016,17(1):677
24 Lal D,Verma M,Behura SK.Codon usage bias in phylum Actinobacteria:relevance to environmental adaptation and host pathogenicity[J].Res Microbiol,2016,167(8):669-677
25 Gun L,Yumiao R,Haixian P.Comprehensive analysis and comparison on the codon usage pattern of whole mycobacterium tuberculosis coding genome from different area[J].Biomed Res Inter,2018,2018:1-7
26 Bera BC,Virmani N,Kumar N.Genetic and codon usage bias analyses of polymerase genes of equine influenza virus and its relation tc evolution[J].BMC Genom,2017,18(1):652
27 Zhou H,Wang H,Huang LF.Heterogeneity in codon usages of sobemovirus genes[J].Archiv Virol,2005,150(8):1591-1605
28程丽,李宜奎,李晓丹.植物CPR基因密码子偏好性及聚类分析[J].分子植物育种,2017,15(5):1672-1682[Cheng L,Li YK,Li XD.Codon usage bias and cluster analysis of plant CPR genes[J].Mol Plant Breeding,2017,15(5):1672-1682]
29李蓉,谢析颖,王雪晶.兰科植物FNR基因的密码子偏好性分析[J].热带作物学报,2018,39(6):1137-1145[Li R,Xie XY,Wang XJ.Codon usage bias of Ferredoxin-NADP+Oxidoreductase(FNR)in Orchidaceae[J].Chin J Trop Crops,2018 2018,39(6):1137-1145]
30赖瑞联,林玉玲,钟春水.龙眼生长素受体基因TIR1密码子偏好性分析[J]·园艺学报,2016,43(4):771-780[Lai RL,Lin YL,Zhong CS.Analysis of codon bias of auxin receptor gene TIR1 in Dimocarpus longan[J].Acta Horticul Sin,2016,43(4):771-780]
31李平,白云凤,冯瑞云.耔粒苋苹果酸酶(NAD-ME)基因密码子偏好性分析[J].应用与环境生物学报,2011,17(1):12-17[Li P,Bai YF,Feng RY.Analysis of codon bias of NAD-ME gene in Amaranthus hypochondriacus[J].Chin J Appl Environ Biol,2011,17(1):12-17]
2 Vervoort EB,Ravestein AV,Peij N.Optimizing heterologous expressionin dictyostelium:importance of 5'codon adaptation[J].Nucleic Acids Res,2000,28(10):2069-2074
3 Jiang Y,Deng F,Wang H.An extensive analysis on the global codon usage pattern of baculoviruses[J].Archives Virol,2008,153(12):2273-2282
4 Liu H,He R,Zhang H.Analysis of synonymous codon usage in Zea mays[J].Mol Biol Rep,2010,37(2):677-684
5 Ma QP,Li C,Wang J.Analysis of synonymous codon usage in FAD7genes from different plant species[J].Genetics Mol Res GMR,2015,14(1):1414-1422
6 Liu Q,Hu H,Wang H.Mutational bias is the driving force for shaping the synonymous codon usage pattern of alternatively spliced genes in rice(Oryza sa liva L.)[J].Mol Genetics Gen,2015,290(2):1-12
7 Singha HS,Chakraborty S,Deka H.Stress induced MAPK genes show distinct pattern of codon usage in Arabidopsis thaliana,Glycine max and Oryza sativa[J].Bioinformation,2014,10(7):436-442
8 Murray EE,Lotzer J,Eberle M.Codon usage in plant genes[J].Nucleic Acids Res,1989,17(2):477-498
9 Lu H,Zhao WM,Zheng Y.Analysis of synonymous codon usage bias in chlamydia[J].Acta Biochim Biophys Sin,2010,37(12):1-10
10 Humphreys DP,Sehdev M,Chapman AP.High-level periplasmic expression in escherichiyotic coli using a eukar signal peptide:importance of codon usage at the 5'end of the coding sequence[J].Protein Exp P urif,2000,20(2):252-264a
11 Li L,Yu XF,Thompson A.Arabidopsis MYRB30 is a direct target of BEST and cooperates with BES1 to regulate brassinosteroid-induced gene expression[J].Plant J,2010,58(2):275-286
12 Lee MM,Schiefelbein J.Cell pattern in the Arabidopsis root epiderAmis determined by lateral inhibition with feedback[J].Plant Cell,2002,14(3):611-618
13 Kim JH,Hyun WY,Nguyen HN.AtMyb7,a subgroup 4 R2R3 Myb,negatively regulates ABA-induced inhibition of seed germination by blocking the expression of the bZIP transcription factor ABI5[J].Pla nt Cell Environ,2015,38(3):559-571
14 Wang N,Zhang W,Qin M.Drought tolerance conferred in soybean(Glycine max L.)by GmMYB84,a novel R2R3-MYB transcription factor[J].Plant Cell Physiol,2017,58(10):1764-1776
15 Lee HG,Seo PJ.The MYB96-HHP module iIntegrates cold and ABA signaling to activate the CBF-COR pathway in Arabidopsis[J].Plant J,2015,82(6):962-977
16 Zhu ZR.MiR-140-3p i.s involved in in-stent restenosis by targeting C-Myb and BCL-2 in peripheral artery disease[J].J Atherosclerosis Thrombosis,2018:44624
17 Lin-Wang K,Bolitho K,Grafton K.An R2R3 MYB transcription factor associated with regulation of the anthocyanin biosynthetic pathway in Rosaceae[J].BMC Plant Biol,2010,10(1):50
18 Hatlestad GJ,Akhavan NA,Sunnadeniya RM.The beet Y locus encodesan anthocyanin MYB-like protein that activates the betalain red pigment pathway[J].Nat Genet,2015,47(1):92-106
19谢礼洋,刘生财,白玉.苋菜甜菜红素合成相关基因AmMYB1的克隆及表达分析[J].西北植物学报,2016,36(6):1080-1090[Xie LY,Liu SC,Bai Y.Cloning and expression analysis of betalain-related transcription factor gene AmMYBl in Amaranthus tricolor L.[J].Acta Bot Bor-Occid Sin,2016,36(6):1080-1090]
20 Sharp PM,Tuohy TMF,Mosurski KR.Codon usage in yeast:cluster analysis clearly differentiates highly and lowly expressed genes[J].Nucleic Acids Res,1986,14(13):5125-5143
21 Peden JF.Analysis of codon usage[J].Univ Nottingham,2000,90(1):73-74
22陈哲,胡福初,王祥和.菠萝密码子使用偏好性分析[J].果树学报.2017,8(8):946-955[Chen Z,Fuchu HU,Wang XH.Analysis of codon usage bias of Ananas comosus with genome sequencing data[J].J Fruit Sci,2017,8(8):946-955]
23 Zhao Y,Hao Z,Xu A.Analysis of codon usage bias of envelope glycoprotein genes in nuclear polyhedrosis virus(NPV)and its relation to evolution[J].BMC Genomics,2016,17(1):677
24 Lal D,Verma M,Behura SK.Codon usage bias in phylum Actinobacteria:relevance to environmental adaptation and host pathogenicity[J].Res Microbiol,2016,167(8):669-677
25 Gun L,Yumiao R,Haixian P.Comprehensive analysis and comparison on the codon usage pattern of whole mycobacterium tuberculosis coding genome from different area[J].Biomed Res Inter,2018,2018:1-7
26 Bera BC,Virmani N,Kumar N.Genetic and codon usage bias analyses of polymerase genes of equine influenza virus and its relation tc evolution[J].BMC Genom,2017,18(1):652
27 Zhou H,Wang H,Huang LF.Heterogeneity in codon usages of sobemovirus genes[J].Archiv Virol,2005,150(8):1591-1605
28程丽,李宜奎,李晓丹.植物CPR基因密码子偏好性及聚类分析[J].分子植物育种,2017,15(5):1672-1682[Cheng L,Li YK,Li XD.Codon usage bias and cluster analysis of plant CPR genes[J].Mol Plant Breeding,2017,15(5):1672-1682]
29李蓉,谢析颖,王雪晶.兰科植物FNR基因的密码子偏好性分析[J].热带作物学报,2018,39(6):1137-1145[Li R,Xie XY,Wang XJ.Codon usage bias of Ferredoxin-NADP+Oxidoreductase(FNR)in Orchidaceae[J].Chin J Trop Crops,2018 2018,39(6):1137-1145]
30赖瑞联,林玉玲,钟春水.龙眼生长素受体基因TIR1密码子偏好性分析[J]·园艺学报,2016,43(4):771-780[Lai RL,Lin YL,Zhong CS.Analysis of codon bias of auxin receptor gene TIR1 in Dimocarpus longan[J].Acta Horticul Sin,2016,43(4):771-780]
31李平,白云凤,冯瑞云.耔粒苋苹果酸酶(NAD-ME)基因密码子偏好性分析[J].应用与环境生物学报,2011,17(1):12-17[Li P,Bai YF,Feng RY.Analysis of codon bias of NAD-ME gene in Amaranthus hypochondriacus[J].Chin J Appl Environ Biol,2011,17(1):12-17]