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[1]赖瑞联,冯新,陈瑾,等.橄榄查尔酮异构酶基因CHI的密码子偏好模式[J].应用与环境生物学报,2017,23(05):945-951.[doi:10.3724/SP.J.1145.2016.11037]
 LAI Ruilian,FENG Xin,CHEN Jin,et al.Codon usage pattern of chalcone isomerase gene (CHI) in Canarium album (Lour.) Raeusch[J].Chinese Journal of Applied & Environmental Biology,2017,23(05):945-951.[doi:10.3724/SP.J.1145.2016.11037]
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橄榄查尔酮异构酶基因CHI的密码子偏好模式()
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《应用与环境生物学报》[ISSN:1006-687X/CN:51-1482/Q]

卷:
23卷
期数:
2017年05期
页码:
945-951
栏目:
生物活性化合物的发现与开发专栏
出版日期:
2017-10-25

文章信息/Info

Title:
Codon usage pattern of chalcone isomerase gene (CHI) in Canarium album (Lour.) Raeusch
作者:
赖瑞联冯新陈瑾韦晓霞陈义挺吴如健
福建省农业科学院果树研究所 福州 350013
Author(s):
LAI Ruilian FENG Xin CHEN Jin WEI Xiaoxia CHEN Yiting** & WU Rujian**
Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
关键词:
橄榄黄酮类化合物查尔酮异构酶密码子偏好模式
Keywords:
Canarium album (Lour.) Raeusch flavonoid chalcone isomerase codon usage pattern
分类号:
S667.501
DOI:
10.3724/SP.J.1145.2016.11037
摘要:
黄酮类化合物是橄榄[Canarium album (Lour.) Raeusch]的重要活性成分,而查尔酮异构酶(Chalcone isomerase,CHI)是黄酮合成的关键酶类之一,了解橄榄查尔酮异构酶基因CHI的密码子偏好模式可为其功能和分子进化研究提供科学依据. 采用CodonW和EMBOSS分析橄榄CHI的密码子偏好性参数,并通过有效密码子数(Effective number of codon,ENc)绘图、中性绘图和偏倚分析探讨单双子叶植物CHI密码子偏好性形成的可能因素,同时分别采用SPSS19.0和MEGA5.2基于密码子偏好性和序列相似性进行聚类分析. 结果显示:橄榄CHI ENc值、G和C的含量(GC)以及密码子第3位上G和C含量(GC3s)分别为50.89、0.451和0.465,表明其密码子偏好性较弱,但倾向使用富含A和U,并以A或U结尾的密码子;单子叶植物CHI的密码子偏好性普遍高于双子叶植物,基于密码子偏好性和核酸序列相似性均能将单双子叶植物进行较准确的归类;密码子碱基成分和相关性分析发现,物种间CHI密码子偏好性受编码区长度的影响较小,而与碱基的组成密切相关;此外,橄榄CHI与模式生物拟南芥、烟草、大肠杆菌和酵母菌基因组均存在较大的密码子偏好性差异. 本研究表明突变压力是单双子叶植物间CHI严格的密码子偏好规律形成的主要作用力,而橄榄CHI外源表达和遗传转化时需要根据宿主基因组偏好模式进行密码子优化和改造. (图2 表4 参44)
Abstract:
Chalcone isomerase (CHI) is one of the key enzymes in the flavonoid synthesis pathway of Canarium album (Lour.) Raeusch. To provide a theoretical basis for further functional and evolutionary analysis of CHI, the codon usage pattern of C. album (Lour.) Raeusch CHI (CaCHI) was analyzed. We used CodonW and EMBOSS to investigate the codon usage bias of CaCHI and the effective number of codon (ENc) plots, neutral drawing, and parity rule 2 plot were subsequently used for the exploration of possible factors that affect the formation of the bias. Moreover, based on codon bias or sequence similarity, the statistical package for the social sciences (SPSS) version 19.0 or MEGA5.2 was used for cluster analysis of CHI in monocotyledon and dicotyledon plants. The results showed that the ENc, GC content (GC), and GC content of the 3rd site (GC3s) were 50.89, 0.451, and 0.465 respectively for CaCHI, which suggests that the codon bias level of CHI in C. album (Lour.) Raeusch was low and biased toward the synonymous codons with A or U on the 3rd site. It was also identified that the codon bias level of CHI in monocotyledons was generally higher than that in dicotyledons. Notably, according to the codon bias and sequence similarity of CHI, the results of phylogenetic tree analysis accurately classified the 40 investigated plants into monocotyledon and dicotyledon groups. Moreover, the correlation analysis revealed that the base composition but not the coding region length greatly affected the codon bias of plants. Additionally, the codon usage bias of CaCHI was quite different from that of model organisms such as Arabidopsis thaliana, Nicotiana sylvestris, Escherichia coli, and Saccharomyces cerevisiae. Our data confirmed that mutation pressure contributed dominantly to the strict codon usage rules in both monocotyledon and dicotyledon plants. Furthermore, it might be extremely essential to perform codon optimizations and modifications according to the codon bias of the host genome for heterologous expression and genetic transformation analysis of CaCHI.

参考文献/References:

1 Goodman DB, Church GM, Kosuri S. Causes and effects of N-terminal codon bias in bacterial genes [J]. Science, 2013, 342 (6157): 475-479
2 Bulmer M. The selection-mutation-drift theory of synonymous codon usage [J]. Genetics, 1991, 129 (3): 897-907
3 Kimura M. Possibility of extensive neutral evolution under stabilizing selection with special reference to nonrandom usage of synonymous codons [J]. PNAS, 1981, 78 (9): 5773-5777
4 Li WH. Models of nearly neutral mutations with particular implications for nonrandom usage of synonymous codons [J]. J Mol Evol, 1987, 24 (4): 337-345
5 Rensing SA, Fritzowsky D, Lang D, Reski R. Protein encoding genes in an ancient plant: analysis of codon usage, retained genes and splice sites in a moss, Physcomitrella patens [J]. BMC Genom, 2005, 6 (1): 1-13
6 Knight RD, Freeland SJ, Landweber LF. A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes [J]. Genome Biol, 2001, 2 (4): 1-13
7 Qin Z, Cai Z, Xia G, Wang M. Synonymous codon usage bias is correlative to intron number and shows disequilibrium among exons in plants [J]. BMC Genom, 2013, 14 (1): 1-11
8 Martínez-Pérez F, Bendena WG, Chang BS, Tobe SS. Influence of codon usage bias on FGLamide-allatostatin mRNA secondary structure [J]. Peptides, 2010, 32 (3): 509-517
9 Shah P, Gilchrist MA. Effect of correlated tRNA abundances on translation errors and evolution of codon usage bias [J]. PLoS Genet, 2010, 6 (9): 1001128
10 Pek HB, Klement M, Ang KS, Chrng BKS, Ow DSW, Lee DY. Exploring codon context bias for synthetic gene design of a thermostable invertase in Escherichia coli [J]. Enzyme Microb Technol, 2015, 75-76: 57-63
11 Pan LL, Wang Y, Hu JH, Ding ZT, Li C. Analysis of codon use features of stearoyl-acyl carrier protein desaturase gene in Camellia sinensis [J]. J Theor Biol, 2013, 334 (19): 80-86
12 Wei L, He J, Jia X, Qi Q, Liang ZS, Ping Y, Liu SY, Sun JC. Analysis of codon usage bias of mitochondrial genome in Bombyx mori and its relation to evolution [J]. BMC Evol Biol, 2014, 14 (1): 262-262
13 Xu C, Dong J, Tong C, Gong X, Wen Q, Zhuge Q. Analysis of synonymous codon usage patterns in seven different citrus species [J]. Evol Bioinform, 2013, 9 (9): 215-228
14 Torre ARDL, Lin YC, Peer YVD, Ingvarson PK. Genome-wide analysis reveals diverged patterns of codon bias, gene expression, and rates of sequence evolution in Picea gene families [J]. Genome Biol Evol, 2015, 7 (4): 1002-1015
15 Nie X, Deng P, Feng K, Liu P, Du X, You FM, Weining S. Comparative analysis of codon usage patterns in chloroplast genomes of the Asteraceae family [J]. Plant Mol Biol Rep, 2013, 32 (4): 828-840
16 Nair RR, Nandhini MB, Monalisha E, Murugan K, Sethuraman T, Nagarajan S, Rao NSP, Ganesh D. Synonymous codon usage in chloroplast genome of Coffea arabica [J]. Bioinformation, 2012, 8 (22): 1096-1104
17 吴如健, 陈 瑾, 胡菡青, 万继锋, 韦晓霞. 橄榄黄酮类化合物研究进展[J]. 福建农业学报, 2015, 30 (1): 106-110 [Wu RJ, Chen J, Hu HQ, Wang JF, Wei XX. Research advancement of flavonoids from Chinese olive [J]. Fujian J Agric Sci, 2015, 30 (1): 106-110]
18 张庆举. 橄榄叶类黄酮合成相关基因cDNA的克隆和生物信息学分析[D]. 福州: 福建农林大学, 2011 [Zhang QJ. The cDNA cloning and bioinformatic analysis of flavonoid biosynthesis-related genes in Chinese olive leaves [D]. Fuzhou: Fujian Agriculture and Forestry University, 2011]
19 李平, 白云凤, 冯瑞云, 王原媛, 张维锋. 籽粒苋苹果酸酶(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, BaiI YF, Feng RY, Wang YY, Zhang WF. Analysis of codon bias of NAD-ME gene in Amaranthus hypochondriacus [J]. Chin J Appl Environ Biol, 2011, 17 (1): 12-17]
20 孙晶, 何涛, 万闰兰, 彭小风, 彭泽. 铁皮石斛尿苷二磷酸葡萄糖焦磷酸化酶基因(UGP)的密码子偏好性分析[J]. 应用与环境生物学报, 2014, 20 (5): 759-766 [Sun J, He T, Wang RL, Peng XF, Peng Z. The codon usage bias of UDP-glucose pyrophosphorylase gene (UGP) in Dendrobium officinale [J]. Chin J Appl Environ Biol, 2014, 20 (5): 759-766]
21 Peden JF. Analysis of codon usage [J]. Univ Nott, 2000, 90 (1): 73-74
22 Rice P, Longden I, Bleasby A. EMBOSS: the european molecular biology open software suite [J]. Trends Genet, 2000, 16 (6): 276-277
23 Shi X, Wang X, Li Z, Zhu QH, Tang W, Ge S, Lou JC. Nucleotide substitution pattern in rice paralogues: implication for negative correlation between the synonymous substitution rate and codon usage bias [J]. Gene, 2006, 376 (2): 199-206
24 杨国锋, 苏昆龙, 赵怡然, 宋智斌, 孙娟. 蒺藜苜蓿叶绿体密码子偏好性分析[J]. 草业学报, 2015, 24 (12): 171-179 [Yang GF, Su KL, Zhao YR, Song ZB, Sun J. Analysis of codon usage in the chloroplast genome of Medicago truncatula [J]. Acta Pratacult Sin, 2015, 24 (12): 171-179]
25 Mathé C, Peresetsky A, Déhais P, Van MM, Rouze P. Classification of Arabidopsis thaliana gene sequences: clustering of coding sequences into two groups according to codon usage improves gene prediction [J]. J Mol Biol, 1999, 285 (5): 1977-1991
26 Sau K, Gupta S, Sau S, Ghosh TC. Synonymous codon usage bias in 16 Staphylococcus aureus phages: implication in phage therapy [J]. Virus Res, 2005, 113 (2): 123-131
27 Subramanian A, Sarkar RR. Data in support of large scale comparative codon usage analysis in Leishmania and Trypanosomatids [J]. Data Brief, 2015, 4: 269-272
28 Sharp PM, Li WH. An evolutionary perspective on synonymous codon usage in unicellular organisms [J]. J Mol Evol, 1986, 24 (1): 28-38
29 Jiang Y, Deng F, Wang H, Hu Z. An extensive analysis on the global codon usage pattern of baculoviruses [J]. Arch Virol, 2008, 153 (12): 2273-2282
30 Murray EE, Lotzer J, Eberle M. Codon usage in plant genes [J]. Nucl Acids Res, 1989, 17 (2): 477-498
31 Ingvarsson PK. Natural selection on synonymous and nonsynonymous mutations shapes patterns of polymorphism in Populus tremula [J]. Mol Biol Evol, 2010, 27 (3): 650-660
32 Ar DLT, Lin YC, Van de PY, Ingvarsson PK. Genome-wide analysis reveals diverged patterns of codon bias, gene expression and rates of sequence evolution in Picea gene families [J]. Genome Biol Evol, 2015, 7 (4): 1002-1015
33 Qiu S, Bergero R, Zeng K, Charlesworth D. Patterns of codon usage bias in Silene latifolia [J]. Mol Biol Evol, 2011, 28 (1): 771-780
34 Zhang L, Guo Y, Luo L, Yue P, Dong ZM, Sun SH, Qiu LJ. Analysis of nuclear gene codon bias on soybean genome and transcriptome [J]. Acta Agron Sin, 2011, 37 (6): 965-974
35 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
36 Liu H, He R, Zhang H, Huang YB, Tian ML, Zhang JJ. Analysis of synonymous codon usage in Zea mays [J]. Mol Biol Rep, 2010, 37 (2): 677-684
37 Liu H, Huang Y, Du X, Chen Z, Zeng X. Patterns of synonymous codon usage bias in the model grass Brachypodium distachyon [J]. Genet Mol Res, 2012, 11 (4): 4695-4706
38 续晨, 蔡小宁, 钱保俐, 贲爱玲. 葡萄基因组密码子使用偏好模式研究[J]. 西北植物学报, 2012, 32 (2): 409-415 [Xu C, Cai XN, Qian BL, Ben AL. Codon usage bias in Vitis vinifera [J]. Acta Bot Bor-Occid Sin, 2012, 32 (2): 409-415]
39 Yang HJ, Liu GS, Zhang ST. Codon usage bias studies and cluster analysis on chloroplastic genes in tobacco [J]. Acta Tabac Sin, 2012, 18 (2): 37-43
40 Novembre JA. Accounting for background nucleotide composition when measuring codon usage bias [J]. Mol Biol Evol, 2002, 19 (8): 1390-1394
41 Christianson ML. Codon usage patterns distort phylogenies from or of DNA sequences [J]. Am J Bot, 2005, 92 (8): 1221-1233
42 赖瑞联, 林玉玲, 钟春水, 赖钟雄. 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, Lai ZX. Analysis of codon bias of auxin receptor gene TIR1 in Dimocarpus longan [J]. Acta Horticult Sin, 2016, 43 (4): 771-780]
43 赖瑞联, 林玉玲, 林梦桦, 谢析颖, 徐涵, 王天池, MIN Kyaw Thu, 赖钟雄. 龙眼生长素响应因子ARF3密码子偏好性分析[EB/OL]. 中国科技论文在线[2016-04-30]. http://www.paper.edu.cn/releasepaper/content/201605-108 [Lai RL, Lin YL, Lin MH, Xu H, Wang TC, Min KT, Lai ZX. Analysis of codon bias of auxin response factor ARF3 in Dimocarpus longan Lour [EB/OL]. Sciencepaper Online [2016-04-30]. http://www.paper.edu.cn/releasepaper/content/201605-108]
44 Li C, Pan LL, Wang Y, Ding ZT. Codon bias of the gene for chloroplast glycerol-3-phosphate acyltransferase in Camellia sinensis (L.) O. Kuntze [J]. Biochem Syst Ecol, 2014, 55 (2): 212-218

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更新日期/Last Update: 2017-10-25