Codon Usage Bias of Chalcone Synthase Gene CHS in Kiwifruit
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摘要: 为了解猕猴桃查尔酮合成酶基因（Chalcone Synthase，CHS）的密码子使用特征，采用CodonW、SPSS、MEGA软件和EMBOSS在线程序等分析猕猴桃CHS密码子偏好性，并构建单双子叶植物CHS系统发育树。研究结果表明，猕猴桃CHS有效密码子数（ENc）、总G和C含量（GC）和密码子第3位上G或C含量（GC3s）分别为57.21、0.533和0.607；同义密码子相对使用度（RSCU）大于1.0的密码子数为30，但不存在偏好性极强的密码子；聚类分析结果发现，基于密码子使用偏好性分类可将单双子叶进行准确归类，而CHS序列相似性聚类结果并不理想；密码子使用频率分析表明，猕猴桃CHS与模式生物拟南芥和大肠杆菌基因组间密码子使用偏好性差异相对较小。研究认为，猕猴桃CHS密码子偏好性较弱，但倾向使用G和C，且以G或C结尾的密码子；单双子叶植物CHS间存在严格的密码子使用法则；此外，拟南芥和大肠杆菌可能是猕猴桃CHS遗传转化和异源表达较为理想的受体系统。Abstract: To investage codon usage characteristic of chalcone synthase gene of kiwifruit, CodonW, SPSS, MEGA software and EMBOSS online program were used to analyse codon usgae bias (CUB) of CHS, and phylogenetic tree of CHS between monocotyledon and dicotyledon was constructed in this paper. The results showed that, the effective number of codons (ENc), total GC content (GC) and GC content on the 3rd site (GC3s) was 57.21, 0.533 and 0.607, respectively. The number of condons, the number of relative synonymous codon usage (RSCU) of which was more than 1.0, was 30, but no codons was with strongly CUB. The cluster tree of CHS based on CUB was closer to the real category system than it did by sequence similarity. According to codon usage frequency, the CUB between CHS of kiwifruit and Arabidopsis thaliana, Escherichia coli were more similar. These results indicated that, the CUB level of CHS was low in kiwifruit, but it was bias toward GC rich codons and synonymous codons with G or C at 3rd codon position. And CHS in monocotyledons and dicotyledons had the distinctive CUB rules. In addition, Arabidopsis thaliana and Escherichia coli migth be the best receptors for genetic transformation and heterologous expression of CHS in kiwifruit.
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Key words:
- Kiwifruit /
- chalcone synthase /
- codon usage bias /
- cluster analysis
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图 1 基于密码子使用偏好性(A)和序列相似性(B)CHS聚类分析
Figure 1. Phylogenetic tree analysis of CHS based on CUB (A) and sequence similarity (B)
图 2 猕猴桃CHS与模式基因组密码子使用频率比较
Figure 2. Comparison of CUB between kiwifruit CHS and representative organism genome
表 1 猕猴桃CHS同义密码子相对使用度
Table 1. RSCU of kiwifruit CHS in Actinidia chinensis Planch
氨基酸 密码子 RSCU 丙氨酸Ala GCA 0.75 GCC 1.63 GCG 0.50 GCT 1.13 精氨酸Arg AGA 0 AGG 1.76 CGA 0.35 CGC 1.76 CGG 1.06 CGT 1.06 天冬酰胺Asn AAC 1.78 AAT 0.22 天冬氨酸Asp GAC 1.16 GAT 0.84 半胱氨酸Cys TGC 1 TGT 1 谷氨酰胺Gln CAA 0.91 CAG 1.09 GAA 0.67 GAG 1.33 甘氨酸Gly GGA 0.52 GGC 0.77 GGG 1.42 GGT 1.29 组氨酸His CAC 0.75 CAT 1.25 异亮氨酸Ile ATA 0.32 ATC 1.42 ATT 1.26 亮氨酸Leu CTA 0.57 CTC 1.86 CTG 0.86 CTT 0.86 TTA 0.29 TTG 1.57 赖氨酸Lys AAA 0.67 AAG 1.33 苯丙氨酸Phe TTC 0.77 TTT 1.23 脯氨酸Pro CCA 0.80 脯氨酸Pro CCC 1.40 CCG 0.60 CCT 1.20 丝氨酸Ser AGC 1.64 AGT 1.09 TCA 0.82 TCC 1.09 TCG 0.55 TCT 0.82 苏氨酸Thr ACA 0.17 ACC 1.57 ACG 0.87 ACT 1.39 酪氨酸Tyr TAC 1.33 TAT 0.67 缬氨酸Val GTA 0.13 GTC 1.29 GTG 1.42 GTT 1.16 注：下划线表示偏好性较强的密码子。 
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[1] MONTEFIORI M, MCGHIE T K, COSTA G, et al. Pigments in the fruit of red-fleshed kiwifruit (Actinidia chinensis and Actinidia deliciosa)[J]. Journal of Agricultural & Food Chemistry, 2005, 53(24):9526-9530. https://www.researchgate.net/publication/12373071_Carotenoid_and_ultrastructure_variations_in_plastids_of_Arum_italicum_Miller_fruit_during_maturation_and_ripening [2] 张亮, 满玉萍, 姜正旺, 等.猕猴桃花青素合成途径基因AcCHS和AcLDOX的克隆与表达分析[J].园艺学报, 2012, 39(11):2124-2132. http://d.wanfangdata.com.cn/Periodical/yyxb201211003 [3] 黄春辉, 葛翠莲, 张晓慧, 等. '红阳'猕猴桃突变体果实花青苷合成相关结构基因的表达分析[J].果树学报, 2014, 31(2):169-174. http://or.nsfc.gov.cn/handle/00001903-5/232023 [4] 杨红丽, 王彦昌, 姜正旺, 等. '红阳'猕猴桃cDNA文库构建及F3H基因的表达初探[J].遗传, 2009, 31(12):1265-1272. http://www.wanfangdata.com.cn/details/detail.do?_type=perio&id=yc200912013 [5] 杨俊, 姜正旺, 王彦昌.红肉猕猴桃DFR基因的克隆及表达分析[J].植物科学学报, 2010, 28(6):673-681. http://www.doc88.com/p-3147462105281.html [6] 王燕, 许锋, 程水源.植物查尔酮合成酶分子生物学研究进展[J].河南农业科学, 2007, 36(8):5-9. http://www.docin.com/p-738962687.html [7] SUN J, TANG W, LIU Y. Transient expression of CHS-RNAi effectively influences the accumulation of anthocyanin in fruit of kiwifruit (Actinidia chinensis)[J]. Chinese Journal of Applied & Environmental Biology, 2014, 20(5):929-933. http://www.chinaagrisci.com/Jwk_zgnykxen/EN/rss_zxly.xml [8] PEK H B, KLEMENT M, ANG K S, et al. Exploring codon context bias for synthetic gene design of a thermostable invertase in Escherichia coli[J]. Enzyme & Microbial Technology, 2015, 75-76:57-63. https://www.sciencedirect.com/science/article/pii/S0141022915000678 [9] RENSING S A, FRITZOWSKY D, LANG D, et al. Protein encoding genes in an ancient plant:analysis of codon usage, retained genes and splice sites in a moss, Physcomitrella patens[J]. BMC Genomics, 2005, 6(1):1-13. doi: 10.1186/1471-2164-6-1 [10] TULLER T, WALDMAN Y Y, KUPIEC M, et al. Translation efficiency is determined by both codon bias and folding energy[J]. Proceedings of the National Academy of Sciences of the United States of America, 2010, 107(8):3645-3650. doi: 10.1073/pnas.0909910107 [11] ZHEN Q, CAI Z, XIA G, et al. Synonymous codon usage bias is correlative to intron number and shows disequilibrium among exons in plants[J]. BMC Genomics, 2013, 14(1):1-11. doi: 10.1186/1471-2164-14-1 [12] SHARP P M, LI W H. An evolutionary perspective on synonymous codon usage in unicellular organisms[J]. Journal of Molecular Evolution, 1986, 24(1):28-38. doi: 10.1007/BF02099948 [13] MURRAY E E, LOTZER J, EBERLE M. Codon usage in plant genes[J]. Nucleic Acids Research, 1989, 17(2):477-498. doi: 10.1093/nar/17.2.477 [14] NOVEMBRE J A. Accounting for background nucleotide composition when measuring codon usage bias[J]. Molecular Biology and Evolution, 2002, 19(8):1390-1394. doi: 10.1093/oxfordjournals.molbev.a004201 [15] 赖瑞联, 林玉玲, 钟春水, 等.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. http://www.wanfangdata.com.cn/details/detail.do?_type=perio&id=yyxb201604017 [16] SHARP P M, COWE E, HIGGINS D G, et al. Codon usage patterns in Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster and Homo sapiens; a review of the considerable within-species diversity[J]. Nucleic Acids Research, 1988, 16(17):8207-8211. doi: 10.1093/nar/16.17.8207 [17] 赖瑞联, 林玉玲, 林梦桦, 等. 龙眼生长素响应因子ARF3密码子偏好性分析[EB/OL]. 北京: 中国科技论文在线[2016-04-30]. [18] 赖志宸, 林玉玲.野生蕉ω-3脂肪酸去饱和酶基因FAD7密码子偏性分析[J].福建农业学报, 2017, 32(5):503-507. http://www.fjnyxb.cn/CN/abstract/abstract3177.shtml [19] 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(5):0945-0951 http://kns.cnki.net/KCMS/detail/detail.aspx?filename=yyhs201705029&dbname=CJFD&dbcode=CJFQ [20] DUAN H, WANG H, MA B, et al. Codon optimization and expression of irisin in Pichia pastoris GS115[J]. International Journal of Biological Macromolecules, 2015, 79(1):21-26. https://www.sciencedirect.com/science/article/pii/S0006291X07020037 [21] Li C, Pan L L, Wang Y, et al. Codon bias of the gene for chloroplast glycerol-3-phosphate acyltransferase in Camellia sinensis (L.) O. Kuntze[J]. Biochemical Systematics & Ecology, 2014, 55(2):212-218. https://www.researchgate.net/publication/286209351_Codon_usage_analysis_in_squalene_synthase_gene -
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