Intercodon dinucleotides affect codon choice in plant genes
Intercodon dinucleotides affect codon choice in plant genes
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DOI：
10.1093/nar/28.17.3339
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发表时间：
2000-09-01
影响因子：
14.9
通讯作者：
Marchetti, S
中科院分区：
文献类型：
--
作者：
De Amicis, F;Marchetti, S
本研究考虑了平均分布于甘蓝型油菜、拟南芥、番茄、烟草、Pisum sativum、Glycine max、Oryza sativa、Triticum aestivum、Hordeum vulgare和Zea mays之间的超过29万个密码子对应的710个cds，确定了每个氨基酸在A、G、C或T作为后续三联体的初始核苷酸时的同义密码子选择；在假设密码子独立组合的情况下，33.4%的病例出现频率与预期差异显著（P = 0.01），这主要是由于普遍存在TpA和CpG互密码子缺失。一般来说，密码子间tpa和CpGs最好分别被CpAs和TpGs取代。在一些情况下，密码子频率也被修改，以避免同四聚体和同三聚体的形成，减少下游{1,2}GG或AG二核苷酸的互密码子apc，以及在某些情况下增加GpA或ApG互密码子。由于TpA、CpG和三聚体缺乏直接或间接占密码子频率显著变化的77%，因此可以得出结论，密码子的使用反映了DNA结构水平上的精确需求。植物物种表现出与系统发育相关的对结构约束的适应性，密码子使用的灵活性反映在探针设计的最佳密码子阵列上。
In this work, 710 CDSs corresponding to over 290 000 codons equally distributed between Brassica napus, Arabidopsis thaliana, Lycopersicon esculentum, Nicotiana tabacum, Pisum sativum, Glycine max, Oryza sativa, Triticum aestivum, Hordeum vulgare and Zea mays were considered, For each amino acid, synonymous codon choice was determined in the presence of A, G, C or T as the initial nucleotide of the subsequent triplet; data were statistically analysed under the hypothesis of an independent assortment of codons, In 33.4% of cases, a frequency significantly (P = 0.01) different from that expected was recorded, This was mainly due to a pervasive intercodon TpA and CpG deficiency. As a general rule, intercodon TpAs and CpGs were preferably replaced by CpAs and TpGs, respectively. In several instances, codon frequencies were also modified to avoid homotetramer and homotrimer formation, to reduce intercodon ApCs downstream {1,2} GG or AG dinucleotides, as well as to increase GpA or ApG intercodons under certain contexts. Since TpA, CpG and homotetra(tri)mer deficiency directly or indirectly accounted for 77% of significant variation in the codon frequency, it can be concluded that codon usage mirrors precise needs at the DNA structure level. Plant species exhibited a phylogenetically-related adaptation to structural constraints, Codon usage flexibility was reflected in strikingly different arrays of optimum codons for probe design.