Tyson H, Dhindsa R
Biology Department, McGill University, Montreal, Quebec, Canada.
DNA Seq. 1995;5(6):339-51. doi: 10.3109/10425179509020865.
Codon preference and asymmetry in usage in the DNA sequences encoding the mature enzyme protein of 24 plant peroxidases from 12 different species were examined. Codon usage in highly conserved/non-conserved areas of the sequences was analysed, as well as possible deficiency/excess in CpG dinucleotides in the pairs of codon positions. Sequence relationships displayed by overall codon usage, dinucleotide frequencies within codons, and amino acid sequences were also studied. The main findings were: (1) Monocots clustered separately from dicots for overall codon usage and dinucleotide frequencies in codon positions 2 and 3, with six and seven clusters respectively discernible among these 24 peroxidase sequences. The monocot/dicot distinction disappeared in the four clusters among the mature protein amino acid sequences. Overall codon usage in sequences from monocotyledon and dicotyledon species differed, the monocots favouring codons with C or G in the third position. (2) Codon usage was biassed in many sequences, asymmetry was particularly noticeable in the monocots. (3) For repeated amino acids within conserved areas, codon preference appeared dependent on the order in which the repeated amino acid occurred, so that its usage of synonymous codons frequently balanced out.
研究了来自12个不同物种的24种植物过氧化物酶成熟酶蛋白编码DNA序列中的密码子偏好和使用不对称性。分析了序列高度保守/非保守区域的密码子使用情况，以及密码子位置对中CpG二核苷酸可能存在的不足/过量情况。还研究了整体密码子使用、密码子内二核苷酸频率和氨基酸序列所显示的序列关系。主要发现如下：(1) 在密码子位置2和3的整体密码子使用和二核苷酸频率方面，单子叶植物与双子叶植物聚类分开，在这24个过氧化物酶序列中分别可辨别出6个和7个聚类。在成熟蛋白氨基酸序列的4个聚类中，单子叶植物/双子叶植物的区分消失了。单子叶植物和双子叶植物物种序列的整体密码子使用情况不同，单子叶植物倾向于第三位为C或G的密码子。(2) 许多序列中的密码子使用存在偏差，不对称性在单子叶植物中尤为明显。(3) 对于保守区域内的重复氨基酸，密码子偏好似乎取决于重复氨基酸出现的顺序，因此其同义密码子的使用频率常常趋于平衡。
