运用CHIPS、CUSP和CodonW等程序分析了双子叶C4植物籽粒苋(Amaranthus hypochondriacus)丙酮酸磷酸二激酶(PPDK)基因的密码子偏好性, 并与马铃薯(Solanum tuberosum)和苜蓿(Medicago truncatula)等双子叶植物及水稻(Oryza sativa)和玉米(Zea mays)等单子叶植物进行了比较, 建立了聚类树状图, 以期在作物高光效基因工程中为籽粒苋PPDK基因选择合适的受体植物提供依据。研究结果表明, 籽粒苋PPDK基因偏好于以A或T结尾的密码子, 与其它几种被比较的双子叶作物的PPDK基因密码子偏好性趋势一致, 而玉米和水稻等单子叶植物更偏好使用以G或C结尾的密码子。PPDK基因密码子使用偏好性的系统聚类分析表明, 籽粒苋与马铃薯和苜蓿等双子叶植物聚为一类, 而稗草(Echinochloa crusgalli)、玉米和高粱(Sorghum bicolor)等单子叶植物聚为一类, 与系统进化地位一致。但单子叶植物水稻的密码子偏好性与籽粒苋较为接近, 与玉米和高粱相差较远。为了选择合适的蛋白质表达系统, 比较并分析了籽粒苋PPDK基因的密码子偏好性与大肠杆菌(Escherichia coli)及酵母菌的异同, 发现其与酵母菌的差异小于大肠杆菌, 表明选择酵母菌表达系统更为合适。
We used CHIPS, CUSP and Codon W online programs to confirm the codon bias of the complete coding sequence of PPDK in the grain Amaranthus hypochondriacus, then compared the codon bias with PPDK genes from different plant species. We constructed a phylogenetic tree based on codon bias to provide a basis for selecting appropriate PPDK receptors for A. hypochondriacus by high-photosynthesis gene engineering. PPDK in A. hypochondriacus and several other dicotyledonous crops was biased toward synonymous codons with A and T at the third codon position, but Zea mays, Oryza sativa and other monocotyledons use the end of the G or C codon. Phylogenetic analysis suggested that PPDK of A. hypochondriacus was evolutionarily closer to dicotyledons such as Solanum tuberosum and Medicago truncatula than the monocotyledons Z. mays, Sorghum bicolor and Echinochloa crusgalli. However, O. sativa is an exception in that the codon bias of PPDK is closer to that of dicotyledons A. hypochondriacus than the monocotyledons Z. mays or S. bicolor. To select the appropriate protein expression system, we compared the PPDK codon bias expression in A. hypochondriacus and Escherichia coli or yeast. Differences between A. hypochondriacus and yeast expression were less than between A. hypochondriacus and E. coli. The yeast system may be more suitable for expressing PPDK of A. hypochondriacus.
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