茎瘤固氮根瘤菌Azorhizobium caulinodans ORS571基因组密码子使用偏好性分析

Analysis of Codon Usage Bias in the Genome of Azorhizobium Caulinodans ORS571

目前对于自生固氮菌和共生固氮菌的密码子使用特征已有较深入的了解,然而对于既可以进行自生固氮又可以共生固氮的固氮菌的认识仍十分有限。本研究采用对应分析、相关分析和卡方检验等方法对具有这一特征的茎瘤固氮根瘤菌ORS571基因组密码子进行分析,以期深入了解该类固氮菌密码子使用特征。以有效密码子数量(ENC)和密码子第3位GC含量(GC3s)分别为x、y轴绘制ENC-plot图谱,同时绘制描述仅受基因组碱基组成影响条件下的ENC和GC3s关系的期望曲线。结果发现,部分基因位于期望曲线上,说明该菌密码子偏好性受到了基因组碱基组成影响。对应分析和相关分析表明,包括固氮相关基因在内的全部基因在对应分析第1向量轴上的坐标值均与密码子适应指数和GC3s呈显著负相关(P<0.05),说明该菌码子偏好性还受基因表达水平和GC3s的影响。22个密码子的使用频率在高表达基因中显著增多,确定为最优密码子。其中21个密码子以G/C结尾,说明最优密码子有强烈的GC3s偏好。

The codon usage of the free-living and symbiotic nitrogen-fixing bacteria has been extensively studied.However,there was little information about the nitrogen-fixing bacteria that had dual capacity for both free-living and symbiotic nitrogen fixation.The codon usage of Azorhizobium caulinodans ORS571 as typical bacterium was investigated by correspondence analysis,correlation analysis and chi square test to gain a better understanding of the codon usage of such bacteria.The ENC-plot was obtained with the effective number of codons（ENC） and GC content at the third position of the codons（GC3s） as x and y axis respectively.In addition,the expected curve was also drawn to reveal the relationship of ENC and GC3s when the codon usage was only subjected to the nucleotide composition constraint.A few genes lied on the expected curve in ENC-plot,indicating nucleotide composition constraint played a role in the codon usage pattern.Correspondence analysis and correlation analysis showed the loading of all genes on the first axis of correspondence analysis correlated negatively and significantly（P〈0.05） with codon adaption index and GC3s.Therefore,codon usage pattern was also influenced by gene expression and GC3s.Moreover,22 codons were identified to be preferred codons with high frequency in highly expressed genes.Among them,21 codons were ended with G/C,indicating high GC3s bias in preferred codons.