Codon usage bias for genes involved in oxalate acetylation degradation pathway
[Objective]This study aimed to explore the condon preference of oxalyl-CoA synthase(AAE3),oxalyl-CoA decarboxylase(OCD)and formate dehydrogenase(FDH)genes involved in the oxalate acetylation degradation pathway among 100 plant species,as well as the factors that influenced condon preference,and analyzed their suitable heterologous expression receptors,which could provide scientific basis for understanding the genetic modification and evolution of AAE3,OCD and FDH genes in plants,and for enhancing their heterologous expression efficiency.[Method]Comprehensively used CodonW 1.4.2,CUSP and Python softwares,through PR2-plot analysis,ENC-plot analysis,rela-tive synonymous codon usage(RSCU)analysis,neutral plot analysis and codon frequency comparison analysis,the base composition characteristics,codon preference and its main influencing factors,high-frequency codons,optimal codons and heterologous expression adaptation receptors of AAE3,OCD,and FDH coding sequences(CDS)were deeply eluci-dated.[Result]The GC content of the CDS sequences of AAE3,OCD and FDH genes varied greatly at different posi-tions,but they all preferred codon ending with G/C.The gene expression levels of AAE3,OCD and FDH genes were low,and the codon preference was weak,with the degree of FDH＞AAE3＞OCD.During evolution,the codon preference of AAE3,OCD and FDH genes was mainly influenced by natural selection,with mutation pressure having little effect.RSCU analysis showed that AAE3,OCD and FDH genes had 31,26 and 27 high-frequency codons,and 19,14 and 9 op-timal codons respectively,among which the optimal codons of AAE3 and FDH genes all ended in G/C,and 8 of the opti-mal codons of OCD gene ended in G/C,accounting for 57.14％of the optimal codons.Arabidopsis thaliana and Nico-tiana tabacum could serve as adaptive receptors for heterologous expression of AAE3,OCD and FDH genes.When Esche-richia coli and Saccharomyces cerevisiae were selected as heterologous expression receptors,more codons(17-19)needed to be modified.[Conclusion]AAE3,OCD and FDH genes exhibit highly similar codon preference characteristics during evolutionary process,and the selection of heterologous expression receptors should prioritize A.thaliana and N.tabacum.
万方数据
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