文献类型：期刊文献

英文题名：Significance and roles of synonymous codon usage in the evolutionary process of Proteus

作者：Jin, Li[1,2];Gao, Han[3];Cao, Xiaoan[2];Han, Shengyi[2,4];Xu, Long[2,4];Ma, Zhongren[1];Shang, Youjun[2];Ma, Xiao-xia[1]

机构：[1]Northwest Minzu Univ, Biomed Res Ctr, Lanzhou 730046, Gansu, Peoples R China;[2]Chinese Acad Agr Sci, Lanzhou Vet Res Inst, State Key Lab Vet Etiol Biol, Lanzhou 730046, Gansu, Peoples R China;[3]East China Univ Sci & Technol, Dept Coll Pharm, Shanghai, Peoples R China;[4]Gansu Agr Univ, Coll Vet Med, Lanzhou, Gansu, Peoples R China

年份：2020

卷号：60

期号：5

起止页码：424

外文期刊名：JOURNAL OF BASIC MICROBIOLOGY

收录：;WOS:【SCI-EXPANDED(收录号:WOS:000527847700006)】；

语种：英文

外文关键词：evolutionary dynamic; genetic niche; nucleotide usage; Proteus; synonymous codon usage

摘要：Proteus spp. bacteria frequently serve as opportunistic pathogens that can infect many animals and show positive survival and existence in various natural environments. The evolutionary pattern of Proteus spp. is an unknown topic, which benefits understanding the different evolutionary dynamics for excellent bacterial adaptation to various environments. Here, the eight whole genomes of different Proteus species were analyzed for the interplay between nucleotide usage and synonymous codon usage. Although the orthologous average nucleotide identity and average nucleotide identity display the genetic diversity of these Proteus species at the genome level, the principal component analysis further shows that these species sustain the specific genetic niche at the aspect of synonymous codon usage patterns. Interestingly, although these Proteus species have A/T rich genes with underrepresented G (guanine) or C (cytosine) at the third codon positions and overrepresented A or T at these positions, some synonymous codons with A or T end are obviously suppressed in usage. The overall codon usage pattern reflected by the effective number of codons (ENC) has a significantly positive correlation with GC3 content (GC content at the third codon position), and ENC has a significantly negative correlation with the adaptation index for these species. These results suggest that the mutation pressure caused by nucleotide composition constraint serves as a dominant evolutionary dynamic driving evolutionary trend of Proteus spp., along with other selections related to natural selection, replication and fine-tune translation, and so on. Taken together, the analyses help to understand the evolutionary interplay between nucleotide and codon usage at the gene level of Proteus.