Bioinformatic analysis of proteins with GGDEF/EAL/HD-GYP domain in Leptospira interrogans
DING Shi-biao1, 2, XIAO Guo-hui2, KONG Liang-liang2, YAN Jie2, LIN Xü-ai2
1.Department of Clinical Laboratory, Zhejiang Hangzhou Red Cross Hospital, Hangzhou 310003, China; 2.Department of Microbiology and Parasitology, College of Medicine, Zhejiang University, Hangzhou 310058, China
Abstract：To further understand the function and regulation of c-di-GMP, the second messenger of bacteria, bioinformatic methods were used to analysis the proteins in Leptospira interrogans with GGDEF or EAL/HD-GYP domain, which regulate the synthesis and delegation of c-di-GMP. Genes, encoded proteins with GGDEF or EAL/HD-GYP domain, in the genome of Leptospira interrogans Lai, were analyzed by PSI-BLAST. The signal peptide sequences were analyzed by Signal P 4.0 software. Protein structures were analyzed by SMART and CCD in NCBI. The transmembrane sequences were detected by EMBNET. Homology analysis of protein sequences were detected by DNAstar. The phylogenetic tree was constructed using Neighbor-joining method. There are 22 proteins of Leptospira interrogans with GGDEF or EAL/HD-GYP domain, most of them contain receptor domain, such as PAS, GAF or REC, and the transmembrane region. Seven proteins with PAS receptor domain are more independent and located in a separate evolutionary branch, while the remaining 6 proteins with GGDEF domain are distributed in different branches. Four proteins with EAL domain and 2 proteins with HD-GYP domain are also more independent and are in the different evolutionary branch. Three proteins coupling GGDEF and EAL domains are more likely to be related to PDE activity, based on the analysis of evolutionary relationships. The genes coded proteins with GGDEF and EAL/HD-GYP domain are widely exist in Leptospira interrogans genome. The analysis of related protein indicated that 1) c-di-GMP signal network with a high degree of complexity; 2) L. interrogans can reflect a hook on the environmental alteration with a sophisticated mechanism.
丁士标, 肖国辉, 孔亮亮, 严杰, 林旭瑷. 问号钩端螺旋体GGDEF和EAL/HD-GYP结构域蛋白生物信息学分析[J]. 中国人兽共患病学报, 2016, 32(2): 109-113.
DING Shi-biao, XIAO Guo-hui, KONG Liang-liang, YAN Jie, LIN Xü-ai. Bioinformatic analysis of proteins with GGDEF/EAL/HD-GYP domain in Leptospira interrogans. Chinese Journal of Zoonoses, 2016, 32(2): 109-113.
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