问号钩端螺旋体GGDEF和EAL/HD-GYP结构域蛋白生物信息学分析

Bioinformatic analysis of proteins with GGDEF/EAL/HD-GYP domain in Leptospira interrogans

目的分析问号钩端螺旋体(钩体)环二鸟苷酸(Cyclic dimeric-GMP,c-di-GMP)调节相关的GGDEF和EAL/HD-GYP结构域蛋白生物信息学结果,为后续的功能研究奠定基础。方法 PSI-BLAST方法分析编码GGDEF和EAL/HDGYP结构域蛋白的基因;利用相应生物信息学软件对蛋白信号肽序列、跨膜序列、蛋白结构、同源性进行分析并构建目的蛋白进化树。结果问号钩体中22个蛋白分别含有GGDEF或EAL/HD-GYP结构域,多数蛋白均有感受器结构域和跨膜区。7个具有PAS输入感受器的GGDEF结构域蛋白进化较为独立,位于单独的一个分支,其余6个GGDEF结构域蛋白则分散在不同的分支上。4个EAL结构域蛋白和2个HD-GYP结构域蛋白进化上也较为独立,分别处于同一进化分支。3个GGDEF和EAL结构域耦合的蛋白在进化关系上更趋向于PDE活性蛋白。结论钩体具有多拷贝的合成和降解c-di-GMP相关蛋白编码基因,表明在钩体中c-di-GMP网络具有高度复杂性,同时反映出钩体对环境条件的改变具有复杂的应对机制。

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 4.0software.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 6proteins with GGDEF domain are distributed in different branches.Four proteins with EAL domain and 2proteins 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.