Phenotypic–genotypic analysis of GGDEF/EAL/HD-GYP domain-encoding genes in Pseudomonas putida
Phenotypic–genotypic analysis of GGDEF/EAL/HD-GYP domain-encoding genes in Pseudomonas putida
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恶臭假单胞菌 GGDEF/EAL/HD-GYP 结构域编码基因的表型和基因型分析
DOI：
10.1111/1758-2229.12808
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发表时间：
2019
影响因子：
3.3
通讯作者：
Qiaoyun Huang
中科院分区：
文献类型：
--
作者：
Hailing Nie;Wenli Chen;Qiaoyun Huang
环状二鸟苷(c-di-GMP)是一种广泛保守的细菌信号分子，调节多种细胞过程，如生物膜的形成、菌落形态和游泳运动。恶臭假单胞菌KT2440基因组上有一大组基因编码具有GGDEF/EAL/HD-Gyp结构域的蛋白，其胞内c-di-GMP水平受带有GGDEF结构域的二鸟苷酸环化酶(DGC)和带有EAL或HD-Gyp结构域的磷酸二酯酶(PDE)控制。然而，这些基因的表型-基因相关性和c-di-GMP代谢在很大程度上是未知的。为此，我们系统构建了42个c-di-GMP代谢相关基因的缺失突变/过表达菌株，并对其表型进行了分析，初步揭示了每个基因在生物膜形成、菌落形态和游泳运动中的作用。随后的蛋白质序列比对和细胞c-di-GMP分析结果表明，42个基因中有25个可能编码DGC，9个基因编码PDE，4个基因编码双功能酶，另外4个基因编码酶失活蛋白。这项研究提供了对这42个基因作用的基本了解，并可以作为研究人员进一步阐明这些GGDEF和EAL/HD-Gyp结构域蛋白功能的工具包。
Cyclic diguanylate (c‐di‐GMP) is a broadly conserved bacterial signalling molecule that modulates diverse cellular processes, such as biofilm formation, colony morphology and swimming motility. The intracellular level of c‐di‐GMP is controlled by diguanylate cyclases (DGCs) with GGDEF domain and phosphodiesterases (PDEs) with either EAL or HD‐GYP domain.Pseudomonas putidaKT2440 has a large group of genes on its genome encoding proteins with GGDEF/EAL/HD‐GYP domains. However, phenotypic–genotypic correlation and c‐di‐GMP metabolism of these genes were largely unknown. Herein, by systematically constructing deletion mutants/overexpression strains of the 42 predicted c‐di‐GMP metabolism–related genes and analysing the phenotypes, we preliminarily revealed the role of each gene in biofilm formation, colony morphology and swimming motility. Subsequent results from protein sequence alignments and cellular c‐di‐GMP assessment indicated that 25 out of the 42 genes were likely to encode DGCs, nine genes were predicted to encode PDEs, four genes encoded bifunctional enzymes and the other four genes encoded enzymatically inactive proteins. This study offers a basic understanding of the roles of these 42 genes and can serve as a toolkit for investigators to further elucidate the functions of these GGDEF and EAL/HD‐GYP domain‐containing proteins.