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 putida KT2440 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.

中文翻译：

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恶臭假单胞菌中GGDEF / EAL / HD-GYP域编码基因的表型-基因型分析。

环状双鸟苷酸（c-di-GMP）是一种广泛保存的细菌信号分子，可调节多种细胞过程，例如生物膜形成，菌落形态和游泳运动。细胞内c-di-GMP的水平由具有GGDEF域的双鸟苷酸环化酶（DGC）和具有EAL或HD-GYP域的磷酸二酯酶（PDE）控制。恶臭假单胞菌KT2440的基因组上有大量的基因编码带有GGDEF / EAL / HD-GYP结构域的蛋白质。然而，这些基因的表型-基因型相关性和c-di-GMP代谢在很大程度上尚不清楚。在本文中，通过系统地构建42个预测的c-di-GMP代谢相关基因的缺失突变体/过表达菌株并分析表型，我们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。蛋白质序列比对和细胞c-di-GMP评估的后续结果表明，42个基因中有25个可能编码DGC，9个基因预计编码PDE，4个基因编码双功能酶，另外4个基因编码无酶活性的蛋白质。 。