The second messenger cyclic dimeric GMP (c-di-GMP) is almost ubiquitous among bacteria as are the c-di-GMP turnover proteins, which mediate the transition between motility and sessility. EAL domain proteins have been characterized as c-di-GMP-specific phosphodiesterases. While most EAL domain proteins contain additional, usually N-terminal, domains, there is a distinct family of proteins with stand-alone EAL domains, exemplified by Salmonella enterica serovar Typhimurium proteins STM3611 (YhjH/PdeH), a c-di-GMP-specific phosphodiesterase, and the enzymatically inactive STM1344 (YdiV/CdgR) and STM1697, which regulate bacterial motility through interaction with the flagellar master regulator, FlhDC. We have analyzed the phylogenetic distribution of EAL-only proteins and their potential functions. Genes encoding EAL-only proteins were found in various bacterial phyla, although most of them were seen in proteobacteria, particularly enterobacteria. Based on the conservation of the active site residues, nearly all stand-alone EAL domains encoded by genomes from phyla other than proteobacteria appear to represent functional phosphodiesterases. Within enterobacteria, EAL-only proteins were found to cluster either with YhjH or with one of the subfamilies of YdiV-related proteins. EAL-only proteins from Shigella flexneri, Klebsiella pneumoniae, and Yersinia enterocolitica were tested for their ability to regulate swimming and swarming motility and formation of the red, dry, and rough (rdar) biofilm morphotype. In these tests, YhjH-related proteins S4210, KPN_01159, KPN_03274, and YE4063 displayed properties typical of enzymatically active phosphodiesterases, whereas S1641 and YE1324 behaved like members of the YdiV/STM1697 subfamily, with Yersinia enterocolitica protein YE1324 shown to downregulate motility in its native host. Of two closely related EAL-only proteins, YE2225 is an active phosphodiesterase, while YE1324 appears to interact with FlhD. These results suggest that in FlhDC-harboring beta- and gammaproteobacteria, some EAL-only proteins evolved to become catalytically inactive and regulate motility and biofilm formation by interacting with FlhDC.IMPORTANCE The EAL domain superfamily consists mainly of proteins with cyclic dimeric GMP-specific phosphodiesterase activity, but individual domains have been classified in three classes according to their functions and conserved amino acid signatures. Proteins that consist solely of stand-alone EAL domains cannot rely on other domains to form catalytically active dimers, and most of them fall into one of two distinct classes: catalytically active phosphodiesterases with well-conserved residues of the active site and the dimerization loop, and catalytically inactive YdiV/CdgR-like proteins that regulate bacterial motility by binding to the flagellar master regulator, FlhDC, and are found primarily in enterobacteria. The presence of apparently inactive EAL-only proteins in the bacteria that do not express FlhD suggests the existence of additional EAL interaction partners.

译文

:第二信使环二聚体GMP(c-di-GMP)在细菌中几乎无处不在,而c-di-GMP周转蛋白则介导运动性和固执性之间的过渡。 EAL域蛋白已被表征为c-di-GMP特异性磷酸二酯酶。虽然大多数EAL结构域蛋白都包含其他(通常是N端)结构域,但是有一个具有独立EAL结构域的独特蛋白家族,例如肠炎沙门氏菌血清鼠伤寒蛋白STM3611(YhjH / PdeH),c-di-GMP-特定的磷酸二酯酶,以及无酶活性的STM1344(YdiV / CdgR)和STM1697,它们通过与鞭毛主调节剂FlhDC相互作用来调节细菌的运动。我们已经分析了仅EAL蛋白的系统发育分布及其潜在功能。在各种细菌门中都发现了仅编码EAL蛋白的基因,尽管其中大多数都出现在变形杆菌,特别是肠杆菌中。基于活性位点残基的保守性,几乎所有由非细菌菌属的门的基因组编码的独立EAL结构域似乎都代表功能性磷酸二酯酶。在肠杆菌中,仅EAL蛋白被发现与YhjH或YdiV相关蛋白的一个亚家族聚集在一起。测试了来自弗氏志贺氏菌,肺炎克雷伯菌和小肠结肠炎耶尔森氏菌的仅EAL蛋白调节游泳和成群运动以及形成红色,干燥和粗糙(rdar)生物膜形态的能力。在这些测试中,YhjH相关蛋白S4210,KPN_01159,KPN_03274和YE4063显示出具有酶促活性的磷酸二酯酶的典型特性,而S1641和YE1324的行为类似于YdiV / STM1697亚家族的成员,而小肠结肠炎耶尔森氏菌蛋白YE1324则可下调其运动能力。主持人。在两个密切相关的仅EAL蛋白质中,YE2225是一种活性磷酸二酯酶,而YE1324似乎与FlhD相互作用。这些结果表明,在具有FlhDC的β和γ变形蛋白细菌中,一些仅EAL的蛋白质通过与FlhDC相互作用而进化为变得无催化活性并调节运动性和生物膜形成。活性,但根据其功能和保守的氨基酸特征,将单个域分为三类。仅由独立的EAL结构域组成的蛋白质不能依靠其他结构域形成催化活性的二聚体,并且大多数属于两种截然不同的类别之一:催化活性的磷酸二酯酶,其具有保守的活性位点残基和二聚环,以及无催化作用的YdiV / CdgR样蛋白,它们通过与鞭毛主调节剂FlhDC结合来调节细菌运动,主要存在于肠杆菌中。细菌中不表达FlhD的仅非EAL活性蛋白的存在表明存在其他EAL相互作用伴侣。

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