A cyclic GMP-dependent signalling pathway regulates bacterial phytopathogenesis

An, Shi-Qi; Chin, Ko‐Hsin; Febrer, Melanie; McCarthy, Yvonne; Yang, Jauo Guey; Liu, Chung Liang; Swarbreck, David; Rogers, Jane; Dow, J. Maxwell; Chou, Shan‐Ho; Ryan, Robert P.

doi:10.1038/emboj.2013.165

Cited by 48 publications

(36 citation statements)

References 21 publications

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“…This indicates that E. coli cells expressing GcyA or GuaX accumulated mostly cGMP but not cAMP, which is consistent with the original reports. 3,4 To further test the utility of the CRP/CRP G system, we cloned two genes encoding putative nucleotide cyclases of unknown substrate specificity. One of these, AZL_d00190, hereby designated guaA, originates from plasmid pAB510d present in Azospillrillum sp.…”

Section: Crp/crp G Reporter-based Discrimination Of Adenylate and Guamentioning

confidence: 99%

Identification of bacterial guanylate cyclases

et al. 2015

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The ability of bacteria to use cGMP as a second messenger has been controversial for decades. Recently, nucleotide cyclases from Rhodospirillum centenum, GcyA, and Xanthomonas campestris, GuaX, have been shown to possess guanylate cyclase activities. Enzymatic activities of these guanylate cyclases measured in vitro were low, which makes interpretation of the assays ambiguous. Protein sequence analysis at present is insufficient to distinguish between bacterial adenylate and guanylate cyclases, both of which belong to nucleotide cyclases of type III. We developed a simple method for discriminating between guanylate and adenylate cyclase activities in a physiologically relevant bacterial system. The method relies on the use of a mutant cAMP receptor protein, CRPG, constructed here. While wild-type CRP is activated exclusively by cAMP,_CRPG can be activated by either cAMP or cGMP. Using CRP- and CRPG-dependent lacZ expression in two E. coli strains, we verified that R. centenum GcyA and X. campestris GuaX have primarily guanylate cyclase activities. Among two other bacterial nucleotide cyclases tested, one, GuaA from Azospillrillum sp. B510, proved to have guanylate cyclase activity, while the other one, Bradyrhizobium japonicum CyaA, turned out to function as an adenylate cyclase. The results obtained with this reporter system were in excellent agreement with direct measurements of cyclic nucleotides secreted by E. coli expressing nucleotide cyclase genes. The simple genetic screen developed here is expected to facilitate identification of bacterial guanylate cyclases and engineering of guanylate cyclases with desired properties.

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Section: Crp/crp G Reporter-based Discrimination Of Adenylate and Guamentioning

confidence: 99%

Identification of bacterial guanylate cyclases

et al. 2015

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“…2). Both compounds are essential signaling molecules in eukaryotes, and, whereas cGMP is used less commonly in eubacteria, cAMP is widely important in Gram-negative bacteria (35, 36). Growing evidence suggests that the similar 3′,5′-cyclic ribonucleotides cCMP and cUMP might also serve as biological second messengers (37, 38).…”

Section: Examples Of Modern Rna-based Signaling Moleculesmentioning

confidence: 99%

The lost language of the RNA World

Nelson

Breaker

2017

Sci. Signal.

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The possibility of an RNA World is based on the notion that life on Earth passed through a primitive phase without proteins, at a time when all genomes and enzymes were composed of ribonucleic acid. Numerous apparent vestiges of this ancient RNA World remain today, including many nucleotide-derived coenzymes, self-processing ribozymes, metabolite-binding riboswitches, and even ribosomes. Intriguingly, many of the most common signaling molecules and second messengers used by modern organisms are also formed from RNA. For example, nucleotide derivatives such as cAMP, ppGpp, and ZTP, as well as the cyclic dinucleotides c-di-GMP and c-di-AMP, are intimately involved in signaling diverse physiological or metabolic changes in bacteria and other organisms. Herein we describe the potential diversity of this ‘lost language’ of the RNA World, and speculate on whether additional components of this ancient communication machinery might remain hidden though still very much relevant to modern cells.

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“…This small cluster contains the K. pneumonia protein MrkH, which is the only tandem PilZ protein with known structure and cellular function. MrkH is a c-di-GMP-binding transcriptional regulator that regulates the expression of mrkABCDF genes to control type 3 fimbriae and biofilm formation 50 . The crystal structure of MrkH shows that the RxxxR and D/NxSxxG motifs are from the canonical C-terminal PilZ domain, and that the N-terminal PilZ domain also contributes to c-di-GMP binding through residues H69, G73 and R108 ( Figure 11A).…”

Section: Ycgr-like Pilz Proteins Exhibit Great Sequence and Functionmentioning

confidence: 99%

“…The crystal structure of MrkH shows that the RxxxR and D/NxSxxG motifs are from the canonical C-terminal PilZ domain, and that the N-terminal PilZ domain also contributes to c-di-GMP binding through residues H69, G73 and R108 ( Figure 11A). MrkH interacts with DNA mainly through a C-terminal helix in a c-di-GMP-dependent fashion 50 .…”

Section: Ycgr-like Pilz Proteins Exhibit Great Sequence and Functionmentioning

confidence: 99%

Large-scale sequence similarity analysis reveals the scope of sequence and function divergence in PilZ domain proteins

Cheang

Sheng

et al. 2020

Preprint

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PilZ domain-containing proteins constitute a superfamily of widely distributed bacterial signalling proteins. Although studies have established the canonical PilZ domain as an adaptor protein domain evolved to specifically bind the second messenger c-di-GMP, mounting evidence suggest that the PilZ domain has undergone enormous divergent evolution to generate a superfamily of proteins that are characterized by a wide range of c-di-GMP-binding affinity, binding partners and cellular functions. The divergent evolution has even generated families of non-canonical PilZ domains that completely lack c-di-GMP binding ability. In this study, we performed a large-scale sequence analysis on more than 28,000 single-and di-domain PilZ proteins using the sequence similarity networking tool created originally to analyse functionally diverse enzyme superfamilies. The sequence similarity networks (SSN) generated by the analysis feature a large number of putative isofunctional protein clusters, and thus, provide an unprecedented panoramic view of the sequence-function relationship and function diversification in PilZ proteins. Some of the protein clusters in the networks are considered as unexplored clusters that contain proteins with completely unknown biological function;whereas others contain one, two or a few functionally known proteins, and therefore, enabling us to infer the cellular function of uncharacterized homologs or orthologs. With the ultimate goal of elucidating the diverse roles played by PilZ proteins in bacterial signal transduction, the work described here will facilitate the annotation of the vast number of PilZ proteins encoded by bacterial genome and help to prioritize functionally unknown PilZ proteins for future studies.3 Importance Although PilZ domain is best known as the protein domain evolved specifically for the binding of the second messenger c-di-GMP, divergent evolution has generated a superfamily of PilZ proteins with a diversity of ligand or protein-binding properties and cellular functions.We analysed the sequences of more than 28,000 PilZ proteins using the sequence similarity networking (SSN) tool to yield a global view of the sequence-function relationship and function diversification in PilZ proteins. The results will facilitate the annotation of the vast number of PilZ proteins encoded by bacterial genomes and help us prioritize PilZ proteins for future studies.

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A cyclic GMP-dependent signalling pathway regulates bacterial phytopathogenesis

Cited by 48 publications

References 21 publications

Identification of bacterial guanylate cyclases

Identification of bacterial guanylate cyclases

The lost language of the RNA World

Large-scale sequence similarity analysis reveals the scope of sequence and function divergence in PilZ domain proteins

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