A Novel Tetrameric PilZ Domain Structure from Xanthomonads

Li, Tso-Ning; Chin, Ko‐Hsin; Fung, Kit-Man; Yang, Ming-Te; Wang, Andrew H.-J.; Chou, Shan‐Ho

doi:10.1371/journal.pone.0022036

Cited by 20 publications

(18 citation statements)

References 63 publications

(101 reference statements)

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“…The binding of cyclic di-GMP was prevented by alanine substitution of R21 and Q24 (Fig. 5A), conserved residues within PilZ domain proteins implicated in nucleotide binding (Li et al, 2011). To determine whether cyclic di-GMP binding is required for the formation of the triprotein complex and regulation of motility, the effect of expressing the R21AQ24A variant of XC_2249 in the XC_2249 mutant background was examined (Fig.…”

Section: Cyclic Di-gmp Binding By Xc_2249 Is Not Required For Motilitmentioning

confidence: 99%

Retracted: Dynamic complex formation between HD‐GYP, GGDEF and PilZ domain proteins regulates motility in Xanthomonas campestris

Ryan

McCarthy

Kiely

et al. 2012

Molecular Microbiology

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SummaryRpfG is a member of a class of wide spread bacterial two-component regulators with an HD-GYP cyclic di-GMP phosphodiesterase domain. In the plant pathogen Xanthomonas campestris, RpfG together with the sensor kinase RpfC regulates multiple factors as a response to the cell-to-cell Diffusible Signalling Factor (DSF). A dynamic physical interaction of RpfG with two diguanylate cyclase (GGDEF) domain proteins controls motility. Here we show that, contrary to expectation, regulation of motility by the GGDEF domain proteins does not depend upon their cyclic di-GMP synthetic activity. Furthermore we show that the complex of RpfG and GGDEF domain proteins recruits a specific PilZ domain 'adaptor' protein, and this complex then interacts with the pilus motor proteins PilU and PiIT. The results support a model in which DSF signalling influences motility through the highly regulated dynamic interaction of proteins that affect pilus action. A specific motif that we identify to be required for HD-GYP domain interaction is conserved in a number of GGDEF domain proteins, suggesting that regulation via interdomain interactions is of broad relevance.

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Section: Cyclic Di-gmp Binding By Xc_2249 Is Not Required For Motilitmentioning

confidence: 99%

Retracted: Dynamic complex formation between HD‐GYP, GGDEF and PilZ domain proteins regulates motility in Xanthomonas campestris

Ryan

McCarthy

Kiely

et al. 2012

Molecular Microbiology

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“…Furthermore, PilZ domain proteins were found to adopt different oligomeric states (Fig. 1), from monomeric to tetrameric (82,83,87,152) (51,52,148,(154)(155)(156), polysaccharide synthesis and translocation (18,149,157), and DNA binding (120,158), are described in this review. It is clear that the PilZ domain functions as a versatile module that can regulate diverse activities in a c-di-GMP-dependent manner.…”

Section: Types Of C-di-gmp Receptorsmentioning

confidence: 92%

Cyclic di-GMP: the First 25 Years of a Universal Bacterial Second Messenger

Römling

Galperin

Gomelsky

2013

Microbiol Mol Biol Rev

1,501

1,698

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SUMMARY Twenty-five years have passed since the discovery of cyclic dimeric (3′→5′) GMP (cyclic di-GMP or c-di-GMP). From the relative obscurity of an allosteric activator of a bacterial cellulose synthase, c-di-GMP has emerged as one of the most common and important bacterial second messengers. Cyclic di-GMP has been shown to regulate biofilm formation, motility, virulence, the cell cycle, differentiation, and other processes. Most c-di-GMP-dependent signaling pathways control the ability of bacteria to interact with abiotic surfaces or with other bacterial and eukaryotic cells. Cyclic di-GMP plays key roles in lifestyle changes of many bacteria, including transition from the motile to the sessile state, which aids in the establishment of multicellular biofilm communities, and from the virulent state in acute infections to the less virulent but more resilient state characteristic of chronic infectious diseases. From a practical standpoint, modulating c-di-GMP signaling pathways in bacteria could represent a new way of controlling formation and dispersal of biofilms in medical and industrial settings. Cyclic di-GMP participates in interkingdom signaling. It is recognized by mammalian immune systems as a uniquely bacterial molecule and therefore is considered a promising vaccine adjuvant. The purpose of this review is not to overview the whole body of data in the burgeoning field of c-di-GMP-dependent signaling. Instead, we provide a historic perspective on the development of the field, emphasize common trends, and illustrate them with the best available examples. We also identify unresolved questions and highlight new directions in c-di-GMP research that will give us a deeper understanding of this truly universal bacterial second messenger.

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“…Many PilZ domain proteins, including the eponymous PilZ protein from P. aeruginosa, belong to type II, which lacks the Nterminal RXXXR motif and is incapable of binding c-di-GMP (26)(27)(28). PilZ type III is a truncated version that forms a stable tetramer via a helical bundle (29); it does not bind c-di-GMP either.…”

Section: Why More Than a Single C-di-gmp Adaptor Protein?mentioning

confidence: 99%

Diversity of Cyclic Di-GMP-Binding Proteins and Mechanisms

2016

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Cyclic di-GMP (c-di-GMP) synthetases and hydrolases (GGDEF, EAL, and HD-GYP domains) can be readily identified in bacterial genome sequences by using standard bioinformatic tools. In contrast, identification of c-di-GMP receptors remains a difficult task, and the current list of experimentally characterized c-di-GMP-binding proteins is likely incomplete. Several classes of c-di-GMP-binding proteins have been structurally characterized; for some others, the binding sites have been identified; and for several potential c-di-GMP receptors, the binding sites remain to be determined. We present here a comparative structural analysis of c-di-GMP-protein complexes that aims to discern the common themes in the binding mechanisms that allow c-di-GMP receptors to bind it with (sub)micromolar affinities despite the 1,000-fold excess of GTP. The available structures show that most receptors use their Arg and Asp/Glu residues to bind c-di-GMP monomers, dimers, or tetramers with stacked guanine bases. The only exception is the EAL domains that bind c-di-GMP monomers in an extended conformation. We show that in c-di-GMPbinding signature motifs, Arg residues bind to the O-6 and N-7 atoms at the Hoogsteen edge of the guanine base, while Asp/Glu residues bind the N-1 and N-2 atoms at its Watson-Crick edge. In addition, Arg residues participate in stacking interactions with the guanine bases of c-di-GMP and the aromatic rings of Tyr and Phe residues. This may account for the presence of Arg residues in the active sites of every receptor protein that binds stacked c-di-GMP. We also discuss the implications of these structural data for the improved understanding of the c-di-GMP signaling mechanisms.

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A Novel Tetrameric PilZ Domain Structure from Xanthomonads

Cited by 20 publications

References 63 publications

Retracted: Dynamic complex formation between HD‐GYP, GGDEF and PilZ domain proteins regulates motility in Xanthomonas campestris

Retracted: Dynamic complex formation between HD‐GYP, GGDEF and PilZ domain proteins regulates motility in Xanthomonas campestris

Cyclic di-GMP: the First 25 Years of a Universal Bacterial Second Messenger

Diversity of Cyclic Di-GMP-Binding Proteins and Mechanisms

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