Riboswitches in Eubacteria Sense the Second Messenger Cyclic Di-GMP

Sudarsan, Narasimhan; Lee, E. R.; Weinberg, Zasha; Moy, Ryan H.; Kim, J. N.; Link, Kristian H.; Breaker, Ronald R.

doi:10.1126/science.1159519

Cited by 633 publications

(770 citation statements)

References 22 publications

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“…These include proteins containing PilZ domains, or even degenerate GGDEF/EAL domains, which have been found to bind c-di-GMP and regulate related downstream processes such as motility and virulence (Amikam & Galperin, 2006;McCarthy et al, 2008;Navarro et al, 2009;Newell et al, 2009;Pratt et al, 2007;Ryjenkov et al, 2006). Besides mediating protein-protein interactions, c-di-GMP has been shown also to regulate protein translation through two classes of c-di-GMP riboswitches (Smith et al, 2011;Sudarsan et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

Comprehensive overexpression analysis of cyclic-di-GMP signalling proteins in the phytopathogen Pectobacterium atrosepticum reveals diverse effects on motility and virulence phenotypes

et al. 2014

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Bis-(39-59)-cyclic dimeric guanosine monophosphate (c-di-GMP) is a ubiquitous bacterial signalling molecule produced by diguanylate cyclases of the GGDEF-domain family. Elevated c-di-GMP levels or increased GGDEF protein expression is frequently associated with the onset of sessility and biofilm formation in numerous bacterial species. Conversely, phosphodiesterasedependent diminution of c-di-GMP levels by EAL-and HD-GYP-domain proteins is often accompanied by increased motility and virulence. In this study, we individually overexpressed 23 predicted GGDEF, EAL or HD-GYP-domain proteins encoded by the phytopathogen Pectobacterium atrosepticum strain SCRI1043. MS-based detection of c-di-GMP and 59-phosphoguanylyl-(39-59)-guanosine in these strains revealed that overexpression of most genes promoted modest 1-10-fold changes in cellular levels of c-di-GMP, with the exception of the GGDEF-domain proteins ECA0659 and ECA3374, which induced 1290-and 7660-fold increases, respectively. Overexpression of most EAL domain proteins increased motility, while overexpression of most GGDEF domain proteins reduced motility and increased poly-b-1,6-N-acetyl-glucosamine-dependent flocculation. In contrast to domain-based predictions, overexpression of the EAL protein ECA3549 or the HD-GYP protein ECA3548 increased c-di-GMP concentrations and reduced motility. Most overexpression constructs altered the levels of secreted cellulases, pectinases and proteases, confirming c-di-GMP regulation of virulence in Pe. atrosepticum. However, there was no apparent correlation between virulence-factor induction and the domain class expressed or cellular c-di-GMP levels, suggesting that regulation was in response to specific effectors within the network, rather than total c-di-GMP concentration. Finally, we demonstrated that the cellular localization patterns vary considerably for GGDEF/EAL/HD-GYP proteins, indicating it is a likely factor restricting specific interactions within the c-di-GMP network.

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Section: Introductionmentioning

confidence: 99%

Comprehensive overexpression analysis of cyclic-di-GMP signalling proteins in the phytopathogen Pectobacterium atrosepticum reveals diverse effects on motility and virulence phenotypes

et al. 2014

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“…These RNA domains, known as riboswitches, are components of a cis-acting genetic control module, which bind to a diverse array of metabolites and control the genes involved in the biosynthesis or degradation of these metabolites (Winkler and Breaker 2005). Riboswitches have also been found that bind second-messenger molecules to regulate fundamental cellular processes (Sudarsan et al 2008). Structural changes within the riboswitch occur upon ligand binding, allowing the riboswitch to interact with an expression platform to modulate gene expression by effects on transcriptional or translational efficiency (Yarnell and Roberts 1999;.…”

Section: Introductionmentioning

confidence: 99%

Identification of a tertiary interaction important for cooperative ligand binding by the glycine riboswitch

Erion¹,

Strobel²

2010

RNA

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The glycine riboswitch has a tandem dual aptamer configuration, where each aptamer is a separate ligand-binding domain, but the aptamers function together to bind glycine cooperatively. We sought to understand the molecular basis of glycine riboswitch cooperativity by comparing sites of tertiary contacts in a series of cooperative and noncooperative glycine riboswitch mutants using hydroxyl radical footprinting, in-line probing, and native gel-shift studies. The results illustrate the importance of a direct or indirect interaction between the P3b hairpin of aptamer 2 and the P1 helix of aptamer 1 in cooperative glycine binding. Furthermore, our data support a model in which glycine binding is sequential; where the binding of glycine to the second aptamer allows tertiary interactions to be made that facilitate binding of a second glycine molecule to the first aptamer. These results provide insight into cooperative ligand binding in RNA macromolecules.

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“…Recent observations indicate that c-di-GMP can act as a riboswitch, binding specific elements (aptamers) in the UTRs of some mRNAs and affecting their stability (Sudarsan et al, 2008). The pgaABCD transcript is characterized by a rather long UTR (234 nt; Wang et al, 2005) and is regulated at the level of mRNA stability by the CsrA protein.…”

Section: Discussionmentioning

confidence: 99%

“…Thus, YddV does not seem to regulate pgaABCD expression by modulating CsrA activity. Since c-di-GMP has been shown to act as a riboswitch, and to be able to increase the chemical and functional half-life of mRNA carrying c-di-GMP-responding elements (Sudarsan et al, 2008), we tested the possibility that the yddV gene affects pgaABCD mRNA stability via its DGC activity. mRNA decay kinetics experiments showed that the pgaA transcript has a half-life of~1.5 min in the MG1655 strain; yddV inactivation did not affect pgaABCD mRNA stability in the MG1655 background (data not shown), suggesting that yddV-dependent pgaABCD regulation is not mediated by mRNA stabilization.…”

Section: Regulation Of Pgaabcd Expression By Dgcsmentioning

confidence: 99%

“…the FleQ regulator in Pseudomonas aeruginosa (Hickman & Harwood, 2008), the VpsT protein in Vibrio cholerae (Krasteva et al, 2010) and the CLP protein in Xanthomonas campestris (Chin et al, 2010). In addition, c-di-GMP can regulate gene expression through direct binding to riboswitch elements in mRNAs (Sudarsan et al, 2008), bypassing the need for c-di-GMPbinding regulatory proteins.…”

Section: Introductionmentioning

confidence: 99%

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The diguanylate cyclase YddV controls production of the exopolysaccharide poly-N-acetylglucosamine (PNAG) through regulation of the PNAG biosynthetic pgaABCD operon

et al. 2010

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In Gram-negative bacteria, production of adhesion factors and extracellular polysaccharides (EPS) is promoted by the activity of diguanylate cyclases (DGCs), a class of enzymes able to catalyse the synthesis of the signal molecule bis-(39,59)-cyclic di-guanylic acid (c-di-GMP). In this report we show that in Escherichia coli, overexpression of the YddV protein, but not of other DGCs such as AdrA and YcdT, induces the production of the EPS poly-N-acetylglucosamine (PNAG) by stimulating expression of pgaABCD, the PNAG-biosynthetic operon. Stimulation of PNAG production and activation of pgaABCD expression by the YddV protein are abolished by inactivation of its GGDEF motif, responsible for DGC activity. Consistent with the effects of YddV overexpression, inactivation of the yddV gene negatively affects pgaABCD transcription and PNAG-mediated biofilm formation. pgaABCD regulation by the yddV gene also takes place in a mutant carrying a partial deletion of the csrA gene, which encodes the main regulator of pgaABCD expression, suggesting that YddV does not regulate pgaABCD through modulation of CsrA activity. Our results demonstrate that PNAG production does not simply respond to intracellular c-di-GMP concentration, but specifically requires the DGC activity of the YddV protein, thus supporting the notion that in E. coli, c-di-GMP biosynthesis by a given DGC protein triggers regulatory events that lead to activation of specific sets of EPS biosynthetic genes or proteins. INTRODUCTIONMost bacteria are able to switch between two different 'lifestyles': single cells (planktonic mode) and biofilm, i.e. a sessile microbial community. Biofilm and planktonic cells differ significantly in their physiology, in their gene expression pattern and even in their morphology. In particular, biofilm cells are characterized by production of adhesion factors and extracellular polysaccharides (EPS), resistance to environmental stresses, and lower sensitivity to antibiotics compared with planktonic cells (Costerton et al., 1995;Anderl et al., 2000;Harrison et al., 2007Harrison et al., , 2009).Transition from planktonic cells to biofilm is regulated by environmental and physiological cues, relayed to the bacterial cell by signal molecules or 'second messengers'. A second messenger, bis-(39,59)-cyclic diguanylic acid, better known as cyclic-di-GMP (c-di-GMP), plays a pivotal role in biofilm formation and maintenance by stimulating production of EPS and adhesion factors (Ross et al., 1991;Simm et al., 2004;Kader et al., 2006;Weber et al., 2006). In addition, c-di-GMP biosynthesis affects important cellular processes, such as morphological differentiation and cell replication in Caulobacter crescentus (Paul et al., 2004), cell motility (Méndez-Ortiz et al., 2006; Jonas et al., 2008) and virulence factor production (Kulasakara et al., 2006;Hammer & Bassler, 2009). In Enterobacteria, c-di-GMP seems to be involved in regulation of adhesion factors, such as curli and cellulose, important for adaptation and survival outside the warm-blooded hos...

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Riboswitches in Eubacteria Sense the Second Messenger Cyclic Di-GMP

Cited by 633 publications

References 22 publications

Comprehensive overexpression analysis of cyclic-di-GMP signalling proteins in the phytopathogen Pectobacterium atrosepticum reveals diverse effects on motility and virulence phenotypes

Comprehensive overexpression analysis of cyclic-di-GMP signalling proteins in the phytopathogen Pectobacterium atrosepticum reveals diverse effects on motility and virulence phenotypes

Identification of a tertiary interaction important for cooperative ligand binding by the glycine riboswitch

The diguanylate cyclase YddV controls production of the exopolysaccharide poly-N-acetylglucosamine (PNAG) through regulation of the PNAG biosynthetic pgaABCD operon

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