Mechanisms of Cyclic-di-GMP Signaling in Bacteria

137

183

Section: Protein-protein Interactions and The Regulation Of Specific mentioning

confidence: 99%

Cell–cell signal-dependent dynamic interactions between HD-GYP and GGDEF domain proteins mediate virulence in Xanthomonas campestris

Ryan

McCarthy²,

Andrade³

et al. 2010

137

183

“…GGDEF and EAL domain proteins, which are involved in the production and degradation, respectively, of bis-(3′-5′)-cyclic dimeric GMP (cyclic-di-GMP), were also detected at a higher abundance (33,34). Cyclic-di-GMP is an important secondary messenger, regulating the transition from a motile planktonic to a surface-associated biofilm lifestyle in a range of bacteria (34,35), for example by up-regulating the production of adhesins and biofilm matrix components (36)(37)(38)(39) or downregulating motility genes (34).…”

Section: Resultsmentioning

confidence: 99%

Bacterial community assembly based on functional genes rather than species

Burke¹,

Steinberg

Rusch

et al. 2011

689

606

The principles underlying the assembly and structure of complex microbial communities are an issue of long-standing concern to the field of microbial ecology. We previously analyzed the community membership of bacterial communities associated with the green macroalga Ulva australis, and proposed a competitive lottery model for colonization of the algal surface in an attempt to explain the surprising lack of similarity in species composition across different algal samples. Here we extend the previous study by investigating the link between community structure and function in these communities, using metagenomic sequence analysis. Despite the high phylogenetic variability in microbial species composition on different U. australis (only 15% similarity between samples), similarity in functional composition was high (70%), and a core of functional genes present across all algal-associated communities was identified that were consistent with the ecology of surface-and hostassociated bacteria. These functions were distributed widely across a variety of taxa or phylogenetic groups. This observation of similarity in habitat (niche) use with respect to functional genes, but not species, together with the relative ease with which bacteria share genetic material, suggests that the key level at which to address the assembly and structure of bacterial communities may not be "species" (by means of rRNA taxonomy), but rather the more functional level of genes.lateral gene transfer | biofilm | ecological model M etagenomic analysis of environmental microbial communities has revealed an enormous and previously unknown microbial diversity, and expanded our knowledge of their function in a variety of environments (1-5). Much still remains unknown, however, such as the principles underlying the assembly and structure of complex microbial communities, an issue of long-standing concern to the field of microbial ecology. To this aim, several recent studies have supported the "neutral hypothesis" (6-8), a largely stochastic model for community assembly, which assumes that species are ecologically equivalent and that community structure is determined by random processes (9, 10). However, there is also evidence that niche or deterministic processes play a role in community structure (11, 12); thus, both niche and neutral processes are likely to affect the assembly of complex microbial communities.Support for these models is based on species abundance distributions, and critical functional aspects, such as the assumption of ecological equivalence, have for the most part not been tested. In this study, we examine the encoded functions of an algalassociated bacterial community and link patterns of function to patterns of community assembly. Following the results of an earlier study (13), we investigate these communities in the context of the lottery hypothesis, a model for community "assembly" derived from studies of eukaryotic communities, such as coral reef fish (14). This hypothesis incorporates both neutral and functional aspects and arg...

“…The bis-(3′-5′)-cyclic dimeric guanosine monophosphate (c-di-GMP) signaling system is one key pathway that allows bacteria to alter their behavior in response to changing environmental conditions (reviewed in refs. [1][2][3][4]. Cyclicdi-GMP is a second messenger that is synthesized by diguanylate cyclases (DGCs) and degraded by specific phosphodiesterases in response to a variety of stimuli, including light, oxidative conditions, cell density, and antibiotics.…”

mentioning

confidence: 99%

Structural basis of differential ligand recognition by two classes of bis-(3′-5′)-cyclic dimeric guanosine monophosphate-binding riboswitches

Smith

Shanahan

Moore

et al. 2011

104

195

The bis-(3′-5′)-cyclic dimeric guanosine monophosphate (c-di-GMP) signaling pathway regulates biofilm formation, virulence, and other processes in many bacterial species and is critical for their survival. Two classes of c-di-GMP-binding riboswitches have been discovered that bind this second messenger with high affinity and regulate diverse downstream genes, underscoring the importance of RNA receptors in this pathway. We have solved the structure of a c-di-GMP-II riboswitch, which reveals that the ligand is bound as part of a triplex formed with a pseudoknot. The structure also shows that the guanine bases of c-di-GMP are recognized through noncanonical pairings and that the phosphodiester backbone is not contacted by the RNA. Recognition is quite different from that observed in the c-di-GMP-I riboswitch, demonstrating that at least two independent solutions for RNA second messenger binding have evolved. We exploited these differences to design a c-di-GMP analog that selectively binds the c-di-GMP-II aptamer over the c-di-GMP-I RNA. There are several bacterial species that contain both types of riboswitches, and this approach holds promise as an important tool for targeting one riboswitch, and thus one gene, over another in a selective fashion.