Cyclic di-GMP Activation of Polynucleotide Phosphorylase Signal-Dependent RNA Processing

Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas,TX 75390-9038, USA.
Journal of Molecular Biology (Impact Factor: 4.33). 02/2011; 407(5):633-9. DOI: 10.1016/j.jmb.2011.02.019
Source: PubMed


The second messenger cyclic diguanylic acid (c-di-GMP) is implicated in key lifestyle decisions of bacteria, including biofilm formation and changes in motility and virulence. Some challenges in deciphering the physiological roles of c-di-GMP are the limited knowledge about the cellular targets of c-di-GMP, the signals that control its levels, and the proportion of free cellular c-di-GMP, if any. Here, we identify the target and the regulatory signal for a c-di-GMP-responsive Escherichia coli ribonucleoprotein complex. We show that a direct c-di-GMP target in E. coli is polynucleotide phosphorylase (PNPase), an important enzyme in RNA metabolism that serves as a 3' polyribonucleotide polymerase or a 3'-to-5' exoribonuclease. We further show that a complex of polynucleotide phosphorylase with the direct oxygen sensors DosC and DosP can perform oxygen-dependent RNA processing. We conclude that c-di-GMP can mediate signal-dependent RNA processing and that macromolecular complexes can compartmentalize c-di-GMP signaling.

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    • "In a study by Tuckerman et al., an E. coli protein complex, termed " degradosome " contained a DGC and PDE which mediate the c-di-GMP-dependent RNA processing (Tuckerman et al., 2011). We used a bacterial adenylate cyclase two-hybrid (BACTH) system to test whether there is a physical interaction between YcgR 3937 and EGcpB or EcpC in D. "
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    ABSTRACT: Dickeya dadantii is a globally dispersed phytopathogen which causes diseases on a wide range of host plants. This pathogen utilizes the type III secretion system (T3SS) to suppress host defense responses, and secretes pectate lyase (Pel) to degrade the plant cell wall. Although the regulatory small RNA (sRNA) RsmB, cyclic diguanylate monophosphate (c-di-GMP), and flagellar regulator have been reported to affect the regulation of these two virulence factors or multiple cell behaviors such as motility and biofilm formation, the linkage between these regulatory components that coordinate the cell behaviors remain unclear. Here we revealed a sophisticated regulatory network that connects the sRNA, c-di-GMP signaling, and flagellar master regulator FlhDC. We propose multi-tiered regulatory mechanisms that link the FlhDC to the T3SS through three distinct pathways including the FlhDC-FliA-YcgR3937 pathway; the FlhDC-EcpC-RpoN-HrpL pathway; and the FlhDC-rsmB-RsmA-HrpL pathway. Among these, EcpC is the most dominant factor for FlhDC to positively regulate T3SS expression.
    No preview · Article · Aug 2015 · Environmental Microbiology
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    • "The ability of a second messenger to have numerous effects on cellular behavior lies in the diversity of c-di-GMP receptors. In other species of bacteria, c-di-GMP has been demonstrated to exert its regulatory effects through proteins with cyclic nucleotide monophosphate domains (Tao et al., 2010), ribonucleoprotein complexes (Tuckerman et al., 2011), transcriptional regulators (Hickman and Harwood, 2008; Krasteva et al., 2010; Fazli et al., 2011), GEMM riboswitches (Sudarsan et al., 2008; Smith et al., 2009; Luo et al., 2013), and PilZ domain-containing proteins (Amikam and Galperin, 2006; Ryjenkov et al., 2006; Bian et al., 2013). To date, only one c-di-GMP-binding protein, the PilZ domain-containing protein PlzA, has been identified in B. burgdorferi (Freedman et al., 2010; Pitzer et al., 2011). "
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    ABSTRACT: In nature, the Lyme disease spirochete Borrelia burgdorferi cycles between the unrelated environments of the Ixodes tick vector and mammalian host. In order to survive transmission between hosts, B. burgdorferi must be able to not only detect changes in its environment, but also rapidly and appropriately respond to these changes. One manner in which this obligate parasite regulates and adapts to its changing environment is through cyclic-di-GMP (c-di-GMP) signaling. c-di-GMP has been shown to be instrumental in orchestrating the adaptation of B. burgdorferi to the tick environment. B. burgdorferi possesses only one set of c-di-GMP-metabolizing genes (one diguanylate cyclase and two distinct phosphodiesterases) and one c-di-GMP-binding PilZ-domain protein designated as PlzA. While studies in the realm of c-di-GMP signaling in B. burgdorferi have exploded in the last few years, there are still many more questions than answers. Elucidation of the importance of c-di-GMP signaling to B. burgdorferi may lead to the identification of mechanisms that are critical for the survival of B. burgdorferi in the tick phase of the enzootic cycle as well as potentially delineate a role (if any) c-di-GMP may play in the transmission and virulence of B. burgdorferi during the enzootic cycle, thereby enabling the development of effective drugs for the prevention and/or treatment of Lyme disease.
    Full-text · Article · May 2014 · Frontiers in Cellular and Infection Microbiology
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    • "The current paradigm indicates that high levels of this messenger are associated with a sessile lifestyle characterized by the formation of biofilms, while low c-di-GMP levels promote biofilm dispersal and swimming motility [29], [30], [31]. Perception of c-di-GMP has been associated with several protein domains [32], [33] and with specific structures in mRNA (riboswitches) [34], [35]. One of the protein domains that has been demonstrated to bind c-di-GMP across the bacterial kingdom is the PilZ domain [4], [24], originally described in cellulose synthases [36], [37]. "
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    ABSTRACT: Diguanylate cyclase and phosphodiesterase enzymatic activities control c-di-GMP levels modulating planktonic versus sessile lifestyle behavior in bacteria. The PilZ domain is described as a sensor of c-di-GMP intracellular levels and the proteins containing a PilZ domain represent the best studied class of c-di-GMP receptors forming part of the c-di-GMP signaling cascade. In P. fluorescens F113 we have found two diguanylate cyclases (WspR, SadC) and one phosphodiesterase (BifA) implicated in regulation of swimming motility and biofilm formation. Here we identify a flgZ gene located in a flagellar operon encoding a protein that contains a PilZ domain. Moreover, we show that FlgZ subcellular localization depends on the c-di-GMP intracellular levels. The overexpression analysis of flgZ in P. fluorescens F113 and P. putida KT2440 backgrounds reveal a participation of FlgZ in Pseudomonas swimming motility regulation. Besides, the epistasis of flgZ over wspR and bifA clearly shows that c-di-GMP intracellular levels produced by the enzymatic activity of the diguanylate cyclase WspR and the phosphodiesterase BifA regulates biofilm formation through FlgZ.
    Full-text · Article · Feb 2014 · PLoS ONE
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