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Chapter 5 : The HD-GYP Domain and Cyclic Di-GMP Signaling

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The HD-GYP Domain and Cyclic Di-GMP Signaling, Page 1 of 2

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Abstract:

A role for the HD-GYP domain in c-di-GMP hydrolysis was then proposed based on examination of the distribution and numbers of GGDEF, EAL, and HD-GYP domains encoded by different bacterial genomes, coupled with the known activities of other members of the HD superfamily of enzymes as metal-dependent hydrolases. This chapter reviews the current understanding of the HD-GYP domain in c-di-GMP signaling. In particular, it discusses (i) the identification of the HD-GYP domain and bioinformatic prediction as a novel c-di-GMP PDE, (ii) the experimental evidence implicating the HD-GYP domain in c-di-GMP degradation, (iii) the biological role of the HD-GYP domain protein RpfG in signal transduction in Xcc, (iv) regulatory interplay between RpfG and other c-di-GMP signaling proteins in Xcc, and (v) emerging information on the role of HD-GYP domain proteins in other bacteria. A role for HD-GYP in c-di-GMP hydrolysis was proposed based on an examination of the distribution and numbers of GGDEF, EAL, and HD-GYP domains encoded by different bacterial genomes, where several genomes encode proteins with the GGDEF and HD-GYP domains but no EAL domain. These findings illustrate two aspects of HD-GYP domain proteins that are consonant with our understanding of the diverse roles of GGDEF and EAL domain proteins. The first is that different HD-GYP domain proteins appear to have distinct regulatory roles.

Citation: Ryan R, McCarthy Y, Dow J. 2010. The HD-GYP Domain and Cyclic Di-GMP Signaling, p 57-67. In Wolfe A, Visick K (ed), The Second Messenger Cyclic Di-GMP. ASM Press, Washington, DC. doi: 10.1128/9781555816667.ch5

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Figures

Image of Figure 1.
Figure 1.

Conservation of amino acid residues and motifs within the HD-GYP domain. (A) Schematic representation of the HD-GYP domain indicating the separation of the regions containing the HD dyad and the GYP motif by a region of high sequence diversity. (B) Alignments of 211 HD-GYP domains encoded by complete microbial genomes (http://www.ncbi.nlm.nih.gov/Complete_Genomes/RRcensus.html) were used to establish conserved residues, and the output was drawn using the WebLogo program (http://weblogo.berkeley.edu). The letters in each position represent amino acid residues found in that position; the height of each letter reflects the fraction of sequences with the corresponding amino acid residue in that position. The residue numbering is from RpfG (XCL.2335) as designated by the SMART nrdb database (http://smart.embl-heidelberg.de).

Citation: Ryan R, McCarthy Y, Dow J. 2010. The HD-GYP Domain and Cyclic Di-GMP Signaling, p 57-67. In Wolfe A, Visick K (ed), The Second Messenger Cyclic Di-GMP. ASM Press, Washington, DC. doi: 10.1128/9781555816667.ch5
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Image of Figure 2.
Figure 2.

Domain architectures of proteins with an HD-GYP domain. The HD-GYP domain can occur singly but is found more often in association with other signaling and regulatory domains, commonly with REC, the receiver domain of two-component regulators. RpfG and PA4781, which are described in the text, have this domain organization. Some proteins with REC and HD-GYP domains such as PA2572 have an additional C-terminal domain that has not been characterized, but has a regulatory role. HD-GYP is also found in association with PilZ and GGDEF domains, with HD domains, with domains related to the C-terminal DNA binding domain of LuxR family regulators (LuxR_C), with HAMP and GAF domains, and with uncharacterized flanking domains. In some proteins, the HDX GK and HHEXXDGXGYP motifs are more widely separated than in the canonical sequence; this is indicated by HD—GYP. TM indicates the proposed transmembrane helix. Organism abbreviations: PA, XC, Rsc, Pfl, PP, CPE, ECA, Mll, Mflv, VV, BP,

Citation: Ryan R, McCarthy Y, Dow J. 2010. The HD-GYP Domain and Cyclic Di-GMP Signaling, p 57-67. In Wolfe A, Visick K (ed), The Second Messenger Cyclic Di-GMP. ASM Press, Washington, DC. doi: 10.1128/9781555816667.ch5
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Image of Figure 3.
Figure 3.

The HD-GYP domain protein RpfG controls multiple functions in Mutation of leads to reduced virulence in plants (top left), reduced production of extracellular enzymes such as protease (top right), reduced motility (bottom right), and increased formation of aggregates in certain media (bottom left).

Citation: Ryan R, McCarthy Y, Dow J. 2010. The HD-GYP Domain and Cyclic Di-GMP Signaling, p 57-67. In Wolfe A, Visick K (ed), The Second Messenger Cyclic Di-GMP. ASM Press, Washington, DC. doi: 10.1128/9781555816667.ch5
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Image of Figure 4.
Figure 4.

Model for role of the HD-GYP domain regulator RpfG in transduction of the DSF cell-cell signal in xanthomonads. The synthesis of the DSF signal requires RpfF, whereas RpfC is a complex sensor kinase responsible for DSF perception. Structural changes that occur upon DSF binding to the RpfC sensory input domain trigger autophosphorylation of RpfC at a histidine (H) residue and phosphorelay to RpfG (solid arrow) via aspartate (D) and histidine (H) residues of the receiver domain (black) and histidine phosphotransfer domain (white) of RpfC, respectively. Phospho-rylation of RpfG activates c-di-GMP degradation by the HD-GYP domain. RpfG may also physically interact with GGDEF domain proteins to influence c-di-GMP concentrations and with other regulators, modulating their activity in transcription (dotted lines). In RpfG influences expression of the CRP-like protein Clp ( ) by an unknown mechanism, leading to activation of a downstream signaling cascade involving other transcriptional regulators, Zur and FhrR (not shown). In ), a second sensor may phosphorylate RpfG in response to DSF. Although shown as a membrane-bound protein, this sensor may equally be located in the cytoplasm.

Citation: Ryan R, McCarthy Y, Dow J. 2010. The HD-GYP Domain and Cyclic Di-GMP Signaling, p 57-67. In Wolfe A, Visick K (ed), The Second Messenger Cyclic Di-GMP. ASM Press, Washington, DC. doi: 10.1128/9781555816667.ch5
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