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Recent studies have identified c‐di‐GMP as a novel secondary messenger molecule that is heavily involved in regulating bacterial biofilm formation, motility, production of pathogenicity factors etc. PilZ domain‐containing proteins have been suggested and subsequently proved to be the c‐di‐GMP receptor. However, considering the diverse biological functions exhibited by c‐di‐GMP, it may be that receptors other than the PilZ domain exist. An essential protein from the plant pathogen Xanthomonas campestris pv. campestris (Xcc) that contains a noncanonical PilZ signature motif yet is critical for Xcc pathogenicity has been cloned, purified and crystallized. Detailed characterization of this protein may reveal an alternative binding mode of c‐di‐GMP and allow a more thorough understanding of how c‐di‐GMP exhibits its diverse effects.  相似文献   

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c‐di‐GMP is a major secondary‐messenger molecule in regulation of bacterial pathogenesis. Therefore, the c‐di‐GMP‐mediated signal transduction network is of considerable interest. The PilZ domain was the first c‐di‐GMP receptor to be predicted and identified. However, every PilZ domain binds c‐di‐GMP with a different binding affinity. Intriguingly, a noncanonical PilZ domain has recently been found to serve as a mediator to link FimXEAL to the PilB or PilT ATPase to control the function of type IV pili (T4P). It is thus essential to determine the structure of the FimXEAL–PilZ complex in order to determine how the binding of c‐di‐GMP to the FimXEAL domain induces conformational change of the adjoining noncanonical PilZ domain, which may transmit information to PilB or PilT to control T4P function. Here, the preparation and preliminary X‐ray diffraction studies of the XccFimXEAL–c‐di‐GMP and XccFimXEAL–c‐di‐GMP–XccPilZ complexes from Xcc (Xanthomonas campestris pv. campesteris) are reported. Detailed studies of these complexes may allow a more thorough understanding of how c‐di‐GMP transmits its effects through the degenerate EAL domain and the noncanonical PilZ domain.  相似文献   

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Bacterial polynucleotide phosphorylase (PNPase) is a 3′–5′ processive exoribonuclease that participates in mRNA turnover and quality control of rRNA precursors in many bacterial species. It also associates with the RNase E scaffold and other components to form a multi‐enzyme RNA degradasome machinery that performs a wider regulatory role in degradation, quality control and maturation of mRNA and noncoding RNA. Several crystal structures of bacterial PNPases, as well as some biological activity studies, have been published. However, how the enzymatic activity of PNPase is regulated is less well understood. Recently, Escherichia coli PNPase was found to be a direct c‐di‐GMP binding target, raising the possibility that c‐di‐GMP may participate in the regulation of RNA processing. Here, the successful cloning, purification and crystallization of S1‐domain‐truncated Xanthomonas campestris PNPase (XcPNPaseΔS1) in the presence of c‐di‐GMP are reported. The crystals belonged to the monoclinic space group C2, with unit‐cell parameters a = 132.76, b = 128.38, c = 133.01 Å, γ = 93.3°, and diffracted to a resolution of 2.00 Å.  相似文献   

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Cyclic diguanosine monophosphate (c‐di‐GMP) is a key signalling molecule involved in regulating many important biological functions in bacteria. The synthesis of c‐di‐GMP is catalyzed by the GGDEF‐domain‐containing diguanylate cyclase (DGC), the activity of which is regulated by the binding of product at the allosteric inhibitory (I) site. However, a significant number of GGDEF domains lack the RxxD motif characteristic of the allosteric I site. Here, the structure of XCC4471GGDEF, the GGDEF domain of a DGC from Xanthomonas campestris, in complex with c‐di‐GMP has been solved. Unexpectedly, the structure of the complex revealed a GGDEF‐domain dimer cross‐linked by two molecules of c‐di‐GMP at the strongly conserved active sites. In the complex (c‐di‐GMP)2 adopts a novel partially intercalated form, with the peripheral guanine bases bound to the guanine‐binding pockets and the two central bases stacked upon each other. Alteration of the residues involved in specific binding to c‐di‐GMP led to dramatically reduced Kd values between XCC4471GGDEF and c‐di‐GMP. In addition, these key residues are strongly conserved among the many thousands of GGDEF‐domain sequences identified to date. These results indicate a new product‐bound form for GGDEF‐domain‐containing proteins obtained via (c‐di‐GMP)2 binding at the active site. This novel XCC4471GGDEF–c‐di‐GMP complex structure may serve as a general model for the design of lead compounds to block the DGC activity of GGDEF‐domain‐containing proteins in X. campestris or other microorganisms that contain multiple GGDEF‐domain proteins.  相似文献   

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PA4608 is a single PilZ domain protein from Pseudomonas aeruginosa that binds to cyclic dimeric guanosine monophosphate (c-di-GMP). Although the monomeric structure of unbound PA4608 has been studied in detail, the molecular details of c-di-GMP binding to this protein are still uncharacterized. Hence, we determined the solution structure of c-di-GMP bound PA4608. We found that PA4608 undergoes conformational changes to expose the c-di-GMP binding site by ejection of the C-terminal 3(10) helix. A dislocation of the C-terminal tail in the presence of c-di-GMP implies that this region acts as a lid that alternately covers and exposes the hydrophobic surface of the binding site. In addition, mutagenesis and NOE data for PA4608 revealed that conserved residues are in contact with the c-di-GMP molecule. The unique structural characteristics of PA4608, including its monomeric state and its ligand binding characteristics, yield insight into its function as a c-di-GMP receptor.  相似文献   

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The bacterial second messenger cyclic diguanylate monophosphate (c‐di‐GMP) mediates multiple aspects of bacterial physiology through binding to various effectors. In some cases, these effectors are single‐domain proteins which only contain a PilZ domain. It remains largely unknown how single‐domain PilZ proteins function and regulate their downstream targets. Recently, a single‐domain PilZ protein, MapZ (PA4608), was identified to inhibit the activity of the methyltransferase CheR1. Here, crystal structures of the C‐terminal domain of CheR1 containing SAH and of CheR1 in complex with c‐di‐GMP‐bound MapZ are reported. It was observed that the binding site of MapZ in CheR1 partially overlaps with the SAH/SAM‐binding pocket. Consequently, binding of MapZ blocks SAH/SAM binding. This provides direct structural evidence on the mechanism of inhibition of CheR1 by MapZ in the presence of c‐di‐GMP.  相似文献   

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Bacterial biofilms are multicellular aggregates encased in an extracellular matrix mainly composed of exopolysaccharides (EPSs), protein and nucleic acids, which determines the architecture of the biofilm. Erwinia amylovora Ea1189 forms a biofilm inside the xylem of its host, which results in vessel plugging and water transport impairment. The production of the EPSs amylovoran and levan is critical for the formation of a mature biofilm. In addition, cyclic dimeric GMP (c‐di‐GMP) has been reported to positively regulate amylovoran biosynthesis and biofilm formation in E. amylovora Ea1189. In this study, we demonstrate that cellulose is synthesized by E. amylovora Ea1189 and is a major modulator of the three‐dimensional characteristics of biofilms formed by this bacterium, and also contributes to virulence during systemic host invasion. In addition, we demonstrate that the activation of cellulose biosynthesis in E. amylovora is a c‐di‐GMP‐dependent process, through allosteric binding to the cellulose catalytic subunit BcsA. We also report that the endoglucanase BcsZ is a key player in c‐di‐GMP activation of cellulose biosynthesis. Our results provide evidence of the complex composition of the extracellular matrix produced by E. amylovora and the implications of cellulose biosynthesis in shaping the architecture of the biofilm and in the expression of one of the main virulence phenotypes of this pathogen.  相似文献   

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Cyclic guanosine 3′,5′‐monophosphate (cyclic GMP) is a second messenger whose role in bacterial signalling is poorly understood. A genetic screen in the plant pathogen Xanthomonas campestris (Xcc) identified that XC_0250, which encodes a protein with a class III nucleotidyl cyclase domain, is required for cyclic GMP synthesis. Purified XC_0250 was active in cyclic GMP synthesis in vitro. The linked gene XC_0249 encodes a protein with a cyclic mononucleotide‐binding (cNMP) domain and a GGDEF diguanylate cyclase domain. The activity of XC_0249 in cyclic di‐GMP synthesis was enhanced by addition of cyclic GMP. The isolated cNMP domain of XC_0249 bound cyclic GMP and a structure–function analysis, directed by determination of the crystal structure of the holo‐complex, demonstrated the site of cyclic GMP binding that modulates cyclic di‐GMP synthesis. Mutation of either XC_0250 or XC_0249 led to a reduced virulence to plants and reduced biofilm formation in vitro. These findings describe a regulatory pathway in which cyclic GMP regulates virulence and biofilm formation through interaction with a novel effector that directly links cyclic GMP and cyclic di‐GMP signalling.  相似文献   

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Riboswitches are RNA molecules that regulate gene expression using conformation change, affected by binding of small molecule ligands. Although a number of ligand‐bound aptamer complex structures have been solved, it is important to know ligand‐free conformations of the aptamers in order to understand the mechanism of specific binding by ligands. In this paper, we use dynamics simulations on a series of models to characterize the ligand‐free and ligand‐bound aptamer domain of the c‐di‐GMP class I (GEMM‐I) riboswitch. The results revealed that the ligand‐free aptamer has a stable state with a folded P2 and P3 helix, an unfolded P1 helix and open binding pocket. The first Mg ions binding to the aptamer is structurally favorable for the successive c‐di‐GMP binding. The P1 helix forms when c‐di‐GMP is successive bound. Three key junctions J1/2, J2/3 and J1/3 in the GEMM‐I riboswitch contributing to the formation of P1 helix have been found. The binding of the c‐di‐GMP ligand to the GEMM‐I riboswitch induces the riboswitch's regulation through the direct allosteric communication network in GEMM‐I riboswitch from the c‐di‐GMP binding sites in the J1/2 and J1/3 junctions to the P1 helix, the indirect ones from those in the J2/3 and P2 communicating to P1 helix via the J1/2 and J1/3 media.  相似文献   

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FleQ is a master regulator that controls bacterial flagellar gene expression. It is a unique enhancer‐binding protein or repressor protein comprising an N‐terminal FleQ domain, an AAA+/ATPase σ54‐interaction domain and a helix–turn–helix DNA‐binding domain. FleN is a putative ATPase with a deviant Walker A motif that works together with FleQ by binding to the FleQ N‐terminal domain to fully express pel, psl and cdr operons in the presence of c‐di‐GMP to enhance biofilm formation. Stenotrophomonas maltophilia is an emerging human pathogen that causes fatal infections in humans. In order to understand the interaction between the FleN and FleQ domains and its effect on S. maltophilia biofilm formation, determination of the FleQ–c‐di‐GMP and FleN–FleQ–c‐di‐GMP complex structures was embarked upon. Towards this goal, the FleQ N‐terminal domain from S. maltophilia was first cloned and expressed in Escherichia coli. Native and SeMet‐labelled FleQ domains were successfully crystallized and diffracted to resolutions of 2.08 and 2.58 Å, respectively.  相似文献   

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PA4608 is a 125 residue protein from Pseudomonas aeruginosa with a recent identification as a PilZ domain and putative bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) adaptor protein that plays a role in bacterial second-messenger regulated processes. The nuclear magnetic resonance (NMR) structure of PA4608 has been determined and c-di-GMP binding has been confirmed by NMR titration studies. The monomeric core structure of PA4608 contains a six-stranded anti-parallel beta barrel flanked by three helices. Conserved surface residues among PA4608 homologs suggest the c-di-GMP binding site is at one end of the barrel and includes residues in the helices as well as in the unstructured N-terminus. Chemical shift changes in PA4608 resonances upon titration with c-di-GMP confirm binding. This evidence supports the hypothesis that proteins containing PilZ domains are the long-sought c-di-GMP adaptor proteins.  相似文献   

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An intracellular second messenger unique to bacteria, c-di-GMP, has gained appreciation as a key player in adaptation and virulence strategies, such as biofilm formation, persistence, and cytotoxicity. Diguanylate cyclases containing GGDEF domains and phosphodiesterases containing either EAL or HD-GYP domains have been identified as the enzymes controlling intracellular c-di-GMP levels, yet little is known regarding signal transmission and the sensory targets for this signaling molecule. Although limited in number, identified c-di-GMP receptors in bacteria are characterized by prominent diversity and multilevel impact. In addition, c-di-GMP has been shown to have immunomodulatory effects in mammals and several eukaryotic c-di-GMP sensors have been proposed. The structural biology of c-di-GMP receptors is a rapidly developing field of research, which holds promise for the development of novel therapeutics against bacterial infections. In this review, we highlight recent advances in identifying bacterial and eukaryotic c-di-GMP signaling mechanisms and emphasize the need for mechanistic structure-function studies on confirmed signaling targets.  相似文献   

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Aims: The primary goal of this study was to characterize the existence of a functional c‐di‐GMP pathway in the bioleaching bacterium Acidithiobacillus ferrooxidans. Methods and Results: A bioinformatic search revealed that the genome sequence of At. ferrooxidans ATCC 23270 codes for several proteins involved in the c‐di‐GMP pathway, including diguanylate cyclases (DGC), phosphodiesterases and PilZ effector proteins. Overexpression in Escherichia coli demonstrated that four At. ferrooxidans genes code for proteins containing GGDEF/EAL domains with functional DGC activity. MS/MS analysis allowed the identification of c‐di‐GMP in nucleotide preparations obtained from At. ferrooxidans cells. In addition, c‐di‐GMP levels in cells grown on the surface of solid energetic substrates such as sulfur prills or pyrite were higher than those measured in ferrous iron planktonic cells. Conclusions: At. ferrooxidans possesses a functional c‐di‐GMP pathway that could play a key role in At. ferrooxidans biofilm formation during bioleaching processes. Significance and Impact of the Study: This is the first global study about the c‐di‐GMP pathway in an acidophilic bacterium of great interest for the biomining industry. It opens a new way to explore the regulation of biofilm formation by biomining micro‐organisms during the bioleaching process.  相似文献   

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In many bacterial pathogens, the second messenger c‐di‐GMP stimulates the production of an exopolysaccharide (EPS) matrix to shield bacteria from assaults of the immune system. How c‐di‐GMP induces EPS biogenesis is largely unknown. Here, we show that c‐di‐GMP allosterically activates the synthesis of poly‐β‐1,6‐N‐acetylglucosamine (poly‐GlcNAc), a major extracellular matrix component of Escherichia coli biofilms. C‐di‐GMP binds directly to both PgaC and PgaD, the two inner membrane components of the poly‐GlcNAc synthesis machinery to stimulate their glycosyltransferase activity. We demonstrate that the PgaCD machinery is a novel type c‐di‐GMP receptor, where ligand binding to two proteins stabilizes their interaction and promotes enzyme activity. This is the first example of a c‐di‐GMP‐mediated process that relies on protein–protein interaction. At low c‐di‐GMP concentrations, PgaD fails to interact with PgaC and is rapidly degraded. Thus, when cells experience a c‐di‐GMP trough, PgaD turnover facilitates the irreversible inactivation of the Pga machinery, thereby temporarily uncoupling it from c‐di‐GMP signalling. These data uncover a mechanism of c‐di‐GMP‐mediated EPS control and provide a frame for c‐di‐GMP signalling specificity in pathogenic bacteria.  相似文献   

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