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https://www.readbyqxmd.com/read/28904996/environmental-and-genetic-determinants-of-biofilm-formation-in-paracoccus-denitrificans
#1
Santosh Kumar, Stephen Spiro
The genome of the denitrifying bacterium Paracoccus denitrificans predicts the expression of a small heme-containing nitric oxide (NO) binding protein, H-NOX. The genome organization and prior work in other bacteria suggest that H-NOX interacts with a diguanylate cyclase that cyclizes GTP to make cyclic di-GMP (cdGMP). Since cdGMP frequently regulates attached growth as a biofilm, we first established conditions for biofilm development by P. denitrificans. We found that adhesion to a polystyrene surface is strongly stimulated by the addition of 10 mM Ca(2+) to rich media...
September 2017: MSphere
https://www.readbyqxmd.com/read/28902153/bacterial-biofilm-control-by-perturbation-of-bacterial-signaling-processes
#2
REVIEW
Tim Holm Jakobsen, Tim Tolker-Nielsen, Michael Givskov
The development of effective strategies to combat biofilm infections by means of either mechanical or chemical approaches could dramatically change today's treatment procedures for the benefit of thousands of patients. Remarkably, considering the increased focus on biofilms in general, there has still not been invented and/or developed any simple, efficient and reliable methods with which to "chemically" eradicate biofilm infections. This underlines the resilience of infective agents present as biofilms and it further emphasizes the insufficiency of today's approaches used to combat chronic infections...
September 13, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28889312/discovering-selective-diguanylate-cyclase-inhibitors-from-pled-to-discrimination-of-the-active-site-of-cyclic-di-gmp-phosphodiesterases
#3
S Rinaldo, G Giardina, F Mantoni, A Paiardini, Alessio Paone, Francesca Cutruzzolà
One of the most important signals involved in controlling biofilm formation is represented by the intracellular second messenger 3',5'-cyclic diguanylic acid (c-di-GMP). Since the pathways involved in c-di-GMP biosynthesis and breakdown are found only in bacteria, targeting c-di-GMP metabolism represents an attractive strategy for the development of biofilm-disrupting drugs. Here, we present the workflow required to perform a structure-based design of inhibitors of diguanylate cyclases, the enzymes responsible for c-di-GMP biosynthesis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28889311/targeting-c-di-gmp-signaling-biofilm-formation-and-bacterial-motility-with-small-molecules
#4
Clement Opoku-Temeng, Herman O Sintim
Bacteria possess several signaling molecules that regulate distinct phenotypes. Cyclic di-GMP (c-di-GMP) has emerged as a ubiquitous second messenger that regulates bacterial virulence, cell cycle, motility, and biofilm formation. The link between c-di-GMP signaling and biofilm formation affords novel strategies for treatment of biofilm-associated infections, which is a major public health problem. The complex c-di-GMP signaling pathway creates a hurdle in the development of small molecule modulators. Nonetheless, some progress has been made in this regard and inhibitors of c-di-GMP metabolizing enzymes that affect biofilm formation and motility have been documented...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28889309/identification-of-c-di-gmp-responsive-riboswitches
#5
Johann Peltier, Olga Soutourina
Bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) is an important signaling molecule for community behavior control, cell morphogenesis, and virulence in bacteria. In addition to protein effectors, this second messenger binds RNA molecules that act as riboswitches to control target gene expression. In this chapter, we describe a method for experimental validation of the functionality of c-di-GMP-responsive riboswitches and the analysis of c-di-GMP control of target gene expression by qRT-PCR and Northern blot...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28889305/detection-of-cyclic-di-gmp-binding-proteins-utilizing-a-biotinylated-cyclic-di-gmp-pull-down-assay
#6
Jacob R Chambers, Karin Sauer
Cyclic di-GMP is an important regulatory messenger molecule that often directly interacts with proteins to alter function. It is therefore important to find potential c-di-GMP binding proteins and verify a direct interaction between them. Here, we describe a pull-down assay using biotinylated-c-di-GMP to capture a specific protein of interest followed by immunoblot analysis to determine relative protein abundance. This method also allows for addition of both specific and nonspecific competitors to determine specificity of c-di-GMP-protein binding...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28889304/use-of-nonradiochemical-dnase-footprinting-to-analyze-c-di-gmp-modulation-of-dna-binding-proteins
#7
Claudine Baraquet, Caroline S Harwood
The transition of bacteria from a planktonic lifestyle to a collaborative, sessile biofilm lifestyle is a regulated process orchestrated by the intracellular second-messenger c-di-GMP (bis-(3'-5')-cyclic dimeric guanosine monophosphate). To modulate this transition, c-di-GMP acts at the transcriptional, posttranscriptional, and posttranslational levels. In this chapter, we describe a method to study of how a transcriptional regulator modulates gene expression in response to c-di-GMP binding. DNase I footprinting is a valuable tool for use in analyzing how regulatory proteins bind to DNA, the location of their binding sites or how c-di-GMP affects their binding to DNA...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28889303/detection-of-c-di-gmp-responsive-dna-binding
#8
Jacob R Chambers, Karin Sauer
Modulation of signal transduction via binding of the secondary messenger molecule cyclic di-GMP to effector proteins is a near universal regulatory schema in bacteria. In particular, direct binding of c-di-GMP to transcriptional regulators has been shown to alter gene expression of a variety of processes. Here, we illustrate a pull-down-based DNA:protein binding reaction to determine the relative importance of c-di-GMP in the binding affinity of a target protein to specific DNA sequences. Specifically, the pull-down-based assay enables DNA binding to be analyzed with differing concentrations of c-di-GMP in the absence/presence of specific and nonspecific competitors...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28889301/determining-phosphodiesterase-activity-radioactive-assay
#9
Barbara I Kazmierczak
Cyclic-di-GMP phosphodiesterases (PDEs) catalyze the hydrolysis of the bacterial second messenger c-di-GMP. This protocol describes a sensitive radioactive assay for PDE activity in which substrate and product can be quickly and easily separated by thin-layer chromatography.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28889300/measuring-cyclic-diguanylate-c-di-gmp-specific-phosphodiesterase-activity-using-the-mant-c-di-gmp-assay
#10
Dorit Eli, Trevor E Randall, Henrik Almblad, Joe J Harrison, Ehud Banin
The second messenger, cyclic diguanylate (c-di-GMP), regulates a variety of bacterial cellular and social behaviors. A key determinant of c-di-GMP levels in cells is its degradation by c-di-GMP-specific phosphodiesterases (PDEs). Here, we describe an assay to determine c-di-GMP degradation rates in vitro using 2'-O-(N'-methylanthraniloyl)-cyclic diguanylate (MANT-c-di-GMP). Additionally, a protocol for the production and purification of recombinant Pseudomonas aeruginosa RocR, a c-di-GMP-specific PDE that may serve as a control in MANT-c-di-GMP assays, is provided...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28889299/fluorescent-2-aminopurine-c-di-gmp-and-gpg-analogs-as-pde-probes
#11
Jie Zhou, Clement Opoku-Temeng, Herman O Sintim
c-di-GMP is widely recognized as an important ubiquitous signaling molecule in bacteria. c-di-GMP phosphodiesterases (PDEs) regulate the intracellular concentration of c-di-GMP and some could be potential drug targets. Here, we describe a class of dinucleotide probes suitable for monitoring the enzymatic activities of c-di-GMP PDEs in real time. Such probes contain fluorescent nucleobases and can be readily cleaved by PDEs, resulting in a change in fluorescence. Fluorescent cyclic and linear dinucleotide probes could be used in diverse applications, such as confirming the activity of an expressed PDE or oligoribonuclease (Orns) or identifying inhibitors of PDEs or Orns using high-throughput screening formats...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28889297/contribution-of-cyclic-di-gmp-in-the-control-of-type-iii-and-type-vi-secretion-in-pseudomonas-aeruginosa
#12
Ronan R McCarthy, Martina Valentini, Alain Filloux
Bacteria produce toxins to enhance their competitiveness in the colonization of an environment as well as during an infection. The delivery of toxins into target cells is mediated by several types of secretion systems, among them our focus is Type III and Type VI Secretion Systems (T3SS and T6SS, respectively). A thorough methodology is provided detailing how to identify if cyclic di-GMP signaling plays a role in the P. aeruginosa toxin delivery mediated by T3SS or T6SS. This includes in vitro preparation of the samples for Western blot analysis aiming at detecting possible c-di-GMP-dependent T3SS/T6SS switch, as well as in vivo analysis using the model organism Galleria mellonella to demonstrate the ecological and pathogenic consequence of the switch between these two secretion systems...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28889296/probing-the-role-of-cyclic-di-gmp-signaling-systems-in-disease-using-chinese-radish
#13
Shi-Qi An, Ji-Liang Tang, J Maxwell Dow
The determination of the genome sequences of pathogenic bacteria has facilitated functional analyses that aim to understand the molecular basis of virulence. In particular, genome sequence information of the pathogen Xanthomonas campestris pathovar campestris has allowed researchers to identify and functionally analyze the role of intracellular signaling involving cyclic di-GMP in black rot disease of crucifers. Here, we describe leaf clipping and spraying methods for testing the virulence of wild type and derived mutants of X...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28889295/analysis-of-c-di-gmp-levels-synthesized-by-a-photoreceptor-protein-in-response-to-different-light-qualities-using-an-in-vitro-enzymatic-assay
#14
Veronika Angerer, Lars-Oliver Essen, Annegret Wilde
Diguanylate cyclases are enzymes that use two GTP molecules to produce one molecule cyclic dimeric guanosine monophosphate (c-di-GMP). This cyclic dinucleotide is an ubiquitous prokaryotic second messenger that controls a variety of cell functions. Several proteins have been described which contain a photoreceptor domain fused to a diguanylate cyclase. The cyanobacterial light sensor Cph2 is responsible for the blue-light induced synthesis of c-di-GMP in Synechocystis sp. PCC 6803. Here, we provide a detailed protocol for an in vitro enzymatic assay with a purified photoreceptor protein using light as the crucial reaction parameter for c-di-GMP synthesis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28889293/type-iv-pili-dependent-motility-as-a-tool-to-determine-the-activity-of-c-di-gmp-modulating-enzymes-in-myxococcus-xanthus
#15
Dorota Skotnicka, Lotte Søgaard-Andersen
The nucleotide-based second messenger bis-(3'-5')-cyclic dimeric GMP (c-di-GMP) regulates multiple processes in bacteria including cellular motility. The rod-shaped Myxococcus xanthus cells move in the direction of their long axis using two distinct motility systems: type IV pili (T4P)-dependent motility and gliding motility. Manipulation of the c-di-GMP level by expression of either an active, heterologous diguanylate cyclase or an active, heterologous phosphodiesterase causes defects in T4P-dependent motility without affecting gliding motility...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28889292/congo-red-stain-identifies-matrix-overproduction-and-is-an-indirect-measurement-for-c-di-gmp-in-many-species-of-bacteria
#16
Christopher J Jones, Daniel J Wozniak
Congo red is a diazo textile dye that has been used to visualize the production of amyloid fibers for nearly a century. Microbiological applications were later developed, especially in identifying strains that produce amyloid appendages called curli and overexpressing polysaccharides in the biofilm matrix. The second messenger cyclic diguanylate (c-di-GMP) regulates the production of biofilm matrix polysaccharides, and therefore Congo red staining of samples can be utilized as an indirect measurement of elevated c-di-GMP production in bacteria...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28889289/cyclic-di-gmp-responsive-transcriptional-reporter-bioassays-in-pseudomonas-aeruginosa
#17
Bradley R Borlee, Grace I Borlee, Kevin H Martin, Yasuhiko Irie
3',5'-cyclic diguanosine monophosphate (cyclic di-GMP) is a bacterial secondary messenger molecule that regulates many important cellular activities and behaviors, such as motility and biofilm formation. While mass spectrometry protocols for quantitative analyses of intracellular cyclic di-GMP concentrations have been developed, they are time intensive, expensive, low-throughput, and incapable of directly monitoring dynamic changes in vivo. In this protocol, we provide a Pseudomonas aeruginosa-specific detailed methodology to assay the intracellular levels of cyclic di-GMP using biological reporters...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28889287/spectrophotometric-and-mass-spectroscopic-methods-for-the-quantification-and-kinetic-evaluation-of-in-vitro-c-di-gmp-synthesis
#18
Geoffrey B Severin, Christopher M Waters
The expression and activity of diguanylate cyclase (DGC) and phosphodiesterase (PDE) enzymes are responsible for modulating and maintaining the intracellular concentration of the bacterial second messenger cyclic diguanosine-monophosphate (c-di-GMP). Here, we describe an in vitro method for the spectrophotometric detection and quantification of DGC catalyzed c-di-GMP synthesis through adaptation of the EnzChek(®) Pyrophosphate Assay Kit. We also outline a method for the quantification of c-di-GMP produced in this in vitro reaction using Ultra-Performance Liquid Chromatography tandem Mass Spectrometry (UPLC-MS/MS)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28889286/detection-of-cyclic-dinucleotides-by-sting
#19
Xiao-Xia Du, Xiao-Dong Su
STING (stimulator of interferon genes) is an essential signaling adaptor protein mediating cytosolic DNA-induced innate immunity for both microbial invasion and self-DNA leakage. STING is also a direct receptor for cytosolic cyclic dinucleotides (CDNs), including the microbial secondary messengers c-di-GMP (3',3'-cyclic di-GMP), 3',3'cGAMP (3',3'-cyclic GMP-AMP), and mammalian endogenous 2',3'cGAMP (2',3'-cyclic GMP-AMP) synthesized by cGAS (cyclic GMP-AMP synthase). Upon CDN binding, STING undergoes a conformational change to enable signal transduction by phosphorylation and finally to active IRF3 (Interferon regulatory factor 3) for type I interferon production...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28889285/identification-and-quantification-of-cyclic-di-guanosine-monophosphate-and-its-linear-metabolites-by-reversed-phase-lc-ms-ms
#20
Heike Bähre, Volkhard Kaever
Cyclic dinucleotides such as bis-(3',5')-cyclic dimeric guanosine monophosphate (3',3'-c-di-GMP) represent an important class of second messengers in bacteria and are involved in numerous (patho)physiological settings. Here, we describe a sensitive and specific quantification method for 3',3'-c-di-GMP by HPLC-coupled tandem mass spectrometry (LC-MS/MS). Additionally, linear 3',3'-c-di-GMP metabolites, i.e., 5'-phosphoguanylyl-3',5'-guanosine (pGpG) and 5'-guanosine monophosphate (5'-GMP), as well as cyclic guanosine monophosphate (3',5'-cGMP) and 3',3' c-di-GMP analogues (2',3'-c-di-GMP and 2',2'-c-di-GMP) can be simultaneously determined by this method...
2017: Methods in Molecular Biology
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