Published in Bioinformatics on October 25, 2005
Principles of c-di-GMP signalling in bacteria. Nat Rev Microbiol (2009) 7.13
Cyclic di-GMP: the first 25 years of a universal bacterial second messenger. Microbiol Mol Biol Rev (2013) 4.69
Roles of cyclic diguanylate in the regulation of bacterial pathogenesis. Annu Rev Microbiol (2007) 4.53
Signals, regulatory networks, and materials that build and break bacterial biofilms. Microbiol Mol Biol Rev (2009) 4.11
Identification of FleQ from Pseudomonas aeruginosa as a c-di-GMP-responsive transcription factor. Mol Microbiol (2008) 4.03
Structural classification of bacterial response regulators: diversity of output domains and domain combinations. J Bacteriol (2006) 3.86
A cyclic-di-GMP receptor required for bacterial exopolysaccharide production. Mol Microbiol (2007) 3.54
Structural and mechanistic determinants of c-di-GMP signalling. Nat Rev Microbiol (2009) 3.39
Structural basis of ligand binding by a c-di-GMP riboswitch. Nat Struct Mol Biol (2009) 3.28
The c-di-GMP binding protein YcgR controls flagellar motor direction and speed to affect chemotaxis by a "backstop brake" mechanism. Mol Cell (2010) 2.76
DgrA is a member of a new family of cyclic diguanosine monophosphate receptors and controls flagellar motor function in Caulobacter crescentus. Proc Natl Acad Sci U S A (2007) 2.42
The structural basis of cyclic diguanylate signal transduction by PilZ domains. EMBO J (2007) 2.39
PilZ domain proteins bind cyclic diguanylate and regulate diverse processes in Vibrio cholerae. J Biol Chem (2007) 2.31
Cyclic di-GMP signaling in bacteria: recent advances and new puzzles. J Bacteriol (2006) 2.13
Get the message out: cyclic-Di-GMP regulates multiple levels of flagellum-based motility. J Bacteriol (2007) 2.13
Crystallographic snapshot of cellulose synthesis and membrane translocation. Nature (2012) 2.10
Subcellular location characteristics of the Pseudomonas aeruginosa GGDEF protein, WspR, indicate that it produces cyclic-di-GMP in response to growth on surfaces. Mol Microbiol (2007) 2.00
You've come a long way: c-di-GMP signaling. Curr Opin Microbiol (2012) 1.93
Structural basis for c-di-GMP-mediated inside-out signaling controlling periplasmic proteolysis. PLoS Biol (2011) 1.93
Structural analysis of the GGDEF-EAL domain-containing c-di-GMP receptor FimX. Structure (2009) 1.79
Escherichia coli biofilms. Curr Top Microbiol Immunol (2008) 1.79
Tetrameric c-di-GMP mediates effective transcription factor dimerization to control Streptomyces development. Cell (2014) 1.74
A complex transcription network controls the early stages of biofilm development by Escherichia coli. J Bacteriol (2006) 1.71
Second messenger regulation of biofilm formation: breakthroughs in understanding c-di-GMP effector systems. Annu Rev Cell Dev Biol (2012) 1.54
Identification and characterization of cyclic diguanylate signaling systems controlling rugosity in Vibrio cholerae. J Bacteriol (2008) 1.54
The cyclic nucleotide monophosphate domain of Xanthomonas campestris global regulator Clp defines a new class of cyclic di-GMP effectors. J Bacteriol (2009) 1.52
Nucleotide binding by the widespread high-affinity cyclic di-GMP receptor MshEN domain. Nat Commun (2016) 1.49
Rrp1, a cyclic-di-GMP-producing response regulator, is an important regulator of Borrelia burgdorferi core cellular functions. Mol Microbiol (2009) 1.45
A CsgD-independent pathway for cellulose production and biofilm formation in Escherichia coli. J Bacteriol (2006) 1.45
A staphylococcal GGDEF domain protein regulates biofilm formation independently of cyclic dimeric GMP. J Bacteriol (2008) 1.45
Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1. Genome Biol (2008) 1.39
Sensing the messenger: the diverse ways that bacteria signal through c-di-GMP. Protein Sci (2012) 1.38
MrkH, a novel c-di-GMP-dependent transcriptional activator, controls Klebsiella pneumoniae biofilm formation by regulating type 3 fimbriae expression. PLoS Pathog (2011) 1.36
Allosteric activation of exopolysaccharide synthesis through cyclic di-GMP-stimulated protein-protein interaction. EMBO J (2012) 1.36
Structural and biochemical determinants of ligand binding by the c-di-GMP riboswitch . Biochemistry (2010) 1.35
The EAL domain protein YciR acts as a trigger enzyme in a c-di-GMP signalling cascade in E. coli biofilm control. EMBO J (2013) 1.32
The FleQ protein from Pseudomonas aeruginosa functions as both a repressor and an activator to control gene expression from the pel operon promoter in response to c-di-GMP. Nucleic Acids Res (2012) 1.32
Structural basis of differential ligand recognition by two classes of bis-(3'-5')-cyclic dimeric guanosine monophosphate-binding riboswitches. Proc Natl Acad Sci U S A (2011) 1.28
Regulation of flagellar motility during biofilm formation. FEMS Microbiol Rev (2013) 1.28
Genetic reductionist approach for dissecting individual roles of GGDEF proteins within the c-di-GMP signaling network in Salmonella. Proc Natl Acad Sci U S A (2009) 1.24
Cellulose as an architectural element in spatially structured Escherichia coli biofilms. J Bacteriol (2013) 1.23
Bioinformatics and experimental analysis of proteins of two-component systems in Myxococcus xanthus. J Bacteriol (2007) 1.21
MucR, a novel membrane-associated regulator of alginate biosynthesis in Pseudomonas aeruginosa. Appl Environ Microbiol (2008) 1.21
Discrete cyclic di-GMP-dependent control of bacterial predation versus axenic growth in Bdellovibrio bacteriovorus. PLoS Pathog (2012) 1.21
Virulence and prodigiosin antibiotic biosynthesis in Serratia are regulated pleiotropically by the GGDEF/EAL domain protein, PigX. J Bacteriol (2007) 1.21
Mechanism of activation of bacterial cellulose synthase by cyclic di-GMP. Nat Struct Mol Biol (2014) 1.20
The response threshold of Salmonella PilZ domain proteins is determined by their binding affinities for c-di-GMP. Mol Microbiol (2012) 1.19
Coordinated cyclic-di-GMP repression of Salmonella motility through YcgR and cellulose. J Bacteriol (2012) 1.18
Iron induces bimodal population development by Escherichia coli. Proc Natl Acad Sci U S A (2013) 1.16
Analysis of a Borrelia burgdorferi phosphodiesterase demonstrates a role for cyclic-di-guanosine monophosphate in motility and virulence. Mol Microbiol (2010) 1.16
Small Regulatory RNAs in the Control of Motility and Biofilm Formation in E. coli and Salmonella. Int J Mol Sci (2013) 1.16
BcsA and BcsB form the catalytically active core of bacterial cellulose synthase sufficient for in vitro cellulose synthesis. Proc Natl Acad Sci U S A (2013) 1.15
Comparative genomics of cyclic-di-GMP signalling in bacteria: post-translational regulation and catalytic activity. Nucleic Acids Res (2010) 1.14
Microbial alginate production, modification and its applications. Microb Biotechnol (2013) 1.14
Identification and characterization of non-cellulose-producing mutants of Gluconacetobacter hansenii generated by Tn5 transposon mutagenesis. J Bacteriol (2013) 1.13
Cyclic di-GMP signaling regulates invasion by Ehrlichia chaffeensis of human monocytes. J Bacteriol (2010) 1.13
Structure of the cytoplasmic region of PelD, a degenerate diguanylate cyclase receptor that regulates exopolysaccharide production in Pseudomonas aeruginosa. J Biol Chem (2012) 1.11
Solution structure of the PilZ domain protein PA4608 complex with cyclic di-GMP identifies charge clustering as molecular readout. J Biol Chem (2011) 1.11
Diguanylate cyclases control magnesium-dependent motility of Vibrio fischeri. J Bacteriol (2006) 1.09
The Anaplasma phagocytophilum PleC histidine kinase and PleD diguanylate cyclase two-component system and role of cyclic Di-GMP in host cell infection. J Bacteriol (2008) 1.09
Cyclic di-GMP is essential for the survival of the lyme disease spirochete in ticks. PLoS Pathog (2011) 1.08
Differential analogue binding by two classes of c-di-GMP riboswitches. J Am Chem Soc (2011) 1.07
LtmA, a novel cyclic di-GMP-responsive activator, broadly regulates the expression of lipid transport and metabolism genes in Mycobacterium smegmatis. Nucleic Acids Res (2012) 1.07
Small RNAs in the control of RpoS, CsgD, and biofilm architecture of Escherichia coli. RNA Biol (2014) 1.07
Evidence for cyclic Di-GMP-mediated signaling in Bacillus subtilis. J Bacteriol (2012) 1.06
Structure and mechanism of purine-binding riboswitches. Q Rev Biophys (2012) 1.06
Identification and characterization of a phosphodiesterase that inversely regulates motility and biofilm formation in Vibrio cholerae. J Bacteriol (2010) 1.04
Systematic functional analysis reveals that a set of seven genes is involved in fine-tuning of the multiple functions mediated by type IV pili in Neisseria meningitidis. Infect Immun (2010) 1.03
Analysis of the Borrelia burgdorferi cyclic-di-GMP-binding protein PlzA reveals a role in motility and virulence. Infect Immun (2011) 1.03
Biofilms and Cyclic di-GMP (c-di-GMP) Signaling: Lessons from Pseudomonas aeruginosa and Other Bacteria. J Biol Chem (2016) 1.02
Identification and molecular characterization of a cyclic-di-GMP effector protein, PlzA (BB0733): additional evidence for the existence of a functional cyclic-di-GMP regulatory network in the Lyme disease spirochete, Borrelia burgdorferi. FEMS Immunol Med Microbiol (2009) 1.01
Molecular and bioengineering strategies to improve alginate and polydydroxyalkanoate production by Azotobacter vinelandii. Microb Cell Fact (2007) 0.99
Integration of the second messenger c-di-GMP into the chemotactic signaling pathway. MBio (2013) 0.99
Diversity of Cyclic Di-GMP-Binding Proteins and Mechanisms. J Bacteriol (2016) 0.99
Functional characterization of core components of the Bacillus subtilis cyclic-di-GMP signaling pathway. J Bacteriol (2013) 0.98
The Anabaena sp. strain PCC 7120 gene all2874 encodes a diguanylate cyclase and is required for normal heterocyst development under high-light growth conditions. J Bacteriol (2008) 0.98
Dimeric c-di-GMP is required for post-translational regulation of alginate production in Pseudomonas aeruginosa. J Biol Chem (2015) 0.98
The diguanylate cyclase, Rrp1, regulates critical steps in the enzootic cycle of the Lyme disease spirochetes. Mol Microbiol (2011) 0.97
A molecular description of cellulose biosynthesis. Annu Rev Biochem (2015) 0.97
Novel candidate virulence factors in rice pathogen Xanthomonas oryzae pv. oryzicola as revealed by mutational analysis. Appl Environ Microbiol (2007) 0.95
GIL, a new c-di-GMP-binding protein domain involved in regulation of cellulose synthesis in enterobacteria. Mol Microbiol (2014) 0.95
Bacterial exopolysaccharides: biosynthesis pathways and engineering strategies. Front Microbiol (2015) 0.94
Cyanobacteriochrome SesA is a diguanylate cyclase that induces cell aggregation in Thermosynechococcus. J Biol Chem (2014) 0.94
Cyclic diguanylate signaling proteins control intracellular growth of Legionella pneumophila. MBio (2011) 0.94
Brucella melitensis cyclic di-GMP phosphodiesterase BpdA controls expression of flagellar genes. J Bacteriol (2011) 0.93
Cyclic di-GMP-mediated repression of swarming motility by Pseudomonas aeruginosa PA14 requires the MotAB stator. J Bacteriol (2014) 0.93
Cyclic di-GMP riboswitch-regulated type IV pili contribute to aggregation of Clostridium difficile. J Bacteriol (2014) 0.91
Cyclic-di-GMP-binding CRP-like protein: a spectacular new role for a veteran signal transduction actor. J Bacteriol (2009) 0.90
Identification of flgZ as a flagellar gene encoding a PilZ domain protein that regulates swimming motility and biofilm formation in Pseudomonas. PLoS One (2014) 0.90
Bacterial Rotary Export ATPases Are Allosterically Regulated by the Nucleotide Second Messenger Cyclic-di-GMP. J Biol Chem (2015) 0.90
Inactivation of cyclic Di-GMP binding protein TDE0214 affects the motility, biofilm formation, and virulence of Treponema denticola. J Bacteriol (2013) 0.89
Systematic Identification of Cyclic-di-GMP Binding Proteins in Vibrio cholerae Reveals a Novel Class of Cyclic-di-GMP-Binding ATPases Associated with Type II Secretion Systems. PLoS Pathog (2015) 0.88
The cyclic-di-GMP signaling pathway in the Lyme disease spirochete, Borrelia burgdorferi. Front Cell Infect Microbiol (2014) 0.88
The cyclic-di-GMP phosphodiesterase BinA negatively regulates cellulose-containing biofilms in Vibrio fischeri. J Bacteriol (2010) 0.88
Cyclic-di-GMP signalling regulates motility and biofilm formation in Bordetella bronchiseptica. Microbiology (2013) 0.87
The diguanylate cyclase GcbA facilitates Pseudomonas aeruginosa biofilm dispersion by activating BdlA. J Bacteriol (2014) 0.86
Three cyanobacteriochromes work together to form a light color-sensitive input system for c-di-GMP signaling of cell aggregation. Proc Natl Acad Sci U S A (2015) 0.86
Structural characterization reveals that a PilZ domain protein undergoes substantial conformational change upon binding to cyclic dimeric guanosine monophosphate. Protein Sci (2010) 0.86
Genetic analysis of the role of yfiR in the ability of Escherichia coli CFT073 to control cellular cyclic dimeric GMP levels and to persist in the urinary tract. Infect Immun (2013) 0.86
C-di-GMP: the dawning of a novel bacterial signalling system. Mol Microbiol (2005) 5.41
Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes. BMC Evol Biol (2003) 4.70
Cyclic di-GMP: the first 25 years of a universal bacterial second messenger. Microbiol Mol Biol Rev (2013) 4.69
Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome. Proc Natl Acad Sci U S A (2003) 3.55
An extracellular calcium-binding domain in bacteria with a distant relationship to EF-hands. FEMS Microbiol Lett (2003) 3.45
A genomic update on clostridial phylogeny: Gram-negative spore formers and other misplaced clostridia. Environ Microbiol (2013) 2.63
The 2010 Nucleic Acids Research Database Issue and online Database Collection: a community of data resources. Nucleic Acids Res (2009) 2.42
Dimeric dUTPases, HisE, and MazG belong to a new superfamily of all-alpha NTP pyrophosphohydrolases with potential "house-cleaning" functions. J Mol Biol (2005) 2.14
The cyanobacterial genome core and the origin of photosynthesis. Proc Natl Acad Sci U S A (2006) 2.11
A novel type of conserved DNA-binding domain in the transcriptional regulators of the AlgR/AgrA/LytR family. Nucleic Acids Res (2002) 2.10
Amidase domains from bacterial and phage autolysins define a family of gamma-D,L-glutamate-specific amidohydrolases. Trends Biochem Sci (2003) 2.06
Common extracellular sensory domains in transmembrane receptors for diverse signal transduction pathways in bacteria and archaea. J Bacteriol (2003) 1.97
Towards BioDBcore: a community-defined information specification for biological databases. Nucleic Acids Res (2010) 1.97
Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations. Proc Natl Acad Sci U S A (2005) 1.93
Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia. Biol Direct (2008) 1.78
Planctomycetes and eukaryotes: a case of analogy not homology. Bioessays (2011) 1.76
Phylogenomic analysis of the Giardia intestinalis transcarboxylase reveals multiple instances of domain fusion and fission in the evolution of biotin-dependent enzymes. J Mol Microbiol Biotechnol (2003) 1.76
The 2013 Nucleic Acids Research Database Issue and the online molecular biology database collection. Nucleic Acids Res (2012) 1.66
Genome sequence of the deep-sea gamma-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy. Proc Natl Acad Sci U S A (2004) 1.62
Inventing the dynamo machine: the evolution of the F-type and V-type ATPases. Nat Rev Microbiol (2007) 1.52
The genome sequence of the psychrophilic archaeon, Methanococcoides burtonii: the role of genome evolution in cold adaptation. ISME J (2009) 1.40
Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1. Genome Biol (2008) 1.39
Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution. Biol Direct (2010) 1.35
The PA14 domain, a conserved all-beta domain in bacterial toxins, enzymes, adhesins and signaling molecules. Trends Biochem Sci (2004) 1.32
Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae. Nucleic Acids Res (2004) 1.31
The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection. Nucleic Acids Res (2013) 1.26
Origin of first cells at terrestrial, anoxic geothermal fields. Proc Natl Acad Sci U S A (2012) 1.26
Towards BioDBcore: a community-defined information specification for biological databases. Database (Oxford) (2011) 1.24
The COMBREX project: design, methodology, and initial results. PLoS Biol (2013) 1.24
The DxDxDG motif for calcium binding: multiple structural contexts and implications for evolution. J Mol Biol (2004) 1.24
Evolutionary primacy of sodium bioenergetics. Biol Direct (2008) 1.23
On the origin of life in the zinc world. 2. Validation of the hypothesis on the photosynthesizing zinc sulfide edifices as cradles of life on Earth. Biol Direct (2009) 1.19
The past and present of sodium energetics: may the sodium-motive force be with you. Biochim Biophys Acta (2008) 1.17
Single domain response regulators: molecular switches with emerging roles in cell organization and dynamics. Curr Opin Microbiol (2009) 1.17
Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20. J Bacteriol (2003) 1.13
Structural insight into the mechanism of c-di-GMP hydrolysis by EAL domain phosphodiesterases. J Mol Biol (2010) 1.12
In Silico Metabolic Model and Protein Expression of Haemophilus influenzae Strain Rd KW20 in Rich Medium. OMICS (2004) 1.10
MASE1 and MASE2: two novel integral membrane sensory domains. J Mol Microbiol Biotechnol (2003) 1.09
Telling bacteria: do not LytTR. Structure (2008) 1.09
Globins synthesize the second messenger bis-(3'-5')-cyclic diguanosine monophosphate in bacteria. J Mol Biol (2009) 1.08
Co-evolution of primordial membranes and membrane proteins. Trends Biochem Sci (2009) 1.07
Sequence conservation in the chagasin family suggests a common trend in cysteine proteinase binding by unrelated protein inhibitors. Protein Sci (2002) 1.03
Cyanobacterial response regulator PatA contains a conserved N-terminal domain (PATAN) with an alpha-helical insertion. Bioinformatics (2006) 1.00
Experimental verification of a sequence-based prediction: F(1)F(0)-type ATPase of Vibrio cholerae transports protons, not Na(+) ions. J Bacteriol (2003) 0.99
The crystal structure of a complex of Campylobacter jejuni dUTPase with substrate analogue sheds light on the mechanism and suggests the "basic module" for dimeric d(C/U)TPases. J Mol Biol (2004) 0.99
Diversity of Cyclic Di-GMP-Binding Proteins and Mechanisms. J Bacteriol (2016) 0.99
New structural and functional contexts of the Dx[DN]xDG linear motif: insights into evolution of calcium-binding proteins. PLoS One (2011) 0.98
GIL, a new c-di-GMP-binding protein domain involved in regulation of cellulose synthesis in enterobacteria. Mol Microbiol (2014) 0.95
Sentra: a database of signal transduction proteins for comparative genome analysis. Nucleic Acids Res (2006) 0.93
Characterization of the N-ATPase, a distinct, laterally transferred Na+-translocating form of the bacterial F-type membrane ATPase. Bioinformatics (2010) 0.92
Sequence analysis and characterization of a novel fibronectin-binding repeat domain from the surface of Streptococcus pneumoniae. OMICS (2004) 0.91
Crystal structure of the bacterial YhcH protein indicates a role in sialic acid catabolism. J Bacteriol (2005) 0.90
Functional analysis of conserved polar residues in Vc-NhaD, Na+/H+ antiporter of Vibrio cholerae. J Biol Chem (2005) 0.89
Structural diversity of calcium-binding proteins in bacteria: single-handed EF-hands? Trends Microbiol (2003) 0.88
Genome Diversity of Spore-Forming Firmicutes. Microbiol Spectr (2013) 0.87
Sequence analysis of GerM and SpoVS, uncharacterized bacterial 'sporulation' proteins with widespread phylogenetic distribution. Bioinformatics (2008) 0.86
Analysis of structure and function of putative surface-exposed proteins encoded in the Streptococcus pneumoniae genome: a bioinformatics-based approach to vaccine and drug design. Crit Rev Biochem Mol Biol (2003) 0.86
Physico-chemical and evolutionary constraints for the formation and selection of first biopolymers: towards the consensus paradigm of the abiogenic origin of life. Chem Biodivers (2007) 0.86
Survival of the fittest before the beginning of life: selection of the first oligonucleotide-like polymers by UV light. BMC Evol Biol (2003) 0.85
Evolution of cytochrome bc complexes: from membrane-anchored dehydrogenases of ancient bacteria to triggers of apoptosis in vertebrates. Biochim Biophys Acta (2013) 0.84
Bacterial second messengers, cGMP and c-di-GMP, in a quest for regulatory dominance. EMBO J (2013) 0.84
Phylogenomic reconstruction of archaeal fatty acid metabolism. Environ Microbiol (2014) 0.84
Salt in the wound: a possible role of Na+ gradient in chlamydial infection. J Mol Microbiol Biotechnol (2004) 0.82
Open questions on the origin of life at anoxic geothermal fields. Orig Life Evol Biosph (2012) 0.80
How many signal peptides are there in bacteria? Environ Microbiol (2013) 0.80
The role of energy in the emergence of biology from chemistry. Orig Life Evol Biosph (2012) 0.80
Genome-based identification and characterization of a putative mucin-binding protein from the surface of Streptococcus pneumoniae. Proteins (2007) 0.79
On the abundance of zinc in the evolutionarily old protein domains. Proc Natl Acad Sci U S A (2010) 0.76
From biofouling to bioremediation: the good, the bad and the vague. Curr Opin Biotechnol (2004) 0.75
Microbial genome analysis: the COG approach. Brief Bioinform (2017) 0.75