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Cyclic AMP Receptor Protein (0):
Recent article
Cyclic AMP Receptor Protein
Abstract
We present three crystal structures of NtcA from the cyanobacterium Anabaena: the apoform, and two ligand-bound forms in complex with either 2-OG or its analogue 2,2-difluoropentanedioic acid. All structures assemble as homodimers, with each subunit composed of an N-terminal effector-binding domain...
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PMID: 20616047
PDF is available here.
PDF is available here.
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Journal of Bacteriology (192)14 2010
Abstract
We used two different approaches to generate apo-Vfr and examined its ability to bind a representative set of virulence gene promoters in the absence and presence of different allosteric effectors. Of the cyclic nucleotides tested, only cAMP was able to restore DNA binding activity to apo-Vfr. In co...
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PMID: 20494996
PDF is available here.
PDF is available here.
Nucleic Acids Research (38)11 2010
Abstract
We successfully constructed a series of DNA plasmids that carry many tandem copies of a DNA-binding site for one sequence-specific DNA-binding protein, such as lambda O, LacI, GalR, CRP and AraC. In this case, the protein-induced Delta Lk was greatly amplified and can be measured experimentally. Ind...
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PMID: 20185570
PDF is available here.
PDF is available here.
Hereditas (Beijing) (32)6 2010
Abstract
Bacteria often sequentially utilize coexisting carbohydrates in environment and firstly select the one (frequently glucose) easiest to metabolize. This phenomenon is known as carbon catabolite repression (CCR). In existing Chinese teaching materials of molecular biology and related courses, unclear...
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PMID: 20566460
PDF is available here.
PDF is available here.
Abstract
We found that many chromosomal genes and environmental stimuli affected MarA-mediated antibiotic resistance. Seven genes affected resistance mediated by MarA in an antibiotic-specific way; these were mostly genes encoding unrelated enzymes, transporters, and unknown proteins. Other genes affected Ma...
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PMID: 20211899
PDF is available here.
PDF is available here.
Abstract
Our data show that diabetes elicits specific changes in secretory protein expression in human salivary glands, thus contributing to the altered oral environment and oral disease associated with diabetes.
© 2010 John Wiley & Sons A/S....
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PMID: 20456617
PDF is available here.
PDF is available here.
BMC Microbiology (10) 2010
Abstract
These results suggest multiple novel features for the regulation of these two adjacent operons. SiaR functions as both a repressor and an activator and SiaR and CRP interact to regulate both operons from a single set of operators....
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PMID: 20843349
PDF is available here.
PDF is available here.
Veterinary Research (41)1 2010
Abstract
Salmonella enterica serovar Choleraesuis (Salmonella Choleraesuis) causes a lethal systemic infection (salmonellosis) in swine. Live attenuated Salmonella Choleraesuis vaccines are effective in preventing the disease, and isolates of Salmonella Choleraesuis with mutations in the cAMP-receptor protein...
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PMID: 19775595
PDF is available here.
PDF is available here.
Journal of Bacteriology (192)1 2010
Abstract
Journal of Bacteriology (192)1 2010
Abstract
We assayed their accumulation under a variety of growth conditions and after exposure to stress. We found that many small proteins accumulate under specific growth conditions or are stress induced. For some genes, the observed changes in protein levels were consistent with known transcriptional regu...
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PMID: 19734316
PDF is available here.
PDF is available here.
Journal of Bacteriology (192)1 2010
Abstract
We further investigated our previous finding that rhaS deletion resulted in a threefold increase in rhaSR promoter activity, suggesting RhaS negative autoregulation of rhaSR. We found that RhaS autoregulation required the cyclic AMP receptor protein (CRP) binding site at rhaSR and that RhaS was able...
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PMID: 19854903
PDF is available here.
PDF is available here.
Abstract
We show that deletion of polyphosphate kinase (PPK), the principal enzyme responsible for synthesis of polyP, resulted in augmented expression of cAMP receptor protein (CRP) and rpoS and lowered H2O2 sensitivity in Salmonella Typhimurium ATCC14028. The binding of cAMP-CRP complex to rpoS promoter an...
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PMID: 20075614
PDF is available here.
PDF is available here.
Abstract
A transcriptional fusion (opgG1::MudJ) to the opgGH operon of Salmonella enterica serovar Typhimurium (S. Typhimurium) LT2, isolated by resistance to mecillinam, was used to study the influence of global regulators RpoS, ppGpp, and cAMP/cAMP-receptor protein (CRP) on expression of the opgGH operon a...
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PMID: 19940937
PDF is available here.
PDF is available here.
Genetika (Moskva) (45)9 2009
Abstract
Gene vfr previously described only in Pseudomonas aeruginosa was cloned, identified, and sequenced in cells of Pseudomonas chlororaphis 449; its localization in the chromosome was determined. Amino acid sequence of the protein encoded by gene vfr in P. chlororaphis 449 was shown to have a 83% identi...
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PMID: 19824540
PDF is available here.
PDF is available here.
Microbiology (155)Pt 7 2009
Abstract
These results suggest that: (i) Vfr enhances toxA expression in PAO1 both directly and indirectly through regA, but not through pvdS; (ii) vfr expression is not regulated by iron; and (iii) both Vfr and PvdS cooperate in the presence of RegA to achieve a maximum level of toxA expression....
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PMID: 19389782
PDF is available here.
PDF is available here.
Nucleic Acids Research (37)8 2009
Abstract
We experimentally tested whether this relationship could be used to engineer novel DNA-protein interactions. Using Escherichia coli CRP as a template, we tested eight designs based on this relationship and found that four worked as predicted. Collectively, these results in this work demonstrate that...
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PMID: 19264798
PDF is available here.
PDF is available here.
Abstract
Bending is not only required to accommodate DNA within the cell but also is a mechanism used by proteins to initiate DNA replication, transcription, and recombination. Determining the angles by which regulatory DNA segments deviate from linearity upon binding of proteins is a necessary step toward a...
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PMID: 19378186
PDF is available here.
PDF is available here.
Abstract
Transcription factors interact at promoters to modulate the transcription of genes. This chapter describes three in vitro methods that can be used to monitor their activity: transcript assays, abortive initiation assays, and potassium permanganate footprinting. These techniques have been developed u...
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PMID: 19378177
PDF is available here.
PDF is available here.
BMC Microbiology (9) 2009
Abstract
The sycO, ypkA and yopJ genes constitute a single operon in Y. pestis. CRP specifically binds to the promoter-proximate region of sycO, and represses the expression of the sycO-ypkA-yopJ operon. A single CRP-dependent promoter is employed for the sycO-ypkA-yopJ operon, but two CRP binding sites (sit...
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PMID: 19703315
PDF is available here.
PDF is available here.
FEBS Letters (582)27 2008
Abstract
We show that the cAMP-cAMP receptor protein complex regulates cqsA expression at the post-transcriptional level. This conclusion is supported by the analysis of cqsA-lacZ fusions, the ectopic expression of cqsA in Deltacrp mutants and by Northern blot analysis showing that cqsA mRNA is unstable in D...
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PMID: 18930049
PDF is available here.
PDF is available here.
Journal of Molecular Biology (383)2 2008
Abstract
We have previously identified 13 H. influenzae CRP sites that differ from canonical (CRP-N) sites in the following features: (1) Both half-sites of these noncanonical (CRP-S) sites have C(6) instead of T(6), although they otherwise have an unusually high level of identity with the binding site conse...
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PMID: 18761017
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (283)45 2008
Abstract
We investigated the transcriptional characteristics of this global regulator. Two distinct transcriptional initiation sites for the rpoS gene, the proximal promoter (P(p)) and the distal promoter (P(d)), were defined by primer extension experiments. Various rpoS::luxAB transcriptional fusions indica...
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PMID: 18713737
PDF is available here.
PDF is available here.
FEMS Microbiology Letters (288)2 2008
Abstract
The Escherichia coli K-12 malI-malX intergenic region contains two divergent promoters, which have been investigated by both mutational and biochemical analysis. The malX promoter drives transcription initiation from a location that is 43 bp upstream from the malX translation start codon. Expression...
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PMID: 19054084
PDF is available here.
PDF is available here.
Infection and Immunity (76)11 2008
Abstract
I footprinting assays mapped transcriptional start sites, core promoter elements, and CRP binding sites within the DNA regions upstream of pla and pst, revealing positive and direct control of these two laterally acquired plasmid genes by CRP. The crp disruption affected both in vitro and in vivo gr...
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PMID: 18710863
PDF is available here.
PDF is available here.
Journal of Molecular Biology (383)1 2008
Abstract
We report the identification of the sRNA (CyaR, cyclic AMP-activated RNA) that promotes decay of the ompX mRNA. The transcription of the cyaR gene is stringently controlled by cAMP-cAMP receptor protein and, unexpectedly, cyaR expression is also up-regulated, directly or indirectly, by sigma(E). In...
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PMID: 18619465
PDF is available here.
PDF is available here.
Journal of Bacteriology (190)22 2008
Abstract
I (topA) mutants. However, its physiological significance has remained unclear. Temperature downshift of a mutant yielded transient growth arrest and a parallel increase in hypernegative supercoiling that was more severe with lower temperature. Both properties were alleviated by overexpression of RN...
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PMID: 18790862
PDF is available here.
PDF is available here.
Molecular Microbiology (70)1 2008
Abstract
We report crystal structures of D. hafniense CprK in the ligand-free (both oxidation states), ligand-bound (reduced) and DNA-bound states, making it the first member of the widespread CRP-FNR superfamily for which a complete structural description of both redox-dependent and allosteric molecular rea...
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PMID: 18717788
PDF is available here.
PDF is available here.
Molecular Microbiology (70)1 2008
Abstract
We found eight SdrP-dependent promoters using in vitro transcription assays. A predicted SdrP binding site similar to that recognized by Escherichia coli CRP was found upstream of each SdrP-dependent promoter. In the wild-type strain, expression of these eight genes tended to increase upon entry int...
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PMID: 18699868
PDF is available here.
PDF is available here.
Journal of Bacteriology (190)20 2008
Abstract
We characterize for the first time the expression of murQ and its regulation by MurR, a member of the poorly characterized RpiR/AlsR family of transcriptional regulators. Deleting murR abolished the extensive lag phase observed for E. coli grown on MurNAc and enhanced murQ transcription some 20-fold...
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PMID: 18723630
PDF is available here.
PDF is available here.
Biotechnology Letters (30)9 2008
Abstract
Escherichia coli W3110 was previously engineered to produce xylitol from a mixture of glucose plus xylose by expressing xylose reductase (CbXR) and deleting xylulokinase (DeltaxylB), combined with either plasmid-based expression of a xylose transporter (XylE or XylFGH) (Khankal et al., J Biotechnol,...
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PMID: 18414795
PDF is available here.
PDF is available here.
Nucleic Acids Research (36)16 2008
Abstract
We have developed novel artificial transcription factors (ATFs) capable of reprogramming innate gene expression circuits in Escherichia coli. These ATFs are composed of zinc finger (ZF) DNA-binding proteins, with distinct specificities, fused to an E. coli cyclic AMP receptor protein (CRP). By rando...
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PMID: 18641039
PDF is available here.
PDF is available here.
Molecules and Cells (26)1 2008
Abstract
We demonstrated interdomain interactions in apo-CRP, using a comparative thermodynamic approach to the intact protein and its isolated domains, which were prepared either by limited proteolysis or using recombinant DNA. Thermal denaturation of the intact apo-CRP, monitored by differential scanning c...
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PMID: 18525238
PDF is available here.
PDF is available here.
Journal of Biotechnology (135)4 2008
Abstract
The glxR (cg0350) gene of Corynebacterium glutamicum ATCC 13032 encodes a DNA-binding transcription regulator of the CRP/FNR protein family. Five genomic DNA regions known to be bound by GlxR provided the seed information for DNA binding site discovery by expectation maximization and Gibbs sampling...
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PMID: 18573287
PDF is available here.
PDF is available here.
Abstract
We identified 2 pyrimidine salvage enzymes, namely, uridine phosphorylase and cytidine deaminase, which were down-regulated in the iscS mutant. Both enzymes are positively regulated by the cAMP receptor protein (CRP). We also identified a novel protein complex, namely, YeiT-YeiA, whose expression le...
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PMID: 18482579
PDF is available here.
PDF is available here.
Journal of Bacteriology (190)13 2008
Abstract
We show a surprising similarity in the altered ligand specificity of four CRP* variants with a single substitution in D53S, G141K, A144T, or L148K, and we propose a common basis for this phenomenon. The increased active protein population caused by an equilibrium shift in these variants is hypothesi...
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PMID: 18456811
PDF is available here.
PDF is available here.
Abstract
We observed that growth of S. marcescens in glucose-rich medium strongly stimulated biofilm formation, which contrasts with previous studies showing that biofilm formation is inhibited by glucose in Escherichia coli and other enteric bacteria. Glucose uptake is known to inversely mediate intracellul...
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PMID: 18424546
PDF is available here.
PDF is available here.
Abstract
The cyclic AMP receptor protein (CRP) of Escherichia coli regulates the activity of more than 150 genes. Allosteric changes in CRP structure accompanied by cAMP binding, initiate transcription through protein binding to specific DNA sequences. Initially, researchers proposed a two-site cAMP-binding...
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PMID: 18338329
PDF is available here.
PDF is available here.
Abstract
Cyclic AMP serves as an intracellular messenger in cells and regulates a variety of biological functions by transmitting information through proteins. These proteins of different functions all consist of a cAMP-binding motif, and the structure of this motif is highly conserved with an exception of t...
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PMID: 18328555
PDF is available here.
PDF is available here.
Journal of Biotechnology (134)3-4 2008
Abstract
We examine the contributions of the native E. coli xylose transporters (the d-xylose/proton symporter XylE and the d-xylose ABC transporter XylFGH) and CRP* to xylitol production in the presence of glucose and xylose. The final batch xylitol titer with strain PC09 (Delta xylB and crp*) is reduced by...
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PMID: 18359531
PDF is available here.
PDF is available here.
Infection and Immunity (76)5 2008
Abstract
We have found that these SNPs resulted in small but significant changes in the expression of a number of genes in M. tuberculosis when a deletion of the Rv3676 CRP was complemented by the BCG allele, compared to complementation by the M. tuberculosis allele. We can explain these changes in gene expr...
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PMID: 18332206
PDF is available here.
PDF is available here.
Nucleic Acids Research (36)8 2008
Abstract
We have investigated the different determinants needed for optimal repression and their spatial requirements. We show that repression requires a complex involving four DNA-bound MelR molecules, and that the global CRP regulator plays little or no role....
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PMID: 18346968
PDF is available here.
PDF is available here.
Molecular Microbiology (68)4 2008
Abstract
We have taken a 'reverse target search' approach by systematic inactivation of Salmonella sRNA genes, and screening 35 sRNA deletion strains for effects on OmpX synthesis. We have identified the Hfq-dependent CyaR (formerly RyeE) sRNA as an ompX repressor. Global transcriptomic profiling following i...
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PMID: 18399940
PDF is available here.
PDF is available here.
Archives of Oral Biology (53)5 2008
Abstract
The higher nuclear and cytoplasmic labeling during the neonatal period may reflect RII involvement in acinar cell differentiation. The accumulation of RII in secretory granules is similar to the pattern of the major salivary proteins, amylase and PSP. The redistribution of RII in these compartments...
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PMID: 18187105
PDF is available here.
PDF is available here.
Molecular Microbiology (68)2 2008
Abstract
We have shown previously that ribosome stalling during translation caused by various reasons leads to mRNA cleavage, resulting in non-stop mRNAs that are eliminated in a tmRNA-dependent manner. Amino acid starvation is a physiological condition in which ribosome stalling is expected to occur more fr...
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PMID: 18284591
PDF is available here.
PDF is available here.
Biophysical Journal (94)6 2008
Abstract
We developed a detailed mathematical model that accounts for all of the known regulatory mechanisms in this system, and studied the effect of inducing the operon with lactose instead of an artificial inducer. In this article, the model is improved to account, in a more detailed way, for the interact...
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PMID: 18065471
PDF is available here.
PDF is available here.
Microbiology (154)Pt 2 2008
Abstract
We have recently demonstrated that the ptxR upstream region contains potential binding sites for multiple regulators, including the virulence factor regulator Vfr. In this study, we identified within the ptxR upstream region, a 25 bp sequence to which Vfr specifically binds. The sequence is located...
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PMID: 18227247
PDF is available here.
PDF is available here.
Nucleic Acids Research (36)3 2008
Abstract
We implement a scalable approach based on thermodynamic molecular properties to model ab initio systems regulated through multiple DNA sites with looping. We show that this approach applied to the lac operon accurately predicts the system behavior for a wide range of cellular conditions, which inclu...
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PMID: 18056082
PDF is available here.
PDF is available here.
Journal of Biochemistry (143)2 2008
Abstract
Interdomain interaction of apo-cyclic AMP receptor protein (apo-CRP) was qualified using its isolated domains. The cAMP-binding domain was prepared by a limited proteolysis, while the DNA-binding domain was constructed as a recombinant protein. Three different regions making interdomain contacts in...
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PMID: 18084042
PDF is available here.
PDF is available here.
Abstract
We describe the use of informatics enabled comparative genomics to identify novel genes under the control of CRP regulator in Mycobacterium tuberculosis (M.tb). An inventory of CRP regulated genes and their operon context in important mycobacterial species such as M. leprae, M. avium subsp. paratube...
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PMID: 18022770
PDF is available here.
PDF is available here.
BMC Genomics (9 Suppl 1)suppl 1 2008
Abstract
We conducted physiological and transcriptomic studies to characterize Fur in Shewanella oneidensis, with regard to its roles in iron and acid tolerance response. A S. oneidensisfur deletion mutant was defective in growth under iron-abundant or acidic environment. However, it coped with iron depletio...
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PMID: 18366600
PDF is available here.
PDF is available here.
Nucleic Acids Research (36)1 2008
Abstract
We have isolated mutations in H. influenzae sxy that greatly elevate translation and thus cause competence to develop in otherwise non-inducing conditions (hypercompetence). In vitro nuclease analysis confirmed the existence of an extensive secondary structure at the 5' end of sxy mRNA that sequeste...
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PMID: 17981840
PDF is available here.
PDF is available here.
Research in Microbiology (159)7-8 2008
Abstract
We report that mutations in components of the catabolite repression system (cyaA and crp) eliminate flagellum production and swimming motility. Exogenous cAMP was able to restore flagellum production to adenylate cyclase mutants, as determined by transmission electron microscopy and PAGE analysis. A...
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PMID: 18718529
PDF is available here.
PDF is available here.
Abstract
We use extensive explicit-solvent molecular dynamics simulations (135 ns) to investigate the allosteric mechanism of CAP. Six trajectories were carried out for apo, singly liganded, and doubly liganded CAP, both in the presence and absence of DNA. Thorough analyses of the dynamics through the constr...
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PMID: 18041838
PDF is available here.
PDF is available here.
Journal of Bacteriology (189)24 2007
Abstract
We determined that expression of pla is controlled by the global regulator cyclic AMP (cAMP) receptor protein (Crp). This transcription factor is well conserved among distantly related bacteria, where it acts as a soluble receptor for the ubiquitous signaling molecule cAMP and controls a global netw...
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PMID: 17933899
PDF is available here.
PDF is available here.
Abstract
We demonstrate that deletion of crp and cya (adenylate cyclase) converts a rugose DeltahapR mutant to a smooth one. The smooth DeltahapR Deltacrp and DeltahapR Deltacya double mutants could be converted back to rugose by complementation with crp and cya, respectively. CRP was found to enhance the ex...
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PMID: 17921282
PDF is available here.
PDF is available here.
Physical Biology (4)4 2007
Abstract
We address this by presenting a cost-benefit theory for gene regulation functions that takes into account temporally varying inputs in the environment and stochastic noise in the biological components. We apply this theory to the well-studied lac operon of E. coli. The present theory explains the sh...
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PMID: 17991990
PDF is available here.
PDF is available here.
Abstract
We exploited a crp (cAMP receptor protein) gene-deleted, virulence plasmid-cured Salmonella choleraesuis mutant with decreased carbon source utilization, designated S.C.-Deltacrp/vpl(-), as a live vaccine strain. Normal weight gain with no clinical signs was observed in pigs immunized with high dose...
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PMID: 17825957
PDF is available here.
PDF is available here.
Biophysical Chemistry (130)1-2 2007
Abstract
We detect important fragments for the function of biomolecular systems and quantify the strength of interaction energies based on quantum chemistry, including the effects of charge transfer, electronic polarization and dispersion force. In this study, by analyzing a protein-DNA complex, we report a...
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PMID: 17656003
PDF is available here.
PDF is available here.
Molecular Microbiology (66)1 2007
Abstract
We identified SiaR as a repressor of sialic acid transport and catabolism in NTHi. Inactivation of siaR resulted in the unregulated expression of the genes in both operons. Unregulated catabolism of sialic acid in the siaR mutant resulted in the reduction of surface sialylation and an increase in se...
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PMID: 17880422
PDF is available here.
PDF is available here.
Journal of Bacteriology (189)19 2007
Abstract
We measured in a systematic way the relation between cellular growth rates and the key parameters of catabolite repression, i.e., the phosphorylated EIIA(Crr) (EIIA(Crr) approximately P) level and the cAMP level, using in vitro and in vivo assays. Different growth rates were obtained by using either...
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PMID: 17675376
PDF is available here.
PDF is available here.