scholarly journals A Dual Binding Site for Integration Host Factor and the Response Regulator CtrA inside the Caulobacter crescentus Replication Origin

2003 ◽  
Vol 185 (18) ◽  
pp. 5563-5572 ◽  
Author(s):  
Rania Siam ◽  
Ann Karen C. Brassinga ◽  
Gregory T. Marczynski
Keyword(s):  
Binding Site ◽  
Replication Origin ◽  
Protein Concentration ◽  
Caulobacter Crescentus ◽  
Response Regulator ◽  
Chromosome Replication ◽  
Integration Host Factor ◽  
Host Factor ◽  
Dna Mutations ◽  
Ihf Protein

ABSTRACT The response regulator CtrA controls chromosome replication by binding to five sites, a, b, c, d, and e, inside the Caulobacter crescentus replication origin (Cori). In this study, we demonstrate that integration host factor (IHF) binds Cori over the central CtrA binding site c. Surprisingly, IHF and CtrA share DNA recognition sequences. Rather than promoting cooperative binding, IHF binding hinders CtrA binding to site c and nearby site d. Unlike other CtrA binding sites, DNA mutations in the CtrA c/IHF site uniquely impair autonomous Cori plasmid replication. These mutations also alter transcription from distant promoters more than 100 bp away. When the CtrA c/IHF site was deleted from the chromosome, these cells grew slowly and became selectively intolerant to a CtrA phosphor-mimic allele (D51E). Since CtrA protein concentration decreases during the cell cycle as IHF protein concentration increases, we propose a model in which IHF displaces CtrA in order to bend Cori and promote efficient chromosome replication.

scholarly journals Conserved Response Regulator CtrA and IHF Binding Sites in the α-Proteobacteria Caulobacter crescentus and Rickettsia prowazekii Chromosomal Replication Origins

2002 ◽  
Vol 184 (20) ◽  
pp. 5789-5799 ◽  
Author(s):  
Ann Karen C. Brassinga ◽  
Rania Siam ◽  
William McSween ◽  
Herbert Winkler ◽  
David Wood ◽  
...  
Keyword(s):  
Binding Sites ◽  
Replication Origin ◽  
Caulobacter Crescentus ◽  
Response Regulator ◽  
Replication Origins ◽  
Rickettsia Prowazekii ◽  
Chromosomal Replication ◽  
Global Response ◽  
Developmental Defects ◽  
Ihf Protein

ABSTRACT CzcR is the Rickettsia prowazekii homolog of the Caulobacter crescentus global response regulator CtrA. CzcR expression partially compensates for developmental defects in ctrA mutant C. crescentus cells, and CzcR binds to all five CtrA binding sites in the C. crescentus replication origin. Conversely, CtrA binds to five similar sites in the putative R. prowazekii replication origin (oriRp). Also, Escherichia coli IHF protein binds over a central CtrA binding site in oriRp. Therefore, CtrA and IHF regulatory proteins have similar binding patterns in both replication origins, and we propose that CzcR is a global cell cycle regulator in R. prowazekii.

scholarly journals Comparative analysis of Caulobacter chromosome replication origins

Microbiology ◽  
2009 ◽  
Vol 155 (4) ◽  
pp. 1215-1225 ◽  
Author(s):  
S. M. Shaheen ◽  
Marie-Claude Ouimet ◽  
Gregory T. Marczynski
Keyword(s):  
Binding Site ◽  
Binding Sites ◽  
Caulobacter Crescentus ◽  
Chromosome Replication ◽  
Integration Host Factor ◽  
Site Directed Mutagenesis ◽  
Replication Origins ◽  
Two Component ◽  
Replication Control ◽  
Dnaa Box

Caulobacter crescentus (CB15) initiates chromosome replication only in stalked cells and not in swarmers. To better understand this dimorphic control of chromosome replication, we isolated replication origins (oris) from freshwater Caulobacter (FWC) and marine Caulobacter (MCS) species. Previous studies implicated integration host factor (IHF) and CcrM DNA methylation sites in replication control. However, ori IHF and CcrM sites identified in the model FWC CB15 were only conserved among closely related FWCs. DnaA boxes and CtrA binding sites are established CB15 ori components. CtrA is a two-component regulator that blocks chromosome replication selectively in CB15 swarmers. DnaA boxes and CtrA sites were found in five FWC and three MCS oris. Usually, a DnaA box and a CtrA site were paired, suggesting that CtrA binding regulates DnaA activity. We tested this hypothesis by site-directed mutagenesis of an MCS10 ori which contains only one CtrA binding site overlapping a critical DnaA box. This overlapping site is unique in the whole MCS10 genome. Selective DnaA box mutations decreased replication, while selective CtrA binding site mutations increased replication of MCS10 ori plasmids. Therefore, both FWC and MCS oris use CtrA to repress replication. Despite this similarity, phylogenetic analysis unexpectedly shows that CtrA usage evolved separately among these Caulobacter oris. We discuss consensus oris and convergent ori evolution in differentiating bacteria.

scholarly journals The Escherichia coli K-12 NarL and NarP Proteins Insulate the nrf Promoter from the Effects of Integration Host Factor

2006 ◽  
Vol 188 (21) ◽  
pp. 7449-7456 ◽  
Author(s):  
Douglas F. Browning ◽  
David J. Lee ◽  
Alan J. Wolfe ◽  
Jeffrey A. Cole ◽  
Stephen J. W. Busby
Keyword(s):  
Escherichia Coli ◽  
Response Regulator ◽  
Regulatory Region ◽  
Enteric Bacteria ◽  
Integration Host Factor ◽  
Host Factor ◽  
Receptor Protein ◽  
E Coli ◽  
Serovar Typhimurium ◽  
K 12

ABSTRACT The Escherichia coli K-12 nrf operon promoter can be activated fully by the FNR protein (regulator of fumarate and nitrate reduction) binding to a site centered at position −41.5. FNR-dependent transcription is suppressed by integration host factor (IHF) binding at position −54, and this suppression is counteracted by binding of the NarL or NarP response regulator at position −74.5. The E. coli acs gene is transcribed from a divergent promoter upstream from the nrf operon promoter. Transcription from the major acsP2 promoter is dependent on the cyclic AMP receptor protein and is modulated by IHF and Fis binding at multiple sites. We show that IHF binding to one of these sites, located at position −127 with respect to the nrf promoter, has a positive effect on nrf promoter activity. This activation is dependent on the face of the DNA helix, independent of IHF binding at other locations, and found only when NarL/NarP are not bound at position −74.5. Binding of NarL/NarP appears to insulate the nrf promoter from the effects of IHF. The acs-nrf regulatory region is conserved in other pathogenic E. coli strains and related enteric bacteria but differs in Salmonella enterica serovar Typhimurium.

scholarly journals Role of Integration Host Factor in the Transcriptional Activation of Flagellar Gene Expression in Caulobacter crescentus

2005 ◽  
Vol 187 (3) ◽  
pp. 949-960 ◽  
Author(s):  
Rachel E. Muir ◽  
James W. Gober
Keyword(s):  
Gene Expression ◽  
Caulobacter Crescentus ◽  
Consensus Sequence ◽  
Integration Host Factor ◽  
Host Factor ◽  
Flagellar Gene ◽  
Class Iii ◽  
Mild Defect ◽  
Flagellar Genes ◽  
Class Iv

ABSTRACT In the Caulobacter crescentus predivisional cell, class III and IV flagellar genes, encoding the extracytoplasmic components of the flagellum, are transcribed in the nascent swarmer compartment. This asymmetric expression pattern is attributable to the compartmentalized activity of the σ54-dependent transcriptional activator FlbD. Additionally, these temporally transcribed flagellar promoters possess a consensus sequence for the DNA-binding protein integration host factor (IHF), located between the upstream FlbD binding site and the promoter sequences. Here, we deleted the C. crescentus gene encoding the β-subunit of the IHF, ihfB (himD), and examined the effect on flagellar gene expression. The ΔihfB strain exhibited a mild defect in cell morphology and impaired motility. Using flagellar promoter reporter fusions, we observed that expression levels of a subset of class III flagellar promoters were decreased by the loss of IHF. However, one of these promoters, fliK-lacZ, exhibited a wild-type cell cycle-regulated pattern of expression in the absence of IHF. Thus, IHF is required for maximal transcription of several late flagellar genes. The ΔihfB strain was found to express significantly reduced amounts of the class IV flagellin, FljL, as a consequence of reduced transcriptional activity. Our results indicate that the motility defect exhibited by the ΔihfB strain is most likely attributable to its failure to accumulate the class IV-encoded 27-kDa flagellin subunit, FljL.

scholarly journals Regulation of podJ Expression during theCaulobacter crescentus Cell Cycle

1999 ◽  
Vol 181 (13) ◽  
pp. 3967-3973 ◽  
Author(s):  
William B. Crymes ◽  
Daolong Zhang ◽  
Bert Ely
Keyword(s):  
Cell Cycle ◽  
Binding Site ◽  
Promoter Activity ◽  
Caulobacter Crescentus ◽  
Response Regulator ◽  
Negative Regulator ◽  
Nucleotide Sequence Analysis ◽  
Global Response ◽  
Temporal Regulation ◽  
Polar Organelle

ABSTRACT The polar organelle development gene, podJ, is expressed during the swarmer-to-stalked cell transition of theCaulobacter crescentus cell cycle. Mutants with insertions that inactivate the podJ gene are nonchemotactic, deficient in rosette formation, and resistant to polar bacteriophage, but they divide normally. In contrast, hyperexpression of podJresults in a lethal cell division defect. Nucleotide sequence analysis of the podJ promoter region revealed a binding site for the global response regulator, CtrA. Deletion of this site results in increased overall promoter activity, suggesting that CtrA is a negative regulator of the podJ promoter. Furthermore, synchronization studies have indicated that temporal regulation is not dependent on the presence of the CtrA binding site. Thus, although the level of podJ promoter activity is dependent on the CtrA binding site, the temporal control of podJ promoter expression is dependent on other factors.

scholarly journals Two-step interrogation then recognition of DNA binding site by Integration Host Factor: an architectural DNA-bending protein

2017 ◽  
Vol 46 (4) ◽  
pp. 1741-1755 ◽  
Author(s):  
Yogambigai Velmurugu ◽  
Paula Vivas ◽  
Mitchell Connolly ◽  
Serguei V Kuznetsov ◽  
Phoebe A Rice ◽  
...  
Keyword(s):  
Dna Binding ◽  
Binding Site ◽  
Dna Bending ◽  
Integration Host Factor ◽  
Host Factor ◽  
Dna Binding Site

Transcriptional regulation of the uptake [NiFe]hydrogenase genes in Rhodobacter capsulatus

2005 ◽  
Vol 33 (1) ◽  
pp. 28-32 ◽  
Author(s):  
P.M. Vignais ◽  
S. Elsen ◽  
A. Colbeau
Keyword(s):  
Gene Expression ◽  
Rhodobacter Capsulatus ◽  
Response Regulator ◽  
Regulatory System ◽  
Integration Host Factor ◽  
Host Factor ◽  
Promoter Recognition ◽  
The Stability ◽  
A Site

Transcription of the hupSL genes, which encode the uptake [NiFe]hydrogenase of Rhodobacter capsulatus, is specifically activated by H2. Three proteins are involved, namely the H2-sensor HupUV, the histidine kinase HupT and the transcriptional activator HupR. hupT and hupUV mutants have the same phenotype, i.e. an increased level of hupSL expression (assayed by phupS::lacZ fusion) in the absence of H2; they negatively control hupSL gene expression. HupT can autophosphorylate its conserved His217, and in vitro phosphotransfer to Asp54 of its cognate response regulator, HupR, was demonstrated. The non-phosphorylated form of HupR binds to an enhancer site (5′-TTG-N5-CAA) of phupS localized at −162/−152 nt and requires integration host factor to activate fully hupSL transcription. HupUV is an O2-insensitive [NiFe]hydrogenase, which interacts with HupT to regulate the phosphorylation state of HupT in response to H2 availability. The N-terminal domain of HupT, encompassing the PAS domain, is required for interaction with HupUV. This interaction with HupT, leading to the formation of a (HupT)2–(HupUV)2 complex, is weakened in the presence of H2, but incubation of HupUV with H2 has no effect on the stability of the heterodimer/tetramer, HupUV–(HupUV)2, equilibrium. HupSL biosynthesis is also under the control of the global two-component regulatory system RegB/RegA, which controls gene expression in response to redox. RegA binds to a site close to the −35 promoter recognition site and to a site overlapping the integration host factor DNA-binding site (5′-TCACACACCATTG, centred at −87 nt) and acts as a repressor.

Sign in / Sign up

Export Citation Format

Share Document