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RNA Polymerase Sigma 54 (0):
Recent article
RNA Polymerase Sigma 54
Abstract
We characterize the initial encounter between the enhancer-dependent Esigma(54) and its cognate activator AAA+ ATPase protein, before ADP+P(i) formation, using a small primed RNA (spRNA) synthesis assay. The results show that in a prehydrolysis state, sufficient activator-dependent rearrangements in...
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PMID: 20439713
PDF is available here.
PDF is available here.
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Microbiology (156)Pt 3 2010
Abstract
We report on the gene expression alterations that follow rpoN inactivation in Escherichia coli O157 : H7 strain Sakai (Sakai rpoN : : kan), and the influence of RpoN on the acid resistance phenotype. Microarray gene expression profiling revealed the differential expression of 103 genes in SakairpoN...
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PMID: 19942657
PDF is available here.
PDF is available here.
Abstract
Regulation of aromatic degradation in obligate anaerobes was studied in the Fe(III)-respiring model organism Geobacter metallireducens GS-15. A two-component system and a sigma54-dependent promoter were identified that are both involved in the regulation of the gene coding for benzoate-coenzyme A li...
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PMID: 19915033
PDF is available here.
PDF is available here.
Journal of Bacteriology (192)1 2010
Abstract
We confirmed that the gabT and gabD genes belong to different transcriptional units, while the gabD and gabR genes form an operon. We also demonstrated that the gabR gene plays a positive regulatory role in gabD and gabT expression. The GabR protein may be a sigma(54)-dependent transcriptional activ...
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PMID: 19854901
PDF is available here.
PDF is available here.
BMC Genomics (10)1 2009
Abstract
An rpoN deletion mutant could not be obtained under all conditions tested. In order to investigate the regulon of the G. sulfurreducens RpoN, an RpoN over-expression strain was made in which an extra copy of the rpoN gene was under the control of a taclac promoter. Combining both the microarray tran...
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PMID: 19624843
PDF is available here.
PDF is available here.
Journal of Bacteriology (190)24 2008
Abstract
We conclude that HP0958 is a posttranscriptional regulator that modulates the amount of the flaA message available for translation in H. pylori....
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PMID: 18931105
PDF is available here.
PDF is available here.
Molecular Cell (32)3 2008
Abstract
We present cryoelectron microscopy reconstructions of bacterial RNAP in complex with sigma(54) alone, and of RNAP-sigma(54) with an AAA+ activator. Together with photo-crosslinking data that establish the location of promoter DNA within the complexes, we explain why the RNAP-sigma(54) closed complex...
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PMID: 18995832
PDF is available here.
PDF is available here.
Molecular Microbiology (70)3 2008
Abstract
We identify the Pr promoter of dmpR as a sigma(70)-dependent promoter that is regulated by a novel mechanism in which sigma(54)-RNA polymerase occupancy of the non-overlapping sigma(54)-Po promoter stimulates sigma(70)-Pr output. In addition, we show that DmpR stimulates its own production through P...
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PMID: 18786144
PDF is available here.
PDF is available here.
Genetika (Moskva) (44)9 2008
Abstract
The control of gene expression in response to an increase in the bacterial population density (Quorum Sensing) involves low-molecular-weight signal molecules (autoinducers, AI). AI-2 and synthase LuxS mediating its synthesis are widely distributed in Gram-negative and Gram-positive bacteria. In this...
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PMID: 18846815
PDF is available here.
PDF is available here.
Microbiology (154)Pt 9 2008
Abstract
We employed microarray analyses to compare gene expression levels in rrp2, rpoN and rpoS mutants of parental strain 297. We identified 98 genes that were similarly regulated by Rrp2, RpoN and RpoS, and an additional 47 genes were determined to be likely regulated by this pathway. The substantial ove...
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PMID: 18757798
PDF is available here.
PDF is available here.
Journal of Molecular Biology (381)1 2008
Abstract
We propose a structural symmetry-based model for homotropic control in the AAA(+) characteristic ring architecture....
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PMID: 18599077
PDF is available here.
PDF is available here.
Abstract
We have constructed and examined an A. baylyi ADP1 strain, ADPWH-Pu-lux-xylR. The Pu promoter in ADPWH-Pu-lux-xylR was specifically induced by toluene, m-, p- and o-xylene. The substrate-induced Pu promoter was highly dependent on the growth medium: it was repressed in rich media until stationary ph...
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PMID: 18363715
PDF is available here.
PDF is available here.
Journal of Bacteriology (190)13 2008
Abstract
We investigated the transcription mechanism for the sulfate starvation-induced expression of these sfn operons. Using an in vivo transcription assay and in vitro DNA-binding experiments, we revealed that SfnR negatively regulates the expression of sfnECR by binding to the downstream region of the tr...
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PMID: 18456803
PDF is available here.
PDF is available here.
Molecular Microbiology (68)3 2008
Abstract
We summarize our current understanding of the interactions the sigma(54) factor makes with the bacterial transcription machinery....
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PMID: 18331472
PDF is available here.
PDF is available here.
Journal of Bacteriology (190)7 2008
Abstract
We performed genetic and biochemical analyses to understand how FlgR activity is controlled to culminate in the expression of sigma(54)-dependent flagellar genes. Our data suggest that the FlgR receiver domain has the capacity for both positive and negative regulation in controlling the activation o...
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PMID: 18223079
PDF is available here.
PDF is available here.
Journal of Molecular Biology (375)5 2008
Abstract
We present a new nucleotide analogue, AMP-AlF(x), which traps PspF, a bacterial enhancer binding protein, in a stable complex with the sigma(54)-RNA polymerase holoenzyme. The crystal structure of AMP-AlF(x)*PspF(1-275) provides new information on protein-nucleotide interactions and suggests that th...
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PMID: 18082766
PDF is available here.
PDF is available here.
Abstract
We studied the role of some global regulators of gene expression on biofilm formation by Escherichia coli K12. The Histone-like proteins H-NS and StpA were shown to play an essential role in the regulation of biofilm formation. Mutant strains deficient in HNS or StpA had lower levels of biofilm form...
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PMID: 19177607
PDF is available here.
PDF is available here.
Journal of Molecular Biology (375)1 2008
Abstract
We demonstrate that prior to DNA melting, only the sigma(54)-factor directly interacts with the promoter in the regulatory switch within the initial closed E sigma(54)-promoter complex and one intermediate E sigma(54)-promoter complex. We establish that activator-induced conformational rearrangement...
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PMID: 18005983
PDF is available here.
PDF is available here.
Abstract
We show that RpoN is required for efficient colonization of sugar beet seedlings by the plant growth-promoting bacterium Pseudomonas fluorescens SBW25, and use phenotypic and bioinformatic approaches to profile the RpoN-dependent traits and genes of P. fluorescens SBW25. RpoN is required for flagell...
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PMID: 17991033
PDF is available here.
PDF is available here.
Trends in Microbiology (15)12 2007
Abstract
Transcriptional activation in bacteria usually involves an activator protein that binds to sites near the target promoter. Some activators of sigma(54)-RNA polymerase holoenzyme, however, can stimulate transcription even when their DNA-binding domains are removed. Recent studies have revealed exampl...
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PMID: 17997097
PDF is available here.
PDF is available here.
Molecular Microbiology (66)3 2007
Abstract
We analysed the functionality of the conserved 'DE' Walker B motif of a bEBP model, phage shock protein F (PspF), to investigate the role of these residues in the sigma(54)-dependent transcription activation process. We established their role in the regulation of PspF self-association and in the rel...
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PMID: 17883390
PDF is available here.
PDF is available here.
Journal of Bacteriology (189)22 2007
Abstract
We showed that expression of the BBK32 gene is influenced by multiple environmental factors and that its regulation is governed by the response regulator Rrp2 and RpoN-RpoS (sigma(54)-sigma(S)) sigma cascade in B. burgdorferi....
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PMID: 17873053
PDF is available here.
PDF is available here.
Microbiology (153)Pt 9 2007
Abstract
We investigated the transcriptional regulation of the sfnAB operon and possible functions of the sfnA gene. RT-PCR analysis revealed that the sfnAB gene cluster, which is similar to homologues of the acyl-CoA dehydrogenase family, was transcribed as an operon, and its expression was regulated by Sfn...
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PMID: 17768252
PDF is available here.
PDF is available here.
Microbiology (153)Pt 9 2007
Abstract
A previously unannotated, putative fliK gene was identified in the Campylobacter jejuni genome based on sequence analysis; deletion mutants in this gene had a 'polyhook' phenotype characteristic of fliK mutants in other genera. The mutants greatly overexpressed the sigma(54)-dependent flagellar hook...
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PMID: 17768253
PDF is available here.
PDF is available here.
Molecular Microbiology (65)6 2007
Abstract
We report here that expression of the Escherichia coli glmS gene is negatively feedback regulated by its product GlcN-6-P at the post-transcriptional level. Initially, we observed that mutants defective for yhbJ, a gene of the rpoN operon, overproduce GlmS. Concomitantly, a glmS mRNA accumulates tha...
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PMID: 17824929
PDF is available here.
PDF is available here.
Molecular Microbiology (65)2 2007
Abstract
We show that: (i) rpoS has a sigma(54)-dependent promoter that requires Rrp2 to activate transcription; (ii) Rrp2Delta123, a constitutively active form of Rrp2, activated sigma(54)-dependent transcription of rpoS/P-lacZ reporter constructs in Escherichia coli; (iii) quantitative reverse transcriptio...
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PMID: 17590233
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (282)25 2007
Abstract
We report analysis of five hyper-suppressor mutants within the beta- and beta'-subunits of core RNA polymerase that allow high levels of transcription from the sigma54-Po promoter in the absence of ppGpp. Using in vitro transcription and competition assays, we present evidence that these core RNA po...
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PMID: 17456470
PDF is available here.
PDF is available here.
Journal of Molecular Biology (369)4 2007
Abstract
We present the solution structure of the C-terminal domain of sigma(54) bound to the -24 promoter element, in which the conserved RpoN box motif inserts into the major groove of the DNA. This structure elucidates the basis for sequence specific recognition of the -24 element, orients sigma(54) on th...
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PMID: 17481658
PDF is available here.
PDF is available here.
Microbiology (153)Pt 5 2007
Abstract
It has been suggested that resistance to class IIa bacteriocins occurs at either a low or a high level. In listerial strains, low-level resistance (2-4-fold) to class IIa bacteriocins is attributed to alterations in membrane lipid composition. In Listeria monocytogenes and Enterococcus faecalis, hig...
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PMID: 17464076
PDF is available here.
PDF is available here.
Abstract
We have constructed an rpoN mutant of Pseudomonas aeruginosa and investigated its importance as a target for antimicrobial agents, such as quinolones and carbapenems. The stationary-phase cells of the rpoN mutant displayed a survival rate approximately 15 times higher than that of the wild-type cell...
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PMID: 17261620
PDF is available here.
PDF is available here.
Abstract
We present SAS-based solution structures of the ATPase domain of the EBP NtrC1 from Aquifex aeolicus in different nucleotide states. Structures of apo protein and that bound to AMPPNP or ADP-BeF(x) (ground-state mimics), ADP-AlF(x) (a transition-state mimic), or ADP (product) show substantial change...
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PMID: 17437715
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (282)13 2007
Abstract
We report activities for PspF(1-275) mutated in the AAA+ conserved sensor I threonine/asparagine motif (PspF(1-275)(T148A), PspF(1-275)(N149A), and PspF(1-275)(N149S)) within the second region of homology. We show that sensor I asparagine plays a direct role in ATP hydrolysis. However, low hydrolysi...
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PMID: 17242399
PDF is available here.
PDF is available here.
Journal of Bacteriology (189)5 2007
Evidence that RpoS (sigmaS) in Borrelia burgdorferi is controlled directly by RpoN (sigma54/sigmaN).
Abstract
We provide biochemical and genetic evidence that RpoN directly controls rpoS in B. burgdorferi....
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PMID: 17158681
PDF is available here.
PDF is available here.
Journal of Bacteriology (189)6 2007
Abstract
Proteins whose synthesis is enhanced by polyamines at the level of translation were identified in a polyamine-requiring mutant cultured in the presence of 0.1% glucose and 0.02% glutamate instead of 0.4% glucose as an energy source. Under these conditions, enhancement of cell growth by polyamines wa...
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PMID: 17220219
PDF is available here.
PDF is available here.
Abstract
Bacterial transcription relies on the binding of dissociable sigma (sigma) factors to RNA polymerase (RNAP) for promoter specificity. The major variant sigma factor (sigma54) forms a stable closed complex with RNAP bound to DNA that rarely spontaneously isomerises to an open complex. ATP hydrolysis...
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PMID: 17157497
PDF is available here.
PDF is available here.
Abstract
We now provide evidence that the invariant threo-nine residue of the GAFTGA motif plays a role in sensing the DNA downstream of the sigma54-RNAP-binding site and in coupling this information to sigma54-RNAP via the conserved regulatory Region I domain of sigma54 during open complex formation....
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PMID: 17090527
PDF is available here.
PDF is available here.
Microbiology (153)Pt 1 2007
Abstract
The Escherichia coli rpoH gene is transcribed from four known and differently regulated promoters: P1, P3, P4 and P5. This study demonstrates that the conserved consensus sequence of the sigma54 promoter in the regulatory region of the rpoH gene, described previously, is a functional promoter, P6. T...
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PMID: 17185540
PDF is available here.
PDF is available here.
Genome Informatics (19) 2007
Abstract
We describe an extension of the promoter description to include SIDD (stress induced duplex destabilization), DNA curvature and stacking energy. Although we report the best result to date for a realistic promoter prediction task, surprisingly, DNA structural properties did not contribute significant...
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PMID: 18546515
PDF is available here.
PDF is available here.
Molecular Microbiology (63)2 2007
Abstract
We screened a pool of random Vibrio vulnificus mutants for their ability to form biofilms. One mutant displaying significantly decreased biofilm-forming activity was found to contain a transposon insertion in the ntrC gene. The ntrC gene encodes a well-known transcriptional activator. We examined ho...
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PMID: 17241201
PDF is available here.
PDF is available here.
Abstract
These results strongly suggest that the expression of the nifB promoter of H. seropedicae is dependent on the NifA and RpoN proteins and that the IHF protein stimulates NifA activation of nifB promoter....
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PMID: 17473889
PDF is available here.
PDF is available here.
Research in Microbiology (157)9 2006
Abstract
We show here that in vitro assessment of bacterial phenotypes, such as adherence and cytotoxicity, are positively correlated with data from in vivo experiments in Drosophila and can be used to assess bacterial virulence in vivo. Manipulation of environmental parameters, such as iron availability, in...
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PMID: 16901681
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (281)44 2006
Abstract
The sigma(54) promoter specificity factor is distinct from other bacterial RNA polymerase (RNAP) sigma factors in that it forms a transcriptionally silent closed complex upon promoter binding. Transcriptional activation occurs through a nucleotide-dependent isomerization of sigma(54), mediated via i...
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PMID: 16926155
PDF is available here.
PDF is available here.
Journal of Bacteriology (188)22 2006
Abstract
We show that the expression of the two pathways is regulated independently. Overlapping promoters recognized by sigma(28) and sigma(70) RNAP holoenzyme transcribe cheOp2, whereas cheOp3 is regulated by one of the four sigma(54) homologues, RpoN3. The different regulation of these operons may reflect...
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PMID: 16963577
PDF is available here.
PDF is available here.
Abstract
We propose a structural model of EBPs in complex with a sigma(54)-RNAP-promoter complex....
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PMID: 16531068
PDF is available here.
PDF is available here.
FEMS Microbiology Letters (263)1 2006
Abstract
We constructed a deletion mutant of rpoN, encoding the alternative sigma factor RpoN, and analyzed its response to osmotic stress. In a minimal medium with 4% NaCl and 1 mM betaine, the mutant showed a similar growth to that of the parental strain, EGD. In the same medium with 4% NaCl and 1 M carnit...
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PMID: 16958851
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (281)37 2006
Abstract
We demonstrate that the identity of the -11-position is critical for promoter discrimination by RpoN1 and RpoN2. Accordingly, purified RpoN proteins with a deletion of Region I, which has been involved in the recognition of the -11-position, did not show differential binding of fliOp and nifUp promo...
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PMID: 16854992
PDF is available here.
PDF is available here.
Journal of Bacteriology (188)13 2006
Abstract
We have identified a two-component signal transduction system (PilR/S) and an alternative sigma factor (sigma 54) that were shown by insertional inactivation to be required for the regulation of fimbrial biogenesis in D. nodosus. Western blots showed that in both pilR and rpoN mutants, fimbrial subu...
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PMID: 16788189
PDF is available here.
PDF is available here.
Journal of Molecular Biology (359)5 2006
Abstract
We present evidence that two flexible modules of beta', the beta' jaw and the beta' clamp and a conserved regulatory Region I domain of sigma(54), jointly contribute to the maintenance of stable DNA strand separation around the trancription start site in OCs formed at sigma(54)-dependent promoters....
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PMID: 16725156
PDF is available here.
PDF is available here.
FEMS Microbiology Letters (259)1 2006
Abstract
Several Helicobacter pylori flagellar genes require sigma(54) for their transcription. Predicted H. pylori sigma(54)-dependent promoters display a preference for A at position -23 instead of C or T as occurs in promoters from most other bacteria. Substitution of the A at position -23 of the H. pylor...
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PMID: 16684097
PDF is available here.
PDF is available here.
Molecular Microbiology (60)5 2006
Abstract
We argue that anti-XylR scFvs operate as bona fide transcriptional inhibitors of the Pu promoter....
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PMID: 16689797
PDF is available here.
PDF is available here.
Molecular Microbiology (60)3 2006
Abstract
We present evidence: (i) that both DksA and ppGpp are required for in vivo sigma54 transcription even though they do not have any major direct effects on sigma54 transcription in reconstituted in vitro transcription and sigma-factor competition assays, (ii) that previously defined mutations renderin...
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PMID: 16629675
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (281)17 2006
Abstract
Although the m-xylene-responsive sigma54 promoter Pu of Pseudomonas putida mt-2, borne by the TOL plasmid pWWO, is one of the strongest known promoters in vivo, its base-line level in the absence of its aromatic inducer is below the limit of any detection procedure. This is unusual because regulator...
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PMID: 16510445
PDF is available here.
PDF is available here.
Microbiology (152)Pt 4 2006
Abstract
The widely conserved phage-shock-protein A (pspA) operon encodes an extracytoplasmic stress response system that is essential for virulence in Yersinia enterocolitica, and has been linked to other important phenotypes in Escherichia coli, Salmonella enterica and Shigella flexneri. Regulation of pspA...
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PMID: 16549664
PDF is available here.
PDF is available here.
Journal of Bacteriology (188)8 2006
Abstract
We present genetic evidence for participation of sigma(L) (sigma(54)) and the two sigma(L)-dependent transcriptional enhancers BkdR and YplP in the cold shock response of Bacillus subtilis JH642. Single-gene deletion of either sigL, bkdR, or yplP resulted in a cold-sensitive phenotype....
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PMID: 16585774
PDF is available here.
PDF is available here.
Journal of Molecular Biology (357)2 2006
Abstract
We compare six high resolution structures (<2.1 A) of the AAA(+) domain of EBP phage shock protein F (PspF) including apo, AMPPNP, Mg(2+)-ATP, and ADP forms. These structures permit a description of the atomic details underpinning the origins of the conformational changes occurring during ATP hydrol...
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PMID: 16430918
PDF is available here.
PDF is available here.
FEMS Microbiology Letters (256)1 2006
Abstract
We ascribe this reduced colonization to the inability of the mutant to utilize certain organic acid components in the root exudates. The dctA mutant failed to grow on succinate and fumarate, and showed reduced growth on malate. All altered properties of the mutant were complemented by the full-lengt...
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PMID: 16487325
PDF is available here.
PDF is available here.
Biochemical Society Transactions (34)Pt 1 2006
Abstract
The sigma54-dependent transcriptional regulator NorR of Ralstonia eutropha H16 activates gene expression in response to nitric oxide (NO). The N-terminal domain of NorR is thought to be involved in signal perception. A C112S exchange within this domain abolished promoter activation by the mutated pr...
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PMID: 16417516
PDF is available here.
PDF is available here.
Molecular Microbiology (59)1 2006
Abstract
We observed a strong enhanced or decreased promoter activity, especially on linear DNA templates in vitro. The relative positioning and orientations of Esigma54, DNA bending protein and enhancer-bound activator on linear DNA were determined by in vitro footprinting analysis. Intriguingly, the locati...
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PMID: 16359326
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (280)50 2005
Abstract
We present the NMR-derived structure of the C-terminal domain of sigma54 from Aquifex aeolicus. This domain (Thr-323 to Gly-389), which contains the highly conserved RpoN box sequence, consists of a poorly structured N-terminal tail followed by a three-helix bundle, which is surprisingly similar to...
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PMID: 16210314
PDF is available here.
PDF is available here.
Journal of Molecular Biology (354)2 2005
Abstract
We have obtained the structure of the complete RNA polymerase from E.coli containing the sigma54 factor within the closed-promoter complex. Comparisons with earlier reconstructions of the core enzyme and the sigma54 holoenzyme reveal the behaviour of this major variant RNA polymerase in defined func...
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PMID: 16246367
PDF is available here.
PDF is available here.