Characterization of divergent NtrA‐dependent promoters in the anaerobically expressed gene cluster coding for hydrogenase 3 components of <i>Escherichia coli</i>

Lutz, Steffi; Böhm, R.; Beier, Andy; Böck, August

doi:10.1111/j.1365-2958.1990.tb02010.x

Cited by 57 publications

(37 citation statements)

References 41 publications

(30 reference statements)

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“…Previously, it was reported that in E. coli the expression offdhF (4) and various hydrogenase genes (6,18,30) required a functional ntrA. We have confirmed that fdhF expression in S. typhimurium also requires ntrA by using transposon insertional inactivation, i.e., introduction of ntrA209::TnlO.…”

Section: Resultssupporting

confidence: 65%

“…In addi-* Corresponding author. tion, the transcription of several genes involved in the synthesis of active hydrogenase has been shown to require NtrA (4,6,18). Unlike the case with other enterobacterial sigma factors, activation of transcription by NtrA has been shown to require accessory, DNA-binding, trans-acting factors that bind to specific UASs that have many of the properties of eucaryotic enhancers (7,8,26).…”

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confidence: 99%

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Mutations in trans that affect formate dehydrogenase (fdhF) gene expression in Salmonella typhimurium

Fasciano

Hallenbeck

1991

J Bacteriol

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Expression of the fdhF locus of Salmonella typhimurium is shown to be dependent upon ntrA and oxrB. However, the oxrB8 mutation is pleiotropic and also affects the expression of hyd, pepT, and chlC, whereas a mutation in ntrA does not. Insertional inactivation with Tn10 and localized mutagenesis permitted the definition and partial characterization of two new genes, fdhS and fdhR, which appear to be involved in the positive regulation of fdhF expression. Both genes were mapped to the 71- to 72-min region of the S. typhimurium chromosome with the gene order fdhS-crp-fdhR-rpsL. Mutations in fdhS specifically affect fdhF expression without affecting the expression of the other anaerobically induced genes or enzymes that were tested, including hyd, pepT, chlC, nitrite reductase, sulfite reductase, and trimethylamine-N-oxide reductase. Both fdhR and fdhS may be involved in fdhF regulation vis-à-vis oxygen, since localized mutagenesis produced alleles of both genes that permitted the aerobic expression of fdhF. However, fdhR may more directly interact with fdhF, since insertional inactivation of fdhS does not abolish aerobic expression of fdhF in fdhR mutant strains. Taken together, these results suggest that fdhS and fdhR act in concert under anaerobic conditions to activate fdhF transcription.

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Section: Resultssupporting

confidence: 65%

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confidence: 99%

Mutations in trans that affect formate dehydrogenase (fdhF) gene expression in Salmonella typhimurium

Fasciano

Hallenbeck

1991

J Bacteriol

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“…So far, only two divergently transcribed s 54 -dependent promoters have been characterized (Charlton et al, 1993;Lutz et al, 1990;Hopper et al, 1994). In Klebsiella pneumoniae, it has been reported that the IHF protein avoids activation of the nifJ promoter by NifA when it is bound to the UAS responsible for activating the divergently transcribed promoter nifH.…”

Section: Discussionmentioning

confidence: 99%

“…The release of FliA from the inhibitory action of FlgM is one of the most important check-points during flagella formation, and it occurs when FlgM is exported out of the cell once the hook-basal body structure is completed. Hence, it is tempting to speculate that cross-regulation mediated by these UASs helps keep these two proteins in equilibrium.So far, only two divergently transcribed s 54 -dependent promoters have been characterized (Charlton et al, 1993;Lutz et al, 1990; Hopper et al, 1994). In Klebsiella pneumoniae, it has been reported that the IHF protein avoids activation of the nifJ promoter by NifA when it is bound to the UAS responsible for activating the divergently transcribed promoter nifH.…”

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Identification of the binding site of the σ 54 hetero-oligomeric FleQ/FleT activator in the flagellar promoters of Rhodobacter sphaeroides

et al. 2009

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Expression of the flagellar genes in Rhodobacter sphaeroides is dependent on one of the four sigma-54 factors present in this bacterium and on the enhancer binding proteins (EBPs) FleQ and FleT. These proteins, in contrast to other well-characterized EBPs, carry out activation as a hetero-oligomeric complex. To further characterize the molecular properties of this complex we mapped the binding sites or upstream activation sequences (UASs) of six different flagellar promoters. In most cases the UASs were identified at approximately 100 bp upstream from the promoter. However, the activity of the divergent promoters flhAp-flgAp, which are separated by only 53 bp, is mainly dependent on a UAS located approximately 200 bp downstream from each promoter. Interestingly, a significant amount of activation mediated by the upstream or contralateral UAS was also detected, suggesting that the architecture of this region is important for the correct regulation of these promoters. Sequence analysis of the regions carrying the potential FleQ/FleT binding sites revealed a conserved motif. In vivo footprinting experiments with the motAp promoter allowed us to identify a protected region that overlaps with this motif. These results allow us to propose a consensus sequence that represents the binding site of the FleQ/ FleT activating complex. INTRODUCTIONPromoter recognition in bacteria is mediated by the RNA polymerase core (E) associated with a sigma factor. There are two families of sigma factors, the s 70 family and that of s 54 . These two families differ not only in their sequence but also in the mechanism that brings about transcriptional initiation. Whereas Es 70 is capable of forming open complex by itself, Es 54 requires an activator protein that, through ATP hydrolysis, allows open complex formation (for reviews, see Buck et al., 2000;Wigneshweraraj et al., 2005). Activator proteins of Es 54 usually bind approximately 100 bp upstream of the promoter sequence, and a DNA loop favours the interaction of the activator with the RNA polymerase holoenzyme bound to the promoter (Reitzer & Magasanik, 1986;Ninfa et al., 1987;Buck et al., 1986;Hoover et al., 1990;Su et al., 1990;Wedel et al., 1990). The mechanism that allows open complex formation is still unknown, but the current model suggests that the activator protein remodels the nucleoprotein complex formed by Es 54 and DNA in order to initiate transcription Cannon et al., 2000;Burrows et al., 2004;Rappas et al., 2007). The DNA region to which the activator proteins bind is known as the upstream activation sequence or UAS (Buck et al., 1986;Morett et al., 1988). It has been shown for the glnA promoter that this region can be moved more than 1000 bp without losing its ability to stimulate transcription (Ninfa et al., 1987). Based on this property, the UASs are also known as enhancers, and the activator proteins as enhancer binding proteins, or EBPs.The s 54 -dependent promoters show a highly conserved consensus sequence, and their main characteristics are the dinucleotides GG ...

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“…The genes are organized in two divergently transcribed operons (2,5,6). The hyc operon, transcribed in the counterclockwise direction, contains hydrogenase 3 structural genes (2), whereas the products of the clockwise-transcribed hyp genes pleiotropically influence the activities of all three hydrogenases of E. coli (6,10).…”

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confidence: 99%

The Escherichia coli fdv gene probably encodes mutS and is located at minute 58.8 adjacent to the hyc-hyp gene cluster

Schlensog¹,

Böck²

1991

J Bacteriol

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Characterization of divergent NtrA‐dependent promoters in the anaerobically expressed gene cluster coding for hydrogenase 3 components of Escherichia coli

Cited by 57 publications

References 41 publications

Mutations in trans that affect formate dehydrogenase (fdhF) gene expression in Salmonella typhimurium

Mutations in trans that affect formate dehydrogenase (fdhF) gene expression in Salmonella typhimurium

Identification of the binding site of the σ 54 hetero-oligomeric FleQ/FleT activator in the flagellar promoters of Rhodobacter sphaeroides

The Escherichia coli fdv gene probably encodes mutS and is located at minute 58.8 adjacent to the hyc-hyp gene cluster

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