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Regine Hengge

Publications and source records attributed to Regine Hengge.

10 recordsLinked to original sources
PubMed2006

Cyclic-di-GMP-mediated signalling within the sigma network of Escherichia coli.

Bis-(3'-5')-cyclic-di-guanosine monophosphate (c-di-GMP) is a bacterial signalling molecule produced by diguanylate cyclases (DGC, carrying GGDEF domains) and degraded by specific phosphodiesterases (PDE, carrying EAL domains). Neither its full physiological impact nor its effector mechanisms are currently understood. Also, the existence of multiple GGDEF/EAL genes in the genomes of most species raises questions about output specificity and robustness of c-di-GMP signalling. Using microarray and gene fusion analyses, we demonstrate that at least five of the 29 GGDEF/EAL genes in Escherichia coli are not only stationary phase-induced under the control of the general stress response master regulator sigma(S) (RpoS), but also exhibit differential control by additional environmental and temporal signals. Two of the corresponding proteins, YdaM (GGDEF only) and YciR (GGDEF + EAL), which in vitro show DGC and PDE activity, respectively, play an antagonistic role in the expression of the biofilm-associated curli fimbriae. This control occurs at the level of transcription of the curli and cellulose regulator CsgD. Moreover, we show that H-NS positively affects curli expression by inversely controlling the expression of ydaM and yciR. Furthermore, we demonstrate a temporally fine-tuned GGDEF cascade in which YdaM controls the expression of another GGDEF protein, YaiC. By genome-wide microarray analysis, evidence is provided that YdaM and YciR strongly and nearly exclusively control CsgD-regulated genes. We conclude that specific GGDEF/EAL proteins have very distinct expression patterns, and when present in physiological amounts, can act in a highly precise, non-global and perhaps microcompartmented manner on a few or even a single specific target(s).

Bacterial Proteins↗
PubMed2006

Role of the spacer between the -35 and -10 regions in sigmas promoter selectivity in Escherichia coli.

In vitro, the sigma(s) subunit of RNA polymerase (RNAP), RpoS, recognizes nearly identical -35 and -10 promoter consensus sequences as the vegetative sigma70. In vivo, promoter selectivity of RNAP holoenzyme containing either sigma(s) (Esigma(s)) or sigma70 (Esigma70) seems to be achieved by the differential ability of the two holoenzymes to tolerate deviations from the promoter consensus sequence. In this study, we suggest that many natural sigma(s)-dependent promoters possess a -35 element, a feature that has been considered as not conserved among sigma(s)-dependent promoters. These -35 hexamers are mostly non-optimally spaced from the -10 region, but nevertheless functional. A +/- 2 bp deviation from the optimal spacer length of 17 bp or the complete absence of a -35 consensus sequence decreases overall promoter activity, but at the same time favours Esigma(s) in its competition with Esigma70 for promoter recognition. On the other hand, the reduction of promoter activity due to shifting of the -35 element can be counterbalanced by an activity-stimulating feature such as A/T-richness of the spacer region without compromising Esigma(s) selectivity. Based on mutational analysis of sigma(s), we suggest a role of regions 2.5 and 4 of sigma(s) in sensing sub-optimally located -35 elements.

Adenine↗
PubMed2006

Poly(A)-polymerase I links transcription with mRNA degradation via sigmaS proteolysis.

Bacteria rapidly adapt to changes in growth conditions through control of transcription and specific mRNA degradation. Interplay of both mechanisms must exist in order to achieve fine-tuned regulation of gene expression. Transcription of the Escherichia coli bolA gene is mediated by the RpoS/sigmaS transcription factor in response to environmental signals. In this report it is shown that the mechanisms of bolA1p mRNA transcription and degradation are tightly connected at the onset of stationary phase and in response to sudden carbon starvation. In stationary phase, bolA1p mRNA levels were reduced 2.5-fold in a poly(A)-polymerase I (PAPI) mutant, explained by the significant threefold reduction in sigmaS protein levels in the same strain. Furthermore, fusions with the rpoS gene, analysis of the stability of sigmaS and the levels of RssB indicate that the absence of PAPI enhances RssB-mediated sigmaS proteolysis specifically in starved cells. The fact that PAPI induces higher cellular levels of a global regulator is a novel finding of wide biological significance. PAPI could work as a linker between transcription and mRNA degradation with the ultimate goal of adapting and surviving to growth-limiting conditions.

Bacterial Proteins↗
PubMed2005

A two-component phosphotransfer network involving ArcB, ArcA, and RssB coordinates synthesis and proteolysis of sigmaS (RpoS) in E. coli.

The general stress sigma factor sigma(S) (RpoS) in Escherichia coli is controlled at the levels of transcription, translation, and proteolysis. Here we demonstrate that the phosphorylated response regulator ArcA is a direct repressor of rpoS transcription that binds to two sites flanking the major rpoS promoter, with the upstream site overlapping an activating cAMP-CRP-binding site. The histidine sensor kinase ArcB not only phosphorylates ArcA, but also the sigma(S) proteolytic targeting factor RssB, and thereby stimulates sigma(S) proteolysis. Thus, ArcB/ArcA/RssB constitute a branched "three-component system", which coordinates rpoS transcription and sigma(S) proteolysis and thereby maintains low sigma(S) levels in rapidly growing cells. We suggest that the redox state of the quinones, which controls autophosphorylation of ArcB, not only monitors oxygen but also energy supply, and we show that the ArcB/ArcA/RssB system is involved in sigma(S) induction during entry into starvation conditions. Moreover, this induction is enhanced by a positive feedback that involves sigma(S)-dependent induction of ArcA, which further reduces sigma(S) proteolysis, probably by competing with RssB for residual phosphorylation by ArcB.

Bacterial Outer Membrane Proteins↗
PubMed2005

Differential ability of sigma(s) and sigma70 of Escherichia coli to utilize promoters containing half or full UP-element sites.

The sigma(s) subunit of RNA polymerase (RNAP) is the master regulator of the general stress response in Escherichia coli. Nevertheless, the selectivity of promoter recognition by the housekeeping sigma70-containing and sigma5-containing RNAP holoenzymes (Esigma70 and Esigma(s) respectively) is not yet fully clarified, as they both recognize nearly identical -35 and -10 promoter consensus sequences. In this study, we show that in a subset of promoters, Esigma(s) favours the presence of a distal UP-element half-site, and at the same time is unable to take advantage of a proximal half-site or a full UP-element. This is reflected by the frequent occurrence of distal UP-element half-sites in natural sigma(s)-dependent promoters and the absence of proximal half-sites. Esigma70, however, exhibits the opposite preference. The presence of the -35 element is a prerequisite for this differential behaviour. In the absence of the -35 element, half or full UP-element sites play no role in sigma selectivity, but the distal subsite leads to an equivalent, if not greater, transcriptional stimulation than the proximal one for both sigma factors. Finally, experiments using single amino acid substitutions of sigma(s) indicate that the foundation for this preference lies in an inability of sigma(s) to interact with the a subunit C-terminal domain.

Amino Acid Sequence↗
PubMed2005

Genome-wide analysis of the general stress response network in Escherichia coli: sigmaS-dependent genes, promoters, and sigma factor selectivity.

The sigmaS (or RpoS) subunit of RNA polymerase is the master regulator of the general stress response in Escherichia coli. While nearly absent in rapidly growing cells, sigmaS is strongly induced during entry into stationary phase and/or many other stress conditions and is essential for the expression of multiple stress resistances. Genome-wide expression profiling data presented here indicate that up to 10% of the E. coli genes are under direct or indirect control of sigmaS and that sigmaS should be considered a second vegetative sigma factor with a major impact not only on stress tolerance but on the entire cell physiology under nonoptimal growth conditions. This large data set allowed us to unequivocally identify a sigmaS consensus promoter in silico. Moreover, our results suggest that sigmaS-dependent genes represent a regulatory network with complex internal control (as exemplified by the acid resistance genes). This network also exhibits extensive regulatory overlaps with other global regulons (e.g., the cyclic AMP receptor protein regulon). In addition, the global regulatory protein Lrp was found to affect sigmaS and/or sigma70 selectivity of many promoters. These observations indicate that certain modules of the sigmaS-dependent general stress response can be temporarily recruited by stress-specific regulons, which are controlled by other stress-responsive regulators that act together with sigma70 RNA polymerase. Thus, not only the expression of genes within a regulatory network but also the architecture of the network itself can be subject to regulation.

Bacterial Proteins↗
PubMed2004

Multiple stress signal integration in the regulation of the complex sigma S-dependent csiD-ygaF-gabDTP operon in Escherichia coli.

The csiD-ygaF-gabDTP region in the Escherichia coli genome represents a cluster of sigma S-controlled genes. Here, we investigated promoter structures, sigma factor dependencies, potential co-regulation and environmental regulatory patterns for all of these genes. We find that this region constitutes a complex operon with expression being controlled by three differentially regulated promoters: (i) csiDp, which affects the expression of all five genes, is cAMP-CRP/sigma S-dependent and activated exclusively upon carbon starvation and stationary phase; (ii) gabDp1, which is sigma S-dependent and exhibits multiple stress induction like sigma S itself; and (iii) gabDp2[previously suggested by Schneider, B.L., Ruback, S., Kiupakis, A.K., Kasbarian, H., Pybus, C., and Reitzer, L. (2002) J. Bacteriol. 184: 6976-6986], which appears to be Nac/sigma 70-controlled and to respond to poor nitrogen sources. In addition, we identify a novel repressor, CsiR, which modulates csiDp activity in a temporal manner during early stationary phase. Finally, we propose a physiological role for sigma S-controlled GabT/D-mediated gamma-aminobutyrate (GABA) catabolism and glutamate accumulation in general stress adaptation. This physiological role is reflected by the activation of the operon-internal gabDp1 promoter under the different conditions that also induce sigma S, which include shifts to acidic pH or high osmolarity as well as starvation or stationary phase.

Bacterial Proteins↗
PubMed2003

Sequential recognition of two distinct sites in sigma(S) by the proteolytic targeting factor RssB and ClpX.

sigma(S) (RpoS), the master regulator of the general stress response in Escherichia coli, is a model system for regulated proteolysis in bacteria. sigma(S) turnover requires ClpXP and the response regulator RssB, whose phosphorylated form exhibits high affinity for sigma(S). Here, we demonstrate that recognition by the RssB/ClpXP system involves two distinct regions in sigma(S). Region 2.5 of sigma(S) (a long alpha-helix) is sufficient for binding of phosphorylated RssB. However, this interaction alone is not sufficient to trigger proteolysis. A second region located in the N-terminal part of sigma(S), which is exposed only upon RssB-sigma(S) interaction, serves as a binding site for the ClpX chaperone. Binding of the ClpX hexameric ring to sigma(S)-derived reporter proteins carrying the ClpX-binding site (but not the RssB-binding site) is also not sufficient to commit the protein to degradation. Our data indicate that RssB plays a second role in the initiation of sigma(S) proteolysis that goes beyond targeting of sigma(S) to ClpX, and suggest a model for the sequence of events in the initiation of sigma(S) proteolysis.

Adenosine Triphosphatases↗
PubMed2003

Dynamic control of Dps protein levels by ClpXP and ClpAP proteases in Escherichia coli.

The Escherichia coli starvation-induced DNA protection protein Dps was observed to be degraded rapidly during exponential growth. This turnover is dependent on the clpP and clpX genes. The clpA gene is not required for Dps proteolysis, suggesting that Dps is a substrate for ClpXP protease but not for ClpAP protease. Dps proteolysis was found to be highly regulated. Upon carbon starvation, Dps is stabilized, which together with increased Dps synthesis allows strong accumulation of Dps in the stationary phase. The addition of glucose to starving cells results in rapid resumption of Dps proteolysis by ClpXP. Oxidative stress also leads to efficient stabilization of Dps. After hyperosmotic shift, however, proteolysis remains unaffected. Thus, regulated proteolysis of Dps strongly contributes to controlling Dps levels under very specific stress conditions. In contrast to the regulated degradation of RpoS by ClpXP, Dps proteolysis is independent of the recognition factor RssB. In addition, during starvation, clpP and, to a somewhat lesser extent, clpA are involved in maintaining ongoing Dps synthesis (acting at the level of Dps translation), which is required for strong Dps accumulation in long-term stationary phase cells. In summary, both ClpXP and ClpAP exert significant control of Dps levels by affecting log phase stability and stationary phase synthesis of Dps respectively.

ATPases Associated with Diverse Cellular Activitie↗