Compiling Sigma-70-Dependent Promoters

Domı́nguez-Cuevas, Patricia; Marqués, Silvia

doi:10.1007/978-1-4419-9084-6_11

Cited by 34 publications

(31 citation statements)

References 180 publications

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“…The scattered distribution of the cluster of genes for each of the three pathways along the chromosome of P. putida suggests that each of the metabolic pathways has been acquired independently, and the presence of genes that encode catabolic enzymes and regulators was indicative of the potentially independent regulation of each segment. In agreement with this proposal are a series of previous studies that indicated that the glucokinase pathway was under catabolite repression control when cells were exposed to alternative C sources such as toluene or succinate, according to a process mediated by the global Crc regulator (5,41), whereas neither of the other two pathways was under catabolic repression (5).…”

Section: Discussionsupporting

confidence: 75%

A Set of Activators and Repressors Control Peripheral Glucose Pathways in Pseudomonas putida To Yield a Common Central Intermediate

2008

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Pseudomonas putida KT2440 channels glucose to the central Entner-Doudoroff intermediate 6-phosphogluconate through three convergent pathways. The genes for these convergent pathways are clustered in three independent regions on the host chromosome. A number of monocistronic units and operons coexist within each of these clusters, favoring coexpression of catabolic enzymes and transport systems. Expression of the three pathways is mediated by three transcriptional repressors, HexR, GnuR, and PtxS, and by a positive transcriptional regulator, GltR-2. In this study, we generated mutants in each of the regulators and carried out transcriptional assays using microarrays and transcriptional fusions. These studies revealed that HexR controls the genes that encode glucokinase/glucose 6-phosphate dehydrogenase that yield 6-phosphogluconate; the genes for the Entner-Doudoroff enzymes that yield glyceraldehyde-3-phosphate and pyruvate; and gap-1, which encodes glyceraldehyde-3-phosphate dehydrogenase. GltR-2 is the transcriptional regulator that controls specific porins for the entry of glucose into the periplasmic space, as well as the gtsABCD operon for glucose transport through the inner membrane. GnuR is the repressor of gluconate transport and gluconokinase responsible for the conversion of gluconate into 6-phosphogluconate. PtxS, however, controls the enzymes for oxidation of gluconate to 2-ketogluconate, its transport and metabolism, and a set of genes unrelated to glucose metabolism.

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Section: Discussionsupporting

confidence: 75%

A Set of Activators and Repressors Control Peripheral Glucose Pathways in Pseudomonas putida To Yield a Common Central Intermediate

2008

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“…This site is located far from the downstream RNA polymerase-binding site. The P todX promoter exhibits a well defined Ϫ10 base pair region, although there is no base pair Ϫ35 consensus region, consistent with the fact that P todX belongs to the ''extended promoter'' type that resembles P. putida 70 -dependent promoters (5). Because TodT binds far from the RNA polymerase-binding site, we hypothesize that DNA bending is required for transcription activation, which implies that the activation mechanism involves a direct contact between TodT and the RNA polymerase.…”

supporting

confidence: 53%

The TodS–TodT two-component regulatory system recognizes a wide range of effectors and works with DNA-bending proteins

Lacal

Büsch

Guazzaroni

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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The TodS and TodT proteins form a previously unrecognized and highly specific two-component regulatory system in which the TodS sensor protein contains two input domains, each of which are coupled to a histidine kinase domain. This system regulates the expression of the genes involved in the degradation of toluene, benzene, and ethylbenzene through the toluene dioxygenase pathway. In contrast to the narrow substrate range of this catabolic pathway, the TodS effector profile is broad. TodS has basal autophosphorylation activity in vitro, which is enhanced by the presence of effectors. Toluene binds to TodS with high affinity (K d ‫؍‬ 684 ؎ 13 nM) and 1:1 stoichiometry. The analysis of the truncated variants of TodS reveals that toluene binds to the N-terminal input domain (K d ‫؍‬ 2.3 ؎ 0.1 M) but not to the C-terminal half. TodS transphosphorylates TodT, which binds to two highly similar DNA binding sites at base pairs ؊107 and ؊85 of the promoter. Integration host factor (IHF) plays a crucial role in the activation process and binds between the upstream TodT boxes and the ؊10 hexamer region. In an IHF-deficient background, expression from the tod promoter drops 8-fold. In vitro transcription assays confirmed the role determined in vivo for TodS, TodT, and IHF. A functional model is presented in which IHF favors the contact between the TodT activator, bound further upstream, and the ␣-subunit of RNA polymerase bound to the downstream promoter element. Once these contacts are established, the tod operon is efficiently transcribed.Pseudomonas ͉ sensor kinase ͉ toluene dioxygenase ͉ transcriptional regulator M any Pseudomonas putida strains are able to use benzene, toluene, and ethylbenzene as the sole carbon and energy source through the toluene dioxygenase (TOD) pathway (1). In this pathway, the aromatic hydrocarbons are oxidized to their corresponding substituted catechols, which are further metabolized to Krebs cycle intermediates (1, 2). The catabolic genes of the TOD pathway form the operon todXFC1C2BADEGIH, which is transcribed from a single promoter called P todX , located upstream from the todX gene (1-3). The todST genes are found downstream and form an independent operon that is expressed constitutively (2, 3).TodS and TodT have been proposed to form a two-component regulatory system (TCS) that regulates the tod catabolic operon in P. putida F1 (3). TodT shows all of the characteristics of a response regulator, whereas sequence-based domain predictions indicate that the 108-kDa TodS belongs to a family of sensor histidine kinases that have not been studied at the biochemical level. TodS is predicted to comprise two supradomains, each containing a PAS͞PAC sensory domain and a histidine kinase domain. The supradomains are separated by the receiver domain of a response regulator. In contrast to other histidine kinases, TodS apparently lacks transmembrane regions (3). The mode of action of this previously unrecognized type of histidine kinase has yet to be established. On the basis of moderate sequence simil...

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“…1B). From this site, the Ϫ35 and Ϫ10 putative sequences were identified, and these consisted of ATGAC-N16-ATGAA sequences, which shared approximately 40 and 80% identity with the Ϫ10 and Ϫ35 70 consensus sequences, respectively (18). To investigate the activities of the promoters responsible for the sigX-oprF and oprF mRNA production, we constructed 5 transcriptional fusions, namely, pAB754, pAB754-2 M, pAB146, pAB89, and pAB148 (Fig.…”

Section: Resultsmentioning

confidence: 99%

Transcription of the oprF Gene of Pseudomonas aeruginosa Is Dependent Mainly on the SigX Sigma Factor and Is Sucrose Induced

et al. 2012

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The OprF porin is the major outer membrane protein of Pseudomonas aeruginosa. OprF is involved in several crucial functions, including cell structure, outer membrane permeability, environmental sensing, and virulence. The oprF gene is preceded by the sigX gene, which encodes the poorly studied extracytoplasmic function (ECF) sigma factor SigX. Three oprF promoters were previously identified. Two intertwined promoters dependent on 70 and SigX are located in the sigX-oprF intergenic region, whereas a promoter dependent on the ECF AlgU lies within the sigX gene. An additional promoter was found in the cmpX-sigX intergenic region. In this study, we dissected the contribution of each promoter region and of each sigma factor to oprF transcription using transcriptional fusions. In Luria-Bertani (LB) medium, the oprF-proximal region (sigX-oprF intergenic region) accounted for about 80% of the oprF transcription, whereas the AlgU-dependent promoter had marginal activity. Using the sigX mutant PAOSX, we observed that the SigX-dependent promoter was largely predominant over the 70 -dependent promoter. oprF transcription was increased in response to low NaCl or high sucrose concentrations, and this induced transcription was strongly impaired in the absence of SigX. The lack of OprF itself increased oprF transcription. Since these conditions led to cell wall alterations, oprF transcription could be activated by signals triggered by perturbation of the cell envelope.

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Compiling Sigma-70-Dependent Promoters

Cited by 34 publications

References 180 publications

A Set of Activators and Repressors Control Peripheral Glucose Pathways in Pseudomonas putida To Yield a Common Central Intermediate

A Set of Activators and Repressors Control Peripheral Glucose Pathways in Pseudomonas putida To Yield a Common Central Intermediate

The TodS–TodT two-component regulatory system recognizes a wide range of effectors and works with DNA-bending proteins

Transcription of the oprF Gene of Pseudomonas aeruginosa Is Dependent Mainly on the SigX Sigma Factor and Is Sucrose Induced

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