Activation and repression of a σ<sup>N</sup>‐dependent promoter naturally lacking upstream activation sequences

Porrúa, Odil; García-González, Vicente; Santero, Eduardo; Shingler, Victoria; Govantes, Fernando

doi:10.1111/j.1365-2958.2009.06779.x

Cited by 20 publications

(49 citation statements)

References 76 publications

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“…These constructs displayed 100-fold and 7-fold induction under nitrogen limitation (data not shown), similar to the 129-fold and 10-fold induction observed with the wild type and ⌬2 fusions. Thus, sequences downstream from PatzT appear to have a marginal contribution to its regulation, and the observed residual NtrC-dependent activation is likely to occur in a UASindependent fashion (i.e., with the activator not bound or nonspecifically bound to DNA) (53), as documented previously for other Pseudomonas NtrC-dependent promoters (41).…”

Section: Transcriptional Organization Of the Atzrstuvw Operonmentioning

confidence: 62%

“…While N -dependent promoters are obligately activated by a group of transcription factors designated enhancer binding proteins (EBPs), belonging to the family of AAAϩ ATPases (49), very few of them are also subjected to negative regulation exerted by members of other regulatory families. AtzR is one of these rare proteins that has been shown to repress a N -dependent promoter (41). Here, we characterized the regulatory cis-and trans-acting elements involved in activation and repression of PatzT, a N -dependent internal promoter responsible for transcription of the four distal genes of the atzRSTUVW operon.…”

Section: Lttrs Andmentioning

confidence: 99%

“…Transcription from the PatzR promoter is activated by the general nitrogen control activator NtrC (16,41). To test whether PatzT transcription was also dependent on NtrC, expression from the PatzT promoter in pMPO805 was tested in P. putida strain MPO201, a KT2442 derivative harboring a deletion of ntrC (16).…”

Section: Transcriptional Organization Of the Atzrstuvw Operonmentioning

confidence: 99%

“…Transcription of atzR is initiated from the Ndependent PatzR promoter, activated by the general nitrogen control protein NtrC, and repressed by AtzR (16). NtrC-dependent activation of atzR is unusual in that it does not require interaction with any upstream or downstream sequence elements (41). AtzR binds a single site overlapping the PatzR promoter N RNA polymerase (E-N ) recognition element and competes with E-N for DNA binding, resulting in decreased promoter occupancy (41).…”

mentioning

confidence: 99%

“…NtrC-dependent activation of atzR is unusual in that it does not require interaction with any upstream or downstream sequence elements (41). AtzR binds a single site overlapping the PatzR promoter N RNA polymerase (E-N ) recognition element and competes with E-N for DNA binding, resulting in decreased promoter occupancy (41). Cyanuric acid interacts with AtzR to alter its conformation on the divergent PatzR-PatzDEF promoter region and activate atzDEF transcription (40).…”

mentioning

confidence: 99%

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Transcriptional Organization and Regulatory Elements of a Pseudomonas sp. Strain ADP Operon Encoding a LysR-Type Regulator and a Putative Solute Transport System

et al. 2012

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cluster of the Pseudomonas sp. strain ADP atrazine-degradative plasmid pADP-1, which carries genes for an outer membrane protein and the components of a putative ABC-type solute transporter, is located downstream from atzR, which encodes the LysR-type transcriptional regulator of the cyanuric acid-degradative operon atzDEF. Here we describe the transcriptional organization of these genes. Our results show that all six genes are cotranscribed from the PatzR promoter to form the atzRSTUVW operon. A second, stronger promoter, PatzT, is found within atzS and directs transcription of the four distal genes. PatzT is N dependent, activated by NtrC in response to nitrogen limitation with the aid of IHF, and repressed by AtzR. A combination of in vivo mutational analysis and primer extension allowed us to locate the PatzT promoter and map the transcriptional start site. Similarly, we used deletion and point mutation analyses, along with in vivo expression studies and in vitro binding assays, to locate the NtrC, IHF, and AtzR binding sites and address their functionality. Our results suggest a regulatory model in which NtrC activates PatzT transcription via DNA looping, while AtzR acts as an antiactivator that diminishes expression by interfering with the activation process. P seudomonas sp. strain ADP (31) is the model organism for bacterial degradation of the s-triazine herbicide atrazine (2-chloro-4-ethylamino-6-isopropylamino-1,3,5-triazine). Pseudomonas sp. strain ADP uses atrazine as the sole nitrogen source via a six-step hydrolytic pathway, carried by the 108-kbp catabolic plasmid pADP-1 (35). The six genes involved in atrazine mineralization are localized in two distinct regions of the plasmid: atzA, atzB, and atzC, responsible for atrazine conversion to cyanuric acid (2,4,6-trihydroxy-1,3,5-triazine), are harbored at three distant positions within a large (Ͼ40-kbp) unstable region featuring multiple direct repeats and transposable elements. The genes involved in cyanuric acid cleavage and ammonium release are clustered in the stable portion of pADP-1 to form the atzDEF operon (reviewed in reference 51).Our previous work has shown that atrazine utilization by Pseudomonas sp. strain ADP is regulated by nitrogen availability in a manner resembling general nitrogen control (15), and the cyanuric acid utilization operon atzDEF is one of the targets for such regulation (16). Expression of atzDEF is induced by the substrate of the pathway, cyanuric acid, and repressed in the presence of a preferential nitrogen source. The product of atzR, the gene transcribed divergently from atzDEF, is a LysR-type transcriptional regulator (LTTR) required for both nitrogen-and cyanuric aciddependent control. Transcription of atzR is initiated from the Ndependent PatzR promoter, activated by the general nitrogen control protein NtrC, and repressed by AtzR (16). NtrC-dependent activation of atzR is unusual in that it does not require interaction with any upstream or downstream sequence elements (41). AtzR binds a single site overlapping...

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Section: Transcriptional Organization Of the Atzrstuvw Operonmentioning

confidence: 62%

Section: Lttrs Andmentioning

confidence: 99%

Section: Transcriptional Organization Of the Atzrstuvw Operonmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Transcriptional Organization and Regulatory Elements of a Pseudomonas sp. Strain ADP Operon Encoding a LysR-Type Regulator and a Putative Solute Transport System

et al. 2012

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Pleiotropic control of antibiotic biosynthesis, flagellar operon expression, biofilm formation, and carbon source utilization by RpoN in Pseudomonas protegens H78

Liu

Shi

Wang

et al. 2018

Appl Microbiol Biotechnol

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The rhizobacterium Pseudomonas protegens H78 biosynthesizes a number of antibiotic compounds, including pyoluteorin, 2,4-diacetylphloroglucinol, and pyrrolnitrin. Here, we investigated the global regulatory function of the nitrogen metabolism-related sigma factor RpoN in P. protegens H78 through RNA-seq and phenotypic analysis. During the mid- to late-log growth phase, transcriptomic profiling revealed that 562 genes were significantly upregulated, and 502 genes were downregulated by at least twofold at the RNA level in the rpoN deletion mutant in comparison with the wild-type strain H78. With respect to antibiotics, Plt biosynthesis and the expression of its operon were positively regulated, while Prn biosynthesis and the expression of its operon were negatively regulated by RpoN. RpoN is responsible for the global activation of operons involved in flagellar biogenesis and assembly, biofilm formation, and bacterial mobility. In contrast, RpoN was shown to negatively control a number of secretion system operons including one type VI secretion system operon (H1-T6SS), two pilus biogenesis operons (Flp/Tad-T4b pili and Csu-T1 pili), and one polysaccharide biosynthetic operon (psl). In addition, two operons that are involved in mannitol and inositol utilization are under the positive regulation of RpoN. Consistent with this result, the ability of H78 to utilize mannitol or inositol as a sole carbon source is positively influenced by RpoN. Taken together, the RpoN-mediated global regulation is mainly involved in flagellar biogenesis and assembly, bacterial mobility, biofilm formation, antibiotic biosynthesis, secretion systems, and carbon utilization in P. protegens H78.

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Bioremediation of atrazine: recent advances and promises

2014

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Activation and repression of a σ^N‐dependent promoter naturally lacking upstream activation sequences

Cited by 20 publications

References 76 publications

Transcriptional Organization and Regulatory Elements of a Pseudomonas sp. Strain ADP Operon Encoding a LysR-Type Regulator and a Putative Solute Transport System

Transcriptional Organization and Regulatory Elements of a Pseudomonas sp. Strain ADP Operon Encoding a LysR-Type Regulator and a Putative Solute Transport System

Pleiotropic control of antibiotic biosynthesis, flagellar operon expression, biofilm formation, and carbon source utilization by RpoN in Pseudomonas protegens H78

Bioremediation of atrazine: recent advances and promises

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Activation and repression of a σN‐dependent promoter naturally lacking upstream activation sequences

Cited by 20 publications

References 76 publications

Transcriptional Organization and Regulatory Elements of a Pseudomonas sp. Strain ADP Operon Encoding a LysR-Type Regulator and a Putative Solute Transport System

Transcriptional Organization and Regulatory Elements of a Pseudomonas sp. Strain ADP Operon Encoding a LysR-Type Regulator and a Putative Solute Transport System

Pleiotropic control of antibiotic biosynthesis, flagellar operon expression, biofilm formation, and carbon source utilization by RpoN in Pseudomonas protegens H78

Bioremediation of atrazine: recent advances and promises

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Activation and repression of a σ^N‐dependent promoter naturally lacking upstream activation sequences