What makes an Escherichia coli promoter sigmaS dependent? Role of the -13/-14 nucleotide promoter positions and region 2.5 of sigmaS

Becker, Gisela; Hengge‐Aronis, Regine

doi:10.1046/j.1365-2958.2001.02313.x

Cited by 41 publications

(82 citation statements)

References 40 publications

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“…Stimulation to a similar extent of E 70 -dependent transcription by the 13C3 G mutation can also be observed in vivo (Fig. 1B), strongly suggesting that a G nucleotide at position Ϫ13 favors E 70 , which is in agreement with previous observations (8,9). The effect of the 15G3 C/ 13C3 G double mutation clearly confirms the preference of E 70 for a G at the Ϫ13 position as well as the importance of the TG for optimal transcription by S -RNA polymerase.…”

Section: Promoter Elements Determinant For Selective Recognition Of Tsupporting

confidence: 92%

“…4), suggesting that the TG motif might affect another step of transcription initiation, possibly initial binding to PaidB. Ϫ13C-The presence of a C nucleotide at position Ϫ13 is widely conserved among S -dependent promoters and has already been proposed to be a specific determinant for S (8,9). The aidB promoter displays this feature, which is indeed necessary for optimal E S -dependent transcription in vivo (Fig.…”

Section: Table Imentioning

confidence: 92%

“…the first nucleotide in the Ϫ10 hexamer. Finally, we changed to T the A nucleotide at position Ϫ6 immediately downstream of the Ϫ10 sequence, because T appears to be conserved at this position in S -dependent promoters (8,9). We examined the effect of the mutations on promoter activity in vivo using a low copy plasmid carrying the PaidB::lacZ transcriptional fusion (Fig.…”

Section: Promoter Elements Determinant For Selective Recognition Of Tmentioning

confidence: 99%

“…Mutagenesis studies on S -dependent promoters have shown that deviations from the consensus CTATACT affect promoter recognition by S in vivo and have substantiated the importance of the Ϫ13C element (8,20,21). Suppression genetics data suggest that the Ϫ13C is directly contacted by the residue Lys-173 of region 2.5 of S (8). Interestingly, the amino acid located at the equivalent position in region 2.5 of 70 is a glutamate residue (Glu-458) that has been proposed to interact with another promoter element located upstream of the Ϫ10, the TG motif (22).…”

mentioning

confidence: 97%

“…The main sequence feature specific for S -dependent promoters would be a C nucleotide immediately upstream of the Ϫ10 promoter element (CTATA(c/a)T at the Ϫ13 position relative to the transcription start (Ϫ13C)); the Ϫ35 element does not appear to be important for promoter recognition by S , although conflicting data on its role have been reported (10, 16 -19). Mutagenesis studies on S -dependent promoters have shown that deviations from the consensus CTATACT affect promoter recognition by S in vivo and have substantiated the importance of the Ϫ13C element (8,20,21). Suppression genetics data suggest that the Ϫ13C is directly contacted by the residue Lys-173 of region 2.5 of S (8).…”

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confidence: 99%

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Nucleotides from –16 to –12 Determine Specific Promoter Recognition by Bacterial σS-RNA Polymerase

Lacour

Kolb

Landini

2003

Journal of Biological Chemistry

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The alternative sigma factor S , mainly active in stationary phase of growth, recognizes in vitro a ؊10 promoter sequence almost identical to the one for the main sigma factor, 70 , thus raising the problem of how specific promoter recognition by S -RNA polymerase (E S ) is achieved in vivo. We investigated the promoter features involved in selective recognition by E S at the strictly S -dependent aidB promoter. We show that the presence of a C nucleotide as first residue of the aidB ؊10 sequence (؊12C), instead of the T nucleotide canonical for 70 -dependent promoters, is the major determinant for selective recognition by E S . The presence of the ؊12C does not allow formation of an open complex fully proficient in transcription initiation by E 70 . The role of ؊12C as specific determinant for promoter recognition by E S was confirmed by sequence analysis of known E S -dependent promoters as well as site-directed mutagenesis at the promoters of the csgB and sprE genes. We propose that E S , unlike E 70 , can recognize both C and T as the first nucleotide in the ؊10 sequence. Additional promoter features such as the presence of a C nucleotide at position ؊13, contributing to open complex formation by E S , and a TG motif found at the unusual ؊16/؊15 location, possibly contributing to initial binding to the promoter, also represent important factors for S -dependent transcription. We propose a new sequence, TG(N) 0 -2 CCATA(c/a)T, as consensus ؊10 sequence for promoters exclusively recognized by E S .Bacterial cells adapt to changing environmental and physiological conditions by modulating gene expression. Sigma ( ) factors of RNA polymerase, as the subunits responsible for promoter recognition, play a major role in programming gene expression. At least seven different subunits have been identified in Escherichia coli; 70 is the main subunit and can carry out transcription from the majority of E. coli promoters. The alternative subunits can direct transcription toward specific sets of genes (i.e. heat-shock, extracellular proteins, etc.) whose transcription is directed by -specific promoter sequences. A partial exception to the typical role for alternative subunits is represented by S , the product of the rpoS gene, mainly expressed in the stationary phase of growth (1-3). Unlike the other subunits, S -RNA polymerase (E S ) 1 can initiate transcription from several promoters also recognized by E 70 , suggesting that they recognize similar promoter sequences (4). The recognition of similar promoter sequences by S and 70 is reflected by their strong similarity in the DNA binding domains (5). The alignment of E S -dependent promoters and the search for an optimal promoter for E S in vitro using the systematic evolution of ligands by exponential enrichment (SELEX) procedure have pointed to a Ϫ10 consensus sequence for E S , CTATA(c/a)T that is very similar to the canonical TATAAT sequence for 70 (6 -10). These results suggest that promoter selectivity between 70 and S might be determined by factors other than promote...

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Section: Promoter Elements Determinant For Selective Recognition Of Tsupporting

confidence: 92%

Section: Table Imentioning

confidence: 92%

Section: Promoter Elements Determinant For Selective Recognition Of Tmentioning

confidence: 99%

mentioning

confidence: 97%

mentioning

confidence: 99%

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Nucleotides from –16 to –12 Determine Specific Promoter Recognition by Bacterial σS-RNA Polymerase

Lacour

Kolb

Landini

2003

Journal of Biological Chemistry

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Functional identification of the prnABCD operon and its regulation in Serratia plymuthica

Liu

Yang

et al. 2018

Appl Microbiol Biotechnol

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The antibiotic pyrrolnitrin (PRN) is a tryptophan-derived secondary metabolite that plays an important role in the biocontrol of plant diseases due to its broad-spectrum of antimicrobial activities. The PRN biosynthetic gene cluster remains to be characterised in Serratia plymuthica, though it is highly conserved in PRN-producing bacteria. To better understand PRN biosynthesis and its regulation in Serratia, the prnABCD operon from S. plymuthica G3 was cloned, sequenced and expressed in Escherichia coli DH5α. Furthermore, an engineered strain prnind which is a conditional mutant of G3 prnABCD under the control of the Ptac promoter was constructed. This mutant was able to overproduce PRN with isopropylthiogalactoside (IPTG) induction by overexpressing prnABCD, whilst behaving as a conditional mutant of G3 prnABCD in the absence of IPTG. These results confirmed that prnABCD is responsible for PRN biosynthesis in strain G3. Further experiments involving lux-/dsRed-based promoter fusions, combined with site-directed mutagenesis of the putative σ extended -10 region in the prnA promoter, and liquid chromatography-mass spectrometry (LC-MS) analysis extended our previous knowledge about G3, revealing that quorum sensing (QS) regulates PRN biosynthesis through cross talk with RpoS, which may directly activated prnABCD transcription. These findings suggest that PRN in S. plymuthica G3 is produced in a tightly controlled manner, and has diverse functions, such as modulation of cell motility, in addition to antimicrobial activities. Meanwhile, the construction of inducible mutants could be a powerful tool to improve PRN production, beyond its potential use for the investigation of the biological function of PRN.

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Cloning of an alkaline phosphatase gene from the moderately thermophilic bacterium Meiothermus ruber and characterization of the recombinant enzyme

et al. 2003

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A gene that codes for an alkaline phosphatase was cloned from the thermophilic bacterium Meiothermus ruber, and its nucleotide sequence was determined. The deduced amino acid sequence indicates that the enzyme precursor including the putative signal sequence is composed of 503 amino acid residues and has an estimated molecular mass of 54,229 Da. Comparison of the peptide sequence with that of the prototype alkaline phosphatase from Escherichia coli revealed conservation of the regions in the vicinity of the corresponding phosphorylation site and metal binding sites. The protein was expressed in E. coli and its enzymatic properties were characterized. In the absence of exogenously added metal ions, activity was negligible; to obtain maximal activity, addition of free Mg2+ ions was required. Zn2+ ions had an inhibitory effect on the activity of the M. ruber enzyme. The pH and temperature optima for activity were found to be 11.0 and 62 degrees C, respectively. The enzyme was moderately thermostable: it retained about 50% activity after incubation for 6 h at 60 degrees C, whereas at 80 degrees C it was completely inactivated within 2 h. The Michaelis constant for cleavage of 4-nitrophenylphosphate was 0.055 mM. While having much in common with other alkaline phosphatases, the M. ruber enzyme presents some unique features, such as a very narrow pH range for activity and an absolute requirement for magnesium for activity.

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What makes an Escherichia coli promoter sigmaS dependent? Role of the -13/-14 nucleotide promoter positions and region 2.5 of sigmaS

Cited by 41 publications

References 40 publications

Nucleotides from –16 to –12 Determine Specific Promoter Recognition by Bacterial σS-RNA Polymerase

Nucleotides from –16 to –12 Determine Specific Promoter Recognition by Bacterial σS-RNA Polymerase

Functional identification of the prnABCD operon and its regulation in Serratia plymuthica

Cloning of an alkaline phosphatase gene from the moderately thermophilic bacterium Meiothermus ruber and characterization of the recombinant enzyme

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