Nucleotide sequences of two Bacillus subtilis promoters used by Bacillus subtilis sigma-28 RNA polymerase

Gilman, Michael; Wiggs, Janey L.; Chamberlin, Michael J.

doi:10.1093/nar/9.22.5991

Cited by 87 publications

(41 citation statements)

References 32 publications

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“…For 1ytABC transcripts, one site was found 8 nucleotides downstream of the end of the characteristic PD promoter consensus ( Fig. 2) (Gilman et al, 1981). This transcript was absent in strain L16006, in which the sigD gene was disrupted, confirming the aD dependence of this site.…”

Section: Fig 4 Alignment Of Domains Of Lytb Andmentioning

confidence: 67%

Sequencing and analysis of the Bacillus subtilis lytRABC divergon: A regulatory unit encompassing the structural genes of the N-acetylmuramoyl-L-alanine amidase and its modifier

Lazarević¹,

Margot²,

Soldo³

et al. 1992

Journal of General Microbiology

220

240

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The regulatory unit of Bociffus subtifis strain 168 encompassing the structural genes of the N-acetylmuramoyl-L-alanine amidase and of its modifier has been sequenced, and found to be a divergon consisting of divergently transcribed operons fytABC and lytR. Proteins LytA, LytB and LytC are endowed with export signal peptides. Mature LytA is a 9-4 kDa, highly acidic polypeptide whose deduced amino acid sequence points to a lipoprotein. LytB and LytC, the modifier and the amidase, are highly basic. After cleavage of the signal sequence their molecular masses are 74.1 and 49.9 kDa, respectively. These two proteins share considerable homology in their N-terminal moieties and have three GSNRY consensus motifs, characteristic of nearly all amidases. The C-terminal moiety of LytB exhibits homology to the product of spoZZD. LytR is a 35 kDa protein which acts as an attenuator of the expression of both fytABC and fytR operons. Transcription of the fytABC operon proceeds from two promoters: PD, identified as P2*-, (Gilman et d , 1984), and an upstream PA. The former only is subject to LytR attenuation. Translational initiation of fytB and fytC is directed by UUG start codons, suggesting that fytA, B and C undergo coupled translation. Transcription of fytR is initiated at two start sites, one of which corresponds to a highly intense PA promoter whereas the other does not seem to share much homology with any of the known promoter consensus sequences. Both promoters are attenuated by LytR. It is confirmed that the synthesis of the amidase is controlled at least in part by SigD, i.e. that it belongs to thefra regulon and that its activity, or part of it, is co-regulated with flagellar motility. The role of the mutations conferring the Sin, Fla and Ifm phenotypes in the expression of the fytABC operon is discussed.

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Section: Fig 4 Alignment Of Domains Of Lytb Andmentioning

confidence: 67%

Sequencing and analysis of the Bacillus subtilis lytRABC divergon: A regulatory unit encompassing the structural genes of the N-acetylmuramoyl-L-alanine amidase and its modifier

Lazarević¹,

Margot²,

Soldo³

et al. 1992

Journal of General Microbiology

220

240

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“…For most alternative factors, however, far fewer promoters are available for comparison, and there is a greater likelihood of sample bias with this smaller pool. For 28 , a total of about 50 promoters in a range of bacteria have been predicted based on sequence similarity (6,7,11), but only about half have been functionally studied. Furthermore, this small number is overrepresented by promoters for a few class 3 flagellar genes from different bacteria.…”

Section: Discussionmentioning

confidence: 99%

Mutational Analysis of the Promoter Recognized by Chlamydia and Escherichia coli σ ²⁸ RNA Polymerase

Yu¹,

Russo²,

Rounds³

et al. 2006

J Bacteriol

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28 RNA polymerase is an alternative RNA polymerase that has been postulated to have a role in developmental gene regulation in Chlamydia. Although a consensus bacterial 28 promoter sequence has been proposed, it is based on a relatively small number of defined promoters, and the promoter structure has not been systematically analyzed. To evaluate the sequence of the 28 -dependent promoter, we performed a comprehensive mutational analysis of the Chlamydia trachomatis hctB promoter, testing the effect of point substitutions on promoter activity. We defined a ؊35 element recognized by chlamydial 28 RNA polymerase that resembles the consensus ؊35 sequence. Within the ؊10 element, however, chlamydial 28 RNA polymerase showed a striking preference for a CGA sequence at positions ؊12 to ؊10 rather than the longer consensus ؊10 sequence. We also observed a strong preference for this CGA sequence by Escherichia coli 28 RNA polymerase, suggesting that this previously unrecognized motif is the critical component of the ؊10 promoter element recognized by 28 RNA polymerase. Although the consensus spacer length is 11 nucleotides (nt), we found that 28 RNA polymerase from both Chlamydia and E. coli transcribed a promoter with either an 11-or 12-nt spacer equally well. Altogether, we found very similar results for 28 RNA polymerase from C. trachomatis and E. coli, suggesting that promoter recognition by this alternative RNA polymerase is well conserved among bacteria. The preferred 28 promoter that we defined in the context of the hctB promoter is TAAAGwwy-n 11/12 -ryCGAwrn, where w is A or T, r is a purine, y is a pyrimidine, n is any nucleotide, and n 11/12 is a spacer of 11 or 12 nt.

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“…The original plasmid which contains promoter PD-1 is pCD4136; it consists of a 2.5-kb PstI fragment of B. subtilis DNA cloned in the vector pHV14 (58). A 1.1-kb PstI-EcoRI fragment from pCD4136 had been subcloned previously into pBR322 and pJH101 to yield pMG102 and pEAK1, respectively (21,30,54).…”

Section: Materuils and Methodsmentioning

confidence: 99%

“…Gillen This work a All of the strains except CB100 are derived from the parent CB25 (originally JH642; Fla' Mot' Che+ Lyt+ trpC2pheA1) and were constructed as described in the text. CB100 is derived from I168 (trpC2) as described in reference 27. subtilis DNA fragments each known to contain a strong CD promoter, denoted a PD (20,21,58). This approach has led previously to identification of the B. subtilis hag gene, encoding the flagellar filament structural protein flagellin, and the cotranscribed motA and motB genes, which are required for the function of the flagellum and motility of the cell (46,47).…”

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confidence: 99%

Identification of flagellar synthesis regulatory and structural genes in a sigma D-dependent operon of Bacillus subtilis

1994

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The SD form of RNA polymerase from BaciUlus subtilis has been shown previously to direct the synthesis of several transcription units bearing genes for flagellin, motility proteins, and autolysins. In this report, we describe an operon of genes transcribed from the orD-dependent promoter PD-We have identified three complete open reading frames and one partial one downstream of this promoter, immediately upstream is the previously identified comF locus. The PD-1 operon encodes the presumptive B. subtilis homologs of two Salmonella typhimurium late flagellar genes,flgM andflgK. Also present in this operon are two genes of unknown function, orfl39 and orfl60, whose products show similarities to the eukaryotic cytoskeletal proteins myosin and vimentin, respectively. orfl39 and orfl60 may encode proteins that form extended a-helical secondary structures and coiled-coil quaternary structures which may be filamentous components of the gram-positive bacterial flagellum. We have characterized the B. subtilisflgM gene further by constructing an in-frame deletion mutation, flgMA80, and creating strains of B. subtilis in which this allele has replaced the wild-type copy. By primer extension analysis of cellular RNA, we have shown that the flgMA80 mutation relieves the block to transcription of two other yD-dependent operons imposed by an unlinked mutation in a gene directing early flagellar synthesis. We conclude that, as in the case of S. typhimurium, early flagellar synthesis in B. subtilis is coupled to late flagellar synthesis through repression of (FD-dependent transcription by theflgM gene product.The specificity of promoter recognition by RNA polymerase, often a key step in bacterial gene expression, is determined by proteins known as sigma (cr) factors that confer recognition of distinct promoter sequences. The gram-positive bacterium Bacillus subtilis possesses many alternative sigma factors and employs them in the temporal and developmental regulation of specific sets of genes, or regulons. B. subtilis cr' is a secondary sigma factor that controls a regulon of genes expressed in exponential and early postexponential growth (19, 20, 42, 46; see reference 26 for a review). Mutations in the structural gene for cD lead to defects in flagellation, motility, and/or chemotaxis functions (28,42). crD is the structural homolog of the enteric flagellar-specific sigma factor crF, and each factor appears to control the transcription of a similar regulon of genes required for flagellar assembly (fla), motility (mot), and potentially chemotaxis (che) functions (for a review, see reference 50). Sigma factors having this same promoter specificity are implicated in flagellar gene expression in a wide variety of bacterial species (26) and appear to form a family of sigma factors with related promoter specificities.The gene expression hierarchy that controls flagellar morphogenesis in the enteric bacteria, the fla/che/mot regulon, has been depicted primarily as a linear pathway (17, 37; see reference 40 for a review). The expressi...

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Nucleotide sequences of two Bacillus subtilis promoters used by Bacillus subtilis sigma-28 RNA polymerase

Cited by 87 publications

References 32 publications

Sequencing and analysis of the Bacillus subtilis lytRABC divergon: A regulatory unit encompassing the structural genes of the N-acetylmuramoyl-L-alanine amidase and its modifier

Sequencing and analysis of the Bacillus subtilis lytRABC divergon: A regulatory unit encompassing the structural genes of the N-acetylmuramoyl-L-alanine amidase and its modifier

Mutational Analysis of the Promoter Recognized by Chlamydia and Escherichia coli σ ²⁸ RNA Polymerase

Identification of flagellar synthesis regulatory and structural genes in a sigma D-dependent operon of Bacillus subtilis

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Nucleotide sequences of two Bacillus subtilis promoters used by Bacillus subtilis sigma-28 RNA polymerase

Cited by 87 publications

References 32 publications

Sequencing and analysis of the Bacillus subtilis lytRABC divergon: A regulatory unit encompassing the structural genes of the N-acetylmuramoyl-L-alanine amidase and its modifier

Sequencing and analysis of the Bacillus subtilis lytRABC divergon: A regulatory unit encompassing the structural genes of the N-acetylmuramoyl-L-alanine amidase and its modifier

Mutational Analysis of the Promoter Recognized by Chlamydia and Escherichia coli σ 28 RNA Polymerase

Identification of flagellar synthesis regulatory and structural genes in a sigma D-dependent operon of Bacillus subtilis

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Mutational Analysis of the Promoter Recognized by Chlamydia and Escherichia coli σ ²⁸ RNA Polymerase