RpoD promoters in Campylobacter jejuni exhibit a strong periodic signal instead of a -35 box.

Lise Petersen, Thomas S. Larsen, David W. Ussery, Stephen L.W. On, Anders S. Krogh

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

Resumé

We have used a hidden Markov model (HMM) to identify the consensus sequence of the RpoD promoters in the genome of Campylobacter jejuni. The identified promoter consensus sequence is unusual compared to other bacteria, in that the region upstream of the TATA-box does not contain a conserved -35 region, but shows a very strong periodic variation in the AT-content and semi-conserved T-stretches, with a period of 10-11 nucleotides. The TATA-box is in some, but not all cases, preceded by a TGx, similar to an extended -10 promoter. We predicted a total of 764 presumed RpoD promoters in the C.jejuni genome, of which 654 were located upstream of annotated genes. A similar promoter was identified in Helicobacter pylori, a close phylogenetic relative of Campylobacter, but not in Escherichia coli, Vibrio cholerae, or six other Proteobacterial genomes, or in Staphylococcus aureus. We used upstream regions of high confidence genes as training data (n=529, for the C.jejuni genome). We found it necessary to limit the training set to genes that are preceded by an intergenic region of >100bp or by a gene oriented in the opposite direction to be able to identify a conserved sequence motif, and ended up with a training set of 175 genes. This leads to the conclusion that the remaining genes (354) are more rarely preceded by a (RpoD) promoter, and consequently that operon structure may be more widespread in C.jejuni than has been assumed by others. Structural predictions of the regions upstream of the TATA-box indicates a region of highly curved DNA, and we assume that this facilitates the wrapping of the DNA around the RNA polymerase holoenzyme, and offsets the absence of a conserved -35 binding motif.
OriginalsprogEngelsk
Artikelnummer12595250
TidsskriftJournal of Molecular Biology
Vol/bind326 (5)
Sider (fra-til)1361-72
Antal sider12
ISSN0022-2836
StatusUdgivet - mar. 2003

Citer dette

Petersen, L., Larsen, T. S., Ussery, D. W., On, S. L. W., & Krogh, A. S. (2003). RpoD promoters in Campylobacter jejuni exhibit a strong periodic signal instead of a -35 box. Journal of Molecular Biology, 326 (5), 1361-72. [12595250].
Petersen, Lise ; Larsen, Thomas S. ; Ussery, David W. ; On, Stephen L.W. ; Krogh, Anders S. . / RpoD promoters in Campylobacter jejuni exhibit a strong periodic signal instead of a -35 box. I: Journal of Molecular Biology. 2003 ; Bind 326 (5). s. 1361-72.
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title = "RpoD promoters in Campylobacter jejuni exhibit a strong periodic signal instead of a -35 box.",
abstract = "We have used a hidden Markov model (HMM) to identify the consensus sequence of the RpoD promoters in the genome of Campylobacter jejuni. The identified promoter consensus sequence is unusual compared to other bacteria, in that the region upstream of the TATA-box does not contain a conserved -35 region, but shows a very strong periodic variation in the AT-content and semi-conserved T-stretches, with a period of 10-11 nucleotides. The TATA-box is in some, but not all cases, preceded by a TGx, similar to an extended -10 promoter. We predicted a total of 764 presumed RpoD promoters in the C.jejuni genome, of which 654 were located upstream of annotated genes. A similar promoter was identified in Helicobacter pylori, a close phylogenetic relative of Campylobacter, but not in Escherichia coli, Vibrio cholerae, or six other Proteobacterial genomes, or in Staphylococcus aureus. We used upstream regions of high confidence genes as training data (n=529, for the C.jejuni genome). We found it necessary to limit the training set to genes that are preceded by an intergenic region of >100bp or by a gene oriented in the opposite direction to be able to identify a conserved sequence motif, and ended up with a training set of 175 genes. This leads to the conclusion that the remaining genes (354) are more rarely preceded by a (RpoD) promoter, and consequently that operon structure may be more widespread in C.jejuni than has been assumed by others. Structural predictions of the regions upstream of the TATA-box indicates a region of highly curved DNA, and we assume that this facilitates the wrapping of the DNA around the RNA polymerase holoenzyme, and offsets the absence of a conserved -35 binding motif.",
author = "Lise Petersen and Larsen, {Thomas S.} and Ussery, {David W.} and On, {Stephen L.W.} and Krogh, {Anders S.}",
year = "2003",
month = "3",
language = "English",
volume = "326 (5)",
pages = "1361--72",
journal = "Journal of Molecular Biology",
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Petersen, L, Larsen, TS, Ussery, DW, On, SLW & Krogh, AS 2003, 'RpoD promoters in Campylobacter jejuni exhibit a strong periodic signal instead of a -35 box.', Journal of Molecular Biology, bind 326 (5), 12595250, s. 1361-72.

RpoD promoters in Campylobacter jejuni exhibit a strong periodic signal instead of a -35 box. / Petersen, Lise; Larsen, Thomas S. ; Ussery, David W. ; On, Stephen L.W.; Krogh, Anders S. .

I: Journal of Molecular Biology, Bind 326 (5), 12595250, 03.2003, s. 1361-72.

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

TY - JOUR

T1 - RpoD promoters in Campylobacter jejuni exhibit a strong periodic signal instead of a -35 box.

AU - Petersen, Lise

AU - Larsen, Thomas S.

AU - Ussery, David W.

AU - On, Stephen L.W.

AU - Krogh, Anders S.

PY - 2003/3

Y1 - 2003/3

N2 - We have used a hidden Markov model (HMM) to identify the consensus sequence of the RpoD promoters in the genome of Campylobacter jejuni. The identified promoter consensus sequence is unusual compared to other bacteria, in that the region upstream of the TATA-box does not contain a conserved -35 region, but shows a very strong periodic variation in the AT-content and semi-conserved T-stretches, with a period of 10-11 nucleotides. The TATA-box is in some, but not all cases, preceded by a TGx, similar to an extended -10 promoter. We predicted a total of 764 presumed RpoD promoters in the C.jejuni genome, of which 654 were located upstream of annotated genes. A similar promoter was identified in Helicobacter pylori, a close phylogenetic relative of Campylobacter, but not in Escherichia coli, Vibrio cholerae, or six other Proteobacterial genomes, or in Staphylococcus aureus. We used upstream regions of high confidence genes as training data (n=529, for the C.jejuni genome). We found it necessary to limit the training set to genes that are preceded by an intergenic region of >100bp or by a gene oriented in the opposite direction to be able to identify a conserved sequence motif, and ended up with a training set of 175 genes. This leads to the conclusion that the remaining genes (354) are more rarely preceded by a (RpoD) promoter, and consequently that operon structure may be more widespread in C.jejuni than has been assumed by others. Structural predictions of the regions upstream of the TATA-box indicates a region of highly curved DNA, and we assume that this facilitates the wrapping of the DNA around the RNA polymerase holoenzyme, and offsets the absence of a conserved -35 binding motif.

AB - We have used a hidden Markov model (HMM) to identify the consensus sequence of the RpoD promoters in the genome of Campylobacter jejuni. The identified promoter consensus sequence is unusual compared to other bacteria, in that the region upstream of the TATA-box does not contain a conserved -35 region, but shows a very strong periodic variation in the AT-content and semi-conserved T-stretches, with a period of 10-11 nucleotides. The TATA-box is in some, but not all cases, preceded by a TGx, similar to an extended -10 promoter. We predicted a total of 764 presumed RpoD promoters in the C.jejuni genome, of which 654 were located upstream of annotated genes. A similar promoter was identified in Helicobacter pylori, a close phylogenetic relative of Campylobacter, but not in Escherichia coli, Vibrio cholerae, or six other Proteobacterial genomes, or in Staphylococcus aureus. We used upstream regions of high confidence genes as training data (n=529, for the C.jejuni genome). We found it necessary to limit the training set to genes that are preceded by an intergenic region of >100bp or by a gene oriented in the opposite direction to be able to identify a conserved sequence motif, and ended up with a training set of 175 genes. This leads to the conclusion that the remaining genes (354) are more rarely preceded by a (RpoD) promoter, and consequently that operon structure may be more widespread in C.jejuni than has been assumed by others. Structural predictions of the regions upstream of the TATA-box indicates a region of highly curved DNA, and we assume that this facilitates the wrapping of the DNA around the RNA polymerase holoenzyme, and offsets the absence of a conserved -35 binding motif.

M3 - Journal article

VL - 326 (5)

SP - 1361

EP - 1372

JO - Journal of Molecular Biology

JF - Journal of Molecular Biology

SN - 0022-2836

M1 - 12595250

ER -