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Rapid changes in gene expression: DNA determinants of promoter regulation by the concentration of the transcription initiating NTP in Bacillus subtilis.

Sojka L, Kouba T, Barvík I, Sanderová H, Maderová Z, Jonák J, Krásny L - Nucleic Acids Res. (2011)

Bottom Line: An important small molecule effector is the initiating nucleoside triphosphate (iNTP).At some promoters, an increasing iNTP concentration stimulates promoter activity, while a decreasing concentration has the opposite effect.Overall, it seems that various sequence combinations can result in promoter regulation by [iNTP] in B. subtilis.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Molecular Genetics of Bacteria, Institute of Microbiology, Academy of Sciences of the Czech Republic.

ABSTRACT
In bacteria, rapid changes in gene expression can be achieved by affecting the activity of RNA polymerase with small molecule effectors during transcription initiation. An important small molecule effector is the initiating nucleoside triphosphate (iNTP). At some promoters, an increasing iNTP concentration stimulates promoter activity, while a decreasing concentration has the opposite effect. Ribosomal RNA (rRNA) promoters from Gram-positive Bacillus subtilis are regulated by the concentration of their iNTP. Yet, the sequences of these promoters do not emulate the sequence characteristics of [iNTP]-regulated rRNA promoters of Gram-negative Escherichia coli. Here, we identified the 3'-promoter region, corresponding to the transcription bubble, as key for B. subtilis rRNA promoter regulation via the concentration of the iNTP. Within this region, the conserved -5T (3 bp downstream from the -10 hexamer) is required for this regulation. Moreover, we identified a second class of [iNTP]-regulated promoters in B. subtilis where the sequence determinants are not limited to the transcription bubble region. Overall, it seems that various sequence combinations can result in promoter regulation by [iNTP] in B. subtilis. Finally, this study demonstrates how the same type of regulation can be achieved with strikingly different promoter sequences in phylogenetically distant species.

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Class I and Class II promoters. (A) Sequences of B. subtilis rrnA P1, rrnJ P1, Pilv, PgcaD, PinfC promoters and their chimeric variants. −35, −10 and +1 are marked. Transcription from Pilv can initiate at either of the two indicated positions. The +1 position that is 7 bp from −10 is the preferred one. The color coding of the construct names indicates similar types of constructs (e.g. green indicates a chimera with the 5′-region from Pveg and the 3′-region from the tested promoter). The color coding of the sequences indicates the origin of the sequence: dark gray, the tested promoter; light gray, Pveg; white, rrnB P1. (B) Graphical comparison of KGTP values for construct Nos 14–33. The respective KGTP values are shown above the bars and also next to the construct sequence in A. The color coding of the bars corresponds to the color coding of the construct names used in panel A of this figure.
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Figure 5: Class I and Class II promoters. (A) Sequences of B. subtilis rrnA P1, rrnJ P1, Pilv, PgcaD, PinfC promoters and their chimeric variants. −35, −10 and +1 are marked. Transcription from Pilv can initiate at either of the two indicated positions. The +1 position that is 7 bp from −10 is the preferred one. The color coding of the construct names indicates similar types of constructs (e.g. green indicates a chimera with the 5′-region from Pveg and the 3′-region from the tested promoter). The color coding of the sequences indicates the origin of the sequence: dark gray, the tested promoter; light gray, Pveg; white, rrnB P1. (B) Graphical comparison of KGTP values for construct Nos 14–33. The respective KGTP values are shown above the bars and also next to the construct sequence in A. The color coding of the bars corresponds to the color coding of the construct names used in panel A of this figure.

Mentions: Next, we created four variants of these promoters: (i) core; (ii) chimeras consisting of the 5′-region (from 3 bp upstream of −35 to the −10 hexamer) from Pveg fused to 3′-regions [from the −10 hexamer (included) to +1] of the tested promoters (analogous to construct No. 4 in Figure 3A); (iii) chimeras consisting of 5′-regions from the tested promoters fused to the 3′-region of Pveg (analogous to construct No. 9 in Figure 3A); and (iv) chimeras consisting of the 5′-region from rrnB P1 and 3′-regions from the tested promoter (Figure 5A).Figure 5.


Rapid changes in gene expression: DNA determinants of promoter regulation by the concentration of the transcription initiating NTP in Bacillus subtilis.

Sojka L, Kouba T, Barvík I, Sanderová H, Maderová Z, Jonák J, Krásny L - Nucleic Acids Res. (2011)

Class I and Class II promoters. (A) Sequences of B. subtilis rrnA P1, rrnJ P1, Pilv, PgcaD, PinfC promoters and their chimeric variants. −35, −10 and +1 are marked. Transcription from Pilv can initiate at either of the two indicated positions. The +1 position that is 7 bp from −10 is the preferred one. The color coding of the construct names indicates similar types of constructs (e.g. green indicates a chimera with the 5′-region from Pveg and the 3′-region from the tested promoter). The color coding of the sequences indicates the origin of the sequence: dark gray, the tested promoter; light gray, Pveg; white, rrnB P1. (B) Graphical comparison of KGTP values for construct Nos 14–33. The respective KGTP values are shown above the bars and also next to the construct sequence in A. The color coding of the bars corresponds to the color coding of the construct names used in panel A of this figure.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3113569&req=5

Figure 5: Class I and Class II promoters. (A) Sequences of B. subtilis rrnA P1, rrnJ P1, Pilv, PgcaD, PinfC promoters and their chimeric variants. −35, −10 and +1 are marked. Transcription from Pilv can initiate at either of the two indicated positions. The +1 position that is 7 bp from −10 is the preferred one. The color coding of the construct names indicates similar types of constructs (e.g. green indicates a chimera with the 5′-region from Pveg and the 3′-region from the tested promoter). The color coding of the sequences indicates the origin of the sequence: dark gray, the tested promoter; light gray, Pveg; white, rrnB P1. (B) Graphical comparison of KGTP values for construct Nos 14–33. The respective KGTP values are shown above the bars and also next to the construct sequence in A. The color coding of the bars corresponds to the color coding of the construct names used in panel A of this figure.
Mentions: Next, we created four variants of these promoters: (i) core; (ii) chimeras consisting of the 5′-region (from 3 bp upstream of −35 to the −10 hexamer) from Pveg fused to 3′-regions [from the −10 hexamer (included) to +1] of the tested promoters (analogous to construct No. 4 in Figure 3A); (iii) chimeras consisting of 5′-regions from the tested promoters fused to the 3′-region of Pveg (analogous to construct No. 9 in Figure 3A); and (iv) chimeras consisting of the 5′-region from rrnB P1 and 3′-regions from the tested promoter (Figure 5A).Figure 5.

Bottom Line: An important small molecule effector is the initiating nucleoside triphosphate (iNTP).At some promoters, an increasing iNTP concentration stimulates promoter activity, while a decreasing concentration has the opposite effect.Overall, it seems that various sequence combinations can result in promoter regulation by [iNTP] in B. subtilis.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Molecular Genetics of Bacteria, Institute of Microbiology, Academy of Sciences of the Czech Republic.

ABSTRACT
In bacteria, rapid changes in gene expression can be achieved by affecting the activity of RNA polymerase with small molecule effectors during transcription initiation. An important small molecule effector is the initiating nucleoside triphosphate (iNTP). At some promoters, an increasing iNTP concentration stimulates promoter activity, while a decreasing concentration has the opposite effect. Ribosomal RNA (rRNA) promoters from Gram-positive Bacillus subtilis are regulated by the concentration of their iNTP. Yet, the sequences of these promoters do not emulate the sequence characteristics of [iNTP]-regulated rRNA promoters of Gram-negative Escherichia coli. Here, we identified the 3'-promoter region, corresponding to the transcription bubble, as key for B. subtilis rRNA promoter regulation via the concentration of the iNTP. Within this region, the conserved -5T (3 bp downstream from the -10 hexamer) is required for this regulation. Moreover, we identified a second class of [iNTP]-regulated promoters in B. subtilis where the sequence determinants are not limited to the transcription bubble region. Overall, it seems that various sequence combinations can result in promoter regulation by [iNTP] in B. subtilis. Finally, this study demonstrates how the same type of regulation can be achieved with strikingly different promoter sequences in phylogenetically distant species.

Show MeSH
Related in: MedlinePlus