Article thumbnail

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

By Luděk Sojka, Tomáš Kouba, Ivan Barvík, Hana Šanderová, Zdeňka Maderová, Jiří Jonák and Libor Krásný


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

Topics: Gene Regulation, Chromatin and Epigenetics
Publisher: Oxford University Press
OAI identifier:
Provided by: PubMed Central

To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.

Suggested articles


  1. (2001). A new mathematical model for relative quantification in real-time RT-PCR.
  2. (1994). A promoter melting region in the primary sigma factor of Bacillus subtilis.
  3. (2008). Advances in bacterial promoter recognition and its control by factors that do not bind DNA.
  4. (2009). Allosteric control of Escherichia coli rRNA promoter complexes by DksA. Genes Dev.,
  5. (2004). An alternative strategy for bacterial ribosome synthesis: Bacillus subtilis rRNA transcription regulation.
  6. (2006). Antagonistic regulation of Escherichia coli ribosomal RNA rrnB P1 promoter activity by GreA and DksA.
  7. (2002). Bacillus subtilis functional genomics : global characterization of the stringent response by proteome and transcriptome analysis.
  8. (2005). Bacillus subtilis ilvB operon: an intersection of global regulons.
  9. (2010). c ˇ kova ´ ,V., S ˇ anderova ´ ,H., Z ˇ ı´dek,L., Nova ´ c ˇ ek,J.,
  10. (2003). Co-overexpression of Escherichia coli RNA polymerase subunits allows isolation and analysis of mutant enzymes lacking lineage-specific sequence insertions.
  11. (1995). Compilation and analysis of Bacillus subtilis sigma A-dependent promoter sequences: evidence for extended contact between RNA polymerase and upstream promoter DNA.
  12. (2001). Contributions of UP elements and the transcription factor FIS to expression from the seven rrn P1 promoters in Escherichia coli.
  13. (1975). Control of expression of the pyr genes in Salmonella typhimurium: effects of variations in uridine and cytidine nucleotide pools.
  14. (2003). Control of rRNA expression by small molecules is dynamic and nonredundant.
  15. (1990). E.coli Fis protein activates ribosomal RNA transcription in vitro and in vivo.
  16. (1999). Effect of mutations in the ‘‘extended -10’’ motif of three Bacillus subtilis sigmaA-RNA polymerase-dependent promoters.
  17. (2007). Effects of DksA, GreA, and GreB on transcription initiation: insights into the mechanism of factors that bind in the secondary channel of RNA polymerase.
  18. (1994). Effects of transcriptional start site sequence and position on nucleotide-sensitive selection of alternative start sites at the pyrC promoter in Escherichia coli.
  19. (2005). Elaborate transcription regulation of the Bacillus subtilis ilv-leu operon involved in the biosynthesis of branched-chain amino acids through global regulators of CcpA,
  20. (1999). Expression, abundance, and RNA polymerase binding properties of the delta factor of Bacillus subtilis.
  21. (2008). Fine structure of the promoter—sigma region 1.2 interaction.
  22. (2008). Futile cycle of transcription initiation and termination modulates the response to nucleotide shortage in S.
  23. (1973). Genetic studies of leucine biosynthesis in Bacillus subtilis.
  24. (2007). Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum.
  25. (2010). Heavy involvement of stringent transcription control depending on the adenine or guanine species of the transcription initiation site in glucose and pyruvate metabolism in Bacillus subtilis.
  26. (1992). Identification of tms-26 as an allele of the gcaD gene, which encodes N-acetylglucosamine 1-phosphate uridyltransferase in Bacillus subtilis.
  27. (1977). Induction of sporulation in Bacillus subtilis by decoyinine and hadacidin.
  28. (1988). Instability of rRNA operons in Bacillus subtilis.
  29. (2003). Measuring control of transcription initiation by changing concentrations of nucleotides and their derivatives.
  30. (1992). Mechanism of initiation of transcription by Bacillus subtilis RNA polymerase at several promoters.
  31. (2001). Mechanism of regulation of transcription initiation by ppGpp. I. Effects of ppGpp on transcription initiation in vivo and in vitro.
  32. (1999). Molecular cloning and comparative sequence analyses of rRNA operons
  33. (2008). Molecular mechanisms underlying the positive stringent response of the Bacillus subtilis ilv-leu operon, involved in the biosynthesis of branched-chain amino acids.
  34. (1987). Mutations of the Escherichia coli lacUV5 promoter resulting in increased expression in Bacillus subtilis.
  35. (2004). Negative Transcriptional regulation of the ilv-leu operon for biosynthesis of branched-chain amino acids through the Bacillus subtilis global regulator TnrA.
  36. (1993). Nucleotide pool-sensitive selection of the transcriptional start site in vivo at the Salmonella typhimurium pyrC and pyrD promoters.
  37. (1990). Overproduction, purification, and characterization of Bacillus subtilis RNA polymerase sigma A factor.
  38. (1998). PhoP-P and RNA polymerase sigmaA holoenzyme are sufficient for transcription of Pho regulon promoters in Bacillus subtilis: PhoP-P activator sites within the coding region stimulate transcription in vitro.
  39. (2004). Phylogeny of Firmicutes with special reference to Mycoplasma (Mollicutes) as inferred from phosphoglycerate kinase amino acid sequence data.
  40. (1996). Plasmids for ectopic integration on Bacillus subtilis.
  41. (2004). Promoter unwinding and promoter clearance by RNA polymerase: detection by single-molecule DNA nanomanipulation.
  42. (1999). Protein-nucleic acid interactions during open complex formation investigated by systematic alteration of the protein and DNA binding partners.
  43. (2008). Regulation of a eukaryotic gene by GTP-dependent start site selection and transcription attenuation.
  44. (1994). Regulation of pyrBI operon expression in Escherichia coli by UTP-sensitive reiterative RNA synthesis during transcriptional initiation.
  45. (2001). Regulation of rRNA transcription correlates with nucleoside triphosphate sensing.
  46. (1981). Response of guanosine 50-triphosphate concentration to nutritional changes and its significance for Bacillus subtilis sporulation.
  47. (2007). Ribosomal protein L20 controls expression of the Bacillus subtilis infC operon via a transcription attenuation mechanism.
  48. (2002). Ribosomes, protein synthesis factors, and tRNA synthetases. In Sonenshein,A.L., Hoch,J.A. and Losick,R. (eds), Bacillus subtilis and Its Closest Relatives: From Genes to Cells.
  49. (2008). RNA polymerase elongation factors.
  50. (2010). RNA polymerase trafficking in Bacillus subtilis cells.
  51. (2006). rRNA promoter regulation by nonoptimal binding of sigma region 1.2: an additional recognition element for RNA polymerase.
  52. (2004). rRNA transcription in Escherichia coli.
  53. (1989). Saturation mutagenesis of an Escherichia coli rRNA promoter and initial characterization of promoter variants.
  54. (2006). Sensitivity of the yeast mitochondrial RNA polymerase to +1 and +2 initiating nucleotides.
  55. (1986). Separation and analysis of the RNA polymerase binding sites of a complex Bacillus subtilis promoter.
  56. (2010). Small subunits of RNA polymerase: localisation, levels and implications for core enzyme composition.
  57. (2000). Structural organization of the RNA polymerase-promoter open complex.
  58. (2006). Subcellular partitioning of transcription factors in Bacillus subtilis.
  59. (1998). The -16 region of Bacillus subtilis and other gram-positive bacterial promoters.
  60. (2010). The delta subunit of RNA polymerase, RpoE, is a global modulator of Streptococcus mutans environmental adaptation.
  61. (1996). The dnaB-pheA (256 -240 ) region of the Bacillus subtilis chromosome containing genes responsible for stress responses , the utilization of plant cell walls and primary metabolism.
  62. (2004). The Escherichia coli Fis promoter is regulated by changes in the levels of its transcription initiation nucleotide CTP.
  63. (2008). The identity of the transcription +1 position is crucial for changes in gene expression in response to amino acid starvation in Bacillus subtilis.
  64. (2009). The interaction of Bacillus subtilis sigmaA with RNA polymerase.
  65. (1981). The role of the delta peptide of the Bacillus subtilis RNA polymerase in promoter selection.
  66. (1996). The rRNA operons of Mycobacterium smegmatis and Mycobacterium tuberculosis: comparison of promoter elements and of neighbouring upstream genes.
  67. (2002). The TRTGn motif stabilizes the transcription initiation open complex.
  68. (2009). Transcription activity of individual rrn operons in Bacillus subtilis mutants deficient in (p)ppGpp synthetase genes, relA, yjbM, and ywaC.
  69. (1997). Transcription regulation by initiating NTP concentration: rRNA synthesis in bacteria.
  70. (2004). Transcriptional organization and posttranscriptional regulation of the Bacillus subtilis branched-chain amino acid biosynthesis genes.
  71. (1992). Transcriptional regulation of the ilv-leu operon of Bacillus subtilis.
  72. (2003). Transcriptional, functional and cytochemical analyses of the veg gene in Bacillus subtilis.