Binding motifs in bacterial gene promoters modulate transcriptional effects of global regulators CRP and ArcA

Journal Article · Wed May 30 04:00:00 EDT 2012 · Gene Regulation and Systems Biology

DOI:https://doi.org/10.4137/GRSB.S9357· OSTI ID:1045100

Leuze, Mike; Karpinets, Tatiana V; Syed, Mustafa H; Beliaev, Alex S; Uberbacher, Edward

Bacterial gene regulation involves transcription factors (TF) that bind to DNA recognition sequences in operon promoters. These recognition sequences, many of which are palindromic, are known as regulatory elements or transcription factor binding sites (TFBS). Some TFs are global regulators that can modulate the expression of hundreds of genes. In this study we examine global regulator half-sites, where a half-site, which we shall call a binding motif (BM), is one half of a palindromic TFBS. We explore the hypothesis that the number of BMs plays an important role in transcriptional regulation, examining empirical data from transcriptional profiling of the CRP and ArcA regulons. We compare the power of BM counts and of full TFBS characteristics to predict induced transcriptional activity. We find that CRP BM counts have a nonlinear effect on CRP-dependent transcriptional activity and predict this activity better than full TFBS quality or location.

• Research Organization: Pacific Northwest National Laboratory (PNNL), Richland, WA (US)
• Sponsoring Organization: USDOE
• DOE Contract Number: AC05-76RL01830
• OSTI ID: 1045100
• Report Number(s): PNNL-SA-86561; KP1601010
• Journal Information: Gene Regulation and Systems Biology, Journal Name: Gene Regulation and Systems Biology Vol. 6
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
60 APPLIED LIFE SCIENCES
DNA
GENE REGULATION
GENES
HYPOTHESIS
PROMOTERS
TRANSCRIPTION FACTORS
bacterial gene promoters
binding motifs
global regulators