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Modulation of extracytoplasmic function (ECF) sigma factor promoter selectivity by spacer region sequence
Ahmed Gaballa1, Veronica Guariglia-Oropeza1, Franziska Dürr1
1Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA.
Nucleic Acids Research
|October 26, 2017
Summary
Bacteria adapt to stress using extracytoplasmic function (ECF) sigma factors. A T-tract DNA motif, alongside core promoter elements, dictates promoter selectivity for these factors, influencing bacterial stress response.
Area of Science:
- Molecular Biology
- Bacterial Genetics
- Gene Regulation
Background:
- Bacteria utilize conditional gene expression for stress adaptation, particularly involving extracytoplasmic function (ECF) sigma factors for cell envelope stress.
- Bacillus subtilis possesses seven ECF sigma factors, with σM, σW, σX, and σV being well-studied regulators of stress-response genes.
- The promoter recognition mechanisms of these ECF sigma factors, particularly the role of core promoter elements (-10 and -35 regions), are not fully elucidated.
Purpose of the Study:
- To investigate the role of DNA sequence motifs beyond the core promoter elements in determining ECF sigma factor promoter selectivity.
- To understand how specific DNA sequences contribute to the differential recognition of promoters by related ECF sigma factors.
- To elucidate the mechanism by which promoter selectivity is modulated, impacting the breadth of gene regulons activated during stress.
Main Methods:
- Experimental analysis of promoter sequences recognized by Bacillus subtilis ECF sigma factors (σM, σW, σX, σV).
- Identification and characterization of a homopolymeric T-tract motif located near the -35 promoter element.
- Assays to determine the contribution of this T-tract motif to promoter activation by different ECF sigma factors.
Main Results:
- A homopolymeric T-tract motif, in conjunction with core promoter sequences, is identified as a key determinant of ECF sigma factor promoter selectivity.
- This T-tract motif exhibits critical importance for promoter activation by σV and variable contributions to activation by σM, σX, and σW.
- The motif is proposed to induce DNA curvature, influencing promoter activity and differential ECF sigma factor binding.
Conclusions:
- The T-tract motif plays a significant role in modulating promoter recognition by ECF sigma factors, thereby fine-tuning bacterial stress responses.
- This finding provides a mechanistic explanation for the overlapping yet distinct promoter specificities observed among ECF sigma factors.
- The differential utilization of this motif offers a strategy for regulating the scope and nature of gene expression during cell envelope stress.
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