Dresden 2017 – scientific programme

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BP: Fachverband Biologische Physik

BP 19: Posters - Computational Biophysics

BP 19.12: Poster

Tuesday, March 21, 2017, 14:00–16:00, P1A

Computational prediction of alternative σ factor control — •Hao Wu, Angelika Diehl, and Georg Fritz — LOEWE Center for Synthetic Microbiology, Philipps University Marburg, Germany

Evolutionary co-variation of residues has been extensively exploited to predict conserved interaction of proteins. Here we used this method to study bacterial alternative σ factors. These subunits of RNA polymerases determine its specificity of promoter recognition and are involved in many gene regulation processes crucial for bacterial survival. One important player in the regulation of σ factor activity are anti-σ factors, which sequester their cognate σ factors in the absence of a stimulus, but to date the determinants of binding specificity are poorly understood. Our computational analysis revealed the interacting pairs of residues featuring crucial domains in σ factors. The amino acid pairs are either positively and negatively charged, or hydrophobic, depending on the phylogenetic group of the σ factor. Furthermore, a few alternative σ factor groups contain no anti-σ factor and instead feature a protein domain fused C-terminally to the σ factor as well as a highly conserved gene in its genomic context. Our analysis suggests a cluster of interactions interfacing between the σ domain and the C-terminal domain of the σ-factor. The second protein is also predicted to contact a number of residues at the same interface, suggesting a function as a co-factor. This study helps us to deepen our understanding of the specificity of interactions between σ factor and anti-σ factor, and provides novel insights into the regulatory mechanism employed by different alternative σ factor groups.