Protein-DNA interactions of oxidative-stress transcription factors OxyR1 and OxyR2 in <em>Aliivibrio fischeri</em>

Abstract

Transcription factors (TFs) are regulatory proteins that bind tightly to specific DNA sequences 15-20 base pairs long. Being sequence-specific DNA-binding proteins, TFs bear the key to the cellular state and control how organisms respond to different environmental stresses. OxyR, a LysR-type transcription factor, binds strongly to H₂O₂ and activates a set of genes whose main purpose is to protect bacteria against oxidative stress. The genome of <em>Aliivibrio fischeri</em> bacteria codes for two different OxyR proteins, OxyR1 and OxyR2. However, the collection of target genes of OxyR1 and OxyR2 in <em>A. fischeri </em>remains to be determined. This study aims to clone, overexpress, and purify OxyR1 and OxyR2 TFs to determine their DNA binding functionality throughout the assessment of their intrinsic DNA-binding preferences. Purified OxyR1 and OxyR2 TFs were used to determine their DNA binding specificity using Systematic Evolution of Ligands by Exponential Enrichment (SELEX-seq).