31Gene duplication and subsequent evolutionary divergence have allowed conserved proteins 32 to develop unique roles. The MarR family of transcription factors (TFs) has undergone extensive 33 duplication and diversification in bacteria, where they act as environmentally-responsive 34 repressors of genes encoding efflux pumps that confer resistance to xenobiotics, including many 35 antimicrobial agents. We have performed structural, functional, and genetic analyses of 36 representative members of the SlyA/RovA lineage of MarR TFs, which retain some ancestral 37 functions, including repression of their own expression and that of divergently-transcribed multi-38 drug efflux pumps, as well as allosteric inhibition by aromatic carboxylate compounds. However, 39 SlyA and RovA have acquired the ability to counter-silence horizontally-acquired genes, which 40 has greatly facilitated the evolution of Enterobacteriaceae by horizontal gene transfer. 41 SlyA/RovA TFs in different species have independently evolved novel regulatory circuits to 42 provide the enhanced levels of expression required for their new role. Moreover, in contrast to 43 MarR, SlyA is not responsive to copper. These observations demonstrate the ability of TFs to 44 acquire new functions as a result of evolutionary divergence of both cis-regulatory sequences and 45 in trans interactions with modulatory ligands.46 Evolution of SlyA Transcription Factors Will, et al.
109been conserved not due to their primordial role in regulating antimicrobial resistance but rather as 110 a consequence of their counter-silencing function, which is essential to maintain the regulated 111 expression of horizontally-acquired genes in Enterobacteriaceae. 112 113 Results 114 Evolution of SlyA Transcription Factors Will, et al. 6 Salicylate-mediated inhibition of SlyA activity. As environmentally-responsive repressors 115 whose conformation and regulatory actions are modulated by small aromatic carboxylates (12, 116 14), MarR family TFs are inhibited by salicylate in vitro (12). In their structural analyses of SlyA-117 DNA interactions, Dolan et al, (33) inferred from our structural data (see below) that salicylate 118 might regulate SlyA. Using electrophoretic mobility shift assays, they demonstrated that salicylate 119 inhibits DNA-binding by SlyA. To confirm that this influences the function of SlyA as a 120 transcriptional regulator, we performed in vitro transcription assays (IVTs) of slyA and the 121 divergently transcribed ydhIJK efflux pump operon. Supercoiled plasmid DNA containing the 122 slyA-ydhIJK region was incubated with RNA polymerase (RNAP) and increasing SlyA 123 concentrations in the presence or absence of salicylate. SlyA repressed slyA transcription 124 approximately 5.3-fold, while ydhI transcription was inhibited ~19-fold (Figure 1A, B). The 125 addition of 2mM sodium salicylate reduced SlyA-mediated repression to 2.8-fold and 3.2-fold, 126 respectively, indicating that the sensitivity to aromatic carboxylates observed in classical MarR 127TFs...