Fig. 2: MarR_73 forms a dimer, binds to IAA and has a DNA binding site upstream of gene 72 to regulate the IAA degradation locus.
From: Diverse MarR bacterial regulators of auxin catabolism in the plant microbiome
a, The crystal structure of dimer MarR_73 at 1.3 Å with IAA bound to each MarR_73 monomer. The MarR_73 primary monomer is shown in orange, while the secondary monomer is shown in purple. All numbers correspond to residue position. Residues 11 and 148 are the first and last observed residues, respectively. The DNA binding helices (residues 70–83, labelled with asterisks) are not positioned in a manner conducive to binding DNA. For example, they are separated by 38 Å (intermonomer distance between the residue 77 Cα positions central to these helices), which is 10 Å further than that observed in complexes of MarRs and DNA (PMID 28124121). It has been shown that ligand binding shifts the MarR DNA binding helices and adjacent loops such that they are unable to bind the major groove of target DNA sequences65. b,c, Key contacts between MarR_73 and the IAA indole ring (b) and the IAA carboxylate (c). IAA is shown in teal. d, Identification of the 24 bp MarR_73 DNA binding sequence between genes 73 and 72 in the Variovorax IAA degradation locus. Binding affinities to DNA were determined using the MarR_73 S28A because of its weakened binding to IAA. KD values are means± s.e.m. from two independent ITC measurements (see Supplementary Table 2 for full binding data). e, Deletion of MarR_73 or MarR_50 causes increased degradation of IAA. IAA was measured from cultures in M9 medium containing succinate and IAA (n = 3). The time of sampling for RNA-seq in f is shown as a dotted line. f, Transcriptomes of V. paradoxus CL14 wild type and deletion mutants reveal the role of MarR_73 and MarR_50 in the regulation of the IAA degradation locus (n = 3). MarR_73 represses the IAA degradation locus and is derepressed by IAA. Deletion of MarR_50 appears to amplify the upregulation of the IAA degradation locus in response to IAA.
