The AibR-isovaleryl coenzyme A regulator and its DNA binding site – a model for the regulation of alternative de novo isovaleryl coenzyme A biosynthesis in Myxococcus xanthus

Abstract

Isovaleryl coenzyme A (IV-CoA) is an important building block of iso-fatty acids. In myxobacteria, IV-CoA is essential for the formation of signaling molecules involved in fruiting body formation. Leucine degradation is the common source of IV-CoA, but a second, de novo biosynthetic route to IV-CoA termed AIB (alternative IV-CoA biosynthesis) was recently discovered in M. xanthus. The AIB-operon contains the TetR-like transcriptional regulator AibR, which we characterize in this study. We demonstrate that IV-CoA binds AibR with micromolar affinity and show by gelshift experiments that AibR interacts with the promoter region of the AIB-operon once IV-CoA is present. We identify an 18-bp near-perfect palindromic repeat as containing the AibR operator and provide evidence that AibR also controls an additional genomic locus coding for a putative acetyl–CoA acetyltransferase. To elucidate atomic details, we determined crystal structures of AibR in the apo, the IV-CoA- and the IV-CoA-DNA-bound state to 1.7 Å, 2.35 Å and 2.92 Å, respectively. IV-CoA induces partial unfolding of an α-helix, which allows sequence-specific interactions between AibR and its operator. This study provides insights into AibR-mediated regulation and shows that AibR functions in an unusual TetR-like manner by blocking transcription not in the ligand-free but in the effector-bound state.

Functional Mechanism of the Efflux Pumps Transcription Regulators From Pseudomonas aeruginosa Based on 3D Structures

“…Among the 280 structures of TetR deposited in the PDB, more than 80 are declared to be associated with ligands. The chemical nature of these ligands is diverse, from a simple benzenediol such as resorcinol interacting with RolR, regulator of the aromatic catabolism from Corynebacterium glutamicum (3AQT, Li et al, 2011 ), to a more complex nucleotide derivative compound like isovaleryl coenzyme A (IV-CoA), an important building block in the formation of iso-fatty acids, interacting with AibR from Myxococcus xanthus (5K7H, 5K7Z; Bock et al, 2017 ). Most of the regulators classically repress the transcription in their apo-form, except for the AibR which is a repressor in a ligand-bound form of a whole operon bearing five genes involved in the biosynthesis process of IV-CoA, once bound to the same ligand.…”

“…The nature of these amino acids varies with the cognate DNA sequence, even though most of the protein/DNA interactions involve the DNA backbone and not the nucleic base. This is the case for AibR presenting seven residues interacting with phosphates backbone and only two involving specific contacts with the base (Bock et al, 2017 ). Nevertheless, one residue is particularly well conserved, a tyrosine (Y42 in TetR and Y40 in QacR) that interacts with the same DNA phosphate as the amine group of the N-terminal residue of α4, reinforcing the DNA binding.…”

Plasmalogens and Photooxidative Stress Signaling in Myxobacteria, and How it Unmasked CarF/TMEM189 as the Δ1′-Desaturase PEDS1 for Human Plasmalogen Biosynthesis

“…The latter operon encodes a transcriptional regulator (AibR), the 3-hydroxy-3-methylglutaryl coenzyme A synthase (MvaS), two subunits of a novel type of decarboxylase (AibA and AibB), and a medium-chain reductase-dehydrogenase (AibC). AibR, when bound to isovaleryl-CoA, downregulates the Aib operon and a gene encoding a putative acetyl-CoA acetyltransferase that likely catalyzes formation of the MvaS substrate acetoacetyl-CoA ( Mahmud et al, 2002 ; Bode et al, 2006 ; Bode et al, 2009 ; Li et al, 2013 ; Bock et al, 2016 ; Bock et al, 2017a ; Bock et al, 2017b ). Interestingly, Aib pathway genes are upregulated upon starvation (when Bkd pathway genes are downregulated), and also in bkd mutants ( Bode et al, 2009 ; Bhat et al, 2014b ; Muñoz-Dorado et al, 2019 ), presumably to ensure supply of isovaleryl-CoA for iso-branched fatty acid synthesis-homeostasis under different conditions.…”