Characterization of Transport Proteins for Aromatic Compounds Derived from Lignin: Benzoate Derivative Binding Proteins

Abstract

In vitro growth experiments have demonstrated that aromatic compounds derived from lignin can be metabolized and represent a major carbon resource for many soil bacteria. However, the proteins that mediate the movement of these metabolites across the cell membrane have not been thoroughly characterized. To address this deficiency, we used a library representative of lignin degradation products and a thermal stability screen to determine ligand specificity for a set of solute-binding proteins (SBPs) from ATP-binding cassette (ABC) transporters. The ligand mapping process identified a set of proteins from Alphaproteobacteria that recognize various benzoate derivatives. Seven high-resolution crystal structures of these proteins in complex with four different aromatic compounds were obtained. The protein–ligand complexes provide details of molecular recognition that can be used to infer binding specificity. This structure–function characterization provides new insight for the biological roles of these ABC transporters and their SBPs, which had been previously annotated as branched-chain amino-acid-binding proteins. The knowledge derived from the crystal structures provides a foundation for development of sequencebased methods to predict the ligand specificity of other uncharacterized transporters. These results also demonstrate that Alphaproteobacteria possess a diverse set of transport capabilities for lignin-derived compounds. Characterization of this new class of transporters improves genomic annotation projects and provides insight into the metabolic potential of soil bacteria.

Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1

“…The transport of small aromatic molecules after lignin degradation is important because these small molecules likely account for a significant source of energy and biomass among lignin-degrading microbes (Michalska et al, 2012). Aromatic compounds derived from lignin degradation could be imported by an ATP-depended mechanism (Paulsen et al, 2000; Chaudhry et al, 2007).…”

“…These transportations are mediated by ATP-binding cassette (ABC) transporters. The bacterial ABC transporter is composed of a transmembrane permease, a cytoplasmic ATPase subunit, and a periplasmic solute-binding protein (SBP) (Michalska et al, 2012). In known lignin degrading bacteria, these SBPs are identified as branched-chain amino acid-binding proteins (Giuliani et al, 2008; Oda et al, 2008).…”

Structural and functional characterization of solute binding proteins for aromatic compounds derived from lignin:p-Coumaric acid and related aromatic acids

“…These bacteria employ a common metabolic strategy that transforms the complex assortment of degradation products into a limited number of aromatic compounds which then proceed through central degradation pathways that perform aromatic ring cleavage . In a previous study, we characterized several solute‐binding proteins (SBPs) that mediate the transport of benzoate‐like compounds that feed directly into central degradation pathways. However, few proteins involved in the transport or metabolism of non‐benzoate compounds such as p ‐coumaric acid (COU), caffeic acid, ferulic acid, or sinapic acid have been experimentally characterized.…”

How Aromatic Compounds Block DNA Binding of HcaR Catabolite Regulator

“…In the presence of hydroxycinnamates, AcHcaR fails to bind to DNA, and operon transcription can proceed. It is believed that hydroxycinnamates enter the cell through the HcaK transporter, although it is known that ATP-binding cassette transporters are also involved in the transport of aromatic compounds (32). The HcaC CoA ligase initiates metabolism by converting these compounds to corresponding hydroxycinnamoyl-CoA thioesters.…”