Lignin, a plant-produced aromatic polymer, represents a significant, yet difficult to utilize, reservoir of organic matter. Understanding lignin bioprocessing is important for comprehending carbon cycling. Biodegradation of this highly resistant material requires multiple classes of extracellular enzymes produced by certain species of fungi and bacteria. In free-radical-based random depolymerization of lignin a number of small aromatic compounds are produced. These molecules are further metabolized by microbes through relatively well-known aerobic and anaerobic pathways. However, mechanisms by which these molecules are imported into cells attracted little attention. We investigated a set of solute-binding proteins (SBPs) of ABC transporters from soil Alphaproteobacteria that mediate transport of lignin degradation products. Functional screens and structural studies were integrated into discovery framework. Detailed characterization enabled us to distinguish four functional groups that show binding preference based on the size of an aliphatic chain and a number of aromatic ring substituents. Multiple crystal structures for protein-ligand complexes for each of these groups provided details of molecular recognition that can be used to infer ligand specificity. The ligand-binding characterization allows for the assignment of specific functions of several SBPs, many of which have been misannotated as branched-chain amino acid-binding proteins. The results demonstrate that Alphaproteobacteria contain a broad spectrum of transport capabilities for lignin-derived compounds. A detailed analysis of this new class of transporters will advance genomic annotation projects and provide insight into the metabolic potential of soil bacteria.
This research has been funded in part by a grant from the NIH grant GM094585, and by the U.S. DOE, BER, under Contract DE-AC02-06CH11357.