The structural basis for high‐affinity uptake of lignin‐derived aromatic compounds by proteobacterial TRAP transporters

Abstract

The organic polymer lignin is a component of plant cell walls, which like (hemi)-cellulose is highly abundant in nature and relatively resistant to degradation. However, extracellular enzymes released by natural microbial consortia can cleave the b-aryl ether linkages in lignin, releasing monoaromatic phenylpropanoids that can be further catabolised by diverse species of bacteria. Biodegradation of lignin is therefore important in global carbon cycling, and its natural abundance also makes it an attractive biotechnological feedstock for the industrial production of commodity chemicals. Whilst the pathways for degradation of lignin-derived aromatics have been extensively characterised, much less is understood about how they are recognised and taken up from the environment. The purple phototrophic bacterium Rhodopseudomonas palustris can grow on a range of phenylpropanoid monomers and is a model organism for studying their uptake and breakdown. R. palustris encodes a tripartite ATP-independent periplasmic (TRAP) transporter (TarPQM) linked to genes encoding phenylpropanoid-degrading enzymes. The periplasmic solute-binding protein component of this transporter, TarP, has previously been shown to bind aromatic substrates. Here, we determine the high-resolution crystal structure of TarP from R. palustris as well as the structures of homologous proteins from the salt marsh bacterium Sagittula stellata and the halophile Chromohalobacter salexigens, which also grow on lignin-derived aromatics. In combination with tryptophan fluorescence ligand-binding assays, our ligand-bound co-crystal structures reveal the molecular basis for highaffinity recognition of phenylpropanoids by these TRAP transporters, which have potential for improving uptake of these compounds for biotechnological transformations of lignin.

The Biocatalytic Potential of Aromatic Ammonia–Lyase from Loktanella atrilutea

“…TRAP periplasmic solute binding proteins are known to be widespread in many bacteria and archaea [21] . TRAPs, such as RPA1782 from R. palustris were shown to possess nanomolar range affinity to lignin‐derived cinnamates, such as coumarate, caffeate and ferulate, [22] suggesting a role in scavenging very low environmental concentrations of these substituted cinnamic acids [23] . Among the closest homologues of La AAL (Table S6), without data for the genomic context of metagenome–derived AL‐11, only the gene encoding AAL from Thetidibacter halocola (with 85 % sequence identity) shows identical genome positioning.…”

Structure, substrate selectivity determinants and membrane interactions of a Glutamate-specific TAXI TRAP binding protein fromVibrio cholerae

“…The vast majority of our understanding of TRAP transporter structure and function comes from the characterization of DctP-type TRAP transporters 4,[7][8][9][10][11][12][13][14][15][16][17][18][19][20] , most prominently, a sialic acid-specific member from Haemophilus influenzae, SiaPQM (HiSiaP is the SBP and HiSiaQM is the fused membrane component) 3,[20][21][22][23][24][25][26] . Work from multiple labs on a variety of TRAP SBPs has revealed that, like SBPs from ATP-binding cassette (ABC) transporters, they utilize a venus flytrap type mechanism, in which the binding of ligand to the open apo state triggers closure of the two α/β globular domains around the substrate 27 .…”