Structural basis for high specificity of octopine binding in the plant pathogen Agrobacterium tumefaciens

Abstract

Agrobacterium pathogens of octopine- and nopaline-types force host plants to produce either octopine or nopaline compounds, which they use as nutrients. Two Agrobacterium ABC-transporters and their cognate periplasmic binding proteins (PBPs) OccJ and NocT import octopine and nopaline/octopine, respectively. Here, we show that both octopine transport and degradation confer a selective advantage to octopine-type A. tumefaciens when it colonizes plants. We report the X-ray structures of the unliganded PBP OccJ and its complex with octopine as well as a structural comparison with NocT and the related PBP LAO from Salmonella enterica, which binds amino acids (lysine, arginine and ornithine). We investigated the specificity of OccJ, NocT and LAO using several ligands such as amino acids, octopine, nopaline and octopine analogues. OccJ displays a high selectivity and nanomolar range affinity for octopine. Altogether, the structural and affinity data allowed to define an octopine binding signature in PBPs and to construct a OccJ mutant impaired in octopine binding, a selective octopine-binding NocT and a non-selective octopine-binding LAO by changing one single residue in these PBPs. We proposed the PBP OccJ as a major trait in the ecological specialization of octopine-type Agrobacterium pathogens when they colonize and exploit the plant host.

The biotroph Agrobacterium tumefaciens thrives in tumors by exploiting a wide spectrum of plant host metabolites

“…When expressed into the plant cell nucleus, the T‐DNA genes divert the host hormonal and metabolic pathways to provoke the development of galls or plant tumors (Deeken et al ., ). In previous work, we paid attention to specific metabolites, the opines, that accumulate in the A. tumefaciens ‐infected plant tumors (Lang et al ., ; El Sahili et al ., ; Marty et al ., ; Tannières et al ., ; Lang et al ., ; Vigouroux et al ., ). Opines, such as agrocinopines, mannopine, nopaline, and octopine, result from the condensation of sugars and amino and organic acids (Dessaux et al ., ).…”

The interplay of protein–ligand and water‐mediated interactions shape affinity and selectivity in the LAO binding protein

“…It is common to observe homologous PBPs that bind the same molecule with different selectivity, as well as PBPs which bind several ligands in the same binding site with different affinity. For this reason, such proteins have been good models to study the structural basis that determine affinity and selectivity in proteins [6,[15][16][17][18][19][20][21][22][23][24][25]. These features have made PBPs a suitable target to develop biosensors [14,[26][27][28][29][30][31] and design new binding abilities [14,32,33].…”

Automatic annotation of protein residues in published papers

“…Slashed_pos Single residue, slashed position (Vigouroux et al, 2017), which under the original Nagel RegEx patterns would have been matched as a single residue. Further examples are given in Table 2. A further decomposition step is performed on the complex matches to extract individual residues from the parent match.…”

“…The contexts and locations across the potential size of such an automatically annotated corpus that can now be generated would enable unsupervised ontology learning, a process that is onerous when performed manually. An example of the annotations generated by pyresid appearing on the full-text article Vigouroux et al (2017) hosted on Europe PMC.…”