Fitness costs restrict niche expansion by generalist niche-constructing pathogens

Abstract

We investigated the molecular and ecological mechanisms involved in niche expansion, or generalism, versus specialization in sympatric plant pathogens. Nopaline-type and octopine-type Agrobacterium tumefaciens engineer distinct niches in their plant hosts that provide different nutrients: nopaline or octopine, respectively. Previous studies revealed that nopaline-type pathogens may expand their niche to also assimilate octopine in the presence of nopaline, but consequences of this phenomenon on pathogen dynamics in planta were not known. Here, we provided molecular insight into how the transport protein NocT can bind octopine as well as nopaline, contributing to niche expansion. We further showed that despite the ability for niche expansion, nopaline-type pathogens had no competitive advantage over octopine-type pathogens in co-infected plants. We also demonstrated that a single nucleotide polymorphism in the nocR gene was sufficient to allow octopine assimilation by nopaline-type strains even in absence of nopaline. The evolved nocR bacteria had higher fitness than their ancestor in octopine-rich transgenic plants but lower fitness in tumors induced by octopine-type pathogens. Overall, this work elucidates the specialization of A. tumefaciens to particular opine niches and explains why generalists do not always spread despite the advantage associated with broader nutritional niches.

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

“…As previously mentioned in Lang et al . 14 , Ser91 seems incompatible with a possible binding of nopaline to OccJ due to steric hindrance. The side chain of Asn202 in OccJ also does not seem in a suitable position to accommodate nopaline or octopine in the conformation observed in NocT because its C β atom is less than 2 Å from nopaline (Fig.…”

“…ITC confirmed the 1:1 binding stoichiometry. NocT also binds octopine, but displays a 1,000 fold lower affinity with a K D of 6.1 ± 0.7 µM in the same range as for nopaline ( K D of 3.7 ± 0.6 µM; 6 , 14 ). Because LAO’s two tryptophan residues lie far from the ligand binding site, no fluorescence intensity change was detected.…”

“…( b ) Comparison between the open unliganded (cyan) and the closed liganded (deep blue) forms of OccJ. A curved arrow indicates the movement of lobe 2 upon ligand binding ( c ) octopine bound to the ligand binding site of OccJ in its annealing Fo-Fc omit map contoured at 4 σ. Hydrogen bonds between octopine and OccJ are shown as dashed lines in black (distances below 3.2 Å) and in magenta (distances between 3.2 and 3.4 Å) ( d ) octopine bound to the ligand binding site in NocT-octopine structure 14 ( e ) closed-up view around the pyruvate moiety of octopine from the superposition of OccJ-octopine and NocT-octopine complexes. Double arrows indicate distances.…”

“…3c ), and is surrounded by 18 residues defining the ligand binding site of OccJ (Table 3 ). Both structures of OccJ and NocT in complex with octopine (PDB code 5ITP for NocT-octopine, 14 ) superimpose with an average RMSD of 1.7 Å over all Cα atoms. They share a very similar binding site around the arginine moiety of octopine (Table 3 and Fig.…”

“…Interestingly, nopaline-type strains are able to assimilate octopine, once nopaline induces the nopaline assimilative pathway 6 . We have recently shown that both octopine and nopaline can bind NocT with similar affinity in the micromolar range and we have characterized their binding mode to NocT at atomic level 14 . OccJ shares 47% sequence identity with NocT and belongs to cluster F within the PBP structural classification 15 .…”