Biology subjects

Ayala-Garcia, P.

Publications and source records attributed to Ayala-Garcia, P..

3 recordsLinked to original sources

bioRxiv2026

Strain-specific early, host-shaped late: the rhizobial transcriptome across symbiosis

The two ends of the rhizobial symbiotic trajectory have only been described separately. Here we report strand-specific RNA-seq of bacteroids of two strains, each against free-living cells of the same strain and alongside its flavonoid response: Sinorhizobium fredii HH103 from soybean (Glycine max), Glycyrrhiza uralensis and Lotus burttii, and Rhizobium tropici CIAT 899 from common bean (Phaseolus vulgaris) and L. burttii, the one legume both strains nodulate. Between 1877 and 2284 genes respond per strain-host combination, and most of that response is host-common: 1171 of 2855 genes respond in all three hosts of HH103 and 1664 of 2703 in both hosts of CIAT 899. What distinguishes the remainder is host identity rather than nodule type, since HH103 bacteroids from the indeterminate-nodule G. uralensis resemble those from L. burttii more than either resembles those from soybean, its natural host. Nitrogen fixation and the stress response are over-represented in every bacteroid and motility is almost entirely repressed, yet the shared core of CIAT 899 is the only repression-dominated gene set here and its translational machinery is induced where that of HH103 is repressed. Dismantling of the early programme is selective: in HH103 the type III apparatus is switched off, the Nod factor operons are attenuated but retained, and the fixABCX operon under a nod box is amplified, so a nod box does not by itself mark a gene as early. CIAT 899, lacking a type III system and placing no nif/fix gene under flavonoid control, keeps that block flat until the nodule, then engages 26 of its 30 genes. Across genera, 26% of responding orthologue pairs are shared in the bacteroid against 5% in the flavonoid response: each bacterium negotiates entry in a dialect of its own and converges on a shared end state whose amplitude, rather than content, the host modulates.

microbiology↗

bioRxiv2026

EveD, a vesicle-associated rhizobial candidate effector shaping nodulation competitiveness and host genotype responses

Bacterial extracellular vesicles (EVs) are an ancestral secretion route that delivers cargoes to host cells. Although rhizobial EVs transport Nod factors and other bacterial components, their role in protein delivery during symbiosis remains unexplored. Here we characterise EveD, a large soluble repeat-containing protein of Sinorhizobium fredii HH103. Its export is independent of the type III secretion system, and EveD is recovered only in EV-containing fractions. eveD expression is not induced by genistein or soybean seed exudates and does not follow the canonical NodD1-TtsI pathway, but partially depends on the symbiotic regulator SyrM. When expressed in plant cells, EveD localises mainly to the cytoplasm, associates with endoplasmic reticulum-like structures and occasionally occurs in the nucleus. The eveD mutant shows increased nodule occupancy relative to the wild type in Glycine max cv. Williams 82. EveD modulates early responses in wild Glycine soja accessions in a genotype-dependent manner, constraining pseudonodule organogenesis in JL2 while promoting it in CH2. These findings identify EveD as an EV-associated rhizobial protein contributing to bacterial competitiveness and genotype-dependent symbiotic responses, and highlight EVs as an additional route for protein export during legume symbiosis.

microbiology↗

bioRxiv2026

A rhizobial extracellular vesicle-conveyed auxin transporter mediates phytohormone mobilization and optimizes rhizobium-legume symbiosis

Bacterial extracellular vesicles (bEVs) are emerging as key players in interkingdom communication, yet their role in delivering functional proteins to host cells during symbiosis remains unexplored. This study shows that Sinorhizobium fredii HH103 packages a PIN-like auxin transporter, AuxT, into bEVs that traffic within the peribacteroid space of soybean nodules. AuxT is chromosomally encoded and constitutively expressed, genetically uncoupled from the flavonoid-inducible auxin biosynthesis machinery located on the symbiotic plasmid. Structural prediction reveals that AuxT adopts an eight-transmembrane-helix architecture with striking homology to plant PIN auxin exporters, despite negligible sequence identity. Molecular docking demonstrates that AuxT binds indole-3-acetic acid within a central cavity, with dimerization inducing ligand-specific conformational changes consistent with transport activity. The auxT mutant exhibits significant symbiotic defects including reduced shoot biomass, nodule number, and nodule mass that are fully restored by complementation. Critically, AuxT-enriched bEVs contain elevated auxin levels, and nodules colonized by the complemented strain accumulate more auxin specifically within the bEVs peribacteroid space, while bacteroids themselves show no auxin retention. We postulate that bEV-associated AuxT mediates localized auxin export into the symbiosome, modulating the host hormonal environment to optimize symbiotic development. This work reveals a previously unrecognized mechanism of interdomain hormonal modulation, where a bacterium uses a structurally convergent transporter and vesicular delivery to actively shape host physiology and to improve the symbiotic performance.

microbiology↗