Biology subjects

Jimenez-Zurdo, J. I.

Publications and source records attributed to Jimenez-Zurdo, J. I..

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

RNase III influences microaerobic symbiotic pathways and RNA regulation in Sinorhizobium meliloti

Bacterial ribonucleases (RNases) are central components of post-transcriptional networks underlying environmental adaptation. However, their contribution to the ecological specialization of bacteria with complex lifestyles, such as nitrogen-fixing legume symbionts, remains poorly understood. Here, we investigated the role of the double-stranded RNase III ortholog (SmRNase III) in Sinorhizobium meliloti, the symbiotic partner of alfalfa (Medicago sativa L.). Loss of SmRNase III function affected the expression of nearly 30% of protein-coding genes and 12% of annotated non-coding RNAs (sRNAs). Remarkably, more than 70% of these changes occurred under the microaerobic conditions typical of symbiotic root nodules. Many SmRNase III-dependent transcripts encode pathways supporting microaerobic metabolism and nitrogen fixation in endosymbiotic bacteroids. Analysis of sequencing read coverage revealed putative consensus cleavage signatures biased toward mRNA 5' untranslated regions, suggesting preferential processing at these sites. Altered expression of sRNAs and/or their predicted mRNA targets further supports a role for SmRNase III in sRNA-mediated silencing. Consistently, in vivo and in vitro assays demonstrated that SmRNase III is required for the repression of nifK (encoding the {beta}-subunit of the nitrogenase MoFe protein) and dctA (encoding a major dicarboxylate transporter) by the antisense sRNA asNifK1 and the trans-sRNA AbcR1, respectively. Our findings reveal a major impact of SmRNase III on shaping the symbiotic transcriptome of S. meliloti and provide a foundation for deeper investigation into the mechanisms and regulatory roles of RNase III activity in rhizobia.

microbiology↗

bioRxiv2025

A single small RNA shapes multiple symbiotic traits in rhizobia

Bacterial small non-coding RNAs (sRNAs) remain understudied in the ecologically crucial nitrogen (N2)-fixing root-nodule Rhizobium-legume symbiosis. The only known rhizobial RNA regulator with broad symbiotic influence is the N-responsive trans-acting sRNA NfeR1, identified in the alfalfa symbiont Sinorhizobium meliloti. To pinpoint NfeR1 function, we profiled its RNA targets using MS2 affinity purification coupled with RNA sequencing (MAPS) in N stressed bacteria, a condition that drives nodulation. NfeR1 targets distinct regions of numerous mRNAs and sRNAs via three redundant anti-Shine-Dalgarno motifs, with silencing as major regulatory outcome. Target mRNAs span pathways differentially regulated throughout symbiosis, including N metabolism, motility, stress adaptation, and cell cycle control. Notably, NfeR1 modulates cell morphology and DNA replication by pervasive regulation of cell cycle mRNAs. It also silences gdhA, repressing glutamine dehydrogenase-dependent N assimilation and enhancing nodulation gene expression, further fine-tuned by a novel RNA feedback loop between NfeR1 and the dual-function sRNA SmelC549. Our findings position NfeR1 as a central hub within a structurally and functionally complex RNA network that coordinates N signaling and symbiotic performance in S. meliloti.

microbiology↗