bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.64898/2026.09.12.750751

The plant specific Histone Lysine Demethylase MtPKDM9B mediates the root nodule symbiosis by controlling H3K27me3 levels and expression of symbiotic genes

Ferrari, M.·Yacullo, M.·Traubenik, S.·Ibarra, E.·Blanco, F. A.·Reynoso, M.·Zanetti, M. E.
View original source ↗Export metadata ↓

Abstract

Under nitrogen limiting conditions, legume plants interact with nitrogen fixing bacteria known as rhizobia, resulting in the formation of a new organ, the nodule. This process is accompanied by dramatic changes in gene expression, which operate at different levels. A previous study revealed that histone methylation is differentially modulated during nodulation. However, the histone methyl transferases and demethylases involved in this modulation have not been characterized. In this study we report the identification of the Medicago truncatula putative histone lysine demethylase MtPKDM9B, which is subject to alternative splicing (AS), and the differential modulation of AS variants at translational level during nodule symbiosis. Knockdown of MtPKDM9B impaired infection by rhizobia, nodule development, bacterial viability and the expression of the leghemoglobin coding gene MtLHB1. MtPKDM9B is the putative ortholog of Arabidopsis EARLY FLOWERING 6 (ELF6/AtPKDM9B) gene involved in the removal of the repressive mark H2K27me3. A combination of ChIP-seq and RNA-seq experiments revealed that MtPKDM9B is required for demethylation of H3K27me3 in regions nearby or contained within gene bodies of symbiotic genes and the upregulation of the cognate mRNAs in response to rhizobia, including those encoding the putative ubiquitin ligase MtPUB2, the MYB transcription factor MtMYB040 and the auxin conjugating enzyme MtGH3 (Gretchen Hagen 3). Our findings illustrate how AS and translational regulation of this plant specific histone lysine demethylase contributes to the removal of the repressive mark H3K27me3, promoting transcriptional activation of symbiotic genes required for the formation of functional nitrogen fixing nodules.

Explore related subjects

plant biologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Ferrari, M., Yacullo, M., Traubenik, S., Ibarra, E., Blanco, F. A., Reynoso, M., Zanetti, M. E.. 2026-09-17. The plant specific Histone Lysine Demethylase MtPKDM9B mediates the root nodule symbiosis by controlling H3K27me3 levels and expression of symbiotic genes. https://doi.org/10.64898/2026.09.12.750751

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Loss of starch synthase IIa alleviates the negative impact of high temperature on rice starch during grain filling

High temperatures during grain filling stage are becoming increasingly frequent, compromising both grain and eating quality and thereby driving demand for heat-resilient cultivars. Such conditions are known to reduce the expression of granule-bound starch synthase I (GBSSI) and starch branching enzyme IIb (BEIIb), which are involved in starch biosynthesis, resulting in a decrease in amylose content and an increase in long-chain amylopectin. Thus, the present study introduced functional mutation in starch synthase IIa (SSIIa) that increases the proportion of short amylopectin chains to genetically compensate for the high-temperature-induced increase in amylopectin long chain. Rice lines carrying the ss2a mutation were grown at two locations with cooler (Akita) and warmer (Okayama) temperatures. Their grain traits, starch structure, and eating quality were compared. The ss2a mutant lines showed an increased proportion of short amylopectin chains as well as an increased apparent amylose content. Furthermore, these alterations in starch structure varied with the grain-filling temperature of the cultivation sites, ultimately affected eating quality. These results suggest that enriching short amylopectin chain via the ss2a mutation can counteract the increase in long amylopectin chain caused by high temperatures during grain filling, thereby maintaining a desirable starch structure and eating quality.

plant biology↗
bioRxiv2026

Analysis of SpCas9 on- and off-target effects in high efficiency multiplex editing in Arabidopsis

RNA-guided nucleases (RGNs), such as Cas9 from Streptococcus pyogenes (SpCas9), are widely used for plant genome editing. Previous surveys for off-targeting, the modification of unintended targets with similarity to the intended target, indicate high specificity of SpCas9 in plant cells. However, off-targeting has not been assessed for efficiency-optimized editing systems combined with extensive multiplexing, which might increase the likelihood of cleavage at unintended sites. We therefore analyzed Arabidopsis thaliana lines that had been extensively mutagenized using zCas9i and up to 29 gRNAs addressing >45 target sites over several rounds of editing. Genomes were sequenced by short- and long-read technologies, and genome-wide variants were catalogued. Our pipeline for variant calling reliably detected RGN-induced mutations at on-targets. When excluding these on-target modifications, variants were detected in edited lines at frequencies similar to those previously reported for spontaneous mutations. In further analyses, we did not find any evidence for an origin of these variants from RGN activity. Our data are thus consistent with high specificity of SpCas9. In contrast, we detected genomic reorganization events upon editing at two complex loci, RPP1 and RPP7, encompassing multiple homologous genes, and also identified an allele by WGS that had escaped detection by amplicon sequencing. We conclude that, while off-targets may efficiently be avoided by selection of specific gRNAs, on-target modifications may be more extensive than intended, especially at complex loci and/or during multiplexing.

plant biology↗
bioRxiv2026

A cellulose synthase interactome uncovers BAG proteins as regulators of cellulose synthase homeostasis

Cellulose synthase complexes build the load-bearing cellulose microfibrils of plant cell walls, yet how the abundance of their catalytic CELLULOSE SYNTHASE A (CESA) subunits is maintained remains unclear. Here, we used multi-bait TurboID proximity labelling with ten cellulose-synthesis-associated baits and six subcellular controls to define a high-confidence cellulose synthase neighbourhood. Stringent spatial and recurrence-based filtering yielded a core network of 119 interactions among 44 proteins and identified three members of the conserved Bcl-2-associated athanogene (BAG) family as previously unrecognised regulators of cellulose synthase homeostasis. BAG1-3 associated with primary-wall CESAs in reciprocal proximity-labelling experiments. Arabidopsis bag mutants showed reduced cellulose accumulation, hypersensitivity to cellulose-synthesis inhibitors, and markedly decreased CESA protein abundance without corresponding changes in CESA transcript levels. Loss of BAG function also increased the accumulation of CESA6 in vacuolar compartments. These findings identify BAG proteins as previously unrecognised regulators of cellulose synthase homeostasis and link a conserved proteostasis-associated protein family to plant cell wall biosynthesis. More broadly, the study establishes multi-bait proximity labelling, combined with cell location-specific controls, as a strategy for resolving dynamic protein networks whose components traffic through multiple subcellular compartments.

plant biology↗