Biology subjects

Alon, M.

Publications and source records attributed to Alon, M..

4 recordsLinked to original sources

bioRxiv2026

Conserved inhibitory mechanisms of root-associated bacteria towardsArabidopsis thaliana and Chlamydomonas reinhardtii

Soil bacteria colonize plants without causing visible disease, yet many suppress host growth. The prevalence and evolutionary reach of this cryptic inhibition are unknown, because phenotyping hundreds of isolates in plants is prohibitively slow. Here we use the unicellular algae Chlamydomonas reinhardtii as a scalable proxy for the green lineage. We screened 148 plant-associated bacteria on Chlamydomonas lawns. Seven of eight Chlamydomonas inhibitors also inhibited the vascular model plant Arabidopsis thaliana. In one of these dual inhibitors, Burkholderia sola MF6, transposon screening and proteomics implicated type VI secretion and tight-adherence pili, and over half the non-inhibitory mutants also failed against Arabidopsis. In the algae, infection triggers rapid deflagellation, then non-lytic regulated cell death. The algal zinc/iron transporter ZIP3 promotes inhibition, whereas the cathepsin X protease CEP12 restrains it, and ZIP3 is epistatic to CEP12. Cryptic inhibition is thus ancient and widespread, and a unicellular algae uncovers it at scale.

plant biology↗

bioRxiv2026

Nodule microbiome functions shape the performance of a wild perennial legume

Nitrogen fixing legume nodules are typically viewed as the product of a bilateral mutualism between host plants and nitrogen-fixing rhizobia, yet nodules also harbor diverse non-rhizobial endophytes whose functional significance remains poorly understood, especially in wild legumes and uncultivated soil. Here, using the wild Mediterranean shrub Calicotome villosa, we performed a soil inoculation experiment to test whether plant performance is linked to the functional composition of the nodule microbiome. Soil inocula from different natural sites produced strong differences in nodulation success, plant biomass, leaf nitrogen concentration, nitrogen fixation rate, and nodule allocation under otherwise uniform conditions. Although Bradyrhizobium dominated all nodules, species composition varied among inoculation sources, and non-rhizobial endophytes reached substantial abundance in some treatments. Functional profiles of the nodule microbiome were significantly associated with plant phenotype, with the strongest coupling observed for traits related to nodule investment. Targeted and genome-wide analyses identified trait-associated genes in both symbionts and endophytes, including genes involved in nitrogen cycling, ammonium transport, denitrification, pyrimidine degradation, sulfur assimilation, and type VI secretion systems. Several of these functions were not part of the canonical symbiosis machinery, yet were strongly associated with plant nitrogen status, biomass accumulation, or nodule mass fraction. Together, our results show that legume performance is better predicted by the collective functional composition of the nodule microbiome than by the primary symbiont alone. These findings support a broader view of nodules as multipartite microbial communities.

ecology↗

bioRxiv2025

Fast and accurate taxonomic domain assignment of short metagenomic reads using BBERT

Shotgun metagenomes from complex environments such as soil uncover vast biodiversity. Yet most short reads produced by shotgun sequencing cannot be taxonomically or functionally annotated, as they lack a sufficiently comprehensive reference, obscuring the true structure and function of microbial communities. We introduce BBERT, a nucleotide large language model optimized for short reads. Testing on a large cohort of soil metagenomes, we found that BBERT identifies bacterial sequence syntax without relying on reference databases, enabling accurate assignment of taxonomic domain, coding potential, and reading frame directly from reads as short as 100 bp. BBERT is small and fast enough to analyze metagenomes using a modest GPU and can be used to convert short metagenomic reads directly to bacterial amino acid sequences for downstream applications. BBERT also improves de-novo metagenomic assembly, reducing mismatches and gaps while accelerating runtime. Using metagenomes from wild legume nodules, we demonstrate that BBERT filtering improves bin quality while significantly accelerating de-novo assembly. By providing fast, reference-free classification of short reads, BBERT unlocks large metagenomic archives for more accurate ecological and evolutionary analyses.

bioinformatics↗

bioRxiv2021

The proteasome regulator PSME4 drives immune evasion and abrogates anti-tumor immunity in NSCLC

Protein degradation by proteasomes is important for the immune response against tumors. Antigens generated by the proteasome promote immune cell infiltration into tumors and improve tumors responses to immunotherapy. For example, immunoproteasomes - a subset of proteasomes induced by inflammatory signals - may improve the response of melanomas to immune checkpoint inhibitors (ICI) by eliciting tumor inflammation. Yet, it is unclear whether and how protein degradation by proteasomes impacts cancer progression and contributes to immune evasion and resistance. Here, we profile the proteasome-cleaved peptides in lung cancers and find that PSME4 serves as a novel inhibitory regulator of the immunoproteasome, playing an anti-inflammatory role in cancer. Biochemical assays combined with scRNA-seq, immunopeptidomics and in vivo analyses demonstrate that PSME4 promotes an immunosuppressive environment around the tumor and abrogates anti-tumor immunity by inhibiting antigen presentation and attenuating tumor inflammation. Furthermore, we find that PSME4 expression is correlated with responsiveness to ICI across several cancer types. Our findings suggest that PSME4-mediated regulation of proteasome activity is a novel mechanism of immune evasion in non-small-cell lung carcinoma and may be targeted therapeutically for restoring anti-tumor immunity. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/464690v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@e87910org.highwire.dtl.DTLVardef@641843org.highwire.dtl.DTLVardef@175092corg.highwire.dtl.DTLVardef@ad34c2_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIMapping the degradation landscape in Non-Small Cell Lung Cancer (NSCLC) uncovers altered proteasome activity and composition C_LIO_LIProteasome regulator PSME4 plays an anti-inflammatory role in NSCLC by attenuating immunoproteasome activity C_LIO_LIPSME4 restricts tumor antigen presentation and cytokine secretion, defining a cold tumor environment C_LIO_LIPSME4 drives tumor immune evasion and is associated with resistance to immunotherapy C_LI

cancer biology↗