Biology subjects

Armbruster, L.

Publications and source records attributed to Armbruster, L..

6 recordsLinked to original sources

bioRxiv2026

The transcription factor SiROCX controls a monocot-specific CAZyme program for host cell wall remodeling during symbiotic root colonization

Intracellular accommodation of beneficial fungi requires controlled remodeling of host cell walls while avoiding activation of plant immune responses. During colonization of monocot roots, the endophytic fungus Serendipita indica induces a suite of carbohydrate-active enzymes (CAZymes) targeting xylan and cellulose. Weighted gene co-expression network analysis identified the basidiomycete-specific transcription factor SiROCX as a key regulator of this monocot-adapted program. DNA affinity purification sequencing (DAP-seq) defined the SiROCX binding motif and revealed a CAZyme-enriched target regulon. Inducible SiROCX overexpression selectively activated motif-containing CAZyme genes and markedly enhanced xylanase and cellulase activities on xylan and native barley root cell walls. Premature activation of this program triggered expression of a plant immune marker despite comparable fungal biomass, indicating that precise temporal control of CAZyme deployment is required to maintain symbiotic compatibility. Together, these findings identify SiROCX as a central regulator of a monocot-adapted cell wall-degrading secretome and reveal a basidiomycete-specific regulatory module that coordinates host cell wall remodeling with immune-compatible symbiotic colonization. SignificanceBeneficial fungi colonize living plant cells, requiring host cell wall remodeling while avoiding immune activation. However, the key transcriptional regulators coordinating this process in basidiomycetes during symbiotic root colonization remain unknown. We identify SiROCX, a conserved basidiomycete-specific transcription factor, as a master activator of a monocot-adapted xylan/cellulose degradation program in the root endophyte Serendipita indica. By integrating in planta co-expression networks, DAP-seq, secretome proteomics, and enzymatic assays, we show that SiROCX overexpression markedly enhances secretion and activity of xylan- and cellulose-degrading enzymes, boosting sugar release from monocot cell walls. These findings reveal a basidiomycete-specific regulatory module for immune-compatible host cell wall remodeling, providing a framework to engineer fungal CAZyme programs for crop symbiosis and biomass conversion.

microbiology↗

bioRxiv2025

A fungal root endophyte functionally complements host immunity and mitigates natural immune variation in Arabidopsis

Beneficial root-associated microbes can enhance plant resilience by complementing aspects of host immunity. The fungal root endophyte Serendipita indica (Si) is known to promote plant growth and confer broad stress tolerance. To assess how natural host genetic variation influences Si-mediated protection, we screened 47 Arabidopsis thaliana accessions for susceptibility to the fungal pathogen Bipolaris sorokiniana (Bs) with and without Si colonization. All accessions benefited from Si, indicating that endophyte-mediated disease mitigation occurs broadly across diverse host genotypes. A focused comparison of two genetically and geographically proximate Swedish accessions, T510 and T530, which displayed the most divergent protection scores, revealed substantial differences in Bs susceptibility. Transcriptome profiling under bi- and tripartite colonization showed conserved defense responses in both accessions. Bs infection downregulated growth- and development-related genes, consistent with a growth-immunity trade-off, with T530 exhibiting higher Bs colonization and a stronger transcriptional response than T510. Co-colonization with Si effectively suppressed pathogen growth and disease symptoms in both accessions. Comparative genomic and transcriptomic analyses identified four immune receptor genes, including the TIR-NLR ISI, present in T510 but absent in T530. An isi T-DNA insertion mutant phenocopied the heightened Bs susceptibility of T530, confirming that ISI contributes to root immunity, while Si-mediated protection remained intact despite increased pathogen susceptibility. Together, these findings demonstrate that fungal endophytes can mitigate the functional consequences of natural immune variation and enhance the resilience of genetically diverse plant populations. HighlightsO_LIS. indica confers broad protection against B. sorokiniana largely independent of host genotype or pathogen susceptibility. C_LIO_LIThe TIR-NLR immune receptor ISI contributes to root immunity but is not essential for S. indica-mediated protection. C_LIO_LIBeneficial endophytes can mitigate natural immune variation effects and support overall plant health. C_LI

ecology↗

bioRxiv2025

Host-adapted enzymatic deconstruction of acetylated xylan enables mutualistic colonization of monocot roots

Intracellular accommodation of mutualistic fungi in plant roots depends on selective remodeling of host cell walls while minimizing activation of plant immune responses. In this study, we identify a host-adapted enzymatic module in the root endophyte Serendipita indica that targets acetylated xylan, a major structural component of monocot cell walls. The glycoside hydrolase SiGH11 cleaves the xylan backbone and releases O-acetylated oligosaccharides, which are subsequently deacetylated by the XynE-like esterase SiAXE. These enzymes are co-expressed within a monocot-specific transcriptional program that is enriched in carbohydrate-active enzymes and sugar transporters. Their combined activity enhances enzymatic degradation and facilitates downstream hydrolysis by exo-xylanases, which reduces the production of apoplastic reactive oxygen species triggered by damage-associated molecular patterns. Functional analysis shows that overexpression of SiAXE promotes early root colonization, while deletion of the gene compromises fungal proliferation during later stages. These findings define a coordinated and immune-compatible strategy for host cell wall deconstruction that enables fungal adaptation and endophytic colonization of monocot roots. In BriefSerendipita indica utilizes a transcriptionally coordinated xylanase and esterase module to degrade acetylated xylan in monocot roots. This enzyme cooperation enhances substrate breakdown, suppresses immune responses, and enables endophytic colonization, illustrating how mutualistic fungi adapt saprotrophic enzymes for host-specific intracellular accommodation. HighlightsO_LIMutualistic fungal endophyte repurposes saprotrophic enzymes to enable monocot-specific intracellular root colonization C_LIO_LICoordinated xylanase and esterase activity remodels host cell walls and dampens immune responses C_LIO_LIExpression of cell wall degrading enzymes is regulated by host species and colonization stage C_LIO_LIResults reveal fungal adaptation to monocot roots along the saprotrophy to symbiosis transition C_LI

plant biology↗

bioRxiv2023

Time-resolved transcriptomics reveal a mechanism of host niche defense: beneficial root endophytes deploy a host-protective antimicrobial GH18-CBM5 chitinase

Associations between plants and beneficial root-endophytic fungi enhance plant performance by improving nutrient uptake, abiotic stress tolerance and disease resistance. To successfully colonize different host plants and defend their host niche against competing microbes, but also to cooperate with beneficial bacterial members of the microbiota, root endophytes such as Sebacinales secrete a multitude of tightly regulated effector-proteins and carbohydrate-active enzymes. However, the functions, specificity, and regulation of these proteins remain poorly understood. In this study, we employ time-resolved transcriptomics to analyse the gene expression profiles of two Sebacinales members interacting with organisms from different kingdoms of life. We identified crucial genes for plant colonization and intermicrobial competition, including a fungal GH18-CBM5 chitinase specifically upregulated in response to the phytopathogenic fungus Bipolaris sorokiniana. This chitinase protects the plant hosts against the pathogen, reducing fungal biomass and disease symptoms in barley and Arabidopsis thaliana. Our findings shed light on interaction partner specific gene expression in Sebacinales endophytes, with potential applications in enhancing plant health and resilience. Bullet pointsO_LIBoth Serendipita indica (Si) and Serendipita vermifera (Sv) show similar transcriptional responses to three host species and the phytopathogen Bipolaris sorokiniana (Bs), indicating common interaction principles between Sebacinales and plant hosts or fungi. C_LIO_LIThese shared mechanisms involve the activation of effector genes like small secreted proteins and carbohydrate-active enzymes. C_LIO_LICooperation with beneficial bacteria elicits only minimal transcriptomic alterations in Sebacinales compared to plants and Bs. C_LIO_LISebacinales respond to Bs by upregulating a specific GH18-CBM5 chitinase unique to Basidiomycota within the fungal kingdom, inhibiting Bs growth and reducing disease symptoms in Arabidopsis thaliana and barley. C_LI

microbiology↗

bioRxiv2020

Mechanisms of up-regulation of Ubiquitin-Proteasome activity in the absence of NatA dependent N-terminal acetylation

N-terminal acetylation is a prominent protein modification and inactivation of N-terminal acetyltransferases (NATs) cause protein homeostasis stress. Using multiplexed protein stability (MPS) profiling with linear ubiquitin fusions as reporters for the activity of the ubiquitin proteasome system (UPS) we observed increased UPS activity in NatA, but not NatB or NatC mutants. We find several mechanisms contributing to this behavior. First, NatA-mediated acetylation of the N-terminal ubiquitin independent degron regulates the abundance of Rpn4, the master regulator of the expression of proteasomal genes. Second, the abundance of several E3 ligases involved in degradation of UFD substrates is increased in cells lacking NatA. Finally, we identify the E3 ligase Tom1 as a novel chain elongating enzyme (E4) involved in the degradation of linear ubiquitin fusions via the formation of branched K11 and K29 ubiquitin chains, independently of the known E4 ligases involved in UFD, leading to enhanced ubiquitination of the UFD substrates.

cell biology↗

bioRxiv2019

The proteomic inventory reveals the chloroplast ribosome as nexus within a diverse protein network

Chloroplast gene expression is tightly regulated and majorly controlled on the level of protein synthesis. Fine-tuning of translation is vital for plant development, acclimation to environmental challenges and for the assembly of major protein complexes such as the photosynthesis machinery. However, many regulatory mediators and the interaction network of chloroplast ribosomes are not known to date. We report here on a deep proteomic analysis of the plastidic ribosome interaction network in Chlamydomonas reinhardtii cells. Affinity-purification of ribosomes was achieved via endogenous affinity tagging of the chloroplast-encoded protein Rpl5, yielding a specific enrichment of >650 chloroplast-localized proteins. The ribosome interaction network was validated for several proteins and provides a new source of mainly conserved factors directly linking translation with central processes such as protein folding, photosystem biogenesis, redox control, RNA maturation, energy and metabolite homeostasis. Our approach provided the first evidence for the existence of a plastidic co-translational acting N-acetyltransferase (cpNAT1). Expression of tagged cpNAT1 confirmed its ribosome-association, and we demonstrated the ability of cpNAT1 to acetylate substrate proteins at their N-terminus. Our dataset establishes that the chloroplast protein synthesis machinery acts as nexus in a highly choreographed, spatially interconnected protein network and underscores its wide-ranging regulatory potential during gene expression. ONE-SENTENCE SUMMARYAffinity purification of Chlamydomonas reinhardtii chloroplast ribosomes and subsequent proteomic analysis revealed a broad spectrum of interactors ranging from global translation control to specific pathways.

biochemistry↗