Biology subjects

Koprivova, A.

Publications and source records attributed to Koprivova, A..

10 recordsLinked to original sources

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

Loss of tRNA uridine thiolation affects mRNA translation, protein production, and sulfur-compound metabolism in Arabidopsis

The uridine at position 34 of tRNA anticodon loops is always modified at variable levels depending on environmental conditions, but a function for this highly conserved modification has not been firmly established. Using Arabidopsis thaliana, we show that the thiolation of U34 is a prerequisite for the subsequent modifications at position 32 and 37 of the tRNALys(UUU) anticodon loop, revealing a novel modification network. Surprisingly, the level of tRNALys(UUU) is strongly increased rather than reduced in the ctu1 or ctu2 mutant backgrounds that prevent these modifications. This suggests the existence of a regulatory feedback loop that drives the transcription of this specific tRNA gene family. Furthermore, we observed that the ability of the ribosome to decode AAA, GAA and CAA codons is impaired when the thiol group is lost, leading to a reduction in protein production, especially for genes enriched in these codons. Finally, we show that loss of tRNA thiolation results in variations in levels of many proteins involved in sulfur-compound metabolism and several sulfur-containing metabolites, suggesting that the level of tRNA thiolation may act as a sensor that regulates these processes.

molecular biology↗

bioRxiv2025

Clade I TGA transcription factors are negative regulators of sulfate uptake and metabolism

Increasing crop nutrient use efficiency can have dual impact; it can significantly reduce costs for fertilizers and mitigate global environmental repercussions caused by nutrient leakage. Understanding nutrient crosstalk in light of global environmental changes is crucial for improving nutrient use efficiency and food security. Here we show that provision of nitrate, but not ammonium, induces sulfate uptake and assimilation. We reveal that TGA1 and TGA4 are negative regulators of sulfate uptake, while other TGAs and the nitrate receptors NRT1.1 and NLP7 are not involved in this regulation. Our results show that TGA1 and TGA4 negatively regulate a larger set of genes involved in S signaling and metabolism, not only under nitrate provision, but also under S-deficiency. Under long-term S-deficiency, tga1 tga4 mutant had increased Cys levels in the shoots and showed better fitness. Additionally, TGA1 and TGA4 play a negative role in pathogen-induced indolic GSLs synthesis under sulfate deficiency. Similarly, clade I TGA TFs negatively regulate camalexin accumulation under pathogenic bacteria infection. Together, our findings suggest that TGA1 and TGA4 play an important role in the crosstalk of nitrate signaling with sulfate metabolism, and affect the function of S-metabolites in the interaction with pathogenic bacteria.

plant biology↗

bioRxiv2025

Multilevel analysis of response to plant growth promoting and pathogenic bacteria in Arabidopsis roots and the role of CYP71A27 in this response

Understanding how plants distinguish between commensal and pathogenic microorganisms is one of the major challenges in the plant microbe interaction research. We previously identified a gene encoding CYP71A27 connected to camalexin, which is necessary for a plant growth promoting (PGP) activity of a number of bacterial strains. To dissect its function, we compared multilevel responses in roots of wild type Arabidopsis and the cyp71A27 mutant to two bacterial strains, a PGP Pseudomonas fluorescens CH267 and a pathogen Burkholderia glumeae PG1. We show that incubation with these bacteria leads to significant and distinct transcriptional reprogramming. This is accompanied by a proteome remodelling in both shoots and roots and profound changes in accumulation of many metabolites, primarily sugars, amino acids, and TCA cycle intermediates, but also by alterations in the ionome. We then analysed the mutant cyp71a27 and identified number of genes and proteins differently regulated, particularly after interaction with the PGP strain, but only a very mild impact of the mutation on root metabolites and exudates. We analysed a variety of mutants in genes differentially regulated by Pseudomonas sp. CH267 in cyp71a27 and revealed that their response to this PGP bacterial strain is similar to cyp71a27. Thus, it seems that CYP71A27 is a non-canonical P-450 without a metabolic function but active in signalling pointing to a regulatory role of the CYP71A27 gene, particularly in interaction with a plant growth promoting bacteria.

plant biology↗

bioRxiv2025

Cysteine signaling in plant pathogen response

The amino acid cysteine is the precursor for a wide range of sulfur-containing functional molecules in plants, including enzyme cofactors and defense compounds. Due to its redox active thiol group cysteine is highly reactive. Synthesis and degradation pathways are present in several subcellular compartments to adjust the intracellular cysteine concentration. However, stress conditions can lead to a transient increase in local cysteine levels. Here we investigate links between cysteine homeostasis and metabolic signaling in Arabidopsis thaliana. The systemic proteome response to cysteine feeding strongly suggests that Arabidopsis seedlings interpret accumulation of cysteine above a certain threshold as a signal for a biotic threat. Cysteine supplementation of Arabidopsis plants via the roots increases their resistance to the hemibiotrophic bacterium Pseudomonas syringae confirming the protective function of the cysteine induced defense pathways. Analysis of mutant plants reveals that the balance of cysteine synthesis between the cytosol and organelles is crucial during Arabidopsis immune response to Pseudomonas syringae. The induction profile of pathogen responsive proteins by cysteine provides insight into potential modes of action. Our results highlight the role of cysteine as a metabolic signal in the plant immune response and add evidence to the emerging concept of intracellular organelles as important players in plant stress signaling.

plant biology↗

bioRxiv2022

Modulation of Arabidopsis growth by volatile organic compounds from a root-derived bacterial community

Plant roots are surrounded by fluctuating biotic and abiotic factors. The living component - the microbiota - is actively shaped by the plant and plays an important role in overall plant health. While it has been shown that specialized metabolites exuded from the plant are involved in shaping host interactions with the microbiota, it is unclear how underground volatile organic compounds (VOCs) influence this communication. This is especially true for root-associated bacteria which are known to release VOCs that can influence plant growth. Using a simplified synthetic bacterial community (SynCom) representing the phylogenetic diversity of bacteria in the root microbiome, we set out to characterize plant growth and defense metabolites when subjected to bacterial VOCs (bVOCs). Moreover, by profiling the SynCom community composition after co-cultivation with the plant, we explored how members of the community influenced each other in our growth setup. Our findings reveal that plant growth promotion can occur via VOCs from a bacterial SynCom, but that the plant response differs for individual community members. In addition, we find that bVOCs are able to repress chemical defense responses in the plant, possibly to facilitate colonization. By removing key species from the SynCom, we find that complex bacteria-bacteria interactions are likely to underlie this phenomenon, and that bVOC-induced modulation of plant responses in the rhizosphere may be an emergent property of bacterial communities rather than depending on individual species.

plant biology↗

bioRxiv2022

Nitrogen and phosphorus deficiencies alter primary and secondary metabolites of soybean roots

Nitrogen (N) and phosphorus (P) are two essential plant macronutrients that can limit plant growth by different mechanisms. We aimed to shed light on how soybean respond to low nitrogen (LN), low phosphorus (LP) and their combined deficiency (LNP). Generally, these conditions triggered changes in gene expression of the same processes, including cell wall organization, defense response, response to oxidative stress, and photosynthesis, however, response was different in each condition. A typical primary response to LN and LP was detected also in soybean, i.e., the enhanced uptake of N and P, respectively, by upregulation of genes for the corresponding transporters. The regulation of genes involved in cell wall organization showed that in LP roots tended to produce more casparian strip, in LN more secondary wall biosynthesis occurred, and in LNP reduction in expression of genes involved in secondary wall production accompanied by cell wall loosening was observed. Flavonoid biosynthesis also showed distinct pattern of regulation in different conditions: more anthocyanin production in LP, and more isoflavonoid production in LN and LNP, which we confirmed also on the metabolite level. Interestingly, in soybean the nutrient deficiencies reduced defense response by lowering expression of genes involved in defense response, suggesting a role of N and P nutrition in plant disease resistance. In conclusion, we provide detailed information on how LN, LP, and LNP affect different processes in soybean roots on the molecular and physiological levels.

plant biology↗

bioRxiv2021

Glutathione contributes to plant defense against parasitic cyst nematodes

Cyst nematodes (CNs) are an important group of root-infecting sedentary endoparasites that severely damage many crop plants worldwide. An infective CN juvenile enters the hosts roots and migrates towards the vascular cylinder, where it induces the formation of syncytial feeding cells, which nourish the CN throughout its parasitic stages. Here, we examined the role of glutathione (L-{gamma}-glutamyl-L-cysteinylglycine, GSH) in Arabidopsis thaliana upon infection with the CN Heterodera schachtii. Arabidopsis lines with mutations pad2, cad2, or zir1 in the glutamate-cysteine ligase (GSH1) gene, which encodes the first enzyme in the glutathione biosynthetic pathway, displayed enhanced CN susceptibility, but susceptibility was reduced for rax1, another GSH1 allele. Biochemical analysis revealed differentially altered thiol levels in these mutants that was independent of nematode infection. All GSH-deficient mutants exhibited impaired activation of defense marker genes as well as genes for biosynthesis of the antimicrobial compound camalexin early in infection. Further analysis revealed a link between glutathione-mediated plant susceptibility to CN infection and the production of camalexin upon nematode infection. These results suggest that GSH levels affects plant susceptibility to CN by fine-tuning the balance between the cellular redox environment and the production of compounds related to defense against infection.

plant biology↗

bioRxiv2021

Rhizobiales commensal bacteria promote Arabidopsis thaliana root growth via host sulfated peptide pathway

Root-associated commensal bacteria that belong to the order Rhizobiales, which also contains symbiotic and pathogenic bacteria, promote primary root growth of Arabidopsis thaliana. However, the molecular mechanism underlying this root growth promotion (RGP) activity remained unclear. Here, we conducted a transcriptomic analysis of A. thaliana roots inoculated with root-associated commensal bacteria of Rhizobiales and sister lineages and revealed common and strain/lineage-specific transcriptional response, possibly mediated by WRKY and ANAC family of transcription factors. We showed that the observed common response was also partly triggered by a wide range of non-pathogenic bacteria, fungi, and a multikingdom synthetic community (SynCom). This response was characterized by a down-regulation of genes related to intracellular redox regulation, suggesting distinctive redox status between pathogenic and non-pathogenic interactions. By integrating with developmental and cell biological experiments, we identified a crucial role of TYROSYLPROTEIN SULFOTRANSFERASE (TPST) in Rhizobiales RGP. Conversely, none of the known TPST-dependent sulfated peptide pathways appeared to be required for this activity, suggesting an unidentified component in the protein sulfation pathway targeted by Rhizobiales RGP. Finally, we show that TPST is needed for RGP exerted by Rhizobiales but not Pseudomonadales isolates, delineating lineage-specific mechanisms to manipulate host root development.

plant biology↗

bioRxiv2020

Shoot-root interaction in control of camalexin exudation in Arabidopsis

Plants exude secondary metabolites from the roots to shape the composition and function of their microbiome. Many of these compounds are known for their anti-microbial activity and are part of the plant immunity, such as the indole-derived phytoalexin camalexin. Here we studied the dynamics of camalexin synthesis and exudation upon induction of Arabidopsis thaliana with a plant growth promotion bacteria Pseudomonas sp. CH267 or a bacterial pathogen Burkholderia glumae PG1. We show that while the camalexin accumulation and exudation is more rapidly but transiently induced upon interaction with the growth promoting strain, the pathogen induces a higher and more stable camalexin levels. The concentration of camalexin in shoots, roots and exudates is well correlated, triggering a question on the origin of the exuded camalexin. By combination of experiments with cut shoots and roots and grafting of wild type plant with mutants in camalexin synthesis we showed that while camalexin can be produced and released by both organs, in intact plant the exuded camalexin originates in the shoots. We show that camalexin synthesis in response to B. glumae PG1 is dependent on cooperation of four CYP71 genes and a loss of function of any of them reduces camalexin synthesis. In conclusion, camalexin synthesis seems to be controlled on a whole plant level and coordinated between shoots and roots.

plant biology↗