Biology subjects

Kopriva, S.

Publications and source records attributed to Kopriva, S..

31 records · Page 2Linked to original sources

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

New insights into the evolution of SPX gene family from algae to legumes; a focus on soybean

BackgroundSPX-containing proteins have been known as key players in phosphate signaling and homeostasis. In Arabidopsis and rice, functions of some SPXs have been characterized, but little is known about their function in other plants, especially in the legumes. ResultsWe analyzed SPX gene family evolution in legumes and in a number of key species from algae to angiosperms. We found that SPX harboring proteins showed fluctuations in domain fusions from algae to the angiosperms with, finally, four classes appearing and being retained in the land plants. Despite these fluctuations, Lysine Surface Cluster (KSC), and the third residue of Phosphate Binding Sites (PBS) showed complete conservation in almost all of SPXs except few proteins in Selaginella moellendorffii and Papaver sumniferum, suggesting they might have different ligand preferences. In addition, we found that the WGD/segmentally or dispersed duplication types were the most frequent contributors to the SPX expansion, and that there is a positive correlation between the amount of WGD contribution to the SPX expansion in individual species and its number of EXS genes. We could also reveal that except SPX class genes, other classes lost the collinearity relationships among Arabidopsis and legume genomes. The sub- or neo-functionalization of the duplicated genes in the legumes makes it difficult to find the functional orthologous genes. Therefore, we used two different methods to identify functional orthologs in soybean and Medicago. High variance in the dynamic and spatial expression pattern of GmSPXs proved the new or sub-functionalization in the paralogs. ConclusionThis comprehensive analysis revealed how SPX gene family evolved from algae to legumes and also discovered several new domains fused to SPX domain in algae. In addition, we hypothesized that there different phosphate sensing mechanisms might occur in S. moellendorffii and P. sumniferum. Finally, we predicted putative functional orthologs of AtSPXs in the legumes, especially, orthologs of AtPHO1 and AtPHO1;H1, involved in long-distance Pi transportation. These findings help to understand evolution of phosphate signaling and might underpin development of new legume varieties with improved phosphate use efficiency.

evolutionary 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↗

bioRxiv2021

The bundle sheath of rice is conditioned to play an active role in water transport as well as sulfur assimilation and jasmonic acid synthesis

Leaves comprise multiple cell types but our knowledge of the patterns of gene expression that underpin their functional specialization is fragmentary. Our understanding and ability to undertake rational redesign of these cells is therefore limited. We aimed to identify genes associated with the incompletely understood bundle sheath of C3 plants, which represents a key target associated with engineering traits such as C4 photosynthesis into rice. To better understand veins, bundle sheath and mesophyll cells of rice we used laser capture microdissection followed by deep sequencing. Gene expression of the mesophyll is conditioned to allow coenzyme metabolism and redox homeostasis as well as photosynthesis. In contrast, the bundle sheath is specialized in water transport, sulphur assimilation and jasmonic acid biosynthesis. Despite the small chloroplast compartment of bundle sheath cells, substantial photosynthesis gene expression was detected. These patterns of gene expression were not associated with presence/absence of particular transcription factors in each cell type, but rather gradients in expression across the leaf. Comparative analysis with C3 Arabidopsis identified a small gene-set preferentially expressed in bundle sheath cells of both species. This included genes encoding transcription factors from fourteen orthogroups, and proteins allowing water transport, sulphate assimilation and jasmonic acid synthesis. The most parsimonious explanation for our findings is that bundle sheath cells from the last common ancestor of rice and Arabidopsis was specialized in this manner, and since the species diverged these patterns of gene expression have been maintained. Significance statementThe role of bundle sheath cells in C4 species have been studied intensively but this is not the case in leaves that use the ancestral C3 pathway. Here, we show that gene expression in the bundle sheath of rice is specialized to allow sulphate and nitrate reduction, water transport and jasmonate synthesis, and comparative analysis with Arabidopsis indicates ancient roles for bundle sheath cells in water transport, sulphur and jasmonate synthesis.

plant biology↗

bioRxiv2021

The SLIM1 transcription factor regulates arsenic sensitivity in Arabidopsis thaliana

The transcriptional regulators of arsenic-induced gene expression remain largely unknown. Sulfur assimilation is tightly linked with arsenic detoxification. Here we report that mutant alleles in the SLIM1 transcription factor are substantially more sensitive to arsenic than cadmium. Arsenic treatment caused high levels of oxidative stress in the slim1 mutants, and slim1 alleles were impaired in both thiol and sulfate accumulation. We further found enhanced arsenic accumulation in roots of slim1 mutants. Transcriptome analyses indicate an important role for SLIM1 in arsenic-induced tolerance mechanisms. The present study identifies the SLIM1 transcription factor as an essential component in arsenic tolerance and arsenic-induced gene expression. Our results suggest that the severe arsenic sensitivity of the slim1 mutants is caused by altered redox status.

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↗

bioRxiv2019

An integrative approach to investigate natural variation in the accumulation of aliphatic glucosinolates in Arabidopsis thaliana

Glucosinolates are a fascinating class of specialised metabolites found in the plants of Brassicacea family. The variation in glucosinolate composition across different Arabidopsis ecotypes could be a result of allelic compositions at different biosynthetic loci. The contribution of methylthioalkylmalate synthase (MAM) genes to diversity of glucosinolate profiles across different Arabidopsis ecotypes has been confirmed by genetic analyses. Different MAM isoforms utilise different chain-elongated substrates for glucosinolate biosynthesis causing thus a variation in chain lengths across different Arabidopsis ecotypes. To further investigate the relationship between the genotype and the associated metabolic phenotype, we studied the diversity of genes and enzymes of glucosinolate biosynthesis. Using Shannon entropy as a measure we revealed that several genes of the pathway show a clear derivation from the expected behaviour, either accumulating non-synonymous SNPs or showing signs of purifying selection. We found that the genotype-phenotype relationship is much more complicated than inferred from the diversity of MAM synthases. We conclude therefore, that the ON/OFF feature of key QTLs is not enough to elucidate the diversity of glucosinolates across different Arabidopsis thaliana ecotypes and that glucosinolate profiles are determined also through the polymorphic residues along the coding regions of multiple metabolic genes.

plant biology↗

bioRxiv2019

Low-glutathione mutants are impaired in growth but do not show an increased sensitivity to moderate water deficit

Glutathione is considered a key metabolite for stress defense and elevated levels have frequently been proposed to positively influence stress tolerance. To investigate whether glutathione affects plant performance and the drought tolerance of plants, wild-type Arabidopsis plants and an allelic series of five mutants (rax1, pad2, cad2, nrc1, and zir1) with reduced glutathione contents between 21 and 63 % compared to wild-type glutathione content were phenotypically characterized for their shoot growth under control and water-limiting conditions using a shoot phenotyping platform. Under non-stress conditions the zir1 mutant with only 21 % glutathione showed a pronounced dwarf phenotype. All other mutants with intermediate glutathione contents up to 62 % in contrast showed consistently slightly smaller shoots than the wild-type. Moderate drought stress imposed through water withdrawal until shoot growth ceased showed that wild-type plants and all mutants responded similarly in terms of chlorophyll fluorescence and growth retardation. These results lead to the conclusion that glutathione is important for general plant performance but that the glutathione content does not affect tolerance to moderate drought conditions typically experienced by crops in the field.

plant biology↗

bioRxiv2019

Metabolic mechanisms of nitrogen substrate utilisation in three rhizosphere bacterial strains investigated using quantitative proteomics

Nitrogen metabolism in the rhizosphere microbiome plays an important role in mediating plant nutrition, particularly under low inputs of mineral fertilisers. However, there is relatively little mechanistic information about which genes and metabolic pathways are induced by rhizosphere bacterial strains to utilise diverse nitrogen substrates. Here we investigate nitrogen substrate utilisation in three taxonomically diverse bacterial strains previously isolated from Arabidopsis roots. The three strains represent taxa that are consistently detected as core members of the plant microbiome: Pseudomonas, Streptomyces and Rhizobium. We use phenotype microarrays to determine the nitrogen substrate preferences of these strains, and compare the experimental results versus computational simulations of genome-scale metabolic network models obtained with EnsembleFBA. Results show that all three strains exhibit generalistic nitrogen substrate preferences, with substrate utilisation being well predicted by EnsembleFBA. Using label-free quantitative proteomics, we document hundreds of proteins in each strain that exhibit differential abundance values following cultivation on five different nitrogen sources: ammonium, glutamate, lysine, serine and urea. Proteomic data show that the three strains use different metabolic strategies to utilise specific nitrogen sources. One diverging trait appears to be their degree of proteomic flexibility, with Pseudomonas sp. Root9 utilising lysine nutrition via widespread protein-level alterations to its flexible metabolic network, whereas Rhizobium sp. Root491 shows relatively stable proteome composition across diverse nitrogen sources. Our results give new protein-level information about the specific transporters and enzymes induced by diverse rhizosphere bacterial strains to utilise organic nitrogen substrates.\n\nImportanceNitrogen is the primary macronutrient required for plant growth. In contemporary agriculture, the vast majority of nitrogen is delivered via mineral fertilisers, which have undesirable environmental consequences such as waterway eutrophication and greenhouse gas production. There is increasing research interest in designing agricultural systems that mimic natural ecosystems, where nitrogen compounds are cycled between plants and soil, with the mineralisation of recalcitrant soil organic-N molecules mediated via microbial metabolism. However, to date there is little mechanistic information about which genes and metabolic pathways are induced by rhizosphere bacterial strains to metabolise organic-N molecules. Here, we use quantitative proteomics to provide new information about the molecular mechanisms utilised by taxonomically diverse rhizosphere bacterial strains to utilise different nitrogen substrates. Furthermore, we generate computational models of bacterial metabolism from a minimal set of experimental information, providing a workflow that can be easily reused to predict nitrogen substrate utilisation in other strains.

microbiology↗

bioRxiv2019

Identification of novel genes involved in phosphate accumulation in Lotus japonicus through Genome Wide Association mapping of root system architecture and anion content

Phosphate is a key nutrient for plants and as it is needed in high quantities. It is highly immobile in the soil and represents a major limiting factor for plant productivity. Plants have evolved different solutions to forage the soil for phosphate and to adapt to phosphate limitation ranging from a profound tuning of their root system architecture and metabolic profile to the evolution of widespread mutualistic interactions, such as those with arbuscular mycorrhizal fungi (AM symbiosis). Despite the prevalence of AM symbiosis throughout land plants, most studies aimed at identifying genes that regulate plant responses to phosphate have been conducted in species incapable of AM symbiosis, such as Arabidopsis. Here we elucidated plant responses and their genetic basis to different phosphate levels in a plant species that is widely used as a model for AM symbiosis: Lotus japonicus. Rather than focusing on a single model strain, we measured root growth and anion content in response to different levels of phosphate in a large panel of Lotus japonicus natural accessions. This allowed us not only to uncover common as well as divergent responses within this species, but also enabled Genome Wide Association Studies by which we identified new genes regulating phosphate homeostasis in Lotus. Under low phosphate conditions, we uncovered a correlation between plant biomass and the decrease of plant phosphate concentration in plant tissues, suggesting a dilution effect. Altogether our data of the genetic and phenotypic variation within a species capable of AM complements studies that have been conducted in Arabidopsis, and advances our understanding of the continuum of genotype by phosphate level interaction that exists throughout dicot plants. Author SummaryPhosphate represents a major limiting factor for plant productivity. Plants have evolved different solutions to adapt to phosphate limitation ranging from a profound tuning of their root system architecture and metabolic profile to the evolution of widespread mutualistic interactions, such as arbuscular mycorrhizal symbiosis. Here we elucidated plant responses and their genetic basis to different phosphate levels in model legume plant species, Lotus japonicus, a plant commonly used for studying arbuscular mycorhizal symbiosis. We investigated Lotus responses to phosphate levels by combining high throughput root system architecture phenotyping and nutrient measurements with a natural variation approach. We investigated relations between root phenotypic responses and nutrient accumulation and we uncovered, under low phosphate conditions, a correlation between plant biomass and the decrease of plant phosphate concentration in plant tissues, suggesting a dilution effect. By means of Genome Wide Association mapping and integration of multiple traits, we identified new genes regulating phosphate homeostasis in Lotus.

plant biology↗

bioRxiv2019

Chloroplasts Require Glutathione Reductase to Balance Reactive Oxygen Species and Maintain Efficient Photosynthesis

O_LIThiol-based redox-regulation is vital to coordinate chloroplast functions depending on illumination. Yet, how the redox-cascades of the thioredoxin and glutathione redox machineries integrate metabolic regulation and reactive oxygen species (ROS) detoxification remains largely unresolved. We investigate if maintaining a highly reducing stromal glutathione redox potential (EGSH) via glutathione reductase (GR) is necessary for functional photosynthesis and plant growth.\nC_LIO_LISince absence of the plastid/mitochondrial GR is embryo-lethal in Arabidopsis thaliana, we used the model moss Physcomitrella patens to create knock-out lines. We dissect the role of GR in chloroplasts by in vivo monitoring stromal EGSH dynamics, and reveal changes in protein abundances by metabolic labelling.\nC_LIO_LIWhereas stromal EGSH is highly reducing in wildtype and clearly responsive to light, the absence of GR leads to a partial oxidation, which is not rescued by light. Photosynthetic performance and plant growth are decreased with increasing light intensities, while ascorbate and zeaxanthin levels are elevated. An adjustment of chloroplast proteostasis is pinpointed by the induction of plastid protein repair and degradation machineries.\nC_LIO_LIOur results indicate that the plastid thioredoxin and glutathione redox systems operate largely independently. They reveal a critical role of GR in maintaining efficient photosynthesis.\nC_LI

plant biology↗