SEARCH · Search bioRxiv

Results for “Plant Biology”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,351 records · Page 75Linked to original sources

bioRxiv2018

Plant-derived coumarins shape the composition of an Arabidopsis synthetic root microbiome

SignificanceThe root microbiome composition is largely determined by the soil inoculum, with a distinct contribution from the host. Yet, the molecular mechanisms with which the host influences its rhizobiome are only beginning to be discovered. Using a hydroponics-based synthetic community approach, we probe the impact of root-exuded specialized metabolites in shaping the root microbiome. We uncover a role for coumarins in structuring the rhizobiome, particularly by limiting the growth of a Pseudomonas strain, for which we propose a mechanism of action. Our findings support the exciting possibility that root-exuded coumarins form a part of the plants adaptive response to iron deficiency that goes beyond iron mobilization to modulate the rhizobiome, and highlights avenues towards engineering the rhizosphere for plant health.\n\nAbstractThe factors that dictate the composition of the root microbiome and its role in plant fitness has been a long-standing question. Recent work has highlighted a major contribution of the soil inoculum in determining the composition of the root microbiome. However, plants are known to conditionally exude a diverse array of unique secondary metabolites, largely varying between species and environmental conditions. Here, we explore the role of specialized metabolites in dictating which bacteria reside in the rhizosphere. We employed a reduced synthetic community (SynCom) of Arabidopsis thaliana root-isolated bacteria to detect community shifts that occur in the absence of the secreted small molecule phytoalexins, flavonoids, and coumarins. We find that lack of coumarin biosynthesis in f6h1 mutant plant lines causes a shift in the root microbial community specifically under iron deficiency. We demonstrate a potential role for iron-mobilizing coumarins in sculpting the A. thaliana root bacterial community by inhibiting the proliferation of a relatively abundant Pseudomonas species via a redox-mediated mechanism. This work establishes a systematic approach enabling elucidation of specific mechanisms by which plant-derived molecules mediate microbial community composition. Our findings expand on the function of conditionally-exuded specialized metabolites and lead to new avenues to effectively engineer the rhizosphere for improving crop growth in alkaline soils, which make up a third of total arable soils.

plant biology↗

bioRxiv2018

Differential responses of antioxidants and dehydrin expression in two switchgrass (Panicum virgatum) cultivars contrasting in drought tolerance

Drought stress is a major limiting factor for plant growth and development in many regions of the world. This study was designed to investigate antioxidant metabolism and dehydrin expression responses to drought stress in two switchgrass cultivars (drought tolerant Alamo, and drought sensitive Dacotah) contrasting in drought tolerance. The plants were subjected to well-watered [100% evapotranspiration (ET)] or drought stress (30%-50% ET) conditions for up to 24 d in growth chambers. Drought stress decreased leaf relative water content (RWC), increased leaf electrolyte leakage (EL), leaf malondialdehyde (MDA) content in two cultivars, but Alamo exhibited higher leaf RWC level, lower leaf EL and MDA when compared to Dacotah at 24 d of drought treatment. Drought stress also increased superoxide dismutase (SOD), catalase (CAT) and ascorbate peroxidase (APX) activities in two cultivars, Alamo had relatively higher SOD, CAT and APX activities and greater abundance of SOD and APX isozymes than Dacotah at 24 d of drought treatment. Alamo had higher abundance of 55 KDa and 18 KDa dehydrin accumulation than Dacotah under drought treatment. Relative genes expression level of PvCAT1, PvAPX2, PvERD and PvPIP1;5 in Alamo were significantly higher than Dacotah at 24 d of drought treatment. These results suggest that increase in antioxidant enzymes and accumulation of dehydrin were highly related with switchgrass drought tolerance. Antioxidant enzyme activity, isozyme expression and dehydrin abundance could provide a useful screening tool to identify relative drought tolerance in switchgrass cultivars.

plant biology↗

bioRxiv2018

Pheophorbide a, a chlorophyll catabolite may regulate jasmonate signalling during dark-induced senescence in Arabidopsis

Chlorophyll degradation is one of the most visible landmarks of leaf senescence. During senescence, chlorophyll is degraded in the multi-step pheophorbide a oxygenase (PAO)/phyllobilin pathway, which is tightly regulated at the transcriptional level. This regulation allows a coordinated and efficient remobilisation of nitrogen towards sink organs. Taking advantage of combined transcriptome and metabolite analyses during dark-induced senescence of Arabidopsis thaliana mutants deficient in key steps of the PAO/phyllobilin pathway, we show an unanticipated role for one of the pathway intermediates, i.e. pheophorbide a. Both jasmonic acid-related gene expression and jasmonic acid precursors specifically accumulated in pao1, deficient in PAO. We propose that pheophorbide a, the last intact porphyrin intermediate of chlorophyll degradation and unique pathway bottleneck, has been recruited as a signalling molecule of the chloroplast metabolic status. Our work challenges the assumption that chlorophyll breakdown is merely a senescence output, but propose that the flux of pheophorbide a through the pathway acts in a feed-forward loop that remodels the nuclear transcriptome and controls the pace of chlorophyll degradation in senescing leaves.\n\nSummaryTranscriptome and metabolite profiles of key chlorophyll breakdown mutants reveal complex interplay between speed of chlorophyll degradation and jasmonic acid signalling\n\nFinancial sourcesThis work was supported by the European Union (Plant Fellow program), the Swiss National Foundation/ERA-NET (grant N{degrees} 163504) and the German Research Foundation (DFG, grant N{degrees} INST 186/822-1).

plant biology↗

bioRxiv2018

CRK2 enhances salt tolerance in Arabidopsis thaliana by regulating endocytosis and callose deposition in connection with PLDα1

High salinity has become an increasingly prevalent source of stress to which plants need to adapt. The receptor-like protein kinases (RLKs), including the cysteine-rich receptor-like kinase (CRK) subfamily, are a highly expanded family of transmembrane proteins in plants and are largely responsible for communication between cells and the extracellular environment. Various CRKs have been implicated in biotic and abiotic stress responses, however their functions on a cellular level remain largely uncharacterized. Here we have shown that CRK2 enhances salt tolerance at the germination stage in Arabidopsis thaliana. We identified CRK2 as a negative regulator of endocytosis, under both normal growth conditions and salt stress. We also established that functional CRK2 is required for salt-induced callose deposition. In doing so, we revealed a novel role for callose deposition, in response to increased salinity, and demonstrated its importance for salt tolerance during germination. Using fluorescently tagged proteins we observed specific changes in CRK2s subcellular localization in response to various stress treatments. Many of CRK2s cellular functions were dependent on phospholipase D (PLD) activity, as were the subcellular localization changes. Thus we propose that CRK2 acts downstream of PLD during salt stress to regulate endocytosis and promote callose deposition, and that CRK2 adopts specific stress-dependent subcellular localization patterns in order to carry out its functions.\n\nOne sentence summaryThe receptor-like kinase CRK2 acts in connection with PLD1 to regulate endocytosis and callose deposition at plasmodesmata, enhancing salt tolerance in Arabidopsis thaliana.

plant biology↗

bioRxiv2018

Antiviral Functions of ARGONAUTE Proteins During Turnip Crinkle Virus Infection Revealed by Image-based Trait Analysis in Arabidopsis

RNA-based silencing functions as an important antiviral immunity mechanism in plants. Plant viruses evolved to encode viral suppressors of RNA silencing (VSRs) that interfere with the function of key components in the silencing pathway. As effectors in the RNA silencing pathway, ARGONAUTE (AGO) proteins are targeted of by some VSRs, such as that encoded by Turnip crinkle virus (TCV). A VSR-deficient TCV mutant was used to identify AGO proteins with antiviral activities during infection. A quantitative phenotyping protocol using an image-based color trait analysis pipeline on the PlantCV platform, with temporal red, green and blue (RGB) imaging and a computational segmentation algorithm, was used to measure plant disease after TCV inoculation. This process captured and analyzed growth and leaf color of Arabidopsis plants in response to virus infection over time. By combining this quantitative phenotypic data with molecular assays to detect local and systemic virus accumulation, AGO2, AGO3, and AGO7 were shown to play antiviral roles during TCV infection. In leaves, AGO2 and AGO7 functioned as prominent non-additive, anti-TCV effectors, while AGO3 played a minor role. Other AGOs were required to protect inflorescence tissues against TCV. Overall, these results indicate that distinct AGO proteins have specialized, modular roles in antiviral defense across different tissues, and demonstrate the effectiveness of image-based phenotyping to quantify disease progression.\n\nAuthor SummaryPlant viruses caused substantial losses in crop production and quality worldwide. Precisely measuring plant health is critical for better understanding the mechanisms underlying plant virus and host interactions. Advances in high-resolution imaging technologies and deep-learning tools have made acquiring and analyzing \"big data\" of disease traits possible. In this study, we have developed a high-throughput, image-based trait phenotyping pipeline to quantify disease severity in Arabidopsis thaliana infected by Turnip Crinkle Virus (TCV). Our aim is to understand how the antiviral RNA silencing machinery is tuned to protect the host from invading virus infection. We focused on ARGONAUTE proteins, which are the effectors in the RNA silencing pathway. A mutant line of TCV with a dysfunctional silencing suppressor (P38) was used to investigate which ago mutation could compensate for the dysfunctional silencing suppressor and facilitate the development of disease symptoms. We demonstrated that specific AGO proteins contribute to protecting leaves from TCV infection in a non-additive manner. Our results also implied that distinct AGOs are required to function collectively to silence TCV in inflorescence tissues. More evidence is still needed to further understand how these antiviral AGOs interact with suppressor proteins molecularly during TCV infection.

plant biology↗

bioRxiv2018

Golden magic: RSH enzymes for (p)ppGpp metabolism in the diatom Phaeodactylum tricornutum.

The nucleotides guanosine tetraphosphate and pentaphosphate (together known as (p)ppGpp or magic spot) are produced in plant plastids from GDP/GTP and ATP by RelA-SpoT homologue (RSH) enzymes. In the model plant Arabidopsis (p)ppGpp regulates chloroplast transcription and translation to affect growth, and is also implicated in acclimation to stress. However, little is known about (p)ppGpp metabolism or its evolution in other photosynthetic eukaryotes. Here we studied (p)ppGpp metabolism in the golden-coloured marine diatom Phaeodactylum tricornutum. We identified three expressed RSH genes in the P. tricornutum genome, and determined the enzymatic activity of the corresponding enzymes by heterologous expression in bacteria. We showed that two P. tricornutum RSH are (p)ppGpp synthetases, despite substitution of a residue within the active site believed critical for activity, and that the third RSH is a bifunctional (p)ppGpp synthetase and hydrolase, the first of its kind demonstrated in a photosynthetic eukaryote. A broad phylogenetic analysis then showed that diatom RSH belong to novel algal RSH clades. Together our work significantly expands the horizons of (p)ppGpp signalling in the photosynthetic eukaryotes by demonstrating an unexpected functional, structural and evolutionary diversity in RSH enzymes from organisms with plastids derived from red algae.\n\nHighlightWe discover RSH enzymes for (p)ppGpp metabolism in the diatom Phaeodactylum tricornutum and show that they have surprising functional and structural features, and belong to novel red-plastid lineage RSH clades.

plant biology↗

bioRxiv2018

Genetic and physical interactions between the organellar mechanosensitive ion channel homologs MSL1, MSL2, and MSL3 reveal a role for inter-organellar communication in plant development

Plant development requires communication on many levels, including between cells and between organelles within a cell. For example, mitochondria and plastids have been proposed to be sensors of environmental stress and to coordinate their responses. Here we present evidence for communication between mitochondria and chloroplasts during leaf and root development, based on genetic and physical interactions between three Mechanosensitive channels of Small conductance-Like (MSL) proteins from Arabidopsis thaliana. MSL proteins are Arabidopsis homologs of the bacterial Mechanosensitive channel of Small conductance (MscS), which relieves cellular osmotic pressure to protect against lysis during hypoosmotic shock. MSL1 localizes to the inner mitochondrial membrane, while MSL2 and MSL3 localize to the inner plastid membrane and are required to maintain plastid osmotic homeostasis during normal growth and development. In this study, we characterized the phenotypic effect of a genetic lesion in MSL1, both in wild type and in msl2 msl3 mutant backgrounds. msl1 single mutants appear wild type for all phenotypes examined. The characteristic leaf rumpling in msl2 msl3 double mutants was exacerbated in the msl1 msl2 msl3 triple mutant. However, the introduction of the msl1 lesion into the msl2 msl3 mutant background suppressed other msl2 msl3 mutant phenotypes, including ectopic callus formation, accumulation of superoxide and hydrogen peroxide in the shoot apical meristem, decreased root length, and reduced number of lateral roots. All these phenotypes could be recovered by molecular complementation with a transgene containing a wild type version of MSL1. In yeast-based interaction studies, MSL1 interacted with itself, but not with MSL2 or MSL3. These results establish that the abnormalities observed in msl2 msl3 double mutants is partially dependent on the presence of functional MSL1 and suggest a possible role for communication between plastid and mitochondria in seedling development.

plant biology↗

bioRxiv2018

The rice G protein γ subunit qPE9-1 positively regulates grain-filling process by interacting with abscisic acid and auxin

The rice genome contains a single G (RGA1) and G{beta} (RGB1) and five G{gamma} subunits. Recent genetic studies have shown that DEP1/qPE9-1, an atypical putative G{gamma} protein, is responsible for dense and erect panicles, but the biochemical and molecular mechanisms underlying control of grain size are not well understood. Here, we report that plants carrying qPE9-1 have more endosperm cells per grain than plants contain the qpe9-1 allele. The qPE9-1 line has a higher rate and longer period of starch accumulation than the qpe9-1 line. Additionally, the expression of several key genes encoding enzymes catalyzing sucrose metabolism and starch biosynthesis is higher in the qPE9-1 line than in the qpe9-1 line, especially from the mid to late grain-filling stage. Grains of the qPE9-1 line also have higher contents of two phytohormones, ABA and IAA. Exogenous application of ABA or IAA enhanced starch accumulation and the expression of genes encoding grain-filling-related enzymes in the grains of qPE9-1, whereas only IAA produced these effects in qpe9-1. Based on these results, we conclude that qPE9-1 promotes endosperm cell proliferation and positively regulates starch accumulation largely through ABA and IAA, which enhance the expression of genes encoding starch biosynthesis during the late grain-filling stage.

plant biology↗

bioRxiv2018

Rhizosphere-enriched microbes as a pool to design synthetic communities for reproducible beneficial outputs

Composts represent a sustainable way to suppress diseases and improve plant growth. Identification of compost-derived microbial communities enriched in the rhizosphere of plants and characterization of their traits, could facilitate the design of microbial synthetic communities (SynComs) that upon soil inoculation could yield consistent beneficial effects towards plants. Here, we characterized a collection of compost-derived bacteria, previously isolated from tomato rhizosphere, for in vitro antifungal activity against soil-borne fungal pathogens and for their potential to change growth parameters in Arabidopsis. We further assessed root-competitive traits in the dominant rhizospheric genus Bacillus. Certain isolated rhizobacteria displayed antifungal activity against the tested pathogens and affected growth of Arabidopsis, and Bacilli members possessed several enzymatic activities. Subsequently, we designed two SynComs with different composition and tested their effect on Arabidopsis and tomato growth and health. SynCom1, consisting of different bacterial genera, displayed negative effect on Arabidopsis in vitro, but promoted tomato growth in pots. SynCom2, consisting of Bacilli, didnt affect Arabidopsis growth, enhanced tomato growth and suppressed Fusarium wilt symptoms. Overall, we found selection of compost-derived microbes with beneficial properties in the rhizosphere of tomato plants, and observed that application of SynComs on poor substrates can yield reproducible plant phenotypes.

plant biology↗

bioRxiv2018

Control of stem-cell niche establishment in Arabidopsis flowers by REVOLUTA and the LEAFY-RAX1 module

Plants retain the ability to produce organs throughout their life by maintaining active stem cell niches called meristems. The shoot apical meristem (SAM) is responsible for the growth of aerial plant structures. In Arabidopsis thaliana, the SAM initially produces leaves during the vegetative phase and later flowers during reproductive development. In the early stages of floral initiation, a group of cells first emerges from the SAM to form a stereotypically organized meristematic structure on its flank. However, the molecular mechanisms underlying the acquisition of this specific meristematic organization remain elusive. We show here that the transcription factors LEAFY (LFY) and REVOLUTA (REV) control two partially redundant pathways controlling meristematic organization in early flower primordia. We found that LFY acts through the transcription factor REGULATOR OF AXILLARY MERISTEM1 (RAX1) and we provide mechanistic insights in how RAX1 allows meristem identity establishment in young flowers. Our work provides a molecular link between the processes of meristem formation and floral identity acquisition in the nascent flower.

plant biology↗

bioRxiv2018

Rapid identification of an Arabidopsis NLR gene conferring susceptibility to Sclerotinia sclerotiorum using time-resolved automated phenotyping

The broad host range necrotrophic fungus Sclerotinia sclerotiorum is a devastating pathogen of many oil and vegetable crops. Plant genes conferring complete resistance against S. sclerotiorum have not been reported. Instead, plant populations challenged by S. sclerotiorum exhibit a continuum of partial resistance designated as quantitative disease resistance (QDR). Because of their complex interplay and their small phenotypic effect, the functional characterization of QDR genes remains limited. How broad host range necrotrophic fungi manipulate plant programmed cell death is for instance largely unknown. Here, we designed a time-resolved automated disease phenotyping pipeline and assessed the kinetics of disease symptoms caused by seven S. sclerotiorum isolates on six A. thaliana natural accessions with unprecedented resolution. We hypothesized that large effect polymorphisms common to the most resistant A. thaliana accessions, but absent from the most susceptible ones, would point towards disease susceptibility genes. This identified highly divergent alleles of the nucleotide-binding site leucine-rich repeat gene LAZ5 in the resistant accessions Rubenzhnoe and Lip-0. Two LAZ5-deficient mutant lines in the Col-0 genetic background showed enhanced QDR to S. sclerotiorum, whereas plants mutated in the closely related CSA1 gene responded like the wild type. These findings illustrate the value of time-resolved image-based phenotyping for unravelling the genetic bases of complex traits such as QDR. Our results suggest that S. sclerotiorum manipulates plant sphingolipid pathways guarded by LAZ5 to trigger programmed cell death and cause disease.

plant biology↗

bioRxiv2018

ETAPOD: A forecast model for prediction of black pod disease Outbreak in Nigeria

The misuse of toxic fungicides by indigenous cocoa farmers in Nigeria stem from their inability to predict the time for black pod disease (BPD) outbreak. Prediction of possible time for BPD outbreak will provide spotlight on areas under massive BPD invasion, minimise fungicide misuse and increase control accuracy. The Multiple Regression Model (MRM): Y=+{beta}1X1+{beta}2X2+...+{beta}nXn where Y is Nx1 matrix of response variable, X1,X2,...Xn are NxK matrices of regressors, and {beta}1,{beta}2,...{beta}n regression coefficients was used in model development. Eight models (MRM1-MRM8) were fitted from real life BPD data. The performances of the models were ascertained using SER, RMSEpred and R-SqAdj. Prediction(s) made by the best fitted model was compared to real life observations (Monthly BPD Occurrence (MBO), Total Annual Occurrence (TAO), and Average Annual Occurrence (AAO), respectively). The preferred model was MRM5 (ETAPOD) followed by MRM4, MRM1, MRM2, and MRM3 in terms of SER (0.22, 0.39, 0.45, 0.45 and 0.45), RMSEpred.(0.30, 039, 0.46, 0.46 and 0.46) and R-SqAdj.(0.67, 0.49, 0.32, 0.32, and 0.31), respectively. Predictions on BPD outbreak made by ETAPOD showed that MBO, TAO and AAO for some selected stations i.e. Owena and Waasimi were 9.05, 72.3 and 6.0% compared with observed BPD values of 9.5, 70.0, and 5.8%, respectively. Adaagba, Iyanfoworogi, and Owode-Igangan had 9.43, 77.8, and 6.5% as their predicted BPD values compared with the observed values of 9.0, 53.5, and 4.46%, respectively. ETAPOD performed better than other models and its predicted values were within the range of real life occurrence.

plant biology↗

bioRxiv2018

The Ca2+ sensor protein CMI1 fine tunes root development, auxin distribution and responses

Signaling cross-talks between auxin, a regulator of plant development and Ca2+, a universal second messenger have been proposed to modulate developmental plasticity in plants. However, the underlying molecular mechanisms are largely unknown. Here we report that in Arabidopsis roots, auxin elicits specific Ca2+ signaling pattern that spatially coincide with the expression pattern of auxin-regulated genes. We identified the EF-hand protein CMI1 (Ca2+ sensor Modulator of ICR1) as an interactor of the ROP effector ICR1 (Interactor of Constitutively active ROP). CMI1 is monomeric in solution, changes its secondary structure at Ca2+ concentrations ranging from 10-9 to 10-8 M and its interaction with ICR1 is Ca2+ dependent, involving a conserved hydrophobic pocket. cmi1 mutants display an increased auxin response including shorter primary roots, longer root hairs, longer hypocotyls and altered lateral root formation while ectopic expression of CMI1 induces root growth arrest and reduced auxin responses at the root tip. When expressed alone, CMI1 is localized at the plasma membrane, the cytoplasm and in nuclei. Interaction of CMI1 and ICR1 results in exclusion of CMI1 from nuclei and suppression of the root growth arrest. CMI1 expression is directly upregulated by auxin while expression of auxin induced genes is enhanced in cmi1 concomitantly with repression of auxin induced Ca2+ increases in the lateral root cap and vasculature, indicating that CMI1 represses early auxin responses. Collectively, our findings identify a crucial function of Ca2+ signaling and CMI1 in root growth and suggest an auxin-Ca2+ regulatory feedback loop that fine tunes root development.

plant biology↗

bioRxiv2018

Genetic determination of stomatal patterning in winter wheat (Triticum aestivum L.)

Leaf stomata are microscopic pores mediating plant-environment interactions. Their role in carbon uptake and transpiration make them prime candidates for improving water use efficiency (WUE). Stomatal density (SD), the number of stomata per unit area, has been shown to be negatively correlated with WUE. However, little is known about the genetic basis of SD in wheat (Triticum aestivum L.), and to what extant genetic variation exists in contemporary wheat germplasm. Here, we evaluated stomatal patterning over two growing seasons in a set of 333 wheat lines, representing the European winter wheat germplasm. Stomatal patterning was mainly determined by two underlying traits, the distance between files of stomata and the distance between stomata within a file. By haplotype association mapping, quantitative trait loci for SD were consistently detected in both seasons on wheat chromosomes (CHR) 2A, 3A and 7B. The single nucleotide polymorphism markers most significantly associated with SD coincided with the genes INDUCER OF CBF EXPRESSION 1 (ICE1) and STOMATAL CYTOKINESIS-DEFECTIVE 1 (SCD1) on CHR 3A, and genes involved in ethylene and auxin signaling on CHR 2A and 7B, respectively. Our study unlocks the phenotypic and genotypic variation for stomatal patterning traits in contemporary wheat germplasm. It provides gene targets for functional validation and practical tools to manipulate SD using marker-assisted selection for crop improvement.

plant biology↗

bioRxiv2018

Priming winter wheat seeds with the bacterial quorum sensing signal N-hexanoyl-L-homoserine lactone (C6-HSL) shows potential to improve plant growth and seed yield

Several model plants are known to respond to bacterial quorum sensing molecules with altered root growth and gene expression patterns and induced resistance to plant pathogens. These compounds may represent novel elicitors that could be applied as seed primers to enhance cereal crop resistance to pathogens and abiotic stress and to improve yields. We investigated whether the acyl-homoserine lactone N-hexanoyl-L-homoserine lactone (C6-HSL) impacted winter wheat (Triticum aestivum L.) seed germination, plant development and productivity, using two Ukrainian varieties, Volodarka and Yatran 60, in both in vitro experiments and field trials. In vitro germination experiments indicated that C6-HSL seed priming had a small but significant positive impact on germination levels (1.2x increase, p < 0.0001), coleoptile and radicle development (1.4x increase, p < 0.0001). Field trials over two growing seasons (2015-16 and 2016-17) also demonstrated significant improvements in biomass at the tillering stage (1.4x increase, p < 0.0001), and crop structure and productivity at maturity including grain yield (1.4 - 1.5x increase, p < 0.0007) and quality (1.3x increase in good grain, p < 0.0001). In some cases variety effects were observed (p [≤] 0.05) suggesting that the effect of C6-HSL seed priming might depend on plant genetics, and some benefits of priming were also evident in F1 plants grown from seeds collected the previous season (p [≤] 0.05). These field-scale findings suggest that bacterial acyl-homoserine lactones such as C6-HSL could be used to improve cereal crop growth and yield and reduce reliance on fungicides and fertilisers to combat pathogens and stress.

plant biology↗

bioRxiv2018

Cell type-specific regulation of nutrient absorption, metabolism and transfer in arbuscular mycorrhizal fungi

Arbuscular mycorrhizal fungi (AMF) establish symbiotic relationships with most land plants, mainly for the purpose of nutrient exchange. Many studies have revealed the regulation of absorption, metabolism, and transfer of nutrients in AMF and the genes involved in these processes. However, the spatial regulation of the genes among the structures comprising each developmental stage are not well understood. Here, we demonstrate the structure-specific transcriptome of the model AMF species, Rhizophagus irregularis. We performed an ultra-low input RNA-seq analysis, SMART-seq2, comparing five extraradical structures, germ tubes, runner hyphae, branched absorbing structures, immature spores, and mature spores. In addition, we reanalyzed the recently reported RNA-seq data comparing intraradical hyphae and arbuscules. Our analyses captured the distinct features of each structure and revealed the structure-specific expression patterns of genes related to absorption, metabolism, and transfer of nutrients. Of note, the transcriptional profiles suggest the distinct functions of branched absorbing structures in nutrient absorption. These findings provide a comprehensive dataset to advance our understanding of the transcriptional dynamics of fungal nutrition in this symbiotic system.

plant biology↗

bioRxiv2018

Cryo-Electron tomography 3D structure and nanoscale model of Arabidopsis thaliana cell wall

Using cryo-electron tomography of vitrified sections of one month-old Arabidopsis thaliana inflorescence stem tissue, we visualized primary and secondary cell walls of xylem tissue. Extensive quantitative and statistical analysis of segmented 3D tomographic data allowed geometrically idealized 3D-CAD model building of prototypic microfibrils, cross-links, and their supramolecular microfibril 3D organization. We propose a prototypic microfibril model where a cellulose core is heavily decorated by a thin sheath of hemicellulose with infrequent but sturdy hemicellulose-based cross-links. Such prototypic microfibrils then adopt a rather unexpected 3D supramolecular organization of high order and complexity. We discuss a possible new role for lignin in plant cell walls at low concentrations with lignin not acting as a matrix but rather as a reinforcement of microfibrils and cross-links. Extensive computational simulations of mechanical properties further revealed that this 3D organization of the cell wall is not optimized for load bearing but instead for flexibility and ductility.\n\nOne Sentence SummaryCryo-electron tomography and mechanical simulations revealed cell wall 3D architecture, optimized for flexibility/ductility.

plant biology↗

bioRxiv2018

How to Build a Fruit: Transcriptomics of a Novel Fruit Type in the Brassiceae

Comparative gene expression studies are invaluable for predicting how existing genetic pathways may be modified or redeployed to produce novel and variable phenotypes. Fruits are ecologically important organs because of their impact on plant fitness and seed dispersal, modifications in which results in morphological variation across species. A novel fruit type in the Brassicaceae known as heteroarthrocarpy enables distinct dispersal methods in a single fruit through segmentation via a lateral joint and variable dehiscence at maturity. Given the close relationship to Arabidopsis, species that exhibit heteroarthrocarpy are powerful models to elucidate how differences in gene expression of a fruit patterning pathway may result in novel fruit types. Transcriptomes of distal, joint, and proximal regions from Erucaria erucarioides and Cakile lanceolata were analyzed to elucidate within and between species differences in whole transcriptome, gene ontology, and fruit patterning expression profiles. Whole transcriptome expression profiles vary between fruit regions in patterns that are consistent with fruit anatomy. These transcriptomic variances do not correlate with changes in gene ontology, as they remain generally stable within and between both species. Upstream regulators in the fruit patterning pathway, FILAMENTOUS FLOWER and YABBY3, are expressed in the distal and proximal regions of E. erucarioides, but not in the joint, implicating alterations in the pathway in heteroarthrocarpic fruits. Downstream gene, INDEHISCENT, is significantly upregulated in the abscissing joint region of C. lanceolata, which suggests repurposing of valve margin genes for novel joint disarticulation in an otherwise indehiscent fruit. In summary, these data are consistent with modifications in fruit patterning genes producing heteroarthrocarpic fruits through different components of the pathway relative to other indehiscent, non-heteroarthrocarpic, species within the family. Our understanding of fruit development in Arabidopsis is now extended to atypical siliques within the Brassicaceae, facilitating future studies on seed shattering in important Brassicaceous crops and pernicious weeds.

plant biology↗