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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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bioRxiv2017

A microbially derived tyrosine sulfated peptide mimics a plant peptide hormone

O_LIThe biotrophic pathogen Xanthomonas oryzae pv. oryzae (Xoo) produces a sulfated peptide named RaxX, which shares similarity to peptides in the PSY (plant peptide containing sulfated tyrosine) family. We hypothesize that RaxX functionally mimics the growth stimulating activity of PSY peptides.\nC_LIO_LIRoot length was measured in Arabidopsis and rice treated with synthetic RaxX peptides. We also used comparative genomic analysis and Reactive Oxygen Species (ROS) burst assay to evaluate the activity of RaxX and PSY peptides.\nC_LIO_LIHere we found that a synthetic sulfated RaxX derivative comprising 13 residues (RaxX13-sY), highly conserved between RaxX and PSY, induces root growth in Arabidopsis and rice in a manner similar to that triggered by PSY. We identified residues that are required for activation of immunity mediated by the rice XA21 receptor but that are not essential for root growth induced by PSY. Finally, we showed that a Xanthomonas strain lacking raxX is impaired in virulence.\nC_LIO_LIThese findings suggest that RaxX serves as a molecular mimic of PSY peptides to facilitate Xoo infection and that XA21 has evolved the ability to recognize and respond specifically to the microbial form of the peptide.\nC_LI

plant biology↗

bioRxiv2017

Transcription Through The Eye Of A Needle: Daily And Annual Cycles Of Gene Expression Variation In Douglas-Fir Needles

BackgroundPerennial growth in plants is the product of interdependent cycles of daily and annual stimuli that induce cycles of growth and dormancy. In conifers, needles are the key perennial organ that integrates daily and seasonal signals from light, temperature, and water availability. To understand the relationship between seasonal rhythms and seasonal gene expression responses in conifers, we examined diurnal and circannual needle mRNA accumulation in Douglas-fir (Pseudotsuga menziesii) needles at diurnal and circannual scales. Using mRNA sequencing, we sampled 6.1x109 microreads from 19 trees and constructed a de novo pan-transcriptome reference that includes 173,882 tree-derived transcripts. Using this reference, we mapped RNA-Seq reads from 179 samples that capture daily, seasonal, and annual variation.\n\nResultsWe identified 12,042 diurnally-cyclic transcripts, 9,299 of which showed homology to annotated genes from other plant genomes, including angiosperm core clock genes. Annual analysis revealed 21,225 an-nually-cyclic transcripts, 17,335 of which showed homology to annotated genes from other plant genomes. The timing of maximum gene expression is associated with light quality at diurnal and photoperiod at annual scales, with two-thirds of transcripts reaching maximum expression +/- 2 hours from sunrise and sunset, and half reaching maximum expression +/- 20 days from winter and summer solstices. Comparison to published microarray-based gene expression studies in spruce (Picea) show that the rank order of expression for 760 putatively orthologous genes was significantly preserved, highlighting the generality of our findings.\n\nConclusionsThis finding highlights the extensive annual and seasonal transcriptome variability demonstrated in conifer needles. At these temporal scales, 29% of expressed transcripts showed a significant diurnal rhythm, and 58.7% showed a significant circannual rhythm. Remarkably, thousands of genes reach their annual peak activity during winter dormancy, a time of metabolic stasis. Photoperiod appears to be a dominant driver of annual transcription patterns in Douglas-fir, and these results may be general for predicting rhythmic transcription patterns in emerging gymnosperm models.

plant biology↗

bioRxiv2017

The Maternal Environment Interacts With Genetic Variation In Regulating Seed Dormancy In Arabidopsis thaliana

Seed dormancy is a complex adaptive trait that controls the timing of seed germination, one of the major fitness components in many plant species. Despite being highly heritable, seed dormancy is extremely plastic and influenced by a wide range of environmental cues. Here, using a set of 92 Arabidopsis thaliana lines from Sweden, we investigate the effect of seed maturation temperature on dormancy variation at the population level. The response to temperature differs dramatically between lines, demonstrating that genotype and the maternal environment interact in controlling the trait. By performing a genome-wide association study (GWAS), we identified several candidate genes that could account for this plasticity, two of which are involved in the photoinduction of germination. Altogether, our results provide insight into both the molecular mechanisms and the evolution of dormancy plasticity, and can serve to improve our understanding of environmentally dependent life-history transitions.\n\nHighlightThe effect of low seed-maturation temperatures on seed dormancy is highly variable in Arabidopsis thaliana accessions from Sweden, denoting strong genotype-environment interactions, and a genome-wide association study identified compelling candidates that could account for this plasticity.

plant biology↗

bioRxiv2017

Escape from bacterial diversity: potential enemy release in invading yellow starthistle (Centaurea solstitialis) microbiomes

O_LIInvasive species could benefit from introduction to locations with favorable species interactions. Microbiomes are an important source of interactions that vary across regions. We examine whether bacterial communities could explain more favorable microbial interactions in highly invasive populations of yellow starthistle.\nC_LIO_LIWe sequenced amplicons of prokaryotic 16S rRNA genes to characterize bacterial community composition in the phyllosphere, ectorhizosphere, and endorhizosphere of plants from seven invading populations in California, USA and eight native populations in Europe. We tested for differentiation of microbiomes by geography, plant compartment, and plant genotype.\nC_LIO_LIBacterial communities differed significantly between native and invaded ranges within plant compartments, with consistently lower diversity in plants from the invaded range. Genera containing known plant pathogens also showed lower diversity in invaded range plants. The diversity of bacteria in roots was positively correlated with plant genotype diversity within both ranges, but this relationship did not explain microbial differences between ranges.\nC_LIO_LIOur findings reveal changes in the composition and diversity of bacterial interactions in invading plants, consistent with observations of altered soil interactions in this invasion. These results call for further study of the sources of variation in microbiomes and the potential for bacteria to facilitate invasion success.\nC_LI

plant biology↗

bioRxiv2017

The Rice XA21 Ectodomain Fused to the Arabidopsis EFR Cytoplasmic Domain Confers Resistance to Xanthomonas oryzae pv. oryzae

O_LIRice (Oryza sativa) plants expressing the XA21 cell surface receptor kinase are resistant to Xanthomonas oryzae pv.oryzae (Xoo) infection. We previously demonstrated that expressing a chimeric protein containing the EFR (ELONGATION FACTOR Tu RECEPTOR) ectodomain and the XA21 endodomain (EFR:XA21) in rice does not confer robust resistance to Xoo.\nC_LIO_LITo test if the XA21 ectodomain is required for Xoo resistance, we produced transgenic rice lines expressing a chimeric protein consisting of the XA21 ectodomain and EFR endodomain (XA21:EFR) and inoculated these lines with Xoo. We also tested if the XA21:EFR rice plants respond to a synthetic sulfated 21 amino acid derivative (RaxX21-sY) derived from the activator of XA21-mediated immunity, RaxX.\nC_LIO_LIWe found that five independently transformed XA21:EFR rice lines displayed resistance to Xoo as measured by lesion length analysis, and showed that five lines express markers of the XA21 defense response (generation of reactive oxygen species and defense response gene expression) after treatment with RaxX21-sY.\nC_LIO_LIOur results indicate that expression of the XA21:EFR chimeric receptor in rice confers resistance to Xoo. These results suggest that the endodomain of the EFR and XA21 immune receptors are interchangeable and the XA21 ectodomain is the key determinant conferring robust resistance to Xoo.\nC_LI

plant biology↗

bioRxiv2017

Could Plants Be Sentient?

Feelings in humans are mental states representing groups of physiological functions that usually have defined behavioural objectives or purpose. Feelings are thought to be coordinated in the brain stem of animals and are evolutionarily ancient. One function of the brain is to prioritise between competing mental states, and thus groups of physiological functions and in turn behaviour. Anger, fear or pain call for immediate action whereas hunger, or thirst, signify longer term needs and a requirement for search. Plants use groups of coordinated physiological activities to deal with defined environmental situations but currently have no known mental state to prioritise any order of response. Plants do have a nervous system based on phloem which is highly cross linked. Its potential for forming a mental state is unknown but it could be used to distinguish between different and even contradictory signals and thus determine a priority of response. The vascular nervous system stretches throughout the whole plant providing the potential for assessment in all parts and commensurate with its self-organising, phenotypically plastic behaviour.

plant biology↗

bioRxiv2017

Phytohormone Inhibitor Treatments Phenocopy Brassinosteroid And Gibberellin Dwarf Mutant Interactions In Maize

Phytohormone biosynthesis produces metabolites with profound effects on plant growth and development. Modulation of hormone levels during developmental events, in response to the environment, by genetic polymorphism, or by chemical application can reveal the plant processes most responsive to a phytohormone. In many cases, chemical inhibitors are applied and the levels of specific phytohormones are measured to determine if, and which, phytohormone is affected by a molecule. In many cases, the sensitivity of biochemical testing has determined multiple pathways affected by a single inhibitor. Genetic studies are not subject to this problem, and a wealth of data about the morphological impacts of hormone biosynthetic inhibition has accumulated through the study of enzyme mutants. We previously identified a complex interplay between brassinosteroid (BR) and gibberellin (GA) in maize, where the interdependence of the two differs dependent on the developmental context. We found that: GA is required for loss of BR to induce retained pistils in the tassel florets (POPIT); BR is required for the loss of GA to induce tiller outgrowth; BR and GA are additive for plant height; BR has no effect on the induction of anther retention in ear florets of GA mutants. In this work, we sought to assess the specificity of three triazole inhibitors of cytochrome P450s by determining their abilities to recapitulate the phenotype of double mutants. The GA biosynthetic inhibitors uniconazole (UCZ) and paclobutrazol (PAC) were applied to the BR biosynthetic mutant na2 and all double mutant phenotypes were recovered in the UCZ treatment. PAC was unable to suppress the retention of pistils in the tassels of nana plant2 (na2) mutant plants. The BR biosynthetic inhibitor propiconazole (PCZ) suppressed tiller outgrowth in the GA biosynthetic mutant dwarf5 (d5). All treatments were additive with genetic mutants for effects on plant height. Due to additional measurements done here but not in previous studies of the double mutants, we detected new interactions between GA and BR biosynthesis affecting plastochron index and tassel branching. These experiments, a refinement of our previous model, and a discussion of the extension of this type of work are presented.

plant biology↗

bioRxiv2017

Methomyl Injury To Carbon Exchange Rates And Related Processes In Cotton

Some insecticides have the potential to cause varying levels of phytotoxicity. This study examined 1) the time courses of photosynthetic injury in cotton (Gossypium hirsutisms L.) leaves treated with methomyl [S-methyl-N-[(methyl carbamoyl)oxy]-thioacetimidate] and 2) the relationships between carbon exchange rate (CER), stomatal conductance, the chlorophyll fluorescence parameter FX/FP, and ribulose-1,5-bisphosphate carboxylase/ oxygenase (rubisco) activity. Plots were sprayed with either 0 or 0.84 kg methomyl{middle dot}ha-1 when cotton was in mid-reproductive growth. Starting on the day of spraying, CER, stomatal conductance, FX/FP, and rubisco activity were measured daily for five consecutive days [4, 28, 52, 76 and 100 hours after spraying (HAS)]. In methomyl-treated leaves, CER decreased within hours after spraying, reached their lowest point at 28 HAS in experiment I and 76 HAS in experiment II, then recovered near-control levels by 100 HAS. At their lowest points, CER of methomyl-treated leaves decreased from 20 to 50% compared to controls. Stomatal conductance, FX/FP, and rubisco activity followed similar patterns to CER. Stomatal conductance was more closely related to CER than were FX/FP and rubisco activity. Chlorophyll fluorescence recovered more quickly than did CER. Rubisco activity did not decrease till after CER. From the parameters measured in this study, stomatal conductance appeared to be the major factor influencing methomyl-induced changes in CER, although all three parameters may be involved in the process of CER change.\n\nAbbreviations

plant biology↗

bioRxiv2017

Cross-talk between active DNA demethylation, resetting of cellular metabolism and shoot apical growth in poplar bud break

Annual dormancy-growth cycle is a developmental and physiological process essential for the survival of temperate and boreal forests. Seasonal control of shoot growth in woody perennials requires specific genetic programs integrated with the environmental signals. The environmental-controlled mechanisms that regulate the shift between winter dormancy to growth promoting genetic program are still unknown. Here, we show that dynamics in genomic DNA methylation (gDNA) levels regulate dormancy-growth cycle in poplar. We proved that the reactivation of cell division in the apical shoot that lead bud break process in spring, is preceded by a progressive reduction of gDNA methylation in apex tissue. We also identified that the induction in apex tissue of a chilling-dependent poplar DEMETER-LIKE 10 (PtaDML10) DNA demethylase precedes shoot growth reactivation. Transgenic poplars showing down-regulation of PtaDML8/10 caused delayed bud break. Genome wide transcriptome and methylome analysis and data mining revealed the gene targets of active DML-dependent DNA demethylation genetically associated to bud break. These data point to a chilling dependent-DEMETER-like DNA demethylase controlling the genetic shift from winter dormancy to a condition that promotes shoot apical vegetative growth in poplar.

plant biology↗

bioRxiv2017

Advances in abscission signaling

Abscission is a process in plants for shedding unwanted organs such as leaves, flowers, fruits, or floral organs. Shedding of leaves in the fall is the most visually obvious display of abscission in nature. The very shape plants take is forged by the processes of growth and abscission. Mankind manipulates abscission in modern agriculture to do things like prevent pre-harvest fruit drop prior to mechanical harvesting in fruit orchards. Abscission occurs specifically at abscission zones that are laid down as the organ that will one day abscise is developed. A sophisticated signaling network initiates abscission when it is time to shed the unwanted organ. In this article, we review recent advances in understanding the signaling mechanisms that activate abscission. Physiological advances and roles for hormones in abscission are also addressed. Finally, we discuss current avenues for basic abscission research and potentially lucrative future directions for its application to modern agriculture.

plant biology↗

bioRxiv2017

Discovery and reduction of nonspecific activities of the major herbicide-resistance gene BAR

Herbicide resistance is a major trait of genetically modified (GM) crops. Currently, resistance to phosphinothricin (also known as glufosinate) is the second most widespread genetically engineered herbicide-resistance trait in crops after glyphosate resistance1,2. Resistance to phosphinothricin in plants is achieved by transgenic expression of the bialaphos resistance (BAR) or phosphinothricin acetyltransferase (PAT) genes, which were initially isolated from the natural herbicide bialaphos-producing soil bacteria Streptomyces hygroscopicus and S. viridochromogenes, respectively3,4. Mechanistically, BAR and PAT encode phosphinothricin acetyltransferase, which transfers an acetyl group from acetyl coenzyme A (acetyl-CoA) to the -NH2 group of phosphinothricin, resulting in herbicide inactivation1. Although early in vitro enzyme assays showed that recombinant BAR and PAT exhibit substrate preference toward phosphinothricin over the 20 proteinogenic amino acids1, whether transgenic expression of BAR and PAT affects plant endogenous metabolism in vivo was not known. Combining metabolomics, plant genetics, and biochemical approaches, we show that transgenic BAR indeed converts two plant endogenous amino acids, aminoadipate and tryptophan, to their respective N-acetylated products in several plant species examined. We report the crystal structures of BAR, and further delineate structural basis for its substrate selectivity and catalytic mechanism. Through structure-guided protein engineering, we generated several BAR variants that display significantly reduced nonspecific activities compared to its wild-type counterpart. Our results demonstrate that transgenic expression of enzymes as a common strategy in modern biotechnology may render unintended metabolic consequences arisen from enzyme promiscuity. Understanding of such phenomena at the mechanistic level will facilitate better design of maximally insulated systems featuring heterologously expressed enzymes.

plant biology↗

bioRxiv2017

Guidance Of Circumnutation Of Climbing Bean Stems: An Ecological Exploration

In this report we explore the guidance of circumnutation of climbing bean stems under the light of general rho/tau theory, a theory that aims to explain how living organisms guide goal-directed movements ecologically. We present some preliminary results on the control of circumnutation by climbing beans, and explore the possibility that the power of movement in plants, more generally, is controlled under ecological principles.

plant biology↗

bioRxiv2017

The Date Palm (Phoenix dactylifera L.) In Siwa Oasis (Egypt): How Ethnographic, Morphometric, And Genetic Analyses Together Explain The Local Agrobiodiversity

The agrobiodiversity of the Siwa oasis (in Egypt), located at the crossroads of ancient Trans-Saharan routes, is evaluated in this article focusing on the date palm (Phoenix dactylifera L.), the oasis \"ecosystem engineer\". This assessment confronts different ontologies: diversity as expressed and maintained by the folk categorization system of the Siwa inhabitants (through the results of an ethnographical analysis) and diversity described by genetic sciences and a morphometric tool based on the size and geometry of the seeds. This work is also an opportunity to evaluate this tool intended for archaeobotany. Beyond a simple instrumentalization of one discipline by another, this study offers a space of mutual enrichment: on the relative importance of the feral and cultivated date palms, the local relevance of the concept of \"cultivar\" and the confirmation of the existence of \"ethnovarieties\".

plant biology↗

bioRxiv2017

Members of the abscisic acid co-receptor PP2C protein family mediate salicylic acid-abscisic acid crosstalk

The interplay between abscisic acid (ABA) and salicylic acid (SA) influences plant responses to various (a)biotic stresses; however, the underlying mechanism(s) for this crosstalk is largely unknown. Here we report that type 2C protein phosphatases (PP2Cs), some of which are negative regulators of ABA signaling, bind SA. SA binding suppressed the ABA-enhanced interaction between these PP2Cs and various ABA receptors belonging to the PYR/PYL/RCAR protein family. Additionally, SA suppressed ABA-enhanced degradation of PP2Cs and ABA-induced stabilization of SnRK2s. Supporting SAs role as a negative regulator of ABA signaling, exogenous SA suppressed ABA-induced gene expression, whereas SA-deficient sid2-1 mutants displayed heightened PP2C degradation and hypersensitivity to ABA-induced suppression of seed germination. Together, these results suggest a new molecular mechanism through which SA antagonizes ABA signaling. A better understanding of the crosstalk between these hormones is important for improving the sustainability of agriculture in the face of climate change.

plant biology↗

bioRxiv2017

The Odd One Out: Aabidopsis Reticulon 20 Has A Role In Lipid Biosynthesis

The family of reticulon proteins has been shown to be involved in a variety of functions in eukaryotic cells including tubulation of the endoplasmic reticulum (ER), formation of cell plates and primary plasmodesmata. Reticulons are integral ER membrane proteins characterised by a reticulon homology domain comprising four transmembrane domains which results in the reticulons sitting in the membrane in a W-topology. Here we report on a subgroup of reticulons with an extended N-terminal domain and in particular on arabidopsis reticulon 20. We show that reticulon 20 is located in a unique punctate pattern on the ER membrane. Its closest homologue reticulon 19 labels the whole ER. We show that mutants in RTN20 or RTN19, respectively, display a significant change in sterol composition in the roots indicating a role in lipid biosynthesis or regulation. A third homologue in this family - 3BETAHSD/D1- is localised to ER exit sites resulting in an intriguing location difference for the three proteins.

plant biology↗

bioRxiv2017

A Role For The F-Box Protein HAWAIIAN SKIRT In Plant miRNA Function

As regulators of gene expression in multicellular organisms, microRNAs (miRNAs) are crucial for growth and development. While a plethora of factors involved in their biogenesis and action in Arabidopsis thaliana have been described, these processes and their fine-tuning are not fully understood in plants. Here, we used plants expressing an artificial miRNA target mimic (MIM) to screen for negative regulators of miR156 activity. We identified a new mutant allele of the F-box protein HAWAIIAN SKIRT (HWS; At3G61590), hws-5, as a suppressor of the MIM156-induced developmental and molecular phenotypes. In hws plants, levels of endogenous miRNAs are increased and their mRNA targets decreased. Plants constitutively expressing full-length HWS - but not a truncated version lacking the F-box domain - display morphological and molecular phenotypes resembling those of mutants defective in miRNA biogenesis and activity. In combination with such mutants, hws loses its delayed floral organ abscission ( skirt) phenotype, suggesting epistasis. Also, the overall hws transcriptome profile partially resembles well-known miRNA mutants hyl1-2 and se-3, indicating action in a common pathway. We thus propose HWS as a novel, F-box dependent regulator of miRNA biogenesis.\n\nSummary statementHAWAIIAN SKIRT is a regulator of Arabidopsis thaliana microRNA biogenesis and acts in an F-box-dependent manner.

plant biology↗

bioRxiv2017

A Collection Of Genetically Engineered Populus Trees Reveals Wood Biomass Traits That Predict Glucose Yield From Enzymatic Hydrolysis

Wood represents a promising source of lignocellulosic biomass for the production of bio-based renewables, especially biofuels. However, woody feedstocks must be improved to become competitive against petroleum. We created a collection of Populus trees consisting of 40 genetically engineered lines to modify and to better understand wood biomass properties. A total of 65 traits were measured in these trees and in the corresponding wild-type clone, including growth parameters, wood anatomical and structural properties, cell wall composition and analytical saccharification. The relationships between saccharification of glucose and biomass traits were investigated using multivariate data analysis methods and mathematical modeling. To circumvent potential trade-offs between biomass production and saccharification potential, we also estimated the \"total-wood glucose yield\" (TWG) expected after pretreatment and 72h of enzymatic hydrolysis from whole trees. A mathematical model estimated TWG from a subset of 22 wood biomass traits with good predictivity (Q2 = 0.8), while saccharification of glucose could be predicted from seven biomass traits (Q2 = 0.49). Among the seven diagnostic traits for saccharification, four also affected biomass production, such as the ratio of S- to G-lignin which was beneficial for saccharification but detrimental for growth. The contents of various matrix polysaccharides appeared important for predicting both saccharification and TWG, including low abundance monosaccharides. In particular, fucose and mannose contents negatively correlated with TWG, apparently by negatively associating with biomass production. Both biomass production and saccharification, and hence TWG, negatively correlated with arabinose and rhamnose contents, suggesting that these low abundance monosaccharides represent markers/targets for improving feedstocks.

plant biology↗

bioRxiv2017

Sequence Features Of MADS-Domain Proteins That Act As Hubs In The Protein-Protein Interaction Network Controlling Flower Development

The development of angiosperm flowers is regulated by homeotic MIKC-type MADS-domain transcription factors that activate or repress target genes via the formation of DNA-bound, organ specific tetrameric complexes. The protein-protein interaction (PPI) capabilities differ considerably between different MIKC-type proteins. The floral homeotic protein SEPALLATA3 (SEP3) acts as a hub that incorporates numerous other MADS-domain proteins into tetrameric complexes that would otherwise not form. However, the molecular mechanisms that underlie these promiscuous interactions remain largely unknown. In this study we created a collection of amino acid substitution mutants of SEP3 to quantify the contribution of individual residues on protein tetramerization during DNA-binding, employing methods of molecular biophysics. We show that leucine residues at certain key positions form a leucine zipper structure that is essential for tetramerization of SEP3, whereas the introduction of physicochemically very similar residues at respective sites impedes the formation of DNA-bound tetramers. Comprehensive molecular evolutionary analyses of MADS-domain proteins from a diverse set of flowering plants revealed exceedingly high conservation of the identified leucine residues within SEP3-subfamily proteins throughout angiosperm evolution. In contrast, MADS-domain proteins that are unable to tetramerize among themselves exhibit preferences for other amino acids at homologous sites. Our findings indicate that the subfamily-specific conservation of amino acid residues at just a few key positions account for subfamily-specific interaction capabilities of MADS-domain transcription factors and shaped the present-day structure of the PPI network controlling flower development.

plant biology↗