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At least 649 records · Page 36Linked to original sources

bioRxiv2018

The chloroplast 2-cysteine peroxiredoxin functions as thioredoxin oxidase in redox regulation of chloroplast metabolism

Thiol-dependent redox regulation controls central processes in plant cells including photosynthesis. Thioredoxins reductively activate e.g. Calvin-Benson cycle enzymes. However the mechanism of oxidative inactivation is unknown despite its importance for efficient regulation. Here, the abundant 2-cysteine peroxiredoxin (2-CysPrx), but not its site-directed variants, mediates rapid inactivation of reductively activated fructose-1,6-bisphosphatase and NADPH-dependent malate dehydrogenase (MDH) in the presence of the proper thioredoxins. Deactivation of phosphoribulokinase and MDH was compromised in 2cysprxAB mutants plants upon light/dark transition compared to wildtype. The decisive role of 2cysprxAB in regulating photosynthesis was evident from reoxidation kinetics of ferredoxin upon darkening of intact leaves since its half time decreased 3.5-times in 2cysprxAB. The disadvantage of inefficient deactivation turned into an advantage in fluctuating light. The results show that the 2-CysPrx serves as electron sink in the thiol network important to oxidize reductively activated proteins and represents the missing link in the reversal of thioredoxin-dependent regulation.

plant biology↗

bioRxiv2018

Seasonal changes of metabolites in phloem sap from Broussonetia papyrifera

Gas chromatography-Mass spectrometry (GC-MS) were employed to analyze the whole metabolites in phloem sap of Broussonetia papyrifera and the seasonal changes of content of these metabolites were also investigated. Thirty-eight metabolites were detected in BP phloem exudates. The highest content (44.59mg g-1) of total metabolites was presented in March. High contents of organic acids and sugars were detected in BP phloem exudates from all growing months. Smaller amounts of fatty acids and alcohols were also detected in BP phloem exudates. Interestingly, some metabolites, such as PI3 kinase inhibitor, Chlorogenic acid, Chelerythrine and palmitic acid, which have properties of bioactivity to anticancer and anti-inflammation, were also detected. Quininic acid was the most abundant organic acid, representing up to 86.3% (average value) of all organic acids. D-fructose, D-glucose, and sucrose were the major soluble sugars in phloem saps and the maximum of sugars content was 19.76mg g-1 (average value) in November. Seasonal changes of contents of metabolites were different among individuals. The metabolites analysis double confirmed that the BP phloem sap can be serviced as an important resource for synthesis of pharmaceutical and human health products.

plant biology↗

bioRxiv2018

Physicochemical characteristics and high sensory acceptability in cappuccinos made with jackfruit seeds replacing cocoa powder

Jackfruit seeds are an under-utilized waste product in many tropical countries. In this work, we demonstrate the potential of roasted jackfruit seeds to substitute for cocoa powder in cappuccino formulations. Two different flours were produced from a hard variety jackfruit by drying or fermenting the seeds prior to roasting. Next, seven formulations were prepared with 50%, 75%, and 100% substitution of cocoa powder with jackfruit seed flours. The acceptance of cappuccinos by consumers (n=126) and quantitative descriptive analysis (QDA(R)) were used to describe the preparations. Physicochemical proprieties were also evaluated. When 50% and 75% cocoa powder was replaced with dry jackfruit seed flour, there was no change in sensory acceptability or technological proprieties; however, it is possible identify advantages to using dry jackfruit seed flour, including moisture reduction and high wettability, solubility and sensory acceptation of the chocolate aroma. The principal component analysis of QDA(R) explained 90% variances; cluster analysis enabled the definition of four groups for six cappuccino preparations. In fact, dry jackfruit seed flour is an innovative cocoa powder substitute; it could be used in food preparations, consequently utilizing this tropical fruit waste by incorporating it as an ingredient in a common product of the human diet.

plant biology↗

bioRxiv2018

Sensitive detection of pre-integration intermediates of LTR retrotransposons in crop plants

Retrotransposons have played an important role in the evolution of host genomes1,2. Their impact on host chromosomes is mainly deduced from the composition of DNA sequences, which have been fixed over evolutionary time. These studies provide important \"snapshots\" reflecting historical activities of transposons but do not predict current transposition potential. We previously reported Sequence-Independent Retrotransposon Trapping (SIRT) as a methodology that, by identification of extrachromosomal linear DNA (eclDNA), revealed the presence of active LTR retrotransposons in Arabidopsis9. Unfortunately, SIRT cannot be applied to large and transposon-rich genomes of crop plants. We have since developed an alternative approach named ALE-seq (amplification of LTR of eclDNAs followed by sequencing). ALE-seq reveals sequences of 5 LTRs of eclDNAs after two-step amplification: in vitro transcription and subsequent reverse transcription. Using ALE-seq in rice, we detected eclDNAs for a novel Copia family LTR retrotransposon, Go-on, which is activated by heat stress. Sequencing of rice accessions revealed that Go-on has preferentially accumulated in indica rice grown at higher temperatures. Furthermore, ALE-seq applied to tomato fruits identified a developmentally regulated Gypsy family of retrotransposons. Importantly, a bioinformatic pipeline adapted for ALE-seq data analyses allows the direct and reference-free annotation of new active retroelements. This pipeline allows assessment of LTR retrotransposon activities in organisms for which genomic sequences and/or reference genomes are unavailable or are of low quality.

plant biology↗

bioRxiv2018

Vascular brassinosteroid receptors confer drought resistance without penalizing plant growth

Drought represents a major threat to food security. Mechanistic data describing plant responses to drought have been studied extensively and genes conferring drought resistance have been introduced into crop plants. However, plants with enhanced drought resistance usually display lower growth, highlighting the need for strategies to uncouple drought resistance from growth. Here, we show that overexpression of BRL3, a vascular-enriched member of the brassinosteroid receptor family, can confer drought stress tolerance in Arabidopsis. Whereas loss-of-function mutations in the ubiquitously expressed BRI1 receptor leads to drought resistance at the expense of growth, overexpression of BRL3 receptor confers drought tolerance without penalizing overall growth. Systematic analyses reveal that upon drought stress, increased BRL3 triggers the accumulation of osmoprotectant metabolites including proline and sugars. Transcriptomic analysis suggests that this results from differential expression of genes in the vascular tissues. Altogether, this data suggests that manipulating BRL3 expression could be used to engineer drought tolerant crops.

plant biology↗

bioRxiv2018

PRX9 and PRX40 are extensin peroxidases essential for maintaining tapetum and microspore cell wall integrity during Arabidopsis anther development

Pollen and microspore development is an essential step in the life cycle of all land plants that generate male gametes. Within flowering plants, pollen development occurs inside of the anther. Here, we report the identification of two class III peroxidase-encoding genes, PRX9 and PRX40, that are genetically redundant and essential for proper anther and pollen development in Arabidopsis thaliana. Arabidopsis double mutants devoid of functional PRX9 and PRX40 are male-sterile. The mutant anthers display swollen, hypertrophic tapetal cells and pollen grains, suggesting disrupted cell wall integrity. These phenotypes ultimately lead to nearly 100%-penetrant pollen degeneration upon anther maturation. Using immunochemical and biochemical approaches, we show that PRX9 and PRX40 are likely extensin peroxidases that contribute to the establishment of tapetal cell wall integrity during anther development. This work identifies PRX9 and PRX40 as the first extensin peroxidases to be described in Arabidopsis and highlights the importance of extensin cross-linking during plant development.

plant biology↗

bioRxiv2018

Temperature response of Rubisco kinetics in Arabidopsis thaliana: thermal breakpoints and implications for reaction mechanisms

Optimization of Rubisco kinetics could improve photosynthetic efficiency, ultimatly resulting in increased crop yield. However, imprecise knowledge of the reaction mechanism and the individual rate constants limit our ability to optimize the enzyme. Membrane inlet mass spectrometery (MIMS) may offer benefits over traditional methods for determining individual rate constants of the Rubisco reaction mechanism, as it can directly monitor concentration changes in CO2, O2, and their isotopologs during assays. However, a direct comparsion of MIMS to the traditional Radiolabel method of determining Rubisco kinetic parameters has not been made. Here, the temperature responses of Rubisco kinetic parameters from Arabidopsis thaliana were measured using the Radiolabel and MIMS methods. The two methods provided comparable parameters above 25 {degrees}C, but temperature responses deviated at low temperature as MIMS derived catalytic rates of carboxylation, oxygenation, and CO2/O2 specificity showed thermal breakpoints. Here we discuss the variability and uncertainty surrounding breakpoints in the Rubisco temperature response and relavance of individual rate constants of the reaction mechanisms to potential breakpoints.

plant biology↗

bioRxiv2018

Plant trichomes and a single gene GLABRA1 contribute to insect community composition on field-grown Arabidopsis thaliana

Background: Genetic variation in plants alters insect abundance and community structure in the field; however, little is known about the importance of a single gene among diverse plant genotypes. In this context, Arabidopsis trichomes provide an excellent system to discern the roles of natural variation and a key gene, GLABRA1, in shaping insect communities. In this study, we transplanted two independent glabrous mutants (gl1-1 and gl1-2) and 17 natural accessions of Arabidopsis thaliana to two localities in Switzerland and Japan.\n\nResults: Fifteen insect species inhabited plant accessions, with 10-30% broad-sense heritability of community indices being detected, such as species richness and diversity. The total abundance of leaf-chewing herbivores was negatively correlated with trichome density at both the field sites, while glucosinolates had variable effects on leaf chewers between the two sites. Interestingly, there was a parallel tendency for the abundance of leaf chewers to be higher on gl1-1 and gl1-2 than for their different parental accessions, Ler-1 and Col-0, respectively. Furthermore, the loss of function in the GLABRA1 gene significantly decreased the resistance of plants to the two predominant chewers, flea beetles and turnip sawflies.\n\nConclusions: Overall, our results indicate that insect community composition on A. thaliana is heritable across two distant field sites, with GLABRA1 playing a key role in altering the abundance of leaf-chewing herbivores. Given that such a trichome variation is widely observed in Brassicaceae plants, the present study exemplifies the community-wide impact of a single plant gene on crucifer-feeding insects in the field.

plant biology↗

bioRxiv2018

Photoperiod sensing of the circadian clock is controlled by ELF3 and GI

ELF3 and GI are two important components of the Arabidopsis circadian clock. They are not only essential for the oscillator function but are also pivotal in mediating light inputs to the oscillator. Lack of either results in a defective oscillator causing severely compromised output pathways, such as photoperiodic flowering and hypocotyl elongation. Although single loss of function mutants of ELF3 and GI have been well-studied, their genetic interaction remains unclear. We generated an elf3 gi double mutant to study their genetic relationship in clock-controlled growth and phase transition phenotypes. We found that ELF3 and GI repress growth differentially during the night and the day, respectively. Circadian clock assays revealed that ELF3 and GI are essential Zeitnehmers that enable the oscillator to synchronize the endogenous cellular mechanisms to external environmental signals. In their absence, the circadian oscillator fails to synchronize to the light-dark cycles even under diurnal conditions. Consequently, clock-mediated photoperiod-responsive growth and development is completely lost in plants lacking both genes, suggesting that ELF3 and GI together convey photoperiod sensing to the central oscillator. Since ELF3 and GI are conserved across flowering plants and represent important breeding and domestication targets, our data highlight the possibility of developing photoperiod-insensitive crops by adjusting the allelic combination of these two key genes.\n\nOne sentence summaryELF3 and GI are essential for circadian clock mediated photoperiod sensing.

plant biology↗

bioRxiv2018

First natural crossover recombination of intact ORFs between two distinct species of the family Closteroviridae

Lettuce chlorosis virus-SP (LCV-SP) (family Closteroviridae, genus Crinivirus), is a new strain of LCV which is able to infect green bean plants and incapable of infecting lettuce crops. In the present study, high throughput and Sanger sequencing of RNA was used to obtain the LCV-SP full-length sequence. The LCV-SP genome comprises 8825 nt and 8672 nt equivalent with RNA1 and RNA2 respectively. RNA1 of LCV-SP contains four ORFs, the proteins encoded by the ORF1a and ORF1b are closely related to LCV RNA1 from California (FJ380118) whereas the 3{acute} end encodes proteins which share high amino acid sequence identity with RNA1 of BnYDV (EU191904). The genomic sequence of RNA2 consists of 8 ORFs, instead of 10 ORFs contained in LCV-California isolate. The distribution of vsiRNA (virus-derived small interfering RNA) along the LCV-SP genome suggested the presence of subgenomic RNAs corresponding with HSP70, P6.4 and P60. Results of the analysis using RDP4 and Simplot programs are the proof of the evidence that LCV-SP is the first recombinant of the family Closteroviridae by crossover recombination of intact ORFs, being the LCV RNA1 (FJ380118) and BnYDV RNA1 (EU191904) the origin of the new LCV strain. Genetic diversity values of virus isolates in the recombinant region obtained after sampling LCV-SP infected green bean between 2011 and 2017 might suggest that the recombinant virus event occurred in the area before this period. The presence of LCV-SP shows the role of recombination as a driving force of evolution within the genus Crinivirus, a globally distributed, emergent genus.

plant biology↗

bioRxiv2018

RCD1 Coordinates Chloroplastic and Mitochondrial Electron Transfer through Interaction with ANAC Transcription Factors

Signaling from chloroplasts and mitochondria, both dependent on reactive oxygen species (ROS), merge at the nuclear protein RADICAL-INDUCED CELL DEATH1 (RCD1). ROS produced in the chloroplasts affect the abundance, thiol redox state and oligomerization of RCD1. RCD1 directly interacts in vivo with ANAC013 and ANAC017 transcription factors, which are the mediators of the ROS-related mitochondrial complex III retrograde signa and suppresses activity of ANAC013 and ANAC017. Inactivation of RCD1 leads to increased expression of ANAC013 and ANAC017-regulated genes belonging to the mitochondrial dysfunction stimulon (MDS), including genes for mitochondrial alternative oxidases (AOXs). Accumulating AOXs and other MDS gene products alter electron transfer pathways in the chloroplasts, leading to diminished production of chloroplastic ROS and increased protection of photosynthetic apparatus from ROS damage. RCD1-dependent regulation affects chloroplastic and mitochondrial retrograde signaling including chloroplast signaling by 3-phosphoadenosine 5-phosphate (PAP). Sensitivity of RCD1 to organellar ROS provides feedback control of nuclear gene expression.

plant biology↗

bioRxiv2018

StomataCounter: a deep learning method applied to automatic stomatal identification and counting

O_LIStomata fulfill an important physiological role and are often phenotyped by researchers in many fields. Currently, no fully automated method exists to perform this task. Researchers typically rely on manual counts of stomata, which is an error-prone method and difficult to reproduce.\nC_LIO_LIWe introduce StomataCounter, an automated stomata counting system using a deep convolutional neural network to identify pores in a variety of different microscopic images. We used a human-in-the-loop approach to train and refine a neural network on a large variety of microscopic images, which helps us achieve robust detection among a number of datasets.\nC_LIO_LIOur network achieves 98.1% identification accuracy on Ginkgo SEM micrographs, and 94.2% transfer accuracy when tested on untrained species.\nC_LIO_LITo facilitate adoption of the method, we make a web tool available under http://www.stomata.science/\nC_LI

plant biology↗

bioRxiv2018

Early in planta detection of Xanthomonas axonopodis pv. punicae in pomegranate using enhanced loop-mediated isothermal amplification assay

Bacterial blight in pomegranate caused by Xanthomonas axonopodis pv. punicae (Xap) is an increasing threat for pomegranate cultivation in India. To prevent the economic losses, it is pivotal to detect the infection in latent stages rather than in later stages. We have developed an enhanced method termed as loop-mediated isothermal amplification (LAMP) technique to evaluate for the latent detection of Xap in pomegranate using six set of specific primers. Three DNA intercalating dyes were used, such as Ethidium bromide, hydroxynaphthol blue (HNB) and SYBR Green resulted in visualising the positivity for LAMP assay. The reaction time and temperature were to be 65{degrees}C from 30 min onwards, for the dyes and its sensitivity was observed up to 10-7 ng in the LAMP assay. For field applicability, LAMP assay detected Xap on 7th day post infection while the PCR amplified Xap after 11th day post infection. Finally, the specificity of LAMP assay was validated to be positive with ten Xap isolates for its accuracy and 29 non-Xap bacterial isolates showed negative results. Moreover, this method could be used as a better alternative to PCR based methods, for early detection of the pathogens.

plant biology↗

bioRxiv2018

Lack of negative density-dependence regulation in a dominant oak tree from a neotropical highland forest

Conspecific negative density-dependence(CNDD) is one of the main mechanisms proposed to regulate species coexistence. Tropical highland forests, in contrast to diverse lowland forests, are commonly dominated by a few tree species. Testing the importance of density-dependence effects on seedling establishment of dominant trees may provide insights on the mechanisms regulating population dynamics and forest composition of tropical highlands. We tested the importance of CNDD regulation on seedling survival and recruitment of Quercus costaricensis, a monodominant oak in the Talamanca highland forests of Costa Rica. We used spatial statistics and generalized linear mixed models to test the effects of conspecific density, distance to the nearest adult, density of Chusquea bamboo shoots, and herbivory on the annual survival probability of 3538 seedlings between 2014 and 2017. We did not find any effect of CNDD on seedling survival. However, bamboo density and herbivory both significantly decreased seedling survival. All seedlings had signs of herbivory and predator satiation may explain the lack of density dependent regulation in this species. We argue that the lack of intraspecific density regulation at the seedling stage may explain the dominance of Q. costaricensis in the highland forests of Costa Rica. Local density of this endemic oak is instead regulated by herbivory and the density of Chusquea.

plant biology↗

bioRxiv2018

Influence of plant growth regulators and nitrogen sources on the production and development of Brachiaria decumbens cv. Basilisk

The aim was to evaluate the effect of seed treatment with plant growth regulators and nitrogen fertilization methods in Brachiaria decumbens cv. Basilisk on the growth and development through germinative characteristics, dry matter yield and physiological composition. Plant growth regulators increased germination and mass yields of plant structures in coated seeds. From the regression estimates, higher germination percentages and root dry mass production were obtained with the use of Plant growth regulators for the initial growth (10.3; 12.8 mL.kg-1 seed, respectively). Leaf and pseudostem mass production had a significant interaction effect between seed type and the use of growth regulator. Coated seeds had greater performance with absence or at lower levels of growth regulators, and embryo quality contributed to the greater formation of plant tissues. More efficient levels (8.85 and 9.57 mL.kg-1 seed) were observed for the yields of plant structures (leaf and pseudostem). Soil N-fertilization resulted in higher dry mass productions of leaf, stem, shoot and root, as well as for root volume. Rates of photoassimilate were increased by soil fertilization and use of plant growth regulators. The use of exogenous hormonal compounds acts on the organogenesis of plant tissues and increases the development of Brachiaria decumbens cv. Basilisk. Soil N-fertilization increase mass yields as it maximizes photosynthetic processes and growth rates.

plant biology↗

bioRxiv2018

Analysis of Transcripts and splice isoforms in Red Clover (Trifolium pratense L.) by single-molecule long-read sequencing

Red clover (Trifolium pratense L.) is an important cool-season legume plant, which is the most widely planted forage legume after alfalfa. Although a draft genome sequence was published already, the sequences and completed structure of mRNA transcripts remain unclear, which limit further explore on red clover. In this study, the red clover transcriptome was sequenced using single-molecule long-read sequencing to identify full-length splice isoforms, and 29,730 novel isoforms from known genes and 2,194 novel isoforms from novel genes were identified. A total of 5,492 alternative splicing events was identified and the majority of alter spliced events in red clover was corrected as intron retention. In addition, of the 15,229 genes detected by SMRT, 8,719 including 1,86,517 transcripts have at least one poly(A) site. Furthermore, we identified 4,333 long non-coding RNAs and 3,762 fusion transcripts. Our results show the feasibility of deep sequencing full-length RNA from red clover transcriptome on a single-molecule level.

plant biology↗

bioRxiv2018

Nucleus- and plastid-targeted annexin 5 promotes reproductive development in Arabidopsis and is essential for pollen and embryo formation

BackgroundPollen development is a strictly controlled post-meiotic process during which microspores differentiate into microgametophytes and profound structural and functional changes occur in organelles. Annexin 5 is a calcium- and lipid-binding protein that is highly expressed in pollen grains and regulates pollen development and physiology. To gain further insights into the role of ANN5 in Arabidopsis development, we performed detailed phenotypic characterization of Arabidopsis plants with modified ANN5 levels. In addition, interaction partners and subcellular localization of ANN5 were analyzed to investigate potential functions of ANN5 at cellular level.\n\nResultsHere, we report that RNAi-mediated suppression of ANN5 results in formation of smaller pollen grains, enhanced pollen lethality, and delayed pollen tube growth. ANN5 RNAi knockdown plants also displayed aberrant development during the transition from the vegetative to generative phase and during embryogenesis, reflected by delayed bolting time and reduced embryo size, respectively. At the subcellular level, ANN5 was delivered to the nucleus, nucleolus, and cytoplasm, and was frequently localized in plastid nucleoids, suggesting a likely role in interorganellar communication. Furthermore, ANN5-YFP co-immunoprecipitated with RABE1b, a putative GTPase, and interaction in planta was confirmed in plastidial nucleoids using FLIM-FRET analysis.\n\nConclusionsOur findings let us to propose that ANN5 influences basal cell homeostasis via modulation of plastid activity during pollen maturation. We hypothesize that the role of ANN5 is to orchestrate the plastidial and nuclear genome activities via protein-protein interactions however not only in maturing pollen but also during the transition from the vegetative to the generative growth and embryo development.

plant biology↗

bioRxiv2018

Ethylene signaling regulates natural variation in the abundance of antifungal acetylated diferuloylsucroses and Fusarium graminearum resistance in maize seedling roots

O_LIThe production and regulation of defensive specialized metabolites plays a central role in pathogen resistance in maize (Zea mays) and other plants. Therefore, identification of genes involved in plant specialized metabolism can contribute to improved disease resistance.\nC_LIO_LIWe used comparative metabolomics to identify previously unknown antifungal metabolites in maize seedling roots, and investigated the genetic and physiological mechanisms underlying their natural variation using quantitative trait locus (QTL) mapping and comparative transcriptomics approaches.\nC_LIO_LITwo maize metabolites, smilaside A (3,6-diferuloyl-3',6'-diacetylsucrose) and smiglaside C (3,6-diferuloyl-2',3',6'-triacetylsucrose), that may contribute to maize resistance against Fusarium graminearum and other fungal pathogens were identified. Elevated expression of an ethylene receptor gene, ETHYLENE INSENSITIVE 2 (ZmEIN2), co-segregated with decreased smilaside A/smiglaside C ratio. Pharmacological and genetic manipulation of ethylene availability and sensitivity in vivo indicated that, whereas ethylene was required for the production of both metabolites, the smilaside A/smiglaside C ratio was negatively regulated by ethylene sensitivity. This ratio, rather than the absolute abundance of these two metabolites, was important for maize seedling root defense against F. graminearum.\nC_LIO_LIEthylene signaling regulates the relative abundance of the two F. graminearum-resistance-related metabolites and affects resistance against F. graminearum in maize seedling roots.\nC_LI

plant biology↗