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bioRxiv2017

Laccaria bicolor MiSSP8 is a small-secreted protein decisive for the establishment of the ectomycorrhizal symbiosis

The ectomycorrhizal symbiosis is a predominant tree-microbe interaction in forest ecosystems sustaining tree growth and health. Its establishment and functioning implies a long-term and intimate relationship between the soil-borne fungi and the roots of trees. Mycorrhiza-induced Small Secreted Proteins (MiSSPs) are hypothesized as keystone symbiotic proteins, required to set up the symbiosis by modifying the host metabolism and/or building the symbiotic interfaces.\n\nL. bicolor MiSSP8 is the third most highly induced MiSSPs in symbiotic tissues and it is also expressed in fruiting bodies. The MiSSP8-RNAi knockdown mutants are strongly impaired in their mycorrhization ability with Populus, with the lack of fungal mantle and Hartig net development due to a lack of hyphal aggregation. MiSSP8 C-terminus displays a repetitive motif containing a kexin cleavage site, recognized by KEX2 in vitro. This suggests MiSSP8 protein might be cleaved into small peptides. Moreover, the MiSSP8 repetitive motif is found in other proteins predicted secreted by both saprotrophic and ectomycorrhizal fungi. Thus, our data indicate that MiSSP8 is a small-secreted protein involved at early stages of ectomycorrhizal symbiosis, likely by regulating hyphal aggregation and pseudoparenchyma formation.

plant biology↗

bioRxiv2017

Role of guard-cell ABA in determining maximal stomatal aperture and prompt vapor-pressure-deficit response

Abscisic acid (ABA) is known to be involved in stomatal closure. However, its role in stomatal response to rapid increases in the vapor pressure deficit (VPD) is unclear. To study this issue, we generated guard cell (GC)-specific ABA-insensitive Arabidopsis plants (GC-specific abi1-1; GCabi). Under normal conditions, the stomatal conductance (gs) and apertures of GCabi plants were greater than those of control plants. This supports GC ABA role as limiting maximal stomatal aperture under non-stressful conditions. When there was a rapid increase in VPD (0.15 to 1 kPa), the gs and stomatal apertures of GCabi decreased in a manner similar that observed in the WT control, but different from that observed in WT plants treated with fusicoccin. Low VPD increased the size of the stomatal apertures of the WT, but not of GCabi. We conclude that GC ABA does not play a significant role in the initial, rapid stomatal closure that occurs in response to an increase in VPD, but is important for stomatal adaptation to ambient VPD. We propose a biphasic angiosperm VPD-sensing model that includes an initial passive-hydraulic, ABA-independent phase and a subsequent ABA-dependent steady-state phase in which stomatal behavior is optimized for ambient VPD conditions.\n\nHighlightGuard-cell ABA does not play a significant role in the immediate closure of stomata following an increase in the VPD, but is important for stomatal adaptation to ambient VPD.

plant biology↗

bioRxiv2017

3D label-free imaging and analysis of Pinus pollen grains using optical diffraction tomography

O_LIThe structure of pollen grains is related to the reproductive function of the plants. Here, three-dimensional (3D) refractive index maps were obtained for individual conifer pollen grains using optical diffraction tomography (ODT).\nC_LIO_LIThe 3D morphological features of pollen grains from pine trees were investigated using measured refractive index maps, in which distinct substructures were clearly distinguished and analyzed.\nC_LIO_LIMorphological and physiochemical parameters of the pollen grains were quantified from the obtained refractive index (RI) maps and used to quantitatively study the interspecific differences of pollen grains from different strains.\nC_LIO_LIOur results demonstrate that ODT can assess the structure of pollen grains. This label-free and rapid 3D imaging approach may provide a new platform for understanding the physiology of pollen grains.\nC_LI

plant biology↗

bioRxiv2017

Effects of polyploidy on response of Dunaliella salina to salinity

In this study, effect of different percentages of polyploid cells of Dunaliella salina in culture medium, on growth and other biochemical parameters of algae under different salinity levels were investigated. The results indicated that concentration 3M NaCl is the optimal concentration of salt, since in this concentration, the highest enhancement in fresh and dry weight, chlorophyll and carotenoids, soluble sugar, glycerol, protein and starch content was observed in comparison with other concentrations. The amount of these metabolites declined in the concentrations under the optimum salinity. The least and highest amounts of MDA were observed at 1 and 4 M NaCl respectively. Polyploidy in optimum concentration of salt, caused further increment of the above growth parameters. In this relation, in most cases, treatment of 0.1% was more effective. The beneficial effects of polyploidy in non-optimal conditions were also found in some parameters such as biomass, chlorophyll, carotenoids, proteins and starch. The activity of antioxidant enzymes CAT, SOD and POD were maximum in 4 M NaCl. Polyploidy affected activity of these antioxidant enzymes in some concentrations of salt. Overall, our results suggest that the microalgae have significantly different responses to salt stress based on ploidy level of the algae.\n\nAbbreviations

plant biology↗

bioRxiv2017

Secondary metabolites and the antimicrobial potential of five different Coleus species in response to salinity stress

Salinity is one of the major abiotic stresses that affects the growth and productivity of plants. The presence of soluble salts at high concentration near the root system restricts the uptake of water by plants. Plants grown under saline conditions possess higher amounts of secondary metabolites compared with those grown under normal conditions. The use of traditional medicine to treat infectious diseases is increasing day by day throughout the world. Developing novel drugs with antimicrobial potential from the source of medicinal plants is receiving attention to replace the use of synthetic drugs and to combat the growth of multi-drug resistant strains. Thus screening of medicinal plant extracts is carried out to evaluate their antimicrobial potency. The present study aimed at determining the secondary metabolites and antimicrobial potential of leaf, stem and root ethanol and chloroform extracts of five different Coleus species; C.aromaticus, C.amboinicus, Cbarbatus, C.forskohlii and C.zeylanicus subjected to salinity stress. The up regulation in the content of plant bioactive compounds along with the antimicrobial activities of ethanol and chloroform extracts under the influence of salinity stress have been observed during the study in Coleus. The leaf, stem and root extracts of all the five Coleus species showed good antimicrobial activity against the tested pathogenic strains. The leaf extracts of Coleus showed higher inhibitory activity compared to the stem and root extracts. Ethanol extracts showed higher anti-microbial activity ranging from 1.5-100 mg/ml compared with the chloroform extracts ranging from 0.97-250 mg/ml respectively. The study revealed that the increased antimicrobial activity with increasing salinity might be due to the up regulation of secondary metabolites. The leaf, stem and root extracts of Coleus showed effective antimicrobial activity against the pathogenic strains even under saline conditions is due to the up regulation of secondary metabolites which provides a scope of developing novel drugs to treat infectious diseases.

plant biology↗

bioRxiv2017

Subtle perturbations of the maize methylome reveal genes and transposons silenced by DNA methylation

DNA methylation is a chromatin modification that can provide epigenetic regulation of gene and transposon expression. Plants utilize several pathways to establish and maintain DNA methylation in specific sequence contexts. The chromomethylase (CMT) genes maintain CHG (where H = A, C or T) methylation. The RNA-directed DNA methylation (RdDM) pathway is important for CHH methylation. Transcriptome analysis was performed in a collection of Zea mays lines carrying mutant alleles for CMT or RdDM-associated genes. While the majority of the transcriptome was not affected, we identified sets of genes and transposon families sensitive to context-specific decreases in DNA methylation in mutant lines. Many of the genes that are up-regulated in CMT mutant lines have high levels of CHG methylation, while genes that are differentially expressed in RdDM mutants are enriched for having nearby mCHH islands, providing evidence that context-specific DNA methylation directly regulates expression of a small number of genes. The analysis of a diverse set of inbred lines revealed that many genes regulated by CMTs exhibit natural variation for DNA methylation and gene expression. Transposon families with differential expression in the mutant genotypes show few defining features, though several families up-regulated in RdDM mutants show enriched expression in endosperm, highlighting the importance for this pathway during reproduction. Taken together, our findings suggest that while the number of genes and transposon families whose expression is reproducibly affected by mild perturbations in context-specific methylation is small, there are distinct patterns for loci impacted by RdDM and CMT mutants.

plant biology↗

bioRxiv2017

Expansion and diversification of the gibberellin receptor GIBBERELLIN INSENSITIVE DWARF1 (GID1) in land plants

Gibberellic acid (gibberellins, GA) controls key developmental processes in the life-cycle of land plants. By interacting with the GIBBERELLIN INSENSITIVE DWARF1 (GID1) receptor, GA regulates the expression of a wide range of genes through different pathways. Here we report the systematic identification and classification of GID1s in 52 plants genomes, encompassing from bryophytes and lycophytes, to several monocots and eudicots. We investigated the evolutionary relationship of GID1s using a comparative genomics framework and found strong support a previously proposed phylogenetic classification of this family in land plants. We identified lineage-specific expansions of particular subfamilies (i.e. GID1ac and GID1b) in different eudicot lineages (e.g. GID1b in legumes). Further, we found both, shared and divergent structural features between GID1ac and GID1b subgroups in eudicots, which provide mechanistic insights on their functions. Gene expression data from several species show that at least one GID1 gene is expressed in every sampled tissue, with a strong bias of GID1b expression towards underground tissues and dry legume seeds (typically with low GA levels). Taken together, our results support that GID1ac retained canonical GA signaling roles, whereas GID1b specialized in conditions of low GA concentrations. We propose that this functional specialization occurred initially at the gene expression level and was later fine-tuned by specific mutations that conferred greater GA affinity to GID1b, including a Phe residue in the GA-binding pocket. Finally, we discuss the importance of our findings to understand the diversification of GA perception mechanisms in land plants.

plant biology↗

bioRxiv2017

Investigating on relationship between effective quantum efficiency and irradiance

AbstractModels describing the relationship between effective quantum efficiency of PS II ({Phi}PSII) and irradiance (I) are routinely used to determine how irradiance influences effective quantum efficiency and photosynthetic electron transport rate (ETR). However, with no single model one can accurately describe the relationship between{Phi} PSII and I, and explain the interdependence between{Phi} PSII and biophysical properties of photosynthetic pigments, especially in plants growing under low level irradiances. Basing on the mechanistic model of photosynthetic electron transport rate we have developed the model of the relationship between{Phi} PSII and I. The new model reveals that{Phi} PSII increases with photochemistry (kP) and heat dissipation (kD). Furthermore, the values of key parameters calculated using the new model were compared with the values calculated with two other empirical models. The new model was perfectly fitted to the light-response curves of{Phi} PSII. The key calculated photosynthetic parameters: maximum{Phi} PSII, maximum ETR and their corresponding saturation irradiance were close to the measured values. In addition, our model associates{Phi} PSII with intrinsic features of photosynthetic pigments. We concluded that{Phi} PSII decreased with increasing I due to the decrease in the effective absorption cross-section of photosynthetic pigments molecules.\n\nHighlightA model of the relationship between effective quantum efficiency of PS II ({Phi}PSII) and irradiance (I) has been developed. Using this new model it was found that{Phi} PSII decreased with increasing I due to the decrease in the effective absorption cross-section of photosynthetic pigments molecules.\n\nAbbreviations

plant biology↗

bioRxiv2017

k-mer grammar uncovers maize regulatory architecture

Only a small percentage of the genome sequence is involved in regulation of gene expression, but to biochemically identify this portion is expensive and laborious. In species like maize, with diverse intergenic regions and lots of repetitive elements, this is an especially challenging problem. While regulatory regions are rare, they do have characteristic chromatin contexts and sequence organization (the grammar) with which they can be identified. We developed a computational framework to exploit this sequence arrangement. The models learn to classify regulatory regions based on sequence features - k-mers. To do this, we borrowed two approaches from the field of natural language processing: (1) \"bag-of-words\" which is commonly used for differentially weighting key words in tasks like sentiment analyses, and (2) a vector-space model using word2vec (vector-k-mers), that captures semantic and linguistic relationships between words. We built \"bag-of-k-mers\" and \"vector-k-mers\" models that distinguish between regulatory and non-regulatory regions with an accuracy above 90%. Our \"bag-of-k-mers\" achieved higher overall accuracy, while the \"vector-k-mers\" models were more useful in highlighting key groups of sequences within the regulatory regions. These models now provide powerful tools to annotate regulatory regions in other maize lines beyond the reference, at low cost and with high accuracy.

plant biology↗

bioRxiv2017

Development of an in vitro pre-mRNA splicing assay using plant nuclear extract

BackgroundPre-mRNA splicing is an essential post-transcriptional process in all eukaryotes. In vitro splicing systems using nuclear or cytoplasmic extracts from mammalian cells, yeast, and Drosophila have provided a wealth of mechanistic insights into assembly and composition of the spliceosome, splicing regulatory proteins and mechanisms of pre-mRNA splicing in non-plant systems. The lack of an in vitro splicing system prepared from plant cells has been a major limitation in splicing research in plants.\n\nResultsHere we report an in vitro splicing assay system using plant nuclear extract. Several lines of evidence indicate that nuclear extract (NE) derived from Arabidopsis seedlings can convert pre-mRNA substrate (LHCB3) into a spliced product. These include: i) generation of an RNA product that corresponds to the size of expected mRNA, ii) a junction-mapping assay using S1 nuclease revealed that the two exons are spliced together, iii) the reaction conditions are similar to those found with non-plant extracts and iv) finally mutations in conserved donor and acceptor sites abolished the production of the spliced product.\n\nConclusionsThis first report on the plant in vitro splicing assay opens new avenues to investigate plant spliceosome assembly and composition, and splicing regulatory mechanisms specific to plants.

plant biology↗

bioRxiv2017

LRX Proteins play a crucial role in pollen grain and pollen tube cell wall development

Leucine-rich repeat extensins (LRXs) are chimeric proteins containing an N-terminal leucine-rich repeat (LRR) and a C-terminal extensin domain. LRXs are involved in cell wall formation in vegetative tissues and required for plant growth. However, the nature of their role in these cellular processes remains to be elucidated. Here, we used a combination of molecular techniques, light microscopy, and transmission electron microscopy to characterize mutants of pollen-expressed LRXs in Arabidopsis thaliana. Mutations in multiple pollen-expressed lrx genes causes severe defects in pollen germination and pollen tube (PT) growth, resulting in a reduced seed set. Physiological experiments demonstrate that manipulating Ca2+ availability partially suppresses the PT growth defects, suggesting that LRX proteins influence Ca2+-related processes. Furthermore, we show that LRX protein localizes to the cell wall, and its LRR-domain (which likely mediates protein-protein interactions) is associated with the plasma membrane. Mechanical analyses by cellular force microscopy and finite element method-based modelling revealed significant changes in the material properties of the cell wall and the fine-tuning of cellular biophysical parameters in the mutants compared to the wild type. The results indicate that LRX proteins might play a role in cell wall-plasma membrane communication, influencing cell wall formation and cellular mechanics.

plant biology↗

bioRxiv2017

A comparison of root and shoot hydraulics, aquaporin expression and leaf gas exchange between two grapevine cultivars reveals differences in hydraulic control mediated by aquaporins

Hydraulics of plants that take different strategies of stomatal control under water stress are still relatively poorly understood. Here we explore how root and shoot hydraulics, gas exchange, aquaporin expression and abscisic acid (ABA) concentration in leaf xylem sap ([ABA]xylem) may be involved and coordinated. A comparison in responses to mild water stress and ABA application was made between two cultivars of Vitis vinifera L. previously classified as isohydric (Grenache) and anisohydric (Syrah). Grenache showed stronger adjustments of leaf, plant, and root hydraulic conductances to decreased soil moisture and a steeper correlation of stomatal conductance (gs) to [ABA]xylem than Syrah resulting in greater conservation of soil moisture, but not necessarily more isohydric behaviour. Under well-watered conditions, changes in vapour pressure deficit (VPD) had a strong influence on gs in both cultivars with adjustments of leaf hydraulic conductance. Grenache was more sensitive to decreases in soil water availability compared to Syrah that rather responded to VPD. There were stronger correlations between plant hydraulic parameters and changes in aquaporin gene expression in leaves and roots of Grenache. Overall, the results reinforce the hypothesis that both hydraulic and chemical signals significantly contribute to the differences in water conservation behaviours of the two cultivars.

plant biology↗

bioRxiv2017

A global comparison of the nutritive values of forage plants grown in contrasting environments

Forage plants are valuable because they maintain wild and domesticated herbivores, and sustain the delivery of meat, milk and other commodities. Forage plants contain different quantities of fibre, lignin, minerals and protein, and vary in the proportion of their tissue that can be digested by herbivores. These nutritive components are important determinants of consumer growth rates, reproductive success and behaviour. A dataset was compiled to quantify variation in forage plant nutritive values within- and between-plant species, and to assess variation between plant functional groups and bioclimatic zones. 1,255 geo-located records containing 3,774 measurements of nutritive values for 136 forage plant species grown in 30 countries were obtained from published articles. Spatial variability in forage nutritive values indicated that climate modified plant nutritive values. Forage plants grown in arid and equatorial regions generally contained less digestible material than those grown in temperate and tundra regions; containing more fibre and lignin, and less protein. These patterns may reveal why herbivore body sizes, digestion and migration strategies are different in warmer and drier regions. This dataset also revealed the capacity for variation in the nutrition provided by forage plants. The proportion of the plant tissue that was digestible ranged between species from 2-91%. The amount of fibre contained within plant material ranged by 23-90%, protein by 2-36%, lignin by 1-21% and minerals by 2-22%. Water contents also varied substantially; ranging from 3-89% of standing biomass. On average, grasses and tree foliage contained the most fibre, whilst herbaceous legumes contained the most protein and tree foliage contained the most lignin. However, there were individual species within each functional group that were highly nutritious. This dataset may be used to identify forage plant species with useful traits which can be cultivated to enhance livestock productivity and inform wild herbivore conservation strategies.

plant biology↗

bioRxiv2017

PWO1 interacts with PcG proteins and histones to regulate Arabidopsis flowering and development.

Polycomb-group (PcG) proteins mediate epigenetic gene regulation by setting H3K27me3 via Polycomb Repressive Complex 2 (PRC2). In plants, it is largely unclear how PcG proteins are recruited to their target genes.\n\nHere, we identified the PWWP-DOMAIN INTERACTOR OF POLYCOMBS1 (PWO1) protein which interacts with all three Arabidopsis PRC2 histone methyltransferases and is required for keeping full H3 occupancy at several Arabidopsis genes. PWO1 localizes and recruits CLF to nuclear speckles in tobacco nuclei, suggesting a role in spatial organization of PcG regulation. PWO1 belongs to a gene family with three members acting redundantly: pwo1 pwo2 pwo3 triple mutants are seedling lethal and show shoot and root meristem arrest, while pwo1 single mutants are early flowering. Interestingly, PWO1s PWWP domain confers binding to histones, which is reduced by a point mutation in a highly conserved residue of this domain and blocked by phosphorylation of H3S28. PWO1 carrying this mutation is not able to fully complement the pwo1 pwo2 pwo3 triple mutant, indicating the requirement of this domain for PWO1 in vivo activity. Thus, the PWO family may present a novel class of histone readers which are involved in recruiting PcG proteins to subnuclear domains and in promoting Arabidopsis development.

plant biology↗

bioRxiv2017

Characterisation of the pathogenicity of strains of Pseudomonas syringae towards cherry and plum

Bacterial canker is a major disease of cherry and other stone fruits caused by several pathovars of Pseudomonas syringae. These are P.s pv. morsprunorum race 1 (Psm R1), P.s pv. morsprunorum race 2 (Psm R2) and P.s pv. syringae (Pss). Psm R1 and R2 were originally designated as races of the same pathovar, however phylogenetic analysis has revealed them to be distantly related. This study characterised the pathogenicity of P. syringae on cherry and plum, in the field and the laboratory. The field experiment identified variation in host cultivar susceptibility to the different pathogen clades. The cherry cultivar Merton Glory exhibited a broad resistance to all clades, whilst cultivar Van showed race-specific resistance. Psm R1 may be divided into a race structure with some strains pathogenic to both cherry and plum and others only pathogenic to plum. The results of laboratory-based pathogenicity tests were compared to results obtained on whole-trees. Only cut shoot inoculations were found to be sensitive enough to detect cultivar variation in susceptibility. Measuring population growth of bacteria in detached leaves reliably discriminated pathogens from non-pathogens. In addition, symptom appearance discriminated Psm races from non-pathogens which triggered a rapid hypersensitive response (HR). The pathogen Pss rapidly induced disease lesions and therefore may exhibit a more necrotrophic lifestyle than hemi-biotrophic Psm races. This in-depth study of pathogenic interactions, identification of host resistance and optimisation of laboratory assays, will provide a framework for future genetic dissection of virulence and host resistance mechanisms.

plant biology↗

bioRxiv2017

The hydrophobin-like OmSSP1 may be an effector in the ericoid mycorrhizal symbiosis

Mutualistic and pathogenic plant-colonizing fungi use effector molecules to manipulate the host cell metabolism to allow plant tissue invasion. Some small secreted proteins (SSPs) have been identified as fungal effectors in both ectomycorrhizal and arbuscular mycorrhizal fungi, but it is currently unknown whether SSPs also play a role as effectors in other mycorrhizal associations. Ericoid mycorrhiza is a specific endomycorrhizal type that involves symbiotic fungi mostly belonging to the Leotiomycetes (Ascomycetes) and plants in the family Ericaceae. Genomic and RNASeq data from the ericoid mycorrhizal fungus Oidiodendron maius led to the identification of several symbiosis-upregulated genes encoding putative SSPs. OmSSP1, the most highly symbiosis up-regulated SSP, was found to share some features with fungal hydrophobins, even though it lacks the Pfam hydrophobin domain. Sequence alignment with other hydrophobins and hydrophobin-like fungal proteins placed OmSSP1 within Class I hydrophobins. However, the predicted features of OmSSP1 may suggest a distinct type of hydrophobin-like proteins. The presence of a predicted signal peptide and a yeast-based signal sequence trap assay demonstrate that OmSSP1 is secreted during symbiosis. OmSSP1 null-mutants showed a reduced capacity to form ericoid mycorrhiza with Vaccinium myrtillus roots, suggesting a role as effectors in the ericoid mycorrhizal interaction.

plant biology↗

bioRxiv2017

Reassessing the evolution of strigolactone synthesis and signalling

Strigolactones (SLs) are an important class of carotenoid-derived signalling molecule in plants, which function both as exogenous signals in the rhizosphere, and as endogenous plant hormones. In flowering plants, SLs are synthesized by a core pathway of four enzymes, and are perceived by the DWARF14 (D14) receptor, leading to degradation of SMAX1-LIKE7 (SMXL7) target proteins in a manner dependent on the SCFMAX2 ubiquitin ligase. The evolutionary history of SLs is poorly understood, and it is not clear whether SL synthesis and signalling are present in all land plant lineages, nor when these traits evolved. We have utilized recently-generated genomic and transcriptomic sequences from across the land plant clade to resolve the origin of each known component of SL synthesis and signalling. We show that all enzymes in the core SL synthesis pathway originated at or before the base of land plants, consistent with the previously observed distribution of SLs themselves in land plant lineages. We also show that the late-acting enzyme LATERAL BRANCHING OXIDOREDUCTASE (LBO) is considerably more ancient than previously thought. We perform a detailed phylogenetic analysis of SMXL proteins, and show that specific SL target proteins only arose in flowering plants. We also assess diversity and protein structure in the SMXL family, identifying several previously unknown clades. Overall, our results suggest that SL synthesis is much more ancient than canonical SL signalling, consistent with the idea that SLs first evolved as rhizosphere signals, and were only recruited much later as hormonal signals.

plant biology↗

bioRxiv2017

Natural Variation of OsLG3 Controls Drought Stress Tolerance in Rice by Inducing ROS Scavenging

BackgroundImproving performance of rice under drought stress has potential to significant impact on rice productivity. Previously we reported that OsLG3 positively control rice grain length and yield.\n\nResultsIn this study, we found that OsLG3 was more strongly expressed in upland rice compared to lowland rice under drought stress condition. Candidate gene association analysis showed that the natural variation in OsLG3 was associated with tolerance to water deficit stress in germinating rice seeds. Transgenic rice with enhanced OsLG3 expression exhibited improved tolerance to drought and that is most likely due to enhanced ROS scavenging efficiency. Phylogenetic analysis and pedigree records indicated that the tolerant allele of OsLG3 has potential to improve drought tolerance of japonica rice.\n\nConclusionsCollectively, our work revealed that the natural variation of OsLG3 contributes to rice drought tolerance and the elite allele of OsLG3 is a promising genetic resource for the development of drought-tolerant and high-yield rice varieties.

plant biology↗