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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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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At least 433 records · Page 24Linked to original sources

bioRxiv2017

Simultaneous CRISPR/Cas9-mediated editing of cassava eIF4E isoforms nCBP-1 and nCBP-2 confers elevated resistance to cassava brown streak disease

Cassava brown streak disease (CBSD) is a major constraint on cassava yields in East and Central Africa and threatens production in West Africa. CBSD is caused by two species of positive sense RNA viruses belonging to the family Potyviridae, genus Ipomovirus: Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV). Diseases caused by the family Potyviridae require the interaction of viral genome-linked protein (VPg) and host eukaryotic translation initiation factor 4E (eIF4E) isoforms. Cassava encodes five eIF4E proteins: eIF4E, eIF(iso)4E-1, eIF(iso)4E-2, novel cap-binding protein-1 (nCBP-1), and nCBP-2. Protein-protein interaction experiments consistently found that VPg proteins associate with cassava nCBPs. CRISPR/Cas9-mediated genome editing was employed to generate ncbp-1, ncbp-2, and ncbp-1/ncbp-2 mutants in cassava cultivar 60444. Challenge with CBSV showed that ncbp-1/ncbp-2 mutants displayed delayed and attenuated CBSD aerial symptoms, as well as reduced severity and incidence of storage root necrosis. Suppressed disease symptoms were correlated with reduced virus titer in storage roots relative to wild-type controls. Our results demonstrate the ability to modify multiple genes simultaneously in cassava to achieve tolerance to CBSD. Future studies will investigate the contribution of remaining eIF4E isoforms on CBSD and translate this knowledge into an optimized strategy for protecting cassava from disease.

plant biology↗

bioRxiv2017

Hypoxia in the grape berry linked to mesocarp cell death: the role of seed respiration and lenticels on the berry pedicel

Mesocarp cell death (CD) during ripening is common in berries of seeded Vitis vinifera L wine cultivars. We examined if hypoxia within berries is linked to CD. Internal oxygen concentration ([O2]) across the mesocarp was measured in berries from Chardonnay and Shiraz, both seeded, and Ruby Seedless, using an oxygen micro-sensor. Steep [O2] gradients were observed across the skin and [O2] decreased toward the middle of the mesocarp. As ripening progressed the minimum [O2] approached zero in the seeded cultivars and correlated to CD. Seed respiration was a large proportion of total berry respiration early in ripening but did not account for O2 deficiency late in ripening. [O2] increased towards the central axis corresponding to the presence of air spaces visualised using x-ray microCT. These connect to lenticels on the pedicel that were critical for berry O2 uptake as a function of temperature, and when blocked caused anoxia in the berry, ethanol accumulation and CD. Lenticel area on Chardonnay pedicels was higher than that for Shiraz probably accounting for the lower sensitivity of Chardonnay berry CD to high temperatures. The implications of hypoxia in grape berries are discussed in terms of its role in ripening and berry water relations.\n\nHighlightGrape berry internal oxygen concentration is dependent upon lenticels on the pedicel and cultivar differences in lenticels may account for temperature sensitivity of cell death in the mesocarp.

plant biology↗

bioRxiv2017

A first global phylogeny of Maize chlorotic mottle virus

Maize chlorotic mottle virus has been rapidly spreading around the globe over the past decade. The interactions of Maize chlorotic mottle virus with potyviridae viruses causes an aggressive synergistic viral condition - maize lethal necrosis, which can cause total yield loss. Maize production in sub-Saharan Africa, where it is the most important cereal, is threatened by the arrival of maize lethal necrosis. We obtained Maize chlorotic mottle virus genome sequences from across East Africa and for the first time from Ecuador and Hawaii, and constructed a phylogeny which highlights the similarity of Chinese to African isolates, and Ecuadorian to Hawaiian isolates. We used a measure of clustering, the adjusted Rand index, to extract region-specific SNPs and coding variation that can be used for diagnostics. The population genetics analysis we performed shows that the majority of sequence diversity is partitioned between populations, with diversity extremely low within China and East Africa.

plant biology↗

bioRxiv2017

Endodermal differentiation is reconstructed by coordination of two parallel signaling systems derived from the stele in roots

The plant roots represent the exquisitely controlled cell fate map in which different cell types undergo a complete status transition from stem cell division and initial fate specification, to the terminal differentiation. The endodermis is initially specified in meristem but further differentiates to form Casparian strips (CSs), the apoplastic barrier in the mature zone for the selective transport between stele and outer tissues, and thus is regarded as plant inner skin. In the Arabidopsis thaliana root the transcription factors SHORTROOT (SHR) regulate asymmetric cell division in cortical initials to separate endodermal and cortex cell layer. In this paper, we utilized synthetic approach to examine the reconstruction of fully functional Casparian strips in plant roots. Our results revealed that SHR serves as a master regulator of a hierarchical signaling cascade that, combined with stele-derived small peptides, is sufficient to rebuild the functional CS in non-endodermal cells. This is a demonstration of the deployment of two parallel signaling systems, in which both apoplastic and symplastic communication were employed, for coordinately specifying the endodermal cell fate.

plant biology↗

bioRxiv2017

Quantitative proteomic analysis of auxin signaling during seedling development

Auxin induces rapid gene expression changes throughout plant development. How these transcriptional responses relate to changes in protein abundance is not well characterized. We have identified auxin regulated proteins in whole seedlings, roots and hypocotyls and at three different time points (30 min, 120 min and 3 hours) using an iTRAQ (isobaric tags for relative and absolute quantification) based quantitative proteomics approach. These profiling experiments detected 4,701 proteins from seedling tissue, 6,740 proteins from root tissue and 3,925 proteins from hypocotyl tissue. Comparisons between the differentially expressed proteins data sets showed little overlap, suggesting that auxin proteomes exhibit both temporal and spatial specificity. Numerous proteins showed significant changes in abundance following auxin treatment independent of changes in cognate transcript abundance. This includes several well characterized proteins with various roles in auxin pathways, suggesting that complex gene regulation mechanisms follow auxin signaling events. Specifically, regulation of translation may play a role as inferred from MapMan categorization analyses and protein interaction networks comprised of auxin regulated proteins. Additionally, functional categorization of auxin regulated proteins indicates rapid and complex metabolic changes occur in both roots and hypocotyls in response to auxin which are not apparent from transcriptome analyses. Altogether these data describe novel auxin-regulated proteomes and are an excellent resource for identifying new downstream signaling components related to auxin-mediated plant growth and development.

plant biology↗

bioRxiv2017

Revisiting criteria for plant miRNA annotation in the era of big data

MicroRNAs (miRNAs) are ~21 nucleotide-long regulatory RNAs that arise from endonucleolytic processing of hairpin precursors. Many function as essential post-transcriptional regulators of target mRNAs and long non-coding RNAs. Alongside miRNAs, plants also produce large numbers of short interfering RNAs (siRNAs), which are distinguished from miRNAs primarily by their biogenesis (typically processed from long double-stranded RNA instead of single-stranded hairpins) and functions (typically via roles in transcriptional regulation instead of post-transcriptional regulation). Next-generation DNA sequencing methods have yielded extensive datasets of plant small RNAs, resulting in many miRNA annotations, occasionally inaccurately curated. The sheer number of endogenous siRNAs compared to miRNAs has been a major factor in the erroneous annotation of siRNAs as miRNAs. Here, we provide updated criteria for the confident annotation of plant miRNAs, suitable for the era of \"big data\" from DNA sequencing. The updated criteria emphasize replication, the minimization of false positives, and they require next-generation sequencing of small RNAs. We argue that improved annotation systems are needed for miRNAs and all other classes of plant small RNAs. Finally, to illustrate the complexities of miRNA and siRNA annotation, we review the evolution and functions of miRNAs and siRNAs in plants.

plant biology↗

bioRxiv2017

Chromatin accessibility changes between Arabidopsis stem cells and mesophyll cells illuminate cell type-specific transcription factor networks

BackgroundCell differentiation is driven by changes in transcription factor (TF) activity and subsequent alterations in transcription. To study this process, differences in TF binding between cell types can be deduced by methods that probe chromatin accessibility. We used cell type-specific nuclei purification followed by the Assay for Transposase Accessible Chromatin (ATAC-seq) to delineate differences in chromatin accessibility and TF regulatory networks between stem cells of the shoot apical meristem (SAM) and differentiated leaf mesophyll cells of Arabidopsis thaliana.\n\nResultsChromatin accessibility profiles of SAM stem cells and leaf mesophyll cells were highly similar at a qualitative level, yet thousands of regions of quantitatively different chromatin accessibility were also identified. We found that chromatin regions preferentially accessible in mesophyll cells tended to also be substantially accessible in the stem cells as compared to the genome-wide average, whereas the converse was not true. Analysis of genomic regions preferentially accessible in each cell type identified hundreds of overrepresented TF binding motifs, highlighting a set of TFs that are likely important for each cell type. Among these, we found evidence for extensive co-regulation of target genes by multiple TFs that are preferentially expressed in one cell type or the other. For example, a set of zinc-finger TFs appear to control a suite of growth-and development-related genes specifically in stem cells, while another TF set co-regulates genes involved in light responses and photosynthesis specifically in mesophyll cells. Interestingly, the TFs within both of these sets also show evidence of extensively co-regulating each other.\n\nConclusionsQuantitative analysis of chromatin accessibility differences between stem cells and differentiated mesophyll cells allowed us to identify TF regulatory networks and downstream target genes that are likely to be functionally important in each cell type. Our findings that mesophyll cell-enriched accessible sites tend to already be substantially accessible in stem cells, but not vice versa, suggests that widespread regulatory element accessibility may be important for the developmental plasticity of stem cells. This work also demonstrates the utility of cell type-specific chromatin accessibility profiling in quickly developing testable models of regulatory control differences between cell types.

plant biology↗

bioRxiv2017

Split personality of Aluminum Activated Malate Transporter family proteins: facilitation of both GABA and malate transport

Plant aluminum activated malate transporters (ALMTs) are currently classified as anion channels; they are also known to be regulated by diverse signals leading to a range of physiological responses. Gamma-aminobutyric acid (GABA) regulation of anion flux through ALMT proteins requires the presence of a specific amino acid motif in ALMTs that shares similarity with a GABA-binding site in mammalian GABAA receptors. Here, we explore why TaALMT1-activation leads to a negative correlation between malate efflux and endogenous GABA concentrations ([GABA]i) in both wheat root tips and in heterologous expression systems. We show that TaALMT1 activation reduces [GABA]i because TaALMT1 facilitates GABA efflux. TaALMT1-expression also leads to GABA transport into cells, demonstrated by a yeast complementation assay and via 14CGABA uptake into TaALMT1-expressing Xenopus laevis oocytes; this was found to be a general feature of all ALMTs we examined. Mutation of the GABA motif (TaALMT1F213C) prevented both GABA influx and efflux, and uncoupled the relationship between malate efflux and [GABA]i. We conclude that ALMTs are likely to act as both GABA and anion transporters in planta. GABA and malate appear to interact with ALMTs in a complex manner regulating each others transport, suggestive of a role for ALMTs in communicating metabolic status.

plant biology↗

bioRxiv2017

The genome sequence of the wild tomato Solanum pimpinellifolium provides insights into salinity tolerance

Solanum pimpinellifolium, a wild relative of cultivated tomato, offers a wealth of breeding potential for several desirable traits such as tolerance to abiotic and biotic stresses. Here, we report the genome and annotation of S. pimpinellifolium LA0480. The LA0480 genome size (811 Mb) and the number of annotated genes (25,970) are within the range observed for other sequenced tomato species. We developed and utilized the Dragon Eukaryotic Analyses Platform (DEAP) to functionally annotate the LA0480 protein-coding genes. Additionally, we used DEAP to compare protein function between S. pimpinellifolium and cultivated tomato. Our data suggest enrichment in genes involved in biotic and abiotic stress responses. Moreover, we present phenotypic data from one field experiment that demonstrate a greater salinity tolerance for fruit-and yield-related traits in S. pimpinellifolium compared with cultivated tomato. To understand the genomic basis for these differences in S. pimpinellifolium and S. lycopersicum, we analyzed 15 genes that have previously been shown to mediate salinity tolerance in plants. We show that S. pimpinellifolium has a higher copy number of the inositol-3-phosphate synthase and phosphatase genes, which are both key enzymes in the production of inositol and its derivatives. Moreover, our analysis indicates that changes occurring in the inositol phosphate pathway may contribute to the observed higher salinity tolerance in LA0480. Altogether, our work provides essential resources to understand and unlock the genetic and breeding potential of S. pimpinellifolium, and to discover the genomic basis underlying its environmental robustness.

plant biology↗

bioRxiv2017

A bacterial GW-effector targets Arabidopsis AGO1 to promote pathogenicity and induces Effector-triggered immunity by disrupting AGO1 homeostasis

Pseudomonas syringae type III effectors were previously shown to suppress the Arabidopsis microRNA (miRNA) pathway through unknown mechanisms. Here, we first show that the HopT1-1 effector promotes bacterial growth by suppressing the Arabidopsis Argonaute 1 (AGO1)-dependent miRNA pathway. We further demonstrate that HopT1-1 interacts with Arabidopsis AGO1 through conserved glycine/tryptophan (GW) motifs, and in turn suppresses miRNA function. This process is not associated with a general decrease in miRNA accumulation. Instead, HopT1-1 reduces the level of AGO1-associated miRNAs in a GW-dependent manner. Therefore, HopT1-1 alters AGO1-miRISC activity, rather than miRNA biogenesis or stability. In addition, we show that the AGO1-binding platform of HopT1-1 is essential to suppress the production of reactive oxygen species (ROS) and of callose deposits during Pattern-triggered immunity (PTI). These data imply that the RNA silencing suppression activity of HopT1-1 is intimately coupled with its virulence function. Overall, these findings provide sound evidence that a bacterial effector has evolved to directly target a plant AGO protein to suppress PTI and cause disease.

plant biology↗

bioRxiv2017

A biophysical dynamic module for the polarisation of auxin efflux carriers PIN-FORMED (PIN)

Intracellular polarisation of auxin efflux carriers is crucial for understanding how auxin gradients form in plants. The polarisation dynamics of auxin efflux carriers PIN-FORMED (PIN) depends on both biomechanical forces as well as chemical, molecular and genetic factors. Biomechanical forces have shown to affect the localisation of PIN transporters to the plasma membrane. We proposed a biophysical module of PIN polarisation that integrates biomechanical, molecular, and cellular processes as well as their non-linear interactions. The module was implemented as a discrete Boolean model and then approximated to a continuous dynamic system, in order to explore the relative contribution of the factors mediating PIN polarisation at the scale of single cell. Our models recovered qualitative behaviours that have been experimentally observed and enabled us to postulate that, in the context of PIN polarisation, the effects of the mechanical forces can predominate over the activity of molecular factors such as the GTPase ROP6 and the CRIB-motif CRIB-motif RIC1.

plant biology↗

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↗