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Results for “plant biology”

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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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At least 235 records · Page 13Linked to original sources

bioRxiv2019

The Arabidopsis Diacylglycerol Kinase 4 is involved in nitric oxide-dependent pollen tube guidance and fertilization

Nitric oxide (NO) is a key signaling molecule that regulates diverse biological processes in both animals and plants. In animals, NO regulates vascular wall tone, neurotransmission and immune response while in plants, NO is essential for development and responses to biotic and abiotic stresses [1-3]. Interestingly, NO is involved in the sexual reproduction of both animals and plants mediating physiological events related to the male gamete [2, 4]. In animals, NO stimulates sperm motility [4] and binding to the plasma membrane of oocytes [5] while in plants, NO mediates pollen-stigma interactions and pollen tube guidance [6, 7]. NO generation in pollen tubes (PTs) has been demonstrated [8] and intracellular responses to NO include cytosolic Ca2+ elevation, actin organization, vesicle trafficking and cell wall deposition [7, 9]. However, the NO-responsive proteins that mediate these responses are still elusive. Here we show that PTs of Arabidopsis lacking the pollen-specific Diacylglycerol Kinase 4 (DGK4) grow slower and become insensitive to NO-dependent growth inhibition and re-orientation responses. Recombinant DGK4 protein yields NO-responsive spectral and catalytic changes in vitro which are compatible with a role in NO perception and signaling in PTs. NO is a fast, diffusible gas and, based on our results, we hypothesize it could serve in long range signaling and/or rapid cell-cell communication functions mediated by DGK4 downstream signaling during the progamic phase of angiosperm reproduction.

plant biology↗

bioRxiv2019

GAL4/GFP enhancer-trap lines for identification and manipulation of cells and tissues in developing Arabidopsis leaves

Understanding developmental processes requires the unambiguous identification of cells and tissues, and the selective manipulation of the properties of those cells and tissues. Both requirements can most efficiently be satisfied through the use of GAL4/GFP enhancer-trap lines. No such lines are available, however, for the study of leaf development in the Columbia-0 reference genotype of Arabidopsis. Here we address this limitation by identifying and characterizing a set of GAL4/GFP enhancer-trap lines in the Columbia-0 background for the specific labeling of cells and tissues during leaf development, and for the targeted expression of genes of interest in those cells and tissues. By using one line in our set to resolve outstanding problems in leaf vein patterning, we show that these lines can be used to address key questions in plant developmental biology.

plant biology↗

bioRxiv2023

Glycome profiling and immunohistochemistry uncover spaceflight-induced changes in non-cellulosic cell wall components in Arabidopsis thaliana seedling roots

A large and diverse library of glycan-directed monoclonal antibodies (mAbs) was used to determine if plant cell walls are modified by low-gravity conditions encountered during spaceflight. This method called glycome profiling (glycomics) revealed global differences in non-cellulosic cell wall epitopes in Arabidopsis thaliana root extracts recovered from RNA purification columns between seedlings grown on the International Space Station-based Vegetable Production System and paired ground (1-g) controls. Immunohistochemistry on 11-day-old seedling primary root sections showed that ten of twenty-two mAbs that exhibited spaceflight-induced increases in binding through glycomics, labeled space-grown roots more intensely than those from the ground. The ten mAbs recognized xyloglucan, xylan, and arabinogalactan epitopes. Notably, three xylem-enriched unsubstituted xylan backbone epitopes were more intensely labeled in space-grown roots than in ground-grown roots, suggesting that the spaceflight environment accelerated root secondary cell wall formation. This study highlights the feasibility of glycomics for high-throughput evaluation of cell wall glycans using only root high alkaline extracts from RNA purification columns, and subsequent validation of these results by immunohistochemistry. This approach will benefit plant space biological studies because it extends the analyses possible from the limited amounts of samples returned from spaceflight and help uncover microgravity-induced tissue-specific changes in plant cell walls.

plant biology↗

bioRxiv2024

Chloroplast Cell-Free Systems from Different Plant Species as a Rapid Prototyping Platform

Climate change poses a significant threat to global agriculture, necessitating innovative solutions. Plant synthetic biology, particularly chloroplast engineering, holds promise as a viable approach to this challenge. Chloroplasts present a variety of advantageous traits for genetic engineering, but the development of genetic tools and genetic part characterization in these organelles is hindered by the lengthy timescales required to generate transplastomic organisms. To address these challenges, we have established a versatile protocol for generating chloroplast-based cell-free gene expression (CFE) systems derived from a diverse range of plant species, including wheat (monocot), spinach, and poplar trees (dicots). We show that these systems work with conventionally used T7 RNA polymerase, as well as the endogenous chloroplast polymerases, allowing for detailed characterization and prototyping of regulatory sequences at both transcription and translation levels. To demonstrate the platform for characterization of promoters and 5 and 3 untranslated regions (UTRs) in higher plant chloroplast gene expression, we analyze a collection of 23 5UTRs, 10 3UTRs, and 6 chloroplast promoters, assessed their expression in spinach and wheat extracts, and found consistency in expression patterns, suggesting cross-species compatibility. Looking forward, our chloroplast CFE systems open new avenues for plant synthetic biology, offering prototyping tools for both understanding gene expression and developing engineered plants, which could help meet the demands of a changing global climate. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/580994v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@a6b24org.highwire.dtl.DTLVardef@2b62org.highwire.dtl.DTLVardef@1203308org.highwire.dtl.DTLVardef@f674a5_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2022

The transcriptional landscape of plant infection by the rice blast fungus Magnaporthe oryzae reveals distinct families of temporally co-regulated and structurally conserved effectors

The rice blast fungus Magnaporthe oryzae causes a devastating disease which threatens global rice production. In spite of intense study, the biology of plant tissue invasion during blast disease remains poorly understood. Here we report a high resolution, transcriptional profiling study of the entire plant-associated development of the blast fungus. Our analysis revealed major temporal changes in fungal gene expression during plant infection. Pathogen gene expression could be classified into 10 modules of temporally co-expressed genes, providing evidence of induction of pronounced shifts in primary and secondary metabolism, cell signalling and transcriptional regulation. A set of 863 genes encoding secreted proteins are differentially expressed at specific stages of infection, and 546 were predicted to be effectors and named MEP (Magnaporthe effector protein) genes. Computational prediction of structurally-related MEPs, including the MAX effector family, revealed their temporal co-regulation in the same co-expression modules. We functionally characterised 32 MEP genes and demonstrate that Mep effectors are predominantly targeted to the cytoplasm of rice cells via the biotrophic interfacial complex (BIC), and use a common unconventional secretory pathway. Taken together, our study reveals major changes in gene expression associated with blast disease and identifies a diverse repertoire of effectors critical to successful infection.

plant biology↗

bioRxiv2021

Regulation of suberin biosynthesis and Casparian strip development in the root endodermis by two plant auxins

The biological function of the auxin phenylacetic acid (PAA) is not well characterized in plants. Although some aspects of its biology; transport, signaling and metabolism have recently been described. Previous work on this phytohormone has suggested that PAA behaves in an identical manner to IAA (indole-3-acetic acid) in promoting plant growth, yet plants require greater concentrations of PAA to elicit the same physiological responses. Here we show that normalized PAA treatment results in the differential expression of a unique list of genes, suggesting that plants can respond differently to the two auxins. This is further explored in endodermal barrier regulation where the two auxins invoke striking differences in the deposition patterns of suberin. We further show that auxin acts antagonistically on Casparian strip (CS) formation as it can circumvent the CS transcriptional machinery to repress CS related genes. Additionally, altered suberin biosynthesis reduces endogenous levels of PAA and CS deficiency represses the biosynthesis of IAA and the levels of both auxins. These findings implicate auxin as a regulator of endodermal barrier formation and highlight a novel role for PAA in root development and differentiation.

plant biology↗

bioRxiv2026

Synthetic activation of gibberellin signaling reveals spatial coordination of root growth

Gibberellins (GAs) influence cell division and elongation, profoundly shaping plant architecture and yield. GA perception occurs when bioactive GAs bind the receptor GID1, promoting DELLA degradation and activating transcriptional programs. While GA signaling in the root endodermis is essential for promoting root elongation, functions of other layers in spatial control of GA responses have not been explored. Here, we developed a synthetic GA (sGA) that does not bind endogenous GID1, together with a modified GID1 (mGID1) engineered to selectively recognize sGA, enabling cell-specific activation of GA signaling in vivo. Using this system in Arabidopsis, we demonstrate that coordinated action of GA signaling in the endodermis, epidermis, and other layers is required for full root elongation. Moreover, cell type-specific expression of GA biosynthetic enzymes indicates the existence of intercellular GA transport. The sGA-mGID1 system provides a versatile platform for spatially precise reprogramming of hormone signaling, enabling synthetic control of developmental processes such as root-shoot growth balance, thereby advancing applications in plant synthetic biology and sustainable crop improvement.

plant biology↗

bioRxiv2024

Genetically encoded Boolean logic operators to sense and integrate phenylpropanoid metabolite levels in plants

O_LISynthetic biology has the potential to revolutionize biotechnology, public health and agriculture. Recent studies have shown the enormous potential of plants as chassis for synthetic biology applications. However, tools to precisely manipulate metabolic pathways for bioproduction in plants are still needed. C_LIO_LIWe have adapted bacterial allosteric transcription factors (aTFs) to control gene expression in plants in a ligand-specific manner. The aTFs used here function as transcription repressors of semi-synthetic promoters, and aTF activity is regulated by specific plant metabolites, especially phenylpropanoid-related molecules. Using these aTFs, we also designed synthetic genetic circuits capable of computing Boolean logic operations. C_LIO_LIThree aTFs, CouR, FapR and TtgR, were able to achieve [~]95% repression of their respective target promoters. For TtgR, a 6-fold de-repression could be triggered by inducing its ligand (naringenin) accumulation, showing its use as biosensor. Moreover, we designed synthetic genetic circuits that use AND, NAND, IMPLY and NIMPLY Boolean logic operations and integrate metabolite levels as input to the circuit. C_LIO_LIWe showed that biosensors can be implemented in plants to detect phenylpropanoid-related metabolites and activate a genetic circuit that follows a pre-defined logic, demonstrating their potential as tools for exerting control over plant metabolic pathways and facilitating the bioproduction of natural products. C_LI

plant biology↗

bioRxiv2021

Single-cell Stereo-seq enables cell type-specific spatial transcriptome characterization in Arabidopsis leaves

Understanding the complex functions of plant leaves requires spatially resolved gene expression profiling with single-cell resolution. However, although in situ gene expression profiling technologies have been developed, this goal has not yet been achieved. Here, we present the first in situ single-cell transcriptome profiling in plant, scStereo-seq (single-cell SpaTial Enhanced REsolution Omics-sequencing), which enabled the bona fide single-cell spatial transcriptome of Arabidopsis leaves. We successfully characterized subtle but significant transcriptomic differences between upper and lower epidermal cells. Furthermore, with high-resolution location information, we discovered the cell type-specific spatial gene expression gradients from main vein to leaf edge. By reconstructing those spatial gradients, we show for the first time the distinct spatial developmental trajectories of vascular cells and guard cells. Our findings show the importance of incorporating spatial information for answering complex biological questions in plant, and scStereo-seq offers a powerful single cell spatially resolved transcriptomic strategy for plant biology.

plant biology↗

bioRxiv2022

Split selectable marker mediated gene stacking in plants

Plant synthetic biology and genetic engineering depend on the controlled expression of transgenes of interest, which relies heavily on the use of Agrobacterium-mediated transformation. Here we establish a novel split selectable marker system using protein splicing elements called "inteins" for Agrobacterium-mediated co-transformation in plants. This method enables robust co-transformation in Arabidopsis and poplar, providing a novel strategy for the simultaneous insertion of multiple genes into both herbaceous and woody plants.

plant biology↗

bioRxiv2021

Saccharide Analysis of Onion Outer Epidermal Walls

BackgroundEpidermal cell walls have special structural and biological roles in the life of the plant. Typically they are multi-ply structures encrusted with waxes and cutin which protect the plant from dehydration and pathogen attack. These characteristics may also reduce chemical and enzymatic deconstruction of the wall for sugar analysis and conversion to biofuels. We have assessed the saccharide composition of the outer epidermal wall of onion scales with different analytical methods. This wall is a particularly useful model for cell wall imaging and mechanics. ResultsEpidermal walls were depolymerized by acidic methanolysis combined with 2 M trifluoracetic acid hydrolysis and the resultant sugars were analyzed by high-performance anion-exchange chromatography with pulsed amperometric detection (HPAEC-PAD). Total sugar yields based on wall dry weight were low (53%). Removal of waxes with chloroform increased the sugar yields to 73% and enzymatic digestion did not improve these yields. Analysis by gas chromatography/mass spectrometry (GC/MS) of per-O-trimethylsilyl (TMS) derivatives of the sugar methyl glycosides produced by acidic methanolysis gave a high yield for galacturonic acid (GalA) but glucose (Glc) was severely reduced. In a complementary fashion, GC/MS analysis of methyl alditols produced by permethylation gave substantial yields for glucose and other neutral sugars, but GalA was severely reduced. Analysis of the walls by 13C solid-state NMR confirmed and extended these results and revealed 15% lipid content after chloroform extraction (potentially cutin and unextractable waxes). ConclusionsAlthough exact values vary with the analytical method, our best estimate is that polysaccharide in the outer epidermal wall of onion scales is comprised of homogalacturonan (~50%), cellulose (~20%), galactan (~10%), xyloglucan (~10%) and smaller amounts of other polysaccharides. Low yields of specific monosaccharides by some methods may be exaggerated in epidermal walls impregnated with waxes and cutin and call for cautious interpretation of the results.

plant biology↗

bioRxiv2025

Hyperspectral Imaging to Quantify Nodules and Detect Biological Nitrogen Fixation in Legumes

Legume root nodules are important for biological nitrogen fixation, a process critical for plants to gain additional nitrogen from the environment. Nodule quantification is valuable for evaluating nitrogen fixation efficiency, assessing symbiotic relationships, monitoring responses to nitrogen, and supporting genetic studies on legume adaptation and productivity. However, accurate quantification of root nodules is difficult and time-consuming due to the complexity of the root system and soil interference. Here, we explore the utility of hyperspectral imaging as a non-destructive tool to detect active fixing root nodules with minimal preparation and show that we can differentiate nodules and root tissues through unique spectral signatures while also distinguishing between fixing and non-fixing nodules. We applied deep learning techniques to develop an automated nodule counting pipeline adaptable across different legume species and under diverse growth conditions. This approach eliminates the need for labor-intensive counting and enables the detection of nodules embedded within dense root tangles with high accuracy. This automated hyperspectral approach offers a promising alternative to support assessments of nodule abundance and their activity across legume species grown under various environments.

plant biology↗

bioRxiv2019

Auxin-dependent xyloglucan remodelling defines differential tissue expansion in Arabidopsis thaliana

Size control is a fundamental question in biology, showing incremental complexity in case of plants whose cells possess a rigid cell wall. The phytohormone auxin is a vital growth regulator with central importance for differential growth control. Here we show that growth inducing and repressing auxin conditions correlate with reduced and enhanced complexity of extracellular xyloglucans, respectively. In agreement, genetic interference with xyloglucan complexity distinctly modulates auxin-dependent differential growth rates. Our work proposes that an auxin-dependent, spatially defined effect on xyloglucan structure and its effect on cell wall mechanics specify differential, gravitropic hypocotyl growth.

plant biology↗

bioRxiv2023

Monitoring single root hairs using a micro-chambered hydroponics system MiCHy reveals a new mode of action of the aminosteroid U73122

When using chemical probes and inhibitors for cell biological studies, the uniform and rapid access of the chemical to the sample is key for the accuracy of the analysis. Until now, however, this could only be accomplished by using expensive equipment and labor-intensive and often lengthy procedures. Here, we introduce MiCHy, a micro-chambered hydroponics system, as an accessible and versatile method for chemical treatments and demonstrate its use for imaging roots of Arabidopsis thaliana, the major model system for plant cell biological research. Using lipid biosensors in combination with established chemicals, such as the phosphoinositol 4-kinase (PI4K) inhibitor phenylarsine oxide and the phosphoinositide-specific phospholipase C (PI-PLC) inhibitor U73122, we demonstrate the suitability of MiCHy for studying the relationship between growth and lipid dynamics in root hairs. We further reveal novel effects of U73122 on the plasma membrane localization of phosphatidylinositol-4-phosphate 5-kinase 3 (PIP5K3), which is the first evidence demonstrating a role for U73122 besides its role as a PI-PLC inhibitor in plants.

plant biology↗

bioRxiv2023

Conservation of heat stress acclimation by the inositol polyphosphate multikinase, IPMK responsible for 4/6-InsP7 production in land plants

Inositol pyrophosphates (PP-InsPs) are soluble cellular messengers that integrate environmental cues to induce adaptive responses in eukaryotes. In plants, the biological functions of various PP-InsP species are poorly understood, largely due to the absence of canonical enzymes present in other eukaryotes. The recent identification of a new PP-InsP isomer with yet unknown enantiomeric identity, 4/6-InsP7 in the eudicot Arabidopsis thaliana, further highlights the intricate PP-InsP signalling network employed by plants. The abundance of 4/6-InsP7 in land plants, the enzyme(s) responsible for its synthesis, and the physiological functions of this species are all currently unknown. In this study, we show that 4/6-InsP7 is the major PP-InsP species present across land plants. Our findings demonstrate that the Arabidopsis inositol polyphosphate multikinase (IPMK) homolog, AtIPK2 generates 4/6-InsP7 in vitro. Furthermore, the cellular level of 4/6-InsP7 is controlled by the two Arabidopsis IPMK isoforms, AtIPK2 and AtIPK2{beta}. Notably, the activity of these IPMK proteins is critical for heat stress acclimation in Arabidopsis. During heat stress, the expression of genes encoding various heat shock proteins controlled by the heat shock factors (HSFs) is affected in the AtIPK2-deficient plants. Furthermore, we show that the transcription activity of HSF is regulated by the AtIPK2 proteins. Our parallel investigations using the liverwort Marchantia polymorpha suggest that the InsP6 kinase activity of IPMK and the role of IPMK in regulating the heat stress response are evolutionarily conserved. Collectively, our study indicates that IPMK has played a critical role in transducing environmental cues for biological processes during land plant evolution.

plant biology↗

bioRxiv2016

Compromised External Validity: Federally Produced Cannabis Does Not Reflect Legal Markets

As the most widely used illicit drug, the basis of the fastest growing major industry in the US, and as a source of numerous under-studied psychoactive compounds, understanding the psychological and physiological effects of Cannabis is essential. The National Institute on Drug Abuse (NIDA) is designated as the sole legal producer of Cannabis for use in US research studies. We sought to compare the chemical profiles of Cannabis varieties that are available to consumers in states that have state-legalized use versus what is available to researchers interested in studying the plant and its effects. Our results demonstrate that the federally produced Cannabis has significantly less variety and lower concentrations of cannabinoids. Current research, which has focused on material that is far less diverse and less potent than that used by the public, limits our understanding of the plants chemical, biological, psychological, medical, and pharmacological properties. Investigation is urgently needed on the diverse forms of Cannabis used by the public in state-legal markets.

plant biology↗

bioRxiv2024

Spatial Transcriptomics Reveals Expression Gradients in Developing Wheat Inflorescences at Cellular Resolution

The diversity of plant inflorescence architectures is specified by gene expression patterns. In wheat (Triticum aestivum), the lanceolate-shaped inflorescence (spike) is defined by rudimentary spikelets at the base which initiate first but subsequently lag in development compared with central spikelets. While previous studies identified gene expression differences between central and basal inflorescence sections, the spatio-temporal dynamics and gradients along the apical-basal axis remain poorly resolved due to bulk tissue-level techniques. Here, using spatial transcriptomics, we profiled 200 genes across four stages of wheat inflorescence development to cellular resolution. Cell segmentation and unsupervised clustering identified 18 expression domains and their enriched genes, revealing dynamic spatio-temporal organisation along the apical-basal axis of the inflorescence. Along this axis, we uncovered distinct and spatially coordinated gene expression gradients patterning meristems prior to the visible delay in basal spikelet development. This study demonstrates the potential for spatial transcriptomics time-series to advance plant developmental biology.

plant biology↗

bioRxiv2020

ConnecTF: A platform to build gene networks by integrating transcription factor-target gene interactions

Deciphering gene regulatory networks (GRNs) is both a promise and challenge of systems biology. The promise is identifying key transcription factors (TFs) that enable an organism to react to changes in its environment. The challenge is constructing GRNs that involve hundreds of TFs and hundreds of thousands of interactions with their genome-wide target genes validated by high-throughput sequencing. To address this challenge, we developed ConnecTF, a species-independent web-based platform for constructing validated GRNs and to refine inferred GRNs via combined analysis of genome-wide studies of TF-target gene binding, TF-target regulation and other TF-centric omic data. We demonstrate the functionality of ConnecTF in three case studies, showing how integration within and across TF-target datasets uncovers biological insights. Case study 1 uses integration of TF-target gene regulation and binding datasets to uncover mode-of-action and identify potential TF partners for 14 TFs in abscisic acid signaling. Case study 2 demonstrates how genome-wide TF-target data and automated functions in ConnecTF are used to conduct precision/recall analysis and pruning of an inferred GRN for nitrogen signaling. In case study 3, we use ConnecTF to chart a network path from NLP7, a master TF in nitrogen signaling, to direct secondary TF2s, to its indirect targets, in an approach called Network Walking. The public version of ConnecTF (https://ConnecTF.org) contains 3,738,278 TF-target interactions for 423 TFs in Arabidopsis, and 839,210 TF-target interactions for 139 TFs in maize. The database and tools in ConnecTF should advance the exploration of GRNs in plant systems biology applications for models and crops.

plant biology↗