Integrative Analysis from the Epigenome to Translatome Uncovers Patterns of Dominant Nuclear Regulation during Transient Stress

Detection and Automated Quantification of Nucleocytoplasmic RNA Fractions in Arabidopsis Using smFISH

Subcellular RNA localization is an underexplored regulatory layer crucial for properly adapting cells to cellular or environmental conditions. Most studies describing RNA localization have been performed by cell fractionation and subsequent RNA quantification from pools of cells, thereby missing information about cell-to-cell variability. RNA single-molecule fluorescent in situ hybridization (smFISH) is an effective technique for detecting single RNA molecules and identifying subcellular accumulation patterns. Nevertheless, obtaining quantitative results from smFISH can be challenging in tissues with high autofluorescence, like in plants. Here, we describe an automated pipeline to detect and quantify nucleocytoplasmic RNA levels from Arabidopsis root smFISH images. This pipeline utilizes free image preprocessing, segmentation, and RNA detection software. The method permits users with any programming skills to analyze batches of images. Suggestions and recommendations for image acquisition, processing, and data analysis are included. This pipeline allows quantitative differences in nucleocytoplasmic distribution at the single-cell level to be studied under different cellular, environmental, and genetic contexts.

A mechanistic integration of hypoxia signaling with energy, redox, and hormonal cues

Oxygen deficiency (hypoxia) occurs naturally in many developing plant tissues but can become a major threat during acute flooding stress. Consequently, plants as aerobic organisms must rapidly acclimate to hypoxia and the associated energy crisis to ensure cellular and ultimately organismal survival. In plants, oxygen sensing is tightly linked with oxygen-controlled protein stability of group VII ETHYLENE-RESPONSE FACTORs (ERFVII), which, when stabilized under hypoxia, act as key transcriptional regulators of hypoxia-responsive genes (HRGs). Multiple signaling pathways feed into hypoxia signaling to fine-tune cellular decision-making under stress. First, ATP shortage upon hypoxia directly affects the energy status and adjusts anaerobic metabolism. Secondly, altered redox homeostasis leads to reactive oxygen and nitrogen species (ROS and RNS) accumulation, evoking signaling and oxidative stress acclimation. Finally, the phytohormone ethylene promotes hypoxia signaling to improve acute stress acclimation, while hypoxia signaling in turn can alter ethylene, auxin, abscisic acid, salicylic acid, and jasmonate signaling to guide development and stress responses. In this Update, we summarize the current knowledge on how energy, redox, and hormone signaling pathways are induced under hypoxia and subsequently integrated at the molecular level to ensure stress-tailored cellular responses. We show that some HRGs are responsive to changes in redox, energy, and ethylene independently of the oxygen status, and we propose an updated HRG list that is more representative for hypoxia marker gene expression. We discuss the synergistic effects of hypoxia, energy, redox, and hormone signaling and their phenotypic consequences in the context of both environmental and developmental hypoxia.

Primed to persevere: Hypoxia regulation from epigenome to protein accumulation in plants

Plant cells regularly encounter hypoxia (low-oxygen conditions) as part of normal growth and development, or in response to environmental stresses such as flooding. In recent years, our understanding of the multi-layered control of hypoxia-responsive gene expression has greatly increased. In this Update, we take a broad look at the epigenetic, transcriptional, translational, and post-translational mechanisms that regulate responses to low-oxygen levels. We highlight how a network of post-translational modifications (including phosphorylation), secondary messengers, transcriptional cascades, and retrograde signals from the mitochondria and endoplasmic reticulum (ER) feed into the control of transcription factor activity and hypoxia-responsive gene transcription. We discuss epigenetic mechanisms regulating the response to reduced oxygen availability, through focussing on active and repressive chromatin modifications and DNA methylation. We also describe current knowledge of the co- and post-transcriptional mechanisms that tightly regulate mRNA translation to coordinate effective gene expression under hypoxia. Finally, we present a series of outstanding questions in the field and consider how new insights into the molecular workings of the hypoxia-triggered regulatory hierarchy could pave the way for developing flood-resilient crops.

Advances in seed hypoxia research

Seeds represent essential stages of the plant life cycle: embryogenesis, the intermittent quiescence phase, and germination. Each stage has its own physiological requirements, genetic program, and environmental challenges. Consequently, the effects of developmental and environmental hypoxia can vary from detrimental to beneficial. Past and recent evidence shows how low-oxygen signaling and metabolic adaptations to hypoxia affect seed development and germination. Here, we review the recent literature on seed biology in relation to hypoxia research and present our perspective on key challenges and opportunities for future investigations.

Hypoxia represses pattern-triggered immune responses in Arabidopsis

Biotic and abiotic stresses frequently co-occur in nature, yet relatively little is known about how plants coordinate the response to combined stresses. Protein degradation by the ubiquitin/proteasome system is central to the regulation of multiple independent stress response pathways in plants. The Arg/N-degron pathway is a subset of the ubiquitin/proteasome system that targets proteins based on their N-termini and has been specifically implicated in the responses to biotic and abiotic stresses, including hypoxia, via accumulation of group VII ETHYLENE RESPONSE FACTOR (ERF-VII) transcription factors that orchestrate the onset of the hypoxia response program. Here, we investigated the role of the Arabidopsis (Arabidopsis thaliana) Arg/N-degron pathway in mediating the crosstalk between combined abiotic and biotic stresses using hypoxia treatments and the flg22 elicitor of pattern-triggered immunity (PTI), respectively. We uncovered a link between the plant transcriptional responses to hypoxia and flg22. Combined hypoxia and flg22 treatments showed that hypoxia represses the flg22 transcriptional program, as well as the expression of pattern recognition receptors, mitogen-activated protein kinase (MAPK) signaling and callose deposition during PTI through mechanisms that are mostly independent from the ERF-VIIs. These findings improve our understanding of the tradeoffs between plant responses to combined abiotic and biotic stresses in the context of our efforts to increase crop resilience to global climate change. Our results also show that the well-known repressive effect of hypoxia on innate immunity in animals also applies to plants.

Widespread position-dependent transcriptional regulatory sequences in plants

Much of what we know about eukaryotic transcription stems from animals and yeast; however, plants evolved separately for over a billion years, leaving ample time for divergence in transcriptional regulation. Here we set out to elucidate fundamental properties of cis-regulatory sequences in plants. Using massively parallel reporter assays across four plant species, we demonstrate the central role of sequences downstream of the transcription start site (TSS) in transcriptional regulation. Unlike animal enhancers that are position independent, plant regulatory elements depend on their position, as altering their location relative to the TSS significantly affects transcription. We highlight the importance of the region downstream of the TSS in regulating transcription by identifying a DNA motif that is conserved across vascular plants and is sufficient to enhance gene expression in a dose-dependent manner. The identification of a large number of position-dependent enhancers points to fundamental differences in gene regulation between plants and animals.

New Insights into the Connections between Flooding/Hypoxia Response and Plant Defenses against Pathogens

The impact of global climate change has highlighted the need for a better understanding of how plants respond to multiple simultaneous or sequential stresses, not only to gain fundamental knowledge of how plants integrate signals and mount a coordinated response to stresses but also for applications to improve crop resilience to environmental stresses. In recent years, there has been a stronger emphasis on understanding how plants integrate stresses and the molecular mechanisms underlying the crosstalk between the signaling pathways and transcriptional programs that underpin plant responses to multiple stresses. The combination of flooding (or resulting hypoxic stress) with pathogen infection is particularly relevant due to the frequent co-occurrence of both stresses in nature. This review focuses on (i) experimental approaches and challenges associated with the study of combined and sequential flooding/hypoxia and pathogen infection, (ii) how flooding (or resulting hypoxic stress) influences plant immunity and defense responses to pathogens, and (iii) how flooding contributes to shaping the soil microbiome and is linked to plants' ability to fight pathogen infection.

AraLeTA: An Arabidopsis leaf expression atlas across diurnal and developmental scales

Mature plant leaves are a composite of distinct cell types, including epidermal, mesophyll, and vascular cells. Notably, the proportion of these cells and the relative transcript concentrations within different cell types may change over time. While gene expression data at a single-cell level can provide cell-type-specific expression values, it is often too expensive to obtain these data for high-resolution time series. Although bulk RNA-seq can be performed in a high-resolution time series, RNA-seq using whole leaves measures average gene expression values across all cell types in each sample. In this study, we combined single-cell RNA-seq data with time-series data from whole leaves to assemble an atlas of cell-type-specific changes in gene expression over time for Arabidopsis (Arabidopsis thaliana). We inferred how the relative transcript concentrations of different cell types vary across diurnal and developmental timescales. Importantly, this analysis revealed 3 subgroups of mesophyll cells with distinct temporal profiles of expression. Finally, we developed tissue-specific gene networks that form a community resource: an Arabidopsis Leaf Time-dependent Atlas (AraLeTa). This allows users to extract gene networks that are confirmed by transcription factor-binding data and specific to certain cell types at certain times of day and at certain developmental stages. AraLeTa is available at https://regulatorynet.shinyapps.io/araleta/.

Water deficit response in nodulated soybean roots: a comprehensive transcriptome and translatome network analysis

BACKGROUND

Soybean establishes a mutualistic interaction with nitrogen-fixing rhizobacteria, acquiring most of its nitrogen requirements through symbiotic nitrogen fixation. This crop is susceptible to water deficit; evidence suggests that its nodulation status-whether it is nodulated or not-can influence how it responds to water deficit. The translational control step of gene expression has proven relevant in plants subjected to water deficit.

RESULTS

Here, we analyzed soybean roots' differential responses to water deficit at transcriptional, translational, and mixed (transcriptional + translational) levels. Thus, the transcriptome and translatome of four combined-treated soybean roots were analyzed. We found hormone metabolism-related genes among the differentially expressed genes (DEGs) at the translatome level in nodulated and water-restricted plants. Also, weighted gene co-expression network analysis followed by differential expression analysis identified gene modules associated with nodulation and water deficit conditions. Protein-protein interaction network analysis was performed for subsets of mixed DEGs of the modules associated with the plant responses to nodulation, water deficit, or their combination.

CONCLUSIONS

Our research reveals that the stand-out processes and pathways in the before-mentioned plant responses partially differ; terms related to glutathione metabolism and hormone signal transduction (2 C protein phosphatases) were associated with the response to water deficit, terms related to transmembrane transport, response to abscisic acid, pigment metabolic process were associated with the response to nodulation plus water deficit. Still, two processes were common: galactose metabolism and branched-chain amino acid catabolism. A comprehensive analysis of these processes could lead to identifying new sources of tolerance to drought in soybean.

Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics

Single-cell and single-nucleus RNA-sequencing technologies capture the expression of plant genes at an unprecedented resolution. Therefore, these technologies are gaining traction in plant molecular and developmental biology for elucidating the transcriptional changes across cell types in a specific tissue or organ, upon treatments, in response to biotic and abiotic stresses, or between genotypes. Despite the rapidly accelerating use of these technologies, collective and standardized experimental and analytical procedures to support the acquisition of high-quality data sets are still missing. In this commentary, we discuss common challenges associated with the use of single-cell transcriptomics in plants and propose general guidelines to improve reproducibility, quality, comparability, and interpretation and to make the data readily available to the community in this fast-developing field of research.

Aethionema arabicum dimorphic seed trait resetting during transition to seedlings

The transition from germinating seeds to emerging seedlings is one of the most vulnerable plant life cycle stages. Heteromorphic diaspores (seed and fruit dispersal units) are an adaptive bet-hedging strategy to cope with spatiotemporally variable environments. While the roles and mechanisms of seedling traits have been studied in monomorphic species, which produce one type of diaspore, very little is known about seedlings in heteromorphic species. Using the dimorphic diaspore model Aethionema arabicum (Brassicaceae), we identified contrasting mechanisms in the germination responses to different temperatures of the mucilaginous seeds (M+ seed morphs), the dispersed indehiscent fruits (IND fruit morphs), and the bare non-mucilaginous M- seeds obtained from IND fruits by pericarp (fruit coat) removal. What follows the completion of germination is the pre-emergence seedling growth phase, which we investigated by comparative growth assays of early seedlings derived from the M+ seeds, bare M- seeds, and IND fruits. The dimorphic seedlings derived from M+ and M- seeds did not differ in their responses to ambient temperature and water potential. The phenotype of seedlings derived from IND fruits differed in that they had bent hypocotyls and their shoot and root growth was slower, but the biomechanical hypocotyl properties of 15-day-old seedlings did not differ between seedlings derived from germinated M+ seeds, M- seeds, or IND fruits. Comparison of the transcriptomes of the natural dimorphic diaspores, M+ seeds and IND fruits, identified 2,682 differentially expressed genes (DEGs) during late germination. During the subsequent 3 days of seedling pre-emergence growth, the number of DEGs was reduced 10-fold to 277 root DEGs and 16-fold to 164 shoot DEGs. Among the DEGs in early seedlings were hormonal regulators, in particular for auxin, ethylene, and gibberellins. Furthermore, DEGs were identified for water and ion transporters, nitrate transporter and assimilation enzymes, and cell wall remodeling protein genes encoding enzymes targeting xyloglucan and pectin. We conclude that the transcriptomes of seedlings derived from the dimorphic diaspores, M+ seeds and IND fruits, undergo transcriptional resetting during the post-germination pre-emergence growth transition phase from germinated diaspores to growing seedlings.

The mechanisms behind the contrasting responses to waterlogging in black-grass (Alopecurus myosuroides) and wheat (Triticum aestivum)

Black-grass (Alopecurus myosuroides ) is one of the most problematic agricultural weeds of Western Europe, causing significant yield losses in winter wheat (Triticum aestivum ) and other crops through competition for space and resources. Previous studies link black-grass patches to water-retaining soils, yet its specific adaptations to these conditions remain unclear. We designed pot-based waterlogging experiments to compare 13 biotypes of black-grass and six cultivars of wheat. These showed that wheat roots induced aerenchyma when waterlogged whereas aerenchyma-like structures were constitutively present in black-grass. Aerial biomass of waterlogged wheat was smaller, whereas waterlogged black-grass was similar or larger. Variability in waterlogging responses within and between these species was correlated with transcriptomic and metabolomic changes in leaves of control or waterlogged plants. In wheat, transcripts associated with regulation and utilisation of phosphate compounds were upregulated and sugars and amino acids concentrations were increased. Black-grass biotypes showed limited molecular responses to waterlogging. Some black-grass amino acids were decreased and one transcript commonly upregulated was previously identified in screens for genes underpinning metabolism-based resistance to herbicides. Our findings provide insights into the different waterlogging tolerances of these species and may help to explain the previously observed patchiness of this weed's distribution in wheat fields.

ERFVII action and modulation through oxygen-sensing in Arabidopsis thaliana

Oxygen is a key signalling component of plant biology, and whilst an oxygen-sensing mechanism was previously described in Arabidopsis thaliana, key features of the associated PLANT CYSTEINE OXIDASE (PCO) N-degron pathway and Group VII ETHYLENE RESPONSE FACTOR (ERFVII) transcription factor substrates remain untested or unknown. We demonstrate that ERFVIIs show non-autonomous activation of root hypoxia tolerance and are essential for root development and survival under oxygen limiting conditions in soil. We determine the combined effects of ERFVIIs in controlling gene expression and define genetic and environmental components required for proteasome-dependent oxygen-regulated stability of ERFVIIs through the PCO N-degron pathway. Using a plant extract, unexpected amino-terminal cysteine sulphonic acid oxidation level of ERFVIIs was observed, suggesting a requirement for additional enzymatic activity within the pathway. Our results provide a holistic understanding of the properties, functions and readouts of this oxygen-sensing mechanism defined through its role in modulating ERFVII stability.

Transcriptional analysis in multiple barley varieties identifies signatures of waterlogging response

Waterlogging leads to major crop losses globally, particularly for waterlogging-sensitive crops such as barley. Waterlogging reduces oxygen availability and results in additional stresses, leading to the activation of hypoxia and stress response pathways that promote plant survival. Although certain barley varieties have been shown to be more tolerant to waterlogging than others and some tolerance-related quantitative trait loci have been identified, the molecular mechanisms underlying this trait are mostly unknown. Transcriptomics approaches can provide very valuable information for our understanding of waterlogging tolerance. Here, we surveyed 21 barley varieties for the differential transcriptional activation of conserved hypoxia-response genes under waterlogging and selected five varieties with different levels of induction of core hypoxia-response genes. We further characterized their phenotypic response to waterlogging in terms of shoot and root traits. RNA sequencing to evaluate the genome-wide transcriptional responses to waterlogging of these selected varieties led to the identification of a set of 98 waterlogging-response genes common to the different datasets. Many of these genes are orthologs of the so-called "core hypoxia response genes," thus highlighting the conservation of plant responses to waterlogging. Hierarchical clustering analysis also identified groups of genes with intrinsic differential expression between varieties prior to waterlogging stress. These genes could constitute interesting candidates to study "predisposition" to waterlogging tolerance or sensitivity in barley.

Conserved and variable heat stress responses of the Heat Shock Factor transcription factor family in maize and Setaria viridis

The Heat Shock Factor (HSF) transcription factor family is a central and required component of plant heat stress responses and acquired thermotolerance. The HSF family has dramatically expanded in plant lineages, often including a repertoire of 20 or more genes. Here we assess and compare the composition, heat responsiveness, and chromatin profiles of the HSF families in maize and Setaria viridis (Setaria), two model C4 panicoid grasses. Both species encode a similar number of HSFs, and examples of both conserved and variable expression responses to a heat stress event were observed between the two species. Chromatin accessibility and genome-wide DNA-binding profiles were generated to assess the chromatin of HSF family members with distinct responses to heat stress. We observed significant variability for both chromatin accessibility and promoter occupancy within similarly regulated sets of HSFs between Setaria and maize, as well as between syntenic pairs of maize HSFs retained following its most recent genome duplication event. Additionally, we observed the widespread presence of TF binding at HSF promoters in control conditions, even at HSFs that are only expressed in response to heat stress. TF-binding peaks were typically near putative HSF-binding sites in HSFs upregulated in response to heat stress, but not in stable or not expressed HSFs. These observations collectively support a complex scenario of expansion and subfunctionalization within this transcription factor family and suggest that within-family HSF transcriptional regulation is a conserved, defining feature of the family.

An antisense intragenic lncRNA SEAIRa mediates transcriptional and epigenetic repression of SERRATE in Arabidopsis

SERRATE (SE) is a core protein for microRNA (miRNA) biogenesis as well as for mRNA alternative splicing. Investigating the regulatory mechanism of SE expression is hence critical to understanding its detailed function in diverse biological processes. However, little about the control of SE expression has been clarified, especially through long noncoding RNA (lncRNA). Here, we identified an antisense intragenic lncRNA transcribed from the 3' end of SE, named SEAIRa. SEAIRa repressed SE expression, which in turn led to serrated leaves. SEAIRa recruited plant U-box proteins PUB25/26 with unreported RNA binding ability and a ubiquitin-like protein related to ubiquitin 1 (RUB1) for H2A monoubiquitination (H2Aub) at exon 11 of SE. In addition, PUB25/26 helped cleave SEAIRa and release the 5' domain fragment, which recruited the PRC2 complex for H3 lysine 27 trimethylation (H3K27me3) deposition at the first exon of SE. The distinct modifications of H2Aub and H3K27me3 at different sites of the SE locus cooperatively suppressed SE expression. Collectively, our results uncover an epigenetic mechanism mediated by the lncRNA SEAIRa that modulates SE expression, which is indispensable for plant growth and development.

Multi-stress resilience in plants recovering from submergence

Submergence limits plants' access to oxygen and light, causing massive changes in metabolism; after submergence, plants experience additional stresses, including reoxygenation, dehydration, photoinhibition and accelerated senescence. Plant responses to waterlogging and partial or complete submergence have been well studied, but our understanding of plant responses during post-submergence recovery remains limited. During post-submergence recovery, whether a plant can repair the damage caused by submergence and reoxygenation and re-activate key processes to continue to grow, determines whether the plant survives. Here, we summarize the challenges plants face when recovering from submergence, primarily focusing on studies of Arabidopsis thaliana and rice (Oryza sativa). We also highlight recent progress in elucidating the interplay among various regulatory pathways, compare post-hypoxia reoxygenation between plants and animals and provide new perspectives for future studies.

Complexity of Abiotic Stress Stimuli: Mimicking Hypoxic Conditions Experimentally on the Basis of Naturally Occurring Environments

Plants require oxygen to respire and produce energy. Plant cells are exposed to low oxygen levels (hypoxia) in different contexts and have evolved conserved molecular responses to hypoxia. Both environmental and developmental factors can influence intracellular oxygen concentrations. In nature, plants can experience hypoxic conditions when the soil becomes saturated with water following heavy precipitation (i.e., waterlogging). Hypoxia can also arise in specific tissues that have poor gas exchange with atmospheric oxygen. In this case, hypoxic niches that are physiologically and developmentally relevant may form. To dissect the molecular mechanisms underlying the regulation of hypoxia response in plants, a wide range of hypoxia-inducing methods have been used in the laboratory setting. Yet, the different characteristics, pros and cons of each of these hypoxia treatments are seldom compared between methods, and with natural forms of hypoxia. In this chapter, we present both environmental and developmental forms of hypoxia that plants encounter in the wild, as well as the different experimental hypoxia treatments used to mimic them in the laboratory setting, with the aim of informing on what experimental approaches might be most appropriate to the questions addressed, including stress signaling and regulation.

Revisiting AGAMOUS-LIKE15, a Key Somatic Embryogenesis Regulator, Using Next Generation Sequencing Analysis in Arabidopsis

AGAMOUS-like 15 (AGL15) is a member of the MADS-domain transcription factor (TF) family. MADS proteins are named for a conserved domain that was originally from an acronym derived from genes expressed in a variety of eukaryotes (MCM1-AGAMOUS-DEFICIENS-SERUM RESPONSE FACTOR). In plants, this family has expanded greatly, with more than one-hundred members generally found in dicots, and the proteins encoded by these genes have often been associated with developmental identity. AGL15 transcript and protein accumulate primarily in embryos and has been found to promote an important process called plant regeneration via somatic embryogenesis (SE). To understand how this TF performs this function, we have previously used microarray technologies to assess direct and indirect responsive targets of this TF. We have now revisited this question using next generation sequencing (NGS) to both characterize in vivo binding sites for AGL15 as well as response to the accumulation of AGL15. We compared these data to the prior microarray results to evaluate the different platforms. The new NGS data brought to light an interaction with brassinosteroid (BR) hormone signaling that was "missed" in prior Gene Ontology analysis from the microarray studies.

The retrograde signaling regulator ANAC017 recruits the MKK9-MPK3/6, ethylene, and auxin signaling pathways to balance mitochondrial dysfunction with growth

In plant cells, mitochondria are ideally positioned to sense and balance changes in energy metabolism in response to changing environmental conditions. Retrograde signaling from mitochondria to the nucleus is crucial for adjusting the required transcriptional responses. We show that ANAC017, the master regulator of mitochondrial stress, directly recruits a signaling cascade involving the plant hormones ethylene and auxin as well as the MAP KINASE KINASE (MKK) 9-MAP KINASE (MPK) 3/6 pathway in Arabidopsis thaliana. Chromatin immunoprecipitation followed by sequencing and overexpression demonstrated that ANAC017 directly regulates several genes of the ethylene and auxin pathways, including MKK9, 1-AMINO-CYCLOPROPANE-1-CARBOXYLATE SYNTHASE 2, and YUCCA 5, in addition to genes encoding transcription factors regulating plant growth and stress responses such as BASIC REGION/LEUCINE ZIPPER MOTIF (bZIP) 60, bZIP53, ANAC081/ATAF2, and RADICAL-INDUCED CELL DEATH1. A time-resolved RNA-seq experiment established that ethylene signaling precedes the stimulation of auxin signaling in the mitochondrial stress response, with a large part of the transcriptional regulation dependent on ETHYLENE-INSENSITIVE 3. These results were confirmed by mutant analyses. Our findings identify the molecular components controlled by ANAC017, which integrates the primary stress responses to mitochondrial dysfunction with whole plant growth via the activation of regulatory and partly antagonistic feedback loops.

Seed-to-Seedling Transition: Novel Aspects

Transition from seed to seedling represents a critical stage in plants’ life cycles. This process includes three significant events in the seeds: (i) tissue hydration, (ii) the mobilization of reserve nutrients, and (iii) the activation of metabolic activity. Global metabolic rearrangements lead to the initiation of radicle growth and the resumption of vegetative development. It requires massive reprogramming of the transcriptome, proteome, metabolome, and attendant signaling pathways, resulting in the silencing of seed-maturation genes and the activation of vegetative growth genes. This Special Issue discusses the mechanisms of genetic, epigenetic, and hormonal switches during seed-to-seedling transitions. Detailed information has also been covered regarding the influence of germination features on seedling establishment.

Function of Cajal Bodies in Nuclear RNA Retention in A. thaliana Leaves Subjected to Hypoxia

Retention of RNA in the nucleus precisely regulates the time and rate of translation and controls transcriptional bursts that can generate profound variability in mRNA levels among identical cells in tissues. In this study, we investigated the function of Cajal bodies (CBs) in RNA retention in A. thaliana leaf nuclei during hypoxia stress was investigated. It was observed that in ncb-1 mutants with a complete absence of CBs, the accumulation of poly(A⁺) RNA in the leaf nuclei was lower than that in wt under stress. Moreover, unlike in root cells, CBs store less RNA, and RNA retention in the nuclei is much less intense. Our results reveal that the function of CBs in the accumulation of RNA in nuclei under stress depends on the plant organ. Additionally, in ncb-1, retention of introns of mRNA RPB1 (largest subunit of RNA polymerase II) mRNA was observed. However, this isoform is highly accumulated in the nucleus. It thus follows that intron retention in transcripts is more important than CBs for the accumulation of RNA in nuclei. Accumulated mRNAs with introns in the nucleus could escape transcript degradation by NMD (nonsense-mediated mRNA decay). From non-fully spliced mRNAs in ncb-1 nuclei, whose levels increase during hypoxia, introns are removed during reoxygenation. Then, the mRNA is transferred to the cytoplasm, and the RPB1 protein is translated. Despite the accumulation of isoforms in nuclei with retention of introns in reoxygenation, ncb-1 coped much worse with long hypoxia, and manifested faster yellowing and shrinkage of leaves.

An oxygen-sensing mechanism for angiosperm adaptation to altitude

Flowering plants (angiosperms) can grow at extreme altitudes, and have been observed growing as high as 6,400 metres above sea level^1,2; however, the molecular mechanisms that enable plant adaptation specifically to altitude are unknown. One distinguishing feature of increasing altitude is a reduction in the partial pressure of oxygen (pO₂). Here we investigated the relationship between altitude and oxygen sensing in relation to chlorophyll biosynthesis—which requires molecular oxygen³—and hypoxia-related gene expression. We show that in etiolated seedlings of angiosperm species, steady-state levels of the phototoxic chlorophyll precursor protochlorophyllide are influenced by sensing of atmospheric oxygen concentration. In Arabidopsis thaliana, this is mediated by the PLANT CYSTEINE OXIDASE (PCO) N-degron pathway substrates GROUP VII ETHYLENE RESPONSE FACTOR transcription factors (ERFVIIs). ERFVIIs positively regulate expression of FLUORESCENT IN BLUE LIGHT (FLU), which represses the first committed step of chlorophyll biosynthesis, forming an inactivation complex with tetrapyrrole synthesis enzymes that are negatively regulated by ERFVIIs, thereby suppressing protochlorophyllide. In natural populations representing diverse angiosperm clades, we find oxygen-dependent altitudinal clines for steady-state levels of protochlorophyllide, expression of inactivation complex components and hypoxia-related genes. Finally, A. thaliana accessions from contrasting altitudes display altitude-dependent ERFVII activity and accumulation. We thus identify a mechanism for genetic adaptation to absolute altitude through alteration of the sensitivity of the oxygen-sensing system.

Plants have adapted to grow at specific altitudes by regulating chlorophyll synthesis in response to ambient oxygen concentration, calibrated by altitude-dependent activity of GROUP VII ETHYLENE RESPONSE FACTOR.

Transcriptional Response of Two Brassica napus Cultivars to Short-Term Hypoxia in the Root Zone

Waterlogging is one major stress for crops and causes multiple problems for plants, for example low gas diffusion, changes in redox potential and accumulation of toxic metabolites. Brassica napus is an important oil crop with high waterlogging sensitivity, which may cause severe yield losses. Its reactions to the stress are not fully understood. In this work the transcriptional response of rapeseed to one aspect of waterlogging, hypoxia in the root zone, was analyzed by RNAseq, including two rapeseed cultivars from different origin, Avatar from Europe and Zhongshuang 9 from Asia. Both cultivars showed a high number of differentially expressed genes in roots after 4 and 24 h of hypoxia. The response included many well-known hypoxia-induced genes such as genes coding for glycolytic and fermentative enzymes, and strongly resembled the hypoxia response of the model organism Arabidopsis thaliana. The carbohydrate status of roots, however, was minimally affected by root hypoxia, with a tendency of carbohydrate accumulation rather than a carbon starvation. Leaves did not respond to the root stress after a 24-h treatment. In agreement with the gene expression data, subsequent experiments with soil waterlogging for up to 14 days revealed no differences in response or tolerance to waterlogging between the two genotypes used in this study. Interestingly, using a 0.1% starch solution for waterlogging, which caused a lowered soil redox potential, resulted in much stronger effects of the stress treatment than using pure water suggesting a new screening method for rapeseed cultivars in future experiments.

Try or Die: Dynamics of Plant Respiration and How to Survive Low Oxygen Conditions

Fluctuations in oxygen (O₂) availability occur as a result of flooding, which is periodically encountered by terrestrial plants. Plant respiration and mitochondrial energy generation rely on O₂ availability. Therefore, decreased O₂ concentrations severely affect mitochondrial function. Low O₂ concentrations (hypoxia) induce cellular stress due to decreased ATP production, depletion of energy reserves and accumulation of metabolic intermediates. In addition, the transition from low to high O₂ in combination with light changes-as experienced during re-oxygenation-leads to the excess formation of reactive oxygen species (ROS). In this review, we will update our current knowledge about the mechanisms enabling plants to adapt to low-O₂ environments, and how to survive re-oxygenation. New insights into the role of mitochondrial retrograde signaling, chromatin modification, as well as moonlighting proteins and mitochondrial alternative electron transport pathways (and their contribution to low O₂ tolerance and survival of re-oxygenation), are presented.

Localization and Functional Roles of Components of the Translation Apparatus in the Eukaryotic Cell Nucleus

Components of the translation apparatus, including ribosomal proteins, have been found in cell nuclei in various organisms. Components of the translation apparatus are involved in various nuclear processes, particularly those associated with genome integrity control and the nuclear stages of gene expression, such as transcription, mRNA processing, and mRNA export. Components of the translation apparatus control intranuclear trafficking; the nuclear import and export of RNA and proteins; and regulate the activity, stability, and functional recruitment of nuclear proteins. The nuclear translocation of these components is often involved in the cell response to stimulation and stress, in addition to playing critical roles in oncogenesis and viral infection. Many components of the translation apparatus are moonlighting proteins, involved in integral cell stress response and coupling of gene expression subprocesses. Thus, this phenomenon represents a significant interest for both basic and applied molecular biology. Here, we provide an overview of the current data regarding the molecular functions of translation factors and ribosomal proteins in the cell nucleus.

Transition from Seeds to Seedlings: Hormonal and Epigenetic Aspects

Transition from seed to seedling is one of the critical developmental steps, dramatically affecting plant growth and viability. Before plants enter the vegetative phase of their ontogenesis, massive rearrangements of signaling pathways and switching of gene expression programs are required. This results in suppression of the genes controlling seed maturation and activation of those involved in regulation of vegetative growth. At the level of hormonal regulation, these events are controlled by the balance of abscisic acid and gibberellins, although ethylene, auxins, brassinosteroids, cytokinins, and jasmonates are also involved. The key players include the members of the LAFL network-the transcription factors LEAFY COTYLEDON1 and 2 (LEC 1 and 2), ABSCISIC ACID INSENSITIVE3 (ABI3), and FUSCA3 (FUS3), as well as DELAY OF GERMINATION1 (DOG1). They are the negative regulators of seed germination and need to be suppressed before seedling development can be initiated. This repressive signal is mediated by chromatin remodeling complexes-POLYCOMB REPRESSIVE COMPLEX 1 and 2 (PRC1 and PRC2), as well as PICKLE (PKL) and PICKLE-RELATED2 (PKR2) proteins. Finally, epigenetic methylation of cytosine residues in DNA, histone post-translational modifications, and post-transcriptional downregulation of seed maturation genes with miRNA are discussed. Here, we summarize recent updates in the study of hormonal and epigenetic switches involved in regulation of the transition from seed germination to the post-germination stage.

The hypoxia-reoxygenation stress in plants

Plants are very plastic in adapting growth and development to changing adverse environmental conditions. This feature will be essential for plants to survive climate changes characterized by extreme temperatures and rainfall. Although plants require molecular oxygen (O2) to live, they can overcome transient low-O2 conditions (hypoxia) until return to standard 21% O2 atmospheric conditions (normoxia). After heavy rainfall, submerged plants in flooded lands undergo transient hypoxia until water recedes and normoxia is recovered. The accumulated information on the physiological and molecular events occurring during the hypoxia phase contrasts with the limited knowledge on the reoxygenation process after hypoxia, which has often been overlooked in many studies in plants. Phenotypic alterations during recovery are due to potentiated oxidative stress generated by simultaneous reoxygenation and reillumination leading to cell damage. Besides processes such as N-degron proteolytic pathway-mediated O2 sensing, or mitochondria-driven metabolic alterations, other molecular events controlling gene expression have been recently proposed as key regulators of hypoxia and reoxygenation. RNA regulatory functions, chromatin remodeling, protein synthesis, and post-translational modifications must all be studied in depth in the coming years to improve our knowledge on hypoxia-reoxygenation transition in plants, a topic with relevance in agricultural biotechnology in the context of global climate change.

Using high-throughput multiple optical phenotyping to decipher the genetic architecture of maize drought tolerance

BACKGROUND

Drought threatens the food supply of the world population. Dissecting the dynamic responses of plants to drought will be beneficial for breeding drought-tolerant crops, as the genetic controls of these responses remain largely unknown.

RESULTS

Here we develop a high-throughput multiple optical phenotyping system to noninvasively phenotype 368 maize genotypes with or without drought stress over a course of 98 days, and collected multiple optical images, including color camera scanning, hyperspectral imaging, and X-ray computed tomography images. We develop high-throughput analysis pipelines to extract image-based traits (i-traits). Of these i-traits, 10,080 were effective and heritable indicators of maize external and internal drought responses. An i-trait-based genome-wide association study reveals 4322 significant locus-trait associations, representing 1529 quantitative trait loci (QTLs) and 2318 candidate genes, many that co-localize with previously reported maize drought responsive QTLs. Expression QTL (eQTL) analysis uncovers many local and distant regulatory variants that control the expression of the candidate genes. We use genetic mutation analysis to validate two new genes, ZmcPGM2 and ZmFAB1A, which regulate i-traits and drought tolerance. Moreover, the value of the candidate genes as drought-tolerant genetic markers is revealed by genome selection analysis, and 15 i-traits are identified as potential markers for maize drought tolerance breeding.

CONCLUSION

Our study demonstrates that combining high-throughput multiple optical phenotyping and GWAS is a novel and effective approach to dissect the genetic architecture of complex traits and clone drought-tolerance associated genes.

Transcriptome Analysis of Arabidopsis thaliana Plants Treated with a New Compound Natolen128, Enhancing Salt Stress Tolerance

Salinity stress is a major threat to agriculture and global food security. Chemical priming is a promising approach to improving salinity stress tolerance in plants. To identify small molecules with the capacity to enhance salinity stress tolerance in plants, chemical screening was performed using Arabidopsis thaliana. We screened 6400 compounds from the Nagoya University Institute of Transformative Bio-Molecule (ITbM) chemical library and identified one compound, Natolen128, that enhanced salinity-stress tolerance. Furthermore, we isolated a negative compound of Natolen128, namely Necolen124, that did not enhance salinity stress tolerance, though it has a similar chemical structure to Natolen128. We conducted a transcriptomic analysis of Natolen128 and Necolen124 to investigate how Natolen128 enhances high-salinity stress tolerance. Our data indicated that the expression levels of 330 genes were upregulated by Natolen128 treatment compared with that of Necolen124. Treatment with Natolen128 increased expression of hypoxia-responsive genes including ethylene biosynthetic enzymes and PHYTOGLOBIN, which modulate accumulation of nitric oxide (NO) level. NO was slightly increased in plants treated with Natolen128. These results suggest that Natolen128 may regulate NO accumulation and thus, improve salinity stress tolerance in A. thaliana.

Sugar modulation of anaerobic-response networks in maize root tips

Sugar supply is a key component of hypoxia tolerance and acclimation in plants. However, a striking gap remains in our understanding of mechanisms governing sugar impacts on low-oxygen responses. Here, we used a maize (Zea mays) root-tip system for precise control of sugar and oxygen levels. We compared responses to oxygen (21 and 0.2%) in the presence of abundant versus limited glucose supplies (2.0 and 0.2%). Low-oxygen reconfigured the transcriptome with glucose deprivation enhancing the speed and magnitude of gene induction for core anaerobic proteins (ANPs). Sugar supply also altered profiles of hypoxia-responsive genes carrying G4 motifs (sources of regulatory quadruplex structures), revealing a fast, sugar-independent class followed more slowly by feast-or-famine-regulated G4 genes. Metabolite analysis showed that endogenous sugar levels were maintained by exogenous glucose under aerobic conditions and demonstrated a prominent capacity for sucrose re-synthesis that was undetectable under hypoxia. Glucose abundance had distinctive impacts on co-expression networks associated with ANPs, altering network partners and aiding persistence of interacting networks under prolonged hypoxia. Among the ANP networks, two highly interconnected clusters of genes formed around Pyruvate decarboxylase 3 and Glyceraldehyde-3-phosphate dehydrogenase 4. Genes in these clusters shared a small set of cis-regulatory elements, two of which typified glucose induction. Collective results demonstrate specific, previously unrecognized roles of sugars in low-oxygen responses, extending from accelerated onset of initial adaptive phases by starvation stress to maintenance and modulation of co-expression relationships by carbohydrate availability.

Linkage analysis, GWAS, transcriptome analysis to identify candidate genes for rice seedlings in response to high temperature stress

BACKGROUND

Rice plants suffer from the rising temperature which is becoming more and more prominent. Mining heat-resistant genes and applying them to rice breeding is a feasible and effective way to solve the problem.

RESULT

Three main biomass traits, including shoot length, dry weight, and fresh weight, changed after abnormally high-temperature treatment in the rice seedling stage of a recombinant inbred lines and the natural indica germplasm population. Based on a comparison of the results of linkage analysis and genome-wide association analysis, two loci with lengths of 57 kb and 69 kb in qDW7 and qFW6, respectively, were associated with the rice response to abnormally high temperatures at the seedling stage. Meanwhile, based on integrated transcriptome analysis, some genes are considered as important candidate genes. Combining with known genes and analysis of homologous genes, it was found that there are eight genes in candidate intervals that need to be focused on in subsequent research.

CONCLUSIONS

The results indicated several relevant loci, which would help researchers to further discover beneficial heat-resistant genes that can be applied to rice heat-resistant breeding.

Linkage analysis, GWAS, transcriptome analysis to identify candidate genes for rice seedlings in response to high temperature stress

BACKGROUND

Rice plants suffer from the rising temperature which is becoming more and more prominent. Mining heat-resistant genes and applying them to rice breeding is a feasible and effective way to solve the problem.

RESULT

Three main biomass traits, including shoot length, dry weight, and fresh weight, changed after abnormally high-temperature treatment in the rice seedling stage of a recombinant inbred lines and the natural indica germplasm population. Based on a comparison of the results of linkage analysis and genome-wide association analysis, two loci with lengths of 57 kb and 69 kb in qDW7 and qFW6, respectively, were associated with the rice response to abnormally high temperatures at the seedling stage. Meanwhile, based on integrated transcriptome analysis, some genes are considered as important candidate genes. Combining with known genes and analysis of homologous genes, it was found that there are eight genes in candidate intervals that need to be focused on in subsequent research.

CONCLUSIONS

The results indicated several relevant loci, which would help researchers to further discover beneficial heat-resistant genes that can be applied to rice heat-resistant breeding.

Valine-Glutamine Proteins in Plant Responses to Oxygen and Nitric Oxide

Multigene families coding for valine-glutamine (VQ) proteins have been identified in all kind of plants but chlorophytes. VQ proteins are transcriptional regulators, which often interact with WRKY transcription factors to regulate gene expression sometimes modulated by reversible phosphorylation. Different VQ-WRKY complexes regulate defense against varied pathogens as well as responses to osmotic stress and extreme temperatures. However, despite these well-known functions, new regulatory activities for VQ proteins are still to be explored. Searching public Arabidopsis thaliana transcriptome data for new potential targets of VQ-WRKY regulation allowed us identifying several VQ protein and WRKY factor encoding genes that were differentially expressed in oxygen-related processes such as responses to hypoxia or ozone-triggered oxidative stress. Moreover, some of those were also differentially regulated upon nitric oxide (NO) treatment. These subsets of VQ and WRKY proteins might combine into different VQ-WRKY complexes, thus representing a potential regulatory core of NO-modulated and O₂-modulated responses. Given the increasing relevance that gasotransmitters are gaining as plant physiology regulators, and particularly considering the key roles exerted by O₂ and NO in regulating the N-degron pathway-controlled stability of transcription factors, VQ and WRKY proteins could be instrumental in regulating manifold processes in plants.

Multiple levels of crosstalk in hormone networks regulating plant defense

Plant hormones are essential for regulating the interactions between plants and their complex biotic and abiotic environments. Each hormone initiates a specific molecular pathway and these different hormone pathways are integrated in a complex network of synergistic, antagonistic and additive interactions. This inter-pathway communication is called hormone crosstalk. By influencing the immune network topology, hormone crosstalk is essential for tailoring plant responses to diverse microbes and insects in diverse environmental and internal contexts. Crosstalk provides robustness to the immune system but also drives specificity of induced defense responses against the plethora of biotic interactors. Recent advances in dry-lab and wet-lab techniques have greatly enhanced our understanding of the broad-scale effects of hormone crosstalk on immune network functioning and have revealed underlying principles of crosstalk mechanisms. Molecular studies have demonstrated that hormone crosstalk is modulated at multiple levels of regulation, such as by affecting protein stability, gene transcription and hormone homeostasis. These new insights into hormone crosstalk regulation of plant defense are reviewed here, with a focus on crosstalk acting on the jasmonic acid pathway in Arabidopsis thaliana, highlighting the transcription factors MYC2 and ORA59 as major targets for modulation by other hormones.

RNAi Mediated Hypoxia Stress Tolerance in Plants

Small RNAs regulate various biological process involved in genome stability, development, and adaptive responses to biotic or abiotic stresses. Small RNAs include microRNAs (miRNAs) and small interfering RNAs (siRNAs). MicroRNAs (miRNAs) are regulators of gene expression that affect the transcriptional and post-transcriptional regulation in plants and animals through RNA interference (RNAi). miRNAs are endogenous small RNAs that originate from the processing of non-coding primary miRNA transcripts folding into hairpin-like structures. The mature miRNAs are incorporated into the RNA-induced silencing complex (RISC) and drive the Argonaute (AGO) proteins towards their mRNA targets. siRNAs are generated from a double-stranded RNA (dsRNA) of cellular or exogenous origin. siRNAs are also involved in the adaptive response to biotic or abiotic stresses. The response of plants to hypoxia includes a genome-wide transcription reprogramming. However, little is known about the involvement of RNA signaling in gene regulation under low oxygen availability. Interestingly, miRNAs have been shown to play a role in the responses to hypoxia in animals, and recent evidence suggests that hypoxia modulates the expression of various miRNAs in plant systems. In this review, we describe recent discoveries on the impact of RNAi on plant responses to hypoxic stress in plants.

The Hypoxic Proteome and Metabolome of Barley (Hordeum vulgare L.) with and without Phytoglobin Priming

Overexpression of phytoglobins (formerly plant hemoglobins) increases the survival rate of plant tissues under hypoxia stress by the following two known mechanisms: (1) scavenging of nitric oxide (NO) in the phytoglobin/NO cycle and (2) mimicking ethylene priming to hypoxia when NO scavenging activates transcription factors that are regulated by levels of NO and O2 in the N-end rule pathway. To map the cellular and metabolic effects of hypoxia in barley (Hordeum vulgare L., cv. Golden Promise), with or without priming to hypoxia, we studied the proteome and metabolome of wild type (WT) and hemoglobin overexpressing (HO) plants in normoxia and after 24 h hypoxia (WT24, HO24). The WT plants were more susceptible to hypoxia than HO plants. The chlorophyll a + b content was lowered by 50% and biomass by 30% in WT24 compared to WT, while HO plants were unaffected. We observed an increase in ROS production during hypoxia treatment in WT seedlings that was not observed in HO seedlings. We identified and quantified 9694 proteins out of which 1107 changed significantly in abundance. Many proteins, such as ion transporters, Ca2+-signal transduction, and proteins related to protein degradation were downregulated in HO plants during hypoxia, but not in WT plants. Changes in the levels of histones indicates that chromatin restructuring plays a role in the priming of hypoxia. We also identified and quantified 1470 metabolites, of which the abundance of >500 changed significantly. In summary the data confirm known mechanisms of hypoxia priming by ethylene priming and N-end rule activation; however, the data also indicate the existence of other mechanisms for hypoxia priming in plants.

RNA-Seq reveals novel genes and pathways associated with hypoxia duration and tolerance in tomato root

Due to climate change, economically important crop plants will encounter flooding periods causing hypoxic stress more frequently. This may lead to reduced yields and endanger food security. As roots are the first organ to be affected by hypoxia, the ability to sense and respond to hypoxic stress is crucial. At the molecular level, therefore, fine-tuning the regulation of gene expression in the root is essential for hypoxia tolerance. Using an RNA-Seq approach, we investigated transcriptome modulation in tomato roots of the cultivar 'Moneymaker', in response to short- (6 h) and long-term (48 h) hypoxia. Hypoxia duration appeared to have a significant impact on gene expression such that the roots of five weeks old tomato plants showed a distinct time-dependent transcriptome response. We observed expression changes in 267 and 1421 genes under short- and long-term hypoxia, respectively. Among these, 243 genes experienced changed expression at both time points. We identified tomato genes with a potential role in aerenchyma formation which facilitates oxygen transport and may act as an escape mechanism enabling hypoxia tolerance. Moreover, we identified differentially regulated genes related to carbon and amino acid metabolism and redox homeostasis. Of particular interest were the differentially regulated transcription factors, which act as master regulators of downstream target genes involved in responses to short and/or long-term hypoxia. Our data suggest a temporal metabolic and anatomic adjustment to hypoxia in tomato root which requires further investigation. We propose that the regulated genes identified in this study are good candidates for further studies regarding hypoxia tolerance in tomato or other crops.

Chloroplast Calcium Signaling in the Spotlight

Calcium has long been known to regulate the metabolism of chloroplasts, concerning both light and carbon reactions of photosynthesis, as well as additional non photosynthesis-related processes. In addition to undergo Ca²⁺ regulation, chloroplasts can also influence the overall Ca²⁺ signaling pathways of the plant cell. Compelling evidence indicate that chloroplasts can generate specific stromal Ca²⁺ signals and contribute to the fine tuning of cytoplasmic Ca²⁺ signaling in response to different environmental stimuli. The recent set up of a toolkit of genetically encoded Ca²⁺ indicators, targeted to different chloroplast subcompartments (envelope, stroma, thylakoids) has helped to unravel the participation of chloroplasts in intracellular Ca²⁺ handling in resting conditions and during signal transduction. Intra-chloroplast Ca²⁺ signals have been demonstrated to occur in response to specific environmental stimuli, suggesting a role for these plant-unique organelles in transducing Ca²⁺-mediated stress signals. In this mini-review we present current knowledge of stimulus-specific intra-chloroplast Ca²⁺ transients, as well as recent advances in the identification and characterization of Ca²⁺-permeable channels/transporters localized at chloroplast membranes. In particular, the potential role played by cMCU, a chloroplast-localized member of the mitochondrial calcium uniporter (MCU) family, as component of plant environmental sensing is discussed in detail, taking into account some specific structural features of cMCU. In summary, the recent molecular identification of some players of chloroplast Ca²⁺ signaling has opened new avenues in this rapidly developing field and will hopefully allow a deeper understanding of the role of chloroplasts in shaping physiological responses in plants.