The plant noncoding transcriptome: a versatile environmental sensor.

Plant noncoding RNA transcripts have gained increasing attention in recent years due to growing evidence that they can regulate developmental plasticity. In this review article, we comprehensively analyze the relationship between noncoding RNA transcripts in plants and their response to environmental cues. We first provide an overview of the various noncoding transcript types, including long and small RNAs, and how the environment modulates their performance. We then highlight the importance of noncoding RNA secondary structure for their molecular and biological functions. Finally, we discuss recent studies that have unveiled the functional significance of specific long noncoding transcripts and their molecular partners within ribonucleoprotein complexes during development and in response to biotic and abiotic stress. Overall, this review sheds light on the fascinating and complex relationship between dynamic noncoding transcription and plant environmental responses, and highlights the need for further research to uncover the underlying molecular mechanisms and exploit the potential of noncoding transcripts for crop resilience in the context of global warming.

Understanding the chemical language mediating maize immunity and environmental adaptation.

Diverse networks of specialized metabolites promote plant fitness by mediating beneficial and antagonistic environmental interactions. In maize (Zea mays), constitutive and dynamically formed cocktails of terpenoids, benzoxazinoids, oxylipins, and phenylpropanoids contribute to plant defense and ecological adaptation. Recent research has highlighted the multifunctional nature of many specialized metabolites, serving not only as elaborate chemical defenses that safeguard against biotic and abiotic stress but also as regulators in adaptive developmental processes and microbiome interactions. Great strides have also been made in identifying the modular pathway networks that drive maize chemical diversity. Translating this knowledge into strategies for enhancing stress resilience traits has the potential to address climate-driven yield losses in one of the world's major food, feed, and bioenergy crops.

Environmental context of phenotypic plasticity in flowering time in sorghum and rice.

Phenotypic plasticity is an important topic in biology and evolution. However, how to generate broadly applicable insights from individual studies remains a challenge. Here, with flowering time observed from a large geographical region for sorghum and rice genetic populations, we examine the consistency of parameter estimation for reaction norms of genotypes across different subsets of environments and searched for potential strategies to inform the study design. Both sample size and environmental mean range of the subset affected the consistency. The subset with either a large range of environmental mean or a large sample size resulted in genetic parameters consistent with the overall pattern. Furthermore, high accuracy through genomic prediction was obtained for reaction norm parameters of untested genotypes using models built from tested genotypes under the subsets of environments with either a large range or a large sample size. With 1428 and 1674 simulated settings, our analyses suggested that the distribution of environmental index values of a site should be considered in designing experiments. Overall, we showed that environmental context was critical, and considerations should be given to better cover the intended range of the environmental variable. Our findings have implications for the genetic architecture of complex traits, plant-environment interaction, and climate adaptation.

Effect of Nutrient Solution Flow on Lettuce Root Morphology in Hydroponics: A Multi-Omics Analysis of Hormone Synthesis and Signal Transduction.

This study examined how the nutrient flow environment affects lettuce root morphology in hydroponics using multi-omics analysis. The results indicate that increasing the nutrient flow rate initially increased indicators such as fresh root weight, root length, surface area, volume, and average diameter before declining, which mirrors the trend observed for shoot fresh weight. Furthermore, a high-flow environment significantly increased root tissue density. Further analysis using Weighted Gene Co-expression Network Analysis (WGCNA) and Weighted Protein Co-expression Network Analysis (WPCNA) identified modules that were highly correlated with phenotypes and hormones. The analysis revealed a significant enrichment of hormone signal transduction pathways. Differences in the expression of genes and proteins related to hormone synthesis and transduction pathways were observed among the different flow conditions. These findings suggest that nutrient flow may regulate hormone levels and signal transmission by modulating the genes and proteins associated with hormone biosynthesis and signaling pathways, thereby influencing root morphology. These findings should support the development of effective methods for regulating the flow of nutrients in hydroponic contexts.

Time-resolved systems analysis of the induction of high photosynthetic capacity in Arabidopsis during acclimation to high light.

Induction of high photosynthetic capacity is a key acclimation response to high light (HL) for many herbaceous dicot plants; however, the signaling pathways that control this response remain largely unknown. Here, a systems biology approach was utilized to characterize the induction of high photosynthetic capacity in strongly and weakly acclimating Arabidopsis thaliana accessions. Plants were grown for 5 wk in a low light (LL) regime, and time-resolved photosynthetic physiological, metabolomic, and transcriptomic responses were measured during subsequent exposure to HL. The induction of high nitrogen (N) assimilation rates early in the HL shift was strongly predictive of the induction of photosynthetic capacity later in the HL shift. Accelerated N assimilation rates depended on the mobilization of existing organic acid (OA) reserves and increased de novo OA synthesis during the induction of high photosynthetic capacity. Enhanced sucrose biosynthesis capacity increased in tandem with the induction of high photosynthetic capacity, and increased starch biosynthetic capacity was balanced by increased starch catabolism. This systems analysis supports a model in which the efficient induction of N assimilation early in the HL shift begins the cascade of events necessary for the induction of high photosynthetic capacity acclimation in HL.

Dynamic response of photorespiration in fluctuating light environments.

Photorespiration is a dynamic process that is intimately linked to photosynthetic carbon assimilation. There is a growing interest in understanding carbon assimilation during dynamic conditions, but the role of photorespiration under such conditions is unclear. In this review, we discuss recent work relevant to the function of photorespiration under dynamic conditions, with a special focus on light transients. This work reveals that photorespiration is a fundamental component of the light induction of assimilation where variable diffusive processes limit CO2 exchange with the atmosphere. Additionally, metabolic interactions between photorespiration and the C3 cycle may help balance fluxes under dynamic light conditions. We further discuss how the energy demands of photorespiration present special challenges to energy balancing during dynamic conditions. We finish the review with an overview of why regulation of photorespiration may be important under dynamic conditions to maintain appropriate fluxes through metabolic pathways related to photorespiration such as nitrogen and one-carbon metabolism.

Plant sizes and shapes above and belowground and their interactions with climate.

Although the above and belowground sizes and shapes of plants strongly influence plant competition, community structure, and plant-environment interactions, plant sizes and shapes remain poorly characterized across climate regimes. We investigated relationships among shoot and root system size and climate. We assembled and analyzed, to our knowledge, the largest global database describing the maximum rooting depth, lateral spread, and shoot size of terrestrial plants - more than doubling the Root Systems of Individual Plants database to 5647 observations. Water availability and growth form greatly influence shoot size, and rooting depth is primarily influenced by temperature seasonality. Shoot size is the strongest predictor of lateral spread, with root system diameter being two times wider than shoot width on average for woody plants. Shoot size covaries strongly with rooting system size; however, the geometries of plants differ considerably across climates, with woody plants in more arid climates having shorter shoots, but deeper, narrower root systems. Additionally, estimates of the depth and lateral spread of plant root systems are likely underestimated at the global scale.

cis-prenyltransferase 3 and α/ß-hydrolase are new determinants of dolichol accumulation in Arabidopsis.

Dolichols (Dols), ubiquitous components of living organisms, are indispensable for cell survival. In plants, as well as other eukaryotes, Dols are crucial for post-translational protein glycosylation, aberration of which leads to fatal metabolic disorders in humans and male sterility in plants. Until now, the mechanisms underlying Dol accumulation remain elusive. In this study, we have analysed the natural variation of the accumulation of Dols and six other isoprenoids among more than 120 Arabidopsis thaliana accessions. Subsequently, by combining QTL and GWAS approaches, we have identified several candidate genes involved in the accumulation of Dols, polyprenols, plastoquinone and phytosterols. The role of two genes implicated in the accumulation of major Dols in Arabidopsis-the AT2G17570 gene encoding a long searched for cis-prenyltransferase (CPT3) and the AT1G52460 gene encoding an α/ß-hydrolase-is experimentally confirmed. These data will help to generate Dol-enriched plants which might serve as a remedy for Dol-deficiency in humans.

Extranuptial nectaries in bromeliads: a new record for Pitcairnia burchellii and perspectives for Bromeliaceae.

Nectar plays important roles in the relationship between plants and other organisms, both within pollination systems and as a defense mechanism. In the latter case, extranuptial nectaries (ENNs) usually attract patrolling arthropods that reduce herbivory. ENNs have been frequently reported within the "xeric clade" of Bromeliaceae, but their occurrence in other groups of bromeliads is largely unexplored, especially considering their position, secretory activity and structure. After observing the presence of ants constantly patrolling the inflorescences of Pitcairnia burchellii Mez, we searched for the presence, secretory activity, and structure of ENNs in this species. We also provide a brief review of the occurrence ENNs in Bromeliaceae. The distribution of nectaries was assessed using ant-exclusion experiments, while structural analysis was performed using standard methods for light and scanning electron microscopy. The presence of sugars in the secretion was assessed by thin-layer chromatography and glucose strip tests. Nectaries in P. burchelli are non-structured glands on the adaxial surface of floral bracts and sepals. Bracts and sepals are distinct spatial units that act over time in the same strategy of floral bud protection. Literature data reveals that ENNs might be more common within Bromeliaceae than previously considered, comprising a homoplastic feature in the family. Future perspectives and evolutionary and taxonomic implications are discussed.

The Chemical Ecology of Benzoxazinoids.

Benzoxazinoids are specialized metabolites that modulate plant physiology and plant interactions with their environment. In this review, we synthesize their multiple functions and ecological relevance. We first provide an overview of benzoxazinoid biosynthesis and highlight known regulatory elements involved in modulating their production. We then outline the role of benzoxazinoids in plant nutrition, vegetative and reproductive growth, and defense. We further summarize benzoxazinoid response to environmental factors such as temperature, drought, CO2, light, or nutrient levels and emphasize their potential role in tolerating abiotic stresses. Finally, we argue that benzoxazinoids act as a strong selective force on different trophic levels by shaping the plant interactions with microbes, insect herbivores, and competitor plants. Understanding the pivotal role of benzoxazinoids in plant biology is crucial to apprehend their impact on (agro)ecosystem functioning and diversity.

Environment-coupled models of leaf metabolism.

The plant leaf is the main site of photosynthesis. This process converts light energy and inorganic nutrients into chemical energy and organic building blocks for the biosynthesis and maintenance of cellular components and to support the growth of the rest of the plant. The leaf is also the site of gas-water exchange and due to its large surface, it is particularly vulnerable to pathogen attacks. Therefore, the leaf's performance and metabolic modes are inherently determined by its interaction with the environment. Mathematical models of plant metabolism have been successfully applied to study various aspects of photosynthesis, carbon and nitrogen assimilation and metabolism, aided suggesting metabolic intervention strategies for optimized leaf performance, and gave us insights into evolutionary drivers of plant metabolism in various environments. With the increasing pressure to improve agricultural performance in current and future climates, these models have become important tools to improve our understanding of plant-environment interactions and to propel plant breeders efforts. This overview article reviews applications of large-scale metabolic models of leaf metabolism to study plant-environment interactions by means of flux-balance analysis. The presented studies are organized in two ways - by the way the environment interactions are modelled - via external constraints or data-integration and by the studied environmental interactions - abiotic or biotic.

Interplay between Coumarin Accumulation, Iron Deficiency and Plant Resistance to Dickeya spp.

Coumarins belong to a group of secondary metabolites well known for their high biological activities including antibacterial and antifungal properties. Recently, an important role of coumarins in plant resistance to pathogens and their release into the rhizosphere upon pathogen infection was discovered. It is also well documented that coumarins play a crucial role in the Arabidopsis thaliana growth under Fe-limited conditions. However, the mechanisms underlying interplay between plant resistance, accumulation of coumarins and Fe status, remain largely unknown. In this work, we investigated the effect of both mentioned factors on the disease severity using the model system of Arabidopsis/Dickeya spp. molecular interactions. We evaluated the disease symptoms in Arabidopsis plants, wild-type Col-0 and its mutants defective in coumarin accumulation, grown in hydroponic cultures with contrasting Fe regimes and in soil mixes. Under all tested conditions, Arabidopsis plants inoculated with Dickeya solani IFB0099 strain developed more severe disease symptoms compared to lines inoculated with Dickeya dadantii 3937. We also showed that the expression of genes encoding plant stress markers were strongly affected by D. solani IFB0099 infection. Interestingly, the response of plants to D. dadantii 3937 infection was genotype-dependent in Fe-deficient hydroponic solution.

Identification and Characterization of Stress-Responsive TAS3-Derived TasiRNAs in Melon.

Small interfering RNAs (siRNA) are key regulators of gene expression that play essential roles in diverse biological processes. Trans-acting siRNAs (tasiRNAs) are a class of plant-endogenous siRNAs that lead the cleavage of nonidentical transcripts. TasiRNAs are usually involved in fine-tuning development. However, increasing evidence supports that tasiRNAs may be involved in stress response. Melon is a crop of great economic importance extensively cultivated in semiarid regions frequently exposed to changing environmental conditions that limit its productivity. However, knowledge of the precise role of siRNAs in general, and of tasiRNAs in particular, in regulating the response to adverse environmental conditions is limited. Here, we provide the first comprehensive analysis of computationally inferred melon-tasiRNAs responsive to two biotic (viroid-infection) and abiotic (cold treatment) stress conditions. We identify two TAS3-loci encoding to length (TAS3-L) and short (TAS3-S) transcripts. The TAS candidates predicted from small RNA-sequencing data were characterized according to their chromosome localization and expression pattern in response to stress. The functional activity of cmTAS genes was validated by transcript quantification and degradome assays of the tasiRNA precursors and their predicted targets. Finally, the functionality of a representative cmTAS3-derived tasiRNA (TAS3-S) was confirmed by transient assays showing the cleavage of ARF target transcripts.

Exploring the protein-protein interaction landscape in plants.

Protein-protein interactions (PPIs) represent an essential aspect of plant systems biology. Identification of key protein players and their interaction networks provide crucial insights into the regulation of plant developmental processes and into interactions of plants with their environment. Despite the great advance in the methods for the discovery and validation of PPIs, still several challenges remain. First, the PPI networks are usually highly dynamic, and the in vivo interactions are often transient and difficult to detect. Therefore, the properties of the PPIs under study need to be considered to select the most suitable technique, because each has its own advantages and limitations. Second, besides knowledge on the interacting partners of a protein of interest, characteristics of the interaction, such as the spatial or temporal dynamics, are highly important. Hence, multiple approaches have to be combined to obtain a comprehensive view on the PPI network present in a cell. Here, we present the progress in commonly used methods to detect and validate PPIs in plants with a special emphasis on the PPI features assessed in each approach and how they were or can be used for the study of plant interactions with their environment.

The era of nitric oxide in plant biology: Twenty years tying up loose ends.

Nitric oxide (NO) is an essential signal molecule to maintain cellular homeostasis in uni and pluricellular organisms. Conceptually, NO intervenes as much in sustaining basal metabolic processes, as in firing cellular responses to changes in internal and external conditions, and also in guiding the return to basal conditions. Behind these unusual capabilities of NO is the chemistry of this molecule, an unstable, reactive, free radical and short half-life gas. It is a lipophilic molecule that crosses all the barriers that biological membranes can impose. The extraordinary impact that the elucidation of physiological processes regulated by NO has had on plants, is comparable to the consequences of the discovery in 1986 that NO is present in animal tissues, and the following deep studies that demonstrated its biological activity regulating blood pressure. In this review, we have summarized and discuss the main discoveries that have emerged at Mar del Plata University over the past 20 years, and that have contributed to understand part of the biology of NO in plants. Besides, these findings are put in context with the progress made by other research groups, and in perspective, emphasizing that the history of NO in plants has just begun.

Integration of multi-omics techniques and physiological phenotyping within a holistic phenomics approach to study senescence in model and crop plants.

The study of senescence in plants is complicated by diverse levels of temporal and spatial dynamics as well as the impact of external biotic and abiotic factors and crop plant management. Whereas the molecular mechanisms involved in developmentally regulated leaf senescence are very well understood, in particular in the annual model plant species Arabidopsis, senescence of other organs such as the flower, fruit, and root is much less studied as well as senescence in perennials such as trees. This review addresses the need for the integration of multi-omics techniques and physiological phenotyping into holistic phenomics approaches to dissect the complex phenomenon of senescence. That became feasible through major advances in the establishment of various, complementary 'omics' technologies. Such an interdisciplinary approach will also need to consider knowledge from the animal field, in particular in relation to novel regulators such as small, non-coding RNAs, epigenetic control and telomere length. Such a characterization of phenotypes via the acquisition of high-dimensional datasets within a systems biology approach will allow us to systematically characterize the various programmes governing senescence beyond leaf senescence in Arabidopsis and to elucidate the underlying molecular processes. Such a multi-omics approach is expected to also spur the application of results from model plants to agriculture and their verification for sustainable and environmentally friendly improvement of crop plant stress resilience and productivity and contribute to improvements based on postharvest physiology for the food industry and the benefit of its customers.

Genome-wide identification of the GDSL-type esterase/lipase protein (GELP) gene family in Ricinus communis and its transcriptional regulation during germination and seedling establishment under different abiotic stresses.

GDSL-type esterase/lipase protein (GELP) genes are crucial in the specialized lipid metabolism, in the responses to abiotic stresses, and in the regulation of plant homeostasis. R. communis is an important oilseed crop species that can sustain growth and productivity when exposed to harsh environmental conditions. Herein, we raised the question of whether the GELP gene family could be involved in the acquisition of R. communis tolerance to abiotic stresses during seed germination and seedling establishment. Thus, we used bioinformatics and transcriptomics to characterize the R. communis GELP gene family. R. communis genome possesses 96 GELP genes that were characterized by extensive bioinformatics, including phylogenetic analysis, subcellular localization, exon-intron distribution, the analysis of regulatory cis-elements, tandem duplication, and physicochemical properties. Transcriptomics indicated that numerous RcGELP genes are readily responsive to high-temperature and salt stresses and might be potential candidates for genome editing techniques to develop abiotic stress-tolerant crops.

An overview of secretion in floral bracts of Tillandsioideae (Bromeliaceae), with emphasis on the secretory scales.

Bromeliaceae display many water-use strategies, from leaf impounding tanks to Crassulacean acid metabolism (CAM) photosynthesis and absorbing trichomes. Recent studies show that trichomes in inflorescences of bromeliads can exude viscous secretions, protecting against various stresses, including excessive water loss. In light of this, and considering the knowledge gap regarding inflorescence trichomes in bromeliads, we aimed to investigate the presence, source and chemical nature of inflorescence secretions in species of the Tillandsioideae (Bromeliaceae) and to describe the anatomy of their floral bracts focusing on trichome structure and position. We conducted a prospection of secretory activity and anatomy in floral bracts in 52 species of Tillandsioideae and 1 early divergent Bromeliaceae species. We used histochemical tests to investigate the presence and nature of secretion combined with standard light microscopy methods. Secretion appears in all studied species of tribe Vrieseeae, in Guzmania species, Wallisia cyanea, Tillandsia streptopylla (Tillandsieae) and Catopsis morreniana (Catopsideae). It is absent in Vriesea guttata (Vrieseeae), Racinaea crispa and various Tillandsia species (Tillandsieae). Secretion is produced by peltate trichomes on the adaxial surface of young bracts and comprises hydrophilic and lipophilic substances. Bract anatomy revealed an internal mucilage-secreting tissue with wide distribution within the subtribe Vrieseinae. Our results point to a broad occurrence of secretion associated with bracteal scales in inflorescences of Tillandsioideae. Secretory function is strongly related to trichomes of the adaxial surface, whereas the indumentum of the abaxial side is lacking or likely associated with water absorption; the latter case is especially related to small, xeric plants. Exudates might engage in colleter-like roles, protecting against desiccation, high-radiation and herbivores. Directions for future research are presented.