Nitrate in 2020: Thirty Years from Transport to Signaling Networks

The Plant Cell, Год журнала: 2020, Номер 32(7), С. 2094 - 2119

Опубликована: Март 13, 2020

Nitrogen (N) is an essential macronutrient for plants and a major limiting factor plant growth crop production. Nitrate the main source of N available to in agricultural soils many natural environments. Sustaining productivity paramount importance current scenario increasing world population, diversification uses, climate change. Plant crops around world, however, still supported by excess application N-rich fertilizers with detrimental economic environmental impacts. Thus, understanding how regulate nitrate uptake metabolism key developing new enhanced use efficiency cope future food demands. The study responses has gained considerable interest over last 30 years. This review provides overview findings research, spanning biochemistry, molecular genetics, genomics, systems biology. We discuss we have reached our view transport, local systemic sensing/signaling, regulatory networks underlying nitrate-controlled outputs plants. hope this summary will serve not only as timeline information repository but also baseline define outstanding questions research.

Язык: Английский

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PLAZA 5.0: extending the scope and power of comparative and functional genomics in plants

Nucleic Acids Research, Год журнала: 2021, Номер 50(D1), С. D1468 - D1474

Опубликована: Окт. 13, 2021

PLAZA is a platform for comparative, evolutionary, and functional plant genomics. It makes broad set of genomes, data types analysis tools available to researchers through user-friendly website, an API, bulk downloads. In this latest release the platform, we are integrating record number 134 high-quality split up over two instances: Dicots 5.0 Monocots 5.0. This genomes corresponds with massive expansion in species when compared 4.0, which offered access 71 species, 89% overall increase. The contains information 5 882 730 genes, offers pre-computed gene families phylogenetic trees 274 684 protein-coding genes. also comes new updated features: BED import functionality workbench, improved interactive visualizations enrichments genome-wide mapping sets, fully redesigned extended API. Taken together, version support biologists working on different within green lineage provides efficient versatile toolbox All releases accessible from portal website: https://bioinformatics.psb.ugent.be/plaza/.

Язык: Английский

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Phenotyping: New Windows into the Plant for Breeders

Annual Review of Plant Biology, Год журнала: 2020, Номер 71(1), С. 689 - 712

Опубликована: Фев. 25, 2020

Plant phenotyping enables noninvasive quantification of plant structure and function interactions with environments. High-capacity reaches hitherto inaccessible phenotypic characteristics. Diverse, challenging, valuable applications have originated among scientists, prebreeders, breeders as they study the diversity genetic resources apply increasingly complex traits to crop improvement. Noninvasive technologies are used analyze experimental breeding populations. We cover most recent research in controlled-environment field for seed, shoot, root traits. Select become state art show promise speeding up process early generations. highlight behind rapid advances proximal remote sensing plants fields. conclude by discussing new disciplines working community: data science, address challenge generating FAIR (findable, accessible, interoperable, reusable) data, robotics, directly on farms.

Язык: Английский

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Advances in “Omics” Approaches for Improving Toxic Metals/Metalloids Tolerance in Plants

Frontiers in Plant Science, Год журнала: 2022, Номер 12

Опубликована: Янв. 4, 2022

Food safety has emerged as a high-urgency matter for sustainable agricultural production. Toxic metal contamination of soil and water significantly affects productivity, which is further aggravated by extreme anthropogenic activities modern practices, leaving food human health at risk. In addition to reducing crop production, increased metals/metalloids toxicity also disturbs plants' demand supply equilibrium. Counterbalancing toxic demands better understanding the complex mechanisms physiological, biochemical, molecular, cellular, plant level that may result in productivity. Consequently, plants have established different internal defense cope with adverse effects metals/metalloids. Nevertheless, these are not adequate overwhelm toxicity. Plants produce several secondary messengers trigger cell signaling, activating numerous transcriptional responses correlated defense. Therefore, recent advances omics approaches such genomics, transcriptomics, proteomics, metabolomics, ionomics, miRNAomics, phenomics enabled characterization molecular regulators associated tolerance, can be deployed developing tolerant plants. This review highlights various response strategies adopted tolerate toxicity, including responses. A seven-(omics)-based design summarized scientific clues reveal stress-responsive genes, proteins, metabolites, miRNAs, trace elements, stress-inducible phenotypes, metabolic pathways could potentially help up face fluctuating environmental conditions. Finally, some bottlenecks future directions been highlighted, enable

Язык: Английский

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Transcriptomics, proteomics, and metabolomics interventions prompt crop improvement against metal(loid) toxicity

Plant Cell Reports, Год журнала: 2024, Номер 43(3)

Опубликована: Фев. 27, 2024

The escalating challenges posed by metal(loid) toxicity in agricultural ecosystems, exacerbated rapid climate change and anthropogenic pressures, demand urgent attention. Soil contamination is a critical issue because it significantly impacts crop productivity. widespread threat of can jeopardize global food security due to contaminated supplies pose environmental risks, contributing soil water pollution thus impacting the whole ecosystem. In this context, plants have evolved complex mechanisms combat stress. Amid array innovative approaches, omics, notably transcriptomics, proteomics, metabolomics, emerged as transformative tools, shedding light on genes, proteins, key metabolites involved stress responses tolerance mechanisms. These identified candidates hold promise for developing high-yielding crops with desirable agronomic traits. Computational biology tools like bioinformatics, biological databases, analytical pipelines support these omics approaches harnessing diverse information facilitating mapping genotype-to-phenotype relationships under conditions. This review explores: (1) multifaceted strategies that use adapt their environment; (2) latest findings metal(loid)-mediated metabolomics studies across various plant species; (3) integration data artificial intelligence high-throughput phenotyping; (4) bioinformatics single and/or multi-omics integration; (5) insights into adaptations future outlooks; (6) capacity advances creating sustainable resilient thrive metal(loid)-contaminated environments.

Язык: Английский

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Systematic Multi-Omics Integration (MOI) Approach in Plant Systems Biology

Frontiers in Plant Science, Год журнала: 2020, Номер 11

Опубликована: Июнь 26, 2020

Across all facets of biology, the rapid progress in high-throughput data generation has enabled us to perform multi-omics systems biology research. Transcriptomics, proteomics, and metabolomics can answer targeted biological questions regarding expression transcripts, proteins, metabolites, independently, but a systematic integration (MOI) comprehensively assimilate, annotate, model these large sets. Previous MOI studies reviews have detailed its usage practicality on various organisms including human, animals, microbes, plants. Plants are especially challenging due poorly annotated genomes, multi-organelles, diverse secondary metabolites. Hence, constructive methodological guidelines how for plants needed, particularly researchers newly embarking this topic. In review, we thoroughly classify verify workflows ensure successful omics with accurate representation. We also propose three levels MOI, namely element-based (level 1), pathway-based 2), mathematical-based 3). These described relation recent publications tools, highlight their function. The drawbacks limitations discussed future improvement toward more amenable strategies plant biology.

Язык: Английский

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Specialized phenolic compounds in seeds: structures, functions, and regulations

Plant Science, Год журнала: 2020, Номер 296, С. 110471 - 110471

Опубликована: Март 19, 2020

Язык: Английский

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Plant Reactome: a knowledgebase and resource for comparative pathway analysis

Nucleic Acids Research, Год журнала: 2019, Номер unknown

Опубликована: Окт. 15, 2019

Abstract Plant Reactome (https://plantreactome.gramene.org) is an open-source, comparative plant pathway knowledgebase of the Gramene project. It uses Oryza sativa (rice) as a reference species for manual curation pathways and extends knowledge to another 82 via gene-orthology projection using data model framework. currently hosts 298 pathways, including metabolic transport transcriptional networks, hormone signaling developmental processes. In addition browsing users can upload analyze their omics data, such gene-expression overlay curated or experimental gene-gene interaction extend knowledge. The team actively engages researchers students on gene by offering workshops online tutorials. supports, implements collaborates with wider community make tools related genes, genomes, Findable, Accessible, Interoperable Re-usable (FAIR).

Язык: Английский

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Multifaceted roles of nitric oxide in tomato fruit ripening: NO-induced metabolic rewiring and consequences for fruit quality traits

Journal of Experimental Botany, Год журнала: 2020, Номер 72(3), С. 941 - 958

Опубликована: Окт. 30, 2020

Nitric oxide (NO) has been implicated as part of the ripening regulatory network in fleshy fruits. However, very little is known about simultaneous action NO on events and metabolic reactions behind ripening-related changes fruit color, taste, aroma nutritional value. Here, we performed an in-depth characterization concomitant tomato (Solanum lycopersicum) transcriptome metabolome associated with delayed-ripening phenotype caused by supplementation at pre-climacteric stage. Approximately one-third was altered response to NO, including a multilevel down-regulation genes, which turn restricted production tissue sensitivity ethylene. also repressed hydrogen peroxide-scavenging enzymes, intensifying nitro-oxidative stress S-nitrosation nitration throughout ripening. Carotenoid, tocopherol, flavonoid ascorbate biosynthesis were differentially affected resulting overaccumulation (25%) flavonoids (60%), impaired lycopene production. In contrast, compounds related taste (sugars, organic acids, amino acids) (volatiles) slightly NO. Our findings indicate that triggers extensive transcriptional rewiring early stage, modifying antioxidant composition minimal impact aroma.

Язык: Английский

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Functional specificity, diversity, and redundancy of Arabidopsis JAZ family repressors in jasmonate and COI1‐regulated growth, development, and defense

New Phytologist, Год журнала: 2021, Номер 231(4), С. 1525 - 1545

Опубликована: Май 19, 2021

Summary In response to jasmonates (JAs), the JA receptor Coronatine Insensitive 1 (COI1) recruits JA‐zinc‐finger inflorescence meristem (ZIM)‐domain (JAZ) family repressors for destruction regulate plant growth, development, and defense. As Arabidopsis encodes 13 JAZ repressors, their functional specificity, diversity, redundancy in JA/COI1‐mediated responses remain unclear. We generated a broad range of jaz mutants based on phylogenetic relationship investigate roles responses. The group I JAZ6 may play an inhibitory role resistance Botrytis cinerea , II (JAZ10)/III (JAZ11/12) JA‐regulated root growth inhibition susceptibility Pseudomonas syringae pv tomato DC3000, IV JAZ3/4/9 flowering time delay defense against insects. JAZs exhibit high apical hook curvature. undecuple jaz1/2/3/4/5/6/7/9/10/11/12 ( jaz1‐7 9‐12 ) mutations enhance suppress phenotypes coi1‐1 time, rosette hypersensitivity curvature, leaf yellowing is blocked by . does not influence stamen wild‐type affects transcriptional profile recovers fraction that This study contributes elucidating members JA/COI1‐regulated

Язык: Английский

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