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Trends in Plant Science Nov 2023Molecular motifs can explain information processing within single cells, while how assemblies of cells collectively achieve this remains less well understood. Plant... (Review)
Review
Molecular motifs can explain information processing within single cells, while how assemblies of cells collectively achieve this remains less well understood. Plant fitness and survival depend upon robust and accurate decision-making in their decentralised multicellular organ systems. Mobile agents, including hormones, metabolites, and RNAs, have a central role in coordinating multicellular collective decision-making, yet mechanisms describing how cell-cell communication scales to organ-level transitions is poorly understood. Here, we explore how unified outputs may emerge in plant organs by distributed information processing across different scales and using different modalities. Mathematical and computational representations of these events are also explored toward understanding how these events take place and are leveraged to manipulate plant development in response to the environment.
PubMed: 38036390
DOI: 10.1016/j.tplants.2023.11.006 -
Plants (Basel, Switzerland) Dec 2023The family of Nuclear Distribution C (NudC) proteins plays a pivotal and evolutionarily conserved role in all eukaryotes. In animal systems, these proteins influence... (Review)
Review
The family of Nuclear Distribution C (NudC) proteins plays a pivotal and evolutionarily conserved role in all eukaryotes. In animal systems, these proteins influence vital cellular processes like cell division, protein folding, nuclear migration and positioning, intracellular transport, and stress response. This review synthesizes past and current research on NudC family members, focusing on their growing importance in plants and intricate contributions to plant growth, development, and stress tolerance. Leveraging information from available genomic databases, we conducted a thorough characterization of NudC family members, utilizing phylogenetic analysis and assessing gene structure, motif organization, and conserved protein domains. Our spotlight on two Arabidopsis genes, and , underscores their indispensable roles in embryogenesis and postembryonic development, stress responses, and tolerance mechanisms. Emphasizing the chaperone activity of plant NudC family members, crucial for mitigating stress effects and enhancing plant resilience, we highlight their potential as valuable targets for enhancing crop performance. Moreover, the structural and functional conservation of NudC proteins across species suggests their potential applications in medical research, particularly in functions related to cell division, microtubule regulation, and associated pathways. Finally, we outline future research avenues centering on the exploration of under investigated functions of NudC proteins in plants.
PubMed: 38202427
DOI: 10.3390/plants13010119 -
Current Opinion in Plant Biology Dec 2023Beneficial microorganisms colonizing internal plant tissues, the endophytes, support their host through plant growth promotion, pathogen protection, and abiotic stress... (Review)
Review
Beneficial microorganisms colonizing internal plant tissues, the endophytes, support their host through plant growth promotion, pathogen protection, and abiotic stress alleviation. Their efficient application in agriculture requires the understanding of the molecular mechanisms and environmental conditions that facilitate in planta accommodation. Accumulating evidence reveals that commensal microorganisms employ similar colonization strategies as their pathogenic counterparts. Fine-tuning of immune response, motility, and metabolic crosstalk accounts for their differentiation. For a holistic perspective, in planta experiments with microbial collections and comprehensive genome data exploration are crucial. This review describes the most recent findings on factors involved in endophytic colonization processes, focusing on bacteria and fungi, and discusses required methodological approaches to unravel their relevance within a community context.
Topics: Endophytes; Symbiosis; Fungi; Plants; Plant Development
PubMed: 37939457
DOI: 10.1016/j.pbi.2023.102483 -
ELife Oct 2023Experiments on tropical trees suggest that new mutations in plants are driven by age rather than number of cell divisions during growth.
Experiments on tropical trees suggest that new mutations in plants are driven by age rather than number of cell divisions during growth.
Topics: Mutation; Plants; Trees; Plant Physiological Phenomena; Tropical Climate; Cell Division; Plant Senescence
PubMed: 37819030
DOI: 10.7554/eLife.89706 -
Frontiers in Plant Science 2023
PubMed: 37767288
DOI: 10.3389/fpls.2023.1279230 -
Planta Apr 2024In this review, we give an overview of plant sequencing efforts and how this impacts plant functional genomics research. Plant genome sequence information greatly... (Review)
Review
In this review, we give an overview of plant sequencing efforts and how this impacts plant functional genomics research. Plant genome sequence information greatly facilitates the studies of plant biology, functional genomics, evolution of genomes and genes, domestication processes, phylogenetic relationships, among many others. More than two decades of sequencing efforts have boosted the number of available sequenced plant genomes. The first plant genome, of Arabidopsis, was published in the year 2000 and currently, 4604 plant genomes from 1482 plant species have been published. Various large sequence initiatives are running, which are planning to produce tens of thousands of sequenced plant genomes in the near future. In this review, we give an overview on the status of sequenced plant genomes and on the use of genome information in different research areas.
Topics: Phylogeny; Genome, Plant; Genomics; Arabidopsis; Domestication
PubMed: 38592421
DOI: 10.1007/s00425-024-04397-z -
IScience Jul 2023Cytosine methylation is an important epigenetic modification involved in regulation of plant development. However, the epigenetic mechanisms governing peanut seed...
Cytosine methylation is an important epigenetic modification involved in regulation of plant development. However, the epigenetic mechanisms governing peanut seed development remain unclear. Herein, we generated DNA methylation profiles of developmental seeds of peanut H2014 and its smaller seed mutant H1314 at 15 and 60 days after pegging (DAP, S1, S4). Accompanying seed development, globally elevated methylation was observed in both lines. The mutant had a higher methylation level of 31.1% than wild type at S4, and 27.1-35.9% of the differentially methylated regions (DMRs) between the two lines were distributed in promoter or genic regions at both stages. Integrated methylome and transcriptome analysis revealed important methylation variations closely associated with seed development. Furthermore, some genes showed significantly negative correlation of expression with the methylation level within promoter or gene body. The results provide insights into the roles of DNA methylation in peanut seed development.
PubMed: 37534185
DOI: 10.1016/j.isci.2023.107062 -
Journal of Genetics and Genomics = Yi... Aug 2023As sessile organisms, plants have evolved sophisticated mechanisms to optimize their growth and development in response to fluctuating nutrient levels. Brassinosteroids... (Review)
Review
As sessile organisms, plants have evolved sophisticated mechanisms to optimize their growth and development in response to fluctuating nutrient levels. Brassinosteroids (BRs) are a group of plant steroid hormones that play critical roles in plant growth and developmental processes as well as plant responses to environmental stimuli. Recently, multiple molecular mechanisms have been proposed to explain the integration of BRs with different nutrient signaling processes to coordinate gene expression, metabolism, growth, and survival. Here, we review recent advances in understanding the molecular regulatory mechanisms of the BR signaling pathway and the multifaceted roles of BR in the intertwined sensing, signaling, and metabolic processes of sugar, nitrogen, phosphorus, and iron. Further understanding and exploring these BR-related processes and mechanisms will facilitate advances in crop breeding for higher resource efficiency.
Topics: Brassinosteroids; Plant Breeding; Plant Growth Regulators; Signal Transduction; Plants; Nutrients; Gene Expression Regulation, Plant
PubMed: 36914050
DOI: 10.1016/j.jgg.2023.03.004 -
The EMBO Journal Jul 2023Brassinosteroids (BRs) are important plant hormones involved in many aspects of development. Here, we show that BRASSINOSTEROID SIGNALING KINASEs (BSKs), key components...
Brassinosteroids (BRs) are important plant hormones involved in many aspects of development. Here, we show that BRASSINOSTEROID SIGNALING KINASEs (BSKs), key components of the BR pathway, are precisely controlled via de-S-acylation mediated by the defense hormone salicylic acid (SA). Most Arabidopsis BSK members are substrates of S-acylation, a reversible protein lipidation that is essential for their membrane localization and physiological function. We establish that SA interferes with the plasma membrane localization and function of BSKs by decreasing their S-acylation levels, identifying ABAPT11 (ALPHA/BETA HYDROLASE DOMAIN-CONTAINING PROTEIN 17-LIKE ACYL PROTEIN THIOESTERASE 11) as an enzyme whose expression is quickly induced by SA. ABAPT11 de-S-acylates most BSK family members, thus integrating BR and SA signaling for the control of plant development. In summary, we show that BSK-mediated BR signaling is regulated by SA-induced protein de-S-acylation, which improves our understanding of the function of protein modifications in plant hormone cross talk.
Topics: Brassinosteroids; Arabidopsis Proteins; Salicylic Acid; Arabidopsis; Plant Growth Regulators; Acylation; Gene Expression Regulation, Plant
PubMed: 37211868
DOI: 10.15252/embj.2022112998 -
Nature Communications Mar 2024Plants exhibit reproducible timing of developmental events at multiple scales, from switches in cell identity to maturation of the whole plant. Control of developmental... (Review)
Review
Plants exhibit reproducible timing of developmental events at multiple scales, from switches in cell identity to maturation of the whole plant. Control of developmental timing likely evolved for similar reasons that humans invented clocks: to coordinate events. However, whereas clocks are designed to run independently of conditions, plant developmental timing is strongly dependent on growth and environment. Using simplified models to convey key concepts, we review how growth-dependent and inherent timing mechanisms interact with the environment to control cyclical and progressive developmental transitions in plants.
Topics: Plants; Plant Development
PubMed: 38531864
DOI: 10.1038/s41467-024-46941-1