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Frontiers in Plant Science 2023The plant homeodomain (PHD) finger with a conserved Cys4-His-Cys3 motif is a common zinc-binding domain, which is widely present in all eukaryotic genomes. The PHD... (Review)
Review
The plant homeodomain (PHD) finger with a conserved Cys4-His-Cys3 motif is a common zinc-binding domain, which is widely present in all eukaryotic genomes. The PHD finger is the "reader" domain of methylation marks in histone H3 and plays a role in the regulation of gene expression patterns. Numerous proteins containing the PHD finger have been found in plants. In this review, we summarize the functional studies on PHD finger proteins in plant growth and development and responses to abiotic stresses in recent years. Some PHD finger proteins, such as VIN3, VILs, and Ehd3, are involved in the regulation of flowering time, while some PHD finger proteins participate in the pollen development, for example, MS, TIP3, and MMD1. Furthermore, other PHD finger proteins regulate the plant tolerance to abiotic stresses, including Alfin1, ALs, and AtSIZ1. Research suggests that PHD finger proteins, as an essential transcription regulator family, play critical roles in various plant biological processes, which is helpful in understanding the molecular mechanisms of novel PHD finger proteins to perform specific function.
PubMed: 38046601
DOI: 10.3389/fpls.2023.1297607 -
Frontiers in Plant Science 2023For the past two decades, the study of alternative splicing (AS) and its involvement in plant development and stress response has grown in popularity. Only recently... (Review)
Review
For the past two decades, the study of alternative splicing (AS) and its involvement in plant development and stress response has grown in popularity. Only recently however, has the focus shifted to the study of how AS regulation (or lack-thereof) affects downstream mRNA and protein landscapes and how these AS regulatory events impact plant development and stress tolerance. In humans, protein phosphorylation represents one of the predominant mechanisms by which AS is regulated and thus the protein kinases governing these phosphorylation events are of interest for further study. Large-scale phosphoproteomic studies in plants have consistently found that RNA splicing-related proteins are extensively phosphorylated, however, the signaling pathways involved in AS regulation have not been resolved. In this mini-review, we summarize our current knowledge of the three major splicing-related protein kinase families in plants that are suggested to mediate AS phospho-regulation and draw comparisons to their metazoan orthologs. We also summarize and contextualize the phosphorylation events identified as occurring on splicing-related protein families to illustrate the high degree to which splicing-related proteins are modified, placing a new focus on elucidating the impacts of AS at the protein and PTM-level.
PubMed: 37780493
DOI: 10.3389/fpls.2023.1249057 -
International Journal of Molecular... Jun 2023Abiotic stress is the adverse effect of any abiotic factor on a plant in a given environment, impacting plants' growth and development. These stress factors, such as... (Review)
Review
Abiotic stress is the adverse effect of any abiotic factor on a plant in a given environment, impacting plants' growth and development. These stress factors, such as drought, salinity, and extreme temperatures, are often interrelated or in conjunction with each other. Plants have evolved mechanisms to sense these environmental challenges and make adjustments to their growth in order to survive and reproduce. In this review, we summarized recent studies on plant stress sensing and its regulatory mechanism, emphasizing signal transduction and regulation at multiple levels. Then we presented several strategies to improve plant growth under stress based on current progress. Finally, we discussed the implications of research on plant response to abiotic stresses for high-yielding crops and agricultural sustainability. Studying stress signaling and regulation is critical to understand abiotic stress responses in plants to generate stress-resistant crops and improve agricultural sustainability.
Topics: Stress, Physiological; Crops, Agricultural; Plant Development; Signal Transduction; Agriculture; Gene Expression Regulation, Plant
PubMed: 37446089
DOI: 10.3390/ijms241310915 -
Journal of Plant Physiology Nov 2023A plant's genome encodes enzymes, transporters and many other proteins which constitute metabolism. Interactions of plants with their environment shape their growth,... (Review)
Review
A plant's genome encodes enzymes, transporters and many other proteins which constitute metabolism. Interactions of plants with their environment shape their growth, development and resilience towards adverse conditions. Although genome sequencing technologies and applications have experienced triumphantly rapid development during the last decades, enabling nowadays a fast and cheap sequencing of full genomes, prediction of metabolic phenotypes from genotype × environment interactions remains, at best, very incomplete. The main reasons are a lack of understanding of how different levels of molecular organisation depend on each other, and how they are constituted and expressed within a setup of growth conditions. Phenotypic plasticity, e.g., of the genetic model plant Arabidopsis thaliana, has provided important insights into plant-environment interactions and the resulting genotype x phenotype relationships. Here, we summarize previous and current findings about plant development in a changing environment and how this might be shaped and reflected in metabolism and its regulation. We identify current challenges in the study of plant development and metabolic regulation and provide an outlook of how methodological workflows might support the application of findings made in model systems to crops and their cultivation.
Topics: Gene-Environment Interaction; Genotype; Phenotype; Crops, Agricultural; Arabidopsis
PubMed: 37839392
DOI: 10.1016/j.jplph.2023.154116 -
Microbial Biotechnology Dec 2023The scientific community increasingly recognized that seed microbiomes are important for plant growth and nutrition. The versatile roles and modulating properties that... (Review)
Review
The scientific community increasingly recognized that seed microbiomes are important for plant growth and nutrition. The versatile roles and modulating properties that microbiomes hold in the context of seeds seem to be an inherited approach to avert adverse conditions. These discoveries attracted extensive interest, especially in staple food crops (SFCs) where grain was consumed as food. Along with the rapid expansion of population and industrialization that posed a severe challenge to the yield of SFCs, microbiologists and botanists began to explore and engineer seed microbiomes, for safer and more fruitful grain production. To utilize seed microbiomes, we present an overall review of the most updated scientific literature on three representative SFCs (wheat, rice and maize) using the 5W1H (Which, Where, What, Why, When and How) method that provides a comprehensive understanding of the issue. These include which factors determine the composition of seed microbiomes? Where do seed microbiomes come from? What are these seed microbes? Why do these microbes choose seeds as their destination and when do microbes settle down and become seed communists? In addition, how do seed microbiomes work and can be manipulated effectively? Therefore, answering the aforementioned questions regarding SFCs seed microbiomes remain fundamental in bridging endophytic research gaps and harnessing their ecological services.
Topics: Seeds; Crops, Agricultural; Plant Development; Microbiota
PubMed: 37815330
DOI: 10.1111/1751-7915.14352 -
Plants (Basel, Switzerland) Oct 2023Glycine-rich RNA binding proteins (GR-RBPs), a branch of RNA binding proteins (RBPs), play integral roles in regulating various aspects of RNA metabolism regulation,... (Review)
Review
Glycine-rich RNA binding proteins (GR-RBPs), a branch of RNA binding proteins (RBPs), play integral roles in regulating various aspects of RNA metabolism regulation, such as RNA processing, transport, localization, translation, and stability, and ultimately regulate gene expression and cell fate. However, our current understanding of GR-RBPs has predominantly been centered on Arabidopsis thaliana, a model plant for investigating plant growth and development. Nonetheless, an increasing body of literature has emerged in recent years, shedding light on the presence and functions of GRPs in diverse crop species. In this review, we not only delineate the distinctive structural domains of plant GR-RBPs but also elucidate several contemporary mechanisms of GR-RBPs in the post-transcriptional regulation of RNA. These mechanisms encompass intricate processes, including RNA alternative splicing, polyadenylation, miRNA biogenesis, phase separation, and RNA translation. Furthermore, we offer an exhaustive synthesis of the diverse roles that GR-RBPs fulfill within crop plants. Our overarching objective is to provide researchers and practitioners in the field of agricultural genetics with valuable insights that may inform and guide the application of plant genetic engineering for enhanced crop development and sustainable agriculture.
PubMed: 37836244
DOI: 10.3390/plants12193504 -
Philosophical Transactions of the Royal... Apr 2024When future conditions are unpredictable, bet-hedging strategies can be advantageous. This can involve isogenic individuals producing different phenotypes, under the... (Review)
Review
When future conditions are unpredictable, bet-hedging strategies can be advantageous. This can involve isogenic individuals producing different phenotypes, under the same environmental conditions. Ecological studies provide evidence that variability in seed germination time has been selected for as a bet-hedging strategy. We demonstrate how variability in germination time found in Arabidopsis could function as a bet-hedging strategy in the face of unpredictable lethal stresses. Despite a body of knowledge on how the degree of seed dormancy versus germination is controlled, relatively little is known about how differences between isogenic seeds in a batch are generated. We review proposed mechanisms for generating variability in germination time and the current limitations and new possibilities for testing the model predictions. We then look beyond germination to the role of variability in seedling and adult plant growth and review new technologies for quantification of noisy gene expression dynamics. We discuss evidence for phenotypic variability in plant traits beyond germination being under genetic control and propose that variability in stress response gene expression could function as a bet-hedging strategy. We discuss open questions about how noisy gene expression could lead to between-plant heterogeneity in gene expression and phenotypes. This article is part of a discussion meeting issue 'Causes and consequences of stochastic processes in development and disease'.
Topics: Humans; Adult; Germination; Seeds; Seedlings; Arabidopsis; Knowledge
PubMed: 38432313
DOI: 10.1098/rstb.2023.0048 -
Plant Molecular Biology Jul 2023Anthocyanins are a family of water-soluble vacuolar pigments present in almost all flowering plants. The chemistry, biosynthesis and functions of these flavonoids have... (Review)
Review
Anthocyanins are a family of water-soluble vacuolar pigments present in almost all flowering plants. The chemistry, biosynthesis and functions of these flavonoids have been intensively studied, in part due to their benefit for human health. Given that they are efficient antioxidants, intense research has been devoted to studying their possible roles against damage caused by reactive oxygen species (ROS). However, the redox homeostasis established between antioxidants and ROS is important for plant growth and development. On the one hand, high levels of ROS can damage DNA, proteins, and lipids, on the other, they are also required for cell signaling, plant development and stress responses. Thus, a balance is needed in which antioxidants can remove excessive ROS, while not precluding ROS from triggering important cellular signaling cascades. In this article, we discuss how anthocyanins and ROS interact and how a deeper understanding of the balance between them could help improve plant productivity, nutritional value, and resistance to stress, while simultaneously maintaining proper cellular function and plant growth.
Topics: Humans; Reactive Oxygen Species; Antioxidants; Anthocyanins; Oxidation-Reduction; Plant Development; Oxidative Stress
PubMed: 37351824
DOI: 10.1007/s11103-023-01362-4 -
International Journal of Molecular... Aug 2023WUSCHEL-related homeobox (WOX) proteins are very important in controlling plant development and stress responses. However, the WOX family members and their role in...
WUSCHEL-related homeobox (WOX) proteins are very important in controlling plant development and stress responses. However, the WOX family members and their role in response to abiotic stresses are largely unknown in melon ( L.). In this study, 11 WOX (CmWOX) transcript factors with conserved WUS and homeobox motif were identified and characterized, and subdivided into modern clade, ancient clade and intermediate clade based on bioinformatic and phylogenetic analysis. Evolutionary analysis revealed that the CmWOX family showed protein variations in Arabidopsis, tomato, cucumber, melon and rice. Alignment of protein sequences uncovered that all CmWOXs had the typical homeodomain, which consisted of conserved amino acids. -element analysis showed that genes may response to abiotic stress. RNA-seq and qRT-PCR results further revealed that the expression of partially genes are associated with cold and drought. and were constitutively expressed under abiotic stresses, may play a role in abiotic processes during plant development. Taken together, this study offers new perspectives on the CmWOX family's interaction and provides the framework for research on the molecular functions of genes.
Topics: Genes, Homeobox; Cucumis melo; Phylogeny; Cucurbitaceae; Multigene Family; Genes, Plant; Arabidopsis; Gene Expression Regulation, Plant; Plant Proteins; Homeodomain Proteins; Arabidopsis Proteins
PubMed: 37569702
DOI: 10.3390/ijms241512326 -
BMC Plant Biology Aug 2023Climate change has exacerbated the effects of abiotic stresses on plant growth and productivity. Drought is one of the most important abiotic stress factors that... (Review)
Review
Climate change has exacerbated the effects of abiotic stresses on plant growth and productivity. Drought is one of the most important abiotic stress factors that interfere with plant growth and development. Plant selection and breeding as well as genetic engineering methods used to improve crop drought tolerance are expensive and time consuming. Plants use a myriad of adaptative mechanisms to cope with the adverse effects of drought stress including the association with beneficial microorganisms such as plant growth promoting rhizobacteria (PGPR). Inoculation of plant roots with different PGPR species has been shown to promote drought tolerance through a variety of interconnected physiological, biochemical, molecular, nutritional, metabolic, and cellular processes, which include enhanced plant growth, root elongation, phytohormone production or inhibition, and production of volatile organic compounds. Therefore, plant colonization by PGPR is an eco-friendly agricultural method to improve plant growth and productivity. Notably, the processes regulated and enhanced by PGPR can promote plant growth as well as enhance drought tolerance. This review addresses the current knowledge on how drought stress affects plant growth and development and describes how PGPR can trigger plant drought stress responses at the physiological, morphological, and molecular levels.
Topics: Droughts; Plant Development; Drought Resistance; Plant Growth Regulators; Acclimatization
PubMed: 37626328
DOI: 10.1186/s12870-023-04403-8