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International Journal of Molecular... Oct 2021Plant development processes are regulated by epigenetic alterations that shape nuclear structure, gene expression, and phenotypic plasticity; these alterations can... (Review)
Review
Plant development processes are regulated by epigenetic alterations that shape nuclear structure, gene expression, and phenotypic plasticity; these alterations can provide the plant with protection from environmental stresses. During plant growth and development, these processes play a significant role in regulating gene expression to remodel chromatin structure. These epigenetic alterations are mainly regulated by transposable elements (TEs) whose abundance in plant genomes results in their interaction with genomes. Thus, TEs are the main source of epigenetic changes and form a substantial part of the plant genome. Furthermore, TEs can be activated under stress conditions, and activated elements cause mutagenic effects and substantial genetic variability. This introduces novel gene functions and structural variation in the insertion sites and primarily contributes to epigenetic modifications. Altogether, these modifications indirectly or directly provide the ability to withstand environmental stresses. In recent years, many studies have shown that TE methylation plays a major role in the evolution of the plant genome through epigenetic process that regulate gene imprinting, thereby upholding genome stability. The induced genetic rearrangements and insertions of mobile genetic elements in regions of active euchromatin contribute to genome alteration, leading to genomic stress. These TE-mediated epigenetic modifications lead to phenotypic diversity, genetic variation, and environmental stress tolerance. Thus, TE methylation is essential for plant evolution and stress adaptation, and TEs hold a relevant military position in the plant genome. High-throughput techniques have greatly advanced the understanding of TE-mediated gene expression and its associations with genome methylation and suggest that controlled mobilization of TEs could be used for crop breeding. However, development application in this area has been limited, and an integrated view of TE function and subsequent processes is lacking. In this review, we explore the enormous diversity and likely functions of the TE repertoire in adaptive evolution and discuss some recent examples of how TEs impact gene expression in plant development and stress adaptation.
Topics: DNA Methylation; DNA Transposable Elements; Epigenesis, Genetic; Plant Development; Plant Physiological Phenomena; Plants; Stress, Physiological
PubMed: 34768817
DOI: 10.3390/ijms222111387 -
Mitochondrion Jul 2020The mitochondrial F-ATP synthase is responsible for coupling the transmembrane proton gradient, generated through the inner membrane by the electron transport chain, to... (Review)
Review
The mitochondrial F-ATP synthase is responsible for coupling the transmembrane proton gradient, generated through the inner membrane by the electron transport chain, to the synthesis of ATP. This enzyme shares a basic architecture with the prokaryotic and chloroplast ones, since it is composed of a catalytic head (F), located in the mitochondrial matrix, a membrane-bound part (F), together with a central and a peripheral stalk. In this review we compare the structural and functional properties of F-ATP synthase in plant mitochondria with those of yeast and mammals. We also present the physiological impact of the alteration of F-ATP synthase in plants, with a special regard to its involvement in cytoplasmic male sterility. Furthermore, we show the involvement of this enzyme in plant stress responses. Finally, we discuss the role of F-ATP synthase in shaping the curvature of the mitochondrial inner membrane and in permeability transition pore formation.
Topics: Gene Expression Regulation, Enzymologic; Mitochondria; Models, Molecular; Plant Proteins; Plants; Protein Conformation; Proton-Translocating ATPases; Stress, Physiological
PubMed: 32534049
DOI: 10.1016/j.mito.2020.06.001 -
The International Journal of... 2013In higher plants, genetic transformation, which is part of the toolbox for the study of living organisms, had been reported only 30 years ago, boosting basic plant... (Review)
Review
In higher plants, genetic transformation, which is part of the toolbox for the study of living organisms, had been reported only 30 years ago, boosting basic plant biology research, generating superior crops, and leading to the new discipline of plant biotechnology. Here, we review its principles and the corresponding molecular tools. In vitro regeneration, through somatic embryogenesis or organogenesis, is discussed because they are prerequisites for the subsequent Agrobacterium tumefaciens-mediated transferred (T)-DNA or direct DNA transfer methods to produce transgenic plants. Important molecular components of the T-DNA are examined, such as selectable marker genes that allow the selection of transformed cells in tissue cultures and are used to follow the gene of interest in the next generations, and reporter genes that have been developed to visualize promoter activities, protein localizations, and protein-protein interactions. Genes of interest are assembled with promoters and termination signals in Escherichia coli by means of GATEWAY-derived binary vectors that represent the current versatile cloning tools. Finally, future promising developments in transgene technology are considered.
Topics: Agrobacterium tumefaciens; Biotechnology; DNA, Bacterial; Escherichia coli; Gene Transfer Techniques; Genes, Plant; Genes, Reporter; Genetic Vectors; Genotype; Plants; Plants, Genetically Modified; Promoter Regions, Genetic; Transgenes
PubMed: 24166431
DOI: 10.1387/ijdb.130232mv -
Plant Physiology Apr 2024Small-molecule phytohormones exert control over plant growth, development, and stress responses by coordinating the patterns of gene expression within and between cells.... (Review)
Review
Small-molecule phytohormones exert control over plant growth, development, and stress responses by coordinating the patterns of gene expression within and between cells. Increasing evidence indicates that currently recognized plant hormones are part of a larger group of regulatory metabolites that have acquired signaling properties during the evolution of land plants. This rich assortment of chemical signals reflects the tremendous diversity of plant secondary metabolism, which offers evolutionary solutions to the daunting challenges of sessility and other unique aspects of plant biology. A major gap in our current understanding of plant regulatory metabolites is the lack of insight into the direct targets of these compounds. Here, we illustrate the blurred distinction between classical phytohormones and other bioactive metabolites by highlighting the major scientific advances that transformed the view of jasmonate from an interesting floral scent to a potent transcriptional regulator. Lessons from jasmonate research generally apply to other phytohormones and thus may help provide a broad understanding of regulatory metabolite-protein interactions. In providing a framework that links small-molecule diversity to transcriptional plasticity, we hope to stimulate future research to explore the evolution, functions, and mechanisms of perception of a broad range of plant regulatory metabolites.
Topics: Cyclopentanes; Oxylipins; Plant Growth Regulators; Gene Expression Regulation, Plant; Signal Transduction; Plants
PubMed: 38290050
DOI: 10.1093/plphys/kiae045 -
Plant, Cell & Environment Mar 2006Resolution and analysis of genes encoding components of the pathways of primary sulphur assimilation have provided the potential to elucidate how sulphur is managed by... (Review)
Review
Resolution and analysis of genes encoding components of the pathways of primary sulphur assimilation have provided the potential to elucidate how sulphur is managed by plants. Individual roles for members of gene families and regulatory mechanisms operating at gene, cellular and whole plant levels have been recognized. Sulphur is taken up and transported around the plant principally as sulphate, catalysed for the most part by a single gene family of highly regulated transporters. Additional regulation occurs in the pathway of reduction of sulphate to sulphide and its incorporation into cysteine, which occurs principally within the plastid. Cellular and whole-plant regulation of uptake, and the assimilatory pathway attempt to balance supply with demand for growth and include mechanisms for re-mobilization and redistribution of sulphur. Furthermore, optimization of sulphur assimilation requires coordination with carbon and nitrogen pathways, and multiple processes have been proposed to contribute to this balance. Present studies on cis and trans elements are focusing on transcriptional regulation, but this regulation still needs to be linked to apparent metabolite sensing. Whilst the components of the assimilatory pathways have been resolved after many years of controversy, uncertainties remain concerning roles of individual genes in gene families, their sub-cellular localization and their significance in balancing sulphur flux to sulphur demand of the plant for growth under variable environmental conditions.
Topics: Anion Transport Proteins; Gene Expression Regulation, Plant; Genes, Plant; Multigene Family; Plants; Signal Transduction; Sulfur
PubMed: 17080593
DOI: 10.1111/j.1365-3040.2005.01470.x -
Current Opinion in Plant Biology Dec 2021Plants react to a myriad of biotic and abiotic environmental signals through specific cellular mechanisms required for survival under stress. Although pathogen... (Review)
Review
Plants react to a myriad of biotic and abiotic environmental signals through specific cellular mechanisms required for survival under stress. Although pathogen perception has been widely studied and characterized, salt stress perception and signaling remain largely elusive. Recent observations, obtained in the model plant Arabidopsis thaliana, show that perception of specific features of pathogens also allows plants to mount salt stress resilience pathways, highlighting the possibility that salt sensing and pathogen perception mechanisms partially overlap. We discuss these overlapping strategies and examine the emerging role of A. thaliana cell wall and plasma membrane components in activating both salt- and pathogen-induced responses, as part of exquisite mechanisms underlying perception of damage and danger. This knowledge helps understanding the complexity of plant responses to pathogens and salinity, leading to new hypotheses that could explain why plants evolved similar strategies to respond to these, at first sight, very different types of stimuli.
Topics: Arabidopsis; Arabidopsis Proteins; Gene Expression Regulation, Plant; Perception; Plants; Salinity; Salt Stress; Stress, Physiological
PubMed: 34856479
DOI: 10.1016/j.pbi.2021.102120 -
Plant, Cell & Environment May 2016Mitochondria play a central role in plant metabolism as they are a major source of ATP through synthesis by the oxidative phosphorylation pathway and harbour key... (Review)
Review
Mitochondria play a central role in plant metabolism as they are a major source of ATP through synthesis by the oxidative phosphorylation pathway and harbour key metabolic reactions such as the TCA cycle. The energy and building blocks produced by mitochondria are essential to drive plant growth and development as well as to provide fuel for responses to abiotic and biotic stresses. The majority of mitochondrial proteins are encoded in the nuclear genome and have to be imported into the organelle. For the regulation of the corresponding genes intricate signalling pathways exist to adjust their expression. Signals directly regulate nuclear gene expression (anterograde signalling) to adjust the protein composition of the mitochondria to the needs of the cell. In parallel, mitochondria communicate back their functional status to the nucleus (retrograde signalling) to prompt transcriptional regulation of responsive genes via largely unknown signalling mechanisms. Plant hormones are the major signalling components regulating all layers of plant development and cellular functions. Increasing evidence is now becoming available that plant hormones are also part of signalling networks controlling mitochondrial function and their biogenesis. This review summarizes recent advances in understanding the interaction of mitochondrial and hormonal signalling pathways.
Topics: Crops, Agricultural; Mitochondria; Plant Development; Plant Growth Regulators; Plants; Signal Transduction
PubMed: 26763171
DOI: 10.1111/pce.12712 -
Philosophical Transactions of the Royal... May 2022Linnaeus's very first opus, written when he was 22 years old, dealt with the analogy that exists between plants and animals in how they 'propagate their species', and a...
Linnaeus's very first opus, written when he was 22 years old, dealt with the analogy that exists between plants and animals in how they 'propagate their species', and a revised version with a plate depicting the union of male and female plants became a foundational text on the sexuality of plants. The question how systems with separate males and females have evolved in sedentary organisms that appear ancestrally bisexual has fascinated biologists ever since. The phenomenon, termed dioecy, has important consequences for plant reproductive success and is of commercial interest since it affects seed quality and fruit production. This theme issue presents a series of articles that synthesize and challenge the current understanding of how plants achieve dioecy. The articles deal with a broad set of taxa, including , , , , and , as well as overarching topics, such as the field's terminology, analogies with animal sex determination systems, evolutionary pathways to dioecy, dosage compensation, and the longevity of the two sexes. In this introduction, we focus on four topics, each addressed by several articles from different angles and with different conclusions. Our highlighting of unclear or controversial issues may help future studies to build on the current understanding and to ask new questions that will expand our knowledge of plant sexual systems. This article is part of the theme issue 'Sex determination and sex chromosome evolution in land plants'.
Topics: Animals; Embryophyta; Plants; Reproduction; Sex Chromosomes
PubMed: 35306895
DOI: 10.1098/rstb.2021.0210 -
International Journal of Biological... Aug 2022Antimicrobial peptides, also known as AMPs, are cationic and amphipathic molecules found in all living organisms, composing part of the defense mechanisms against... (Review)
Review
Antimicrobial peptides, also known as AMPs, are cationic and amphipathic molecules found in all living organisms, composing part of the defense mechanisms against various pathogens, including fungi, viruses, bacteria, and nematodes. AMPs derived from plants are the focus of this review because they have gained attention as alternative molecules to overcome pathogen resistance as well as new drugs to combat cancer. Plant AMPs are generally classified based on their sequences and structures, as thionins, defensins, hevein-like peptides, knottins, stable-like peptides, lipid transfer proteins, snakins, and cyclotides. Although there are studies reporting the toxicity of plant AMPs to nontarget cells or limitations of oral administration, synthetic AMPs with reduced toxicity or allergenicity, or greater resistance to peptidases can be designed by using different bioinformatics tools. Thus, this review provides information about the classification of plant AMPs, their characteristics, mechanisms of action, hemolytic and cytotoxic potential, possible applications in the medical field, and finally, the use of bioinformatics to help design synthetic AMPs with improved features.
Topics: Antimicrobial Peptides; Computational Biology; Fungi; Plants
PubMed: 35700843
DOI: 10.1016/j.ijbiomac.2022.06.043 -
International Journal of Molecular... Jan 2023Plants are constantly exposed to environmental stresses. Local stimuli sensed by one part of a plant are translated into long-distance signals that can influence the... (Review)
Review
Plants are constantly exposed to environmental stresses. Local stimuli sensed by one part of a plant are translated into long-distance signals that can influence the activities in distant tissues. Changes in levels of phytohormones in distant parts of the plant occur in response to various local stimuli. The regulation of hormone levels can be mediated by long-distance electrical signals, which are also induced by local stimulation. We consider the crosstalk between electrical signals and phytohormones and identify interaction points, as well as provide insights into the integration nodes that involve changes in pH, Ca and ROS levels. This review also provides an overview of our current knowledge of how electrical signals and hormones work together to induce a systemic response.
Topics: Plant Growth Regulators; Plants; Signal Transduction; Electricity; Stress, Physiological
PubMed: 36614284
DOI: 10.3390/ijms24010847