-
The International Journal of... 2012Broad comparative studies at the level of developmental processes are necessary to fully understand the evolution of development and phenotypes. The concept of dynamical... (Review)
Review
Broad comparative studies at the level of developmental processes are necessary to fully understand the evolution of development and phenotypes. The concept of dynamical patterning modules (DPMs) provides a framework for studying developmental processes in the context of wide comparative analyses. DPMs are defined as sets of ancient, conserved gene products and molecular networks, in conjunction with the physical morphogenetic and patterning processes they mobilize in the context of multicellularity. The theoretical framework based on DPMs originally postulated that each module generates a key morphological motif of the basic animal body plans and organ forms. Here, we use a previous definition of the plant multicellular body plan and describe the basic DPMs underlying the main features of plant development. For each DPM, we identify characteristic molecules and molecular networks, and when possible, the physical processes they mobilize. We then briefly review the phyletic distribution of these molecules across the various plant lineages. Although many of the basic plant DPMs are significantly different from those of animals, the framework established by a DPM perspective on plant development is essential for comparative analyses aiming to provide a truly mechanistic explanation for organic development across all plant and animal lineages.
Topics: Biological Evolution; Epigenesis, Genetic; Gene Expression Regulation, Plant; Plant Development; Plants
PubMed: 23319343
DOI: 10.1387/ijdb.120027mb -
International Journal of Molecular... Jun 2020Hydrogen sulfide (HS), once recognized only as a poisonous gas, is now considered the third endogenous gaseous transmitter, along with nitric oxide (NO) and carbon... (Review)
Review
Hydrogen sulfide (HS), once recognized only as a poisonous gas, is now considered the third endogenous gaseous transmitter, along with nitric oxide (NO) and carbon monoxide (CO). Multiple lines of emerging evidence suggest that HS plays positive roles in plant growth and development when at appropriate concentrations, including seed germination, root development, photosynthesis, stomatal movement, and organ abscission under both normal and stress conditions. HS influences these processes by altering gene expression and enzyme activities, as well as regulating the contents of some secondary metabolites. In its regulatory roles, HS always interacts with either plant hormones, other gasotransmitters, or ionic signals, such as abscisic acid (ABA), ethylene, auxin, CO, NO, and Ca. Remarkably, HS also contributes to the post-translational modification of proteins to affect protein activities, structures, and sub-cellular localization. Here, we review the functions of HS at different stages of plant development, focusing on the S-sulfhydration of proteins mediated by HS and the crosstalk between HS and other signaling molecules.
Topics: Air Pollutants; Gene Expression Regulation, Plant; Hydrogen Sulfide; Plant Development; Plant Physiological Phenomena; Plant Proteins; Plants; Signal Transduction
PubMed: 32605208
DOI: 10.3390/ijms21134593 -
International Journal of Molecular... Jul 2019The DUF642 protein family is found exclusively in spermatophytes and is represented by 10 genes in Arabidopsis and in most of the 24 plant species analyzed to date. Even... (Review)
Review
The DUF642 protein family is found exclusively in spermatophytes and is represented by 10 genes in Arabidopsis and in most of the 24 plant species analyzed to date. Even though the primary structure of DUF642 proteins is highly conserved in different spermatophyte species, studies of their expression patterns in Arabidopsis have shown that the spatial-temporal expression pattern for each gene is specific and consistent with the phenotypes of the mutant plants studied so far. Additionally, the regulation of DUF642 gene expression by hormones and environmental stimuli was specific for each gene, showing both up- and down-regulation depending of the analyzed tissue and the intensity or duration of the stimuli. These expression patterns suggest that the DUF642 genes are involved throughout the development and growth of plants. In general, changes in the expression patterns of DUF642 genes can be related to changes in pectin methyl esterase activity and/or to changes in the degree of methyl-esterified homogalacturonans during plant development in different cell types. Thus, the regulation of pectin methyl esterases mediated by DUF642 genes could contribute to the regulation of the cell wall properties during plant growth.
Topics: Cell Wall; Gene Expression Regulation, Plant; Genes, Plant; Plant Development; Plant Proteins
PubMed: 31284602
DOI: 10.3390/ijms20133333 -
Journal of Experimental Botany Nov 2017Cuticles, which are composed of a variety of aliphatic molecules, impregnate epidermal cell walls forming diffusion barriers that cover almost all the aerial surfaces in... (Review)
Review
Cuticles, which are composed of a variety of aliphatic molecules, impregnate epidermal cell walls forming diffusion barriers that cover almost all the aerial surfaces in higher plants. In addition to revealing important roles for cuticles in protecting plants against water loss and other environmental stresses and aggressions, mutants with permeable cuticles show major defects in plant development, such as abnormal organ formation as well as altered seed germination and viability. However, understanding the mechanistic basis for these developmental defects represents a significant challenge due to the pleiotropic nature of phenotypes and the altered physiological status/viability of some mutant backgrounds. Here we discuss both the basis of developmental phenotypes associated with defects in cuticle function and mechanisms underlying developmental processes that implicate cuticle modification. Developmental abnormalities in cuticle mutants originate at early developmental time points, when cuticle composition and properties are very difficult to measure. Nonetheless, we aim to extract principles from existing data in order to pinpoint the key cuticle components and properties required for normal plant development. Based on our analysis, we will highlight several major questions that need to be addressed and technical hurdles that need to be overcome in order to advance our current understanding of the developmental importance of plant cuticles.
Topics: Gene Expression Regulation, Plant; Organogenesis, Plant; Phenotype; Plant Development; Plant Epidermis
PubMed: 28992283
DOI: 10.1093/jxb/erx313 -
Biomolecules Sep 2022The hormonal system plays a decisive role in the control of plant growth and development [...].
The hormonal system plays a decisive role in the control of plant growth and development [...].
Topics: Plant Development; Plant Growth Regulators
PubMed: 36139144
DOI: 10.3390/biom12091305 -
Journal of Integrative Plant Biology Oct 2018Pectins are complex cell wall polysaccharides important for many aspects of plant development. Recent studies have discovered extensive physical interactions between... (Review)
Review
Pectins are complex cell wall polysaccharides important for many aspects of plant development. Recent studies have discovered extensive physical interactions between pectins and other cell wall components, implicating pectins in new molecular functions. Pectins are often localized in spatially-restricted patterns, and some of these non-uniform pectin distributions contribute to multiple aspects of plant development, including the morphogenesis of cells and organs. Furthermore, a growing number of mutants affecting cell wall composition have begun to reveal the distinct contributions of different pectins to plant development. This review discusses the interactions of pectins with other cell wall components, the functions of pectins in controlling cellular morphology, and how non-uniform pectin composition can be an important determinant of developmental processes.
Topics: Cell Wall; Pectins; Plant Development
PubMed: 29727062
DOI: 10.1111/jipb.12662 -
Current Opinion in Plant Biology Feb 2019Plants integrate a wide range of cellular, developmental, and environmental signals to regulate complex patterns of gene expression. Recent advances in genomic... (Review)
Review
Plants integrate a wide range of cellular, developmental, and environmental signals to regulate complex patterns of gene expression. Recent advances in genomic technologies enable differential gene expression analysis at a systems level, allowing for improved inference of the network of regulatory interactions between genes. These gene regulatory networks, or GRNs, are used to visualize the causal regulatory relationships between regulators and their downstream target genes. Accordingly, these GRNs can represent spatial, temporal, and/or environmental regulations and can identify functional genes. This review summarizes recent computational approaches applied to different types of gene expression data to infer GRNs in the context of plant growth and development. Three stages of GRN inference are described: first, data collection and analysis based on the dataset type; second, network inference application based on data availability and proposed hypotheses; and third, validation based on in silico, in vivo, and in planta methods. In addition, this review relates data collection strategies to biological questions, organizes inference algorithms based on statistical methods and data types, discusses experimental design considerations, and provides guidelines for GRN inference with an emphasis on the benefits of integrative approaches, especially when a priori information is limited. Finally, this review concludes that computational frameworks integrating large-scale heterogeneous datasets are needed for a more accurate (e.g. fewer false interactions), detailed (e.g. discrimination between direct versus indirect interactions), and comprehensive (e.g. genetic regulation under various conditions and spatial locations) inference of GRNs.
Topics: Computational Biology; Gene Regulatory Networks; Models, Genetic; Plant Development; Reproducibility of Results
PubMed: 30445315
DOI: 10.1016/j.pbi.2018.10.005 -
Journal of Genetics and Genomics = Yi... Oct 2019Plants grow in dynamic environments where they receive diverse environmental signals. Swift and precise control of gene expression is essential for plants to align their... (Review)
Review
Plants grow in dynamic environments where they receive diverse environmental signals. Swift and precise control of gene expression is essential for plants to align their development and metabolism with fluctuating surroundings. Modifications on histones serve as "histone code" to specify chromatin and gene activities. Different modifications execute distinct functions on the chromatin, promoting either active transcription or gene silencing. Histone writers, erasers, and readers mediate the regulation of histone modifications by catalyzing, removing, and recognizing modifications, respectively. Growing evidence indicates the important function of histone modifications in plant development and environmental responses. Histone modifications also serve as environmental memory for plants to adapt to environmental changes. Here we review recent progress on the regulation of histone modifications in plants, the impact of histone modifications on environment-controlled developmental transitions including germination and flowering, and the role of histone modifications in environmental memory.
Topics: Chromatin; Flowers; Gene Expression Regulation, Plant; Germination; Histones; Plant Development
PubMed: 31813758
DOI: 10.1016/j.jgg.2019.09.005 -
Plant Physiology Apr 2021
Topics: Biological Phenomena; Cell Membrane; Plant Development; Plant Growth Regulators; Signal Transduction
PubMed: 33822219
DOI: 10.1093/plphys/kiaa107 -
Seminars in Cell & Developmental Biology Jan 2021Vascular plants, unlike bryophytes, have a strong root-shoot dichotomy in which the tissue systems are mutually interdependent; roots are completely dependent on shoots... (Review)
Review
Vascular plants, unlike bryophytes, have a strong root-shoot dichotomy in which the tissue systems are mutually interdependent; roots are completely dependent on shoots for photosynthetic sugars, and shoots are completely dependent on roots for water and mineral nutrients. Long-distance communication between shoot and root is therefore critical for the growth, development and survival of vascular plants, especially with regard to variable environmental conditions. However, this long-distance signalling does not appear an ancestral feature of land plants, and has likely arisen in vascular plants to service the radical alterations in body-plan seen in this taxon. In this review, we examine the defined hormonal root-to-shoot and shoot-to-root signalling pathways that coordinate the growth of vascular plants, with a particular view to understanding how these pathways may have evolved. We highlight the completely divergent roles of isopentenyl-adenine and trans-zeatin cytokinin species in long-distance signalling, and ask whether cytokinin can really be considered as a single class of hormones in the light of recent research. We also discuss the puzzlingly sparse evidence for auxin as a shoot-to-root signal, the evolutionary re-purposing of strigolactones and gibberellins as hormonal signals, and speculate on the possible role of sugars as long-distance signals. We conclude by discussing the 'design principles' of long-distance signalling in vascular plants.
Topics: Gene Expression Regulation, Plant; Plant Development; Plant Growth Regulators
PubMed: 32576500
DOI: 10.1016/j.semcdb.2020.06.011