The m<sup>6</sup>A writers, readers, and erasers regulate plant development and respond to biotic/abiotic stresses

Chrysanthemum indicum is an important medicinal plant that has a particularly strong effect on bacteria and viruses and has antioxidant, anti-inflammatory, and immunomodulatory properties. The genes of the TCP family, a group of plant-specific transcription factors (TFs), have been found to play a crucial role in the regulation of plant growth and development as well as resistance to abiotic stress. Nevertheless, no systematic analysis of the TCP family genes in C. indicum has been performed so far. In the present study, a total of 26 non-redundant CiTCP genes were identified in the genome of C. indicum. The TCP genes were categorized into three subgroups on the basis of the phylogenetic analysis: 7, 9, and 10 genes belonged to the CIN subgroup, CYC/TB1 subgroup, and PCF subgroup, respectively. All CiTCPs were unevenly distributed across the 9 chromosomes. TCP genes in the same subgroup showed similar gene structures and conserved motifs. Gene duplication analysis revealed that segmental duplications had a significant effect on the expansion of CiTCP genes. The analysis of cis-elements revealed that CiTCP genes may be involved in the regulation of plant development, hormone response and response to abiotic stress. Expression profile analysis of the transcriptome data indicated that CiTCP genes exhibited similar or distinct expressions within different tissues and under different abiotic stresses. According to the results of quantitative RT-PCR (qRT-PCR), the expression of 15 selected genes responded strongly to various abiotic stress factors. The results of our studies could provide comprehensive insights into the TCP family genes of C. indicum for further functional investigations.

Two ancient and highly divergent actin-based cytoskeletal systems have evolved in angiosperms. Plant genomes encode complex actin and actin binding protein (ABP) gene families, most of which are phylogenetically grouped into gene classes with distinct vegetative or constitutive and reproductive expression patterns. In Arabidopsis thaliana, ectopic expression of high levels of a reproductive class actin, ACT1, in vegetative tissues causes severe dwarfing of plants with aberrant organization of most plant organs and cell types due to a severely altered actin cytoskeletal architecture. Overexpression of the vegetative class actin ACT2 to similar levels, however, produces insignificant phenotypic changes. We proposed that the misexpression of the pollen-specific ACT1 in vegetative cell types affects the dynamics of actin due to its inappropriate interaction with endogenous vegetative ABPs. To examine the functionally distinct interactions among the major classes of actins and ABPs, we ectopically coexpressed reproductive profilin (PRF4) or actin-depolymerizing factor (ADF) isovariants (e.g., ADF7) with ACT1. Our results demonstrated that the coexpression of these reproductive, but not vegetative, ABP isovariants suppressed the ectopic ACT1 expression phenotypes and restored wild-type stature and normal actin cytoskeletal architecture to the double transgenic plants. Thus, the actins and ABPs appear to have evolved class-specific, protein-protein interactions that are essential to the normal regulation of plant growth and development.

One of the most intriguing questions in life science is how living organisms develop and maintain their predominant form and shape via the cascade of the processes of differentiation starting from the single cell. Mathematical modeling of these developmental processes could be a very important tool to properly describe the complex processes of evolution and geometry of morphogenesis in time and space. Here, we summarize the most important biological knowledge on plant development, exploring the different layers of investigation in developmental processes such as plant morphology, genetics, plant physiology, molecular biology and epigenetics. As knowledge on the fundamentals of plant embryogenesis, growth and development is constantly improving, we gather here the latest data on genetic, molecular and hormonal regulation of plant development together with the basic background knowledge. Special emphasis is placed on the regulation of cell cycle progression, on the role of the signal molecules phytohormones in plant development and on the details of plant meristems (loci containing plant stem cells) function. We also explore several proposed biological models regarding regulating plant development. The information presented here could be used as a basis for mathematical modeling and computer simulation of developmental processes in plants.

In Arabidopsis thaliana, the endosomal-localized Na+/H+ antiporters NHX5 and NHX6 regulate ion and pH homeostasis and are important for plant growth and development. However, the mechanism by which these endosomal NHXs function in plant development is not well understood. Auxin modulates plant growth and development through the formation of concentration gradients in plant tissue to control cell division and expansion. Here, we identified a role for NHX5 and NHX6 in the establishment and maintenance of auxin gradients in embryo and root tissues. We observed developmental impairment and abnormal cell division in embryo and root tissues in the double knockout nhx5 nhx6, consistent with these tissues showing high expression of NHX5 and NHX6. Through confocal microscopy imaging with the DR5::GFP auxin reporter, we identify defects in the perception, accumulation and redistribution of auxin in nhx5 nhx6 cells. Furthermore, we find that the steady-state levels of the PIN-FORMED (PIN) auxin efflux carriers PIN1 and PIN2 are reduced in nhx5 nhx6 root cells. Our results demonstrate that NHX5 and NHX6 function in auxin-mediated plant development by maintaining PIN abundance at the plasma membrane, and provide new insight into the regulation of plant development by endosomal NHX antiporters.

Plant growth and development are greatly affected by the environment. Many genes have been identified to be involved in regulating plant development and adaption of abiotic stress. Apart from protein-coding genes, more and more evidence indicates that non-coding RNAs (ncRNAs), including small RNAs and long ncRNAs (lncRNAs), can target plant developmental and stress-responsive mRNAs, regulatory genes, DNA regulatory regions, and proteins to regulate the transcription of various genes at the transcriptional, posttranscriptional, and epigenetic level. Currently, the molecular regulatory mechanisms of sRNAs and lncRNAs controlling plant development and abiotic response are being deeply explored. In this review, we summarize the recent research progress of small RNAs and lncRNAs in plants, focusing on the signal factors, expression characters, targets functions, and interplay network of ncRNAs and their targets in plant development and abiotic stress responses. The complex molecular regulatory pathways among small RNAs, lncRNAs, and targets in plants are also discussed. Understanding molecular mechanisms and functional implications of ncRNAs in various abiotic stress responses and development will benefit us in regard to the use of ncRNAs as potential character-determining factors in molecular plant breeding.

BackgroundThe phytohormone auxin mediates a stunning array of plant development through the functions of AUXIN RESPONSE FACTORs (ARFs), which belong to transcription factors and are present as a protein family comprising 10–43 members so far identified in different plant species. Plant development is also subject to regulation by TRANSPARENT TESTA GLABRA (TTG) proteins, such as NtTTG2 that we recently characterized in tobacco Nicotiana tabacum. To find the functional linkage between TTG and auxin in the regulation of plant development, we performed de novo assembly of the tobacco transcriptome to identify candidates of NtTTG2-regulated ARF genes.ResultsThe role of NtTTG2 in tobacco growth and development was studied by analyzing the biological effects of gene silencing and overexpression. The NtTTG2 gene silencing causes repressive effects on vegetative growth, floral anthocyanin synthesis, flower colorization, and seed production. By contrast, the plant growth and development processes are promoted by NtTTG2 overexpression. The growth/developmental function of NtTTG2 associates with differential expression of putative ARF genes identified by de novo assembly of the tobacco transcriptome. The transcriptome contains a total of 54,906 unigenes, including 30,124 unigenes (54.86%) with annotated functions and at least 8,024 unigenes (14.61%) assigned to plant growth and development. The transcriptome also contains 455 unigenes (0.83%) related to auxin responses, including 40 putative ARF genes. Based on quantitative analyses, the expression of the putative genes is either promoted or inhibited by NtTTG2.ConclusionsThe biological effects of the NtTTG2 gene silencing and overexpression suggest that NtTTG2 is an essential regulator of growth and development in tobacco. The effects of the altered NtTTG2 expression on expression levels of putative ARF genes identified in the transcriptome suggest that NtTTG2 functions in relation to ARF transcription factors.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-14-806) contains supplementary material, which is available to authorized users.

Cell cycle regulation is of pivotal importance for plant growth and development. Although plant cell division shares basic mechanisms with all eukaryotes, plants have evolved novel molecules orchestrating the cell cycle. Some regulatory proteins, such as cyclins and inhibitors of cyclin-dependent kinases, are particularly numerous in plants, possibly reflecting the remarkable ability of plants to modulate their postembryonic development. Many plant cells also can continue DNA replication in the absence of mitosis, a process known as endoreduplication, causing polyploidy. Here, we review the molecular mechanisms that regulate cell division and endoreduplication and we discuss our understanding, albeit very limited, on how the cell cycle is integrated with plant development.

Cytokinins (CKs) are well-established as important phytohormonal regulators of plant growth and development. An increasing number of studies have also revealed the function of these hormones in plant responses to biotic and abiotic stresses. While the function of certain CK classes, including trans-zeatin and isopentenyladenine-type CKs, have been studied in detail, the role of cis-zeatin-type CKs (cZs) in plant development and in mediating environmental interactions is less well defined. Here we provide a comprehensive summary of the current knowledge about abundance, metabolism and activities of cZs in plants. We outline the history of their analysis and the metabolic routes comprising cZ biosynthesis and degradation. Further we provide an overview of changes in the pools of cZs during plant development and environmental interactions. We summarize studies that investigate the role of cZs in regulating plant development and defence responses to pathogen and herbivore attack and highlight their potential role as 'novel' stress-response markers. Since the functional roles of cZs remain largely based on correlative data and genetic manipulations of their biosynthesis, inactivation and degradation are few, we suggest experimental approaches using transgenic plants altered in cZ levels to further uncover their roles in plant growth and environmental interactions and their potential for crop improvement.

<p indent="0mm">Nitric oxide (NO) is an important gaseous signaling molecule widely distributed in living organisms, it modulates protein stability and enzyme activities mainly through post-translational modifications, including <italic>S</italic>-nitrosylation and tyrosine nitration. NO regulates multiple physiological processes during plant development and stress responses. Moreover, the complex interplay among NO and phytohormones, reactive oxygen species and other signaling molecules precisely regulates various stages of plant growth and development to maintain normal life activities. Here, we review the synthesis and metabolism of NO, and provide insights into the mechanism and biological significance of NO in the regulation of plant development and stress responses.

Cytokinins are a class of plant hormones that regulate diverse aspects of plant growth and development. During the past decade, genetic and genomic approaches have succeeded in identifying many genes involved in the de novo synthesis, activation, inactivation, and signaling of cytokinin. Characterization of these genes has not only helped to define basic schemes of cytokinin biosynthesis and signaling, but has also demonstrated that cytokinins play a crucial role in numerous developmental processes. Furthermore, recent studies in rice have highlighted cytokinins as promising targets for crop improvement. This chapter gives an overview of our current understanding of the cytokinin biosynthesis and signaling pathways, and summarizes recent findings on the molecular basis for cytokinin involvement in plant development.

The precise control of free auxin (indole-3-acetic acid, IAA) gradient, which is orchestrated by biosynthesis, conjugation, degradation, hydrolyzation, and transport, is critical for all aspects of plant growth and development. Of these, the GRETCHEN HAGEN 3 (GH3) acyl acid amido synthetase family, pivotal in conjugating IAA with amino acids, has garnered significant interest. Recent advances in understanding GH3-dependent IAA conjugation have positioned GH3 functional elucidation as a hot topic of research. This review aims to consolidate and discuss recent findings on (i) the enzymatic mechanisms driving GH3 activity, (ii) the influence of chemical inhibitor on GH3 function, and (iii) the transcriptional regulation of GH3 and its impact on plant development and stress response. Additionally, we explore the distinct biological functions attributed to IAA-amino acid conjugates.

Plant reproduction comprises an interlocking array of developmental pathways which include the formation of the sexual organs, the generation of germ linesde novo, and the operation of the mechanisms which regulate epigenetic imprinting and the system of self-incompatibility found in m any angiosperms. Little is known of how these processes are regulated at a molecular level, with the exception of the floral organs which are determined by families of homeotic genes operating in a heterochronic fashion. In dioecious and monoecious plants the expression of these ‘floral’ genes must be modulated by sexdeterm ination sequences, situated in some circumstances on sex chromosomes. Older, physiological data indicate that sex can be determined by growth regulators, particularly gibberellic acid (GA) and cytokinins, and it is possible that sex-determination genes establish local concentrations of growth regulators at the apex, which in turn influence the expression of the homeotic floral genes. Evidence from anther development indicates genes involved in differentiation of the male and female germ lines to be regulated by defined promoter, enhancer, and silencer regions, but few data are available on the sequences directing the initiation and regulation of meiosis; certainly parallels can be drawn with similar events in microorganisms, and useful complementation strategies may be devised, but significant differences do exist between yeasts and higher plants suggesting that more appropriate parallels should be drawn with multicellular eukaryotes such as nematodes. The loci involved in epigenetic imprinting and self-incompatibility are important because they affect both male and female developmental pathways. Nothing is known of the regulatory sequences which direct the epigenetic imprinting of the sperm and central cell genomes, but information is becoming available on the promoter regions of theS(incompatibility)-locus. Interestingly, sequences directing expression in male and female tissues are contained within a single 5' stretch within the locus, and these prom oters also induce expression in different cell types in the anther and pistil depending on the type of self-incompatibility involved. Regulation of reproductive development in plants is apparently not very stringent, for there are examples in both male and female germ lines of reversion to an embryonic condition (apomixis and microspore embryogenesis); whether this reflects the highly dedifferentiated state of these cells or differences in the regulation of somatic and reproductive development remains to be determined.

In grapevines, the MYB transcription factors play an important regulatory role in the phenylpropanoid pathway including proanthocyanidin, anthocyanin, and flavonoid biosynthesis. However, the role of MYB in abiotic stresses is not clear. In this study, an R2R3-MYB transcription factor, VyMYB24, was isolated from a high drought-tolerant Chinese wild Vitis species V. yanshanesis. Our findings demonstrated that it was involved in plant development and drought tolerance. VyMYB24 is a nuclear protein and is significantly induced by drought stress. When over-expressed in tobacco, VyMYB24 caused plant dwarfing including plant height, leaf area, flower size, and seed weight. The GA1+3 content in transgenic plants was reduced significantly, and spraying exogenous gibberellin could recover the dwarf phenotype of VyMYB24 transgenic plants, suggesting that VyMYB24 might inhibit plant development by the regulation of gibberellin (GA) metabolism. Under drought stress, the VyMYB24 transgenic plants improved their tolerance to drought with a lower wilting rate, lower relative electrical conductivity, and stronger roots. Compared to wild-type tobacco plants, VyMYB24 transgenic plants accumulated less reactive oxygen, accompanied by increased antioxidant enzyme activity and upregulated gene expression levels of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) genes. In addition, transgenic plants accumulated more proline, and their related synthetic genes NtP5CR and NtP5CS genes were significantly upregulated when exposed to drought. Besides, abiotic stress-responsive genes, NtDREB, NtERD10C, NtERD10D, and NtLEA5, were upregulated significantly in VyMYB24 transgenic plants. These results indicate that VyMYB24 plays a positive regulatory role in response to drought stress and also regulates plant development, which provides new evidence to further explore the molecular mechanism of drought stress of the MYB gene family.

GDSL esterases/lipases (GELPs), present throughout all living organisms, have been a very attractive research subject in plant science due mainly to constantly emerging properties and functions in plant growth and development under both normal and stressful conditions. This review summarizes the advances in research on plant GELPs in several model plants and crops, including Arabidopsis, rice, maize and tomato, while focusing on the roles of GELPs in regulating plant development and plant–environment interactions. In addition, the possible regulatory network and mechanisms of GELPs have been discussed.

Auxin is among the key growth regulators that play diverse roles in virtually all aspects of plant growth and development. Intensive investigations during the past two decades have helped in elucidation of auxin perception and signal transduction mechanisms operative in plants. In addition to its primary role in regulating plant development, several studies in recent years have provided unflinching evidence for the involvement of auxin in abiotic stress responses. Functional genomics studies and genome-wide expression analysis have revealed altered expression of auxin-responsive genes, such as Aux/IAA, GH3, SAURs, and ARFs, under abiotic stress conditions. Variations in endogenous levels of auxin at global and local levels under various abiotic stress conditions have been associated with phenotypic changes and provided intriguing evidences regarding its role in response to environmental changes. Modulation of reactive oxygen species (ROS) levels in response to exogenous auxin as well as to drought, salinity, and ABA have indicated towards a complex relationship network between auxin, ROS, and abiotic stresses in plants. The advent of recent functional genomics technologies has led to identification of several candidate genes that may modulate crosstalk between auxin and abiotic stresses. This chapter discusses auxin homeostasis, signal transduction mechanisms, and how these processes are modulated under abiotic stresses, thus emphasizing on the emerging roles of auxin as a key integrator of abiotic stress pathways and plant development.