Transcriptional mechanisms regulating gene expression and determining cell fates in plant development

Transcriptional regulatory mechanisms that control transcriptional regulators, target genes, and their interactions provide new insights into general development processes throughout the life cycle of the plant. Although different molecular mechanisms that regulate plant growth and development have been identified, detailed transcriptional mechanisms that control gene expression, modulate developmental programmes, and determine cell fates in plant development are not fully understood. To increase our understanding on transcriptional mechanisms regulating diverse processes in plant development, we have reviewed the regulation of transcription during the process of development including transcriptional mechanisms regulating root, stem, leaf, flower, seed, embryo, endosperm, ovule, fruit, and chloroplast development. We have summarized the interaction, expression, transport, signaling events of transcriptional regulators and their targets in a number of model plants and highlighted the involvement of hormones and microRNAs in plant development. Understanding the precise transcriptional mechanisms regulating gene expression in plant development will be valuable for plant molecular breeding.

Arabidopsis AtBECLIN 1/AtAtg6/AtVps30 is essential for pollen germination and plant development

Pollen germination on the surface of compatible stigmatic tissues is an essential step for plant fertilization. Here we report that the Arabidopsis mutant bcll is male sterile as a result of the failure ofpollen germination. We show that the bcll mutant allele cannot be transmitted by male gametophytes and no homozygous bcll mutants were obtained. Analysis of pollen developmental stages indicates that the bcll mutation affects pollen germination but not pollen maturation. Molecular analysis demonstrates that the failure of pollen germination was caused by the disruption of AtBECLIN 1. AtBECLIN 1 is expressed predominantly in mature pollen and encodes a protein with significant homology to Beclin1/Atg6/Vps30 required for the processes of autophagy and vacuolar protein sorting （VPS） in yeast. We also show that AtBECLIN 1 is required for normal plant development, and that genes related to autophagy, VPS and the glycosylphosphatidylinositol anchor system, were affected by the deficiency of AtBECLIN 1.

The cytochrome P450 superfamily: Key players in plant development and defense

The cytochrome P450 （CYP） superfamily is the largest enzymatic protein family in plants, and it also widely exists in mammals, fungi, bacteria, insects and so on. Members of this superfamily are involved in multiple metabolic pathways with distinct and complex functions, playing important roles in a vast array of reactions. As a result, numerous secondary metabolites are synthesized that function as growth and developmental signals or protect plants from various biotic and abiotic stresses. Here, we summarize the characterization of CYPs, as well as their phylogenetic classification. We also focus on recent advances in elucidating the roles of CYPs in mediating plant growth and development as well as biotic and abiotic stresses responses, providing insights into their potential utilization in plant breeding.

Emerging role of jasmonic acid in woody plant development

Jasmonic acid is a crucial phytohormone that plays a pivotal role,serving as a regulator to balancing plant development and resistance.However,there are analogous and distinctive characteristics exhibited in JA biosynthesis,perception,and signal transduction pathways in both herbaceous and woody plants.Moreover,the majority of research subjects have predominantly focused on the function of JA in model or herbaceous plants.Consequently,there is a significant paucity of studies investigating JA regulation networks in woody plants,particularly concerning post-transcriptional regulatory events such as alternative splicing(AS).This review article aims to conduct a comprehensive summary of advancements that JA signals regulate plant development across various woody species,comparing the analogous features and regulatory differences to herbaceous counterparts.In addition,we summarized the involvement of AS events including splicing factor(SF)and transcripts in the JA regulatory network,highlighting the effectiveness of high-throughput proteogenomic methods.A better understanding of the JA signaling pathway in woody plants has pivotal implications for forestry production,including optimizing plant management and enhancing secondary metabolite production.

The TELOMERE REPEAT BINDING proteins TRB4 and TRB5 function as transcriptional activators of PRC2-controlled genes to regulate plant development

Plant-specific transcriptional regulators called TELOMERE REPEAT BINDING proteins(TRBs)combine two DNA-binding domains,the GH1 domain,which binds to linker DNA and is shared with H1 histones,and the Myb/SANT domain,which specifically recognizes the telobox DNA-binding site motif.TRB1,TRB2,and TRB3 proteins recruit Polycomb group complex 2(PRC2)to deposit H3K27me3 and JMJ14 to remove H3K4me3 at gene promoters containing telobox motifs to repress transcription.Here,we demonstrate that TRB4 and TRB5,two related paralogs belonging to a separate TRB clade conserved in spermatophytes,regulate the transcription of several hundred genes involved in developmental responses to environmental cues.TRB4 binds to several thousand sites in the genome,mainly at transcription start sites and promoter regions of transcriptionally active and H3K4me3-marked genes,but,unlike TRB1,it is not enriched at H3K27me3-marked gene bodies.However,TRB4 can physically interact with the catalytic components of PRC2,SWINGER,and CURLY LEAF(CLF).Unexpectedly,we show that TRB4 and TRB5 are required for distinctive phenotypic traits observed in clf mutant plants and thus function as transcriptional activators of several hundred CLF-controlled genes,including key flowering genes.We further demonstrate that TRB4 shares multiple target genes with TRB1 and physically and genetically interacts with members of both TRB clades.Collectively,these results reveal that TRB proteins engage in both positive and negative interactions with other members of the family to regulate plant development through both PRC2-dependent and-independent mechanisms.

Sulfated peptides and their receptors:Key regulators of plant development and stress adaptation

Four distinct types of sulfated peptides have been identified in Arabidopsis thaliana.These peptides play crucial roles in regulating plant development and stress adaptation.Recent studies have revealed that Xan-thomonas and Meloidogyne can secrete plant-like sulfated peptides,exploiting the plant sulfated peptide signaling pathway to suppress plant immunity.Over the past three decades,receptors for these four types of sulfated peptides have been identified,all of which belong to the leucine-rich repeat receptor-like protein kinase subfamily.A number of regulatory proteins have been demonstrated to play important roles in their corresponding signal transduction pathways.In this review,we comprehensively summarize the discov-eries of sulfated peptides and their receptors,mainly in Arabidopsis thaliana.We also discuss their known biological functions in plant development and stress adaptation.Finally,we put forward a number of ques-tions for reference in future studies.

The Mechanisms of Brassinosteroids＇ Action： From Signal Transduction to Plant Development

Brassinosteroids play diverse roles in plant growth and development. Plants deficient in brassinosteroid （BR） biosynthesis or defective in signal transduction show many abnormal developmental phenotypes, indicating the importance of both BR biosynthesis and the signaling pathway in regulating these biological processes. Recently, using genetics, proteomics, genomics, cell biology, and many other approaches, more components involved in the BR signaling pathway were identified. Furthermore, the physiological, cellular, and molecular mechanisms by which BRs regulate various aspects of plant development, are being discovered. These include root development, anther and pollen development and formation, stem elongation, vasculature differentiation, and cellulose biosynthesis, suggesting that the biological functions of BRs are far beyond promoting cell elongation, This review will focus on the up-to-date progresses about regulatory mechanisms of the BR signaling pathway and the physiological and molecular mechanisms whereby BRs regulate plant growth and development.

DNA cytosine methylation in plant development

Cytosine bases of the nuclear genome in higher plants are often extensively methylated.Cytosine methylation has been implicated in the silencing of both transposable elements （TEs） and endogenous genes,and loss of methylation may have severe functional consequences.The recent methylation profiling of the entire Arabidopsis genome has provided novel insights into the extent and pattern of cytosine methylation and its relationships with gene activity.In addition,the fresh studies also revealed the more dynamic nature of this epigenetic modification across plant development than previously believed.Cytosine methylation of gene promoter regions usually inhibits transcription,but methylation in coding regions （gene-body methylation） does not generally affect gene expression.Active demethylation （though probably act synergistically with passive loss of methylation） of promoters by the 5-methyl cytosine DNA glycosylase or DEMETER （DME） is required for the uni-parental expression of imprinting genes in endosperm,which is essential for seed viability.The opinion that cytosine methylation is indispensible for normal plant development has been reinforced by using single or combinations of diverse loss-of-function mutants for DNA methyltransferases,DNA glycosylases,components involved in siRNA biogenesis and chromatin remodeling factors.Patterns of cytosine methylation in plants are usually faithfully maintained across organismal generations by the concerted action of epigenetic inheritance and progressive correction of strayed patterns.However,some variant methylation patterns may escape from being corrected and hence produce novel epialleles in the affected somatic cells.This,coupled with the unique property of plants to produce germline cells late during development,may enable the newly acquired epialleles to be inherited to future generations,which if visible to selection may contribute to adaptation and evolution.

Knights in Action： Lectin Receptor-Like Kinases in Plant Development and Stress Responses

The Receptor-Like Kinase （RLK） is a vast protein family with over 600 genes in Arabidopsis and 1100 in rice. The Lectin RLK （LecRLK） family is believed to play crucial roles in saccharide signaling as well as stress perception. All the LecRLKs possess three domains： an N-terminal lectin domain, an intermediate transmembrane domain, and a C-terminal kinase domain. On the basis of lectin domain variability, LecRLKs have been subgrouped into three subclasses： L-, G-, and C-type LecRLKs. While the previous studies on LecRLKs were dedicated to classification, comparative structural analysis and expression analysis by promoter-based studies, most of the recent studies on LecRLKs have laid special emphasis on the potential of this gene family in regulating biotic/abiotic stress and developmental pathways in plants, thus mak- ing the prospects of studying the LecRLK-mediated regulatory mechanism exceptionally promising. In this review, we have described in detail the LecRLK gene family with respect to a historical, evolutionary, and structural point of view. Furthermore, we have laid emphasis on the LecRLKs roles in development, stress conditions, and hormonal response. We have also discussed the exciting research prospects offered by the current knowledge on the LecRLK gene family. The multitude of the LecRLK gene family members and their functional diversity mark these genes as both interesting and worthy candidates for further analysis, especially in the field of crop improvement.

Genomic basis for light control of plant development

Light is one of the key environmental signals regulating plant growth and development.Therefore,understanding the mechanisms by which light controls plant development has long been of great interest to plant biologists.Traditional genetic and molecular approaches have successfully identified key regulatory factors in light signaling,but recent genomic studies have revealed massive reprogramming of plant transcriptomes by light,identified binding sites across the entire genome of several pivotal transcription factors in light signaling,and discovered the involvement of epigenetic regulation in light-regulated gene expression.This review summarizes the key genomic work conducted in the last decade which provides new insights into light control of plant development.

Phosphatidic acid plays key roles regulating plant development and stress responses

Phospholipids, including phosphatidic acid （PA）, phosphatidylcholine （PC）, phosphatidylethanolamine （PE）, phosphatidylglycerol （PC）, phosphatidylserine （PS） and phosphoinositides, have emerged as an important class of cellular messenger molecules in various cellular and physiological processes, of which PA attracts much attention of researchers. In addition to its effect on stimulating vesicle trafficking, many studies have demonstrated that PA plays a crucial role in various signaling pathways by binding target proteins and regulating their activity and subcellular localization. Here, we summarize the functional mechanisms and target proteins underlying PA-mediated regulation of cellular signaling, development, hormonal responses, and stress responses in plants.

Effects of light emitting diode lights on plant growth,development and traits a meta-analysis

The various monochromatic Light Emitting Diode(LED)lights are widely used in growth facility for cultivating various plants,particularly horticultural crops because of their higher luminous efficiency,lower radiation and power consumption than the traditional white fluorescent lamp light.However,considerable inconsistent effects have been reported in literature.We conducted a meta-analysis to assess the effects of different colors of LED light on plant growth,development and various traits.Compared to the light from white fluorescent lamps,the red LED light significantly changed 4 out 26 plant characteristics by at least 37%,and blue LED light significantly increased 5 of 26 assessed characteristics by 37%or more.The combination of red/blue LED lights only significantly increased dry weight by 161%among 25 plant characteristics analyzed.Compared to the white LED light,red LED light significantly decreased 2 of 9 plant characteristics by at least 36%,and blue LED light significantly decreased only 1 of 9 plant characteristics,total chlorophyll content,by 42%.In the moderators analyzed,plant taxonomic families significantly influenced the effects of LED lights on shoot dry weight,and plant life cycles and plant taxonomic families significantly affected the effect on stomatal conductance.Through systematic meta-analysis,we found that the effect of LED on plant growth and quality traits was speciesspecific,and the effect was affected by the cultivation conditions.Therefore,we suggest that researchers be more targeted to experiment,and collect traits associated with practical production,especially related to the quality of product data,such as carotenoids,anthocyanin and other antioxidant compounds.This article is to provide more data with practical application,guide the application of LED in horticultural plant factory.

Expanding roles for pectins in plant development

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 composi- tion 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.

TRAF proteins as key regulators of plant development and stress responses

Tumor necrosis factor receptor-associated factor(TRAF)proteins are conserved in higher eukaryotes and play key roles in transducing cellular signals across different organelles.They are characterized by their C-terminal region(TRAF-C domain)containing seven to eight antiparallelβ-sheets,also known as the meprin and TRAF-C homology(MATH)domain.Over the past few decades,significant progress has been made toward understanding the diverse roles of TRAF proteins in mammals and plants.Compared to other eukaryotic species,the Arabidopsis thaliana and rice(Oryza sativa)genomes encode many more TRAF/MATH domaincontaining proteins;these plant proteins cluster into five classes:TRAF/MATH-only,MATH-BPM,MATH-UBP(ubiquitin protease),Seven in absentia(SINA),and MATH-Filament and MATHPEARLI-4 proteins,suggesting parallel evolution of TRAF proteins in plants.Increasing evidence now indicates that plant TRAF proteins form central signaling networks essential for multiple biological processes,such as vegetative and reproductive development,autophagosome formation,plant immunity,symbiosis,phytohormone signaling,and abiotic stress responses.Here,we summarize recent advances and highlight future prospects for understanding on the molecular mechanisms by which TRAF proteins act in plant development and stress responses.

Understanding Plant Development and Stress Responses through Integrative Approaches

As the name reflects, integrative plant biology is the core topic of JIPB. In the past few years JIPB has been pursuing the development of this area, to assist the scientific community to bring together all possible research tools to understand plant growth, development and stress responses in micro- and macro-scales. As part of these efforts, JIPB and Yantai University organized the 1st International Symposium on Integrative Plant Biology in the seaside town of Yantai during August 10-12, 2009 （Figure 1） The symposium was co-sponsored by Botanical Society of China, Chinese Society for Cell Biology, Genetics Society of China, and Chinese Society for Plant Physiology.

Asymmetric cell division in plant development

Asymmetric cell division(ACD) is a fundamental process that generates new cell types during development in eukaryotic species.In plant development,post-embryonic organogenesis driven by ACD is universal and more important than in animals,in which organ pattern is preset during embryogenesis.Thus,plant development provides a powerful system to study molecular mechanisms underlying ACD.During the past decade,tremendous progress has been made in our understanding of the key components and mechanisms involved in this important process in plants.Here,we present an overview of how ACD is determined and regulated in multiple biological processes in plant development and compare their conservation and specificity among different model cell systems.We also summarize the molecular roles and mechanisms of the phytohormones in the regulation of plant ACD.Finally,we conclude with the overarching paradigms and principles that govern plant ACD and consider how new technologies can be exploited to fill the knowledge gaps and make new advances in the field.

Introduction of Institute of Medicinal Plant Development

Institute of Medicinal Plant Development (IMPLAD), affiliated with the Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), was established in August 1983. IMPLAD, headquartered in the Zhongguancun Scientific and Technical Zone, Beijing, China, owns three branch institutes with total over 333 hectares of land in the subtropical regions of southern China, located in

A Botanist’s Cognitive View on Plant Growth: Cross-Talk between Developmental and Sensitivity Networks

An alteration in plant phenotypes assisted by their responses to the environmental stimuli (=tropism) has been fundamental to understand the “plant sensitivity ” that plays a crucial role in plants’ adaptive success. Plants succeed through the deployment of moderators controlling polar auxin-transport determining organ bending. Stimulus-specific effectors can be synthesized by the outer peripheral cells at the bending sites where they target highly conserved cellular processes and potentially persuade the plant sensitivity at large. Remarkably, the peripheral cells require different time-intervals to achieve the threshold expression-levels of stimulus-specific molecular responders. After stimulus perception, tropic curvatures (especially at growing root-apices) are duly coordinated via integrated chemical and electrical signalling which is the key to cellular communications. Thus, the acquired phenotypic alterations are the perplexed outcome of plant’s developmental pace, complemented by the sensitivity. A novel aspect of this study is to advance our understanding of plant developmental-programming and the extent of plant-sensitivity, determining the plant growth and their future applications.

SPATULA as a Versatile Tool in Plant:The Progress and Perspectives of SPATULA(SPT)Transcriptional Factor

With the rapid development of modern molecular biology and bioinformatics,many studies have proved that transcription factors play an important role in regulating the growth and development of plants.SPATULA(SPT)belongs to the bHLH transcription family and participates in many processes of regulating plant growth and development.This review systemically summarizes the multiple roles of SPT in plant growth,development,and stress response,including seed germination,flowering,leaf size,carpel development,and root elongation,which is helpful for us to better understand the functions of SPT.

Developmental Genetics Analysis for Plant Height in indica Hybrid Rice Across Environments

The developmental genetics of plant height was analyzed from two groups of three-line indica hybrid rice at two environmental conditions based on the NCII design, using the additive-dominant developmental genetics models and the statistic methods. The results showed that the rice genotypes and environmental conditions could both affect plant height, and the effects of environment on plant height decreased gradually with plant development. Additive and dominant effects both governed the performance of plant height at all developmental stages. However, the degrees of effect varied among the rice genotypes. Moreover, the interaction between environments and genotypes also affected plant height. The genetic effects differed at most developmental stages. Furthermore, the expressJon of additive effect was more active than that of dominant effect. Conditional interaction effects with environment also influenced plant height during genetic development, especially at the eady stage. Mid-parent heterosis （HMP） increased gradually with the developmental stage of plant height, and maximized at the latest stage, whereas the heterosis over the better parent （HBP） showed small differences among the genotypes, and kept stable at the later stage, with positive numeric value. At most developmental stages, conditional HMP was positively significant, while conditional HBP was negatively significant. All above results suggest that HMP and HBP have some new expressions in all developmental periods and the levels and directions are quite different.