Agricultural and Biological Sciences › Plant Science

Plant Molecular Biology Research

Works Count: 61849

Wikipedia

Description

This cluster of papers focuses on the molecular mechanisms underlying plant development, with a particular emphasis on the roles of microRNAs, auxin, gene expression regulation, epigenetic mechanisms, transcription factors, genome-wide analyses, cytokinin signaling, and the control of flowering time.

Keywords

Plant; Development; MicroRNA; Auxin; Gene Expression; Epigenetic Regulation; Transcription Factors; Genome-wide Analysis; Cytokinin Signaling; Flowering Time

MicroRNAs

2004-01-01

David P. Bartel

‘Green revolution’ genes encode mutant gibberellin response modulators

1999-07-01

Jinrong Peng , Donald E. Richards , Nigel M. Hartley +7 more

Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high‐salinity stresses using a full‐length cDNA microarray

2002-08-01

Motoaki Seki , Mari Narusaka , Junko Ishida +7 more

Summary Full‐length cDNAs are essential for functional analysis of plant genes in the post‐sequencing era of the Arabidopsis genome. Recently, cDNA microarray analysis has been developed for quantitative analysis of … Summary Full‐length cDNAs are essential for functional analysis of plant genes in the post‐sequencing era of the Arabidopsis genome. Recently, cDNA microarray analysis has been developed for quantitative analysis of global and simultaneous analysis of expression profiles. We have prepared a full‐length cDNA microarray containing ≈7000 independent, full‐length cDNA groups to analyse the expression profiles of genes under drought, cold (low temperature) and high‐salinity stress conditions over time. The transcripts of 53, 277 and 194 genes increased after cold, drought and high‐salinity treatments, respectively, more than fivefold compared with the control genes. We also identified many highly drought‐, cold‐ or high‐salinity‐ stress‐inducible genes. However, we observed strong relationships in the expression of these stress‐responsive genes based on Venn diagram analysis, and found 22 stress‐inducible genes that responded to all three stresses. Several gene groups showing different expression profiles were identified by analysis of their expression patterns during stress‐responsive gene induction. The cold‐inducible genes were classified into at least two gene groups from their expression profiles. DREB1A was included in a group whose expression peaked at 2 h after cold treatment. Among the drought, cold or high‐salinity stress‐inducible genes identified, we found 40 transcription factor genes (corresponding to ≈11% of all stress‐inducible genes identified), suggesting that various transcriptional regulatory mechanisms function in the drought, cold or high‐salinity stress signal transduction pathways.

Prediction of Plant MicroRNA Targets

2002-08-01

Matthew W. Rhoades , Brenda J. Reinhart , Lee P. Lim +3 more

View PDF Chat

Efflux-dependent auxin gradients establish the apical–basal axis of Arabidopsis

2003-11-01

Jiří Friml , Anne Vieten , Michael Sauer +5 more

The F-box protein TIR1 is an auxin receptor

2005-05-01

Nihal Dharmasiri , Sunethra Dharmasiri , Mark Estelle

Auxin: Regulation, Action, and Interaction

2005-02-08

Andrew W. Woodward

• Background The phytohormone auxin is critical for plant growth and orchestrates many developmental processes. • Scope This review considers the complex array of mechanisms plants use to control auxin … • Background The phytohormone auxin is critical for plant growth and orchestrates many developmental processes. • Scope This review considers the complex array of mechanisms plants use to control auxin levels, the movement of auxin through the plant, the emerging view of auxin-signalling mechanisms, and several interactions between auxin and other phytohormones. Though many natural and synthetic compounds exhibit auxin-like activity in bioassays, indole-3-acetic acid (IAA) is recognized as the key auxin in most plants. IAA is synthesized both from tryptophan (Trp) using Trp-dependent pathways and from an indolic Trp precursor via Trp-independent pathways; none of these pathways is fully elucidated. Plants can also obtain IAA by β-oxidation of indole-3-butyric acid (IBA), a second endogenous auxin, or by hydrolysing IAA conjugates, in which IAA is linked to amino acids, sugars or peptides. To permanently inactivate IAA, plants can employ conjugation and direct oxidation. Consistent with its definition as a hormone, IAA can be transported the length of the plant from the shoot to the root; this transport is necessary for normal development, and more localized transport is needed for tropic responses. Auxin signalling is mediated, at least in large part, by an SCFTIR1 E3 ubiquitin ligase complex that accelerates Aux/IAA repressor degradation in response to IAA, thereby altering gene expression. Two classes of auxin-induced genes encode negatively acting products (the Aux/IAA transcriptional repressors and GH3 family of IAA conjugating enzymes), suggesting that timely termination of the auxin signal is crucial. Auxin interaction with other hormone signals adds further challenges to understanding auxin response. • Conclusions Nearly six decades after the structural elucidation of IAA, many aspects of auxin metabolism, transport and signalling are well established; however, more than a few fundamental questions and innumerable details remain unresolved.

View PDF Chat

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

2008-02-17

Shawn Cokus , Suhua Feng , Xiaoyu Zhang +7 more

An “Electronic Fluorescent Pictograph” Browser for Exploring and Analyzing Large-Scale Biological Data Sets

2007-08-07

Deborah R. Winter , Ben Vinegar , Hardeep K. Nahal-Bose +3 more

The exploration of microarray data and data from other high-throughput projects for hypothesis generation has become a vital aspect of post-genomic research. For the non-bioinformatics specialist, however, many of the … The exploration of microarray data and data from other high-throughput projects for hypothesis generation has become a vital aspect of post-genomic research. For the non-bioinformatics specialist, however, many of the currently available tools provide overwhelming amounts of data that are presented in a non-intuitive way.In order to facilitate the interpretation and analysis of microarray data and data from other large-scale data sets, we have developed a tool, which we have dubbed the electronic Fluorescent Pictograph - or eFP - Browser, available at http://www.bar.utoronto.ca/, for exploring microarray and other data for hypothesis generation. This eFP Browser engine paints data from large-scale data sets onto pictographic representations of the experimental samples used to generate the data sets. We give examples of using the tool to present Arabidopsis gene expression data from the AtGenExpress Consortium (Arabidopsis eFP Browser), data for subcellular localization of Arabidopsis proteins (Cell eFP Browser), and mouse tissue atlas microarray data (Mouse eFP Browser).The eFP Browser software is easily adaptable to microarray or other large-scale data sets from any organism and thus should prove useful to a wide community for visualizing and interpreting these data sets for hypothesis generation.

View PDF Chat

Local, Efflux-Dependent Auxin Gradients as a Common Module for Plant Organ Formation

2003-11-01

Eva Benková , Marta Michniewicz , Michael Sauer +4 more

View PDF Chat

Gene silencing by microRNAs: contributions of translational repression and mRNA decay

2011-01-18

Eric Huntzinger , Elisa Izaurralde

FT Protein Movement Contributes to Long-Distance Signaling in Floral Induction of Arabidopsis

2007-04-20

Laurent Corbesier , Coral Vincent , Seonghoe Jang +7 more

In plants, seasonal changes in day length are perceived in leaves, which initiate long-distance signaling that induces flowering at the shoot apex. The identity of the long-distance signal has yet … In plants, seasonal changes in day length are perceived in leaves, which initiate long-distance signaling that induces flowering at the shoot apex. The identity of the long-distance signal has yet to be determined. In Arabidopsis, activation of FLOWERING LOCUS T (FT) transcription in leaf vascular tissue (phloem) induces flowering. We found that FT messenger RNA is required only transiently in the leaf. In addition, FT fusion proteins expressed specifically in phloem cells move to the apex and move long distances between grafted plants. Finally, we provide evidence that FT does not activate an intermediate messenger in leaves. We conclude that FT protein acts as a long-distance signal that induces Arabidopsis flowering.

A Plant miRNA Contributes to Antibacterial Resistance by Repressing Auxin Signaling

2006-04-21

Lionel Navarro , Patrice Dunoyer , Florence Jay +5 more

Plants and animals activate defenses after perceiving pathogen-associated molecular patterns (PAMPs) such as bacterial flagellin. In Arabidopsis , perception of flagellin increases resistance to the bacterium Pseudomonas syringae , although … Plants and animals activate defenses after perceiving pathogen-associated molecular patterns (PAMPs) such as bacterial flagellin. In Arabidopsis , perception of flagellin increases resistance to the bacterium Pseudomonas syringae , although the molecular mechanisms involved remain elusive. Here, we show that a flagellin-derived peptide induces a plant microRNA (miRNA) that negatively regulates messenger RNAs for the F-box auxin receptors TIR1, AFB2, and AFB3. Repression of auxin signaling restricts P. syringae growth, implicating auxin in disease susceptibility and miRNA-mediated suppression of auxin signaling in resistance.

Control of leaf morphogenesis by microRNAs

2003-08-20

Javier F. Palatnik , Edwards Allen , Xuelin Wu +4 more

Establishing, maintaining and modifying DNA methylation patterns in plants and animals

2010-02-09

Julie A. Law , Steven E. Jacobsen

The Arabidopsis F-box protein TIR1 is an auxin receptor

2005-05-01

Stefan Kepinski , Ottoline Leyser

PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences

2002-01-01

Magali Lescot

PlantCARE is a database of plant cis-acting regulatory elements, enhancers and repressors. Regulatory elements are represented by positional matrices, consensus sequencesand individual sites on particular promoter sequences. Links to the … PlantCARE is a database of plant cis-acting regulatory elements, enhancers and repressors. Regulatory elements are represented by positional matrices, consensus sequencesand individual sites on particular promoter sequences. Links to the EMBL, TRANSFAC and MEDLINE databases are provided when available. Data about the transcription sites are extracted mainly from the literature, supplemented with an increasing number of in silico predicted data. Apart from a general description for specific transcription factor sites, levels of confidence for the experimental evidence, functional information and the position on the promoter are given as well. New features have been implemented to search for plant cis-acting regulatory elements in a query sequence. Furthermore, links are now provided to a new clustering and motif search method to investigate clusters of co-expressed genes. New regulatory elements can be sent automatically and will be added to the database after curation. The PlantCARE relational database is available via the World Wide Web at http://sphinx.rug.ac.be:8080/PlantCARE/.

View PDF Chat

The Microprocessor complex mediates the genesis of microRNAs

2004-11-01

Richard I. Gregory , Kai-ping Yan , Govindasamy Amuthan +4 more

Two Transcription Factors, DREB1 and DREB2, with an EREBP/AP2 DNA Binding Domain Separate Two Cellular Signal Transduction Pathways in Drought- and Low-Temperature-Responsive Gene Expression, Respectively, in Arabidopsis

1998-08-01

Qiang Liu , Mie Kasuga , Yoh Sakuma +4 more

Plant growth is greatly affected by drought and low temperature. Expression of a number of genes is induced by both drought and low temperature, although these stresses are quite different. … Plant growth is greatly affected by drought and low temperature. Expression of a number of genes is induced by both drought and low temperature, although these stresses are quite different. Previous experiments have established that a cis-acting element named DRE (for dehydration-responsive element) plays an important role in both dehydration- and low-temperature-induced gene expression in Arabidopsis. Two cDNA clones that encode DRE binding proteins, DREB1A and DREB2A, were isolated by using the yeast one-hybrid screening technique. The two cDNA libraries were prepared from dehydrated and cold-treated rosette plants, respectively. The deduced amino acid sequences of DREB1A and DREB2A showed no significant sequence similarity, except in the conserved DNA binding domains found in the EREBP and APETALA2 proteins that function in ethylene-responsive expression and floral morphogenesis, respectively. Both the DREB1A and DREB2A proteins specifically bound to the DRE sequence in vitro and activated the transcription of the β-glucuronidase reporter gene driven by the DRE sequence in Arabidopsis leaf protoplasts. Expression of the DREB1A gene and its two homologs was induced by low-temperature stress, whereas expression of the DREB2A gene and its single homolog was induced by dehydration. Overexpression of the DREB1A cDNA in transgenic Arabidopsis plants not only induced strong expression of the target genes under unstressed conditions but also caused dwarfed phenotypes in the transgenic plants. These transgenic plants also revealed freezing and dehydration tolerance. In contrast, overexpression of the DREB2A cDNA induced weak expression of the target genes under unstressed conditions and caused growth retardation of the transgenic plants. These results indicate that two independent families of DREB proteins, DREB1 and DREB2, function as trans-acting factors in two separate signal transduction pathways under low-temperature and dehydration conditions, respectively.

A gene expression map of Arabidopsis thaliana development

2005-04-03

Markus Schmid , Timothy S. Davison , Stefan R. Henz +6 more

A MicroRNA as a Translational Repressor of APETALA2 in Arabidopsis Flower Development

2003-08-05

Xuemei Chen

Plant microRNAs (miRNAs) show a high degree of sequence complementarity to, and are believed to guide the cleavage of, their target messenger RNAs. Here, I show that miRNA172, which can … Plant microRNAs (miRNAs) show a high degree of sequence complementarity to, and are believed to guide the cleavage of, their target messenger RNAs. Here, I show that miRNA172, which can base-pair with the messenger RNA of a floral homeotic gene, APETALA2, regulates APETALA2 expression primarily through translational inhibition. Elevated miRNA172 accumulation results in floral organ identity defects similar to those in loss-of-function apetala2 mutants. Elevated levels of mutant APETALA2 RNA with disrupted miRNA172 base pairing, but not wild-type APETALA2 RNA, result in elevated levels of APETALA2 protein and severe floral patterning defects. Therefore, miRNA172 likely acts in cell-fate specification as a translational repressor of APETALA2 in Arabidopsis flower development.

View PDF Chat

The war of the whorls: genetic interactions controlling flower development

1991-09-01

Enrico Coen , Elliot M. Meyerowitz

Genome-wide High-Resolution Mapping and Functional Analysis of DNA Methylation in Arabidopsis

2006-09-01

Xiaoyu Zhang , Junshi Yazaki , Ambika Sundaresan +7 more

View PDF Chat

Arabidopsis Transcription Factors: Genome-Wide Comparative Analysis Among Eukaryotes

2000-12-15

José Luis Riechmann , Jacqueline E. Heard , Greg S. Martin +7 more

The completion of the Arabidopsis thaliana genome sequence allows a comparative analysis of transcriptional regulators across the three eukaryotic kingdoms. Arabidopsis dedicates over 5% of its genome to code for … The completion of the Arabidopsis thaliana genome sequence allows a comparative analysis of transcriptional regulators across the three eukaryotic kingdoms. Arabidopsis dedicates over 5% of its genome to code for more than 1500 transcription factors, about 45% of which are from families specific to plants. Arabidopsis transcription factors that belong to families common to all eukaryotes do not share significant similarity with those of the other kingdoms beyond the conserved DNA binding domains, many of which have been arranged in combinations specific to each lineage. The genome-wide comparison reveals the evolutionary generation of diversity in the regulation of transcription.

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

2008-04-18

Ryan Lister , Ronan C. O’Malley , Julian Tonti‐Filippini +4 more

View PDF Chat

Clock Mutants of Drosophila melanogaster

1971-09-01

Ronald J. Konopka , Seymour Benzer

Three mutants have been isolated in which the normal 24-hour rhythm is drastically changed. One mutant is arrhythmic; another has a period of 19 hr; a third has a period … Three mutants have been isolated in which the normal 24-hour rhythm is drastically changed. One mutant is arrhythmic; another has a period of 19 hr; a third has a period of 28 hr. Both the eclosion rhythm of a population and the locomotor activity of individual flies are affected. All these mutations appear to involve the same functional gene on the X chromosome.

View PDF Chat

Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA Targets

2005-01-01

Benjamin P. Lewis , Christopher B. Burge , David P. Bartel

RNA silencing in plants

2004-09-15

David C. Baulcombe

Role of MicroRNAs in Plant and Animal Development

2003-07-17

James C. Carrington , Victor Ambros

Small RNAs, including microRNAs (miRNAs) and short interfering RNAs (siRNAs), are key components of an evolutionarily conserved system of RNA-based gene regulation in eukaryotes. They are involved in many molecular … Small RNAs, including microRNAs (miRNAs) and short interfering RNAs (siRNAs), are key components of an evolutionarily conserved system of RNA-based gene regulation in eukaryotes. They are involved in many molecular interactions, including defense against viruses and regulation of gene expression during development. miRNAs interfere with expression of messenger RNAs encoding factors that control developmental timing, stem cell maintenance, and other developmental and physiological processes in plants and animals. miRNAs are negative regulators that function as specificity determinants, or guides, within complexes that inhibit protein synthesis (animals) or promote degradation (plants) of mRNA targets.

The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray)

2006-09-15

Gerald A. Tuskan , Stephen DiFazio , Stefan Jansson +7 more

We report the draft genome of the black cottonwood tree, Populus trichocarpa . Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 … We report the draft genome of the black cottonwood tree, Populus trichocarpa . Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis , ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.

View PDF Chat

Target mimicry provides a new mechanism for regulation of microRNA activity

2007-07-22

José M. Franco‐Zorrilla , Adrián Vallí , Marco Todesco +7 more

Rapid Flow Cytometric Analysis of the Cell Cycle in Intact Plant Tissues

1983-06-03

David W. Galbraith , Kristi R. Harkins , Joyce M. Maddox +3 more

Mechanical chopping of plant tissues in the presence of mithramycin released intact nuclei representative of the cells within the tissues. The amount of nuclear DNA in the homogenates of monocotyledonous … Mechanical chopping of plant tissues in the presence of mithramycin released intact nuclei representative of the cells within the tissues. The amount of nuclear DNA in the homogenates of monocotyledonous and dicotyledonous plants was accurately and rapidly determined by flow microfluorometry, and the distribution of nuclei involved in the cell cycle was charted for tissues selected from different physical locations or developmental stages.

FLOWERING LOCUS C Encodes a Novel MADS Domain Protein That Acts as a Repressor of Flowering

1999-05-01

Scott D. Michaels , Richard M. Amasino

Winter-annual ecotypes of Arabidopsis are relatively late flowering, unless the flowering of these ecotypes is promoted by exposure to cold (vernalization). This vernalization-suppressible, late-flowering phenotype results from the presence of … Winter-annual ecotypes of Arabidopsis are relatively late flowering, unless the flowering of these ecotypes is promoted by exposure to cold (vernalization). This vernalization-suppressible, late-flowering phenotype results from the presence of dominant, late-flowering alleles at two loci, FRIGIDA (FRI) and FLOWERING LOCUS C (FLC). In this study, we report that flc null mutations result in early flowering, demonstrating that the role of active FLC alleles is to repress flowering. FLC was isolated by positional cloning and found to encode a novel MADS domain protein. The levels of FLC mRNA are regulated positively by FRI and negatively by LUMINIDEPENDENS. FLC is also negatively regulated by vernalization. Overexpression of FLC from a heterologous promoter is sufficient to delay flowering in the absence of an active FRI allele. We propose that the level of FLC activity acts through a rheostat-like mechanism to control flowering time in Arabidopsis and that modulation of FLC expression is a component of the vernalization response.

Origin, Biogenesis, and Activity of Plant MicroRNAs

2009-02-01

Olivier Voinnet

View PDF Chat

Role of WUSCHEL in Regulating Stem Cell Fate in the Arabidopsis Shoot Meristem

1998-12-01

Klaus Mayer , Heiko Schoof , Achim Haecker +3 more

View PDF Chat

microRNA-Directed Phasing during Trans-Acting siRNA Biogenesis in Plants

2005-04-01

Edwards Allen , Zhixin Xie , Adam M Gustafson +1 more

Regulation of Flowering Time and Floral Organ Identity by a MicroRNA and Its APETALA2-Like Target Genes

2003-10-10

Milo J. Aukerman , Hajime Sakai

MicroRNAs (miRNAs) are approximately 21-nucleotide noncoding RNAs that have been identified in both animals and plants. Although in animals there is direct evidence implicating particular miRNAs in the control of … MicroRNAs (miRNAs) are approximately 21-nucleotide noncoding RNAs that have been identified in both animals and plants. Although in animals there is direct evidence implicating particular miRNAs in the control of developmental timing, to date it is not known whether plant miRNAs also play a role in regulating temporal transitions. Through an activation-tagging approach, we demonstrate that miRNA 172 (miR172) causes early flowering and disrupts the specification of floral organ identity when overexpressed in Arabidopsis. miR172 normally is expressed in a temporal manner, consistent with its proposed role in flowering time control. The regulatory target of miR172 is a subfamily of APETALA2 (AP2) transcription factor genes. We present evidence that miR172 downregulates these target genes by a translational mechanism rather than by RNA cleavage. Gain-of-function and loss-of-function analyses indicate that two of the AP2-like target genes normally act as floral repressors, supporting the notion that miR172 regulates flowering time by downregulating AP2-like target genes.

View PDF Chat

psRNATarget: a plant small RNA target analysis server

2011-05-27

Xinbin Dai , Patrick X. Zhao

Plant endogenous non-coding short small RNAs (20–24 nt), including microRNAs (miRNAs) and a subset of small interfering RNAs (ta-siRNAs), play important role in gene expression regulatory networks (GRNs). For example, … Plant endogenous non-coding short small RNAs (20–24 nt), including microRNAs (miRNAs) and a subset of small interfering RNAs (ta-siRNAs), play important role in gene expression regulatory networks (GRNs). For example, many transcription factors and development-related genes have been reported as targets of these regulatory small RNAs. Although a number of miRNA target prediction algorithms and programs have been developed, most of them were designed for animal miRNAs which are significantly different from plant miRNAs in the target recognition process. These differences demand the development of separate plant miRNA (and ta-siRNA) target analysis tool(s). We present psRNATarget, a plant small RNA target analysis server, which features two important analysis functions: (i) reverse complementary matching between small RNA and target transcript using a proven scoring schema, and (ii) target-site accessibility evaluation by calculating unpaired energy (UPE) required to ‘open’ secondary structure around small RNA’s target site on mRNA. The psRNATarget incorporates recent discoveries in plant miRNA target recognition, e.g. it distinguishes translational and post-transcriptional inhibition, and it reports the number of small RNA/target site pairs that may affect small RNA binding activity to target transcript. The psRNATarget server is designed for high-throughput analysis of next-generation data with an efficient distributed computing back-end pipeline that runs on a Linux cluster. The server front-end integrates three simplified user-friendly interfaces to accept user-submitted or preloaded small RNAs and transcript sequences; and outputs a comprehensive list of small RNA/target pairs along with the online tools for batch downloading, key word searching and results sorting. The psRNATarget server is freely available at http://plantgrn.noble.org/psRNATarget/ .

View PDF Chat

MEME: discovering and analyzing DNA and protein sequence motifs

2006-07-01

Timothy L. Bailey , N. Williams , C. Misleh +1 more

MEME (Multiple EM for Motif Elicitation) is one of the most widely used tools for searching for novel ‘signals’ in sets of biological sequences. Applications include the discovery of new … MEME (Multiple EM for Motif Elicitation) is one of the most widely used tools for searching for novel ‘signals’ in sets of biological sequences. Applications include the discovery of new transcription factor binding sites and protein domains. MEME works by searching for repeated, ungapped sequence patterns that occur in the DNA or protein sequences provided by the user. Users can perform MEME searches via the web server hosted by the National Biomedical Computation Resource ( http://meme.nbcr.net ) and several mirror sites. Through the same web server, users can also access the Motif Alignment and Search Tool to search sequence databases for matches to motifs encoded in several popular formats. By clicking on buttons in the MEME output, users can compare the motifs discovered in their input sequences with databases of known motifs, search sequence databases for matches to the motifs and display the motifs in various formats. This article describes the freely accessible web server and its architecture, and discusses ways to use MEME effectively to find new sequence patterns in biological sequences and analyze their significance.

View PDF Chat

Aux/IAA proteins repress expression of reporter genes containing natural and highly active synthetic auxin response elements.

1997-11-01

Tim Ulmasov , Jane Murfett , Gretchen Hagen +1 more

A highly active synthetic auxin response element (AuxRE), referred to as DR5, was created by performing site-directed mutations in a natural composite AuxRE found in the soybean GH3 promoter. DR5 … A highly active synthetic auxin response element (AuxRE), referred to as DR5, was created by performing site-directed mutations in a natural composite AuxRE found in the soybean GH3 promoter. DR5 consisted of tandem direct repeats of 11 bp that included the auxin-responsive TGTCTC element. The DR5 AuxRE showed greater auxin responsiveness than a natural composite AuxRE and the GH3 promoter when assayed by transient expression in carrot protoplasts or in stably transformed Arabidopsis seedlings, and it provides a useful reporter gene for studying auxin-responsive transcription in wild-type plants and mutants. An auxin response transcription factor, ARF1, bound with specificity to the DR5 AuxRE in vitro and interacted with Aux/IAA proteins in a yeast two-hybrid system. Cotransfection experiments with natural and synthetic AuxRE reporter genes and effector genes encoding Aux/IAA proteins showed that overexpression of Aux/IAA proteins in carrot protoplasts resulted in specific repression of TGTCTC AuxRE reporter gene expression.

View PDF Chat

The PIN auxin efflux facilitator network controls growth and patterning in Arabidopsis roots

2005-01-01

Ikram Blilou , Jian Xu , Marjolein Wildwater +7 more

View PDF Chat

TRANSCRIPTIONAL REGULATORY NETWORKS IN CELLULAR RESPONSES AND TOLERANCE TO DEHYDRATION AND COLD STRESSES

2006-04-07

Kazuko Yamaguchi‐Shinozaki , Kazuo Shinozaki

Plant growth and productivity are greatly affected by environmental stresses such as drought, high salinity, and low temperature. Expression of a variety of genes is induced by these stresses in … Plant growth and productivity are greatly affected by environmental stresses such as drought, high salinity, and low temperature. Expression of a variety of genes is induced by these stresses in various plants. The products of these genes function not only in stress tolerance but also in stress response. In the signal transduction network from perception of stress signals to stress-responsive gene expression, various transcription factors and cis-acting elements in the stress-responsive promoters function for plant adaptation to environmental stresses. Recent progress has been made in analyzing the complex cascades of gene expression in drought and cold stress responses, especially in identifying specificity and cross talk in stress signaling. In this review article, we highlight transcriptional regulation of gene expression in response to drought and cold stresses, with particular emphasis on the role of transcription factors and cis-acting elements in stress-inducible promoters.

MicroRNAs AND THEIR REGULATORY ROLES IN PLANTS

2006-01-31

Matthew W. Jones-Rhoades , David P. Bartel , Bonnie Bartel

MicroRNAs (miRNAs) are small, endogenous RNAs that regulate gene expression in plants and animals. In plants, these approximately 21-nucleotide RNAs are processed from stem-loop regions of long primary transcripts by … MicroRNAs (miRNAs) are small, endogenous RNAs that regulate gene expression in plants and animals. In plants, these approximately 21-nucleotide RNAs are processed from stem-loop regions of long primary transcripts by a Dicer-like enzyme and are loaded into silencing complexes, where they generally direct cleavage of complementary mRNAs. Although plant miRNAs have some conserved functions extending beyond development, the importance of miRNA-directed gene regulation during plant development is now particularly clear. Identified in plants less than four years ago, miRNAs are already known to play numerous crucial roles at each major stage of development-typically at the cores of gene regulatory networks, targeting genes that are themselves regulators, such as those encoding transcription factors and F-box proteins.

Computational Identification of Plant MicroRNAs and Their Targets, Including a Stress-Induced miRNA

2004-06-01

Matthew W. Jones-Rhoades , David P. Bartel

View PDF Chat

Novel and Stress-Regulated MicroRNAs and Other Small RNAs from Arabidopsis[W]

2004-08-01

Ramanjulu Sunkar , Jian‐Kang Zhu

Abstract MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are small noncoding RNAs that have recently emerged as important regulators of mRNA degradation, translational repression, and chromatin modification. In Arabidopsis thaliana, … Abstract MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are small noncoding RNAs that have recently emerged as important regulators of mRNA degradation, translational repression, and chromatin modification. In Arabidopsis thaliana, 43 miRNAs comprising 15 families have been reported thus far. In an attempt to identify novel and abiotic stress regulated miRNAs and siRNAs, we constructed a library of small RNAs from Arabidopsis seedlings exposed to dehydration, salinity, or cold stress or to the plant stress hormone abscisic acid. Sequencing of the library and subsequent analysis revealed 26 new miRNAs from 34 loci, forming 15 new families. Two of the new miRNAs from three loci are members of previously reported miR171 and miR319 families. Some of the miRNAs are preferentially expressed in specific tissues, and several are either upregulated or downregulated by abiotic stresses. Ten of the miRNAs are highly conserved in other plant species. Fifty-one potential targets with diverse function were predicted for the newly identified miRNAs based on sequence complementarity. In addition to miRNAs, we identified 102 other novel endogenous small RNAs in Arabidopsis. These findings suggest that a large number of miRNAs and other small regulatory RNAs are encoded by the Arabidopsis genome and that some of them may play important roles in plant responses to environmental stresses as well as in development and genome maintenance.

View PDF Chat

The Stem Cell Population of Arabidopsis Shoot Meristems Is Maintained by a Regulatory Loop between the CLAVATA and WUSCHEL Genes

2000-03-01

Heiko Schoof , Michael Lenhard , Achim Haecker +3 more

View PDF Chat

Plant hormone-mediated regulation of stress responses

2016-04-14

Vivek Verma , Pratibha Ravindran , Prakash P. Kumar

Being sessile organisms, plants are often exposed to a wide array of abiotic and biotic stresses. Abiotic stress conditions include drought, heat, cold and salinity, whereas biotic stress arises mainly … Being sessile organisms, plants are often exposed to a wide array of abiotic and biotic stresses. Abiotic stress conditions include drought, heat, cold and salinity, whereas biotic stress arises mainly from bacteria, fungi, viruses, nematodes and insects. To adapt to such adverse situations, plants have evolved well-developed mechanisms that help to perceive the stress signal and enable optimal growth response. Phytohormones play critical roles in helping the plants to adapt to adverse environmental conditions. The elaborate hormone signaling networks and their ability to crosstalk make them ideal candidates for mediating defense responses. Recent research findings have helped to clarify the elaborate signaling networks and the sophisticated crosstalk occurring among the different hormone signaling pathways. In this review, we summarize the roles of the major plant hormones in regulating abiotic and biotic stress responses with special focus on the significance of crosstalk between different hormones in generating a sophisticated and efficient stress response. We divided the discussion into the roles of ABA, salicylic acid, jasmonates and ethylene separately at the start of the review. Subsequently, we have discussed the crosstalk among them, followed by crosstalk with growth promoting hormones (gibberellins, auxins and cytokinins). These have been illustrated with examples drawn from selected abiotic and biotic stress responses. The discussion on seed dormancy and germination serves to illustrate the fine balance that can be enforced by the two key hormones ABA and GA in regulating plant responses to environmental signals. The intricate web of crosstalk among the often redundant multitudes of signaling intermediates is just beginning to be understood. Future research employing genome-scale systems biology approaches to solve problems of such magnitude will undoubtedly lead to a better understanding of plant development. Therefore, discovering additional crosstalk mechanisms among various hormones in coordinating growth under stress will be an important theme in the field of abiotic stress research. Such efforts will help to reveal important points of genetic control that can be useful to engineer stress tolerant crops.

View PDF Chat

PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants

2016-10-12

Jinpu Jin , Feng Tian , De-Chang Yang +4 more

With the goal of providing a comprehensive, high-quality resource for both plant transcription factors (TFs) and their regulatory interactions with target genes, we upgraded plant TF database PlantTFDB to version … With the goal of providing a comprehensive, high-quality resource for both plant transcription factors (TFs) and their regulatory interactions with target genes, we upgraded plant TF database PlantTFDB to version 4.0 (http://planttfdb.cbi.pku.edu.cn/). In the new version, we identified 320 370 TFs from 165 species, presenting a more comprehensive genomic TF repertoires of green plants. Besides updating the pre-existing abundant functional and evolutionary annotation for identified TFs, we generated three new types of annotation which provide more directly clues to investigate functional mechanisms underlying: (i) a set of high-quality, non-redundant TF binding motifs derived from experiments; (ii) multiple types of regulatory elements identified from high-throughput sequencing data; (iii) regulatory interactions curated from literature and inferred by combining TF binding motifs and regulatory elements. In addition, we upgraded previous TF prediction server, and set up four novel tools for regulation prediction and functional enrichment analyses. Finally, we set up a novel companion portal PlantRegMap (http://plantregmap.cbi.pku.edu.cn) for users to access the regulation resource and analysis tools conveniently.

View PDF Chat

bZIP transcription factors in Arabidopsis

2002-03-01

Marc Jakoby , Bernd Weißhaar , Wolfgang Dröge‐Laser +4 more

MicroRNAs in plants

2002-07-01

Brenda J. Reinhart , Earl G. Weinstein , Matthew W. Rhoades +2 more

MicroRNAs (miRNAs) are an extensive class of ∼22-nucleotide noncoding RNAs thought to regulate gene expression in metazoans. We find that miRNAs are also present in plants, indicating that this class … MicroRNAs (miRNAs) are an extensive class of ∼22-nucleotide noncoding RNAs thought to regulate gene expression in metazoans. We find that miRNAs are also present in plants, indicating that this class of noncoding RNA arose early in eukaryotic evolution. In this paper 16 Arabidopsis miRNAs are described, many of which have differential expression patterns in development. Eight are absolutely conserved in the rice genome. The plant miRNA loci potentially encode stem–loop precursors similar to those processed by Dicer (a ribonuclease III) in animals. Mutation of an Arabidopsis Dicer homolog, CARPEL FACTORY, prevents the accumulation of miRNAs, showing that similar mechanisms direct miRNA processing in plants and animals. The previously described roles of CARPEL FACTORY in the development of Arabidopsis embryos, leaves, and floral meristems suggest that the miRNAs could play regulatory roles in the development of plants as well as animals.

View PDF Chat

Asperous coordinates regenerative timing by regulating damage-induced WNT Signaling

2025-06-25

Si Cave , Manashi Sonowal , Chloe Van Hazel +2 more

Tissue regeneration requires precise control of signaling pathways to direct proliferation, differentiation, and patterning. While early responses to injury are well characterized, how differentiation is coordinated during later stages remains … Tissue regeneration requires precise control of signaling pathways to direct proliferation, differentiation, and patterning. While early responses to injury are well characterized, how differentiation is coordinated during later stages remains unclear. Here, we identify Asperous (Aspr), an EGF-repeat protein, as a regeneration-specific regulator in Drosophila wing discs. Aspr is dispensable for wing development but is strongly induced within 24 hours post-injury. Maintaining aspr expression inhibits differentiation and alters reparative growth, while loss impairs regeneration. Structural and expression analyses show Aspr is a membrane-associated extracellular protein secreted in extracellular vesicles (EVs), where it co-localizes with the WNT ligand Wingless (Wg). We find Aspr regulates post-injury but not developmental Wg signaling, potentially by influencing its secretion or availability via EVs. These findings suggest Aspr regulates WNT activity to ensure proper timing of cell fate specification during regeneration, revealing a mechanism by which signaling dynamics are temporally controlled during tissue repair.

Root-derived cytokinin regulates Arabidopsis flowering time through components of the age pathway

2025-06-25

Isabel Bartrina , Sören Werner , Andreas Schenke +3 more | PLANT PHYSIOLOGY

Abstract The transition to flowering is governed by different pathways integrating endogenous and exogenous signals. Here, we evaluated the role of the phytohormone cytokinin (CK) in regulating Arabidopsis thaliana flowering … Abstract The transition to flowering is governed by different pathways integrating endogenous and exogenous signals. Here, we evaluated the role of the phytohormone cytokinin (CK) in regulating Arabidopsis thaliana flowering time. By analyzing key mutants in CK metabolism, transport and signalling, we found that the hormone promotes flowering under both long-day (LD) and short-day (SD) conditions, with a stronger impact on flowering under SDs. Genetic analyses indicated that both trans- and cis-zeatin regulate the floral transition, while isopentenyladenine plays a minor role. Blocking CK export from roots and reciprocal grafting experiments revealed that root-derived CK is an important flowering signal. Perception and transmission of the CK flowering signal depended on distinct CK receptors, phosphotransmitter proteins and several B-type response regulators. Further, CK functioned through floral integrators such as OVEREXPRESSION OF CONSTANS1 (SOC1) and components of the age pathway. The CK status of plants affected the levels of the age pathway microRNAs miR156 and miR172. Cytokinin-promoted flowering required the miR156-target SQUAMOSA PROMOTER BINDING PROTEIN-LIKE15 (SPL15) and miR172, and the late-flowering phenotype of LD-grown CK-deficient plants depended on miR172-targeted APETALA2 (AP2)-like genes encoding floral repressors. Collectively, this study shows that CK regulates flowering time through the two-component signaling system and components of the age pathway, providing a genetic framework for future investigations.

Identification of flowering time loci in the C genome affecting flowering under a short-day condition by using an oilseed Brassica napus population carrying genome contents of six B. oleracea

2025-06-24

Karanjot Singh Gill , Juthy Abedin Nupur , Guanqun Chen +3 more | Euphytica

Amyloplast imaging system in Arabidopsis ovule integument

2025-06-24

M Fujiwara , Ryuuichi D. Itoh | CYTOLOGIA

Understanding the changes in endogenous GA3 in relation to developmental transitions in cauliflower (Brassica oleracea var. botrytis L.)

2025-06-24

Sohamkumar Luhana , Shrawan Singh , Shipra Nagar +6 more | PLoS ONE

Cauliflower is a crop with intricate developmental transitions influenced by both external and internal cues. Plant growth regulators (PGRs) play a key role in developmental transitions and plant responses to … Cauliflower is a crop with intricate developmental transitions influenced by both external and internal cues. Plant growth regulators (PGRs) play a key role in developmental transitions and plant responses to environmental factors. The present study aimed to investigate the endogenous levels of gibberellins (GAs) (i) at six different developmental stages and (ii) at four time points in four varieties of cauliflower using high-performance liquid chromatography (HPLC). The Pusa Ashwini, Pusa Sharad, Pusa Shukti, and Pusa Snowball Kt-25 varieties represent all four thermosensory-based maturity groups: early (20–27 °C), mid-early (15–20 °C), mid-late (12–16 °C), and late or snowball (10–16 °C), respectively. GA 3 content was highest in Pusa Shukti (4.020 ppm) and lowest in Pusa Ashwini (3.091 ppm). A higher endogenous GA 3 concentration was recorded at the bolting stage (4.118 ppm), seedling stage (4.057 ppm), and curd initiation stage (3.722 ppm), suggesting its role in stalk elongation. The difference in GA 3 content was significant between curd (3.613 ppm) and leaf tissues (2.947 ppm) at the full curd stage and nonsignificant between stalk (3.948 ppm) and leaf tissues (4.118 ppm) at the bolting stage. Regarding the time points, the GA 3 content was highest in Pusa Sharad (4.311 ppm) and lowest in Pusa Ashwini (2.990 ppm). GA 3 content showed a significant positive correlation with duration to crucial developmental transitions, namely the curd initiation stage, the full curd stage, and the bolting stage. The study highlights the role of endogenous gibberellins in plant development and suggests their potential for benefiting seed production.

Gaining insights into epigenetic memories through artificial intelligence and omics science in plants

2025-06-24

Judit Dobránszki , Valya Vassileva , D. Agius +6 more | Journal of Integrative Plant Biology

ABSTRACT Plants exhibit remarkable abilities to learn, communicate, memorize, and develop stimulus‐dependent decision‐making circuits. Unlike animals, plant memory is uniquely rooted in cellular, molecular, and biochemical networks, lacking specialized organs … ABSTRACT Plants exhibit remarkable abilities to learn, communicate, memorize, and develop stimulus‐dependent decision‐making circuits. Unlike animals, plant memory is uniquely rooted in cellular, molecular, and biochemical networks, lacking specialized organs for these functions. Consequently, plants can effectively learn and respond to diverse challenges, becoming used to recurring signals. Artificial intelligence (AI) and machine learning (ML) represent the new frontiers of biological sciences, offering the potential to predict crop behavior under environmental stresses associated with climate change. Epigenetic mechanisms, serving as the foundational blueprints of plant memory, are crucial in regulating plant adaptation to environmental stimuli. They achieve this adaptation by modulating chromatin structure and accessibility, which contribute to gene expression regulation and allow plants to adapt dynamically to changing environmental conditions. In this review, we describe novel methods and approaches in AI and ML to elucidate how plant memory occurs in response to environmental stimuli and priming mechanisms. Furthermore, we explore innovative strategies exploiting transgenerational memory for plant breeding to develop crops resilient to multiple stresses. In this context, AI and ML can aid in integrating and analyzing epigenetic data of plant stress responses to optimize the training of the parental plants.

Distinct domains of ENHANCER OF PINOID hold information for its polarization required for auxin-mediated cotyledon and flower development in Arabidopsis

2025-06-23

Michaela Matthes , Nicole Yun , Miriam Luichtl +7 more | PLoS Genetics

The Arabidopsis ENHANCER OF PINOID (ENP) protein and the AGC-kinase PINOID (PID) synergistically impact on polarization and function of the auxin transporter PIN-FORMED1 (PIN1) required for plant leaf and flower … The Arabidopsis ENHANCER OF PINOID (ENP) protein and the AGC-kinase PINOID (PID) synergistically impact on polarization and function of the auxin transporter PIN-FORMED1 (PIN1) required for plant leaf and flower organ development. ENP offers a PID-independent input for PIN-function since enp pid double mutants lead to cotyledon- and flower-less plants in contrast to pid single mutants, which develop cotyledons and abnormal albeit fertile flowers. This indicates that ENP, which depicts a similar polar localization as PIN1, is a potential interactor of PINs including PIN1. Here we show that the modular structure of ENP predicted by AlphaFold separates the capability for its own cellular polarization and its function linked to polar PIN1 activity. The part of ENP from aa1 to aa470 is subdivided into three structured domains. They are supportive and/or essential for cellular polarity. In contrast, the C-terminus, which is an intrinsically disordered region (IDR), is completely dispensable for polarity but essential for ENP-mediated PIN1-function. FLIM-FRET shows ENP to be closely associated with the plasma membrane and its IDR to significantly interact with PINs. Moreover, the modification status of two prominent phosphorylation sites in the IDR determines ENPs stability and its capability in supporting PIN1. Our results show ENP to be an element in the assumed PIN-multiprotein complex and explain its impact on PID-independent PIN1 activity.

An Antagonism Between Ethylene Signaling and DNA Methylation Orchestrates the Progression of Leaf Senescence in Non‐heading Chinese Cabbage

2025-06-23

Dingyu Zhang , Yong Luo , Han Wang +7 more | Advanced Science

Leaf senescence significantly impacts both the yield and quality of non-heading Chinese cabbage (NHCC). Despite its importance, the molecular mechanisms underlying the initiation and progression of leaf senescence in NHCC … Leaf senescence significantly impacts both the yield and quality of non-heading Chinese cabbage (NHCC). Despite its importance, the molecular mechanisms underlying the initiation and progression of leaf senescence in NHCC remain poorly understood. Here, transcriptome changes are first profiled, and found that ethylene (ET) and salicylic acid (SA) signaling pathways are activated during leaf senescence. Further mining of ET, SA, and DNA methylation pathway genes identified that EIN3A and CMT2 are induced and repressed, respectively, during leaf senescence. A whole-genome bisulfite sequencing (WGBS) analysis revealed a global reduction of DNA methylation during leaf senescence, with the most dramatic decline occurring in the 1 kb regions upstream of transcription start sites (TSS) and downstream of transcription end sites (TES). Knocking down of EIN3A and CMT2 via virus-induced gene silencing (VIGS) demonstrated that EIN3A is crucial for ET- and age-triggered leaf senescence, while CMT2 plays an inhibitory role. It further showed that EIN3A directly represses the expression of CMT2 to release its "braking" role on senescence-associated genes (SAGs) expression. Thus, the study uncovers a pivotal antagonistic interaction between ET signaling and DNA methylation, which may be involved in setting the pace for the progression of leaf senescence in NHCC.

Engineering saline-alkali-tolerant apple rootstock by knocking down MdGH3 genes in M9-T337

2025-06-23

Fang Zhi , Tianle Fan , Li Jia +7 more | Stress Biology

Soil salinization and alkalization have become an increasingly severe global issues, significantly limiting both the yield and quality of apples (Malus × domestica). M9-T337 is a widely used apple dwarfing … Soil salinization and alkalization have become an increasingly severe global issues, significantly limiting both the yield and quality of apples (Malus × domestica). M9-T337 is a widely used apple dwarfing rootstock; however, it is sensitive to saline-alkali stress. Therefore, developing saline-alkali tolerant apple rootstocks is essential. In this study, we utilized RNAi (RNA interference) technology to knock down GH3 genes in the M9-T337 background, aiming to engineer a dwarfing and stress-tolerant apple rootstock. We found that MdGH3 RNAi plants exhibited superior morphology compared to M9-T337 under saline-alkali stress conditions, characterized by more robust root systems, increased plant height, a lower Na+/K+ ratio, and enhanced photosynthetic and antioxidant capacities. Moreover, when MdGH3 RNAi plants were used as rootstocks, the GL-3/MdGH3 RNAi plants also displayed greater plant height, root vitality, photosynthetic ability, and antioxidant capacity compared to GL-3 grafted onto M9-T337 rootstock. Taken together, our study constructed a saline-alkali-tolerant apple rootstock by knocking down MdGH3 genes.

Arabidopsis RabGDIs are essential for the asymmetric division of zygotes and embryonic patterning

2025-06-23

Guimin Yin , Yanan Wu , Weiqi Wang +6 more | bioRxiv (Cold Spring Harbor Laboratory)

An asymmetric division of zygotes sets up the apical-basal body axis and starts the life cycle of angiosperms. In addition to specific expression of transcription factors and polar distribution of … An asymmetric division of zygotes sets up the apical-basal body axis and starts the life cycle of angiosperms. In addition to specific expression of transcription factors and polar distribution of auxin, vesicular trafficking-mediated endomembrane dynamics are critical for zygotic division and embryonic patterning. As key regulators of vesicular trafficking, whether Rab GTPases play a role in these processes is unclear. We report that Arabidopsis guanine nucleotide dissociation inhibitors for Rab (RabGDIs) are essential for the asymmetric division of zygotes and embryonic patterning likely through regulating the dynamic targeting of canonical Rab GTPases, especially Rab5. Arabidopsis RabGDIs specifically interact with canonical Rab GTPases. Functional loss of Arabidopsis RabGDI1 and RabGDI2 compromises the asymmetry of zygotic division, cell fate determination, and embryonic patterning. Polar distribution of vacuolar dynamics was disrupted in zygotes and 1-cell embryo of gdi1 gdi2, suggesting a key role of RabGDIs in vacuolar dynamics. Furthermore, genetic interference of canonical Rab5, a key regulator of vacuolar trafficking and biogenesis, in zygotes leads to similar defects, consistent with the disturbed localization of Rab5 in gdi1 gdi2 embryos. Results presented demonstrate the key role of RabGDIs through Rab GTPases in asymmetric division of zygotes and embryonic patterning.

Cold Stress Memory Genes in Cucumber are Widely Regulated by “Hit-and-Run” Model

2025-06-23

Qinghua Di , Lu Liu , Yan Yan +6 more | Journal of Plant Growth Regulation

Zinc Finger-Homeodomain Transcription Factor: A New Player in Plant Growth, Stress Response, and Quality Regulation

2025-06-23

Aizong Shen , Meili Lv , Y.J. Ge +5 more | Agronomy

Zinc finger-homeodomain (ZF-HD) transcription factors are a unique class that only exist in plants and are essential for plant growth and development, various stress responses, and quality formation and regulation. … Zinc finger-homeodomain (ZF-HD) transcription factors are a unique class that only exist in plants and are essential for plant growth and development, various stress responses, and quality formation and regulation. In recent years, an increasing number of reports regarding this class of transcription factors have been published, identifying their novel functions. In this paper, the evolution, structural characteristics, and subfamily classification of ZF-HD transcription factors are comprehensively introduced and the roles of the ZF-HD in abiotic and biotic stress responses, plant hormone signal transduction, and quality regulation are extensively investigated. In future studies, more efforts should be focused on the in-depth exploration of the mechanisms through which the ZF-HD could act at various stages of plant growth and development. We also determine the current research status and future directions related to the ZF-HD, with the aim of providing a comprehensive knowledge base and research insights for the further exploration of ZF-HD transcription factors in plant molecular biology.

Molecular Bonsai: Elucidating the design principles for engineering plant organ size

2025-06-22

Tawni Bull , James B. Blair , Shirley Sutton +2 more | bioRxiv (Cold Spring Harbor Laboratory)

Enhancements to crop morphology, such as the semi-dwarfing that helped drive the green revolution, are often driven by changes in gene dosage. These changes are challenging to translate across varieties … Enhancements to crop morphology, such as the semi-dwarfing that helped drive the green revolution, are often driven by changes in gene dosage. These changes are challenging to translate across varieties and species, which slows the pace of crop improvement. Synthetic transcription factors (SynTFs) offer a rapid alternative to generate targeted alterations to gene dosage. However, the complexity of developmental pathways makes it unclear how to best apply them to predictably engineer morphology. In this work, we explore if mathematical modeling can guide SynTF-based expression modulation of genes in the signaling pathway of the phytohormone, gibberellin (GA), which is a central regulator of cell expansion, to elucidate the design principles for engineering organ size. We demonstrate that modulation of GA signaling gene expression can generate consistent dwarfing across tissues in both controlled and variable environments in the model plant Arabidopsis thaliana, and that the degree of dwarfing is dependent on the strength of regulation as predicted by modeling. We further validate the predictive power of the model by demonstrating its capacity to accurately predict the qualitative impacts of different regulatory architectures for both increasing and decreasing organ size. Finally, we show that these insights can be generalized for engineering organ size in the crop Solanum lycopersicum (tomato). This work creates a framework for predictable engineering of an agriculturally important trait, organ size, across tissues and plant species. It also serves as a proof-of-concept for how mathematical models can guide SynTF-based alterations in gene dosage to enable bottom-up design of plant phenotypes.

F‐Actin Polarization and Microtubule Integrity Direct Regeneration Patterns and Polarity of Cell Outgrowth in Wound‐Induced Reprogramming

2025-06-22

Yi‐Ting Huang , Y. C. James Yen , Joop E. M. Vermeer +2 more | Plant Cell & Environment

ABSTRACT Plants have developed a high regenerative capacity to repair damaged tissues and regenerate new organs in response to injury. When wounded, cells detect mechanical forces through their cytoskeletons and … ABSTRACT Plants have developed a high regenerative capacity to repair damaged tissues and regenerate new organs in response to injury. When wounded, cells detect mechanical forces through their cytoskeletons and transmit molecular signals to the nucleus, triggering cell reprogramming. As mechanosensing and cell reprogramming have been studied separately, the connection between these processes and the role of cytoskeletal networks in regeneration is still unclear. This study used Physcomitrium patens to investigate the spatiotemporal dynamics of actin filaments and microtubules during wound‐induced cell reprogramming. Upon laser‐induced wounding, we observed a rapid and localized accumulation of F‐actin at the plasma membrane of the neighboring cells next to the wounding site, whereas microtubules showed no immediate discernible changes. Disruption of F‐actin severely impaired overall regeneration, leading to significant reductions in the reprogramming rate. Perturbations of microtubules primarily impacted regenerative cell divisions. Depolymerization of cytoskeletal networks altered regeneration patterns, reflected in the higher ratio of cell outgrowth to division and the outgrowth polarity. These findings underscore the functional role of the cytoskeleton in regulating cell reprogramming. This study reveals that early cytoskeletal polarization after wounding guides the polarity of cell outgrowth, providing new insights into how plants regenerate from mechanical damage.

Targeted Editing of the miR529/miR156-IPA1 Regulatory Module via the CRISPR/Cas9 System for Developing Ideal Plant Architecture Traits in Rice

2025-06-21

A. Shanthinie , S. Varanavasiappan , K. K. Kumar +5 more | Plant Molecular Biology Reporter

DEAD-box protein SMA1 activates immunity likely through the formation of nuclear condensates with EDS1 in Arabidopsis

2025-06-21

Xudong Li , Chengming Liu , Jinge Du +7 more | Cell Reports

Co-transcriptional splicing changes combine with reduced productive transcription initiation for cold-induced repression of FLC

2025-06-21

Robert Maple , Govind Menon , Susan Duncan +5 more | bioRxiv (Cold Spring Harbor Laboratory)

The Arabidopsis floral repressor locus FLC is epigenetically silenced during winter cold to align flowering with spring. During weeks of cold exposure, FLC transcription is progressively reduced both by transcriptional … The Arabidopsis floral repressor locus FLC is epigenetically silenced during winter cold to align flowering with spring. During weeks of cold exposure, FLC transcription is progressively reduced both by transcriptional repression mediated by FLC antisense transcription, and epigenetic silencing implemented through a Polycomb-mediated epigenetic switch. In the warm, FLC is transcriptionally repressed by coordinated changes in transcription initiation and RNA PolII speed in a mechanism involving proximal termination. Whether similar mechanisms contribute to the cold-induced FLC transcriptional repression is unknown. Here, we combine mathematical modelling and transcription profiling to investigate FLC transcriptional changes during the cold. We find different dynamics of spliced and unspliced transcripts during cold exposure with only a small change in PolII speed. We also show that, unlike short-term cold, long-term cold temperatures drive an increase in splicing rates while simultaneously reducing productive transcription at FLC. This process is influenced by antisense COOLAIR transcription but does not rely on proximal COOLAIR termination. Cold-induced transcriptional repression of FLC thus involves a decoupling of changes in productive transcription initiation from PolII speed and rates of co-transcriptional splicing, a different mechanism to that repressing FLC in the warm.

Overexpression of SEPALLATA3-like Gene SnMADS37 Generates Green Petal-Tip Flowers in Solanum nigrum

2025-06-20

Siming Yuan , Chunlan Piao , Xinyu Zhang +1 more | Plants

The SEPALLATA3 (SEP3)-like MADS-box genes play crucial roles in determining petal identity and development in the petunia and tomato of Solanaceae. Solanum nigrum is a self-pollinating plant in the Solanaceae … The SEPALLATA3 (SEP3)-like MADS-box genes play crucial roles in determining petal identity and development in the petunia and tomato of Solanaceae. Solanum nigrum is a self-pollinating plant in the Solanaceae family, and produces white flowers. However, the mechanisms controlling the transition from green to white petals during flower development remain poorly understood. In this study, we isolated a flower-specific SEP3-like gene, SnMADS37, from S. nigrum, and investigated its potential role in chlorophyll metabolism during petal development. Our results show that quantitative RT-PCR analysis demonstrates that SnMADS37 is exclusively expressed in petals and stamens during early floral bud development. Overexpression of SnMADS37 clearly enhanced the number of petals, promoting the formation of additional petal-like tissues in stamens and extra organs in some fruits. Moreover, fully opened transformed petals exhibited notable chlorophyll accumulation at their tips and veins, whereas silencing of Snmads37 clearly inhibited petal expansion and reduced green pigmentation in early flower buds. Additionally, the transformed green petals exhibited distinct conical epidermal cells in the green regions, similar to wild type (WT) petals. Our results demonstrate that SnMADS37 plays a critical role in regulating petal identity, expansion, and chlorophyll metabolism during petal development. These findings provide new insights into the functional diversification of SEP3-like MADS-box genes in angiosperms.

Advances in ERECTA Family Regulation of Female Gametophyte Development in Arabidopsis thaliana

2025-06-20

Han Su , Xiaohu Jiang , Yanfen Liu +5 more | Plants

The female gametophyte is central to the reproductive success of flowering plants, with its development being tightly controlled by an intricate network of genes and signaling pathways. A deeper understanding … The female gametophyte is central to the reproductive success of flowering plants, with its development being tightly controlled by an intricate network of genes and signaling pathways. A deeper understanding of these regulatory mechanisms is essential for uncovering the complexities of plant growth and development. Recent studies have shed light on various aspects of female gametophyte development, highlighting the role of specific gene and signaling networks. Among these, the ERECTA family of leucine-rich repeat receptor-like kinase (RLK) in Arabidopsis thaliana has emerged as a key player, influencing multiple biological processes, particularly those governing reproductive development of the female gametophyte. This review focuses on the significant progress made in understanding the ERECTA family’s involvement in germline cell development, emphasizing its functional roles and signaling mechanisms in female gametophyte development.

<scp>BZR2</scp>‐<scp>GRF5</scp> acts as a hub module in regulating in vitro regeneration through brassinosteroid–auxin crosstalk in hybrid sweetgum

2025-06-20

Ying Li , Wenhao Ma , P Wang +7 more | New Phytologist

Summary In vitro plant regeneration is critical for germplasm multiplication, conservation, and genetic improvement in woody plants, primarily via two pathways: somatic embryogenesis (SE) and organogenesis. Brassinosteroids (BR) and auxin … Summary In vitro plant regeneration is critical for germplasm multiplication, conservation, and genetic improvement in woody plants, primarily via two pathways: somatic embryogenesis (SE) and organogenesis. Brassinosteroids (BR) and auxin are key hormones regulating plant regeneration. However, the synergistic mechanism between these hormones in hybrid sweetgum remains poorly understood. We demonstrated that LsfBZR1/2 in the BR signaling pathway interacts with LsfGRF2/3/5. Functional characterization revealed that overexpression of either LsfBZR2 or LsfGRF5 significantly promoted callus proliferation while suppressing somatic embryo formation during SE, and enhanced shoot regeneration efficiency in organogenesis. LsfBZR2‐LsfGRF5 module was found to differentially regulate the auxin efflux gene LsfWAG2 in a tissue‐specific manner. During SE, LsfBZR2 overexpression suppresses LsfWAG2 expression, leading to auxin accumulation that promotes embryogenic callus (EC) proliferation. Conversely, in the organogenesis pathway, LsfBZR2 overexpression enhanced LsfWAG2 expression, which reduced auxin levels and consequently accelerated shoot regeneration. This study represents the first identification of the LsfBZR2‐LsfGRF5 module as a central regulator with dual functions in different tissues of hybrid sweetgum. Through the crosstalk between BR and auxin, this module influences both SE and organogenesis. Our study provides evidence supporting the elucidation of the molecular mechanism of in vitro regeneration in hybrid sweetgum, which is of great significance for breeding and large‐scale production.

Homeodomain leucine zipper protein controls the lobed leaf formation by modulating auxin distribution in watermelon

2025-06-20

Yimei Zhou , Chen Chuchu , Shu-Xu Yi +5 more | Theoretical and Applied Genetics

Multifaceted roles of FD gene family in flowering, plant architecture, and adaptation

2025-06-20

Hui Yang , Meiling Zhong , Yucheng Liu +5 more | Frontiers in Plant Science

FD gene family encodes transcription factors with a basic region/leucine zipper (bZIP) domain that play an essential role in floral transition regulation, which is vital for plants’ reproduction. Recent studies … FD gene family encodes transcription factors with a basic region/leucine zipper (bZIP) domain that play an essential role in floral transition regulation, which is vital for plants’ reproduction. Recent studies have uncovered additional functions for FD gene family in plant development, hormone signaling, and response to environmental cues. These pleiotropic roles make them promising targets for modern crops’ breeding. Here, we systematically review the diverse functions and regulation mechanisms of FD gene family in model plants and several crops, to provide important insights into their roles. By summarizing the current understanding of their molecular mechanisms, we aim to highlight their potential as key targets for improving crop yield, stress tolerance, and adaptation to changing climates. Furthermore, we propose future research directions, these efforts will pave the way for the effective utilization of them in modern crop breeding programs.

Small signaling peptides define leaf longevity

2025-06-20

Liping Qiu , Rong Lu , Zhiyuan Zhang +4 more | Frontiers in Plant Science

NAC Transcription Factor LpNAC22 Positively Regulates Drought Tolerance in Perennial Ryegrass

2025-06-19

Zhiquan Qiang , Zhen Zeng , Dengke Ma +3 more | Plant Cell & Environment

ABSTRACT Drought serves as a major environmental stress that restricts both the yield and quality of perennial ryegrass. Therefore, it is important to identify the essential genes that determine drought … ABSTRACT Drought serves as a major environmental stress that restricts both the yield and quality of perennial ryegrass. Therefore, it is important to identify the essential genes that determine drought tolerance in perennial ryegrasses. In this paper, we isolated a drought‐induced NAC transcription factor LpNAC22 . Transcriptional activity assays in yeast and plant cells indicated that LpNAC22 has transcriptional activation function. Subcellular localization observations revealed that LpNAC22 localized in the nucleus, compatible with its function as a transcription factor. LpNAC22 overexpression plants had enhanced drought tolerance and reduced cell membrane damage, whereas the knockdown of LpNAC22 in perennial ryegrass reduced plant drought tolerance and led to aggravated cell membrane damage. Late embryogenesis abundant (LEA), well‐known stress resistance proteins, can protect the cell membrane from damage during drought conditions. DNA affinity purification sequencing and transcriptional regulation analysis demonstrated that LpNAC22 upregulates two LEA family genes, LpLEA1 and LpLEA2‐1 , by directly binding to their promoters. Furthermore, we demonstrated that overexpression of LpLEA1 and LpLEA2‐1 in Arabidopsis enhanced drought tolerance and reduced cell membrane damage under drought conditions. Our findings provide evidence that LpNAC22 improves drought resistance by modulating the transcription of LEA family genes in perennial ryegrass.

Key Genes BpMYB80 and BpMYB59 Play Important Roles in Regulating Floral Development in Birch Male Flower Mutants

2025-06-19

Zhongjia Yuan , Yang Liu , Xinyan Gao +6 more | Plant Physiology and Biochemistry

Novel plant cell suspension platforms for saffron apocarotenoid production and its impact on carotenoid and volatile profiles

2025-06-19

María Lobato-Gómez , Markus Laurel , Marta Vázquez‐Vilar +4 more | Plant Biotechnology Journal

Summary Saffron apocarotenoids, including crocins, picrocrocin and safranal, are valuable metabolites with pharmaceutical and cosmetic potential. However, their natural plant sources are difficult to cultivate, which limits large‐scale production. The … Summary Saffron apocarotenoids, including crocins, picrocrocin and safranal, are valuable metabolites with pharmaceutical and cosmetic potential. However, their natural plant sources are difficult to cultivate, which limits large‐scale production. The identification of carotenoid cleavage dioxygenases (CCDs), which catalyse the first and most critical step in their biosynthesis, has enabled the production of these apocarotenoids in heterologous plant systems. In this study, we aimed to generate plant cell suspensions expressing Crocus sativus CCD2 and Gardenia jasminoides CCD4a , along with a bacterial phytoene synthase to enhance carotenoid biosynthesis and CsUGT93P1 , which improves crocin stability. Transgenic cell suspensions were established from Nicotiana benthamiana plants and Nicotiana tabacum cv. BY‐2 cells. In BY‐2 cells expressing GjCCD4a , crocin accumulation reached 770 μg/g DW, which further increased upon methyl jasmonate elicitation. Remarkably, the BY‐2 transgenic cells exhibited an 18,000‐fold increase in β‐cyclocitral content compared to wild‐type cells. The best‐performing N. benthamiana and BY‐2 lines were successfully cultivated in wave bioreactors, demonstrating their potential for saffron apocarotenoid production. In the BY‐2 bioreactor, apart from saffron apocarotenoids, phytoene and notably high amounts of lycopene were produced, adding value to the platform and indicating a remodelling of the carotenoid pathway. This study establishes the viability and lays the foundation for the scalable production of saffron apocarotenoids and carotenoids in plant cell suspensions.

Alternative Splicing of Functional Genes in Plant Growth, Development, and Stress Responses

2025-06-19

Guan Liu , Hanhui Wang , Huan Gao +5 more | International Journal of Molecular Sciences

In plants, alternative splicing (AS) is a crucial post-transcriptional regulatory mechanism that generates diverse mature transcripts from precursor mRNA, with the resulting functional proteins regulating a wide range of plant … In plants, alternative splicing (AS) is a crucial post-transcriptional regulatory mechanism that generates diverse mature transcripts from precursor mRNA, with the resulting functional proteins regulating a wide range of plant life activities. The regulation of AS is intricate and complex, playing pivotal roles in controlling plant biological processes like seed germination, flowering time control, growth, and development, as well as responses to abiotic and biotic stresses. The regulation of AS is a multilayered and intricately coordinated network system, primarily involving two core components: cis-regulatory elements and trans-acting factors on pre-mRNA. The precise execution of AS relies on the splicing factors by recognizing cis-elements to modulate splice site selection. Regulated by their own sequence variation, environmental cues, and identification of different spliceosomes, functional genes enable AS to achieve precise spatiotemporal regulation, thereby allowing plants to dynamically respond to developmental signals and environmental challenges. Here, we provide a comprehensive overview of AS patterns, functional genes, and splicing factors undergoing AS and its regulatory mechanisms during different processes, highlighting how AS-mediated gene regulation contributes to plant development and stress response, and offering potential strategies for improving plant adaptation by manipulation of AS-regulated genes.

Genome-wide identification and expression analysis of RWP-RK genes in Pyropia haitanensis reveals their roles in gametogenesis

2025-06-19

Hongchang Ding , Huiping Ma , Long-Chen Tang +1 more | Journal of Applied Phycology

ELD1 mediates photoperiodic flowering via OsCCA1 alternative splicing and interacts with phytochrome signaling in rice

2025-06-19

Liang Cai , Benyuan Hao , Zhuang Xu +7 more | Nature Communications

Molecular mechanisms underlying the early steps of floral initiation in seasonal flowering genotypes of cultivated strawberry

2025-06-19

Freya Maria Rosemarie Ziegler , Amélia Gaston , Karine Guy +7 more | Frontiers in Plant Science

Floral initiation is essential for sexual reproduction in angiosperms and plays a critical role in determining crop yields. In cultivated strawberry, however, the molecular mechanisms underlying floral initiation remain poorly … Floral initiation is essential for sexual reproduction in angiosperms and plays a critical role in determining crop yields. In cultivated strawberry, however, the molecular mechanisms underlying floral initiation remain poorly understood, with most studies focusing on a single genotype under controlled conditions. To gain more insight into this process, we conducted a field-based study in two countries using two seasonal flowering cultivars. Our investigation focused on the early stages of floral initiation, analyzing samples that captured key developmental stages of the shoot apical meristem. Differential gene expression analysis of leaf and terminal bud tissues revealed an enrichment of genes involved in carbohydrate metabolism and phytohormone signaling pathways in leaves. Additionally, we observed enrichment of protein classes related to cytoskeleton organization, cell cycle regulation, and chromatin structure during early floral initiation. We also identified genes associated with the photoperiodic pathway, including well-known floral integrators such as TFL1 and SOC1 , along with several other genes linked to phytohormone regulation, such as XTH23 , PP2 and EIN3 .

Genome-wide identification, transcriptional profiling, and miRNA-binding site analysis of the LBD gene family in the camphor tree

2025-06-19

Jiaqi Zhang , Lian Shan , Haoran Qi +3 more | Frontiers in Plant Science

Cinnamomum camphora (Lauraceae), an evergreen arborescent species endemic to East Asian ecosystems, is ecologically and economically prized for three cardinal attributes: decay-resistant xylem, aesthetic canopy architecture, and pharmacologically active terpenoid … Cinnamomum camphora (Lauraceae), an evergreen arborescent species endemic to East Asian ecosystems, is ecologically and economically prized for three cardinal attributes: decay-resistant xylem, aesthetic canopy architecture, and pharmacologically active terpenoid emissions. The plant-specific Lateral Organ Boundaries Domain (LBD) transcription factors mediate phylogenetically conserved developmental pathways governing lateral organogenesis and secondary metabolism across embryophytes. Despite multiple published C. camphora genome assemblies, functional characterization of LBD transcription factors in this species remains limited. We systematically identified 40 LBD genes through whole-genome analysis and characterized their structural features, evolutionary relationships, and expression patterns. Five are intron-free, while seven genes harbor two or more introns each. Detailed annotation of CcLBD promoter regions identified 33 cis-regulatory elements linked to hormone signaling and stress adaptation. Transcriptional dynamics of the 40 CcLBD genes were profiled across seven tissues of the camphor tree using short-read RNA-Seq, revealing that 22 genes were highly expressed in flowers and 12 were predominantly expressed in roots, suggesting potential roles in reproductive organ development and root formation in C. camphora . Phylogenetic analysis classified all CcLBD proteins into two clades, each harboring a conserved lateral organ boundaries (LOB) domain. Integrative omics analyses (small RNA-seq and degradome data) further implicated miR408 and miR2950c in post-transcriptional regulation of CcLBD5 via mRNA cleavage. These results establish a framework for the functional dissection of LBD-mediated developmental and stress-response pathways in C. camphora .

Mechanisms driving functional divergence of transcription factor paralogs

2025-06-19

I. J. Higgins , Sarah G. Choudury , Aman Y. Husbands | New Phytologist

Summary Transcription factors (TFs) are core components of the regulatory toolkits that control gene expression. The sophistication of these regulatory toolkits dramatically increased during Eukaryotic evolution, accomplished in part by … Summary Transcription factors (TFs) are core components of the regulatory toolkits that control gene expression. The sophistication of these regulatory toolkits dramatically increased during Eukaryotic evolution, accomplished in part by the duplication of existing TFs and the subsequent repurposing of these new paralogs. This process, termed functional divergence, drove the evolution of increasingly elaborate programs of gene expression and, in turn, cellular and organismal complexity. Mechanisms generating functional divergence of TF paralogs are thus of significant interest. Here, we review the numerous mechanisms that can lead to divergence of TF paralogs, drawing on studies from across Eukaryota but with a special emphasis on the plant kingdom. We end by placing these mechanisms back into a broader evolutionary context.

Molecular tipping points in plant cell surface H+ homeostasis and signaling

2025-06-18

Kaltra Xhelilaj , Anja T. Fuglsang , Julien Gronnier +1 more | Quantitative Plant Biology

Nitrate enhances salt tolerance of wild jujube by regulating nutrient homeostasis and nitrate transporters

2025-06-18

Ayimaiti Abudoukayoumu , Yunfei Li , Yue Sun +3 more | Plant Stress

Escaping endogenous miRNA post-transcriptional silencing of JrGRF4b enhanced transformation efficiency in woody plants

2025-06-18

Baoxin Li , Mengting Pan , Dezheng Wu +2 more | Frontiers in Plant Science

The stable expression of transgenes was critically influenced by post-transcriptional regulatory mechanisms in transgenic plants. In this study, we investigated the influence of endogenous miRNA-mediated silencing on heterologous gene expression … The stable expression of transgenes was critically influenced by post-transcriptional regulatory mechanisms in transgenic plants. In this study, we investigated the influence of endogenous miRNA-mediated silencing on heterologous gene expression by introducing walnut ( Juglans regia L.)-derived Growth-Regulating Factors 4 ( JrGRF4b ), disrupting miR396-mediated silencing of replace- JrGRF4b ( rJrGRF4b ), and Jr-miR396a into birch ( Betula platyphylla Suk.). While JrGRF4b overexpression showed no significant improvement in transformation efficiency due to Bp-miR396 -mediated suppression, transgenic lines expressing rJrGRF4b exhibited a 2.53% increase in transformation efficiency, along with significantly enhanced callus diameter, adventitious bud height, root elongation, cellular expansion, and shoot primordia proliferation compared to control ( **p &lt;0.01). In contrast, Jr-miR396a -overexpressing plants displayed growth inhibition through suppression of endogenous BpGRFs . The results showed that escaping endogenous miRNA regulation by targeted site modification of rJrGRF4b significantly improved transgene performance in woody plants. Thus, comprehensive evaluation of post-transcriptional epigenetic regulation between transgenes and endogenous miRNAs in recipient plants was demonstrated to be important, and targeted escape from such miRNA-mediated suppression was shown to ensure stable and high-efficiency transgene expression.

A xyloglucan endotransglucosylase/hydrolase gene, IbXTH16, increases cold tolerance in transgenic sweetpotato

2025-06-18

Tao Yu , Jiaquan Pan , Sitong Liu +2 more | Frontiers in Genetics

Introduction Low temperature is a key environmental factor that threaten sweetpotato growth and development. In-depth studies on the gene functions underlying cold resistance are important for genetic engineering in sweetpotato. … Introduction Low temperature is a key environmental factor that threaten sweetpotato growth and development. In-depth studies on the gene functions underlying cold resistance are important for genetic engineering in sweetpotato. Methods The IbXTH16 gene was cloned using a homologous cloning approach. Its expression was detected in sweetpotato leaves subjected to low-temperature stress and brassinosteroid treatment. Subsequently, the IbXTH16 gene was introduced into sweetpotato variety Lizixiang to generate IbXTH16 -overexpressing plants, thereby enabling the functional validation of the IbXTH16 . Results and discussion The IbXTH16 gene was cloned from the cold-tolerant variety LHS21. Its 879 bp coding sequence encoded a 292 aa protein with a molecular weight of 32.983 kDa and a pI of 8.47. The 2039 bp genomic sequence of IbXTH16 contained two exons and one intron. The IbXTH16 protein was localized in the cell membrane. IbXTH16 was strongly induced by 4°C and brassinosteroid. IbXTH16 positively regulates cold tolerance of sweetpotato by activating the BR and proline pathways.

A chaperonin <scp>BnaC01</scp>.<scp>CCT8</scp> contributes to silique length and seed weight by affecting auxin and jasmonic acid signalling in Brassica napus

2025-06-18

Zhaoyang Qu , Ze Tian , Liqing Wei +7 more | Plant Biotechnology Journal

Summary Seed weight (SW), which is directly influenced by silique length (SL), is a critical agronomic trait significantly affecting both the quality and yield of rapeseed. In this study, a … Summary Seed weight (SW), which is directly influenced by silique length (SL), is a critical agronomic trait significantly affecting both the quality and yield of rapeseed. In this study, a shorter silique length ( ssl ) mutant was generated through ethyl methane sulfonate mutagenesis, exhibiting reduced SL and SW compared to the wild type. Utilizing a map‐based cloning approach, BnaC01.CCT8 , a member of the chaperonin containing T‐complex polypeptide‐1 (CCT) family, was identified as the gene responsible for restoring the ssl phenotype. A missense mutation from alanine to valine (A507V) in BnaC01.CCT8 was identified as crucial for its functional activity, as evidenced by the genetic complementation of BnaC01.CCT8 and BnaC01.CCT8 A507V in the Arabidopsis cct8‐2 background. Moreover, overexpression of BnaC01.CCT8 in Brassica napus significantly enhanced SL, SW and seed yield per plant. Conversely, CRISPR/Cas9‐mediated bnac01.cct8 knockout lines exhibited reduced SL and SW. Transcriptome analysis and hormone content detection indicated that BnaC01.CCT8 positively regulated SL and SW primarily by modulating auxin and jasmonic acid signalling, thereby affecting the length of epidermal cells in the silique wall. Furthermore, BnaC01.CCT8 interacted with BnaA09.ARF18 (AUXIN‐RESPONSE FACTOR 18), contributing to the regulation of SL and SW, while the A507V mutation disrupted this interaction. Haplotype analysis demonstrated that several SNP differences in BnaC01.CCT8 were significantly associated with variations in SL and SW among germplasm resources, revealing superior alleles of BnaC01.CCT8 . The identification and functional analysis of BnaC01.CCT8 provide new insights into the mechanisms regulating SL and SW and present a valuable target for the genetic enhancement of rapeseed yield.

Cotyledon opening during seedling deetiolation is determined by ABA-mediated splicing regulation

2025-06-18

Guiomar Martín , Ana Confraria , Isain Zapata +3 more | EMBO Reports

Abstract During seedling deetiolation, plants adjust their development to expose photosynthetic tissues to sunlight, enabling the transition from heterotrophic to autotrophic growth. While various plant hormones are known to influence … Abstract During seedling deetiolation, plants adjust their development to expose photosynthetic tissues to sunlight, enabling the transition from heterotrophic to autotrophic growth. While various plant hormones are known to influence this process, the role of abscisic acid (ABA) remains unclear. Here, we reveal that ABA plays a major role in controlling the dynamics of cotyledon aperture during seedling deetiolation. In the dark, ABA accumulates in the cotyledons to effectively repress their opening. However, light exposure reverses this effect, allowing the cotyledons to open. Our findings indicate that ABA-mediated regulation of cotyledon dynamics is accompanied by genome-wide rearrangements in both transcriptional and splicing patterns. We demonstrate that ABA-dependent adjustments of cotyledon and splicing dynamics in response to light depend on the positive role of two splicing factors, RS40 and RS41. Moreover, we identify transcriptional and posttranscriptional mechanisms that control the activity of these proteins. Altogether, this work sheds light on the interplay between light and ABA, highlighting cotyledon opening as a new developmental outcome, and identifying alternative splicing as the underlying layer of gene regulation.

Brassinosteroids: Biosynthesis, Signaling, and Hormonal Crosstalk as Related to Fruit Yield and Quality

2025-06-18

Divya Aryal , Fernando Alférez | Plants

Brassinosteroids (BRs) are plant growth regulators (PGRs) with pleiotropic effects on plant growth and development. They play a role in seed germination, vegetative and reproductive growth, photosynthetic efficiency, vascular differentiation, … Brassinosteroids (BRs) are plant growth regulators (PGRs) with pleiotropic effects on plant growth and development. They play a role in seed germination, vegetative and reproductive growth, photosynthetic efficiency, vascular differentiation, fruit yield, quality, and resilience to biotic and abiotic stresses. They engage in crosstalk with other hormones like auxin, gibberellins, ethylene and abscisic acid, influencing all plant growth and development aspects. Studies on the effect of BRs on the reproductive growth of fruit crops are accumulating, given the potential of this PGR as a management tool in agriculture. This review explores the multifaceted roles of BRs in fruit crop maturation. From their biosynthesis and signal transduction pathways to their influence on fruit production, development, and maturation, we focus on the effect of this plant hormone on different aspects of fruit yield and quality, including fruit set and firmness, sugar accumulation, and fruit development. We address BRs' interaction with different hormones at molecular and physiological levels in regulating these processes in climacteric and non-climacteric fruits. We also identify areas where knowledge is still lacking regarding hormonal crosstalk involving BRs in the regulation of developmental processes governing fruit quality and yield so knowledge generated can inform management decisions in fruit crop production.

lncRNA-mRNA-miRNA Networks in Arabidopsis thaliana Exposed to Micro-Nanoplastics

2025-06-18

Roberta Galbo , Domenico Giosa , Gaetano M. Gargiulo +7 more | International Journal of Plant Biology

Long non-coding RNAs (lncRNAs) are key regulators of genetic networks in numerous biological processes. Micro-nanoplastics represent a novel abiotic stress, having a direct xenobiotic impact on plant cells, while the … Long non-coding RNAs (lncRNAs) are key regulators of genetic networks in numerous biological processes. Micro-nanoplastics represent a novel abiotic stress, having a direct xenobiotic impact on plant cells, while the regulation of lncRNAs in Arabidopsis thaliana under this kind of abiotic stress remains largely unclear. We explored RNA-seq data sets of A. thaliana roots treated with two types of micro-nanoplastics: transparent polyethylene terephthalate (Tr-PET) and blue polyethylene terephthalate (Bl-PET) to reveal known and new unannotated lncRNAs. Our findings showed that the Tr-PET changed the expression of 104 lncRNAs, while the Bl-PET changed the expression of just 19. We speculate on the possible significance of the differential expressions for plant tolerance and resistance to micro-nanoplastic stress. A key finding of this work is that the studied lncRNAs tend to regulate their neighboring protein-coding genes. Consistent with this regulatory role, their promoters were found to contain cis-acting regulatory elements responsive to abscisic acid, light, MeJA, MYC/MYB, and other stress-related signals. Furthermore, some of the miRNAs that participate in plant development and defense were also predicted to be sponged by the differentially expressed lncRNAs. In summary, this study adds to our knowledge of A. thaliana lncRNAs through the discovery of new transcripts, describing their expression under micro-nanoplastic stress, and revealing their possible roles in post-transcriptional gene regulation.

Molecular Characterization of CnHd3a and Spatial Expression of Its Alternative Splicing Forms Associated with Flowering Transition and Flower Development in Coconut Palm (Cocos nucifera L.)

2025-06-18

Pariya Maneeprasert , Siriwan Thaisakun , Theerachai Thanananta +3 more | Genes

The flowering transition is a critical process determining the onset of reproductive development and fruit production. The molecular mechanisms underlying this process in coconuts are poorly understood; however, recent studies … The flowering transition is a critical process determining the onset of reproductive development and fruit production. The molecular mechanisms underlying this process in coconuts are poorly understood; however, recent studies have identified CnHd3a as a potential regulator of the floral transition in coconuts. In this study, we characterized the molecular structure of CnHd3a and analyzed its alternative splicing forms in tall and dwarf varieties of coconut palms during the flowering transition. We used qRT-PCR to measure the expression levels of CnHd3a at different developmental stages. CnHd3a was expressed in leaves and the shoot apical meristem (SAM) during the flowering transition in both coconut varieties and flower tissues during flower development. Interestingly, the expression levels of complex isoforms of CnHd3a were higher in the leaves of dwarf coconuts than in those of tall coconuts, suggesting their involvement in shortening the vegetative growth phase of dwarf coconuts. The gene structure of CnHd3a was found to be conserved across different plant species, indicating the evolutionary conservation of the floral transition process. Our findings provide insight into the molecular mechanisms underlying the floral transition and flower development processes in coconut palm. The tissue-specific expression patterns of CnHd3a isoforms show their potential roles in growth and development. Further investigations focusing on the functional characterization of CnHd3a isoforms will have practical implications for coconut breeding and cultivation strategies.

CbuERF114, an Ethylene Responsive Factor, Regulates Floral Transition in Catalpa bungei

2025-06-18

Yue Fei , Chengcheng Yao , Jiwen Hu +7 more | Plant Physiology and Biochemistry

AtDIVARICATA1 promotes flowering through regulating flowering integrators and GA biosynthesis in Arabidopsis

2025-06-18

Dong Li , Xumin Wang , Tiantian Liu +7 more | International Journal of Biological Macromolecules

Transcriptional Regulation of Sugar Accumulation and Composition in Jujube Fruit: The Roles of ZjSWEET15 and ZjSUS2 Genes

2025-06-18

Zhe Zhang , Yanqiu Geng , Yun Xing +5 more | Scientia Horticulturae

Mechanisms and Regulation of Senescence: An Overview on Hormonal and Oxidative Perspective

2025-06-17

Lily Pal | International Journal For Multidisciplinary Research

Senescence in plants represents a crucial developmental phase involving the regulated degradation of cellular components, enabling the remobilization of nutrients to support growth and reproduction. This review focuses on cotyledon … Senescence in plants represents a crucial developmental phase involving the regulated degradation of cellular components, enabling the remobilization of nutrients to support growth and reproduction. This review focuses on cotyledon senescence occurring during early seedling development. Cotyledon senescence is characterized by complex physiological, biochemical, and molecular processes including chlorophyll degradation, macromolecular breakdown, and dynamic hormonal signaling. Hormones such as ethylene, cytokinins, and abscisic acid (ABA) play antagonistic roles in regulating the timing and progression of senescence. Additionally, the interplay between reactive oxygen species (ROS) and antioxidant defense systems forms a pivotal aspect of senescence regulation, acting both as cellular damage agents and signaling molecules. Despite significant advances, the signaling networks linking embryonic axis development with cotyledon senescence continues to be lacking. Unraveling these pathways may offer insights into seedling establishment and improve our knowledge of plant developmental biology.

Revisiting the Role of MicroRNAs in the Battle against Abiotic Stress

2025-06-17

Shalini Dhiman , Raman Tikoria , Mohd Sajid Ali +7 more | CRC Press eBooks

Exploring sucrose and non-NPK essential nutrient signaling for precision control of flowering time

2025-06-17

Gibeom Baek , Na-Hyun Shin , Jinmi Yoon +1 more | Plant Biotechnology Reports