Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Simple network motifs can capture key characteristics of the floral transition in Arabidopsis.

ABSTRACT: The floral transition is a key decision during plant development. While different species have evolved diverse pathways to respond to different environmental cues to flower in the correct season, key properties such as irreversibility and robustness to fluctuating signals appear to be conserved. We have used mathematical modeling to demonstrate how minimal regulatory networks of core components are sufficient to capture these behaviors. Simplified models inevitably miss finer details of the biological system, yet they provide a tractable route to understanding the overall system behavior. We combined models with experimental data to qualitatively reproduce characteristics of the floral transition and to quantitatively scale the network to fit with available leaf numbers. Our study highlights the value of pursuing an iterative approach combining modeling with experimental work to capture key features of complex systems.

SUBMITTER: Pullen N

PROVIDER: S-EPMC4106512 | biostudies-literature | 2013 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Simple network motifs can capture key characteristics of the floral transition in Arabidopsis.

Pullen Nick N Jaeger Katja E KE Wigge Philip A PA Morris Richard J RJ

Plant signaling & behavior 20130829 11

The floral transition is a key decision during plant development. While different species have evolved diverse pathways to respond to different environmental cues to flower in the correct season, key properties such as irreversibility and robustness to fluctuating signals appear to be conserved. We have used mathematical modeling to demonstrate how minimal regulatory networks of core components are sufficient to capture these behaviors. Simplified models inevitably miss finer details of the biol ...[more]

PMID: 23989666

Similar Datasets

VDAC1 Negatively Regulates Floral Transition in Arabidopsis thaliana.

Project description:Voltage-dependent anion channels (VDACs) are the most important proteins in mitochondria. They localize to the outer mitochondrial membrane and contribute to the metabolite transport between the mitochondria and cytoplasm, which aids plant growth regulation. Here, we report that Arabidopsis thaliana VDAC1 is involved in the floral transition, with the loss of AtVDAC1 function, resulting in an early-flowering phenotype. AtVDAC1 is expressed ubiquitously in Arabidopsis. To identify the flowering pathway integrators that may be responsible for AtVDAC1's function during the floral transition, an RNA-seq analysis was performed. In total, 106 differentially expressed genes (DEGs) were identified between wild-type and atvdac1-5 mutant seedlings. However, none were involved in flowering-related pathways. In contrast, AtVDAC1 physically associated with FLOWERING LOCUS T. Thus, in the floral transition, AtVDAC1 may function partly through the FLOWERING LOCUS T protein.

| S-EPMC8584032 | biostudies-literature

EBS is a bivalent histone reader that regulates floral phase transition in Arabidopsis.

Project description:The ability of cells to perceive and translate versatile cues into differential chromatin and transcriptional states is critical for many biological processes1-5. In plants, timely transition to a flowering state is crucial for successful reproduction6-9. EARLY BOLTING IN SHORT DAY (EBS) is a negative transcriptional regulator that prevents premature flowering in Arabidopsis thaliana10,11. We found that EBS contains bivalent bromo-adjacent homology (BAH)-plant homeodomain (PHD) reader modules that bind H3K27me3 and H3K4me3, respectively. We observed co-enrichment of a subset of EBS-associated genes with H3K4me3, H3K27me3, and Polycomb repressor complex 2 (PRC2). Notably, EBS adopted an autoinhibition mode to mediate its switch in binding preference between H3K27me3 and H3K4me3. This binding balance was critical because disruption of either EBS-H3K27me3 or EBS-H3K4me3 interaction induced early floral transition. Our results identify a bivalent chromatin reader capable of recognizing two antagonistic histone marks, and we propose a distinct mechanism of interaction between active and repressive chromatin states.

| S-EPMC6556434 | biostudies-literature

The inhibitory effect of ABA on floral transition is mediated by ABI5 in Arabidopsis.

Project description:Seed germination and flowering initiation are both transitions responding to similar seasonal cues. This study shows that ABSCISIC ACID-INSENSITIVE MUTANT 5 (ABI5), a bZIP transcription factor, which plays an important role in the abscisic acid (ABA)-arrested seed germination, is robustly associated with the floral transition in Arabidopsis. Under long-day conditions, overexpression of ABI5 could delay floral transition through upregulating FLOWERING LOCUS C (FLC) expression. In contrast, ectopically overexpressing FLC in an abi5 mutant reversed the earlier flowering phenotype. Further analysis indicated that transactivation of FLC could be promoted by ABI5 and/or other abscisic acid-responsive element (ABRE)-binding factors (ABFs). The expression of FLC that was promoted by ABI5 and/or other ABFs could be blocked in a triple SNF1-related protein kinase (SnRK) mutant, snrk2.2/2.3/2.6, despite the presence of ABA. In sharp contrast, when SnRK2.6 was coexpressed, the reduction of transactivity of FLC was reverted in mesophyll protoplasts of snrk2.2/2.3/2.6. Additional results from analysing transgenic plants carrying mutations of phosphoamino acids (ABI5 ( S42AS145AT201A )), which are conserved in ABI5, suggested that SnRK2-mediated ABI5 and/or ABF phosphorylation may be crucial for promoting FLC expression. The transgenic plants ABI5 ( S42AS145AT201A ) were insensitive to ABA in seed germination, in addition to having an earlier flowering phenotype. Direct binding of ABI5 to the ABRE/G-box promoter elements existing in FLC was demonstrated by chromatin immunoprecipitation. Mutations at the ABRE/G-box regions in FLC promoter sequences abolished the ABI5-promoted transactivation of FLC. In summary, these results may decipher the inhibitory effect of ABA on floral transition in Arabidopsis.

| S-EPMC3542054 | biostudies-literature

C-terminal domain phosphatase-like 1 (CPL1) is involved in floral transition in Arabidopsis.

Project description:BackgroundRNA polymerase II plays critical roles in transcription in eukaryotic organisms. C-terminal Domain Phosphatase-like 1 (CPL1) regulates the phosphorylation state of the C-terminal domain of RNA polymerase II subunit B1, which is critical in determining RNA polymerase II activity. CPL1 plays an important role in miRNA biogenesis, plant growth and stress responses. Although cpl1 mutant showes delayed-flowering phenotype, the molecular mechanism behind CPL1's role in floral transition is still unknown.ResultsTo study the role of CPL1 during the floral transition, we first tested phenotypes of cpl1-3 mutant, which harbors a point-mutation. The cpl1-3 mutant contains a G-to-A transition in the second exon, which results in an amino acid substitution from Glu to Lys (E116K). Further analyses found that the mutated amino acid (Glu) was conserved in these species. As a result, we found that the cpl1-3 mutant experienced delayed flowering under both long- and short-day conditions, and CPL1 is involved in the vernalization pathway. Transcriptome analysis identified 109 genes differentially expressed in the cpl1 mutant, with 2 being involved in floral transition. Differential expression of the two flowering-related DEGs was further validated by qRT-PCR.ConclusionsFlowering genetic pathways analysis coupled with transciptomic analysis provides potential genes related to floral transition in the cpl1-3 mutant, and a framework for future studies of the molecular mechanisms behind CPL1's role in floral transition.

| S-EPMC8418720 | biostudies-literature

transition-Transcriptome of floral transition

Project description:transition-Transcriptome of floral transition

| PRJNA477336 | ENA

Cell division and morphological changes in the shoot apex of Arabidopsis thaliana during floral transition.

Project description:Eight-week-old vegetative plants of Arabidopsis thaliana, ecotype Columbia, were induced to flower by a single long day (LD). In this experimental system, it is known that the last component of the floral stimulus moves from the leaves to the apex 24-36 h after the start of the LD, and the first floral meristem is initiated by the shoot apical meristem (SAM) at 44-56 h (Corbesier et al., 1996, The Plant Journal 9: 947-952). Here we show that the rate of cell division is increased at floral transition in all SAM parts but not in the sub-apical pith cells. Mitotic activity starts to increase 24 h after the start of the LD and is two- to three-fold higher at peak times than that in non-induced plants. This activation is followed by the start of SAM enlargement at 44 h, SAM doming at 48 h, and the elongation of apical internodes (bolting) at 52 h.

| S-EPMC4242243 | biostudies-literature

transition-Transcriptome of floral transition

Project description:ngs2015_01_transition-transition-Identification of transcripts and long non-coding transcripts in wild-type mature rosette leaves of Arabidopsis thaliana during a photoperiodic switch inducing floral transition.-Arabidopsis thaliana Col-0 plants were grown in soil, in growth chamber under white fluorescent light, under short-day (8 hours light/16 hours dark, SD) or long-day (16 hours light/8 hours dark, LD) conditions. Temperature in SD was 21°C during the light period and 18°C during the dark, humidity (65%) remained constant. In LD, temperature (21°C) and humidity (70%) remained constant. Plants were cultured for 4 weeks in individual pot, in SD then transferred in LD. Plants were analysed at different time points before transfer (T0) and after two, three and five days of transfer (T2, T3, T5). The second pair of leaves was collected before dusk, at Zeitgeber time 15 (ZT15) considering ZT 0 the switched on of the light. Three biological replicates were performed. The floral transition occurs between T0 and T5 based on AP1:GUS marker, a inflorescence meristem is not yet visible during this developmental window at the center of the rosette.

2019-04-17 | GSE116123 | GEO

Molecular condensation of the CO/NF-YB/NF-YC/FT complex gates floral transition in Arabidopsis

Project description:The plant master photoperiodic regulator CONSTANS (CO) interacts with Nuclear Factor-Y subunits B2 (NF-YB2) and C9 (NF-YC9) and transcriptionally activates the florigen gene FLOWERING LOCUS T (FT), regulating floral transition. However, the molecular mechanism of the functional four-component complex assembly in the nucleus remains elusive. We report that co-phase separation of CO with NF-YB2/NF-YC9/FT precisely controls heterogeneous CO assembly and FT transcriptional activation. In response to light signals, CO proteins form functional percolation clusters from a diffuse distribution in a B-box-motif-dependent manner. Multivalent coassembly with NF-YC9 and NF-YB2 prevents inhibitory condensate formation and is necessary to maintain proper CO assembly and material properties. The intrinsically disordered region (IDR) of NF-YC9, containing a polyglutamine motif, fine-tunes the functional properties of CO/NF-YB/NF-YC condensates. Specific FT promoter recognition with polyelectrolyte partitioning also enables the fluidic functional properties of CO/NF-YB/NF-YC/FT condensates. Our findings offer novel insights into the tunable macromolecular condensation of the CO/NF-YB/NF-YC/FT complex in controlling flowering in the photoperiod control.

| S-SCDT-10_1038-S44318-024-00293-0 | biostudies-other

The sugar transporter SWEET10 acts downstream of FLOWERING LOCUS T during floral transition of Arabidopsis thaliana.

Project description:BACKGROUND:Floral transition initiates reproductive development of plants and occurs in response to environmental and endogenous signals. In Arabidopsis thaliana, this process is accelerated by several environmental cues, including exposure to long days. The photoperiod-dependent promotion of flowering involves the transcriptional induction of FLOWERING LOCUS T (FT) in the phloem of the leaf. FT encodes a mobile protein that is transported from the leaves to the shoot apical meristem, where it forms part of a regulatory complex that induces flowering. Whether FT also has biological functions in leaves of wild-type plants remains unclear. RESULTS:In order to address this issue, we first studied the leaf transcriptomic changes associated with FT overexpression in the companion cells of the phloem. We found that FT induces the transcription of SWEET10, which encodes a bidirectional sucrose transporter, specifically in the leaf veins. Moreover, SWEET10 is transcriptionally activated by long photoperiods, and this activation depends on FT and one of its earliest target genes SUPPRESSOR OF CONSTANS OVEREXPRESSION 1 (SOC1). The ectopic expression of SWEET10 causes early flowering and leads to higher levels of transcription of flowering-time related genes in the shoot apex. CONCLUSIONS:Collectively, our results suggest that the FT-signaling pathway activates the transcription of a sucrose uptake/efflux carrier during floral transition, indicating that it alters the metabolism of flowering plants as well as reprogramming the transcription of floral regulators in the shoot meristem.

| S-EPMC6998834 | biostudies-literature

SHORT VEGETATIVE PHASE reduces gibberellin biosynthesis at the Arabidopsis shoot apex to regulate the floral transition.

Project description:In Arabidopsis thaliana environmental and endogenous cues promote flowering by activating expression of a small number of integrator genes. The MADS box transcription factor SHORT VEGETATIVE PHASE (SVP) is a critical inhibitor of flowering that directly represses transcription of these genes. However, we show by genetic analysis that the effect of SVP cannot be fully explained by repressing known floral integrator genes. To identify additional SVP functions, we analyzed genome-wide transcriptome data and show that GIBBERELLIN 20 OXIDASE 2, which encodes an enzyme required for biosynthesis of the growth regulator gibberellin (GA), is upregulated in svp mutants. GA is known to promote flowering, and we find that svp mutants contain elevated levels of GA that correlate with GA-related phenotypes such as early flowering and organ elongation. The ga20ox2 mutation suppresses the elevated GA levels and partially suppresses the growth and early flowering phenotypes of svp mutants. In wild-type plants, SVP expression in the shoot apical meristem falls when plants are exposed to photoperiods that induce flowering, and this correlates with increased expression of GA20ox2. Mutations that impair the photoperiodic flowering pathway prevent this downregulation of SVP and the strong increase in expression of GA20ox2. We conclude that SVP delays flowering by repressing GA biosynthesis as well as integrator gene expression and that, in response to inductive photoperiods, repression of SVP contributes to the rise in GA at the shoot apex, promoting rapid induction of flowering.

| S-EPMC4084417 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data