Prediction and analysis of phenotypes in the Arabidopsis clock mutant <i>prr7 prr9</i> using the Framework Model v2 (FMv2)

Data, FMv2 model and simulations for the Chew et al. 2017 paper (bioRxiv https://doi.org/10.1101/105437 ), updated 2022 as bioRxiv https://doi.org/10.1101/105437v2, mostly on the prr7 prr9 double mutant, with controls in lsf1 and prr7 single mutants. This is one of the outputs from the EU TiMet project, https://fairdomhub.org/projects/92.

This data archive was updated during submisson to the journal _in Silico _Plants in 2022, and a Snapshot was published. NB the updates are not changing the core data, or the FMv2 model that has been public for some years, just enhancing annotations and adding supporting data files, including from follow-up studies. We will add the paper and its DOI to this Investigation when it's published. The same Snapshot will likely be shared on the University of Edinburgh Datashare and on Zenodo.

We request that users gives appropriate credit to the authors of any data released here, as a norm of academic practice, including data released under CC-0 licence.

DOI: 10.15490/fairdomhub.1.investigation.123.1

Zenodo URL: None

Created at: 10th May 2022 at 19:19

Contents

Test of FMv2, study Laurel & Hardy 1

Modelling and experiments for FMv2 as a whole; Testing Framework Model version 2 (FMv2)

Biomass, leaf number and metabolites

Biomass, leaf number and metabolites in Col0 (WT), prr7, prr7prr9, and lsf1.
Metabolite data from plants after 28 days of growth were analysed most (27 days 'end of night', 28 days 'end of day' and 'end of night').
The data file also includes data from 21 days of growth ('end of day' and 'end of night'), which is useful for comparison to early-flowering plants not tested here, such as the lhycca1 double mutant, that flower before 28 days, altering their physiology.

Laurel and Hardy 1 - experimental data (.mat file)

Experimental data, in MATLAB binary file format.

  • LH1_data.mat

Laurel and Hardy 1 - Experimental data (excel)

Biomass and metabolite data for Laurel and Hardy 1.

  • LH1_experimental_data.xlsx

FMv2 simulation

No description specified

Laurel and Hardy 1 - simulation data (.mat file)

Model simulation data for Laurel and Hardy 1, in MATLAB binary format.

  • plot_LH1_biomass_and_carbon_pools.mat

Laurel and Hardy 1 mean data and simulations

Excel spreadsheet with data and simulations used to prepare figures for publication, see Metadata sheet for conditions.
Data Fresh (not dry) rosette leaf biomass, measured in samples of 5 plants each on multiple days, as mean and SD;
Simulation outputs from FMv2 for Col Wild Type plants, lsf1, and two simulations for prr7prr9 where the mutation affects only starch degradation or both starch degradation and malate/fumarate store mobilisation.

Starch levels in carbon units (not C6) measured on on
...

  • Laurel and Hardy 1_DDS.xlsx

Construction of Framework Model version 2 (FMv2)

Modelling and experiments for FMv2 components.

TiMet WP1.1a Metabolite analysis of clock mutants

Metabolite analysis in clock mutants: Col-0 parent and mutants gi-201, toc1-101 and prr7prr9; WS parent and lhy/cca1 double mutant. Plants grown in Golm and harvested at End of Day and End of Night, , assays 22 major metabolites. More detail on TiMet wiki if required. Heteroscedastic t-tests to highlight most significant changes, without multiple-testing correction.

TiMet WP1.1a metabolite data, ED-EN in clock mutants

Analysis of carbon metabolites in clock mutants by Anna Flis and Ronan Sulpice, Mark Stitt lab

  • Clock mutant ED-EN LC-MS data from AnnaF_stats_2.xlsx

TiMet WP1.1, Clock gene expression in clock mutants

RNA timeseries data from TiMet for clock genes in prr7 prr9 and Col wild-type plants under 12L:12D cycle and LL

TiMet WP1.1 qRT-PCR LD to LL and DD

RNA levels for control amplicons and multiple clock genes in 2 WT (Col, Ws) and 5 clock mutants of Arabidopsis, in biological duplicates, from three conditions: Diurnal cycle (12L/12D), Extended night (DD), Extended light (LL), harvested every 2 hours. Numbers are in transcript copy per cell, obtained assuming 1 g FW contains 25000000 cells.
Comments:
Data from LD are concateneted with DD and LL for better visualization. Toc1-101 (col-0) gi-201 (col-0) prr7-3 prr9-1 (col-0) , lhy cca1 (ws) elf3-4
...

  • ShowExperiment.action?experimentId=2841

Defining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure

Our understanding of the complex, transcriptional feedback loops in the circadian clock mechanism has depended upon quantitative, timeseries data from disparate sources. We measure clock gene RNA profiles in Arabidopsis thaliana seedlings, grown with or without exogenous sucrose, or in soil-grown plants and in wild-type and mutant backgrounds. The RNA profiles were strikingly robust across the experimental conditions, so current mathematical models are likely to be broadly applicable in leaf
...

Composition of FMv2

Combination of multiple sub-models to form Framework Model version 2

Arabidopsis - starch and the circadian clock, Model 2 (Seaton et al., 2013)

A model of the circadian regulation of starch turnover, as published in Seaton, Ebenhoeh, Millar, Pokhilko, "Regulatory principles and experimental approaches to the circadian control of starch turnover", J. Roy. Soc. Interface, 2013. This model is referred to as "Model Variant 2".
The other model variants are all available from www.plasmo.ed.ac.uk as stated in the publication.
Note that the 'P2011' circadian clock model was modified for this publication (as described), in order to replicate the
...

  • PLM_78.xml
  • model.shtml?accession=PLM_78

Modelling circadian regulation of flowering time and hypocotyl elongation, Seaton et al., 2015

Matlab model (could not be represented in SBML) from publication with abstract:
Clock-regulated pathways coordinate the response of many developmental processes to changes in photoperiod and temperature. We model two of the best-understood clock output pathways in Arabidopsis, which control key regulators of flowering and elongation growth. In flowering, the model predicted regulatory links from the clock to CYCLING DOF FACTOR 1 (CDF1) and FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (FKF1) transcription.
...

  • 1031Supplementary%20File%201%20-%20MATLAB%20code.zip
  • model.shtml?accession=PLM_1010

Chew_et_al_2014_Framework_Model version 1, Matlab and Simile

This record includes Matlab and Simile format versions of the Arabidopsis Framework Model version 1, FMv1 (Chew et al, PNAS 2014; http://www.pnas.org/content/early/2014/08/27/1410238111), copied from the PlaSMo resource (www.plasmo.ed.ac.uk), PLM_ID=76. The model description is in the Supplementary Materials of the publication, which should be uploaded somewhere here also but I don't see how to do it.

The FMv1 links the following sub-models:
1. Arabidopsis leaf carbohydrate model (Rasse and
...

  • model.shtml?accession=PLM_76
  • 134MATLAB%20Framework%20Model.zip
  • 1020Framework%20Model%20in%20Simile.zip
  • timet-logo-sm.png

Framework Model v2

Framework Model for Arabidopsis vegetative growth, version 2 (FMv2), as described in Chew et al. bioRxiv 2017 (https://doi.org/10.1101/105437; please see linked Article file).

The FMv2 model record on FAIRDOMHub has the following versions, which represent the same FMv2 model:
Version 1 is an archive of the github repository of MATLAB code for the Framework Model v2, downloaded from https://github.com/danielseaton/frameworkmodel on 06/02/17. This version was not licensed for further use and was
...

  • frameworkmodel

Linking circadian time to growth rate quantitatively via carbon metabolism

Summary paragraph

Predicting a multicellular organism’s phenotype quantitatively from its genotype is challenging, as genetic effects must propagate up time and length scales. Circadian clocks are intracellular regulators that control temporal gene expression patterns and hence metabolism, physiology and behaviour, from sleep/wake cycles in mammals to flowering in plants
1–3
. Clock genes are rarely essential but appropriate alleles can confer a competitive advantage
4,5
and have been repeatedly
...

Simulating clock gene expression with model P2011.1.2

Comparison of simulated wild-type and prr7prr9 double mutant under 12L:12D cycles. Simulation with CVODE simulator via SBSI v1.5 framework.

TiMet WP1.1 qRT-PCR LD to LL and DD

RNA levels for control amplicons and multiple clock genes in 2 WT (Col, Ws) and 5 clock mutants of Arabidopsis, in biological duplicates, from three conditions: Diurnal cycle (12L/12D), Extended night (DD), Extended light (LL), harvested every 2 hours. Numbers are in transcript copy per cell, obtained assuming 1 g FW contains 25000000 cells.
Comments:
Data from LD are concateneted with DD and LL for better visualization. Toc1-101 (col-0) gi-201 (col-0) prr7-3 prr9-1 (col-0) , lhy cca1 (ws) elf3-4
...

  • ShowExperiment.action?experimentId=2841

P2011.1.2 simulations of clock genes under LD cycles

for Chew, Seaton et al. paper Figure 1

  • TiMEt WP1_1 prr79 sims P2011.zip

P2011.1.2 simulations vs. data for WT, normalised for plots

For Chew, Seaton et al. Figure 1

  • SBSI plots final.xlsx

P2011.1.2 simulations and data in prr7 prr9 mutant, normalised for plots

For Chew, Seaton et al. Figure 1

  • SBSI 79 plots final.xlsx

Arabidopsis clock model P2011.1.2

This version is P2011.1.2, model ID PLM_71 version 1. Dynamics identical to P2011.1.1 of the Pokhilko et al. 2012 publication.

http://www.plasmo.ed.ac.uk/plasmo/models/download.shtml?accession=PLM_71&version=1

  • PLM_71.xml

P2011.1.2_directupload

Exactly the same as model 243, but uploaded as a file rather than copied from PlaSMo.

  • PLM_71.xml

Analysis of Framework Model version 2 (FMv2)

Simulations, parameter sensitivity analysis etc. for FMv2

Sensitivity analysis of FMv2

effects of 1% increase in each parameter, more detailed analysis of water content

Sensitivity analysis results (.mat file)

Model analysis results in binary Matlab format

  • sens_analysis_results_WT.mat

Relationship among FMv2 outputs

correlations of starch mobilisation and fresh weight under single parameter changes

Sensitivity analysis results (.mat file)

Model analysis results in binary Matlab format

  • sens_analysis_results_WT.mat

Test of FMv2, study Laurel & Hardy 2

Modelling and experiments for FMv2 as a whole; Testing Framework Model version 2 (FMv2)

Biomass and metabolites

Biomass (fresh mass, dry mass), leaf numbers, leaf area, gas exchange and 12 metabolites in Col0 (WT), prr7prr9, and lsf1 (presented in the preprint/paper) and pgm (not analysed further).

Laurel and Hardy 2 - experimental data (.mat file)

Experimental data for Laurel and Hardy 2, in MATLAB binary format.

  • LH2_data.mat

Laurel and Hardy 2 - Experimental data (excel)

Mean and SD data for metabolites and biomass, along with metadata used to simulate this experiment.

  • Laurel and Hardy 2 - experimental data (excel).xlsx

Laurel and Hardy 2 - complete data

Complete excel spradsheets for Laurel and Hardy 2, including data for the pgm mutant that were not analysed in the Chew et al. 2017 preprint/publication.
Data include fresh and dry biomass, gas exchange, leaf numbers and metabolites in Col0 (WT), prr7prr9, pgm and lsf1 plants.
Metabolite data are from plants after 27 days of growth (end of night) and 28 days (end of day and end of night).

  • Laurel and Hardy 2 - complete data.zip

FMv2 simulation

Simulation data from FMv2 calibrated for experiment L&H2, an experiment run at 18.5C instead of the 20.5C of the replicate and related studies. The Excel file includes the mean and SD of the relevant experimental data, and the figure panels.

Laurel and Hardy 2 - simulation data (.mat file)

Simulation data for Laurel and Hardy 2, in MATLAB binary format.

  • plot_LH2_biomass_and_carbon_pools.mat

Laurel and Hardy 2 mean data and simulations

Excel spreadsheet with data and simulations used to prepare figures for publication, see Metadata sheet for conditions. Data Fresh (not dry) rosette leaf biomass, measured in samples of 5 plants each on multiple days, as mean and SD; Simulation outputs from FMv2 for Col Wild Type plants, lsf1, and two simulations for prr7prr9 where the mutation affects only starch degradation or both starch degradation and malate/fumarate store mobilisation.

Starch levels in carbon units (not C6) measured on on
...

  • Laurel and Hardy 2 with malate and fumarate_DDS.xlsx

Test of FMv2, study Laurel & Hardy 3

Modelling and experiments for FMv2 as a whole; Testing Framework Model version 2 (FMv2)

Biomass and metabolites

Biomass (fresh mass, dry mass), leaf numbers, leaf area, gas exchange and 12 metabolites in Col0 (WT), prr7prr9, and pgm at days 29 and 35, presented in the preprint/publication, with most data also for Col and lhycca1 at days 21/22/23, not analysed further.

We suggest that the lower carbon assimilation rate measured in lhycca1 (see gas exchange data) might allow a calibirated simulation in the FMv2 model in future to incorporate the indirect effects of nightly carbon starvation in this genotype
...

Laurel and Hardy 3 - experimental data (.mat file)

Experimental data for Laurel and Hardy 3, in MATLAB binary format.

  • LH3_data.mat

Laurel and Hardy 3 - Experimental data (excel)

No description specified

  • Laurel and Hardy 3 - experimental data (excel).xlsx

Laurel and Hardy 3 - complete data

Excel spreadsheets for biomass, leaf number, gas exchange and metabolites, including pgm and lhycca1.
Key data are for 27-28 day old plants for Col and prr7prr9, analysed for the preprint/publication.
Gas exchange data for lhycca1 showed lower Assimilation per unit area than Col, prr7prr9; A in pgm was higher than Col.
Metabolite data were also collected for Col and lhycca1 at 18 days, before the lhycca1 flowered, but these are marked as unreliable.

  • Laurel and Hardy 3 - complete data.zip

FMv2 simulation

No description specified

Laurel and Hardy 3 - simulation data (.mat file)

Simulation data for Laurel and Hardy 3, in MATLAB binary format.

  • plot_LH3_biomass_and_carbon_pools.mat

Laurel and Hardy 3 mean data and simulations

Excel spreadsheet with data and simulations used to prepare figures for publication, see Metadata sheet for conditions. Data Fresh (not dry) rosette leaf biomass, measured in samples of 5 plants each on multiple days, as mean and SD; Simulation outputs from FMv2 for Col Wild Type plants, and two simulations for prr7prr9 where the mutation affects only starch degradation or both starch degradation and malate/fumarate store mobilisation.

Starch levels in carbon units (not C6) measured on on days
...

  • Laurel and Hardy 3 with malate and fumarate_DDS.xlsx

Test of FMv2, study Gibberellins 1

Modelling and experiments for FMv2 as a whole; Testing Framework Model version 2 (FMv2)

Biomass and metabolites

Biomass and metabolites in Col0 (WT) and prr7prr9, with and without exogenous gibberellins (GA)

All biomass data for study Gibberellins 1

Biomass data for individual plants at day 35, fresh and dry weights, as well as mean and SD, from study Gibberellins 1

  • GA_Biomass of full sets_AJM.xlsx

Biomass and metabolite data for study Gibberellins 1

Excel sheet with mean and SD biomass data and charts, individual metabolite replicates, mean, SD and charts
Details on Read.ME worksheet

  • GA experiment - biomass + metabolite_AJM.xlsx

Circadian period analysis

Luciferase reporter gene assay for circadian period of seedlings in constant light, for Col0 (WT) and prr7prr9, with and without exogenous gibberellins (GA). Supplementary Figure 11f in Chew et al., _in Silico _Plants.

Raw and processed data, together with circadian period analysis and summary statistics, are available from BioDare.ed.ac.uk: choose https://biodare.ed.ac.uk/experiment ("Browse Public Resources" on the Login screen), then you can link to https://biodare.ed.ac.uk/robust/ShowExperiment.action?experimentId=3838,
...

Test of FMv2, follow-on: mechanisms of malate/fumarate accumulation

Follow-up to the validation experiments on FMv2, testing candidate mechanisms for high malate and fumarate accumulation in the Arabidopsis double mutant prr7prr9 and its parent accession Col. New collaborations with the groups of Teresa Fitzpatrick and TiMet partner Samuel Zeeman.

Assimilation and partitioning of 14CO2 at night

Follow-up to the validation experiments on FMv2, testing candidate mechanisms for high malate and fumarate accumulation in the Arabidopsis double mutant prr7prr9 and its parent accession Col.

In this study, 14CO2 labelling was used to test the rate of carbon assimilation in the dark at the end of the subjective night (starting about ZT21), which is indicative of PEPC activity in forming malate, and the subsequent partitioning of this labelled C into various cellular fractions. The short-period
...

Carbon assimilation and partitioning in darkness

14CO2 assimilation in the night-time, in plants of Col, prr7prr9; Ws, lhycca1 genotypes at 18 and 28 days, and partitioning among cellular fractions.

  • Labelling data from Gavin George_AJM2.xlsx

Thiamine vitamers

Follow-up to the validation experiments on FMv2, testing candidate mechanisms for high malate and fumarate accumulation in the Arabidopsis double mutant prr7prr9 and its parent accession Col.

In this study, thiamine vitamers were quantified to test whether the essential cofactor TDP had altered enzyme activities to affect the malate and fumarate levels, using existing plant samples harvested from am earlier L&H study.

Testing thiamine metabolites in Col and prr7prr9

Excel file with data on levels of thiamine and its metabolites TMP and active cofactor TDP, tested in Col and prr7prr9 samples from study Laurel and Hardy 3.
Altered levels of TDP could potentially affect enzymes with TDP cofactors that metabolise malate and fumarate levels, altering their levels in prr7prr9.

  • Thiamin Geneva results 10_05_2015_AJM.xlsx

Tests of FMv2, compilations and figures

Assorted files prepared during the publication process of the FMv2, its validation and testing, mostly focussed on the Arabidopsis double mutant prr7prr9 and its parent accession Col.
Data from other studies that are described separately, and linked by Atribution to the File records under this Study.

Biomass, leaf area and gas exchange data

Biomass, leaf number and gas exchange data for Col0 (WT), prr7prr9, and lsf1, compiled from four studies: L&H1-3 and the 'no GA' controls of Gibberellins 1.

Four-study data compilation with charts

Excel workbook with included Read.Me sheet, including FW and DW biomass data derived from files linked elsewhere;
a compilation of the rosette area and gas exchange data for every plant measured of the Col, lsf1 and prr7prr9 genotypes;
statistical analysis across the experiments;
and charts of the compiled data, some of which are presented as figure panels in the 2022 versions.

  • Biomass_FW_DW_gas_exchange_data.xlsx

Test of FMv2, photoperiodic flowering and hypocotyl elongation

Model simulations compared to experimental data from the literature (publications from Mizuno lab are linked), testing the FMv2.

Mizuno lab, Flowering time in clock mutants

Leaf number at flowering data from literature for prr7 prr9 and Col wild-type plants under long photoperiods and short photoperiods

Flowering time in WT vs prr7prr9 (Nakamichi et al, 2007)

No description specified

  • nakamichi2007_WT_vs_prr7prr9_flowering_data.xlsx

Arabidopsis clock-associated pseudo-response regulators PRR9, PRR7 and PRR5 coordinately and positively regulate flowering time through the canonical CONSTANS-dependent photoperiodic pathway

Photoperiodism allows organisms to measure daylength, or external photoperiod, and to anticipate coming seasons. Daylength measurement requires the integration of light signal and temporal information by the circadian clock. In the long-day plant Arabidopsis thaliana, CONSTANS (CO) plays a crucial role in integrating the circadian rhythm and environmental light signals into the photoperiodic flowering pathway. Nevertheless, the molecular mechanism by which the circadian clock modulates the cyclic
...

Mizuno lab, Hypocotyl length in clock mutants

Seedling hypocotyl data from literature for prr7 prr9 and Col wild-type plants under various photoperiods

Hypocotyl lengths in WT vs prr7prr9 across photoperiods (Niwa et al, 2009)

No description specified

  • niwa2009_WT_vs_prr7prr9_hypocotyl_data.xlsx

The circadian clock regulates the photoperiodic response of hypocotyl elongation through a coincidence mechanism in Arabidopsis thaliana

The plant circadian clock generates rhythms with a period close to 24 h, and it controls a wide range of physiological and developmental oscillations in habitats under natural light/dark cycles. Among clock-controlled developmental events, the best characterized is the photoperiodic control of flowering time in Arabidopsis thaliana. Recently, it was also reported that the clock regulates a daily and rhythmic elongation of hypocotyls. Here, we report that the promotion of hypocotyl elongation is
...

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Citation
Millar, A., Chew, Y. H., Seaton, D., & Mengin, V. (2022). Prediction and analysis of phenotypes in the Arabidopsis clock mutant prr7 prr9 using the Framework Model v2 (FMv2). FAIRDOMHub. https://doi.org/10.15490/FAIRDOMHUB.1.INVESTIGATION.123.1
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Created: 10th May 2022 at 19:19

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