Matt Hannah

1
Systems-level analysis of plant low-temperature
responses

• Matt Hannah
• hannah_at_mpimp-golm.mpg.de

2
Overview Freezing tolerance and cold acclimation
Introduction Cold acclimation Signaling
pathways Outlook

• Freezing tolerance and cold acclimation
• Consensus cold responsive genes
• Functional testing to identify key processes
• Natural variation of freezing tolerance
• Cold - circadian clock interactions
• Transcriptional regulation of freezing tolerance
• Systems-level analysis of signaling
• Identifying candidate small molecule signals
• Dynamic response to temperature and light

3
Overview Freezing tolerance and cold acclimation
Introduction Cold acclimation Signaling
pathways Outlook

• Frost limits crop yield and distribution
• Basic nonacclimated (NA) freezing tolerance
• Many plants increase freezing tolerance after
  acclimation (ACC) at low nonfreezing temperatures
• During ACC there are complex changes in gene
  expression, metabolite levels and physiology

4
Overview Freezing tolerance and cold acclimation
Introduction Cold acclimation Signaling
pathways Outlook
Xin Browse (2000) Plant Cell Environ 23, 893
5
Consensus changes and functional testing Natural
variation of freezing tolerance Cold circadian
interactions Transcriptional regulation
Introduction Cold acclimation Signaling
pathways Outlook

• Nine Arabidopsis accessions
• Mature rosette, before and after 14 d cold
  acclimation _at_ 4C
• Quantitative determination of freezing tolerance
  by leaf electrolyte leakage (LT50)
• Expression profiling - Affymetrix ATH1 array
• Metabolite profiling GCMS
• 3 independent experiments

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Introduction Cold acclimation Signaling
pathways Outlook
Consensus changes and functional testing Natural
variation of freezing tolerance Cold circadian
interactions Transcriptional regulation
Consensus cold regulated genes
Hannah et al. (2005) PLoS Genetics 1, e26
7
Introduction Cold acclimation Signaling
pathways Outlook
Consensus changes and functional testing Natural
variation of freezing tolerance Cold circadian
interactions Transcriptional regulation
Functional analysis of bulk transcriptional
changes
Hannah et al. (2005) PLoS Genetics 1, e26
8
Introduction Cold acclimation Signaling
pathways Outlook
Consensus changes and functional testing Natural
variation of freezing tolerance Cold circadian
interactions Transcriptional regulation
Considerable natural variation of freezing
tolerance
Hannah et al. (2006) Plant Physiology 142, 98
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Introduction Cold acclimation Signaling
pathways Outlook
Consensus changes and functional testing Natural
variation of freezing tolerance Cold circadian
interactions Transcriptional regulation
ACC freezing tolerance correlates with habitat
temperature
Hannah et al. (2006) Plant Physiology 142, 98
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Introduction Cold acclimation Signaling
pathways Outlook
Consensus changes and functional testing Natural
variation of freezing tolerance Cold circadian
interactions Transcriptional regulation
Global transcript changes correlate with ACC
capacity.....
Hannah et al. (2006) Plant Physiology 142, 98
11
Introduction Cold acclimation Signaling
pathways Outlook
Consensus changes and functional testing Natural
variation of freezing tolerance Cold circadian
interactions Transcriptional regulation
.....but global metabolite changes do not
Hannah et al. (2006) Plant Physiology 142, 98
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Introduction Cold acclimation Signaling
pathways Outlook
Consensus changes and functional testing Natural
variation of freezing tolerance Cold circadian
interactions Transcriptional regulation
Genes correlating with ACC LT50 CBF-regulon
enriched
Vogel et al. (2005) Plant J 41, 195
Hannah et al. (2006) Plant Physiology 142, 98
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Introduction Cold acclimation Signaling
pathways Outlook
Consensus changes and functional testing Natural
variation of freezing tolerance Cold circadian
interactions Transcriptional regulation
Functional analysis reveals the most abundant
changes
Hannah et al. (2006) Plant Physiology 142, 98
14
Introduction Cold acclimation Signaling
pathways Outlook
Consensus changes and functional testing Natural
variation of freezing tolerance Cold circadian
interactions Transcriptional regulation
Up-regulation of flavonoid biosynthesis for high
ACC?
Tohge et al. (2005) Plant J 42, 218
Hannah et al. (2006) Plant Physiology 142, 98
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Introduction Cold acclimation Signaling
pathways Outlook
Consensus changes and functional testing Natural
variation of freezing tolerance Cold circadian
interactions Transcriptional regulation
Tenela is metabolically similar to ACC plants
Hannah et al. (2006) Plant Physiology 142, 98
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Introduction Cold acclimation Signaling
pathways Outlook
Consensus changes and functional testing Natural
variation of freezing tolerance Cold circadian
interactions Transcriptional regulation
Tenela has constitutively high freezing tolerance
Cook et al. (2004) PNAS 101, 15243
Hannah et al. (2006) Plant Physiology 142, 98
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Introduction Cold acclimation Signaling
pathways Outlook
Consensus changes and functional testing Natural
variation of freezing tolerance Cold circadian
interactions Transcriptional regulation

• Acclimated freezing tolerance correlates with
  minimum habitat temperature
• Acclimation capacity correlates with global
  transcript, but not metabolite, changes
• Metabolites and transcripts, including
  transcription factors, correlate with freezing
  tolerance
• Several functional groups and pathways may be of
  particular importance
• The CBF pathway may naturally enhance freezing
  tolerance prior to cold exposure

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Introduction Cold acclimation Signaling
pathways Outlook
Consensus changes and functional testing Natural
variation of freezing tolerance Cold circadian
interactions Transcriptional regulation
Interactions between cold and the circadian clock
Circadian cycle in continuous conditions,
period 24h
Diurnal cycle under day/night input
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Introduction Cold acclimation Signaling
pathways Outlook
Consensus changes and functional testing Natural
variation of freezing tolerance Cold circadian
interactions Transcriptional regulation
Major diurnal contribution to cold-responsive
genes
Bläsing et al. (2005) Plant Cell 17, 3257
Bieniawska et al. Submitted
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Introduction Cold acclimation Signaling
pathways Outlook
Consensus changes and functional testing Natural
variation of freezing tolerance Cold circadian
interactions Transcriptional regulation
Major diurnal contribution to cold-responsive
genes
Bieniawska et al. Submitted
21
Introduction Cold acclimation Signaling
pathways Outlook
Consensus changes and functional testing Natural
variation of freezing tolerance Cold circadian
interactions Transcriptional regulation
Coordinate time-of-day regulation underlying PC
1, 2, 4
Edwards et al. (2006) Plant Cell 18, 639
Bieniawska et al. Submitted
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Introduction Cold acclimation Signaling
pathways Outlook
Consensus changes and functional testing Natural
variation of freezing tolerance Cold circadian
interactions Transcriptional regulation
The Arabidopsis circadian clock
LUX
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Introduction Cold acclimation Signaling
pathways Outlook
Consensus changes and functional testing Natural
variation of freezing tolerance Cold circadian
interactions Transcriptional regulation
Cold damps cycles under diurnal conditions
Bieniawska et al. Submitted
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Introduction Cold acclimation Signaling
pathways Outlook
Consensus changes and functional testing Natural
variation of freezing tolerance Cold circadian
interactions Transcriptional regulation
Cold disrupts cycles in continuous light
Bieniawska et al. Submitted
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Introduction Cold acclimation Signaling
pathways Outlook
Consensus changes and functional testing Natural
variation of freezing tolerance Cold circadian
interactions Transcriptional regulation
Cold differentially clamps clock output gene
expression
Bieniawska et al. Submitted
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Introduction Cold acclimation Signaling
pathways Outlook
Consensus changes and functional testing Natural
variation of freezing tolerance Cold circadian
interactions Transcriptional regulation
Clock function at low temperature (Diurnal
conditions)
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Introduction Cold acclimation Signaling
pathways Outlook
Consensus changes and functional testing Natural
variation of freezing tolerance Cold circadian
interactions Transcriptional regulation
Cold effects on the circadian clock
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Introduction Cold acclimation Signaling
pathways Outlook
Consensus changes and functional testing Natural
variation of freezing tolerance Cold circadian
interactions Transcriptional regulation
cold-response is time-of-day dependent
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Introduction Cold acclimation Signaling
pathways Outlook
Consensus changes and functional testing Natural
variation of freezing tolerance Cold circadian
interactions Transcriptional regulation
Extensive diurnal gating of cold-induced TFs
Bieniawska et al. Submitted
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Introduction Cold acclimation Signaling
pathways Outlook
Consensus changes and functional testing Natural
variation of freezing tolerance Cold circadian
interactions Transcriptional regulation
Transcriptional regulation of freezing tolerance
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Introduction Cold acclimation Signaling
pathways Outlook
Identifying small molecule signals Dynamic
networks
A systems approach to identify small molecule
signals

• Aims
• Metabolites acting as signals in planta
• Genes controlling metabolites
• Co-regulated genes
• Data
• 100 different conditions
• Genetic/environment/chemical variation

Hannah et al. Submitted
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Introduction Cold acclimation Signaling
pathways Outlook
Identifying small molecule signals Dynamic
networks
Sucrose correlation versus 6h treatment in
seedlings
Solfanelli et al. (2005) Plant Physiol. 140, 637
Hannah et al. Submitted
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Introduction Cold acclimation Signaling
pathways Outlook
Identifying small molecule signals Dynamic
networks
Leucine correlation versus transgenic line with
2 increase
Hannah et al. Submitted
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Introduction Cold acclimation Signaling
pathways Outlook
Identifying small molecule signals Dynamic
networks
Dynamic environmental response networks

• Aims
• Understand environmental responses
• Signaling networks
• Small molecules
• Regulatory genes
• Predict MetaboliteTranscriptCondition
• Data
• 8 different conditions, 23 timepoints
• Enironmental variation

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Introduction Cold acclimation Signaling
pathways Outlook
Identifying small molecule signals Dynamic
networks
Dynamic environmental response networks
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Introduction Cold acclimation Signaling
pathways Outlook
Identifying small molecule signals Dynamic
networks
Analysis overview
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Introduction Cold acclimation Signaling
pathways Outlook
Identifying small molecule signals Dynamic
networks
Time dependent co-regulation

• shifted co-response
• Co-response noise
• many treatments
• Variable time shifts

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Introduction Cold acclimation Signaling
pathways Outlook
Identifying small molecule signals Dynamic
networks
TF target prediction using multiple short
timecourses
Redestig et al. (2007) BMC Bioinf. 8, 454
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Introduction Cold acclimation Signaling
pathways Outlook
Identifying small molecule signals Dynamic
networks
Exemplar temperature-light responses transcripts
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Introduction Cold acclimation Signaling
pathways Outlook
Identifying small molecule signals Dynamic
networks
Exemplar temperature-light responses metabolites
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Introduction Cold acclimation Signaling
pathways Outlook

• Identify transcriptional regulatory networks
  underlying plant responses to temperature and
  light
• Investigate small molecule signaling in response
  to environmental perturbation
• Use forward genetics to dissect signaling
  cascades
• Investigate the importance of these cascades for
  plant adaptation and survival

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Acknowledgements

• Lothar Willmitzer
• Dirk Hincha
• Arnd Heyer
• Cold
• Carmen Espinoza
• Zuzanna Bieniawska
• Armin Schlereth
• Ronan Sulpice
• Candidate signals
• Alisdair Fernie
• Dirk Steinhauser
• Metanomics

• Dynamic networks
• Henning Redestig
• Camila Caldana
• Andrea Leisse