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Interaction with diurnal and circadian regulation results in dynamic metabolic and transcriptional changes during cold acclimation in Arabidopsis.

Espinoza C, Degenkolbe T, Caldana C, Zuther E, Leisse A, Willmitzer L, Hincha DK, Hannah MA - PLoS ONE (2010)

Bottom Line: Levels of some conventional cold induced metabolites, such as γ-aminobutyric acid, galactinol, raffinose and putrescine, exhibited diurnal and circadian oscillations and transcripts encoding their biosynthetic enzymes often also cycled and preceded their cold-induction, in agreement with transcriptional regulation.However, the accumulation of other cold-responsive metabolites, for instance homoserine, methionine and maltose, did not have consistent transcriptional regulation, implying that metabolic reconfiguration involves complex transcriptional and post-transcriptional mechanisms.These data demonstrate the importance of understanding cold acclimation in the correct day-night context, and are further supported by our demonstration of impaired cold acclimation in a circadian mutant.

View Article: PubMed Central - PubMed

Affiliation: Max-Planck-Institute of Molecular Plant Physiology, Potsdam, Germany.

ABSTRACT
In plants, there is a large overlap between cold and circadian regulated genes and in Arabidopsis, we have shown that cold (4°C) affects the expression of clock oscillator genes. However, a broader insight into the significance of diurnal and/or circadian regulation of cold responses, particularly for metabolic pathways, and their physiological relevance is lacking. Here, we performed an integrated analysis of transcripts and primary metabolites using microarrays and gas chromatography-mass spectrometry. As expected, expression of diurnally regulated genes was massively affected during cold acclimation. Our data indicate that disruption of clock function at the transcriptional level extends to metabolic regulation. About 80% of metabolites that showed diurnal cycles maintained these during cold treatment. In particular, maltose content showed a massive night-specific increase in the cold. However, under free-running conditions, maltose was the only metabolite that maintained any oscillations in the cold. Furthermore, although starch accumulates during cold acclimation we show it is still degraded at night, indicating significance beyond the previously demonstrated role of maltose and starch breakdown in the initial phase of cold acclimation. Levels of some conventional cold induced metabolites, such as γ-aminobutyric acid, galactinol, raffinose and putrescine, exhibited diurnal and circadian oscillations and transcripts encoding their biosynthetic enzymes often also cycled and preceded their cold-induction, in agreement with transcriptional regulation. However, the accumulation of other cold-responsive metabolites, for instance homoserine, methionine and maltose, did not have consistent transcriptional regulation, implying that metabolic reconfiguration involves complex transcriptional and post-transcriptional mechanisms. These data demonstrate the importance of understanding cold acclimation in the correct day-night context, and are further supported by our demonstration of impaired cold acclimation in a circadian mutant.

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Contribution of low temperature and diurnal regulation to the variation in transcripts and metabolites in diurnal and circadian time courses.PCA (Principal Component Analysis) was applied to transcript (A) and metabolite (B) profiling datasets from diurnal and circadian time courses. The color indicates the different light and temperature conditions of the studied time courses: light/dark cycles either at 20°C (red) or 4°C (dark blue) and continuous light at 20°C (orange) or 4°C (light blue). Circadian time courses are denoted by c in lowercase. Sampling time is indicated by ZT (zeitgeber, in hours). PC1 and PC2 correspond to principal component 1 and 2, respectively. Each point in (A) represents a single transcript profile, whilst in (B) it represents the mean metabolite profile of five biological replicates.
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pone-0014101-g002: Contribution of low temperature and diurnal regulation to the variation in transcripts and metabolites in diurnal and circadian time courses.PCA (Principal Component Analysis) was applied to transcript (A) and metabolite (B) profiling datasets from diurnal and circadian time courses. The color indicates the different light and temperature conditions of the studied time courses: light/dark cycles either at 20°C (red) or 4°C (dark blue) and continuous light at 20°C (orange) or 4°C (light blue). Circadian time courses are denoted by c in lowercase. Sampling time is indicated by ZT (zeitgeber, in hours). PC1 and PC2 correspond to principal component 1 and 2, respectively. Each point in (A) represents a single transcript profile, whilst in (B) it represents the mean metabolite profile of five biological replicates.

Mentions: Principal Component Analysis (PCA) was used to determine the main contributions to variation in the data. Figure 2 shows that temperature was responsible for the primary difference in both transcript and metabolite datasets. Principal Component 1 (PC1) separates samples of cold treated plants from those at 20°C, and explains 38% and 67% of the variation for the transcript and metabolite data, respectively. Time zero samples (ZT14) clustered together with samples at 20°C, and subsequent time points from the cold series showed progressively larger separation from time 0, as expected from previous publications [5], [12], [14]. Interestingly, in L/L separation of samples based on metabolite changes in the cold progressed more rapidly than in L/D, with earlier time points segregating more strongly from the control samples. Diurnal variation was also clearly visible and underlies PC2, which explains 13% and 12% of the variation for the transcript and metabolite data, respectively. In case of transcripts, diurnal patterns are apparent in Figure 2 where samples from time points that differ by 24 h mostly group together in the L/D 20°C time course. In addition, L/D and L/L samples at 20°C are also separated by PCA as L/L samples are more tightly grouped than the L/D samples, highlighting the greater contribution of diurnal regulation to sample variation. For the metabolites, where both L/L and L/D were additionally studied in the cold, the contribution of diurnal regulation was less pronounced at 4°C than 20°C, consistent with a disruption of the clock by cold [1].


Interaction with diurnal and circadian regulation results in dynamic metabolic and transcriptional changes during cold acclimation in Arabidopsis.

Espinoza C, Degenkolbe T, Caldana C, Zuther E, Leisse A, Willmitzer L, Hincha DK, Hannah MA - PLoS ONE (2010)

Contribution of low temperature and diurnal regulation to the variation in transcripts and metabolites in diurnal and circadian time courses.PCA (Principal Component Analysis) was applied to transcript (A) and metabolite (B) profiling datasets from diurnal and circadian time courses. The color indicates the different light and temperature conditions of the studied time courses: light/dark cycles either at 20°C (red) or 4°C (dark blue) and continuous light at 20°C (orange) or 4°C (light blue). Circadian time courses are denoted by c in lowercase. Sampling time is indicated by ZT (zeitgeber, in hours). PC1 and PC2 correspond to principal component 1 and 2, respectively. Each point in (A) represents a single transcript profile, whilst in (B) it represents the mean metabolite profile of five biological replicates.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2990718&req=5

pone-0014101-g002: Contribution of low temperature and diurnal regulation to the variation in transcripts and metabolites in diurnal and circadian time courses.PCA (Principal Component Analysis) was applied to transcript (A) and metabolite (B) profiling datasets from diurnal and circadian time courses. The color indicates the different light and temperature conditions of the studied time courses: light/dark cycles either at 20°C (red) or 4°C (dark blue) and continuous light at 20°C (orange) or 4°C (light blue). Circadian time courses are denoted by c in lowercase. Sampling time is indicated by ZT (zeitgeber, in hours). PC1 and PC2 correspond to principal component 1 and 2, respectively. Each point in (A) represents a single transcript profile, whilst in (B) it represents the mean metabolite profile of five biological replicates.
Mentions: Principal Component Analysis (PCA) was used to determine the main contributions to variation in the data. Figure 2 shows that temperature was responsible for the primary difference in both transcript and metabolite datasets. Principal Component 1 (PC1) separates samples of cold treated plants from those at 20°C, and explains 38% and 67% of the variation for the transcript and metabolite data, respectively. Time zero samples (ZT14) clustered together with samples at 20°C, and subsequent time points from the cold series showed progressively larger separation from time 0, as expected from previous publications [5], [12], [14]. Interestingly, in L/L separation of samples based on metabolite changes in the cold progressed more rapidly than in L/D, with earlier time points segregating more strongly from the control samples. Diurnal variation was also clearly visible and underlies PC2, which explains 13% and 12% of the variation for the transcript and metabolite data, respectively. In case of transcripts, diurnal patterns are apparent in Figure 2 where samples from time points that differ by 24 h mostly group together in the L/D 20°C time course. In addition, L/D and L/L samples at 20°C are also separated by PCA as L/L samples are more tightly grouped than the L/D samples, highlighting the greater contribution of diurnal regulation to sample variation. For the metabolites, where both L/L and L/D were additionally studied in the cold, the contribution of diurnal regulation was less pronounced at 4°C than 20°C, consistent with a disruption of the clock by cold [1].

Bottom Line: Levels of some conventional cold induced metabolites, such as γ-aminobutyric acid, galactinol, raffinose and putrescine, exhibited diurnal and circadian oscillations and transcripts encoding their biosynthetic enzymes often also cycled and preceded their cold-induction, in agreement with transcriptional regulation.However, the accumulation of other cold-responsive metabolites, for instance homoserine, methionine and maltose, did not have consistent transcriptional regulation, implying that metabolic reconfiguration involves complex transcriptional and post-transcriptional mechanisms.These data demonstrate the importance of understanding cold acclimation in the correct day-night context, and are further supported by our demonstration of impaired cold acclimation in a circadian mutant.

View Article: PubMed Central - PubMed

Affiliation: Max-Planck-Institute of Molecular Plant Physiology, Potsdam, Germany.

ABSTRACT
In plants, there is a large overlap between cold and circadian regulated genes and in Arabidopsis, we have shown that cold (4°C) affects the expression of clock oscillator genes. However, a broader insight into the significance of diurnal and/or circadian regulation of cold responses, particularly for metabolic pathways, and their physiological relevance is lacking. Here, we performed an integrated analysis of transcripts and primary metabolites using microarrays and gas chromatography-mass spectrometry. As expected, expression of diurnally regulated genes was massively affected during cold acclimation. Our data indicate that disruption of clock function at the transcriptional level extends to metabolic regulation. About 80% of metabolites that showed diurnal cycles maintained these during cold treatment. In particular, maltose content showed a massive night-specific increase in the cold. However, under free-running conditions, maltose was the only metabolite that maintained any oscillations in the cold. Furthermore, although starch accumulates during cold acclimation we show it is still degraded at night, indicating significance beyond the previously demonstrated role of maltose and starch breakdown in the initial phase of cold acclimation. Levels of some conventional cold induced metabolites, such as γ-aminobutyric acid, galactinol, raffinose and putrescine, exhibited diurnal and circadian oscillations and transcripts encoding their biosynthetic enzymes often also cycled and preceded their cold-induction, in agreement with transcriptional regulation. However, the accumulation of other cold-responsive metabolites, for instance homoserine, methionine and maltose, did not have consistent transcriptional regulation, implying that metabolic reconfiguration involves complex transcriptional and post-transcriptional mechanisms. These data demonstrate the importance of understanding cold acclimation in the correct day-night context, and are further supported by our demonstration of impaired cold acclimation in a circadian mutant.

Show MeSH