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Circadian Profiling of the Arabidopsis Proteome Using 2D-DIGE.

Choudhary MK, Nomura Y, Shi H, Nakagami H, Somers DE - Front Plant Sci (2016)

Bottom Line: Clock-generated biological rhythms provide an adaptive advantage to an organism, resulting in increased fitness and survival.The phasing of maximum expression for the cyclic proteins was similar for both datasets, with a nearly even distribution of peak phases across the time series.Taken together, this study provides new insights into the importance of post-transcriptional circadian control of plant physiology and metabolism.

View Article: PubMed Central - PubMed

Affiliation: Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology Pohang, South Korea.

ABSTRACT
Clock-generated biological rhythms provide an adaptive advantage to an organism, resulting in increased fitness and survival. To better elucidate the plant response to the circadian system, we surveyed protein oscillations in Arabidopsis seedlings under constant light. Using large-scale two-dimensional difference in gel electrophoresis (2D-DIGE) the abundance of more than 1000 proteins spots was reproducibly resolved quantified and profiled across a circadian time series. A comparison between phenol-extracted samples and RuBisCO-depleted extracts identified 71 and 40 rhythmically-expressed proteins, respectively, and between 30 and 40% of these derive from non-rhythmic transcripts. These included proteins influencing transcriptional regulation, translation, metabolism, photosynthesis, protein chaperones, and stress-mediated responses. The phasing of maximum expression for the cyclic proteins was similar for both datasets, with a nearly even distribution of peak phases across the time series. STRING clustering analysis identified two interaction networks with a notable number of oscillating proteins: plastid-based and cytosolic chaperones and 10 proteins involved in photosynthesis. The oscillation of the ABA receptor, PYR1/RCAR11, with peak expression near dusk adds to a growing body of evidence that intimately ties ABA signaling to the circadian system. Taken together, this study provides new insights into the importance of post-transcriptional circadian control of plant physiology and metabolism.

No MeSH data available.


Related in: MedlinePlus

RuBisCO activase protein oscillation in constant light. Immunodetection of RuBisCO activase (RCA) protein abundance. Ten-day-old Arabidopsis Col-0 seedlings grown under LD cycles were released to continuous light and harvested at the indicated time. White and gray bars indicate subjective day and night. Protein level was quantitated relative to histone H3 and normalized to the level of LL25. Error bars indicate s.e.m. from two biological replicates.
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Figure 5: RuBisCO activase protein oscillation in constant light. Immunodetection of RuBisCO activase (RCA) protein abundance. Ten-day-old Arabidopsis Col-0 seedlings grown under LD cycles were released to continuous light and harvested at the indicated time. White and gray bars indicate subjective day and night. Protein level was quantitated relative to histone H3 and normalized to the level of LL25. Error bars indicate s.e.m. from two biological replicates.

Mentions: Peak RCA protein abundance was early-day phased for both methods and slightly phase-delayed relative to peak RCA mRNA abundance (Figures 4D–F). We validated these results by immunoblot using whole seedling extracts grown under the same entrainment and free-running conditions. Peak RCA levels occurred at the same phase and with similar amplitude as that obtained from the two 2D-DIGE data sets (Figure 5). Both approaches resolved oscillations with a two-fold or less range in abundance, indicating a high degree of sensitivity and reproducibility using 2D-DIGE/MS.


Circadian Profiling of the Arabidopsis Proteome Using 2D-DIGE.

Choudhary MK, Nomura Y, Shi H, Nakagami H, Somers DE - Front Plant Sci (2016)

RuBisCO activase protein oscillation in constant light. Immunodetection of RuBisCO activase (RCA) protein abundance. Ten-day-old Arabidopsis Col-0 seedlings grown under LD cycles were released to continuous light and harvested at the indicated time. White and gray bars indicate subjective day and night. Protein level was quantitated relative to histone H3 and normalized to the level of LL25. Error bars indicate s.e.m. from two biological replicates.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4940426&req=5

Figure 5: RuBisCO activase protein oscillation in constant light. Immunodetection of RuBisCO activase (RCA) protein abundance. Ten-day-old Arabidopsis Col-0 seedlings grown under LD cycles were released to continuous light and harvested at the indicated time. White and gray bars indicate subjective day and night. Protein level was quantitated relative to histone H3 and normalized to the level of LL25. Error bars indicate s.e.m. from two biological replicates.
Mentions: Peak RCA protein abundance was early-day phased for both methods and slightly phase-delayed relative to peak RCA mRNA abundance (Figures 4D–F). We validated these results by immunoblot using whole seedling extracts grown under the same entrainment and free-running conditions. Peak RCA levels occurred at the same phase and with similar amplitude as that obtained from the two 2D-DIGE data sets (Figure 5). Both approaches resolved oscillations with a two-fold or less range in abundance, indicating a high degree of sensitivity and reproducibility using 2D-DIGE/MS.

Bottom Line: Clock-generated biological rhythms provide an adaptive advantage to an organism, resulting in increased fitness and survival.The phasing of maximum expression for the cyclic proteins was similar for both datasets, with a nearly even distribution of peak phases across the time series.Taken together, this study provides new insights into the importance of post-transcriptional circadian control of plant physiology and metabolism.

View Article: PubMed Central - PubMed

Affiliation: Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology Pohang, South Korea.

ABSTRACT
Clock-generated biological rhythms provide an adaptive advantage to an organism, resulting in increased fitness and survival. To better elucidate the plant response to the circadian system, we surveyed protein oscillations in Arabidopsis seedlings under constant light. Using large-scale two-dimensional difference in gel electrophoresis (2D-DIGE) the abundance of more than 1000 proteins spots was reproducibly resolved quantified and profiled across a circadian time series. A comparison between phenol-extracted samples and RuBisCO-depleted extracts identified 71 and 40 rhythmically-expressed proteins, respectively, and between 30 and 40% of these derive from non-rhythmic transcripts. These included proteins influencing transcriptional regulation, translation, metabolism, photosynthesis, protein chaperones, and stress-mediated responses. The phasing of maximum expression for the cyclic proteins was similar for both datasets, with a nearly even distribution of peak phases across the time series. STRING clustering analysis identified two interaction networks with a notable number of oscillating proteins: plastid-based and cytosolic chaperones and 10 proteins involved in photosynthesis. The oscillation of the ABA receptor, PYR1/RCAR11, with peak expression near dusk adds to a growing body of evidence that intimately ties ABA signaling to the circadian system. Taken together, this study provides new insights into the importance of post-transcriptional circadian control of plant physiology and metabolism.

No MeSH data available.


Related in: MedlinePlus