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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

Functional classification of the phenol-extracted circadian-regulated proteins by GO analysis. Percentage GO terms were displayed for three GO vocabularies: (A) Cellular component, (B) Biological process, and (C) Molecular function. (D–F) Results for same categories obtained from RuBisCO-depleted protein extracts.
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Figure 6: Functional classification of the phenol-extracted circadian-regulated proteins by GO analysis. Percentage GO terms were displayed for three GO vocabularies: (A) Cellular component, (B) Biological process, and (C) Molecular function. (D–F) Results for same categories obtained from RuBisCO-depleted protein extracts.

Mentions: For further characterization we performed GO analysis using TAIR Slim GO for cellular component, molecular function and biological process. The cellular component representation is extremely similar for both the protein extraction procedures, but there is slightly less representation of chloroplast and plastid protein in the RuBisCO-depleted extracts (48 vs. 50%), possibly reflecting the removal of RuBisCO (Figure 6A). Within the molecular function category, proteins involved in enzymatic activity and protein and nucleotide binding are the major players in both data sets. At the biological process level proteins related to stress response and protein metabolism are the major contributors (Figure 6). Thus, the two types of extractions displayed a high degree of similarity in the relative contribution of three different GO vocabularies examined.


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

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

Functional classification of the phenol-extracted circadian-regulated proteins by GO analysis. Percentage GO terms were displayed for three GO vocabularies: (A) Cellular component, (B) Biological process, and (C) Molecular function. (D–F) Results for same categories obtained from RuBisCO-depleted protein extracts.
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4940426&req=5

Figure 6: Functional classification of the phenol-extracted circadian-regulated proteins by GO analysis. Percentage GO terms were displayed for three GO vocabularies: (A) Cellular component, (B) Biological process, and (C) Molecular function. (D–F) Results for same categories obtained from RuBisCO-depleted protein extracts.
Mentions: For further characterization we performed GO analysis using TAIR Slim GO for cellular component, molecular function and biological process. The cellular component representation is extremely similar for both the protein extraction procedures, but there is slightly less representation of chloroplast and plastid protein in the RuBisCO-depleted extracts (48 vs. 50%), possibly reflecting the removal of RuBisCO (Figure 6A). Within the molecular function category, proteins involved in enzymatic activity and protein and nucleotide binding are the major players in both data sets. At the biological process level proteins related to stress response and protein metabolism are the major contributors (Figure 6). Thus, the two types of extractions displayed a high degree of similarity in the relative contribution of three different GO vocabularies examined.

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