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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

Interaction networks within circadian protein data sets. (A) Phenol-extracted and (B) RuBisCO-extracted data sets. Network mapping performed using the STRING protein interaction algorithm based on the STRING database using high confidence parameters. Proteins not connected with network were removed for better visualization. Line colors indicate the types of evidence for each association. Circled groupings indicate (a) chaperone-related and (b,c) photosynthesis-related networks.
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Figure 7: Interaction networks within circadian protein data sets. (A) Phenol-extracted and (B) RuBisCO-extracted data sets. Network mapping performed using the STRING protein interaction algorithm based on the STRING database using high confidence parameters. Proteins not connected with network were removed for better visualization. Line colors indicate the types of evidence for each association. Circled groupings indicate (a) chaperone-related and (b,c) photosynthesis-related networks.

Mentions: The STRING database allows accumulated protein-protein interaction data to be assembled and viewed as interaction networks (Szklarczyk et al., 2015). Using STRING we identified and focus on groupings of rhythmic proteins associated with photosynthesis (the phenol-extracted and RuBisCO-depleted data sets) and chaperones (phenol-extracted data set; Figure 7).


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

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

Interaction networks within circadian protein data sets. (A) Phenol-extracted and (B) RuBisCO-extracted data sets. Network mapping performed using the STRING protein interaction algorithm based on the STRING database using high confidence parameters. Proteins not connected with network were removed for better visualization. Line colors indicate the types of evidence for each association. Circled groupings indicate (a) chaperone-related and (b,c) photosynthesis-related networks.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 7: Interaction networks within circadian protein data sets. (A) Phenol-extracted and (B) RuBisCO-extracted data sets. Network mapping performed using the STRING protein interaction algorithm based on the STRING database using high confidence parameters. Proteins not connected with network were removed for better visualization. Line colors indicate the types of evidence for each association. Circled groupings indicate (a) chaperone-related and (b,c) photosynthesis-related networks.
Mentions: The STRING database allows accumulated protein-protein interaction data to be assembled and viewed as interaction networks (Szklarczyk et al., 2015). Using STRING we identified and focus on groupings of rhythmic proteins associated with photosynthesis (the phenol-extracted and RuBisCO-depleted data sets) and chaperones (phenol-extracted data set; Figure 7).

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