Construction of a chloroplast protein interaction network and functional mining of photosynthetic proteins in Arabidopsis thaliana

Yu, Qing; Li, Guang; Wang, Guan; Sun, Jing; Wang, Peng Cheng; Wang, Chen; Mi, Hua Ling; Wei, Min; Cui, Jian; Cui, Yong; Chong, Kang; Li, Yi Xue; Li, Yu Hua; Zhao, Zhongming; Shi, Tie Liu; Yang, Zhong‐Nan

doi:10.1038/cr.2008.286

Cited by 43 publications

(39 citation statements)

References 71 publications

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“…All information concerning peptide and protein identifications are deposited in the PRoteomics IDEntifications (PRIDE) database (20). To extract plastid phosphoproteins, we matched this dataset against a chloroplast proteome reference table that was assembled from the overlap of two previously published chloroplast proteome datasets (SI Appendix, Table S1) (10,21). Altogether, 1,657 spectra, 294 phosphopeptides, and 149 phosphoproteins matched with chloroplast proteins (SI Appendix, Table S2).…”

Section: Resultsmentioning

confidence: 99%

Comparative phosphoproteome profiling reveals a function of the STN8 kinase in fine-tuning of cyclic electron flow (CEF)

Reiland

Finazzi

Endler

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

142

133

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Important aspects of photosynthetic electron transport efficiency in chloroplasts are controlled by protein phosphorylation. Two thylakoid-associated kinases, STN7 and STN8, have distinct roles in shortand long-term photosynthetic acclimation to changes in light quality and quantity. Although some substrates of STN7 and STN8 are known, the complexity of this regulatory kinase system implies that currently unknown substrates connect photosynthetic performance with the regulation of metabolic and regulatory functions. We performed an unbiased phosphoproteome-wide screen with Arabidopsis WT and stn8 mutant plants to identify unique STN8 targets. The phosphorylation status of STN7 was not affected in stn8, indicating that kinases other than STN8 phosphorylate STN7 under standard growth conditions. Among several putative STN8 substrates, PGRL1-A is of particular importance because of its possible role in the modulation of cyclic electron transfer. The STN8 phosphorylation site on PGRL1-A is absent in both monocotyledonous plants and algae. In dicots, spectroscopic measurements with Arabidopsis WT, stn7, stn8, and stn7/stn8 double-mutant plants indicate a STN8-mediated slowing down of the transition from cyclic to linear electron flow at the onset of illumination. This finding suggests a possible link between protein phosphorylation by STN8 and fine-tuning of cyclic electron flow during this critical step of photosynthesis, when the carbon assimilation is not commensurate to the electron flow capacity of the chloroplast.phosphoproteomics | Arabidopsis thaliana I n the field of chloroplast biogenesis, interest in protein phosphorylation historically focused on photosynthesis-related proteins, with the initial discovery of thylakoid membrane protein phosphorylation dating back to the late 1970s (1-4). Almost a decade later, AtpB, RNA-binding proteins, and transcription factors were recognized as phosphoproteins in thylakoid membranes and stroma fractions (5-7). Because of recent large-scale functional genomics and phosphoproteomics approaches, ∼200 chloroplast phosphoproteins are known today, and several kinases have been identified that are most likely involved in their phosphorylation (8). However, the exact kinase/substrate relationships are not known for most of the proteins, and efforts are underway to identify in vivo substrates of known kinases. Phosphoproteomics data suggest that chloroplast functions are regulated by a highly complex phosphoprotein network in which one kinase phosphorylates several substrates and one substrate is probably phosphorylated by several kinases at different sites (9, 10).Although we currently do not understand all nodes in the chloroplast phosphoprotein network, candidate proteins and experimental tools are available to address the above questions. Two of the best-characterized chloroplast kinases are STN7 and STN8. STN7 is the ortholog of the Stt7 kinase from Chlamydomonas reinhardtii that was identified in screens for strains with a defect in state transitions (11). This process ba...

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Section: Resultsmentioning

confidence: 99%

Comparative phosphoproteome profiling reveals a function of the STN8 kinase in fine-tuning of cyclic electron flow (CEF)

Reiland

Finazzi

Endler

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

142

133

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“…1). After several false starts owing to lack of sensitivity of mass spectrometers and high false discovery rates of the algorithms used to predict chloroplast transit sequences, the chloroplast proteome is now thought to contain about 2000 proteins (Millar et al, 2006;Yu et al, 2008;Zybailov et al, 2008). To validate these predictions, it will be necessary to test experimentally the localization of at least a subset of the proteins.…”

Section: Systems Biology In Anterograde Regulation Chloroplast Proteomentioning

confidence: 99%

Signaling between Chloroplasts and the Nucleus: Can a Systems Biology Approach Bring Clarity to a Complex and Highly Regulated Pathway?

Jung

Chory

2009

Plant Physiology

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“…The set of 1,476 nuclear genes encoding chloroplast proteins was extracted from a previously compiled list of 1,808 chloroplast proteins (Yu et al, 2008), selecting those proteins that had been reliably assigned to chloroplasts and adding known chloroplast proteins not already on the list. The set of 1,323 nuclear genes for mitochondrial proteins was compiled by extracting mitochondrial proteins validated by the presence of at least one EST in the SUBA (Heazlewood et al, 2007) and the MitoP2 (Elstner et al, 2009) databases.…”

Section: Gene Sets and Microarray Expression Datamentioning

confidence: 99%

Intracompartmental and Intercompartmental Transcriptional Networks Coordinate the Expression of Genes for Organellar Functions

et al. 2011

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(X.W., G.H., K.F.X.M.)Genes for mitochondrial and chloroplast proteins are distributed between the nuclear and organellar genomes. Organelle biogenesis and metabolism, therefore, require appropriate coordination of gene expression in the different compartments to ensure efficient synthesis of essential multiprotein complexes of mixed genetic origin. Whereas organelle-to-nucleus signaling influences nuclear gene expression at the transcriptional level, organellar gene expression (OGE) is thought to be primarily regulated posttranscriptionally. Here, we show that intracompartmental and intercompartmental transcriptional networks coordinate the expression of genes for organellar functions. Nearly 1,300 ATH1 microarray-based transcriptional profiles of nuclear and organellar genes for mitochondrial and chloroplast proteins in the model plant Arabidopsis (Arabidopsis thaliana) were analyzed. The activity of genes involved in organellar energy production (OEP) or OGE in each of the organelles and in the nucleus is highly coordinated. Intracompartmental networks that link the OEP and OGE gene sets serve to synchronize the expression of nucleus-and organelle-encoded proteins. At a higher regulatory level, coexpression of organellar and nuclear OEP/OGE genes typically modulates chloroplast functions but affects mitochondria only when chloroplast functions are perturbed. Under conditions that induce energy shortage, the intercompartmental coregulation of photosynthesis genes can even override intracompartmental networks. We conclude that dynamic intracompartmental and intercompartmental transcriptional networks for OEP and OGE genes adjust the activity of organelles in response to the cellular energy state and environmental stresses, and we identify candidate cis-elements involved in the transcriptional coregulation of nuclear genes. Regarding the transcriptional regulation of chloroplast genes, novel tentative target genes of s factors are identified.

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Construction of a chloroplast protein interaction network and functional mining of photosynthetic proteins in Arabidopsis thaliana

Cited by 43 publications

References 71 publications

Comparative phosphoproteome profiling reveals a function of the STN8 kinase in fine-tuning of cyclic electron flow (CEF)

Comparative phosphoproteome profiling reveals a function of the STN8 kinase in fine-tuning of cyclic electron flow (CEF)

Signaling between Chloroplasts and the Nucleus: Can a Systems Biology Approach Bring Clarity to a Complex and Highly Regulated Pathway?

Intracompartmental and Intercompartmental Transcriptional Networks Coordinate the Expression of Genes for Organellar Functions

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