Biochemistry, proteomics, and phosphoproteomics of plant mitochondria from non-photosynthetic cells

Havelund, Jesper Foged; Thelen, Jay J.; Møller, Ian Max

doi:10.3389/fpls.2013.00051

Cited by 34 publications

(28 citation statements)

References 91 publications

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“…This should facilitate renewed plastid phosphorylation network analysis and linkage between (novel) plastid kinases, such as ABC1Ks (Lundquist et al, 2012) and candidate plastid substrates. According to a recent review (Havelund et al, 2013), 64 mitochondrial proteins (with 103 p-sites) were found to be phosphorylated. This number was increased to 168 proteins (from set A) in this study.…”

Section: Over-and Underrepresentation Of Phosphorylation In Cellular mentioning

confidence: 99%

Meta-Analysis of Arabidopsis thaliana Phospho-Proteomics Data Reveals Compartmentalization of Phosphorylation Motifs

et al. 2014

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ORCID ID: 0000-0001-9536-0487 (K.J.v.W.)Protein (de)phosphorylation plays an important role in plants. To provide a robust foundation for subcellular phosphorylation signaling network analysis and kinase-substrate relationships, we performed a meta-analysis of 27 published and unpublished in-house mass spectrometry-based phospho-proteome data sets for Arabidopsis thaliana covering a range of processes, (non)photosynthetic tissue types, and cell cultures. This resulted in an assembly of 60,366 phospho-peptides matching to 8141 nonredundant proteins. Filtering the data for quality and consistency generated a set of medium and a set of high confidence phospho-proteins and their assigned phospho-sites. The relation between single and multiphosphorylated peptides is discussed. The distribution of p-proteins across cellular functions and subcellular compartments was determined and showed overrepresentation of protein kinases. Extensive differences in frequency of pY were found between individual studies due to proteomics and mass spectrometry workflows. Interestingly, pY was underrepresented in peroxisomes but overrepresented in mitochondria. Using motif-finding algorithms motif-x and MMFPh at high stringency, we identified compartmentalization of phosphorylation motifs likely reflecting localized kinase activity. The filtering of the data assembly improved signal/noise ratio for such motifs. Identified motifs were linked to kinases through (bioinformatic) enrichment analysis. This study also provides insight into the challenges/pitfalls of using large-scale phospho-proteomic data sets to nonexperts.

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Section: Over-and Underrepresentation Of Phosphorylation In Cellular mentioning

confidence: 99%

Meta-Analysis of Arabidopsis thaliana Phospho-Proteomics Data Reveals Compartmentalization of Phosphorylation Motifs

et al. 2014

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“…No studies to date have specifically examined the role of reversible protein phosphorylation in the mitochondrial IMS of any organism despite targeted proteomics studies revealing the presence of a number of protein kinases and protein phosphatases in this subcompartment (Salvi et al, 2005;Pagliarini and Dixon, 2006;Vögtle et al, 2012;Duncan et al, 2013). To date, 10 protein kinases have been localized to the plant mitchondrion, but none specifically to the IMS (Havelund et al, 2013). Furthermore, recent elucidation of the IMS proteome of yeast identified a number of IMS proteins that have been previously documented in whole mitochondria phosphoproteomics studies to be phosphorylated (Vögtle et al, 2012).…”

Section: Atslp2-atmia40 Protein Complex Negatively Regulates Ga Biosymentioning

confidence: 99%

Activation of Mitochondrial Protein Phosphatase SLP2 by MIA40 Regulates Seed Germination

et al. 2016

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Reversible protein phosphorylation catalyzed by protein kinases and phosphatases represents the most prolific and wellcharacterized posttranslational modification known. Here, we demonstrate that Arabidopsis (Arabidopsis thaliana) Shewanella-like protein phosphatase 2 (AtSLP2) is a bona fide Ser/Thr protein phosphatase that is targeted to the mitochondrial intermembrane space (IMS) where it interacts with the mitochondrial oxidoreductase import and assembly protein 40 (AtMIA40), forming a protein complex. Interaction with AtMIA40 is necessary for the phosphatase activity of AtSLP2 and is dependent on the formation of disulfide bridges on AtSLP2. Furthermore, by utilizing atslp2 null mutant, AtSLP2 complemented and AtSLP2 overexpressing plants, we identify a function for the AtSLP2-AtMIA40 complex in negatively regulating gibberellic acid-related processes during seed germination. Results presented here characterize a mitochondrial IMS-localized protein phosphatase identified in photosynthetic eukaryotes as well as a protein phosphatase target of the highly conserved eukaryotic MIA40 IMS oxidoreductase.

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“…In the intervening years, a number of more focused proteomic studies have been performed mainly on Arabidopsis mitochondria, swelling the number of identified plant mitochondrial proteins to 660 nonredundant proteins (Heazlewood et al, 2004;Duncan et al, 2011;Klodmann et al, 2011;Lee et al, 2012;Tan et al, 2012). Missing from this list are many essential plant mitochondrial activities, including regulatory proteins, transcription factors, metabolite translocators, and the wealth of tRNA synthases and pentatricopeptide repeat (PPR) proteins (Havelund et al, 2013).…”

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confidence: 99%

The Potato Tuber Mitochondrial Proteome

et al. 2013

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Mitochondria are called the powerhouses of the cell. To better understand the role of mitochondria in maintaining and regulating metabolism in storage tissues, highly purified mitochondria were isolated from dormant potato tubers (Solanum tuberosum 'Folva') and their proteome investigated. Proteins were resolved by one-dimensional gel electrophoresis, and tryptic peptides were extracted from gel slices and analyzed by liquid chromatography-tandem mass spectrometry using an Orbitrap XL. Using four different search programs, a total of 1,060 nonredundant proteins were identified in a quantitative manner using normalized spectral counts including as many as 5-fold more "extreme" proteins (low mass, high isoelectric point, hydrophobic) than previous mitochondrial proteome studies. We estimate that this compendium of proteins represents a high coverage of the potato tuber mitochondrial proteome (possibly as high as 85%). The dynamic range of protein expression spanned 1,800-fold and included nearly all components of the electron transport chain, tricarboxylic acid cycle, and protein import apparatus. Additionally, we identified 71 pentatricopeptide repeat proteins, 29 membrane carriers/transporters, a number of new proteins involved in coenzyme biosynthesis and iron metabolism, the pyruvate dehydrogenase kinase, and a type 2C protein phosphatase that may catalyze the dephosphorylation of the pyruvate dehydrogenase complex. Systematic analysis of prominent posttranslational modifications revealed that more than 50% of the identified proteins harbor at least one modification. The most prominently observed class of posttranslational modifications was oxidative modifications. This study reveals approximately 500 new or previously unconfirmed plant mitochondrial proteins and outlines a facile strategy for unbiased, near-comprehensive identification of mitochondrial proteins and their modified forms.

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Biochemistry, proteomics, and phosphoproteomics of plant mitochondria from non-photosynthetic cells

Cited by 34 publications

References 91 publications

Meta-Analysis of Arabidopsis thaliana Phospho-Proteomics Data Reveals Compartmentalization of Phosphorylation Motifs

Meta-Analysis of Arabidopsis thaliana Phospho-Proteomics Data Reveals Compartmentalization of Phosphorylation Motifs

Activation of Mitochondrial Protein Phosphatase SLP2 by MIA40 Regulates Seed Germination

The Potato Tuber Mitochondrial Proteome

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