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Abstract
Plant peroxisomes are required for a number of fundamental physiological processes, such as primary and secondary metabolism, development and stress response. Indexing the dynamic peroxisome proteome is prerequisite to fully understanding the importance of these organelles. Mass Spectrometry (MS)-based proteome analysis has allowed the identification of novel peroxisomal proteins and pathways in a relatively high-throughput fashion and significantly expanded the list of proteins and biochemical reactions in plant peroxisomes. In this chapter, we summarize the experimental proteomic studies performed in plants, compile a list of ~200 confirmed Arabidopsis peroxisomal proteins, and discuss the diverse plant peroxisome functions with an emphasis on the role of Arabidopsis MS-based proteomics in discovering new peroxisome functions. Many plant peroxisome proteins and biochemical pathways are specific to plants, substantiating the complexity, plasticity and uniqueness of plant peroxisomes. Mapping the full plant peroxisome proteome will provide a knowledge base for the improvement of crop production, quality and stress tolerance.
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Affiliation(s)
- Ronghui Pan
- MSU-Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
| | - Jianping Hu
- MSU-Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA.
- Plant Biology Department, Michigan State University, East Lansing, MI, 48824, USA.
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Liu SL, Pan AQ, Adams KL. Protein subcellular relocalization of duplicated genes in Arabidopsis. Genome Biol Evol 2014; 6:2501-15. [PMID: 25193306 PMCID: PMC4202327 DOI: 10.1093/gbe/evu191] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Gene duplications during eukaroytic evolution, by successive rounds of polyploidy and by smaller scale duplications, have provided an enormous reservoir of new genes for the evolution of new functions. Preservation of many duplicated genes can be ascribed to changes in sequences, expression patterns, and functions. Protein subcellular relocalization (protein targeting to a new location within the cell) is another way that duplicated genes can diverge. We studied subcellular relocalization of gene pairs duplicated during the evolution of the Brassicaceae including gene pairs from the alpha whole genome duplication that occurred at the base of the family. We analyzed experimental localization data from green fluorescent protein experiments for 128 duplicate pairs in Arabidopsis thaliana, revealing 19 pairs with subcellular relocalization. Many more of the duplicate pairs with relocalization than with the same localization showed an accelerated rate of amino acid sequence evolution in one duplicate, and one gene showed evidence for positive selection. We studied six duplicate gene pairs in more detail. We used gene family analysis with several pairs to infer which gene shows relocalization. We identified potential sequence mutations through comparative analysis that likely result in relocalization of two duplicated gene products. We show that four cases of relocalization have new expression patterns, compared with orthologs in outgroup species, including two with novel expression in pollen. This study provides insights into subcellular relocalization of evolutionarily recent gene duplicates and features of genes whose products have been relocalized.
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Affiliation(s)
- Shao-Lun Liu
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada Present address: Department of Life Science, Tunghai University, Taichung, Taiwan
| | - An Qi Pan
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada Present address: Mintec Inc., Vancouver, BC, Canada
| | - Keith L Adams
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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Braun HP, Binder S, Brennicke A, Eubel H, Fernie AR, Finkemeier I, Klodmann J, König AC, Kühn K, Meyer E, Obata T, Schwarzländer M, Takenaka M, Zehrmann A. The life of plant mitochondrial complex I. Mitochondrion 2014; 19 Pt B:295-313. [PMID: 24561573 DOI: 10.1016/j.mito.2014.02.006] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 01/28/2014] [Accepted: 02/12/2014] [Indexed: 12/29/2022]
Abstract
The mitochondrial NADH dehydrogenase complex (complex I) of the respiratory chain has several remarkable features in plants: (i) particularly many of its subunits are encoded by the mitochondrial genome, (ii) its mitochondrial transcripts undergo extensive maturation processes (e.g. RNA editing, trans-splicing), (iii) its assembly follows unique routes, (iv) it includes an additional functional domain which contains carbonic anhydrases and (v) it is, indirectly, involved in photosynthesis. Comprising about 50 distinct protein subunits, complex I of plants is very large. However, an even larger number of proteins are required to synthesize these subunits and assemble the enzyme complex. This review aims to follow the complete "life cycle" of plant complex I from various molecular perspectives. We provide arguments that complex I represents an ideal model system for studying the interplay of respiration and photosynthesis, the cooperation of mitochondria and the nucleus during organelle biogenesis and the evolution of the mitochondrial oxidative phosphorylation system.
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Affiliation(s)
- Hans-Peter Braun
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany.
| | - Stefan Binder
- Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, 89069 Ulm, Germany
| | - Axel Brennicke
- Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, 89069 Ulm, Germany
| | - Holger Eubel
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Iris Finkemeier
- Plant Sciences, Ludwig Maximilians Universität München, Grosshadernerstr. 2-4, 82152 Planegg-Martinsried, Germany
| | - Jennifer Klodmann
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Ann-Christine König
- Plant Sciences, Ludwig Maximilians Universität München, Grosshadernerstr. 2-4, 82152 Planegg-Martinsried, Germany
| | - Kristina Kühn
- Institut für Biologie/Molekulare Zellbiologie der Pflanzen, Humboldt Universität zu Berlin, Philippstraße 13, 10115 Berlin, Germany
| | - Etienne Meyer
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Toshihiro Obata
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Markus Schwarzländer
- INRES - Chemical Signalling, Rheinische Friedrich-Wilhelms-Universität Bonn, Friedrich-Ebert-Allee 144, D-53113 Bonn, Germany
| | - Mizuki Takenaka
- Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, 89069 Ulm, Germany
| | - Anja Zehrmann
- Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, 89069 Ulm, Germany
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Kaur N, Hu J. Defining the plant peroxisomal proteome: from Arabidopsis to rice. FRONTIERS IN PLANT SCIENCE 2011; 2:103. [PMID: 22645559 PMCID: PMC3355810 DOI: 10.3389/fpls.2011.00103] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Accepted: 12/08/2011] [Indexed: 05/08/2023]
Abstract
Peroxisomes are small subcellular organelles mediating a multitude of processes in plants. Proteomics studies over the last several years have yielded much needed information on the composition of plant peroxisomes. In this review, the status of peroxisome proteomics studies in Arabidopsis and other plant species and the cumulative advances made through these studies are summarized. A reference Arabidopsis peroxisome proteome is generated, and some unique aspects of Arabidopsis peroxisomes that were uncovered through proteomics studies and hint at unanticipated peroxisomal functions are also highlighted. Knowledge gained from Arabidopsis was utilized to compile a tentative list of peroxisome proteins for the model monocot plant, rice. Differences in the peroxisomal proteome between these two model plants were drawn, and novel facets in rice were expounded upon. Finally, we discuss about the current limitations of experimental proteomics in decoding the complete and dynamic makeup of peroxisomes, and complementary and integrated approaches that would be beneficial to defining the peroxisomal metabolic and regulatory roadmaps. The synteny of genomes in the grass family makes rice an ideal model to study peroxisomes in cereal crops, in which these organelles have received much less attention, with the ultimate goal to improve crop yield.
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Affiliation(s)
- Navneet Kaur
- MSU-DOE Plant Research Laboratory, Michigan State UniversityEast Lansing, MI, USA
| | - Jianping Hu
- MSU-DOE Plant Research Laboratory, Michigan State UniversityEast Lansing, MI, USA
- Plant Biology Department, Michigan State UniversityEast Lansing, MI, USA
- *Correspondence: Jianping Hu, MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA. e-mail:
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Armbruster U, Hertle A, Makarenko E, Zühlke J, Pribil M, Dietzmann A, Schliebner I, Aseeva E, Fenino E, Scharfenberg M, Voigt C, Leister D. Chloroplast proteins without cleavable transit peptides: rare exceptions or a major constituent of the chloroplast proteome? MOLECULAR PLANT 2009; 2:1325-35. [PMID: 19995733 DOI: 10.1093/mp/ssp082] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Most chloroplast proteins (cp proteins) are nucleus-encoded, synthesized on cytosolic ribosomes as precursor proteins containing a presequence (cTP), and post-translationally imported via the Tic/Toc complex into the organelle, where the cTP is removed. Only a few unambiguous instances of cp proteins that do not require cTPs (non-canonical cp proteins) have been reported so far. However, the survey of data from large-scale proteomic studies presented here suggests that the fraction of such proteins in the total cp proteome might be as large as approximately 30%. To explore this discrepancy, we chose a representative set of 28 putative non-canonical cp proteins, and used in vitro import and Red Fluorescent Protein (RFP)-fusion assays to determine their sub-cellular destinations. Four proteins, including embryo defective 1211, glycolate oxidase 2, protein disulfide isomerase-like protein (PDII), and a putative glutathione S-transferase, could be unambiguously assigned to the chloroplast. Several others ('potential cp proteins') were found to be imported into chloroplasts in vitro, but failed to localize to the organelle when RFP was fused to their C-terminal ends. Extrapolations suggest that the fraction of cp proteins that enter the inner compartments of the organelle, although they lack a cTP, might be as large as 11.4% of the total cp proteome. Our data also support the idea that cytosolic proteins that associate with the cp outer membrane might account for false positive cp proteins obtained in earlier studies.
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Affiliation(s)
- Ute Armbruster
- Lehrstuhl für Botanik, Department Biologie I, Ludwig-Maximilians-Universität München, Menzinger Str. 67, D-80638 München, Germany
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