1
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Müller B. Iron transport mechanisms and their evolution focusing on chloroplasts. JOURNAL OF PLANT PHYSIOLOGY 2023; 288:154059. [PMID: 37586271 DOI: 10.1016/j.jplph.2023.154059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 07/26/2023] [Accepted: 07/28/2023] [Indexed: 08/18/2023]
Abstract
Iron (Fe) is an essential element for photosynthetic organisms, required for several vital biological functions. Photosynthesis, which takes place in the chloroplasts of higher plants, is the major Fe consumer. Although the components of the root Fe uptake system in dicotyledonous and monocotyledonous plants have been extensively studied, the Fe transport mechanisms of chloroplasts in these two groups of plants have received little attention. This review focuses on the comparative analysis of Fe transport processes in the evolutionary ancestors of chloroplasts (cyanobacteria) with the processes in embryophytes and green algae (Viridiplantae). The aim is to summarize how chloroplasts are integrated into cellular Fe homeostasis and how Fe transporters and Fe transport mechanisms have been modified by evolution.
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Affiliation(s)
- Brigitta Müller
- Department of Plant Physiology and Molecular Biology, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, H-1117, Hungary.
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2
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Gutiérrez Y, Fresch M, Hellmann SL, Hankeln T, Scherber C, Brockmeyer J. A multifactorial proteomics approach to sex‐specific effects of diet composition and social environment in an omnivorous insect. Ecol Evol 2021. [DOI: 10.1002/ece3.7676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Yeisson Gutiérrez
- Centro de Bioinformática y Biología Computacional de Colombia – BIOS Manizales Colombia
| | - Marion Fresch
- Department Food Chemistry Institute for Biochemistry and Technical Biochemistry University of Stuttgart Stuttgart Germany
| | - Sören L. Hellmann
- Institute of Organismic and Molecular Evolutionary Biology University of Mainz Mainz Germany
| | - Thomas Hankeln
- Institute of Organismic and Molecular Evolutionary Biology University of Mainz Mainz Germany
| | - Christoph Scherber
- Institute of Landscape Ecology University of Münster Münster Germany
- Centre for Biodiversity Monitoring Zoological Research Museum Alexander Koenig Bonn Germany
| | - Jens Brockmeyer
- Department Food Chemistry Institute for Biochemistry and Technical Biochemistry University of Stuttgart Stuttgart Germany
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3
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Bayer RG, Stael S, Teige M. Chloroplast Isolation and Enrichment of Low-Abundance Proteins by Affinity Chromatography for Identification in Complex Proteomes. Methods Mol Biol 2021; 2261:535-547. [PMID: 33421013 DOI: 10.1007/978-1-0716-1186-9_34] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Comprehensive knowledge of the proteome is a crucial prerequisite to understand dynamic changes in biological systems. Particularly low-abundance proteins are of high relevance in these processes as these are often proteins involved in signal transduction and acclimation responses. Although technological advances resulted in a tremendous increase in protein identification sensitivity by mass spectrometry (MS), the dynamic range in protein abundance is still the most limiting problem for the detection of low-abundance proteins in complex proteomes. These proteins will typically escape detection in shotgun MS experiments due to the presence of high-abundance proteins. Therefore, specific enrichment strategies are still required to overcome this technical limitation of MS-based protein discovery. We have searched for novel signal transduction proteins, more specifically kinases and calcium-binding proteins, and here we describe different approaches for enrichment of these low-abundance proteins from isolated chloroplasts from pea and Arabidopsis for subsequent proteomic analysis by MS. These approaches could be extended to include other signal transduction proteins and target different organelles.
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Affiliation(s)
- Roman G Bayer
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Simon Stael
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
- VIB Department of Plant Systems Biology, Ghent University, Ghent, Belgium
| | - Markus Teige
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria.
- Max Perutz Labs, Department of Biochemistry and Cell Biology, University of Vienna, Vienna, Austria.
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4
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Ebner JN, Ritz D, von Fumetti S. Comparative proteomics of stenotopic caddisfly Crunoecia irrorata identifies acclimation strategies to warming. Mol Ecol 2019; 28:4453-4469. [PMID: 31478292 PMCID: PMC6856850 DOI: 10.1111/mec.15225] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/28/2019] [Accepted: 07/29/2019] [Indexed: 12/23/2022]
Abstract
Species' ecological preferences are often deduced from habitat characteristics thought to represent more or less optimal conditions for physiological functioning. Evolution has led to stenotopic and eurytopic species, the former having decreased niche breadths and lower tolerances to environmental variability. Species inhabiting freshwater springs are often described as being stenotopic specialists, adapted to the stable thermal conditions found in these habitats. Whether due to past local adaptation these species have evolved or have lost intra-generational adaptive mechanisms to cope with increasing thermal variability has, to our knowledge, never been investigated. By studying how the proteome of a stenotopic species changes as a result of increasing temperatures, we investigate if the absence or attenuation of molecular mechanisms is indicative of local adaptation to freshwater springs. An understanding of compensatory mechanisms is especially relevant as spring specialists will experience thermal conditions beyond their physiological limits due to climate change. In this study, the stenotopic species Crunoecia irrorata (Trichoptera: Lepidostomatidae, Curtis 1834) was acclimated to 10, 15 and 20°C for 168 hr. We constructed a homology-based database and via liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based shotgun proteomics identified 1,358 proteins. Differentially abundant proteins and protein norms of reaction revealed candidate proteins and molecular mechanisms facilitating compensatory responses such as trehalose metabolism, tracheal system alteration and heat-shock protein regulation. A species-specific understanding of compensatory physiologies challenges the characterization of species as having narrow tolerances to environmental variability if that characterization is based on occurrences and habitat characteristics alone.
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Affiliation(s)
- Joshua N. Ebner
- Geoecology Research GroupDepartment of Environmental SciencesUniversity of BaselBaselSwitzerland
| | - Danilo Ritz
- Proteomics Core FacilityBiozentrumUniversity of BaselBaselSwitzerland
| | - Stefanie von Fumetti
- Geoecology Research GroupDepartment of Environmental SciencesUniversity of BaselBaselSwitzerland
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5
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Abstract
In this chapter, we describe some of the approaches we employ in the analysis of iTRAQ data in our group, with an emphasis on practical issues that can occur in larger multi-run projects. Our pipeline starts with a well-established iTRAQ workflow, makes use of protein level quantitation using ProteinPilot, and continues either via a global analysis in the presence of a common reference, or by identifying pairwise comparisons of interest and applying a method taking the protein ratios and protein ratio confidence measures into consideration. Additionally we describe what issues can occur in the more subtle scenarios involving composite databases in multi-run situations, and an approach applicable in that setting.
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6
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Eisenhut M, Hoecker N, Schmidt SB, Basgaran RM, Flachbart S, Jahns P, Eser T, Geimer S, Husted S, Weber APM, Leister D, Schneider A. The Plastid Envelope CHLOROPLAST MANGANESE TRANSPORTER1 Is Essential for Manganese Homeostasis in Arabidopsis. MOLECULAR PLANT 2018; 11:955-969. [PMID: 29734002 DOI: 10.1016/j.molp.2018.04.008] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 04/26/2018] [Accepted: 04/27/2018] [Indexed: 05/18/2023]
Abstract
The transition metal manganese (Mn) is indispensable for photoautotrophic growth since photosystem II (PSII) employs an inorganic Mn4CaO5 cluster for water splitting. Here, we show that the Arabidopsis membrane protein CHLOROPLAST MANGANESE TRANSPORTER1 (CMT1) is involved in chloroplast Mn homeostasis. CMT1 is the closest homolog of the previously characterized thylakoid Mn transporter PHOTOSYNTHESIS-AFFECTED MUTANT71 (PAM71). In contrast to PAM71, CMT1 resides at the chloroplast envelope and is ubiquitously expressed. Nonetheless, like PAM71, the expression of CMT1 can also alleviate the Mn-sensitive phenotype of yeast mutant Δpmr1. The cmt1 mutant is severely suppressed in growth, chloroplast ultrastructure, and PSII activity owing to a decrease in the amounts of pigments and thylakoid membrane proteins. The importance of CMT1 for chloroplast Mn homeostasis is demonstrated by the significant reduction in chloroplast Mn concentrations in cmt1-1, which exhibited reduced Mn binding in PSII complexes. Moreover, CMT1 expression is downregulated in Mn-surplus conditions. The pam71 cmt1-1double mutant resembles the cmt1-1 single mutant rather than pam71 in most respects. Taken together, our results suggest that CMT1 mediates Mn2+ uptake into the chloroplast stroma, and that CMT1 and PAM71 function sequentially in Mn delivery to PSII across the chloroplast envelope and the thylakoid membrane.
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Affiliation(s)
- Marion Eisenhut
- Biochemie der Pflanzen, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany.
| | - Natalie Hoecker
- Molekularbiologie der Pflanzen (Botanik), Department Biologie I, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Sidsel Birkelund Schmidt
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre (CPSC), Faculty of Science, University of Copenhagen, 1871 Frederiksberg, Denmark
| | - Rubek Merina Basgaran
- Biochemie der Pflanzen, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Samantha Flachbart
- Biochemie der Pflanzen, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Peter Jahns
- Biochemie der Pflanzen, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Tabea Eser
- Molekularbiologie der Pflanzen (Botanik), Department Biologie I, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Stefan Geimer
- Zellbiologie/Elektronenmikroskopie NW I/B1, Universität Bayreuth, 95447 Bayreuth, Germany
| | - Søren Husted
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre (CPSC), Faculty of Science, University of Copenhagen, 1871 Frederiksberg, Denmark
| | - Andreas P M Weber
- Biochemie der Pflanzen, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Dario Leister
- Molekularbiologie der Pflanzen (Botanik), Department Biologie I, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Anja Schneider
- Molekularbiologie der Pflanzen (Botanik), Department Biologie I, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany.
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7
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Ruiz-May E, Sørensen I, Fei Z, Zhang S, Domozych DS, Rose JKC. The Secretome and N-Glycosylation Profiles of the Charophycean Green Alga, Penium margaritaceum, Resemble Those of Embryophytes. Proteomes 2018; 6:E14. [PMID: 29561781 PMCID: PMC6027541 DOI: 10.3390/proteomes6020014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 03/13/2018] [Accepted: 03/14/2018] [Indexed: 11/16/2022] Open
Abstract
The secretome can be defined as the population of proteins that are secreted into the extracellular environment. Many proteins that are secreted by eukaryotes are N-glycosylated. However, there are striking differences in the diversity and conservation of N-glycosylation patterns between taxa. For example, the secretome and N-glycosylation structures differ between land plants and chlorophyte green algae, but it is not clear when this divergence took place during plant evolution. A potentially valuable system to study this issue is provided by the charophycean green algae (CGA), which is the immediate ancestors of land plants. In this study, we used lectin affinity chromatography (LAC) coupled with mass spectrometry to characterize the secretome including secreted N-glycoproteins of Penium margaritaceum, which is a member of the CGA. The identified secreted proteins and N-glycans were compared to those known from the chlorophyte green alga Chlamydomonas reinhardtii and the model land plant, Arabidopsis thaliana, to establish their evolutionary context. Our approach allowed the identification of cell wall proteins and proteins modified with N-glycans that are identical to those of embryophytes, which suggests that the P. margaritaceum secretome is more closely related to those of land plants than to those of chlorophytes. The results of this study support the hypothesis that many of the proteins associated with plant cell wall modification as well as other extracellular processes evolved prior to the colonization of terrestrial habitats.
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Affiliation(s)
- Eliel Ruiz-May
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A. C., Cluster BioMimic, Carretera Antigua a Coatepec 351, Congregación el Haya, CP 91070 Xalapa, Veracruz, Mexico.
| | - Iben Sørensen
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
| | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, NY 14853, USA.
- U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA.
| | - Sheng Zhang
- Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA.
| | - David S Domozych
- Department of Biology and Skidmore Microscopy Imaging Center, Skidmore College, Saratoga Springs, NY 12866, USA.
| | - Jocelyn K C Rose
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
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8
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Gu Y, He L, Zhao C, Wang F, Yan B, Gao Y, Li Z, Yang K, Xu J. Biochemical and Transcriptional Regulation of Membrane Lipid Metabolism in Maize Leaves under Low Temperature. FRONTIERS IN PLANT SCIENCE 2017; 8:2053. [PMID: 29250095 PMCID: PMC5714865 DOI: 10.3389/fpls.2017.02053] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 11/16/2017] [Indexed: 05/03/2023]
Abstract
Membrane lipid modulation is one of the major strategies plants have developed for cold acclimation. In this study, a combined lipidomic and transcriptomic analysis was conducted, and the changes in glycerolipids contents and species, and transcriptional regulation of lipid metabolism in maize leaves under low temperature treatment (5°C) were investigated. The lipidomic analysis showed an increase in the phospholipid phosphatidic acid (PA) and a decrease in phosphatidylcholine (PC). And an increase in digalactosyldiacylglycerol and a decrease in monogalactosyldiacylglycerol of the galactolipid class. The results implied an enhanced turnover of PC to PA to serve as precursors for galactolipid synthesis under following low temperature treatment. The analysis of changes in abundance of various lipid molecular species suggested major alterations of different pathways of plastidic lipids synthesis in maize under cold treatment. The synchronous transcriptomic analysis revealed that genes involved in phospholipid and galactolipid synthesis pathways were significantly up-regulated, and a comprehensive gene-metabolite network was generated illustrating activated membrane lipids adjustment in maize leaves following cold treatment. This study will help to understand the regulation of glycerolipids metabolism at both biochemical and molecular biological levels in 18:3 plants and to decipher the roles played by lipid remodeling in cold response in major field crop maize.
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Affiliation(s)
- Yingnan Gu
- Key Laboratory of Modern Agricultural Cultivation and Crop Germplasm Improvement of Heilongjiang Province, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China
- Remote Sensing Technique Center of Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Lin He
- Key Laboratory of Modern Agricultural Cultivation and Crop Germplasm Improvement of Heilongjiang Province, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Changjiang Zhao
- Key Laboratory of Modern Agricultural Cultivation and Crop Germplasm Improvement of Heilongjiang Province, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Feng Wang
- Key Laboratory of Modern Agricultural Cultivation and Crop Germplasm Improvement of Heilongjiang Province, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Bowei Yan
- Key Laboratory of Modern Agricultural Cultivation and Crop Germplasm Improvement of Heilongjiang Province, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Yuqiao Gao
- Key Laboratory of Modern Agricultural Cultivation and Crop Germplasm Improvement of Heilongjiang Province, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Zuotong Li
- Key Laboratory of Modern Agricultural Cultivation and Crop Germplasm Improvement of Heilongjiang Province, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Kejun Yang
- Key Laboratory of Modern Agricultural Cultivation and Crop Germplasm Improvement of Heilongjiang Province, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China
- *Correspondence: Kejun Yang, Jingyu Xu,
| | - Jingyu Xu
- Key Laboratory of Modern Agricultural Cultivation and Crop Germplasm Improvement of Heilongjiang Province, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, China
- *Correspondence: Kejun Yang, Jingyu Xu,
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9
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Synergism of proteomics and mRNA sequencing for enzyme discovery. J Biotechnol 2016; 235:132-8. [DOI: 10.1016/j.jbiotec.2015.12.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 12/07/2015] [Accepted: 12/14/2015] [Indexed: 12/14/2022]
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10
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Bionda T, Gross LE, Becker T, Papasotiriou DG, Leisegang MS, Karas M, Schleiff E. Eukaryotic Hsp70 chaperones in the intermembrane space of chloroplasts. PLANTA 2016; 243:733-47. [PMID: 26669598 DOI: 10.1007/s00425-015-2440-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 11/27/2015] [Indexed: 06/05/2023]
Abstract
MAIN CONCLUSION Multiple eukaryotic Hsp70 typically localized in the cytoplasm are also distributed to the intermembrane space of chloroplasts and might thereby represent the missing link in energizing protein translocation. Protein translocation into organelles is a central cellular process that is tightly regulated. It depends on signals within the preprotein and on molecular machines catalyzing the process. Molecular chaperones participate in transport and translocation of preproteins into organelles to control folding and to provide energy for the individual steps. While most of the processes are explored and the components are identified, the transfer of preproteins into and across the intermembrane space of chloroplasts is not yet understood. The existence of an energy source in this compartment is discussed, because the required transit peptide length for successful translocation into chloroplasts is shorter than that found for mitochondria where energy is provided exclusively by matrix chaperones. Furthermore, a cytosolic-type Hsp70 homologue was proposed as component of the chloroplast translocon in the intermembrane space energizing the initial translocation. The molecular identity of such intermembrane space localized Hsp70 remained unknown, which led to a controversy concerning its existence. We identified multiple cytosolic Hsp70s by mass spectrometry on isolated, thermolysin-treated Medicago sativa chloroplasts. The localization of these Hsp70s of M. sativa or Arabidopsis thaliana in the intermembrane space was confirmed by a self-assembly GFP-based in vivo system. The localization of cytosolic Hsp70s in the stroma of chloroplasts or different mitochondrial compartments could not be observed. Similarly, we could not identify any cytosolic Hsp90 in the intermembrane space of chloroplast. With respect to our results we discuss the possible targeting and function of the Hsp70 found in the intermembrane space.
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Affiliation(s)
- Tihana Bionda
- Molecular Cell Biology of Plants, Goethe University, Max von Laue Str. 9, 60438, Frankfurt, Germany
- Institute of Biochemistry II, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Lucia E Gross
- Molecular Cell Biology of Plants, Goethe University, Max von Laue Str. 9, 60438, Frankfurt, Germany
| | - Thomas Becker
- Molecular Cell Biology of Plants, Goethe University, Max von Laue Str. 9, 60438, Frankfurt, Germany
- Biochemistry and Molecular Biology, ZBMZ, and BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, Stefan-Meier-Str. 17, 79104, Freiburg, Germany
| | - Dimitrios G Papasotiriou
- Pharmaceutical Chemistry, Goethe University, Max von Laue Str. 9, 60438, Frankfurt, Germany
- Syngenta Ltd., Jealott's Hill International Research Centre, Bracknell, Berkshire, RG42 6EY, UK
| | - Matthias S Leisegang
- Molecular Cell Biology of Plants, Goethe University, Max von Laue Str. 9, 60438, Frankfurt, Germany
- Institute for Cardiovascular Physiology, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Michael Karas
- Pharmaceutical Chemistry, Goethe University, Max von Laue Str. 9, 60438, Frankfurt, Germany
| | - Enrico Schleiff
- Molecular Cell Biology of Plants, Goethe University, Max von Laue Str. 9, 60438, Frankfurt, Germany.
- Molecular Cell Biology of Plants, Cluster of Excellence Frankfurt, Goethe University, Max von Laue Str. 9, 60438, Frankfurt, Germany.
- Buchmann Institut for Molecular Life Sciences, Max von Laue Str. 9, 60438, Frankfurt, Germany.
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11
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Paul P, Chaturvedi P, Selymesi M, Ghatak A, Mesihovic A, Scharf KD, Weckwerth W, Simm S, Schleiff E. The membrane proteome of male gametophyte in Solanum lycopersicum. J Proteomics 2016; 131:48-60. [DOI: 10.1016/j.jprot.2015.10.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Revised: 09/21/2015] [Accepted: 10/08/2015] [Indexed: 12/11/2022]
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12
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Provan F, Nilsen MM, Larssen E, Uleberg KE, Sydnes MO, Lyng E, Øysæd KB, Baussant T. An evaluation of coral lophelia pertusa mucus as an analytical matrix for environmental monitoring: A preliminary proteomic study. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2016; 79:647-657. [PMID: 27484144 DOI: 10.1080/15287394.2016.1210494] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
For the environmental monitoring of coral, mucus appears to be an appropriate biological matrix due to its array of functions in coral biology and the non-intrusive manner in which it can be collected. The aim of the present study was to evaluate the feasibility of using mucus of the stony coral Lophelia pertusa (L. pertusa) as an analytical matrix for discovery of biomarkers used for environmental monitoring. More specifically, to assess whether a mass-spectrometry-based proteomic approach can be applied to characterize the protein composition of coral mucus and changes related to petroleum discharges at the seafloor. Surface-enhanced laser desorption/ionization-time of flight mass spectrometry (SELDI-TOF MS) screening analyses of orange and white L. pertusa showed that the mucosal protein composition varies significantly with color phenotype, a pattern not reported prior to this study. Hence, to reduce variability from phenotype difference, L. pertusa white individuals only were selected to characterize in more detail the basal protein composition in mucus using liquid chromatography, mass spectrometry, mass spectrometry (LC-MS/MS). In total, 297 proteins were identified in L. pertusa mucus of unexposed coral individuals. Individuals exposed to drill cuttings in the range 2 to 12 mg/L showed modifications in coral mucus protein composition compared to unexposed corals. Although the results were somewhat inconsistent between individuals and require further validation in both the lab and the field, this study demonstrated preliminary encouraging results for discovery of protein markers in coral mucus that might provide more comprehensive insight into potential consequences attributed to anthropogenic stressors and may be used in future monitoring of coral health.
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Affiliation(s)
- Fiona Provan
- a International Research Institute of Stavanger (IRIS), Biomiljø , Randaberg , Norway
| | - Mari Mæland Nilsen
- a International Research Institute of Stavanger (IRIS), Biomiljø , Randaberg , Norway
| | - Eivind Larssen
- a International Research Institute of Stavanger (IRIS), Biomiljø , Randaberg , Norway
| | - Kai-Erik Uleberg
- a International Research Institute of Stavanger (IRIS), Biomiljø , Randaberg , Norway
| | - Magne O Sydnes
- a International Research Institute of Stavanger (IRIS), Biomiljø , Randaberg , Norway
- b Faculty of Science and Technology, Department of Mathematics and Natural Science , University of Stavanger , Stavanger , Norway
| | - Emily Lyng
- a International Research Institute of Stavanger (IRIS), Biomiljø , Randaberg , Norway
| | - Kjell Birger Øysæd
- a International Research Institute of Stavanger (IRIS), Biomiljø , Randaberg , Norway
| | - Thierry Baussant
- a International Research Institute of Stavanger (IRIS), Biomiljø , Randaberg , Norway
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13
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Boudichevskaia A, Heckwolf M, Kaldenhoff R. T-DNA insertion in aquaporin gene AtPIP1;2 generates transcription profiles reminiscent of a low CO2 response. PLANT, CELL & ENVIRONMENT 2015; 38:2286-2298. [PMID: 25850563 DOI: 10.1111/pce.12547] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 03/22/2015] [Indexed: 06/04/2023]
Abstract
Results from CO2 diffusion studies and characterization of Arabidopsis thaliana aquaporin AtPIP1;2 T-DNA insertion lines support the idea that specific aquaporins facilitate the diffusion of CO2 through biological membranes. However, their function as CO2 diffusion facilitators in plant physiology is still a matter of debate. Assuming that a lack of AtPIP1;2 causes a characteristic transcriptional response, we compared data from a AtPIP1;2 T-DNA insertion line obtained by Illumina sequencing, Affymetrix chip analysis and quantitative RT-PCR to the transcriptome of plants grown under drought stress or under low CO2 conditions. The plant reaction to the deficit of AtPIP1;2 was unlike drought stress responses but comparable with that of low CO2 conditions. In addition, we observed a phenotype characteristic to plants grown under low CO2 . The findings support the hypothesis that the AtPIP1;2 function in plant physiology is not to facilitate water but CO2 diffusion.
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Affiliation(s)
| | - Marlies Heckwolf
- Applied Plant Science, Darmstadt University of Technology, Darmstadt, D-64287, Germany
- Department of Energy Great Lakes Bioenergy Research Center, Department of Agronomy, University of Wisconsin, Madison, WI, 53703, USA
| | - Ralf Kaldenhoff
- Applied Plant Science, Darmstadt University of Technology, Darmstadt, D-64287, Germany
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14
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Chloroplast isolation and affinity chromatography for enrichment of low-abundant proteins in complex proteomes. Methods Mol Biol 2015; 1295:211-23. [PMID: 25820724 DOI: 10.1007/978-1-4939-2550-6_16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Detailed knowledge of the proteome is crucial to advance the biological sciences. Low-abundant proteins are of particular interest to many biologists as they include, for example those proteins involved in signal transduction. Recent technological advances resulted in a tremendous increase in protein identification sensitivity by mass spectrometry (MS). However, the dynamic range in protein abundance still forms a fundamental problem that limits the detection of low-abundant proteins in complex proteomes. These proteins will typically escape detection in shotgun MS experiments due to the presence of other proteins at an abundance several-fold higher in order of magnitude. Therefore, specific enrichment strategies are required to overcome this technical limitation of MS-based protein discovery. We have searched for novel signal transduction proteins, more specifically kinases and calcium-binding proteins, and here we describe different approaches for enrichment of these low-abundant proteins from isolated chloroplasts from pea and Arabidopsis for subsequent proteomic analysis by MS. These approaches could be extended to include other signal transduction proteins and target different organelles.
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15
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Proteomic Analysis of the Defense Response of Wheat to the Powdery Mildew Fungus, Blumeria graminis f. sp. tritici. Protein J 2014; 33:513-24. [DOI: 10.1007/s10930-014-9583-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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16
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Pascovici D, Gardiner DM, Song X, Breen E, Solomon PS, Keighley T, Molloy MP. Coverage and Consistency: Bioinformatics Aspects of the Analysis of Multirun iTRAQ Experiments with Wheat Leaves. J Proteome Res 2013; 12:4870-81. [DOI: 10.1021/pr400531y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Dana Pascovici
- Australian
Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia
| | - Donald M. Gardiner
- CSIRO Plant Industry, Queensland Bioscience
Precinct, 306 Carmody Road, Brisbane, QLD 4067, Australia
| | - Xiaomin Song
- Australian
Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia
| | - Edmond Breen
- Australian
Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia
| | - Peter S. Solomon
- Plant
Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Tim Keighley
- Australian
Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia
| | - Mark P. Molloy
- Australian
Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia
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17
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Agrawal GK, Sarkar A, Righetti PG, Pedreschi R, Carpentier S, Wang T, Barkla BJ, Kohli A, Ndimba BK, Bykova NV, Rampitsch C, Zolla L, Rafudeen MS, Cramer R, Bindschedler LV, Tsakirpaloglou N, Ndimba RJ, Farrant JM, Renaut J, Job D, Kikuchi S, Rakwal R. A decade of plant proteomics and mass spectrometry: translation of technical advancements to food security and safety issues. MASS SPECTROMETRY REVIEWS 2013; 32:335-65. [PMID: 23315723 DOI: 10.1002/mas.21365] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 09/10/2012] [Accepted: 09/10/2012] [Indexed: 05/21/2023]
Abstract
Tremendous progress in plant proteomics driven by mass spectrometry (MS) techniques has been made since 2000 when few proteomics reports were published and plant proteomics was in its infancy. These achievements include the refinement of existing techniques and the search for new techniques to address food security, safety, and health issues. It is projected that in 2050, the world's population will reach 9-12 billion people demanding a food production increase of 34-70% (FAO, 2009) from today's food production. Provision of food in a sustainable and environmentally committed manner for such a demand without threatening natural resources, requires that agricultural production increases significantly and that postharvest handling and food manufacturing systems become more efficient requiring lower energy expenditure, a decrease in postharvest losses, less waste generation and food with longer shelf life. There is also a need to look for alternative protein sources to animal based (i.e., plant based) to be able to fulfill the increase in protein demands by 2050. Thus, plant biology has a critical role to play as a science capable of addressing such challenges. In this review, we discuss proteomics especially MS, as a platform, being utilized in plant biology research for the past 10 years having the potential to expedite the process of understanding plant biology for human benefits. The increasing application of proteomics technologies in food security, analysis, and safety is emphasized in this review. But, we are aware that no unique approach/technology is capable to address the global food issues. Proteomics-generated information/resources must be integrated and correlated with other omics-based approaches, information, and conventional programs to ensure sufficient food and resources for human development now and in the future.
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Affiliation(s)
- Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry, PO Box 13265, Kathmandu, Nepal.
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18
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Champagne A, Boutry M. Proteomics of nonmodel plant species. Proteomics 2013; 13:663-73. [PMID: 23125178 DOI: 10.1002/pmic.201200312] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Revised: 10/17/2012] [Accepted: 10/22/2012] [Indexed: 01/10/2023]
Abstract
Until recently, large scale proteomic investigations in the plant field have only been possible for a few model species for which the whole genome sequence had been fully determined. In contrast, for many other species with a strong economic interest as sources of human food and animal feed, as well as industrial and pharmacological molecules, little was known about their genome sequence and identifying the proteome in these species was still considered challenging. However, progress has been made as a result of several recent advances in proteomics tools, e.g. in MS technology and data search programs, and the increasing availability of genomic and cDNA sequences from various species. Moreover, next-generation sequencing technologies now make it possible to rapidly determine, at a reasonable cost, the genome or RNA sequence of species not currently considered as models, thus considerably expanding the plant sequence databases. This review will show how these advances make it possible to identify a large set of proteins, even for species for which few sequences are currently available.
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Affiliation(s)
- Antoine Champagne
- Institut des Sciences de la Vie, Université catholique de Louvain, Croix du Sud 4-15, Louvain-la-Neuve, Belgium
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19
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Timmins-Schiffman E, Nunn BL, Goodlett DR, Roberts SB. Shotgun proteomics as a viable approach for biological discovery in the Pacific oyster. CONSERVATION PHYSIOLOGY 2013; 1:cot009. [PMID: 27293593 PMCID: PMC4732435 DOI: 10.1093/conphys/cot009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 04/10/2013] [Accepted: 04/11/2013] [Indexed: 05/03/2023]
Abstract
Shotgun proteomics offers an efficient means to characterize proteins in a complex mixture, particularly when sufficient genomic resources are available. In order to assess the practical application of shotgun proteomics in the Pacific oyster (Crassostrea gigas), liquid chromatography coupled with tandem mass spectrometry was used to characterize the gill proteome. Using information from the recently published Pacific oyster genome, 1043 proteins were identified. Biological samples (n = 4) and corresponding technical replicates (three) were similar in both specific proteins identified and expression, as determined by normalized spectral abundance factor. A majority of the proteins identified (703) were present in all biological samples. Functional analysis of the protein repertoire illustrates that these proteins represent a wide range of biological processes, supporting the dynamic function of the gill. These insights are important for understanding environmental influences on the oyster, because the gill tissue acts as the interface between the oyster and its environment. In silico analysis indicated that this sequencing effort identified a large proportion of the complete gill proteome. Together, these data demonstrate that shotgun sequencing is a viable approach for biological discovery and will play an important role in future studies of oyster physiology.
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Affiliation(s)
- Emma Timmins-Schiffman
- School of Aquatic and Fishery Sciences, University of Washington, Box 355020, Seattle, WA 98195, USA
| | - Brook L. Nunn
- Genomic Sciences, University of Washington, Box 355065, Seattle, WA 98195, USA
| | - David R. Goodlett
- Medicinal Chemistry, University of Washington, Box 357610, Seattle, WA 98195, USA
| | - Steven B. Roberts
- School of Aquatic and Fishery Sciences, University of Washington, Box 355020, Seattle, WA 98195, USA
- Corresponding author: School of Aquatic and Fishery Sciences, University of Washington, Box 355020, Seattle, WA 98195, USA. Tel: +1 206 685 3742.
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20
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Schulze WX, Sanggaard KW, Kreuzer I, Knudsen AD, Bemm F, Thøgersen IB, Bräutigam A, Thomsen LR, Schliesky S, Dyrlund TF, Escalante-Perez M, Becker D, Schultz J, Karring H, Weber A, Højrup P, Hedrich R, Enghild JJ. The protein composition of the digestive fluid from the venus flytrap sheds light on prey digestion mechanisms. Mol Cell Proteomics 2012; 11:1306-19. [PMID: 22891002 PMCID: PMC3494193 DOI: 10.1074/mcp.m112.021006] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Revised: 07/26/2012] [Indexed: 11/06/2022] Open
Abstract
The Venus flytrap (Dionaea muscipula) is one of the most well-known carnivorous plants because of its unique ability to capture small animals, usually insects or spiders, through a unique snap-trapping mechanism. The animals are subsequently killed and digested so that the plants can assimilate nutrients, as they grow in mineral-deficient soils. We deep sequenced the cDNA from Dionaea traps to obtain transcript libraries, which were used in the mass spectrometry-based identification of the proteins secreted during digestion. The identified proteins consisted of peroxidases, nucleases, phosphatases, phospholipases, a glucanase, chitinases, and proteolytic enzymes, including four cysteine proteases, two aspartic proteases, and a serine carboxypeptidase. The majority of the most abundant proteins were categorized as pathogenesis-related proteins, suggesting that the plant's digestive system evolved from defense-related processes. This in-depth characterization of a highly specialized secreted fluid from a carnivorous plant provides new information about the plant's prey digestion mechanism and the evolutionary processes driving its defense pathways and nutrient acquisition.
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Affiliation(s)
- Waltraud X. Schulze
- From the ‡Max Planck Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Kristian W. Sanggaard
- §Department of Molecular Biology and Genetics, Aarhus University, Gustav Wiedsvej 10C, 8000 Aarhus C, Denmark
| | - Ines Kreuzer
- ¶Department of Molecular Plant Physiology & Biophysics, Universität Würzburg, Julius-von-Sachs-Platz 2, 97082 Würzburg, Germany
| | - Anders D. Knudsen
- §Department of Molecular Biology and Genetics, Aarhus University, Gustav Wiedsvej 10C, 8000 Aarhus C, Denmark
| | - Felix Bemm
- ‖Department of Bioinformatics, Biozentrum, Am Hubland, Universität Würzburg, D-97074 Wuerzburg, Germany
| | - Ida B. Thøgersen
- §Department of Molecular Biology and Genetics, Aarhus University, Gustav Wiedsvej 10C, 8000 Aarhus C, Denmark
| | - Andrea Bräutigam
- ‡‡Department of Plant Biochemistry, Heinrich-Heine-Universitaet Duesseldorf, Universitaetsstrasse 1, 40225 Duesseldorf, Germany
| | - Line R. Thomsen
- §Department of Molecular Biology and Genetics, Aarhus University, Gustav Wiedsvej 10C, 8000 Aarhus C, Denmark
| | - Simon Schliesky
- ‡‡Department of Plant Biochemistry, Heinrich-Heine-Universitaet Duesseldorf, Universitaetsstrasse 1, 40225 Duesseldorf, Germany
| | - Thomas F. Dyrlund
- §Department of Molecular Biology and Genetics, Aarhus University, Gustav Wiedsvej 10C, 8000 Aarhus C, Denmark
| | - Maria Escalante-Perez
- ¶Department of Molecular Plant Physiology & Biophysics, Universität Würzburg, Julius-von-Sachs-Platz 2, 97082 Würzburg, Germany
| | - Dirk Becker
- ¶Department of Molecular Plant Physiology & Biophysics, Universität Würzburg, Julius-von-Sachs-Platz 2, 97082 Würzburg, Germany
| | - Jörg Schultz
- ‖Department of Bioinformatics, Biozentrum, Am Hubland, Universität Würzburg, D-97074 Wuerzburg, Germany
| | - Henrik Karring
- §§University of Southern Denmark, Institute of Chemical Engineering, Biotechnology and Environmental Technology, Niels Bohrs Allé 1, 5230 Odense M, Denmark
| | - Andreas Weber
- ‡‡Department of Plant Biochemistry, Heinrich-Heine-Universitaet Duesseldorf, Universitaetsstrasse 1, 40225 Duesseldorf, Germany
| | - Peter Højrup
- ¶¶Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Rainer Hedrich
- ¶Department of Molecular Plant Physiology & Biophysics, Universität Würzburg, Julius-von-Sachs-Platz 2, 97082 Würzburg, Germany
- ‖‖Zoology Department, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Jan J. Enghild
- §Department of Molecular Biology and Genetics, Aarhus University, Gustav Wiedsvej 10C, 8000 Aarhus C, Denmark
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Abstract
High-throughput identification of proteins with the latest generation of hybrid high-resolution mass spectrometers is opening new perspectives in microbiology. I present, here, an overview of tandem mass spectrometry technology and bioinformatics for shotgun proteomics that make 2D-PAGE approaches obsolete. Non-labelling quantitative approaches have become more popular than labelling techniques on most proteomic platforms because they are easier to carry out while their quantitative outcome is rather robust. Parameters for recording mass spectrometry data, however, need to be chosen carefully and statistics to assess the confidence of the results should not be neglected. Interestingly, next-generation sequencing methodologies make any microbial model quickly amenable to proteomics, leading to the documentation of a wide range of organisms from diverse environments. Some recent discoveries made using microbial proteomics have challenged some biological dogma, such as: (i) initiation of the translation does not occur predominantly from ATG codons in some microorganisms, (ii) non-canonical initiation codons are used to regulate the production of specific but important proteins and (iii) a gene may code for multiple polypeptide species, heterogeneous in terms of sequences. Microbial diversity and microbial physiology can now be revisited by means of exhaustive comparative proteomic surveys where thousands of proteins are detected and quantified. Proteogenomics, consisting of better annotating of genomes with the help of proteomic evidence, is paving the way for integrated multi-omic approaches in microbiology. Finally, meta-proteomic tools and approaches are emerging for tackling the high complexity of the microbial world as a whole, opening new perspectives for assessing how microbial communities function.
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Affiliation(s)
- Jean Armengaud
- CEA, DSV, IBEB, Lab Biochim System Perturb, F-30207 Bagnols-sur-Cèze, France.
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22
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Roston RL, Gao J, Murcha MW, Whelan J, Benning C. TGD1, -2, and -3 proteins involved in lipid trafficking form ATP-binding cassette (ABC) transporter with multiple substrate-binding proteins. J Biol Chem 2012; 287:21406-15. [PMID: 22544736 PMCID: PMC3375562 DOI: 10.1074/jbc.m112.370213] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 04/27/2012] [Indexed: 11/06/2022] Open
Abstract
Members of the ATP-binding cassette (ABC) transporter family are essential proteins in species as diverse as archaea and humans. Their domain architecture has remained relatively fixed across these species, with rare exceptions. Here, we show one exception to be the trigalactosyldiacylglycerol 1, 2, and 3 (TGD1, -2, and -3) putative lipid transporter located at the chloroplast inner envelope membrane. TGD2 was previously shown to be in a complex of >500 kDa. We demonstrate that this complex also contains TGD1 and -3 and is very stable because it cannot be broken down by gentle denaturants to form a "core" complex similar in size to standard ABC transporters. The complex was purified from Pisum sativum (pea) chloroplast envelopes by native gel electrophoresis and examined by mass spectrometry. Identified proteins besides TGD1, -2, or -3 included a potassium efflux antiporter and a TIM17/22/23 family protein, but these were shown to be in separate high molecular mass complexes. Quantification of the complex components explained the size of the complex because 8-12 copies of the substrate-binding protein (TGD2) were found per functional transporter.
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Affiliation(s)
- Rebecca L. Roston
- From the Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 and
| | - Jinpeng Gao
- From the Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 and
| | - Monika W. Murcha
- the Australian Research Council Centre of Excellence Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - James Whelan
- the Australian Research Council Centre of Excellence Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Christoph Benning
- From the Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 and
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23
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Translational plant proteomics: a perspective. J Proteomics 2012; 75:4588-601. [PMID: 22516432 DOI: 10.1016/j.jprot.2012.03.055] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2011] [Revised: 02/25/2012] [Accepted: 03/25/2012] [Indexed: 11/21/2022]
Abstract
Translational proteomics is an emerging sub-discipline of the proteomics field in the biological sciences. Translational plant proteomics aims to integrate knowledge from basic sciences to translate it into field applications to solve issues related but not limited to the recreational and economic values of plants, food security and safety, and energy sustainability. In this review, we highlight the substantial progress reached in plant proteomics during the past decade which has paved the way for translational plant proteomics. Increasing proteomics knowledge in plants is not limited to model and non-model plants, proteogenomics, crop improvement, and food analysis, safety, and nutrition but to many more potential applications. Given the wealth of information generated and to some extent applied, there is the need for more efficient and broader channels to freely disseminate the information to the scientific community. This article is part of a Special Issue entitled: Translational Proteomics.
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24
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Pudelski B, Schock A, Hoth S, Radchuk R, Weber H, Hofmann J, Sonnewald U, Soll J, Philippar K. The plastid outer envelope protein OEP16 affects metabolic fluxes during ABA-controlled seed development and germination. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:1919-36. [PMID: 22155670 PMCID: PMC3295387 DOI: 10.1093/jxb/err375] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Revised: 10/15/2011] [Accepted: 10/21/2011] [Indexed: 05/20/2023]
Abstract
Previously, the OEP16.1 channel pore in the outer envelope membrane of mature pea (Pisum sativum) chloroplasts in vitro has been characterized to be selective for amino acids. Isolation of OEP16.2, a second OEP16 isoform from pea, in the current study allowed membrane localization and gene expression of OEP16 to be followed throughout seed development and germination of Arabidopsis thaliana and P. sativum. Thereby it can be shown on the transcript and protein level that the isoforms OEP16.1 and OEP16.2 in both plant species are alternating: whereas OEP16.1 is prominent in early embryo development and first leaves of the growing plantlet, OEP16.2 dominates in late seed development stages, which are associated with dormancy and desiccation, as well as early germination events. Further, OEP16.2 expression in seeds is under control of the phytohormone abscisic acid (ABA), leading to an ABA-hypersensitive phenotype of germinating oep16 knockout mutants. In consequence, the loss of OEP16 causes metabolic imbalance, in particular that of amino acids during seed development and early germination. It is thus concluded that in vivo OEP16 most probably functions in shuttling amino acids across the outer envelope of seed plastids.
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Affiliation(s)
- Birgit Pudelski
- Biochemie und Physiologie der Pflanzen, Department Biologie I, Botanik, Ludwig-Maximilians-Universität München, D-82152 Planegg-Martinsried, Germany
- Munich Centre for Integrated Protein Science CiPSM, Ludwig-Maximilians-Universität München, D-81377 München, Germany
| | - Annette Schock
- Biochemie und Physiologie der Pflanzen, Department Biologie I, Botanik, Ludwig-Maximilians-Universität München, D-82152 Planegg-Martinsried, Germany
- Munich Centre for Integrated Protein Science CiPSM, Ludwig-Maximilians-Universität München, D-81377 München, Germany
| | - Stefan Hoth
- Molekulare Pflanzenphysiologie, Department Biologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstrasse 5, D-91058 Erlangen, Germany
- Pflanzenphysiologie, Biozentrum Klein Flottbek, Universität Hamburg, Ohnhorststrabe 18, D-22609 Hamburg, Germany
| | - Ruslana Radchuk
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), Corrensstrasse 3, D-06466 Gatersleben, Germany
| | - Hans Weber
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), Corrensstrasse 3, D-06466 Gatersleben, Germany
| | - Jörg Hofmann
- Biochemie, Department Biologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstrasse 5, D-91058 Erlangen, Germany
| | - Uwe Sonnewald
- Biochemie, Department Biologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstrasse 5, D-91058 Erlangen, Germany
| | - Jürgen Soll
- Biochemie und Physiologie der Pflanzen, Department Biologie I, Botanik, Ludwig-Maximilians-Universität München, D-82152 Planegg-Martinsried, Germany
- Munich Centre for Integrated Protein Science CiPSM, Ludwig-Maximilians-Universität München, D-81377 München, Germany
| | - Katrin Philippar
- Biochemie und Physiologie der Pflanzen, Department Biologie I, Botanik, Ludwig-Maximilians-Universität München, D-82152 Planegg-Martinsried, Germany
- Munich Centre for Integrated Protein Science CiPSM, Ludwig-Maximilians-Universität München, D-81377 München, Germany
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25
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Stael S, Rocha AG, Wimberger T, Anrather D, Vothknecht UC, Teige M. Cross-talk between calcium signalling and protein phosphorylation at the thylakoid. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:1725-33. [PMID: 22197893 PMCID: PMC3970089 DOI: 10.1093/jxb/err403] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The role of protein phosphorylation for adjusting chloroplast functions to changing environmental needs is well established, whereas calcium signalling in the chloroplast is only recently becoming appreciated. The work presented here explores the potential cross-talk between calcium signalling and protein phosphorylation in chloroplasts and provides the first evidence for targets of calcium-dependent protein phosphorylation at the thylakoid membrane. Thylakoid proteins were screened for calcium-dependent phosphorylation by 2D gel electrophoresis combined with phospho-specific labelling and PsaN, CAS, and VAR1, among other proteins, were identified repeatedly by mass spectrometry. Subsequently their calcium-dependent phosphorylation was confirmed in kinase assays using the purified proteins and chloroplast extracts. This is the first report on the protein targets of calcium-dependent phosphorylation of thylakoid proteins and provides ground for further studies in this direction.
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Affiliation(s)
- Simon Stael
- Department of Biochemistry and Cell Biology, MFPL, University of Vienna, Dr. Bohrgasse 9, A-1030, Vienna, Austria
| | - Agostinho G. Rocha
- Department of Biology I, Botany, LMU Munich, Großhaderner Str. 2, D-82152 Planegg-Martinsried, Germany
| | - Terje Wimberger
- Department of Biochemistry and Cell Biology, MFPL, University of Vienna, Dr. Bohrgasse 9, A-1030, Vienna, Austria
| | - Dorothea Anrather
- Mass Spectrometry Facility, MFPL, University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria
| | - Ute C. Vothknecht
- Department of Biology I, Botany, LMU Munich, Großhaderner Str. 2, D-82152 Planegg-Martinsried, Germany
- Center for Integrated Protein Science (Munich) at the Department of Biology of the LMU Munich, D-81377 Munich, Germany
| | - Markus Teige
- Department of Biochemistry and Cell Biology, MFPL, University of Vienna, Dr. Bohrgasse 9, A-1030, Vienna, Austria
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26
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Ajjawi I, Coku A, Froehlich JE, Yang Y, Osteryoung KW, Benning C, Last RL. A J-like protein influences fatty acid composition of chloroplast lipids in Arabidopsis. PLoS One 2011; 6:e25368. [PMID: 22028775 PMCID: PMC3196505 DOI: 10.1371/journal.pone.0025368] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Accepted: 09/01/2011] [Indexed: 12/26/2022] Open
Abstract
A comprehensive understanding of the lipid and fatty acid metabolic machinery is needed for optimizing production of oils and fatty acids for fuel, industrial feedstocks and nutritional improvement in plants. T-DNA mutants in the poorly annotated Arabidopsis thaliana gene At1g08640 were identified as containing moderately high levels (50–100%) of 16∶1Δ7 and 18∶1Δ9 leaf fatty acids and subtle decreases (5–30%) of 16∶3 and 18∶3 (http://www.plastid.msu.edu/). TLC separation of fatty acids in the leaf polar lipids revealed that the chloroplastic galactolipids monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol (DGDG) were the main lipid types affected by this mutation. Analysis of the inferred amino acid sequence of At1g08640 predicted the presence of a transit peptide, three transmembrane domains and an N-terminal J-like domain, and the gene was named CJD1 for Chloroplast J-like Domain 1. GFP reporter experiments and in vitro chloroplast import assays demonstrated CJD1 is a chloroplast membrane protein. Screening of an Arabidopsis cDNA library by yeast-2-hybrid (Y2H) using the J-like domain of CJD1 as bait identified a plastidial inner envelope protein (Accumulation and Replication of Chloroplasts 6, ARC6) as the primary interacting partner in the Y2H assay. ARC6 plays a central role in chloroplast division and binds CJD1 via its own J-like domain along with an adjacent conserved region whose function is not fully known. These results provide a starting point for future investigations of how mutations in CJD1 affect lipid composition.
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Affiliation(s)
- Imad Ajjawi
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Ardian Coku
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - John E. Froehlich
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
- Michigan State University (MSU)–Department of Engineering (DOE) Plant Research Laboratories, Michigan State University, East Lansing, Michigan, United States of America
| | - Yue Yang
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Katherine W. Osteryoung
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Christoph Benning
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Robert L. Last
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
- * E-mail:
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27
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Agrawal GK, Bourguignon J, Rolland N, Ephritikhine G, Ferro M, Jaquinod M, Alexiou KG, Chardot T, Chakraborty N, Jolivet P, Doonan JH, Rakwal R. Plant organelle proteomics: collaborating for optimal cell function. MASS SPECTROMETRY REVIEWS 2011; 30:772-853. [PMID: 21038434 DOI: 10.1002/mas.20301] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2009] [Revised: 02/02/2010] [Accepted: 02/02/2010] [Indexed: 05/10/2023]
Abstract
Organelle proteomics describes the study of proteins present in organelle at a particular instance during the whole period of their life cycle in a cell. Organelles are specialized membrane bound structures within a cell that function by interacting with cytosolic and luminal soluble proteins making the protein composition of each organelle dynamic. Depending on organism, the total number of organelles within a cell varies, indicating their evolution with respect to protein number and function. For example, one of the striking differences between plant and animal cells is the plastids in plants. Organelles have their own proteins, and few organelles like mitochondria and chloroplast have their own genome to synthesize proteins for specific function and also require nuclear-encoded proteins. Enormous work has been performed on animal organelle proteomics. However, plant organelle proteomics has seen limited work mainly due to: (i) inter-plant and inter-tissue complexity, (ii) difficulties in isolation of subcellular compartments, and (iii) their enrichment and purity. Despite these concerns, the field of organelle proteomics is growing in plants, such as Arabidopsis, rice and maize. The available data are beginning to help better understand organelles and their distinct and/or overlapping functions in different plant tissues, organs or cell types, and more importantly, how protein components of organelles behave during development and with surrounding environments. Studies on organelles have provided a few good reviews, but none of them are comprehensive. Here, we present a comprehensive review on plant organelle proteomics starting from the significance of organelle in cells, to organelle isolation, to protein identification and to biology and beyond. To put together such a systematic, in-depth review and to translate acquired knowledge in a proper and adequate form, we join minds to provide discussion and viewpoints on the collaborative nature of organelles in cell, their proper function and evolution.
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Affiliation(s)
- Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), P.O. Box 13265, Sanepa, Kathmandu, Nepal.
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Ekblom R, Galindo J. Applications of next generation sequencing in molecular ecology of non-model organisms. Heredity (Edinb) 2011; 107:1-15. [PMID: 21139633 PMCID: PMC3186121 DOI: 10.1038/hdy.2010.152] [Citation(s) in RCA: 630] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2010] [Revised: 09/10/2010] [Accepted: 11/02/2010] [Indexed: 11/09/2022] Open
Abstract
As most biologists are probably aware, technological advances in molecular biology during the last few years have opened up possibilities to rapidly generate large-scale sequencing data from non-model organisms at a reasonable cost. In an era when virtually any study organism can 'go genomic', it is worthwhile to review how this may impact molecular ecology. The first studies to put the next generation sequencing (NGS) to the test in ecologically well-characterized species without previous genome information were published in 2007 and the beginning of 2008. Since then several studies have followed in their footsteps, and a large number are undoubtedly under way. This review focuses on how NGS has been, and can be, applied to ecological, population genetic and conservation genetic studies of non-model species, in which there is no (or very limited) genomic resources. Our aim is to draw attention to the various possibilities that are opening up using the new technologies, but we also highlight some of the pitfalls and drawbacks with these methods. We will try to provide a snapshot of the current state of the art for this rapidly advancing and expanding field of research and give some likely directions for future developments.
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Affiliation(s)
- R Ekblom
- Department of Animal and Plant Sciences, University of Sheffield, UK.
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Franssen SU, Shrestha RP, Bräutigam A, Bornberg-Bauer E, Weber APM. Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing. BMC Genomics 2011; 12:227. [PMID: 21569327 PMCID: PMC3224338 DOI: 10.1186/1471-2164-12-227] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2010] [Accepted: 05/11/2011] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The garden pea, Pisum sativum, is among the best-investigated legume plants and of significant agro-commercial relevance. Pisum sativum has a large and complex genome and accordingly few comprehensive genomic resources exist. RESULTS We analyzed the pea transcriptome at the highest possible amount of accuracy by current technology. We used next generation sequencing with the Roche/454 platform and evaluated and compared a variety of approaches, including diverse tissue libraries, normalization, alternative sequencing technologies, saturation estimation and diverse assembly strategies. We generated libraries from flowers, leaves, cotyledons, epi- and hypocotyl, and etiolated and light treated etiolated seedlings, comprising a total of 450 megabases. Libraries were assembled into 324,428 unigenes in a first pass assembly.A second pass assembly reduced the amount to 81,449 unigenes but caused a significant number of chimeras. Analyses of the assemblies identified the assembly step as a major possibility for improvement. By recording frequencies of Arabidopsis orthologs hit by randomly drawn reads and fitting parameters of the saturation curve we concluded that sequencing was exhaustive. For leaf libraries we found normalization allows partial recovery of expression strength aside the desired effect of increased coverage. Based on theoretical and biological considerations we concluded that the sequence reads in the database tagged the vast majority of transcripts in the aerial tissues. A pathway representation analysis showed the merits of sampling multiple aerial tissues to increase the number of tagged genes. All results have been made available as a fully annotated database in fasta format. CONCLUSIONS We conclude that the approach taken resulted in a high quality - dataset which serves well as a first comprehensive reference set for the model legume pea. We suggest future deep sequencing transcriptome projects of species lacking a genomics backbone will need to concentrate mainly on resolving the issues of redundancy and paralogy during transcriptome assembly.
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Affiliation(s)
- Susanne U Franssen
- Institute for Evolution and Biodiversity, Westfalian Wilhelms University, Hüfferstrasse 1, 48149 Münster, Germany
| | - Roshan P Shrestha
- Department of Plant Biology, Michigan State University, 48823 East Lansing, MI, USA
| | - Andrea Bräutigam
- Department of Plant Biology, Michigan State University, 48823 East Lansing, MI, USA
- Institute of Plant Biochemistry, Heinrich Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, Westfalian Wilhelms University, Hüfferstrasse 1, 48149 Münster, Germany
| | - Andreas PM Weber
- Department of Plant Biology, Michigan State University, 48823 East Lansing, MI, USA
- Institute of Plant Biochemistry, Heinrich Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany
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Tarantino D, Morandini P, Ramirez L, Soave C, Murgia I. Identification of an Arabidopsis mitoferrinlike carrier protein involved in Fe metabolism. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2011; 49:520-9. [PMID: 21371898 DOI: 10.1016/j.plaphy.2011.02.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Accepted: 02/03/2011] [Indexed: 05/22/2023]
Abstract
Iron has a major role in mitochondrial as well as in chloroplast metabolism, however the processes involved in organelle iron transport in plants are only partially understood. To identify mitochondrial iron transporters in Arabidopsis, we searched for proteins homologous to the Danio rerio (zebrafish) Mitoferrin2 MFRN2, a mitochondrial iron importer in non-erythroid cells. Among the identified putative Arabidopsis mitoferrinlike proteins, we focused on that one encoded by At5g42130, which we named AtMfl1 (MitoFerrinLike1). AtMfl1 expression strongly correlates with genes coding for proteins involved in chloroplast metabolism. Such an unexpected result is supported by the identification by different research groups, of the protein encoded by At5g42130 and of its homologs from various plant species in the inner chloroplastic envelope membrane proteome. Notably, neither the protein encoded by At5g42130 nor its homologs from other plant species have been identified in the mitochondrial proteome. AtMfl1 gene expression is dependent on Fe supply: AtMfl1 transcript strongly accumulates under Fe excess, moderately under Fe sufficiency and weakly under Fe deficiency. In order to understand the physiological role of AtMfl1, we isolated and characterized two independent AtMfl1 KO mutants, atmfl1-1 and atmfl1-2: both show reduced vegetative growth. When grown under conditions of Fe excess, atmfl1-1 and atmfl1-2 mutants (seedlings, rosette leaves) contain less total Fe than wt and also reduced expression of the iron storage ferritin AtFer1. Taken together, these results suggest that Arabidopsis mitoferrinlike gene AtMfl1 is involved in Fe transport into chloroplasts, under different conditions of Fe supply and that suppression of its expression alters plant Fe accumulation in various developmental stages.
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Affiliation(s)
- Delia Tarantino
- Sezione di Fisiologia e Biochimica delle Piante, Dipartimento di Biologia, Università degli Studi di Milano, via Celoria 26, 20133 Italy
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Bayer RG, Stael S, Csaszar E, Teige M. Mining the soluble chloroplast proteome by affinity chromatography. Proteomics 2011; 11:1287-99. [PMID: 21365755 PMCID: PMC3531887 DOI: 10.1002/pmic.201000495] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Revised: 12/15/2010] [Accepted: 12/29/2010] [Indexed: 12/28/2022]
Abstract
Chloroplasts are fundamental organelles enabling plant photoautotrophy. Besides their outstanding physiological role in fixation of atmospheric CO(2), they harbor many important metabolic processes such as biosynthesis of amino acids, vitamins or hormones. Technical advances in MS allowed the recent identification of most chloroplast proteins. However, for a deeper understanding of chloroplast function it is important to obtain a complete list of constituents, which is so far limited by the detection of low-abundant proteins. Therefore, we developed a two-step strategy for the enrichment of low-abundant soluble chloroplast proteins from Pisum sativum and their subsequent identification by MS. First, chloroplast protein extracts were depleted from the most abundant protein ribulose-1,5-bisphosphate carboxylase/oxygenase by SEC or heating. Further purification was carried out by affinity chromatography, using ligands specific for ATP- or metal-binding proteins. By these means, we were able to identify a total of 448 proteins including 43 putative novel chloroplast proteins. Additionally, the chloroplast localization of 13 selected proteins was confirmed using yellow fluorescent protein fusion analyses. The selected proteins included a phosphoglycerate mutase, a cysteine protease, a putative protein kinase and an EF-hand containing substrate carrier protein, which are expected to exhibit important metabolic or regulatory functions.
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Affiliation(s)
- Roman G Bayer
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Austria
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Reiland S, Grossmann J, Baerenfaller K, Gehrig P, Nunes-Nesi A, Fernie AR, Gruissem W, Baginsky S. Integrated proteome and metabolite analysis of the de-etiolation process in plastids from rice (Oryza sativa L.). Proteomics 2011; 11:1751-63. [PMID: 21433289 DOI: 10.1002/pmic.201000703] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Revised: 12/14/2010] [Accepted: 01/11/2011] [Indexed: 12/16/2022]
Abstract
We have analyzed the dynamics of the rice etioplast membrane proteome during the early phase of de-etiolation using iTRAQ-based relative protein quantification. Several hundred plastid proteins were identified from enriched membranes, including 36 putative transporters. Hierarchical clustering revealed the coordinated light induction of thylakoid membrane proteins with proteins involved in translation and fatty acid metabolism. No other functional category of identified proteins showed a similarly consistent light induction, and no consistent changes were observed for the identified transporters. This suggests that the etioplast metabolism is already primed to accommodate the metabolic changes that occur during the onset of photosynthesis. This hypothesis was further tested in metabolite profiling experiments. Here, the changes upon illumination are mostly restricted to a decrease in the concentration of some amino acids and an increase in the concentrations of aspartic acid, malic acid, fumaric acid, and succinic acid. These changes are consistent with a rapid activation of photosynthesis and subsequent rapid production of storage carbohydrates and proteins. The information at the proteome level and the parallel measurements of metabolite accumulation both support the view that only minor metabolic network reconstruction and modification of enzyme levels occurs during the first 4 h of etioplast to chloroplast differentiation.
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Affiliation(s)
- Sonja Reiland
- Department of Biology, Plant Biotechnology, ETH Zurich, Zurich, Switzerland
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Weber APM, Linka N. Connecting the plastid: transporters of the plastid envelope and their role in linking plastidial with cytosolic metabolism. ANNUAL REVIEW OF PLANT BIOLOGY 2011; 62:53-77. [PMID: 21526967 DOI: 10.1146/annurev-arplant-042110-103903] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Plastids have a multitude of functions in eukaryotic cells, ranging from photosynthesis to storage, and a role in essential biosynthetic pathways. All plastids are of either primary or higher-order endosymbiotic origin. That is, either a photosynthetic cyanobacterium was integrated into a mitochondriate eukaryotic host cell (primary endosymbiosis) or a plastid-bearing eukaryotic cell merged with another eukaryotic cell (secondary or higher-order endosymbioses), thereby passing on the plastid between various eukaryotic lineages. For all of these endosymbioses to become functional, it was essential to establish metabolic connections between organelle and host cell. Here, we review the present understanding of metabolite exchange between plastids and the surrounding cytosol in the context of the endosymbiotic origin of plastids in various eukaryotic lineages. We show that only a small number of transporters that can be traced down to the primary endosymbiotic event are conserved between plastids of diverse origins.
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Affiliation(s)
- Andreas P M Weber
- Institute of Plant Biochemistry, Heinrich-Heine Universität Düsseldorf, 40225 Düsseldorf, Germany.
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Bräutigam A, Kajala K, Wullenweber J, Sommer M, Gagneul D, Weber KL, Carr KM, Gowik U, Maß J, Lercher MJ, Westhoff P, Hibberd JM, Weber AP. An mRNA blueprint for C4 photosynthesis derived from comparative transcriptomics of closely related C3 and C4 species. PLANT PHYSIOLOGY 2011; 155:142-56. [PMID: 20543093 PMCID: PMC3075794 DOI: 10.1104/pp.110.159442] [Citation(s) in RCA: 181] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Accepted: 06/09/2010] [Indexed: 05/18/2023]
Abstract
C(4) photosynthesis involves alterations to the biochemistry, cell biology, and development of leaves. Together, these modifications increase the efficiency of photosynthesis, and despite the apparent complexity of the pathway, it has evolved at least 45 times independently within the angiosperms. To provide insight into the extent to which gene expression is altered between C(3) and C(4) leaves, and to identify candidates associated with the C(4) pathway, we used massively parallel mRNA sequencing of closely related C(3) (Cleome spinosa) and C(4) (Cleome gynandra) species. Gene annotation was facilitated by the phylogenetic proximity of Cleome and Arabidopsis (Arabidopsis thaliana). Up to 603 transcripts differ in abundance between these C(3) and C(4) leaves. These include 17 transcription factors, putative transport proteins, as well as genes that in Arabidopsis are implicated in chloroplast movement and expansion, plasmodesmatal connectivity, and cell wall modification. These are all characteristics known to alter in a C(4) leaf but that previously had remained undefined at the molecular level. We also document large shifts in overall transcription profiles for selected functional classes. Our approach defines the extent to which transcript abundance in these C(3) and C(4) leaves differs, provides a blueprint for the NAD-malic enzyme C(4) pathway operating in a dicotyledon, and furthermore identifies potential regulators. We anticipate that comparative transcriptomics of closely related species will provide deep insight into the evolution of other complex traits.
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Bräutigam A, Gowik U. What can next generation sequencing do for you? Next generation sequencing as a valuable tool in plant research. PLANT BIOLOGY (STUTTGART, GERMANY) 2010; 12:831-41. [PMID: 21040298 DOI: 10.1111/j.1438-8677.2010.00373.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Next generation sequencing (NGS) technologies have opened fascinating opportunities for the analysis of plants with and without a sequenced genome on a genomic scale. During the last few years, NGS methods have become widely available and cost effective. They can be applied to a wide variety of biological questions, from the sequencing of complete eukaryotic genomes and transcriptomes, to the genome-scale analysis of DNA-protein interactions. In this review, we focus on the use of NGS for plant transcriptomics, including gene discovery, transcript quantification and marker discovery for non-model plants, as well as transcript annotation and quantification, small RNA discovery and antisense transcription analysis for model plants. We discuss the experimental design for analysis of plants with and without a sequenced genome, including considerations on sampling, RNA preparation, sequencing platforms and bioinformatics tools for data analysis. NGS technologies offer exciting new opportunities for the plant sciences, especially for work on plants without a sequenced genome, since large sequence resources can be generated at moderate cost.
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Affiliation(s)
- A Bräutigam
- Institute of Plant Biochemistry, Heinrich-Heine University, Düsseldorf, Germany.
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Salem M, Rexroad CE, Wang J, Thorgaard GH, Yao J. Characterization of the rainbow trout transcriptome using Sanger and 454-pyrosequencing approaches. BMC Genomics 2010; 11:564. [PMID: 20942956 PMCID: PMC3091713 DOI: 10.1186/1471-2164-11-564] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2010] [Accepted: 10/13/2010] [Indexed: 12/28/2022] Open
Abstract
Background Rainbow trout are important fish for aquaculture and recreational fisheries and serves as a model species for research investigations associated with carcinogenesis, comparative immunology, toxicology and evolutionary biology. However, to date there is no genome reference sequence to facilitate the development of molecular technologies that utilize high-throughput characterizations of gene expression and genetic variation. Alternatively, transcriptome sequencing is a rapid and efficient means for gene discovery and genetic marker development. Although a large number (258,973) of EST sequences are publicly available, the nature of rainbow trout duplicated genome hinders assembly and complicates annotation. Results High-throughput deep sequencing of the Swanson rainbow trout doubled-haploid transcriptome using 454-pyrosequencing technology yielded ~1.3 million reads with an average length of 344 bp, a total of 447 million bases. De novo assembly of the sequences yielded 151,847 Tentative Consensus (TC) sequences (average length of 662 bp) and 224,391 singletons. A combination assembly of both the 454-pyrosequencing ESTs and the pre-existing sequences resulted in 161,818 TCs (average length of 758 bp) and 261,071 singletons. Gene Ontology analysis of the combination assembly showed high similarities to transcriptomes of other fish species with known genome sequences. Conclusion The 454 library significantly increased the suite of ESTs available for rainbow trout, allowing improved assembly and annotation of the transcriptome. Furthermore, the 454 sequencing enables functional genome research in rainbow trout, providing a wealth of sequence data to serve as a reference transcriptome for future studies including identification of paralogous sequences and/or allelic variation, digital gene expression and proteomic research.
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Affiliation(s)
- Mohamed Salem
- Laboratory of Animal Biotechnology and Genomics, Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA
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Pudelski B, Kraus S, Soll J, Philippar K. The plant PRAT proteins - preprotein and amino acid transport in mitochondria and chloroplasts. PLANT BIOLOGY (STUTTGART, GERMANY) 2010; 12 Suppl 1:42-55. [PMID: 20712620 DOI: 10.1111/j.1438-8677.2010.00357.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The membrane proteins of the plant preprotein and amino acid transporter (PRAT) superfamily all share common structural elements, such as four membrane-spanning alpha-helices. Interestingly they display diverse localisation to outer and inner membranes of chloroplasts and mitochondria. Furthermore, they fulfil different functions in preprotein translocation as well as amino acid transport across these membranes. This review summarises current knowledge on precursor protein import and amino acid transport in plastids and mitochondria and provides an overview of the distinct tasks and features of members of the PRAT superfamily in the model plant Arabidopsis thaliana.
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Affiliation(s)
- B Pudelski
- Biochemie und Physiologie der Pflanzen, Department Biologie I, Botanik, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
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Schilmiller AL, Miner DP, Larson M, McDowell E, Gang DR, Wilkerson C, Last RL. Studies of a biochemical factory: tomato trichome deep expressed sequence tag sequencing and proteomics. PLANT PHYSIOLOGY 2010; 153:1212-23. [PMID: 20431087 PMCID: PMC2899918 DOI: 10.1104/pp.110.157214] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2010] [Accepted: 04/27/2010] [Indexed: 05/18/2023]
Abstract
Shotgun proteomics analysis allows hundreds of proteins to be identified and quantified from a single sample at relatively low cost. Extensive DNA sequence information is a prerequisite for shotgun proteomics, and it is ideal to have sequence for the organism being studied rather than from related species or accessions. While this requirement has limited the set of organisms that are candidates for this approach, next generation sequencing technologies make it feasible to obtain deep DNA sequence coverage from any organism. As part of our studies of specialized (secondary) metabolism in tomato (Solanum lycopersicum) trichomes, 454 sequencing of cDNA was combined with shotgun proteomics analyses to obtain in-depth profiles of genes and proteins expressed in leaf and stem glandular trichomes of 3-week-old plants. The expressed sequence tag and proteomics data sets combined with metabolite analysis led to the discovery and characterization of a sesquiterpene synthase that produces beta-caryophyllene and alpha-humulene from E,E-farnesyl diphosphate in trichomes of leaf but not of stem. This analysis demonstrates the utility of combining high-throughput cDNA sequencing with proteomics experiments in a target tissue. These data can be used for dissection of other biochemical processes in these specialized epidermal cells.
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Affiliation(s)
- Anthony L Schilmiller
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319, USA.
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EST analysis reveals putative genes involved in glycyrrhizin biosynthesis. BMC Genomics 2010; 11:268. [PMID: 20423525 PMCID: PMC2886062 DOI: 10.1186/1471-2164-11-268] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2009] [Accepted: 04/28/2010] [Indexed: 12/29/2022] Open
Abstract
Background Glycyrrhiza uralensis is one of the most popular medicinal plants in the world and is also widely used in the flavoring of food and tobacco. Due to limited genomic and transcriptomic data, the biosynthetic pathway of glycyrrhizin, the major bioactive compound in G. uralensis, is currently unclear. Identification of candidate genes involved in the glycyrrhizin biosynthetic pathway will significantly contribute to the understanding of the biosynthetic and medicinal chemistry of this compound. Results We used the 454 GS FLX platform and Titanium regents to produce a substantial expressed sequence tag (EST) dataset from the vegetative organs of G. uralensis. A total of 59,219 ESTs with an average read length of 409 bp were generated. 454 ESTs were combined with the 50,666 G. uralensis ESTs in GenBank. The combined ESTs were assembled into 27,229 unique sequences (11,694 contigs and 15,535 singletons). A total of 20,437 unique gene elements representing approximately 10,000 independent transcripts were annotated using BLAST searches (e-value ≤ 1e-5) against the SwissProt, KEGG, TAIR, Nr and Nt databases. The assembled sequences were annotated with gene names and Gene Ontology (GO) terms. With respect to the genes related to glycyrrhizin metabolism, genes encoding 16 enzymes of the 18 total steps of the glycyrrhizin skeleton synthesis pathway were found. To identify novel genes that encode cytochrome P450 enzymes and glycosyltransferases, which are related to glycyrrhizin metabolism, a total of 125 and 172 unigenes were found to be homologous to cytochrome P450s and glycosyltransferases, respectively. The cytochrome P450 candidate genes were classified into 32 CYP families, while the glycosyltransferase candidate genes were classified into 45 categories by GO analysis. Finally, 3 cytochrome P450 enzymes and 6 glycosyltransferases were selected as the candidates most likely to be involved in glycyrrhizin biosynthesis through an organ-specific expression pattern analysis based on real-time PCR. Conclusions Using the 454 GS FLX platform and Titanium reagents, our study provides a high-quality EST database for G. uralensis. Based on the EST analysis, novel candidate genes related to the secondary metabolite pathway of glycyrrhizin, including novel genes encoding cytochrome P450s and glycosyltransferases, were found. With the assistance of organ-specific expression pattern analysis, 3 unigenes encoding cytochrome P450s and 6 unigenes encoding glycosyltransferases were selected as the candidates most likely to be involved in glycyrrhizin biosynthesis.
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Walters JR, Harrison RG. Combined EST and proteomic analysis identifies rapidly evolving seminal fluid proteins in Heliconius butterflies. Mol Biol Evol 2010; 27:2000-13. [PMID: 20375075 DOI: 10.1093/molbev/msq092] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Seminal fluid proteins (SFPs) directly influence a wide range of reproductive processes, including fertilization, sperm storage, egg production, and immune response. Like many other reproductive proteins, the molecular evolution of SFPs is generally characterized by rapid and frequently adaptive evolution. However, the evolutionary processes underlying this often-documented pattern have not yet been confidently determined. A robust understanding of the processes governing SFP evolution will ultimately require identifying SFPs and characterizing their evolution in many different taxa, often where only limited genomic resources are available. Here, we report the first comprehensive molecular genetic and evolutionary analysis of SFPs conducted in Lepidoptera (moths and butterflies). We have identified 51 novel SFPs from two species of Heliconius butterflies (Heliconius erato and Heliconius melpomene) by combining "indirect" bioinformatic and expression analyses of expressed sequence tags from male accessory gland and wing tissues with "direct" proteomic analyses of spermatophores. Proteomic analyses identified fewer SFPs than the indirect criteria but gave consistent results. Of 51 SFPs, 40 were identified in both species but fewer than half could be functionally annotated via similarity searches (Blast, IPRscan, etc.). The majority of annotated Heliconius SFPs were predicted to be chymotrypsins. Comparisons of Heliconius SFPs with those from fruit fly, mosquito, honeybee, and cricket suggest that gene turnover is high among these proteins and that SFPs are rarely conserved across insect orders. Pairwise estimates of evolutionary rates between SFPs and nonreproductive proteins show that, on average, Heliconius SFPs are evolving rapidly. At least one of these SFPs is evolving adaptively (dN/dS > 1), implicating a role for positive selection in this rapid evolution. This work establishes a strong precedent for future research on the causes and consequences of reproductive protein evolution in the Lepidoptera. Butterflies and moths have an extremely rich history of organismal research, which will provide an informative ecological context for further molecular evolutionary investigations.
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Affiliation(s)
- James R Walters
- Department of Ecology and Evolutionary Biology, Cornell University, USA.
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Abstract
Chloroplasts are the defining organelle of photoautotrophic plant cells. Photosynthetic light reactions and electron transport are the functions of an elaborate thylakoid membrane system inside chloroplasts. The lipid composition of photosynthetic membranes is characterized by a substantial fraction of nonphosphorous galactoglycerolipids reflecting the need of sessile plants to conserve phosphorus. Lipid transport and assembly of glycerolipids play an essential role in the biogenesis of the photosynthetic apparatus in developing chloroplasts. During chloroplast biogenesis, fatty acids are synthesized in the plastid and are exported to the endoplasmic reticulum, where they are incorporated into membrane lipids. Alternatively, lipids can also be assembled de novo at the inner envelope membrane of plastids in many plants. A rich repertoire of lipid exchange mechanisms involving the thylakoid membranes, the chloroplast inner and outer envelope membranes, and the endoplasmic reticulum is emerging. Studies of thylakoid biogenesis provide new insights into the general mechanisms of intermembrane lipid transfer.
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Affiliation(s)
- Christoph Benning
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA.
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Thompson R, Burstin J, Gallardo K. Post-genomics studies of developmental processes in legume seeds. PLANT PHYSIOLOGY 2009; 151:1023-9. [PMID: 19675147 PMCID: PMC2773076 DOI: 10.1104/pp.109.143966] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Affiliation(s)
- Richard Thompson
- INRA, UMR Genetics and Ecophysiology of Grain Legumes, F-21065 Dijon, France.
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Bräutigam A, Weber APM. Proteomic analysis of the proplastid envelope membrane provides novel insights into small molecule and protein transport across proplastid membranes. MOLECULAR PLANT 2009; 2:1247-61. [PMID: 19995728 DOI: 10.1093/mp/ssp070] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Proplastids are undifferentiated plastids of meristematic tissues that synthesize amino acids for protein synthesis, fatty acids for membrane lipid production, and purines and pyrimidines for DNA and RNA synthesis. Unlike chloroplasts, proplastids depend on supply, with reducing power, energy, and precursor metabolites from the remainder of the cell. Comparing proplastid and chloroplast envelope proteomes and the corresponding transcriptomes of leaves and shoot apex revealed a clearly distinct composition of the proplastid envelope. It is geared towards import of metabolic precursors and export of product metabolites for the rapidly dividing cell. The analysis also suggested a new role for the triosephosphate translocator in meristematic tissues, identified the route of organic nitrogen import into proplastids, and detected an adenine nucleotide exporter. The protein import complex contains the import receptors Toc120 and Toc132 and lacks the redox sensing complex subunits of Tic32, Tic55, and Tic62, which mirrors the expression patterns of the corresponding genes in leaves and the shoot apex. We further show that the protein composition of the internal membrane system is similar to etioplasts, as it is dominated by the ATP synthase complex and thus remarkably differs from that of chloroplast thylakoids.
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Affiliation(s)
- Andrea Bräutigam
- Institut für Biochemie der Pflanzen, Heinrich Heine Universität, Universitätsstrasse 1, D-40225 Düsseldorf, Germany.
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Morozova O, Hirst M, Marra MA. Applications of new sequencing technologies for transcriptome analysis. Annu Rev Genomics Hum Genet 2009; 10:135-51. [PMID: 19715439 DOI: 10.1146/annurev-genom-082908-145957] [Citation(s) in RCA: 340] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Transcriptome analysis has been a key area of biological inquiry for decades. Over the years, research in the field has progressed from candidate gene-based detection of RNAs using Northern blotting to high-throughput expression profiling driven by the advent of microarrays. Next-generation sequencing technologies have revolutionized transcriptomics by providing opportunities for multidimensional examinations of cellular transcriptomes in which high-throughput expression data are obtained at a single-base resolution.
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Affiliation(s)
- Olena Morozova
- BC Cancer Agency, Genome Sciences Center, Vancouver, BC V5Z 4S6, Canada.
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Dassanayake M, Haas JS, Bohnert HJ, Cheeseman JM. Shedding light on an extremophile lifestyle through transcriptomics. THE NEW PHYTOLOGIST 2009; 183:764-775. [PMID: 19549131 DOI: 10.1111/j.1469-8137.2009.02913.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The tropical intertidal ecosystem is defined by trees - mangroves - which are adapted to an extreme and extremely variable environment. The genetic basis underlying these adaptations is, however, virtually unknown. Based on advances in pyrosequencing, we present here the first transcriptome analysis for plants for which no prior genomic information was available. We selected the mangroves Rhizophora mangle (Rhizophoraceae) and Heritiera littoralis (Malvaceae) as ecologically important extremophiles employing markedly different physiological and life-history strategies for survival and dominance in this extreme environment. For maximal representation of conditional transcripts, mRNA was obtained from a variety of developmental stages, tissues types, and habitats. For each species, a normalized cDNA library of pooled mRNAs was analysed using GSFLX pyrosequencing. A total of 537,635 sequences were assembled de novo and annotated as > 13,000 distinct gene models for each species. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology annotations highlighted remarkable similarities in the mangrove transcriptome profiles, which differed substantially from the model plants Arabidopsis and Populus. Similarities in the two species suggest a unique mangrove lifestyle overarching the effects of transcriptome size, habitat, tissue type, developmental stage, and biogeographic and phylogenetic differences between them.
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Affiliation(s)
- M Dassanayake
- Department of Plant Biology, University of Illinois, 505 South Goodwin Avenue, Urbana, IL 61801 USA
| | - J S Haas
- Office of Networked Information Technologies (ONIT), School of Integrative Biology, University of Illinois, 505 South Goodwin Avenue, Urbana, IL 61801 USA
| | - H J Bohnert
- Department of Plant Biology, University of Illinois, 505 South Goodwin Avenue, Urbana, IL 61801 USA
| | - J M Cheeseman
- Department of Plant Biology, University of Illinois, 505 South Goodwin Avenue, Urbana, IL 61801 USA
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Jouhet J, Gray JC. Interaction of actin and the chloroplast protein import apparatus. J Biol Chem 2009; 284:19132-41. [PMID: 19435889 PMCID: PMC2707226 DOI: 10.1074/jbc.m109.012831] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2009] [Revised: 05/08/2009] [Indexed: 11/06/2022] Open
Abstract
Actin filaments are major components of the cytoskeleton and play numerous essential roles, including chloroplast positioning and plastid stromule movement, in plant cells. Actin is present in pea chloroplast envelope membrane preparations and is localized at the surface of the chloroplasts, as shown by agglutination of intact isolated chloroplasts by antibodies to actin. To identify chloroplast envelope proteins involved in actin binding, we have carried out actin co-immunoprecipitation and co-sedimentation experiments on detergent-solubilized pea chloroplast envelope membranes. Proteins co-immunoprecipitated with actin were identified by mass spectrometry and by Western blotting and included the Toc159, Toc75, Toc34, and Tic110 components of the TOC-TIC protein import apparatus. A direct interaction of actin with Escherichia coli-expressed Toc159, but not Toc33, was shown by co-sedimentation experiments, suggesting that Toc159 is the component of the TOC complex that interacts with actin on the cytosolic side of the outer envelope membrane. The physiological significance of this interaction is unknown, but it may play a role in the import of nuclear-encoded photosynthesis proteins.
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Affiliation(s)
- Juliette Jouhet
- From the Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, United Kingdom
| | - John C. Gray
- From the Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, United Kingdom
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