A Pan-plant Protein Complex Map Reveals Deep Conservation and Novel Assemblies
Plants are foundational for global ecological and economic systems, but most plant proteins remain uncharacterized. Protein interaction networks often suggest protein functions and open new avenues to characterize genes and proteins. We therefore systematically determined protein complexes from 13 p...
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| Published in | Cell Vol. 181; no. 2; pp. 460 - 474.e14 |
|---|---|
| Main Authors | , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
Elsevier Inc
16.04.2020
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| Subjects | |
| Online Access | Get full text |
| ISSN | 0092-8674 1097-4172 1097-4172 |
| DOI | 10.1016/j.cell.2020.02.049 |
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| Abstract | Plants are foundational for global ecological and economic systems, but most plant proteins remain uncharacterized. Protein interaction networks often suggest protein functions and open new avenues to characterize genes and proteins. We therefore systematically determined protein complexes from 13 plant species of scientific and agricultural importance, greatly expanding the known repertoire of stable protein complexes in plants. By using co-fractionation mass spectrometry, we recovered known complexes, confirmed complexes predicted to occur in plants, and identified previously unknown interactions conserved over 1.1 billion years of green plant evolution. Several novel complexes are involved in vernalization and pathogen defense, traits critical for agriculture. We also observed plant analogs of animal complexes with distinct molecular assemblies, including a megadalton-scale tRNA multi-synthetase complex. The resulting map offers a cross-species view of conserved, stable protein assemblies shared across plant cells and provides a mechanistic, biochemical framework for interpreting plant genetics and mutant phenotypes.
[Display omitted]
•A global snapshot of protein organization in plants from deep proteomics profiling•Biochemical fractionation reveals stable protein complexes conserved across plants•Many observed complexes have previously only been inferred in plants by gene content•Known molecular modules are elaborated in plants with novel subunits and organization
This massive plant proteomics project, using co-fractionation mass spectrometry to measure the amounts and associations of over two million proteins from 13 diverse plant species, reveals stable protein complexes shared across plant cells and provides a framework for interpreting plant genetics and mutant phenotypes. |
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| AbstractList | Plants are foundational to global ecological and economic systems, yet most plant proteins remain uncharacterized. Protein interaction networks often suggest protein functions and open new avenues to characterize genes and proteins. We therefore systematically determined protein complexes from 13 plant species of scientific and agricultural importance, greatly expanding the known repertoire of stable protein complexes in plants. Using co-fractionation mass spectrometry, we recovered known complexes, confirmed complexes predicted to occur in plants, and identified previously unknown interactions conserved over 1.1 billion years of green plant evolution. Several novel complexes are involved in vernalization and pathogen defense, traits critical to agriculture. We also observed plant analogs of animal complexes with distinct molecular assemblies, including a megadalton-scale tRNA multi-synthetase complex. The resulting map offers a cross-species view of conserved, stable protein assemblies shared across plant cells and provides a mechanistic, biochemical framework for interpreting plant genetics and mutant phenotypes. This massive plant proteomics project, using co-fractionation-mass spectrometry to measure the amounts and associations of over two million proteins from 13 diverse plant species, reveals stable protein complexes shared across plant cells and provides a framework for interpreting plant genetics and mutant phenotypes. Plants are foundational for global ecological and economic systems, but most plant proteins remain uncharacterized. Protein interaction networks often suggest protein functions and open new avenues to characterize genes and proteins. We therefore systematically determined protein complexes from 13 plant species of scientific and agricultural importance, greatly expanding the known repertoire of stable protein complexes in plants. By using co-fractionation mass spectrometry, we recovered known complexes, confirmed complexes predicted to occur in plants, and identified previously unknown interactions conserved over 1.1 billion years of green plant evolution. Several novel complexes are involved in vernalization and pathogen defense, traits critical for agriculture. We also observed plant analogs of animal complexes with distinct molecular assemblies, including a megadalton-scale tRNA multi-synthetase complex. The resulting map offers a cross-species view of conserved, stable protein assemblies shared across plant cells and provides a mechanistic, biochemical framework for interpreting plant genetics and mutant phenotypes. Plants are foundational for global ecological and economic systems, but most plant proteins remain uncharacterized. Protein interaction networks often suggest protein functions and open new avenues to characterize genes and proteins. We therefore systematically determined protein complexes from 13 plant species of scientific and agricultural importance, greatly expanding the known repertoire of stable protein complexes in plants. By using co-fractionation mass spectrometry, we recovered known complexes, confirmed complexes predicted to occur in plants, and identified previously unknown interactions conserved over 1.1 billion years of green plant evolution. Several novel complexes are involved in vernalization and pathogen defense, traits critical for agriculture. We also observed plant analogs of animal complexes with distinct molecular assemblies, including a megadalton-scale tRNA multi-synthetase complex. The resulting map offers a cross-species view of conserved, stable protein assemblies shared across plant cells and provides a mechanistic, biochemical framework for interpreting plant genetics and mutant phenotypes. Plants are foundational for global ecological and economic systems, but most plant proteins remain uncharacterized. Protein interaction networks often suggest protein functions and open new avenues to characterize genes and proteins. We therefore systematically determined protein complexes from 13 plant species of scientific and agricultural importance, greatly expanding the known repertoire of stable protein complexes in plants. By using co-fractionation mass spectrometry, we recovered known complexes, confirmed complexes predicted to occur in plants, and identified previously unknown interactions conserved over 1.1 billion years of green plant evolution. Several novel complexes are involved in vernalization and pathogen defense, traits critical for agriculture. We also observed plant analogs of animal complexes with distinct molecular assemblies, including a megadalton-scale tRNA multi-synthetase complex. The resulting map offers a cross-species view of conserved, stable protein assemblies shared across plant cells and provides a mechanistic, biochemical framework for interpreting plant genetics and mutant phenotypes.Plants are foundational for global ecological and economic systems, but most plant proteins remain uncharacterized. Protein interaction networks often suggest protein functions and open new avenues to characterize genes and proteins. We therefore systematically determined protein complexes from 13 plant species of scientific and agricultural importance, greatly expanding the known repertoire of stable protein complexes in plants. By using co-fractionation mass spectrometry, we recovered known complexes, confirmed complexes predicted to occur in plants, and identified previously unknown interactions conserved over 1.1 billion years of green plant evolution. Several novel complexes are involved in vernalization and pathogen defense, traits critical for agriculture. We also observed plant analogs of animal complexes with distinct molecular assemblies, including a megadalton-scale tRNA multi-synthetase complex. The resulting map offers a cross-species view of conserved, stable protein assemblies shared across plant cells and provides a mechanistic, biochemical framework for interpreting plant genetics and mutant phenotypes. Plants are foundational for global ecological and economic systems, but most plant proteins remain uncharacterized. Protein interaction networks often suggest protein functions and open new avenues to characterize genes and proteins. We therefore systematically determined protein complexes from 13 plant species of scientific and agricultural importance, greatly expanding the known repertoire of stable protein complexes in plants. By using co-fractionation mass spectrometry, we recovered known complexes, confirmed complexes predicted to occur in plants, and identified previously unknown interactions conserved over 1.1 billion years of green plant evolution. Several novel complexes are involved in vernalization and pathogen defense, traits critical for agriculture. We also observed plant analogs of animal complexes with distinct molecular assemblies, including a megadalton-scale tRNA multi-synthetase complex. The resulting map offers a cross-species view of conserved, stable protein assemblies shared across plant cells and provides a mechanistic, biochemical framework for interpreting plant genetics and mutant phenotypes. [Display omitted] •A global snapshot of protein organization in plants from deep proteomics profiling•Biochemical fractionation reveals stable protein complexes conserved across plants•Many observed complexes have previously only been inferred in plants by gene content•Known molecular modules are elaborated in plants with novel subunits and organization This massive plant proteomics project, using co-fractionation mass spectrometry to measure the amounts and associations of over two million proteins from 13 diverse plant species, reveals stable protein complexes shared across plant cells and provides a framework for interpreting plant genetics and mutant phenotypes. |
| Author | Papoulas, Ophelia Wan, Cuihong Roux, Stanley J. Dong, Oliver Xiaoou Ronald, Pamela C. McWhite, Claire D. Salmi, Mari L. Drew, Kevin Chen, Z. Jeffrey June, Viviana Cox, Rachael M. Kwon, Taejoon Browning, Karen S. Marcotte, Edward M. |
| AuthorAffiliation | 2 Department of Plant Pathology and The Genome Center, University of California, Davis, CA 95616, USA, and Joint Bioenergy Institute, Emeryville, CA 94608, USA 1 Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA 3 Department of Biomedical Engineering/School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulju-gun, Ulsan, 44919, Republic of Korea 4 Hubei Key Lab of Genetic Regulation & Integrative Biology, School of Life Sciences, Central China Normal University, No. 152 Luoyu Road, Wuhan 430079, PR China |
| AuthorAffiliation_xml | – name: 3 Department of Biomedical Engineering/School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulju-gun, Ulsan, 44919, Republic of Korea – name: 2 Department of Plant Pathology and The Genome Center, University of California, Davis, CA 95616, USA, and Joint Bioenergy Institute, Emeryville, CA 94608, USA – name: 1 Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA – name: 4 Hubei Key Lab of Genetic Regulation & Integrative Biology, School of Life Sciences, Central China Normal University, No. 152 Luoyu Road, Wuhan 430079, PR China |
| Author_xml | – sequence: 1 givenname: Claire D. orcidid: 0000-0001-7346-3047 surname: McWhite fullname: McWhite, Claire D. organization: Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA – sequence: 2 givenname: Ophelia surname: Papoulas fullname: Papoulas, Ophelia organization: Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA – sequence: 3 givenname: Kevin surname: Drew fullname: Drew, Kevin organization: Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA – sequence: 4 givenname: Rachael M. surname: Cox fullname: Cox, Rachael M. organization: Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA – sequence: 5 givenname: Viviana surname: June fullname: June, Viviana organization: Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA – sequence: 6 givenname: Oliver Xiaoou surname: Dong fullname: Dong, Oliver Xiaoou organization: Department of Plant Pathology and The Genome Center, University of California, Davis, Davis, CA 95616, USA – sequence: 7 givenname: Taejoon surname: Kwon fullname: Kwon, Taejoon organization: Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulju-gun, Ulsan 44919, Republic of Korea – sequence: 8 givenname: Cuihong surname: Wan fullname: Wan, Cuihong organization: Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA – sequence: 9 givenname: Mari L. surname: Salmi fullname: Salmi, Mari L. organization: Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA – sequence: 10 givenname: Stanley J. surname: Roux fullname: Roux, Stanley J. organization: Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA – sequence: 11 givenname: Karen S. surname: Browning fullname: Browning, Karen S. organization: Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA – sequence: 12 givenname: Z. Jeffrey surname: Chen fullname: Chen, Z. Jeffrey organization: Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA – sequence: 13 givenname: Pamela C. surname: Ronald fullname: Ronald, Pamela C. organization: Department of Plant Pathology and The Genome Center, University of California, Davis, Davis, CA 95616, USA – sequence: 14 givenname: Edward M. surname: Marcotte fullname: Marcotte, Edward M. email: marcotte@icmb.utexas.edu organization: Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/32191846$$D View this record in MEDLINE/PubMed |
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| Issue | 2 |
| Keywords | protein interactions comparative proteomics pathogen defense plants co-fractionation mass spectrometry (CF-MS) cross-linking mass spectrometry (CL-MS) evolution protein complexes interaction-to-phenotype |
| Language | English |
| License | Copyright © 2020 Elsevier Inc. All rights reserved. |
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| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 These authors contributed equally to this work Lead Contact: Edward M. Marcotte AUTHOR CONTRIBUTIONS Conceptualization and Methodology, CDM, OP, EMM; Software, CDM, KD; Investigation, OP, CDM, CW, RMC, VJ, OXD; Formal Analysis and visualization, CDM; Writing – Original Draft, OP, CDM, EMM; Writing – Review & Editing, CDM, OP, VJ, OXD, KSB, ZJC, PCR, EMM; Funding Acquisition, CDM, KD, ZJC, PCR, EMM; Fern transcriptome, CDM, TK, MLS, SJR, EMM; Resources, SJR, ZJC, KSB, PCR, EMM; Supervision, EMM |
| ORCID | 0000-0001-7346-3047 |
| OpenAccessLink | http://www.cell.com/article/S0092867420302269/pdf |
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| SubjectTerms | animals co-fractionation mass spectrometry (CF-MS) comparative proteomics cross-linking mass spectrometry (CL-MS) economic systems enzymes evolution genes interaction-to-phenotype mass spectrometry Mass Spectrometry - methods mutants pathogen defense pathogens phenotype plant genetics plant proteins Plant Proteins - genetics Plant Proteins - metabolism plants Plants - genetics Plants - metabolism protein complexes Protein Interaction Mapping - methods Protein Interaction Maps - physiology protein interactions Proteomics - methods transfer RNA vernalization |
| Title | A Pan-plant Protein Complex Map Reveals Deep Conservation and Novel Assemblies |
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