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Pulido P, Zagari N, Manavski N, Gawronski P, Matthes A, Scharff LB, Meurer J, Leister D. CHLOROPLAST RIBOSOME ASSOCIATED Supports Translation under Stress and Interacts with the Ribosomal 30S Subunit. PLANT PHYSIOLOGY 2018; 177:1539-1554. [PMID: 29914890 PMCID: PMC6084680 DOI: 10.1104/pp.18.00602] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 06/09/2018] [Indexed: 05/07/2023]
Abstract
Chloroplast ribosomes, which originated from cyanobacteria, comprise a large subunit (50S) and a small subunit (30S) containing ribosomal RNAs (rRNAs) and various ribosomal proteins. Genes for many chloroplast ribosomal proteins, as well as proteins with auxiliary roles in ribosome biogenesis or functioning, reside in the nucleus. Here, we identified Arabidopsis (Arabidopsis thaliana) CHLOROPLAST RIBOSOME ASSOCIATED (CRASS), a member of the latter class of proteins, based on the tight coexpression of its mRNA with transcripts for nucleus-encoded chloroplast ribosomal proteins. CRASS was acquired during the evolution of embryophytes and is localized to the chloroplast stroma. Loss of CRASS results in minor defects in development, photosynthetic efficiency, and chloroplast translation activity under controlled growth conditions, but these phenotypes are greatly exacerbated under stress conditions induced by the translational inhibitors lincomycin and chloramphenicol or by cold treatment. The CRASS protein comigrates with chloroplast ribosomal particles and coimmunoprecipitates with the 16S rRNA and several chloroplast ribosomal proteins, particularly the plastid ribosomal proteins of the 30S subunit (PRPS1 and PRPS5). The association of CRASS with PRPS1 and PRPS5 is independent of rRNA and is not detectable in yeast two-hybrid experiments, implying that either CRASS interacts indirectly with PRPS1 and PRPS5 via another component of the small ribosomal subunit or that it recognizes structural features of the multiprotein/rRNA particle. CRASS plays a role in the biogenesis and/or stability of the chloroplast ribosome that becomes critical under certain stressful conditions when ribosomal activity is compromised.
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Affiliation(s)
- Pablo Pulido
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University, Munich, D-82152 Planegg-Martinsried, Germany
- Copenhagen Plant Science Center, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Nicola Zagari
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University, Munich, D-82152 Planegg-Martinsried, Germany
- Copenhagen Plant Science Center, University of Copenhagen, 1871 Frederiksberg C, Denmark
- Centro Ricerca e Innovazione, Fondazione Edmund Mach, I-38010 San Michele all'Adige, Italy
| | - Nikolay Manavski
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University, Munich, D-82152 Planegg-Martinsried, Germany
| | - Piotr Gawronski
- Copenhagen Plant Science Center, University of Copenhagen, 1871 Frederiksberg C, Denmark
- Department of Plant Genetics, Breeding, and Biotechnology, Warsaw University of Life Sciences, 02-776 Warsaw, Poland
| | - Annemarie Matthes
- Copenhagen Plant Science Center, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Lars B Scharff
- Copenhagen Plant Science Center, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Jörg Meurer
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University, Munich, D-82152 Planegg-Martinsried, Germany
| | - Dario Leister
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University, Munich, D-82152 Planegg-Martinsried, Germany
- Copenhagen Plant Science Center, University of Copenhagen, 1871 Frederiksberg C, Denmark
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102
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Helle S, Bray F, Verbeke J, Devassine S, Courseaux A, Facon M, Tokarski C, Rolando C, Szydlowski N. Proteome Analysis of Potato Starch Reveals the Presence of New Starch Metabolic Proteins as Well as Multiple Protease Inhibitors. FRONTIERS IN PLANT SCIENCE 2018; 9:746. [PMID: 29963063 PMCID: PMC6013586 DOI: 10.3389/fpls.2018.00746] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 05/15/2018] [Indexed: 05/20/2023]
Abstract
Starch bound proteins mainly include enzymes from the starch biosynthesis pathway. Recently, new functions in starch molecular assembly or active protein targeting were also proposed for starch associated proteins. The potato genome sequence reveals 77 loci encoding starch metabolizing enzymes with the identification of previously unknown putative isoforms. Here we show by bottom-up proteomics that most of the starch biosynthetic enzymes in potato remain associated with starch even after washing with SDS or protease treatment of the granule surface. Moreover, our study confirmed the presence of PTST1 (Protein Targeting to Starch), ESV1 (Early StarVation1) and LESV (Like ESV), that have recently been identified in Arabidopsis. In addition, we report on the presence of a new isoform of starch synthase, SS6, containing both K-X-G-G-L catalytic motifs. Furthermore, multiple protease inhibitors were also identified that are cleared away from starch by SDS and thermolysin treatments. Our results indicate that SS6 may play a yet uncharacterized function in starch biosynthesis and open new perspectives both in understanding storage starch metabolism as well as breeding improved potato lines.
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Affiliation(s)
- Stanislas Helle
- Univ. Lille, CNRS, UMR8576 – UGSF – Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
- Univ. Lille, CNRS, USR 3290 – MSAP – Miniaturisation pour la Synthèse, l’Analyse et la Protéomique, Lille, France
| | - Fabrice Bray
- Univ. Lille, CNRS, USR 3290 – MSAP – Miniaturisation pour la Synthèse, l’Analyse et la Protéomique, Lille, France
| | - Jérémy Verbeke
- Univ. Lille, CNRS, USR 3290 – MSAP – Miniaturisation pour la Synthèse, l’Analyse et la Protéomique, Lille, France
| | - Stéphanie Devassine
- Univ. Lille, CNRS, USR 3290 – MSAP – Miniaturisation pour la Synthèse, l’Analyse et la Protéomique, Lille, France
| | - Adeline Courseaux
- Univ. Lille, CNRS, UMR8576 – UGSF – Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Maud Facon
- Univ. Lille, CNRS, UMR8576 – UGSF – Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
- Univ. Lille, CNRS, USR 3290 – MSAP – Miniaturisation pour la Synthèse, l’Analyse et la Protéomique, Lille, France
| | - Caroline Tokarski
- Univ. Lille, CNRS, USR 3290 – MSAP – Miniaturisation pour la Synthèse, l’Analyse et la Protéomique, Lille, France
| | - Christian Rolando
- Univ. Lille, CNRS, USR 3290 – MSAP – Miniaturisation pour la Synthèse, l’Analyse et la Protéomique, Lille, France
| | - Nicolas Szydlowski
- Univ. Lille, CNRS, UMR8576 – UGSF – Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
- Univ. Lille, CNRS, USR 3290 – MSAP – Miniaturisation pour la Synthèse, l’Analyse et la Protéomique, Lille, France
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103
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Marchand J, Heydarizadeh P, Schoefs B, Spetea C. Ion and metabolite transport in the chloroplast of algae: lessons from land plants. Cell Mol Life Sci 2018; 75:2153-2176. [PMID: 29541792 PMCID: PMC5948301 DOI: 10.1007/s00018-018-2793-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 03/01/2018] [Accepted: 03/07/2018] [Indexed: 12/28/2022]
Abstract
Chloroplasts are endosymbiotic organelles and play crucial roles in energy supply and metabolism of eukaryotic photosynthetic organisms (algae and land plants). They harbor channels and transporters in the envelope and thylakoid membranes, mediating the exchange of ions and metabolites with the cytosol and the chloroplast stroma and between the different chloroplast subcompartments. In secondarily evolved algae, three or four envelope membranes surround the chloroplast, making more complex the exchange of ions and metabolites. Despite the importance of transport proteins for the optimal functioning of the chloroplast in algae, and that many land plant homologues have been predicted, experimental evidence and molecular characterization are missing in most cases. Here, we provide an overview of the current knowledge about ion and metabolite transport in the chloroplast from algae. The main aspects reviewed are localization and activity of the transport proteins from algae and/or of homologues from other organisms including land plants. Most chloroplast transporters were identified in the green alga Chlamydomonas reinhardtii, reside in the envelope and participate in carbon acquisition and metabolism. Only a few identified algal transporters are located in the thylakoid membrane and play role in ion transport. The presence of genes for putative transporters in green algae, red algae, diatoms, glaucophytes and cryptophytes is discussed, and roles in the chloroplast are suggested. A deep knowledge in this field is required because algae represent a potential source of biomass and valuable metabolites for industry, medicine and agriculture.
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Affiliation(s)
- Justine Marchand
- Metabolism, Bioengineering of Microalgal Molecules and Applications (MIMMA), Mer Molécules Santé, IUML, FR 3473 CNRS, Le Mans University, 72000, Le Mans, France
| | - Parisa Heydarizadeh
- Metabolism, Bioengineering of Microalgal Molecules and Applications (MIMMA), Mer Molécules Santé, IUML, FR 3473 CNRS, Le Mans University, 72000, Le Mans, France
| | - Benoît Schoefs
- Metabolism, Bioengineering of Microalgal Molecules and Applications (MIMMA), Mer Molécules Santé, IUML, FR 3473 CNRS, Le Mans University, 72000, Le Mans, France.
| | - Cornelia Spetea
- Department of Biological and Environmental Sciences, University of Gothenburg, 40530, Göteborg, Sweden.
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104
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Ahmed MS, Shahjaman M, Kabir E, Kamruzzaman M. Prediction of Protein Acetylation Sites using Kernel Naive Bayes Classifier Based on Protein Sequences Profiling. Bioinformation 2018; 14:213-218. [PMID: 30108418 PMCID: PMC6077816 DOI: 10.6026/97320630014213] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 04/29/2018] [Accepted: 04/29/2018] [Indexed: 12/11/2022] Open
Abstract
Lysine acetylation is one of the decisive categories of protein post-translational modification (PTM), it is convoluted in many significant cellular developments and severe diseases in the biological system. The experimental identification of protein-acetylated sites is painstaking, time-consuming and expensive. Hence, there is significant interest in the development of computational approaches for consistent prediction of acetylation sites using protein sequences. Features selection from protein sequences plays a significant role for acetylation sites prediction. We describe an improved feature selection approach for acetylation sites prediction based on kernel naive Bayes classifier (KNBC). We have shown that KNBC generated from selected features by a new feature selection method outperforms than the existing methods for identification of acetylation sites. The sensitivity, specificity, ACC (Accuracy), MCC (Matthews Correlation Coefficient) and AUC (Area under Curve of ROC) in our proposed method are as follows 80.71%, 93.39%, 76.73%, 41.37% and 83.0% with the optimum window size is 47. Thus the kernel naive Bayes classifier finds application in acetylation site prediction.
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Affiliation(s)
- Md. Shakil Ahmed
- Department of Statistics, University of Rajshahi, Rajshahi-6205, Bangladesh
| | - Md. Shahjaman
- Department of Statistics, Begum Rokeya University, Rangpur-5400, Bangladesh
| | - Enamul Kabir
- School of Agricultural, Computational and Environmental Sciences, University of Southern Queensland, Australia
| | - Md. Kamruzzaman
- Data Science for Knowledge Creation Research Center, Seoul National University, Korea
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105
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Sun Q, Li YY, Wang Y, Zhao HH, Zhao TY, Zhang ZY, Li DW, Yu JL, Wang XB, Zhang YL, Han CG. Brassica yellows virus P0 protein impairs the antiviral activity of NbRAF2 in Nicotiana benthamiana. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:3127-3139. [PMID: 29659986 PMCID: PMC5972614 DOI: 10.1093/jxb/ery131] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 03/24/2018] [Indexed: 05/29/2023]
Abstract
In interactions between poleroviruses and their hosts, few cellular proteins have been identified that directly interact with the multifunctional virus P0 protein. To help explore the functions of P0, we identified a Brassica yellows virus genotype A (BrYV-A) P0BrA-interacting protein from Nicotiana benthamiana, Rubisco assembly factor 2 (NbRAF2), which localizes in the nucleus, cell periphery, chloroplasts, and stromules. We found that its C-terminal domain (amino acids 183-211) is required for self-interaction. A split ubiquitin membrane-bound yeast two-hybrid system and co-immunoprecipitation assays showed that NbRAF2 interacted with P0BrA, and co-localized in the nucleus and at the cell periphery. Interestingly, the nuclear pool of NbRAF2 decreased in the presence of P0BrA and during BrYV-A infection, and the P0BrA-mediated reduction of nuclear NbRAF2 required dual localization of NbRAF2 in the chloroplasts and nucleus. Tobacco rattle virus-based virus-induced gene silencing of NbRAF2 promoted BrYV-A infection in N. benthamiana, and the overexpression of nuclear NbRAF2 inhibited BrYV-A accumulation. Potato leafroll virus P0PL also interacted with NbRAF2 and decreased its nuclear accumulation, indicating that NbRAF2 may be a common target of poleroviruses. These results suggest that nuclear NbRAF2 possesses antiviral activity against BrYV-A infection, and that BrYV-A P0BrA interacts with NbRAF2 and alters its localization pattern to facilitate virus infection.
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Affiliation(s)
- Qian Sun
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory of Plant Pathology, China Agricultural University, Beijing, P. R. China
| | - Yuan-Yuan Li
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory of Plant Pathology, China Agricultural University, Beijing, P. R. China
| | - Ying Wang
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory of Plant Pathology, China Agricultural University, Beijing, P. R. China
| | - Hang-Hai Zhao
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory of Plant Pathology, China Agricultural University, Beijing, P. R. China
| | - Tian-Yu Zhao
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory of Plant Pathology, China Agricultural University, Beijing, P. R. China
| | - Zong-Ying Zhang
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory of Plant Pathology, China Agricultural University, Beijing, P. R. China
| | - Da-Wei Li
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, P. R., China
| | - Jia-Lin Yu
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, P. R., China
| | - Xian-Bing Wang
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, P. R., China
| | - Yong-Liang Zhang
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, P. R., China
| | - Cheng-Gui Han
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory of Plant Pathology, China Agricultural University, Beijing, P. R. China
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106
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Fichman Y, Koncz Z, Reznik N, Miller G, Szabados L, Kramer K, Nakagami H, Fromm H, Koncz C, Zilberstein A. SELENOPROTEIN O is a chloroplast protein involved in ROS scavenging and its absence increases dehydration tolerance in Arabidopsis thaliana. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 270:278-291. [PMID: 29576081 DOI: 10.1016/j.plantsci.2018.02.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Revised: 02/26/2018] [Accepted: 02/27/2018] [Indexed: 06/08/2023]
Abstract
The evolutionary conserved family of Selenoproteins performs redox-regulatory functions in bacteria, archaea and eukaryotes. Among them, members of the SELENOPROTEIN O (SELO) subfamily are located in mammalian and yeast mitochondria, but their functions are thus far enigmatic. Screening of T-DNA knockout mutants for resistance to the proline analogue thioproline (T4C), identified mutant alleles of the plant SELO homologue in Arabidopsis thaliana. Absence of SELO resulted in a stress-induced transcriptional activation instead of silencing of mitochondrial proline dehydrogenase, and also high elevation of Δ(1)-pyrroline-5-carboxylate dehydrogenase involved in degradation of proline, thereby alleviating T4C inhibition and lessening drought-induced proline accumulation. Unlike its animal homologues, SELO was localized to chloroplasts of plants ectopically expressing SELO-GFP. The protein was co-fractionated with thylakoid membrane complexes, and co-immunoprecipitated with FNR, PGRL1 and STN7, all involved in regulating PSI and downstream electron flow. The selo mutants displayed extended survival under dehydration, accompanied by longer photosynthetic activity, compared with wild-type plants. Enhanced expression of genes encoding ROS scavenging enzymes in the unstressed selo mutant correlated with higher oxidant scavenging capacity and reduced methyl viologen damage. The study elucidates SELO as a PSI-related component involved in regulating ROS levels and stress responses.
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Affiliation(s)
- Yosef Fichman
- School of Plant Sciences and Food Security, Tel Aviv University, P.O. Box 39040, Tel Aviv 6997801, Israel
| | - Zsuzsa Koncz
- Department of Plant Developmental Biology, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, D-50829 Cologne, Germany
| | - Noam Reznik
- School of Plant Sciences and Food Security, Tel Aviv University, P.O. Box 39040, Tel Aviv 6997801, Israel
| | - Gad Miller
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - László Szabados
- Institute of Plant Biology, Biological Research Center of Hungarian Academy of Sciences, Temesvári krt. 62/64, H-6724 Szeged, Hungary
| | - Katharina Kramer
- Protein Mass Spectrometry Group, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, D-50829 Cologne, Germany
| | - Hirofumi Nakagami
- Protein Mass Spectrometry Group, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, D-50829 Cologne, Germany
| | - Hillel Fromm
- School of Plant Sciences and Food Security, Tel Aviv University, P.O. Box 39040, Tel Aviv 6997801, Israel
| | - Csaba Koncz
- Department of Plant Developmental Biology, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, D-50829 Cologne, Germany; Institute of Plant Biology, Biological Research Center of Hungarian Academy of Sciences, Temesvári krt. 62/64, H-6724 Szeged, Hungary
| | - Aviah Zilberstein
- School of Plant Sciences and Food Security, Tel Aviv University, P.O. Box 39040, Tel Aviv 6997801, Israel.
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107
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Nowack ECM, Weber APM. Genomics-Informed Insights into Endosymbiotic Organelle Evolution in Photosynthetic Eukaryotes. ANNUAL REVIEW OF PLANT BIOLOGY 2018; 69:51-84. [PMID: 29489396 DOI: 10.1146/annurev-arplant-042817-040209] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The conversion of free-living cyanobacteria to photosynthetic organelles of eukaryotic cells through endosymbiosis transformed the biosphere and eventually provided the basis for life on land. Despite the presumable advantage conferred by the acquisition of photoautotrophy through endosymbiosis, only two independent cases of primary endosymbiosis have been documented: one that gave rise to the Archaeplastida, and the other to photosynthetic species of the thecate, filose amoeba Paulinella. Here, we review recent genomics-informed insights into the primary endosymbiotic origins of cyanobacteria-derived organelles. Furthermore, we discuss the preconditions for the evolution of nitrogen-fixing organelles. Recent genomic data on previously undersampled cyanobacterial and protist taxa provide new clues to the origins of the host cell and endosymbiont, and proteomic approaches allow insights into the rearrangement of the endosymbiont proteome during organellogenesis. We conclude that in addition to endosymbiotic gene transfers, horizontal gene acquisitions from a broad variety of prokaryotic taxa were crucial to organelle evolution.
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Affiliation(s)
- Eva C M Nowack
- Microbial Symbiosis and Organelle Evolution Group, Biology Department, Heinrich Heine University, 40225 Düsseldorf, Germany;
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, 40225 Düsseldorf, Germany;
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108
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Zoschke R, Bock R. Chloroplast Translation: Structural and Functional Organization, Operational Control, and Regulation. THE PLANT CELL 2018; 30:745-770. [PMID: 29610211 PMCID: PMC5969280 DOI: 10.1105/tpc.18.00016] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/26/2018] [Accepted: 04/01/2018] [Indexed: 05/20/2023]
Abstract
Chloroplast translation is essential for cellular viability and plant development. Its positioning at the intersection of organellar RNA and protein metabolism makes it a unique point for the regulation of gene expression in response to internal and external cues. Recently obtained high-resolution structures of plastid ribosomes, the development of approaches allowing genome-wide analyses of chloroplast translation (i.e., ribosome profiling), and the discovery of RNA binding proteins involved in the control of translational activity have greatly increased our understanding of the chloroplast translation process and its regulation. In this review, we provide an overview of the current knowledge of the chloroplast translation machinery, its structure, organization, and function. In addition, we summarize the techniques that are currently available to study chloroplast translation and describe how translational activity is controlled and which cis-elements and trans-factors are involved. Finally, we discuss how translational control contributes to the regulation of chloroplast gene expression in response to developmental, environmental, and physiological cues. We also illustrate the commonalities and the differences between the chloroplast and bacterial translation machineries and the mechanisms of protein biosynthesis in these two prokaryotic systems.
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Affiliation(s)
- Reimo Zoschke
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Ralph Bock
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
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109
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Lee DW, Hwang I. Evolution and Design Principles of the Diverse Chloroplast Transit Peptides. Mol Cells 2018; 41:161-167. [PMID: 29487274 PMCID: PMC5881089 DOI: 10.14348/molcells.2018.0033] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 02/06/2018] [Indexed: 11/27/2022] Open
Abstract
Chloroplasts are present in organisms belonging to the kingdom Plantae. These organelles are thought to have originated from photosynthetic cyanobacteria through endosymbiosis. During endosymbiosis, most cyanobacterial genes were transferred to the host nucleus. Therefore, most chloroplast proteins became encoded in the nuclear genome and must return to the chloroplast after translation. The N-terminal cleavable transit peptide (TP) is necessary and sufficient for the import of nucleus-encoded interior chloroplast proteins. Over the past decade, extensive research on the TP has revealed many important characteristic features of TPs. These studies have also shed light on the question of how the many diverse TPs could have evolved to target specific proteins to the chloroplast. In this review, we summarize the characteristic features of TPs. We also highlight recent advances in our understanding of TP evolution and provide future perspectives about this important research area.
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Affiliation(s)
- Dong Wook Lee
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang 37673,
Korea
| | - Inhwan Hwang
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang 37673,
Korea
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673,
Korea
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110
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Ashihara H, Stasolla C, Fujimura T, Crozier A. Purine salvage in plants. PHYTOCHEMISTRY 2018; 147:89-124. [PMID: 29306799 DOI: 10.1016/j.phytochem.2017.12.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 12/10/2017] [Accepted: 12/14/2017] [Indexed: 05/04/2023]
Abstract
Purine bases and nucleosides are produced by turnover of nucleotides and nucleic acids as well as from some cellular metabolic pathways. Adenosine released from the S-adenosyl-L-methionine cycle is linked to many methyltransferase reactions, such as the biosynthesis of caffeine and glycine betaine. Adenine is produced by the methionine cycles, which is related to other biosynthesis pathways, such those for the production of ethylene, nicotianamine and polyamines. These purine compounds are recycled for nucleotide biosynthesis by so-called "salvage pathways". However, the salvage pathways are not merely supplementary routes for nucleotide biosynthesis, but have essential functions in many plant processes. In plants, the major salvage enzymes are adenine phosphoribosyltransferase (EC 2.4.2.7) and adenosine kinase (EC 2.7.1.20). AMP produced by these enzymes is converted to ATP and utilised as an energy source as well as for nucleic acid synthesis. Hypoxanthine, guanine, inosine and guanosine are salvaged to IMP and GMP by hypoxanthine/guanine phosphoribosyltransferase (EC 2.4.2.8) and inosine/guanosine kinase (EC 2.7.1.73). In contrast to de novo purine nucleotide biosynthesis, synthesis by the salvage pathways is extremely favourable, energetically, for cells. In addition, operation of the salvage pathway reduces the intracellular levels of purine bases and nucleosides which inhibit other metabolic reactions. The purine salvage enzymes also catalyse the respective formation of cytokinin ribotides, from cytokinin bases, and cytokinin ribosides. Since cytokinin bases are the active form of cytokinin hormones, these enzymes act to maintain homeostasis of cellular cytokinin bioactivity. This article summarises current knowledge of purine salvage pathways and their possible function in plants and purine salvage activities associated with various physiological phenomena are reviewed.
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Affiliation(s)
- Hiroshi Ashihara
- Department of Biology, Ochanomizu University, Bunkyo-ku, Tokyo, 112-8610, Japan.
| | - Claudio Stasolla
- Department of Plant Science, University of Manitoba, Winnipeg, R3T 2N2, Canada
| | - Tatsuhito Fujimura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Alan Crozier
- Department of Nutrition, University of California, Davis, CA, 95616-5270, USA
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111
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A plastidial pantoate transporter with a potential role in pantothenate synthesis. Biochem J 2018; 475:813-825. [DOI: 10.1042/bcj20170883] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/26/2018] [Accepted: 01/30/2018] [Indexed: 11/17/2022]
Abstract
The pantothenate (vitamin B5) synthesis pathway in plants is not fully defined because the subcellular site of its ketopantoate → pantoate reduction step is unclear. However, the pathway is known to be split between cytosol, mitochondria, and potentially plastids, and inferred to involve mitochondrial or plastidial transport of ketopantoate or pantoate. No proteins that mediate these transport steps have been identified. Comparative genomic and transcriptomic analyses identified Arabidopsis thaliana BASS1 (At1g78560) and its maize (Zea mays) ortholog as candidates for such a transport role. BASS1 proteins belong to the bile acid : sodium symporter family and share similarity with the Salmonella enterica PanS pantoate/ketopantoate transporter and with predicted bacterial transporters whose genes cluster on the chromosome with pantothenate synthesis genes. Furthermore, Arabidopsis BASS1 is co-expressed with genes related to metabolism of coenzyme A, the cofactor derived from pantothenate. Expression of Arabidopsis or maize BASS1 promoted the growth of a S. enterica panB panS mutant strain when pantoate, but not ketopantoate, was supplied, and increased the rate of [3H]pantoate uptake. Subcellular localization of green fluorescent protein fusions in Nicotiana tabacum BY-2 cells demonstrated that Arabidopsis BASS1 is targeted solely to the plastid inner envelope. Two independent Arabidopsis BASS1 knockout mutants accumulated pantoate ∼10-fold in leaves and had smaller seeds. Taken together, these data indicate that BASS1 is a physiologically significant plastidial pantoate transporter and that the pantoate reduction step in pantothenate biosynthesis could be at least partly localized in plastids.
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Gao L, Lu Z, Ding L, Guo J, Wang M, Ling N, Guo S, Shen Q. Role of Aquaporins in Determining Carbon and Nitrogen Status in Higher Plants. Int J Mol Sci 2018; 19:E35. [PMID: 29342938 PMCID: PMC5795985 DOI: 10.3390/ijms19010035] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 12/17/2017] [Accepted: 12/19/2017] [Indexed: 01/01/2023] Open
Abstract
Aquaporins (AQPs) are integral membrane proteins facilitating the transport of water and some small neutral molecules across cell membranes. In past years, much effort has been made to reveal the location of AQPs as well as their function in water transport, photosynthetic processes, and stress responses in higher plants. In the present review, we paid attention to the character of AQPs in determining carbon and nitrogen status. The role of AQPs during photosynthesis is characterized as its function in transporting water and CO₂ across the membrane of chloroplast and thylakoid; recalculated results from published studies showed that over-expression of AQPs contributed to 25% and 50% increases in stomatal conductance (gs) and mesophyll conductance (gm), respectively. The nitrogen status in plants is regulated by AQPs through their effect on water flow as well as urea and NH₄⁺ uptake, and the potential role of AQPs in alleviating ammonium toxicity is discussed. At the same time, root and/or shoot AQP expression is quite dependent on both N supply amounts and forms. Future research directions concerning the function of AQPs in regulating plant carbon and nitrogen status as well as C/N balance are also highlighted.
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Affiliation(s)
- Limin Gao
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China.
| | - Zhifeng Lu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China.
| | - Lei Ding
- Institut des Sciences de la Vie, Université Catholique de Louvain, Louvain-la-Neuve B-1348, Belgium.
| | - Junjie Guo
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China.
| | - Min Wang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China.
| | - Ning Ling
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China.
| | - Shiwei Guo
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China.
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China.
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113
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Lee DW, Yoo YJ, Razzak MA, Hwang I. Prolines in Transit Peptides Are Crucial for Efficient Preprotein Translocation into Chloroplasts. PLANT PHYSIOLOGY 2018; 176:663-677. [PMID: 29158328 PMCID: PMC5761803 DOI: 10.1104/pp.17.01553] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 11/17/2017] [Indexed: 05/20/2023]
Abstract
Chloroplasts import many preproteins that can be classified based on their physicochemical properties. The cleavable N-terminal transit peptide (TP) of chloroplast preproteins contains all the information required for import into chloroplasts through Toc/Tic translocons. The question of whether and how the physicochemical properties of preproteins affect TP-mediated import into chloroplasts has not been elucidated. Here, we present evidence that Pro residues in TP mediate efficient translocation through the chloroplast envelope membranes for proteins containing transmembrane domains (TMDs) or proteins prone to aggregation. By contrast, the translocation of soluble proteins through the chloroplast envelope membranes is less dependent on TP prolines. Proless TPs failed to mediate protein translocation into chloroplasts; instead, these mutant TPs led to protein mistargeting to the chloroplast envelope membranes or nonspecific protein aggregation during import into chloroplasts. The mistargeting of TMD-containing proteins caused by Pro-less TPs in wild-type protoplasts was mimicked by wild-type TPs in hsp93-V protoplasts, in which preprotein translocation is compromised. We propose that the physicochemical properties of chloroplast proteins affect protein translocation through the chloroplast envelope, and prolines in TP have a crucial role in the efficient translocation of TMD-containing proteins.
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Affiliation(s)
- Dong Wook Lee
- Division of Integrative Biosciences and Biotechnology, and Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea
| | - Yun-Joo Yoo
- Division of Integrative Biosciences and Biotechnology, and Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea
| | - Md Abdur Razzak
- Division of Integrative Biosciences and Biotechnology, and Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea
| | - Inhwan Hwang
- Division of Integrative Biosciences and Biotechnology, and Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea
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Hooper CM, Stevens TJ, Saukkonen A, Castleden IR, Singh P, Mann GW, Fabre B, Ito J, Deery MJ, Lilley KS, Petzold CJ, Millar AH, Heazlewood JL, Parsons HT. Multiple marker abundance profiling: combining selected reaction monitoring and data-dependent acquisition for rapid estimation of organelle abundance in subcellular samples. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:1202-1217. [PMID: 29024340 PMCID: PMC5863471 DOI: 10.1111/tpj.13743] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 09/25/2017] [Accepted: 09/28/2017] [Indexed: 05/20/2023]
Abstract
Measuring changes in protein or organelle abundance in the cell is an essential, but challenging aspect of cell biology. Frequently-used methods for determining organelle abundance typically rely on detection of a very few marker proteins, so are unsatisfactory. In silico estimates of protein abundances from publicly available protein spectra can provide useful standard abundance values but contain only data from tissue proteomes, and are not coupled to organelle localization data. A new protein abundance score, the normalized protein abundance scale (NPAS), expands on the number of scored proteins and the scoring accuracy of lower-abundance proteins in Arabidopsis. NPAS was combined with subcellular protein localization data, facilitating quantitative estimations of organelle abundance during routine experimental procedures. A suite of targeted proteomics markers for subcellular compartment markers was developed, enabling independent verification of in silico estimates for relative organelle abundance. Estimation of relative organelle abundance was found to be reproducible and consistent over a range of tissues and growth conditions. In silico abundance estimations and localization data have been combined into an online tool, multiple marker abundance profiling, available in the SUBA4 toolbox (http://suba.live).
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Affiliation(s)
- Cornelia M. Hooper
- ARC Centre of Excellence in Plant Energy BiologyThe University of Western AustraliaPerthWA6009Australia
| | | | - Anna Saukkonen
- Department of BiochemistryUniversity of CambridgeCambridgeCB2 1QRUK
| | - Ian R. Castleden
- ARC Centre of Excellence in Plant Energy BiologyThe University of Western AustraliaPerthWA6009Australia
| | - Pragya Singh
- Joint BioEnergy InstituteLawrence Berkeley National LaboratoryBerkeleyCA94702USA
| | - Gregory W. Mann
- Joint BioEnergy InstituteLawrence Berkeley National LaboratoryBerkeleyCA94702USA
| | - Bertrand Fabre
- Department of BiochemistryUniversity of CambridgeCambridgeCB2 1QRUK
| | - Jun Ito
- Joint BioEnergy InstituteLawrence Berkeley National LaboratoryBerkeleyCA94702USA
| | - Michael J Deery
- Department of BiochemistryUniversity of CambridgeCambridgeCB2 1QRUK
| | | | | | - A. Harvey Millar
- ARC Centre of Excellence in Plant Energy BiologyThe University of Western AustraliaPerthWA6009Australia
| | - Joshua L. Heazlewood
- Joint BioEnergy InstituteLawrence Berkeley National LaboratoryBerkeleyCA94702USA
- School of BioSciencesThe University of MelbourneMelbourneVIC3010Australia
| | - Harriet T. Parsons
- Department of BiochemistryUniversity of CambridgeCambridgeCB2 1QRUK
- Copenhagen University, Plant and Environmental SciencesFrederiksberg1871Denmark
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115
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Zhang S, Zhang Z, Wen Z, Gu C, An YQC, Bales C, DiFonzo C, Song Q, Wang D. Fine mapping of the soybean aphid-resistance genes Rag6 and Rag3c from Glycine soja 85-32. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:2601-2615. [PMID: 28887657 DOI: 10.1007/s00122-017-2979-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 08/30/2017] [Indexed: 05/07/2023]
Abstract
KEY MESSAGE Rag6 and Rag3c were delimited to a 49-kb interval on chromosome 8 and a 150-kb interval on chromosome 16, respectively. Structural variants in the exons of candidate genes were identified. The soybean aphid, an invasive species, has significantly threatened soybean production in North America since 2000. Host-plant resistance is known as an ideal management strategy for aphids. Two novel aphid-resistance loci, Rag6 and Rag3c, from Glycine soja 85-32, were previously detected in a 10.5-cM interval on chromosome 8 and a 7.5-cM interval on chromosome 16, respectively. Defining the exact genomic position of these two genes is critical for improving the effectiveness of marker-assisted selection for aphid resistance and for identification of the functional genes. To pinpoint the locations of Rag6 and Rag3c, four populations segregating for Rag6 and Rag3c were used to fine map these two genes. The availability of the Illumina Infinium SoySNP50K/8K iSelect BeadChip, combined with single-nucleotide polymorphism (SNP) markers discovered through the whole-genome re-sequencing of E12901, facilitated the fine mapping process. Rag6 was refined to a 49-kb interval on chromosome 8 with four candidate genes, including three clustered nucleotide-binding site leucine-rich repeat (NBS-LRR) genes and an amine oxidase encoding gene. Rag3c was refined to a 150-kb interval on chromosome 16 with 11 candidate genes, two of which are a LRR gene and a lipase gene. Moreover, by sequencing the whole-genome exome-capture of the resistant source (E12901), structural variants were identified in the exons of the candidate genes of Rag6 and Rag3c. The closely linked SNP markers and the candidate gene information presented in this study will be significant resources for integrating Rag6 and Rag3c into elite cultivars and for future functional genetics studies.
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Affiliation(s)
- Shichen Zhang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue St., Rm. A384E, East Lansing, MI, 48824-1325, USA
| | - Zhongnan Zhang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue St., Rm. A384E, East Lansing, MI, 48824-1325, USA
| | - Zixiang Wen
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue St., Rm. A384E, East Lansing, MI, 48824-1325, USA
| | - Cuihua Gu
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue St., Rm. A384E, East Lansing, MI, 48824-1325, USA
| | - Yong-Qiang Charles An
- Plant Genetic Research Unit, Agricultural Research Service, United States Department of Agriculture, at Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Carmille Bales
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue St., Rm. A384E, East Lansing, MI, 48824-1325, USA
| | - Chris DiFonzo
- Department of Entomology, Michigan State University, East Lansing, MI, 48824, USA
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, 20705, USA
| | - Dechun Wang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue St., Rm. A384E, East Lansing, MI, 48824-1325, USA.
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Wang Z, Tang K, Zhang D, Wan Y, Wen Y, Lu Q, Wang L. High-throughput m6A-seq reveals RNA m6A methylation patterns in the chloroplast and mitochondria transcriptomes of Arabidopsis thaliana. PLoS One 2017; 12:e0185612. [PMID: 29131848 PMCID: PMC5683568 DOI: 10.1371/journal.pone.0185612] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 09/16/2017] [Indexed: 12/22/2022] Open
Abstract
This study is the first to comprehensively characterize m6A patterns in the Arabidopsis chloroplast and mitochondria transcriptomes based on our open accessible data deposited in NCBI's Gene Expression Omnibus with GEO Series accession number of GSE72706. Over 86% of the transcripts were methylated by m6A in the two organelles. Over 550 and 350 m6A sites were mapped, with ~5.6 to ~5.8 and ~4.6 to ~4.9 m6A sites per transcript, to the chloroplast and mitochondria genome, respectively. The overall m6A methylation extent in the two organelles was greatly higher than that in the nucleus. The m6A motif sequences in the transcriptome of two organelles were similar to the nuclear motifs, suggesting that selection of the m6A motifs for RNA methylation was conserved between the nucleus and organelle transcriptomes. The m6A patterns of rRNAs and tRNAs in the organelle were similar to those in the nucleus. However, the m6A patterns in coding RNAs were distinct between the nucleus and the organelle, suggesting that that regulation of the m6A methylation patterns may be different between the nuclei and the organelles. The extensively methylated transcripts in the two organelles were mainly associated with rRNA, ribosomal proteins, photosystem reaction proteins, tRNA, NADH dehydrogenase and redox. On average, 64% and 79% of the transcripts in the two organelles showed differential m6A methylation across three organs of the leaves, flowers and roots. The m6A methylation extent in the chloroplast was higher than that in the mitochondria. This study provides deep insights into the m6A methylation topology and differentiation in the plant organelle transcriptomes.
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Affiliation(s)
- Zegang Wang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Kai Tang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, United States of America
| | - Dayong Zhang
- Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yizhen Wan
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, United States of America
- * E-mail:
| | - Yan Wen
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Quanyou Lu
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Lei Wang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
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Majsec K, Bhuiyan NH, Sun Q, Kumari S, Kumar V, Ware D, van Wijk KJ. The Plastid and Mitochondrial Peptidase Network in Arabidopsis thaliana: A Foundation for Testing Genetic Interactions and Functions in Organellar Proteostasis. THE PLANT CELL 2017; 29:2687-2710. [PMID: 28947489 PMCID: PMC5728138 DOI: 10.1105/tpc.17.00481] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/29/2017] [Accepted: 09/21/2017] [Indexed: 05/17/2023]
Abstract
Plant plastids and mitochondria have dynamic proteomes. Protein homeostasis in these organelles is maintained by a proteostasis network containing protein chaperones, peptidases, and their substrate recognition factors. However, many peptidases, as well as their functional connections and substrates, are poorly characterized. This review provides a systematic insight into the organellar peptidase network in Arabidopsis thaliana We present a compendium of known and putative Arabidopsis peptidases and inhibitors, and compare the distribution of plastid and mitochondrial peptidases to the total peptidase complement. This comparison shows striking biases, such as the (near) absence of cysteine and aspartic peptidases and peptidase inhibitors, whereas other peptidase families were exclusively organellar; reasons for such biases are discussed. A genome-wide mRNA-based coexpression data set was generated based on quality controlled and normalized public data, and used to infer additional plastid peptidases and to generate a coexpression network for 97 organellar peptidase baits (1742 genes, making 2544 edges). The graphical network includes 10 modules with specialized/enriched functions, such as mitochondrial protein maturation, thermotolerance, senescence, or enriched subcellular locations such as the thylakoid lumen or chloroplast envelope. The peptidase compendium, including the autophagy and proteosomal systems, and the annotation based on the MEROPS nomenclature of peptidase clans and families, is incorporated into the Plant Proteome Database.
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Affiliation(s)
- Kristina Majsec
- Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
| | - Nazmul H Bhuiyan
- School for Integrative Plant Sciences, Section Plant Biology, Cornell University, Ithaca, New York 14853
| | - Qi Sun
- Computational Biology Service Unit, Cornell University, Ithaca, New York 14853
| | - Sunita Kumari
- Cold Spring Harbor laboratory, Cold Spring Harbor, New York 17724
| | - Vivek Kumar
- Cold Spring Harbor laboratory, Cold Spring Harbor, New York 17724
| | - Doreen Ware
- Cold Spring Harbor laboratory, Cold Spring Harbor, New York 17724
| | - Klaas J van Wijk
- School for Integrative Plant Sciences, Section Plant Biology, Cornell University, Ithaca, New York 14853
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Li QP, Wang S, Gou JY. A split ubiquitin system to reveal topology and released peptides of membrane proteins. BMC Biotechnol 2017; 17:69. [PMID: 28865427 PMCID: PMC5581432 DOI: 10.1186/s12896-017-0391-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 08/28/2017] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Membrane proteins define biological functions of membranes in cells. Extracellular peptides of transmembrane proteins receive signals from pathogens or environments, and are the major targets of drug developments. Despite of their essential roles, membrane proteins remain elusive in topological studies due to technique difficulties in their expressions and purifications. METHODS First, the target gene is cloned into a destination vector to fuse with C terminal ubiquitin at the N or C terminus. Then, Cub vector with target gene and NubWT or NubG vectors are transformed into AP4 or AP5 yeast cells, respectively. After mating, the diploid cells are dipped onto selection medium to check the growth. Topology of the target protein is determined according to Table 1. RESULTS We present a split ubiquitin topology (SUT) analysis system to study the topology and truncation peptide of membrane proteins in a simple yeast experiment. In the SUT system, transcription activator (TA) fused with a nucleo-cytoplasmic protein shows strong auto-activation with both positive and negative control vectors. TA fused with the cytoplasmic end of membrane proteins activates reporter genes only with positive control vector with a wild type N terminal ubiquitin (NubWT). However, TA fused with the extracellular termini of membrane proteins can't activate reporter genes even with NubWT. Interestingly,TA fused with the released peptide of a membrane protein shows autoactivation in the SUT system. CONCLUSION The SUT system is a simple and fast experimental procedure complementary to computational predictions and large scale proteomic techniques. The preliminary data from SUT are valuable for pathogen recognitions and new drug developments.
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Affiliation(s)
- Qiu-Ping Li
- Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Shuai Wang
- Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Jin-Ying Gou
- Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China.
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119
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Two interacting PPR proteins are major Arabidopsis editing factors in plastid and mitochondria. Proc Natl Acad Sci U S A 2017; 114:8877-8882. [PMID: 28760958 DOI: 10.1073/pnas.1705780114] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
RNA editing is converting hundreds of cytosines into uridines during organelle gene expression of land plants. The pentatricopeptide repeat (PPR) proteins are at the core of this posttranscriptional RNA modification. Even if a PPR protein defines the editing site, a DYW domain of the same or another PPR protein is believed to catalyze the deamination. To give insight into the organelle RNA editosome, we performed tandem affinity purification of the plastidial CHLOROPLAST BIOGENESIS 19 (CLB19) PPR editing factor. Two PPR proteins, dually targeted to mitochondria and chloroplasts, were identified as potential partners of CLB19. These two proteins, a P-type PPR and a member of a small PPR-DYW subfamily, were shown to interact in yeast. Insertional mutations resulted in embryo lethality that could be rescued by embryo-specific complementation. A transcriptome analysis of these complemented plants showed major editing defects in both organelles with a very high PPR type specificity, indicating that the two proteins are core members of E+-type PPR editosomes.
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120
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Hartings S, Paradies S, Karnuth B, Eisfeld S, Mehsing J, Wolff C, Levey T, Westhoff P, Meierhoff K. The DnaJ-Like Zinc-Finger Protein HCF222 Is Required for Thylakoid Membrane Biogenesis in Plants. PLANT PHYSIOLOGY 2017; 174:1807-1824. [PMID: 28572458 PMCID: PMC5490910 DOI: 10.1104/pp.17.00401] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 05/31/2017] [Indexed: 05/22/2023]
Abstract
To understand the biogenesis of the thylakoid membrane in higher plants and to identify auxiliary proteins required to build up this highly complex membrane system, we have characterized the allelic nuclear mutants high chlorophyll fluorescence222-1 (hcf222-1) and hcf222-2 and isolated the causal gene by map-based cloning. In the ethyl methanesulfonate-induced mutant hcf222-1, the accumulation of the cytochrome b6f (Cytb6f) complex was reduced to 30% compared with the wild type. Other thylakoid membrane complexes accumulated to normal levels. The T-DNA knockout mutant hcf222-2 showed a more severe defect with respect to thylakoid membrane proteins and accumulated only 10% of the Cytb6f complex, accompanied by a reduction in photosystem II, the photosystem II light-harvesting complex, and photosystem I. HCF222 encodes a protein of 99 amino acids in Arabidopsis (Arabidopsis thaliana) that has similarities to the cysteine-rich zinc-binding domain of DnaJ chaperones. The insulin precipitation assay demonstrated that HCF222 has disulfide reductase activity in vitro. The protein is conserved in higher plants and bryophytes but absent in algae and cyanobacteria. Confocal fluorescence microscopy showed that a fraction of HCF222-green fluorescent protein was detectable in the endoplasmic reticulum but that it also could be recognized in chloroplasts. A fusion construct of HCF222 containing a plastid transit peptide targets the protein into chloroplasts and was able to complement the mutational defect. These findings indicate that the chloroplast-targeted HCF222 is indispensable for the maturation and/or assembly of the Cytb6f complex and is very likely involved in thiol-disulfide biochemistry at the thylakoid membrane.
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Affiliation(s)
- Stephanie Hartings
- Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University Düsseldorf, 40225 Duesseldorf, Germany
| | - Susanne Paradies
- Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University Düsseldorf, 40225 Duesseldorf, Germany
| | - Bianca Karnuth
- Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University Düsseldorf, 40225 Duesseldorf, Germany
| | - Sabrina Eisfeld
- Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University Düsseldorf, 40225 Duesseldorf, Germany
| | - Jasmin Mehsing
- Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University Düsseldorf, 40225 Duesseldorf, Germany
| | - Christian Wolff
- Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University Düsseldorf, 40225 Duesseldorf, Germany
| | - Tatjana Levey
- Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University Düsseldorf, 40225 Duesseldorf, Germany
| | - Peter Westhoff
- Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University Düsseldorf, 40225 Duesseldorf, Germany
| | - Karin Meierhoff
- Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University Düsseldorf, 40225 Duesseldorf, Germany
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Shen J, Williams-Carrier R, Barkan A. PSA3, a Protein on the Stromal Face of the Thylakoid Membrane, Promotes Photosystem I Accumulation in Cooperation with the Assembly Factor PYG7. PLANT PHYSIOLOGY 2017; 174:1850-1862. [PMID: 28522455 PMCID: PMC5490921 DOI: 10.1104/pp.17.00524] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 05/17/2017] [Indexed: 05/16/2023]
Abstract
PSI is a large protein-pigment complex located in the thylakoid membrane in cyanobacteria, plants, and algae. Although the structure and components of PSI are well characterized, mechanisms that orchestrate its assembly are poorly understood. In this study, we discovered a novel nucleus-encoded protein, Photosystem I Assembly3 (PSA3), that is required for PSI accumulation. PSA3 is conserved among green photosynthetic eukaryotes but is lacking in cyanobacteria. Mutations in the psa3 gene cause the specific loss of PSI in Arabidopsis (Arabidopsis thaliana) and maize (Zea mays). Ribosome profiling and pulse-labeling analyses showed that chloroplast- encoded PSI subunits are synthesized at normal rates in psa3 mutants, indicating that PSA3 is involved in the biogenesis of PSI at a posttranslational step. PSA3 resides on the stromal face of the thylakoid membrane, where it is found in a complex that is slightly smaller than PSI. Structural predictions suggest that PSA3 binds a basic peptide in a manner that is sensitive to the oxidation state of Cys pairs flanking the predicted peptide binding groove. PSA3 and the previously described PSI biogenesis factor PYG7 interact in yeast two-hybrid and bimolecular fluorescence complementation assays, and they are found in thylakoid membrane complexes of similar size. These and other results indicate that PSA3 cooperates with PYG7 to promote the stable assembly of PSI, and that the PsaC subunit is likely to be the primary target of their action.
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Affiliation(s)
- Jie Shen
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | | | - Alice Barkan
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
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122
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Szabò I, Spetea C. Impact of the ion transportome of chloroplasts on the optimization of photosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:3115-3128. [PMID: 28338935 DOI: 10.1093/jxb/erx063] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Ions play fundamental roles in all living cells, and their gradients are often essential to fuel transport, regulate enzyme activities, and transduce energy within cells. Regulation of their homeostasis is essential for cell metabolism. Recent results indicate that modulation of ion fluxes might also represent a useful strategy to regulate one of the most important physiological processes taking place in chloroplasts, photosynthesis. Photosynthesis is highly regulated, due to its unique role as a cellular engine for growth in the light. Controlling the balance between ATP and NADPH synthesis is a critical task, and availability of these molecules can limit the overall photosynthetic yield. Photosynthetic organisms optimize photosynthesis in low light, where excitation energy limits CO2 fixation, and minimize photo-oxidative damage in high light by dissipating excess photons. Despite extensive studies of these phenomena, the mechanism governing light utilization in plants is still poorly understood. In this review, we provide an update of the recently identified chloroplast-located ion channels and transporters whose function impacts photosynthetic efficiency in plants.
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Affiliation(s)
- Ildikò Szabò
- Department of Biology, University of Padova, Italy; CNR Institute of Neuroscience, Padova, Italy
| | - Cornelia Spetea
- Department of Biological and Environmental Sciences, University of Gothenburg, 40530 Gothenburg, Sweden
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123
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Fristedt R. Chloroplast function revealed through analysis of GreenCut2 genes. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2111-2120. [PMID: 28369575 DOI: 10.1093/jxb/erx082] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Chloroplasts are the green plastids responsible for light-powered photosynthetic reactions and carbon assimilation in the plant cell. Our knowledge of chloroplast functions is constantly increasing and we now know this plastid is predicted to house around 3000 proteins. However, even with generous estimates, we do not know the function of more than 10-15% of these proteins. The next frontier in chloroplast research is to identify and characterize the function of the whole chloroplast proteome, a challenging task due to the inherent complexity a proteome possesses. A logical starting point is to identify and study proteins that have been determined experimentally to be localized in the chloroplast, conserved only among the photosynthetic lineage. These are the proteins with the most probable and important roles in chloroplast function. This review gives an introduction to the GreenCut2, a collection of proteins present only in photosynthetic organisms. By using recent large scale proteomics data, this cut was narrowed to include only those proteins experimentally verified to be localized in the chloroplast, and more specifically to the photosynthetic thylakoid membrane. By using highly informative bioinformatic approaches, the theoretical functional prediction for several of these uncharacterized GreenCut2 proteins is discussed.
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Affiliation(s)
- Rikard Fristedt
- Biophysics of Photosynthesis, Faculty of Sciences, VU University Amsterdam,Amsterdam,the Netherlands
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124
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South PF, Walker BJ, Cavanagh AP, Rolland V, Badger M, Ort DR. Bile Acid Sodium Symporter BASS6 Can Transport Glycolate and Is Involved in Photorespiratory Metabolism in Arabidopsis thaliana. THE PLANT CELL 2017; 29:808-823. [PMID: 28351992 PMCID: PMC5435425 DOI: 10.1105/tpc.16.00775] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 02/08/2017] [Accepted: 03/28/2017] [Indexed: 05/19/2023]
Abstract
Photorespiration is an energy-intensive process that recycles 2-phosphoglycolate, a toxic product of the Rubisco oxygenation reaction. The photorespiratory pathway is highly compartmentalized, involving the chloroplast, peroxisome, cytosol, and mitochondria. Though the soluble enzymes involved in photorespiration are well characterized, very few membrane transporters involved in photorespiration have been identified to date. In this work, Arabidopsis thaliana plants containing a T-DNA disruption of the bile acid sodium symporter BASS6 show decreased photosynthesis and slower growth under ambient, but not elevated CO2 Exogenous expression of BASS6 complemented this photorespiration mutant phenotype. In addition, metabolite analysis and genetic complementation of glycolate transport in yeast showed that BASS6 was capable of glycolate transport. This is consistent with its involvement in the photorespiratory export of glycolate from Arabidopsis chloroplasts. An Arabidopsis double knockout line of both BASS6 and the glycolate/glycerate transporter PLGG1 (bass6, plgg1) showed an additive growth defect, an increase in glycolate accumulation, and reductions in photosynthetic rates compared with either single mutant. Our data indicate that BASS6 and PLGG1 partner in glycolate export from the chloroplast, whereas PLGG1 alone accounts for the import of glycerate. BASS6 and PLGG1 therefore balance the export of two glycolate molecules with the import of one glycerate molecule during photorespiration.
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Affiliation(s)
- Paul F South
- Global Change and Photosynthesis Research Unit, U.S. Department of Agriculture/Agricultural Research Service, Urbana, Illinois 61801
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801
| | - Berkley J Walker
- Global Change and Photosynthesis Research Unit, U.S. Department of Agriculture/Agricultural Research Service, Urbana, Illinois 61801
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801
| | - Amanda P Cavanagh
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801
| | - Vivien Rolland
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of Biology, College of Medicine, Biology and Environment, The Australian National University, Canberra ACT 0200, Australia
| | - Murray Badger
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Research School of Biology, College of Medicine, Biology and Environment, The Australian National University, Canberra ACT 0200, Australia
| | - Donald R Ort
- Global Change and Photosynthesis Research Unit, U.S. Department of Agriculture/Agricultural Research Service, Urbana, Illinois 61801
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801
- Department of Plant Biology, University of Illinois, Urbana, Illinois 61801
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125
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Bienvenut WV, Scarpelli JP, Dumestier J, Meinnel T, Giglione C. EnCOUNTer: a parsing tool to uncover the mature N-terminus of organelle-targeted proteins in complex samples. BMC Bioinformatics 2017; 18:182. [PMID: 28320318 PMCID: PMC5359831 DOI: 10.1186/s12859-017-1595-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 03/10/2017] [Indexed: 01/01/2023] Open
Abstract
Background Characterization of mature protein N-termini by large scale proteomics is challenging. This is especially true for proteins undergoing cleavage of transit peptides when they are targeted to specific organelles, such as mitochondria or chloroplast. Protein neo-N-termini can be located up to 100–150 amino acids downstream from the initiator methionine and are not easily predictable. Although some bioinformatics tools are available, they usually require extensive manual validation to identify the exact N-terminal position. The situation becomes even more complex when post-translational modifications take place at the neo-N-terminus. Although N-terminal acetylation occurs mostly in the cytosol, it is also observed in some organelles such as chloroplast. To date, no bioinformatics tool is available to define mature protein starting positions, the associated N-terminus acetylation status and/or yield for each proteoform. In this context, we have developed the EnCOUNTer tool (i) to score all characterized peptides using discriminating parameters to identify bona fide mature protein N-termini and (ii) to determine the N-terminus acetylation yield of the most reliable ones. Results Based on large scale proteomics analyses using the SILProNAQ methodology, tandem mass spectrometry favoured the characterization of thousands of peptides. Data processing using the EnCOUNTer tool provided an efficient and rapid way to extract the most reliable mature protein N-termini. Selected peptides were subjected to N-terminus acetylation yield determination. In an A. thaliana cell lysate, 1232 distinct proteotypic N-termini were characterized of which 648 were located at the predicted protein N-terminus (position 1/2) and 584 were located further downstream (starting at position > 2). A large number of these N-termini were associated with various well-defined maturation processes occurring on organelle-targeted proteins (mitochondria, chloroplast and peroxisome), secreted proteins or membrane-targeted proteins. It was also possible to highlight some protein alternative starts, splicing variants or erroneous protein sequence predictions. Conclusions The EnCOUNTer tool provides a unique way to extract accurately the most relevant mature proteins N-terminal peptides from large scale experimental datasets. Such data processing allows the identification of the exact N-terminus position and the associated acetylation yield. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1595-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Willy Vincent Bienvenut
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris Saclay, 91198, Gif-sur-Yvette Cedex, France.
| | - Jean-Pierre Scarpelli
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris Saclay, 91198, Gif-sur-Yvette Cedex, France
| | - Johan Dumestier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris Saclay, 91198, Gif-sur-Yvette Cedex, France
| | - Thierry Meinnel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris Saclay, 91198, Gif-sur-Yvette Cedex, France
| | - Carmela Giglione
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris Saclay, 91198, Gif-sur-Yvette Cedex, France
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Zufferey M, Montandon C, Douet V, Demarsy E, Agne B, Baginsky S, Kessler F. The novel chloroplast outer membrane kinase KOC1 is a required component of the plastid protein import machinery. J Biol Chem 2017; 292:6952-6964. [PMID: 28283569 DOI: 10.1074/jbc.m117.776468] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 02/28/2017] [Indexed: 11/06/2022] Open
Abstract
The biogenesis and maintenance of cell organelles such as mitochondria and chloroplasts require the import of many proteins from the cytosol, a process that is controlled by phosphorylation. In the case of chloroplasts, the import of hundreds of different proteins depends on translocons at the outer and inner chloroplast membrane (TOC and TIC, respectively) complexes. The essential protein TOC159 functions thereby as an import receptor. It has an N-terminal acidic (A-) domain that extends into the cytosol, controls receptor specificity, and is highly phosphorylated in vivo However, kinases that phosphorylate the TOC159 A-domain to enable protein import have remained elusive. Here, using co-purification with TOC159 from Arabidopsis, we discovered a novel component of the chloroplast import machinery, the regulatory kinase at the outer chloroplast membrane 1 (KOC1). We found that KOC1 is an integral membrane protein facing the cytosol and stably associates with TOC. Moreover, KOC1 phosphorylated the A-domain of TOC159 in vitro, and in mutant koc1 chloroplasts, preprotein import efficiency was diminished. koc1 Arabidopsis seedlings had reduced survival rates after transfer from the dark to the light in which protein import into plastids is required to rapidly complete chloroplast biogenesis. In summary, our data indicate that KOC1 is a functional component of the TOC machinery that phosphorylates import receptors, supports preprotein import, and contributes to efficient chloroplast biogenesis.
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Affiliation(s)
- Mónica Zufferey
- From the Laboratory of Plant Physiology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - Cyrille Montandon
- the College of Agriculture and Life Sciences, Cornell University, Ithaca, New York 14853
| | - Véronique Douet
- From the Laboratory of Plant Physiology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - Emilie Demarsy
- the Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland, and
| | - Birgit Agne
- Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, 06099 Halle (Saale), Germany
| | - Sacha Baginsky
- Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, 06099 Halle (Saale), Germany
| | - Felix Kessler
- From the Laboratory of Plant Physiology, University of Neuchâtel, 2000 Neuchâtel, Switzerland,
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Mei J, Li F, Liu X, Hu G, Fu Y, Liu W. Newly identified CSP41b gene localized in chloroplasts affects leaf color in rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 256:39-45. [PMID: 28167036 DOI: 10.1016/j.plantsci.2016.12.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 12/02/2016] [Accepted: 12/08/2016] [Indexed: 05/05/2023]
Abstract
A rice mutant with light-green leaves was discovered from a transgenic line of Oryza sativa. The mutant has reduced chlorophyll content and abnormal chloroplast morphology throughout its life cycle. Genetic analysis revealed that a single nuclear-encoded recessive gene is responsible for the mutation, here designated as lgl1. To isolate the lgl1 gene, a high-resolution physical map of the chromosomal region around the lgl1 gene was made using a mapping population consisting of 1984 mutant individuals. The lgl1 gene was mapped in the 76.5kb region between marker YG4 and marker YG5 on chromosome 12. Sequence analysis revealed that there was a 39bp deletion within the fourth exon of the candidate gene Os12g0420200 (TIGR locus Os12g23180) encoding a chloroplast stem-loop-binding protein of 41kDa b (CSP41b). The lgl1 mutation was rescued by transformation with the wild type CSP41b gene. Accordingly, the CSP41b gene is identified as the LGL1 gene. CSP41b was transcribed in various tissues and was mainly expressed in leaves. Expression of CSP41b-GFP fusion protein indicated that CSP41b is localized in chloroplasts. The expression levels of some key genes involved in chlorophyll biosynthesis and photosynthesis, such as ChlD, ChlI, Hema1, Ygl1, POR, Cab1R, Cab2R, PsaA, and rbcL, was significantly changed in the lgl1 mutant. Our results demonstrate that CSP41b is a novel gene required for normal leaf color and chloroplast morphology in rice.
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Affiliation(s)
- Jiasong Mei
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang 310006, China
| | - Feifei Li
- School of Agriculture and Food Science, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Xuri Liu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang 310006, China
| | - Guocheng Hu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang 310006, China
| | - Yaping Fu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang 310006, China
| | - Wenzhen Liu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang 310006, China.
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Knoch D, Riewe D, Meyer RC, Boudichevskaia A, Schmidt R, Altmann T. Genetic dissection of metabolite variation in Arabidopsis seeds: evidence for mQTL hotspots and a master regulatory locus of seed metabolism. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1655-1667. [PMID: 28338798 PMCID: PMC5444479 DOI: 10.1093/jxb/erx049] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
To gain insight into genetic factors controlling seed metabolic composition and its relationship to major seed properties, an Arabidopsis recombinant inbred line (RIL) population, derived from accessions Col-0 and C24, was studied using an MS-based metabolic profiling approach. Relative intensities of 311 polar primary metabolites were used to identify associated genomic loci and to elucidate their interactions by quantitative trait locus (QTL) mapping. A total of 786 metabolic QTLs (mQTLs) were unequally distributed across the genome, forming several hotspots. For the branched-chain amino acid leucine, mQTLs and candidate genes were elucidated in detail. Correlation studies displayed links between metabolite levels, seed protein content, and seed weight. Principal component analysis revealed a clustering of samples, with PC1 mapping to a region on the short arm of chromosome IV. The overlap of this region with mQTL hotspots indicates the presence of a potential master regulatory locus of seed metabolism. As a result of database queries, a series of candidate regulatory genes, including bZIP10, were identified within this region. Depending on the search conditions, metabolic pathway-derived candidate genes for 40-61% of tested mQTLs could be determined, providing an extensive basis for further identification and characterization of hitherto unknown genes causal for natural variation of Arabidopsis seed metabolism.
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Affiliation(s)
- Dominic Knoch
- Department of Molecular Genetics/Heterosis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Seeland/OT Gatersleben, Germany
| | - David Riewe
- Department of Molecular Genetics/Heterosis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Seeland/OT Gatersleben, Germany
| | - Rhonda Christiane Meyer
- Department of Molecular Genetics/Heterosis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Seeland/OT Gatersleben, Germany
| | - Anastassia Boudichevskaia
- Department of Breeding Research/Genome Plasticity, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Seeland/OT Gatersleben, Germany
| | - Renate Schmidt
- Department of Breeding Research/Genome Plasticity, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Seeland/OT Gatersleben, Germany
| | - Thomas Altmann
- Department of Molecular Genetics/Heterosis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Seeland/OT Gatersleben, Germany
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Clayton H, Saladié M, Rolland V, Sharwood R, Macfarlane T, Ludwig M. Loss of the Chloroplast Transit Peptide from an Ancestral C 3 Carbonic Anhydrase Is Associated with C 4 Evolution in the Grass Genus Neurachne. PLANT PHYSIOLOGY 2017; 173:1648-1658. [PMID: 28153918 PMCID: PMC5338660 DOI: 10.1104/pp.16.01893] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 01/31/2017] [Indexed: 06/01/2023]
Abstract
Neurachne is the only known grass lineage containing closely related C3, C3-C4 intermediate, and C4 species, making it an ideal taxon with which to study the evolution of C4 photosynthesis in the grasses. To begin dissecting the molecular changes that led to the evolution of C4 photosynthesis in this group, the complementary DNAs encoding four distinct β-carbonic anhydrase (CA) isoforms were characterized from leaf tissue of Neurachne munroi (C4), Neurachne minor (C3-C4), and Neurachne alopecuroidea (C3). Two genes (CA1 and CA2) each encode two different isoforms: CA1a/CA1b and CA2a/CA2b. Transcript analyses found that CA1 messenger RNAs were significantly more abundant than transcripts from the CA2 gene in the leaves of each species examined, constituting ∼99% of all β-CA transcripts measured. Localization experiments using green fluorescent protein fusion constructs showed that, while CA1b is a cytosolic CA in all three species, the CA1a proteins are differentially localized. The N. alopecuroidea and N. minor CA1a isoforms were imported into chloroplasts of Nicotiana benthamiana leaf cells, whereas N. munroi CA1a localized to the cytosol. Sequence analysis indicated an 11-amino acid deletion in the amino terminus of N. munroi CA1a relative to the C3 and C3-C4 proteins, suggesting that chloroplast targeting of CA1a is the ancestral state and that loss of a functional chloroplast transit peptide in N. munroi CA1a is associated with the evolution of C4 photosynthesis in Neurachne spp. Remarkably, this mechanism is homoplastic with the evolution of the C4-associated CA in the dicotyledonous genus Flaveria, although the actual mutations in the two lineages differ.
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Affiliation(s)
- Harmony Clayton
- School of Molecular Sciences, University of Western Australia, Perth, Western Australia 6009, Australia (H.C., M.S., M.L.)
- Australian Research Council Centre for Translational Photosynthesis, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia (V.R., R.S.); and
- Western Australian Herbarium, Science and Conservation Division, Department of Parks and Wildlife, Perth, Western Australia 6152, Australia (T.M.)
| | - Montserrat Saladié
- School of Molecular Sciences, University of Western Australia, Perth, Western Australia 6009, Australia (H.C., M.S., M.L.)
- Australian Research Council Centre for Translational Photosynthesis, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia (V.R., R.S.); and
- Western Australian Herbarium, Science and Conservation Division, Department of Parks and Wildlife, Perth, Western Australia 6152, Australia (T.M.)
| | - Vivien Rolland
- School of Molecular Sciences, University of Western Australia, Perth, Western Australia 6009, Australia (H.C., M.S., M.L.)
- Australian Research Council Centre for Translational Photosynthesis, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia (V.R., R.S.); and
- Western Australian Herbarium, Science and Conservation Division, Department of Parks and Wildlife, Perth, Western Australia 6152, Australia (T.M.)
| | - Robert Sharwood
- School of Molecular Sciences, University of Western Australia, Perth, Western Australia 6009, Australia (H.C., M.S., M.L.)
- Australian Research Council Centre for Translational Photosynthesis, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia (V.R., R.S.); and
- Western Australian Herbarium, Science and Conservation Division, Department of Parks and Wildlife, Perth, Western Australia 6152, Australia (T.M.)
| | - Terry Macfarlane
- School of Molecular Sciences, University of Western Australia, Perth, Western Australia 6009, Australia (H.C., M.S., M.L.)
- Australian Research Council Centre for Translational Photosynthesis, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia (V.R., R.S.); and
- Western Australian Herbarium, Science and Conservation Division, Department of Parks and Wildlife, Perth, Western Australia 6152, Australia (T.M.)
| | - Martha Ludwig
- School of Molecular Sciences, University of Western Australia, Perth, Western Australia 6009, Australia (H.C., M.S., M.L.);
- Australian Research Council Centre for Translational Photosynthesis, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia (V.R., R.S.); and
- Western Australian Herbarium, Science and Conservation Division, Department of Parks and Wildlife, Perth, Western Australia 6152, Australia (T.M.)
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Muñoz-Nortes T, Pérez-Pérez JM, Ponce MR, Candela H, Micol JL. The ANGULATA7 gene encodes a DnaJ-like zinc finger-domain protein involved in chloroplast function and leaf development in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:870-884. [PMID: 28008672 DOI: 10.1111/tpj.13466] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 12/16/2016] [Accepted: 12/19/2016] [Indexed: 06/06/2023]
Abstract
The characterization of mutants with altered leaf shape and pigmentation has previously allowed the identification of nuclear genes that encode plastid-localized proteins that perform essential functions in leaf growth and development. A large-scale screen previously allowed us to isolate ethyl methanesulfonate-induced mutants with small rosettes and pale green leaves with prominent marginal teeth, which were assigned to a phenotypic class that we dubbed Angulata. The molecular characterization of the 12 genes assigned to this phenotypic class should help us to advance our understanding of the still poorly understood relationship between chloroplast biogenesis and leaf morphogenesis. In this article, we report the phenotypic and molecular characterization of the angulata7-1 (anu7-1) mutant of Arabidopsis thaliana, which we found to be a hypomorphic allele of the EMB2737 gene, which was previously known only for its embryonic-lethal mutations. ANU7 encodes a plant-specific protein that contains a domain similar to the central cysteine-rich domain of DnaJ proteins. The observed genetic interaction of anu7-1 with a loss-of-function allele of GENOMES UNCOUPLED1 suggests that the anu7-1 mutation triggers a retrograde signal that leads to changes in the expression of many genes that normally function in the chloroplasts. Many such genes are expressed at higher levels in anu7-1 rosettes, with a significant overrepresentation of those required for the expression of plastid genome genes. Like in other mutants with altered expression of plastid-encoded genes, we found that anu7-1 exhibits defects in the arrangement of thylakoidal membranes, which appear locally unappressed.
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Affiliation(s)
- Tamara Muñoz-Nortes
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, Elche, 03202, Spain
| | - José Manuel Pérez-Pérez
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, Elche, 03202, Spain
| | - María Rosa Ponce
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, Elche, 03202, Spain
| | - Héctor Candela
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, Elche, 03202, Spain
| | - José Luis Micol
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, Elche, 03202, Spain
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Grabsztunowicz M, Koskela MM, Mulo P. Post-translational Modifications in Regulation of Chloroplast Function: Recent Advances. FRONTIERS IN PLANT SCIENCE 2017; 8:240. [PMID: 28280500 PMCID: PMC5322211 DOI: 10.3389/fpls.2017.00240] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 02/08/2017] [Indexed: 05/08/2023]
Abstract
Post-translational modifications (PTMs) of proteins enable fast modulation of protein function in response to metabolic and environmental changes. Phosphorylation is known to play a major role in regulating distribution of light energy between the Photosystems (PS) I and II (state transitions) and in PSII repair cycle. In addition, thioredoxin-mediated redox regulation of Calvin cycle enzymes has been shown to determine the efficiency of carbon assimilation. Besides these well characterized modifications, recent methodological progress has enabled identification of numerous other types of PTMs in various plant compartments, including chloroplasts. To date, at least N-terminal and Lys acetylation, Lys methylation, Tyr nitration and S-nitrosylation, glutathionylation, sumoylation and glycosylation of chloroplast proteins have been described. These modifications impact DNA replication, control transcriptional efficiency, regulate translational machinery and affect metabolic activities within the chloroplast. Moreover, light reactions of photosynthesis as well as carbon assimilation are regulated at multiple levels by a number of PTMs. It is likely that future studies will reveal new metabolic pathways to be regulated by PTMs as well as detailed molecular mechanisms of PTM-mediated regulation.
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Affiliation(s)
| | | | - Paula Mulo
- Molecular Plant Biology, Department of Biochemistry, University of TurkuTurku, Finland
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Wang C, Yamamoto H, Narumiya F, Munekage YN, Finazzi G, Szabo I, Shikanai T. Fine-tuned regulation of the K + /H + antiporter KEA3 is required to optimize photosynthesis during induction. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:540-553. [PMID: 27783435 DOI: 10.1111/tpj.13405] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 10/17/2016] [Accepted: 10/17/2016] [Indexed: 05/22/2023]
Abstract
KEA3 is a thylakoid membrane localized K+ /H+ antiporter that regulates photosynthesis by modulating two components of proton motive force (pmf), the proton gradient (∆pH) and the electric potential (∆ψ). We identified a mutant allele of KEA3, disturbed proton gradient regulation (dpgr) based on its reduced non-photochemical quenching (NPQ) in artificial (CO2 -free with low O2 ) air. This phenotype was enhanced in the mutant backgrounds of PSI cyclic electron transport (pgr5 and crr2-1). In ambient air, reduced NPQ was observed during induction of photosynthesis in dpgr, the phenotype that was enhanced after overnight dark adaptation. In contrast, the knockout allele of kea3-1 exhibited a high-NPQ phenotype during steady state in ambient air. Consistent with this kea3-1 phenotype in ambient air, the membrane topology of KEA3 indicated a proton efflux from the thylakoid lumen to the stroma. The dpgr heterozygotes showed a semidominant and dominant phenotype in artificial and ambient air, respectively. In dpgr, the protein level of KEA3 was unaffected but the downregulation of its activity was probably disturbed. Our findings suggest that fine regulation of KEA3 activity is necessary for optimizing photosynthesis.
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Affiliation(s)
- Caijuan Wang
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
| | - Hiroshi Yamamoto
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
- CREST, Japan Science and Technology Agency, Chiyoda-ku, Tokyo, 102-0076, Japan
| | - Fumika Narumiya
- Graduate School of Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0101, Japan
- Sakai City Institute of Public Health, Sakai, Osaka, 590-0953, Japan
| | - Yuri Nakajima Munekage
- Graduate School of Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0101, Japan
- Department of Bioscience, School of Science and Technology, Kwansei Gakuin University, Sandan, Hyogo, 669-1337, Japan
| | - Giovanni Finazzi
- UMR 5168 Laboratoire de Physiologie Cellulaire Végétale (LPCV) CNRS/UJF/INRA/CEA, Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV), CEA Grenoble, 38054, Grenoble, France
| | - Ildiko Szabo
- Department of Biology, University of Padova, Padova, 35121, Italy
| | - Toshiharu Shikanai
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
- CREST, Japan Science and Technology Agency, Chiyoda-ku, Tokyo, 102-0076, Japan
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Stein O, Avin-Wittenberg T, Krahnert I, Zemach H, Bogol V, Daron O, Aloni R, Fernie AR, Granot D. Arabidopsis Fructokinases Are Important for Seed Oil Accumulation and Vascular Development. FRONTIERS IN PLANT SCIENCE 2017; 7:2047. [PMID: 28119723 PMCID: PMC5222831 DOI: 10.3389/fpls.2016.02047] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 12/21/2016] [Indexed: 05/25/2023]
Abstract
Sucrose (a disaccharide made of glucose and fructose) is the primary carbon source transported to sink organs in many plants. Since fructose accounts for half of the hexoses used for metabolism in sink tissues, plant fructokinases (FRKs), the main fructose-phosphorylating enzymes, are likely to play a central role in plant development. However, to date, their specific functions have been the subject of only limited study. The Arabidopsis genome contains seven genes encoding six cytosolic FRKs and a single plastidic FRK. T-DNA knockout mutants for five of the seven FRKs were identified and used in this study. Single knockouts of the FRK mutants did not exhibit any unusual phenotype. Double-mutants of AtFRK6 (plastidic) and AtFRK7 showed normal growth in soil, but yielded dark, distorted seeds. The seed distortion could be complemented by expression of the well-characterized tomato SlFRK1, confirming that a lack of FRK activity was the primary cause of the seed phenotype. Seeds of the double-mutant germinated, but failed to establish on 1/2 MS plates. Seed establishment was made possible by the addition of glucose or sucrose, indicating reduced seed storage reserves. Metabolic profiling of the double-mutant seeds revealed decreased TCA cycle metabolites and reduced fatty acid metabolism. Examination of the mutant embryo cells revealed smaller oil bodies, the primary storage reserve in Arabidopsis seeds. Quadruple and penta FRK mutants showed growth inhibition and leaf wilting. Anatomical analysis revealed smaller trachea elements and smaller xylem area, accompanied by necrosis around the cambium and the phloem. These results demonstrate overlapping and complementary roles of the plastidic AtFRK6 and the cytosolic AtFRK7 in seed storage accumulation, and the importance of AtFRKs for vascular development.
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Affiliation(s)
- Ofer Stein
- Volcani Center, Institute of Plant Sciences, Agricultural Research OrganizationBet Dagan, Israel
- Robert H. Smith Faculty of Agriculture, Institute of Plant Sciences and Genetics in Agriculture, Food and Environment, Hebrew University of JerusalemRehovot, Israel
| | - Tamar Avin-Wittenberg
- Max-Planck-Institut für Molekulare PflanzenphysiologiePotsdam-Golm, Germany
- Department of Plant and Environmental Sciences, Hebrew University of JerusalemGivat Ram, Jerusalem, Israel
| | - Ina Krahnert
- Max-Planck-Institut für Molekulare PflanzenphysiologiePotsdam-Golm, Germany
| | - Hanita Zemach
- Volcani Center, Institute of Plant Sciences, Agricultural Research OrganizationBet Dagan, Israel
| | - Vlada Bogol
- Volcani Center, Institute of Plant Sciences, Agricultural Research OrganizationBet Dagan, Israel
| | - Oksana Daron
- Department of Life Sciences, Ben-Gurion UniversityBeer-Sheva, Israel
| | - Roni Aloni
- Department of Plant Sciences, Tel Aviv UniversityTel Aviv, Israel
| | - Alisdair R. Fernie
- Max-Planck-Institut für Molekulare PflanzenphysiologiePotsdam-Golm, Germany
| | - David Granot
- Volcani Center, Institute of Plant Sciences, Agricultural Research OrganizationBet Dagan, Israel
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134
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Lundquist PK, Mantegazza O, Stefanski A, Stühler K, Weber APM. Surveying the Oligomeric State of Arabidopsis thaliana Chloroplasts. MOLECULAR PLANT 2017; 10:197-211. [PMID: 27794502 DOI: 10.1016/j.molp.2016.10.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 10/17/2016] [Accepted: 10/18/2016] [Indexed: 05/08/2023]
Abstract
Blue native-PAGE (BN-PAGE) resolves protein complexes in their native state. When combined with immunoblotting, it can be used to identify the presence of high molecular weight complexes at high resolution for any protein, given a suitable antibody. To identify proteins in high molecular weight complexes on a large scale and to bypass the requirement for specific antibodies, we applied a tandem mass spectrometry (MS/MS) approach to BN-PAGE-resolved chloroplasts. Fractionation of the gel into six bands allowed identification and label-free quantification of 1000 chloroplast proteins with native molecular weight separation. Significantly, this approach achieves a depth of identification comparable with traditional shotgun proteomic analyses of chloroplasts, indicating much of the known chloroplast proteome is amenable to MS/MS identification under our fractionation scheme. By limiting the number of fractionation bands to six, we facilitate scaled-up comparative analyses, as we demonstrate with the reticulata chloroplast mutant displaying a reticulated leaf phenotype. Our comparative proteomics approach identified a candidate interacting protein of RETICULATA as well as effects on lipid remodeling proteins, amino acid metabolic enzymes, and plastid division machinery. We additionally highlight selected proteins from each sub-compartment of the chloroplast that provide novel insight on known or hypothesized protein complexes to further illustrate the utility of this approach. Our results demonstrate the high sensitivity and reproducibility of this technique, which is anticipated to be widely adaptable to other sub-cellular compartments.
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Affiliation(s)
- Peter K Lundquist
- Institute for Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany.
| | - Otho Mantegazza
- Institute for Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Anja Stefanski
- Molecular Proteomics Laboratory, BMFZ, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Kai Stühler
- Molecular Proteomics Laboratory, BMFZ, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Andreas P M Weber
- Institute for Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany
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135
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Nawaz G, Kang H. Chloroplast- or Mitochondria-Targeted DEAD-Box RNA Helicases Play Essential Roles in Organellar RNA Metabolism and Abiotic Stress Responses. FRONTIERS IN PLANT SCIENCE 2017; 8:871. [PMID: 28596782 PMCID: PMC5442247 DOI: 10.3389/fpls.2017.00871] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 05/10/2017] [Indexed: 05/04/2023]
Abstract
The yields and productivity of crops are greatly diminished by various abiotic stresses, including drought, cold, heat, and high salinity. Chloroplasts and mitochondria are cellular organelles that can sense diverse environmental stimuli and alter gene expression to cope with adverse environmental stresses. Organellar gene expression is mainly regulated at posttranscriptional levels, including RNA processing, intron splicing, RNA editing, RNA turnover, and translational control, during which a variety of nucleus-encoded RNA-binding proteins (RBPs) are targeted to chloroplasts or mitochondria where they play essential roles in organellar RNA metabolism. DEAD-box RNA helicases (RHs) are enzymes that can alter RNA structures and affect RNA metabolism in all living organisms. Although a number of DEAD-box RHs have been found to play important roles in RNA metabolism in the nucleus and cytoplasm, our understanding on the roles of DEAD-box RHs in the regulation of RNA metabolism in chloroplasts and mitochondria is only at the beginning. Considering that organellar RNA metabolism and gene expression are tightly regulated by anterograde signaling from the nucleus, it is imperative to determine the functions of nucleus-encoded organellar RBPs. In this review, we summarize the emerging roles of nucleus-encoded chloroplast- or mitochondria-targeted DEAD-box RHs in organellar RNA metabolism and plant response to diverse abiotic stresses.
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137
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Botella C, Jouhet J, Block MA. Importance of phosphatidylcholine on the chloroplast surface. Prog Lipid Res 2017; 65:12-23. [DOI: 10.1016/j.plipres.2016.11.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 11/04/2016] [Accepted: 11/06/2016] [Indexed: 12/11/2022]
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138
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Bienvenut WV, Giglione C, Meinnel T. SILProNAQ: A Convenient Approach for Proteome-Wide Analysis of Protein N-Termini and N-Terminal Acetylation Quantitation. Methods Mol Biol 2017; 1574:17-34. [PMID: 28315241 DOI: 10.1007/978-1-4939-6850-3_3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Protein N-terminal modifications have recently been involved in overall proteostasis through their impact on cell fate and protein life time. This explains the development of new approaches to characterize more precisely the N-terminal end of mature proteins. Although few approaches are available to perform N-terminal enrichment based on positive or negative discriminations, these methods are usually restricted to the enrichment in N-terminal peptides and their characterization by mass spectrometry. Recent investigation highlights both (1) the knowledge of the N-terminal acetylation status of most cytosolic proteins and (2) post-translational addition of this modification on the N-terminus of nuclear coded chloroplast proteins imported in the plastid and after the cleavage of the transit peptide. The workflow involves stable isotope labeling to assess N-acetylation rates followed by Strong Cation eXchange (SCX ) fractionation of the samples to provide protein N-terminal enriched fractions. Combined with mass spectrometry analyses, the technology finally requires extensive data processing. This last step aims first at discriminating the most relevant mature N-termini from the characterized peptides, next at determining its experimental position and then at calculating the N-terminal acetylation yield. Stable-Isotope Protein N-terminal Acetylation Quantification (SILProNAQ) is a complete workflow combining wet-lab techniques together with dry-lab processing to determine the N-terminal acetylation yield of mature proteins for a clearly defined localization.
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Affiliation(s)
- Willy V Bienvenut
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris Saclay, Bâtiment 21, Avenue de la Terrassee, 91198, Gif-sur-Yvette cedex, France.
| | - Carmela Giglione
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris Saclay, Bâtiment 21, Avenue de la Terrassee, 91198, Gif-sur-Yvette cedex, France
| | - Thierry Meinnel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris Saclay, Bâtiment 21, Avenue de la Terrassee, 91198, Gif-sur-Yvette cedex, France
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139
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Lee CP, Maksaev G, Jensen GS, Murcha MW, Wilson ME, Fricker M, Hell R, Haswell ES, Millar AH, Sweetlove LJ. MSL1 is a mechanosensitive ion channel that dissipates mitochondrial membrane potential and maintains redox homeostasis in mitochondria during abiotic stress. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:809-825. [PMID: 27505616 PMCID: PMC5195915 DOI: 10.1111/tpj.13301] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 08/04/2016] [Accepted: 08/05/2016] [Indexed: 05/18/2023]
Abstract
Mitochondria must maintain tight control over the electrochemical gradient across their inner membrane to allow ATP synthesis while maintaining a redox-balanced electron transport chain and avoiding excessive reactive oxygen species production. However, there is a scarcity of knowledge about the ion transporters in the inner mitochondrial membrane that contribute to control of membrane potential. We show that loss of MSL1, a member of a family of mechanosensitive ion channels related to the bacterial channel MscS, leads to increased membrane potential of Arabidopsis mitochondria under specific bioenergetic states. We demonstrate that MSL1 localises to the inner mitochondrial membrane. When expressed in Escherichia coli, MSL1 forms a stretch-activated ion channel with a slight preference for anions and provides protection against hypo-osmotic shock. In contrast, loss of MSL1 in Arabidopsis did not prevent swelling of isolated mitochondria in hypo-osmotic conditions. Instead, our data suggest that ion transport by MSL1 leads to dissipation of mitochondrial membrane potential when it becomes too high. The importance of MSL1 function was demonstrated by the observation of a higher oxidation state of the mitochondrial glutathione pool in msl1-1 mutants under moderate heat- and heavy-metal-stress. Furthermore, we show that MSL1 function is not directly implicated in mitochondrial membrane potential pulsing, but is complementary and appears to be important under similar conditions.
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Affiliation(s)
- Chun Pong Lee
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Bayliss Building M316, 35 Stirling Highway, Crawley, 6009, Western Australia, Australia
| | - Grigory Maksaev
- Department of Biology, Washington University in Saint Louis, One Brookings Drive, Mailcode 1137, Saint Louis, MO, 63130, USA
| | - Gregory S Jensen
- Department of Biology, Washington University in Saint Louis, One Brookings Drive, Mailcode 1137, Saint Louis, MO, 63130, USA
| | - Monika W Murcha
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Bayliss Building M316, 35 Stirling Highway, Crawley, 6009, Western Australia, Australia
| | - Margaret E Wilson
- Department of Biology, Washington University in Saint Louis, One Brookings Drive, Mailcode 1137, Saint Louis, MO, 63130, USA
| | - Mark Fricker
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Ruediger Hell
- Department of Plant Molecular Biology, Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 360, D-69120, Heidelberg, Germany
| | - Elizabeth S Haswell
- Department of Biology, Washington University in Saint Louis, One Brookings Drive, Mailcode 1137, Saint Louis, MO, 63130, USA
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Bayliss Building M316, 35 Stirling Highway, Crawley, 6009, Western Australia, Australia
| | - Lee J Sweetlove
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
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140
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Morita R, Nakagawa M, Takehisa H, Hayashi Y, Ichida H, Usuda S, Ichinose K, Abe H, Shirakawa Y, Sato T, Fujiwara MT, Itoh RD, Abe T. Heavy-ion beam mutagenesis identified an essential gene for chloroplast development under cold stress conditions during both early growth and tillering stages in rice. Biosci Biotechnol Biochem 2016; 81:271-282. [PMID: 27804786 DOI: 10.1080/09168451.2016.1249452] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
We isolated a cold sensitive virescent1 (csv1) mutant from a rice (Oryza sativa L.) population mutagenized by carbon ion irradiation. The mutant exhibited chlorotic leaves during the early growth stages, and produced normal green leaves as it grew. The growth of csv1 plants displayed sensitivity to low temperatures. In addition, the mutant plants that were transferred to low temperatures at the fifth leaf stage produced chlorotic leaves subsequently. Genetic and molecular analyses revealed translocation of a 13-kb genomic fragment that disrupted the causative gene (CSV1; LOC_Os05g34040). CSV1 encodes a plastid-targeted oxidoreductase-like protein conserved among land plants, green algae, and cyanobacteria. Furthermore, CSV1 transcripts were more abundant in immature than in mature leaves, and they did not markedly increase or decrease with temperature. Taken together, our results indicate that CSV1 supports chloroplast development under cold stress conditions, in both the early growth and tillering stages in rice.
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Affiliation(s)
- Ryouhei Morita
- a Nishina Center for Accelerator-Based Science, RIKEN, Wako , Japan
| | - Mayu Nakagawa
- a Nishina Center for Accelerator-Based Science, RIKEN, Wako , Japan
| | - Hinako Takehisa
- a Nishina Center for Accelerator-Based Science, RIKEN, Wako , Japan
| | - Yoriko Hayashi
- a Nishina Center for Accelerator-Based Science, RIKEN, Wako , Japan
| | - Hiroyuki Ichida
- a Nishina Center for Accelerator-Based Science, RIKEN, Wako , Japan
| | - Sachiko Usuda
- a Nishina Center for Accelerator-Based Science, RIKEN, Wako , Japan
| | | | - Hiroshi Abe
- a Nishina Center for Accelerator-Based Science, RIKEN, Wako , Japan
| | - Yuki Shirakawa
- a Nishina Center for Accelerator-Based Science, RIKEN, Wako , Japan
| | - Tadashi Sato
- a Nishina Center for Accelerator-Based Science, RIKEN, Wako , Japan.,b Graduate School of Agricultural Science, Tohoku University , Sendai , Japan
| | - Makoto T Fujiwara
- a Nishina Center for Accelerator-Based Science, RIKEN, Wako , Japan.,c Faculty of Science and Technology , Sophia University , Tokyo , Japan
| | - Ryuuichi D Itoh
- d Faculty of Science , University of the Ryukyus , Nishihara, Japan
| | - Tomoko Abe
- a Nishina Center for Accelerator-Based Science, RIKEN, Wako , Japan
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141
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A multi-step peptidolytic cascade for amino acid recovery in chloroplasts. Nat Chem Biol 2016; 13:15-17. [PMID: 27820795 DOI: 10.1038/nchembio.2227] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 08/24/2016] [Indexed: 12/28/2022]
Abstract
Plastids (including chloroplasts) are subcellular sites for a plethora of proteolytic reactions, required in functions ranging from protein biogenesis to quality control. Here we show that peptides generated from pre-protein maturation within chloroplasts of Arabidopsis thaliana are degraded to amino acids by a multi-step peptidolytic cascade consisting of oligopeptidases and aminopeptidases, effectively allowing the recovery of single amino acids within these organelles.
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142
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Króliczewski J, Piskozub M, Bartoszewski R, Króliczewska B. ALB3 Insertase Mediates Cytochrome b 6 Co-translational Import into the Thylakoid Membrane. Sci Rep 2016; 6:34557. [PMID: 27698412 PMCID: PMC5048292 DOI: 10.1038/srep34557] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 09/15/2016] [Indexed: 01/10/2023] Open
Abstract
The cytochrome b6 f complex occupies an electrochemically central position in the electron-transport chain bridging the photosynthetic reaction center of PS I and PS II. In plants, the subunits of these thylakoid membrane protein complexes are both chloroplast and nuclear encoded. How the chloroplast-encoded subunits of multi-spanning cytochrome b6 are targeted and inserted into the thylakoid membrane is not fully understood. Experimental approaches to evaluate the cytochrome b6 import mechanism in vivo have been limited to bacterial membranes and were not a part of the chloroplast environment. To evaluate the mechanism governing cytochrome b6 integration in vivo, we performed a comparative analysis of both native and synthetic cytochrome b6 insertion into purified thylakoids. Using biophysical and biochemical methods, we show that cytochrome b6 insertion into the thylakoid membrane is a non-spontaneous co-translational process that involves ALB3 insertase. Furthermore, we provided evidence that CSP41 (chloroplast stem-loop-binding protein of 41 kDa) interacts with RNC-cytochrome b6 complexes, and may be involved in cytochrome b6 (petB) transcript stabilization or processing.
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Affiliation(s)
- Jarosław Króliczewski
- Laboratory of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Wrocław Poland
| | - Małgorzata Piskozub
- Amplicon Sp. z o. o., Wrocław, Poland
- Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Rafał Bartoszewski
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - Bożena Króliczewska
- Department of Animal Physiology and Biostructure, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
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143
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Yamamoto H, Fan X, Sugimoto K, Fukao Y, Peng L, Shikanai T. CHLORORESPIRATORY REDUCTION 9 is a Novel Factor Required for Formation of Subcomplex A of the Chloroplast NADH Dehydrogenase-Like Complex. PLANT & CELL PHYSIOLOGY 2016; 57:2122-2132. [PMID: 27481895 DOI: 10.1093/pcp/pcw130] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 07/12/2016] [Indexed: 06/06/2023]
Abstract
In vascular plants, the chloroplast NADH dehydrogenase-like (NDH) complex, a homolog of respiratory NADH:quinone oxidoreductase (Complex I), mediates plastoquinone reduction using ferredoxin as an electron donor in cyclic electron transport around PSI in the thylakoid membrane. In angiosperms, chloroplast NDH is composed of five subcomplexes and forms a supercomplex with PSI. The modular assembly of stroma-protruded subcomplex A, which corresponds to the Q module of Complex I, was recently reported. However, the factors involved in the specific assembly steps have not been completely identified. Here, we isolated an Arabidopsis mutant, chlororespiratory reduction 9 (crr9), defective in NDH activity. The CRR9 gene encodes a novel stromal protein without any known functional domains or motifs. CRR9 is highly conserved in cyanobacteria and land plants but not in green algae, which do not have chloroplast NDH. Blue native-PAGE and immunoblot analyses of thylakoid proteins indicated that formation of subcomplex A was impaired in crr9 CRR9 was specifically required for the accumulation of NdhK, a subcomplex A subunit, in NDH assembly intermediates in the stroma. Furthermore, two-dimensional clear native/SDS-PAGE analysis of the stroma fraction indicated that incorporation of NdhM into NDH assembly intermediate complex 400 was impaired in crr9 These results suggest that CRR9 is a novel factor required for the formation of NDH subcomplex A.
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Affiliation(s)
- Hiroshi Yamamoto
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, 606-8502 Japan
- CREST, Japan Science and Technology Agency Chiyoda-ku Tokyo, 102-0076 Japan
| | - Xiangyuan Fan
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Kazuhiko Sugimoto
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, 606-8502 Japan
| | - Yoichiro Fukao
- Department of Bioinformatics, Ritsumeikan University, Kusatsu, Shiga, 525-8577 Japan
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192 Japan
| | - Lianwei Peng
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Toshiharu Shikanai
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, 606-8502 Japan
- CREST, Japan Science and Technology Agency Chiyoda-ku Tokyo, 102-0076 Japan
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144
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Riggs JW, Rockwell NC, Cavales PC, Callis J. Identification of the Plant Ribokinase and Discovery of a Role for Arabidopsis Ribokinase in Nucleoside Metabolism. J Biol Chem 2016; 291:22572-22582. [PMID: 27601466 DOI: 10.1074/jbc.m116.754689] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 09/06/2016] [Indexed: 12/30/2022] Open
Abstract
Ribose can be used for energy or as a component of several important biomolecules, but for it to be used in either capacity it must first be phosphorylated by ribokinase (RBSK). RBSK proteins are part of the phosphofructokinase-B (pfkB) family of carbohydrate kinases. Sequence comparisons of pfkB proteins from the model plant Arabidopsis thaliana with the human and Escherichia coli RBSK identified a single candidate RBSK, At1g17160 (AtRBSK). AtRBSK is more similar to predicted RBSKs from other plant species and known mammalian and prokaryotic RBSK than to all other PfkB proteins in Arabidopsis AtRBSK contains a predicted chloroplast transit peptide, and we confirmed plastid localization using AtRBSK fused to YFP. Structure prediction software verified that the AtRBSK sequence mapped onto a known RBSK structure. Kinetic parameters of purified recombinant AtRBSK were determined to be Kmribose = 150 μm ± 17 μm, KmATP = 45 μm ± 5.6 μm, and kcat = 2.0 s-1 Substrate inhibition was observed for AtRBSK (KiATP = 2.44 mm ± 0.36 mm), as has been demonstrated for other RBSK proteins. Ribose accumulated in Arabidopsis plants lacking AtRBSK. Such plants grew normally unless media was supplemented with ribose, which led to chlorosis and growth inhibition. Both chlorosis and ribose accumulation were abolished upon the introduction of a transgene expressing AtRBSK-MYC, demonstrating that the loss of protein is responsible for ribose hypersensitivity. Ribose accumulation in plants lacking AtRBSK was reduced in plants also deficient in the nucleoside ribohydrolase NSH1, linking AtRBSK activity to nucleoside metabolism.
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Affiliation(s)
- John W Riggs
- From the Department of Molecular and Cellular Biology, University of California, Davis, California 95616
| | - Nathan C Rockwell
- From the Department of Molecular and Cellular Biology, University of California, Davis, California 95616
| | - Philip C Cavales
- From the Department of Molecular and Cellular Biology, University of California, Davis, California 95616
| | - Judy Callis
- From the Department of Molecular and Cellular Biology, University of California, Davis, California 95616
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145
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Baslam M, Oikawa K, Kitajima-Koga A, Kaneko K, Mitsui T. Golgi-to-plastid trafficking of proteins through secretory pathway: Insights into vesicle-mediated import toward the plastids. PLANT SIGNALING & BEHAVIOR 2016; 11:e1221558. [PMID: 27700755 PMCID: PMC5058459 DOI: 10.1080/15592324.2016.1221558] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 07/31/2016] [Accepted: 08/01/2016] [Indexed: 05/22/2023]
Abstract
The diversity of protein targeting pathways to plastids and their regulation in response to developmental and metabolic status is a key issue in the regulation of cellular function in plants. The general import pathways that target proteins into and across the plastid envelope with changes in gene expression are critical for plant development by regulating the response to physiological and metabolic changes within the cell. Glycoprotein targeting to complex plastids involves routing through the secretory pathway, among others. However, the mechanisms of trafficking via this system remain poorly understood. The present article discusses our results in site-specific N-glycosylation of nucleotide pyrophosphatase/phosphodiesterases (NPPs) glycoproteins and highlights protein delivery in Golgi/plastid pathway via the secretory pathway. Furthermore, we outline the hypotheses that explain the mechanism for importing vesicles trafficking with nucleus-encoded proteins into plastids.
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Affiliation(s)
- Marouane Baslam
- Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, Niigata, Japan
- Graduate School of Science and Technology, Niigata University, Ikarashi, Niigata, Japan
| | - Kazusato Oikawa
- Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, Niigata, Japan
| | - Aya Kitajima-Koga
- Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, Niigata, Japan
| | - Kentaro Kaneko
- Graduate School of Science and Technology, Niigata University, Ikarashi, Niigata, Japan
| | - Toshiaki Mitsui
- Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, Niigata, Japan
- Graduate School of Science and Technology, Niigata University, Ikarashi, Niigata, Japan
- CONTACT Toshiaki Mitsui Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, Niigata, 9502181, R3T 2N2 Japan
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146
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Pradedova EV, Nimaeva OD, Truchan IS, Salyaev RK. Glutathione transferase activity of vacuoles, plastids, and tissue extracts of red beetroot. BIOCHEMISTRY (MOSCOW) SUPPLEMENT SERIES A: MEMBRANE AND CELL BIOLOGY 2016. [DOI: 10.1134/s1990747816020082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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147
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Nishimura K, Kato Y, Sakamoto W. Chloroplast Proteases: Updates on Proteolysis within and across Suborganellar Compartments. PLANT PHYSIOLOGY 2016; 171:2280-93. [PMID: 27288365 PMCID: PMC4972267 DOI: 10.1104/pp.16.00330] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Indexed: 05/08/2023]
Abstract
Chloroplasts originated from the endosymbiosis of ancestral cyanobacteria and maintain transcription and translation machineries for around 100 proteins. Most endosymbiont genes, however, have been transferred to the host nucleus, and the majority of the chloroplast proteome is composed of nucleus-encoded proteins that are biosynthesized in the cytosol and then imported into chloroplasts. How chloroplasts and the nucleus communicate to control the plastid proteome remains an important question. Protein-degrading machineries play key roles in chloroplast proteome biogenesis, remodeling, and maintenance. Research in the past few decades has revealed more than 20 chloroplast proteases, which are localized to specific suborganellar locations. In particular, two energy-dependent processive proteases of bacterial origin, Clp and FtsH, are central to protein homeostasis. Processing endopeptidases such as stromal processing peptidase and thylakoidal processing peptidase are involved in the maturation of precursor proteins imported into chloroplasts by cleaving off the amino-terminal transit peptides. Presequence peptidases and organellar oligopeptidase subsequently degrade the cleaved targeting peptides. Recent findings have indicated that not only intraplastidic but also extraplastidic processive protein-degrading systems participate in the regulation and quality control of protein translocation across the envelopes. In this review, we summarize current knowledge of the major chloroplast proteases in terms of type, suborganellar localization, and diversification. We present details of these degradation processes as case studies according to suborganellar compartment (envelope, stroma, and thylakoids). Key questions and future directions in this field are discussed.
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Affiliation(s)
- Kenji Nishimura
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
| | - Yusuke Kato
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
| | - Wataru Sakamoto
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
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148
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Hirano T, Tanidokoro K, Shimizu Y, Kawarabayasi Y, Ohshima T, Sato M, Tadano S, Ishikawa H, Takio S, Takechi K, Takano H. Moss Chloroplasts Are Surrounded by a Peptidoglycan Wall Containing D-Amino Acids. THE PLANT CELL 2016; 28:1521-32. [PMID: 27325639 PMCID: PMC4981129 DOI: 10.1105/tpc.16.00104] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 06/11/2016] [Indexed: 05/08/2023]
Abstract
It is believed that the plastids in green plants lost peptidoglycan (i.e., a bacterial cell wall-containing d-amino acids) during their evolution from an endosymbiotic cyanobacterium. Although wall-like structures could not be detected in the plastids of green plants, the moss Physcomitrella patens has the genes required to generate peptidoglycan (Mur genes), and knocking out these genes causes defects in chloroplast division. Here, we generated P patens knockout lines (∆Pp-ddl) for a homolog of the bacterial peptidoglycan-synthetic gene encoding d-Ala:d-Ala ligase. ∆Pp-ddl had a macrochloroplast phenotype, similar to other Mur knockout lines. The addition of d-Ala-d-Ala (DA-DA) to the medium suppressed the appearance of giant chloroplasts in ∆Pp-ddl, but the addition of l-Ala-l-Ala (LA-LA), DA-LA, LA-DA, or d-Ala did not. Recently, a metabolic method for labeling bacterial peptidoglycan was established using ethynyl-DA-DA (EDA-DA) and click chemistry to attach an azide-modified fluorophore to the ethynyl group. The ∆Pp-ddl line complemented with EDA-DA showed that moss chloroplasts are completely surrounded by peptidoglycan. Our findings strongly suggest that the moss plastids have a peptidoglycan wall containing d-amino acids. By contrast, no plastid phenotypes were observed in the T-DNA tagged ddl mutant lines of Arabidopsis thaliana.
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Affiliation(s)
- Takayuki Hirano
- Graduate School of Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan
| | - Koji Tanidokoro
- Graduate School of Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan
| | - Yasuhiro Shimizu
- Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan
| | - Yutaka Kawarabayasi
- Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
| | - Toshihisa Ohshima
- Faculty of Engineering, Osaka Institute of Technology, Asahi-ku, Osaka 535-8585, Japan
| | - Momo Sato
- Graduate School of Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan
| | - Shinji Tadano
- Graduate School of Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan
| | - Hayato Ishikawa
- Graduate School of Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan
| | - Susumu Takio
- Graduate School of Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan Center for Marine Environment Studies, Kumamoto University, Kumamoto 860-8555, Japan
| | - Katsuaki Takechi
- Graduate School of Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan
| | - Hiroyoshi Takano
- Graduate School of Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan Institute of Pulsed Power Science, Kumamoto University, Kumamoto 860-8555, Japan
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149
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Abstract
DNA methylation is an epigenetic mechanism that has important functions in transcriptional silencing and is associated with repressive histone methylation (H3K9me). To further investigate silencing mechanisms, we screened a mutagenized Arabidopsis thaliana population for expression of SDCpro-GFP, redundantly controlled by DNA methyltransferases DRM2 and CMT3. Here, we identify the hypomorphic mutant mthfd1-1, carrying a mutation (R175Q) in the cytoplasmic bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase (MTHFD1). Decreased levels of oxidized tetrahydrofolates in mthfd1-1 and lethality of loss-of-function demonstrate the essential enzymatic role of MTHFD1 in Arabidopsis. Accumulation of homocysteine and S-adenosylhomocysteine, genome-wide DNA hypomethylation, loss of H3K9me and transposon derepression indicate that S-adenosylmethionine-dependent transmethylation is inhibited in mthfd1-1. Comparative analysis of DNA methylation revealed that the CMT3 and CMT2 pathways involving positive feedback with H3K9me are mostly affected. Our work highlights the sensitivity of epigenetic networks to one-carbon metabolism due to their common S-adenosylmethionine-dependent transmethylation and has implications for human MTHFD1-associated diseases.
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150
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Grahl S, Reiter B, Gügel IL, Vamvaka E, Gandini C, Jahns P, Soll J, Leister D, Rühle T. The Arabidopsis Protein CGLD11 Is Required for Chloroplast ATP Synthase Accumulation. MOLECULAR PLANT 2016; 9:885-99. [PMID: 26979383 DOI: 10.1016/j.molp.2016.03.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 02/29/2016] [Accepted: 03/07/2016] [Indexed: 05/15/2023]
Abstract
ATP synthases in chloroplasts (cpATPase) and mitochondria (mtATPase) are responsible for ATP production during photosynthesis and oxidative phosphorylation, respectively. Both enzymes consist of two multisubunit complexes, the membrane-bound coupling factor O and the soluble coupling factor 1. During cpATPase biosynthesis, several accessory factors facilitate subunit production and orchestrate complex assembly. Here, we describe a new auxiliary protein in Arabidopsis thaliana, which is required for cpATPase accumulation. AtCGLD11 (CONSERVED IN THE GREEN LINEAGE AND DIATOMS 11) is a protein without any known functional domain and shows dual localization to chloroplasts and mitochondria. Loss of AtCGLD11 function results in reduced levels of cpATPase and impaired photosynthetic performance with lower rates of ATP synthesis. In yeast two-hybrid experiments, AtCGLD11 interacts with the β subunits of the cpATPase and mtATPase. Our results suggest that AtCGLD11 functions in F1 assembly during cpATPase biogenesis, while its role in mtATPase biosynthesis may not, or not yet, be essential.
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Affiliation(s)
- Sabine Grahl
- Lehrstuhl für Biochemie und Physiologie der Pflanzen (Botanik), Department Biologie I, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany; Munich Centre for Integrated Protein Science CiPSM, Ludwig-Maximilians Universität München, Butenandtstr. 5 - 13, 81377 Munich, Germany
| | - Bennet Reiter
- Lehrstuhl für Molekularbiologie der Pflanzen (Botanik), Department Biologie I, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Irene Luise Gügel
- Lehrstuhl für Biochemie und Physiologie der Pflanzen (Botanik), Department Biologie I, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany; Munich Centre for Integrated Protein Science CiPSM, Ludwig-Maximilians Universität München, Butenandtstr. 5 - 13, 81377 Munich, Germany
| | - Evgenia Vamvaka
- Lehrstuhl für Molekularbiologie der Pflanzen (Botanik), Department Biologie I, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Chiara Gandini
- Lehrstuhl für Molekularbiologie der Pflanzen (Botanik), Department Biologie I, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Peter Jahns
- Plant Biochemistry, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Jürgen Soll
- Lehrstuhl für Biochemie und Physiologie der Pflanzen (Botanik), Department Biologie I, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany; Munich Centre for Integrated Protein Science CiPSM, Ludwig-Maximilians Universität München, Butenandtstr. 5 - 13, 81377 Munich, Germany
| | - Dario Leister
- Lehrstuhl für Molekularbiologie der Pflanzen (Botanik), Department Biologie I, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany.
| | - Thilo Rühle
- Lehrstuhl für Molekularbiologie der Pflanzen (Botanik), Department Biologie I, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
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