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Song C, Li Y, Yang M, Li T, Hou Y, Liu Y, Xu C, Liu J, Millar AH, Wang N, Li L. Protein aggregation in plant mitochondria lacking Lon1 inhibits translation and induces unfolded protein responses. PLANT, CELL & ENVIRONMENT 2024. [PMID: 38988259 DOI: 10.1111/pce.15035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 06/20/2024] [Accepted: 06/27/2024] [Indexed: 07/12/2024]
Abstract
Loss of Lon1 led to stunted plant growth and accumulation of nuclear-encoded mitochondrial proteins including Lon1 substrates. However, an in-depth label-free proteomics quantification of mitochondrial proteins in lon1 revealed that the majority of mitochondrial-encoded proteins decreased in abundance. Additionally, we found that lon1 mutants contained protein aggregates in the mitochondrial that were enriched in metabolic enzymes, ribosomal subunits and PPR-containing proteins of the translation apparatus. These mutants exhibited reduced general mitochondrial translation as well as deficiencies in RNA splicing and editing. These findings support the role of Lon1 in maintaining a functional translational apparatus for mitochondrial-encoded gene translation. Transcriptome analysis of lon1 revealed a mitochondrial unfolded protein response reminiscent of the mitochondrial retrograde signalling dependent on the transcription factor ANAC017. Notably, lon1 mutants exhibited transiently elevated ethylene production, and the shortened hypocotyl observed in lon1 mutants during skotomorphogenesis was partially alleviated by ethylene inhibitors. Furthermore, the short root phenotype was partially ameliorated by introducing a mutation in the ethylene receptor ETR1. Interestingly, the upregulation of only a select few target genes was linked to ETR1-mediated ethylene signalling. Together this provides multiple steps in the link between loss of Lon1 and signalling responses to restore mitochondrial protein homoeostasis in plants.
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Affiliation(s)
- Ce Song
- Frontiers Science Center for Cell Responses, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, China
| | - Yuanyuan Li
- Frontiers Science Center for Cell Responses, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, China
| | - Mengmeng Yang
- Frontiers Science Center for Cell Responses, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, China
| | - Tiantian Li
- Frontiers Science Center for Cell Responses, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, China
| | - Yuqi Hou
- Frontiers Science Center for Cell Responses, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, China
| | - Yinyin Liu
- Frontiers Science Center for Cell Responses, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, China
| | - Chang Xu
- Frontiers Science Center for Cell Responses, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, China
| | - Jinjian Liu
- Key Laboratory of Radiopharmacokinetics for Innovative Drugs, Chinese Academy of Medical Sciences, and Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, Crawley, Western Australia, Australia
| | - Ningning Wang
- Frontiers Science Center for Cell Responses, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, China
| | - Lei Li
- Frontiers Science Center for Cell Responses, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, China
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2
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Wittmann DT, Peter FE, Strätker SM, Ortega-Rodés P, Grimm B, Hedtke B. Dual plastid targeting of protoporphyrinogen oxidase 2 in Amaranthaceae promotes herbicide tolerance. PLANT PHYSIOLOGY 2024; 195:713-727. [PMID: 38330186 PMCID: PMC11060682 DOI: 10.1093/plphys/kiae062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 02/10/2024]
Abstract
Plant tetrapyrrole biosynthesis (TPB) takes place in plastids and provides the chlorophyll and heme required for photosynthesis and many redox processes throughout plant development. TPB is strictly regulated, since accumulation of several intermediates causes photodynamic damage and cell death. Protoporphyrinogen oxidase (PPO) catalyzes the last common step before TPB diverges into chlorophyll and heme branches. Land plants possess two PPO isoforms. PPO1 is encoded as a precursor protein with a transit peptide, but in most dicotyledonous plants PPO2 does not possess a cleavable N-terminal extension. Arabidopsis (Arabidopsis thaliana) PPO1 and PPO2 localize in chloroplast thylakoids and envelope membranes, respectively. Interestingly, PPO2 proteins in Amaranthaceae contain an N-terminal extension that mediates their import into chloroplasts. Here, we present multiple lines of evidence for dual targeting of PPO2 to thylakoid and envelope membranes in this clade and demonstrate that PPO2 is not found in mitochondria. Transcript analyses revealed that dual targeting in chloroplasts involves the use of two transcription start sites and initiation of translation at different AUG codons. Among eudicots, the parallel accumulation of PPO1 and PPO2 in thylakoid membranes is specific for the Amaranthaceae and underlies PPO2-based herbicide resistance in Amaranthus species.
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Affiliation(s)
- Daniel T Wittmann
- Institute of Biology/Plant Physiology, Humboldt-Universität zu Berlin, Philippstr. 13 (Building 12), 10115 Berlin, Germany
| | - Franziska E Peter
- Institute of Biology/Plant Physiology, Humboldt-Universität zu Berlin, Philippstr. 13 (Building 12), 10115 Berlin, Germany
| | - Sarah Melissa Strätker
- Institute of Biology/Plant Physiology, Humboldt-Universität zu Berlin, Philippstr. 13 (Building 12), 10115 Berlin, Germany
| | - Patricia Ortega-Rodés
- Institute of Biology/Plant Physiology, Humboldt-Universität zu Berlin, Philippstr. 13 (Building 12), 10115 Berlin, Germany
- Lab. Fisiología Vegetal, Dpto. Biología Vegetal, Facultad de Biología, Universidad de La Habana, 10400 La Habana, Cuba
| | - Bernhard Grimm
- Institute of Biology/Plant Physiology, Humboldt-Universität zu Berlin, Philippstr. 13 (Building 12), 10115 Berlin, Germany
| | - Boris Hedtke
- Institute of Biology/Plant Physiology, Humboldt-Universität zu Berlin, Philippstr. 13 (Building 12), 10115 Berlin, Germany
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3
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Zhang Y, Jaime SM, Bulut M, Graf A, Fernie AR. The conditional mitochondrial protein complexome in the Arabidopsis thaliana root and shoot. PLANT COMMUNICATIONS 2023; 4:100635. [PMID: 37291828 PMCID: PMC10504587 DOI: 10.1016/j.xplc.2023.100635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 02/23/2023] [Accepted: 06/02/2023] [Indexed: 06/10/2023]
Abstract
Protein complexes are important for almost all biological processes. Hence, to fully understand how cells work, it is also necessary to characterize protein complexes and their dynamics in response to various cellular cues. Moreover, the dynamics of protein interaction play crucial roles in regulating the (dis)association of protein complexes and, in turn, regulating biological processes such as metabolism. Here, mitochondrial protein complexes were investigated by blue native PAGE and size-exclusion chromatography under conditions of oxidative stress in order to monitor their dynamic (dis)associations. Rearrangements of enzyme interactions and changes in protein complex abundance were observed in response to oxidative stress induced by menadione treatment. These included changes in enzymatic protein complexes involving γ-amino butyric acid transaminase (GABA-T), Δ-ornithine aminotransferase (Δ-OAT), or proline dehydrogenase 1 (POX1) that are expected to affect proline metabolism. Menadione treatment also affected interactions between several enzymes of the tricarboxylic acid (TCA) cycle and the abundance of complexes of the oxidative phosphorylation pathway. In addition, we compared the mitochondrial complexes of roots and shoots. Considerable differences between the two tissues were observed in the mitochondrial import/export apparatus, the formation of super-complexes in the oxidative phosphorylation pathway, and specific interactions between enzymes of the TCA cycle that we postulate may be related to the metabolic/energetic requirements of roots and shoots.
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Affiliation(s)
- Youjun Zhang
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria; Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Silvia Martínez Jaime
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Mustafa Bulut
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Alexander Graf
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
| | - Alisdair R Fernie
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria; Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
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4
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Sun Y, Li J, Zhang L, Lin R. Regulation of chloroplast protein degradation. J Genet Genomics 2023:S1673-8527(23)00049-8. [PMID: 36863685 DOI: 10.1016/j.jgg.2023.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 02/02/2023] [Accepted: 02/14/2023] [Indexed: 03/04/2023]
Abstract
Chloroplasts are unique organelles that not only provide sites for photosynthesis and many metabolic processes, but also are sensitive to various environmental stresses. Chloroplast proteins are encoded by genes from both nuclear and chloroplast genomes. During chloroplast development and responses to stresses, the robust protein quality control systems are essential for regulation of protein homeostasis and the integrity of chloroplast proteome. In this review, we summarize the regulatory mechanisms of chloroplast protein degradation refer to protease system, ubiquitin-proteasome system, and the chloroplast autophagy. These mechanisms symbiotically play a vital role in chloroplast development and photosynthesis under both normal or stress conditions.
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Affiliation(s)
- Yang Sun
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, Henan 475001, China
| | - Jialong Li
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Lixin Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, Henan 475001, China.
| | - Rongcheng Lin
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
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Gao LL, Hong ZH, Wang Y, Wu GZ. Chloroplast proteostasis: A story of birth, life, and death. PLANT COMMUNICATIONS 2023; 4:100424. [PMID: 35964157 PMCID: PMC9860172 DOI: 10.1016/j.xplc.2022.100424] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/02/2022] [Accepted: 08/10/2022] [Indexed: 06/02/2023]
Abstract
Protein homeostasis (proteostasis) is a dynamic balance of protein synthesis and degradation. Because of the endosymbiotic origin of chloroplasts and the massive transfer of their genetic information to the nucleus of the host cell, many protein complexes in the chloroplasts are constituted from subunits encoded by both genomes. Hence, the proper function of chloroplasts relies on the coordinated expression of chloroplast- and nucleus-encoded genes. The biogenesis and maintenance of chloroplast proteostasis are dependent on synthesis of chloroplast-encoded proteins, import of nucleus-encoded chloroplast proteins from the cytosol, and clearance of damaged or otherwise undesired "old" proteins. This review focuses on the regulation of chloroplast proteostasis, its interaction with proteostasis of the cytosol, and its retrograde control over nuclear gene expression. We also discuss significant issues and perspectives for future studies and potential applications for improving the photosynthetic performance and stress tolerance of crops.
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Affiliation(s)
- Lin-Lin Gao
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Zheng-Hui Hong
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yinsong Wang
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Guo-Zhang Wu
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
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6
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Rozov SM, Deineko EV. Increasing the Efficiency of the Accumulation of Recombinant Proteins in Plant Cells: The Role of Transport Signal Peptides. PLANTS (BASEL, SWITZERLAND) 2022; 11:2561. [PMID: 36235427 PMCID: PMC9572730 DOI: 10.3390/plants11192561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
The problem with increasing the yield of recombinant proteins is resolvable using different approaches, including the transport of a target protein to cell compartments with a low protease activity. In the cell, protein targeting involves short-signal peptide sequences recognized by intracellular protein transport systems. The main systems of the protein transport across membranes of the endoplasmic reticulum and endosymbiotic organelles are reviewed here, as are the major types and structure of the signal sequences targeting proteins to the endoplasmic reticulum and its derivatives, to plastids, and to mitochondria. The role of protein targeting to certain cell organelles depending on specific features of recombinant proteins and the effect of this targeting on the protein yield are discussed, in addition to the main directions of the search for signal sequences based on their primary structure. This knowledge makes it possible not only to predict a protein localization in the cell but also to reveal the most efficient sequences with potential biotechnological utility.
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7
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Ghifari AS, Teixeira PF, Kmiec B, Singh N, Glaser E, Murcha MW. The dual-targeted prolyl aminopeptidase PAP1 is involved in proline accumulation in response to stress and during pollen development. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:78-93. [PMID: 34460901 DOI: 10.1093/jxb/erab397] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
Plant endosymbiotic organelles such as mitochondria and chloroplasts harbour a wide array of biochemical reactions. As a part of protein homeostasis to maintain organellar activity and stability, unwanted proteins and peptides need to be completely degraded in a stepwise mechanism termed the processing pathway, where at the last stage single amino acids are released by aminopeptidases. Here, we determined the molecular and physiological functions of a prolyl aminopeptidase homologue PAP1 (At2g14260) that is able to release N-terminal proline. Transcript analyses demonstrate that an alternative transcription start site gives rise to two alternative transcripts, generating two in-frame proteins PAP1.1 and PAP1.2. Subcellular localization studies revealed that the longer isoform PAP1.1, which contains a 51 residue N-terminal extension, is exclusively targeted to chloroplasts, while the truncated isoform PAP1.2 is located in the cytosol. Distinct expression patterns in different tissues and developmental stages were observed. Investigations into the physiological role of PAP1 using loss-of-function mutants revealed that PAP1 activity may be involved in proline homeostasis and accumulation, required for pollen development and tolerance to osmotic stress. Enzymatic activity, subcellular location, and expression patterns of PAP1 suggest a role in the chloroplastic peptide processing pathway and proline homeostasis.
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Affiliation(s)
- Abi S Ghifari
- School of Molecular Sciences, The University of Western Australia, Crawley, Perth WA, Australia
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Perth WA, Australia
| | - Pedro F Teixeira
- Department of Biochemistry and Biophysics, Arrhenius Laboratory for Natural Sciences, Stockholm University, Stockholm, Sweden
| | - Beata Kmiec
- Department of Biochemistry and Biophysics, Arrhenius Laboratory for Natural Sciences, Stockholm University, Stockholm, Sweden
| | - Neha Singh
- School of Molecular Sciences, The University of Western Australia, Crawley, Perth WA, Australia
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Perth WA, Australia
| | - Elzbieta Glaser
- Department of Biochemistry and Biophysics, Arrhenius Laboratory for Natural Sciences, Stockholm University, Stockholm, Sweden
| | - Monika W Murcha
- School of Molecular Sciences, The University of Western Australia, Crawley, Perth WA, Australia
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Perth WA, Australia
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8
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Sun JL, Li JY, Wang MJ, Song ZT, Liu JX. Protein Quality Control in Plant Organelles: Current Progress and Future Perspectives. MOLECULAR PLANT 2021; 14:95-114. [PMID: 33137518 DOI: 10.1016/j.molp.2020.10.011] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 10/09/2020] [Accepted: 10/28/2020] [Indexed: 05/20/2023]
Abstract
The endoplasmic reticulum, chloroplasts, and mitochondria are major plant organelles for protein synthesis, photosynthesis, metabolism, and energy production. Protein homeostasis in these organelles, maintained by a balance between protein synthesis and degradation, is essential for cell functions during plant growth, development, and stress resistance. Nucleus-encoded chloroplast- and mitochondrion-targeted proteins and ER-resident proteins are imported from the cytosol and undergo modification and maturation within their respective organelles. Protein folding is an error-prone process that is influenced by both developmental signals and environmental cues; a number of mechanisms have evolved to ensure efficient import and proper folding and maturation of proteins in plant organelles. Misfolded or damaged proteins with nonnative conformations are subject to degradation via complementary or competing pathways: intraorganelle proteases, the organelle-associated ubiquitin-proteasome system, and the selective autophagy of partial or entire organelles. When proteins in nonnative conformations accumulate, the organelle-specific unfolded protein response operates to restore protein homeostasis by reducing protein folding demand, increasing protein folding capacity, and enhancing components involved in proteasome-associated protein degradation and autophagy. This review summarizes recent progress on the understanding of protein quality control in the ER, chloroplasts, and mitochondria in plants, with a focus on common mechanisms shared by these organelles during protein homeostasis.
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Affiliation(s)
- Jing-Liang Sun
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310027, China
| | - Jin-Yu Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310027, China
| | - Mei-Jing Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310027, China
| | - Ze-Ting Song
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310027, China
| | - Jian-Xiang Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310027, China.
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9
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Wang H, Liu S, Dai X, Yang Y, Luo Y, Gao Y, Liu X, Wei W, Wang H, Xu X, Reddy ASN, Jaiswal P, Li W, Liu B, Gu L. PSDX: A Comprehensive Multi-Omics Association Database of Populus trichocarpa With a Focus on the Secondary Growth in Response to Stresses. FRONTIERS IN PLANT SCIENCE 2021; 12:655565. [PMID: 34122478 PMCID: PMC8195342 DOI: 10.3389/fpls.2021.655565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/26/2021] [Indexed: 05/16/2023]
Abstract
Populus trichocarpa (P. trichocarpa) is a model tree for the investigation of wood formation. In recent years, researchers have generated a large number of high-throughput sequencing data in P. trichocarpa. However, no comprehensive database that provides multi-omics associations for the investigation of secondary growth in response to diverse stresses has been reported. Therefore, we developed a public repository that presents comprehensive measurements of gene expression and post-transcriptional regulation by integrating 144 RNA-Seq, 33 ChIP-seq, and six single-molecule real-time (SMRT) isoform sequencing (Iso-seq) libraries prepared from tissues subjected to different stresses. All the samples from different studies were analyzed to obtain gene expression, co-expression network, and differentially expressed genes (DEG) using unified parameters, which allowed comparison of results from different studies and treatments. In addition to gene expression, we also identified and deposited pre-processed data about alternative splicing (AS), alternative polyadenylation (APA) and alternative transcription initiation (ATI). The post-transcriptional regulation, differential expression, and co-expression network datasets were integrated into a new P. trichocarpa Stem Differentiating Xylem (PSDX) database (http://forestry.fafu.edu.cn/db/SDX), which further highlights gene families of RNA-binding proteins and stress-related genes. The PSDX also provides tools for data query, visualization, a genome browser, and the BLAST option for sequence-based query. Much of the data is also available for bulk download. The availability of PSDX contributes to the research related to the secondary growth in response to stresses in P. trichocarpa, which will provide new insights that can be useful for the improvement of stress tolerance in woody plants.
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Affiliation(s)
- Huiyuan Wang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sheng Liu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiufang Dai
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Yongkang Yang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yunjun Luo
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yubang Gao
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xuqing Liu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wentao Wei
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huihui Wang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xi Xu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Anireddy S. N. Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, United States
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Bo Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Bo Liu,
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Lianfeng Gu,
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10
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Abstract
Messenger RNAs (mRNAs) consist of a coding region (open reading frame (ORF)) and two untranslated regions (UTRs), 5'UTR and 3'UTR. Ribosomes travel along the coding region, translating nucleotide triplets (called codons) to a chain of amino acids. The coding region was long believed to mainly encode the amino acid content of proteins, whereas regulatory signals reside in the UTRs and in other genomic regions. However, in recent years we have learned that the ORF is expansively populated with various regulatory signals, or codes, which are related to all gene expression steps and additional intracellular aspects. In this paper, we review the current knowledge related to overlapping codes inside the coding regions, such as the influence of synonymous codon usage on translation speed (and, in turn, the effect of translation speed on protein folding), ribosomal frameshifting, mRNA stability, methylation, splicing, transcription and more. All these codes come together and overlap in the ORF sequence, ensuring production of the right protein at the right time.
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Affiliation(s)
- Shaked Bergman
- Department of Biomedical Engineering, Tel-Aviv University, Tel Aviv, Israel
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11
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Mackenzie SA, Kundariya H. Organellar protein multi-functionality and phenotypic plasticity in plants. Philos Trans R Soc Lond B Biol Sci 2019; 375:20190182. [PMID: 31787051 PMCID: PMC6939364 DOI: 10.1098/rstb.2019.0182] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
With the increasing impact of climate instability on agricultural and ecological systems has come a heightened sense of urgency to understand plant adaptation mechanisms in more detail. Plant species have a remarkable ability to disperse their progeny to a wide range of environments, demonstrating extraordinary resiliency mechanisms that incorporate epigenetics and transgenerational stability. Surprisingly, some of the underlying versatility of plants to adapt to abiotic and biotic stress emerges from the neofunctionalization of organelles and organellar proteins. We describe evidence of possible plastid specialization and multi-functional organellar protein features that serve to enhance plant phenotypic plasticity. These features appear to rely on, for example, spatio-temporal regulation of plastid composition, and unusual interorganellar protein targeting and retrograde signalling features that facilitate multi-functionalization. Although we report in detail on three such specializations, involving MSH1, WHIRLY1 and CUE1 proteins in Arabidopsis, there is ample reason to believe that these represent only a fraction of what is yet to be discovered as we begin to elaborate cross-species diversity. Recent observations suggest that plant proteins previously defined in one context may soon be rediscovered in new roles and that much more detailed investigation of proteins that show subcellular multi-targeting may be warranted. This article is part of the theme issue ‘Linking the mitochondrial genotype to phenotype: a complex endeavour’.
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Affiliation(s)
- Sally A Mackenzie
- Departments of Biology and Plant Science, The Pennsylvania State University, 362 Frear North Building, University Park, PA 16802, USA
| | - Hardik Kundariya
- Departments of Biology and Plant Science, The Pennsylvania State University, 362 Frear North Building, University Park, PA 16802, USA
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12
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Moyet L, Salvi D, Bouchnak I, Miras S, Perrot L, Seigneurin-Berny D, Kuntz M, Rolland N. Calmodulin is involved in the dual subcellular location of two chloroplast proteins. J Biol Chem 2019; 294:17543-17554. [PMID: 31578278 PMCID: PMC6873194 DOI: 10.1074/jbc.ra119.010846] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Indexed: 12/02/2022] Open
Abstract
Cell compartmentalization is an essential process by which eukaryotic cells separate and control biological processes. Although calmodulins are well-known to regulate catalytic properties of their targets, we show here their involvement in the subcellular location of two plant proteins. Both proteins exhibit a dual location, namely in the cytosol in addition to their association to plastids (where they are known to fulfil their role). One of these proteins, ceQORH, a long-chain fatty acid reductase, was analyzed in more detail, and its calmodulin-binding site was identified by specific mutations. Such a mutated form is predominantly targeted to plastids at the expense of its cytosolic location. The second protein, TIC32, was also shown to be dependent on its calmodulin-binding site for retention in the cytosol. Complementary approaches (bimolecular fluorescence complementation and reverse genetics) demonstrated that the calmodulin isoform CAM5 is specifically involved in the retention of ceQORH in the cytosol. This study identifies a new role for calmodulin and sheds new light on the intriguing CaM-binding properties of hundreds of plastid proteins, despite the fact that no CaM or CaM-like proteins were identified in plastids.
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Affiliation(s)
- Lucas Moyet
- Laboratoire de Physiologie Cellulaire & Végétale, Université Grenoble Alpes, INRA, CNRS, CEA, IRIG-LPCV, 38000 Grenoble, France
| | - Daniel Salvi
- Laboratoire de Physiologie Cellulaire & Végétale, Université Grenoble Alpes, INRA, CNRS, CEA, IRIG-LPCV, 38000 Grenoble, France
| | - Imen Bouchnak
- Laboratoire de Physiologie Cellulaire & Végétale, Université Grenoble Alpes, INRA, CNRS, CEA, IRIG-LPCV, 38000 Grenoble, France
| | - Stéphane Miras
- Laboratoire de Physiologie Cellulaire & Végétale, Université Grenoble Alpes, INRA, CNRS, CEA, IRIG-LPCV, 38000 Grenoble, France
| | - Laura Perrot
- Laboratoire de Physiologie Cellulaire & Végétale, Université Grenoble Alpes, INRA, CNRS, CEA, IRIG-LPCV, 38000 Grenoble, France
| | - Daphné Seigneurin-Berny
- Laboratoire de Physiologie Cellulaire & Végétale, Université Grenoble Alpes, INRA, CNRS, CEA, IRIG-LPCV, 38000 Grenoble, France
| | - Marcel Kuntz
- Laboratoire de Physiologie Cellulaire & Végétale, Université Grenoble Alpes, INRA, CNRS, CEA, IRIG-LPCV, 38000 Grenoble, France
| | - Norbert Rolland
- Laboratoire de Physiologie Cellulaire & Végétale, Université Grenoble Alpes, INRA, CNRS, CEA, IRIG-LPCV, 38000 Grenoble, France
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Lee DW, Lee S, Lee J, Woo S, Razzak MA, Vitale A, Hwang I. Molecular Mechanism of the Specificity of Protein Import into Chloroplasts and Mitochondria in Plant Cells. MOLECULAR PLANT 2019; 12:951-966. [PMID: 30890495 DOI: 10.1016/j.molp.2019.03.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 02/19/2019] [Accepted: 03/10/2019] [Indexed: 05/04/2023]
Abstract
Plants possess both types of endosymbiotic organelles, chloroplasts and mitochondria. Transit peptides and presequences function as signal sequences for specific import into chloroplasts and mitochondria, respectively. However, how these highly similar signal sequences confer the protein import specificity remains elusive. Here, we show that mitochondrial- or chloroplast-specific import involves two distinct steps, specificity determination and translocation across envelopes, which are mediated by the N-terminal regions and functionally interchangeable C-terminal regions, respectively, of transit peptides and presequences. A domain harboring multiple-arginine and hydrophobic sequence motifs in the N-terminal regions of presequences was identified as the mitochondrial specificity factor. The presence of this domain and the absence of arginine residues in the N-terminal regions of otherwise common targeting signals confers specificity of protein import into mitochondria and chloroplasts, respectively. AtToc159, a chloroplast import receptor, also contributes to determining chloroplast import specificity. We propose that common ancestral sequences were functionalized into mitochondrial- and chloroplast-specific signal sequences by the presence and absence, respectively, of multiple-arginine and hydrophobic sequence motifs in the N-terminal region.
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Affiliation(s)
- Dong Wook Lee
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Sumin Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Junho Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Seungjin Woo
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Md Abdur Razzak
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Alessandro Vitale
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale Delle Ricerche, Milano, Italy
| | - 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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14
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Tsitsekian D, Daras G, Alatzas A, Templalexis D, Hatzopoulos P, Rigas S. Comprehensive analysis of Lon proteases in plants highlights independent gene duplication events. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2185-2197. [PMID: 30590727 PMCID: PMC6460959 DOI: 10.1093/jxb/ery440] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 11/28/2018] [Indexed: 05/10/2023]
Abstract
The degradation of damaged proteins is essential for cell viability. Lon is a highly conserved ATP-dependent serine-lysine protease that maintains proteostasis. We performed a comparative genome-wide analysis to determine the evolutionary history of Lon proteases. Prokaryotes and unicellular eukaryotes retained a single Lon copy, whereas multicellular eukaryotes acquired a peroxisomal copy, in addition to the mitochondrial gene, to sustain the evolution of higher order organ structures. Land plants developed small Lon gene families. Despite the Lon2 peroxisomal paralog, Lon genes triplicated in the Arabidopsis lineage through sequential evolutionary events including whole-genome and tandem duplications. The retention of Lon1, Lon4, and Lon3 triplicates relied on their differential and even contrasting expression patterns, distinct subcellular targeting mechanisms, and functional divergence. Lon1 seems similar to the pre-duplication ancestral gene unit, whereas the duplication of Lon3 and Lon4 is evolutionarily recent. In the wider context of plant evolution, papaya is the only genome with a single ancestral Lon1-type gene. The evolutionary trend among plants is to acquire Lon copies with ambiguous pre-sequences for dual-targeting to mitochondria and chloroplasts, and a substrate recognition domain that deviates from the ancestral Lon1 type. Lon genes constitute a paradigm of dynamic evolution contributing to understanding the functional fate of gene duplicates.
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Affiliation(s)
- Dikran Tsitsekian
- Department of Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Gerasimos Daras
- Department of Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Anastasios Alatzas
- Department of Biotechnology, Agricultural University of Athens, Athens, Greece
| | | | | | - Stamatis Rigas
- Department of Biotechnology, Agricultural University of Athens, Athens, Greece
- Correspondence:
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15
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Qian Y, Lynch JH, Guo L, Rhodes D, Morgan JA, Dudareva N. Completion of the cytosolic post-chorismate phenylalanine biosynthetic pathway in plants. Nat Commun 2019. [PMID: 30604768 DOI: 10.1038/s41467-018-07969-7962] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
In addition to being a vital component of proteins, phenylalanine is also a precursor of numerous aromatic primary and secondary metabolites with broad physiological functions. In plants phenylalanine is synthesized predominantly via the arogenate pathway in plastids. Here, we describe the structure, molecular players and subcellular localization of a microbial-like phenylpyruvate pathway for phenylalanine biosynthesis in plants. Using a reverse genetic approach and metabolic flux analysis, we provide evidence that the cytosolic chorismate mutase is responsible for directing carbon flux towards cytosolic phenylalanine production via the phenylpyruvate pathway. We also show that an alternative transcription start site of a known plastidial enzyme produces a functional cytosolic prephenate dehydratase that catalyzes the conversion of prephenate to phenylpyruvate, the intermediate step between chorismate mutase and phenylpyruvate aminotransferase. Thus, our results complete elucidation of phenylalanine biosynthesis via phenylpyruvate in plants, showing that this pathway splits from the known plastidial arogenate pathway at chorismate, instead of prephenate as previously thought, and the complete pathway is localized in the cytosol.
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Affiliation(s)
- Yichun Qian
- Department of Horticulture and Landscape Architecture, Purdue University, 625 Agriculture Mall Dr., West Lafayette, IN, 47907-2010, USA
| | - Joseph H Lynch
- Department of Biochemistry, Purdue University, 175 South University St., West Lafayette, IN, 47907-2063, USA
| | - Longyun Guo
- Department of Biochemistry, Purdue University, 175 South University St., West Lafayette, IN, 47907-2063, USA
| | - David Rhodes
- Department of Horticulture and Landscape Architecture, Purdue University, 625 Agriculture Mall Dr., West Lafayette, IN, 47907-2010, USA
| | - John A Morgan
- Department of Biochemistry, Purdue University, 175 South University St., West Lafayette, IN, 47907-2063, USA
- Davidson School of Chemical Engineering, Purdue University, 480 Stadium Mall Dr., West Lafayette, IN, 47907-2100, USA
| | - Natalia Dudareva
- Department of Horticulture and Landscape Architecture, Purdue University, 625 Agriculture Mall Dr., West Lafayette, IN, 47907-2010, USA.
- Department of Biochemistry, Purdue University, 175 South University St., West Lafayette, IN, 47907-2063, USA.
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA.
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16
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Qian Y, Lynch JH, Guo L, Rhodes D, Morgan JA, Dudareva N. Completion of the cytosolic post-chorismate phenylalanine biosynthetic pathway in plants. Nat Commun 2019; 10:15. [PMID: 30604768 PMCID: PMC6318282 DOI: 10.1038/s41467-018-07969-2] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 12/05/2018] [Indexed: 01/10/2023] Open
Abstract
In addition to being a vital component of proteins, phenylalanine is also a precursor of numerous aromatic primary and secondary metabolites with broad physiological functions. In plants phenylalanine is synthesized predominantly via the arogenate pathway in plastids. Here, we describe the structure, molecular players and subcellular localization of a microbial-like phenylpyruvate pathway for phenylalanine biosynthesis in plants. Using a reverse genetic approach and metabolic flux analysis, we provide evidence that the cytosolic chorismate mutase is responsible for directing carbon flux towards cytosolic phenylalanine production via the phenylpyruvate pathway. We also show that an alternative transcription start site of a known plastidial enzyme produces a functional cytosolic prephenate dehydratase that catalyzes the conversion of prephenate to phenylpyruvate, the intermediate step between chorismate mutase and phenylpyruvate aminotransferase. Thus, our results complete elucidation of phenylalanine biosynthesis via phenylpyruvate in plants, showing that this pathway splits from the known plastidial arogenate pathway at chorismate, instead of prephenate as previously thought, and the complete pathway is localized in the cytosol.
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Affiliation(s)
- Yichun Qian
- Department of Horticulture and Landscape Architecture, Purdue University, 625 Agriculture Mall Dr., West Lafayette, IN, 47907-2010, USA
| | - Joseph H Lynch
- Department of Biochemistry, Purdue University, 175 South University St., West Lafayette, IN, 47907-2063, USA
| | - Longyun Guo
- Department of Biochemistry, Purdue University, 175 South University St., West Lafayette, IN, 47907-2063, USA
| | - David Rhodes
- Department of Horticulture and Landscape Architecture, Purdue University, 625 Agriculture Mall Dr., West Lafayette, IN, 47907-2010, USA
| | - John A Morgan
- Department of Biochemistry, Purdue University, 175 South University St., West Lafayette, IN, 47907-2063, USA.,Davidson School of Chemical Engineering, Purdue University, 480 Stadium Mall Dr., West Lafayette, IN, 47907-2100, USA
| | - Natalia Dudareva
- Department of Horticulture and Landscape Architecture, Purdue University, 625 Agriculture Mall Dr., West Lafayette, IN, 47907-2010, USA. .,Department of Biochemistry, Purdue University, 175 South University St., West Lafayette, IN, 47907-2063, USA. .,Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA.
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17
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Cabout S, Leask MP, Varghese S, Yi J, Peters B, Conze LL, Köhler C, Brownfield L. The meiotic regulator JASON utilizes alternative translation initiation sites to produce differentially localized forms. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:4205-4217. [PMID: 28922756 PMCID: PMC5853252 DOI: 10.1093/jxb/erx222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 06/06/2017] [Indexed: 06/07/2023]
Abstract
The JASON (JAS) protein plays an important role in maintaining an organelle band across the equator of male meiotic cells during the second division, with its loss leading to unreduced pollen in Arabidopsis. In roots cells, JAS localizes to the Golgi, tonoplast and plasma membrane. Here we explore the mechanism underlying the localization of JAS. Overall, our data show that leaky ribosom scanning and alternative translation initiation sites (TISs) likely leads to the formation of two forms of JAS: a long version with an N-terminal Golgi localization signal and a short version with a different N-terminal signal targeting the protein to the plasma membrane. The ratio of the long and short forms of JAS is developmentally regulated, with both being produced in roots but the short form being predominant and functional during meiosis. This regulation of TISs in meiocytes ensures that the short version of JAS is formed during meiosis to ensure separation of chromosome groups and the production of reduced pollen. We hypothesize that increased occurrence of unreduced pollen under stress conditions may be a consequence of altered usage of JAS TISs during stress.
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Affiliation(s)
- Simon Cabout
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Megan P Leask
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Shiny Varghese
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Jun Yi
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Benjamin Peters
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Lei Liu Conze
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Claudia Köhler
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
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18
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Nishimura K, Kato Y, Sakamoto W. Essentials of Proteolytic Machineries in Chloroplasts. MOLECULAR PLANT 2017; 10:4-19. [PMID: 27585878 DOI: 10.1016/j.molp.2016.08.005] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 08/17/2016] [Accepted: 08/21/2016] [Indexed: 05/22/2023]
Abstract
Plastids are unique organelles that can alter their structure and function in response to environmental and developmental stimuli. Chloroplasts are one type of plastid and are the sites for various metabolic processes, including photosynthesis. For optimal photosynthetic activity, the chloroplast proteome must be properly shaped and maintained through regulated proteolysis and protein quality control mechanisms. Enzymatic functions and activities are conferred by protein maturation processes involving consecutive proteolytic reactions. Protein abundances are optimized by the balanced protein synthesis and degradation, which is depending on the metabolic status. Malfunctioning proteins are promptly degraded. Twenty chloroplast proteolytic machineries have been characterized to date. Specifically, processing peptidases and energy-driven processive proteases are the major players in chloroplast proteome biogenesis, remodeling, and maintenance. Recently identified putative proteases are potential regulators of photosynthetic functions. Here we provide an updated, comprehensive overview of chloroplast protein degradation machineries and discuss their importance for photosynthesis. Wherever possible, we also provide structural insights into chloroplast proteases that implement regulated proteolysis of substrate proteins/peptides.
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Affiliation(s)
- Kenji Nishimura
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan
| | - Yusuke Kato
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan
| | - Wataru Sakamoto
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan.
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19
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Ioannidi E, Rigas S, Tsitsekian D, Daras G, Alatzas A, Makris A, Tanou G, Argiriou A, Alexandrou D, Poethig S, Hatzopoulos P, Kanellis AK. Trichome patterning control involves TTG1 interaction with SPL transcription factors. PLANT MOLECULAR BIOLOGY 2016; 92:675-687. [PMID: 27631431 DOI: 10.1007/s11103-016-0538-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 08/29/2016] [Indexed: 05/10/2023]
Abstract
Epidermal cell differentiation is a paramount and conserved process among plants. In Arabidopsis, a ternary complex formed by MYB, bHLH transcription factors and TTG1 modulates unicellular trichome morphogenesis. The formation of multicellular glandular trichomes of the xerophytic shrub Cistus creticus that accumulate labdane-type diterpenes, has attained much attention renowned for its medicinal properties. Here, we show that C. creticus TTG1 (CcTTG1) interacts with the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPLA/B) proteins, putative homologs of AtSPL4/5 that in turn interact with AtTTG1. These interactions occur between proteins from evolutionarily distant species supporting the conserved function of TTG1-SPL complex. Overexpression of AtSPL4 and AtSPL5 decreased the expression of GLABRA2 (AtGL2), the major regulator of trichome morphogenesis, resulting in trichome reduction on the adaxial surface of cauline leaves, thereby illuminating the significance of TTG1-SPLs interactions in trichome formation control. AtGL2 and AtSPL4 have opposite expression patterns during early stages of leaf development. We postulate an antagonistic effect between SPLs and the heterogeneous MYB-bHLH factors binding to TTG1. Hence, the SPLs potentially rearrange the complex, attenuating its transcriptional activity to control trichome distribution.
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Affiliation(s)
- Eugenia Ioannidi
- Group of Biotechnology of Pharmaceutical Plants, Laboratory of Pharmacognosy, Department of Pharmaceutical Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Stamatis Rigas
- Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece
| | - Dikran Tsitsekian
- Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece
| | - Gerasimos Daras
- Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece
| | - Anastasios Alatzas
- Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece
| | - Antonis Makris
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece
| | - Georgia Tanou
- Group of Biotechnology of Pharmaceutical Plants, Laboratory of Pharmacognosy, Department of Pharmaceutical Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Department of Agricultural Sciences, Aristotle University of Thessaloniki, 541 24, Thessaloniki, Greece
| | | | - Dimitrios Alexandrou
- Group of Biotechnology of Pharmaceutical Plants, Laboratory of Pharmacognosy, Department of Pharmaceutical Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Scott Poethig
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104-6313, USA
| | - Polydefkis Hatzopoulos
- Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece.
| | - Angelos K Kanellis
- Group of Biotechnology of Pharmaceutical Plants, Laboratory of Pharmacognosy, Department of Pharmaceutical Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece.
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20
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Identification of a second PAD1 in Brettanomyces bruxellensis LAMAP2480. Antonie van Leeuwenhoek 2016; 110:291-296. [PMID: 27771809 DOI: 10.1007/s10482-016-0793-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 10/18/2016] [Indexed: 12/13/2022]
Abstract
Volatile phenols are aromatic compounds produced by some yeasts of the genus Brettanomyces as defense against the toxicity of hydroxycinnamic acids (p-coumaric acid, ferulic acid and caffeic acid). The origin of these compounds in winemaking involves the sequential action of two enzymes: coumarate decarboxylase and vinylphenol reductase. The first one converts hydroxycinnamic acids into hydroxystyrenes, which are then reduced to ethyl derivatives by vinylphenol reductase. Volatile phenols derived from p-coumaric acid (4-vinylphenol and 4-ethylphenol) have been described as the major contributors to self-defeating aromas associated with stable, gouache, wet mouse, etc., which generates large economic losses in the wine industry. The gene responsible for the production of 4-vinylphenol from p-coumaric acid has been identified as PAD1, which encodes a phenylacrylic acid decarboxylase. PAD1 has been described for many species, among them Candida albicans, Candida dubliniensis, Debaryomyces hansenii and Pichia anomala. In Brettanomyces bruxellensis LAMAP2480, a 666 bp reading frame (DbPAD) encodes a coumarate decarboxylase. Recent studies have reported the existence of a new reading frame belonging to DbPAD called DbPAD2 of 531 bp, which could encode a protein with similar enzymatic activity to PAD1. The present study confirmed that the transformation of Saccharomyces cerevisiae strain BY4722 with reading frame DbPAD2 under the control of the B. bruxellensis ACT1 promoter, encodes an enzyme with coumarate decarboxylase activity. This work has provided deeper insight into the origin of aroma defects in wine due to contamination by Brettanomyces spp.
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21
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Young PG, Bartel B. Pexophagy and peroxisomal protein turnover in plants. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1863:999-1005. [PMID: 26348128 DOI: 10.1016/j.bbamcr.2015.09.005] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 08/26/2015] [Accepted: 09/02/2015] [Indexed: 01/21/2023]
Abstract
Peroxisomes are dynamic, vital organelles that sequester a variety of oxidative reactions and their toxic byproducts from the remainder of the cell. The oxidative nature of peroxisomal metabolism predisposes the organelle to self-inflicted damage, highlighting the need for a mechanism to dispose of damaged peroxisomes. In addition, the metabolic requirements of plant peroxisomes change during development, and obsolete peroxisomal proteins are degraded. Although pexophagy, the selective autophagy of peroxisomes, is an obvious mechanism for executing such degradation, pexophagy has only recently been described in plants. Several recent studies in the reference plant Arabidopsis thaliana implicate pexophagy in the turnover of peroxisomal proteins, both for quality control and during functional transitions of peroxisomal content. In this review, we describe our current understanding of the occurrence, roles, and mechanisms of pexophagy in plants.
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Affiliation(s)
- Pierce G Young
- Department of BioSciences, Rice University, Houston, TX 77005, USA.
| | - Bonnie Bartel
- Department of BioSciences, Rice University, Houston, TX 77005, USA.
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22
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Vélez-Bermúdez IC, Carretero-Paulet L, Legnaioli T, Ludevid D, Pagès M, Riera M. Novel CK2α and CK2β subunits in maize reveal functional diversification in subcellular localization and interaction capacity. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 235:58-69. [PMID: 25900566 DOI: 10.1016/j.plantsci.2015.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 03/06/2015] [Accepted: 03/07/2015] [Indexed: 05/17/2023]
Abstract
In plants, CK2α/β subunits are encoded by multigenic families. They assemble as heterotetrameric holoenzymes or remain as individual subunits and are usually located in distinct cell compartments. Here we revise the number of maize CK2α/β genes, bringing them up to a total of eight (four CK2α catalytic and four CK2β regulatory subunits). We characterize CK2β4, which presents nuclear localization and interacts with CK2α1, CK2α3, CK2β1, and CK2β3. We also describe two CK2α isoforms (CK2α2 and CK2α4) containing N-terminal extensions that correspond to putative cTPs (chloroplast transit peptides). These cTPs are functional and responsible for the subcellular localization of CK2α2 and CK2α4 in chloroplasts. Phylogenetic analysis of the CK2α gene family, further supported by the gene structure and architecture of conserved protein domains, reveals the evolutionary expansion and diversification of this family. The subcellular localization of all four CK2α isoforms was found to be altered when were co-expressed with CK2β, thereby pointing to the latter as regulators of CK2α localization.
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Affiliation(s)
- I C Vélez-Bermúdez
- Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Campus UAB - Edifici CRAG, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain
| | - L Carretero-Paulet
- Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Campus UAB - Edifici CRAG, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain
| | - T Legnaioli
- Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Campus UAB - Edifici CRAG, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain
| | - D Ludevid
- Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Campus UAB - Edifici CRAG, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain
| | - M Pagès
- Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Campus UAB - Edifici CRAG, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain
| | - M Riera
- Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Campus UAB - Edifici CRAG, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain.
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23
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Daras G, Rigas S, Tsitsekian D, Iacovides TA, Hatzopoulos P. Potassium transporter TRH1 subunits assemble regulating root-hair elongation autonomously from the cell fate determination pathway. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 231:131-7. [PMID: 25575998 DOI: 10.1016/j.plantsci.2014.11.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Revised: 11/24/2014] [Accepted: 11/28/2014] [Indexed: 05/17/2023]
Abstract
Trichoblasts of trh1 plants form root-hair initiation sites that fail to undergo tip growth resulting in a tiny root-hair phenotype. TRH1 belongs to Arabidopsis KT/KUP/HAK potassium transporter family controlling root-hair growth and gravitropism. Double mutant combinations between trh1 and root-hair mutants affecting cell fate or root-hair initiation exhibited additive phenotypes, suggesting that TRH1 acts independently and developmentally downstream of root-hair initiation. Bimolecular Fluorescence Complementation (BiFC), upon TRH1-YFP(C) and TRH1-YFP(N) co-transformation into tobacco epidermal cells, led to fluorescence emission indicative of TRH1 subunit homodimerization. Yeast two-hybrid analysis revealed two types of interactions. The hydrophilic segment between the second and the third transmembrane domain extending from residues Q105 to T141 is competent for a relatively weak interaction, whereas the region at the C-terminal beyond the last transmembrane domain, extending from amino acids R565 to A729, strongly self-interacts. These domains likely facilitate the co-assembly of TRH1 subunits forming an active K(+) transport system within cellular membrane structures. The results support the role of TRH1 acting as a convergence point between the developmental root-hair pathway and the environmental/hormonal signaling pathway to preserve auxin homeostasis ensuring plant adaptation in changing environments.
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Affiliation(s)
- Gerasimos Daras
- Department of Biotechnology, Agricultural University of Athens, Iera Odos 75,118 55, Athens, Greece.
| | - Stamatis Rigas
- Department of Biotechnology, Agricultural University of Athens, Iera Odos 75,118 55, Athens, Greece.
| | - Dikran Tsitsekian
- Department of Biotechnology, Agricultural University of Athens, Iera Odos 75,118 55, Athens, Greece.
| | - Tefkros A Iacovides
- Department of Biotechnology, Agricultural University of Athens, Iera Odos 75,118 55, Athens, Greece.
| | - Polydefkis Hatzopoulos
- Department of Biotechnology, Agricultural University of Athens, Iera Odos 75,118 55, Athens, Greece.
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van Wijk KJ. Protein maturation and proteolysis in plant plastids, mitochondria, and peroxisomes. ANNUAL REVIEW OF PLANT BIOLOGY 2015; 66:75-111. [PMID: 25580835 DOI: 10.1146/annurev-arplant-043014-115547] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Plastids, mitochondria, and peroxisomes are key organelles with dynamic proteomes in photosynthetic eukaryotes. Their biogenesis and activity must be coordinated and require intraorganellar protein maturation, degradation, and recycling. The three organelles together are predicted to contain ∼200 presequence peptidases, proteases, aminopeptidases, and specific protease chaperones/adaptors, but the substrates and substrate selection mechanisms are poorly understood. Similarly, lifetime determinants of organellar proteins, such as N-end degrons and tagging systems, have not been identified, but the substrate recognition mechanisms likely share similarities between organelles. Novel degradomics tools for systematic analysis of protein lifetime and proteolysis could define such protease-substrate relationships, degrons, and protein lifetime. Intraorganellar proteolysis is complemented by autophagy of whole organelles or selected organellar content, as well as by cytosolic protein ubiquitination and degradation by the proteasome. This review summarizes (putative) plant organellar protease functions and substrate-protease relationships. Examples illustrate key proteolytic events.
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Affiliation(s)
- Klaas J van Wijk
- Department of Plant Biology, Cornell University, Ithaca, New York 14853;
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Berim A, Kim MJ, Gang DR. Identification of a unique 2-oxoglutarate-dependent flavone 7-O-demethylase completes the elucidation of the lipophilic flavone network in basil. PLANT & CELL PHYSIOLOGY 2015; 56:126-136. [PMID: 25378691 DOI: 10.1093/pcp/pcu152] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Small molecule demethylation is considered unusual in plants. Of the studied instances, the N-demethylation of nicotine is catalyzed by a Cyt P450 monooxygenase, while the O-dealkylation of alkaloids in Papaver somniferum is mediated by 2-oxoglutarate-dependent dioxygenases (2-ODDs). This report describes a 2-ODD regiospecifically catalyzing the 7-O-demethylation of methoxylated flavones in peltate trichomes of sweet basil (Ocimum basilicum L.). Three candidate 2-ODDs were identified in the basil trichome transcriptome database. Only the candidate designated ObF7ODM1 was found to be active with and highly specific for the proposed natural substrates, gardenin B and 8-hydroxysalvigenin. Of the characterized 2-ODDs, ObF7ODM1 is most closely related to O-demethylases from Papaver. The demethylase activity in trichomes from four basil chemotypes matches well with the abundance of ObF7ODM1 peptides and transcripts in the same trichome preparations. Treatment of basil plants with a 2-ODD inhibitor prohexadione-calcium significantly reduced the accumulation of 7-O-demethylated flavone nevadensin, confirming the involvement of a 2-ODD in its formation. Notably, the full-length open reading frame of ObF7ODM1 contains a second in-frame AUG codon 57 nucleotides downstream of the first translation initiation codon. Both AUG codons are recognized by bacterial translation machinery during heterologous gene expression. The N-truncated ObF7ODM1 is nearly inactive. The N-terminus essential for activity is unique to ObF7ODM1 and does not align with the sequences of other 2-ODDs. Further studies will reveal whether alternative translation initiation plays a role in regulating the O-demethylase activity in planta. Molecular identification of the flavone 7-O-demethylase completes the biochemical elucidation of the lipophilic flavone network in basil.
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Affiliation(s)
- Anna Berim
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
| | - Min-Jeong Kim
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
| | - David R Gang
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
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Tuller T, Zur H. Multiple roles of the coding sequence 5' end in gene expression regulation. Nucleic Acids Res 2014; 43:13-28. [PMID: 25505165 PMCID: PMC4288200 DOI: 10.1093/nar/gku1313] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The codon composition of the coding sequence's (ORF) 5′ end first few dozen codons is known to be distinct to that of the rest of the ORF. Various explanations for the unusual codon distribution in this region have been proposed in recent years, and include, among others, novel regulatory mechanisms of translation initiation and elongation. However, due to the fact that many overlapping regulatory signals are suggested to be associated with this relatively short region, its research is challenging. Here, we review the currently known signals that appear in this region, the theories related to the way they regulate translation and affect the organismal fitness, and the debates they provoke.
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Affiliation(s)
- Tamir Tuller
- Department of Biomedical Engineering, the Engineering Faculty, Tel Aviv University, Tel Aviv, Israel The Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Hadas Zur
- Department of Biomedical Engineering, the Engineering Faculty, Tel Aviv University, Tel Aviv, Israel
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Murcha MW, Kmiec B, Kubiszewski-Jakubiak S, Teixeira PF, Glaser E, Whelan J. Protein import into plant mitochondria: signals, machinery, processing, and regulation. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:6301-35. [PMID: 25324401 DOI: 10.1093/jxb/eru399] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The majority of more than 1000 proteins present in mitochondria are imported from nuclear-encoded, cytosolically synthesized precursor proteins. This impressive feat of transport and sorting is achieved by the combined action of targeting signals on mitochondrial proteins and the mitochondrial protein import apparatus. The mitochondrial protein import apparatus is composed of a number of multi-subunit protein complexes that recognize, translocate, and assemble mitochondrial proteins into functional complexes. While the core subunits involved in mitochondrial protein import are well conserved across wide phylogenetic gaps, the accessory subunits of these complexes differ in identity and/or function when plants are compared with Saccharomyces cerevisiae (yeast), the model system for mitochondrial protein import. These differences include distinct protein import receptors in plants, different mechanistic operation of the intermembrane protein import system, the location and activity of peptidases, the function of inner-membrane translocases in linking the outer and inner membrane, and the association/regulation of mitochondrial protein import complexes with components of the respiratory chain. Additionally, plant mitochondria share proteins with plastids, i.e. dual-targeted proteins. Also, the developmental and cell-specific nature of mitochondrial biogenesis is an aspect not observed in single-celled systems that is readily apparent in studies in plants. This means that plants provide a valuable model system to study the various regulatory processes associated with protein import and mitochondrial biogenesis.
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Affiliation(s)
- Monika W Murcha
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia
| | - Beata Kmiec
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, SE-10691 Stockholm, Sweden
| | - Szymon Kubiszewski-Jakubiak
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia
| | - Pedro F Teixeira
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, SE-10691 Stockholm, Sweden
| | - Elzbieta Glaser
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, SE-10691 Stockholm, Sweden
| | - James Whelan
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Science, La Trobe University, Bundoora, Victoria, 3086, Australia
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Rigas S, Daras G, Tsitsekian D, Alatzas A, Hatzopoulos P. Evolution and significance of the Lon gene family in Arabidopsis organelle biogenesis and energy metabolism. FRONTIERS IN PLANT SCIENCE 2014; 5:145. [PMID: 24782883 PMCID: PMC3990055 DOI: 10.3389/fpls.2014.00145] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 03/26/2014] [Indexed: 05/18/2023]
Abstract
Lon is the first identified ATP-dependent protease highly conserved across all kingdoms. Model plant species Arabidopsis thaliana has a small Lon gene family of four members. Although these genes share common structural features, they have distinct properties in terms of gene expression profile, subcellular targeting and substrate recognition motifs. This supports the notion that their functions under different environmental conditions are not necessarily redundant. This article intends to unravel the biological role of Lon proteases in energy metabolism and plant growth through an evolutionary perspective. Given that plants are sessile organisms exposed to diverse environmental conditions and plant organelles are semi-autonomous, it is tempting to suggest that Lon genes in Arabidopsis are paralogs. Adaptive evolution through repetitive gene duplication events of a single archaic gene led to Lon genes with complementing sets of subfunctions providing to the organism rapid adaptability for canonical development under different environmental conditions. Lon1 function is adequately characterized being involved in mitochondrial biogenesis, modulating carbon metabolism, oxidative phosphorylation and energy supply, all prerequisites for seed germination and seedling establishment. Lon is not a stand-alone proteolytic machine in plant organelles. Lon in association with other nuclear-encoded ATP-dependent proteases builds up an elegant nevertheless, tight interconnected circuit. This circuitry channels properly and accurately, proteostasis and protein quality control among the distinct subcellular compartments namely mitochondria, chloroplasts, and peroxisomes.
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Affiliation(s)
| | | | | | | | - Polydefkis Hatzopoulos
- *Correspondence: Polydefkis Hatzopoulos, Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, Athens 118 55, Greece e-mail:
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