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Nakanishi K, Li H, Ichino T, Tatsumi K, Osakabe K, Watanabe B, Shimomura K, Yazaki K. Peroxisomal 4-coumaroyl-CoA ligases participate in shikonin production in Lithospermum erythrorhizon. PLANT PHYSIOLOGY 2024; 195:2843-2859. [PMID: 38478427 DOI: 10.1093/plphys/kiae157] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 02/18/2024] [Indexed: 08/02/2024]
Abstract
4-Coumaroyl-CoA ligase (4CL) is a key enzyme in the phenylpropanoid pathway, which is involved in the biosynthesis of various specialized metabolites such as flavonoids, coumarins, lignans, and lignin. Plants have several 4CLs showing divergence in sequence: Class I 4CLs involved in lignin metabolism, Class II 4CLs associated with flavonoid metabolism, and atypical 4CLs and 4CL-like proteins of unknown function. Shikonin, a Boraginaceae-specific specialized metabolite in red gromwell (Lithospermum erythrorhizon), is biosynthesized from p-hydroxybenzoic acid, and the involvement of 4CL in its biosynthesis has long been debated. In this study, we demonstrated the requirement of 4CL for shikonin biosynthesis using a 4CL-specific inhibitor. In silico analysis of the L. erythrorhizon genome revealed the presence of at least 8 4CL genes, among which the expression of 3 (Le4CL3, Le4CL4, and Le4CL5) showed a positive association with shikonin production. Phylogenetic analysis indicated that Le4CL5 belongs to Class I 4CLs, while Le4CL3 and Le4CL4 belong to clades that are distant from Class I and Class II. Interestingly, both Le4CL3 and Le4CL4 have peroxisome targeting signal 1 in their C-terminal region, and subcellular localization analysis revealed that both localize to the peroxisome. We targeted each of the 3 Le4CL genes by CRISPR/Cas9-mediated mutagenesis and observed remarkably lower shikonin production in Le4CL3-ge and Le4CL4-ge genome-edited lines compared with the vector control. We, therefore, conclude that peroxisomal Le4CL3 and Le4CL4 are responsible for shikonin production and propose a model for metabolite-specific 4CL distribution in L. erythrorhizon.
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Affiliation(s)
- Kohei Nakanishi
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Hao Li
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Takuji Ichino
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
- Laboratory of Medicinal Cell Biology, Kobe Pharmaceutical University, Kobe, Hyogo 658-8558, Japan
| | - Kanade Tatsumi
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Keishi Osakabe
- Graduate School of Technology, Industrial and Social Science, Tokushima University, Tokushima, Tokushima 770-8503, Japan
| | - Bunta Watanabe
- Chemistry Laboratory, The Jikei University School of Medicine, Chofu, Tokyo 182-8570, Japan
| | - Koichiro Shimomura
- Graduate School of Life Science, Toyo University, 1-1-1 Izumino, Itakura, Ora, Gunma 374-0193, Japan
| | - Kazufumi Yazaki
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
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2
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Miyazawa SI, Ujino-Ihara T, Miyama T, Tahara K, Tobita H, Suzuki Y, Nishiguchi M. Different photorespiratory mechanisms in conifer leaves, where peroxisomes have intrinsically low catalase activity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1004-1020. [PMID: 37162489 DOI: 10.1111/tpj.16276] [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: 07/15/2022] [Revised: 04/28/2023] [Accepted: 05/03/2023] [Indexed: 05/11/2023]
Abstract
Photorespiration is an essential metabolic mechanism associated with photosynthesis; however, little is known about the photorespiratory pathway of conifer gymnosperms. Metabolite analyses of the leaves of 27 tree species showed that the mean glycerate content in conifer leaves was lower than that in angiosperm leaves. We performed experiments where [13 C]-serine was fed to detached shoots of a conifer (Cryptomeria japonica), via the transpiration stream, and compared the labeling patterns of photorespiratory metabolites with those of an angiosperm tree (Populus nigra), because glycerate is produced from serine via hydroxypyruvate in peroxisomes. In P. nigra, hydroxypyruvate, glycerate and glycine were labeled with 13 C, whereas in C. japonica, glycolate and a non-canonical photorespiratory metabolite, formate, were also labeled, suggesting that an H2 O2 -mediated non-enzymatic decarboxylation (NED) reaction occurs in C. japonica. We analyzed changes in the metabolite contents of leaves kept in the dark and leaves exposed to illuminated photorespiration-promoting conditions: a positive relationship between formate and serine levels in C. japonica implied that the active C1 -metabolism pathway synthesizes serine from formate. Leaf gas exchange analyses revealed that CO2 produced through NED was recaptured by chloroplasts. Database analysis of the peroxisomal targeting signal motifs of an H2 O2 -scavenging enzyme, catalase, derived from various species, including nine coniferous species, as well as analyses of peroxisomal fractions isolated from C. japonica and P. nigra leaves indicated that conifer peroxisomes had less catalase activity. These results suggest that NED and the subsequent C1 metabolism are involved in the photorespiratory pathway of conifer leaves, where peroxisomes have intrinsically low catalase activity.
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Affiliation(s)
- Shin-Ichi Miyazawa
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute (FFPRI), 1 Matsunosato, Tsukuba, Japan
| | - Tokuko Ujino-Ihara
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute (FFPRI), 1 Matsunosato, Tsukuba, Japan
| | - Takafumi Miyama
- Department of Disaster Prevention, Meteorology and Hydrology, Forestry and Forest Products Research Institute (FFPRI), 1 Matsunosato, Tsukuba, Japan
| | - Ko Tahara
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute (FFPRI), 1 Matsunosato, Tsukuba, Japan
| | - Hiroyuki Tobita
- Department of Plant Ecology, Forestry and Forest Products Research Institute (FFPRI), 1 Matsunosato, Tsukuba, Japan
| | - Yuji Suzuki
- Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Japan
| | - Mitsuru Nishiguchi
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute (FFPRI), 1 Matsunosato, Tsukuba, Japan
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3
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Mano S, Hayashi Y, Hikino K, Otomo M, Kanai M, Nishimura M. Ubiquitin-conjugating activity by PEX4 is required for efficient protein transport to peroxisomes in Arabidopsis thaliana. J Biol Chem 2022; 298:102038. [PMID: 35595097 PMCID: PMC9190015 DOI: 10.1016/j.jbc.2022.102038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 11/08/2022] Open
Abstract
Protein transport to peroxisomes requires various proteins, such as receptors in the cytosol and components of the transport machinery on peroxisomal membranes. The Arabidopsis apem (aberrant peroxisome morphology) mutant apem7 shows decreased efficiency of peroxisome targeting signal 1–dependent protein transport to peroxisomes. In apem7 mutants, peroxisome targeting signal 2–dependent protein transport is also disturbed, and plant growth is repressed. The APEM7 gene encodes a protein homologous to peroxin 4 (PEX4), which belongs to the ubiquitin-conjugating (UBC) protein family; however, the UBC activity of Arabidopsis PEX4 remains to be investigated. Here, we show using electron microscopy and immunoblot analysis using specific PEX4 antibodies and in vitro transcription/translation assay that PEX4 localizes to peroxisomal membranes and possesses UBC activity. We found that the substitution of proline with leucine by apem7 mutation alters ubiquitination of PEX4. Furthermore, substitution of the active-site cysteine residue at position 90 in PEX4, which was predicted to be a ubiquitin-conjugation site, with alanine did not restore the apem7 phenotype. Taken together, these findings indicate that abnormal ubiquitination in the apem7 mutant alters ubiquitin signaling during the process of protein transport, suggesting that the UBC activity of PEX4 is indispensable for efficient protein transport to peroxisomes.
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Affiliation(s)
- Shoji Mano
- Department of Cell Biology, National Institute for Basic Biology, Myodaiji, Okazaki, Japan; Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Myodaiji, Okazaki, Japan.
| | - Yasuko Hayashi
- Graduate School of Science and Technology, Niigata University, Ikarashi, Niigata, Japan
| | - Kazumi Hikino
- Department of Cell Biology, National Institute for Basic Biology, Myodaiji, Okazaki, Japan
| | - Masayoshi Otomo
- Graduate School of Science and Technology, Niigata University, Ikarashi, Niigata, Japan
| | - Masatake Kanai
- Department of Cell Biology, National Institute for Basic Biology, Myodaiji, Okazaki, Japan
| | - Mikio Nishimura
- Department of Cell Biology, National Institute for Basic Biology, Myodaiji, Okazaki, Japan
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4
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Tanaka M, Takahashi R, Hamada A, Terai Y, Ogawa T, Sawa Y, Ishikawa T, Maruta T. Distribution and Functions of Monodehydroascorbate Reductases in Plants: Comprehensive Reverse Genetic Analysis of Arabidopsis thaliana Enzymes. Antioxidants (Basel) 2021; 10:antiox10111726. [PMID: 34829597 PMCID: PMC8615211 DOI: 10.3390/antiox10111726] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/22/2021] [Accepted: 10/27/2021] [Indexed: 11/16/2022] Open
Abstract
Monodehydroascorbate reductase (MDAR) is an enzyme involved in ascorbate recycling. Arabidopsis thaliana has five MDAR genes that encode two cytosolic, one cytosolic/peroxisomal, one peroxisomal membrane-attached, and one chloroplastic/mitochondrial isoform. In contrast, tomato plants possess only three enzymes, lacking the cytosol-specific enzymes. Thus, the number and distribution of MDAR isoforms differ according to plant species. Moreover, the physiological significance of MDARs remains poorly understood. In this study, we classify plant MDARs into three classes: class I, chloroplastic/mitochondrial enzymes; class II, peroxisomal membrane-attached enzymes; and class III, cytosolic/peroxisomal enzymes. The cytosol-specific isoforms form a subclass of class III and are conserved only in Brassicaceae plants. With some exceptions, all land plants and a charophyte algae, Klebsormidium flaccidum, contain all three classes. Using reverse genetic analysis of Arabidopsis thaliana mutants lacking one or more isoforms, we provide new insight into the roles of MDARs; for example, (1) the lack of two isoforms in a specific combination results in lethality, and (2) the role of MDARs in ascorbate redox regulation in leaves can be largely compensated by other systems. Based on these findings, we discuss the distribution and function of MDAR isoforms in land plants and their cooperation with other recycling systems.
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Affiliation(s)
- Mio Tanaka
- Graduate School of Natural Science and Technology, Shimane University, 1060 Nishikawatsu, Matsue 690-8504, Shimane, Japan; (M.T.); (A.H.); (T.O.); (T.I.)
- Department of Life Science and Biotechnology, Faculty of Life and Environmental Science, Shimane University, 1060 Nishikawatsu, Matsue 690-8504, Shimane, Japan; (R.T.); (Y.T.); (Y.S.)
| | - Ryuki Takahashi
- Department of Life Science and Biotechnology, Faculty of Life and Environmental Science, Shimane University, 1060 Nishikawatsu, Matsue 690-8504, Shimane, Japan; (R.T.); (Y.T.); (Y.S.)
| | - Akane Hamada
- Graduate School of Natural Science and Technology, Shimane University, 1060 Nishikawatsu, Matsue 690-8504, Shimane, Japan; (M.T.); (A.H.); (T.O.); (T.I.)
- Department of Life Science and Biotechnology, Faculty of Life and Environmental Science, Shimane University, 1060 Nishikawatsu, Matsue 690-8504, Shimane, Japan; (R.T.); (Y.T.); (Y.S.)
| | - Yusuke Terai
- Department of Life Science and Biotechnology, Faculty of Life and Environmental Science, Shimane University, 1060 Nishikawatsu, Matsue 690-8504, Shimane, Japan; (R.T.); (Y.T.); (Y.S.)
| | - Takahisa Ogawa
- Graduate School of Natural Science and Technology, Shimane University, 1060 Nishikawatsu, Matsue 690-8504, Shimane, Japan; (M.T.); (A.H.); (T.O.); (T.I.)
- Department of Life Science and Biotechnology, Faculty of Life and Environmental Science, Shimane University, 1060 Nishikawatsu, Matsue 690-8504, Shimane, Japan; (R.T.); (Y.T.); (Y.S.)
- Institute of Agricultural and Life Sciences, Academic Assembly, Shimane University, 1060 Nishikawatsu, Matsue 690-8504, Shimane, Japan
| | - Yoshihiro Sawa
- Department of Life Science and Biotechnology, Faculty of Life and Environmental Science, Shimane University, 1060 Nishikawatsu, Matsue 690-8504, Shimane, Japan; (R.T.); (Y.T.); (Y.S.)
| | - Takahiro Ishikawa
- Graduate School of Natural Science and Technology, Shimane University, 1060 Nishikawatsu, Matsue 690-8504, Shimane, Japan; (M.T.); (A.H.); (T.O.); (T.I.)
- Department of Life Science and Biotechnology, Faculty of Life and Environmental Science, Shimane University, 1060 Nishikawatsu, Matsue 690-8504, Shimane, Japan; (R.T.); (Y.T.); (Y.S.)
- Institute of Agricultural and Life Sciences, Academic Assembly, Shimane University, 1060 Nishikawatsu, Matsue 690-8504, Shimane, Japan
| | - Takanori Maruta
- Graduate School of Natural Science and Technology, Shimane University, 1060 Nishikawatsu, Matsue 690-8504, Shimane, Japan; (M.T.); (A.H.); (T.O.); (T.I.)
- Department of Life Science and Biotechnology, Faculty of Life and Environmental Science, Shimane University, 1060 Nishikawatsu, Matsue 690-8504, Shimane, Japan; (R.T.); (Y.T.); (Y.S.)
- Institute of Agricultural and Life Sciences, Academic Assembly, Shimane University, 1060 Nishikawatsu, Matsue 690-8504, Shimane, Japan
- Correspondence: ; Tel.: +81-882-32-6585
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5
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Lim SL, Voon CP, Guan X, Yang Y, Gardeström P, Lim BL. In planta study of photosynthesis and photorespiration using NADPH and NADH/NAD + fluorescent protein sensors. Nat Commun 2020; 11:3238. [PMID: 32591540 PMCID: PMC7320160 DOI: 10.1038/s41467-020-17056-0] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 06/09/2020] [Indexed: 12/21/2022] Open
Abstract
The challenge of monitoring in planta dynamic changes of NADP(H) and NAD(H) redox states at the subcellular level is considered a major obstacle in plant bioenergetics studies. Here, we introduced two circularly permuted yellow fluorescent protein sensors, iNAP and SoNar, into Arabidopsis thaliana to monitor the dynamic changes in NADPH and the NADH/NAD+ ratio. In the light, photosynthesis and photorespiration are linked to the redox states of NAD(P)H and NAD(P) pools in several subcellular compartments connected by the malate-OAA shuttles. We show that the photosynthetic increases in stromal NADPH and NADH/NAD+ ratio, but not ATP, disappear when glycine decarboxylation is inhibited. These observations highlight the complex interplay between chloroplasts and mitochondria during photosynthesis and support the suggestions that, under normal conditions, photorespiration supplies a large amount of NADH to mitochondria, exceeding its NADH-dissipating capacity, and the surplus NADH is exported from the mitochondria to the cytosol through the malate-OAA shuttle.
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Affiliation(s)
- Shey-Li Lim
- School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong, China
| | - Chia Pao Voon
- School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong, China
| | - Xiaoqian Guan
- School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong, China
| | - Yi Yang
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China
| | - Per Gardeström
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87, Umeå, Sweden
| | - Boon Leong Lim
- School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong, China.
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China.
- HKU Shenzhen Institute of Research and Innovation, Shenzhen, China.
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6
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You X, Zhu S, Zhang W, Zhang J, Wang C, Jing R, Chen W, Wu H, Cai Y, Feng Z, Hu J, Yan H, Kong F, Zhang H, Zheng M, Ren Y, Lin Q, Cheng Z, Zhang X, Lei C, Jiang L, Wang H, Wan J. OsPEX5 regulates rice spikelet development through modulating jasmonic acid biosynthesis. THE NEW PHYTOLOGIST 2019; 224:712-724. [PMID: 31264225 DOI: 10.1111/nph.16037] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 06/23/2019] [Indexed: 06/09/2023]
Abstract
Spikelet is the primary reproductive structure and a critical determinant of grain yield in rice. The molecular mechanisms regulating rice spikelet development still remain largely unclear. Here, we report that mutations in OsPEX5, which encodes a peroxisomal targeting sequence 1 (PTS1) receptor protein, cause abnormal spikelet morphology. We show that OsPEX5 can physically interact with OsOPR7, an enzyme involved in jasmonic acid (JA) biosynthesis and is required for its import into peroxisome. Similar to Ospex5 mutant, the knockout mutant of OsOPR7 generated via CRISPR-Cas9 technology has reduced levels of endogenous JA and also displays an abnormal spikelet phenotype. Application of exogenous JA can partially rescue the abnormal spikelet phenotype of Ospex5 and Osopr7. Furthermore, we show that OsMYC2 directly binds to the promoters of OsMADS1, OsMADS7 and OsMADS14 to activate their expression, and subsequently regulate spikelet development. Our results suggest that OsPEX5 plays a critical role in regulating spikelet development through mediating peroxisomal import of OsOPR7, therefore providing new insights into regulation of JA biosynthesis in plants and expanding our understanding of the biological role of JA in regulating rice reproduction.
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Affiliation(s)
- Xiaoman You
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shanshan Zhu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agriculture Sciences, Beijing, 100081, China
| | - Wenwei Zhang
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jie Zhang
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chunming Wang
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ruonan Jing
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weiwei Chen
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agriculture Sciences, Beijing, 100081, China
| | - Hongming Wu
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yue Cai
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhiming Feng
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jinlong Hu
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Haigang Yan
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fei Kong
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Huan Zhang
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ming Zheng
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yulong Ren
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agriculture Sciences, Beijing, 100081, China
| | - Qibing Lin
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agriculture Sciences, Beijing, 100081, China
| | - Zhijun Cheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agriculture Sciences, Beijing, 100081, China
| | - Xin Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agriculture Sciences, Beijing, 100081, China
| | - Cailin Lei
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agriculture Sciences, Beijing, 100081, China
| | - Ling Jiang
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Haiyang Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agriculture Sciences, Beijing, 100081, China
| | - Jianmin Wan
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agriculture Sciences, Beijing, 100081, China
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7
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Abstract
Our knowledge of the proteome of plant peroxisomes is far from being complete, and the functional complexity and plasticity of this cell organelle are amazingly high particularly in plants, as exemplified by the model species Arabidopsis thaliana. Plant-specific peroxisome functions that have been uncovered only recently include, for instance, the participation of peroxisomes in phylloquinone and biotin biosynthesis. Experimental proteome studies have been proved very successful in defining the proteome of Arabidopsis peroxisomes but this approach also faces significant challenges and limitations. Complementary to experimental approaches, computational methods have emerged as important powerful tools to define the proteome of soluble matrix proteins of plant peroxisomes. Compared to other cell organelles such as mitochondria, plastids and the ER, the simultaneous operation of two major import pathways for soluble proteins in peroxisomes is rather atypical. Novel machine learning prediction approaches have been developed for peroxisome targeting signals type 1 (PTS1) and revealed high sensitivity and specificity, as validated by in vivo subcellular targeting analyses in diverse transient plant expression systems. Accordingly, the algorithms allow the correct prediction of many novel peroxisome-targeted proteins from plant genome sequences and the discovery of additional organelle functions. In contrast, the prediction of PTS2 proteins largely remains restricted to genome searches by conserved patterns contrary to more advanced machine learning methods. Here, we summarize and discuss the capabilities and accuracies of available prediction algorithms for PTS1 and PTS2 carrying proteins.
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Affiliation(s)
- Sigrun Reumann
- Department of Plant Biochemistry and Infection Biology, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr. 18, 22609, Hamburg, Germany.
| | - Gopal Chowdhary
- KIIT School of Biotechnology, Campus XI, KIIT University, Bhubaneswar, 751024, India
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8
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Cao S, Li H, Yao X, Li L, Jiang L, Zhang Q, Zhang J, Liu D, Lu H. Enzymatic characterization of two acetyl-CoA synthetase genes from Populus trichocarpa. SPRINGERPLUS 2016; 5:818. [PMID: 27390658 PMCID: PMC4916118 DOI: 10.1186/s40064-016-2532-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 06/07/2016] [Indexed: 11/10/2022]
Abstract
The acetyl-CoA synthetase (ACS) family is a subfamily of adenylate-forming enzymes, which has a close evolutionary relationship with the 4-coumarate:CoA ligase (4CL) family. In this study, two ACS genes were cloned from Populus trichocarpa and were named PtrACS1 and PtrACS2. Bioinformatics characterization of PtrACS1 and PtrACS2 showed that they contained the key ACS residues and a putative peroxisome targeting sequence 1 (PTS1) at the end of the C-terminal sequence. Real-time PCR results showed that PtrACS1 and PtrACS2 were expressed in the phloem, xylem, leaves, and roots of one-year-old P. trichocarpa, but were expressed primarily in the leaves. The ACS enzyme activity was higher in leaves than other tissues in P. trichocarpa. Two overexpressed recombinant proteins showed no catalytic activity toward the substrates of 4CL, but did have notable catalytic activity toward sodium acetate and substrates of ACS. The relative activities of PtrACS1 and PtrACS2 were 194.16 ± 11.23 and 422.25 ± 21.69 μM min(-1) mg(-1), respectively. The K m and V max of PtrACS1 were 0.25 mM and 698.85 μM min(-1) mg(-1), while those for PtrACS2 were 0.72 mM and 245.96 μM min(-1) mg(-1), respectively. Our results revealed that both proteins belong to the ACS family, and provide a theoretical foundation for the identification and functional analysis of members of the adenylate-forming enzyme superfamily.
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Affiliation(s)
- Shan Cao
- College of Life Sciences and Biotechnology, Beijing Forestry University, No. 35 Qinghua East Road, Haidian District, Beijing, 100083 People's Republic of China.,National Engineering Laboratory for Tree Breeding, Beijing, 100083 People's Republic of China
| | - Hui Li
- College of Life Sciences and Biotechnology, Beijing Forestry University, No. 35 Qinghua East Road, Haidian District, Beijing, 100083 People's Republic of China.,National Engineering Laboratory for Tree Breeding, Beijing, 100083 People's Republic of China
| | - Xiaoyun Yao
- College of Life Sciences and Biotechnology, Beijing Forestry University, No. 35 Qinghua East Road, Haidian District, Beijing, 100083 People's Republic of China.,National Engineering Laboratory for Tree Breeding, Beijing, 100083 People's Republic of China
| | - Lihong Li
- College of Life Sciences and Biotechnology, Beijing Forestry University, No. 35 Qinghua East Road, Haidian District, Beijing, 100083 People's Republic of China.,National Engineering Laboratory for Tree Breeding, Beijing, 100083 People's Republic of China
| | - Luyao Jiang
- College of Life Sciences and Biotechnology, Beijing Forestry University, No. 35 Qinghua East Road, Haidian District, Beijing, 100083 People's Republic of China.,National Engineering Laboratory for Tree Breeding, Beijing, 100083 People's Republic of China
| | - Qiang Zhang
- College of Life Sciences and Biotechnology, Beijing Forestry University, No. 35 Qinghua East Road, Haidian District, Beijing, 100083 People's Republic of China.,National Engineering Laboratory for Tree Breeding, Beijing, 100083 People's Republic of China
| | - Jiaxue Zhang
- College of Life Sciences and Biotechnology, Beijing Forestry University, No. 35 Qinghua East Road, Haidian District, Beijing, 100083 People's Republic of China.,National Engineering Laboratory for Tree Breeding, Beijing, 100083 People's Republic of China
| | - Di Liu
- College of Life Sciences and Biotechnology, Beijing Forestry University, No. 35 Qinghua East Road, Haidian District, Beijing, 100083 People's Republic of China
| | - Hai Lu
- College of Life Sciences and Biotechnology, Beijing Forestry University, No. 35 Qinghua East Road, Haidian District, Beijing, 100083 People's Republic of China.,National Engineering Laboratory for Tree Breeding, Beijing, 100083 People's Republic of China
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9
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Reumann S, Chowdhary G, Lingner T. Characterization, prediction and evolution of plant peroxisomal targeting signals type 1 (PTS1s). BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1863:790-803. [PMID: 26772785 DOI: 10.1016/j.bbamcr.2016.01.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 01/01/2016] [Accepted: 01/04/2016] [Indexed: 12/22/2022]
Abstract
Our knowledge of the proteome of plant peroxisomes and their functional plasticity is far from being complete, primarily due to major technical challenges in experimental proteome research of the fragile cell organelle. Several unexpected novel plant peroxisome functions, for instance in biotin and phylloquinone biosynthesis, have been uncovered recently. Nevertheless, very few regulatory and membrane proteins of plant peroxisomes have been identified and functionally described up to now. To define the matrix proteome of plant peroxisomes, computational methods have emerged as important powerful tools. Novel prediction approaches of high sensitivity and specificity have been developed for peroxisome targeting signals type 1 (PTS1) and have been validated by in vivo subcellular targeting analyses and thermodynamic binding studies with the cytosolic receptor, PEX5. Accordingly, the algorithms allow the correct prediction of many novel peroxisome-targeted proteins from plant genome sequences and the discovery of additional organelle functions. In this review, we provide an overview of methodologies, capabilities and accuracies of available prediction algorithms for PTS1 carrying proteins. We also summarize and discuss recent quantitative, structural and mechanistic information of the interaction of PEX5 with PTS1 carrying proteins in relation to in vivo import efficiency. With this knowledge, we develop a model of how proteins likely evolved peroxisomal targeting signals in the past and still nowadays, in which order the two import pathways might have evolved in the ancient eukaryotic cell, and how the secondary loss of the PTS2 pathway probably happened in specific organismal groups.
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Affiliation(s)
- S Reumann
- Department of Plant Biochemistry and Infection Biology, Biocentre Klein Flottbek, University of Hamburg, D-22609 Hamburg, Germany; Centre for Organelle Research, University of Stavanger, N-4036 Stavanger, Norway.
| | - G Chowdhary
- Centre for Organelle Research, University of Stavanger, N-4036 Stavanger, Norway; KIIT School of Biotechnology, Campus XI, KIIT University, I-751024 Bhubaneswar, India.
| | - T Lingner
- Department of Bioinformatics, Institute for Microbiology and Genetics, D-37077 Goettingen, Germany.
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10
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Li J, Liu J, Wang G, Cha JY, Li G, Chen S, Li Z, Guo J, Zhang C, Yang Y, Kim WY, Yun DJ, Schumaker KS, Chen Z, Guo Y. A chaperone function of NO CATALASE ACTIVITY1 is required to maintain catalase activity and for multiple stress responses in Arabidopsis. THE PLANT CELL 2015; 27:908-25. [PMID: 25700484 PMCID: PMC4558663 DOI: 10.1105/tpc.114.135095] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 01/20/2015] [Accepted: 02/04/2015] [Indexed: 05/19/2023]
Abstract
Catalases are key regulators of reactive oxygen species homeostasis in plant cells. However, the regulation of catalase activity is not well understood. In this study, we isolated an Arabidopsis thaliana mutant, no catalase activity1-3 (nca1-3) that is hypersensitive to many abiotic stress treatments. The mutated gene was identified by map-based cloning as NCA1, which encodes a protein containing an N-terminal RING-finger domain and a C-terminal tetratricopeptide repeat-like helical domain. NCA1 interacts with and increases catalase activity maximally in a 240-kD complex in planta. In vitro, NCA1 interacts with CATALASE2 (CAT2) in a 1:1 molar ratio, and the NCA1 C terminus is essential for this interaction. CAT2 activity increased 10-fold in the presence of NCA1, and zinc ion binding of the NCA1 N terminus is required for this increase. NCA1 has chaperone protein activity that may maintain the folding of catalase in a functional state. NCA1 is a cytosol-located protein. Expression of NCA1 in the mitochondrion of the nca1-3 mutant does not rescue the abiotic stress phenotypes of the mutant, while expression in the cytosol or peroxisome does. Our results suggest that NCA1 is essential for catalase activity.
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Affiliation(s)
- Jing Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Juntao Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Guoqiang Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Joon-Yung Cha
- Division of Applied Life Sciences (BK21 Plus Program), Gyeongsang National University, Jinju City 660-701, Korea
| | - Guannan Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - She Chen
- National Institute of Biological Sciences, Beijing 102206, China
| | - Zhen Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jinghua Guo
- College of Life Science, Beijing Normal University, Beijing 100875, China
| | - Caiguo Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yongqing Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Woe-Yeon Kim
- Division of Applied Life Sciences (BK21 Plus Program), Gyeongsang National University, Jinju City 660-701, Korea
| | - Dae-Jin Yun
- Division of Applied Life Sciences (BK21 Plus Program), Gyeongsang National University, Jinju City 660-701, Korea
| | - Karen S Schumaker
- School of Plant Sciences, University of Arizona, Tucson, Arizona 85721
| | - Zhongzhou Chen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yan Guo
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China National Center for Plant Gene Research, Beijing 100193, China
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11
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Gnanasambandam A, Anderson DJ, Mills E, Brumbley SM. Heterologous C-terminal signals effectively target fluorescent fusion proteins to leaf peroxisomes in diverse plant species. JOURNAL OF PLANT PHYSIOLOGY 2012; 169:830-833. [PMID: 22386008 DOI: 10.1016/j.jplph.2012.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 12/06/2011] [Accepted: 01/11/2012] [Indexed: 05/31/2023]
Abstract
Peroxisomes are functionally diverse organelles that are wholly dependent on import of nuclear-encoded proteins. The signals that direct proteins into these organelles are either found at the C-terminus (type 1 peroxisomal targeting signal; PTS1) or N-terminus (type 2 peroxisomal targeting signal; PTS2) of the protein. Based on a limited number of tests in heterologous systems, PTS1 signals appear to be conserved across species. To further test the generality of this conclusion and to establish the extent to which the PTS1 signals can be relied on for biotechnological purposes across species, we tested two PTS1 signals for their ability to target fluorescent proteins in diverse plant species. Transient assays following microprojectile bombardment showed that the six amino acid PTS1 sequence (RAVARL) from spinach glycolate oxidase effectively targets green fluorescent fusion protein to the leaf peroxisomes in all 20 crops tested, including four monocots (sugarcane, wheat, corn and onion) and 16 dicots (carrot, cucumber, broccoli, tomato, lettuce, turnip, radish, cauliflower, cabbage, capsicum, celery, tobacco, petunia, beetroot, eggplant and coriander). Similarly, results indicated that the 10 amino acid PTS1 sequence (IHHPRELSRL) from pumpkin malate synthase effectively targets red fluorescent fusion protein to the leaf peroxisomes in all four crops tested including monocot (sugarcane) and dicot (cabbage, celery and pumpkin) species. These signal sequences should be useful metabolic engineering tools to direct recombinant proteins to the leaf peroxisomes in diverse plant species of biotechnological interest.
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12
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Kamigaki A, Kondo M, Mano S, Hayashi M, Nishimura M. Suppression of peroxisome biogenesis factor 10 reduces cuticular wax accumulation by disrupting the ER network in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2009; 50:2034-46. [PMID: 19892830 DOI: 10.1093/pcp/pcp152] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Peroxisome biogenesis factor 10 (PEX10) is a component of the peroxisomal matrix protein import machinery. To analyze the physiological function of PEX10, we used transgenic AtPEX10i Arabidopsis plants that had suppressed expression of the PEX10 gene due to RNA interference. AtPEX10i plants had patches of paleness on leaves, and abnormal floral organs that were typical of cuticular wax-deficient mutants. Quantitative analysis of cuticular wax revealed that the amount of wax in AtPEX10i plants was indeed lower than that in control plants. This result was confirmed by toluidine blue staining and scanning electron microscopic analysis of AtPEX10i. The CER1, CER4, WAX2 and SHN1 genes are known to be responsible for wax biosynthesis in Arabidopsis. Of these, CER1, CER4 and WAX2 were found to be localized on the endoplasmic reticulum (ER). In AtPEX10i plants, the expression of these genes was down-regulated, and CER1, CER4 and WAX2 were mislocalized to the cytosol. We also found that AtPEX10i plants had defects in ER morphology. Based on these results, we propose that PEX10 is essential for the maintenance of ER morphology and for the expression of CER1, CER4, WAX2 and SHN1 genes, which contribute to the biosynthesis of cuticular wax.
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Affiliation(s)
- Akane Kamigaki
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, 444-8585, Japan
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13
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Kaur N, Reumann S, Hu J. Peroxisome biogenesis and function. THE ARABIDOPSIS BOOK 2009; 7:e0123. [PMID: 22303249 PMCID: PMC3243405 DOI: 10.1199/tab.0123] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Peroxisomes are small and single membrane-delimited organelles that execute numerous metabolic reactions and have pivotal roles in plant growth and development. In recent years, forward and reverse genetic studies along with biochemical and cell biological analyses in Arabidopsis have enabled researchers to identify many peroxisome proteins and elucidate their functions. This review focuses on the advances in our understanding of peroxisome biogenesis and metabolism, and further explores the contribution of large-scale analysis, such as in sillco predictions and proteomics, in augmenting our knowledge of peroxisome function In Arabidopsis.
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Affiliation(s)
| | - Sigrun Reumann
- Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, N-4036 Stavanger, Norway
| | - Jianping Hu
- MSU-DOE Plant Research Laboratory and
- Plant Biology Department, Michigan State University, East Lansing, MI 48824
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14
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Reumann S, Quan S, Aung K, Yang P, Manandhar-Shrestha K, Holbrook D, Linka N, Switzenberg R, Wilkerson CG, Weber APM, Olsen LJ, Hu J. In-depth proteome analysis of Arabidopsis leaf peroxisomes combined with in vivo subcellular targeting verification indicates novel metabolic and regulatory functions of peroxisomes. PLANT PHYSIOLOGY 2009; 150:125-43. [PMID: 19329564 PMCID: PMC2675712 DOI: 10.1104/pp.109.137703] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2009] [Accepted: 03/23/2009] [Indexed: 05/18/2023]
Abstract
Peroxisomes are metabolically diverse organelles with essential roles in plant development. The major protein constituents of plant peroxisomes are well characterized, whereas only a few low-abundance and regulatory proteins have been reported to date. We performed an in-depth proteome analysis of Arabidopsis (Arabidopsis thaliana) leaf peroxisomes using one-dimensional gel electrophoresis followed by liquid chromatography and tandem mass spectrometry. We detected 65 established plant peroxisomal proteins, 30 proteins whose association with Arabidopsis peroxisomes had been previously demonstrated only by proteomic data, and 55 putative novel proteins of peroxisomes. We subsequently tested the subcellular targeting of yellow fluorescent protein fusions for selected proteins and confirmed the peroxisomal localization for 12 proteins containing predicted peroxisome targeting signals type 1 or 2 (PTS1/2), three proteins carrying PTS-related peptides, and four proteins that lack conventional targeting signals. We thereby established the tripeptides SLM> and SKV> (where > indicates the stop codon) as new PTS1s and the nonapeptide RVx(5)HF as a putative new PTS2. The 19 peroxisomal proteins conclusively identified from this study potentially carry out novel metabolic and regulatory functions of peroxisomes. Thus, this study represents an important step toward defining the complete plant peroxisomal proteome.
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Affiliation(s)
- Sigrun Reumann
- Michigan State University-Department of Energy Plant Research Laboratory , Michigan State University, East Lansing, Michigan 48824, USA
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15
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Shinozaki A, Sato N, Hayashi Y. Peroxisomal targeting signals in green algae. PROTOPLASMA 2009; 235:57-66. [PMID: 19214701 DOI: 10.1007/s00709-009-0031-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2008] [Accepted: 01/05/2009] [Indexed: 05/27/2023]
Abstract
Peroxisomal enzymatic proteins contain targeting signals (PTS) to enable their import into peroxisomes. These targeting signals have been identified as PTS1 and PTS2 in mammalian, yeast, and higher plant cells; however, no PTS2-like amino acid sequences have been observed in enzymes from the genome database of Cyanidiochyzon merolae (Bangiophyceae), a primitive red algae. In studies on the evolution of PTS, it is important to know when their sequences came to be the peroxisomal targeting signals for all living organisms. To this end, we identified a number of genes in the genome database of the green algae Chlamydomonas reinhardtii, which contains amino acid sequences similar to those found in plant PTS. In order to determine whether these sequences function as PTS in green algae, we expressed modified green fluorescent proteins (GFP) fused to these putative PTS peptides under the cauliflower mosaic virus 35S promoter. To confirm whether granular structures containing GFP-PTS fusion proteins accumulated in the peroxisomes of Closterium ehrenbergii, we observed these cells after the peroxisomes were stained with 3, 3'-diaminobenzidine. Our results confirm that the GFP-PTS fusion proteins indeed accumulated in the peroxisomes of these green algae. These findings suggest that the peroxisomal transport system for PTS1 and PTS2 is conserved in green algal cells and that our fusion proteins can be used to visualize peroxisomes in live cells.
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Affiliation(s)
- Akiko Shinozaki
- Graduate School of Science and Technology, Niigata University, 8050 Ikarashi, Ninotyou, Niigata city, Niigata, 950-2181, Japan
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16
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Ahumada I, Cairó A, Hemmerlin A, González V, Pateraki I, Bach TJ, Rodríguez-Concepción M, Campos N, Boronat A. Characterisation of the gene family encoding acetoacetyl-CoA thiolase in Arabidopsis. FUNCTIONAL PLANT BIOLOGY : FPB 2008; 35:1100-1111. [PMID: 32688858 DOI: 10.1071/fp08012] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2008] [Accepted: 07/30/2008] [Indexed: 05/26/2023]
Abstract
Thiolases are ubiquitous enzymes involved in many essential biochemical processes. Biosynthetic thiolases, also known as acetoacetyl-CoA thiolases (AACT), catalyse a reversible Claisen-type condensation of two acetyl-CoA molecules to form acetoacetyl-CoA. Here, we report the characterisation of two genes from Arabidopsis thaliana L., ACT1 and ACT2, which encode two closely related AACT isoforms (AACT1 and AACT2, respectively). Transient expression of constructs encoding AACT1 and AACT2 fused to GFP revealed that the two proteins show a different subcellular localisation. While AACT1 is found in peroxisomes, AACT2 localises in the cytosol and the nucleus. The peroxisomal localisation of AACT1 depends on the presence of a C-terminal peroxisomal targeting sequence (PTS1) motif (Ser-Ala-Leu) not previously found in other organisms. ACT1 and ACT2 genes are also differentially expressed. Whereas ACT2 is expressed at relatively high level in all plant tissues, the expression of ACT1 is restricted to roots and inflorescences and its transcript is present at very low levels. The obtained results are in agreement with the involvement of AACT2 in catalysing the first step of the mevalonate pathway. The metabolic function of AACT1 is not clear at present, although its particular peroxisomal localisation might exclude a role in isoprenoid biosynthesis.
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Affiliation(s)
- Iván Ahumada
- Departament de Bioquímica i Biologia Molecular, Facultat de Biologia, Universitat de Barcelona, Avda. Diagonal 645, 08028 Barcelona, Spain
| | - Albert Cairó
- Departament de Bioquímica i Biologia Molecular, Facultat de Biologia, Universitat de Barcelona, Avda. Diagonal 645, 08028 Barcelona, Spain
| | - Andréa Hemmerlin
- Centre National de la Recherche Scientifique, UPR 2357, Institut de Biologie Moléculaire des Plantes, 28 rue Goethe, 67083 Strasbourg Cedex, France
| | - Víctor González
- Departament de Bioquímica i Biologia Molecular, Facultat de Biologia, Universitat de Barcelona, Avda. Diagonal 645, 08028 Barcelona, Spain
| | - Irene Pateraki
- Departament de Bioquímica i Biologia Molecular, Facultat de Biologia, Universitat de Barcelona, Avda. Diagonal 645, 08028 Barcelona, Spain
| | - Thomas J Bach
- Centre National de la Recherche Scientifique, UPR 2357, Institut de Biologie Moléculaire des Plantes, 28 rue Goethe, 67083 Strasbourg Cedex, France
| | - Manuel Rodríguez-Concepción
- Departament de Bioquímica i Biologia Molecular, Facultat de Biologia, Universitat de Barcelona, Avda. Diagonal 645, 08028 Barcelona, Spain
| | - Narciso Campos
- Departament de Bioquímica i Biologia Molecular, Facultat de Biologia, Universitat de Barcelona, Avda. Diagonal 645, 08028 Barcelona, Spain
| | - Albert Boronat
- Departament de Bioquímica i Biologia Molecular, Facultat de Biologia, Universitat de Barcelona, Avda. Diagonal 645, 08028 Barcelona, Spain
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17
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Kamada-Nobusada T, Hayashi M, Fukazawa M, Sakakibara H, Nishimura M. A putative peroxisomal polyamine oxidase, AtPAO4, is involved in polyamine catabolism in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2008; 49:1272-82. [PMID: 18703589 DOI: 10.1093/pcp/pcn114] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
We characterized three Arabidopsis polyamine oxidase genes, AtPAO2, AtPAO3 and AtPAO4. Transient expression of these genes as monomeric red fluorescent protein fusion proteins in Arabidopsis root cells revealed that all are peroxisomal proteins. Quantitative analysis of their transcripts in various organs suggested that AtPAO4 is the major isoform in root peroxisomes. Analysis of recombinant AtPAO4 protein indicated that it is a flavoprotein that catalyzed the oxidative conversion of spermine to spermidine. AtPAO4-deficient mutants established by using T-DNA insertion and RNA interference techniques had markedly increased spermine and decreased spermidine levels in the roots. These results suggest that AtPAO4 is a root peroxisomal polyamine oxidase that participates in polyamine catabolism. Microarray analysis showed that AtPAO4 deficiency induced alterations in the expression of genes related to the drought stress response and flavonoid biosynthesis.
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Affiliation(s)
- Tomoe Kamada-Nobusada
- Division of Cell Mechanisms, Department of Cell Biology, National Institute for Basic Biology, Okazaki, 444-8585 Japan
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18
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Arai Y, Hayashi M, Nishimura M. Proteomic analysis of highly purified peroxisomes from etiolated soybean cotyledons. PLANT & CELL PHYSIOLOGY 2008; 49:526-39. [PMID: 18281324 DOI: 10.1093/pcp/pcn027] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
To identify previously unknown peroxisomal proteins, we established an optimized method for isolating highly purified peroxisomes from etiolated soybean cotyledons using Percoll density gradient centrifugation followed by iodixanol density gradient centrifugation. Proteins in highly purified peroxisomes were separated by two-dimensional PAGE. We performed peptide mass fingerprinting of proteins separated in the gel with matrix-assisted laser desorption ionization time-of-flight mass spectrometry and used the peptide mass fingerprints to search a non-redundant soybean expressed sequence tag database. We succeeded in assigning 92 proteins to 70 sequences in the database. Among them, proteins encoded by 30 sequences were judged to be located in peroxisomes. These included enzymes for fatty acid beta-oxidation, the glyoxylate cycle, photorespiratory glycolate metabolism, stress response and metabolite transport. We also show experimental evidence that plant peroxisomes contain a short-chain dehydrogenase/reductase family protein, enoyl-CoA hydratase/isomerase family protein, 3-hydroxyacyl-CoA dehydrogenase-like protein and a voltage-dependent anion-selective channel protein.
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Affiliation(s)
- Yuko Arai
- Department of Cell Biology, National Institute for Basic Biology, Okazaki 444-8585 Japan
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19
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Ma C, Reumann S. Improved prediction of peroxisomal PTS1 proteins from genome sequences based on experimental subcellular targeting analyses as exemplified for protein kinases from Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2008; 59:3767-79. [PMID: 18836189 DOI: 10.1093/jxb/ern221] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Due to current experimental limitations in peroxisome proteome research, the identification of low-abundance regulatory proteins such as protein kinases largely relies on computational protein prediction. To test and improve the identification of regulatory proteins by such a prediction-based approach, the Arabidopsis genome was screened for genes that encode protein kinases with predicted type 1 or type 2 peroxisome targeting signals (PTS1 or PTS2). Upon transient expression in onion epidermal cells, the predicted PTS1 domains of four of the seven protein kinases re-directed the reporter protein, enhanced yellow green fluorescent (EYFP), to peroxisomes and were thus verified as functional PTS1 domains. The full-length fusions, however, remained cytosolic, suggesting that PTS1 exposure is induced by specific signals. To investigate why peroxisome targeting of three other kinases was incorrectly predicted and ultimately to improve the prediction algorithms, selected amino acid residues located upstream of PTS1 tripeptides were mutated and the effect on subcellular targeting of the reporter protein was analysed. Acidic residues in close proximity to major PTS1 tripeptides were demonstrated to inhibit protein targeting to plant peroxisomes even in the case of the prototypical PTS1 tripeptide SKL>, whereas basic residues function as essential auxiliary targeting elements in front of weak PTS1 tripeptides such as SHL>. The functional characterization of these inhibitory and essential enhancer-targeting elements allows their consideration in predictive algorithms to improve the prediction accuracy of PTS1 proteins from genome sequences.
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Affiliation(s)
- Changle Ma
- Department of Plant Biochemistry, Georg-August-University of Goettingen, Albrecht-von-Haller-Institute for Plant Sciences, Justus-von-Liebig-Weg 11, D-37077 Goettingen, Germany
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20
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Reumann S, Babujee L, Ma C, Wienkoop S, Siemsen T, Antonicelli GE, Rasche N, Lüder F, Weckwerth W, Jahn O. Proteome analysis of Arabidopsis leaf peroxisomes reveals novel targeting peptides, metabolic pathways, and defense mechanisms. THE PLANT CELL 2007; 19:3170-93. [PMID: 17951448 PMCID: PMC2174697 DOI: 10.1105/tpc.107.050989] [Citation(s) in RCA: 165] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2007] [Revised: 09/12/2007] [Accepted: 09/24/2007] [Indexed: 05/18/2023]
Abstract
We have established a protocol for the isolation of highly purified peroxisomes from mature Arabidopsis thaliana leaves and analyzed the proteome by complementary gel-based and gel-free approaches. Seventy-eight nonredundant proteins were identified, of which 42 novel proteins had previously not been associated with plant peroxisomes. Seventeen novel proteins carried predicted peroxisomal targeting signals (PTS) type 1 or type 2; 11 proteins contained PTS-related peptides. Peroxisome targeting was supported for many novel proteins by in silico analyses and confirmed for 11 representative full-length fusion proteins by fluorescence microscopy. The targeting function of predicted and unpredicted signals was investigated and SSL>, SSI>, and ASL> were established as novel functional PTS1 peptides. In contrast with the generally accepted confinement of PTS2 peptides to the N-terminal domain, the bifunctional transthyretin-like protein was demonstrated to carry internally a functional PTS2. The novel enzymes include numerous enoyl-CoA hydratases, short-chain dehydrogenases, and several enzymes involved in NADP and glutathione metabolism. Seven proteins, including beta-glucosidases and myrosinases, support the currently emerging evidence for an important role of leaf peroxisomes in defense against pathogens and herbivores. The data provide new insights into the biology of plant peroxisomes and improve the prediction accuracy of peroxisome-targeted proteins from genome sequences.
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Affiliation(s)
- Sigrun Reumann
- Department of Plant Biochemistry, Georg-August-University of Goettingen, Albrecht-von-Haller-Institute for Plant Sciences, D-37077 Goettingen, Germany.
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21
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Zolman BK, Nyberg M, Bartel B. IBR3, a novel peroxisomal acyl-CoA dehydrogenase-like protein required for indole-3-butyric acid response. PLANT MOLECULAR BIOLOGY 2007; 64:59-72. [PMID: 17277896 DOI: 10.1007/s11103-007-9134-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2006] [Accepted: 01/03/2007] [Indexed: 05/13/2023]
Abstract
Indole-3-butyric acid (IBA) is an endogenous auxin that acts in Arabidopsis primarily via its conversion to the principal auxin indole-3-acetic acid (IAA). Genetic and biochemical evidence indicates that this conversion is similar to peroxisomal fatty acid beta-oxidation, but the specific enzymes catalyzing IBA beta-oxidation have not been identified. We identified an IBA-response mutant (ibr3) with decreased responses to the inhibitory effects of IBA on root elongation or the stimulatory effects of IBA on lateral root formation. However, ibr3 mutants respond normally to other forms of auxin, including IAA. The mutant seedlings germinate and develop normally, even in the absence of sucrose, suggesting that fatty acid beta-oxidation is unaffected. Additionally, double mutants between ibr3 and acx3, which is defective in an acyl-CoA oxidase acting in fatty acid beta-oxidation, have enhanced IBA resistance, consistent with a distinct role for IBR3. Positional cloning revealed that IBR3 encodes a putative acyl-CoA dehydrogenase with a consensus peroxisomal targeting signal. Based on the singular defect of this mutant in responding to IBA, we propose that IBR3 may act directly in the oxidation of IBA to IAA.
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Affiliation(s)
- Bethany K Zolman
- Department of Biology, University of Missouri-St Louis, One University Boulevard, R223 Research Building, St Louis, MO 63121, USA.
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22
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Li Y, Cao J, Huang L, Yu X, Xiang X. BcMF13, a new reproductive organ-specific gene from Brassica rapa. ssp. chinensis, affects pollen development. Mol Biol Rep 2007; 35:207-14. [PMID: 17387632 DOI: 10.1007/s11033-007-9072-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2006] [Accepted: 02/26/2007] [Indexed: 10/23/2022]
Abstract
A transcript-derived fragment (GenBank accession number DN237920.1) accumulated in the wild-type flower buds of Chinese cabbage (Brassica campestris L. ssp. chinensis Makino, syn. B. rapa ssp. chinensis) was isolated and further investigated. The full length DNA and cDNA of the fragment were cloned by rapid amplification of cDNA ends. The gene, BcMF13, encodes a protein of 73 amino acids and is interrupted by an intron of 106 bp (GenBank accession number EF158459). Southern blot analysis revealed that BcMF13 could be a single-copy gene in the Chinese cabbage genome. Sequence blast analysis showed that BcMF13 was a new gene. In EST database, those sequences share 96-98% identity with BcMF13 cDNA all came from flower buds, microspores, anthers of Brassica, which proved BcMF13 homologs closely related to the development of male gametogenesis in Brassica. RT-PCR discovered that it is exclusively expressed in stage four and five flower buds of fertile line, strongly expressed in stamens. Successful suppression of BcMF13 gene expression by RNA antisense strategy greatly reduced the normal pollen grains, suggesting that BcMF13 was essential in pollen development in Brassica.
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Affiliation(s)
- Yanyan Li
- Lab of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, 282 Kaixuan Road, Hangzhou, 310029, China
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Hayashi M, Nishimura M. Arabidopsis thaliana--a model organism to study plant peroxisomes. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2006; 1763:1382-91. [PMID: 17005266 DOI: 10.1016/j.bbamcr.2006.08.014] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2006] [Revised: 07/28/2006] [Accepted: 08/18/2006] [Indexed: 10/24/2022]
Abstract
In higher plants, peroxisomes have been believed to play a pivotal role in three metabolic pathways, which are lipid breakdown, photorespiration and H2O2-detoxificaton. Recently, significant progress in the study of plant peroxisomes was established by forward-/reverse-genetics and post-genomic approaches using Arabidopsis thaliana, the first higher plant to have its entire genome sequenced. These studies illustrated that plant peroxisomes have more diverse functions than we previously thought. Research using Arabidopsis thaliana is improving our understanding of the function of plant peroxisomes.
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Affiliation(s)
- Makoto Hayashi
- National Institute for Basic Biology, Okazaki 444-8585, Japan
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Lee JR, Jang HH, Park JH, Jung JH, Lee SS, Park SK, Chi YH, Moon JC, Lee YM, Kim SY, Kim JY, Yun DJ, Cho MJ, Lee KO, Lee SY. Cloning of two splice variants of the rice PTS1 receptor, OsPex5pL and OsPex5pS, and their functional characterization using pex5-deficient yeast and Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2006; 47:457-66. [PMID: 16792693 DOI: 10.1111/j.1365-313x.2006.02797.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Using the rice PEX14 cDNA as a bait in a yeast two-hybrid assay, two splice variants of the type I peroxisomal targeting signal (PTS1) receptor, OsPex5pL and OsPex5pS, were cloned from a pathogen-treated rice leaf cDNA library. The proteins were produced from a single gene by alternative splicing, which generated a full-length variant, OsPEX5L, and a variant that lacked exon 7, OsPEX5S. OsPex5pL contained 11 copies of the pentapeptide motif WXXXF/Y in its N-terminus, and seven tetratricopeptide repeats in its C-terminus. Expression of OsPEX5L and OsPEX5S predominantly occurred in leaf tissues, and was induced by various stresses, such as exposure to the pathogen Magnaporthe grisea, and treatment with fungal elicitor, methyl viologen, NaCl or hydrogen peroxide. The Arabidopsis T-DNA insertional pex5 mutant, Atpex5, which does not germinate in the absence of sucrose and was resistant to indole-3-butyric acid (IBA), was perfectly rescued by over-expression of OsPex5pL, but not by OsPex5pS. Using transient expression of OsPex5pL and OsPex5pS in the Atpex5 mutant, we show that OsPex5pL translocates both PTS1- and PTS2-containing proteins into the peroxisome by interacting with OsPex7p, whereas OsPex5pS is involved only in PTS1-dependent import in Arabidopsis.
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Affiliation(s)
- Jung Ro Lee
- Environmental Biotechnology National Core Research Center, Gyeongsang National University, Jinju 660-701, Korea
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Mano S, Nakamori C, Nito K, Kondo M, Nishimura M. The Arabidopsis pex12 and pex13 mutants are defective in both PTS1- and PTS2-dependent protein transport to peroxisomes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2006; 47:604-18. [PMID: 16813573 DOI: 10.1111/j.1365-313x.2006.02809.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Peroxisome biogenesis requires various complex processes including organelle division, enlargement and protein transport. We have been studying a number of Arabidopsis apm mutants that display aberrant peroxisome morphology. Two of these mutants, apm2 and apm4, showed green fluorescent protein fluorescence in the cytosol as well as in peroxisomes, indicating a decrease of efficiency of peroxisome targeting signal 1 (PTS1)-dependent protein transport to peroxisomes. Interestingly, both mutants were defective in PTS2-dependent protein transport. Plant growth was more inhibited in apm4 than apm2 mutants, apparently because protein transport was more severely decreased in apm4 than in apm2 mutants. APM2 and APM4 were found to encode proteins homologous to the peroxins PEX13 and PEX12, respectively, which are thought to be involved in transporting matrix proteins into peroxisomes in yeasts and mammals. We show that APM2/PEX13 and APM4/PEX12 are localized on peroxisomal membranes, and that APM2/PEX13 interacts with PEX7, a cytosolic PTS2 receptor. Additionally, a PTS1 receptor, PEX5, was found to stall on peroxisomal membranes in both mutants, suggesting that PEX12 and PEX13 are components that are involved in protein transport on peroxisomal membranes in higher plants. Proteins homologous to PEX12 and PEX13 have previously been found in Arabidopsis but it is not known whether they are involved in protein transport to peroxisomes. Our findings reveal that APM2/PEX13 and APM4/PEX12 are responsible for matrix protein import to peroxisomes in planta.
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Affiliation(s)
- Shoji Mano
- Department of Cell Biology, National Institute for Basic Biology, Okazaki 444-8585, Japan
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26
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Oishi H, Ebina M. Isolation of cDNA and enzymatic properties of betaine aldehyde dehydrogenase from Zoysia tenuifolia. JOURNAL OF PLANT PHYSIOLOGY 2005; 162:1077-86. [PMID: 16255165 DOI: 10.1016/j.jplph.2005.01.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
We isolated cDNAs encoding betaine aldehyde dehydrogenase (BADH, EC 1.2.1.8) from the salt-tolerant Poaceae, Zoysia tenuifolia by polymerase chain reactions. Zoysia betaine aldehyde dehydrogenase 1 (ZBD1) is 1892bp long and codes for 507 amino acids. The deduced amino acid sequence of ZBD1 is 88% similar to the sequence of rice BADH. Ten cDNA clones were isolated from a cDNA Library of salt-treated Z. tenuifolia by using the ZBD1 fragment as a probe. The proteins coded in some clones were more homologous to BBD2, the cytosolic BADH of barley, than to ZBD1. To investigate their enzymatic properties, ZBD1 and spinach BADH were expressed in Escherichia coli and purified. The optimal pH of ZBD1 was 9.5, which was more alkaline than that of spinach BADH. ZBD1 was less tolerant to NaCl than spinach BADH. ZBD1 showed not only BADH activity but also aminoaldehyde dehydrogenase activity. The Km values of ZBD1 for betaine aldehyde, 4-aminobutyraldehyde (AB-ald), and 3-aminopropionaldehyde (AP-ald) were 291, 49, and 4.0 microM, respectively. ZBD1 showed higher specific activities for AB-ald and AP-ald than did spinach BADH.
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Affiliation(s)
- Hideki Oishi
- Japan Grassland Farming and Forage Seed Association, Forage Crop Research Institute, Nishinasuno, Tochigi, Japan.
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Bi X, Khush GS, Bennett J. The Rice Nucellin Gene Ortholog OsAsp1 Encodes an Active Aspartic Protease Without a Plant-specific Insert and is Strongly Expressed in Early Embryo. ACTA ACUST UNITED AC 2005; 46:87-98. [PMID: 15659452 DOI: 10.1093/pcp/pci002] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The barley nucellin gene was reported to be nucellus specific in its expression and was hypothesized to play a role in the programmed cell death of the nucellus as an aspartic protease. Here we provide direct evidence that the rice ortholog encodes an active aspartic protease, but we prefer the name aspartic protease1 (OsAsp1) to nucellin after a detailed analysis of its expression pattern in rice and barley. Northern blots, RT-PCR and RNA in situ hybridization showed that OsAsp1 is expressed most abundantly in zygotic embryos 1-2 d after fertilization. It is also expressed in pollen, nucellus, ovary wall, shoot and root meristem, coleoptiles of immature seeds, and somatic embryos. A parallel study in barley showed that the barley nucellin gene was expressed not only in the nucellus but also strongly in embryos. Recombinant protein proOsAsp1 expressed in the bacterium Escherichia coli refolded and autolysed at acidic pH 3.5 in vitro, and the mature peptide displayed protease activity. Nucellin has three close homologs in rice on chromosomes 11 and 12 and in Arabidopsis on chromosomes 1 and 4. They lack the plant-specific insert that distinguishes the typical plant aspartic protease from aspartic proteases of other organisms. They constitute a new class of aspartic protease that is present in both monocots and dicots but whose function remains to be explored further.
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MESH Headings
- Amino Acid Sequence
- Aspartic Acid Endopeptidases/genetics
- Base Sequence
- Chromosome Mapping
- Chromosomes, Plant/genetics
- Cloning, Molecular
- DNA, Plant/genetics
- Gene Expression Regulation, Developmental
- Gene Expression Regulation, Enzymologic
- Gene Expression Regulation, Plant
- Genes, Plant
- Hordeum/enzymology
- Hordeum/genetics
- Molecular Sequence Data
- Oryza/embryology
- Oryza/enzymology
- Oryza/genetics
- Peptide Mapping
- Phylogeny
- Plant Proteins/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Plant/genetics
- RNA, Plant/metabolism
- Recombinant Proteins/genetics
- Sequence Homology, Amino Acid
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Affiliation(s)
- Xuezhi Bi
- Plant Breeding, Genetics and Biochemistry Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines.
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Hayashi M, Yagi M, Nito K, Kamada T, Nishimura M. Differential contribution of two peroxisomal protein receptors to the maintenance of peroxisomal functions in Arabidopsis. J Biol Chem 2005; 280:14829-35. [PMID: 15637057 DOI: 10.1074/jbc.m411005200] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Peroxisomes in higher plant cells are known to differentiate in function depending on the cell type. Because of the functional differentiation, plant peroxisomes are subdivided into several classes, such as glyoxysomes and leaf peroxisomes. These peroxisomal functions are maintained by import of newly synthesized proteins containing one of two peroxisomal targeting signals known as PTS1 and PTS2. These targeting signals are known to be recognized by the cytosolic receptors, Pex5p and Pex7p, respectively. To demonstrate the contribution of Pex5p and Pex7p to the maintenance of peroxisomal functions in plants, double-stranded RNA constructs were introduced into the genome of Arabidopsis thaliana. Expression of the PEX5 and PEX7 genes was efficiently reduced by the double-stranded RNA-mediated interference in the transgenic Arabidopsis. The Pex5p-deficient Arabidopsis showed reduced activities for both glyoxysomal and leaf peroxisomal functions. An identical phenotype was observed in a transgenic Arabidopsis overexpressing functionally defective Pex5p. In contrast, the Pex7p-deficient Arabidopsis showed reduced activity for glyoxysomal function but not for leaf peroxisomal function. Analyses of peroxisomal protein import in the transgenic Arabidopsis revealed that Pex5p was involved in import of both PTS1-containing proteins and PTS2-containing proteins, whereas Pex7p contributed to the import of only PTS2-containing proteins. Overall, the results indicated that Pex5p and Pex7p play different roles in the maintenance of glyoxysomal and leaf peroxisomal functions in plants.
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Affiliation(s)
- Makoto Hayashi
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, Japan.
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Abstract
Peroxisomes, one of single membrane-bound organelles, are present ubiquitously in eukaryotic cells. They were originally identified as organelles for production of hydrogen peroxide, the degradation of its hydrogen peroxide, and metabolism of fatty acids, which are functions common to almost all the organisms. Meanwhile, photorespiration and assimilation of symbiotically induced nitrogen are plant-specific functions. Recent postgenetic approaches such as transcriptome and proteome showed that plant peroxisomes are differentiated in various tissues, and revealed that peroxisomes have more important roles in various metabolic processes including biosynthesis of plant hormones than we speculated. All peroxisomal proteins, including metabolic enzymes in the matrix, membrane proteins, and factors responsible for peroxisome biogenesis, are nuclear encoded, and are provided from the outside of peroxisomes. Peroxisome biogenesis, such as protein transport, division, and enlargement, requires various complicated steps and is one of the most intriguing topics. Analyses using peroxisome biogenesis mutants and the whole-scale sequencing projects among several organisms revealed the existence of essential factors responsible for peroxisome biogenesis such as peroxins. This review addresses a comprehensive issue relating to function and biogenesis of plant peroxisomes and Arabidopsis mutants that have been accelerating our understanding of peroxisomes in planta.
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Affiliation(s)
- Shoji Mano
- Department of Cell Biology, National Institute for Basic Biology Okazaki 444-8585, Japan
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Reumann S, Ma C, Lemke S, Babujee L. AraPerox. A database of putative Arabidopsis proteins from plant peroxisomes. PLANT PHYSIOLOGY 2004; 136:2587-608. [PMID: 15333753 PMCID: PMC523325 DOI: 10.1104/pp.104.043695] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2004] [Revised: 06/14/2004] [Accepted: 06/16/2004] [Indexed: 05/17/2023]
Abstract
To identify unknown proteins from plant peroxisomes, the Arabidopsis genome was screened for proteins with putative major or minor peroxisome targeting signals type 1 or 2 (PTS1 or PTS2), as defined previously (Reumann S [2004] Plant Physiol 135: 783-800). About 220 and 60 proteins were identified that carry a putative PTS1 or PTS2, respectively. To further support postulated targeting to peroxisomes, several prediction programs were applied and the putative targeting domains analyzed for properties conserved in peroxisomal proteins and for PTS conservation in homologous plant expressed sequence tags. The majority of proteins with a major PTS and medium to high overall probability of peroxisomal targeting represent novel nonhypothetical proteins and include several enzymes involved in beta-oxidation of unsaturated fatty acids and branched amino acids, and 2-hydroxy acid oxidases with a predicted function in fatty acid alpha-oxidation, as well as NADP-dependent dehydrogenases and reductases. In addition, large protein families with many putative peroxisomal isoforms were recognized, including acyl-activating enzymes, GDSL lipases, and small thioesterases. Several proteins are homologous to prokaryotic enzymes of a novel aerobic hybrid degradation pathway for aromatic compounds and proposed to be involved in peroxisomal biosynthesis of plant hormones like jasmonic acid, auxin, and salicylic acid. Putative regulatory proteins of plant peroxisomes include protein kinases, small heat shock proteins, and proteases. The information on subcellular targeting prediction, homology, and in silico expression analysis for these Arabidopsis proteins has been compiled in the public database AraPerox to accelerate discovery and experimental investigation of novel metabolic and regulatory pathways of plant peroxisomes.
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Affiliation(s)
- Sigrun Reumann
- Georg-August-University of Goettingen, Albrecht-von-Haller-Institute for Plant Sciences, Department for Plant Biochemistry, D-37077 Goettingen, Germany.
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Reumann S. Specification of the peroxisome targeting signals type 1 and type 2 of plant peroxisomes by bioinformatics analyses. PLANT PHYSIOLOGY 2004; 135:783-800. [PMID: 15208424 PMCID: PMC514115 DOI: 10.1104/pp.103.035584] [Citation(s) in RCA: 167] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2003] [Revised: 01/22/2004] [Accepted: 01/22/2004] [Indexed: 05/18/2023]
Abstract
To specify the C-terminal peroxisome targeting signal type 1 (PTS1) and the N-terminal PTS2 for higher plants, a maximum number of plant cDNAs and expressed sequence tags that are homologous to PTS1- and PTS2-targeted plant proteins was retrieved from the public databases and the primary structure of their targeting domains was analyzed for conserved properties. According to their high overall frequency in the homologs and their widespread occurence in different orthologous groups, nine major PTS1 tripeptides ([SA][RK][LM]> without AKM> plus SRI> and PRL>) and two major PTS2 nonapeptides (R[LI]x5HL) were defined that are considered good indicators for peroxisomal localization if present in unknown proteins. A lower but significant number of homologs contained 1 of 11 minor PTS1 tripeptides or of 9 minor PTS2 nonapeptides, many of which have not been identified before in plant peroxisomal proteins. The region adjacent to the PTS peptides was characterized by specific conserved properties as well, such as a pronounced incidence of basic and Pro residues and a high positive net charge, which probably play an auxiliary role in peroxisomal targeting. By contrast, several peptides with assumed peroxisomal targeting properties were not found in any of the 550 homologs and hence play--if at all--only a minor role in peroxisomal targeting. Based on the definition of these major and minor PTS and on the recognition of additional conserved properties, the accuracy of predicting peroxisomal proteins can be raised and plant genomes can be screened for novel proteins of peroxisomes more successfully.
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Affiliation(s)
- Sigrun Reumann
- Albrecht-von-Haller-Institute for Plant Sciences, Department for Plant Biochemistry, D-37077 Goettingen, Germany
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Arimura SI, Yamamoto J, Aida GP, Nakazono M, Tsutsumi N. Frequent fusion and fission of plant mitochondria with unequal nucleoid distribution. Proc Natl Acad Sci U S A 2004; 101:7805-8. [PMID: 15136720 PMCID: PMC419687 DOI: 10.1073/pnas.0401077101] [Citation(s) in RCA: 198] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2004] [Accepted: 03/25/2004] [Indexed: 11/18/2022] Open
Abstract
The balance between mitochondrial fusion and fission influences the reticular shape of mitochondria in yeasts. Little is known about whether mitochondria fusion occurs in plants. Plant mitochondria are usually more numerous and more grain-shaped than animal mitochondria. BLAST searches of the nuclear and mitochondrial genome sequences of Arabidopsis thaliana did not find any obvious homologue of mitochondrial fusion genes found in animals and yeasts. To determine whether mitochondrial fusion actually occurs in plants, we labeled mitochondria in onion epidermal cells with a mitochondria-targeted, photoconvertible fluorescent protein Kaede and then altered the fluorescence of some of the mitochondria within a cell from green to red. Frequent and transient fusion of red and green mitochondria was demonstrated by the appearance of yellow mitochondria that subsequently redivided. We also show that mitochondrial fission occasionally occurs without an equal distribution of the nucleoid (DNA-protein complex in mitochondria), resulting in the coexistence of mitochondria containing various amounts of DNA within a single cell. The heterogeneity of DNA contents in mitochondria may be overcome by the frequent and transient fusion of mitochondria.
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Affiliation(s)
- Shin-ichi Arimura
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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Marchesini S, Erard N, Glumoff T, Hiltunen JK, Poirier Y. Modification of the monomer composition of polyhydroxyalkanoate synthesized in Saccharomyces cerevisiae expressing variants of the beta-oxidation-associated multifunctional enzyme. Appl Environ Microbiol 2004; 69:6495-9. [PMID: 14602605 PMCID: PMC262279 DOI: 10.1128/aem.69.11.6495-6499.2003] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Expression by Saccharomyces cerevisiae of a polyhydroxyalkanoate (PHA) synthase modified at the carboxy end by the addition of a peroxisome targeting signal derived from the last 34 amino acids of the Brassica napus isocitrate lyase (ICL) and containing the terminal tripeptide Ser-Arg-Met resulted in the synthesis of PHA. The ability of the terminal peptide Ser-Arg-Met and of the 34-amino-acid peptide from the B. napus ICL to target foreign proteins to the peroxisome of S. cerevisiae was demonstrated with green fluorescent protein fusions. PHA synthesis was found to be dependent on the presence of both the enzymes generating the beta-oxidation intermediate 3-hydroxyacyl-coenzyme A (3-hydroxyacyl-[CoA]) and the peroxin-encoding PEX5 gene, demonstrating the requirement for a functional peroxisome and a beta-oxidation cycle for PHA synthesis. Using a variant of the S. cerevisiae beta-oxidation multifunctional enzyme with a mutation inactivating the B domain of the R-3-hydroxyacyl-CoA dehydrogenase, it was possible to modify the PHA monomer composition through an increase in the proportion of the short-chain monomers of five and six carbons.
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Affiliation(s)
- Silvia Marchesini
- Laboratoire de Biotechnologie Végétale, Département de Biologie Moléculaire Végétale, Université de Lausanne, CH-1015 Lausanne, Switzerland
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Hayashi M, Nishimura M. Entering a new era of research on plant peroxisomes. CURRENT OPINION IN PLANT BIOLOGY 2003; 6:577-82. [PMID: 14611956 DOI: 10.1016/j.pbi.2003.09.012] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Peroxisomes are globular organelles, of approximately 1 microm in diameter, that are found ubiquitously in eukaryotic cells. In higher plants, peroxisomes have been believed to play a pivotal role in three metabolic pathways: lipid breakdown, photorespiration and H2O2-detoxificaton. However, recent progress using Arabidopsis mutants has suggested that peroxisomes have more diverse functions than are known at present. Extensive studies using genetic and post-genomic approaches will renovate our present understanding of the functions of peroxisomes in plants.
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Affiliation(s)
- Makoto Hayashi
- National Institute for Basic Biology, Okazaki 444-8585, Japan
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35
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Kamada T, Nito K, Hayashi H, Mano S, Hayashi M, Nishimura M. Functional differentiation of peroxisomes revealed by expression profiles of peroxisomal genes in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2003; 44:1275-89. [PMID: 14701923 DOI: 10.1093/pcp/pcg173] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
It is well known that peroxisomal matrix proteins contain one of two targeting signals, PTS1 and PTS2. We comprehensively surveyed genes related to peroxisomal function and biogenesis in the entire Arabidopsis genome sequence. Here, we identified 256 gene candidates of PTS1- and PTS2-containing proteins and another 30 genes of non-PTS-containing proteins. Of these, only 29 proteins have been reported to be functionally characterized as peroxisomal proteins in higher plants. We extensively investigated expression profiles of genes described above in various organs of Arabidopsis: Statistical analyses of these expression profiles revealed that peroxisomal genes could be divided into five groups. One group showed ubiquitous expression in all organs examined, while the other four were classified as showing organ-specific expression in seedlings, cotyledons, roots and in both cotyledons and leaves. These data proposed more detailed description of differentiation of plant peroxisomes.
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Affiliation(s)
- Tomoe Kamada
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, 444-8585 Japan
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36
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Costa MA, Collins RE, Anterola AM, Cochrane FC, Davin LB, Lewis NG. An in silico assessment of gene function and organization of the phenylpropanoid pathway metabolic networks in Arabidopsis thaliana and limitations thereof. PHYTOCHEMISTRY 2003; 64:1097-112. [PMID: 14568076 DOI: 10.1016/s0031-9422(03)00517-x] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The Arabidopsis genome sequencing in 2000 gave to science the first blueprint of a vascular plant. Its successful completion also prompted the US National Science Foundation to launch the Arabidopsis 2010 initiative, the goal of which is to identify the function of each gene by 2010. In this study, an exhaustive analysis of The Institute for Genomic Research (TIGR) and The Arabidopsis Information Resource (TAIR) databases, together with all currently compiled EST sequence data, was carried out in order to determine to what extent the various metabolic networks from phenylalanine ammonia lyase (PAL) to the monolignols were organized and/or could be predicted. In these databases, there are some 65 genes which have been annotated as encoding putative enzymatic steps in monolignol biosynthesis, although many of them have only very low homology to monolignol pathway genes of known function in other plant systems. Our detailed analysis revealed that presently only 13 genes (two PALs, a cinnamate-4-hydroxylase, a p-coumarate-3-hydroxylase, a ferulate-5-hydroxylase, three 4-coumarate-CoA ligases, a cinnamic acid O-methyl transferase, two cinnamoyl-CoA reductases) and two cinnamyl alcohol dehydrogenases can be classified as having a bona fide (definitive) function; the remaining 52 genes currently have undetermined physiological roles. The EST database entries for this particular set of genes also provided little new insight into how the monolignol pathway was organized in the different tissues and organs, this being perhaps a consequence of both limitations in how tissue samples were collected and in the incomplete nature of the EST collections. This analysis thus underscores the fact that even with genomic sequencing, presumed to provide the entire suite of putative genes in the monolignol-forming pathway, a very large effort needs to be conducted to establish actual catalytic roles (including enzyme versatility), as well as the physiological function(s) for each member of the (multi)gene families present and the metabolic networks that are operative. Additionally, one key to identifying physiological functions for many of these (and other) unknown genes, and their corresponding metabolic networks, awaits the development of technologies to comprehensively study molecular processes at the single cell level in particular tissues and organs, in order to establish the actual metabolic context.
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Affiliation(s)
- Michael A Costa
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
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37
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Igarashi D, Miwa T, Seki M, Kobayashi M, Kato T, Tabata S, Shinozaki K, Ohsumi C. Identification of photorespiratory glutamate:glyoxylate aminotransferase (GGAT) gene in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2003; 33:975-987. [PMID: 12631323 DOI: 10.1046/j.1365-313x.2003.01688.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
In the photorespiratory process, peroxisomal glutamate:glyoxylate aminotransferase (GGAT) catalyzes the reaction of glutamate and glyoxylate to 2-oxoglutarate and glycine. Although GGAT has been assumed to play important roles for the transamination in photorespiratory carbon cycles, the gene encoding GGAT has not been identified. Here, we report that an alanine:2-oxoglutarate aminotransferase (AOAT)-like protein functions as GGAT in peroxisomes. Arabidopsis has four genes encoding AOAT-like proteins and two of them (namely AOAT1 and AOAT2) contain peroxisomal targeting signal 1 (PTS1). The expression analysis of mRNA encoding AOATs and EST information suggested that AOAT1 was the major protein in green leaves. When AOAT1 fused to green fluorescent protein (GFP) was expressed in BY-2 cells, it was found to be localized to peroxisomes depending on PTS1. By screening of Arabidopsis T-DNA insertion lines, an AOAT1 knockout line (aoat1-1) was isolated. The activity of GGAT and alanine:glyoxylate aminotransferase (AGAT) in the above-ground tissues of aoat1-1 was reduced drastically and, AOAT and glutamate:pyruvate aminotransferase (GPAT) activity also decreased. Peroxisomal GGAT was detected in the wild type but not in aoat1-1. The growth rate was repressed in aoat1-1 grown under high irradiation or without sugar, though differences were slight in aoat1-1 grown under low irradiation, high-CO2 (0.3%) or high-sugar (3% sucrose) conditions. These phenotypes resembled those of photorespiration-deficient mutants. Glutamate levels increased and serine levels decreased in aoat1-1 grown in normal air conditions. Based on these results, it was concluded that AOAT1 is targeted to peroxisomes, functions as a photorespiratory GGAT, plays a markedly important role for plant growth and the metabolism of amino acids.
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Affiliation(s)
- Daisuke Igarashi
- Institute of Life Sciences, Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki 210-8681, Japan
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Fukao Y, Hayashi M, Nishimura M. Proteomic analysis of leaf peroxisomal proteins in greening cotyledons of Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2002; 43:689-96. [PMID: 12154131 DOI: 10.1093/pcp/pcf101] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Leaf peroxisomes are present in greening cotyledons and contain enzymes of the glycolate pathway that functions in photorespiration. However, only a few leaf peroxisomal proteins, that is hydroxypyruvate reductase (HPR), glycolate oxidase (GO) and alanine:glyoxylate aminotransferase 1 (AGT1), have been characterized, and other functions in leaf peroxisomes have not been solved. To better understand the functions of leaf peroxisomes, we established a method to isolate leaf peroxisomes of greening cotyledons. We analyzed 53 proteins by MALDI-TOF MS and then identified 29 proteins. Among them, five proteins are related to the glycolate pathway, four proteins function in scavenging of hydrogen peroxide and additionally 20 novel leaf peroxisomal proteins were identified. In particular, protein kinases and protein phosphatase were first identified as peroxisomal proteins suggesting that protein phosphorylation is one of the regulatory mechanisms in leaf peroxisomes. Novel leaf peroxisomal proteins contained five PTS1-like proteins that have sequences where one amino acid is substituted with another one in PTS1 sequences. The PTS1 motif was suggested to have novel PTS1 sequences.
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Affiliation(s)
- Youichiro Fukao
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, 444-8585 Japan
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Hodges M. Enzyme redundancy and the importance of 2-oxoglutarate in plant ammonium assimilation. JOURNAL OF EXPERIMENTAL BOTANY 2002; 53:905-16. [PMID: 11912233 DOI: 10.1093/jexbot/53.370.905] [Citation(s) in RCA: 156] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Ammonium is the reduced nitrogen form available to plants for assimilation into amino acids. This is achieved by the GS/GOGAT pathway that requires carbon skeletons in the form of 2-oxoglutarate. To date, the exact enzymatic origin of this organic acid for plant ammonium assimilation is unknown. Isocitrate dehydrogenases and aspartate aminotransferases have been proposed to carry out this function. Since different (iso)forms located in several subcellular compartments are present within a plant cell, recent efforts have concentrated on evaluating the involvement of these enzymes in ammonium assimilation. Furthermore, several observations indicate that 2-oxoglutarate is a good candidate as a metabolic signal to regulate the co-ordination of C and N metabolism. This will be discussed with respect to recent advances in bacterial signalling processes involving a 2-oxoglutarate binding protein called PII.
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Affiliation(s)
- Michael Hodges
- Institut de Biotechnologie des Plantes, CNRS UMR8618, Université Paris Sud-XI, 91405 Orsay Cedex, France.
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Mano S, Nakamori C, Hayashi M, Kato A, Kondo M, Nishimura M. Distribution and characterization of peroxisomes in Arabidopsis by visualization with GFP: dynamic morphology and actin-dependent movement. PLANT & CELL PHYSIOLOGY 2002; 43:331-41. [PMID: 11917088 DOI: 10.1093/pcp/pcf037] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Peroxisomes were visualized in living cells of various tissues in transgenic Arabidopsis by green fluorescent protein (GFP) through the addition of the peroxisomal targeting signal 1 (PTS1) or PTS2. The observation using confocal laser scanning microscopy revealed that the GFP fluorescence signals were detected as spherical spots in all cells of two kinds of transgenic plants. Immunoelectron microscopic analysis using antibodies against the peroxisomal marker protein, catalase, showed the presence of GFP in peroxisomes, confirming that GFP was correctly transported into peroxisomes by PTS1 or PTS2 pathways. It has been also revealed that peroxisomes are motile organelles whose movement might be caused by cytoplasmic flow. The movement of peroxisomes was more prominent in root cells than that in leaves, and divided into two categories: a relatively slow, random, vibrational movement and a rapid movement. Treatment with anti-actin and anti-tubulin drugs revealed that actin filaments involve in the rapid movement of peroxisomes. Moreover, abnormal large peroxisomes are present as clusters at the onset of germination, and these clusters disappear in a few days. Interestingly, tubular peroxisomes were also observed in the hypocotyl. These findings indicate that the shape, size, number and movement of peroxisomes in living cells are dynamic and changeable rather than uniform.
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Affiliation(s)
- Shoji Mano
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, 444-8585, Japan
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Nito K, Yamaguchi K, Kondo M, Hayashi M, Nishimura M. Pumpkin peroxisomal ascorbate peroxidase is localized on peroxisomal membranes and unknown membranous structures. PLANT & CELL PHYSIOLOGY 2001; 42:20-7. [PMID: 11158440 DOI: 10.1093/pcp/pce003] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
To investigate the roles of peroxisomal membrane proteins in the reversible conversion of glyoxysomes to leaf peroxisomes, we characterized several membrane proteins of glyoxysomes. One of them was identified as an ascorbate peroxidase (pAPX) that is localized on glyoxysomal membranes. Its cDNA was isolated by immunoscreening. The deduced amino acid sequence encoded by the cDNA insert does not have a peroxisomal targeting signal (PTS), suggesting that pAPX is imported by one or more PTS-independent pathways. Subcellular fractionation of 3- and 5-d-old cotyledons of pumpkin revealed that pAPX was localized not only in the glyoxysomal fraction, but also in the ER fraction. A magnesium shift experiment showed that the density of pAPX in the ER fraction did not increase in the presence of Mg(2+), indicating that pAPX is not localized in the rough ER. Immunocytochemical analysis using a transgenic Arabidopsis which expressed pumpkin pAPX showed that pAPX was localized on peroxisomal membranes, and also on a unknown membranous structure in green cotyledons. The overall results suggested that pAPX is transported to glyoxysomal membranes via this unknown membranous structure.
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Affiliation(s)
- K Nito
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, 444-8585 Japan
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Hayashi M, Nito K, Toriyama-Kato K, Kondo M, Yamaya T, Nishimura M. AtPex14p maintains peroxisomal functions by determining protein targeting to three kinds of plant peroxisomes. EMBO J 2000; 19:5701-10. [PMID: 11060021 PMCID: PMC305803 DOI: 10.1093/emboj/19.21.5701] [Citation(s) in RCA: 94] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We previously isolated an Arabidopsis: peroxisome-deficient ped2 mutant by its resistance to 2,4-dichlorophenoxybutyric acid. Here, we describe the isolation of a gene responsible for this deficiency, called the PED2 gene, by positional cloning and confirmed its identity by complementation analysis. The amino acid sequence of the predicted protein product is similar to that of human Pex14p, which is a key component of the peroxisomal protein import machinery. Therefore, we decided to call it AT:Pex14p. Analyses of the ped2 mutant revealed that AT:Pex14p controls intracellular transport of both peroxisome targeting signal (PTS)1- and PTS2-containing proteins into three different types of peroxisomes, namely glyoxysomes, leaf peroxisomes and unspecialized peroxisomes. Mutation in the PED2 gene results in reduction of enzymes in all of these functionally differentiated peroxisomes. The reduction in these enzymes induces pleiotropic defects, such as fatty acid degradation, photorespiration and the morphology of peroxisomes. These data suggest that the AT:Pex14p has a common role in maintaining physiological functions of each of these three kinds of plant peroxisomes by determining peroxisomal protein targeting.
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Affiliation(s)
- M Hayashi
- Department of Cell Biology, National Institute for Basic Biology, Okazaki 444-8585, Japan
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Froman BE, Edwards PC, Bursch AG, Dehesh K. ACX3, a novel medium-chain acyl-coenzyme A oxidase from Arabidopsis. PLANT PHYSIOLOGY 2000; 123:733-42. [PMID: 10859203 PMCID: PMC59041 DOI: 10.1104/pp.123.2.733] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/1999] [Accepted: 03/06/2000] [Indexed: 05/18/2023]
Abstract
In a database search for homologs of acyl-coenzyme A oxidases (ACX) in Arabidopsis, we identified a partial genomic sequence encoding an apparently novel member of this gene family. Using this sequence information we then isolated the corresponding full-length cDNA from etiolated Arabidopsis cotyledons and have characterized the encoded recombinant protein. The polypeptide contains 675 amino acids. The 34 residues at the amino terminus have sequence similarity to the peroxisomal targeting signal 2 of glyoxysomal proteins, including the R-[I/Q/L]-X5-HL-XL-X15-22-C consensus sequence, suggesting a possible microsomal localization. Affinity purification of the encoded recombinant protein expressed in Escherichia coli followed by enzymatic assay, showed that this enzyme is active on C8:0- to C14:0-coenzyme A with maximal activity on C12:0-coenzyme A, indicating that it has medium-chain-specific activity. These data indicate that the protein reported here is different from previously characterized classes of ACX1, ACX2, and short-chain ACX (SACX), both in sequence and substrate chain-length specificity profile. We therefore, designate this new gene AtACX3. The temporal and spatial expression patterns of AtACX3 during development and in various tissues were similar to those of the AtSACX and other genes expressed in glyoxysomes. Currently available database information indicates that AtACX3 is present as a single copy gene.
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De Bellis L, Gonzali S, Alpi A, Hayashi H, Hayashi M, Nishimura M. Purification and characterization of a novel pumpkin short-chain acyl-coenzyme A oxidase with structural similarity to acyl-coenzyme A dehydrogenases. PLANT PHYSIOLOGY 2000; 123:327-34. [PMID: 10806249 PMCID: PMC59006 DOI: 10.1104/pp.123.1.327] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/1999] [Accepted: 02/03/2000] [Indexed: 05/20/2023]
Abstract
A novel pumpkin (Cucurbita pepo) short-chain acyl-coenzyme A (CoA) oxidase (ACOX) was purified to homogeneity by hydrophobic-interaction, hydroxyapatite, affinity, and anion-exchange chromatography. The purified enzyme is a tetrameric protein, consisting of apparently identical 47-kD subunits. The protein structure of this oxidase differs from other plant and mammalian ACOXs, but is similar to the protein structure of mammalian mitochondrial acyl-CoA dehydrogenase (ACDH) and the recently identified plant mitochondrial ACDH. Subcellular organelle separation by sucrose density gradient centrifugation revealed that the enzyme is localized in glyoxysomes, whereas no immunoreactive bands of similar molecular weight were detected in mitochondrial fractions. The enzyme selectively catalyzes the oxidation of CoA esters of fatty acids with 4 to 10 carbon atoms, and exhibits the highest activity on C-6 fatty acids. Apparently, the enzyme has no activity on CoA esters of branched-chain or dicarboxylic fatty acids. The enzyme is slightly inhibited by high concentrations of substrate and it is not inhibited by Triton X-100 at concentrations up to 0.5% (v/v). The characteristics of this novel ACOX enzyme are discussed in relation to other ACOXs and ACDHs.
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Affiliation(s)
- L De Bellis
- Dipartimento di Biologia, via Provinciale Lecce-Monteroni, 73100 Lecce, Italy.
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Mano S, Hayashi M, Nishimura M. Light regulates alternative splicing of hydroxypyruvate reductase in pumpkin. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 1999; 17:309-20. [PMID: 10097389 DOI: 10.1046/j.1365-313x.1999.00378.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Hydroxypyruvate reductase (HPR) is a leaf peroxisomal enzyme that functions in the glycolate pathway of photorespiration in plants. We have obtained two highly similar cDNAs for pumpkin HPR (HPR1 and HPR2). It has been revealed that two HPR mRNAs might be produced by alternative splicing from a single type of pre-mRNA. The HPR1 protein, but not the HPR2 protein, was found to have a targeting sequence into leaf peroxisomes at the C-terminus, suggesting that alternative splicing controls the subcellular localization of the two HPR proteins. Immunoblot analysis and subcellular fractionation experiments showed that HPR1 and HPR2 proteins are localized in leaf peroxisomes and the cytosol, respectively. Moreover, indirect fluorescence microscopy and analyses of transgenic tobacco cultured cells and Arabidopsis thaliana expressing fusion proteins with green fluorescent protein (GFP) revealed the different subcellular localizations of the two HPR proteins. Both mRNAs were induced developmentally and by light, but with quantitative differences. Almost equal amounts of the mRNAs were detected in pumpkin cotyledons grown in darkness, but treatment with light greatly enhanced the production of HPR2 mRNA. These findings indicate that light regulates alternative splicing of HPR mRNA, suggesting the presence of a novel mechanism of mRNA maturation, namely light-regulated alternative splicing, in higher plants.
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Affiliation(s)
- S Mano
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, Japan
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Kragler F, Lametschwandtner G, Christmann J, Hartig A, Harada JJ. Identification and analysis of the plant peroxisomal targeting signal 1 receptor NtPEX5. Proc Natl Acad Sci U S A 1998; 95:13336-41. [PMID: 9789089 PMCID: PMC23804 DOI: 10.1073/pnas.95.22.13336] [Citation(s) in RCA: 74] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/1998] [Accepted: 08/31/1998] [Indexed: 11/18/2022] Open
Abstract
Protein translocation into peroxisomes takes place via recognition of a peroxisomal targeting signal present at either the extreme C termini (PTS1) or N termini (PTS2) of matrix proteins. In mammals and yeast, the peroxisomal targeting signal receptor, Pex5p, recognizes the PTS1 consisting of -SKL or variants thereof. Although many plant peroxisomal matrix proteins are transported through the PTS1 pathway, little is known about the PTS1 receptor or any other peroxisome assembly protein from plants. We cloned tobacco (Nicotiana tabacum) cDNAs encoding Pex5p (NtPEX5) based on the protein's interaction with a PTS1-containing protein in the yeast two-hybrid system. Nucleotide sequence analysis revealed that the tobacco Pex5p contains seven tetratricopeptide repeats and that NtPEX5 shares greater sequence similarity with its homolog from humans than from yeast. Expression of NtPEX5 fusion proteins, consisting of the N-terminal part of yeast Pex5p and the C-terminal region of NtPEX5, in a Saccharomyces cerevisiae pex5 mutant restored protein translocation into peroxisomes. These experiments confirmed the identity of the tobacco protein as a PTS1 receptor and indicated that components of the peroxisomal translocation apparatus are conserved functionally. Two-hybrid assays showed that NtPEX5 interacts with a wide range of PTS1 variants that also interact with the human Pex5p. Interestingly, the C-terminal residues of some of these peptides deviated from the established plant PTS1 consensus sequence. We conclude that there are significant sequence and functional similarities between the plant and human Pex5ps.
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Affiliation(s)
- F Kragler
- Section of Plant Biology, Division of Biological Sciences, University of California, One Shields Avenue, Davis, CA 95616, USA
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