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Sng BJR, Jeong YJ, Leong SH, Jeong JC, Lee J, Rajani S, Kim CY, Jang IC. Genome-wide identification of cannabinoid biosynthesis genes in non-drug type Cannabis (Cannabis sativa L.) cultivar. J Cannabis Res 2024; 6:35. [PMID: 39244597 PMCID: PMC11380790 DOI: 10.1186/s42238-024-00246-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/28/2024] [Indexed: 09/09/2024] Open
Abstract
BACKGROUND Cannabis sativa cultivars can be classified as marijuana or hemp, depending on its amount of the psychoactive cannabinoid Δ9-tetrahydrocannabinolic acid (THCA). Hemp Cheungsam is a non-drug type Cannabis sativa that is characterized by low THCA content. However, the transcripts and expression profile of cannabinoid biosynthesis pathway genes of hemp Cheungsam have not been investigated. METHODS RNA-sequencing (RNA-seq) was performed on three different tissue types (flower, leaf, and stem) of hemp Cheungsam to understand their transcriptomes. The expression of cannabinoid biosynthesis pathway genes was further analyzed in each tissue type. Multiple sequence alignment and conserved domain analyses were used to investigate the homologs of cannbinoid biosynthesis genes. RESULTS We found that the cannabinoid biosynthesis pathway was mainly expressed in the flowers of hemp Cheungsam, similar to other Cannabis cultivars. However, expression of cannabidiolic acid (CBDA) synthase was much higher than THCA synthase and cannabichromenic acid (CBCA) synthase, suggesting that the transcription profile favors CBDA biosynthesis. Sequence analysis of cannabinoid biosynthesis pathway genes suggested the identity of orthologs in hemp Cheungsam. CONCLUSIONS Cannabinoid biosynthesis in hemp Cheungsam mostly occurs in the flowers, compared to other plant organs. While CBDA synthase expression is high, THCA and CBCA synthase expression is considerably low, indicating lesser THCA biosynthesis and thus low THCA content. Sequence analysis of key genes (CBDA, THCA, and CBCA synthases) of the cannabinoid biosynthetic pathway indicates that orthologs are present in hemp Cheungsam.
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Affiliation(s)
- Benny Jian Rong Sng
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Yu Jeong Jeong
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Korea
| | - Sing Hui Leong
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Jae Cheol Jeong
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Korea
| | - Jiyoung Lee
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Korea
| | - Sarojam Rajani
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Cha Young Kim
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Korea.
| | - In-Cheol Jang
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore.
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2
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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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3
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Rashan EH, Bartlett AK, Khana DB, Zhang J, Jain R, Smith AJ, Baker ZN, Cook T, Caldwell A, Chevalier AR, Pfleger BF, Yuan P, Amador-Noguez D, Simcox JA, Pagliarini DJ. ACAD10 and ACAD11 enable mammalian 4-hydroxy acid lipid catabolism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.574893. [PMID: 38260250 PMCID: PMC10802472 DOI: 10.1101/2024.01.09.574893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Fatty acid β-oxidation (FAO) is a central catabolic pathway with broad implications for organismal health. However, various fatty acids are largely incompatible with standard FAO machinery until they are modified by other enzymes. Included among these are the 4-hydroxy acids (4-HAs)-fatty acids hydroxylated at the 4 (γ) position-which can be provided from dietary intake, lipid peroxidation, and certain drugs of abuse. Here, we reveal that two atypical and poorly characterized acyl-CoA dehydrogenases (ACADs), ACAD10 and ACAD11, drive 4-HA catabolism in mice. Unlike other ACADs, ACAD10 and ACAD11 feature kinase domains N-terminal to their ACAD domains that phosphorylate the 4-OH position as a requisite step in the conversion of 4-hydroxyacyl-CoAs into 2-enoyl-CoAs-conventional FAO intermediates. Our ACAD11 cryo-EM structure and molecular modeling reveal a unique binding pocket capable of accommodating this phosphorylated intermediate. We further show that ACAD10 is mitochondrial and necessary for catabolizing shorter-chain 4-HAs, whereas ACAD11 is peroxisomal and enables longer-chain 4-HA catabolism. Mice lacking ACAD11 accumulate 4-HAs in their plasma while comparable 3- and 5-hydroxy acids remain unchanged. Collectively, this work defines ACAD10 and ACAD11 as the primary gatekeepers of mammalian 4-HA catabolism and sets the stage for broader investigations into the ramifications of aberrant 4-HA metabolism in human health and disease.
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Affiliation(s)
- Edrees H. Rashan
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Abigail K. Bartlett
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Daven B. Khana
- Department of Microbiology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jingying Zhang
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Raghav Jain
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Andrew J. Smith
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Zakery N. Baker
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Taylor Cook
- Department of Chemical and Biological Engineering, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Alana Caldwell
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Autumn R. Chevalier
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Brian F. Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Peng Yuan
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Daniel Amador-Noguez
- Department of Microbiology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Judith A. Simcox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - David J. Pagliarini
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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4
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Deng Q, Jiang H, Hu J, Pan R. Identification of Auxiliary Organellar Targeting Signals for Plant Peroxisomes Using Bioinformatic Analysis of Large Protein Sequence Datasets Followed by Experimental Validation. Methods Mol Biol 2024; 2792:265-275. [PMID: 38861094 DOI: 10.1007/978-1-0716-3802-6_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
Eukaryotic cells are compartmentalized by membrane-bounded organelles to ensure that specific biochemical reactions and cellular functions occur in a spatially restricted manner. The subcellular localization of proteins is largely determined by their intrinsic targeting signals, which are mainly constituted by short peptides. A complete organelle targeting signal may contain a core signal (CoreS) as well as auxiliary signals (AuxiS). However, the AuxiS is often not as well characterized as the CoreS. Peroxisomes house many key steps in photorespiration, besides other crucial functions in plants. Peroxisome targeting signal type 1 (PTS1), which is carried by most peroxisome matrix proteins, was initially recognized as a C-terminal tripeptide with a "canonical" consensus of [S/A]-[K/R]-[L/M]. Many studies have shown the existence of auxiliary targeting signals upstream of PTS1, but systematic characterizations are lacking. Here, we designed an analytical strategy to characterize the auxiliary targeting signals for plant peroxisomes using large datasets and statistics followed by experimental validations. This method may also be applied to deciphering the auxiliary targeting signals for other organelles, whose organellar targeting depends on a core peptide with assistance from a nearby auxiliary signal.
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Affiliation(s)
- Qianwen Deng
- College of Agriculture and Biotechnology & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
- Zhijiang Lab, Hangzhou, China
| | - Hangjin Jiang
- Center for Data Science, Zhejiang University, Hangzhou, China
| | - Jianping Hu
- Michigan State University-Department of Energy Plant Research Laboratory and Plant Biology Department, Michigan State University, East Lansing, MI, USA
| | - Ronghui Pan
- College of Agriculture and Biotechnology & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China.
- Zhijiang Lab, Hangzhou, China.
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5
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Feng Y, Shao S, Zhou X, Wei W, Liu X, Tang Y, Hua Y, Zheng J, Zhang Y, Ying X. Enhancing the Catalytic Activity of Glycolate Oxidase from Chlamydomonas reinhardtii through Semi-Rational Design. Microorganisms 2023; 11:1689. [PMID: 37512862 PMCID: PMC10385363 DOI: 10.3390/microorganisms11071689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/25/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Glycolate oxidase is a peroxisomal flavoprotein catalyzing the oxidation of glycolate to glyoxylate and plays crucial metabolic roles in green algae, plants, and animals. It could serve as a biocatalyst for enzymatic production of glyoxylate, a fine chemical with a wide variety of applications in perfumery, flavor, and the pharmaceutical and agrochemical industries. However, the low catalytic activity of native glycolate oxidase and low levels of active enzyme in heterologous expression limit its practical use in industrial biocatalysis. Herein, the glycolate oxidase from Chlamydomonas reinhardtii (CreGO) was selected through phylogenetic tree analysis, and its low level of soluble expression in E. coli BL21(DE3) was improved through the use of the glutathione thioltransferase (GST), the choice of the vector pET22b and the optimization of induction conditions. The semi-rational design of the fusion enzyme GST-Gly-Ser-Gly-CreGO led to the superior variant GST-Gly-Ser-Gly-CreGO-Y27S/V111G/V212R with the kcat/Km value of 29.2 s-1·mM-1, which was six times higher than that of the wild type. In contrast to GST-Gly-Ser-Gly-CreGO, 5 mg/mL of crude enzyme GST-Gly-Ser-Gly-CreGO-Y27S/V111G/V212R together with 25 μg/mL of catalase catalyzed the oxidation of 300 mM of methyl glycolate for 8 h, increasing the yield from 50.4 to 93.5%.
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Affiliation(s)
- Yingting Feng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Shuai Shao
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xueting Zhou
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Wan Wei
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xun Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yi Tang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yuhao Hua
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jianyong Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yinjun Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xiangxian Ying
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
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6
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Hoernstein SNW, Özdemir B, van Gessel N, Miniera AA, Rogalla von Bieberstein B, Nilges L, Schweikert Farinha J, Komoll R, Glauz S, Weckerle T, Scherzinger F, Rodriguez-Franco M, Müller-Schüssele SJ, Reski R. A deeply conserved protease, acylamino acid-releasing enzyme (AARE), acts in ageing in Physcomitrella and Arabidopsis. Commun Biol 2023; 6:61. [PMID: 36650210 PMCID: PMC9845386 DOI: 10.1038/s42003-023-04428-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 01/05/2023] [Indexed: 01/18/2023] Open
Abstract
Reactive oxygen species (ROS) are constant by-products of aerobic life. In excess, ROS lead to cytotoxic protein aggregates, which are a hallmark of ageing in animals and linked to age-related pathologies in humans. Acylamino acid-releasing enzymes (AARE) are bifunctional serine proteases, acting on oxidized proteins. AARE are found in all domains of life, albeit under different names, such as acylpeptide hydrolase (APEH/ACPH), acylaminoacyl peptidase (AAP), or oxidized protein hydrolase (OPH). In humans, AARE malfunction is associated with age-related pathologies, while their function in plants is less clear. Here, we provide a detailed analysis of AARE genes in the plant lineage and an in-depth analysis of AARE localization and function in the moss Physcomitrella and the angiosperm Arabidopsis. AARE loss-of-function mutants have not been described for any organism so far. We generated and analysed such mutants and describe a connection between AARE function, aggregation of oxidized proteins and plant ageing, including accelerated developmental progression and reduced life span. Our findings complement similar findings in animals and humans, and suggest a unified concept of ageing may exist in different life forms.
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Affiliation(s)
- Sebastian N W Hoernstein
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104, Freiburg, Germany
| | - Buğra Özdemir
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104, Freiburg, Germany
- Euro-BioImaging Bio-Hub, EMBL Heidelberg, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Nico van Gessel
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104, Freiburg, Germany
| | - Alessandra A Miniera
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104, Freiburg, Germany
| | - Bruno Rogalla von Bieberstein
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104, Freiburg, Germany
- Department of Anesthesiology, University Hospital Würzburg, Oberduerrbacher Strasse 6, 97072, Würzburg, Germany
| | - Lars Nilges
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104, Freiburg, Germany
| | - Joana Schweikert Farinha
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104, Freiburg, Germany
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Ramona Komoll
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104, Freiburg, Germany
- Heraeus Medical GmbH, Philipp-Reis-Straße 8-13, 61273, Wehrheim, Germany
| | - Stella Glauz
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104, Freiburg, Germany
| | - Tim Weckerle
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104, Freiburg, Germany
- Zymo Research Europe GmbH, Muelhauser Strasse 9, 79110, Freiburg, Germany
| | - Friedrich Scherzinger
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104, Freiburg, Germany
- Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103, Leipzig, Germany
| | - Marta Rodriguez-Franco
- Cell Biology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104, Freiburg, Germany
| | - Stefanie J Müller-Schüssele
- Molecular Botany, Department of Biology, Technical University of Kaiserslautern, Erwin-Schrödinger-Strasse 70, 67663, Kaiserslautern, Germany
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104, Freiburg, Germany.
- Signalling Research Centres BIOSS and CIBSS, Schaenzlestrasse 18, 79104, Freiburg, Germany.
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7
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Kunze M. Computational Evaluation of Peroxisomal Targeting Signals in Metazoa. Methods Mol Biol 2023; 2643:391-404. [PMID: 36952201 DOI: 10.1007/978-1-0716-3048-8_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Most soluble proteins enclosed in peroxisomes encode either type-1 or type-2 peroxisomal targeting signals (PTS1 or PTS2), which act as postal codes and define the proteins' intracellular destination. Thus, various computational programs have been developed to evaluate the probability of specific peptide sequences for being a functional PTS or to scan the primary sequence of proteins for such signals. Among these prediction algorithms the PTS1-predictor ( https://mendel.imp.ac.at/pts1/ ) has been amply used, but the research logic of this and other PTS1 prediction tools is occasionally misjudged giving rise to characteristic pitfalls. Here, a proper utilization of the PTS1-predictor is introduced together with a framework of additional tests to increase the validity of the interpretation of results. Moreover, a list of possible causes for a mismatch between results of such predictions and experimental outcomes is provided. However, the foundational arguments apply to other prediction tools for PTS1 motifs as well.
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Affiliation(s)
- Markus Kunze
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna, Vienna, Austria.
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8
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Hochreiter B, Schmid JA, Berger J, Kunze M. Estimating the Interaction Strength Between PTS1-Peptides and Their Receptor PEX5 in Living Cells Using Flow-Cytometer-Based FRET (flowFRET) Measurements. Methods Mol Biol 2023; 2643:413-434. [PMID: 36952203 DOI: 10.1007/978-1-0716-3048-8_30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
The import of many peroxisomal matrix proteins is initiated by the interaction of type-1 peroxisomal targeting signals (PTS1) residing at the extreme C-terminus of cargo proteins and their receptor protein PEX5. This interaction has been amply investigated by biophysical methods using isolated proteins and peptides or heterologous systems such as two-hybrid assays. However, a recently developed novel application of Fluorescence resonance energy transfer (FRET) allows a quantifying measurement of this interaction in living cells. This method combines the systematic measurement of FRET-efficiency in a high number of cells with a well-suited normalization protocol and a fitting algorithm, which together allow the estimation of numerical values for the apparent interaction strength that correlates with other measures of binding strength but can be obtained under rather physiological conditions.
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Affiliation(s)
- Bernhard Hochreiter
- Institute for Vascular Biology and Thrombosis Research, Medical University of Vienna, Vienna, Austria.
| | - Johannes A Schmid
- Institute for Vascular Biology and Thrombosis Research, Medical University of Vienna, Vienna, Austria
| | - Johannes Berger
- Department of Pathobiology of the Nervous System, Medical University of Vienna, Vienna, Austria
| | - Markus Kunze
- Department of Pathobiology of the Nervous System, Medical University of Vienna, Vienna, Austria.
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9
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Mei X, Hu L, Song Y, Zhou C, Mu R, Xie X, Li J, Xiang L, Weng Q, Yang Z. Heterologous Expression and Characterization of Tea ( Camellia sinensis) Polyamine Oxidase Homologs and Their Involvement in Stresses. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:11880-11891. [PMID: 36106904 DOI: 10.1021/acs.jafc.2c01549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Polyamine oxidase (PAO) is a key enzyme maintaining polyamine homeostasis, which affects plant physiological activities. Until now, the gene members and function of PAOs in tea (Camellia sinenesis) have not been fully identified. Here, through the expression in Escherichia coli and Nicotiana benthamiana, we identified six genes annotated as CsPAO in tea genome and transcriptome and determined their enzyme reaction modes and gene expression profiles in tea cultivar 'Yinghong 9'. We found that CsPAO1,2,3 could catalyze spermine, thermospermine, and norspermidine, and CsPAO2,3 could catalyze spermidine in the back-conversion mode, which indicated that the precursor of γ-aminobutyric acid might originate from the oxidation of putrescin but not spermidine. We further investigated the changes of CsPAO activity with temperature and pH and their stability. Kinetic parameters suggested that CsPAO2 was the major PAO modifying polyamine composition in tea, and it could be inactivated by β-hydroxyethylhydrazine and aminoguanidine. Putrescine content and CsPAO2 expression were high in tea flowers. CsPAO2 responded to wound, drought, and salt stress; CsPAO1 might be the main member responding to cold stress; anoxia induced CsPAO3. We conclude that in terms of phylogenetic tree, enzyme characteristics, and expression profile, CsPAO2 might be the dominant CsPAO in the polyamine degradation pathway.
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Affiliation(s)
- Xin Mei
- College of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Duyun 558000, China
| | - Liuhong Hu
- College of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Duyun 558000, China
| | - Yuyan Song
- College of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Duyun 558000, China
| | - Caibi Zhou
- College of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Duyun 558000, China
| | - Ren Mu
- College of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Duyun 558000, China
| | - Xintai Xie
- College of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Duyun 558000, China
| | - Jing Li
- College of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Duyun 558000, China
| | - Lan Xiang
- College of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Duyun 558000, China
| | - Qingbei Weng
- College of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Duyun 558000, China
| | - Ziyin Yang
- South China Botanical Garden, Chinese Academy of Sciences, Xingke Road 723, Tianhe District, Guangzhou 510650, China
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10
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Tarafdar S, Chowdhary G. Translating the Arabidopsis thaliana Peroxisome Proteome Insights to Solanum lycopersicum: Consensus Versus Diversity. Front Cell Dev Biol 2022; 10:909604. [PMID: 35912119 PMCID: PMC9328179 DOI: 10.3389/fcell.2022.909604] [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: 03/31/2022] [Accepted: 06/06/2022] [Indexed: 11/25/2022] Open
Abstract
Peroxisomes are small, single-membrane specialized organelles present in all eukaryotic organisms. The peroxisome is one of the nodal centers of reactive oxygen species homeostasis in plants, which are generated in a high amount due to various stress conditions. Over the past decade, there has been extensive study on peroxisomal proteins and their signaling pathways in the model plant Arabidopsis thaliana, and a lot has been deciphered. However, not much impetus has been given to studying the peroxisome proteome of economically important crops. Owing to the significance of peroxisomes in the physiology of plants during normal and stress conditions, understating its proteome is of much importance. Hence, in this paper, we have made a snapshot of putative peroxisomal matrix proteins in the economically important vegetable crop tomato (Solanum lycopersicum, (L.) family Solanaceae). First, a reference peroxisomal matrix proteome map was generated for Arabidopsis thaliana using the available proteomic and localization studies, and proteins were categorized into various groups as per their annotations. This was used to create the putative peroxisomal matrix proteome map for S. lycopersicum. The putative peroxisome proteome in S. lycopersicum retains the basic framework: the bulk of proteins had peroxisomal targeting signal (PTS) type 1, a minor group had PTS2, and the catalase family retained its characteristic internal PTS. Apart from these, a considerable number of S. lycopersicum orthologs did not contain any "obvious" PTS. The number of PTS2 isoforms was found to be reduced in S. lycopersicum. We further investigated the PTS1s in the case of both the plant species and generated a pattern for canonical and non-canonical PTS1s. The number of canonical PTS1 proteins was comparatively lesser in S. lycopersicum. The non-canonical PTS1s were found to be comparable in both the plant species; however, S. lycopersicum showed greater diversity in the composition of the signal tripeptide. Finally, we have tried to address the lacunas and probable strategies to fill those gaps.
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Affiliation(s)
| | - Gopal Chowdhary
- Plant Molecular Biology Laboratory, School of Biotechnology, KIIT, Bhubaneswar, India
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Deng Q, Li H, Feng Y, Xu R, Li W, Zhu R, Akhter D, Shen X, Hu J, Jiang H, Pan R. Defining upstream enhancing and inhibiting sequence patterns for plant peroxisome targeting signal type 1 using large-scale in silico and in vivo analyses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:567-582. [PMID: 35603488 PMCID: PMC9542071 DOI: 10.1111/tpj.15840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/01/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
Peroxisomes are universal eukaryotic organelles essential to plants and animals. Most peroxisomal matrix proteins carry peroxisome targeting signal type 1 (PTS1), a C-terminal tripeptide. Studies from various kingdoms have revealed influences from sequence upstream of the tripeptide on peroxisome targeting, supporting the view that positive charges in the upstream region are the major enhancing elements. However, a systematic approach to better define the upstream elements influencing PTS1 targeting capability is needed. Here, we used protein sequences from 177 plant genomes to perform large-scale and in-depth analysis of the PTS1 domain, which includes the PTS1 tripeptide and upstream sequence elements. We identified and verified 12 low-frequency PTS1 tripeptides and revealed upstream enhancing and inhibiting sequence patterns for peroxisome targeting, which were subsequently validated in vivo. Follow-up analysis revealed that nonpolar and acidic residues have relatively strong enhancing and inhibiting effects, respectively, on peroxisome targeting. However, in contrast to the previous understanding, positive charges alone do not show the anticipated enhancing effect and that both the position and property of the residues within these patterns are important for peroxisome targeting. We further demonstrated that the three residues immediately upstream of the tripeptide are the core influencers, with a 'basic-nonpolar-basic' pattern serving as a strong and universal enhancing pattern for peroxisome targeting. These findings have significantly advanced our knowledge of the PTS1 domain in plants and likely other eukaryotic species as well. The principles and strategies employed in the present study may also be applied to deciphering auxiliary targeting signals for other organelles.
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Affiliation(s)
- Qianwen Deng
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
- ZJU‐Hangzhou Global Scientific and Technological Innovation CenterZhejiang UniversityHangzhou310027China
| | - He Li
- Center for Data ScienceZhejiang UniversityHangzhou310058China
| | - Yanlei Feng
- ZJU‐Hangzhou Global Scientific and Technological Innovation CenterZhejiang UniversityHangzhou310027China
| | - Ruonan Xu
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
| | - Weiran Li
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
| | - Rui Zhu
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
| | - Delara Akhter
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
- Department of Genetics and Plant BreedingSylhet Agricultural UniversitySylhet3100Bangladesh
| | - Xingxing Shen
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
| | - Jianping Hu
- Department of Energy Plant Research Laboratory and Plant Biology DepartmentMichigan State UniversityEast LansingMichigan48824USA
| | - Hangjin Jiang
- Center for Data ScienceZhejiang UniversityHangzhou310058China
| | - Ronghui Pan
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
- ZJU‐Hangzhou Global Scientific and Technological Innovation CenterZhejiang UniversityHangzhou310027China
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Vasilev J, Mix AK, Heimerl T, Maier UG, Moog D. Inferred Subcellular Localization of Peroxisomal Matrix Proteins of Guillardia theta Suggests an Important Role of Peroxisomes in Cryptophytes. FRONTIERS IN PLANT SCIENCE 2022; 13:889662. [PMID: 35783940 PMCID: PMC9244630 DOI: 10.3389/fpls.2022.889662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
Peroxisomes participate in several important metabolic processes in eukaryotic cells, such as the detoxification of reactive oxygen species (ROS) or the degradation of fatty acids by β-oxidation. Recently, the presence of peroxisomes in the cryptophyte Guillardia theta and other "chromalveolates" was revealed by identifying proteins for peroxisomal biogenesis. Here, we investigated the subcellular localization of candidate proteins of G. theta in the diatom Phaeodactylum tricornutum, either possessing a putative peroxisomal targeting signal type 1 (PTS1) sequence or factors lacking a peroxisomal targeting signal but known to be involved in β-oxidation. Our results indicate important contributions of the peroxisomes of G. theta to the carbohydrate, ether phospholipid, nucleotide, vitamin K, ROS, amino acid, and amine metabolisms. Moreover, our results suggest that in contrast to many other organisms, the peroxisomes of G. theta are not involved in the β-oxidation of fatty acids, which exclusively seems to occur in the cryptophyte's mitochondria.
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Affiliation(s)
- Jana Vasilev
- Laboratory for Cell Biology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Ann-Kathrin Mix
- Laboratory for Cell Biology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Thomas Heimerl
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Uwe G. Maier
- Laboratory for Cell Biology, Department of Biology, Philipps-University Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Daniel Moog
- Laboratory for Cell Biology, Department of Biology, Philipps-University Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
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Kataya A, Gautam N, Jamshed M, Muench DG, Samuel MA, Thelen JJ, Moorhead GB. Identification of Arabidopsis Protein Kinases That Harbor Functional Type 1 Peroxisomal Targeting Signals. Front Cell Dev Biol 2022; 10:745883. [PMID: 35242755 PMCID: PMC8886021 DOI: 10.3389/fcell.2022.745883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 01/25/2022] [Indexed: 12/25/2022] Open
Abstract
Peroxisomes are eukaryotic specific organelles that perform diverse metabolic functions including fatty acid β-oxidation, reactive species metabolism, photorespiration, and responses to stress. However, the potential regulation of these functions by post-translational modifications, including protein phosphorylation, has had limited study. Recently, we identified and catalogued a large number of peroxisomal phosphorylated proteins, implicating the presence of protein kinases in this organelle. Here, we employed available prediction models coupled with sequence conservation analysis to identify 31 protein kinases from the Arabidopsis kinome (all protein kinases) that contain a putative, non-canonical peroxisomal targeting signal type 1 (PTS1). From this, twelve C-terminal domain-PTS1s were demonstrated to be functional in vivo, targeting enhanced yellow fluorescent protein to peroxisomes, increasing the list of presumptive peroxisomal protein kinases to nineteen. Of the twelve protein kinases with functional PTS1s, we obtained full length clones for eight and demonstrated that seven target to peroxisomes in vivo. Screening homozygous mutants of the presumptive nineteen protein kinases revealed one candidate (GPK1) that harbors a sugar-dependence phenotype, suggesting it is involved in regulating peroxisomal fatty acid β-oxidation. These results present new opportunities for investigating the regulation of peroxisome functions.
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Affiliation(s)
- Amr Kataya
- Department of Chemistry, Bioscience, and Environmental Engineering, University of Stavanger, Stavanger, Norway.,Department of Biological Sciences, University of Calgary, Calgary, AB, Canada.,Christopher S. Bond Life Sciences Center, Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | - Nitija Gautam
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Muhammad Jamshed
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Douglas G Muench
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Marcus A Samuel
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Jay J Thelen
- Christopher S. Bond Life Sciences Center, Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | - Greg B Moorhead
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
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Záhonová K, Treitli SC, Le T, Škodová-Sveráková I, Hanousková P, Čepička I, Tachezy J, Hampl V. Anaerobic derivates of mitochondria and peroxisomes in the free-living amoeba Pelomyxa schiedti revealed by single-cell genomics. BMC Biol 2022; 20:56. [PMID: 35227266 PMCID: PMC8887013 DOI: 10.1186/s12915-022-01247-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 02/03/2022] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Mitochondria and peroxisomes are the two organelles that are most affected during adaptation to microoxic or anoxic environments. Mitochondria are known to transform into anaerobic mitochondria, hydrogenosomes, mitosomes, and various transition stages in between, collectively called mitochondrion-related organelles (MROs), which vary in enzymatic capacity. Anaerobic peroxisomes were identified only recently, and their putatively most conserved function seems to be the metabolism of inositol. The group Archamoebae includes anaerobes bearing both anaerobic peroxisomes and MROs, specifically hydrogenosomes in free-living Mastigamoeba balamuthi and mitosomes in the human pathogen Entamoeba histolytica, while the organelles within the third lineage represented by Pelomyxa remain uncharacterized. RESULTS We generated high-quality genome and transcriptome drafts from Pelomyxa schiedti using single-cell omics. These data provided clear evidence for anaerobic derivates of mitochondria and peroxisomes in this species, and corresponding vesicles were tentatively identified in electron micrographs. In silico reconstructed MRO metabolism harbors respiratory complex II, electron-transferring flavoprotein, a partial TCA cycle running presumably in the reductive direction, pyruvate:ferredoxin oxidoreductase, [FeFe]-hydrogenases, a glycine cleavage system, a sulfate activation pathway, and an expanded set of NIF enzymes for iron-sulfur cluster assembly. When expressed in the heterologous system of yeast, some of these candidates localized into mitochondria, supporting their involvement in the MRO metabolism. The putative functions of P. schiedti peroxisomes could be pyridoxal 5'-phosphate biosynthesis, amino acid and carbohydrate metabolism, and hydrolase activities. Unexpectedly, out of 67 predicted peroxisomal enzymes, only four were also reported in M. balamuthi, namely peroxisomal processing peptidase, nudix hydrolase, inositol 2-dehydrogenase, and D-lactate dehydrogenase. Localizations in yeast corroborated peroxisomal functions of the latter two. CONCLUSIONS This study revealed the presence and partially annotated the function of anaerobic derivates of mitochondria and peroxisomes in P. schiedti using single-cell genomics, localizations in yeast heterologous systems, and transmission electron microscopy. The MRO metabolism resembles that of M. balamuthi and most likely reflects the state in the common ancestor of Archamoebae. The peroxisomal metabolism is strikingly richer in P. schiedti. The presence of myo-inositol 2-dehydrogenase in the predicted peroxisomal proteome corroborates the situation in other Archamoebae, but future experimental evidence is needed to verify additional functions of this organelle.
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Affiliation(s)
- Kristína Záhonová
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic.
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.
| | | | - Tien Le
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Ingrid Škodová-Sveráková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Pavla Hanousková
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jan Tachezy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Vladimír Hampl
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic.
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González-Gordo S, Palma JM, Corpas FJ. Peroxisomal Proteome Mining of Sweet Pepper ( Capsicum annuum L.) Fruit Ripening Through Whole Isobaric Tags for Relative and Absolute Quantitation Analysis. FRONTIERS IN PLANT SCIENCE 2022; 13:893376. [PMID: 35615143 PMCID: PMC9125320 DOI: 10.3389/fpls.2022.893376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/21/2022] [Indexed: 05/05/2023]
Abstract
Peroxisomes are ubiquitous organelles from eukaryotic cells characterized by an active nitro-oxidative metabolism. They have a relevant metabolic plasticity depending on the organism, tissue, developmental stage, or physiological/stress/environmental conditions. Our knowledge of peroxisomal metabolism from fruits is very limited but its proteome is even less known. Using sweet pepper (Capsicum annuum L.) fruits at two ripening stages (immature green and ripe red), it was analyzed the proteomic peroxisomal composition by quantitative isobaric tags for relative and absolute quantitation (iTRAQ)-based protein profiling. For this aim, it was accomplished a comparative analysis of the pepper fruit whole proteome obtained by iTRAQ versus the identified peroxisomal protein profile from Arabidopsis thaliana. This allowed identifying 57 peroxisomal proteins. Among these proteins, 49 were located in the peroxisomal matrix, 36 proteins had a peroxisomal targeting signal type 1 (PTS1), 8 had a PTS type 2, 5 lacked this type of peptide signal, and 8 proteins were associated with the membrane of this organelle. Furthermore, 34 proteins showed significant differences during the ripening of the fruits, 19 being overexpressed and 15 repressed. Based on previous biochemical studies using purified peroxisomes from pepper fruits, it could be said that some of the identified peroxisomal proteins were corroborated as part of the pepper fruit antioxidant metabolism (catalase, superoxide dismutase, ascorbate peroxidase, monodehydroascorbate reductase, dehydroascorbate reductaseglutathione reductase, 6-phosphogluconate dehydrogenase and NADP-isocitrate dehydrogenase), the β-oxidation pathway (acyl-coenzyme A oxidase, 3-hydroxyacyl-CoA dehydrogenase, enoyl-CoA hydratase), while other identified proteins could be considered "new" or "unexpected" in fruit peroxisomes like urate oxidase (UO), sulfite oxidase (SO), 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase (METE1), 12-oxophytodienoate reductase 3 (OPR3) or 4-coumarate-CoA ligase (4CL), which participate in different metabolic pathways such as purine, sulfur, L-methionine, jasmonic acid (JA) or phenylpropanoid metabolisms. In summary, the present data provide new insights into the complex metabolic machinery of peroxisomes in fruit and open new windows of research into the peroxisomal functions during fruit ripening.
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Pex7 selectively imports PTS2 target proteins to peroxisomes and is required for anthracnose disease development in Colletotrichum scovillei. Fungal Genet Biol 2021; 157:103636. [PMID: 34742890 DOI: 10.1016/j.fgb.2021.103636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 10/29/2021] [Accepted: 10/29/2021] [Indexed: 11/22/2022]
Abstract
Pex7 is a shuttling receptor that imports matrix proteins with a type 2 peroxisomal targeting signal (PTS2) to peroxisomes. The Pex7-mediated PTS2 protein import contributes to crucial metabolic processes such as the fatty acid β-oxidation and glucose metabolism in a number of fungi, but cellular roles of Pex7 between the import of PTS2 target proteins and metabolic processes have not been fully understood. In this study, we investigated the functional roles of CsPex7, a homolog of the yeast Pex7, by targeted gene deletion in the pepper anthracnose fungus Colletotrichum scovillei. CsPex7 was required for carbon source utilization, scavenging of reactive oxygen species, conidial production, and disease development in C. scovillei. The expression of fluorescently tagged PTS2 signal of hexokinases and 3-ketoacyl-CoA thiolases showed that peroxisomal localization of the hexokinase CsGlk1 PTS2 is dependent on CsPex7, but those of the 3-ketoacyl-CoA thiolases are independent on CsPex7. In addition, GFP-tagged CsPex7 proteins were intensely localized to the peroxisomes on glucose-containing media, indicating a role of CsPex7 in glucose utilization. Collectively, these findings indicate that CsPex7 selectively recognizes specific PTS2 signal for import of PTS2-containing proteins to peroxisomes, thereby mediating peroxisomal targeting efficiency of PTS2-containing proteins in C. scovillei. On pepper fruits, the ΔCspex7 mutant exhibited significantly reduced virulence, in which excessive accumulation of hydrogen peroxide was observed in the pepper cells. We think the reduced virulence results from the abnormality in hydrogen peroxide metabolism of the ΔCspex7 mutant. Our findings provide insight into the cellular roles of CsPex7 in PTS2 protein import system.
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Sunstrum FG, Liu HL, Jancsik S, Madilao LL, Bohlmann J, Irmisch S. 4-Coumaroyl-CoA ligases in the biosynthesis of the anti-diabetic metabolite montbretin A. PLoS One 2021; 16:e0257478. [PMID: 34618820 PMCID: PMC8496819 DOI: 10.1371/journal.pone.0257478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/01/2021] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Montbretins are rare specialized metabolites found in montbretia (Crocosmia x crocosmiiflora) corms. Montbretin A (MbA) is of particular interest as a novel therapeutic for type-2 diabetes and obesity. There is no scalable production system for this complex acylated flavonol glycoside. MbA biosynthesis has been reconstructed in Nicotiana benthamiana using montbretia genes for the assembly of MbA from its various different building blocks. However, in addition to smaller amounts of MbA, the therapeutically inactive montbretin B (MbB) was the major product of this metabolic engineering effort. MbA and MbB differ in a single hydroxyl group of their acyl side chains, which are derived from caffeoyl-CoA and coumaroyl-CoA, respectively. Biosynthesis of both MbA and MbB also require coumaroyl-CoA for the formation of the myricetin core. Caffeoyl-CoA and coumaroyl-CoA are formed in the central phenylpropanoid pathway by acyl activating enzymes (AAEs) known as 4-coumaroyl-CoA ligases (4CLs). Here we investigated a small family of montbretia AAEs and 4CLs, and their possible contribution to montbretin biosynthesis. RESULTS Transcriptome analysis for gene expression patterns related to montbretin biosynthesis identified eight different montbretia AAEs belonging to four different clades. Enzyme characterization identified 4CL activity for two clade IV members, Cc4CL1 and Cc4CL2, converting different hydroxycinnamic acids into the corresponding CoA thioesters. Both enzymes preferred coumaric acid over caffeic acid as a substrate in vitro. While expression of montbretia AAEs did not enhance MbA biosynthesis in N. benthamiana, we demonstrated that both Cc4CLs can be used to activate coumaric and caffeic acid towards flavanone biosynthesis in yeast (Saccharomyces cerevisiae). CONCLUSIONS Montbretia expresses two functional 4CLs, but neither of them is specific for the formation of caffeoyl-CoA. Based on differential expression analysis and phylogeny Cc4CL1 is most likely involved in MbA biosynthesis, while Cc4CL2 may contribute to lignin biosynthesis. Both Cc4CLs can be used for flavanone production to support metabolic engineering of MbA in yeast.
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Affiliation(s)
- Frederick G. Sunstrum
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hannah L. Liu
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sharon Jancsik
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lufiani L. Madilao
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Joerg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sandra Irmisch
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
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Jiang Y, Wang D, Yao Y, Eubel H, Künzler P, Møller IM, Xu D. MULocDeep: A deep-learning framework for protein subcellular and suborganellar localization prediction with residue-level interpretation. Comput Struct Biotechnol J 2021; 19:4825-4839. [PMID: 34522290 PMCID: PMC8426535 DOI: 10.1016/j.csbj.2021.08.027] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/16/2021] [Accepted: 08/16/2021] [Indexed: 12/18/2022] Open
Abstract
Prediction of protein localization plays an important role in understanding protein function and mechanisms. In this paper, we propose a general deep learning-based localization prediction framework, MULocDeep, which can predict multiple localizations of a protein at both subcellular and suborganellar levels. We collected a dataset with 44 suborganellar localization annotations in 10 major subcellular compartments—the most comprehensive suborganelle localization dataset to date. We also experimentally generated an independent dataset of mitochondrial proteins in Arabidopsis thaliana cell cultures, Solanum tuberosum tubers, and Vicia faba roots and made this dataset publicly available. Evaluations using the above datasets show that overall, MULocDeep outperforms other major methods at both subcellular and suborganellar levels. Furthermore, MULocDeep assesses each amino acid’s contribution to localization, which provides insights into the mechanism of protein sorting and localization motifs. A web server can be accessed at http://mu-loc.org.
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Affiliation(s)
- Yuexu Jiang
- Department of Electrical Engineering and Computer Science, Bond Life Sciences Center, Columbia, MO, USA
| | - Duolin Wang
- Department of Electrical Engineering and Computer Science, Bond Life Sciences Center, Columbia, MO, USA
| | - Yifu Yao
- Department of Electrical Engineering and Computer Science, Bond Life Sciences Center, Columbia, MO, USA
| | - Holger Eubel
- Institute of Plant Genetics, Leibniz University Hannover, Hannover, Germany
| | - Patrick Künzler
- Institute of Plant Genetics, Leibniz University Hannover, Hannover, Germany
| | - Ian Max Møller
- Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, DK-4200 Slagelse, Denmark
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, Bond Life Sciences Center, Columbia, MO, USA
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Subcellular Localizations of Catalase and Exogenously Added Fatty Acid in Chlamydomonas reinhardtii. Cells 2021; 10:cells10081940. [PMID: 34440712 PMCID: PMC8391285 DOI: 10.3390/cells10081940] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 02/01/2023] Open
Abstract
Fatty acids are important biological components, yet the metabolism of fatty acids in microalgae is not clearly understood. Previous studies found that Chlamydomonas reinhardtii, the model microalga, incorporates exogenously added fatty acids but metabolizes them differently from animals and yeast. Furthermore, a recent metabolic flux analysis found that the majority of lipid turnover in C. reinhardtii is the recycling of acyl chains from and to membranes, rather than β -oxidation. This indicates that for the alga, the maintenance of existing acyl chains may be more valuable than their breakdown for energy. To gain cell-biological knowledge of fatty acid metabolism in C. reinhardtii, we conducted microscopy analysis with fluorescent probes. First, we found that CAT1 (catalase isoform 1) is in the peroxisomes while CAT2 (catalase isoform 2) is localized in the endoplasmic reticulum, indicating the alga is capable of detoxifying hydrogen peroxide that would be produced during β-oxidation in the peroxisomes. Second, we compared the localization of exogenously added FL-C16 (fluorescently labelled palmitic acid) with fluorescently marked endosomes, mitochondria, peroxisomes, lysosomes, and lipid droplets. We found that exogenously added FL-C16 are incorporated and compartmentalized via a non-endocytic route within 10 min. However, the fluorescence signals from FL-C16 did not colocalize with any marked organelles, including peroxisomes. During triacylglycerol accumulation, the fluorescence signals from FL-C16 were localized in lipid droplets. These results support the idea that membrane turnover is favored over β-oxidation in C. reinhardtii. The knowledge gained in these analyses would aid further studies of the fatty acid metabolism.
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Lackus ND, Schmidt A, Gershenzon J, Köllner TG. A peroxisomal β-oxidative pathway contributes to the formation of C6-C1 aromatic volatiles in poplar. PLANT PHYSIOLOGY 2021; 186:891-909. [PMID: 33723573 PMCID: PMC8195509 DOI: 10.1093/plphys/kiab111] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 02/19/2021] [Indexed: 05/06/2023]
Abstract
Benzenoids (C6-C1 aromatic compounds) play important roles in plant defense and are often produced upon herbivory. Black cottonwood (Populus trichocarpa) produces a variety of volatile and nonvolatile benzenoids involved in various defense responses. However, their biosynthesis in poplar is mainly unresolved. We showed feeding of the poplar leaf beetle (Chrysomela populi) on P. trichocarpa leaves led to increased emission of the benzenoid volatiles benzaldehyde, benzylalcohol, and benzyl benzoate. The accumulation of salicinoids, a group of nonvolatile phenolic defense glycosides composed in part of benzenoid units, was hardly affected by beetle herbivory. In planta labeling experiments revealed that volatile and nonvolatile poplar benzenoids are produced from cinnamic acid (C6-C3). The biosynthesis of C6-C1 aromatic compounds from cinnamic acid has been described in petunia (Petunia hybrida) flowers where the pathway includes a peroxisomal-localized chain shortening sequence, involving cinnamate-CoA ligase (CNL), cinnamoyl-CoA hydratase/dehydrogenase (CHD), and 3-ketoacyl-CoA thiolase (KAT). Sequence and phylogenetic analysis enabled the identification of small CNL, CHD, and KAT gene families in P. trichocarpa. Heterologous expression of the candidate genes in Escherichia coli and characterization of purified proteins in vitro revealed enzymatic activities similar to those described in petunia flowers. RNA interference-mediated knockdown of the CNL subfamily in gray poplar (Populus x canescens) resulted in decreased emission of C6-C1 aromatic volatiles upon herbivory, while constitutively accumulating salicinoids were not affected. This indicates the peroxisomal β-oxidative pathway participates in the formation of volatile benzenoids. The chain shortening steps for salicinoids, however, likely employ an alternative pathway.
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Affiliation(s)
- Nathalie D Lackus
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Axel Schmidt
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Jonathan Gershenzon
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Tobias G Köllner
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
- Author for communication:
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21
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Costello R, Emms DM, Kelly S. Gene Duplication Accelerates the Pace of Protein Gain and Loss from Plant Organelles. Mol Biol Evol 2021; 37:969-981. [PMID: 31750917 PMCID: PMC7086175 DOI: 10.1093/molbev/msz275] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Organelle biogenesis and function is dependent on the concerted action of both organellar-encoded (if present) and nuclear-encoded proteins. Differences between homologous organelles across the Plant Kingdom arise, in part, as a result of differences in the cohort of nuclear-encoded proteins that are targeted to them. However, neither the rate at which differences in protein targeting accumulate nor the evolutionary consequences of these changes are known. Using phylogenomic approaches coupled to ancestral state estimation, we show that the plant organellar proteome has diversified in proportion with molecular sequence evolution such that the proteomes of plant chloroplasts and mitochondria lose or gain on average 3.6 proteins per million years. We further demonstrate that changes in organellar protein targeting are associated with an increase in the rate of molecular sequence evolution and that such changes predominantly occur in genes with regulatory rather than metabolic functions. Finally, we show that gain and loss of protein target signals occurs at a higher rate following gene duplication, revealing that gene and genome duplication are a key facilitator of plant organelle evolution.
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Affiliation(s)
- Rona Costello
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - David M Emms
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Steven Kelly
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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22
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Jawahir V, Zolman BK. Long chain acyl CoA synthetase 4 catalyzes the first step in peroxisomal indole-3-butyric acid to IAA conversion. PLANT PHYSIOLOGY 2021; 185:120-136. [PMID: 33631795 PMCID: PMC8133310 DOI: 10.1093/plphys/kiaa002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 10/08/2020] [Indexed: 06/12/2023]
Abstract
Indole-3-butyric acid (IBA) is an endogenous storage auxin important for maintaining appropriate indole-3-acetic acid (IAA) levels, thereby influencingprimary root elongation and lateral root development. IBA is metabolized into free IAA in peroxisomes in a multistep process similar to fatty acid β-oxidation. We identified LONG CHAIN ACYL-COA SYNTHETASE 4 (LACS4) in a screen for enhanced IBA resistance in primary root elongation in Arabidopsis thaliana. LACSs activate substrates by catalyzing the addition of CoA, the necessary first step for fatty acids to participate in β-oxidation or other metabolic pathways. Here, we describe the novel role of LACS4 in hormone metabolism and postulate that LACS4 catalyzes the addition of CoA onto IBA, the first step in its β-oxidation. lacs4 is resistant to the effects of IBA in primary root elongation and dark-grown hypocotyl elongation, and has reduced lateral root density. lacs6 also is resistant to IBA, although both lacs4 and lacs6 remain sensitive to IAA in primary root elongation, demonstrating that auxin responses are intact. LACS4 has in vitro enzymatic activity on IBA, but not IAA or IAA conjugates, and disruption of LACS4 activity reduces the amount of IBA-derived IAA in planta. We conclude that, in addition to activity on fatty acids, LACS4 and LACS6 also catalyze the addition of CoA onto IBA, the first step in IBA metabolism and a necessary step in generating IBA-derived IAA.
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Affiliation(s)
- Vanessica Jawahir
- Department of Biology, University of Missouri – St Louis, St Louis, Missouri 63121, USA
| | - Bethany Karlin Zolman
- Department of Biology, University of Missouri – St Louis, St Louis, Missouri 63121, USA
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23
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Tyagi S, Singh K, Upadhyay SK. Molecular characterization revealed the role of catalases under abiotic and arsenic stress in bread wheat (Triticum aestivum L.). JOURNAL OF HAZARDOUS MATERIALS 2021; 403:123585. [PMID: 32810714 DOI: 10.1016/j.jhazmat.2020.123585] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 07/01/2020] [Accepted: 07/13/2020] [Indexed: 06/11/2023]
Abstract
Catalases are crucial antioxidant enzymes that reduce the excessive level of H2O2 caused by various environmental stresses and metal toxicity and hence protect the plant cells. In this study, a total of ten TaCAT genes, forming three homeologous groups, were identified in the genome of bread wheat (Triticum aestivum L.) and named as per the wheat gene symbolization guidelines. The identified catalases were characterized for various structural and physicochemical features. The proximal active-site (F(D/A)RERIPERVVHAKGASA) and heme-ligand (R(I/V)F(S/A)Y(A/S)DTQ) signature motifs, catalytic residues and peroxisomal targeting peptides were found conserved. Phylogenetic analysis clustered TaCATs into three classes, which showed conserved functional specialization based on their tissue specific expression. Modulated spatio-temporal expression of various TaCAT genes and alteration in total catalase enzyme activity during heat, drought, salt and arsenic (AsIII and AsV) treatment suggested their roles in abiotic stress response and arsenic tolerance. Molecular cloning and overexpression of TaCAT3-B gene in Escherichia coli showed tolerance against heat, drought, salt and varied concentrations of AsIII and AsV treatments. The results further confirmed their role in stress tolerance and recommended that these genes can be used in future stress management strategies for the development of abiotic and arsenic stress resistant transgenic crops.
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Affiliation(s)
- Shivi Tyagi
- Department of Botany, Panjab University, Chandigarh, 160014, India
| | - Kashmir Singh
- Department of Biotechnology, Panjab University, Chandigarh, 160014, India
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24
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Singh P, Preu L, Beuerle T, Kaufholdt D, Hänsch R, Beerhues L, Gaid M. A promiscuous coenzyme A ligase provides benzoyl-coenzyme A for xanthone biosynthesis in Hypericum. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:1472-1490. [PMID: 33031578 DOI: 10.1111/tpj.15012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/11/2020] [Accepted: 09/23/2020] [Indexed: 05/09/2023]
Abstract
Benzoic acid-derived compounds, such as polyprenylated benzophenones and xanthones, attract the interest of scientists due to challenging chemical structures and diverse biological activities. The genus Hypericum is of high medicinal value, as exemplified by H. perforatum. It is rich in benzophenone and xanthone derivatives, the biosynthesis of which requires the catalytic activity of benzoate-coenzyme A (benzoate-CoA) ligase (BZL), which activates benzoic acid to benzoyl-CoA. Despite remarkable research so far done on benzoic acid biosynthesis in planta, all previous structural studies of BZL genes and proteins are exclusively related to benzoate-degrading microorganisms. Here, a transcript for a plant acyl-activating enzyme (AAE) was cloned from xanthone-producing Hypericum calycinum cell cultures using transcriptomic resources. An increase in the HcAAE1 transcript level preceded xanthone accumulation after elicitor treatment, as previously observed with other pathway-related genes. Subcellular localization of reporter fusions revealed the dual localization of HcAAE1 to cytosol and peroxisomes owing to a type 2 peroxisomal targeting signal. This result suggests the generation of benzoyl-CoA in Hypericum by the CoA-dependent non-β-oxidative route. A luciferase-based substrate specificity assay and the kinetic characterization indicated that HcAAE1 exhibits promiscuous substrate preference, with benzoic acid being the sole aromatic substrate accepted. Unlike 4-coumarate-CoA ligase and cinnamate-CoA ligase enzymes, HcAAE1 did not accept 4-coumaric and cinnamic acids, respectively. The substrate preference was corroborated by in silico modeling, which indicated valid docking of both benzoic acid and its adenosine monophosphate intermediate in the HcAAE1/BZL active site cavity.
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Affiliation(s)
- Poonam Singh
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Mendelssohnstraße 1, Braunschweig, 38106, Germany
| | - Lutz Preu
- Institute of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Beethovenstraße 55, Braunschweig, 38106, Germany
| | - Till Beuerle
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Mendelssohnstraße 1, Braunschweig, 38106, Germany
| | - David Kaufholdt
- Institute of Plant Biology, Technische Universität Braunschweig, Humboldtstraße 1, Braunschweig, 38106, Germany
| | - Robert Hänsch
- Institute of Plant Biology, Technische Universität Braunschweig, Humboldtstraße 1, Braunschweig, 38106, Germany
- Center of Molecular Ecophysiology (CMEP) - College of Resources and Environment, Southwest University No. 2, Tiansheng Road, Chongqing, 400715, P.R. China
| | - Ludger Beerhues
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Mendelssohnstraße 1, Braunschweig, 38106, Germany
- Centre of Pharmaceutical Engineering, Technische Universität Braunschweig, Franz-Liszt-Straße 35 A, Braunschweig, 38106, Germany
| | - Mariam Gaid
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Mendelssohnstraße 1, Braunschweig, 38106, Germany
- Centre of Pharmaceutical Engineering, Technische Universität Braunschweig, Franz-Liszt-Straße 35 A, Braunschweig, 38106, Germany
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25
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Wang X, Sheng X, Tian X, Zhang Y, Li Y. Organelle movement and apical accumulation of secretory vesicles in pollen tubes of Arabidopsis thaliana depend on class XI myosins. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:1685-1697. [PMID: 33067901 DOI: 10.1111/tpj.15030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 09/12/2020] [Accepted: 09/18/2020] [Indexed: 06/11/2023]
Abstract
F-actin and myosin XI play important roles in plant organelle movement. A few myosin XI genes in the genome of Arabidopsis are mainly expressed in mature pollen, which suggests that they may play a crucial role in pollen germination and pollen tube tip growth. In this study, a genetic complementation assay was conducted in a myosin xi-c (myo11c1) myosin xi-e (myo11c2) double mutant, and fluorescence labeling combined with microscopic observation was applied. We found that myosin XI-E (Myo11C2)-green fluorescent protein (GFP) restored the slow pollen tube growth and seed deficiency phenotypes of the myo11c1 myo11c2 double mutant and Myo11C2-GFP partially colocalized with mitochondria, peroxisomes and Golgi stacks. Furthermore, decreased mitochondrial movement and subapical accumulation were detected in myo11c1 myo11c2 double mutant pollen tubes. Fluorescence recovery after photobleaching experiments showed that the fluorescence recoveries of GFP-RabA4d and AtPRK1-GFP at the pollen tube tip of the myo11c1 myo11c2 double mutant were lower than those of the wild type were after photobleaching. These results suggest that Myo11C2 may be associated with mitochondria, peroxisomes and Golgi stacks, and play a crucial role in organelle movement and apical accumulation of secretory vesicles in pollen tubes of Arabidopsis thaliana.
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Affiliation(s)
- Xingjuan Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xiaojing Sheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xiulin Tian
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yu Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yan Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
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26
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Xia FN, Zeng B, Liu HS, Qi H, Xie LJ, Yu LJ, Chen QF, Li JF, Chen YQ, Jiang L, Xiao S. SINAT E3 Ubiquitin Ligases Mediate FREE1 and VPS23A Degradation to Modulate Abscisic Acid Signaling. THE PLANT CELL 2020; 32:3290-3310. [PMID: 32753431 PMCID: PMC7534459 DOI: 10.1105/tpc.20.00267] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/13/2020] [Accepted: 07/31/2020] [Indexed: 05/09/2023]
Abstract
In plants, the ubiquitin-proteasome system, endosomal sorting, and autophagy are essential for protein degradation; however, their interplay remains poorly understood. Here, we show that four Arabidopsis (Arabidopsis thaliana) E3 ubiquitin ligases, SEVEN IN ABSENTIA OF ARABIDOPSIS THALIANA1 (SINAT1), SINAT2, SINAT3, and SINAT4, regulate the stabilities of FYVE DOMAIN PROTEIN REQUIRED FOR ENDOSOMAL SORTING1 (FREE1) and VACUOLAR PROTEIN SORTING23A (VPS23A), key components of the endosomal sorting complex required for transport-I, to modulate abscisic acid (ABA) signaling. GFP-SINAT1, GFP-SINAT2, and GFP-SINAT4 primarily localized to the endosomal and autophagic vesicles. SINATs controlled FREE1 and VPS23A ubiquitination and proteasomal degradation. SINAT overexpressors showed increased ABA sensitivity, ABA-responsive gene expression, and PYRABACTIN RESISTANCE1-LIKE4 protein levels. Furthermore, the SINAT-FREE1/VPS23A proteins were codegraded by the vacuolar pathway. In particular, during recovery post-ABA exposure, SINATs formed homo- and hetero-oligomers in vivo, which were disrupted by the autophagy machinery. Taken together, our findings reveal a novel mechanism by which the proteasomal and vacuolar turnover systems regulate ABA signaling in plants.
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Affiliation(s)
- Fan-Nv Xia
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Baiquan Zeng
- College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, People's Republic of China
| | - Hui-Shan Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Hua Qi
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Li-Juan Xie
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Lu-Jun Yu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Qin-Fang Chen
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Jian-Feng Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Yue-Qin Chen
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Liwen Jiang
- Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, People's Republic of China
| | - Shi Xiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
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Aconitase: To Be or not to Be Inside Plant Glyoxysomes, That Is the Question. BIOLOGY 2020; 9:biology9070162. [PMID: 32664680 PMCID: PMC7407140 DOI: 10.3390/biology9070162] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/08/2020] [Accepted: 07/10/2020] [Indexed: 12/26/2022]
Abstract
After the discovery in 1967 of plant glyoxysomes, aconitase, one the five enzymes involved in the glyoxylate cycle, was thought to be present in the organelles, and although this was found not to be the case around 25 years ago, it is still suggested in some textbooks and recent scientific articles. Genetic research (including the study of mutants and transcriptomic analysis) is becoming increasingly important in plant biology, so metabolic pathways must be presented correctly to avoid misinterpretation and the dissemination of bad science. The focus of our study is therefore aconitase, from its first localization inside the glyoxysomes to its relocation. We also examine data concerning the role of the enzyme malate dehydrogenase in the glyoxylate cycle and data of the expression of aconitase genes in Arabidopsis and other selected higher plants. We then propose a new model concerning the interaction between glyoxysomes, mitochondria and cytosol in cotyledons or endosperm during the germination of oil-rich seeds.
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28
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Baune MC, Lansing H, Fischer K, Meyer T, Charton L, Linka N, von Schaewen A. The Arabidopsis Plastidial Glucose-6-Phosphate Transporter GPT1 is Dually Targeted to Peroxisomes via the Endoplasmic Reticulum. THE PLANT CELL 2020; 32:1703-1726. [PMID: 32111666 PMCID: PMC7203913 DOI: 10.1105/tpc.19.00959] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/28/2020] [Accepted: 02/28/2020] [Indexed: 05/22/2023]
Abstract
Studies on Glucose-6-phosphate (G6P)/phosphate translocator isoforms GPT1 and GPT2 reported the viability of Arabidopsis (Arabidopsis thaliana) gpt2 mutants, whereas heterozygous gpt1 mutants exhibited a variety of defects during fertilization/seed set, indicating that GPT1 is essential for this process. Among other functions, GPT1 was shown to be important for pollen and embryo-sac development. Because our previous work on the irreversible part of the oxidative pentose phosphate pathway (OPPP) revealed comparable effects, we investigated whether GPT1 may dually localize to plastids and peroxisomes. In reporter fusions, GPT2 localized to plastids, but GPT1 also localized to the endoplasmic reticulum (ER) and around peroxisomes. GPT1 contacted two oxidoreductases and also peroxins that mediate import of peroxisomal membrane proteins from the ER, hinting at dual localization. Reconstitution in yeast (Saccharomyces cerevisiae) proteoliposomes revealed that GPT1 preferentially exchanges G6P for ribulose-5-phosphate (Ru5P). Complementation analyses of heterozygous +/gpt1 plants demonstrated that GPT2 is unable to compensate for GPT1 in plastids, whereas GPT1 without the transit peptide (enforcing ER/peroxisomal localization) increased gpt1 transmission significantly. Because OPPP activity in peroxisomes is essential for fertilization, and immunoblot analyses hinted at the presence of unprocessed GPT1-specific bands, our findings suggest that GPT1 is indispensable in both plastids and peroxisomes. Together with its G6P-Ru5P exchange preference, GPT1 appears to play a role distinct from that of GPT2 due to dual targeting.
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Affiliation(s)
- Marie-Christin Baune
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Hannes Lansing
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Kerstin Fischer
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Tanja Meyer
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Lennart Charton
- Biochemie der Pflanzen, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Nicole Linka
- Biochemie der Pflanzen, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Antje von Schaewen
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
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29
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Kataya ARA, Elshobaky A, Heidari B, Dugassa NF, Thelen JJ, Lillo C. Multi-targeted trehalose-6-phosphate phosphatase I harbors a novel peroxisomal targeting signal 1 and is essential for flowering and development. PLANTA 2020; 251:98. [PMID: 32306103 PMCID: PMC7214503 DOI: 10.1007/s00425-020-03389-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 04/10/2020] [Indexed: 05/13/2023]
Abstract
This work reveals information about new peroxisomal targeting signals type 1 and identifies trehalose-6-phosphate phosphatase I as multitargeted and is implicated in plant development, reproduction, and stress response. A putative, non-canonical peroxisomal targeting signal type 1 (PTS1) Pro-Arg-Met > was identified in the extreme C-terminus of trehalose-6-phosphate phosphatase (TPP)I. TPP catalyzes the final step of trehalose synthesis, and the enzyme was previously characterized to be nuclear only (Krasensky et al. in Antioxid Redox Signal 21(9):1289-1304, 2014). Here we show that the TPPI C-terminal decapeptide ending with Pro-Arg-Met > or Pro-Lys-Met > can indeed function as a PTS1. Upon transient expression in two plant expression systems, the free C- or N-terminal end led to the full-length TPPI targeting to peroxisomes and plastids, respectively. The nucleus and nucleolus targeting of the full-length TPPI was observed in both cases. The homozygous T-DNA insertion line of TPPI showed a pleiotropic phenotype including smaller leaves, shorter roots, delayed flowering, hypersensitivity to salt, and a sucrose dependent seedling development. Our results identify novel PTS1s, and TPPI as a protein multi-targeted to peroxisomes, plastids, nucleus, and nucleolus. Altogether our findings implicate an essential role for TPPI in development, reproduction, and cell signaling.
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Affiliation(s)
- Amr R A Kataya
- Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, 4036, Stavanger, Norway.
- Department of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.
| | - Ahmed Elshobaky
- Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, 4036, Stavanger, Norway
- Botany Department, Faculty of Science, Mansoura University, Mansoura, 35516, Egypt
| | - Behzad Heidari
- Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, 4036, Stavanger, Norway
- Department of Plant Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Nemie-Feyissa Dugassa
- Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, 4036, Stavanger, Norway
| | - Jay J Thelen
- Department of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Cathrine Lillo
- Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, 4036, Stavanger, Norway
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30
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Abstract
The past several decades have witnessed tremendous growth in the protein targeting, transport and translocation field. Major advances were made during this time period. Now the molecular details of the targeting factors, receptors and the membrane channels that were envisioned in Blobel's Signal Hypothesis in the 1970s have been revealed by powerful structural methods. It is evident that there is a myriad of cytosolic and membrane associated systems that accurately sort and target newly synthesized proteins to their correct membrane translocases for membrane insertion or protein translocation. Here we will describe the common principles for protein transport in prokaryotes and eukaryotes.
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31
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Lansing H, Doering L, Fischer K, Baune MC, Schaewen AV. Analysis of potential redundancy among Arabidopsis 6-phosphogluconolactonase isoforms in peroxisomes. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:823-836. [PMID: 31641750 DOI: 10.1093/jxb/erz473] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 10/10/2019] [Indexed: 05/21/2023]
Abstract
Recent work revealed that PGD2, an Arabidopsis 6-phosphogluconate dehydrogenase (6-PGD) catalysing the third step of the oxidative pentose-phosphate pathway (OPPP) in peroxisomes, is essential during fertilization. Earlier studies on the second step, catalysed by PGL3, a dually targeted Arabidopsis 6-phosphogluconolactonase (6-PGL), reported the importance of OPPP reactions in plastids but their irrelevance in peroxisomes. Assuming redundancy of 6-PGL activity in peroxisomes, we examined the sequences of other higher plant enzymes. In tomato, there exist two 6-PGL isoforms with the strong PTS1 motif SKL. However, their analysis revealed problems regarding peroxisomal targeting: reporter-PGL detection in peroxisomes required construct modification, which was also applied to the Arabidopsis isoforms. The relative contribution of PGL3 versus PGL5 during fertilization was assessed by mutant crosses. Reduced transmission ratios were found for pgl3-1 (T-DNA-eliminated PTS1) and also for knock-out allele pgl5-2. The prominent role of PGL3 showed as compromised growth of pgl3-1 seedlings on sucrose and higher activity of mutant PGL3-1 versus PGL5 using purified recombinant proteins. Evidence for PTS1-independent uptake was found for PGL3-1 and other Arabidopsis PGL isoforms, indicating that peroxisome import may be supported by a piggybacking mechanism. Thus, multiple redundancy at the level of the second OPPP step in peroxisomes explains the occurrence of pgl3-1 mutant plants.
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Affiliation(s)
- Hannes Lansing
- Molekulare Physiologie der Pflanzen, Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Schlossplatz 7, D-48149 Münster, Germany
| | - Lennart Doering
- Molekulare Physiologie der Pflanzen, Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Schlossplatz 7, D-48149 Münster, Germany
| | - Kerstin Fischer
- Molekulare Physiologie der Pflanzen, Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Schlossplatz 7, D-48149 Münster, Germany
| | - Marie-Christin Baune
- Molekulare Physiologie der Pflanzen, Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Schlossplatz 7, D-48149 Münster, Germany
| | - Antje Von Schaewen
- Molekulare Physiologie der Pflanzen, Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Schlossplatz 7, D-48149 Münster, Germany
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Kunze M. The type-2 peroxisomal targeting signal. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1867:118609. [PMID: 31751594 DOI: 10.1016/j.bbamcr.2019.118609] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 11/08/2019] [Accepted: 11/13/2019] [Indexed: 12/13/2022]
Abstract
The type-2 peroxisomal targeting signal (PTS2) is one of two peptide motifs destining soluble proteins for peroxisomes. This signal acts as amphiphilic α-helix exposing the side chains of all conserved residues to the same side. PTS2 motifs are recognized by a bipartite protein complex consisting of the receptor PEX7 and a co-receptor. Cargo-loaded receptor complexes are translocated across the peroxisomal membrane by a transient pore and inside peroxisomes, cargo proteins are released and processed in many, but not all species. The components of the bipartite receptor are re-exported into the cytosol by a ubiquitin-mediated and ATP-driven export mechanism. Structurally, PTS2 motifs resemble other N-terminal targeting signals, whereas the functional relation to the second peroxisomal targeting signal (PTS1) is unclear. Although only a few PTS2-carrying proteins are known in humans, subjects lacking a functional import mechanism for these proteins suffer from the severe inherited disease rhizomelic chondrodysplasia punctata.
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Affiliation(s)
- Markus Kunze
- Medical University of Vienna, Center for Brain Research, Department of Pathobiology of the Nervous System, Spitalgasse 4, 1090 Vienna, Austria.
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Polyamine oxidase 2 is involved in regulating excess spermidine contents during seed germination and early seedling development in Arabidopsis thaliana. Biochem Biophys Res Commun 2019; 516:1248-1251. [DOI: 10.1016/j.bbrc.2019.07.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 07/06/2019] [Indexed: 11/20/2022]
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Nair P, Mall M, Sharma P, Khan F, Nagegowda DA, Rout PK, Gupta MM, Pandey A, Shasany AK, Gupta AK, Shukla AK. Characterization of a class III peroxidase from Artemisia annua: relevance to artemisinin metabolism and beyond. PLANT MOLECULAR BIOLOGY 2019; 100:527-541. [PMID: 31093899 DOI: 10.1007/s11103-019-00879-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 05/04/2019] [Indexed: 05/25/2023]
Abstract
A class III peroxidase from Artemisia annua has been shown to indicate the possibility of cellular localization-based role diversity, which may have implications in artemisinin catabolism as well as lignification. Artemisia annua derives its importance from the antimalarial artemisinin. The -O-O- linkage in artemisinin makes peroxidases relevant to its metabolism. Earlier, we identified three peroxidase-coding genes from A. annua, whereby Aa547 showed higher expression in the low-artemisinin plant stage whereas Aa528 and Aa540 showed higher expression in the artemisinin-rich plant stage. Here we carried out tertiary structure homology modelling of the peroxidases for docking studies. Maximum binding affinity for artemisinin was shown by Aa547. Further, Aa547 showed greater binding affinity for post-artemisinin metabolite, deoxyartemisinin, as compared to pre-artemisinin metabolites (dihydroartemisinic hydroperoxide, artemisinic acid, dihydroartemisinic acid). It also showed significant binding affinity for the monolignol, coniferyl alcohol. Moreover, Aa547 expression was related inversely to artemisinin content and directly to total lignin content as indicated by its transient silencing and overexpression in A. annua. Artemisinin reduction assay also indicated inverse relationship between Aa547 expression and artemisinin content. Subcellular localization using GFP fusion suggested that Aa547 is peroxisomal. Nevertheless, dual localization (intracellular/extracellular) of Aa547 could not be ruled out due to its effect on both, artemisinin and lignin. Taken together, this indicates possibility of localization-based role diversity for Aa547, which may have implications in artemisinin catabolism as well as lignification in A. annua.
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Affiliation(s)
- Priya Nair
- CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, U.P., 226015, India
| | - Maneesha Mall
- CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, U.P., 226015, India
| | - Pooja Sharma
- CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, U.P., 226015, India
| | - Feroz Khan
- CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, U.P., 226015, India
| | - Dinesh A Nagegowda
- CSIR-Central Institute of Medicinal and Aromatic Plants, Research Centre, Bengaluru, Karnataka, 560065, India
| | - Prasant K Rout
- CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, U.P., 226015, India
| | - Madan M Gupta
- CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, U.P., 226015, India
| | - Alok Pandey
- CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, U.P., 226015, India
| | - Ajit K Shasany
- CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, U.P., 226015, India
| | - Anil K Gupta
- CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, U.P., 226015, India
| | - Ashutosh K Shukla
- CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, U.P., 226015, India.
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Kataya ARA, Muench DG, Moorhead GB. A Framework to Investigate Peroxisomal Protein Phosphorylation in Arabidopsis. TRENDS IN PLANT SCIENCE 2019; 24:366-381. [PMID: 30683463 DOI: 10.1016/j.tplants.2018.12.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 12/11/2018] [Accepted: 12/20/2018] [Indexed: 06/09/2023]
Abstract
Peroxisomes perform essential roles in a range of cellular processes, highlighted by lipid metabolism, reactive species detoxification, and response to a variety of stimuli. The ability of peroxisomes to grow, divide, respond to changing cellular needs, interact with other organelles, and adjust their proteome as required, suggest that, like other organelles, their specialized roles are highly regulated. Similar to most other cellular processes, there is an emerging role for protein phosphorylation to regulate these events. In this review, we establish a knowledge framework of key players that control protein phosphorylation events in the plant peroxisome (i.e., the protein kinases and phosphatases), and highlight a vastly expanded set of (phospho)substrates.
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Affiliation(s)
- Amr R A Kataya
- Department of Chemistry, Bioscience, and Environmental Engineering, University of Stavanger, Stavanger, 4036, Norway; Department of Biological Sciences, University of Calgary, Calgary, T2N 1N4, Canada; www.katayaproject.com.
| | - Douglas G Muench
- Department of Biological Sciences, University of Calgary, Calgary, T2N 1N4, Canada
| | - Greg B Moorhead
- Department of Biological Sciences, University of Calgary, Calgary, T2N 1N4, Canada
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Mandal D, Sinharoy S. A Toolbox for Nodule Development Studies in Chickpea: A Hairy-Root Transformation Protocol and an Efficient Laboratory Strain of Mesorhizobium sp. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:367-378. [PMID: 30398908 DOI: 10.1094/mpmi-09-18-0264-ta] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
A Mesorhizobium sp. produces root nodules in chickpea. Chickpea and model legume Medicago truncatula are members of the inverted repeat-lacking clade (IRLC). The rhizobia, after internalization into the plant cell, are called bacteroids. Nodule-specific cysteine-rich peptides in IRLC legumes guide bacteroids to a terminally differentiated swollen (TDS) form. Bacteroids in chickpea are less TDS than those in Medicago spp. Nodule development in chickpea indicates recent evolutionary diversification and merits further study. A hairy-root transformation protocol and an efficient laboratory strain are prerequisites for performing any genetic study on nodulation. We have standardized a protocol for composite plant generation in chickpea with a transformation frequency above 50%, as shown by fluorescent markers. This protocol also works well in different ecotypes of chickpea. Localization of subcellular markers in these transformed roots is similar to the localization observed in transformed Medicago roots. When checked inside transformed nodules, peroxisomes were concentrated along the periphery of the nodules, while endoplasmic reticulum and Golgi bodies surrounded the symbiosomes. Different Mesorhizobium strains were evaluated for their ability to initiate nodule development and efficiency of nitrogen fixation. Inoculation with different strains resulted in different shapes of TDS bacteroids with variable nitrogen fixation. Our study provides a toolbox to study nodule development in the crop legume chickpea.
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Affiliation(s)
- Drishti Mandal
- National Institute of Plant Genome Research, New Delhi 110067, India
| | - Senjuti Sinharoy
- National Institute of Plant Genome Research, New Delhi 110067, India
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37
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Patel KJ, Kao Y, Llinas RJ, Bartel B. A PEX5 missense allele preferentially disrupts PTS1 cargo import into Arabidopsis peroxisomes. PLANT DIRECT 2019; 3:e00128. [PMID: 31236542 PMCID: PMC6508846 DOI: 10.1002/pld3.128] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 01/09/2019] [Accepted: 03/03/2019] [Indexed: 06/09/2023]
Abstract
The sorting of eukaryotic proteins to various organellar destinations requires receptors that recognize cargo protein targeting signals and facilitate transport into the organelle. One such receptor is the peroxin PEX5, which recruits cytosolic cargo carrying a peroxisome-targeting signal (PTS) type 1 (PTS1) for delivery into the peroxisomal lumen (matrix). In plants and mammals, PEX5 is also indirectly required for peroxisomal import of proteins carrying a PTS2 signal because PEX5 binds the PTS2 receptor, bringing the associated PTS2 cargo to the peroxisome along with PTS1 cargo. Despite PEX5 being the PTS1 cargo receptor, previously identified Arabidopsis pex5 mutants display either impairment of both PTS1 and PTS2 import or defects only in PTS2 import. Here we report the first Arabidopsis pex5 mutant with an exclusive PTS1 import defect. In addition to markedly diminished GFP-PTS1 import and decreased pex5-2 protein accumulation, this pex5-2 mutant shows typical peroxisome-related defects, including inefficient β-oxidation and reduced growth. Growth at reduced or elevated temperatures ameliorated or exacerbated pex5-2 peroxisome-related defects, respectively, without markedly changing pex5-2 protein levels. In contrast to the diminished PTS1 import, PTS2 processing was only slightly impaired and PTS2-GFP import appeared normal in pex5-2. This finding suggests that even minor peroxisomal localization of the PTS1 protein DEG15, the PTS2-processing protease, is sufficient to maintain robust PTS2 processing.
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Affiliation(s)
- Khushali J. Patel
- Department of BioSciencesRice UniversityHoustonTexas
- Present address:
Graduate School of Biomedical SciencesBaylor College of MedicineHoustonTexas
| | - Yun‐Ting Kao
- Department of BioSciencesRice UniversityHoustonTexas
- Present address:
Department of Cell Biology and Molecular GeneticsUniversity of MarylandCollege ParkMaryland
| | | | - Bonnie Bartel
- Department of BioSciencesRice UniversityHoustonTexas
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38
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Chen Z, Zheng W, Chen L, Li C, Liang T, Chen Z, Xu H, Han Y, Kong L, Zhao X, Wang F, Wang Z, Chen S. Green Fluorescent Protein- and Discosoma sp. Red Fluorescent Protein-Tagged Organelle Marker Lines for Protein Subcellular Localization in Rice. FRONTIERS IN PLANT SCIENCE 2019; 10:1421. [PMID: 31749824 PMCID: PMC6848374 DOI: 10.3389/fpls.2019.01421] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 10/14/2019] [Indexed: 05/23/2023]
Abstract
The subcellular localization of proteins is a fundamental aspect of protein functions. Determining the subcellular localization is important for understanding the biological functions of proteins. Here, we developed a set of rice organelle marker lines, in which the expressing fluorescent organelle markers could be used as comparative standards in determining the subcellular localization of the protein of interest. We constructed green fluorescent protein (GFP)- and/or Discosoma sp. red fluorescent protein (DsRed)-tagged organelle markers targeted to the endoplasmic reticulum (ER), mitochondria, Golgi apparatus, peroxisome, actin cytoskeleton, plastid, tonoplast, plasma membrane, and nucleus, respectively. The utility of the rice marker lines for protein subcellular localization studies was demonstrated by detecting a nucleus-localized OsWRKY45 and a mitochondria-associated NbHxk1 in protoplasts of the GFP-OsH2B and the ScCOX4-DsRed lines, respectively. Using a sheath-inoculation method, followed by a live-cell imaging, we detected co-localization of a Magnaporthe oryzae PWL2:mCherry : NLS fusion with the nucleus marker in the GFP-OsH2B rice epidermal cells, confirming the translocation of the M. oryzae effector PWL2 into host cells, and further demonstrating the feasibility of using the organelle marker lines for studying dynamics of proteins in rice cells in the interactions between rice and pathogens. The set of organelle marker lines developed in the present study, provides a valuable resource for protein subcellular localization studies in rice.
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Affiliation(s)
- Ziqiang Chen
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Wenhui Zheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Temasek Life Sciences Laboratory, and the Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Longhai Chen
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Chenlu Li
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Tingmin Liang
- Marine and Agricultural Biotechnology Laboratory, Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Zaijie Chen
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Huibing Xu
- Marine and Agricultural Biotechnology Laboratory, Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Yijuan Han
- Marine and Agricultural Biotechnology Laboratory, Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Lan Kong
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Xu Zhao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Feng Wang
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
- *Correspondence: Feng Wang, ; Zonghua Wang, ; Songbiao Chen,
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Marine and Agricultural Biotechnology Laboratory, Institute of Oceanography, Minjiang University, Fuzhou, China
- *Correspondence: Feng Wang, ; Zonghua Wang, ; Songbiao Chen,
| | - Songbiao Chen
- Marine and Agricultural Biotechnology Laboratory, Institute of Oceanography, Minjiang University, Fuzhou, China
- *Correspondence: Feng Wang, ; Zonghua Wang, ; Songbiao Chen,
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Xu Z, Sun M, Jiang X, Sun H, Dang X, Cong H, Qiao F. Glycinebetaine Biosynthesis in Response to Osmotic Stress Depends on Jasmonate Signaling in Watermelon Suspension Cells. FRONTIERS IN PLANT SCIENCE 2018; 9:1469. [PMID: 30369936 PMCID: PMC6194323 DOI: 10.3389/fpls.2018.01469] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 09/18/2018] [Indexed: 05/02/2023]
Abstract
Glycinebetaine is an important non-toxic osmoprotectant, which is accumulated in higher plants under various stresses. The biosynthesis of glycinebetaine achieved via is a two-step oxidation from choline and betaine aldehyde, catalyzed by choline monooxygenase (CMO) and betaine aldehyde dehydrogenase (BADH), respectively. Up-regulated gene expression of BADH and CMO induced by stress is clearly observed, but the signal transduction is poorly understood. Here, glycinebetaine accumulation in response to osmotic stress and growth recovery induced by exogenous glycinebetaine were observed in a watermelon cell line. When tracing back to the genome sequence of watermelon, it shows that there exists only one member of ClCMO or ClBADH corresponding to glycinebetaine biosynthesis. Both genes harbor a CGTCA-motif in their promoter region which is involved in methyl jasmonate (MeJA)-responsiveness. Amongst MeJA, Ethephon, abscisic acid (ABA), and salicylic acid (SA), MeJA was most effective in gene inducing the expression of ClCMO and ClBADH, and the accumulation of glycinebetaine could also reach an amount comparable to that after osmotic stress by mannitol. Moreover, when ibuprofen (IBU), a JA biosynthesis inhibitor, was pre-perfused into the cells before osmotic stress, glycinebetaine accumulation was suppressed significantly. Interestingly, newly grown cells can keep a high content of glycinebetaine when they are sub-cultured from osmotic stressed cells. This study suggests that osmotic stress induced glycinebetaine biosynthesis occurs via JA signal transduction and not only plays a key role in osmotic stress resistance but also contributes to osmotic stress hardening.
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Affiliation(s)
- Zijian Xu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Mengli Sun
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Xuefei Jiang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Huapeng Sun
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture, Danzhou, China
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, China
| | - Xuanmin Dang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture, Danzhou, China
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, China
| | - Hanqing Cong
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture, Danzhou, China
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, China
| | - Fei Qiao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture, Danzhou, China
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, China
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Mukai S, Matsuzaki T, Fujiki Y. The cytosolic peroxisome-targeting signal (PTS)-receptors, Pex7p and Pex5pL, are sufficient to transport PTS2 proteins to peroxisomes. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018; 1866:441-449. [PMID: 30296498 DOI: 10.1016/j.bbamcr.2018.10.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 09/14/2018] [Accepted: 10/02/2018] [Indexed: 12/28/2022]
Abstract
Proteins harboring peroxisome-targeting signal type-2 (PTS2) are recognized in the cytosol by mobile PTS2 receptor Pex7p and associate with a longer isoform Pex5pL of the PTS1 receptor. Trimeric PTS2 protein-Pex7p-Pex5pL complexes are translocated to peroxisomes in mammalian cells. However, it remains unclear whether Pex5pL and Pex7p are sufficient cytosolic components in transporting of PTS2 proteins to peroxisomes. Here, we construct a semi-intact cell import system to define the cytosolic components required for the peroxisomal PTS2 protein import and show that the PTS2 pre-import complexes comprising Pex7p, Pex5p, and Hsc70 isolated from the cytosol of pex14 Chinese hamster ovary cell mutant ZP161 is import-competent. PTS2 reporter proteins are transported to peroxisomes by recombinant Pex7p and Pex5pL in semi-intact cells devoid of the cytosol. Furthermore, PTS2 proteins are translocated to peroxisomes in the presence of a non-hydrolyzable ATP analogue, adenylyl imidodiphosphate, and N-ethylmaleimide, suggesting that ATP-dependent chaperones including Hsc70 are dispensable for PTS2 protein import. Taken together, we suggest that Pex7p and Pex5pL are the minimal cytosolic factors in the transport of PTS2 proteins to peroxisomes.
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Affiliation(s)
- Satoru Mukai
- Department of Biology, Faculty of Sciences, Kyushu University, 744 Motooka Nishi-ku, Fukuoka 819-0395, Japan
| | - Takashi Matsuzaki
- Department of Biology, Faculty of Sciences, Kyushu University, 744 Motooka Nishi-ku, Fukuoka 819-0395, Japan
| | - Yukio Fujiki
- Division of Organelle Homeostasis, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
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Takahashi Y, Ono K, Akamine Y, Asano T, Ezaki M, Mouri I. Highly-expressed polyamine oxidases catalyze polyamine back conversion in Brachypodium distachyon. JOURNAL OF PLANT RESEARCH 2018; 131:341-348. [PMID: 29063977 DOI: 10.1007/s10265-017-0989-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 10/04/2017] [Indexed: 05/25/2023]
Abstract
To understand the polyamine (PA) catabolic pathways in Brachypodium distachyon, we focused on the flavin-containing polyamine oxidase enzymes (PAO), and characterized them at the molecular and biochemical levels. Five PAO isoforms were identified from database searches, and we named them BdPAO1 to BdPAO5. By gene expression analysis using above-ground tissues such as leaf, stem and inflorescence, it was revealed that BdPAO2 is the most abundant PAO gene in normal growth conditions, followed by BdPAO3 and BdPAO4. BdPAO1 and BdPAO5 were expressed at very low levels. All Arabidopsis thaliana and rice orthologs belonging to the same clade as BdPAO2, BdPAO3 and BdPAO4 have conserved peroxisome-targeting signal sequences at their C-termini. Amino acid sequences of BdPAO2 and BdPAO4 also showed such a sequence, but BdPAO3 did not. We selected the gene with the highest expression level (BdPAO2) and the peroxisome-targeting signal lacking PAO (BdPAO3) for biochemical analysis of substrate specificity and catabolic pathways. BdPAO2 catalyzed conversion of spermine (Spm) or thermospermine to spermidine (Spd), and Spd to putrescine, but its most-favored substrate was Spd. In contrast, BdPAO3 favored Spm as substrate and catalyzed conversion of tetraamines to Spd. These results indicated that the major PAOs in B. distachyon have back-conversion activity.
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Affiliation(s)
- Yoshihiro Takahashi
- Department of Applied Chemistry and Biochemistry, Faculty of Engineering, Kyushu Sangyo University, 2-3-1 Matsukadai Higashi-ku, Fukuoka, 813-8503, Japan.
| | - Kaede Ono
- Department of Applied Chemistry and Biochemistry, Faculty of Engineering, Kyushu Sangyo University, 2-3-1 Matsukadai Higashi-ku, Fukuoka, 813-8503, Japan
| | - Yuuta Akamine
- Department of Applied Chemistry and Biochemistry, Faculty of Engineering, Kyushu Sangyo University, 2-3-1 Matsukadai Higashi-ku, Fukuoka, 813-8503, Japan
| | - Takuya Asano
- Department of Applied Chemistry and Biochemistry, Faculty of Engineering, Kyushu Sangyo University, 2-3-1 Matsukadai Higashi-ku, Fukuoka, 813-8503, Japan
| | - Masatoshi Ezaki
- Department of Applied Chemistry and Biochemistry, Faculty of Engineering, Kyushu Sangyo University, 2-3-1 Matsukadai Higashi-ku, Fukuoka, 813-8503, Japan
| | - Itsupei Mouri
- Department of Applied Chemistry and Biochemistry, Faculty of Engineering, Kyushu Sangyo University, 2-3-1 Matsukadai Higashi-ku, Fukuoka, 813-8503, Japan
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Incarbone M, Ritzenthaler C, Dunoyer P. Peroxisomal Targeting as a Sensitive Tool to Detect Protein-Small RNA Interactions through in Vivo Piggybacking. FRONTIERS IN PLANT SCIENCE 2018; 9:135. [PMID: 29479364 PMCID: PMC5812032 DOI: 10.3389/fpls.2018.00135, 10.3389/fphys.2018.00135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 01/24/2018] [Indexed: 06/26/2024]
Abstract
Peroxisomes are organelles that play key roles in eukaryotic metabolism. Their protein complement is entirely imported from the cytoplasm thanks to a unique pathway that is able to translocate folded proteins and protein complexes across the peroxisomal membrane. The import of molecules bound to a protein targeted to peroxisomes is an active process known as 'piggybacking' and we have recently shown that P15, a virus-encoded protein possessing a peroxisomal targeting sequence, is able to piggyback siRNAs into peroxisomes. Here, we extend this observation by analyzing the small RNA repertoire found in peroxisomes of P15-expressing plants. A direct comparison with the P15-associated small RNA retrieved during immunoprecipitation (IP) experiments, revealed that in vivo piggybacking coupled to peroxisome isolation could be a more sensitive means to determine the various small RNA species bound by a given protein. This increased sensitivity of peroxisome isolation as opposed to IP experiments was also striking when we analyzed the small RNA population bound by the Tomato bushy stunt virus-encoded P19, one of the best characterized viral suppressors of RNA silencing (VSR), artificially targeted to peroxisomes. These results support that peroxisomal targeting should be considered as a novel/alternative experimental approach to assess in vivo interactions that allows detection of labile binding events. The advantages and limitations of this approach are discussed.
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Affiliation(s)
| | | | - Patrice Dunoyer
- Institut de Biologie Moléculaire des Plantes du CNRS, UPR2357, Université de Strasbourg, Strasbourg, France
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Kao YT, Gonzalez KL, Bartel B. Peroxisome Function, Biogenesis, and Dynamics in Plants. PLANT PHYSIOLOGY 2018; 176:162-177. [PMID: 29021223 PMCID: PMC5761812 DOI: 10.1104/pp.17.01050] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 10/09/2017] [Indexed: 05/19/2023]
Abstract
Recent advances highlight understanding of the diversity of peroxisome contributions to plant biology and the mechanisms through which these essential organelles are generated.
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Affiliation(s)
- Yun-Ting Kao
- Department of Biosciences, Rice University, Houston, Texas 77005
| | - Kim L Gonzalez
- Department of Biosciences, Rice University, Houston, Texas 77005
| | - Bonnie Bartel
- Department of Biosciences, Rice University, Houston, Texas 77005
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44
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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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45
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Abstract
Despite of their economical and nutritional interest, the biology of fruits is still little studied in comparison with reports of other plant organs such as leaves and roots. Accordingly, research at subcellular and molecular levels is necessary not only to understand the physiology of fruits, but also to improve crop qualities. Efforts addressed to gain knowledge of the peroxisome proteome and how it interacts with the overall metabolism of fruits will provide tools to be used in breeding strategies of agricultural species with added value. In this work, special attention will be paid to peroxisomal proteins involved in the metabolism of reactive oxygen species (ROS) due to the relevant role of these compounds at fruit ripening. The proteome of peroxisomes purified from sweet pepper (Capsicum annuum L.) fruit is reported, where an iron-superoxide dismutase (Fe-SOD) was localized in these organelles, besides other antioxidant enzymes such as catalase and a Mn-SOD, as well as enzymes involved in the metabolism of carbohydrates, malate, lipids and fatty acids, amino acids, the glyoxylate cycle and in the potential organelles' movements.
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46
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Kunze M. Predicting Peroxisomal Targeting Signals to Elucidate the Peroxisomal Proteome of Mammals. Subcell Biochem 2018; 89:157-199. [PMID: 30378023 DOI: 10.1007/978-981-13-2233-4_7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Peroxisomes harbor a plethora of proteins, but the peroxisomal proteome as the entirety of all peroxisomal proteins is still unknown for mammalian species. Computational algorithms can be used to predict the subcellular localization of proteins based on their amino acid sequence and this method has been amply used to forecast the intracellular fate of individual proteins. However, when applying such algorithms systematically to all proteins of an organism the prediction of its peroxisomal proteome in silico should be possible. Therefore, a reliable detection of peroxisomal targeting signals (PTS ) acting as postal codes for the intracellular distribution of the encoding protein is crucial. Peroxisomal proteins can utilize different routes to reach their destination depending on the type of PTS. Accordingly, independent prediction algorithms have been developed for each type of PTS, but only those for type-1 motifs (PTS1) have so far reached a satisfying predictive performance. This is partially due to the low number of peroxisomal proteins limiting the power of statistical analyses and partially due to specific properties of peroxisomal protein import, which render functional PTS motifs inactive in specific contexts. Moreover, the prediction of the peroxisomal proteome is limited by the high number of proteins encoded in mammalian genomes, which causes numerous false positive predictions even when using reliable algorithms and buries the few yet unidentified peroxisomal proteins. Thus, the application of prediction algorithms to identify all peroxisomal proteins is currently ineffective as stand-alone method, but can display its full potential when combined with other methods.
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Affiliation(s)
- Markus Kunze
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna, Vienna, Austria.
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47
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Incarbone M, Ritzenthaler C, Dunoyer P. Peroxisomal Targeting as a Sensitive Tool to Detect Protein-Small RNA Interactions through in Vivo Piggybacking. FRONTIERS IN PLANT SCIENCE 2018; 9:135. [PMID: 29479364 PMCID: PMC5812032 DOI: 10.3389/fpls.2018.00135] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 01/24/2018] [Indexed: 05/09/2023]
Abstract
Peroxisomes are organelles that play key roles in eukaryotic metabolism. Their protein complement is entirely imported from the cytoplasm thanks to a unique pathway that is able to translocate folded proteins and protein complexes across the peroxisomal membrane. The import of molecules bound to a protein targeted to peroxisomes is an active process known as 'piggybacking' and we have recently shown that P15, a virus-encoded protein possessing a peroxisomal targeting sequence, is able to piggyback siRNAs into peroxisomes. Here, we extend this observation by analyzing the small RNA repertoire found in peroxisomes of P15-expressing plants. A direct comparison with the P15-associated small RNA retrieved during immunoprecipitation (IP) experiments, revealed that in vivo piggybacking coupled to peroxisome isolation could be a more sensitive means to determine the various small RNA species bound by a given protein. This increased sensitivity of peroxisome isolation as opposed to IP experiments was also striking when we analyzed the small RNA population bound by the Tomato bushy stunt virus-encoded P19, one of the best characterized viral suppressors of RNA silencing (VSR), artificially targeted to peroxisomes. These results support that peroxisomal targeting should be considered as a novel/alternative experimental approach to assess in vivo interactions that allows detection of labile binding events. The advantages and limitations of this approach are discussed.
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48
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Robin GP, Kleemann J, Neumann U, Cabre L, Dallery JF, Lapalu N, O’Connell RJ. Subcellular Localization Screening of Colletotrichum higginsianum Effector Candidates Identifies Fungal Proteins Targeted to Plant Peroxisomes, Golgi Bodies, and Microtubules. FRONTIERS IN PLANT SCIENCE 2018; 9:562. [PMID: 29770142 PMCID: PMC5942036 DOI: 10.3389/fpls.2018.00562] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 04/10/2018] [Indexed: 05/20/2023]
Abstract
The genome of the hemibiotrophic anthracnose fungus, Colletotrichum higginsianum, encodes a large inventory of putative secreted effector proteins that are sequentially expressed at different stages of plant infection, namely appressorium-mediated penetration, biotrophy and necrotrophy. However, the destinations to which these proteins are addressed inside plant cells are unknown. In the present study, we selected 61 putative effector genes that are highly induced in appressoria and/or biotrophic hyphae. We then used Agrobacterium-mediated transformation to transiently express them as N-terminal fusions with fluorescent proteins in cells of Nicotiana benthamiana for imaging by confocal microscopy. Plant compartments labeled by the fusion proteins in N. benthamiana were validated by co-localization with specific organelle markers, by transient expression of the proteins in the true host plant, Arabidopsis thaliana, and by transmission electron microscopy-immunogold labeling. Among those proteins for which specific subcellular localizations could be verified, nine were imported into plant nuclei, three were imported into the matrix of peroxisomes, three decorated cortical microtubule arrays and one labeled Golgi stacks. Two peroxisome-targeted proteins harbored canonical C-terminal tripeptide signals for peroxisome import via the PTS1 (peroxisomal targeting signal 1) pathway, and we showed that these signals are essential for their peroxisome localization. Our findings provide valuable information about which host processes are potentially manipulated by this pathogen, and also reveal plant peroxisomes, microtubules, and Golgi as novel targets for fungal effectors.
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Affiliation(s)
- Guillaume P. Robin
- UMR BIOGER, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Jochen Kleemann
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Ulla Neumann
- Central Microscopy, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Lisa Cabre
- UMR BIOGER, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Jean-Félix Dallery
- UMR BIOGER, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Nicolas Lapalu
- UMR BIOGER, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Richard J. O’Connell
- UMR BIOGER, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Versailles, France
- *Correspondence: Richard J. O’Connell,
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49
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Kalel VC, Erdmann R. Unraveling of the Structure and Function of Peroxisomal Protein Import Machineries. Subcell Biochem 2018; 89:299-321. [PMID: 30378029 DOI: 10.1007/978-981-13-2233-4_13] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Peroxisomes are dynamic organelles of eukaryotic cells performing a wide range of functions including fatty acid oxidation, peroxide detoxification and ether-lipid synthesis in mammals. Peroxisomes lack their own DNA and therefore have to import proteins post-translationally. Peroxisomes can import folded, co-factor bound and even oligomeric proteins. The involvement of cycling receptors is a special feature of peroxisomal protein import. Complex machineries of peroxin (PEX) proteins mediate peroxisomal matrix and membrane protein import. Identification of PEX genes was dominated by forward genetic techniques in the early 90s. However, recent developments in proteomic techniques has revolutionized the detailed characterization of peroxisomal protein import. Here, we summarize the current knowledge on peroxisomal protein import with emphasis on the contribution of proteomic approaches to our understanding of the composition and function of the peroxisomal protein import machineries.
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Affiliation(s)
- Vishal C Kalel
- Department of Systems Biochemistry, Faculty of Medicine, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Universitätsstr. 150, 44801, Bochum, Germany.
| | - Ralf Erdmann
- Department of Systems Biochemistry, Faculty of Medicine, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Universitätsstr. 150, 44801, Bochum, Germany
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50
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Yang T, Nagy I, Mancinotti D, Otterbach SL, Andersen TB, Motawia MS, Asp T, Geu-Flores F. Transcript profiling of a bitter variety of narrow-leafed lupin to discover alkaloid biosynthetic genes. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5527-5537. [PMID: 29155974 PMCID: PMC5853437 DOI: 10.1093/jxb/erx362] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 09/25/2017] [Indexed: 05/21/2023]
Abstract
Lupins (Lupinus spp.) are nitrogen-fixing legumes that accumulate toxic alkaloids in their protein-rich beans. These anti-nutritional compounds belong to the family of quinolizidine alkaloids (QAs), which are of interest to the pharmaceutical and chemical industries. To unleash the potential of lupins as protein crops and as sources of QAs, a thorough understanding of the QA pathway is needed. However, only the first enzyme in the pathway, lysine decarboxylase (LDC), is known. Here, we report the transcriptome of a high-QA variety of narrow-leafed lupin (L. angustifolius), obtained using eight different tissues and two different sequencing technologies. In addition, we present a list of 33 genes that are closely co-expressed with LDC and that represent strong candidates for involvement in lupin alkaloid biosynthesis. One of these genes encodes a copper amine oxidase able to convert the product of LDC, cadaverine, into 1-piperideine, as shown by heterologous expression and enzyme assays. Kinetic analysis revealed a low KM value for cadaverine, supporting a role as the second enzyme in the QA pathway. Our transcriptomic data set represents a crucial step towards the discovery of enzymes, transporters, and regulators involved in lupin alkaloid biosynthesis.
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Affiliation(s)
- Ting Yang
- Section for Plant Biochemistry, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Denmark
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Denmark
| | - Istvan Nagy
- Section of Crop Genetics and Biotechnology, Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Davide Mancinotti
- Section for Plant Biochemistry, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Denmark
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Denmark
| | - Sophie Lisa Otterbach
- Section for Plant Biochemistry, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Denmark
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Denmark
| | - Trine Bundgaard Andersen
- Section for Plant Biochemistry, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Denmark
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Denmark
| | - Mohammed Saddik Motawia
- Section for Plant Biochemistry, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Denmark
| | - Torben Asp
- Section of Crop Genetics and Biotechnology, Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Fernando Geu-Flores
- Section for Plant Biochemistry, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Denmark
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Denmark
- Correspondence:
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