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Gomez-Cano F, Chu YH, Cruz-Gomez M, Abdullah HM, Lee YS, Schnell DJ, Grotewold E. Exploring Camelina sativa lipid metabolism regulation by combining gene co-expression and DNA affinity purification analyses. Plant J 2022; 110:589-606. [PMID: 35064997 DOI: 10.1111/tpj.15682] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 01/18/2022] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
Camelina (Camelina sativa) is an annual oilseed plant that is gaining momentum as a biofuel cover crop. Understanding gene regulatory networks is essential to deciphering plant metabolic pathways, including lipid metabolism. Here, we take advantage of a growing collection of gene expression datasets to predict transcription factors (TFs) associated with the control of Camelina lipid metabolism. We identified approximately 350 TFs highly co-expressed with lipid-related genes (LRGs). These TFs are highly represented in the MYB, AP2/ERF, bZIP, and bHLH families, including a significant number of homologs of well-known Arabidopsis lipid and seed developmental regulators. After prioritizing the top 22 TFs for further validation, we identified DNA-binding sites and predicted target genes for 16 out of the 22 TFs tested using DNA affinity purification followed by sequencing (DAP-seq). Enrichment analyses of targets supported the co-expression prediction for most TF candidates, and the comparison to Arabidopsis revealed some common themes, but also aspects unique to Camelina. Within the top potential lipid regulators, we identified CsaMYB1, CsaABI3AVP1-2, CsaHB1, CsaNAC2, CsaMYB3, and CsaNAC1 as likely involved in the control of seed fatty acid elongation and CsaABI3AVP1-2 and CsabZIP1 as potential regulators of the synthesis and degradation of triacylglycerols (TAGs), respectively. Altogether, the integration of co-expression data and DNA-binding assays permitted us to generate a high-confidence and short list of Camelina TFs involved in the control of lipid metabolism during seed development.
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Affiliation(s)
- Fabio Gomez-Cano
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, Room 212, Biochemistry Building, East Lansing, MI, 48824-6473, USA
| | - Yi-Hsuan Chu
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, Room 212, Biochemistry Building, East Lansing, MI, 48824-6473, USA
| | - Mariel Cruz-Gomez
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, Room 212, Biochemistry Building, East Lansing, MI, 48824-6473, USA
| | - Hesham M Abdullah
- Department of Plant Biology, Michigan State University, 612 Wilson Road, Room 166, East Lansing, MI, 48824-1312, USA
- Biotechnology Department, Faculty of Agriculture, Al-Azhar University, Cairo, 11651, Egypt
| | - Yun Sun Lee
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, Room 212, Biochemistry Building, East Lansing, MI, 48824-6473, USA
| | - Danny J Schnell
- Department of Plant Biology, Michigan State University, 612 Wilson Road, Room 166, East Lansing, MI, 48824-1312, USA
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, Room 212, Biochemistry Building, East Lansing, MI, 48824-6473, USA
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Abstract
X-linked adrenoleukodystrophy (ALD) is a neurometabolic disorder affecting the adrenal glands, testes, spinal cord and brain. The disease is caused by mutations in the ABCD1 gene resulting in a defect in peroxisomal degradation of very long-chain fatty acids and their accumulation in plasma and tissues. Males with ALD have a near 100% life-time risk to develop myelopathy. The life-time prevalence to develop progressive cerebral white matter lesions (known as cerebral ALD) is about 60%. Adrenal insufficiency occurs in about 80% of male patients. In adulthood, 80% of women with ALD also develop myelopathy, but adrenal insufficiency or cerebral ALD are very rare. The complex clinical presentation and the absence of a genotype-phenotype correlation are complicating our understanding of the disease. In an attempt to understand the pathophysiology of ALD various model systems have been developed. While these model systems share the basic genetics and biochemistry of ALD they fail to fully recapitulate the complex neurodegenerative etiology of ALD. Each model system recapitulates certain aspects of the disorder. This exposes the complexity of ALD and therefore the challenge to create a comprehensive model system to fully understand ALD. In this review, we provide an overview of the different ALD modeling strategies from single-celled to multicellular organisms and from in vitro to in vivo approaches, and introduce how emerging iPSC-derived technologies could improve the understanding of this highly complex disorder.
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Affiliation(s)
- Roberto Montoro
- Department of Pediatric Neurology, Emma Children's Hospital, Amsterdam UMC, Amsterdam Leukodystrophy Center, Amsterdam NeuroscienceUniversity of AmsterdamAmsterdamThe Netherlands
| | - Vivi M. Heine
- Department of Child and Youth Psychiatry, Amsterdam UMC, Amsterdam NeuroscienceVrije Universiteit AmsterdamAmsterdamThe Netherlands
- Department of Complex Trait Genetics, Centre for Neurogenomics and Cognitive Research, Amsterdam NeuroscienceVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Stephan Kemp
- Department of Pediatric Neurology, Emma Children's Hospital, Amsterdam UMC, Amsterdam Leukodystrophy Center, Amsterdam NeuroscienceUniversity of AmsterdamAmsterdamThe Netherlands
- Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam UMC, Amsterdam Gastroenterology & MetabolismUniversity of AmsterdamAmsterdamThe Netherlands
| | - Marc Engelen
- Department of Pediatric Neurology, Emma Children's Hospital, Amsterdam UMC, Amsterdam Leukodystrophy Center, Amsterdam NeuroscienceUniversity of AmsterdamAmsterdamThe Netherlands
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Yan M, Xue C, Xiong Y, Meng X, Li B, Shen R, Lan P. Proteomic dissection of the similar and different responses of wheat to drought, salinity and submergence during seed germination. J Proteomics 2020; 220:103756. [PMID: 32201361 DOI: 10.1016/j.jprot.2020.103756] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 03/02/2020] [Accepted: 03/17/2020] [Indexed: 12/11/2022]
Abstract
Wheat (Triticum aestivum L.) is one of the major crops worldwide and its production is inevitably subjected to various biotic/abiotic stresses during the life cycle. Drought, salinity and flooding are among the most severe abiotic stresses restricting wheat yields and could occur at very early stages such as seed germination. How wheat seed germination responds to these different stresses remains incomplete. To fill the information gap, a label-free proteomic analysis was applied to decipher the proteomic profiling of the germinating wheat seeds subjected to PEG, NaCl and submergence treatments. In total, 4295 proteins were detected, of which 465, 397 and 732 showed significant alterations in abundance under those stresses when compared with control. A common denominator found in the response observed to all three stresses are changes related to small molecule metabolic processes, and particularly in pathways associated with phenylpropanoid biosynthesis and fatty acid degradation. It was also noticeable that pathways like cysteine and methionine metabolism in the PEG or submergence treatment and starch and sucrose metabolism in the submergence treatment are specifically pronounced. Functional analysis of putative proteins participating in these pathways revealed distinct responsive patterns across different stresses. SIGNIFICANCE: Wheat (Triticum aestivum L.) is one of the most important staple crops in the world, but its growth and productivity are frequently restrained by stresses such as drought, salinity and flooding. To date, many resources have been documented to investigate how wheat responds and adapts to these individual stresses during plant development and yield formation, but little attention was paid to the understandings of the internal link between different conditions, especially during the germination process, a critical stage that determines the optimal growth of wheat. In this study, we carried out the proteome profiling of the germinating seeds of a common wheat cultivar, Chinese Spring, subjected to PEG, NaCl and submergence stresses. We found that the phenylpropanoid biosynthesis and fatty acid degradation pathways were enriched as the ubiquitous stress responses, while some pathways were stress-specific, for instance, starch and sucrose metabolism against submergence. The changes in some of the altered processes were further validated by physiological and molecular approaches. Our results suggest that the overall pathway profiles concerned with the three stresses were similar, but the specific procedures and components in each process varied greatly. The altered proteins and processes can be taken as effective candidates in future breeding and agronomic modification researches.
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Affiliation(s)
- Mingke Yan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Caiwen Xue
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Xiong
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiangxiang Meng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bingjuan Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Renfang Shen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Ping Lan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Pan R, Liu J, Hu J. Peroxisomes in plant reproduction and seed-related development. J Integr Plant Biol 2019; 61:784-802. [PMID: 30578613 DOI: 10.1111/jipb.12765] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 12/18/2018] [Indexed: 05/21/2023]
Abstract
Peroxisomes are small multi-functional organelles essential for plant development and growth. Plant peroxisomes play various physiological roles, including phytohormone biosynthesis, lipid catabolism, reactive oxygen species metabolism and many others. Mutant analysis demonstrated key roles for peroxisomes in plant reproduction, seed development and germination and post-germinative seedling establishment; however, the underlying mechanisms remain to be fully elucidated. This review summarizes findings that reveal the importance and complexity of the role of peroxisomes in the pertinent processes. The β-oxidation pathway plays a central role, whereas other peroxisomal pathways are also involved. Understanding the biochemical and molecular mechanisms of these peroxisomal functions will be instrumental to the improvement of crop plants.
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Affiliation(s)
- Ronghui Pan
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Jun Liu
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Jianping Hu
- MSU-Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, USA
- Plant Biology Department, Michigan State University, East Lansing, MI, USA
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Wang J, Lin W, Yin Z, Wang L, Dong S, An J, Lin Z, Yu H, Shi L, Lin S, Chen S. Comprehensive evaluation of fuel properties and complex regulation of intracellular transporters for high oil production in developing seeds of Prunus sibirica for woody biodiesel. Biotechnol Biofuels 2019; 12:6. [PMID: 30622648 PMCID: PMC6318995 DOI: 10.1186/s13068-018-1347-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 12/24/2018] [Indexed: 05/17/2023]
Abstract
BACKGROUND Based on our previous studies of 17 Prunus sibirica germplasms, one plus tree with high quality and quantity of seed oils has emerged as novel potential source of biodiesel. To better develop P. sibirica seed oils as woody biodiesel, a concurrent exploration of oil content, FA composition, biodiesel yield and fuel properties as well as prediction model construction for fuel properties was conducted on developing seeds to determine the optimal seed harvest time for producing high-quality biodiesel. Oil synthesis required supply of carbon source, energy and FA, but their transport mechanisms still remains enigmatic. Our recent 454 sequencing of P. sibirica could provide long-read sequences to identify membrane transporters for a better understanding of regulatory mechanism for high oil production in developing seeds. RESULTS To better develop the seed oils of P. sibirica as woody biodiesel, we firstly focused on a temporal and comparative evaluation of growth tendency, oil content, FA composition, biodiesel yield and fuel properties as well as model construction for biodiesel property prediction in different developing seeds from P. sibirica plus tree (accession AS-80), revealing that the oils from developing seeds harvested after 60 days after flowering (DAF) could be as novel potential feedstock for producing biodiesel with ideal fuel property. To gain new insight into membrane transport mechanism for high oil yield in developing seeds of P. sibirica, we presented a global analysis of transporter based on our recent 454 sequencing data of P. sibirica. We annotated a total of 116 genes for membrane-localized transporters at different organelles (plastid, endoplasmatic reticulum, tonoplast, mitochondria and peroxisome), of which some specific transporters were identified to be involved in carbon allocation, metabolite transport and energy supply for oil synthesis by both RT-PCR and qRT-PCR. Importantly, the transporter-mediated model was well established for high oil synthesis in developing P. sibirica seeds. Our findings could help to reveal molecular mechanism of increased oil production and may also present strategies for engineering oil accumulation in oilseed plants. CONCLUSIONS This study presents a temporal and comparative evaluation of developing P. sibirica seed oils as a potential feedstock for producing high-quality biodiesel and a global identification for membrane transporters was to gain better insights into regulatory mechanism of high oil production in developing seeds of P. sibirica. Our findings may present strategies for developing woody biodiesel resources and engineering oil accumulation.
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Affiliation(s)
- Jia Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Biotechnology, School of Soil and Water Conservation, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, 100083 China
| | - Weijun Lin
- Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
| | - Zhongdong Yin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Biotechnology, School of Soil and Water Conservation, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, 100083 China
| | - Libing Wang
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 China
| | - ShuBin Dong
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Biotechnology, School of Soil and Water Conservation, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, 100083 China
| | - Jiyong An
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Biotechnology, School of Soil and Water Conservation, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, 100083 China
| | - Zixin Lin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Biotechnology, School of Soil and Water Conservation, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, 100083 China
| | - Haiyan Yu
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 China
| | - Lingling Shi
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Biotechnology, School of Soil and Water Conservation, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, 100083 China
| | - Shanzhi Lin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Biotechnology, School of Soil and Water Conservation, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, 100083 China
| | - Shaoliang Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Biotechnology, School of Soil and Water Conservation, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, 100083 China
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Li N, Xu C, Li-Beisson Y, Philippar K. Fatty Acid and Lipid Transport in Plant Cells. Trends Plant Sci 2016; 21:145-158. [PMID: 26616197 DOI: 10.1016/j.tplants.2015.10.011] [Citation(s) in RCA: 150] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 09/29/2015] [Accepted: 10/15/2015] [Indexed: 05/18/2023]
Abstract
Fatty acids (FAs) and lipids are essential - not only as membrane constituents but also for growth and development. In plants and algae, FAs are synthesized in plastids and to a large extent transported to the endoplasmic reticulum for modification and lipid assembly. Subsequently, lipophilic compounds are distributed within the cell, and thus are transported across most membrane systems. Membrane-intrinsic transporters and proteins for cellular FA/lipid transfer therefore represent key components for delivery and dissemination. In addition to highlighting their role in lipid homeostasis and plant performance, different transport mechanisms for land plants and green algae - in the model systems Arabidopsis thaliana, Chlamydomonas reinhardtii - are compared, thereby providing a current perspective on protein-mediated FA and lipid trafficking in photosynthetic cells.
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Affiliation(s)
- Nannan Li
- Research Center of Bioenergy and Bioremediation (RCBB), College of Resources and Environment, Southwest University, Beibei District, Chongqing, 400715, P.R. China
| | - Changcheng Xu
- Biology Department, Brookhaven National Laboratory, 50 Bell Avenue, Upton, NY 11973-5000, USA
| | - Yonghua Li-Beisson
- Institute of Environmental Biology and Biotechnology, The French Atomic and Alternative Energy Commission, Unité Mixte de Recherche 7265, Commissariat à l'Energie Atomique (CEA) Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - Katrin Philippar
- Department of Biology I, Ludwig-Maximilians-University München, 82152 Planegg-Martinsried, Germany.
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Huang LM, Lai CP, Chen LFO, Chan MT, Shaw JF. Arabidopsis SFAR4 is a novel GDSL-type esterase involved in fatty acid degradation and glucose tolerance. Bot Stud 2015; 56:33. [PMID: 28510842 PMCID: PMC5432905 DOI: 10.1186/s40529-015-0114-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 11/16/2015] [Indexed: 05/02/2023]
Abstract
BACKGROUND SFARs (seed fatty acid reducers) belonging to the GDSL lipases/esterases family have been reported to reduce fatty acid storage and composition in mature Arabidopsis seeds. GDSL lipases/esterases are hydrolytic enzymes that possess multifunctional properties, such as broad substrate specificity, regiospecificity, and stereoselectivity. Studies on the physiological functions and biochemical characteristics of GDSL lipases/esterases in plants are limited, so it is important to elucidate the molecular functions of GDSL-type genes. RESULTS We found that SFAR4 (At3g48460), a fatty acid reducer belonging to the Arabidopsis GDSL lipases/esterases family, was intensely expressed in embryo protrusion, early seedlings, and pollen. The characterization of recombinant SFAR4 protein indicated that it has short-length p-nitrophenyl esterase activity. In addition, SFAR4 enhanced the expression of genes involved in fatty acid metabolism during seed germination and seedling development. SFAR4 elevated the expression of COMATOSE, which transports fatty acids into peroxisomes, and of LACS6 and LACS7, which deliver long-chain acetyl-CoA for β-oxidation. Furthermore, SFAR4 increased the transcription of PED1 and PNC1, which function in importing peroxisomal ATP required for fatty acid degradation. SFAR4 has another function on tolerance to high glucose concentrations but had no significant effects on the expression of the glucose sensor HXK1. CONCLUSIONS The results demonstrated that SFAR4 is a GDSL-type esterase involved in fatty acid metabolism during post-germination and seedling development in Arabidopsis. We suggested that SFAR4 plays an important role in fatty acid degradation, thus reducing the fatty acid content.
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Affiliation(s)
- Li-Min Huang
- Institute of Biotechnology, National Cheng Kung University, No. 1, University Road, Tainan City, 701 Taiwan
- Academia Sinica Biotechnology Center in Southern Taiwan, Academia Sinica, No. 59, Siraya Blvd., SinShih Dist., Tainan, 74145 Taiwan
| | - Chia-Ping Lai
- Department of Food and Beverage Management, Far East University, No. 49, Zhonghua Rd., Xinshi Dist., Tainan City, 74448 Taiwan
| | - Long-Fang O. Chen
- Institute of Biotechnology, National Cheng Kung University, No. 1, University Road, Tainan City, 701 Taiwan
- Institute of Plant and Microbial Biology, Academia Sinica, No. 128, Sec. 2, Academia Road, Nankang, Taipei, 115 Taiwan
| | - Ming-Tsair Chan
- Institute of Biotechnology, National Cheng Kung University, No. 1, University Road, Tainan City, 701 Taiwan
- Agriculture Biotechnology Research Center, Academia Sinica, No. 128, Sec. 2, Academia Road, Nankang, Taipei, 115 Taiwan
- Academia Sinica Biotechnology Center in Southern Taiwan, Academia Sinica, No. 59, Siraya Blvd., SinShih Dist., Tainan, 74145 Taiwan
| | - Jei-Fu Shaw
- Institute of Biotechnology, National Cheng Kung University, No. 1, University Road, Tainan City, 701 Taiwan
- Department of Biological Science and Technology, I-Shou University, No. 1, Sec. 1, Syuecheng Rd., Dashu District, Kaohsiung City, 84001 Taiwan
- Agricultural Biotechnology Center, National Chung Hsing University, 250 Kuo Kuang Rd., Taichung, Taichung, 402 Taiwan
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Abstract
SIGNIFICANCE Reduction-oxidation (Redox) status operates as a major integrator of subcellular and extracellular metabolism and is simultaneously itself regulated by metabolic processes. Redox status not only dominates cellular metabolism due to the prominence of NAD(H) and NADP(H) couples in myriad metabolic reactions but also acts as an effective signal that informs the cell of the prevailing environmental conditions. After relay of this information, the cell is able to appropriately respond via a range of mechanisms, including directly affecting cellular functioning and reprogramming nuclear gene expression. RECENT ADVANCES The facile accession of Arabidopsis knockout mutants alongside the adoption of broad-scale post-genomic approaches, which are able to provide transcriptomic-, proteomic-, and metabolomic-level information alongside traditional biochemical and emerging cell biological techniques, has dramatically advanced our understanding of redox status control. This review summarizes redox status control of metabolism and the metabolic control of redox status at both cellular and subcellular levels. CRITICAL ISSUES It is becoming apparent that plastid, mitochondria, and peroxisome functions influence a wide range of processes outside of the organelles themselves. While knowledge of the network of metabolic pathways and their intraorganellar redox status regulation has increased in the last years, little is known about the interorganellar redox signals coordinating these networks. A current challenge is, therefore, synthesizing our knowledge and planning experiments that tackle redox status regulation at both inter- and intracellular levels. FUTURE DIRECTIONS Emerging tools are enabling ever-increasing spatiotemporal resolution of metabolism and imaging of redox status components. Broader application of these tools will likely greatly enhance our understanding of the interplay of redox status and metabolism as well as elucidating and characterizing signaling features thereof. We propose that such information will enable us to dissect the regulatory hierarchies that mediate the strict coupling of metabolism and redox status which, ultimately, determine plant growth and development.
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Affiliation(s)
- Peter Geigenberger
- 1 Department of Biology I, Ludwig Maximilian University Munich , Planegg-Martinsried, Germany
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Mendiondo GM, Medhurst A, van Roermund CW, Zhang X, Devonshire J, Scholefield D, Fernández J, Axcell B, Ramsay L, Waterham HR, Waugh R, Theodoulou FL, Holdsworth MJ. Barley has two peroxisomal ABC transporters with multiple functions in β-oxidation. J Exp Bot 2014; 65:4833-47. [PMID: 24913629 PMCID: PMC4144768 DOI: 10.1093/jxb/eru243] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
In oilseed plants, peroxisomal β-oxidation functions not only in lipid catabolism but also in jasmonate biosynthesis and metabolism of pro-auxins. Subfamily D ATP-binding cassette (ABC) transporters mediate import of β-oxidation substrates into the peroxisome, and the Arabidopsis ABCD protein, COMATOSE (CTS), is essential for this function. Here, the roles of peroxisomal ABCD transporters were investigated in barley, where the main storage compound is starch. Barley has two CTS homologues, designated HvABCD1 and HvABCD2, which are widely expressed and present in embryo and aleurone tissues during germination. Suppression of both genes in barley RNA interference (RNAi) lines indicated roles in metabolism of 2,4-dichlorophenoxybutyrate (2,4-DB) and indole butyric acid (IBA), jasmonate biosynthesis, and determination of grain size. Transformation of the Arabidopsis cts-1 null mutant with HvABCD1 and HvABCD2 confirmed these findings. HvABCD2 partially or completely complemented all tested phenotypes of cts-1. In contrast, HvABCD1 failed to complement the germination and establishment phenotypes of cts-1 but increased the sensitivity of hypocotyls to 100 μM IBA and partially complemented the seed size phenotype. HvABCD1 also partially complemented the yeast pxa1/pxa2Δ mutant for fatty acid β-oxidation. It is concluded that the core biochemical functions of peroxisomal ABC transporters are largely conserved between oilseeds and cereals but that their physiological roles and importance may differ.
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Affiliation(s)
- Guillermina M Mendiondo
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Anne Medhurst
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Carlo W van Roermund
- Laboratory of Genetic Metabolic Diseases, Academic Medical Centre, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands
| | - Xuebin Zhang
- Biological Chemistry and Crop Protection Department, Rothamsted Research, Harpenden AL5 2JQ, UK
| | - Jean Devonshire
- Plant Biology and Crop Science Department, Rothamsted Research, Harpenden AL5 2JQ, UK
| | - Duncan Scholefield
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - José Fernández
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Barry Axcell
- SABMiller plc., SABMiller House, Church Street, West Woking, Surrey GU21 6HS, UK
| | - Luke Ramsay
- Division of Plant Sciences, College of life Sciences, University of Dundee and The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Hans R Waterham
- Laboratory of Genetic Metabolic Diseases, Academic Medical Centre, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands
| | - Robbie Waugh
- Division of Plant Sciences, College of life Sciences, University of Dundee and The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Frederica L Theodoulou
- Biological Chemistry and Crop Protection Department, Rothamsted Research, Harpenden AL5 2JQ, UK
| | - Michael J Holdsworth
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
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Liu F, Zhao X, Zhang L, Tang T, Lu C, Chen G, Wang X, Bu C, Zhao X. RNA-seq profiling the transcriptome of secondary seed dormancy in canola (Brassica napus L.). Chin Sci Bull 2014. [DOI: 10.1007/s11434-014-0371-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Goto-Yamada S, Mano S, Nakamori C, Kondo M, Yamawaki R, Kato A, Nishimura M. Chaperone and Protease Functions of LON Protease 2 Modulate the Peroxisomal Transition and Degradation with Autophagy. ACTA ACUST UNITED AC 2014; 55:482-96. [DOI: 10.1093/pcp/pcu017] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Quan S, Yang P, Cassin-Ross G, Kaur N, Switzenberg R, Aung K, Li J, Hu J. Proteome analysis of peroxisomes from etiolated Arabidopsis seedlings identifies a peroxisomal protease involved in β-oxidation and development. Plant Physiol 2013; 163:1518-38. [PMID: 24130194 PMCID: PMC3850190 DOI: 10.1104/pp.113.223453] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Plant peroxisomes are highly dynamic organelles that mediate a suite of metabolic processes crucial to development. Peroxisomes in seeds/dark-grown seedlings and in photosynthetic tissues constitute two major subtypes of plant peroxisomes, which had been postulated to contain distinct primary biochemical properties. Multiple in-depth proteomic analyses had been performed on leaf peroxisomes, yet the major makeup of peroxisomes in seeds or dark-grown seedlings remained unclear. To compare the metabolic pathways of the two dominant plant peroxisomal subtypes and discover new peroxisomal proteins that function specifically during seed germination, we performed proteomic analysis of peroxisomes from etiolated Arabidopsis (Arabidopsis thaliana) seedlings. The detection of 77 peroxisomal proteins allowed us to perform comparative analysis with the peroxisomal proteome of green leaves, which revealed a large overlap between these two primary peroxisomal variants. Subcellular targeting analysis by fluorescence microscopy validated around 10 new peroxisomal proteins in Arabidopsis. Mutant analysis suggested the role of the cysteine protease RESPONSE TO DROUGHT21A-LIKE1 in β-oxidation, seed germination, and growth. This work provides a much-needed road map of a major type of plant peroxisome and has established a basis for future investigations of peroxisomal proteolytic processes to understand their roles in development and in plant interaction with the environment.
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Çakır B, Kılıçkaya O. Whole-genome survey of the putative ATP-binding cassette transporter family genes in Vitis vinifera. PLoS One 2013; 8:e78860. [PMID: 24244377 PMCID: PMC3823996 DOI: 10.1371/journal.pone.0078860] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2013] [Accepted: 09/20/2013] [Indexed: 11/18/2022] Open
Abstract
The ATP-binding cassette (ABC) protein superfamily constitutes one of the largest protein families known in plants. In this report, we performed a complete inventory of ABC protein genes in Vitis vinifera, the whole genome of which has been sequenced. By comparison with ABC protein members of Arabidopsis thaliana, we identified 135 putative ABC proteins with 1 or 2 NBDs in V. vinifera. Of these, 120 encode intrinsic membrane proteins, and 15 encode proteins missing TMDs. V. vinifera ABC proteins can be divided into 13 subfamilies with 79 “full-size,” 41 “half-size,” and 15 “soluble” putative ABC proteins. The main feature of the Vitis ABC superfamily is the presence of 2 large subfamilies, ABCG (pleiotropic drug resistance and white-brown complex homolog) and ABCC (multidrug resistance-associated protein). We identified orthologs of V. vinifera putative ABC transporters in different species. This work represents the first complete inventory of ABC transporters in V. vinifera. The identification of Vitis ABC transporters and their comparative analysis with the Arabidopsis counterparts revealed a strong conservation between the 2 species. This inventory could help elucidate the biological and physiological functions of these transporters in V. vinifera.
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Affiliation(s)
- Birsen Çakır
- Department of Horticulture, Faculty of Agriculture, Ege University, Bornova, Izmir, Turkey
- * E-mail:
| | - Ozan Kılıçkaya
- Graduate School of Natural and Applied Sciences, Department of Biotechnology, Ege University, Bornova, Izmir, Turkey
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14
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León J. Role of plant peroxisomes in the production of jasmonic acid-based signals. Subcell Biochem 2013; 69:299-313. [PMID: 23821155 DOI: 10.1007/978-94-007-6889-5_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
Jasmonates are a family of oxylipins derived from linolenic acid that control plant responses to biotic and abiotic stress factors and also regulate plant growth and development. Jasmonic acid (JA) is synthesized through the octadecanoid pathway that involves the translocation of lipid intermediates from the chloroplast membranes to the cytoplasm and later on into peroxisomes. The peroxisomal steps of the pathway involve the reduction of cis-(+)-12-oxophytodienoic acid (12-OPDA) and dinor-OPDA, which are the final products of the choroplastic phase of the biosynthetic pathway acting on 18:3 and 16:3 fatty acids, respectively. Further shortening of the carbon side-chain by successive rounds of β-oxidation reactions are required to complete JA biosynthesis. After peroxisomal reactions are completed, (+)-7-iso-JA is synthesized and then transported to the cytoplasm where is conjugated to the amino acid isoleucine to form the bioactive form of the hormone (+)-7-iso-JA-Ile (JA-Ile). Further regulatory activity of JA-Ile triggering gene activation in the jasmonate-dependent signaling cascades is exerted through a process mediated by the perception via the E3 ubiquitin ligase COI1 and further ligand-activated interaction with the family of JAZ repressor proteins. Upon interaction, JAZ are ubiquitinated and degraded by the proteasome, thus releasing transcription factors such as MYC2 from repression and allowing the activation of JA-responsive genes.
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Affiliation(s)
- José León
- Instituto de Biología Molecular y Celular de Plantas, CSIC - Universidad Politécnica de Valencia, Valencia, Spain,
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15
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Abstract
The transition from seed to seedling is an important step in the life cycle of plants, which is fuelled primarily by the breakdown of triacylglycerol (TAG) in 'oilseed' species. TAG is stored within cytosolic oil bodies, while the pathway for fatty acid β-oxidation resides in the peroxisome. Although the enzymology of fatty acid β-oxidation has been relatively well characterised, the processes by which fatty acids are liberated from oil bodies and enter the peroxisome are less well understood and, together with metabolite, cofactor and co-substrate transporters, represent key targets for future research in order to understand co-ordination of peroxisomal metabolism with that of other subcellular compartments.
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Affiliation(s)
- Frederica L Theodoulou
- Biological Chemistry and Crop Protection Department, Rothamsted Research, West Common, Harpenden, Hertfordshire, UK
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16
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Dave A, Graham IA. Oxylipin Signaling: A Distinct Role for the Jasmonic Acid Precursor cis-(+)-12-Oxo-Phytodienoic Acid (cis-OPDA). Front Plant Sci 2012; 3:42. [PMID: 22645585 PMCID: PMC3355751 DOI: 10.3389/fpls.2012.00042] [Citation(s) in RCA: 128] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 02/19/2012] [Indexed: 05/18/2023]
Abstract
Oxylipins are lipid-derived compounds, many of which act as signals in the plant response to biotic and abiotic stress. They include the phytohormone jasmonic acid (JA) and related jasmonate metabolites cis-(+)-12-oxo-phytodienoic acid (cis-OPDA), methyl jasmonate, and jasmonoyl-L-isoleucine (JA-Ile). Besides the defense response, jasmonates are involved in plant growth and development and regulate a range of processes including glandular trichome development, reproduction, root growth, and senescence. cis-OPDA is known to possess a signaling role distinct from JA-Ile. The non-enzymatically derived phytoprostanes are structurally similar to cis-OPDA and induce a common set of genes that are not responsive to JA in Arabidopsis thaliana. A novel role for cis-OPDA in seed germination regulation has recently been uncovered based on evidence from double mutants and feeding experiments showing that cis-OPDA interacts with abscisic acid (ABA), inhibits seed germination, and increases ABA INSENSITIVE5 (ABI5) protein abundance. Large amounts of cis-OPDA are esterified to galactolipids in A. thaliana and the resulting compounds, known as Arabidopsides, are thought to act as a rapidly available source of cis-OPDA.
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Affiliation(s)
- Anuja Dave
- Department of Biology, Centre for Novel Agricultural Products, University of YorkYork, UK
| | - Ian A. Graham
- Department of Biology, Centre for Novel Agricultural Products, University of YorkYork, UK
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17
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Chao WS, Foley ME, Doğramacı M, Anderson JV, Horvath DP. Alternating temperature breaks dormancy in leafy spurge seeds and impacts signaling networks associated with HY5. Funct Integr Genomics 2011; 11:637-49. [PMID: 21947436 DOI: 10.1007/s10142-011-0253-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Revised: 09/10/2011] [Accepted: 09/13/2011] [Indexed: 01/28/2023]
Abstract
Non-after-ripened seeds of the herbaceous perennial weed leafy spurge do not germinate when imbibed at a constant temperature (C), but transfer to an alternating temperature (A) induced germination. Changes in the transcriptome of seeds during 1 and 3 days of alternating temperature and germinated seeds were compared with seeds incubated at constant temperature. Statistical analysis revealed that 597, 1,491, and 1,329 genes were differentially expressed (P < 0.05) for the comparisons of 21-day C vs. 21-day C + 1-day A, 21-day C vs. 21-day C + 3-day A, and 21-day C vs. 21-day C + Germ (germination), respectively. Functional classifications based on gene set and sub-network enrichment analysis were performed to identify pathways and gene sub-networks that underlie transcriptome changes in the seeds as they germinate. Sugars, plant hormones, photomorphogenesis, and reactive oxygen species were overrepresented at 21-day C + 1-day A. At 21-day C + 3-day A, an increase in cellular activities was observed as the number of overrepresented pathways greatly increased. Many of the metabolic pathways were involved in the biosynthesis of amino acids, macromolecules, and energy and carbon skeleton production for subsequent germination. The 21-day C + 3-day A and 21-day C + Germ pathways and sub-networks were similar and included an overrepresentation of the amino acid biosynthetic pathways; however, 21-day C + Germ seeds have an even wider array of cellular activities such as translation-related pathways, which are most likely for seedling growth. RT-qPCR analysis indicated that the up- and down-regulation of HISTONE H3, GASA2, DREBIII-1, CHS, AOS, PIF3, PLD α1, and LEA may be germination-related since their expression was dramatically changed only in the 21-day C + Germ seeds. Finally, both short-term alternating temperature and short-term light exposure up-regulated the expression targets of the central hub HY5 in leafy spurge and Arabidopsis, respectively, indicating that a signaling network involving HY5 is important for germination.
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18
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Zhang X, De Marcos Lousa C, Schutte-Lensink N, Ofman R, Wanders RJ, Baldwin SA, Baker A, Kemp S, Theodoulou FL. Conservation of targeting but divergence in function and quality control of peroxisomal ABC transporters: an analysis using cross-kingdom expression. Biochem J 2011; 436:547-57. [PMID: 21476988 DOI: 10.1042/bj20110249] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
ABC (ATP-binding cassette) subfamily D transporters are found in all eukaryotic kingdoms and are known to play essential roles in mammals and plants; however, their number, organization and physiological contexts differ. Via cross-kingdom expression experiments, we have explored the conservation of targeting, protein stability and function between mammalian and plant ABCD transporters. When expressed in tobacco epidermal cells, the mammalian ABCD proteins ALDP (adrenoleukodystrophy protein), ALDR (adrenoleukodystrophy-related protein) and PMP70 (70 kDa peroxisomal membrane protein) targeted faithfully to peroxisomes and P70R (PMP70-related protein) targeted to the ER (endoplasmic reticulum), as in the native host. The Arabidopsis thaliana peroxin AtPex19_1 interacted with human peroxisomal ABC transporters both in vivo and in vitro, providing an explanation for the fidelity of targeting. The fate of X-linked adrenoleukodystrophy disease-related mutants differed between fibroblasts and plant cells. In fibroblasts, levels of ALDP in some 'protein-absent' mutants were increased by low-temperature culture, in some cases restoring function. In contrast, all mutant ALDP proteins examined were stable and correctly targeted in plant cells, regardless of their fate in fibroblasts. ALDR complemented the seed germination defect of the Arabidopsis cts-1 mutant which lacks the peroxisomal ABCD transporter CTS (Comatose), but neither ALDR nor ALDP was able to rescue the defect in fatty acid β-oxidation in establishing seedlings. Taken together, our results indicate that the mechanism for trafficking of peroxisomal membrane proteins is shared between plants and mammals, but suggest differences in the sensing and turnover of mutant ABC transporter proteins and differences in substrate specificity and/or function.
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Affiliation(s)
- Xuebin Zhang
- Biological Chemistry Department, Rothamsted Research, Harpenden, Herts. AL5 2JQ, UK
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19
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Abstract
Most plant seeds are dispersed in a dry, mature state. If these seeds are non-dormant and the environmental conditions are favourable, they will pass through the complex process of germination. In this review, recent progress made with state-of-the-art techniques including genome-wide gene expression analyses that provided deeper insight into the early phase of seed germination, which includes imbibition and the subsequent plateau phase of water uptake in which metabolism is reactivated, is summarized. The physiological state of a seed is determined, at least in part, by the stored mRNAs that are translated upon imbibition. Very early upon imbibition massive transcriptome changes occur, which are regulated by ambient temperature, light conditions, and plant hormones. The hormones abscisic acid and gibberellins play a major role in regulating early seed germination. The early germination phase of Arabidopsis thaliana culminates in testa rupture, which is followed by the late germination phase and endosperm rupture. An integrated view on the early phase of seed germination is provided and it is shown that it is characterized by dynamic biomechanical changes together with very early alterations in transcript, protein, and hormone levels that set the stage for the later events. Early seed germination thereby contributes to seed and seedling performance important for plant establishment in the natural and agricultural ecosystem.
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Affiliation(s)
- Karin Weitbrecht
- Botany/Plant Physiology, Institute for Biology II, Faculty of Biology, University of Freiburg, Schänzlestr. 1, D-79104 Freiburg, Germany
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20
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Goto S, Mano S, Nakamori C, Nishimura M. Arabidopsis ABERRANT PEROXISOME MORPHOLOGY9 is a peroxin that recruits the PEX1-PEX6 complex to peroxisomes. Plant Cell 2011; 23:1573-87. [PMID: 21487094 PMCID: PMC3101541 DOI: 10.1105/tpc.110.080770] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Peroxisomes have pivotal roles in several metabolic processes, such as the detoxification of H₂O₂ and β-oxidation of fatty acids, and their functions are tightly regulated by multiple factors involved in peroxisome biogenesis, including protein transport. This study describes the isolation of an embryonic lethal Arabidopsis thaliana mutant, aberrant peroxisome morphology9 (apem9), which is compromised in protein transport into peroxisomes. The APEM9 gene was found to encode an unknown protein. Compared with apem9 having the nucleotide substitution, the knockdown mutants showed severe defects in peroxisomal functions and plant growth. We showed that expression of APEM9 altered PEROXIN6 (PEX6) subcellular localization from the cytosol to peroxisomes. In addition, we showed that PEX1 and PEX6 comprise a heterooligomer and that this complex was recruited to peroxisomal membranes via protein-protein interactions of APEM9 with PEX6. These findings show that APEM9 functions as an anchoring protein, similar to Pex26 in mammals and Pex15p in yeast. Interestingly, however, the identities of amino acids among these anchoring proteins are quite low. These results indicate that although the association of the PEX1-PEX6 complex with peroxisomal membranes is essential for peroxisomal functions, the protein that anchors this complex evolved uniquely in plants.
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Affiliation(s)
- Shino Goto
- Department of Cell Biology, National Institute for Basic Biology, Okazaki 444-8585, Japan
- Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies, Okazaki 444-8585, Japan
| | - Shoji Mano
- Department of Cell Biology, National Institute for Basic Biology, Okazaki 444-8585, Japan
- Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies, Okazaki 444-8585, Japan
| | - Chihiro Nakamori
- Department of Cell Biology, National Institute for Basic Biology, Okazaki 444-8585, Japan
| | - Mikio Nishimura
- Department of Cell Biology, National Institute for Basic Biology, Okazaki 444-8585, Japan
- Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies, Okazaki 444-8585, Japan
- Address correspondence to
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21
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Dave A, Hernández ML, He Z, Andriotis VM, Vaistij FE, Larson TR, Graham IA. 12-oxo-phytodienoic acid accumulation during seed development represses seed germination in Arabidopsis. Plant Cell 2011; 23:583-99. [PMID: 21335376 PMCID: PMC3077774 DOI: 10.1105/tpc.110.081489] [Citation(s) in RCA: 168] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2010] [Revised: 01/21/2011] [Accepted: 02/02/2011] [Indexed: 05/18/2023]
Abstract
Arabidopsis thaliana COMATOSE (CTS) encodes an ABC transporter involved in peroxisomal import of substrates for β-oxidation. Various cts alleles and mutants disrupted in steps of peroxisomal β-oxidation have previously been reported to exhibit a severe block on seed germination. Oxylipin analysis on cts, acyl CoA oxidase1 acyl CoA oxidase2 (acx1 acx2), and keto acyl thiolase2 dry seeds revealed that they contain elevated levels of 12-oxo-phytodienoic acid (OPDA), jasmonic acid (JA), and JA-Ile. Oxylipin and transcriptomic analysis showed that accumulation of these oxylipins occurs during late seed maturation in cts. Analysis of double mutants generated by crossing cts with mutants in the JA biosynthesis pathway indicate that OPDA, rather than JA or JA-Ile, contributes to the block on germination in cts seeds. We found that OPDA was more effective at inhibiting wild-type germination than was JA and that this effect was independent of CORONATINE INSENSITIVE1 but was synergistic with abscisic acid (ABA). Consistent with this, OPDA treatment increased ABA INSENSITIVE5 protein abundance in a manner that parallels the inhibitory effect of OPDA and OPDA+ABA on seed germination. These results demonstrate that OPDA acts along with ABA to regulate seed germination in Arabidopsis.
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22
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Theodoulou FL, Zhang X, De Marcos Lousa C, Nyathi Y, Baker A. Peroxisomal Transport Systems: Roles in Signaling and Metabolism. Signaling and Communication in Plants 2011. [DOI: 10.1007/978-3-642-14369-4_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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23
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Schwember AR, Bradford KJ. Quantitative trait loci associated with longevity of lettuce seeds under conventional and controlled deterioration storage conditions. J Exp Bot 2010; 61:4423-36. [PMID: 20693410 PMCID: PMC2955753 DOI: 10.1093/jxb/erq248] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Revised: 06/16/2010] [Accepted: 07/19/2010] [Indexed: 05/20/2023]
Abstract
Lettuce (Lactuca sativa L.) seeds have poor shelf life and exhibit thermoinhibition (fail to germinate) above ∼25°C. Seed priming (controlled hydration followed by drying) alleviates thermoinhibition by increasing the maximum germination temperature, but reduces lettuce seed longevity. Controlled deterioration (CD) or accelerated ageing storage conditions (i.e. elevated temperature and relative humidity) are used to study seed longevity and to predict potential seed lifetimes under conventional storage conditions. Seeds produced in 2002 and 2006 of a recombinant inbred line (RIL) population derived from a cross between L. sativa cv. Salinas×L. serriola accession UC96US23 were utilized to identify quantitative trait loci (QTLs) associated with seed longevity under CD and conventional storage conditions. Multiple longevity-associated QTLs were identified under both conventional and CD storage conditions for control (non-primed) and primed seeds. However, seed longevity was poorly correlated between the two storage conditions, suggesting that deterioration processes under CD conditions are not predictive of ageing in conventional storage conditions. Additionally, the same QTLs were not identified when RIL populations were grown in different years, indicating that lettuce seed longevity is strongly affected by production environment. Nonetheless, a major QTL on chromosome 4 [Seed longevity 4.1 (Slg4.1)] was responsible for almost 23% of the phenotypic variation in viability of the conventionally stored control seeds of the 2006 RIL population, with improved longevity conferred by the Salinas allele. QTL analyses may enable identification of mechanisms responsible for the sensitivity of primed seeds to CD conditions and breeding for improved seed longevity.
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Affiliation(s)
| | - Kent J. Bradford
- Department of Plant Sciences, One Shields Avenue, University of California, Davis, CA 95616-8780 USA
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24
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Nyathi Y, De Marcos Lousa C, van Roermund CW, Wanders RJA, Johnson B, Baldwin SA, Theodoulou FL, Baker A. The Arabidopsis peroxisomal ABC transporter, comatose, complements the Saccharomyces cerevisiae pxa1 pxa2Delta mutant for metabolism of long-chain fatty acids and exhibits fatty acyl-CoA-stimulated ATPase activity. J Biol Chem 2010; 285:29892-902. [PMID: 20659892 PMCID: PMC2943281 DOI: 10.1074/jbc.m110.151225] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Revised: 07/08/2010] [Indexed: 12/26/2022] Open
Abstract
The Arabidopsis ABC transporter Comatose (CTS; AtABCD1) is required for uptake into the peroxisome of a wide range of substrates for β-oxidation, but it is uncertain whether CTS itself is the transporter or if the transported substrates are free acids or CoA esters. To establish a system for its biochemical analysis, CTS was expressed in Saccharomyces cerevisiae. The plant protein was correctly targeted to yeast peroxisomes, was assembled into the membrane with its nucleotide binding domains in the cytosol, and exhibited basal ATPase activity that was sensitive to aluminum fluoride and abrogated by mutation of a conserved Walker A motif lysine residue. The yeast pxa1 pxa2Δ mutant lacks the homologous peroxisomal ABC transporter and is unable to grow on oleic acid. Consistent with its exhibiting a function in yeast akin to that in the plant, CTS rescued the oleate growth phenotype of the pxa1 pxa2Δ mutant, and restored β-oxidation of fatty acids with a range of chain lengths and varying degrees of desaturation. When expressed in yeast peroxisomal membranes, the basal ATPase activity of CTS could be stimulated by fatty acyl-CoAs but not by fatty acids. The implications of these findings for the function and substrate specificity of CTS are discussed.
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Affiliation(s)
- Yvonne Nyathi
- From the Centre for Plant Sciences, Faculty of Biological Sciences, and
| | | | - Carlo W. van Roermund
- the Departments of Pediatrics and Clinical Chemistry, Laboratory of Genetic Metabolic Diseases, Academic Medical Centre, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands, and
| | - Ronald J. A. Wanders
- the Departments of Pediatrics and Clinical Chemistry, Laboratory of Genetic Metabolic Diseases, Academic Medical Centre, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands, and
| | - Barbara Johnson
- From the Centre for Plant Sciences, Faculty of Biological Sciences, and
| | - Stephen A. Baldwin
- the Institute of Membrane and Systems Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | | | - Alison Baker
- From the Centre for Plant Sciences, Faculty of Biological Sciences, and
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25
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Kanai M, Nishimura M, Hayashi M. A peroxisomal ABC transporter promotes seed germination by inducing pectin degradation under the control of ABI5. Plant J 2010; 62:936-947. [PMID: 20345608 DOI: 10.1111/j.1365-313x.2010.04205.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Seed dormancy is essential for most plants to control the timing of germination. In Arabidopsis thaliana, PED3 is a single-copy gene encoding an ATP-binding cassette transporter that is required for peroxisomal fatty acid beta-oxidation. PED3 is involved in the import of several biologically important molecules into the peroxisome, including very-long-chain fatty acids associated with the breakdown of seed-reserve lipids, and precursors of auxin and jasmonic acid. The germination of ped3 mutants is significantly impaired, suggesting that PED3 regulates dormancy and germination. A transcriptome analysis revealed that many genes containing the core motif of the ABA responsive element (ABRE) in their promoter regions, and the ABA insensitive 5 (ABI5) transcription factor that binds to ABRE, are abnormally up-regulated in imbibed ped3 seeds. Expression of polygalacturonase inhibiting proteins (PGIPs) is also up-regulated specifically in ped3 after imbibition. By contrast, the ped3 abi5 double mutant does not show any of these expression patterns. The results indicate that the abi5 mutation normalizes PGIP expression and rescues the impaired germination phenotype of the ped3 mutant. PGIPs are known to act as inhibitors of polygalacturonases that degrade pectin. The amount of PGIP1 transcript regulates the timing of radicle protrusion. The impaired germination of ped3 could also be rescued by removal of pectin from the seed coat using exogenous polygalacturonase or acidic conditions. Overall, our results suggest that PED3, a peroxisomal ABC transporter, promotes seed germination by suppressing PGIPs under the control of ABI5.
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Affiliation(s)
- Masatake Kanai
- Department of Cell Biology, National Institute for Basic Biology, Okazaki 444-8585, Japan
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26
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Pracharoenwattana I, Zhou W, Smith SM. Fatty acid beta-oxidation in germinating Arabidopsis seeds is supported by peroxisomal hydroxypyruvate reductase when malate dehydrogenase is absent. Plant Mol Biol 2010; 72:101-9. [PMID: 19812894 DOI: 10.1007/s11103-009-9554-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Accepted: 09/25/2009] [Indexed: 05/09/2023]
Abstract
Peroxisomal malate dehydrogenase (PMDH) oxidises NADH produced by fatty acid beta-oxidation during seed germination and seedling growth. Arabidopsis thaliana beta-oxidation mutants exhibit seed dormancy or impaired seed germination and failure of seedlings to degrade triacylglycerol (TAG), but the pmdh1 pmdh2 null mutant germinates readily and degrades TAG slowly during seedling growth. We reasoned that in the pmdh1 pmdh2 mutant an alternative means of oxidising NADH operates to allow a slow rate of beta-oxidation, such as NADH and NAD(+) transport across the peroxisomal membrane or activity of another peroxisomal oxido-reductase. Here we show that peroxisomal hydroxypyruvate reductase (HPR) is present in germinating seeds and although knocking out HPR has little effect on germination and early seedling growth, when knocked out in combination with PMDH it exacerbates the pmdh1 pmdh2 phenotype. It greatly increases the proportion of dormant seeds and reduces the rate of seed germination. Seedlings have increased sucrose dependence and resistance to 2,4-dichlorophenoxybutyric acid (2,4-DB), and slower rate of TAG breakdown. When PMDH is absent, malate is lower in amount in germinating seeds and when HPR is also absent, serine (the immediate precursor of hydroxypyruvate) is much higher. These results indicate that HPR can oxidise NADH at sufficient rate in the absence of PMDH to support beta-oxidation and hence seed germination. We conclude that while HPR normally plays little role in seed germination our results support the growing body of evidence that peroxisomal NADH cannot be exported to the cytosol for oxidation but is oxidised by resident oxido-reductases.
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Affiliation(s)
- Itsara Pracharoenwattana
- Australian Research Council Centre of Excellence in Plant Energy Biology and Centre of Excellence for Plant Metabolomics, Molecular and Chemical Sciences Building M316, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
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27
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Abstract
Due to the presence of plastids, eukaryotic photosynthetic cells represent the most highly compartmentalized eukaryotic cells. This high degree of compartmentation requires the transport of solutes across intracellular membrane systems by specific membrane transporters. In this review, we summarize the recent progress on functionally characterized intracellular plant membrane transporters and we link transporter functions to Arabidopsis gene identifiers and to the transporter classification system. In addition, we outline challenges in further elucidating the plant membrane permeome and we provide an outline of novel approaches for the functional characterization of membrane transporters.
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Affiliation(s)
- Nicole Linka
- Institute of Plant Biochemistry, Heinrich-Heine Universität Düsseldorf, Geb. 26.03.01, Universitätsstrasse 1, Düsseldorf, Germany
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Linkies A, Schuster-Sherpa U, Tintelnot S, Leubner-Metzger G, Müller K. Peroxidases identified in a subtractive cDNA library approach show tissue-specific transcript abundance and enzyme activity during seed germination of Lepidium sativum. J Exp Bot 2009; 61:491-502. [PMID: 19884228 PMCID: PMC2803213 DOI: 10.1093/jxb/erp318] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2009] [Revised: 10/06/2009] [Accepted: 10/12/2009] [Indexed: 05/06/2023]
Abstract
The micropylar endosperm is a major regulator of seed germination in endospermic species, to which the close Brassicaceae relatives Arabidopsis thaliana and Lepidium sativum (cress) belong. Cress seeds are about 20 times larger than the seeds of Arabidopsis. This advantage was used to construct a tissue-specific subtractive cDNA library of transcripts that are up-regulated late in the germination process specifically in the micropylar endosperm of cress seeds. The library showed that a number of transcripts known to be up-regulated late during germination are up-regulated in the micropylar endosperm cap. Detailed germination kinetics of SALK lines carrying insertions in genes present in our library showed that the identified transcripts do indeed play roles during germination. Three peroxidases were present in the library. These peroxidases were identified as orthologues of Arabidopsis AtAPX01, AtPrx16, and AtPrxIIE. The corresponding SALK lines displayed significant germination phenotypes. Their transcripts were quantified in specific cress seed tissues during germination in the presence and absence of ABA and they were found to be regulated in a tissue-specific manner. Peroxidase activity, and particularly its regulation by ABA, also differed between radicles and micropylar endosperm caps. Possible implications of this tissue-specificity are discussed.
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Affiliation(s)
| | | | | | | | - Kerstin Müller
- University of Freiburg, Faculty of Biology, Institute for Biology II, Botany/Plant Physiology, Schänzlestr. 1, D-79104 Freiburg, Germany
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Holman TJ, Jones PD, Russell L, Medhurst A, Ubeda Tomás S, Talloji P, Marquez J, Schmuths H, Tung SA, Taylor I, Footitt S, Bachmair A, Theodoulou FL, Holdsworth MJ. The N-end rule pathway promotes seed germination and establishment through removal of ABA sensitivity in Arabidopsis. Proc Natl Acad Sci U S A 2009; 106:4549-54. [PMID: 19255443 DOI: 10.1073/pnas.0810280106] [Citation(s) in RCA: 152] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The N-end rule pathway targets protein degradation through the identity of the amino-terminal residue of specific protein substrates. Two components of this pathway in Arabidopsis thaliana, PROTEOLYSIS6 (PRT6) and arginyl-tRNA:protein arginyltransferase (ATE), were shown to regulate seed after-ripening, seedling sugar sensitivity, seedling lipid breakdown, and abscisic acid (ABA) sensitivity of germination. Sensitivity of prt6 mutant seeds to ABA inhibition of endosperm rupture reduced with after-ripening time, suggesting that seeds display a previously undescribed window of sensitivity to ABA. Reduced root growth of prt6 alleles and the ate1 ate2 double mutant was rescued by exogenous sucrose, and the breakdown of lipid bodies and seed-derived triacylglycerol was impaired in mutant seedlings, implicating the N-end rule pathway in control of seed oil mobilization. Epistasis analysis indicated that PRT6 control of germination and establishment, as exemplified by ABA and sugar sensitivity, as well as storage oil mobilization, occurs at least in part via transcription factors ABI3 and ABI5. The N-end rule pathway of protein turnover is therefore postulated to inactivate as-yet unidentified key component(s) of ABA signaling to influence the seed-to-seedling transition.
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Yazaki K, Shitan N, Sugiyama A, Takanashi K. Chapter 6 Cell and Molecular Biology of ATP‐Binding Cassette Proteins in Plants. International Review of Cell and Molecular Biology 2009; 276:263-99. [DOI: 10.1016/s1937-6448(09)76006-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Linka N, Theodoulou FL, Haslam RP, Linka M, Napier JA, Neuhaus HE, Weber APM. Peroxisomal ATP import is essential for seedling development in Arabidopsis thaliana. Plant Cell 2008; 20:3241-57. [PMID: 19073763 PMCID: PMC2630453 DOI: 10.1105/tpc.108.062042] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Several recent proteomic studies of plant peroxisomes indicate that the peroxisomal matrix harbors multiple ATP-dependent enzymes and chaperones. However, it is unknown whether plant peroxisomes are able to produce ATP by substrate-level phosphorylation or whether external ATP fuels the energy-dependent reactions within peroxisomes. The existence of transport proteins that supply plant peroxisomes with energy for fatty acid oxidation and other ATP-dependent processes has not previously been demonstrated. Here, we describe two Arabidopsis thaliana genes that encode peroxisomal adenine nucleotide carriers, PNC1 and PNC2. Both proteins, when fused to enhanced yellow fluorescent protein, are targeted to peroxisomes. Complementation of a yeast mutant deficient in peroxisomal ATP import and in vitro transport assays using recombinant transporter proteins revealed that PNC1 and PNC2 catalyze the counterexchange of ATP with ADP or AMP. Transgenic Arabidopsis lines repressing both PNC genes were generated using ethanol-inducible RNA interference. A detailed analysis of these plants showed that an impaired peroxisomal ATP import inhibits fatty acid breakdown during early seedling growth and other beta-oxidation reactions, such as auxin biosynthesis. We show conclusively that PNC1 and PNC2 are essential for supplying peroxisomes with ATP, indicating that no other ATP generating systems exist inside plant peroxisomes.
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Affiliation(s)
- Nicole Linka
- Institut für Biochemie der Pflanzen, Heinrich-Heine Universität Düsseldorf, D-40225 Düsseldorf, Germany.
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Dietrich D, Schmuths H, De Marcos Lousa C, Baldwin JM, Baldwin SA, Baker A, Theodoulou FL, Holdsworth MJ. Mutations in the Arabidopsis peroxisomal ABC transporter COMATOSE allow differentiation between multiple functions in planta: insights from an allelic series. Mol Biol Cell 2008; 20:530-43. [PMID: 19019987 DOI: 10.1091/mbc.e08-07-0745] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
COMATOSE (CTS), the Arabidopsis homologue of human Adrenoleukodystrophy protein (ALDP), is required for import of substrates for peroxisomal beta-oxidation. A new allelic series and a homology model based on the bacterial ABC transporter, Sav1866, provide novel insights into structure-function relations of ABC subfamily D proteins. In contrast to ALDP, where the majority of mutations result in protein absence from the peroxisomal membrane, all CTS mutants produced stable protein. Mutation of conserved residues in the Walker A and B motifs in CTS nucleotide-binding domain (NBD) 1 resulted in a null phenotype but had little effect in NBD2, indicating that the NBDs are functionally distinct in vivo. Two alleles containing mutations in NBD1 outside the Walker motifs (E617K and C631Y) exhibited resistance to auxin precursors 2,4-dichlorophenoxybutyric acid (2,4-DB) and indole butyric acid (IBA) but were wild type in all other tests. The homology model predicted that the transmission interfaces are domain-swapped in CTS, and the differential effects of mutations in the conserved "EAA motif" of coupling helix 2 supported this prediction, consistent with distinct roles for each NBD. Our findings demonstrate that CTS functions can be separated by mutagenesis and the structural model provides a framework for interpretation of phenotypic data.
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Affiliation(s)
- Daniela Dietrich
- Department of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
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33
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León J. Peroxisome proliferation in Arabidopsis: The challenging identification of ligand perception and downstream signaling is closer. Plant Signal Behav 2008; 3:671-3. [PMID: 19704821 PMCID: PMC2634552 DOI: 10.4161/psb.3.9.5780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2008] [Accepted: 02/25/2008] [Indexed: 05/03/2023]
Abstract
Peroxisomes are subcellular organelles with multiple functions mediated by their plasticity and dynamic behavior in plants. Changes in their shape, size, number and enzyme content occur in response to developmental and metabolic cues as well as environmental conditions. The number of peroxisomes per cell is thus mainly determined by its capacity to proliferate. In mammals, peroxisome proliferators such as the hypolipidemic drug clofibrate are perceived by the Peroxisome Proliferator-Activated Receptors (PPARs) nuclear receptors. Therein, activated transcription of the peroxisome biogenesis PEX11 genes and the recruitment of dynamin-related proteins lead to peroxisome proliferation. We recently reported that Arabidopsis thaliana, despite of lacking a PPAR homolog protein, activated the proliferation of peroxisomes in response to clofibrate. Concomitantly, clofibrate activated the expression of wound-responsive genes through the jasmonic acid signaling master regulator COI1 F-box protein. Besides, wounding activated the expression of the peroxisome biogenesis-related PEX1 and PEX14 genes, but not of PEX11 or DRP3A, which analogously to mammals, code for the main regulators of peroxisome proliferation in Arabidopsis. Thus, wounding did not activate peroxisome proliferation. Noteworthy, jasmonic acid-treated plants contained fewer but larger peroxisomes. Despite of the cross-talk between clofibrate- and wound-induced signaling, the proliferation of peroxisomes and the wound-activated defense remained uncoupled.
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Affiliation(s)
- José León
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV); Ciudad Politécnica de la Innovación; Valencia, Spain
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Savidor A, Donahoo RS, Hurtado-Gonzales O, Land ML, Shah MB, Lamour KH, McDonald WH. Cross-species global proteomics reveals conserved and unique processes in Phytophthora sojae and Phytophthora ramorum. Mol Cell Proteomics 2008; 7:1501-16. [PMID: 18316789 PMCID: PMC2500229 DOI: 10.1074/mcp.m700431-mcp200] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2007] [Revised: 01/23/2008] [Indexed: 11/06/2022] Open
Abstract
Phytophthora ramorum and Phytophthora sojae are destructive plant pathogens. P. sojae has a narrow host range, whereas P. ramorum has a wide host range. A global proteomics comparison of the vegetative (mycelium) and infective (germinating cyst) life stages of P. sojae and P. ramorum was conducted to identify candidate proteins involved in host range, early infection, and vegetative growth. Sixty-two candidates for early infection, 26 candidates for vegetative growth, and numerous proteins that may be involved in defining host specificity were identified. In addition, common life stage proteomic trends between the organisms were observed. In mycelia, proteins involved in transport and metabolism of amino acids, carbohydrates, and other small molecules were up-regulated. In the germinating cysts, up-regulated proteins associated with lipid transport and metabolism, cytoskeleton, and protein synthesis were observed. It appears that the germinating cyst catabolizes lipid reserves through the beta-oxidation pathway to drive the extensive protein synthesis necessary to produce the germ tube and initiate infection. Once inside the host, the pathogen switches to vegetative growth in which energy is derived from glycolysis and utilized for synthesis of amino acids and other molecules that assist survival in the plant tissue.
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Affiliation(s)
- Alon Savidor
- Graduate School of Genome Science and Technology, University of Tennessee-Oak Ridge National Laboratory Oak Ridge, Oak Ridge, Tennessee 37830, USA
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35
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Verrier PJ, Bird D, Burla B, Dassa E, Forestier C, Geisler M, Klein M, Kolukisaoglu U, Lee Y, Martinoia E, Murphy A, Rea PA, Samuels L, Schulz B, Spalding EJ, Yazaki K, Theodoulou FL. Plant ABC proteins--a unified nomenclature and updated inventory. Trends Plant Sci 2008; 13:151-9. [PMID: 18299247 DOI: 10.1016/j.tplants.2008.02.001] [Citation(s) in RCA: 459] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2007] [Revised: 01/21/2008] [Accepted: 02/14/2008] [Indexed: 05/18/2023]
Abstract
The ABC superfamily comprises both membrane-bound transporters and soluble proteins involved in a broad range of processes, many of which are of considerable agricultural, biotechnological and medical potential. Completion of the Arabidopsis and rice genome sequences has revealed a particularly large and diverse complement of plant ABC proteins in comparison with other organisms. Forward and reverse genetics, together with heterologous expression, have uncovered many novel roles for plant ABC proteins, but this progress has been accompanied by a confusing proliferation of names for plant ABC genes and their products. A consolidated nomenclature will provide much-needed clarity and a framework for future research.
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Affiliation(s)
- Paul J Verrier
- Biomathematics and Bioinformatics Department, Rothamsted Research, Harpenden, AL5 2JQ, UK
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36
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Castillo MC, León J. Expression of the beta-oxidation gene 3-ketoacyl-CoA thiolase 2 (KAT2) is required for the timely onset of natural and dark-induced leaf senescence in Arabidopsis. J Exp Bot 2008; 59:2171-9. [PMID: 18441338 PMCID: PMC2413277 DOI: 10.1093/jxb/ern079] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2008] [Revised: 02/22/2008] [Accepted: 02/25/2008] [Indexed: 05/20/2023]
Abstract
The onset of leaf senescence is regulated by a complex mechanism involving positive and negative regulators. Among positive regulators, jasmonic acid (JA) accumulates in senescing leaves and the JA-insensitive coi1-1 mutant displays delayed leaf senescence in Arabidopsis. A strong activated expression of the gene coding for the JA-biosynthetic beta-oxidation enzyme 3-ketoacyl-CoA thiolase 2 (KAT2) in natural and dark-induced senescing leaves of Arabidopsis thaliana is reported here. By using KAT2::GUS and KAT2::LUC transgenic plants, it was observed that dark-induced KAT2 activation occurred both in excised leaves as well as in whole darkened plants. The KAT2 activation associated with dark-induced senescence occurred soon after a move to darkness, and it preceded the detection of symptoms and the expression of senescence-associated gene (SAG) markers. Transgenic plants with reduced expression of the KAT2 gene showed a significant delayed senescence both in natural and dark-induced processes. The rapid induction of the KAT2 gene in senescence-promoting conditions as well as the delayed senescence phenotype and the reduced SAG expression in KAT2 antisense transgenic plants, point to KAT2 as an essential component for the timely onset of leaf senescence in Arabidopsis.
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Affiliation(s)
| | - José León
- To whom correspondence should be addressed. E-mail:
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37
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Abstract
Storage oil mobilization starts with the onset of seed germination. Oil bodies packed with triacylglycerol (TAG) exist in close proximity with glyoxysomes, the single membrane-bound organelles that house most of the biochemical machinery required to convert fatty acids derived from TAG to 4-carbon compounds. The 4-carbon compounds in turn are converted to soluble sugars that are used to fuel seedling growth. Biochemical analysis over the last 50 years has identified the main pathways involved in this process, including beta-oxidation, the glyoxylate cycle, and gluconeogenesis. In the last few years molecular genetic dissection of the overall process in the model oilseed species Arabidopsis has provided new insight into its complexity, particularly with respect to the specific role played by individual enzymatic steps and the subcellular compartmentalization of the glyoxylate cycle. Both abscisic acid (ABA) and sugars inhibit storage oil mobilization and a substantial degree of the control appears to operate at the transcriptional level.
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Affiliation(s)
- Ian A Graham
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5YW, United Kingdom.
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38
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Abstract
The transition between dormancy and germination represents a critical stage in the life cycle of higher plants and is an important ecological and commercial trait. In this review we present current knowledge of the molecular control of this trait in Arabidopsis thaliana, focussing on important components functioning during the developmental phases of seed maturation, after-ripening and imbibition. Establishment of dormancy during seed maturation is regulated by networks of transcription factors with overlapping and discrete functions. Following desiccation, after-ripening determines germination potential and, surprisingly, recent observations suggest that transcriptional and post-transcriptional processes occur in the dry seed. The single-cell endosperm layer that surrounds the embryo plays a crucial role in the maintenance of dormancy, and transcriptomics approaches are beginning to uncover endosperm-specific genes and processes. Molecular genetic approaches have provided many new components of hormone signalling pathways, but also indicate the importance of hormone-independent pathways and of natural variation in key regulatory loci. The influence of environmental signals (particularly light) following after-ripening, and the effect of moist chilling (stratification) are increasingly being understood at the molecular level. Combined postgenomics, physiology and molecular genetics approaches are beginning to provide an unparalleled understanding of the molecular processes underlying dormancy and germination.
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Affiliation(s)
- Michael J Holdsworth
- Department of Agricultural and Environmental Sciences, School of BioSciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Leónie Bentsink
- Department of Molecular Plant Physiology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Wim J J Soppe
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
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Carrera E, Holman T, Medhurst A, Dietrich D, Footitt S, Theodoulou FL, Holdsworth MJ. Seed after-ripening is a discrete developmental pathway associated with specific gene networks in Arabidopsis. Plant J 2008; 53:214-24. [PMID: 18028281 PMCID: PMC2254144 DOI: 10.1111/j.1365-313x.2007.03331.x] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2007] [Revised: 09/10/2007] [Accepted: 09/17/2007] [Indexed: 05/18/2023]
Abstract
After-ripening (AR) is a time and environment regulated process occurring in the dry seed, which determines the germination potential of seeds. Both metabolism and perception of the phytohormone abscisic acid (ABA) are important in the initiation and maintenance of dormancy. However, molecular mechanisms that regulate the capacity for dormancy or germination through AR are unknown. To understand the relationship between ABA and AR, we analysed genome expression in Arabidopsis thaliana mutants defective in seed ABA synthesis (aba1-1) or perception (abi1-1). Even though imbibed mutant seeds showed no dormancy, they exhibited changes in global gene expression resulting from dry AR that were comparable with changes occurring in wild-type (WT) seeds. Core gene sets were identified that were positively or negatively regulated by dry seed storage. Each set included a gene encoding repression or activation of ABA function (LPP2 and ABA1, respectively), thereby suggesting a mechanism through which dry AR may modulate subsequent germination potential in WT seeds. Application of exogenous ABA to after-ripened WT seeds did not reimpose characteristics of freshly harvested seeds on imbibed seed gene expression patterns. It was shown that secondary dormancy states reinstate AR status-specific gene expression patterns. A model is presented that separates the action of ABA in seed dormancy from AR and dry storage regulated gene expression. These results have major implications for the study of genetic mechanisms altered in seeds as a result of crop domestication into agriculture, and for seed behaviour during dormancy cycling in natural ecosystems.
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Affiliation(s)
- Esther Carrera
- Crop Performance and Improvement Division, Rothamsted ResearchHarpenden, Hertfordshire AL5 2JQ, UK
| | - Tara Holman
- Department of Agricultural and Environmental Sciences, School of BioSciences, University of NottinghamNottingham LE12 5RD, UK
| | - Anne Medhurst
- Department of Agricultural and Environmental Sciences, School of BioSciences, University of NottinghamNottingham LE12 5RD, UK
| | - Daniela Dietrich
- Crop Performance and Improvement Division, Rothamsted ResearchHarpenden, Hertfordshire AL5 2JQ, UK
- Department of Agricultural and Environmental Sciences, School of BioSciences, University of NottinghamNottingham LE12 5RD, UK
| | - Steven Footitt
- Crop Performance and Improvement Division, Rothamsted ResearchHarpenden, Hertfordshire AL5 2JQ, UK
| | - Frederica L Theodoulou
- Crop Performance and Improvement Division, Rothamsted ResearchHarpenden, Hertfordshire AL5 2JQ, UK
| | - Michael J Holdsworth
- Department of Agricultural and Environmental Sciences, School of BioSciences, University of NottinghamNottingham LE12 5RD, UK
- Correspondence (fax +44 0 1159516233; e-mail )
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Zheng BS, Rönnberg E, Viitanen L, Salminen TA, Lundgren K, Moritz T, Edqvist J. Arabidopsis sterol carrier protein-2 is required for normal development of seeds and seedlings. J Exp Bot 2008; 59:3485-99. [PMID: 18687588 PMCID: PMC2529247 DOI: 10.1093/jxb/ern201] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2008] [Revised: 06/27/2008] [Accepted: 07/04/2008] [Indexed: 05/20/2023]
Abstract
The Arabidopsis thaliana sterol carrier protein-2 (AtSCP2) is a small, basic and peroxisomal protein that in vitro enhances the transfer of lipids between membranes. AtSCP2 and all other plant SCP-2 that have been identified are single-domain polypeptides, whereas in many other eukaryotes SCP-2 domains are expressed in the terminus of multidomain polypeptides. The AtSCP2 transcript is expressed in all analysed tissues and developmental stages, with the highest levels in floral tissues and in maturing seeds. The expression of AtSCP2 is highly correlated with the multifunctional protein-2 (MFP2) involved in beta-oxidation. A. thaliana Atscp2-1 plants deficient in AtSCP2 show altered seed morphology, a delayed germination, and are dependent on an exogenous carbon source to avoid a delayed seedling establishment. Metabolomic investigations revealed 110 variables (putative metabolites) that differed in relative concentration between Atscp2-1 and normal A. thaliana wild-type seedlings. Microarray analysis revealed that many genes whose expression is altered in mutants with a deficiency in the glyoxylate pathway, also have a changed expression level in Atscp2-1.
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Affiliation(s)
- Bing Song Zheng
- Department of Plant Biology and Forest Genetics, Swedish University of Agricultural Sciences, PO Box 7080, 750 07 Uppsala, Sweden
- School of Forestry and Biotechnology, Zhejiang Forestry University, 311300, Lin An, China
| | - Elin Rönnberg
- Department of Plant Biology and Forest Genetics, Swedish University of Agricultural Sciences, PO Box 7080, 750 07 Uppsala, Sweden
| | - Lenita Viitanen
- Department of Biochemistry and Pharmacy, Åbo Akademi University, Artillerigatan 6 A III, FIN-20520 Turku, Finland
| | - Tiina A. Salminen
- Department of Biochemistry and Pharmacy, Åbo Akademi University, Artillerigatan 6 A III, FIN-20520 Turku, Finland
| | - Krister Lundgren
- Umeå Plant Science Center, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden
| | - Thomas Moritz
- Umeå Plant Science Center, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden
| | - Johan Edqvist
- IFM Biology, Linköping University, 581 83 Linköping, Sweden
- To whom correspondence should be addressed:
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Abstract
Seed dormancy provides a mechanism for plants to delay germination until conditions are optimal for survival of the next generation. Dormancy release is regulated by a combination of environmental and endogenous signals with both synergistic and competing effects. Molecular studies of dormancy have correlated changes in transcriptomes, proteomes, and hormone levels with dormancy states ranging from deep primary or secondary dormancy to varying degrees of release. The balance of abscisic acid (ABA):gibberellin (GA) levels and sensitivity is a major, but not the sole, regulator of dormancy status. ABA promotes dormancy induction and maintenance, whereas GA promotes progression from release through germination; environmental signals regulate this balance by modifying the expression of biosynthetic and catabolic enzymes. Mediators of environmental and hormonal response include both positive and negative regulators, many of which are feedback-regulated to enhance or attenuate the response. The net result is a slightly heterogeneous response, thereby providing more temporal options for successful germination.
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Affiliation(s)
- Ruth Finkelstein
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, California 93106-9610, USA.
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42
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Hooks MA, Turner JE, Murphy EC, Johnston KA, Burr S, Jarosławski S. The Arabidopsis ALDP protein homologue COMATOSE is instrumental in peroxisomal acetate metabolism. Biochem J 2007; 406:399-406. [PMID: 17581114 PMCID: PMC2049035 DOI: 10.1042/bj20070258] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The Arabidopsis acn (acetate non-utilizing) mutants were isolated by fluoroacetate-resistant germination and seedling establishment. We report the characterization of the acn2 mutant. Physiological analyses of acn2 showed that it possessed characteristics similar to those of the mutants cts (COMATOSE)-1 and pxa [peroxisomal ABC (ATP-binding-cassette) transporter]1. The acn2 locus was mapped to within 3 cM of the CTS gene on the bottom arm of chromosome IV using CAPS (cleavage amplification polymorphism) and SSLP (simple sequence-length polymorphism) markers. Crossing acn2 and cts-1 failed to restore the fluoroacetate-sensitive phenotype, suggesting that these mutations were allelic. Sequencing of the ACN2 locus revealed a C-->T nonsense mutation in exon 13, which would have resulted in the elimination of the C-terminal hemitransporter domain of the encoded protein. Neither the full-length CTS protein nor the truncated protein was detected on immunoblots using either C-terminal- or N-terminal-specific anti-CTS antibodies respectively, demonstrating the absence of the entire CTS protein in acn2 mutants. Emerged seedlings of both cts-1 and pxa1 alleles displayed increased resistance to FAc (monofluoroacetic acid) compared with the corresponding wild-type seedlings. Complementation studies showed that mutation of the CTS gene was responsible for the FAc-resistant phenotype, as when the wild-type protein was expressed in both the cts-1 and pxa1 mutant lines, the strains became FAc-sensitive. Feeding studies confirmed that both acn2 and cts-1 mutants were compromised in their ability to convert radiolabelled acetate into soluble carbohydrate. These results demonstrate a role for the ABC protein CTS in providing acetate to the glyoxylate cycle in developing seedlings.
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Affiliation(s)
- Mark A Hooks
- School of Biological Sciences, University of Wales Bangor, Bangor, Gwynedd LL57 2UW, Wales, UK.
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43
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Footitt S, Dietrich D, Fait A, Fernie AR, Holdsworth MJ, Baker A, Theodoulou FL. The COMATOSE ATP-binding cassette transporter is required for full fertility in Arabidopsis. Plant Physiol 2007; 144:1467-80. [PMID: 17468211 PMCID: PMC1914130 DOI: 10.1104/pp.107.099903] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
COMATOSE (CTS) encodes a peroxisomal ATP-binding cassette transporter required not only for beta-oxidation of storage lipids during germination and establishment, but also for biosynthesis of jasmonic acid and conversion of indole butyric acid to indole acetic acid. cts mutants exhibited reduced fertilization, which was rescued by genetic complementation, but not by exogenous application of jasmonic acid or indole acetic acid. Reduced fertilization was also observed in thiolase (kat2-1) and peroxisomal acyl-Coenzyme A synthetase mutants (lacs6-1,lacs7-1), indicating a general role for beta-oxidation in fertility. Genetic analysis revealed reduced male transmission of cts alleles and both cts pollen germination and tube growth in vitro were impaired in the absence of an exogenous carbon source. Aniline blue staining of pollinated pistils demonstrated that pollen tube growth was affected only when both parents bore the cts mutation, indicating that expression of CTS in either male or female tissues was sufficient to support pollen tube growth in vivo. Accordingly, abundant peroxisomes were detected in a range of maternal tissues. Although gamma-aminobutyric acid levels were reduced in flowers of cts mutants, they were unchanged in kat2-1, suggesting that alterations in gamma-aminobutyric acid catabolism do not contribute to the reduced fertility phenotype through altered pollen tube targeting. Taken together, our data support an important role for beta-oxidation in fertility in Arabidopsis (Arabidopsis thaliana) and suggest that this pathway could play a role in the mobilization of lipids in both pollen and female tissues.
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Affiliation(s)
- Steven Footitt
- Crop Performance and Improvement Division, Rothamsted Research, Harpenden, Hertfordshire, UK
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Abstract
The degradation of fatty acids in plants occurs primarily in the peroxisomes through the beta-oxidation cycle. Enzymes that are involved in various aspects of beta-oxidation have been identified recently and shown to act biochemically on a diversity of fatty acids and derivatives. Analysis of several mutants has revealed essential roles for beta-oxidation in the breakdown of reserve triacylglycerols, seed development, seed germination and post-germinative growth before the establishment of photosynthesis. Beta-oxidation has also a considerable importance during the vegetative and reproductive growth phases, and plays a role in plant responses to stress, particularly in the synthesis of jasmonic acid.
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Affiliation(s)
- Simon Goepfert
- Department of Plant Molecular Biology, Biophore, University of Lausanne, CH-1015 Lausanne, Switzerland
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Carrera E, Holman T, Medhurst A, Peer W, Schmuths H, Footitt S, Theodoulou FL, Holdsworth MJ. Gene expression profiling reveals defined functions of the ATP-binding cassette transporter COMATOSE late in phase II of germination. Plant Physiol 2007; 143:1669-79. [PMID: 17322332 PMCID: PMC1851828 DOI: 10.1104/pp.107.096057] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Phase II of germination represents a key developmental stage of plant growth during which imbibed seeds either enter stage III of germination, completing the germination process via radicle protrusion, or remain dormant. In this study, we analyzed the influence of the peroxisomal ATP-binding cassette transporter COMATOSE (CTS) on the postimbibition seed transcriptome of Arabidopsis (Arabidopsis thaliana) and also investigated interactions between gibberellin (GA) and CTS function. A novel method for analysis of transcriptome datasets allowed visualization of developmental signatures of seeds, showing that cts-1 retains the capacity to after ripen, indicating a germination block late in phase II. Expression of the key GA biosynthetic genes GA3ox1 and 2 was greatly reduced in cts seeds and genetic analysis suggested that CTS was epistatic to RGL2, a germination-repressing DELLA protein that is degraded by GA. Comparative analysis of seed transcriptome datasets indicated that specific cohorts of genes were influenced by GA and CTS. CTS function was required for expression of the flavonoid biosynthetic pathway. Confocal imaging demonstrated the exclusive accumulation of flavonoids in the epidermis of wild-type seeds. In contrast, flavonoids were absent from cts and kat2-1 mutant seeds, but accumulated following the application of sucrose, indicating an essential role for beta-oxidation in inducing flavonoid biosynthetic genes. These results demonstrate that CTS functions very late in phase II of germination and that its function is required for the expression of specific gene sets related to an important biochemical pathway associated with seedling establishment and survival.
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Affiliation(s)
- Esther Carrera
- Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
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Abstract
The mechanisms controlling seed dormancy in Arabidopsis (Arabidopsis thaliana) have been characterized by proteomics using the dormant (D) accession Cvi originating from the Cape Verde Islands. Comparative studies carried out with freshly harvested dormant and after-ripened non-dormant (ND) seeds revealed a specific differential accumulation of 32 proteins. The data suggested that proteins associated with metabolic functions potentially involved in germination can accumulate during after-ripening in the dry state leading to dormancy release. Exogenous application of abscisic acid (ABA) to ND seeds strongly impeded their germination, which physiologically mimicked the behavior of D imbibed seeds. This application resulted in an alteration of the accumulation pattern of 71 proteins. There was a strong down-accumulation of a major part (90%) of these proteins, which were involved mainly in energetic and protein metabolisms. This feature suggested that exogenous ABA triggers proteolytic mechanisms in imbibed seeds. An analysis of de novo protein synthesis by two-dimensional gel electrophoresis in the presence of [(35)S]-methionine disclosed that exogenous ABA does not impede protein biosynthesis during imbibition. Furthermore, imbibed D seeds proved competent for de novo protein synthesis, demonstrating that impediment of protein translation was not the cause of the observed block of seed germination. However, the two-dimensional protein profiles were markedly different from those obtained with the ND seeds imbibed in ABA. Altogether, the data showed that the mechanisms blocking germination of the ND seeds by ABA application are different from those preventing germination of the D seeds imbibed in basal medium.
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Affiliation(s)
- Kamel Chibani
- Institut National de la Recherche Agronomique-Institut National Agronomique Paris-Grignon, Chaire de Physiologie Végétale, Unité Mixte de Recherche 204, F-75231 Paris cedex 05, France
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Rottensteiner H, Theodoulou FL. The ins and outs of peroxisomes: Co-ordination of membrane transport and peroxisomal metabolism. Biochimica et Biophysica Acta (BBA) - Molecular Cell Research 2006; 1763:1527-40. [PMID: 17010456 DOI: 10.1016/j.bbamcr.2006.08.012] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2006] [Revised: 08/15/2006] [Accepted: 08/18/2006] [Indexed: 11/28/2022]
Abstract
Peroxisomes perform a range of metabolic functions which require the movement of substrates, co-substrates, cofactors and metabolites across the peroxisomal membrane. In this review, we discuss the evidence for and against specific transport systems involved in peroxisomal metabolism and how these operate to co-ordinate biochemical reactions within the peroxisome with those in other compartments of the cell.
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Affiliation(s)
- Hanspeter Rottensteiner
- Medical Faculty of the Ruhr-University of Bochum, Department of Physiological Chemistry, Section of Systems Biochemistry, 44780 Bochum, Germany.
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