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Flutre T, Le Cunff L, Fodor A, Launay A, Romieu C, Berger G, Bertrand Y, Terrier N, Beccavin I, Bouckenooghe V, Roques M, Pinasseau L, Verbaere A, Sommerer N, Cheynier V, Bacilieri R, Boursiquot JM, Lacombe T, Laucou V, This P, Péros JP, Doligez A. A genome-wide association and prediction study in grapevine deciphers the genetic architecture of multiple traits and identifies genes under many new QTLs. G3 (BETHESDA, MD.) 2022; 12:6575896. [PMID: 35485948 PMCID: PMC9258538 DOI: 10.1093/g3journal/jkac103] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/21/2022] [Indexed: 12/11/2022]
Abstract
To cope with the challenges facing agriculture, speeding-up breeding programs is a worthy endeavor, especially for perennial species such as grapevine, but requires understanding the genetic architecture of target traits. To go beyond the mapping of quantitative trait loci in bi-parental crosses, we exploited a diversity panel of 279 Vitis vinifera L. cultivars planted in 5 blocks in the vineyard. This panel was phenotyped over several years for 127 traits including yield components, organic acids, aroma precursors, polyphenols, and a water stress indicator. The panel was genotyped for 63k single nucleotide polymorphisms by combining an 18K microarray and genotyping-by-sequencing. The experimental design allowed to reliably assess the genotypic values for most traits. Marker densification via genotyping-by-sequencing markedly increased the proportion of genetic variance explained by single nucleotide polymorphisms, and 2 multi-single nucleotide polymorphism models identified quantitative trait loci not found by a single nucleotide polymorphism-by-single nucleotide polymorphism model. Overall, 489 reliable quantitative trait loci were detected for 41% more response variables than by a single nucleotide polymorphism-by-single nucleotide polymorphism model with microarray-only single nucleotide polymorphisms, many new ones compared with the results from bi-parental crosses. A prediction accuracy higher than 0.42 was obtained for 50% of the response variables. Our overall approach as well as quantitative trait locus and prediction results provide insights into the genetic architecture of target traits. New candidate genes and the application into breeding are discussed.
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Affiliation(s)
- Timothée Flutre
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France.,Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, 91190 Gif-sur-Yvette, France
| | - Loïc Le Cunff
- UMT Géno-Vigne, 34398 Montpellier, France.,IFV, 30240 Le Grau-du-Roi, France
| | - Agota Fodor
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Amandine Launay
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Charles Romieu
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Gilles Berger
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Yves Bertrand
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Nancy Terrier
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France
| | | | | | - Maryline Roques
- UMT Géno-Vigne, 34398 Montpellier, France.,IFV, 30240 Le Grau-du-Roi, France
| | - Lucie Pinasseau
- SPO, Univ Montpellier, INRAE, Institut Agro, 34060 Montpellier, France
| | - Arnaud Verbaere
- SPO, Univ Montpellier, INRAE, Institut Agro, 34060 Montpellier, France
| | - Nicolas Sommerer
- SPO, Univ Montpellier, INRAE, Institut Agro, 34060 Montpellier, France
| | | | - Roberto Bacilieri
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Jean-Michel Boursiquot
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Thierry Lacombe
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Valérie Laucou
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Patrice This
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Jean-Pierre Péros
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Agnès Doligez
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
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Jurdak R, Rodrigues GDAG, Chaumont N, Schivre G, Bourbousse C, Barneche F, Bou Dagher Kharrat M, Bailly C. Intracellular reactive oxygen species trafficking participates in seed dormancy alleviation in Arabidopsis seeds. THE NEW PHYTOLOGIST 2022; 234:850-866. [PMID: 35175638 DOI: 10.1111/nph.18038] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/03/2022] [Indexed: 06/14/2023]
Abstract
Reactive oxygen species (ROS) release seed dormancy through an unknown mechanism. We used different seed dormancy-breaking treatments to decipher the dynamics and localization of ROS production during seed germination. We studied the involvement of ROS in the breaking of Arabidopsis seed dormancy by cold stratification, gibberellic acid (GA3 ) and light. We characterized the effects of these treatments on abscisic acid and gibberellins biosynthesis and signalling pathways. ROS, mitochondrial redox status and peroxisomes were visualized and/or quantified during seed imbibition. Finally, we performed a cytogenetic characterization of the nuclei from the embryonic axes during seed germination. We show that mitochondria participate in the early ROS production during seed imbibition and that a possible involvement of peroxisomes in later stages should still be analysed. At the time of radicle protrusion, ROS accumulated within the nucleus, which correlated with nuclear expansion and chromatin decompaction. Taken together, our results provide evidence of the role of ROS trafficking between organelles and of the nuclear redox status in the regulation of seed germination by dormancy.
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Affiliation(s)
- Rana Jurdak
- IBPS, CNRS, UMR 7622 Biologie du Développement, Sorbonne Université, Paris, F-75005, France
- Biodiversity and Functional Genomics Laboratory, Université Saint-Joseph de Beyrouth, Beyrouth, 1107 2050, Lebanon
| | - Guilherme de Almeida Garcia Rodrigues
- IBPS, CNRS, UMR 7622 Biologie du Développement, Sorbonne Université, Paris, F-75005, France
- Plant Physiology Lab, Federal University of Santa Catarina (UFSC), Florianópolis, SC, 88040-900, Brazil
| | - Nicole Chaumont
- IBPS, CNRS, UMR 7622 Biologie du Développement, Sorbonne Université, Paris, F-75005, France
| | - Geoffrey Schivre
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, F-75005, France
- Université Paris-Saclay, Orsay, F-91405, France
| | - Clara Bourbousse
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, F-75005, France
| | - Fredy Barneche
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, F-75005, France
| | - Magda Bou Dagher Kharrat
- Biodiversity and Functional Genomics Laboratory, Université Saint-Joseph de Beyrouth, Beyrouth, 1107 2050, Lebanon
| | - Christophe Bailly
- IBPS, CNRS, UMR 7622 Biologie du Développement, Sorbonne Université, Paris, F-75005, France
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Shelp BJ, Aghdam MS, Flaherty EJ. γ-Aminobutyrate (GABA) Regulated Plant Defense: Mechanisms and Opportunities. PLANTS (BASEL, SWITZERLAND) 2021; 10:1939. [PMID: 34579473 PMCID: PMC8468876 DOI: 10.3390/plants10091939] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 02/07/2023]
Abstract
Global climate change and associated adverse abiotic and biotic stress conditions affect plant growth and development, and agricultural sustainability in general. Abiotic and biotic stresses reduce respiration and associated energy generation in mitochondria, resulting in the elevated production of reactive oxygen species (ROS), which are employed to transmit cellular signaling information in response to the changing conditions. Excessive ROS accumulation can contribute to cell damage and death. Production of the non-protein amino acid γ-aminobutyrate (GABA) is also stimulated, resulting in partial restoration of respiratory processes and energy production. Accumulated GABA can bind directly to the aluminum-activated malate transporter and the guard cell outward rectifying K+ channel, thereby improving drought and hypoxia tolerance, respectively. Genetic manipulation of GABA metabolism and receptors, respectively, reveal positive relationships between GABA levels and abiotic/biotic stress tolerance, and between malate efflux from the root and heavy metal tolerance. The application of exogenous GABA is associated with lower ROS levels, enhanced membrane stability, changes in the levels of non-enzymatic and enzymatic antioxidants, and crosstalk among phytohormones. Exogenous GABA may be an effective and sustainable tolerance strategy against multiple stresses under field conditions.
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Affiliation(s)
- Barry J. Shelp
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Morteza Soleimani Aghdam
- Department of Horticultural Science, Imam Khomeini International University, Qazvin 34148-96818, Iran;
| | - Edward J. Flaherty
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada;
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Joshi V, Penalosa A, Joshi M, Rodriguez S. Regulation of Oxalate Metabolism in Spinach Revealed by RNA-Seq-Based Transcriptomic Analysis. Int J Mol Sci 2021; 22:ijms22105294. [PMID: 34069886 PMCID: PMC8157348 DOI: 10.3390/ijms22105294] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 01/12/2023] Open
Abstract
Although spinach (Spinacia oleracea L.) is considered to be one of the most nutrient-rich leafy vegetables, it is also a potent accumulator of anti-nutritional oxalate. Reducing oxalate content would increase the nutritional value of spinach by enhancing the dietary bioavailability of calcium and other minerals. This study aimed to investigate the proposed hypothesis that a complex network of genes associated with intrinsic metabolic and physiological processes regulates oxalate homeostasis in spinach. Transcriptomic (RNA-Seq) analysis of the leaf and root tissues of two spinach genotypes with contrasting oxalate phenotypes was performed under normal physiological conditions. A total of 2308 leaf- and 1686 root-specific differentially expressed genes (DEGs) were identified in the high-oxalate spinach genotype. Gene Ontology (GO) analysis of DEGs identified molecular functions associated with various enzymatic activities, while KEGG pathway analysis revealed enrichment of the metabolic and secondary metabolite pathways. The expression profiles of genes associated with distinct physiological processes suggested that the glyoxylate cycle, ascorbate degradation, and photorespiratory pathway may collectively regulate oxalate in spinach. The data support the idea that isocitrate lyase (ICL), ascorbate catabolism-related genes, and acyl-activating enzyme 3 (AAE3) all play roles in oxalate homeostasis in spinach. The findings from this study provide the foundation for novel insights into oxalate metabolism in spinach.
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Affiliation(s)
- Vijay Joshi
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843, USA
- Texas A&M AgriLife Research and Extension Center, Uvalde, TX 78801, USA;
- Correspondence: ; Tel.: +1-830-988-6137
| | - Arianne Penalosa
- College of Science, University of Texas, Arlington, TX 76019, USA; (A.P.); (S.R.)
| | - Madhumita Joshi
- Texas A&M AgriLife Research and Extension Center, Uvalde, TX 78801, USA;
| | - Sierra Rodriguez
- College of Science, University of Texas, Arlington, TX 76019, USA; (A.P.); (S.R.)
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Schmitz J, Hüdig M, Meier D, Linka N, Maurino VG. The genome of Ricinus communis encodes a single glycolate oxidase with different functions in photosynthetic and heterotrophic organs. PLANTA 2020; 252:100. [PMID: 33170407 PMCID: PMC7655567 DOI: 10.1007/s00425-020-03504-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 10/23/2020] [Indexed: 06/11/2023]
Abstract
The biochemical characterization of glycolate oxidase in Ricinus communis hints to different physiological functions of the enzyme depending on the organ in which it is active. Enzymatic activities of the photorespiratory pathway are not restricted to green tissues but are present also in heterotrophic organs. High glycolate oxidase (GOX) activity was detected in the endosperm of Ricinus communis. Phylogenetic analysis of the Ricinus L-2-hydroxy acid oxidase (Rc(L)-2-HAOX) family indicated that Rc(L)-2-HAOX1 to Rc(L)-2-HAOX3 cluster with the group containing streptophyte long-chain 2-hydroxy acid oxidases, whereas Rc(L)-2-HAOX4 clusters with the group containing streptophyte GOX. Rc(L)-2-HAOX4 is the closest relative to the photorespiratory GOX genes of Arabidopsis. We obtained Rc(L)-2-HAOX4 as a recombinant protein and analyze its kinetic properties in comparison to the Arabidopsis photorespiratory GOX. We also analyzed the expression of all Rc(L)-2-HAOXs and conducted metabolite profiling of different Ricinus organs. Phylogenetic analysis indicates that Rc(L)-2-HAOX4 is the only GOX encoded in the Ricinus genome (RcGOX). RcGOX has properties resembling those of the photorespiratory GOX of Arabidopsis. We found that glycolate, the substrate of GOX, is highly abundant in non-green tissues, such as roots, embryo of germinating seeds and dry seeds. We propose that RcGOX fulfills different physiological functions depending on the organ in which it is active. In autotrophic organs it oxidizes glycolate into glyoxylate as part of the photorespiratory pathway. In fast growing heterotrophic organs, it is most probably involved in the production of serine to feed the folate pathway for special demands of those tissues.
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Affiliation(s)
- Jessica Schmitz
- Plant Molecular Physiology and Biotechnology Division, Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University, and Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
| | - Meike Hüdig
- Plant Molecular Physiology and Biotechnology Division, Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University, and Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
- Molecular Plant Physiology Division, Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Dieter Meier
- Plant Molecular Physiology and Biotechnology Division, Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University, and Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
| | - Nicole Linka
- Institute for Plant Biochemistry, Heinrich Heine University, and Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
| | - Veronica G Maurino
- Plant Molecular Physiology and Biotechnology Division, Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University, and Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany.
- Molecular Plant Physiology Division, Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, Kirschallee 1, 53115, Bonn, Germany.
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Gramazio P, Takayama M, Ezura H. Challenges and Prospects of New Plant Breeding Techniques for GABA Improvement in Crops: Tomato as an Example. FRONTIERS IN PLANT SCIENCE 2020; 11:577980. [PMID: 33014001 PMCID: PMC7500313 DOI: 10.3389/fpls.2020.577980] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/20/2020] [Indexed: 05/28/2023]
Abstract
Over the last seven decades, γ-aminobutyric acid (GABA) has attracted great attention from scientists for its ubiquity in plants, animals and microorganisms and for its physiological implications as a signaling molecule involved in multiple pathways and processes. Recently, the food and pharmaceutical industries have also shown significantly increased interest in GABA, because of its great potential benefits for human health and the consumer demand for health-promoting functional compounds, resulting in the release of a plethora of GABA-enriched products. Nevertheless, many crop species accumulate appreciable GABA levels in their edible parts and could help to meet the daily recommended intake of GABA for promoting positive health effects. Therefore, plant breeders are devoting much effort into breeding elite varieties with improved GABA contents. In this regard, tomato (Solanum lycopersicum), the most produced and consumed vegetable worldwide and a fruit-bearing model crop, has received much consideration for its accumulation of remarkable GABA levels. Although many different strategies have been implemented, from classical crossbreeding to induced mutagenesis, new plant breeding techniques (NPBTs) have achieved the best GABA accumulation results in red ripe tomato fruits along with shedding light on GABA metabolism and gene functions. In this review, we summarize, analyze and compare all the studies that have substantially contributed to tomato GABA breeding with further discussion and proposals regarding the most recent NPBTs that could bring this process to the next level of precision and efficiency. This document also provides guidelines with which researchers of other crops might take advantage of the progress achieved in tomato for more efficient GABA breeding programs.
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Affiliation(s)
- Pietro Gramazio
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Mariko Takayama
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Tsukuba Plant Innovation Research Center (T-PIRC), University of Tsukuba, Tsukuba, Japan
| | - Hiroshi Ezura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Tsukuba Plant Innovation Research Center (T-PIRC), University of Tsukuba, Tsukuba, Japan
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Zhang Z, Liang X, Lu L, Xu Z, Huang J, He H, Peng X. Two glyoxylate reductase isoforms are functionally redundant but required under high photorespiration conditions in rice. BMC PLANT BIOLOGY 2020; 20:357. [PMID: 32727356 PMCID: PMC7391683 DOI: 10.1186/s12870-020-02568-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 07/22/2020] [Indexed: 05/31/2023]
Abstract
BACKGROUND The glyoxylate reductase (GR) multigene family has been described in various plant species, their isoforms show different biochemical features in plants. However, few studies have addressed the biological roles of GR isozymes, especially for rice. RESULTS Here, we report a detailed analysis of the enzymatic properties and physiological roles of OsGR1 and OsGR2 in rice. The results showed that both enzymes prefer NADPH to NADH as cofactor, and the NADPH-dependent glyoxylate reducing activity represents the major GR activity in various tissues and at different growth stages; and OsGR1 proteins were more abundant than OsGR2, which is also a major contributor to total GR activities. By generating and characterizing various OsGR-genetically modified rice lines, including overexpression, single and double-knockout lines, we found that no phenotypic differences occur among the various transgenic lines under normal growth conditions, while a dwarfish growth phenotype was noticed under photorespiration-promoted conditions. CONCLUSION Our results suggest that OsGR1 and OsGR2, with distinct enzymatic characteristics, function redundantly in detoxifying glyoxylate in rice plants under normal growth conditions, whereas both are simultaneously required under high photorespiration conditions.
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Affiliation(s)
- Zhisheng Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, China
| | - Xiu Liang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, China
| | - Lei Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, China
| | - Zheng Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, China
| | - Jiayu Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, China
| | - Han He
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xinxiang Peng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China.
- Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, China.
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Fernie AR, Bauwe H. Wasteful, essential, evolutionary stepping stone? The multiple personalities of the photorespiratory pathway. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:666-677. [PMID: 31904886 DOI: 10.1111/tpj.14669] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/30/2019] [Accepted: 12/11/2019] [Indexed: 05/08/2023]
Abstract
The photorespiratory pathway, in short photorespiration, is a metabolic repair system that enables the CO2 fixation enzyme Rubisco to sustainably operate in the presence of oxygen, that is, during oxygenic photosynthesis of plants and cyanobacteria. Photorespiration is necessary because an auto-inhibitory metabolite, 2-phosphoglycolate (2PG), is produced when Rubisco binds oxygen instead of CO2 as a substrate and must be removed, to avoid collapse of metabolism, and recycled as efficiently as possible. The basic principle of recycling 2PG very likely evolved several billion years ago in connection with the evolution of oxyphotobacteria. It comprises the multi-step combination of two molecules of 2PG to form 3-phosphoglycerate. The biochemistry of this process dictates that one out of four 2PG carbons is lost as CO2 , which is a long-standing plant breeders' concern because it represents by far the largest fraction of respiratory processes that reduce gross-photosynthesis of major crops down to about 50% and less, lowering potential yields. In addition to the ATP needed for recycling of the 2PG carbon, extra energy is needed for the refixation of liberated equal amounts of ammonia. It is thought that the energy costs of photorespiration have an additional negative impact on crop yields in at least some environments. This paper discusses recent advances concerning the origin and evolution of photorespiration, and gives an overview of contemporary and envisioned strategies to engineer the biochemistry of, or even avoid, photorespiration.
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Affiliation(s)
- Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Hermann Bauwe
- Plant Physiology Department, University of Rostock, Albert-Einstein-Straße 3, D-18051, Rostock, Germany
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Singh D, Singh CK, Taunk J, Jadon V, Pal M, Gaikwad K. Genome wide transcriptome analysis reveals vital role of heat responsive genes in regulatory mechanisms of lentil (Lens culinaris Medikus). Sci Rep 2019; 9:12976. [PMID: 31506558 PMCID: PMC6736890 DOI: 10.1038/s41598-019-49496-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 08/23/2019] [Indexed: 01/29/2023] Open
Abstract
The present study reports the role of morphological, physiological and reproductive attributes viz. membrane stability index (MSI), osmolytes accumulations, antioxidants activities and pollen germination for heat stress tolerance in contrasting genotypes. Heat stress increased proline and glycine betaine (GPX) contents, induced superoxide dismutase (SOD), ascorbate peroxidase (APX) and glutathione peroxidase (GPX) activities and resulted in higher MSI in PDL-2 (tolerant) compared to JL-3 (sensitive). In vitro pollen germination of tolerant genotype was higher than sensitive one under heat stress. In vivo stressed pollens of tolerant genotype germinated well on stressed stigma of sensitive genotype, while stressed pollens of sensitive genotype did not germinate on stressed stigma of tolerant genotype. De novo transcriptome analysis of both the genotypes showed that number of contigs ranged from 90,267 to 104,424 for all the samples with N50 ranging from 1,755 to 1,844 bp under heat stress and control conditions. Based on assembled unigenes, 194,178 high-quality Single Nucleotide Polymorphisms (SNPs), 141,050 microsatellites and 7,388 Insertion-deletions (Indels) were detected. Expression of 10 genes was evaluated using quantitative Real Time Polymerase Chain Reaction (RT-qPCR). Comparison of differentially expressed genes (DEGs) under different combinations of heat stress has led to the identification of candidate DEGs and pathways. Changes in expression of physiological and pollen phenotyping related genes were also reaffirmed through transcriptome data. Cell wall and secondary metabolite pathways are found to be majorly affected under heat stress. The findings need further analysis to determine genetic mechanism involved in heat tolerance of lentil.
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Affiliation(s)
- Dharmendra Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Chandan Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Jyoti Taunk
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Vasudha Jadon
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Madan Pal
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Kishor Gaikwad
- ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
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Podlešáková K, Ugena L, Spíchal L, Doležal K, De Diego N. Phytohormones and polyamines regulate plant stress responses by altering GABA pathway. N Biotechnol 2018; 48:53-65. [PMID: 30048769 DOI: 10.1016/j.nbt.2018.07.003] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 06/20/2018] [Accepted: 07/21/2018] [Indexed: 11/16/2022]
Abstract
In plants, γ-aminobutyric acid (GABA) accumulates rapidly in response to environmental stress and variations in its endogenous concentration have been shown to affect plant growth. Exogenous application of GABA has also conferred higher stress tolerance by modulating the expression of genes involved in plant signalling, transcriptional regulation, hormone biosynthesis, reactive oxygen species production and polyamine metabolism. Plant hormones play critical roles in adaptation of plants to adverse environmental conditions through a sophisticated crosstalk among them. Several studies have provided evidence for the relationships between GABA, polyamines and hormones such as abscisic acid, cytokinins, auxins, gibberellins and ethylene, among others, focussing on the effect that one specific group of compounds exerts over the metabolic and signalling pathways of others. In this review, we bring together information obtained from plants exposed to several stress conditions and discuss the possible links among these different groups of molecules. The analysis supports the view that highly conserved pathways connect primary and secondary metabolism, with an overlap of regulatory functions related to stress responses and tolerance among phytohormones, amino acids and polyamines.
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Affiliation(s)
- Kateřina Podlešáková
- Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, CZ-78371, Czech Republic.
| | - Lydia Ugena
- Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, CZ-78371, Czech Republic.
| | - Lukáš Spíchal
- Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, CZ-78371, Czech Republic.
| | - Karel Doležal
- Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, CZ-78371, Czech Republic.
| | - Nuria De Diego
- Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, CZ-78371, Czech Republic.
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11
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γ-Aminobutyric Acid (GABA): Biosynthesis, Role, Commercial Production, and Applications. STUDIES IN NATURAL PRODUCTS CHEMISTRY 2018. [DOI: 10.1016/b978-0-444-64057-4.00013-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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12
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Kopečná M, Vigouroux A, Vilím J, Končitíková R, Briozzo P, Hájková E, Jašková L, von Schwartzenberg K, Šebela M, Moréra S, Kopečný D. The ALDH21 gene found in lower plants and some vascular plants codes for a NADP + -dependent succinic semialdehyde dehydrogenase. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:229-243. [PMID: 28749584 DOI: 10.1111/tpj.13648] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 07/19/2017] [Accepted: 07/24/2017] [Indexed: 06/07/2023]
Abstract
Lower plant species including some green algae, non-vascular plants (bryophytes) as well as the oldest vascular plants (lycopods) and ferns (monilophytes) possess a unique aldehyde dehydrogenase (ALDH) gene named ALDH21, which is upregulated during dehydration. However, the gene is absent in flowering plants. Here, we show that ALDH21 from the moss Physcomitrella patens codes for a tetrameric NADP+ -dependent succinic semialdehyde dehydrogenase (SSALDH), which converts succinic semialdehyde, an intermediate of the γ-aminobutyric acid (GABA) shunt pathway, into succinate in the cytosol. NAD+ is a very poor coenzyme for ALDH21 unlike for mitochondrial SSALDHs (ALDH5), which are the closest related ALDH members. Structural comparison between the apoform and the coenzyme complex reveal that NADP+ binding induces a conformational change of the loop carrying Arg-228, which seals the NADP+ in the coenzyme cavity via its 2'-phosphate and α-phosphate groups. The crystal structure with the bound product succinate shows that its carboxylate group establishes salt bridges with both Arg-121 and Arg-457, and a hydrogen bond with Tyr-296. While both arginine residues are pre-formed for substrate/product binding, Tyr-296 moves by more than 1 Å. Both R121A and R457A variants are almost inactive, demonstrating a key role of each arginine in catalysis. Our study implies that bryophytes but presumably also some green algae, lycopods and ferns, which carry both ALDH21 and ALDH5 genes, can oxidize SSAL to succinate in both cytosol and mitochondria, indicating a more diverse GABA shunt pathway compared with higher plants carrying only the mitochondrial ALDH5.
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Affiliation(s)
- Martina Kopečná
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71, Olomouc, Czech Republic
| | - Armelle Vigouroux
- Institute for Integrative Biology of the Cell (I2BC), CNRS-CEA-Univ. Paris-Sud, Université Paris-Saclay, Avenue de la Terrasse, F-91198, Gif-sur-Yvette, France
| | - Jan Vilím
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71, Olomouc, Czech Republic
| | - Radka Končitíková
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71, Olomouc, Czech Republic
| | - Pierre Briozzo
- Institut Jean-Pierre Bourgin, INRA-AgroParisTech, Université Paris-Saclay, Route de Saint-Cyr, F-78026, Versailles, France
| | - Eva Hájková
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71, Olomouc, Czech Republic
| | - Lenka Jašková
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71, Olomouc, Czech Republic
| | | | - Marek Šebela
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71, Olomouc, Czech Republic
| | - Solange Moréra
- Institute for Integrative Biology of the Cell (I2BC), CNRS-CEA-Univ. Paris-Sud, Université Paris-Saclay, Avenue de la Terrasse, F-91198, Gif-sur-Yvette, France
| | - David Kopečný
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71, Olomouc, Czech Republic
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13
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Zarei A, Brikis CJ, Bajwa VS, Chiu GZ, Simpson JP, DeEll JR, Bozzo GG, Shelp BJ. Plant Glyoxylate/Succinic Semialdehyde Reductases: Comparative Biochemical Properties, Function during Chilling Stress, and Subcellular Localization. FRONTIERS IN PLANT SCIENCE 2017; 8:1399. [PMID: 28855911 PMCID: PMC5558127 DOI: 10.3389/fpls.2017.01399] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 07/27/2017] [Indexed: 05/18/2023]
Abstract
Plant NADPH-dependent glyoxylate/succinic semialdehyde reductases 1 and 2 (cytosolic GLYR1 and plastidial/mitochondrial GLYR2) are considered to be of particular importance under abiotic stress conditions. Here, the apple (Malus × domestica Borkh.) and rice (Oryza sativa L.) GLYR1s and GLYR2s were characterized and their kinetic properties were compared to those of previously characterized GLYRs from Arabidopsis thaliana [L.] Heynh. The purified recombinant GLYRs had an affinity for glyoxylate and succinic semialdehyde, respectively, in the low micromolar and millimolar ranges, and were inhibited by NADP+. Comparison of the GLYR activity in cell-free extracts from wild-type Arabidopsis and a glyr1 knockout mutant revealed that approximately 85 and 15% of the cellular GLYR activity is cytosolic and plastidial/mitochondrial, respectively. Recovery of GLYR activity in purified mitochondria from the Arabidopsis glyr1 mutant, free from cytosolic GLYR1 or plastidial GLYR2 contamination, provided additional support for the targeting of GLYR2 to mitochondria, as well as plastids. The growth of plantlets or roots of various Arabidopsis lines with altered GLYR activity responded differentially to succinic semialdehyde or glyoxylate under chilling conditions. Taken together, these findings highlight the potential regulation of highly conserved plant GLYRs by NADPH/NADP+ ratios in planta, and their roles in the reduction of toxic aldehydes in plants subjected to chilling stress.
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Affiliation(s)
- Adel Zarei
- Department of Plant Agriculture, University of Guelph, GuelphON, Canada
| | | | | | - Greta Z. Chiu
- Department of Plant Agriculture, University of Guelph, GuelphON, Canada
| | | | - Jennifer R. DeEll
- Ontario Ministry of Agriculture, Food and Rural Affairs, SimcoeON, Canada
| | - Gale G. Bozzo
- Department of Plant Agriculture, University of Guelph, GuelphON, Canada
| | - Barry J. Shelp
- Department of Plant Agriculture, University of Guelph, GuelphON, Canada
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14
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Keech O, Gardeström P, Kleczkowski LA, Rouhier N. The redox control of photorespiration: from biochemical and physiological aspects to biotechnological considerations. PLANT, CELL & ENVIRONMENT 2017; 40:553-569. [PMID: 26791824 DOI: 10.1111/pce.12713] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Revised: 12/28/2015] [Accepted: 01/13/2016] [Indexed: 06/05/2023]
Abstract
Photorespiration is a complex and tightly regulated process occurring in photosynthetic organisms. This process can alter the cellular redox balance, notably via the production and consumption of both reducing and oxidizing equivalents. Under certain circumstances, these equivalents, as well as reactive oxygen or nitrogen species, can become prominent in subcellular compartments involved in the photorespiratory process, eventually promoting oxidative post-translational modifications of proteins. Keeping these changes under tight control should therefore be of primary importance. In order to review the current state of knowledge about the redox control of photorespiration, we primarily performed a careful description of the known and potential redox-regulated or oxidation sensitive photorespiratory proteins, and examined in more details two interesting cases: the glycerate kinase and the glycine cleavage system. When possible, the potential impact and subsequent physiological regulations associated with these changes have been discussed. In the second part, we reviewed the extent to which photorespiration contributes to cellular redox homeostasis considering, in particular, the set of peripheral enzymes associated with the canonical photorespiratory pathway. Finally, some recent biotechnological strategies to circumvent photorespiration for future growth improvements are discussed in the light of these redox regulations.
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Affiliation(s)
- Olivier Keech
- Department of Plant Physiology, UPSC, Umeå University, S-90187, Umeå, Sweden
| | - Per Gardeström
- Department of Plant Physiology, UPSC, Umeå University, S-90187, Umeå, Sweden
| | | | - Nicolas Rouhier
- INRA, UMR 1136 Interactions Arbres/Microorganismes, Centre INRA Nancy Lorraine, 54280, Champenoux, France
- Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes, Faculté des Sciences et Technologies, 54506, Vandoeuvre-lès-Nancy, France
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15
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Brikis CJ, Zarei A, Trobacher CP, DeEll JR, Akama K, Mullen RT, Bozzo GG, Shelp BJ. Ancient Plant Glyoxylate/Succinic Semialdehyde Reductases: GLYR1s Are Cytosolic, Whereas GLYR2s Are Localized to Both Mitochondria and Plastids. FRONTIERS IN PLANT SCIENCE 2017; 8:601. [PMID: 28484477 PMCID: PMC5399074 DOI: 10.3389/fpls.2017.00601] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 04/03/2017] [Indexed: 05/18/2023]
Abstract
Plant NADPH-dependent glyoxylate/succinic semialdehyde reductases 1 and 2 (GLYR1 and GLYR2) are considered to be involved in detoxifying harmful aldehydes, thereby preserving plant health during exposure to various abiotic stresses. Phylogenetic analysis revealed that the two GLYR isoforms appeared in the plant lineage prior to the divergence of the Chlorophyta and Streptophyta, which occurred approximately 750 million years ago. Green fluorescent protein fusions of apple (Malus x domestica Borkh.), rice (Oryza sativa L.) and Arabidopsis thaliana [L.] Heynh GLYRs were transiently expressed in tobacco (Nicotiana tabaccum L.) suspension cells or Arabidopsis protoplasts, as well in methoxyfenozide-induced, stably transformed Arabidopsis seedlings. The localization of apple GLYR1 confirmed that this isoform is cytosolic, whereas apple, rice and Arabidopsis GLYR2s were localized to both mitochondria and plastids. These findings highlight the potential involvement of GLYRs within distinct compartments of the plant cell.
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Affiliation(s)
| | - Adel Zarei
- Department of Plant Agriculture, University of Guelph, GuelphON, Canada
| | | | - Jennifer R. DeEll
- Ontario Ministry of Agriculture Food and Rural Affairs, SimcoeON, Canada
| | - Kazuhito Akama
- Department of Biological Science, Shimane UniversityMatsue, Japan
| | - Robert T. Mullen
- Department of Molecular and Cellular Biology, University of Guelph, GuelphON, Canada
| | - Gale G. Bozzo
- Department of Plant Agriculture, University of Guelph, GuelphON, Canada
| | - Barry J. Shelp
- Department of Plant Agriculture, University of Guelph, GuelphON, Canada
- *Correspondence: Barry J. Shelp,
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16
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Payá-Milans M, Aznar-Moreno JA, Balbuena TS, Haslam RP, Gidda SK, Pérez-Hormaeche J, Mullen RT, Thelen JJ, Napier JA, Salas JJ, Garcés R, Martínez-Force E, Venegas-Calerón M. Sunflower HaGPAT9-1 is the predominant GPAT during seed development. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 252:42-52. [PMID: 27717477 DOI: 10.1016/j.plantsci.2016.07.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 07/04/2016] [Accepted: 07/07/2016] [Indexed: 05/25/2023]
Abstract
In oil crops, triacylglycerol biosynthesis is an important metabolic pathway in which glycerol-3-phosphate acyltransferase (GPAT) performs the first acylation step. Mass spectrometry analysis of developing sunflower (Helianthus annuus) seed membrane fractions identified an abundant GPAT, HaGPAT9 isoform 1, with a N-terminal peptide that possessed two phosphorylated residues with possible regulatory function. HaGPAT9-1 belongs to a broad eukaryotic GPAT family, similar to mammalian GPAT3, and it represents one of the two sunflower GPAT9 isoforms, sharing 90% identity with HaGPAT9-2. Both sunflower genes are expressed during seed development and in vegetative tissues, with HaGPAT9-1 transcripts accumulating at relatively higher levels than those for HaGPAT9-2. Green fluorescent protein tagging of HaGPAT9-1 confirmed its subcellular accumulation in the endoplasmic reticulum. Despite their overall sequence similarities, the two sunflower isoforms displayed significant differences in their enzymatic activities. For instance, HaGPAT9-1 possesses in vivo GPAT activity that rescues the lethal phenotype of the cmy228 yeast strain, while in vitro assays revealed a preference of HaGPAT9-1 for palmitoyl-, oleoyl- and linoleoyl-CoAs of one order of magnitude, with the highest increase in yield for oleoyl- and linoleoyl-CoAs. By contrast, no enzymatic activity could be detected for HaGPAT9-2, even though its over-expression modified the TAG profile of yeast.
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Affiliation(s)
- Miriam Payá-Milans
- Department of Biochemistry and Molecular Biology of Plant Products, Instituto de la Grasa (CSIC), Campus Universitario Pablo de Olavide, 41013 Seville, Spain; Department of Entomology & Plant Pathology, University of Tennessee, Knoxville, TN 37996, United States
| | - Jose Antonio Aznar-Moreno
- Department of Biochemistry and Molecular Biology of Plant Products, Instituto de la Grasa (CSIC), Campus Universitario Pablo de Olavide, 41013 Seville, Spain; Department of Biochemistry & Molecular Biophysics, Kansas State University, Manhattan, KS 66506, United States
| | - Tiago S Balbuena
- Department of Biochemistry and Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211, United States; Department of Technology, São Paulo State University, Jaboticabal, São Paulo, Brazil
| | - Richard P Haslam
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom
| | - Satinder K Gidda
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Javier Pérez-Hormaeche
- Department of Biochemistry and Molecular Biology of Plant Products, Instituto de la Grasa (CSIC), Campus Universitario Pablo de Olavide, 41013 Seville, Spain
| | - Robert T Mullen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Jay J Thelen
- Department of Biochemistry and Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211, United States
| | - Johnathan A Napier
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom
| | - Joaquín J Salas
- Department of Biochemistry and Molecular Biology of Plant Products, Instituto de la Grasa (CSIC), Campus Universitario Pablo de Olavide, 41013 Seville, Spain
| | - Rafael Garcés
- Department of Biochemistry and Molecular Biology of Plant Products, Instituto de la Grasa (CSIC), Campus Universitario Pablo de Olavide, 41013 Seville, Spain
| | - Enrique Martínez-Force
- Department of Biochemistry and Molecular Biology of Plant Products, Instituto de la Grasa (CSIC), Campus Universitario Pablo de Olavide, 41013 Seville, Spain
| | - Mónica Venegas-Calerón
- Department of Biochemistry and Molecular Biology of Plant Products, Instituto de la Grasa (CSIC), Campus Universitario Pablo de Olavide, 41013 Seville, Spain.
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17
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Mekonnen DW, Ludewig F. Phenotypic and chemotypic studies using Arabidopsis and yeast reveal that GHB converts to SSA and induce toxicity. PLANT MOLECULAR BIOLOGY 2016; 91:429-40. [PMID: 27037708 DOI: 10.1007/s11103-016-0475-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 03/29/2016] [Indexed: 05/04/2023]
Abstract
γ-Hydroxybutyric acid (GHB) is a naturally occurring compound. It is detected in organisms such as yeasts, plants and mammals. GHB is produced from the reduction of succinic semialdehyde (SSA) by the activity of GHB dehydrogenase. Arabidopsis genome contains two GHB dehydrogenase encoding genes. The accumulation of GHB in ssadh mutants led to the speculation that GHB is the cause of aberrant phenotypes. Conversely, the accumulation of GHB in Arabidopsis plants subjected to abiotic stresses was described as a way of avoiding SSA induced damage. To resolve these contrasting views on GHB, we examined the effect of exogenous GHB and SSA on the growth of yeast and Arabidopsis plants. GHB concentrations up to 1.5 mM didn't affect shoots of Arabidopsis plants; however, root growth was inhibited. In contrast, 0.3 mM SSA has severely affected the growth of plants. Treatment of yeast wild-type strain with 10 mM SSA and 10 mM GHB didn't affect the growth. However, the growth of yeast uga2 mutant was greatly inhibited by the same concentration of SSA, but not GHB. Metabolic analysis and enzyme activity assay on native gel showed that Arabidopsis, but not yeast, possesses a GHB dehydrogenase activity that converts GHB back to SSA. The enzymatic assay has also indicated the existence of an additional GHB dehydrogenase encoding gene(s) in Arabidopsis genome. Taken together, we conclude that GHB is less toxic than SSA. Its accumulation in ssadh mutants and during abiotic stresses is a response to avoid the SSA induced damage.
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Affiliation(s)
- Dereje Worku Mekonnen
- Cologne Biocenter, Botanical Institute II, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany.
| | - Frank Ludewig
- Cologne Biocenter, Botanical Institute II, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
- Division of Biochemistry, Department Biology, University Erlangen-Nuremberg, Staudtstr. 5, 91058, Erlangen, Germany
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18
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Dellero Y, Jossier M, Schmitz J, Maurino VG, Hodges M. Photorespiratory glycolate-glyoxylate metabolism. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3041-52. [PMID: 26994478 DOI: 10.1093/jxb/erw090] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Photorespiration is one of the major carbon metabolism pathways in oxygen-producing photosynthetic organisms. This pathway recycles 2-phosphoglycolate (2-PG), a toxic metabolite, to 3-phosphoglycerate when ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) uses oxygen instead of carbon dioxide. The photorespiratory cycle is in competition with photosynthetic CO2 fixation and it is accompanied by carbon, nitrogen and energy losses. Thus, photorespiration has become a target to improve crop yields. Moreover, during the photorespiratory cycle intermediate metabolites that are toxic to Calvin-Benson cycle and RuBisCO activities, such as 2-PG, glycolate and glyoxylate, are produced. Thus, the presence of an efficient 2-PG/glycolate/glyoxylate 'detoxification' pathway is required to ensure normal development of photosynthetic organisms. Here we review our current knowledge concerning the enzymes that carry out the glycolate-glyoxylate metabolic steps of photorespiration from glycolate production in the chloroplasts to the synthesis of glycine in the peroxisomes. We describe the properties of the proteins involved in glycolate-glyoxylate metabolism in Archaeplastida and the phenotypes observed when knocking down/out these specific photorespiratory players. Advances in our understanding of the regulation of glycolate-glyoxylate metabolism are highlighted.
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Affiliation(s)
- Younès Dellero
- Institut of Plant Sciences Paris-Saclay, Université Paris-Sud, CNRS, INRA, Université d'Evry, Université Paris Diderot, Université Paris-Saclay, Bât 630, 91405 Orsay Cedex, France
| | - Mathieu Jossier
- Institut of Plant Sciences Paris-Saclay, Université Paris-Sud, CNRS, INRA, Université d'Evry, Université Paris Diderot, Université Paris-Saclay, Bât 630, 91405 Orsay Cedex, France
| | - Jessica Schmitz
- Institute of Developmental and Molecular Biology of Plants, Plant Molecular Physiology and Biotechnology Group, Heinrich-Heine-Universität, and Cluster of Excellence on Plant Sciences (CEPLAS), Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Veronica G Maurino
- Institute of Developmental and Molecular Biology of Plants, Plant Molecular Physiology and Biotechnology Group, Heinrich-Heine-Universität, and Cluster of Excellence on Plant Sciences (CEPLAS), Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Michael Hodges
- Institut of Plant Sciences Paris-Saclay, Université Paris-Sud, CNRS, INRA, Université d'Evry, Université Paris Diderot, Université Paris-Saclay, Bât 630, 91405 Orsay Cedex, France
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19
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Hodges M, Dellero Y, Keech O, Betti M, Raghavendra AS, Sage R, Zhu XG, Allen DK, Weber APM. Perspectives for a better understanding of the metabolic integration of photorespiration within a complex plant primary metabolism network. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3015-26. [PMID: 27053720 DOI: 10.1093/jxb/erw145] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Photorespiration is an essential high flux metabolic pathway that is found in all oxygen-producing photosynthetic organisms. It is often viewed as a closed metabolic repair pathway that serves to detoxify 2-phosphoglycolic acid and to recycle carbon to fuel the Calvin-Benson cycle. However, this view is too simplistic since the photorespiratory cycle is known to interact with several primary metabolic pathways, including photosynthesis, nitrate assimilation, amino acid metabolism, C1 metabolism and the Krebs (TCA) cycle. Here we will review recent advances in photorespiration research and discuss future priorities to better understand (i) the metabolic integration of the photorespiratory cycle within the complex network of plant primary metabolism and (ii) the importance of photorespiration in response to abiotic and biotic stresses.
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Affiliation(s)
- Michael Hodges
- Institute of Plant Sciences Paris-Saclay, Université Paris-Sud, CNRS, INRA, Université d'Evry, 91405 Orsay Cedex, France
| | - Younès Dellero
- Institute of Plant Sciences Paris-Saclay, Université Paris-Sud, CNRS, INRA, Université d'Evry, 91405 Orsay Cedex, France
| | - Olivier Keech
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, SE-90187 Umeå, Sweden
| | - Marco Betti
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, Universidad de Sevilla, 141012 Sevilla, Spain
| | - Agepati S Raghavendra
- School of Life Sciences, Department of Plant Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Rowan Sage
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S3B2, Canada
| | - Xin-Guang Zhu
- CAS-MPG Partner Institutes for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
| | - Doug K Allen
- United States Department of Agriculture-Agricultural Research Service, Plant Genetics Research Unit, Donald Danforth Plant Science Center, St Louis, MO 63132, USA
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine-Universität, Universitätsstraße 1, and Cluster of Excellence on Plant Sciences, 40225 Düsseldorf, Germany
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20
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Maurino VG, Engqvist MKM. 2-Hydroxy Acids in Plant Metabolism. THE ARABIDOPSIS BOOK 2015; 13:e0182. [PMID: 26380567 PMCID: PMC4568905 DOI: 10.1199/tab.0182] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Glycolate, malate, lactate, and 2-hydroxyglutarate are important 2-hydroxy acids (2HA) in plant metabolism. Most of them can be found as D- and L-stereoisomers. These 2HA play an integral role in plant primary metabolism, where they are involved in fundamental pathways such as photorespiration, tricarboxylic acid cycle, glyoxylate cycle, methylglyoxal pathway, and lysine catabolism. Recent molecular studies in Arabidopsis thaliana have helped elucidate the participation of these 2HA in in plant metabolism and physiology. In this chapter, we summarize the current knowledge about the metabolic pathways and cellular processes in which they are involved, focusing on the proteins that participate in their metabolism and cellular/intracellular transport in Arabidopsis.
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Affiliation(s)
- Veronica G. Maurino
- institute of Developmental and Molecular Biology of Plants, Plant Molecular Physiology and Biotechnology Group, Heinrich Heine University, Universitätsstraße 1, and Cluster of Excellence on Plant Sciences (CEPLAS), 40225 Düsseldorf, Germany
| | - Martin K. M. Engqvist
- institute of Developmental and Molecular Biology of Plants, Plant Molecular Physiology and Biotechnology Group, Heinrich Heine University, Universitätsstraße 1, and Cluster of Excellence on Plant Sciences (CEPLAS), 40225 Düsseldorf, Germany
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Takayama M, Ezura H. How and why does tomato accumulate a large amount of GABA in the fruit? FRONTIERS IN PLANT SCIENCE 2015; 6:612. [PMID: 26322056 PMCID: PMC4530592 DOI: 10.3389/fpls.2015.00612] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 07/23/2015] [Indexed: 05/19/2023]
Abstract
Gamma-aminobutyric acid (GABA) has received much attention as a health-promoting functional compound, and several GABA-enriched foods have been commercialized. In higher plants, GABA is primarily metabolized via a short pathway called the GABA shunt. The GABA shunt bypasses two steps (the oxidation of α-ketoglutarate to succinate) of the tricarboxylic acid (TCA) cycle via reactions catalyzed by three enzymes: glutamate decarboxylase, GABA transaminase, and succinic semialdehyde dehydrogenase. The GABA shunt plays a major role in primary carbon and nitrogen metabolism and is an integral part of the TCA cycle under stress and non-stress conditions. Tomato is one of the major crops that accumulate a relatively high level of GABA in its fruits. The GABA levels in tomato fruits dramatically change during fruit development; the GABA levels increase from flowering to the mature green stage and then rapidly decrease during the ripening stage. Although GABA constitutes up to 50% of the free amino acids at the mature green stage, the molecular mechanism of GABA accumulation and the physiological function of GABA during tomato fruit development remain unclear. In this review, we summarize recent studies of GABA accumulation in tomato fruits and discuss the potential biological roles of GABA in tomato fruit development.
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Affiliation(s)
| | - Hiroshi Ezura
- *Correspondence: Hiroshi Ezura, The Ezura Laboratory, Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki 305-8572, Japan,
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Mustroph A, Barding GA, Kaiser KA, Larive CK, Bailey-Serres J. Characterization of distinct root and shoot responses to low-oxygen stress in Arabidopsis with a focus on primary C- and N-metabolism. PLANT, CELL & ENVIRONMENT 2014; 37:2366-80. [PMID: 24450922 DOI: 10.1111/pce.12282] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 01/10/2014] [Accepted: 01/12/2014] [Indexed: 05/02/2023]
Abstract
Oxygen deficiency, caused by flooding of all or a portion of a plant, leads to significant gene regulatory and metabolic responses associated with survival. When oxygen-deprived in light, aerial organs and root systems respond in distinct manners because of their respective autotrophy and heterotrophy, as well as intrinsic differences in cell biology and organ function. To better understand organ-specific responses to oxygen deficiency, we monitored changes in the metabolome of roots and shoots of Arabidopsis thaliana seedlings using gas chromatography-mass spectrometry and (1) H-nuclear magnetic resonance spectroscopy. Only roots accumulated high amounts of γ-aminobutyrate (GABA) and lactate, whereas both organs accumulated alanine (Ala) upon hypoxia. Meta-analysis of gene regulation data revealed higher induction of mRNAs coding for fermentative enzymes in roots as compared with shoots. However, the elevation in GABA level was not correlated with changes in transcript abundance, supporting the proposal that post-translational mechanisms are important in metabolic acclimation to hypoxia. The biosynthesis, degradation and function of GABA and Ala during oxygen deprivation and re-aeration is discussed. Finally, a systematic survey of low-oxygen mediated regulation of genes associated with primary metabolism across organs and cell types reveals exciting new avenues for future studies.
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Aznar-Moreno JA, Venegas Calerón M, Martínez-Force E, Garcés R, Mullen R, Gidda SK, Salas JJ. Sunflower (Helianthus annuus) long-chain acyl-coenzyme A synthetases expressed at high levels in developing seeds. PHYSIOLOGIA PLANTARUM 2014; 150:363-73. [PMID: 24102504 DOI: 10.1111/ppl.12107] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 08/27/2013] [Accepted: 08/29/2013] [Indexed: 05/18/2023]
Abstract
Long chain fatty acid synthetases (LACSs) activate the fatty acid chains produced by plastidial de novo biosynthesis to generate acyl-CoA derivatives, important intermediates in lipid metabolism. Oilseeds, like sunflower, accumulate high levels of triacylglycerols (TAGs) in their seeds to nourish the embryo during germination. This requires that sunflower seed endosperm supports very active glycerolipid synthesis during development. Sunflower seed plastids produce large amounts of fatty acids, which must be activated through the action of LACSs, in order to be incorporated into TAGs. We cloned two different LACS genes from developing sunflower endosperm, HaLACS1 and HaLACS2, which displayed sequence homology with Arabidopsis LACS9 and LACS8 genes, respectively. These genes were expressed at high levels in developing seeds and exhibited distinct subcellular distributions. We generated constructs in which these proteins were fused to green fluorescent protein and performed transient expression experiments in tobacco cells. The HaLACS1 protein associated with the external envelope of tobacco chloroplasts, whereas HaLACS2 was strongly bound to the endoplasmic reticulum. Finally, both proteins were overexpressed in Escherichia coli and recovered as active enzymes in the bacterial membranes. Both enzymes displayed similar substrate specificities, with a very high preference for oleic acid and weaker activity toward stearic acid. On the basis of our findings, we discuss the role of these enzymes in sunflower oil synthesis.
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Affiliation(s)
- Jose A Aznar-Moreno
- Instituto de la Grasa (CSIC), Department of Biochemistry and Molecular Biology of Plant Products, 41012, Sevilla, Spain
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Ito J, Parsons HT, Heazlewood JL. The Arabidopsis cytosolic proteome: the metabolic heart of the cell. FRONTIERS IN PLANT SCIENCE 2014; 5:21. [PMID: 24550929 PMCID: PMC3914213 DOI: 10.3389/fpls.2014.00021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Accepted: 01/19/2014] [Indexed: 05/09/2023]
Abstract
The plant cytosol is the major intracellular fluid that acts as the medium for inter-organellar crosstalk and where a plethora of important biological reactions take place. These include its involvement in protein synthesis and degradation, stress response signaling, carbon metabolism, biosynthesis of secondary metabolites, and accumulation of enzymes for defense and detoxification. This central role is highlighted by estimates indicating that the majority of eukaryotic proteins are cytosolic. Arabidopsis thaliana has been the subject of numerous proteomic studies on its different subcellular compartments. However, a detailed study of enriched cytosolic fractions from Arabidopsis cell culture has been performed only recently, with over 1,000 proteins reproducibly identified by mass spectrometry. The number of proteins allocated to the cytosol nearly doubles to 1,802 if a series of targeted proteomic characterizations of complexes is included. Despite this, few groups are currently applying advanced proteomic approaches to this important metabolic space. This review will highlight the current state of the Arabidopsis cytosolic proteome since its initial characterization a few years ago.
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Affiliation(s)
- Jun Ito
- Joint BioEnergy Institute, Emeryville, CAUSA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CAUSA
| | - Harriet T. Parsons
- Joint BioEnergy Institute, Emeryville, CAUSA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CAUSA
- Department of Plant and Environmental Sciences, University of Copenhagen, CopenhagenDenmark
| | - Joshua L. Heazlewood
- Joint BioEnergy Institute, Emeryville, CAUSA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CAUSA
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Galland M, Huguet R, Arc E, Cueff G, Job D, Rajjou L. Dynamic proteomics emphasizes the importance of selective mRNA translation and protein turnover during Arabidopsis seed germination. Mol Cell Proteomics 2014; 13:252-68. [PMID: 24198433 PMCID: PMC3879618 DOI: 10.1074/mcp.m113.032227] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 10/23/2013] [Indexed: 01/02/2023] Open
Abstract
During seed germination, the transition from a quiescent metabolic state in a dry mature seed to a proliferative metabolic state in a vigorous seedling is crucial for plant propagation as well as for optimizing crop yield. This work provides a detailed description of the dynamics of protein synthesis during the time course of germination, demonstrating that mRNA translation is both sequential and selective during this process. The complete inhibition of the germination process in the presence of the translation inhibitor cycloheximide established that mRNA translation is critical for Arabidopsis seed germination. However, the dynamics of protein turnover and the selectivity of protein synthesis (mRNA translation) during Arabidopsis seed germination have not been addressed yet. Based on our detailed knowledge of the Arabidopsis seed proteome, we have deepened our understanding of seed mRNA translation during germination by combining two-dimensional gel-based proteomics with dynamic radiolabeled proteomics using a radiolabeled amino acid precursor, namely [(35)S]-methionine, in order to highlight de novo protein synthesis, stability, and turnover. Our data confirm that during early imbibition, the Arabidopsis translatome keeps reflecting an embryonic maturation program until a certain developmental checkpoint. Furthermore, by dividing the seed germination time lapse into discrete time windows, we highlight precise and specific patterns of protein synthesis. These data refine and deepen our knowledge of the three classical phases of seed germination based on seed water uptake during imbibition and reveal that selective mRNA translation is a key feature of seed germination. Beyond the quantitative control of translational activity, both the selectivity of mRNA translation and protein turnover appear as specific regulatory systems, critical for timing the molecular events leading to successful germination and seedling establishment.
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Affiliation(s)
- Marc Galland
- From ‡INRA, Jean-Pierre Bourgin Institute (IJPB, UMR1318 INRA-AgroParisTech), Laboratory of Excellence “Saclay Plant Sciences” (LabEx SPS), F-78026 Versailles, France
- §AgroParisTech, Chair of Plant Physiology, F-75231 Paris, France
| | - Romain Huguet
- ¶CNRS/Bayer CropScience Joint Laboratory (UMR5240), F-69263 Lyon, France
| | - Erwann Arc
- From ‡INRA, Jean-Pierre Bourgin Institute (IJPB, UMR1318 INRA-AgroParisTech), Laboratory of Excellence “Saclay Plant Sciences” (LabEx SPS), F-78026 Versailles, France
- §AgroParisTech, Chair of Plant Physiology, F-75231 Paris, France
| | - Gwendal Cueff
- From ‡INRA, Jean-Pierre Bourgin Institute (IJPB, UMR1318 INRA-AgroParisTech), Laboratory of Excellence “Saclay Plant Sciences” (LabEx SPS), F-78026 Versailles, France
- §AgroParisTech, Chair of Plant Physiology, F-75231 Paris, France
| | - Dominique Job
- §AgroParisTech, Chair of Plant Physiology, F-75231 Paris, France
- ¶CNRS/Bayer CropScience Joint Laboratory (UMR5240), F-69263 Lyon, France
| | - Loïc Rajjou
- From ‡INRA, Jean-Pierre Bourgin Institute (IJPB, UMR1318 INRA-AgroParisTech), Laboratory of Excellence “Saclay Plant Sciences” (LabEx SPS), F-78026 Versailles, France
- §AgroParisTech, Chair of Plant Physiology, F-75231 Paris, France
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Hoover GJ, Jørgensen R, Rochon A, Bajwa VS, Merrill AR, Shelp BJ. Identification of catalytically important amino acid residues for enzymatic reduction of glyoxylate in plants. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:2663-71. [PMID: 24076009 DOI: 10.1016/j.bbapap.2013.09.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 09/15/2013] [Accepted: 09/18/2013] [Indexed: 02/06/2023]
Abstract
NADPH-dependent glyoxylate reductases from Arabidopsis thaliana (AtGLYR) convert both glyoxylate and succinic semialdehyde into their corresponding hydroxyacid equivalents. The primary sequence of cytosolic AtGLYR1 reveals several sequence elements that are consistent with the β-HAD (β-hydroxyacid dehydrogenase) protein family, whose members include 3-hydroxyisobutyrate dehydrogenase, tartronate semialdehyde reductase and 6-phosphogluconate dehydrogenase. Here, site-directed mutagenesis was utilized to identify catalytically important amino acid residues for glyoxylate reduction in AtGLYR1. Kinetic studies and binding assays established that Lys170 is essential for catalysis, Phe231, Asp239, Ser121 and Thr95 are more important in substrate binding than in catalysis, and Asn174 is more important in catalysis. The low activity of the mutant enzymes precluded kinetic studies with succinic semialdehyde. The crystal structure of AtGLYR1 in the absence of substrate was solved to 2.1Å by molecular replacement using a previously unrecognized member of the β-HAD family, cytokine-like nuclear factor, thereby enabling the 3-D structure of the protein to be modeled with substrate and co-factor. Structural alignment of AtGLYR1 with β-HAD family members provided support for the essentiality of Lys170, Phe173, Asp239, Ser121, Asn174 and Thr95 in the active site and preliminary support for an acid/base catalytic mechanism involving Lys170 as the general acid and a conserved active-site water molecule. This information established that AtGLYR1 is a member of the β-HAD protein family. Sequence and activity comparisons indicated that AtGLYR1 and the plastidial AtGLYR2 possess structural features that are absent in Arabidopsis hydroxypyruvate reductases and probably account for their stronger preference for glyoxylate over hydroxypyruvate.
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Affiliation(s)
- Gordon J Hoover
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada
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27
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Koivistoinen OM, Kuivanen J, Barth D, Turkia H, Pitkänen JP, Penttilä M, Richard P. Glycolic acid production in the engineered yeasts Saccharomyces cerevisiae and Kluyveromyces lactis. Microb Cell Fact 2013; 12:82. [PMID: 24053654 PMCID: PMC3850452 DOI: 10.1186/1475-2859-12-82] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 09/15/2013] [Indexed: 11/24/2022] Open
Abstract
Background Glycolic acid is a C2 hydroxy acid that is a widely used chemical compound. It can be polymerised to produce biodegradable polymers with excellent gas barrier properties. Currently, glycolic acid is produced in a chemical process using fossil resources and toxic chemicals. Biotechnological production of glycolic acid using renewable resources is a desirable alternative. Results The yeasts Saccharomyces cerevisiae and Kluyveromyces lactis are suitable organisms for glycolic acid production since they are acid tolerant and can grow in the presence of up to 50 g l-1 glycolic acid. We engineered S. cerevisiae and K. lactis for glycolic acid production using the reactions of the glyoxylate cycle to produce glyoxylic acid and then reducing it to glycolic acid. The expression of a high affinity glyoxylate reductase alone already led to glycolic acid production. The production was further improved by deleting genes encoding malate synthase and the cytosolic form of isocitrate dehydrogenase. The engineered S. cerevisiae strain produced up to about 1 g l-1 of glycolic acid in a medium containing d-xylose and ethanol. Similar modifications in K. lactis resulted in a much higher glycolic acid titer. In a bioreactor cultivation with d-xylose and ethanol up to 15 g l-1 of glycolic acid was obtained. Conclusions This is the first demonstration of engineering yeast to produce glycolic acid. Prior to this work glycolic acid production through the glyoxylate cycle has only been reported in bacteria. The benefit of a yeast host is the possibility for glycolic acid production also at low pH, which was demonstrated in flask cultivations. Production of glycolic acid was first shown in S. cerevisiae. To test whether a Crabtree negative yeast would be better suited for glycolic acid production we engineered K. lactis in the same way and demonstrated it to be a better host for glycolic acid production.
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Affiliation(s)
- Outi M Koivistoinen
- VTT Technical Research Centre of Finland, Tietotie 2, Espoo FI-02044, P,O, Box 1000, VTT, Finland.
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28
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Fernie AR, Bauwe H, Eisenhut M, Florian A, Hanson DT, Hagemann M, Keech O, Mielewczik M, Nikoloski Z, Peterhänsel C, Roje S, Sage R, Timm S, von Cammerer S, Weber APM, Westhoff P. Perspectives on plant photorespiratory metabolism. PLANT BIOLOGY (STUTTGART, GERMANY) 2013; 15:748-753. [PMID: 23231538 DOI: 10.1111/j.1438-8677.2012.00693.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 09/21/2012] [Indexed: 06/01/2023]
Abstract
Being intimately intertwined with (C3) photosynthesis, photorespiration is an incredibly high flux-bearing pathway. Traditionally, the photorespiratory cycle was viewed as closed pathway to refill the Calvin-Benson cycle with organic carbon. However, given the network nature of metabolism, it hence follows that photorespiration will interact with many other pathways. In this article, we review current understanding of these interactions and attempt to define key priorities for future research, which will allow us greater fundamental comprehension of general metabolic and developmental consequences of perturbation of this crucial metabolic process.
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Affiliation(s)
- A R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
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29
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Koike S, Matsukura C, Takayama M, Asamizu E, Ezura H. Suppression of γ-Aminobutyric Acid (GABA) Transaminases Induces Prominent GABA Accumulation, Dwarfism and Infertility in the Tomato (Solanum lycopersicum L.). ACTA ACUST UNITED AC 2013; 54:793-807. [DOI: 10.1093/pcp/pct035] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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30
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Deleu C, Faes P, Niogret MF, Bouchereau A. Effects of the inhibitor of the γ-aminobutyrate-transaminase, vinyl-γ-aminobutyrate, on development and nitrogen metabolism in Brassica napus seedlings. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2013; 64:60-9. [PMID: 23370302 DOI: 10.1016/j.plaphy.2012.12.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 12/20/2012] [Indexed: 05/23/2023]
Abstract
γ-aminobutyrate-transaminase (EC 2.6.1.19) catalyzes the first step of the catabolism of γ-aminobutyric acid (GABA), a non-protein amino acid well-known to accumulate in plant in response to environmental stimuli. Recent studies reinforce more and more the role of its metabolism in carbon and/or nitrogen metabolisms and as a signalling molecule in developmental processes. Here we investigated the effects of inhibition of γ-aminobutyrate-transaminase (GABA-T) in seedlings of Brassica napus, using vinyl-GABA (VGB) as a specific inhibitor of GABA-T to prevent enzyme activity. Root growth was reduced by 44% in VGB-treated seedlings but was less inhibited when VGB was associated with exogenous GABA and was not reduced with exogenous GABA alone. Measurements of GABA content in seedlings grown on VGB, GABA or VGB + GABA demonstrated that GABA level in root was not linked with the root length reduction, suggesting that GABA was not the sole component acting in root growth inhibition. Besides, metabolic profiling revealed that in root, VGB-treatment caused a twofold increase in content of almost all amino acids, except for alanine whose content was 19-fold higher than in control. In order to test the involvement of alanine accumulation on growth we studied the effects of exogenous alanine. High alanine content slightly reduced root growth suggesting that VGB-induced alanine accumulation was not responsible for root length reduction. We conclude that root growth inhibition in plants whose GABA catabolism was impaired could result at least partly from the disruption of the primary metabolism as a whole rather than direct effect of GABA on cellular growth process.
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Affiliation(s)
- Carole Deleu
- Université Rennes 1, UMR1349 IGEPP, F-35000 Rennes, France.
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31
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Shimajiri Y, Ozaki K, Kainou K, Akama K. Differential subcellular localization, enzymatic properties and expression patterns of γ-aminobutyric acid transaminases (GABA-Ts) in rice (Oryza sativa). JOURNAL OF PLANT PHYSIOLOGY 2013; 170:196-201. [PMID: 23122787 DOI: 10.1016/j.jplph.2012.09.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Revised: 09/13/2012] [Accepted: 09/24/2012] [Indexed: 05/05/2023]
Abstract
γ-Aminobutyric acid transaminase (GABA-T) catalyzes the conversion of GABA to succinic semialdehyde. The rice (Oryza sativa) genome possesses four putative GABA-T genes, which exhibit high amino acid identity (73-82%) but differ in length of the N-terminal region. Transient expression of GABA-T-green fluorescent fusion proteins in onion epidermal cells demonstrated that two of the four enzymes were targeted to mitochondria, a third to chloroplasts, and the fourth to cytosol. Enzymatic analysis of three organelle-targeted GABA-Ts revealed that they used pyruvate and glyoxylate as amino acceptors and that two of the enzymes functioned in mitochondria and chloroplasts at similar levels of activity, whereas the second mitochondrial enzyme displayed very low activity. Transcriptional analysis demonstrated that two of the four genes were more highly expressed in the vegetative organs tested, but exhibited a different pattern during seed maturation. Together, these results suggest that members of the rice GABA-T gene family vary in many respects, such as intracellular targeting, enzymatic activity and regulation of gene expression.
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Affiliation(s)
- Yasuka Shimajiri
- Department of Biological Science, Shimane University, 1060 Nishikawatsu-chou, Matsue 690-8504, Japan
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32
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Gururaj HB, Padma MN, Giridhar P, Ravishankar GA. Functional validation of Capsicum frutescens aminotransferase gene involved in vanillylamine biosynthesis using Agrobacterium mediated genetic transformation studies in Nicotiana tabacum and Capsicum frutescens calli cultures. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 195:96-105. [PMID: 22921003 DOI: 10.1016/j.plantsci.2012.06.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 06/24/2012] [Accepted: 06/26/2012] [Indexed: 06/01/2023]
Abstract
Capsaicinoid biosynthesis involves the participation of two substrates viz. vanillylamine and C(9)-C(11) fatty acid moieties. Vanillylamine which is a derivative of vanillin is synthesized through a transaminase reaction in the phenylpropanoid pathway of capsaicinoid synthesis. Here we report the functional validation of earlier reported putative aminotransferase gene for vanillylamine biosynthesis in heterologous system using Agrobacterium mediated genetic transformation studies in Nicotiana tabacum and Capsicum frutescens calli cultures. Molecular analysis tools comprising PCR and Southern blot analysis have shown the integration of the foreign gene in N. tabacum and C. frutescens calli cultures. The study shows the production of vanillylamine in transformed N. tabacum callus cultures and also the reduction of vanillylamine production when whole gene based antisense binary vector construct was used in transformation of C. frutescens callus cultures. Vanillylamine production, aminotransferase assay with Western blot analysis for crude proteins of transformants established the production of putative aminotransferase (pAMT) protein in alternate plant. The result is a clear evidence of involvement of the reported putative aminotransferase responsible for vanillylamine biosynthesis in capsaicinoid biosynthesis pathway, confirming the gene function through functional validation.
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Affiliation(s)
- Harishchandra B Gururaj
- Plant Cell Biotechnology Department, Central Food Technological Research Institute, (Constituent laboratory of Council of Scientific and Industrial Research, CSIR), Mysore 570020, India
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Ching SLK, Gidda SK, Rochon A, van Cauwenberghe OR, Shelp BJ, Mullen RT. Glyoxylate reductase isoform 1 is localized in the cytosol and not peroxisomes in plant cells. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2012; 54:152-68. [PMID: 22309191 DOI: 10.1111/j.1744-7909.2012.01103.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Glyoxylate reductase (GLYR) is a key enzyme in plant metabolism which catalyzes the detoxification of both photorespiratory glyoxylate and succinic semialdehdye, an intermediate of the γ-aminobutyrate (GABA) pathway. Two isoforms of GLYR exist in plants, GLYR1 and GLYR2, and while GLYR2 is known to be localized in plastids, GLYR1 has been reported to be localized in either peroxisomes or the cytosol. Here, we reappraised the intracellular localization of GLYR1 in Arabidopsis thaliana L. Heynh (ecotype Lansberg erecta) using both transiently-transformed suspension cells and stably-transformed plants, in combination with fluorescence microscopy. The results indicate that GLYR1 is localized exclusively to the cytosol regardless of the species, tissue and/or cell type, or exposure of plants to environmental stresses that would increase flux through the GABA pathway. Moreover, the C-terminal tripeptide sequence of GLYR1, -SRE, despite its resemblance to a type 1 peroxisomal targeting signal, is not sufficient for targeting to peroxisomes. Collectively, these results define the cytosol as the intracellular location of GLYR1 and provide not only important insight to the metabolic roles of GLYR1 and the compartmentation of the GABA and photorespiratory pathways in plant cells, but also serve as a useful reference for future studies of proteins proposed to be localized to peroxisomes and/or the cytosol.
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Affiliation(s)
- Steven L K Ching
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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Shelp BJ, Mullen RT, Waller JC. Compartmentation of GABA metabolism raises intriguing questions. TRENDS IN PLANT SCIENCE 2012; 17:57-9. [PMID: 22226724 DOI: 10.1016/j.tplants.2011.12.006] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 12/11/2011] [Accepted: 12/20/2011] [Indexed: 05/21/2023]
Abstract
This synopsis covers the compartmentation of γ-aminobutyrate (GABA) metabolism, highlighting recent progress with Arabidopsis (Arabidopsis thaliana) and raising questions about mitochondrial GABA and succinic semialdehyde (SSA) transport, the fate of succinic semialdehyde once it exits mitochondria, and biochemical interactions between GABA metabolism and related processes such as photorespiration.
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Affiliation(s)
- Barry J Shelp
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada N1G 2W1.
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35
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Fellerer C, Schweiger R, Schöngruber K, Soll J, Schwenkert S. Cytosolic HSP90 cochaperones HOP and FKBP interact with freshly synthesized chloroplast preproteins of Arabidopsis. MOLECULAR PLANT 2011; 4:1133-45. [PMID: 21596689 DOI: 10.1093/mp/ssr037] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Most chloroplast and mitochondrial proteins are synthesized in the cytosol of the plant cell and have to be imported into the organelles post-translationally. Molecular chaperones play an important role in preventing protein aggregation of freshly translated preproteins and assist in maintaining the preproteins in an import competent state. Preproteins can associate with HSP70, HSP90, and 14-3-3 proteins in the cytosol. In this study, we analyzed a large set of wheat germ-translated chloroplast preproteins with respect to their chaperone binding. Our results demonstrate that the formation of distinct 14-3-3 or HSP90 containing preprotein complexes is a common feature in post-translational protein transport in addition to preproteins that seem to interact solely with HSP70. We were able to identify a diverse and extensive class of preproteins as HSP90 substrates, thus providing a tool for the investigation of HSP90 client protein association. The analyses of chimeric HSP90 and 14-3-3 binding preproteins with exchanged transit peptides indicate an involvement of both the transit peptide and the mature part of the proteins, in HSP90 binding. We identified two partner components of the HSP90 cycle, which were present in the preprotein containing high-molecular-weight complexes, the HSP70/HSP90 organizing protein HOP, as well as the immunophilin FKBP73. The results establish chloroplast preproteins as a general class of HSP90 client proteins in plants using HOP and FKBP as novel cochaperones.
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Affiliation(s)
- Christine Fellerer
- Department of Biology I, Botany, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 2-4, D-82152 Planegg-Martinsried, Germany
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Toyokura K, Watanabe K, Oiwaka A, Kusano M, Tameshige T, Tatematsu K, Matsumoto N, Tsugeki R, Saito K, Okada K. Succinic semialdehyde dehydrogenase is involved in the robust patterning of Arabidopsis leaves along the adaxial-abaxial axis. PLANT & CELL PHYSIOLOGY 2011; 52:1340-53. [PMID: 21690177 DOI: 10.1093/pcp/pcr079] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Polarity along the adaxial-abaxial axis of the leaf is essential for leaf development and morphogenesis. One of the genes that encodes a putative transcription factor regulating adaxial-abaxial polarity, FILAMENTOUS FLOWER (FIL), is expressed in the abaxial region of the leaf primordia. However, the molecular mechanisms controlling the polarized expression of FIL remain unclear. Here, we analyzed an enlarged fil expression domain1 (enf1) mutant of Arabidopsis, which forms both abaxialized leaves and adaxialized leaves. The ENF1 gene encodes SUCCINIC SEMIALDEHYDE DEHYDROGENASE (SSADH), which catalyzes the conversion of succinic semialdehyde (SSA) to succinate. The enf1 phenotype was suppressed by an additional mutation in GAMMA-AMINOBUTYRIC ACID AMINOTRANSFERASE1 (GABAT1), which encodes an SSA-producing enzyme, suggesting that SSA or its derivatives is the metabolite responsible for the defect in the adaxial-abaxial axis-dependent gene expression of enf1. In the shoot apical meristem, GABAT1 was expressed in the outermost layer but SSADH was not. Exogenous application of SSA induced adaxial characters on the abaxial side of the newly developed leaves. We suggest that a GABA shunt metabolite, SSA or its close derivatives, is involved in the robust leaf patterning and structure along the adaxial-abaxial axis.
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Affiliation(s)
- Koichi Toyokura
- Department of Botany, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502 Japan
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Yıldırım V, Ozcan S, Becher D, Büttner K, Hecker M, Ozcengiz G. Characterization of proteome alterations in Phanerochaete chrysosporium in response to lead exposure. Proteome Sci 2011; 9:12. [PMID: 21388532 PMCID: PMC3063812 DOI: 10.1186/1477-5956-9-12] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Accepted: 03/09/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Total soluble proteome alterations of white rot fungus Phanerochaete chrysosporium in response to different doses (25, 50 and 100 μM) of Pb (II) were characterized by 2DE in combination with MALDI-TOF-MS. RESULTS Dose-dependent molecular response to Pb (II) involved a total of 14 up-regulated and 21 down-regulated proteins. The induction of an isoform of glyceraldehyde 3-phosphate dehydrogenase, alcohol dehydrogenase class V, mRNA splicing factor, ATP-dependent RNA helicase, thioredoxin reductase and actin required a Pb (II) dose of at least 50 μM. Analysis of the proteome dynamics of mid-exponential phase cells of P. chrysosporium subjected to 50 μM lead at exposure time intervals of 1, 2, 4 and 8 h, identified a total of 23 proteins in increased and 67 proteins in decreased amount. Overall, the newly induced/strongly up-regulated proteins involved in (i) amelioration of lipid peroxidation products, (ii) defense against oxidative damage and redox metabolism, (iii) transcription, recombination and DNA repair (iv) a yet unknown function represented by a putative protein. CONCLUSION The present study implicated the particular role of the elements of DNA repair, post-tanscriptional regulation and heterotrimeric G protein signaling in response to Pb (II) stress as shown for the first time for a basidiomycete.
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Affiliation(s)
- Volkan Yıldırım
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey.
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Timm S, Florian A, Jahnke K, Nunes-Nesi A, Fernie AR, Bauwe H. The hydroxypyruvate-reducing system in Arabidopsis: multiple enzymes for the same end. PLANT PHYSIOLOGY 2011; 155:694-705. [PMID: 21205613 PMCID: PMC3032460 DOI: 10.1104/pp.110.166538] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Accepted: 12/21/2010] [Indexed: 05/18/2023]
Abstract
Hydroxypyruvate (HP) is an intermediate of the photorespiratory pathway that originates in the oxygenase activity of the key enzyme of photosynthetic CO(2) assimilation, Rubisco. In course of this high-throughput pathway, a peroxisomal transamination reaction converts serine to HP, most of which is subsequently reduced to glycerate by the NADH-dependent peroxisomal enzyme HP reductase (HPR1). In addition, a NADPH-dependent cytosolic HPR2 provides an efficient extraperoxisomal bypass. The combined deletion of these two enzymes, however, does not result in a fully lethal photorespiratory phenotype, indicating even more redundancy in the photorespiratory HP-into-glycerate conversion. Here, we report on a third enzyme, HPR3 (At1g12550), in Arabidopsis (Arabidopsis thaliana), which also reduces HP to glycerate and shows even more activity with glyoxylate, a more upstream intermediate of the photorespiratory cycle. The deletion of HPR3 by T-DNA insertion mutagenesis results in slightly altered leaf concentrations of the photorespiratory intermediates HP, glycerate, and glycine, indicating a disrupted photorespiratory flux, but not in visible alteration of the phenotype. On the other hand, the combined deletion of HPR1, HPR2, and HPR3 causes increased growth retardation, decreased photochemical efficiency, and reduced oxygen-dependent gas exchange in comparison with the hpr1xhpr2 double mutant. Since in silico analysis and proteomic studies from other groups indicate targeting of HPR3 to the chloroplast, this enzyme could provide a compensatory bypass for the reduction of HP and glyoxylate within this compartment.
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Affiliation(s)
- Stefan Timm
- Department of Plant Physiology, University of Rostock, D-18059 Rostock, Germany.
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Dhanoa PK, Richardson LGL, Smith MD, Gidda SK, Henderson MPA, Andrews DW, Mullen RT. Distinct pathways mediate the sorting of tail-anchored proteins to the plastid outer envelope. PLoS One 2010; 5:e10098. [PMID: 20418952 PMCID: PMC2854689 DOI: 10.1371/journal.pone.0010098] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2009] [Accepted: 03/11/2010] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Tail-anchored (TA) proteins are a distinct class of membrane proteins that are sorted post-translationally to various organelles and function in a number of important cellular processes, including redox reactions, vesicular trafficking and protein translocation. While the molecular targeting signals and pathways responsible for sorting TA proteins to their correct intracellular destinations in yeasts and mammals have begun to be characterized, relatively little is known about TA protein biogenesis in plant cells, especially for those sorted to the plastid outer envelope. METHODOLOGY/PRINCIPAL FINDINGS Here we investigated the biogenesis of three plastid TA proteins, including the 33-kDa and 34-kDa GTPases of the translocon at the outer envelope of chloroplasts (Toc33 and Toc34) and a novel 9-kDa protein of unknown function that we define here as an outer envelope TA protein (OEP9). Using a combination of in vivo and in vitro assays we show that OEP9 utilizes a different sorting pathway than that used by Toc33 and Toc34. For instance, while all three TA proteins interact with the cytosolic OEP chaperone/receptor, AKR2A, the plastid targeting information within OEP9 is distinct from that within Toc33 and Toc34. Toc33 and Toc34 also appear to differ from OEP9 in that their insertion is dependent on themselves and the unique lipid composition of the plastid outer envelope. By contrast, the insertion of OEP9 into the plastid outer envelope occurs in a proteinaceous-dependent, but Toc33/34-independent manner and membrane lipids appear to serve primarily to facilitate normal thermodynamic integration of this TA protein. CONCLUSIONS/SIGNIFICANCE Collectively, the results provide evidence in support of at least two sorting pathways for plastid TA outer envelope proteins and shed light on not only the complex diversity of pathways involved in the targeting and insertion of proteins into plastids, but also the molecular mechanisms that underlie the delivery of TA proteins to their proper intracellular locations in general.
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Affiliation(s)
- Preetinder K. Dhanoa
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Lynn G. L. Richardson
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Matthew D. Smith
- Department of Biology, Wilfrid Laurier University, Waterloo, Ontario, Canada
| | - Satinder K. Gidda
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Matthew P. A. Henderson
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - David W. Andrews
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Robert T. Mullen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
- * E-mail:
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Abstract
Molecular modelling suggests that a group of proteins in plants known as the β-hydroxyacid dehydrogenases, or the hydroxyisobutyrate dehydrogenase superfamily, includes enzymes that reduce succinic semialdehyde and glyoxylate to γ-hydroxybutyrate and glycolate respectively. Recent biochemical and expression studies reveal that NADPH-dependent cytosolic (termed GLYR1) and plastidial (termed GLYR2) isoforms of succinic semialdehyde/glyoxylate reductase exist in Arabidopsis. Succinic semialdehyde and glyoxylate are typically generated in leaves via two distinct metabolic pathways, γ-aminobutyrate and glycolate respectively. In the present review, it is proposed that the GLYRs function in the detoxification of both aldehydes during stress and contribute to redox balance. Outstanding questions are highlighted in a scheme for the subcellular organization of the detoxification mechanism in Arabidopsis.
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Lapetina S, Mader CC, Machida K, Mayer BJ, Koleske AJ. Arg interacts with cortactin to promote adhesion-dependent cell edge protrusion. ACTA ACUST UNITED AC 2009; 185:503-19. [PMID: 19414610 PMCID: PMC2700396 DOI: 10.1083/jcb.200809085] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The molecular mechanisms by which the Abelson (Abl) or Abl-related gene (Arg) kinases interface with the actin polymerization machinery to promote cell edge protrusions during cell–matrix adhesion are unclear. In this study, we show that interactions between Arg and the Arp2/3 complex regulator cortactin are essential to mediate actin-based cell edge protrusion during fibroblast adhesion to fibronectin. Arg-deficient and cortactin knockdown fibroblasts exhibit similar defects in adhesion-dependent cell edge protrusion, which can be restored via reexpression of Arg and cortactin. Arg interacts with cortactin via both binding and catalytic events. The cortactin Src homology (SH) 3 domain binds to a Pro-rich motif in the Arg C terminus. Arg mediates adhesion-dependent phosphorylation of cortactin, creating an additional binding site for the Arg SH2 domain. Mutation of residues that mediate Arg–cortactin interactions abrogate the abilities of both proteins to support protrusions, and the Nck adapter, which binds phosphocortactin, is also required. These results demonstrate that interactions between Arg, cortactin, and Nck1 are critical to promote adhesion-dependent cell edge protrusions.
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Affiliation(s)
- Stefanie Lapetina
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
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Clark SM, Di Leo R, Van Cauwenberghe OR, Mullen RT, Shelp BJ. Subcellular localization and expression of multiple tomato gamma-aminobutyrate transaminases that utilize both pyruvate and glyoxylate. JOURNAL OF EXPERIMENTAL BOTANY 2009; 60:3255-67. [PMID: 19470656 PMCID: PMC2718222 DOI: 10.1093/jxb/erp161] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2009] [Revised: 04/24/2009] [Accepted: 04/27/2009] [Indexed: 05/20/2023]
Abstract
Gamma-aminobutyric acid transaminase (GABA-T) catalyses the breakdown of GABA to succinic semialdehyde. In this report, three GABA-T isoforms were identified in the tomato (Solanum lycopersicum L.) plant. The deduced amino acid sequences of the three isoforms are highly similar over most of their coding regions with the exception of their N-terminal regions. Transient expression of the individual full-length GABA-T isoforms fused to the green fluorescent protein in tobacco suspension-cultured cells revealed their distinct subcellular localizations to the mitochondrion, plastid or cytosol, and that the specific targeting of the mitochondrion- and plastid-localized isoforms is mediated by their predicted N-terminal presequences. Removal of the N-terminal targeting presequences from the mitochondrion and plastid GABA-T isoforms yielded good recovery of the soluble recombinant proteins in Escherichia coli when they were co-expressed with the GroES/EL molecular chaperone complex. Activity assays indicated that all three recombinant isoforms possess both pyruvate- and glyoxylate-dependent GABA-T activities, although the mitochondrial enzyme has a specific activity that is significantly higher than that of its plastid and cytosolic counterparts. Finally, differential expression patterns of the three GABA-T isoforms in reproductive tissues, but not vegetative tissues, suggest unique roles for each enzyme in developmental processes. Overall, these findings, together with recent information about rice and pepper GABA-Ts, indicate that the subcellular distribution of GABA-T in the plant kingdom is highly variable.
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Affiliation(s)
- Shawn M. Clark
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Rosa Di Leo
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | | | - Robert T. Mullen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Barry J. Shelp
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, Canada N1G 2W1
- To whom correspondence should be addressed. E-mail:
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Foyer CH, Bloom AJ, Queval G, Noctor G. Photorespiratory metabolism: genes, mutants, energetics, and redox signaling. ANNUAL REVIEW OF PLANT BIOLOGY 2009; 60:455-84. [PMID: 19575589 DOI: 10.1146/annurev.arplant.043008.091948] [Citation(s) in RCA: 360] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Photorespiration is a high-flux pathway that operates alongside carbon assimilation in C(3) plants. Because most higher plant species photosynthesize using only the C(3) pathway, photorespiration has a major impact on cellular metabolism, particularly under high light, high temperatures, and CO(2) or water deficits. Although the functions of photorespiration remain controversial, it is widely accepted that this pathway influences a wide range of processes from bioenergetics, photosystem II function, and carbon metabolism to nitrogen assimilation and respiration. Crucially, the photorespiratory pathway is a major source of H(2)O(2) in photosynthetic cells. Through H(2)O(2) production and pyridine nucleotide interactions, photorespiration makes a key contribution to cellular redox homeostasis. In so doing, it influences multiple signaling pathways, particularly those that govern plant hormonal responses controlling growth, environmental and defense responses, and programmed cell death. The potential influence of photorespiration on cell physiology and fate is thus complex and wide ranging. The genes, pathways, and signaling functions of photorespiration are considered here in the context of whole plant biology, with reference to future challenges and human interventions to diminish photorespiratory flux.
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Affiliation(s)
- Christine H Foyer
- School of Agriculture, Food, and Rural Development, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom.
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Clark SM, Di Leo R, Dhanoa PK, Van Cauwenberghe OR, Mullen RT, Shelp BJ. Biochemical characterization, mitochondrial localization, expression, and potential functions for an Arabidopsis gamma-aminobutyrate transaminase that utilizes both pyruvate and glyoxylate. JOURNAL OF EXPERIMENTAL BOTANY 2009; 60:1743-57. [PMID: 19264755 PMCID: PMC2671622 DOI: 10.1093/jxb/erp044] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2008] [Revised: 01/31/2009] [Accepted: 02/04/2009] [Indexed: 05/18/2023]
Abstract
Gamma-aminobutyrate transaminase (GABA-T) catalyses the breakdown of GABA to succinic semialdehyde. In this report, the previously identified Arabidopsis thaliana (L.) Heyhn GABA-T (AtGABA-T) was characterized in more detail. Full-length AtGABA-T contains an N-terminal 36 amino acid long targeting pre-sequence (36 amino acids) that is both sufficient and necessary for targeting the enzyme to mitochondria. Removal of the pre-sequence encoding this N-terminal targeting domain and co-expression of the resulting truncated AtGABA-T cDNA with the GroES/EL molecular chaperone complex in Escherichia coli yielded good recovery of the soluble recombinant proteins. Activity assays indicated that purified recombinant GABA-T has both pyruvate- and glyoxylate-dependent activities, but cannot utilize 2-oxoglutarate as amino acceptor. Kinetic parameters for glyoxylate- and pyruvate-dependent GABA-T activities were similar, with physiologically relevant affinities. Assays of GABA-T activity in cell-free leaf extracts from wild-type Arabidopsis and two knockout mutants in different genetic backgrounds confirmed that the native enzyme possesses both pyruvate- and glyoxylate-dependent activities. The GABA-T transcript was present throughout the plant, but its expression was highest in roots and increased as a function of leaf development. A GABA-T with dual functions suggests the potential for interaction between GABA metabolism and photorespiratory glyoxylate production.
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Affiliation(s)
- Shawn M. Clark
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Rosa Di Leo
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Preetinder K. Dhanoa
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | | | - Robert T. Mullen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Barry J. Shelp
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, Canada N1G 2W1
- To whom correspondence should be addressed. E-mail:
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Timm S, Nunes-Nesi A, Pärnik T, Morgenthal K, Wienkoop S, Keerberg O, Weckwerth W, Kleczkowski LA, Fernie AR, Bauwe H. A cytosolic pathway for the conversion of hydroxypyruvate to glycerate during photorespiration in Arabidopsis. THE PLANT CELL 2008; 20:2848-59. [PMID: 18952776 PMCID: PMC2590732 DOI: 10.1105/tpc.108.062265] [Citation(s) in RCA: 160] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2008] [Revised: 08/28/2008] [Accepted: 10/02/2008] [Indexed: 05/17/2023]
Abstract
Deletion of any of the core enzymes of the photorespiratory cycle, one of the major pathways of plant primary metabolism, results in severe air-sensitivity of the respective mutants. The peroxisomal enzyme hydroxypyruvate reductase (HPR1) represents the only exception to this rule. This indicates the presence of extraperoxisomal reactions of photorespiratory hydroxypyruvate metabolism. We have identified a second hydroxypyruvate reductase, HPR2, and present genetic and biochemical evidence that the enzyme provides a cytosolic bypass to the photorespiratory core cycle in Arabidopsis thaliana. Deletion of HPR2 results in elevated levels of hydroxypyruvate and other metabolites in leaves. Photosynthetic gas exchange is slightly altered, especially under long-day conditions. Otherwise, the mutant closely resembles wild-type plants. The combined deletion of both HPR1 and HPR2, however, results in distinct air-sensitivity and a dramatic reduction in photosynthetic performance. These results suggest that photorespiratory metabolism is not confined to chloroplasts, peroxisomes, and mitochondria but also extends to the cytosol. The extent to which cytosolic reactions contribute to the operation of the photorespiratory cycle in varying natural environments is not yet known, but it might be dynamically regulated by the availability of NADH in the context of peroxisomal redox homeostasis.
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Affiliation(s)
- Stefan Timm
- University of Rostock, BioScience Institute, Plant Physiology Department, D-18051 Rostock, Germany
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Hwang YT, McCartney AW, Gidda SK, Mullen RT. Localization of the Carnation Italian ringspot virus replication protein p36 to the mitochondrial outer membrane is mediated by an internal targeting signal and the TOM complex. BMC Cell Biol 2008; 9:54. [PMID: 18811953 PMCID: PMC2573885 DOI: 10.1186/1471-2121-9-54] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2008] [Accepted: 09/23/2008] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Carnation Italian ringspot virus (CIRV) is a positive-strand RNA virus that causes massive structural alterations of mitochondria in infected host cells, the most conspicuous being the formation of numerous internal vesicles/spherules that are derived from the mitochondrial outer membrane and serve as the sites for viral RNA replication. While the membrane-bound components of the CIRV replication complex, including a 36-kD RNA-binding protein (p36), are known to be essential for these changes in mitochondrial morphology and are relatively well characterized in terms of their roles in nascent viral RNA synthesis, how these proteins are specifically targeted and inserted into mitochondria is poorly defined. RESULTS Here we report on the molecular signal responsible for sorting p36 to the mitochondrial outer membrane. Using a combination of gain-of-function assays with portions of p36 fused to reporter proteins and domain-swapping assays with p36 and another closely-related viral RNA-binding protein, p33, that sorts specifically to the peroxisomal boundary membrane, we show that the mitochondrial targeting information in p36 resides within its two transmembrane domains (TMDs) and intervening hydrophilic loop sequence. Comprehensive mutational analysis of these regions in p36 revealed that the primary targeting determinants are the moderate hydrophobicity of both TMDs and the positively-charged face of an amphipathic helix within the intervening loop sequence. We show also using bimolecular fluorescence complementation (BiFC) that p36 interacts with certain components of the translocase complex in the mitochondrial outer membrane (TOM), but not with the sorting and assembly machinery (SAM). CONCLUSION Our results provide insight to how viruses, such as CIRV, exploit specific host-cell protein sorting pathways to facilitate their replication. The characterization of the targeting and insertion of p36 into the mitochondrial outer membrane also sheds light on the mechanisms involved in sorting of host-cell membrane proteins to mitochondria, a process that has been largely unexplored in plants.
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Affiliation(s)
- Yeen Ting Hwang
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Andrew W McCartney
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
- JD Irving, Limited, Woodlands Division, 1350 Regent Street, Fredericton, New Brunswick, E3C 2G6, Canada
| | - Satinder K Gidda
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Robert T Mullen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
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Allan WL, Simpson JP, Clark SM, Shelp BJ. Gamma-hydroxybutyrate accumulation in Arabidopsis and tobacco plants is a general response to abiotic stress: putative regulation by redox balance and glyoxylate reductase isoforms. JOURNAL OF EXPERIMENTAL BOTANY 2008; 59:2555-64. [PMID: 18495640 PMCID: PMC2423657 DOI: 10.1093/jxb/ern122] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2007] [Revised: 03/30/2008] [Accepted: 04/01/2008] [Indexed: 05/18/2023]
Abstract
Enzymes that reduce the aldehyde chemical grouping (i.e. H-C=O) to its corresponding alcohol are probably crucial in maintaining plant health during stress. Succinic semialdehyde (SSA) is a mitochondrially-generated intermediate in the metabolism of gamma-aminobutyrate (GABA), which accumulates in response to a variety of biotic and abiotic stresses. SSA can be reduced to gamma-hydroxybutyrate (GHB) under oxygen deficiency and high light conditions. Recent evidence indicates that distinct cytosolic and plastidial glyoxylate reductase isoforms from Arabidopsis (designated herein after as AtGR1 and AtGR2, respectively) catalyse the in vitro conversion of SSA to GHB, as well as glyoxylate to glycolate, via NADPH-dependent reactions. In the present report, the responses of GHB and related amino acids, as well as NADP(+) and NADPH, were monitored in leaves from Arabidopsis or tobacco plants subjected to various abiotic stresses (i.e. Arabidopsis during exposure to salinity, drought, submergence, cold, or heat; tobacco during exposure to, and recovery from, submergence). Time-course experiments revealed that GHB accumulated in both Arabidopsis and tobacco plants subjected to stress, and that this accumulation was generally accompanied by higher GABA and alanine levels, higher NADPH/NADP(+) ratio, and lower glutamate levels. Furthermore, the analysis of gene expression in Arabidopsis revealed that the relative abundance of GR1 (salinity, drought, submergence, cold, and heat) and GR2 (cold and heat) transcripts was enhanced by the stress tested. Thus, GHB accumulation in plants is a general response to abiotic stress and appears to be regulated by both biochemical and transcriptional processes.
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Affiliation(s)
| | | | | | - Barry J. Shelp
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, Canada N1G 2W1
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