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Bar-Even A. Daring metabolic designs for enhanced plant carbon fixation. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 273:71-83. [PMID: 29907311 DOI: 10.1016/j.plantsci.2017.12.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 12/16/2017] [Accepted: 12/16/2017] [Indexed: 05/07/2023]
Abstract
Increasing agricultural productivity is one of the major challenges our society faces. While multiple strategies to enhance plant carbon fixation have been suggested, and partially implemented, most of them are restricted to relatively simple modifications of endogenous metabolism, i.e., "low hanging fruit". Here, I portray the next generation of metabolic solutions to increase carbon fixation rate and yield. These strategies involve major rewiring of central metabolism, including dividing Rubisco's catalysis between several enzymes, replacing Rubisco with a different carboxylation reaction, substituting the Calvin Cycle with alternative carbon fixation pathways, and engineering photorespiration bypass routes that do not release carbon. While the barriers for implementing these elaborated metabolic architectures are quite significant, if we truly want to revolutionize carbon fixation, only daring engineering efforts will lead the way.
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Affiliation(s)
- Arren Bar-Even
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
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Yishai O, Lindner SN, Gonzalez de la Cruz J, Tenenboim H, Bar-Even A. The formate bio-economy. Curr Opin Chem Biol 2016; 35:1-9. [DOI: 10.1016/j.cbpa.2016.07.005] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 06/28/2016] [Accepted: 07/05/2016] [Indexed: 10/21/2022]
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Jacoby RP, Millar AH, Taylor NL. Assessment of respiration in isolated plant mitochondria using Clark-type electrodes. Methods Mol Biol 2015; 1305:165-185. [PMID: 25910734 DOI: 10.1007/978-1-4939-2639-8_12] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Mitochondrial respiration involves two key gas exchanges, the consumption of oxygen and the release of carbon dioxide. The ability to measure the consumption of oxygen via Clark-type electrodes has been one of the key techniques for advancing our knowledge of mitochondrial function in whole organisms, tissue samples, cells, and isolated subcellular fractions. In plants, oxygen electrode analyses provided the first evidence for some of the unique respiratory properties of plant mitochondria. This chapter briefs the principles of respiration and oxidative phosphorylation, how oxygen consumption measurements can be used to assess the quality of isolated mitochondrial preparations, and how these measurements can answer important questions in plant biochemistry and physiology. Finally, it presents instructions on assembling the oxygen electrode apparatus and how to conduct various assays.
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Affiliation(s)
- Richard P Jacoby
- Plant Energy Biology, Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
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Bar-Even A, Noor E, Flamholz A, Milo R. Design and analysis of metabolic pathways supporting formatotrophic growth for electricity-dependent cultivation of microbes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:1039-47. [PMID: 23123556 DOI: 10.1016/j.bbabio.2012.10.013] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 10/05/2012] [Accepted: 10/25/2012] [Indexed: 11/29/2022]
Abstract
Electrosynthesis is a promising approach that enables the biological production of commodities, like fuels and fine chemicals, using renewably produced electricity. Several techniques have been proposed to mediate the transfer of electrons from the cathode to living cells. Of these, the electroproduction of formate as a mediator seems especially promising: formate is readily soluble, of low toxicity and can be produced at relatively high efficiency and at reasonable current density. While organisms that are capable of formatotrophic growth, i.e. growth on formate, exist naturally, they are generally less suitable for bulk cultivation and industrial needs. Hence, it may be helpful to engineer a model organism of industrial relevance, such as E. coli, for growth on formate. There are numerous metabolic pathways that can potentially support formatotrophic growth. Here we analyze these diverse pathways according to various criteria including biomass yield, thermodynamic favorability, chemical motive force, kinetics and the practical challenges posed by their expression. We find that the reductive glycine pathway, composed of the tetrahydrofolate system, the glycine cleavage system, serine hydroxymethyltransferase and serine deaminase, is a promising candidate to support electrosynthesis in E. coli. The approach presented here exemplifies how combining different computational approaches into a systematic analysis methodology provides assistance in redesigning metabolism. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
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Affiliation(s)
- Arren Bar-Even
- Department of Plant Sciences, The Weizmann Institute of Science, Rehovot, Israel.
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Bar-Even A, Noor E, Milo R. A survey of carbon fixation pathways through a quantitative lens. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:2325-42. [PMID: 22200662 DOI: 10.1093/jxb/err417] [Citation(s) in RCA: 133] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
While the reductive pentose phosphate cycle is responsible for the fixation of most of the carbon in the biosphere, it has several natural substitutes. In fact, due to the characterization of three new carbon fixation pathways in the last decade, the diversity of known metabolic solutions for autotrophic growth has doubled. In this review, the different pathways are analysed and compared according to various criteria, trying to connect each of the different metabolic alternatives to suitable environments or metabolic goals. The different roles of carbon fixation are discussed; in addition to sustaining autotrophic growth it can also be used for energy conservation and as an electron sink for the recycling of reduced electron carriers. Our main focus in this review is on thermodynamic and kinetic aspects, including thermodynamically challenging reactions, the ATP requirement of each pathway, energetic constraints on carbon fixation, and factors that are expected to limit the rate of the pathways. Finally, possible metabolic structures of yet unknown carbon fixation pathways are suggested and discussed.
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Affiliation(s)
- Arren Bar-Even
- Department of Plant Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
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Lee CP, Eubel H, Millar AH. Diurnal changes in mitochondrial function reveal daily optimization of light and dark respiratory metabolism in Arabidopsis. Mol Cell Proteomics 2010; 9:2125-39. [PMID: 20601493 DOI: 10.1074/mcp.m110.001214] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Biomass production by plants is often negatively correlated with respiratory rate, but the value of this rate changes dramatically during diurnal cycles, and hence, biomass is the cumulative result of complex environment-dependent metabolic processes. Mitochondria in photosynthetic plant tissues undertake substantially different metabolic roles during light and dark periods that are dictated by substrate availability and the functional capacity of mitochondria defined by their protein composition. We surveyed the heterogeneity of the mitochondrial proteome and its function during a typical night and day cycle in Arabidopsis shoots. This used a staged, quantitative analysis of the proteome across 10 time points covering 24 h of the life of 3-week-old Arabidopsis shoots grown under 12-h dark and 12-h light conditions. Detailed analysis of enzyme capacities and substrate-dependent respiratory processes of isolated mitochondria were also undertaken during the same time course. Together these data reveal a range of dynamic changes in mitochondrial capacity and uncover day- and night-enhanced protein components. Clear diurnal changes were evident in mitochondrial capacities to drive the TCA cycle and to undertake functions associated with nitrogen and sulfur metabolism, redox poise, and mitochondrial antioxidant defense. These data quantify the nature and nuances of a daily rhythm in Arabidopsis mitochondrial respiratory capacity.
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Affiliation(s)
- Chun Pong Lee
- Australian Research Council Centre of Excellence in Plant Energy Biology, Molecular and Chemical Sciences Building M310 University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia
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Parys E, Jastrzebski H. Mitochondria from leaf mesophyll cells of C(4) plants are deficient in the H protein of glycine decarboxylase complex. JOURNAL OF PLANT PHYSIOLOGY 2008; 165:1061-9. [PMID: 17945380 DOI: 10.1016/j.jplph.2007.07.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2007] [Revised: 07/16/2007] [Accepted: 07/16/2007] [Indexed: 05/09/2023]
Abstract
Mesophyll mitochondria from green leaves of the C(4) plants Zea mays (NADP-ME-type), Panicum miliaceum (NAD-ME-type) and Panicum maximum (PEP-CK-type) oxidized NADH, malate and succinate at relatively high rates with respiratory control, but glycine was not oxidized. Among the mitochondrial proteins involved in glycine oxidation, the L, P and T proteins of glycine decarboxylase complex (GDC) and serine hydroxymethyltransferase (SHMT) were present, while the H protein of GDC was undetectable. In contrast, mesophyll mitochondria from etiolated leaves of Z. mays oxidized glycine at a slow rate and with no respiratory control, and contained the H protein as well as the other GDC proteins and SHMT. The T and P proteins and SHMT were present in the mitochondria from etiolated leaves at significantly higher levels than in those from green leaves of Z. mays. The content of the L protein was almost identical in all three C(4) plants examined and close to the value obtained for mesophyll mitochondria from the C(3) plant Pisum sativum, whereas the other GDC proteins and SHMT were less abundant than the L protein. We discuss possible reasons for the H protein's absence in mesophyll mitochondria of C(4) plants, as well as the role(s) the other GDC components could play in its absence.
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Affiliation(s)
- Eugeniusz Parys
- Department of Plant Physiology, University of Warsaw, Poland.
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Ito J, Heazlewood JL, Millar AH. Analysis of the Soluble ATP-Binding Proteome of Plant Mitochondria Identifies New Proteins and Nucleotide Triphosphate Interactions within the Matrix. J Proteome Res 2006; 5:3459-69. [PMID: 17137349 DOI: 10.1021/pr060403j] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The interactions of ATP inside plant mitochondria were investigated by identifying the soluble nucleotide binding proteome captured using immobilized ATP. Selected proteins were separated by 1D SDS-PAGE and 2D IEF-SDS-PAGE and identified by ESI-Q-TOF MS/MS. A range of highly enriched proteins were identified from the mitochondrial proteome, including 14-3-3 proteins and RNA binding proteins, as well as proteins known to contain nucleotide binding domains and/or to be inhibited or stimulated by ATP.
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Affiliation(s)
- Jun Ito
- ARC Centre of Excellence in Plant Energy Biology and School of Biomedical, Biomolecular and Chemical Sciences, The University of Western Australia, 35 Stirling Highway, M316, Crawley 6009, WA, Australia
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Tcherkez G. Viewpoint: How large is the carbon isotope fractionation of the photorespiratory enzyme glycine decarboxylase? FUNCTIONAL PLANT BIOLOGY : FPB 2006; 33:911-920. [PMID: 32689301 DOI: 10.1071/fp06098] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2006] [Accepted: 08/02/2006] [Indexed: 06/11/2023]
Abstract
Despite the intense effort developed over the past 10 years to determine the 12C / 13C isotope fractionation associated with photorespiration, much uncertainty remains about the amplitude, and even the sign, of the 12C / 13C isotope fractionation of glycine decarboxylase, the enzyme that produces CO2 during the photorespiratory cycle. In fact, leaf gas-exchange data have repeatedly indicated that CO2 evolved by photorespiration is depleted in 13C compared with the source material, while glycine decarboxylase has mostly favoured 13C in vitro. Here I give theoretical insights on the glycine decarboxylase reaction and show that (i), both photorespiration and glycine decarboxylation must favour the same carbon isotope - the in vitro measurements being probably adulterated by the high sensitivity of the enzyme to assay conditions and the possible reversibility of the reaction in these conditions, and (ii), simplified quantum chemistry considerations as well as comparisons with other pyridoxal 5'-phosphate-dependent decarboxylases indicate that the carbon isotope fractionation favour the 12C isotope by ~20‰, a value that is consistent with the value of the photorespiratory fractionation (f) obtained by gas-exchange experiments.
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Affiliation(s)
- Guillaume Tcherkez
- Laboratoire d'Ecophysiologie Végétale, CNRS UMR 8079, Bâtiment 362, Université Paris XI, 91405 Orsay, France. Email
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Taylor NL, Heazlewood JL, Day DA, Millar AH. Differential impact of environmental stresses on the pea mitochondrial proteome. Mol Cell Proteomics 2005; 4:1122-33. [PMID: 15914488 DOI: 10.1074/mcp.m400210-mcp200] [Citation(s) in RCA: 152] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Exposure to adverse environmental conditions causes oxidative stress in many organisms, leading either to disease and debilitation or to response and tolerance. Mitochondria are a key site of oxidative stress and of cellular response and play important roles in cell survival. We analyzed the response of mitochondria in pea (Pisum sativum) plants to the common stresses associated with drought, cold, and herbicides. These treatments all altered photosynthetic and respiratory rates of pea leaves to various extents, but only herbicides significantly increased lipid peroxidation product accumulation. Mitochondria isolated from the stressed pea plants maintained their electron transport chain activity, but changes were evident in the abundance of uncoupling proteins, non-phosphorylating respiratory pathways, and oxidative modification of lipoic acid moieties on mitochondrial proteins. These data suggest that herbicide treatment placed a severe oxidative stress on mitochondria, whereas chilling and particularly drought were milder stresses. Detailed analysis of the soluble proteome of mitochondria by gel electrophoresis and mass spectrometry revealed differential degradation of key matrix enzymes during treatments with chilling being significantly more damaging than drought. Differential induction of heat shock proteins and specific losses of other proteins illustrated the diversity of response to these stresses at the protein level. Cross-species matching was required for mass spectrometry identification of nine proteins because only a limited number of pea cDNAs have been sequenced, and the full pea genome is not available. Blue-native separation of intact respiratory chain complexes revealed little if any change in response to environmental stresses. Together these data suggest that although many of the molecular events identified by chemical stresses of mitochondria from a range of model eukaryotes are also apparent during environmental stress of plants, their extent and significance can vary substantially.
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Affiliation(s)
- Nicolas L Taylor
- The Plant Molecular Biology Group, Biochemistry and Molecular Biology, School of Biomedical and Chemical Sciences, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia
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Taylor NL, Rudhe C, Hulett JM, Lithgow T, Glaser E, Day DA, Millar AH, Whelan J. Environmental stresses inhibit and stimulate different protein import pathways in plant mitochondria. FEBS Lett 2003; 547:125-30. [PMID: 12860399 DOI: 10.1016/s0014-5793(03)00691-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The impact of various environmental stresses (drought, chilling or herbicide treatment) on the capacity of plant mitochondria to import precursor proteins was investigated. Drought treatment stimulated import and processing of various precursor proteins via the general import pathway. The stimulatory effect of drought on the general import pathway was due to an increased rate of import, was accompanied by an increased rate of processing, and could be attributed to the presequence of the precursor protein. Interestingly, drought decreased the import of the F(A)d subunit of ATP synthase suggesting a bypass of the point of stimulation during import of this precursor. Both chilling and herbicide treatment of plants, on the other hand, caused inhibition of import with all precursors tested. No decrease in processing of imported proteins was observed by these stress treatments. Western analysis of several mitochondrial proteins indicated that the steady-state level of several mitochondrial components, including the TOM20 receptor and the core subunits of the cytochrome bc(1) complex responsible for processing, remained largely unchanged. Thus environmental stresses differentially affect import of precursor proteins in a complicated manner dependent on the import pathway utilised.
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Affiliation(s)
- Nicolas L Taylor
- Plant Molecular Biology Group, Biochemistry and Molecular Biology, School of Biomedical and Chemical Sciences, The University of Western Australia, 35 Stirling Highway, 6009, Crawley, WA, Australia
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Taylor NL, Day DA, Millar AH. Environmental stress causes oxidative damage to plant mitochondria leading to inhibition of glycine decarboxylase. J Biol Chem 2002; 277:42663-8. [PMID: 12213810 DOI: 10.1074/jbc.m204761200] [Citation(s) in RCA: 155] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A cytotoxic product of lipid peroxidation, 4-hydroxy-2-nonenal (HNE), rapidly inhibited glycine, malate/pyruvate, and 2-oxoglutarate-dependent O2 consumption by pea leaf mitochondria. Dose- and time-dependence of inhibition showed that glycine oxidation was the most severely affected with a K(0.5) of 30 microm. Several mitochondrial proteins containing lipoic acid moieties differentially lost their reactivity to a lipoic acid antibody following HNE treatment. The most dramatic loss of antigenicity was seen with the 17-kDa glycine decarboxylase complex (GDC) H-protein, which was correlated with the loss of glycine-dependent O2 consumption. Paraquat treatment of pea seedlings induced lipid peroxidation, which resulted in the rapid loss of glycine-dependent respiration and loss of H-protein reactivity with lipoic acid antibodies. Pea plants exposed to chilling and water deficit responded similarly. In contrast, the damage to other lipoic acid-containing mitochondrial enzymes was minor under these conditions. The implication of the acute sensitivity of glycine decarboxylase complex H-protein to lipid peroxidation products is discussed in the context of photorespiration and potential repair mechanisms in plant mitochondria.
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Affiliation(s)
- Nicolas L Taylor
- Plant Molecular Biology Group, School of Biomedical and Chemical Sciences, Faculty of Life and Physical Sciences, The University of Western Australia, Crawley, WA 6009, Western Australia, Australia
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