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Weng M, Zhang D, Wang H, Yang C, Lin H, Pan Y, Lin Y. Long non-coding RNAs and their potential function in response to postharvest senescence of Sparassis latifolia during cold storage. Sci Rep 2024; 14:747. [PMID: 38185662 PMCID: PMC10772075 DOI: 10.1038/s41598-023-46744-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 11/04/2023] [Indexed: 01/09/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) have been shown to play crucial roles in response to aging processes. However, how lncRNAs regulate postharvest senescence of Sparassis latifolia (S. latifolia) with oriented polypropylene (OPP) film packing during cold storage remains unclear. In this study, we performed RNA-seq using the fruiting bodies of S. latifolia stored at 4 ℃ for 0, 8, 16 and 24 days after harvest, and profiled the lncRNA and mRNA transcriptome, respectively. In total, 1003 putative lncRNAs were identified, and there were 495, 483 and 162 differentially expressed (DE) lncRNAs, and 3680, 3941 and 1870 differentially expressed mRNAs after 8, 16 and 24 days of storage, respectively, compared to 0 day of storage. Target genes of differentially expressed lncRNAs were found to significantly associate with carbon and energy metabolism, response to abiotic stimulus, amino acid biosynthesis and metabolism, and protein synthesis and transcription. In addition, DE-lncRNA-mRNA co-expression networks in response to aging stress were also constructed. Taken together, these results confirm the regulatory role of lncRNAs in postharvest senescence of S. latifolia and will facilitate for improving preservation method.
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Affiliation(s)
- Mengting Weng
- Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China
- National and Local Joint Engineering Research Center for Breeding & Cultivation of Featured Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China
| | - Di Zhang
- Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China
- National and Local Joint Engineering Research Center for Breeding & Cultivation of Featured Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China
| | - Hongyu Wang
- Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China
- National and Local Joint Engineering Research Center for Breeding & Cultivation of Featured Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China
| | - Chi Yang
- Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China
- National and Local Joint Engineering Research Center for Breeding & Cultivation of Featured Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China
| | - Hongyi Lin
- Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China
- National and Local Joint Engineering Research Center for Breeding & Cultivation of Featured Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China
| | - Yanfang Pan
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Yanquan Lin
- Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China.
- National and Local Joint Engineering Research Center for Breeding & Cultivation of Featured Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China.
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He Q, Jin J, Li P, Zhu H, Wang Z, Fan W, Yang JL. Involvement of SlSTOP1 regulated SlFDH expression in aluminum tolerance by reducing NAD + to NADH in the tomato root apex. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:387-401. [PMID: 36471650 DOI: 10.1111/tpj.16054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
Formate dehydrogenase (FDH; EC 1.2.1.2.) has been implicated in plant responses to a variety of stresses, including aluminum (Al) stress in acidic soils. However, the role of this enzyme in Al tolerance is not yet fully understood, and how FDH gene expression is regulated is unknown. Here, we report the identification and functional characterization of the tomato (Solanum lycopersicum) SlFDH gene. SlFDH encodes a mitochondria-localized FDH with Km values of 2.087 mm formate and 29.1 μm NAD+ . Al induced the expression of SlFDH in tomato root tips, but other metals did not, as determined by quantitative reverse transcriptase-polymerase chain reaction. CRISPR/Cas9-generated SlFDH knockout lines were more sensitive to Al stress and formate than wild-type plants. Formate failed to induce SlFDH expression in the tomato root apex, but NAD+ accumulated in response to Al stress. Co-expression network analysis and interaction analysis between genomic DNA and transcription factors (TFs) using PlantRegMap identified seven TFs that might regulate SlFDH expression. One of these TFs, SlSTOP1, positively regulated SlFDH expression by directly binding to its promoter, as demonstrated by a dual-luciferase reporter assay and electrophoretic mobility shift assay. The Al-induced expression of SlFDH was completely abolished in Slstop1 mutants, indicating that SlSTOP1 is a core regulator of SlFDH expression under Al stress. Taken together, our findings demonstrate that SlFDH plays a role in Al tolerance and reveal the transcriptional regulatory mechanism of SlFDH expression in response to Al stress in tomato.
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Affiliation(s)
- Qiyu He
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jianfeng Jin
- Department of Horticulture, Zhejiang University, Zijingang Campus, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Pengfei Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Huihui Zhu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhanqi Wang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, 313000, China
| | - Wei Fan
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, China
| | - Jian Li Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
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Cheng N, Paris V, Rao X, Wang X, Nakata PA. A conserved oxalyl-coenzyme A decarboxylase in oxalate catabolism. PLANT SIGNALING & BEHAVIOR 2022; 17:2062555. [PMID: 35510715 PMCID: PMC9090294 DOI: 10.1080/15592324.2022.2062555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 06/14/2023]
Abstract
The ability to biosynthesize oxalic acid can provide beneficial functions to plants; however, uncontrolled or prolonged exposure to this strong organic acid results in multiple physiological problems. Such problems include a disruption of membrane integrity, mitochondrial function, metal chelation, and free radical formation. Recent work suggests that a CoA-dependent pathway of oxalate catabolism plays a critical role in regulating tissue oxalate concentrations in plants. Although this CoA-dependent pathway of oxalate catabolism is important, large gaps in our knowledge of the enzymes catalyzing each step remain. Evidence that an oxalyl-CoA decarboxylase (OXC) catalyzes the second step in this pathway, accelerating the conversion of oxalyl-CoA to formyl-CoA, has been reported. Induction studies revealed that OXC gene expression was upregulated in response to an exogenous oxalate supply. Phylogenetic analysis indicates that OXCs are conserved across plant species. Evolutionarily the plant OXCs can be separated into dicot and monocot classes. Multiple sequence alignments and molecular modeling suggest that OXCs have similar functionality with three conserved domains, the N-terminal PYR domain, the middle R domain, and the C-terminal PP domain. Further study of this CoA-dependent pathway of oxalate degradation would benefit efforts to develop new strategies to improve the nutrition quality of crops.
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Affiliation(s)
- Ninghui Cheng
- USDA-ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Texas, United States
| | - Vincent Paris
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Texas, United States
| | - Xiaolan Rao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, P. R. China
| | - Xiaoqiang Wang
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Texas, United States
| | - Paul A. Nakata
- USDA-ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Texas, United States
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4
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The structure-function relationships and physiological roles of MnSOD mutants. Biosci Rep 2022; 42:231385. [PMID: 35662317 PMCID: PMC9208312 DOI: 10.1042/bsr20220202] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 05/10/2022] [Accepted: 06/01/2022] [Indexed: 11/17/2022] Open
Abstract
In this review, we focus on understanding the structure–function relationships of numerous manganese superoxide dismutase (MnSOD) mutants to investigate the role that various amino acids play to maintain enzyme quaternary structure or the active site structure, catalytic potential and metal homeostasis in MnSOD, which is essential to maintain enzyme activity. We also observe how polymorphisms of MnSOD are linked to pathologies and how post-translational modifications affect the antioxidant properties of MnSOD. Understanding how modified forms of MnSOD may act as tumor promoters or suppressors by altering the redox status in the body, ultimately aid in generating novel therapies that exploit the therapeutic potential of mutant MnSODs or pave the way for the development of synthetic SOD mimics.
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Lian T, Wang X, Li S, Jiang H, Zhang C, Wang H, Jiang L. Comparative Transcriptome Analysis Reveals Mechanisms of Folate Accumulation in Maize Grains. Int J Mol Sci 2022; 23:ijms23031708. [PMID: 35163628 PMCID: PMC8836222 DOI: 10.3390/ijms23031708] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 02/05/2023] Open
Abstract
Previously, the complexity of folate accumulation in the early stages of maize kernel development has been reported, but the mechanisms of folate accumulation are unclear. Two maize inbred lines, DAN3130 and JI63, with different patterns of folate accumulation and different total folate contents in mature kernels were used to investigate the transcriptional regulation of folate metabolism during late stages of kernel formation by comparative transcriptome analysis. The folate accumulation during DAP 24 to mature kernels could be controlled by circumjacent pathways of folate biosynthesis, such as pyruvate metabolism, glutamate metabolism, and serine/glycine metabolism. In addition, the folate variation between these two inbred lines was related to those genes among folate metabolism, such as genes in the pteridine branch, para-aminobenzoate branch, serine/tetrahydrofolate (THF)/5-methyltetrahydrofolate cycle, and the conversion of THF monoglutamate to THF polyglutamate. The findings provided insight into folate accumulation mechanisms during maize kernel formation to promote folate biofortification.
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Affiliation(s)
- Tong Lian
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (T.L.); (S.L.); (C.Z.)
- Plant Genetics, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya 572000, China
| | - Xuxia Wang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (X.W.); (H.J.)
| | - Sha Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (T.L.); (S.L.); (C.Z.)
| | - Haiyang Jiang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (X.W.); (H.J.)
| | - Chunyi Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (T.L.); (S.L.); (C.Z.)
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya 572000, China
| | - Huan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (T.L.); (S.L.); (C.Z.)
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (X.W.); (H.J.)
- National Agricultural Science and Technology Center, Chengdu 610213, China
- Correspondence: (H.W.); (L.J.)
| | - Ling Jiang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (T.L.); (S.L.); (C.Z.)
- Correspondence: (H.W.); (L.J.)
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6
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Zhang Y, Giese J, Kerbler SM, Siemiatkowska B, Perez de Souza L, Alpers J, Medeiros DB, Hincha DK, Daloso DM, Stitt M, Finkemeier I, Fernie AR. Two mitochondrial phosphatases, PP2c63 and Sal2, are required for posttranslational regulation of the TCA cycle in Arabidopsis. MOLECULAR PLANT 2021; 14:1104-1118. [PMID: 33798747 DOI: 10.1016/j.molp.2021.03.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 01/26/2021] [Accepted: 03/29/2021] [Indexed: 05/22/2023]
Abstract
Protein phosphorylation is a well-established post-translational mechanism that regulates protein functions and metabolic pathways. It is known that several plant mitochondrial proteins are phosphorylated in a reversible manner. However, the identities of the protein kinases/phosphatases involved in this mechanism and their roles in the regulation of the tricarboxylic acid (TCA) cycle remain unclear. In this study, we isolated and characterized plants lacking two mitochondrially targeted phosphatases (Sal2 and PP2c63) along with pyruvate dehydrogenase kinase (PDK). Protein-protein interaction analysis, quantitative phosphoproteomics, and enzymatic analyses revealed that PDK specifically regulates pyruvate dehydrogenase complex (PDC), while PP2c63 nonspecifically regulates PDC. When recombinant PP2c63 and Sal2 proteins were added to mitochondria isolated from mutant plants, protein-protein interaction and enzymatic analyses showed that PP2c63 directly phosphorylates and modulates the activity of PDC, while Sal2 only indirectly affects TCA cycle enzymes. Characterization of steady-state metabolite levels and fluxes in the mutant lines further revealed that these phosphatases regulate flux through the TCA cycle, and that altered metabolism in the sal2 pp2c63 double mutant compromises plant growth. These results are discussed in the context of current models of the control of respiration in plants.
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Affiliation(s)
- Youjun Zhang
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria.
| | - Jonas Giese
- Institute of Plant Biology and Biotechnology, University of Muenster, Schlossplatz 7, 48149 Muenster, Germany
| | - Sandra M Kerbler
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Beata Siemiatkowska
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Leonardo Perez de Souza
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Jessica Alpers
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - David Barbosa Medeiros
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Dirk K Hincha
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Danilo M Daloso
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Ceará, Brasil
| | - Mark Stitt
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Iris Finkemeier
- Institute of Plant Biology and Biotechnology, University of Muenster, Schlossplatz 7, 48149 Muenster, Germany.
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria.
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7
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Effect of Met/Leu substitutions on the stability of NAD+-dependent formate dehydrogenases from Gossypium hirsutum. Appl Microbiol Biotechnol 2021; 105:2787-2798. [PMID: 33754169 DOI: 10.1007/s00253-021-11232-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 02/24/2021] [Accepted: 03/10/2021] [Indexed: 10/21/2022]
Abstract
NAD+-dependent formate dehydrogenases (FDHs) are extensively used in the regeneration of NAD(P)H and the reduction of CO2 to formate. In addition to their industrial importance, FDHs also play a crucial role in the maintenance of a reducing environment to combat oxidative stress in plants. Therefore, it is important to investigate the response of NAD+-dependent FDH against both temperature and H2O2, to understand the defense mechanisms, and to increase its stability under oxidative stress conditions. In the present study, we characterized the oxidative and thermal stability of NAD+-dependent FDH isolated from cotton, Gossypium hirsutum (GhFDH), by investigating the effect of Met/Leu substitutions in the positions of 225, 234, and 243. Results showed that the single mutant, M234L (0.72 s-1 mM-1), and the triple mutant, M225L/M234L/M243L (0.55 s-1 mM-1), have higher catalytic efficiency than the native enzyme. Substitution of methionine by leucine on the position of 243 increased the free energy gain by 670 J mol-1. The most remarkable results in chemical stability were seen for double and triple mutants, cumulatively. Double and triple substitution of Met to Leu (M225L/M243L and M225L/M243L/M234L) reduce the kefin by a factor of 2 (12.3×10-5 and 12.8×10-5 s-1, respectively.Key points• The closer the residue to NAD+, in which we substituted methionine to leucine, the lower the stability against H2O2 we observed.• The significant gain in the Tm value for the M243L mutant was observed as +5°C.• Residue 234 occupies a critical position for oxidation defense mechanisms. Graphical abstract (a) Methionine amino acids on the protein surface are susceptible to oxidative stress and can be converted to methionine sulfoxide by reactive oxygen derivatives (such as hydrogen peroxide). Therefore, they are critical regions in the change of protein conformation and loss of activity. (b) Replacing the amino acid methionine, which is susceptible to oxidation due to the sulfur group, with the oxidation-resistant leucine amino acid is an important strategy in increasing oxidative stability.
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Kotrasová V, Keresztesová B, Ondrovičová G, Bauer JA, Havalová H, Pevala V, Kutejová E, Kunová N. Mitochondrial Kinases and the Role of Mitochondrial Protein Phosphorylation in Health and Disease. Life (Basel) 2021; 11:life11020082. [PMID: 33498615 PMCID: PMC7912454 DOI: 10.3390/life11020082] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 02/07/2023] Open
Abstract
The major role of mitochondria is to provide cells with energy, but no less important are their roles in responding to various stress factors and the metabolic changes and pathological processes that might occur inside and outside the cells. The post-translational modification of proteins is a fast and efficient way for cells to adapt to ever changing conditions. Phosphorylation is a post-translational modification that signals these changes and propagates these signals throughout the whole cell, but it also changes the structure, function and interaction of individual proteins. In this review, we summarize the influence of kinases, the proteins responsible for phosphorylation, on mitochondrial biogenesis under various cellular conditions. We focus on their role in keeping mitochondria fully functional in healthy cells and also on the changes in mitochondrial structure and function that occur in pathological processes arising from the phosphorylation of mitochondrial proteins.
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Affiliation(s)
- Veronika Kotrasová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51 Bratislava, Slovakia; (V.K.); (B.K.); (G.O.); (J.A.B.); (H.H.); (V.P.)
| | - Barbora Keresztesová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51 Bratislava, Slovakia; (V.K.); (B.K.); (G.O.); (J.A.B.); (H.H.); (V.P.)
- First Faculty of Medicine, Institute of Biology and Medical Genetics, Charles University, 128 00 Prague, Czech Republic
| | - Gabriela Ondrovičová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51 Bratislava, Slovakia; (V.K.); (B.K.); (G.O.); (J.A.B.); (H.H.); (V.P.)
| | - Jacob A. Bauer
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51 Bratislava, Slovakia; (V.K.); (B.K.); (G.O.); (J.A.B.); (H.H.); (V.P.)
| | - Henrieta Havalová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51 Bratislava, Slovakia; (V.K.); (B.K.); (G.O.); (J.A.B.); (H.H.); (V.P.)
| | - Vladimír Pevala
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51 Bratislava, Slovakia; (V.K.); (B.K.); (G.O.); (J.A.B.); (H.H.); (V.P.)
| | - Eva Kutejová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51 Bratislava, Slovakia; (V.K.); (B.K.); (G.O.); (J.A.B.); (H.H.); (V.P.)
- Correspondence: (E.K.); (N.K.)
| | - Nina Kunová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51 Bratislava, Slovakia; (V.K.); (B.K.); (G.O.); (J.A.B.); (H.H.); (V.P.)
- First Faculty of Medicine, Institute of Biology and Medical Genetics, Charles University, 128 00 Prague, Czech Republic
- Correspondence: (E.K.); (N.K.)
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Thermodynamic buffering, stable non-equilibrium and establishment of the computable structure of plant metabolism. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 146:23-36. [PMID: 30444975 DOI: 10.1016/j.pbiomolbio.2018.11.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 11/02/2018] [Accepted: 11/12/2018] [Indexed: 01/09/2023]
Abstract
The equilibria of coenzyme nucleotides and substrates established in plant cells generate simple rules that govern the plant metabolome and provide optimal conditions for the non-equilibrium fluxes of major metabolic processes such as ATP synthesis, CO2 fixation, and mitochondrial respiration. Fast and abundant enzymes, such as adenylate kinase, carbonic anhydrase or malate dehydrogenase, provide constant substrate flux for these processes. These "buffering" enzymes follow the Michaelis-Menten (MM) kinetics and operate near equilibrium. The non-equilibrium "engine" enzymes, such as ATP synthase, Rubisco or the respiratory complexes, follow the modified version of MM kinetics due to their high concentration and low concentration of their substrates. The equilibrium reactions serve as control gates for the non-equilibrium flux through the engine enzymes establishing the balance of the fluxes of load and consumption of metabolic components. Under the coordinated operation of buffering and engine enzymes, the concentrations of free and Mg-bound adenylates and of free Mg2+ are set, serving as feedback signals from the adenylate metabolome. Those are linked to various cell energetics parameters, including membrane potentials. Also, internal levels of reduced and oxidized pyridine nucleotides are established in the coordinated operation of malate dehydrogenase and respiratory components, with proton concentration as a feedback from pyridine nucleotide pools. Non-coupled pathways of respiration serve to equilibrate the levels of pyridine nucleotides, adenylates, and as a pH stat. This stable non-equilibrium organizes the fluxes of energy spatially and temporally, controlling the rates of major metabolic fluxes that follow thermodynamically and kinetically defined computational principles.
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Schwechheimer SK, Becker J, Peyriga L, Portais JC, Sauer D, Müller R, Hoff B, Haefner S, Schröder H, Zelder O, Wittmann C. Improved riboflavin production with Ashbya gossypii from vegetable oil based on 13C metabolic network analysis with combined labeling analysis by GC/MS, LC/MS, 1D, and 2D NMR. Metab Eng 2018; 47:357-373. [PMID: 29654833 DOI: 10.1016/j.ymben.2018.04.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 02/13/2018] [Accepted: 04/11/2018] [Indexed: 11/29/2022]
Abstract
The fungus Ashbya gossypii is an important industrial producer of riboflavin, i.e. vitamin B2. In order to meet the constantly increasing demands for improved production processes, it appears essential to better understand the underlying metabolic pathways of the vitamin. Here, we used a highly sophisticated set-up of parallel 13C tracer studies with labeling analysis by GC/MS, LC/MS, 1D, and 2D NMR to resolve carbon fluxes in the overproducing strain A. gossypii B2 during growth and subsequent riboflavin production from vegetable oil as carbon source, yeast extract, and supplemented glycine. The studies provided a detailed picture of the underlying metabolism. Glycine was exclusively used as carbon-two donor of the vitamin's pyrimidine ring, which is part of its isoalloxazine ring structure, but did not contribute to the carbon-one metabolism due to the proven absence of a functional glycine cleavage system. The pools of serine and glycine were closely connected due to a highly reversible serine hydroxymethyltransferase. Transmembrane formate flux simulations revealed that the one-carbon metabolism displayed a severe bottleneck during initial riboflavin production, which was overcome in later phases of the cultivation by intrinsic formate accumulation. The transiently limiting carbon-one pool was successfully replenished by time-resolved feeding of small amounts of formate and serine, respectively. This increased the intracellular availability of glycine, serine, and formate and resulted in a final riboflavin titer increase of 45%.
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Affiliation(s)
| | - Judith Becker
- Institute of Systems Biotechnology, Saarland University, Germany
| | - Lindsay Peyriga
- Université de Toulouse; INSA, UPS, INP, Toulouse, France; INRA, UMR792 Ingénerie des Systèmes Biologiques et des Procédés, Toulouse, France; CNRS, UMR5504, Toulouse, France
| | - Jean-Charles Portais
- Université de Toulouse; INSA, UPS, INP, Toulouse, France; INRA, UMR792 Ingénerie des Systèmes Biologiques et des Procédés, Toulouse, France; CNRS, UMR5504, Toulouse, France
| | - Daniel Sauer
- Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Birgit Hoff
- BASF SE, White Biotechnology Research, Ludwigshafen, Germany
| | - Stefan Haefner
- BASF SE, White Biotechnology Research, Ludwigshafen, Germany
| | | | - Oskar Zelder
- BASF SE, White Biotechnology Research, Ludwigshafen, Germany
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McNeilly D, Schofield A, Stone SL. Degradation of the stress-responsive enzyme formate dehydrogenase by the RING-type E3 ligase Keep on Going and the ubiquitin 26S proteasome system. PLANT MOLECULAR BIOLOGY 2018; 96:265-278. [PMID: 29270890 DOI: 10.1007/s11103-017-0691-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 12/08/2017] [Indexed: 06/07/2023]
Abstract
KEG is involved in mediating the proteasome-dependent degradation of FDH, a stress-responsive enzyme. The UPS may function to suppress FDH mediated stress responses under favorable growth conditions. Formate dehydrogenase (FDH) has been studied in bacteria and yeasts for the purpose of industrial application of NADH co-factor regeneration. In plants, FDH is regarded as a universal stress protein involved in responses to various abiotic and biotic stresses. Here we show that FDH abundance is regulated by the ubiquitin proteasome system (UPS). FDH is ubiquitinated in planta and degraded by the 26S proteasome. Interaction assays identified FDH as a potential substrate for the RING-type ubiquitin ligase Keep on Going (KEG). KEG is capable of attaching ubiquitin to FDH in in vitro assays and the turnover of FDH was increased when co-expressed with a functional KEG in planta, suggesting that KEG contributes to FDH degradation. Consistent with a role in regulating FDH abundance, transgenic plants overexpressing KEG were more sensitive to the inhibitory effects of formate. In addition, FDH is a phosphoprotein and dephosphorylation was found to increase the stability of FDH in degradation assays. Based on results from this and previous studies, we propose a model where KEG mediates the ubiquitination and subsequent degradation of phosphorylated FDH and, in response to unfavourable growth conditions, reduction in FDH phosphorylation levels may prohibit turnover allowing the stabilized FDH to facilitate stress responses.
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Affiliation(s)
- Daryl McNeilly
- Department of Biology, Dalhousie University, Halifax, NS, B3H4R2, Canada
| | - Andrew Schofield
- Department of Biology, Dalhousie University, Halifax, NS, B3H4R2, Canada
| | - Sophia L Stone
- Department of Biology, Dalhousie University, Halifax, NS, B3H4R2, Canada.
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12
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Fang D, Yang W, Deng Z, An X, Zhao L, Hu Q. Proteomic Investigation of Metabolic Changes of Mushroom (Flammulina velutipes) Packaged with Nanocomposite Material during Cold Storage. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:10368-10381. [PMID: 29111700 DOI: 10.1021/acs.jafc.7b04393] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Metabolic changes of mushroom (Flammulina velutipes) applied with polyethylene (PE) material (Normal-PM) or nanocomposite reinforced PE packaging material (Nano-PM) were monitored using tandem mass tags (TMT) labeling combined with two-dimensional liquid chromatography-tandem mass spectrometry (2D LC-MS/MS) technique. A total of 429 proteins were investigated as differentially expressed proteins (DEPs) among treatments after a cold storage period. A total of 232 DEPs were up-regulated and 65 DEPs were down-regulated in Nano-PM packed F. velutipes compared to that of Normal-PM. The up-regulated DEPs were mainly involved in amino acid synthesis and metabolism, signal transduction, and response to stress while the down-regulated DEPs were largely located in mitochondrion and participated in carbohydrate metabolic, amino acid synthesis and metabolism, and organic acid metabolic. It was also revealed that Nano-PM could inhibit the carbohydrate and energy metabolism bioprocess, promote amino acids biosynthesis, enhance antioxidant system, and improve its resistance to stress, resulting in a further extended shelf life of F. velutipes.
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Affiliation(s)
- Donglu Fang
- College of Food Science and Technology, Nanjing Agricultural University , Nanjing, Jiangsu 210095, P.R. China
| | - Wenjian Yang
- College of Food Science and Engineering, Nanjing University of Finance and Economics , Nanjing, Jiangsu 210046, P.R. China
| | - Zilong Deng
- Department of Food Science & Technology, Oregon State University , Corvallis, Oregon 97331-6602, United States
| | - Xinxin An
- College of Food Science and Technology, Nanjing Agricultural University , Nanjing, Jiangsu 210095, P.R. China
| | - Liyan Zhao
- College of Food Science and Technology, Nanjing Agricultural University , Nanjing, Jiangsu 210095, P.R. China
| | - Qiuhui Hu
- College of Food Science and Technology, Nanjing Agricultural University , Nanjing, Jiangsu 210095, P.R. China
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13
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You C, Chen L, He H, Wu L, Wang S, Ding Y, Ma C. iTRAQ-based proteome profile analysis of superior and inferior Spikelets at early grain filling stage in japonica Rice. BMC PLANT BIOLOGY 2017; 17:100. [PMID: 28592253 PMCID: PMC5463490 DOI: 10.1186/s12870-017-1050-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 05/29/2017] [Indexed: 05/03/2023]
Abstract
BACKGROUND Large-panicle rice varieties often fail to achieve their yield potential due to poor grain filling of late-flowering inferior spikelets (IS). The physiological and molecular mechanisms of poor IS grain filling, and whether an increase in assimilate supply could regulate protein abundance and consequently improve IS grain filling for japonica rice with large panicles is still partially understood. RESULTS A field experiment was performed with two spikelet removal treatments at anthesis in the large-panicle japonica rice line W1844, including removal of the top 1/3 of spikelets (T1) and removal of the top 2/3 of spikelets (T2), with no spikelet removal as a control (T0). The size, weight, setting rate, and grain filling rate of IS were significantly increased after spikelet removing. The biological functions of the differentially expressed proteins (DEPs) between superior and inferior spikelets as well as the response of IS to the removal of superior spikelets (SS) were investigated by using iTRAQ at 10 days post anthesis. A total of 159, 87, and 28 DEPs were identified from group A (T0-SS/T0-IS), group B (T0-SS/T2-IS), and group C (T2-IS/T0-IS), respectively. Among these, 104, 63, and 22 proteins were up-regulated, and 55, 24, and 6 proteins were down-regulated, respectively. Approximately half of these DEPs were involved in carbohydrate metabolism (sucrose-to-starch metabolism and energy metabolism) and protein metabolism (protein synthesis, folding, degradation, and storage). CONCLUSIONS Reduced endosperm cell division and decreased activities of key enzymes associated with sucrose-starch metabolism and nitrogen metabolism are mainly attributed to the poor sink strength of IS. In addition, due to weakened photosynthesis and respiration, IS are unable to obtain a timely supply of materials and energy after fertilization, which might be resulted in the stagnation of IS development. Finally, an increased abundance of 14-3-3 protein in IS could be involved in the inhibition of starch synthesis. The removal of SS contributed to transfer of assimilates to IS and enhanced enzymatic activities of carbon metabolism (sucrose synthase, starch branching enzyme, soluble starch synthase, and pullulanase) and nitrogen metabolism (aspartate amino transferase and alanine amino transferase), promoting starch and protein synthesis in IS. In addition, improvements in energy metabolism (greater abundance of pyrophosphate-fructose 6-phosphate 1-phosphotransferase) might be played a vital role in inducing the initiation of grain filling. These results collectively demonstrate that carbohydrate supply is the main cause of poor IS grain filling.
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Affiliation(s)
- Cuicui You
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 People’s Republic of China
- College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095 People’s Republic of China
| | - Lin Chen
- College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095 People’s Republic of China
| | - Haibing He
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 People’s Republic of China
| | - Liquan Wu
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 People’s Republic of China
| | - Shaohua Wang
- College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095 People’s Republic of China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, 210095 People’s Republic of China
| | - Yanfeng Ding
- College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095 People’s Republic of China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, 210095 People’s Republic of China
| | - Chuanxi Ma
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 People’s Republic of China
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Cheng L, Wang Y, He Q, Li H, Zhang X, Zhang F. Comparative proteomics illustrates the complexity of drought resistance mechanisms in two wheat (Triticum aestivum L.) cultivars under dehydration and rehydration. BMC PLANT BIOLOGY 2016; 16:188. [PMID: 27576435 PMCID: PMC5006382 DOI: 10.1186/s12870-016-0871-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 08/10/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND Drought stress is one of the most adverse environmental constraints to plant growth and productivity. Comparative proteomics of drought-tolerant and sensitive wheat genotypes is a strategy to understand the complexity of molecular mechanism of wheat in response to drought. This study attempted to extend findings regarding the potential proteomic dynamics in wheat under drought stress and to enrich the research content of drought tolerance mechanism. RESULTS A comparative proteomics approach was applied to analyze proteome change of Xihan No. 2 (a drought-tolerant cultivar) and Longchun 23 (a drought-sensitive cultivar) subjected to a range of dehydration treatments (18 h, 24 h and 48 h) and rehydration treatment (R24 h) using 2-DE, respectively. Quantitative image analysis showed a total of 172 protein spots in Xihan No. 2 and 215 spots from Longchun 23 with their abundance significantly altered (p < 0.05) more than 2.5-fold. Out of these spots, a total of 84 and 64 differentially abundant proteins were identified by MALDI-TOF/TOF MS in Xihan No. 2 and Longchun 23, respectively. Most of these identified proteins were involved in metabolism, photosynthesis, defence and protein translation/processing/degradation in both two cultivars. In addition, the proteins involved in redox homeostasis, energy, transcription, cellular structure, signalling and transport were also identified. Furthermore, the comparative analysis of drought-responsive proteome allowed for the general elucidation of the major mechanisms associated with differential responses to drought of both two cultivars. These cellular processes work more cooperatively to re-establish homeostasis in Xihan No. 2 than Longchun 23. The resistance mechanisms of Xihan No. 2 mainly included changes in the metabolism of carbohydrates and amino acids as well as in the activation of more antioxidation and defense systems and in the levels of proteins involved in ATP synthesis and protein degradation/refolding. CONCLUSIONS This study revealed that the levels of a number of proteins involved in various cellular processes were affected by drought stress in two wheat cultivars with different drought tolerance. The results showed that there exist specific responses to drought in Xihan No. 2 and Longchun 23. The proposed hypothetical model would explain the interaction of these identified proteins that are associated with drought-responses in two cultivars, and help in developing strategies to improve drought tolerance in wheat.
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Affiliation(s)
- Lixiang Cheng
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Research & Testing Center, Gansu Agricultural University, Lanzhou, China
| | - Yuping Wang
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Research & Testing Center, Gansu Agricultural University, Lanzhou, China
| | - Qiang He
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Research & Testing Center, Gansu Agricultural University, Lanzhou, China
| | - Huijun Li
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Research & Testing Center, Gansu Agricultural University, Lanzhou, China
- Wuwei Agricultural and Animal Husbandry Bureau, Wuwei, China
| | - Xiaojing Zhang
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Research & Testing Center, Gansu Agricultural University, Lanzhou, China
- Gansu Dingxi Academy of Agricultural Science, Dingxi, China
| | - Feng Zhang
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Research & Testing Center, Gansu Agricultural University, Lanzhou, China
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15
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Igamberdiev AU, Eprintsev AT. Organic Acids: The Pools of Fixed Carbon Involved in Redox Regulation and Energy Balance in Higher Plants. FRONTIERS IN PLANT SCIENCE 2016; 7:1042. [PMID: 27471516 PMCID: PMC4945632 DOI: 10.3389/fpls.2016.01042] [Citation(s) in RCA: 185] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 07/04/2016] [Indexed: 05/18/2023]
Abstract
Organic acids are synthesized in plants as a result of the incomplete oxidation of photosynthetic products and represent the stored pools of fixed carbon accumulated due to different transient times of conversion of carbon compounds in metabolic pathways. When redox level in the cell increases, e.g., in conditions of active photosynthesis, the tricarboxylic acid (TCA) cycle in mitochondria is transformed to a partial cycle supplying citrate for the synthesis of 2-oxoglutarate and glutamate (citrate valve), while malate is accumulated and participates in the redox balance in different cell compartments (via malate valve). This results in malate and citrate frequently being the most accumulated acids in plants. However, the intensity of reactions linked to the conversion of these compounds can cause preferential accumulation of other organic acids, e.g., fumarate or isocitrate, in higher concentrations than malate and citrate. The secondary reactions, associated with the central metabolic pathways, in particularly with the TCA cycle, result in accumulation of other organic acids that are derived from the intermediates of the cycle. They form the additional pools of fixed carbon and stabilize the TCA cycle. Trans-aconitate is formed from citrate or cis-aconitate, accumulation of hydroxycitrate can be linked to metabolism of 2-oxoglutarate, while 4-hydroxy-2-oxoglutarate can be formed from pyruvate and glyoxylate. Glyoxylate, a product of either glycolate oxidase or isocitrate lyase, can be converted to oxalate. Malonate is accumulated at high concentrations in legume plants. Organic acids play a role in plants in providing redox equilibrium, supporting ionic gradients on membranes, and acidification of the extracellular medium.
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Affiliation(s)
- Abir U. Igamberdiev
- Department of Biology, Memorial University of Newfoundland, St. John’sNL, Canada
- *Correspondence: Abir U. Igamberdiev,
| | - Alexander T. Eprintsev
- Department of Biochemistry and Cell Physiology, Voronezh State UniversityVoronezh, Russia
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16
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Tereshina EV, Laskavy VN, Ivanenko SI. Four components of the conjugated redox system in organisms: Carbon, nitrogen, sulfur, oxygen. BIOCHEMISTRY (MOSCOW) 2015; 80:1186-200. [DOI: 10.1134/s0006297915090096] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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17
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Shingaki-Wells R, Millar AH, Whelan J, Narsai R. What happens to plant mitochondria under low oxygen? An omics review of the responses to low oxygen and reoxygenation. PLANT, CELL & ENVIRONMENT 2014; 37:2260-77. [PMID: 24575773 DOI: 10.1111/pce.12312] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 02/09/2014] [Accepted: 02/16/2014] [Indexed: 05/19/2023]
Abstract
Floods can rapidly submerge plants, limiting oxygen to the extent that oxidative phosphorylation no longer generates adequate ATP supplies. Low-oxygen tolerant plants, such as rice, are able to adequately respond to low oxygen by successfully remodelling primary and mitochondrial metabolism to partially counteract the energy crisis that ensues. In this review, we discuss how plants respond to low-oxygen stress at the transcriptomic, proteomic, metabolomic and enzyme activity levels, particularly focusing on mitochondria and interacting pathways. The role of reactive oxygen species and nitrite as an alternative electron acceptor as well as their links to respiratory chain components is discussed. By making intra-kingdom as well as cross-kingdom comparisons, conserved mechanisms of anoxia tolerance are highlighted as well as tolerance mechanisms that are specific to anoxia-tolerant rice during germination and in coleoptiles. We discuss reoxygenation as an often overlooked, yet essential stage of this environmental stress and consider the possibility that changes occurring during low oxygen may also provide benefits upon re-aeration. Finally, we consider what it takes to be low-oxygen tolerant and argue that alternative mechanisms of ATP production, glucose signalling, starch/sucrose signalling as well as reverse metabolism of fermentation end products promote the survival of rice after this debilitating stress.
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Affiliation(s)
- Rachel Shingaki-Wells
- ARC Centre of Excellence in Plant Energy Biology, Bayliss Building University of Western Australia, Crawley, Western Australia, 6009, Australia
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18
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Schertl P, Braun HP. Respiratory electron transfer pathways in plant mitochondria. FRONTIERS IN PLANT SCIENCE 2014; 5:163. [PMID: 24808901 PMCID: PMC4010797 DOI: 10.3389/fpls.2014.00163] [Citation(s) in RCA: 155] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 04/07/2014] [Indexed: 05/18/2023]
Abstract
The respiratory electron transport chain (ETC) couples electron transfer from organic substrates onto molecular oxygen with proton translocation across the inner mitochondrial membrane. The resulting proton gradient is used by the ATP synthase complex for ATP formation. In plants, the ETC is especially intricate. Besides the "classical" oxidoreductase complexes (complex I-IV) and the mobile electron transporters cytochrome c and ubiquinone, it comprises numerous "alternative oxidoreductases." Furthermore, several dehydrogenases localized in the mitochondrial matrix and the mitochondrial intermembrane space directly or indirectly provide electrons for the ETC. Entry of electrons into the system occurs via numerous pathways which are dynamically regulated in response to the metabolic state of a plant cell as well as environmental factors. This mini review aims to summarize recent findings on respiratory electron transfer pathways in plants and on the involved components and supramolecular assemblies.
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Affiliation(s)
| | - Hans-Peter Braun
- Abteilung Pflanzenproteomik, Institut für Pflanzengenetik, Leibniz Universität HannoverHannover, Germany
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19
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Chen CJ, Lai CC, Tseng MC, Liu YC, Liu YH, Chiou LW, Tsai FJ. A novel titanium dioxide-polydimethylsiloxane plate for phosphopeptide enrichment and mass spectrometry analysis. Anal Chim Acta 2014; 812:105-13. [DOI: 10.1016/j.aca.2014.01.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 12/25/2013] [Accepted: 01/06/2014] [Indexed: 01/01/2023]
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20
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Yoshida K, Noguchi K, Motohashi K, Hisabori T. Systematic Exploration of Thioredoxin Target Proteins in Plant Mitochondria. ACTA ACUST UNITED AC 2013; 54:875-92. [DOI: 10.1093/pcp/pct037] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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21
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Havelund JF, Thelen JJ, Møller IM. Biochemistry, proteomics, and phosphoproteomics of plant mitochondria from non-photosynthetic cells. FRONTIERS IN PLANT SCIENCE 2013; 4:51. [PMID: 23494127 PMCID: PMC3595712 DOI: 10.3389/fpls.2013.00051] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 02/26/2013] [Indexed: 05/24/2023]
Abstract
Mitochondria fulfill some basic roles in all plant cells. They supply the cell with energy in the form of ATP and reducing equivalents [NAD(P)H] and they provide the cell with intermediates for a range of biosynthetic pathways. In addition to this, mitochondria contribute to a number of specialized functions depending on the tissue and cell type, as well as environmental conditions. We will here review the biochemistry and proteomics of mitochondria from non-green cells and organs, which differ from those of photosynthetic organs in a number of respects. We will briefly cover purification of mitochondria and general biochemical properties such as oxidative phosphorylation. We will then mention a few adaptive properties in response to water stress, seed maturation and germination, and the ability to function under hypoxic conditions. The discussion will mainly focus on Arabidopsis cell cultures, etiolated germinating rice seedlings and potato tubers as model plants. It will cover the general proteome as well as the posttranslational modification protein phosphorylation. To date 64 phosphorylated mitochondrial proteins with a total of 103 phosphorylation sites have been identified.
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Affiliation(s)
- Jesper F. Havelund
- Department of Molecular Biology and Genetics, Science and Technology, Aarhus UniversitySlagelse, Denmark
| | - Jay J. Thelen
- Department of Biochemistry and Interdisciplinary Plant Group, University of Missouri-ColumbiaColumbia, MO, USA
| | - Ian M. Møller
- Department of Molecular Biology and Genetics, Science and Technology, Aarhus UniversitySlagelse, Denmark
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22
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Dahal D, Mooney BP, Newton KJ. Specific changes in total and mitochondrial proteomes are associated with higher levels of heterosis in maize hybrids. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 72:70-83. [PMID: 22607058 DOI: 10.1111/j.1365-313x.2012.05056.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The phenomenon of hybrid vigor (heterosis) has long been harnessed by plant breeders to improve world food production. However, the changes that are essential for heterotic responses and the mechanisms responsible for heterosis remain undefined. Large increases in biomass and yield in high-heterosis hybrids suggest that alterations in bioenergetic processes may contribute to heterosis. Progeny from crosses between various inbred lines vary in the extent of vigor observed. Field-grown maize F₁ hybrids that consistently exhibited either low or high heterosis across a variety of environments were examined for changes in proteins that may be correlated with increased plant vigor and yield. Unpollinated ears at the time of flowering (ear shoots) were selected for the studies because they are metabolically active, rich in mitochondria, and the sizes of the ears are diagnostic of yield heterosis. Total protein and mitochondrial proteomes were compared among low- and higher-heterosis hybrids. Two-dimensional difference gel electrophoresis was used to identify allelic and/or isoform differences linked to heterosis. Identification of differentially regulated spots by mass spectrometry revealed proteins involved in stress responses as well as primary carbon and protein metabolism. Many of these proteins were identified in multiple spots, but analysis of their abundances by label-free mass spectrometry suggested that most of the expression differences were due to isoform variation rather than overall protein amount. Thus, our proteomics studies suggest that expression of specific alleles and/or post-translational modification of specific proteins correlate with higher levels of heterosis.
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Affiliation(s)
- Diwakar Dahal
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
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23
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Ahsan N, Swatek KN, Zhang J, Miernyk JA, Xu D, Thelen JJ. "Scanning mutagenesis" of the amino acid sequences flanking phosphorylation site 1 of the mitochondrial pyruvate dehydrogenase complex. FRONTIERS IN PLANT SCIENCE 2012; 3:153. [PMID: 22811682 PMCID: PMC3397410 DOI: 10.3389/fpls.2012.00153] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 06/19/2012] [Indexed: 06/01/2023]
Abstract
The mitochondrial pyruvate dehydrogenase complex (mtPDC) is regulated by reversible seryl-phosphorylation of the E1α subunit by a dedicated, intrinsic kinase. The phospho-complex is reactivated when dephosphorylated by an intrinsic PP2C-type protein phosphatase. Both the position of the phosphorylated Ser-residue and the sequences of the flanking amino acids are highly conserved. We have used the synthetic peptide-based kinase client (KiC) assay plus recombinant pyruvate dehydrogenase E1α and E1α-kinase to perform "scanning mutagenesis" of the residues flanking the site of phosphorylation. Consistent with the results from "phylogenetic analysis" of the flanking sequences, the direct peptide-based kinase assays tolerated very few changes. Even conservative changes such as Leu, Ile, or Val for Met, or Glu for Asp, gave very marked reductions in phosphorylation. Overall the results indicate that regulation of the mtPDC by reversible phosphorylation is an extreme example of multiple, interdependent instances of co-evolution.
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Affiliation(s)
- Nagib Ahsan
- Department of Biochemistry, University of MissouriColumbia, MO, USA
- Interdisciplinary Plant Group, University of MissouriColumbia, MO, USA
| | - Kirby N. Swatek
- Department of Biochemistry, University of MissouriColumbia, MO, USA
- Interdisciplinary Plant Group, University of MissouriColumbia, MO, USA
| | - Jingfen Zhang
- Interdisciplinary Plant Group, University of MissouriColumbia, MO, USA
- Department of Computer Science, University of MissouriColumbia, MO, USA
| | - Ján A. Miernyk
- Department of Biochemistry, University of MissouriColumbia, MO, USA
- Interdisciplinary Plant Group, University of MissouriColumbia, MO, USA
- Plant Genetics Research Unit, USDA, Agricultural Research Service, University of MissouriColumbia, MO, USA
| | - Dong Xu
- Interdisciplinary Plant Group, University of MissouriColumbia, MO, USA
- Department of Computer Science, University of MissouriColumbia, MO, USA
| | - Jay J. Thelen
- Department of Biochemistry, University of MissouriColumbia, MO, USA
- Interdisciplinary Plant Group, University of MissouriColumbia, MO, USA
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24
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Klodmann J, Senkler M, Rode C, Braun HP. Defining the protein complex proteome of plant mitochondria. PLANT PHYSIOLOGY 2011; 157:587-98. [PMID: 21841088 PMCID: PMC3192552 DOI: 10.1104/pp.111.182352] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Accepted: 08/10/2011] [Indexed: 05/18/2023]
Abstract
A classical approach, protein separation by two-dimensional blue native/sodium dodecyl sulfate-polyacrylamide gel electrophoresis, was combined with tandem mass spectrometry and up-to-date computer technology to characterize the mitochondrial "protein complex proteome" of Arabidopsis (Arabidopsis thaliana) in so far unrivaled depth. We further developed the novel GelMap software package to annotate and evaluate two-dimensional blue native/sodium dodecyl sulfate gels. The software allows (1) annotation of proteins according to functional and structural correlations (e.g. subunits of a distinct protein complex), (2) assignment of comprehensive protein identification lists to individual gel spots, and thereby (3) selective display of protein complexes of low abundance. In total, 471 distinct proteins were identified by mass spectrometry, several of which form part of at least 35 different mitochondrial protein complexes. To our knowledge, numerous protein complexes were described for the first time (e.g. complexes including pentatricopeptide repeat proteins involved in nucleic acid metabolism). Discovery of further protein complexes within our data set is open to everybody via the public GelMap portal at www.gelmap.de/arabidopsis_mito.
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25
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Komatsu S, Yamamoto A, Nakamura T, Nouri MZ, Nanjo Y, Nishizawa K, Furukawa K. Comprehensive analysis of mitochondria in roots and hypocotyls of soybean under flooding stress using proteomics and metabolomics techniques. J Proteome Res 2011; 10:3993-4004. [PMID: 21766870 DOI: 10.1021/pr2001918] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Flooding is a serious problem for soybeans because it reduces growth and grain yield. Proteomic and metabolomic techniques were used to examine whether mitochondrial function is altered in soybeans by flooding stress. Mitochondrial fractions were purified from the roots and hypocotyls of 4-day-old soybean seedlings that had been flooded for 2 days. Mitochondrial matrix and membrane proteins were separated by two-dimensional polyacrylamide gel electrophoresis and blue-native polyacrylamide gel electrophoresis, respectively. Differentially expressed proteins and metabolites were identified using mass spectrometry. Proteins and metabolites related to the tricarboxylic acid cycle and γ-amino butyrate shunt were up-regulated by flooding stress, while inner membrane carrier proteins and proteins related to complexes III, IV, and V of the electron transport chains were down-regulated. The amounts of NADH and NAD were increased; however, ATP was significantly decreased by flooding stress. These results suggest that flooding directly impairs electron transport chains, although NADH production increases in the mitochondria through the tricarboxylic acid cycle.
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Affiliation(s)
- Setsuko Komatsu
- National Institute of Crop Science, Tsukuba 305-8518, Japan.
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Wojtasik W, Kulma A, Kostyn K, Szopa J. The changes in pectin metabolism in flax infected with Fusarium. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2011; 49:862-872. [PMID: 21435891 DOI: 10.1016/j.plaphy.2011.03.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Accepted: 02/27/2011] [Indexed: 05/30/2023]
Abstract
Fusarium culmorum and Fusarium oxysporum are the most common fungal pathogens of flax (Linum usitatissimum L.), thus leading to the greatest losses in crop yield. A subtractive cDNA library was constructed from flax seedlings exposed for two days to F. oxysporum. This revealed a set of genes that are potentially involved in the flax defense responses. Two of those genes directly participate in cell wall sugar polymer metabolism: UDP-D-glucuronate 4-epimerase (GAE; EC 5.1.3.6) and formate dehydrogenase (FDH; EC 1.2.1.2). GAE delivers the main substrate for pectin biosynthesis, and decreases were detected in its mRNA level after Fusarium infection. FDH participates in the metabolism of formic acid, and the expression level of its gene increased after Fusarium infection. However, metabolite profiling analysis disclosed that the pectin content in the infected plants remained unchanged, but that there were reductions in both the levels of the soluble sugars that serve as pectin precursors, and in the level of formic acid. Since formic acid is the product of pectin demethylesterification, the level of mRNAs coding for pectin methylesterase (EC 3.1.1.11) in the infected flax was measured, revealing a decrease in its expression upon plant infection. Transgenic flax plants overexpressing fungal polygalacturonase (EC 3.2.1.15) and rhamnogalacturonase (EC 3.2.1.-) showed a decrease in the pectin content and an elevated level of formic acid, but the level of expression of the FDH gene remained unchanged. It is suspected that the expression of the formate dehydrogenase gene is directly controlled by the pathogen in the early stage of infection, and additionally by pectin degradation in the later stages.
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Affiliation(s)
- Wioleta Wojtasik
- Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland
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Lee CP, Eubel H, O'Toole N, Millar AH. Combining proteomics of root and shoot mitochondria and transcript analysis to define constitutive and variable components in plant mitochondria. PHYTOCHEMISTRY 2011; 72:1092-108. [PMID: 21296373 DOI: 10.1016/j.phytochem.2010.12.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Revised: 10/28/2010] [Accepted: 12/03/2010] [Indexed: 05/08/2023]
Abstract
Mitochondria undertake respiration in plant cells, but through metabolic plasticity utilize differ proportions of substrates and deliver different proportions of products to cellular metabolic and biosynthetic pathways. In Arabidopsis the mitochondrial proteome from shoots and cell culture have been reported, but there has been little information on mitochondria in roots. We compare the root mitochondrial proteome with mitochondria isolated from photosynthetic shoots to define the role of protein abundance in these differences. The major differences observed were in the abundance and/or activities of enzymes in the TCA cycle and the mitochondrial enzymes involved in photorespiration. Metabolic pathways linked to TCA cycle and photorespiration were also altered, namely cysteine, formate and one-carbon metabolism, as well as amino acid metabolism focused on 2-oxoglutarate generation. Comparisons to microarray analysis of these same tissues showed a positive correlation between mRNA and mitochondrial protein abundance, but still ample evidence for the role of post-transcriptional processes in defining mitochondrial composition. Broader comparisons of transcript abundances for mitochondrial components across Arabidopsis tissues provided additional evidence for specialization of plant mitochondria, and clustering of these data in functional groups showed the constitutive vs variably expressed components of plant mitochondria.
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Affiliation(s)
- Chun Pong Lee
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
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28
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Hirani TA, Tovar-Méndez A, Miernyk JA, Randall DD. Asp295 stabilizes the active-site loop structure of pyruvate dehydrogenase, facilitating phosphorylation of ser292 by pyruvate dehydrogenase-kinase. Enzyme Res 2011; 2011:939068. [PMID: 21318135 PMCID: PMC3034952 DOI: 10.4061/2011/939068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Accepted: 11/05/2010] [Indexed: 01/22/2023] Open
Abstract
We have developed an in vitro system for detailed analysis of reversible phosphorylation of the plant mitochondrial pyruvate dehydrogenase complex, comprising recombinant Arabidopsis thalianaα2β2-heterotetrameric pyruvate dehydrogenase (E1) plus A. thaliana E1-kinase (AtPDK). Upon addition of MgATP, Ser292, which is located within the active-site loop structure of E1α, is phosphorylated. In addition to Ser292, Asp295 and Gly297 are highly conserved in the E1α active-site loop sequences. Mutation of Asp295 to Ala, Asn, or Leu greatly reduced phosphorylation of Ser292, while mutation of Gly297 had relatively little effect. Quantitative two-hybrid analysis was used to show that mutation of Asp295 did not substantially affect binding of AtPDK to E1α. When using pyruvate as a variable substrate, the Asp295 mutant proteins had modest changes in kcat, Km, and kcat/Km values. Therefore, we propose that Asp295 plays an important role in stabilizing the active-site loop structure, facilitating transfer of the γ-phosphate from ATP to the Ser residue at regulatory site one of E1α.
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Affiliation(s)
- Tripty A Hirani
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
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29
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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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30
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David P, des Francs-Small CC, Sévignac M, Thareau V, Macadré C, Langin T, Geffroy V. Three highly similar formate dehydrogenase genes located in the vicinity of the B4 resistance gene cluster are differentially expressed under biotic and abiotic stresses in Phaseolus vulgaris. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 121:87-103. [PMID: 20182695 DOI: 10.1007/s00122-010-1293-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2009] [Accepted: 01/28/2010] [Indexed: 05/06/2023]
Abstract
In higher plants, formate dehydrogenase (FDH, EC1.2.1.2.) catalyzes the NAD-linked oxidation of formate to CO(2), and FDH transcript accumulation has been reported after various abiotic stresses. By sequencing a Phaseolus vulgaris BAC clone encompassing a CC-NBS-LRR gene rich region of the B4 resistance gene cluster, we identified three FDH-encoding genes. FDH is present as a single copy gene in the Arabidopsis thaliana genome, and public database searches confirm that FDH is a low copy gene in plant genomes, since only 33 FDH homologs were identified from 27 plant species. Three independent prediction programs (Predotar, TargetP and Mitoprot) used on this large subset of 33 plant FDHs, revealed that mitochondrial localization of FDH might be the rule in higher plants. A phylogenetic analysis suggests a scenario of local FDH gene duplication in an ancestor of the Phaseoleae followed by another more recent duplication event after bean/soybean divergence. The expression levels of two common bean FDH genes under different treatments were investigated by quantitative RT-PCR analysis. FDH genes are differentially up-regulated after biotic and abiotic stresses (infection with the fungus Colletotrichum lindemuthianum, and dark treatment, respectively). The present study provides the first report of FDH transcript accumulation after biotic stress, suggesting the involvement of FDH in the pathogen resistance process.
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Affiliation(s)
- Perrine David
- Institut de Biotechnologie des Plantes, UMR-CNRS 8618, bât. 630, Université Paris-Sud, 91405, Orsay, France
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31
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Ito J, Taylor NL, Castleden I, Weckwerth W, Millar AH, Heazlewood JL. A survey of the Arabidopsis thaliana mitochondrial phosphoproteome. Proteomics 2009; 9:4229-40. [PMID: 19688752 DOI: 10.1002/pmic.200900064] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Plant mitochondria play central roles in cellular energy production, metabolism and stress responses. Recent phosphoproteomic studies in mammalian and yeast mitochondria have presented evidence indicating that protein phosphorylation is a likely regulatory mechanism across a broad range of important mitochondrial processes. This study investigated protein phosphorylation in purified mitochondria from cell suspensions of the model plant Arabidopsis thaliana using affinity enrichment and proteomic tools. Eighteen putative phosphoproteins consisting of mitochondrial metabolic enzymes, HSPs, a protease and several proteins of unknown function were detected on 2-DE separations of Arabidopsis mitochondrial proteins and affinity-enriched phosphoproteins using the Pro-Q Diamond phospho-specific in-gel dye. Comparisons with mitochondrial phosphoproteomes of yeast and mouse indicate that these three species share few validated phosphoproteins. Phosphorylation sites for seven of the eighteen mitochondrial proteins were characterized by titanium dioxide enrichment and MS/MS. In the process, 71 phosphopeptides from Arabidopsis proteins which are not present in mitochondria but found as contaminants in various types of mitochondrial preparations were also identified, indicating the low level of phosphorylation of mitochondrial components compared with other cellular components in Arabidopsis. Information gained from this study provides a better understanding of protein phosphorylation at both the subcellular and the cellular level in Arabidopsis.
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Affiliation(s)
- Jun Ito
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Western Australia, Australia
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32
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Abstract
A major scientific challenge at the present time for cancer research is the determination of the underlying biological basis for cancer development. It is further complicated by the heterogeneity of cancer's origin. Understanding the molecular basis of cancer requires studying the dynamic and spatial interactions among proteins in cells, signaling events among cancer cells, and interactions between the cancer cells and the tumor microenvironment. Recently, it has been proposed that large-scale protein expression analysis of cancer cell proteomes promises to be valuable for investigating mechanisms of cancer transformation. Advances in mass spectrometry technologies and bioinformatics tools provide a tremendous opportunity to qualitatively and quantitatively interrogate dynamic protein-protein interactions and differential regulation of cellular signaling pathways associated with tumor development. In this review, progress in shotgun proteomics technologies for examining the molecular basis of cancer development will be presented and discussed.
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Affiliation(s)
- Emily I Chen
- Department of Cell Biology, 10550 North Torrey Pines Road, SR11, The Scripps Research Institute, La Jolla, CA 92037, USA
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Abstract
The term 'Proteomics' was introduced in 1997 to describe a growing interest in the study of the proteome - the expressed protein set of an organism. As this new discipline evolved, it quickly became obvious that proteomics would be a very complex and ambitious undertaking, perhaps even more so than genomics, which had engendered it. New techniques for both the separation and analysis/identification of proteins were emerging or being refined, and these facilitated the development of this new field. Many proteomics experiments are now routine in some laboratories. In this chapter we describe a typical proteomics experiment, using examples from our laboratory: the separation of complex mixtures of proteins by 2-dimensional electrophoresis and subsequent identification of a protein spot by mass spectrometry with two commonly used instruments: MALDI-QqTOF and ESI-ion trap.
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34
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Andreadeli A, Flemetakis E, Axarli I, Dimou M, Udvardi MK, Katinakis P, Labrou NE. Cloning and characterization of Lotus japonicus formate dehydrogenase: a possible correlation with hypoxia. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:976-84. [PMID: 19281876 DOI: 10.1016/j.bbapap.2009.02.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2008] [Revised: 02/12/2009] [Accepted: 02/13/2009] [Indexed: 10/21/2022]
Abstract
Formate dehydrogenases (FDHs, EC 1.2.1.2) comprise a group of enzymes found in both prokaryotes and eukaryotes that catalyse the oxidation of formate to CO(2). FDH1 from the model legume Lotus japonicus (LjFDH1) was cloned and expressed in E. coli BL21(DE3) as soluble active protein. The enzyme was purified using affinity chromatography on Cibacron blue 3GA-Sepharose. The enzymatic properties of the recombinant enzyme were investigated and the kinetic parameters (K(m), k(cat)) for a number of substrates were determined. Molecular modelling studies were also employed to create a model of LjFDH1, based on the known structure of the Pseudomonas sp. 101 enzyme. The molecular model was used to help interpret biochemical data concerning substrate specificity and catalytic mechanism of the enzyme. The temporal expression pattern of LjFDH1 gene was studied by real-time RT-PCR in various plant organs and during the development of nitrogen-fixing nodules. Furthermore, the spatial transcript accumulation during nodule development and in young seedpods was determined by in situ RNA-RNA hybridization. These results considered together indicate a possible role of formate oxidation by LjFDH1 in plant tissues characterized by relative hypoxia.
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Affiliation(s)
- A Andreadeli
- Department of Agricultural Biotechnology, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
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35
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Igamberdiev AU, Hill RD. Plant mitochondrial function during anaerobiosis. ANNALS OF BOTANY 2009; 103:259-68. [PMID: 18586697 PMCID: PMC2707300 DOI: 10.1093/aob/mcn100] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2008] [Revised: 04/29/2008] [Accepted: 05/21/2008] [Indexed: 05/17/2023]
Abstract
BACKGROUND Under hypoxic conditions, plant mitochondria preserve the capacity to oxidize external NADH, NADPH and tricarboxylic acid cycle substrates. Nitrite serves as an alternative electron acceptor at the level of cytochrome oxidase, with possibly complex III and the alternative oxidase also being involved. Nitric oxide is a significant product of the reaction, which has a high affinity for cytochrome c oxidase, inhibiting it. The excess NO is scavenged by hypoxically induced class 1 haemoglobin in the reaction involving ascorbate. SCOPE By using nitrite, mitochondria retain a limited capacity for ATP synthesis. NADH, produced from glycolysis during anaerobiosis and oxidized in the mitochondrial electron transport chain, should shift the composition of metabolites formed during anaerobiosis with increased conversion of pyruvate to alanine and greater involvement of other transamination reactions, such as those involving gamma-aminobutyric acid formation. CONCLUSIONS Anaerobic mitochondrial metabolism may have a more significant role than previously thought in alleviating the effects of anoxia on plant cells. There is a need to re-examine mitochondrial carbon and nitrogen metabolism under anoxia to establish the extent of this involvement.
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Affiliation(s)
- Abir U. Igamberdiev
- Department of Biology, Memorial University of Newfoundland, St John's, NL, Canada, A1B 3X9
| | - Robert D. Hill
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada, R3T 2N2
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36
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Lee CP, Eubel H, O'Toole N, Millar AH. Heterogeneity of the Mitochondrial Proteome for Photosynthetic and Non-photosynthetic Arabidopsis Metabolism. Mol Cell Proteomics 2008; 7:1297-316. [DOI: 10.1074/mcp.m700535-mcp200] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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37
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Krause F. Detection and analysis of protein–protein interactions in organellar and prokaryotic proteomes by native gel electrophoresis: (Membrane) protein complexes and supercomplexes. Electrophoresis 2006; 27:2759-81. [PMID: 16817166 DOI: 10.1002/elps.200600049] [Citation(s) in RCA: 144] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
It is an essential and challenging task to unravel protein-protein interactions in their actual in vivo context. Native gel systems provide a separation platform allowing the analysis of protein complexes on a rather proteome-wide scale in a single experiment. This review focus on blue-native (BN)-PAGE as the most versatile and successful gel-based approach to separate soluble and membrane protein complexes of intricate protein mixtures derived from all biological sources. BN-PAGE is a charge-shift method with a running pH of 7.5 relying on the gentle binding of anionic CBB dye to all membrane and many soluble protein complexes, leading to separation of protein species essentially according to their size and superior resolution than other fractionation techniques can offer. The closely related colorless-native (CN)-PAGE, whose applicability is restricted to protein species with intrinsic negative net charge, proved to provide an especially mild separation capable of preserving weak protein-protein interactions better than BN-PAGE. The essential conditions determining the success of detecting protein-protein interactions are the sample preparations, e.g. the efficiency/mildness of the detergent solubilization of membrane protein complexes. A broad overview about the achievements of BN- and CN-PAGE studies to elucidate protein-protein interactions in organelles and prokaryotes is presented, e.g. the mitochondrial protein import machinery and oxidative phosphorylation supercomplexes. In many cases, solubilization with digitonin was demonstrated to facilitate an efficient and particularly gentle extraction of membrane protein complexes prone to dissociation by treatment with other detergents. In general, analyses of protein interactomes should be carried out by both BN- and CN-PAGE.
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Affiliation(s)
- Frank Krause
- Department of Chemistry, Physical Biochemistry, Darmstadt University of Technology, Germany.
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38
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Hopper RK, Carroll S, Aponte AM, Johnson DT, French S, Shen RF, Witzmann FA, Harris RA, Balaban RS. Mitochondrial matrix phosphoproteome: effect of extra mitochondrial calcium. Biochemistry 2006; 45:2524-36. [PMID: 16489745 PMCID: PMC1415274 DOI: 10.1021/bi052475e] [Citation(s) in RCA: 204] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Post-translational modification of mitochondrial proteins by phosphorylation or dephosphorylation plays an essential role in numerous cell signaling pathways involved in regulating energy metabolism and in mitochondrion-induced apoptosis. Here we present a phosphoproteomic screen of the mitochondrial matrix proteins and begin to establish the protein phosphorylations acutely associated with calcium ions (Ca(2+)) signaling in porcine heart mitochondria. Forty-five phosphorylated proteins were detected by gel electrophoresis-mass spectrometry of Pro-Q Diamond staining, while many more Pro-Q Diamond-stained proteins evaded mass spectrometry detection. Time-dependent (32)P incorporation in intact mitochondria confirmed the extensive matrix protein phosphoryation and revealed the dynamic nature of this process. Classes of proteins that were detected included all of the mitochondrial respiratory chain complexes, as well as enzymes involved in intermediary metabolism, such as pyruvate dehydrogenase (PDH), citrate synthase, and acyl-CoA dehydrogenases. These data demonstrate that the phosphoproteome of the mitochondrial matrix is extensive and dynamic. Ca(2+) has previously been shown to activate various dehydrogenases, promote the generation of reactive oxygen species (ROS), and initiate apoptosis via cytochrome c release. To evaluate the Ca(2+) signaling network, the effects of a Ca(2+) challenge sufficient to release cytochrome c were evaluated on the mitochondrial phosphoproteome. Novel Ca(2+)-induced dephosphorylation was observed in manganese superoxide dismutase (MnSOD) as well as the previously characterized PDH. A Ca(2+) dose-dependent dephosphorylation of MnSOD was associated with an approximately 2-fold maximum increase in activity; neither the dephosphorylation nor activity changes were induced by ROS production in the absence of Ca(2+). These data demonstrate the use of a phosphoproteome screen in determining mitochondrial signaling pathways and reveal new pathways for Ca(2+) modification of mitochondrial function at the level of MnSOD.
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Affiliation(s)
- Rachel K. Hopper
- From the Laboratory of Cardiac Energetics, National Heart Lung and Blood Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, 20892
| | - Stefanie Carroll
- From the Laboratory of Cardiac Energetics, National Heart Lung and Blood Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, 20892
| | - Angel M. Aponte
- From the Proteomics Core Facility, National Heart Lung and Blood Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, 20892
| | - D. Thor Johnson
- From the Department of Biochemisty and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, 46202-2111
| | - Stephanie French
- From the Laboratory of Cardiac Energetics, National Heart Lung and Blood Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, 20892
| | - Rong-Fong Shen
- From the Proteomics Core Facility, National Heart Lung and Blood Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, 20892
| | - Frank A. Witzmann
- From the Department of Biochemisty and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, 46202-2111
| | - Robert A. Harris
- From the Department of Biochemisty and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, 46202-2111
| | - Robert S. Balaban
- From the Laboratory of Cardiac Energetics, National Heart Lung and Blood Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, 20892
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Singh J, Kumar D, Ramakrishnan N, Singhal V, Jervis J, Garst JF, Slaughter SM, DeSantis AM, Potts M, Helm RF. Transcriptional response of Saccharomyces cerevisiae to desiccation and rehydration. Appl Environ Microbiol 2006; 71:8752-63. [PMID: 16332871 PMCID: PMC1317403 DOI: 10.1128/aem.71.12.8752-8763.2005] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A transcriptional analysis of the response of Saccharomyces cerevisiae strain BY4743 to controlled air-drying (desiccation) and subsequent rehydration under minimal glucose conditions was performed. Expression of genes involved in fatty acid oxidation and the glyoxylate cycle was observed to increase during drying and remained in this state during the rehydration phase. When the BY4743 expression profile for the dried sample was compared to that of a commercially prepared dry active yeast, strikingly similar expression changes were observed. The fact that these two samples, dried by different means, possessed very similar transcriptional profiles supports the hypothesis that the response to desiccation is a coordinated event independent of the particular conditions involved in water removal. Similarities between "stationary-phase-essential genes" and those upregulated during desiccation were also noted, suggesting commonalities in different routes to reduced metabolic states. Trends in extracellular and intracellular glucose and trehalose levels suggested that the cells were in a "holding pattern" during the rehydration phase, a concept that was reinforced by cell cycle analyses. Application of a "redescription mining" algorithm suggested that sulfur metabolism is important for cell survival during desiccation and rehydration.
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Affiliation(s)
- Jatinder Singh
- Virginia Tech Center for Genomics, Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
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40
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Møller IM, Kristensen BK. Protein oxidation in plant mitochondria detected as oxidized tryptophan. Free Radic Biol Med 2006; 40:430-5. [PMID: 16443157 DOI: 10.1016/j.freeradbiomed.2005.08.036] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2005] [Revised: 08/20/2005] [Accepted: 08/22/2005] [Indexed: 12/28/2022]
Abstract
The formation of N-formylkynurenine by dioxygenation of tryptophan was detected in peptides from rice leaf and potato tuber mitochondria. Proteins in matrix and membrane fractions were separated by two-dimensional gel electrophoresis and identified using a Q-TOF mass spectrometer. N-Formylkynurenine was detected in 29 peptides representing 17 different proteins. With one exception, the oxidation-sensitive aconitase, all of these proteins were either redox active themselves or subunits in redox-active enzyme complexes. The same site was modified in (i) several adjacent spots containing the P protein of the glycine decarboxylase complex, (ii) two different isoforms of the mitochondrial processing peptidase in complex III, and (iii) the same tryptophan residues in Mn-superoxide dismutase in both rice and potato mitochondria. This indicates that Trp oxidation is a selective process.
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Affiliation(s)
- Ian M Møller
- Department of Agricultural Sciences, The Royal Veterinary and Agricultural University, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark.
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41
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Pagliarini DJ, Dixon JE. Mitochondrial modulation: reversible phosphorylation takes center stage? Trends Biochem Sci 2006; 31:26-34. [PMID: 16337125 DOI: 10.1016/j.tibs.2005.11.005] [Citation(s) in RCA: 197] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2005] [Revised: 10/07/2005] [Accepted: 11/21/2005] [Indexed: 11/25/2022]
Abstract
In the past 1.5 billion years, mitochondria have evolved from oxygen-scavenging bacterial symbionts into primary control centers for energy production and cellular life-and-death processes in eukaryotes. This maturation of mitochondrial function has necessitated the coevolution of various mechanisms of communication with the rest of the cell. Emerging evidence indicates that reversible phosphorylation, the most prevalent form of cellular posttranslational modification, is an important and largely overlooked means of regulating mitochondrial functions. The steadily increasing number of reported mitochondrial kinases, phosphatases and phosphoproteins suggests that phosphorylation is likely to emerge as a common theme in the regulation of mitochondrial processes.
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Affiliation(s)
- David J Pagliarini
- Department of Pharmacology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0721, USA
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42
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Eubel H, Braun HP, Millar AH. Blue-native PAGE in plants: a tool in analysis of protein-protein interactions. PLANT METHODS 2005; 1:11. [PMID: 16287510 PMCID: PMC1308860 DOI: 10.1186/1746-4811-1-11] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2005] [Accepted: 11/16/2005] [Indexed: 05/05/2023]
Abstract
Intact protein complexes can be separated by apparent molecular mass using a standard polyacrylamide gel electrophoresis system combining mild detergents and the dye Coomassie Blue. Referring to the blue coloured gel and the gentle method of solubilization yielding native and enzymatically active protein complexes, this technique has been named Blue-Native Polyacrylamide Gel-Electrophoresis (BN-PAGE). BN-PAGE has become the method of choice for the investigation of the respiratory protein complexes of the electron transfer chains of a range of organisms, including bacteria, yeasts, animals and plants. It allows the separation in two dimensions of extremely hydrophobic protein sets for analysis and also provides information on their native interactions. In this review we discuss the capabilities of BN-PAGE in proteomics and the wider investigation of protein:protein interactions with a focus on its use and potential in plant science.
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Affiliation(s)
- Holger Eubel
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, 35 Stirling Hwy, Crawley 6009, Perth, Australia
| | - Hans-Peter Braun
- Abteilung Angewandte Genetik, Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, 35 Stirling Hwy, Crawley 6009, Perth, Australia
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43
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Soanes DM, Talbot NJ. A bioinformatic tool for analysis of EST transcript abundance during infection-related development by Magnaporthe grisea. MOLECULAR PLANT PATHOLOGY 2005; 6:503-512. [PMID: 20565675 DOI: 10.1111/j.1364-3703.2005.00298.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
SUMMARY Information regarding the levels of mRNA transcript abundance under different conditions, or in specific tissue types, can be obtained by analysis of the frequency of EST sequences in randomly sequenced cDNA libraries. Here we report a bioinformatics tool, which provides a means of identifying genes that are differentially expressed during pathogenesis-related development by the rice blast fungus Magnaporthe grisea. A total of 31 534 M. grisea ESTs were obtained from dbEST at NCBI, clustered into 8821 unique sequences (unisequences) and manually annotated. Transcript profiles were then calculated for 958 unigenes identified from eight different cDNA libraries. The data were integrated into the Consortium for Functional Genomics of Microbial Eukaryotes (COGEME) database (http://cogeme.ex.ac.uk/) and a web-based front end was designed to allow users to access and interrogate the generated datasets.
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Affiliation(s)
- Darren M Soanes
- School of Biological and Chemical Sciences, University of Exeter, Washington Singer Laboratories, Perry Road, Exeter EX4 4QG, UK
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Dhingra V, Gupta M, Andacht T, Fu ZF. New frontiers in proteomics research: A perspective. Int J Pharm 2005; 299:1-18. [PMID: 15979831 DOI: 10.1016/j.ijpharm.2005.04.010] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2004] [Revised: 03/01/2005] [Accepted: 04/04/2005] [Indexed: 12/12/2022]
Abstract
Substantial advances have been made in the fundamental understanding of human biology, ranging from DNA structure to identification of diseases associated with genetic abnormalities. Genome sequence information is becoming available in unprecedented amounts. The absence of a direct functional correlation between gene transcripts and their corresponding proteins, however, represents a significant roadblock for improving the efficiency of biological discoveries. The success of proteomics depends on the ability to identify and analyze protein products in a cell or tissue and, this is reliant on the application of several key technologies. Proteomics is in its exponential growth phase. Two-dimensional electrophoresis complemented with mass spectrometry provides a global view of the state of the proteins from the sample. Proteins identification is a requirement to understand their functional diversity. Subtle difference in protein structure and function can contribute to complexity and diversity of life. This review focuses on the progress and the applications of proteomics science with special reference to integration of the evolving technologies involved to address biological questions.
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Affiliation(s)
- Vikas Dhingra
- Department of Pathology, University of Georgia, Athens, GA 30602, USA.
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Ebstrup T, Saalbach G, Egsgaard H. A proteomics study ofin vitro cyst germination and appressoria formation inPhytophthora infestans. Proteomics 2005; 5:2839-48. [PMID: 15996011 DOI: 10.1002/pmic.200401173] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A proteomics study using two-dimensional gel electrophoresis (2-DE) and mass spectrometry was performed on Phytophthora infestans. Proteins from cysts, germinated cysts and appressoria grown in vitro were isolated and separated by 2-DE. Statistical quantitative analysis of the protein spots from five independent experiments of each developmental stage revealed significant up-regulation of ten spots on gels from germinated cysts compared to cysts. Five spots were significantly up-regulated on gels from appressoria compared to germinated cysts and one of these up-regulated spots was not detectable on gels from cysts. In addition, one spot was significantly down-regulated and another spot not detectable on the gels from appressoria. The corresponding proteins to 13 of these spots were identified with high confidence using tandem mass spectrometry and database searches. The functions of the proteins that were up-regulated in germinated cysts and appressoria can be grouped into the following categories: protein synthesis (e.g. a DEAD box RNA helicase), amino acid metabolism, energy metabolism and reactive oxygen species scavenging. The spot not detected in appressoria was identified as the P. infestans crinkling- and necrosis-inducing protein CRN2. The identified proteins are most likely involved in the establishment of the infection of the host plant.
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Affiliation(s)
- Tine Ebstrup
- Biosystems Department, Risoe National Laboratory, Roskilde, Denmark.
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Chapter 5 Phosphorylation-specific analysis strategies for mass spectrometry: enhanced detection of phosphorylated proteins and peptides. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/s0166-526x(05)46005-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Millar AH, Heazlewood JL, Kristensen BK, Braun HP, Møller IM. The plant mitochondrial proteome. TRENDS IN PLANT SCIENCE 2005; 10:36-43. [PMID: 15642522 DOI: 10.1016/j.tplants.2004.12.002] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The plant mitochondrial proteome might contain as many as 2000-3000 different gene products, each of which might undergo post-translational modification. Recent studies using analytical methods, such as one-, two- and three-dimensional gel electrophoresis and one- and two-dimensional liquid chromatography linked on-line with tandem mass spectrometry, have identified >400 mitochondrial proteins, including subunits of mitochondrial respiratory complexes, supercomplexes, phosphorylated proteins and oxidized proteins. The results also highlight a range of new mitochondrial proteins, new mitochondrial functions and possible new mechanisms for regulating mitochondrial metabolism. More than 70 identified proteins in Arabidopsis mitochondrial samples lack similarity to any protein of known function. In some cases, unknown proteins were found to form part of protein complexes, which allows a functional context to be defined for them. There are indications that some of these proteins add novel activities to mitochondrial protein complexes in plants.
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Affiliation(s)
- A Harvey Millar
- Plant Molecular Biology Group, School of Biomedical and Chemical Sciences, University of Western Australia, Crawley 6009, W.A., Australia.
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Tishkov VI, Popov VO. Catalytic mechanism and application of formate dehydrogenase. BIOCHEMISTRY (MOSCOW) 2004. [DOI: 10.1007/pl00021765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Tishkov VI, Popov VO. Catalytic mechanism and application of formate dehydrogenase. BIOCHEMISTRY (MOSCOW) 2004; 69:1252-67. [PMID: 15627379 DOI: 10.1007/s10541-005-0071-x] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
NAD+-dependent formate dehydrogenase (FDH) is an abundant enzyme that plays an important role in energy supply of methylotrophic microorganisms and in response to stress in plants. FDH belongs to the superfamily of D-specific 2-hydroxy acid dehydrogenases. FDH is widely accepted as a model enzyme to study the mechanism of hydride ion transfer in the active center of dehydrogenases because the reaction catalyzed by the enzyme is devoid of proton transfer steps and implies a substrate with relatively simple structure. FDH is also widely used in enzymatic syntheses of optically active compounds as a versatile biocatalyst for NAD(P)H regeneration consumed in the main reaction. This review covers the late developments in cloning genes of FDH from various sources, studies of its catalytic mechanism and physiological role, and its application for new chiral syntheses.
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Affiliation(s)
- V I Tishkov
- Department of Chemical Enzymology, Faculty of Chemistry, Lomonosov Moscow State University, Moscow 119992, Russia.
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Jensen ON. Modification-specific proteomics: characterization of post-translational modifications by mass spectrometry. Curr Opin Chem Biol 2004; 8:33-41. [PMID: 15036154 DOI: 10.1016/j.cbpa.2003.12.009] [Citation(s) in RCA: 375] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Post-translational modifications generate tremendous diversity, complexity and heterogeneity of gene products, and their determination is one of the main challenges in proteomics research. Recent developments in mass spectrometry based approaches for systematic, qualitative and quantitative determination of modified proteins promise to bring new insights on the dynamics and spatio-temporal control of protein activities by post-translational modifications, and reveal their roles in biological processes and pathogenic conditions. Combinations of affinity-based enrichment and extraction methods, multidimensional separation technologies and mass spectrometry are particularly attractive for systematic investigation of post-translationally modified proteins in proteomics.
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Affiliation(s)
- Ole Nørregaard Jensen
- Protein Research Group, Department of Biochemistry & Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark.
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