1
|
Burgess SJ, Taha H, Yeoman JA, Iamshanova O, Chan KX, Boehm M, Behrends V, Bundy JG, Bialek W, Murray JW, Nixon PJ. Identification of the Elusive Pyruvate Reductase of Chlamydomonas reinhardtii Chloroplasts. PLANT & CELL PHYSIOLOGY 2016; 57:82-94. [PMID: 26574578 PMCID: PMC4722173 DOI: 10.1093/pcp/pcv167] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 10/27/2015] [Indexed: 05/19/2023]
Abstract
Under anoxic conditions the green alga Chlamydomonas reinhardtii activates various fermentation pathways leading to the creation of formate, acetate, ethanol and small amounts of other metabolites including d-lactate and hydrogen. Progress has been made in identifying the enzymes involved in these pathways and their subcellular locations; however, the identity of the enzyme involved in reducing pyruvate to d-lactate has remained unclear. Based on sequence comparisons, enzyme activity measurements, X-ray crystallography, biochemical fractionation and analysis of knock-down mutants, we conclude that pyruvate reduction in the chloroplast is catalyzed by a tetrameric NAD(+)-dependent d-lactate dehydrogenase encoded by Cre07.g324550. Its expression during aerobic growth supports a possible function as a 'lactate valve' for the export of lactate to the mitochondrion for oxidation by cytochrome-dependent d-lactate dehydrogenases and by glycolate dehydrogenase. We also present a revised spatial model of fermentation based on our immunochemical detection of the likely pyruvate decarboxylase, PDC3, in the cytoplasm.
Collapse
Affiliation(s)
- Steven J Burgess
- Department of Life Sciences, Sir Ernst Chain Building-Wolfson Laboratories, Imperial College London, S. Kensington Campus, London SW7 2AZ, UK Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK These authors contributed equally to this work
| | - Hussein Taha
- Department of Life Sciences, Sir Ernst Chain Building-Wolfson Laboratories, Imperial College London, S. Kensington Campus, London SW7 2AZ, UK These authors contributed equally to this work Present address: Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, BE1410, Brunei Darussalam
| | - Justin A Yeoman
- Department of Life Sciences, Sir Ernst Chain Building-Wolfson Laboratories, Imperial College London, S. Kensington Campus, London SW7 2AZ, UK
| | - Oksana Iamshanova
- Department of Life Sciences, Sir Ernst Chain Building-Wolfson Laboratories, Imperial College London, S. Kensington Campus, London SW7 2AZ, UK
| | - Kher Xing Chan
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Marko Boehm
- Department of Life Sciences, Sir Ernst Chain Building-Wolfson Laboratories, Imperial College London, S. Kensington Campus, London SW7 2AZ, UK
| | - Volker Behrends
- Department of Biomolecular Medicine, Sir Alexander Fleming Building, Imperial College London, S. Kensington Campus, London SW7 2AZ, UK
| | - Jacob G Bundy
- Department of Biomolecular Medicine, Sir Alexander Fleming Building, Imperial College London, S. Kensington Campus, London SW7 2AZ, UK
| | - Wojciech Bialek
- Department of Life Sciences, Sir Ernst Chain Building-Wolfson Laboratories, Imperial College London, S. Kensington Campus, London SW7 2AZ, UK
| | - James W Murray
- Department of Life Sciences, Sir Ernst Chain Building-Wolfson Laboratories, Imperial College London, S. Kensington Campus, London SW7 2AZ, UK
| | - Peter J Nixon
- Department of Life Sciences, Sir Ernst Chain Building-Wolfson Laboratories, Imperial College London, S. Kensington Campus, London SW7 2AZ, UK
| |
Collapse
|
2
|
Zones JM, Blaby IK, Merchant SS, Umen JG. High-Resolution Profiling of a Synchronized Diurnal Transcriptome from Chlamydomonas reinhardtii Reveals Continuous Cell and Metabolic Differentiation. THE PLANT CELL 2015; 27:2743-69. [PMID: 26432862 PMCID: PMC4682324 DOI: 10.1105/tpc.15.00498] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 07/27/2015] [Accepted: 09/14/2015] [Indexed: 05/18/2023]
Abstract
The green alga Chlamydomonas reinhardtii is a useful model organism for investigating diverse biological processes, such as photosynthesis and chloroplast biogenesis, flagella and basal body structure/function, cell growth and division, and many others. We combined a highly synchronous photobioreactor culture system with frequent temporal sampling to characterize genome-wide diurnal gene expression in Chlamydomonas. Over 80% of the measured transcriptome was expressed with strong periodicity, forming 18 major clusters. Genes associated with complex structures and processes, including cell cycle control, flagella and basal bodies, ribosome biogenesis, and energy metabolism, all had distinct signatures of coexpression with strong predictive value for assigning and temporally ordering function. Importantly, the frequent sampling regime allowed us to discern meaningful fine-scale phase differences between and within subgroups of genes and enabled the identification of a transiently expressed cluster of light stress genes. Coexpression was further used both as a data-mining tool to classify and/or validate genes from other data sets related to the cell cycle and to flagella and basal bodies and to assign isoforms of duplicated enzymes to their cognate pathways of central carbon metabolism. Our diurnal coexpression data capture functional relationships established by dozens of prior studies and are a valuable new resource for investigating a variety of biological processes in Chlamydomonas and other eukaryotes.
Collapse
Affiliation(s)
- James Matt Zones
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132 Division of Biological Sciences, University of California San Diego, La Jolla, California 92093
| | - Ian K Blaby
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095 Institute of Genomics and Proteomics, University of California, Los Angeles, California 90095
| | - James G Umen
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| |
Collapse
|
3
|
Banti V, Giuntoli B, Gonzali S, Loreti E, Magneschi L, Novi G, Paparelli E, Parlanti S, Pucciariello C, Santaniello A, Perata P. Low oxygen response mechanisms in green organisms. Int J Mol Sci 2013; 14:4734-61. [PMID: 23446868 PMCID: PMC3634410 DOI: 10.3390/ijms14034734] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 02/20/2013] [Accepted: 02/21/2013] [Indexed: 01/04/2023] Open
Abstract
Low oxygen stress often occurs during the life of green organisms, mostly due to the environmental conditions affecting oxygen availability. Both plants and algae respond to low oxygen by resetting their metabolism. The shift from mitochondrial respiration to fermentation is the hallmark of anaerobic metabolism in most organisms. This involves a modified carbohydrate metabolism coupled with glycolysis and fermentation. For a coordinated response to low oxygen, plants exploit various molecular mechanisms to sense when oxygen is either absent or in limited amounts. In Arabidopsis thaliana, a direct oxygen sensing system has recently been discovered, where a conserved N-terminal motif on some ethylene responsive factors (ERFs), targets the fate of the protein under normoxia/hypoxia. In Oryza sativa, this same group of ERFs drives physiological and anatomical modifications that vary in relation to the genotype studied. The microalga Chlamydomonas reinhardtii responses to low oxygen seem to have evolved independently of higher plants, posing questions on how the fermentative metabolism is modulated. In this review, we summarize the most recent findings related to these topics, highlighting promising developments for the future.
Collapse
Affiliation(s)
- Valeria Banti
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant’Anna, Via Mariscoglio 34, Pisa 56124, Italy; E-Mails: (V.B.); (B.G.); (S.G.); (G.N.); (E.P.); (S.P.); (C.P.); (A.S.)
| | - Beatrice Giuntoli
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant’Anna, Via Mariscoglio 34, Pisa 56124, Italy; E-Mails: (V.B.); (B.G.); (S.G.); (G.N.); (E.P.); (S.P.); (C.P.); (A.S.)
| | - Silvia Gonzali
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant’Anna, Via Mariscoglio 34, Pisa 56124, Italy; E-Mails: (V.B.); (B.G.); (S.G.); (G.N.); (E.P.); (S.P.); (C.P.); (A.S.)
| | - Elena Loreti
- Institute of Agricultural Biology and Biotechnology, National Research Council, Via Moruzzi 1, Pisa 56100, Italy; E-Mail:
| | - Leonardo Magneschi
- Institute of Plant Biochemistry and Biotechnology, University of Münster, Schlossplatz 8, Münster 48143, Germany; E-Mail:
| | - Giacomo Novi
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant’Anna, Via Mariscoglio 34, Pisa 56124, Italy; E-Mails: (V.B.); (B.G.); (S.G.); (G.N.); (E.P.); (S.P.); (C.P.); (A.S.)
| | - Eleonora Paparelli
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant’Anna, Via Mariscoglio 34, Pisa 56124, Italy; E-Mails: (V.B.); (B.G.); (S.G.); (G.N.); (E.P.); (S.P.); (C.P.); (A.S.)
| | - Sandro Parlanti
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant’Anna, Via Mariscoglio 34, Pisa 56124, Italy; E-Mails: (V.B.); (B.G.); (S.G.); (G.N.); (E.P.); (S.P.); (C.P.); (A.S.)
| | - Chiara Pucciariello
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant’Anna, Via Mariscoglio 34, Pisa 56124, Italy; E-Mails: (V.B.); (B.G.); (S.G.); (G.N.); (E.P.); (S.P.); (C.P.); (A.S.)
| | - Antonietta Santaniello
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant’Anna, Via Mariscoglio 34, Pisa 56124, Italy; E-Mails: (V.B.); (B.G.); (S.G.); (G.N.); (E.P.); (S.P.); (C.P.); (A.S.)
| | - Pierdomenico Perata
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant’Anna, Via Mariscoglio 34, Pisa 56124, Italy; E-Mails: (V.B.); (B.G.); (S.G.); (G.N.); (E.P.); (S.P.); (C.P.); (A.S.)
| |
Collapse
|