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Dupuis S, Lingappa UF, Mayali X, Sindermann ES, Chastain JL, Weber PK, Stuart R, Merchant SS. Scarcity of fixed carbon transfer in a model microbial phototroph-heterotroph interaction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.26.577492. [PMID: 38328118 PMCID: PMC10849638 DOI: 10.1101/2024.01.26.577492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Although the green alga Chlamydomonas reinhardtii has long served as a reference organism, few studies have interrogated its role as a primary producer in microbial interactions. Here, we quantitatively investigated C. reinhardtii's capacity to support a heterotrophic microbe using the established coculture system with Mesorhizobium japonicum , a vitamin B 12 -producing α-proteobacterium. Using stable isotope probing and nanoscale secondary ion mass spectrometry (nanoSIMS), we tracked the flow of photosynthetic fixed carbon and consequent bacterial biomass synthesis under continuous and diurnal light with single-cell resolution. We found that more 13 C fixed by the alga was taken up by bacterial cells under continuous light, invalidating the hypothesis that the alga's fermentative degradation of starch reserves during the night would boost M. japonicum heterotrophy. 15 NH 4 assimilation rates and changes in cell size revealed that M. japonicum cells reduced new biomass synthesis in coculture with the alga but continued to divide - a hallmark of nutrient limitation often referred to as reductive division. Despite this sign of starvation, the bacterium still synthesized vitamin B 12 and supported the growth of a B 12 -dependent C. reinhardtii mutant. Finally, we showed that bacterial proliferation could be supported solely by the algal lysis that occurred in coculture, highlighting the role of necromass in carbon cycling. Collectively, these results reveal the scarcity of fixed carbon in this microbial trophic relationship (particularly under environmentally relevant light regimes), demonstrate B 12 exchange even during bacterial starvation, and underscore the importance of quantitative approaches for assessing metabolic coupling in algal-bacterial interactions.
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Pang X, Nawrocki WJ, Cardol P, Zheng M, Jiang J, Fang Y, Yang W, Croce R, Tian L. Weak acids produced during anaerobic respiration suppress both photosynthesis and aerobic respiration. Nat Commun 2023; 14:4207. [PMID: 37452043 PMCID: PMC10349137 DOI: 10.1038/s41467-023-39898-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 07/02/2023] [Indexed: 07/18/2023] Open
Abstract
While photosynthesis transforms sunlight energy into sugar, aerobic and anaerobic respiration (fermentation) catabolizes sugars to fuel cellular activities. These processes take place within one cell across several compartments, however it remains largely unexplored how they interact with one another. Here we report that the weak acids produced during fermentation down-regulate both photosynthesis and aerobic respiration. This effect is mechanistically explained with an "ion trapping" model, in which the lipid bilayer selectively traps protons that effectively acidify subcellular compartments with smaller buffer capacities - such as the thylakoid lumen. Physiologically, we propose that under certain conditions, e.g., dim light at dawn, tuning down the photosynthetic light reaction could mitigate the pressure on its electron transport chains, while suppression of respiration could accelerate the net oxygen evolution, thus speeding up the recovery from hypoxia. Since we show that this effect is conserved across photosynthetic phyla, these results indicate that fermentation metabolites exert widespread feedback control over photosynthesis and aerobic respiration. This likely allows algae to better cope with changing environmental conditions.
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Affiliation(s)
- Xiaojie Pang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Wojciech J Nawrocki
- Department of Physics and Astronomy and LaserLab Amsterdam Faculty of Science, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands
- Laboratoire de Biologie du Chloroplaste et Perception de la Lumière chez les Microalgues, UMR7141, Centre National de la Recherche Scientifique, Sorbonne Université, Institut de Biologie Physico-Chimique, 13 Rue Pierre et Marie Curie, 75005, Paris, France
| | - Pierre Cardol
- Génétique et Physiologie des Microalgues, InBioS/Phytosystems, Institut de Botanique, Université de Liège, B22, 4000, Liège, Belgium
| | - Mengyuan Zheng
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Jingjing Jiang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China
| | - Yuan Fang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Wenqiang Yang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Roberta Croce
- Department of Physics and Astronomy and LaserLab Amsterdam Faculty of Science, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands
| | - Lijin Tian
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
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Three genomes in the algal genus Volvox reveal the fate of a haploid sex-determining region after a transition to homothallism. Proc Natl Acad Sci U S A 2021; 118:2100712118. [PMID: 34011609 PMCID: PMC8166075 DOI: 10.1073/pnas.2100712118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Evolutionary transitions between species with separate sexes and species in which individuals have both sex functions have wide-ranging biological implications. It is largely unknown how such transitions occur in systems with haploid male- and female-determining chromosomes in algae and bryophytes. We investigated such a transition in the algal genus Volvox by making whole-genome sequences of two closely related species, one of which is heterothallic (with distinct males and females) and the other homothallic (with only bisexual, self-compatible individuals). The heterothallic species harbors a sex-determining region (SDR), while the homothallic species retains a nearly intact female-derived SDR-like region and separate regions containing key male genes. Thus, an ancestral female has probably become homothallic by acquiring genes that confer male functions. Transitions between separate sexes (dioecy) and other mating systems are common across eukaryotes. Here, we study a change in a haploid dioecious green algal species with male- and female-determining chromosomes (U and V). The genus Volvox is an oogamous (with large, immotile female gametes and small, motile male gametes) and includes both heterothallic species (with distinct male and female genotypes, associated with a mating-type system that prevents fusion of gametes of the same sex) and homothallic species (bisexual, with the ability to self-fertilize). We date the origin of an expanded sex-determining region (SDR) in Volvox to at least 75 Mya, suggesting that homothallism represents a breakdown of dioecy (heterothallism). We investigated the involvement of the SDR of the U and V chromosomes in this transition. Using de novo whole-genome sequences, we identified a heteromorphic SDR of ca 1 Mbp in male and female genotypes of the heterothallic species Volvox reticuliferus and a homologous region (SDLR) in the closely related homothallic species Volvox africanus, which retained several different hallmark features of an SDR. The V. africanus SDLR includes a large region resembling the female SDR of the presumptive heterothallic ancestor, whereas most genes from the male SDR are absent. However, we found a multicopy array of the male-determining gene, MID, in a different genomic location from the SDLR. Thus, in V. africanus, an ancestrally female genotype may have acquired MID and thereby gained male traits.
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Water oxidation by photosystem II is the primary source of electrons for sustained H 2 photoproduction in nutrient-replete green algae. Proc Natl Acad Sci U S A 2020; 117:29629-29636. [PMID: 33168746 PMCID: PMC7703569 DOI: 10.1073/pnas.2009210117] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Photosynthetic H2 production in the green alga Chlamydomonas reinhardtii is catalyzed by O2-sensitive [FeFe]-hydrogenases, which accept electrons from photosynthetically reduced ferredoxin and reduce protons to H2. Since the process occurs downstream of photosystem I, the contribution of photosystem II (PSII) in H2 photoproduction has long been a subject of debate. Indeed, water oxidation by PSII results in O2 accumulation in chloroplasts, which inhibits H2 evolution. Therefore, clear evidence for direct water biophotolysis resulting in simultaneous H2 and O2 releases in algae has never been presented. This paper demonstrates that sustained H2 photoproduction in C. reinhardtii is directly linked to PSII-dependent water oxidation and brings insights into regulation of PSII activity and H2 production by CO2/HCO3– under microoxic conditions. The unicellular green alga Chlamydomonas reinhardtii is capable of photosynthetic H2 production. H2 evolution occurs under anaerobic conditions and is difficult to sustain due to 1) competition between [FeFe]-hydrogenase (H2ase), the key enzyme responsible for H2 metabolism in algae, and the Calvin–Benson–Bassham (CBB) cycle for photosynthetic reductants and 2) inactivation of H2ase by O2 coevolved in photosynthesis. Recently, we achieved sustainable H2 photoproduction by shifting algae from continuous illumination to a train of short (1 s) light pulses, interrupted by longer (9 s) dark periods. This illumination regime prevents activation of the CBB cycle and redirects photosynthetic electrons to H2ase. Employing membrane-inlet mass spectrometry and H218O, we now present clear evidence that efficient H2 photoproduction in pulse-illuminated algae depends primarily on direct water biophotolysis, where water oxidation at the donor side of photosystem II (PSII) provides electrons for the reduction of protons by H2ase downstream of photosystem I. This occurs exclusively in the absence of CO2 fixation, while with the activation of the CBB cycle by longer (8 s) light pulses the H2 photoproduction ceases and instead a slow overall H2 uptake is observed. We also demonstrate that the loss of PSII activity in DCMU-treated algae or in PSII-deficient mutant cells can be partly compensated for by the indirect (PSII-independent) H2 photoproduction pathway, but only for a short (<1 h) period. Thus, PSII activity is indispensable for a sustained process, where it is responsible for more than 92% of the final H2 yield.
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Petrova EV, Kukarskikh GP, Krendeleva TE, Antal TK. The Mechanisms and Role of Photosynthetic Hydrogen Production by Green Microalgae. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720030169] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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7
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Algae-Bacteria Consortia as a Strategy to Enhance H 2 Production. Cells 2020; 9:cells9061353. [PMID: 32486026 PMCID: PMC7348838 DOI: 10.3390/cells9061353] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/25/2020] [Accepted: 05/26/2020] [Indexed: 12/11/2022] Open
Abstract
Biological hydrogen production by microalgae is a potential sustainable, renewable and clean source of energy. However, many barriers limiting photohydrogen production in these microorganisms remain unsolved. In order to explore this potential and make biohydrogen industrially affordable, the unicellular microalga Chlamydomonas reinhardtii is used as a model system to solve barriers and identify new approaches that can improve hydrogen production. Recently, Chlamydomonas–bacteria consortia have opened a new window to improve biohydrogen production. In this study, we review the different consortia that have been successfully employed and analyze the factors that could be behind the improved H2 production.
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Bunbury F, Helliwell KE, Mehrshahi P, Davey MP, Salmon DL, Holzer A, Smirnoff N, Smith AG. Responses of a Newly Evolved Auxotroph of Chlamydomonas to B 12 Deprivation. PLANT PHYSIOLOGY 2020; 183:167-178. [PMID: 32079734 PMCID: PMC7210614 DOI: 10.1104/pp.19.01375] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 02/04/2020] [Indexed: 05/10/2023]
Abstract
The corrinoid B12 is synthesized only by prokaryotes yet is widely required by eukaryotes as an enzyme cofactor. Microalgae have evolved B12 dependence on multiple occasions, and we previously demonstrated that experimental evolution of the non-B12-requiring alga Chlamydomonas reinhardtii in media supplemented with B12 generated a B12-dependent mutant (hereafter metE7). This clone provides a unique opportunity to study the physiology of a nascent B12 auxotroph. Our analyses demonstrate that B12 deprivation of metE7 disrupts C1 metabolism, causes an accumulation of starch and triacylglycerides, and leads to a decrease in photosynthetic pigments, proteins, and free amino acids. B12 deprivation also caused a substantial increase in reactive oxygen species, which preceded rapid cell death. Survival could be improved without compromising growth by simultaneously depriving the cells of nitrogen, suggesting a type of cross protection. Significantly, we found further improvements in survival under B12 limitation and an increase in B12 use efficiency after metE7 underwent a further period of experimental evolution, this time in coculture with a B12-producing bacterium. Therefore, although an early B12-dependent alga would likely be poorly adapted to coping with B12 deprivation, association with B12-producers can ensure long-term survival whilst also providing a suitable environment for evolving mechanisms to tolerate B12 limitation better.
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Affiliation(s)
- Freddy Bunbury
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom
| | - Katherine E Helliwell
- Marine Biological Association of the United Kingdom, Citadel Hill, Plymouth EX4 4PY, United Kingdom
- School of Biosciences, University of Exeter, Exeter, PL1 2PB, United Kingdom
| | - Payam Mehrshahi
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom
| | - Matthew P Davey
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom
| | - Deborah L Salmon
- School of Biosciences, University of Exeter, Exeter, PL1 2PB, United Kingdom
| | - Andre Holzer
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom
| | - Nicholas Smirnoff
- School of Biosciences, University of Exeter, Exeter, PL1 2PB, United Kingdom
| | - Alison G Smith
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom
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9
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Subramanian V, Wecker MSA, Gerritsen A, Boehm M, Xiong W, Wachter B, Dubini A, González-Ballester D, Antonio RV, Ghirardi ML. Ferredoxin5 Deletion Affects Metabolism of Algae during the Different Phases of Sulfur Deprivation. PLANT PHYSIOLOGY 2019; 181:426-441. [PMID: 31350361 PMCID: PMC6776842 DOI: 10.1104/pp.19.00457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 06/23/2019] [Indexed: 06/10/2023]
Abstract
Ferredoxin5 (FDX5), a minor ferredoxin protein in the alga Chlamydomonas (Chlamydomonas reinhardtii), helps maintain thylakoid membrane integrity in the dark. Sulfur (S) deprivation has been used to achieve prolonged hydrogen production in green algae. Here, we propose that FDX5 is involved in algal responses to S-deprivation as well as to the dark. Specifically, we tested the role of FDX5 in both the initial aerobic and subsequent anaerobic phases of S-deprivation. Under S-deprived conditions, absence of FDX5 causes a distinct delay in achieving anoxia by affecting photosynthetic O2 evolution, accompanied by reduced acetate uptake, lower starch accumulation, and delayed/lower fermentative metabolite production, including photohydrogen. We attribute these differences to transcriptional and/or posttranslational regulation of acetyl-CoA synthetase and ADP-Glc pyrophosphorylase, and increased stability of the PSII D1 protein. Interestingly, increased levels of FDX2 and FDX1 were observed in the mutant under oxic, S-replete conditions, strengthening our previously proposed hypothesis that other ferredoxins compensate in response to a lack of FDX5. Taken together, the results of our omics and pull-down experiments confirmed biochemical and physiological results, suggesting that FDX5 may have other effects on Chlamydomonas metabolism through its interaction with multiple redox partners.
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Affiliation(s)
| | - Matt S A Wecker
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401
- GeneBiologics, LLC, Boulder, Colorado 80303
| | - Alida Gerritsen
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Marko Boehm
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Wei Xiong
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Benton Wachter
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Alexandra Dubini
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | | | - Regina V Antonio
- University Federal de Santa Catarina, Florianopolis, 476 Santa Catarina, Brazil
| | - Maria L Ghirardi
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401
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Mejias SH, Bahrami-Dizicheh Z, Liutkus M, Sommer DJ, Astashkin A, Kodis G, Ghirlanda G, Cortajarena AL. Repeat proteins as versatile scaffolds for arrays of redox-active FeS clusters. Chem Commun (Camb) 2019; 55:3319-3322. [PMID: 30829362 PMCID: PMC6484676 DOI: 10.1039/c8cc06827e] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Molecular string of beads: modular extension of a protein backbone builds a chain of electroactive clusters.
Arrays of one, two and four electron-transfer active [4Fe–4S] clusters were constructed on modular tetratricopeptide repeat protein scaffolds, with the number of clusters determined solely by the size of the scaffold. The constructs show reversible redox activity and transient charge stabilization necessary to facilitate charge transfer.
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Affiliation(s)
- Sara H Mejias
- CIC biomaGUNE Paseo de Miramón 182, E-20014 Donostia-San Sebastian, Spain
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Ghirardi M, Subramanian V, Wecker M, Smolinski S, Antonio R, Xiong W, Gonzalez-Ballester D, Dubini A. Survey of the anaerobic metabolism of various laboratory wild-type Chlamydomonas reinhardtii strains. ALGAL RES 2018. [DOI: 10.1016/j.algal.2018.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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12
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Düner M, Lambertz J, Mügge C, Hemschemeier A. The soluble guanylate cyclase CYG12 is required for the acclimation to hypoxia and trophic regimes in Chlamydomonas reinhardtii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:311-337. [PMID: 29161457 DOI: 10.1111/tpj.13779] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Revised: 11/03/2017] [Accepted: 11/09/2017] [Indexed: 05/27/2023]
Abstract
Oxygenic phototrophs frequently encounter environmental conditions that result in intracellular energy crises. Growth of the unicellular green alga Chlamydomonas reinhardtii in hypoxia in the light depends on acclimatory responses of which the induction of photosynthetic cyclic electron flow is essential. The microalga cannot grow in the absence of molecular oxygen (O2 ) in the dark, although it possesses an elaborate fermentation metabolism. Not much is known about how the microalga senses and signals the lack of O2 or about its survival strategies during energy crises. Recently, nitric oxide (NO) has emerged to be required for the acclimation of C. reinhardtii to hypoxia. In this study, we show that the soluble guanylate cyclase (sGC) CYG12, a homologue of animal NO sensors, is also involved in this response. CYG12 is an active sGC, and post-transcriptional down-regulation of the CYG12 gene impairs hypoxic growth and gene expression in C. reinhardtii. However, it also results in a disturbed photosynthetic apparatus under standard growth conditions and the inability to grow heterotrophically. Transcriptome profiles indicate that the mis-expression of CYG12 results in a perturbation of responses that, in the wild-type, maintain the cellular energy budget. We suggest that CYG12 is required for the proper operation of the photosynthetic apparatus which, in turn, is essential for survival in hypoxia and darkness.
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Affiliation(s)
- Melis Düner
- Department of Plant Biochemistry, Workgroup Photobiotechnology, Faculty of Biology and Biotechnology, Ruhr-University of Bochum, Universitätsstr. 150, 44801, Bochum, Germany
| | - Jan Lambertz
- Department of Plant Biochemistry, Workgroup Photobiotechnology, Faculty of Biology and Biotechnology, Ruhr-University of Bochum, Universitätsstr. 150, 44801, Bochum, Germany
| | - Carolin Mügge
- Junior Research Group for Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-University of Bochum, Universitätsstr. 150, 44801, Bochum, Germany
| | - Anja Hemschemeier
- Department of Plant Biochemistry, Workgroup Photobiotechnology, Faculty of Biology and Biotechnology, Ruhr-University of Bochum, Universitätsstr. 150, 44801, Bochum, Germany
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Bourke MF, Marriott PJ, Glud RN, Hasler-Sheetal H, Kamalanathan M, Beardall J, Greening C, Cook PL. Metabolism in anoxic permeable sediments is dominated by eukaryotic dark fermentation. NATURE GEOSCIENCE 2017; 10:30-35. [PMID: 28070216 PMCID: PMC5217482 DOI: 10.1038/ngeo2843] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 10/21/2016] [Indexed: 05/27/2023]
Abstract
Permeable sediments are common across continental shelves and are critical contributors to marine biogeochemical cycling. Organic matter in permeable sediments is dominated by microalgae, which as eukaryotes have different anaerobic metabolic pathways to prokaryotes such as bacteria and archaea. Here we present analyses of flow-through reactor experiments showing that dissolved inorganic carbon is produced predominantly as a result of anaerobic eukaryotic metabolic activity. In our experiments, anaerobic production of dissolved inorganic carbon was consistently accompanied by large dissolved H2 production rates, suggesting the presence of fermentation. The production of both dissolved inorganic carbon and H2 persisted following administration of broad spectrum bactericidal antibiotics, but ceased following treatment with metronidazole. Metronidazole inhibits the ferredoxin/hydrogenase pathway of fermentative eukaryotic H2 production, suggesting that pathway as the source of H2 and dissolved inorganic carbon production. Metabolomic analysis showed large increases in lipid production at the onset of anoxia, consistent with documented pathways of anoxic dark fermentation in microalgae. Cell counts revealed a predominance of microalgae in the sediments. H2 production was observed in dark anoxic cultures of diatoms (Fragilariopsis sp.) and a chlorophyte (Pyramimonas) isolated from the study site, substantiating the hypothesis that microalgae undertake fermentation. We conclude that microalgal dark fermentation could be an important energy-conserving pathway in permeable sediments.
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Affiliation(s)
- Michael F Bourke
- Water Studies Centre, School of Chemistry, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - Philip J. Marriott
- Australian Centre for Research on Separation Science, School of Chemistry, Monash University, Wellington Road, VIC 3800, Australia
| | - Ronnie N. Glud
- University of Southern Denmark, Nordic Centre for Earth Evolution, Odense M-5230, Denmark
- Scottish Association for Marine Science, Oban PA37 1QA, UK
- University of Aarhus, Arctic Research Centre, Aarhus, Denmark
| | - Harald Hasler-Sheetal
- University of Southern Denmark, Nordic Centre for Earth Evolution, Odense M-5230, Denmark
- University of Southern Denmark, Villum Center for Bioanalytical Sciences, Odense M-5230, Denmark
| | - Manoj Kamalanathan
- Department of Marine Biology, Texas A&M University. Galveston, TX, 77554 USA
| | - John Beardall
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Chris Greening
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Perran L.M. Cook
- Water Studies Centre, School of Chemistry, Monash University, Wellington Road, Clayton, VIC 3800, Australia
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van Lis R, Popek M, Couté Y, Kosta A, Drapier D, Nitschke W, Atteia A. Concerted Up-regulation of Aldehyde/Alcohol Dehydrogenase (ADHE) and Starch in Chlamydomonas reinhardtii Increases Survival under Dark Anoxia. J Biol Chem 2016; 292:2395-2410. [PMID: 28007962 DOI: 10.1074/jbc.m116.766048] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 12/21/2016] [Indexed: 11/06/2022] Open
Abstract
Aldehyde/alcohol dehydrogenases (ADHEs) are bifunctional enzymes that commonly produce ethanol from acetyl-CoA with acetaldehyde as intermediate and play a key role in anaerobic redox balance in many fermenting bacteria. ADHEs are also present in photosynthetic unicellular eukaryotes, where their physiological role and regulation are, however, largely unknown. Herein we provide the first molecular and enzymatic characterization of the ADHE from the photosynthetic microalga Chlamydomonas reinhardtii Purified recombinant ADHE catalyzed the reversible NADH-mediated interconversions of acetyl-CoA, acetaldehyde, and ethanol but seemed to be poised toward the production of ethanol from acetaldehyde. Phylogenetic analysis of the algal fermentative enzyme supports a vertical inheritance from a cyanobacterial-related ancestor. ADHE was located in the chloroplast, where it associated in dimers and higher order oligomers. Electron microscopy analysis of ADHE-enriched stromal fractions revealed fine spiral structures, similar to bacterial ADHE spirosomes. Protein blots showed that ADHE is regulated under oxic conditions. Up-regulation is observed in cells exposed to diverse physiological stresses, including zinc deficiency, nitrogen starvation, and inhibition of carbon concentration/fixation capacity. Analyses of the overall proteome and fermentation profiles revealed that cells with increased ADHE abundance exhibit better survival under dark anoxia. This likely relates to the fact that greater ADHE abundance appeared to coincide with enhanced starch accumulation, which might reflect ADHE-mediated anticipation of anaerobic survival.
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Affiliation(s)
- Robert van Lis
- From the Aix Marseille Université, CNRS, BIP-UMR 7281, 13402 Marseille, France.,LBE, INRA, 11100 Narbonne, France
| | - Marion Popek
- From the Aix Marseille Université, CNRS, BIP-UMR 7281, 13402 Marseille, France
| | - Yohann Couté
- the Université Grenoble Alpes, BIG-BGE, 38000 Grenoble, France.,the Commissariat à l'Energie Atomique, BIG-BGE, 38000 Grenoble, France.,INSERM, BGE, 38000 Grenoble, France
| | - Artemis Kosta
- the Microscopy Core Facility, FR3479 Institut de Microbiologie de la Méditerranée, 13402 Marseille cedex 20, France, and
| | - Dominique Drapier
- the Institut de Biologie Physico-Chimique, UMR7141 CNRS-UPMC, 75005 Paris, France
| | - Wolfgang Nitschke
- From the Aix Marseille Université, CNRS, BIP-UMR 7281, 13402 Marseille, France
| | - Ariane Atteia
- From the Aix Marseille Université, CNRS, BIP-UMR 7281, 13402 Marseille, France,
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15
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Liran O, Semyatich R, Milrad Y, Eilenberg H, Weiner I, Yacoby I. Microoxic Niches within the Thylakoid Stroma of Air-Grown Chlamydomonas reinhardtii Protect [FeFe]-Hydrogenase and Support Hydrogen Production under Fully Aerobic Environment. PLANT PHYSIOLOGY 2016; 172:264-71. [PMID: 27443604 PMCID: PMC5074601 DOI: 10.1104/pp.16.01063] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 07/18/2016] [Indexed: 05/20/2023]
Abstract
Photosynthetic hydrogen production in the microalga Chlamydomonas reinhardtii is catalyzed by two [FeFe]-hydrogenase isoforms, HydA1 and HydA2, both irreversibly inactivated upon a few seconds exposure to atmospheric oxygen. Until recently, it was thought that hydrogenase is not active in air-grown microalgal cells. In contrast, we show that the entire pool of cellular [FeFe]-hydrogenase remains active in air-grown cells due to efficient scavenging of oxygen. Using membrane inlet mass spectrometry, (18)O2 isotope, and various inhibitors, we were able to dissect the various oxygen uptake mechanisms. We found that both chlororespiration, catalyzed by plastid terminal oxidase, and Mehler reactions, catalyzed by photosystem I and Flavodiiron proteins, significantly contribute to oxygen uptake rate. This rate is considerably enhanced with increasing light, thus forming local anaerobic niches at the proximity of the stromal face of the thylakoid membrane. Furthermore, we found that in transition to high light, the hydrogen production rate is significantly enhanced for a short duration (100 s), thus indicating that [FeFe]-hydrogenase functions as an immediate sink for surplus electrons in aerobic as well as in anaerobic environments. In summary, we show that an anaerobic locality in the chloroplast preserves [FeFe]-hydrogenase activity and supports continuous hydrogen production in air-grown microalgal cells.
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Affiliation(s)
- Oded Liran
- Department of Molecular Biology and Ecology of Plants, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Rinat Semyatich
- Department of Molecular Biology and Ecology of Plants, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Yuval Milrad
- Department of Molecular Biology and Ecology of Plants, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Haviva Eilenberg
- Department of Molecular Biology and Ecology of Plants, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Iddo Weiner
- Department of Molecular Biology and Ecology of Plants, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Iftach Yacoby
- Department of Molecular Biology and Ecology of Plants, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
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16
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Rai V, Karthikaichamy A, Das D, Noronha S, Wangikar PP, Srivastava S. Multi-omics Frontiers in Algal Research: Techniques and Progress to Explore Biofuels in the Postgenomics World. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2016; 20:387-99. [DOI: 10.1089/omi.2016.0065] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Vineeta Rai
- Department of Biosciences and Bioengineering, Proteomics Laboratory, Indian Institute of Technology Bombay, Mumbai, India
| | | | - Debasish Das
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Guwahati, India
- DBT PAN IIT Centre for Bioenergy, Indian Institute of Technology, Bombay, Mumbai, India
| | - Santosh Noronha
- DBT PAN IIT Centre for Bioenergy, Indian Institute of Technology, Bombay, Mumbai, India
- Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Pramod P. Wangikar
- DBT PAN IIT Centre for Bioenergy, Indian Institute of Technology, Bombay, Mumbai, India
- Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Proteomics Laboratory, Indian Institute of Technology Bombay, Mumbai, India
- DBT PAN IIT Centre for Bioenergy, Indian Institute of Technology, Bombay, Mumbai, India
- Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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17
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Olson AC, Carter CJ. The Involvement of hybrid cluster protein 4, HCP4, in Anaerobic Metabolism in Chlamydomonas reinhardtii. PLoS One 2016; 11:e0149816. [PMID: 26930496 PMCID: PMC4773151 DOI: 10.1371/journal.pone.0149816] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 02/04/2016] [Indexed: 12/28/2022] Open
Abstract
The unicellular green algae Chlamydomonas reinhardtii has long been studied for its unique fermentation pathways and has been evaluated as a candidate organism for biofuel production. Fermentation in C. reinhardtii is facilitated by a network of three predominant pathways producing four major byproducts: formate, ethanol, acetate and hydrogen. Previous microarray studies identified many genes as being highly up-regulated during anaerobiosis. For example, hybrid cluster protein 4 (HCP4) was found to be one of the most highly up-regulated genes under anoxic conditions. Hybrid cluster proteins have long been studied for their unique spectroscopic properties, yet their biological functions remain largely unclear. To probe its role during anaerobiosis, HCP4 was silenced using artificial microRNAs (ami-hcp4) followed by extensive phenotypic analyses of cells grown under anoxic conditions. Both the expression of key fermentative enzymes and their respective metabolites were significantly altered in ami-hcp4, with nitrogen uptake from the media also being significantly different than wild-type cells. The results strongly suggest a role for HCP4 in regulating key fermentative and nitrogen utilization pathways.
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Affiliation(s)
- Adam C. Olson
- Integrated Biosciences Graduate Program, University of Minnesota, Duluth, MN, 55812, United States of America
| | - Clay J. Carter
- Department of Plant Biology, University of Minnesota, Saint Paul, MN, 55108, United States of America
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18
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Li X, Zhang R, Patena W, Gang SS, Blum SR, Ivanova N, Yue R, Robertson JM, Lefebvre PA, Fitz-Gibbon ST, Grossman AR, Jonikas MC. An Indexed, Mapped Mutant Library Enables Reverse Genetics Studies of Biological Processes in Chlamydomonas reinhardtii. THE PLANT CELL 2016; 28:367-87. [PMID: 26764374 PMCID: PMC4790863 DOI: 10.1105/tpc.15.00465] [Citation(s) in RCA: 232] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 11/30/2015] [Accepted: 01/11/2016] [Indexed: 05/18/2023]
Abstract
The green alga Chlamydomonas reinhardtii is a leading unicellular model for dissecting biological processes in photosynthetic eukaryotes. However, its usefulness has been limited by difficulties in obtaining mutants in specific genes of interest. To allow generation of large numbers of mapped mutants, we developed high-throughput methods that (1) enable easy maintenance of tens of thousands of Chlamydomonas strains by propagation on agar media and by cryogenic storage, (2) identify mutagenic insertion sites and physical coordinates in these collections, and (3) validate the insertion sites in pools of mutants by obtaining >500 bp of flanking genomic sequences. We used these approaches to construct a stably maintained library of 1935 mapped mutants, representing disruptions in 1562 genes. We further characterized randomly selected mutants and found that 33 out of 44 insertion sites (75%) could be confirmed by PCR, and 17 out of 23 mutants (74%) contained a single insertion. To demonstrate the power of this library for elucidating biological processes, we analyzed the lipid content of mutants disrupted in genes encoding proteins of the algal lipid droplet proteome. This study revealed a central role of the long-chain acyl-CoA synthetase LCS2 in the production of triacylglycerol from de novo-synthesized fatty acids.
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Affiliation(s)
- Xiaobo Li
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Ru Zhang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Weronika Patena
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Spencer S Gang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Sean R Blum
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Nina Ivanova
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Rebecca Yue
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Jacob M Robertson
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Paul A Lefebvre
- Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Sorel T Fitz-Gibbon
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Arthur R Grossman
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Martin C Jonikas
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
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19
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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.
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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
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20
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Abstract
In response to demands for sustainable domestic fuel sources, research into biofuels has become increasingly important. Many challenges face biofuels in their effort to replace petroleum fuels, but rational strain engineering of algae and photosynthetic organisms offers a great deal of promise. For decades, mutations and stress responses in photosynthetic microbiota were seen to result in production of exciting high-energy fuel molecules, giving hope but minor capability for design. However, '-omics' techniques for visualizing entire cell processing has clarified biosynthesis and regulatory networks. Investigation into the promising production behaviors of the model organism C. reinhardtii and its mutants with these powerful techniques has improved predictability and understanding of the diverse, complex interactions within photosynthetic organisms. This new equipment has created an exciting new frontier for high-throughput, predictable engineering of photosynthetically produced carbon-neutral biofuels.
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Affiliation(s)
- Hanna R Aucoin
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, CO, 80401, USA
| | - Joseph Gardner
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, CO, 80401, USA
| | - Nanette R Boyle
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, CO, 80401, USA.
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21
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Shtaida N, Khozin-Goldberg I, Boussiba S. The role of pyruvate hub enzymes in supplying carbon precursors for fatty acid synthesis in photosynthetic microalgae. PHOTOSYNTHESIS RESEARCH 2015; 125:407-22. [PMID: 25846135 DOI: 10.1007/s11120-015-0136-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 03/27/2015] [Indexed: 05/15/2023]
Abstract
Photosynthetic microalgae are currently the focus of basic and applied research due to an ever-growing interest in renewable energy resources. This review discusses the role of carbon-unit supply for the production of acetyl-CoA, a direct precursor of fatty acid biosynthesis and the primary building block of the growing acyl chains for the purpose of triacylglycerol (TAG) production in photosynthetic microalgae under stressful conditions. It underscores the importance of intraplastidic acetyl-CoA generation for storage lipid accumulation. The main focus is placed on two enzymatic steps linking the central carbon metabolism and fatty acid synthesis, namely the reactions catalyzed by the plastidic isoform of pyruvate kinase and the chloroplastic pyruvate dehydrogenase complex. Alternative routes for plastidic acetyl-CoA synthesis are also reviewed. A separate section is devoted to recent advances in functional genomics studies related to fatty acid and TAG biosynthesis.
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Affiliation(s)
- Nastassia Shtaida
- Microalgal Biotechnology Laboratory, French Associates Institute for Agriculture and Biotechnology of Drylands, J. Blaustein Institutes of Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 84990, Midreshet Ben-Gurion, Israel
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22
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Gonzalez-Ballester D, Jurado-Oller JL, Fernandez E. Relevance of nutrient media composition for hydrogen production in Chlamydomonas. PHOTOSYNTHESIS RESEARCH 2015; 125:395-406. [PMID: 25952745 DOI: 10.1007/s11120-015-0152-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 04/29/2015] [Indexed: 05/23/2023]
Abstract
Microalgae are capable of biological H2 photoproduction from water, solar energy, and a variety of organic substrates. Acclimation responses to different nutrient regimes finely control photosynthetic activity and can influence H2 production. Hence, nutrient stresses are an interesting scenario to study H2 production in photosynthetic organisms. In this review, we mainly focus on the H2-production mechanisms in Chlamydomonas reinhardtii and the physiological relevance of the nutrient media composition when producing H2.
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Affiliation(s)
- David Gonzalez-Ballester
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Córdoba, Campus de Rabanales, Edif. Severo Ochoa, 14071, Córdoba, Spain,
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23
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Antal TK, Krendeleva TE, Tyystjärvi E. Multiple regulatory mechanisms in the chloroplast of green algae: relation to hydrogen production. PHOTOSYNTHESIS RESEARCH 2015; 125:357-81. [PMID: 25986411 DOI: 10.1007/s11120-015-0157-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Accepted: 05/11/2015] [Indexed: 05/10/2023]
Abstract
A complex regulatory network in the chloroplast of green algae provides an efficient tool for maintenance of energy and redox balance in the cell under aerobic and anaerobic conditions. In this review, we discuss the structural and functional organizations of electron transport pathways in the chloroplast, and regulation of photosynthesis in the green microalga Chlamydomonas reinhardtii. The focus is on the regulatory mechanisms induced in response to nutrient deficiency stress and anoxia and especially on the role of a hydrogenase-mediated reaction in adaptation to highly reducing conditions and ATP deficiency in the cell.
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Affiliation(s)
- Taras K Antal
- Faculty of Biology, Moscow State University, Vorobyevi Gory, Moscow, 119992, Russia,
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24
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Ji C, Cao X, Liu H, Qu J, Yao C, Zou H, Xue S. Investigating Cellular Responses During Photohydrogen Production by the Marine Microalga Tetraselmis subcordiformis by Quantitative Proteome Analysis. Appl Biochem Biotechnol 2015; 177:649-61. [DOI: 10.1007/s12010-015-1769-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 07/17/2015] [Indexed: 11/24/2022]
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25
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Huwald D, Schrapers P, Kositzki R, Haumann M, Hemschemeier A. Characterization of unusual truncated hemoglobins of Chlamydomonas reinhardtii suggests specialized functions. PLANTA 2015; 242:167-85. [PMID: 25893868 DOI: 10.1007/s00425-015-2294-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 03/27/2015] [Indexed: 05/04/2023]
Abstract
Annotated hemoglobin genes in Chlamydomonas reinhardtii form functional globins, despite unusual architectures. Spectral characteristics show subtle biochemical differences. Multiple globins might help the alga to cope with its versatile environment. The unicellular green alga C. reinhardtii is a photosynthetic, often soil-dwelling organism, subjected to a changeable environment in nature. The alga contains 12 genes encoding so-called truncated hemoglobins that feature a two-on-two helical fold instead of the three-on-three helix arrangement of the long-studied vertebrate globins or plant symbiotic and non-symbiotic hemoglobins. In plants, non-symbiotic hemoglobins often play a role in acclimation to stress, and we could show recently that one of the C. reinhardtii globin genes is vital for anoxic growth. Here, three further globin encoding transcripts (Cre16.g661000.t1.1, Cre16.g661300.t2.1 and Cre16.g662750.t1.2) were heterologously expressed along with the recently studied THB1. UV-Vis and X-ray absorption spectroscopy analyses show that the sequences indeed encode functional hemoglobins, despite their uncommon primary sequences, which include long C-termini without any predictable function, or a split heme-binding domain. The proteins show some variations regarding the coordination of the heme iron or the interaction with diatomic ligands, indicating different functionalities. The respective transcripts are not responsive to the nitrogen source, in contrast to results reported for THB1, but they accumulate in darkness. This work advances experimental data on the very large globin family in general, and, more specifically, on hemoglobins in photosynthetic organisms.
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Affiliation(s)
- Dennis Huwald
- Work Group Photobiotechnology, Department of Plant Biochemistry, Faculty of Biology and Biotechnology, Ruhr-University of Bochum, Universitätsstr. 150, ND2/134, 44801, Bochum, Germany
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26
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Yang W, Catalanotti C, Wittkopp TM, Posewitz MC, Grossman AR. Algae after dark: mechanisms to cope with anoxic/hypoxic conditions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 82:481-503. [PMID: 25752440 DOI: 10.1111/tpj.12823] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 02/28/2015] [Accepted: 03/03/2015] [Indexed: 06/04/2023]
Abstract
Chlamydomonas reinhardtii is a unicellular, soil-dwelling (and aquatic) green alga that has significant metabolic flexibility for balancing redox equivalents and generating ATP when it experiences hypoxic/anoxic conditions. The diversity of pathways available to ferment sugars is often revealed in mutants in which the activities of specific branches of fermentative metabolism have been eliminated; compensatory pathways that have little activity in parental strains under standard laboratory fermentative conditions are often activated. The ways in which these pathways are regulated and integrated have not been extensively explored. In this review, we primarily discuss the intricacies of dark anoxic metabolism in Chlamydomonas, but also discuss aspects of dark oxic metabolism, the utilization of acetate, and the relatively uncharacterized but critical interactions that link chloroplastic and mitochondrial metabolic networks.
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Affiliation(s)
- Wenqiang Yang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Claudia Catalanotti
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Tyler M Wittkopp
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Matthew C Posewitz
- Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, CO, 80401, USA
| | - Arthur R Grossman
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
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27
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Costa RL, Oliveira TV, Ferreira JDS, Cardoso VL, Batista FRX. Prospective technology on bioethanol production from photofermentation. BIORESOURCE TECHNOLOGY 2015; 181:330-337. [PMID: 25678298 DOI: 10.1016/j.biortech.2015.01.090] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 01/20/2015] [Accepted: 01/22/2015] [Indexed: 06/04/2023]
Abstract
The most important global demand is the energy supply from alternative source. Ethanol may be considered an environmental friendly fuel that has been produced by feedstock. The production of ethanol by microalgae represent a process with reduced environmental impact with efficient CO2 fixation and requiring less arable land. This work studied the production of ethanol from green alga Chlamydomonas reinhardtii through the cellular metabolism in a light/dark cycle at 25 °C in a TAP medium with sulfur depletion. The parameters evaluated were inoculum concentration and the medium supplementation with mixotrophic carbon sources. The combination of C.reinhardtii and Rhodobacter capsulatus through a hybrid or co-culture systems was also investigated as well. C.reinhardtii maintained in TAP-S produced 19.25±4.16 g/L (ethanol). In addition, in a hybrid system, with medium initially supplemented with milk whey permeated and the algal effluent used by R. capsulatus, the ethanol production achieved 19.94±2.67 g/L.
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Affiliation(s)
- Rosangela Lucio Costa
- School of Chemical Engineering, Federal University of Uberlandia. Av. Joao Naves de Avila 2121, Santa Monica 38408-144, Uberlandia, MG, Brazil
| | - Thamayne Valadares Oliveira
- School of Chemical Engineering, Federal University of Uberlandia. Av. Joao Naves de Avila 2121, Santa Monica 38408-144, Uberlandia, MG, Brazil
| | - Juliana de Souza Ferreira
- School of Chemical Engineering, Federal University of Uberlandia. Av. Joao Naves de Avila 2121, Santa Monica 38408-144, Uberlandia, MG, Brazil
| | - Vicelma Luiz Cardoso
- School of Chemical Engineering, Federal University of Uberlandia. Av. Joao Naves de Avila 2121, Santa Monica 38408-144, Uberlandia, MG, Brazil
| | - Fabiana Regina Xavier Batista
- School of Chemical Engineering, Federal University of Uberlandia. Av. Joao Naves de Avila 2121, Santa Monica 38408-144, Uberlandia, MG, Brazil.
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28
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Clowez S, Godaux D, Cardol P, Wollman FA, Rappaport F. The involvement of hydrogen-producing and ATP-dependent NADPH-consuming pathways in setting the redox poise in the chloroplast of Chlamydomonas reinhardtii in anoxia. J Biol Chem 2015; 290:8666-76. [PMID: 25691575 DOI: 10.1074/jbc.m114.632588] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Photosynthetic microalgae are exposed to changing environmental conditions. In particular, microbes found in ponds or soils often face hypoxia or even anoxia, and this severely impacts their physiology. Chlamydomonas reinhardtii is one among such photosynthetic microorganisms recognized for its unusual wealth of fermentative pathways and the extensive remodeling of its metabolism upon the switch to anaerobic conditions. As regards the photosynthetic electron transfer, this remodeling encompasses a strong limitation of the electron flow downstream of photosystem I. Here, we further characterize the origin of this limitation. We show that it stems from the strong reducing pressure that builds up upon the onset of anoxia, and this pressure can be relieved either by the light-induced synthesis of ATP, which promotes the consumption of reducing equivalents, or by the progressive activation of the hydrogenase pathway, which provides an electron transfer pathway alternative to the CO2 fixation cycle.
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Affiliation(s)
- Sophie Clowez
- From the Institut de Biologie Physico-Chimique, UMR 7141 CNRS-UPMC, 13 Rue P et M Curie, 75005 Paris, France, and
| | - Damien Godaux
- the Laboratoire de Génétique et Physiologie des Microalgues, Phytosystems, Department of Life Sciences, Institute of Botany, 27 Bld. du Rectorat, University of Liège, B-4000 Liège, Belgium
| | - Pierre Cardol
- the Laboratoire de Génétique et Physiologie des Microalgues, Phytosystems, Department of Life Sciences, Institute of Botany, 27 Bld. du Rectorat, University of Liège, B-4000 Liège, Belgium
| | - Francis-André Wollman
- From the Institut de Biologie Physico-Chimique, UMR 7141 CNRS-UPMC, 13 Rue P et M Curie, 75005 Paris, France, and
| | - Fabrice Rappaport
- From the Institut de Biologie Physico-Chimique, UMR 7141 CNRS-UPMC, 13 Rue P et M Curie, 75005 Paris, France, and
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29
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Roy A, Sommer DJ, Schmitz RA, Brown CL, Gust D, Astashkin A, Ghirlanda G. A De Novo Designed 2[4Fe-4S] Ferredoxin Mimic Mediates Electron Transfer. J Am Chem Soc 2014; 136:17343-9. [DOI: 10.1021/ja510621e] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Anindya Roy
- Department
of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Dayn Joseph Sommer
- Department
of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Robert Arthur Schmitz
- Department
of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Chelsea Lynn Brown
- Department
of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Devens Gust
- Department
of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Andrei Astashkin
- Department
of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Giovanna Ghirlanda
- Department
of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
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Yang W, Catalanotti C, D'Adamo S, Wittkopp TM, Ingram-Smith CJ, Mackinder L, Miller TE, Heuberger AL, Peers G, Smith KS, Jonikas MC, Grossman AR, Posewitz MC. Alternative acetate production pathways in Chlamydomonas reinhardtii during dark anoxia and the dominant role of chloroplasts in fermentative acetate production. THE PLANT CELL 2014; 26:4499-518. [PMID: 25381350 PMCID: PMC4277214 DOI: 10.1105/tpc.114.129965] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 07/15/2014] [Accepted: 10/15/2014] [Indexed: 05/18/2023]
Abstract
Chlamydomonas reinhardtii insertion mutants disrupted for genes encoding acetate kinases (EC 2.7.2.1) (ACK1 and ACK2) and a phosphate acetyltransferase (EC 2.3.1.8) (PAT2, but not PAT1) were isolated to characterize fermentative acetate production. ACK1 and PAT2 were localized to chloroplasts, while ACK2 and PAT1 were shown to be in mitochondria. Characterization of the mutants showed that PAT2 and ACK1 activity in chloroplasts plays a dominant role (relative to ACK2 and PAT1 in mitochondria) in producing acetate under dark, anoxic conditions and, surprisingly, also suggested that Chlamydomonas has other pathways that generate acetate in the absence of ACK activity. We identified a number of proteins associated with alternative pathways for acetate production that are encoded on the Chlamydomonas genome. Furthermore, we observed that only modest alterations in the accumulation of fermentative products occurred in the ack1, ack2, and ack1 ack2 mutants, which contrasts with the substantial metabolite alterations described in strains devoid of other key fermentation enzymes.
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Affiliation(s)
- Wenqiang Yang
- Carnegie Institution for Science, Department of Plant Biology, Stanford, California 94305
| | - Claudia Catalanotti
- Carnegie Institution for Science, Department of Plant Biology, Stanford, California 94305
| | - Sarah D'Adamo
- Colorado School of Mines, Department of Chemistry and Geochemistry, Golden, Colorado 80401
| | - Tyler M Wittkopp
- Carnegie Institution for Science, Department of Plant Biology, Stanford, California 94305 Stanford University, Department of Biology, Stanford, California 94305
| | - Cheryl J Ingram-Smith
- Clemson University, Department of Genetics and Biochemistry, Clemson, South Carolina 29634
| | - Luke Mackinder
- Carnegie Institution for Science, Department of Plant Biology, Stanford, California 94305
| | - Tarryn E Miller
- Colorado School of Mines, Department of Chemistry and Geochemistry, Golden, Colorado 80401
| | - Adam L Heuberger
- Colorado State University, Proteomics and Metabolomics Facility, Fort Collins, Colorado 80523
| | - Graham Peers
- Colorado State University, Department of Biology, Fort Collins, Colorado 80523
| | - Kerry S Smith
- Clemson University, Department of Genetics and Biochemistry, Clemson, South Carolina 29634
| | - Martin C Jonikas
- Carnegie Institution for Science, Department of Plant Biology, Stanford, California 94305
| | - Arthur R Grossman
- Carnegie Institution for Science, Department of Plant Biology, Stanford, California 94305
| | - Matthew C Posewitz
- Colorado School of Mines, Department of Chemistry and Geochemistry, Golden, Colorado 80401
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Subramanian V, Dubini A, Astling DP, Laurens LML, Old WM, Grossman AR, Posewitz MC, Seibert M. Profiling Chlamydomonas metabolism under dark, anoxic H2-producing conditions using a combined proteomic, transcriptomic, and metabolomic approach. J Proteome Res 2014; 13:5431-51. [PMID: 25333711 DOI: 10.1021/pr500342j] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Chlamydomonas reinhardtii is well adapted to survive under different environmental conditions due to the unique flexibility of its metabolism. Here we report metabolic pathways that are active during acclimation to anoxia, but were previously not thoroughly studied under dark, anoxic H2-producing conditions in this model green alga. Proteomic analyses, using 2D-differential in-gel electrophoresis in combination with shotgun mass fingerprinting, revealed increased levels of proteins involved in the glycolytic pathway downstream of 3-phosphoglycerate, the glyoxylate pathway, and steps of the tricarboxylic acid (TCA) reactions. Upregulation of the enzyme, isocitrate lyase (ICL), was observed, which was accompanied by increased intracellular succinate levels, suggesting the functioning of glyoxylate pathway reactions. The ICL-inhibitor study revealed presence of reverse TCA reactions under these conditions. Contributions of the serine-isocitrate lyase pathway, glycine cleavage system, and c1-THF/serine hydroxymethyltransferase pathway in the acclimation to dark anoxia were found. We also observed increased levels of amino acids (AAs) suggesting nitrogen reorganization in the form of de novo AA biosynthesis during anoxia. Overall, novel routes for reductant utilization, in combination with redistribution of carbon and nitrogen, are used by this alga during acclimation to O2 deprivation in the dark.
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Kukuczka B, Magneschi L, Petroutsos D, Steinbeck J, Bald T, Powikrowska M, Fufezan C, Finazzi G, Hippler M. Proton Gradient Regulation5-Like1-Mediated Cyclic Electron Flow Is Crucial for Acclimation to Anoxia and Complementary to Nonphotochemical Quenching in Stress Adaptation. PLANT PHYSIOLOGY 2014; 165:1604-1617. [PMID: 24948831 PMCID: PMC4119042 DOI: 10.1104/pp.114.240648] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
To investigate the functional importance of Proton Gradient Regulation5-Like1 (PGRL1) for photosynthetic performances in the moss Physcomitrella patens, we generated a pgrl1 knockout mutant. Functional analysis revealed diminished nonphotochemical quenching (NPQ) as well as decreased capacity for cyclic electron flow (CEF) in pgrl1. Under anoxia, where CEF is induced, quantitative proteomics evidenced severe down-regulation of photosystems but up-regulation of the chloroplast NADH dehydrogenase complex, plastocyanin, and Ca2+ sensors in the mutant, indicating that the absence of PGRL1 triggered a mechanism compensatory for diminished CEF. On the other hand, proteins required for NPQ, such as light-harvesting complex stress-related protein1 (LHCSR1), violaxanthin de-epoxidase, and PSII subunit S, remained stable. To further investigate the interrelation between CEF and NPQ, we generated a pgrl1 npq4 double mutant in the green alga Chlamydomonas reinhardtii lacking both PGRL1 and LHCSR3 expression. Phenotypic comparative analyses of this double mutant, together with the single knockout strains and with the P. patens pgrl1, demonstrated that PGRL1 is crucial for acclimation to high light and anoxia in both organisms. Moreover, the data generated for the C. reinhardtii double mutant clearly showed a complementary role of PGRL1 and LHCSR3 in managing high light stress response. We conclude that both proteins are needed for photoprotection and for survival under low oxygen, underpinning a tight link between CEF and NPQ in oxygenic photosynthesis. Given the complementarity of the energy-dependent component of NPQ (qE) and PGRL1-mediated CEF, we suggest that PGRL1 is a capacitor linked to the evolution of the PSII subunit S-dependent qE in terrestrial plants.
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Affiliation(s)
- Bernadeta Kukuczka
- Institute of Plant Biology and Biotechnology, University of Münster, 48143 Muenster, Germany (B.K., L.M., D.P., J.S., T.B., C.F., M.H.);Centre National Recherche Scientifique, Unité Mixte Recherche 5168, Laboratoire Physiologie Cellulaire et Végétale, F-38054 Grenoble, France (D.P., G.F.);Commissariat à l'Energie Atomique et Energies Alternatives, l'Institut de Recherches en Technologies et Sciences pour le Vivant, F-38054 Grenoble, France (D.P., G.F.);Institut National Recherche Agronomique, Unité Mixte Recherche 1200, F-38054 Grenoble, France (D.P., G.F.);Université Grenoble Alpes, F-38041 Grenoble, France (D.P., G.F.); andDepartment of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C 1871, Denmark (M.P.)
| | - Leonardo Magneschi
- Institute of Plant Biology and Biotechnology, University of Münster, 48143 Muenster, Germany (B.K., L.M., D.P., J.S., T.B., C.F., M.H.);Centre National Recherche Scientifique, Unité Mixte Recherche 5168, Laboratoire Physiologie Cellulaire et Végétale, F-38054 Grenoble, France (D.P., G.F.);Commissariat à l'Energie Atomique et Energies Alternatives, l'Institut de Recherches en Technologies et Sciences pour le Vivant, F-38054 Grenoble, France (D.P., G.F.);Institut National Recherche Agronomique, Unité Mixte Recherche 1200, F-38054 Grenoble, France (D.P., G.F.);Université Grenoble Alpes, F-38041 Grenoble, France (D.P., G.F.); andDepartment of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C 1871, Denmark (M.P.)
| | - Dimitris Petroutsos
- Institute of Plant Biology and Biotechnology, University of Münster, 48143 Muenster, Germany (B.K., L.M., D.P., J.S., T.B., C.F., M.H.);Centre National Recherche Scientifique, Unité Mixte Recherche 5168, Laboratoire Physiologie Cellulaire et Végétale, F-38054 Grenoble, France (D.P., G.F.);Commissariat à l'Energie Atomique et Energies Alternatives, l'Institut de Recherches en Technologies et Sciences pour le Vivant, F-38054 Grenoble, France (D.P., G.F.);Institut National Recherche Agronomique, Unité Mixte Recherche 1200, F-38054 Grenoble, France (D.P., G.F.);Université Grenoble Alpes, F-38041 Grenoble, France (D.P., G.F.); andDepartment of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C 1871, Denmark (M.P.)
| | - Janina Steinbeck
- Institute of Plant Biology and Biotechnology, University of Münster, 48143 Muenster, Germany (B.K., L.M., D.P., J.S., T.B., C.F., M.H.);Centre National Recherche Scientifique, Unité Mixte Recherche 5168, Laboratoire Physiologie Cellulaire et Végétale, F-38054 Grenoble, France (D.P., G.F.);Commissariat à l'Energie Atomique et Energies Alternatives, l'Institut de Recherches en Technologies et Sciences pour le Vivant, F-38054 Grenoble, France (D.P., G.F.);Institut National Recherche Agronomique, Unité Mixte Recherche 1200, F-38054 Grenoble, France (D.P., G.F.);Université Grenoble Alpes, F-38041 Grenoble, France (D.P., G.F.); andDepartment of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C 1871, Denmark (M.P.)
| | - Till Bald
- Institute of Plant Biology and Biotechnology, University of Münster, 48143 Muenster, Germany (B.K., L.M., D.P., J.S., T.B., C.F., M.H.);Centre National Recherche Scientifique, Unité Mixte Recherche 5168, Laboratoire Physiologie Cellulaire et Végétale, F-38054 Grenoble, France (D.P., G.F.);Commissariat à l'Energie Atomique et Energies Alternatives, l'Institut de Recherches en Technologies et Sciences pour le Vivant, F-38054 Grenoble, France (D.P., G.F.);Institut National Recherche Agronomique, Unité Mixte Recherche 1200, F-38054 Grenoble, France (D.P., G.F.);Université Grenoble Alpes, F-38041 Grenoble, France (D.P., G.F.); andDepartment of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C 1871, Denmark (M.P.)
| | - Marta Powikrowska
- Institute of Plant Biology and Biotechnology, University of Münster, 48143 Muenster, Germany (B.K., L.M., D.P., J.S., T.B., C.F., M.H.);Centre National Recherche Scientifique, Unité Mixte Recherche 5168, Laboratoire Physiologie Cellulaire et Végétale, F-38054 Grenoble, France (D.P., G.F.);Commissariat à l'Energie Atomique et Energies Alternatives, l'Institut de Recherches en Technologies et Sciences pour le Vivant, F-38054 Grenoble, France (D.P., G.F.);Institut National Recherche Agronomique, Unité Mixte Recherche 1200, F-38054 Grenoble, France (D.P., G.F.);Université Grenoble Alpes, F-38041 Grenoble, France (D.P., G.F.); andDepartment of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C 1871, Denmark (M.P.)
| | - Christian Fufezan
- Institute of Plant Biology and Biotechnology, University of Münster, 48143 Muenster, Germany (B.K., L.M., D.P., J.S., T.B., C.F., M.H.);Centre National Recherche Scientifique, Unité Mixte Recherche 5168, Laboratoire Physiologie Cellulaire et Végétale, F-38054 Grenoble, France (D.P., G.F.);Commissariat à l'Energie Atomique et Energies Alternatives, l'Institut de Recherches en Technologies et Sciences pour le Vivant, F-38054 Grenoble, France (D.P., G.F.);Institut National Recherche Agronomique, Unité Mixte Recherche 1200, F-38054 Grenoble, France (D.P., G.F.);Université Grenoble Alpes, F-38041 Grenoble, France (D.P., G.F.); andDepartment of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C 1871, Denmark (M.P.)
| | - Giovanni Finazzi
- Institute of Plant Biology and Biotechnology, University of Münster, 48143 Muenster, Germany (B.K., L.M., D.P., J.S., T.B., C.F., M.H.);Centre National Recherche Scientifique, Unité Mixte Recherche 5168, Laboratoire Physiologie Cellulaire et Végétale, F-38054 Grenoble, France (D.P., G.F.);Commissariat à l'Energie Atomique et Energies Alternatives, l'Institut de Recherches en Technologies et Sciences pour le Vivant, F-38054 Grenoble, France (D.P., G.F.);Institut National Recherche Agronomique, Unité Mixte Recherche 1200, F-38054 Grenoble, France (D.P., G.F.);Université Grenoble Alpes, F-38041 Grenoble, France (D.P., G.F.); andDepartment of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C 1871, Denmark (M.P.)
| | - Michael Hippler
- Institute of Plant Biology and Biotechnology, University of Münster, 48143 Muenster, Germany (B.K., L.M., D.P., J.S., T.B., C.F., M.H.);Centre National Recherche Scientifique, Unité Mixte Recherche 5168, Laboratoire Physiologie Cellulaire et Végétale, F-38054 Grenoble, France (D.P., G.F.);Commissariat à l'Energie Atomique et Energies Alternatives, l'Institut de Recherches en Technologies et Sciences pour le Vivant, F-38054 Grenoble, France (D.P., G.F.);Institut National Recherche Agronomique, Unité Mixte Recherche 1200, F-38054 Grenoble, France (D.P., G.F.);Université Grenoble Alpes, F-38041 Grenoble, France (D.P., G.F.); andDepartment of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C 1871, Denmark (M.P.)
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Helliwell KE, Scaife MA, Sasso S, Araujo APU, Purton S, Smith AG. Unraveling vitamin B12-responsive gene regulation in algae. PLANT PHYSIOLOGY 2014; 165:388-97. [PMID: 24627342 PMCID: PMC4012597 DOI: 10.1104/pp.113.234369] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Photosynthetic microalgae play a vital role in primary productivity and biogeochemical cycling in both marine and freshwater systems across the globe. However, the growth of these cosmopolitan organisms depends on the bioavailability of nutrients such as vitamins. Approximately one-half of all microalgal species requires vitamin B12 as a growth supplement. The major determinant of algal B12 requirements is defined by the isoform of methionine synthase possessed by an alga, such that the presence of the B12-independent methionine synthase (METE) enables growth without this vitamin. Moreover, the widespread but phylogenetically unrelated distribution of B12 auxotrophy across the algal lineages suggests that the METE gene has been lost multiple times in evolution. Given that METE expression is repressed by the presence of B12, prolonged repression by a reliable source of the vitamin could lead to the accumulation of mutations and eventually gene loss. Here, we probe METE gene regulation by B12 and methionine/folate cycle metabolites in both marine and freshwater microalgal species. In addition, we identify a B12-responsive element of Chlamydomonas reinhardtii METE using a reporter gene approach. We show that complete repression of the reporter occurs via a region spanning -574 to -90 bp upstream of the METE start codon. A proteomics study reveals that two other genes (S-Adenosylhomocysteine hydrolase and Serine hydroxymethyltransferase2) involved in the methionine-folate cycle are also repressed by B12 in C. reinhardtii. The strong repressible nature and high sensitivity of the B12-responsive element has promising biotechnological applications as a cost-effective regulatory gene expression tool.
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Liu J, Chakraborty S, Hosseinzadeh P, Yu Y, Tian S, Petrik I, Bhagi A, Lu Y. Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. Chem Rev 2014; 114:4366-469. [PMID: 24758379 PMCID: PMC4002152 DOI: 10.1021/cr400479b] [Citation(s) in RCA: 549] [Impact Index Per Article: 54.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Jing Liu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Saumen Chakraborty
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Parisa Hosseinzadeh
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yang Yu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shiliang Tian
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Igor Petrik
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ambika Bhagi
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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Perrineau MM, Zelzion E, Gross J, Price DC, Boyd J, Bhattacharya D. Evolution of salt tolerance in a laboratory reared population ofChlamydomonas reinhardtii. Environ Microbiol 2014; 16:1755-66. [DOI: 10.1111/1462-2920.12372] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 12/15/2013] [Indexed: 01/10/2023]
Affiliation(s)
| | - Ehud Zelzion
- Department of Ecology, Evolution and Natural Resources
| | | | - Dana C. Price
- Department of Ecology, Evolution and Natural Resources
| | - Jeffrey Boyd
- Department of Biochemistry and Microbiology; Rutgers University; New Brunswick New Jersey 08901 USA
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Photobiological hydrogen production: Bioenergetics and challenges for its practical application. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2013. [DOI: 10.1016/j.jphotochemrev.2013.05.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Roy A, Sarrou I, Vaughn MD, Astashkin AV, Ghirlanda G. De Novo Design of an Artificial Bis[4Fe-4S] Binding Protein. Biochemistry 2013; 52:7586-94. [DOI: 10.1021/bi401199s] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anindya Roy
- Department
of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Iosifina Sarrou
- Department
of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Michael D. Vaughn
- Department
of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Andrei V. Astashkin
- Department
of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Giovanna Ghirlanda
- Department
of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
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Yang S, Guarnieri MT, Smolinski S, Ghirardi M, Pienkos PT. De novo transcriptomic analysis of hydrogen production in the green alga Chlamydomonas moewusii through RNA-Seq. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:118. [PMID: 23971877 PMCID: PMC3846465 DOI: 10.1186/1754-6834-6-118] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 08/05/2013] [Indexed: 05/04/2023]
Abstract
BACKGROUND Microalgae can make a significant contribution towards meeting global renewable energy needs in both carbon-based and hydrogen (H2) biofuel. The development of energy-related products from algae could be accelerated with improvements in systems biology tools, and recent advances in sequencing technology provide a platform for enhanced transcriptomic analyses. However, these techniques are still heavily reliant upon available genomic sequence data. Chlamydomonas moewusii is a unicellular green alga capable of evolving molecular H2 under both dark and light anaerobic conditions, and has high hydrogenase activity that can be rapidly induced. However, to date, there is no systematic investigation of transcriptomic profiling during induction of H2 photoproduction in this organism. RESULTS In this work, RNA-Seq was applied to investigate transcriptomic profiles during the dark anaerobic induction of H2 photoproduction. 156 million reads generated from 7 samples were then used for de novo assembly after data trimming. BlastX results against NCBI database and Blast2GO results were used to interpret the functions of the assembled 34,136 contigs, which were then used as the reference contigs for RNA-Seq analysis. Our results indicated that more contigs were differentially expressed during the period of early and higher H2 photoproduction, and fewer contigs were differentially expressed when H2-photoproduction rates decreased. In addition, C. moewusii and C. reinhardtii share core functional pathways, and transcripts for H2 photoproduction and anaerobic metabolite production were identified in both organisms. C. moewusii also possesses similar metabolic flexibility as C. reinhardtii, and the difference between C. moewusii and C. reinhardtii on hydrogenase expression and anaerobic fermentative pathways involved in redox balancing may explain their different profiles of hydrogenase activity and secreted anaerobic metabolites. CONCLUSIONS Herein, we have described a workflow using commercial software to analyze RNA-Seq data without reference genome sequence information, which can be applied to other unsequenced microorganisms. This study provided biological insights into the anaerobic fermentation and H2 photoproduction of C. moewusii, and the first transcriptomic RNA-Seq dataset of C. moewusii generated in this study also offer baseline data for further investigation (e.g. regulatory proteins related to fermentative pathway discussed in this study) of this organism as a H2-photoproduction strain.
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Affiliation(s)
| | | | - Sharon Smolinski
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Maria Ghirardi
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
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Ghysels B, Godaux D, Matagne RF, Cardol P, Franck F. Function of the chloroplast hydrogenase in the microalga Chlamydomonas: the role of hydrogenase and state transitions during photosynthetic activation in anaerobiosis. PLoS One 2013; 8:e64161. [PMID: 23717558 PMCID: PMC3662714 DOI: 10.1371/journal.pone.0064161] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 04/10/2013] [Indexed: 01/12/2023] Open
Abstract
Like a majority of photosynthetic microorganisms, the green unicellular alga Chlamydomonas reinhardtii may encounter O2 deprived conditions on a regular basis. In response to anaerobiosis or in a respiration defective context, the photosynthetic electron transport chain of Chlamydomonas is remodeled by a state transition process to a conformation that favours the photoproduction of ATP at the expense of reductant synthesis. In some unicellular green algae including Chlamydomonas, anoxia also triggers the induction of a chloroplast-located, oxygen sensitive hydrogenase, which accepts electrons from reduced ferredoxin to convert protons into molecular hydrogen. Although microalgal hydrogen evolution has received much interest for its biotechnological potential, its physiological role remains unclear. By using specific Chlamydomonas mutants, we demonstrate that the state transition ability and the hydrogenase function are both critical for induction of photosynthesis in anoxia. These two processes are thus important for survival of the cells when they are transiently placed in an anaerobic environment.
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Affiliation(s)
- Bart Ghysels
- Laboratory of Bioenergetics, Institute of Plant Biology B22, University of Liège, Liège, Belgium
| | - Damien Godaux
- Laboratory of Genetics of Microorganisms, Institute of Plant Biology B22, University of Liège, Liège, Belgium
| | - René F. Matagne
- Laboratory of Genetics of Microorganisms, Institute of Plant Biology B22, University of Liège, Liège, Belgium
| | - Pierre Cardol
- Laboratory of Genetics of Microorganisms, Institute of Plant Biology B22, University of Liège, Liège, Belgium
| | - Fabrice Franck
- Laboratory of Bioenergetics, Institute of Plant Biology B22, University of Liège, Liège, Belgium
- * E-mail:
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40
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Catalanotti C, Yang W, Posewitz MC, Grossman AR. Fermentation metabolism and its evolution in algae. FRONTIERS IN PLANT SCIENCE 2013; 4:150. [PMID: 23734158 PMCID: PMC3660698 DOI: 10.3389/fpls.2013.00150] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 05/02/2013] [Indexed: 05/20/2023]
Abstract
Fermentation or anoxic metabolism allows unicellular organisms to colonize environments that become anoxic. Free-living unicellular algae capable of a photoautotrophic lifestyle can also use a range of metabolic circuitry associated with different branches of fermentation metabolism. While algae that perform mixed-acid fermentation are widespread, the use of anaerobic respiration is more typical of eukaryotic heterotrophs. The occurrence of a core set of fermentation pathways among the algae provides insights into the evolutionary origins of these pathways, which were likely derived from a common ancestral eukaryote. Based on genomic, transcriptomic, and biochemical studies, anaerobic energy metabolism has been examined in more detail in Chlamydomonas reinhardtii (Chlamydomonas) than in any other photosynthetic protist. This green alga is metabolically flexible and can sustain energy generation and maintain cellular redox balance under a variety of different environmental conditions. Fermentation metabolism in Chlamydomonas appears to be highly controlled, and the flexible use of the different branches of fermentation metabolism has been demonstrated in studies of various metabolic mutants. Additionally, when Chlamydomonas ferments polysaccharides, it has the ability to eliminate part of the reductant (to sustain glycolysis) through the production of H2, a molecule that can be developed as a source of renewable energy. To date, little is known about the specific role(s) of the different branches of fermentation metabolism, how photosynthetic eukaryotes sense changes in environmental O2 levels, and the mechanisms involved in controlling these responses, at both the transcriptional and post-transcriptional levels. In this review, we focus on fermentation metabolism in Chlamydomonas and other protists, with only a brief discussion of plant fermentation when relevant, since it is thoroughly discussed in other articles in this volume.
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Affiliation(s)
- Claudia Catalanotti
- Department of Plant Biology, Carnegie Institution for ScienceStanford, CA, USA
| | - Wenqiang Yang
- Department of Plant Biology, Carnegie Institution for ScienceStanford, CA, USA
| | - Matthew C. Posewitz
- Department of Chemistry and Geochemistry, Colorado School of MinesGolden, CO, USA
| | - Arthur R. Grossman
- Department of Plant Biology, Carnegie Institution for ScienceStanford, CA, USA
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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.
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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.)
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Takahashi H, Clowez S, Wollman FA, Vallon O, Rappaport F. Cyclic electron flow is redox-controlled but independent of state transition. Nat Commun 2013; 4:1954. [PMID: 23760547 PMCID: PMC3709502 DOI: 10.1038/ncomms2954] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 04/29/2013] [Indexed: 11/23/2022] Open
Abstract
Photosynthesis is the biological process that feeds the biosphere with reduced carbon. The assimilation of CO2 requires the fine tuning of two co-existing functional modes: linear electron flow, which provides NADPH and ATP, and cyclic electron flow, which only sustains ATP synthesis. Although the importance of this fine tuning is appreciated, its mechanism remains equivocal. Here we show that cyclic electron flow as well as formation of supercomplexes, thought to contribute to the enhancement of cyclic electron flow, are promoted in reducing conditions with no correlation with the reorganization of the thylakoid membranes associated with the migration of antenna proteins towards Photosystems I or II, a process known as state transition. We show that cyclic electron flow is tuned by the redox power and this provides a mechanistic model applying to the entire green lineage including the vast majority of the cases in which state transition only involves a moderate fraction of the antenna.
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Affiliation(s)
- Hiroko Takahashi
- Institut de Biologie Physico-Chimique, UMR 7141 CNRS-UPMC, 13 rue P et M Curie, 75005 Paris, France
- These authors contributed equally to this work
| | - Sophie Clowez
- Institut de Biologie Physico-Chimique, UMR 7141 CNRS-UPMC, 13 rue P et M Curie, 75005 Paris, France
- These authors contributed equally to this work
| | - Francis-André Wollman
- Institut de Biologie Physico-Chimique, UMR 7141 CNRS-UPMC, 13 rue P et M Curie, 75005 Paris, France
| | - Olivier Vallon
- Institut de Biologie Physico-Chimique, UMR 7141 CNRS-UPMC, 13 rue P et M Curie, 75005 Paris, France
| | - Fabrice Rappaport
- Institut de Biologie Physico-Chimique, UMR 7141 CNRS-UPMC, 13 rue P et M Curie, 75005 Paris, France
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Burgess SJ, Tredwell G, Molnàr A, Bundy JG, Nixon PJ. Artificial microRNA-mediated knockdown of pyruvate formate lyase (PFL1) provides evidence for an active 3-hydroxybutyrate production pathway in the green alga Chlamydomonas reinhardtii. J Biotechnol 2012; 162:57-66. [DOI: 10.1016/j.jbiotec.2012.05.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2011] [Revised: 04/02/2012] [Accepted: 05/30/2012] [Indexed: 12/17/2022]
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Atteia A, van Lis R, Tielens AGM, Martin WF. Anaerobic energy metabolism in unicellular photosynthetic eukaryotes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:210-23. [PMID: 22902601 DOI: 10.1016/j.bbabio.2012.08.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Revised: 07/30/2012] [Accepted: 08/05/2012] [Indexed: 12/25/2022]
Abstract
Anaerobic metabolic pathways allow unicellular organisms to tolerate or colonize anoxic environments. Over the past ten years, genome sequencing projects have brought a new light on the extent of anaerobic metabolism in eukaryotes. A surprising development has been that free-living unicellular algae capable of photoautotrophic lifestyle are, in terms of their enzymatic repertoire, among the best equipped eukaryotes known when it comes to anaerobic energy metabolism. Some of these algae are marine organisms, common in the oceans, others are more typically soil inhabitants. All these species are important from the ecological (O(2)/CO(2) budget), biotechnological, and evolutionary perspectives. In the unicellular algae surveyed here, mixed-acid type fermentations are widespread while anaerobic respiration, which is more typical of eukaryotic heterotrophs, appears to be rare. The presence of a core anaerobic metabolism among the algae provides insights into its evolutionary origin, which traces to the eukaryote common ancestor. The predicted fermentative enzymes often exhibit an amino acid extension at the N-terminus, suggesting that these proteins might be compartmentalized in the cell, likely in the chloroplast or the mitochondrion. The green algae Chlamydomonas reinhardtii and Chlorella NC64 have the most extended set of fermentative enzymes reported so far. Among the eukaryotes with secondary plastids, the diatom Thalassiosira pseudonana has the most pronounced anaerobic capabilities as yet. From the standpoints of genomic, transcriptomic, and biochemical studies, anaerobic energy metabolism in C. reinhardtii remains the best characterized among photosynthetic protists. This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems.
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Affiliation(s)
- Ariane Atteia
- Unité de Bioénergétique et Ingénierie des Protéines-UMR 7281, CNRS-Aix-Marseille Univ, 31 Chemin Joseph Aiguier, 13402 Marseille, France
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Murthy UMN, Wecker MSA, Posewitz MC, Gilles-Gonzalez MA, Ghirardi ML. Novel FixL homologues in Chlamydomonas reinhardtii bind heme and O(2). FEBS Lett 2012; 586:4282-8. [PMID: 22801216 DOI: 10.1016/j.febslet.2012.06.052] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Revised: 06/26/2012] [Accepted: 06/28/2012] [Indexed: 11/17/2022]
Abstract
Genome inspection revealed nine putative heme-binding, FixL-homologous proteins in Chlamydomonas reinhardtii. The heme-binding domains from two of these proteins, FXL1 and FXL5 were cloned, expressed in Escherichia coli, purified and characterized. The recombinant FXL1 and FXL5 domains stained positively for heme, while mutations in the putative ligand-binding histidine FXL1-H200S and FXL5-H200S resulted in loss of heme binding. The FXL1 and FXL5 [Fe(II), bound O(2)] had Soret absorption maxima around 415 nm, and weaker absorptions at longer wavelengths, in concurrence with the literature. Ligand-binding measurements showed that FXL1 and FXL5 bind O(2) with moderate affinity, 135 and 222 μM, respectively. This suggests that Chlamydomonas may use the FXL proteins in O(2)-sensing mechanisms analogous to that reported in nitrogen-fixing bacteria to regulate gene expression.
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Affiliation(s)
- U M Narayana Murthy
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
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Swirsky Whitney LA, Novi G, Perata P, Loreti E. Distinct mechanisms regulating gene expression coexist within the fermentative pathways in Chlamydomonas reinhardtii. ScientificWorldJournal 2012; 2012:565047. [PMID: 22792045 PMCID: PMC3385630 DOI: 10.1100/2012/565047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Accepted: 03/21/2012] [Indexed: 12/12/2022] Open
Abstract
Under dark anoxia, the unicellular green algae Chlamydomonas reinhardtii may produce hydrogen by means of its hydrogenase enzymes, in particular HYD1, using reductants derived from the degradation of intercellular carbon stores. Other enzymes belonging to the fermentative pathways compete for the same reductants. A complete understanding of the mechanisms determining the activation of one pathway rather than another will help us engineer Chlamydomonas for fermentative metabolite production, including hydrogen. We examined the expression pattern of the fermentative genes PDC3, LDH1, ADH2, PFL1, and PFR1 in response to day-night cycles, continuous light, continuous darkness, and low or high oxygen availability, which are all conditions that vary on a regular basis in Chlamydomonas' natural environment. We found that all genes except PFL1 show daily fluctuations in expression, and that PFR1 differentiated itself from the others in that it is clearly responsive to low oxygen, where as PDC3, LDH1, and ADH2 are primarily under diurnal regulation. Our results provide evidence that there exist at least three different regulatory mechanisms within the fermentative pathways and suggest that the fermentative pathways are not redundant but rather that availability of a variety of pathways allows for a differential metabolic response to different environmental conditions.
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Bailey-Serres J, Fukao T, Gibbs DJ, Holdsworth MJ, Lee SC, Licausi F, Perata P, Voesenek LACJ, van Dongen JT. Making sense of low oxygen sensing. TRENDS IN PLANT SCIENCE 2012; 17:129-38. [PMID: 22280796 DOI: 10.1016/j.tplants.2011.12.004] [Citation(s) in RCA: 289] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2011] [Revised: 12/06/2011] [Accepted: 12/13/2011] [Indexed: 05/21/2023]
Abstract
Plant-specific group VII Ethylene Response Factor (ERF) transcription factors have emerged as pivotal regulators of flooding and low oxygen responses. In rice (Oryza sativa), these proteins regulate contrasting strategies of flooding survival. Recent studies on Arabidopsis thaliana group VII ERFs show they are stabilized under hypoxia but destabilized under oxygen-replete conditions via the N-end rule pathway of targeted proteolysis. Oxygen-dependent sequestration at the plasma membrane maintains at least one of these proteins, RAP2.12, under normoxia. Remarkably, SUB1A, the rice group VII ERF that enables prolonged submergence tolerance, appears to evade oxygen-regulated N-end rule degradation. We propose that the turnover of group VII ERFs is of ecological relevance in wetland species and might be manipulated to improve flood tolerance of crops.
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Affiliation(s)
- Julia Bailey-Serres
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, CA 92521-0124, USA.
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Magneschi L, Catalanotti C, Subramanian V, Dubini A, Yang W, Mus F, Posewitz MC, Seibert M, Perata P, Grossman AR. A mutant in the ADH1 gene of Chlamydomonas reinhardtii elicits metabolic restructuring during anaerobiosis. PLANT PHYSIOLOGY 2012; 158:1293-305. [PMID: 22271746 PMCID: PMC3291268 DOI: 10.1104/pp.111.191569] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Accepted: 01/21/2012] [Indexed: 05/20/2023]
Abstract
The green alga Chlamydomonas reinhardtii has numerous genes encoding enzymes that function in fermentative pathways. Among these, the bifunctional alcohol/acetaldehyde dehydrogenase (ADH1), highly homologous to the Escherichia coli AdhE enzyme, is proposed to be a key component of fermentative metabolism. To investigate the physiological role of ADH1 in dark anoxic metabolism, a Chlamydomonas adh1 mutant was generated. We detected no ethanol synthesis in this mutant when it was placed under anoxia; the two other ADH homologs encoded on the Chlamydomonas genome do not appear to participate in ethanol production under our experimental conditions. Pyruvate formate lyase, acetate kinase, and hydrogenase protein levels were similar in wild-type cells and the adh1 mutant, while the mutant had significantly more pyruvate:ferredoxin oxidoreductase. Furthermore, a marked change in metabolite levels (in addition to ethanol) synthesized by the mutant under anoxic conditions was observed; formate levels were reduced, acetate levels were elevated, and the production of CO(2) was significantly reduced, but fermentative H(2) production was unchanged relative to wild-type cells. Of particular interest is the finding that the mutant accumulates high levels of extracellular glycerol, which requires NADH as a substrate for its synthesis. Lactate production is also increased slightly in the mutant relative to the control strain. These findings demonstrate a restructuring of fermentative metabolism in the adh1 mutant in a way that sustains the recycling (oxidation) of NADH and the survival of the mutant (similar to wild-type cell survival) during dark anoxic growth.
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Affiliation(s)
- Leonardo Magneschi
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305, USA.
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Catalanotti C, Dubini A, Subramanian V, Yang W, Magneschi L, Mus F, Seibert M, Posewitz MC, Grossman AR. Altered fermentative metabolism in Chlamydomonas reinhardtii mutants lacking pyruvate formate lyase and both pyruvate formate lyase and alcohol dehydrogenase. THE PLANT CELL 2012; 24:692-707. [PMID: 22353371 PMCID: PMC3315241 DOI: 10.1105/tpc.111.093146] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Revised: 01/05/2012] [Accepted: 01/25/2012] [Indexed: 05/20/2023]
Abstract
Chlamydomonas reinhardtii, a unicellular green alga, often experiences hypoxic/anoxic soil conditions that activate fermentation metabolism. We isolated three Chlamydomonas mutants disrupted for the pyruvate formate lyase (PFL1) gene; the encoded PFL1 protein catalyzes a major fermentative pathway in wild-type Chlamydomonas cells. When the pfl1 mutants were subjected to dark fermentative conditions, they displayed an increased flux of pyruvate to lactate, elevated pyruvate decarboxylation, ethanol accumulation, diminished pyruvate oxidation by pyruvate ferredoxin oxidoreductase, and lowered H(2) production. The pfl1-1 mutant also accumulated high intracellular levels of lactate, succinate, alanine, malate, and fumarate. To further probe the system, we generated a double mutant (pfl1-1 adh1) that is unable to synthesize both formate and ethanol. This strain, like the pfl1 mutants, secreted lactate, but it also exhibited a significant increase in the levels of extracellular glycerol, acetate, and intracellular reduced sugars and a decrease in dark, fermentative H(2) production. Whereas wild-type Chlamydomonas fermentation primarily produces formate and ethanol, the double mutant reroutes glycolytic carbon to lactate and glycerol. Although the metabolic adjustments observed in the mutants facilitate NADH reoxidation and sustained glycolysis under dark, anoxic conditions, the observed changes could not have been predicted given our current knowledge of the regulation of fermentation metabolism.
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Affiliation(s)
- Claudia Catalanotti
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305, USA.
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Tsaousis AD, Leger MM, Stairs CAW, Roger AJ. The Biochemical Adaptations of Mitochondrion-Related Organelles of Parasitic and Free-Living Microbial Eukaryotes to Low Oxygen Environments. CELLULAR ORIGIN, LIFE IN EXTREME HABITATS AND ASTROBIOLOGY 2012. [DOI: 10.1007/978-94-007-1896-8_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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