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Steensma AK, Shachar-Hill Y, Walker BJ. The carbon-concentrating mechanism of the extremophilic red microalga Cyanidioschyzon merolae. PHOTOSYNTHESIS RESEARCH 2023; 156:247-264. [PMID: 36780115 PMCID: PMC10154280 DOI: 10.1007/s11120-023-01000-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 01/27/2023] [Indexed: 05/03/2023]
Abstract
Cyanidioschyzon merolae is an extremophilic red microalga which grows in low-pH, high-temperature environments. The basis of C. merolae's environmental resilience is not fully characterized, including whether this alga uses a carbon-concentrating mechanism (CCM). To determine if C. merolae uses a CCM, we measured CO2 uptake parameters using an open-path infra-red gas analyzer and compared them to values expected in the absence of a CCM. These measurements and analysis indicated that C. merolae had the gas-exchange characteristics of a CCM-operating organism: low CO2 compensation point, high affinity for external CO2, and minimized rubisco oxygenation. The biomass δ13C of C. merolae was also consistent with a CCM. The apparent presence of a CCM in C. merolae suggests the use of an unusual mechanism for carbon concentration, as C. merolae is thought to lack a pyrenoid and gas-exchange measurements indicated that C. merolae primarily takes up inorganic carbon as carbon dioxide, rather than bicarbonate. We use homology to known CCM components to propose a model of a pH-gradient-based CCM, and we discuss how this CCM can be further investigated.
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Affiliation(s)
- Anne K Steensma
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
- Michigan State University - Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, USA
| | - Yair Shachar-Hill
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Berkley J Walker
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA.
- Michigan State University - Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, USA.
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Perez Saura P, Chabi M, Corato A, Cardol P, Remacle C. Cell adaptation of the extremophilic red microalga Galdieria sulphuraria to the availability of carbon sources. FRONTIERS IN PLANT SCIENCE 2022; 13:978246. [PMID: 36186036 PMCID: PMC9520601 DOI: 10.3389/fpls.2022.978246] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 08/16/2022] [Indexed: 06/12/2023]
Abstract
Global energy demand and fossil fuels impact on climate can be partially managed by an increase in the use of biofuels for transports and industries. Biodiesel production is generally preceded by a transesterification process of the green biomass triacylglycerols that generates large amounts of glycerol as a by-product. In this study, the extremophilic red microalga Galdieria sulphuraria 074W was cultivated in heterotrophy. The microalgal growth parameters and biomass composition were compared when grown on an equivalent molar concentration of carbon of either glucose or glycerol as unique carbon source. The maximal biomass reached in these two conditions was not significantly different (∼2.5 g.L-1). Fatty acid profile, protein and storage carbohydrate contents were also statistically similar, irrespectively of the metabolized carbon source. We also observed that the pigment content of G. sulphuraria cells decreased during heterotrophic growth compared to photoautotrophic cultivated cells, and that this diminution was more important in the presence of glucose than glycerol: cells were yellowish in the presence of glucose and green in the presence of glycerol. The pigmentation was restored when glucose was totally consumed in the medium, suggesting that the presence of glucose repressed pigment synthesis. Based on this observation, a transcriptome analysis was performed in order to better understand the mechanisms involved in the loss of color mediated by darkness and by glucose in G. sulphuraria. Three conditions were analyzed: heterotrophy with glycerol or glucose and phototrophy. This allowed us to understand the transcriptional response of cells to light and dark environments both at the nuclear and chloroplast levels, and to show that transcription of gene families, acquired by horizontal gene transfer, such as sugar, amino acid, or acetate transporters, were involved in the response to the availability of different (in)organic sources.
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Miyagishima SY, Tanaka K. The Unicellular Red Alga Cyanidioschyzon merolae-The Simplest Model of a Photosynthetic Eukaryote. PLANT & CELL PHYSIOLOGY 2021; 62:926-941. [PMID: 33836072 PMCID: PMC8504449 DOI: 10.1093/pcp/pcab052] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/01/2021] [Indexed: 05/13/2023]
Abstract
Several species of unicellular eukaryotic algae exhibit relatively simple genomic and cellular architecture. Laboratory cultures of these algae grow faster than plants and often provide homogeneous cellular populations exposed to an almost equal environment. These characteristics are ideal for conducting experiments at the cellular and subcellular levels. Many microalgal lineages have recently become genetically tractable, which have started to evoke new streams of studies. Among such algae, the unicellular red alga Cyanidioschyzon merolae is the simplest organism; it possesses the minimum number of membranous organelles, only 4,775 protein-coding genes in the nucleus, and its cell cycle progression can be highly synchronized with the diel cycle. These properties facilitate diverse omics analyses of cellular proliferation and structural analyses of the intracellular relationship among organelles. C. merolae cells lack a rigid cell wall and are thus relatively easily disrupted, facilitating biochemical analyses. Multiple chromosomal loci can be edited by highly efficient homologous recombination. The procedures for the inducible/repressive expression of a transgene or an endogenous gene in the nucleus and for chloroplast genome modification have also been developed. Here, we summarize the features and experimental techniques of C. merolae and provide examples of studies using this alga. From these studies, it is clear that C. merolae-either alone or in comparative and combinatory studies with other photosynthetic organisms-can provide significant insights into the biology of photosynthetic eukaryotes.
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Affiliation(s)
- Shin-Ya Miyagishima
- * Corresponding authors: Shin-Ya Miyagishima, E-mail: ; Fax, +81-55-981-9412; Kan Tanaka, E-mail:
| | - Kan Tanaka
- * Corresponding authors: Shin-Ya Miyagishima, E-mail: ; Fax, +81-55-981-9412; Kan Tanaka, E-mail:
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Curien G, Lyska D, Guglielmino E, Westhoff P, Janetzko J, Tardif M, Hallopeau C, Brugière S, Dal Bo D, Decelle J, Gallet B, Falconet D, Carone M, Remacle C, Ferro M, Weber AP, Finazzi G. Mixotrophic growth of the extremophile Galdieria sulphuraria reveals the flexibility of its carbon assimilation metabolism. THE NEW PHYTOLOGIST 2021; 231:326-338. [PMID: 33764540 PMCID: PMC8252106 DOI: 10.1111/nph.17359] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 03/18/2021] [Indexed: 05/04/2023]
Abstract
Galdieria sulphuraria is a cosmopolitan microalga found in volcanic hot springs and calderas. It grows at low pH in photoautotrophic (use of light as a source of energy) or heterotrophic (respiration as a source of energy) conditions, using an unusually broad range of organic carbon sources. Previous data suggested that G. sulphuraria cannot grow mixotrophically (simultaneously exploiting light and organic carbon as energy sources), its photosynthetic machinery being repressed by organic carbon. Here, we show that G. sulphuraria SAG21.92 thrives in photoautotrophy, heterotrophy and mixotrophy. By comparing growth, biomass production, photosynthetic and respiratory performances in these three trophic modes, we show that addition of organic carbon to cultures (mixotrophy) relieves inorganic carbon limitation of photosynthesis thanks to increased CO2 supply through respiration. This synergistic effect is lost when inorganic carbon limitation is artificially overcome by saturating photosynthesis with added external CO2 . Proteomic and metabolic profiling corroborates this conclusion suggesting that mixotrophy is an opportunistic mechanism to increase intracellular CO2 concentration under physiological conditions, boosting photosynthesis by enhancing the carboxylation activity of Ribulose-1,5-bisphosphate carboxylase-oxygenase (Rubisco) and decreasing photorespiration. We discuss possible implications of these findings for the ecological success of Galdieria in extreme environments and for biotechnological applications.
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Affiliation(s)
- Gilles Curien
- Laboratoire de Physiologie Cellulaire et Végétale. Université Grenoble AlpesCNRSCEAINRAeGrenoble Cedex 938054France
| | - Dagmar Lyska
- Institute of Plant BiochemistryCluster of Excellence on Plant Sciences (CEPLAS)Heinrich Heine UniversityDüsseldorf40225Germany
| | - Erika Guglielmino
- Laboratoire de Physiologie Cellulaire et Végétale. Université Grenoble AlpesCNRSCEAINRAeGrenoble Cedex 938054France
| | - Phillip Westhoff
- Institute of Plant BiochemistryCluster of Excellence on Plant Sciences (CEPLAS)Heinrich Heine UniversityDüsseldorf40225Germany
| | - Janina Janetzko
- Institute of Plant BiochemistryCluster of Excellence on Plant Sciences (CEPLAS)Heinrich Heine UniversityDüsseldorf40225Germany
| | - Marianne Tardif
- EdyP Laboratoire Biologie à Grande Echelle, Université Grenoble AlpesCEAInsermBGE U1038Grenoble Cedex 938054France
| | - Clément Hallopeau
- Laboratoire de Physiologie Cellulaire et Végétale. Université Grenoble AlpesCNRSCEAINRAeGrenoble Cedex 938054France
| | - Sabine Brugière
- EdyP Laboratoire Biologie à Grande Echelle, Université Grenoble AlpesCEAInsermBGE U1038Grenoble Cedex 938054France
| | - Davide Dal Bo
- Laboratoire de Physiologie Cellulaire et Végétale. Université Grenoble AlpesCNRSCEAINRAeGrenoble Cedex 938054France
| | - Johan Decelle
- Laboratoire de Physiologie Cellulaire et Végétale. Université Grenoble AlpesCNRSCEAINRAeGrenoble Cedex 938054France
| | - Benoit Gallet
- Institut de Biologie StructuraleUniversité Grenoble AlpesCNRSCEA71 Avenue des MartyrsGrenoble38044France
| | - Denis Falconet
- Laboratoire de Physiologie Cellulaire et Végétale. Université Grenoble AlpesCNRSCEAINRAeGrenoble Cedex 938054France
| | - Michele Carone
- Genetics and Physiology of MicroalgaeInBios/Phytosystems Research UnitUniversity of LiegeLiège4000Belgium
| | - Claire Remacle
- Genetics and Physiology of MicroalgaeInBios/Phytosystems Research UnitUniversity of LiegeLiège4000Belgium
| | - Myriam Ferro
- EdyP Laboratoire Biologie à Grande Echelle, Université Grenoble AlpesCEAInsermBGE U1038Grenoble Cedex 938054France
| | - Andreas P.M. Weber
- Institute of Plant BiochemistryCluster of Excellence on Plant Sciences (CEPLAS)Heinrich Heine UniversityDüsseldorf40225Germany
| | - Giovanni Finazzi
- Laboratoire de Physiologie Cellulaire et Végétale. Université Grenoble AlpesCNRSCEAINRAeGrenoble Cedex 938054France
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Bucking the trend of pollinator decline: the population genetics of a range expanding bumblebee. Evol Ecol 2021. [DOI: 10.1007/s10682-021-10111-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Parys E, Krupnik T, Kułak I, Kania K, Romanowska E. Photosynthesis of the Cyanidioschyzon merolae cells in blue, red, and white light. PHOTOSYNTHESIS RESEARCH 2021; 147:61-73. [PMID: 33231791 PMCID: PMC7728651 DOI: 10.1007/s11120-020-00796-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/06/2020] [Indexed: 05/19/2023]
Abstract
Photosynthesis and respiration rates, pigment contents, CO2 compensation point, and carbonic anhydrase activity in Cyanidioschizon merolae cultivated in blue, red, and white light were measured. At the same light quality as during the growth, the photosynthesis of cells in blue light was significantly lowered, while under red light only slightly decreased as compared with white control. In white light, the quality of light during growth had no effect on the rate of photosynthesis at low O2 and high CO2 concentration, whereas their atmospheric level caused only slight decrease. Blue light reduced markedly photosynthesis rate of cells grown in white and red light, whereas the effect of red light was not so great. Only cells grown in the blue light showed increased respiration rate following the period of both the darkness and illumination. Cells grown in red light had the greatest amount of chlorophyll a, zeaxanthin, and β-carotene, while those in blue light had more phycocyanin. The dependence on O2 concentration of the CO2 compensation point and the rate of photosynthesis indicate that this alga possessed photorespiration. Differences in the rate of photosynthesis at different light qualities are discussed in relation to the content of pigments and transferred light energy together with the possible influence of related processes. Our data showed that blue and red light regulate photosynthesis in C. merolae for adjusting its metabolism to unfavorable for photosynthesis light conditions.
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Affiliation(s)
- Eugeniusz Parys
- Department of Molecular Plant Physiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Tomasz Krupnik
- Department of Molecular Plant Physiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Ilona Kułak
- Department of Molecular Plant Physiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Kinga Kania
- Department of Molecular Plant Physiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Elżbieta Romanowska
- Department of Molecular Plant Physiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland.
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Schneider K, Venn B, Mühlhaus T. TMEA: A Thermodynamically Motivated Framework for Functional Characterization of Biological Responses to System Acclimation. ENTROPY 2020; 22:e22091030. [PMID: 33286800 PMCID: PMC7597090 DOI: 10.3390/e22091030] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 09/07/2020] [Accepted: 09/11/2020] [Indexed: 12/16/2022]
Abstract
The objective of gene set enrichment analysis (GSEA) in modern biological studies is to identify functional profiles in huge sets of biomolecules generated by high-throughput measurements of genes, transcripts, metabolites, and proteins. GSEA is based on a two-stage process using classical statistical analysis to score the input data and subsequent testing for overrepresentation of the enrichment score within a given functional coherent set. However, enrichment scores computed by different methods are merely statistically motivated and often elusive to direct biological interpretation. Here, we propose a novel approach, called Thermodynamically Motivated Enrichment Analysis (TMEA), to account for the energy investment in biological relevant processes. Therefore, TMEA is based on surprisal analysis, which offers a thermodynamic-free energy-based representation of the biological steady state and of the biological change. The contribution of each biomolecule underlying the changes in free energy is used in a Monte Carlo resampling procedure resulting in a functional characterization directly coupled to the thermodynamic characterization of biological responses to system perturbations. To illustrate the utility of our method on real experimental data, we benchmark our approach on plant acclimation to high light and compare the performance of TMEA with the most frequently used method for GSEA.
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Takemura T, Imamura S, Kobayashi Y, Tanaka K. Construction of a Selectable Marker Recycling System and the Use in Epitope Tagging of Multiple Nuclear Genes in the Unicellular Red Alga Cyanidioschyzon merolae. PLANT & CELL PHYSIOLOGY 2018; 59:2308-2316. [PMID: 30099537 DOI: 10.1093/pcp/pcy156] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 07/30/2018] [Indexed: 06/08/2023]
Abstract
The nuclear genome of the unicellular red alga Cyanidioschyzon merolae can be modified by homologous recombination with exogenously introduced DNA. However, it is presently difficult to modify multiple chromosome loci because of the limited number of available positive selectable markers. In this study, we constructed a modified URA5.3 gene (URA5.3T), which can be repeatedly used for nuclear genome transformation, as well as two plasmid vectors for 3× FLAG- or 3× Myc-epitope tagging of nuclear-encoded proteins using URA5.3T. In the URA5.3T marker, the promoter region and open reading frame were located between directly repeated URA5.3 terminator sequences, and the URA5.3 gene can be eliminated by 5-fluoroorotic acid selection through homologous recombination. To demonstrate the utility of the constructed system, a 3× FLAG-tag and 3× Myc-tag were introduced at the C-termini of two of the six Rab proteins in C. merolae, CmRab18 and CmRab7, respectively, and the differential expression levels were successfully monitored by immunoblot analysis using these epitope tags. The URA5.3T marker's introduction and elimination cycle can be repeated. Thus, we have constructed a marker recycling system for C. merolae nuclear transformation. A novel procedure to obtain a high plating efficiency of C. merolae cells on solid gellan gum plates is also presented.
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Affiliation(s)
- Tokiaki Takemura
- Laboratory for Chemistry and Life Science, Institute of Innovative Science, Tokyo Institute of Technology, Nagatsuta, Yokohama, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta, Yokohama, Japan
| | - Sousuke Imamura
- Laboratory for Chemistry and Life Science, Institute of Innovative Science, Tokyo Institute of Technology, Nagatsuta, Yokohama, Japan
| | - Yuki Kobayashi
- Laboratory for Chemistry and Life Science, Institute of Innovative Science, Tokyo Institute of Technology, Nagatsuta, Yokohama, Japan
| | - Kan Tanaka
- Laboratory for Chemistry and Life Science, Institute of Innovative Science, Tokyo Institute of Technology, Nagatsuta, Yokohama, Japan
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Affiliation(s)
- Maria Mittag
- Friedrich Schiller University Jena, Jena, Germany.
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