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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] [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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Zou Y, Sabljić I, Horbach N, Dauphinee AN, Åsman A, Sancho Temino L, Minina EA, Drag M, Stael S, Poreba M, Ståhlberg J, Bozhkov PV. Thermoprotection by a cell membrane-localized metacaspase in a green alga. THE PLANT CELL 2024; 36:665-687. [PMID: 37971931 PMCID: PMC10896300 DOI: 10.1093/plcell/koad289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 10/10/2023] [Accepted: 11/12/2023] [Indexed: 11/19/2023]
Abstract
Caspases are restricted to animals, while other organisms, including plants, possess metacaspases (MCAs), a more ancient and broader class of structurally related yet biochemically distinct proteases. Our current understanding of plant MCAs is derived from studies in streptophytes, and mostly in Arabidopsis (Arabidopsis thaliana) with 9 MCAs with partially redundant activities. In contrast to streptophytes, most chlorophytes contain only 1 or 2 uncharacterized MCAs, providing an excellent platform for MCA research. Here we investigated CrMCA-II, the single type-II MCA from the model chlorophyte Chlamydomonas (Chlamydomonas reinhardtii). Surprisingly, unlike other studied MCAs and similar to caspases, CrMCA-II dimerizes both in vitro and in vivo. Furthermore, activation of CrMCA-II in vivo correlated with its dimerization. Most of CrMCA-II in the cell was present as a proenzyme (zymogen) attached to the plasma membrane (PM). Deletion of CrMCA-II by genome editing compromised thermotolerance, leading to increased cell death under heat stress. Adding back either wild-type or catalytically dead CrMCA-II restored thermoprotection, suggesting that its proteolytic activity is dispensable for this effect. Finally, we connected the non-proteolytic role of CrMCA-II in thermotolerance to the ability to modulate PM fluidity. Our study reveals an ancient, MCA-dependent thermotolerance mechanism retained by Chlamydomonas and probably lost during the evolution of multicellularity.
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Affiliation(s)
- Yong Zou
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-756 51 Uppsala, Sweden
| | - Igor Sabljić
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-756 51 Uppsala, Sweden
| | - Natalia Horbach
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, 50-370 Wroclaw, Poland
| | - Adrian N Dauphinee
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-756 51 Uppsala, Sweden
| | - Anna Åsman
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-756 51 Uppsala, Sweden
| | - Lucia Sancho Temino
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-756 51 Uppsala, Sweden
| | - Elena A Minina
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-756 51 Uppsala, Sweden
| | - Marcin Drag
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, 50-370 Wroclaw, Poland
| | - Simon Stael
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-756 51 Uppsala, Sweden
| | - Marcin Poreba
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, 50-370 Wroclaw, Poland
| | - Jerry Ståhlberg
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-756 51 Uppsala, Sweden
| | - Peter V Bozhkov
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-756 51 Uppsala, Sweden
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Bafort Q, Prost L, Aydogdu E, Van de Vloet A, Casteleyn G, Van de Peer Y, De Clerck O. Studying Whole-Genome Duplication Using Experimental Evolution of Chlamydomonas. Methods Mol Biol 2023; 2545:351-372. [PMID: 36720822 DOI: 10.1007/978-1-0716-2561-3_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
In this chapter, we present the use of Chlamydomonas reinhardtii in experiments designed to study the evolutionary impacts of whole genome duplication. We shortly introduce the algal species and depict why it is an excellent model for experimental evolution. Subsequently, we discuss the most relevant steps and methods in the design of a ploidy-related Chlamydomonas experiment. These steps include strain selection, ploidy determination, different methods of making diplo- and polyploid Chlamydomonas cells, replication, culturing conditions, preservation, and the ways to quantify phenotypic and genotypic change.
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Affiliation(s)
- Quinten Bafort
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium. .,Department of Biology, Ghent University, Ghent, Belgium. .,VIB Center for Plant Systems Biology, VIB, Ghent, Belgium.
| | - Lucas Prost
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium. .,Department of Biology, Ghent University, Ghent, Belgium. .,VIB Center for Plant Systems Biology, VIB, Ghent, Belgium.
| | - Eylem Aydogdu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Antoine Van de Vloet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Department of Biology, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Griet Casteleyn
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Department of Biology, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
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Barati B, Zafar FF, Qian L, Wang S, El-Fatah Abomohra A. Bioenergy characteristics of microalgae under elevated carbon dioxide. FUEL 2022; 321:123958. [DOI: 10.1016/j.fuel.2022.123958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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Liang D, Wang X, Fan W. Potential application of Au core labeling for tracking Ag nanoparticles in the aquatic and biological system. WATER RESEARCH 2022; 215:118280. [PMID: 35305490 DOI: 10.1016/j.watres.2022.118280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
The entering of silver nanoparticles (Ag NPs) in natural environments constantly increases due to their widespread production and application. While the environmental behavior, impacts, and fate of Ag NPs were critically assessed, the main challenge represents continuous tracking and quantification of Ag NPs in environmental and biological matrices. A group of labeled Ag NPs with gold cores (Au@Ag NPs) was developed for distinguishing between pristine Ag NPs and their other forms, and we comprehensively compared their physicochemical properties, environmental behavior, and biological effects with unlabeled Ag NPs. The electron transfer process from the Au core to the Ag shell gradually decreased with the increase of Ag shell thickness, then the inhibition of Ag+ release induced by the Au core was gradually alleviated, but the generation of superoxide radicals was intensified sharply. Then, the effect of the Au core on the dissolution capacity and free radicals' generation significantly altered the biological toxicity of Ag NPs, and the influence degree was related to the test organism's species. Nevertheless, the Au core retained the surface properties of Ag NPs, leading to the uptake of Au@Ag NPs, entirely consistent with the behavior of unlabeled Ag NPs. These findings confirmed that Au core labeling provides new opportunities for tracking Ag NPs in environmental and biological systems, and the exposure conditions and test organisms should be carefully assessed before employing the Au core labeling technology.
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Affiliation(s)
- Dingyuan Liang
- School of Space and Environment, Beihang University, Beijing 100191, China
| | - Xiangrui Wang
- Life science, The Hong Kong University of Science and Technology, Hong Kong 100025, China
| | - Wenhong Fan
- School of Space and Environment, Beihang University, Beijing 100191, China; Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University, Beijing 100191, China.
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Volpe C, Vadstein O, Andersen G, Andersen T. Nanocosm: a well plate photobioreactor for environmental and biotechnological studies. LAB ON A CHIP 2021; 21:2027-2039. [PMID: 34008610 DOI: 10.1039/d0lc01250e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Phytoplankton are key primary producers at the bottom of the aquatic food chain. They are a highly diverse group of organisms essential for the functioning of our ecosystems and because of their characteristics, their biomass is considered for various commercial applications. A full appreciation of their abundance, diversity and potential is only feasible by using systems that enable simultaneous testing of strains and/or variables in a fast and easy way. A major bottleneck is the lack of a cost-effective method with the capacity for complex experimental set-ups that enable fast and reproducible screening and analysis. In this study, we present nanocosm, a versatile LED-based micro-scale photobioreactor (PBR) that allows simultaneous testing of multiple variables such as temperature and light within the same plate. Every well can be independently controlled for intensity, temporal variation and light type (RGB, white, UV). We show that our systems guarantee homogeneous conditions because of controlled temperature and evaporation and adjustments for light crosstalk. By ensuring controlled environmental conditions the nanocosm is suitable for running factorial experimental designs where each well can be used as an independent micro-PBR. To validate culture performances, we assess well-to-well reproducibility and our results show minimal well-to-well variability for all the conditions tested. Possible modes of operation and application are discussed together with future development of the system.
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Affiliation(s)
- Charlotte Volpe
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, N-7491, Trondheim, Norway.
| | - Olav Vadstein
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, N-7491, Trondheim, Norway.
| | | | - Tom Andersen
- Department of Biosciences, Section for Aquatic Biology and Toxicology (AQUA), University of Oslo, N-0316, Oslo, Norway
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Jackson HO, Taunt HN, Mordaka PM, Smith AG, Purton S. The Algal Chloroplast as a Testbed for Synthetic Biology Designs Aimed at Radically Rewiring Plant Metabolism. FRONTIERS IN PLANT SCIENCE 2021; 12:708370. [PMID: 34630459 PMCID: PMC8497815 DOI: 10.3389/fpls.2021.708370] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/10/2021] [Indexed: 05/04/2023]
Abstract
Sustainable and economically viable support for an ever-increasing global population requires a paradigm shift in agricultural productivity, including the application of biotechnology to generate future crop plants. Current genetic engineering approaches aimed at enhancing the photosynthetic efficiency or composition of the harvested tissues involve relatively simple manipulations of endogenous metabolism. However, radical rewiring of central metabolism using new-to-nature pathways, so-called "synthetic metabolism", may be needed to really bring about significant step changes. In many cases, this will require re-programming the metabolism of the chloroplast, or other plastids in non-green tissues, through a combination of chloroplast and nuclear engineering. However, current technologies for sophisticated chloroplast engineering ("transplastomics") of plants are limited to just a handful of species. Moreover, the testing of metabolic rewiring in the chloroplast of plant models is often impractical given their obligate phototrophy, the extended time needed to create stable non-chimeric transplastomic lines, and the technical challenges associated with regeneration of whole plants. In contrast, the unicellular green alga, Chlamydomonas reinhardtii is a facultative heterotroph that allows for extensive modification of chloroplast function, including non-photosynthetic designs. Moreover, chloroplast engineering in C. reinhardtii is facile, with the ability to generate novel lines in a matter of weeks, and a well-defined molecular toolbox allows for rapid iterations of the "Design-Build-Test-Learn" (DBTL) cycle of modern synthetic biology approaches. The recent development of combinatorial DNA assembly pipelines for designing and building transgene clusters, simple methods for marker-free delivery of these clusters into the chloroplast genome, and the pre-existing wealth of knowledge regarding chloroplast gene expression and regulation in C. reinhardtii further adds to the versatility of transplastomics using this organism. Herein, we review the inherent advantages of the algal chloroplast as a simple and tractable testbed for metabolic engineering designs, which could then be implemented in higher plants.
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Affiliation(s)
- Harry O. Jackson
- Department of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Henry N. Taunt
- Department of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Pawel M. Mordaka
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Alison G. Smith
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Saul Purton
- Department of Structural and Molecular Biology, University College London, London, United Kingdom
- *Correspondence: Saul Purton
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Folcik AM, Haire T, Cutshaw K, Riddle M, Shola C, Nassani S, Rice P, Richardson B, Shah P, Nazamoddini-Kachouie N, Palmer A. Computer-Assisted Tracking of Chlamydomonas Species. FRONTIERS IN PLANT SCIENCE 2020; 10:1616. [PMID: 32076424 PMCID: PMC7006616 DOI: 10.3389/fpls.2019.01616] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 11/18/2019] [Indexed: 06/10/2023]
Abstract
The green algae Chlamydomonas reinhardtii is a model system for motility in unicellular organisms. Photo-, gravi-, and chemotaxis have previously been associated with C. reinhardtii, and observing the extent of these responses within a population of cells is crucial for refining our understanding of how this organism responds to changing environmental conditions. However, manually tracking and modeling a statistically viable number of samples of these microorganisms is an unreasonable task. We hypothesized that automated particle tracking systems are now sufficiently advanced to effectively characterize such populations. Here, we present an automated method to observe C. reinhardtii motility that allows us to identify individual cells as well as global information on direction, speed, and size. Nutrient availability effects on wild-type C. reinhardtii swimming speeds, as well as changes in speed and directionality in response to light, were characterized using this method. We also provide for the first time the swimming speeds of several motility-deficient mutant lines. While our present effort is focused around the unicellular green algae, C. reinhardtii, we confirm the general utility of this approach using Chlamydomonas moewusii, another member of this genus which contains over 300 species. Our work provides new tools for evaluating and modeling motility in this model organism and establishes the methodology for conducting similar experiments on other unicellular microorganisms.
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Affiliation(s)
- Alexandra M. Folcik
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL, United States
| | - Timothy Haire
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL, United States
| | - Kirstin Cutshaw
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL, United States
| | - Melissa Riddle
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL, United States
| | - Catherine Shola
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL, United States
| | - Sararose Nassani
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL, United States
| | - Paul Rice
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL, United States
| | - Brianna Richardson
- Department of Aerospace, Physics, and Space Sciences, Florida Institute of Technology, Melbourne, FL, United States
| | - Pooja Shah
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL, United States
| | | | - Andrew Palmer
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL, United States
- Department of Ocean Engineering and Marine Sciences, Florida Institute of Technology, Melbourne, FL, United States
- Aldrin Space Institute, Florida Institute of Technology, Melbourne, FL, United States
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9
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Young R, Purton S. CITRIC: cold-inducible translational readthrough in the chloroplast of Chlamydomonas reinhardtii using a novel temperature-sensitive transfer RNA. Microb Cell Fact 2018; 17:186. [PMID: 30474564 PMCID: PMC6260665 DOI: 10.1186/s12934-018-1033-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 11/16/2018] [Indexed: 01/17/2023] Open
Abstract
Background The chloroplast of eukaryotic microalgae such as Chlamydomonas reinhardtii is a potential platform for metabolic engineering and the production of recombinant proteins. In industrial biotechnology, inducible expression is often used so that the translation or function of the heterologous protein does not interfere with biomass accumulation during the growth stage. However, the existing systems used in bacterial or fungal platforms do not transfer well to the microalgal chloroplast. We sought to develop a simple inducible expression system for the microalgal chloroplast, exploiting an unused stop codon (TGA) in the plastid genome. We have previously shown that this codon can be translated as tryptophan when we introduce into the chloroplast genome a trnWUCA gene encoding a plastidial transfer RNA with a modified anticodon sequence, UCA. Results A mutated version of our trnWUCA gene was developed that encodes a temperature-sensitive variant of the tRNA. This allows transgenes that have been modified to contain one or more internal TGA codons to be translated differentially according to the culture temperature, with a gradient of recombinant protein accumulation from 35 °C (low/off) to 15 °C (high). We have named this the CITRIC system, an acronym for cold-inducible translational readthrough in chloroplasts. The exact induction behaviour can be tailored by altering the number of TGA codons within the transgene. Conclusions CITRIC adds to the suite of genetic engineering tools available for the microalgal chloroplast, allowing a greater degree of control over the timing of heterologous protein expression. It could also be used as a heat-repressible system for studying the function of essential native genes in the chloroplast. The genetic components of CITRIC are entirely plastid-based, so no engineering of the nuclear genome is required. Electronic supplementary material The online version of this article (10.1186/s12934-018-1033-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rosanna Young
- Algal Research Group, Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK.,Department of Medicine, Sir Alexander Fleming Building, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Saul Purton
- Algal Research Group, Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK.
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