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Kowalczyk J, Kłodawska K, Zych M, Burczyk J, Malec P. Ubiquitin-like and ubiquitinylated proteins associated with the maternal cell walls of Scenedesmus obliquus 633 as identified by immunochemistry and LC-MS/MS proteomics. PROTOPLASMA 2024:10.1007/s00709-024-01994-3. [PMID: 39365352 DOI: 10.1007/s00709-024-01994-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 09/23/2024] [Indexed: 10/05/2024]
Abstract
The cell walls of green algae Scenedesmus obliquus are complex, polymeric structures including an inner cellulose layer surrounded by an algaenan-containing trilaminar sheath. The process of autosporulation leads to the formation of sporangial (maternal) cell walls, which are released into the medium after sporangial autolysis. In this study, a fraction of maternal cell wall material (CWM) was isolated from the stationary phase cultures of Scenedesmus obliquus 633 and subjected to immunofluorescence microscopy using polyclonal anti-ubiquitin antibodies. The water-extracted polypeptide fraction from the maternal cell walls was then analyzed using immunoblotting and LC-MS/MS. An immunoanalysis showed the presence of several peptides reactive with polyclonal anti-ubiquitin serum, with apparent molecular masses of c. 12, 70, 120, 200, and > 250 kDa. Cell wall-associated peptides were identified on the basis of LC-MS/MS spectra across NCBI databases, including the Scenedesmaceae family (58 records), the Chlorophyceae class (37 records), and Chlamydomonas reinhardtii (18 records) corresponding to the signatures of 95 identified proteins. In particular, three signatures identified ubiquitin and ubiquitin-related proteins. In the maternal cell walls, immunoblotting analysis, immunofluorescence microscopy, and LC-MS/MS proteomics collectively demonstrated the presence of ubiquitin-like epitopes, ubiquitin-specific peptide signatures, and several putative ubiquitin conjugates of a higher molecular mass. These results support the presence of ubiquitin-like proteins in the extramembranous compartment of Scenedesmus obliquus 633 and suggest that protein ubiquitination plays a significant role in the formation and functional integrity of the maternal cell walls in green algae.
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Affiliation(s)
- Justyna Kowalczyk
- Department of Plant Physiology and Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387, Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, 30-348, Kraków, Poland
| | - Kinga Kłodawska
- Department of Plant Physiology and Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387, Kraków, Poland
| | - Maria Zych
- Department of Pharmacognosy and Phytochemistry, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, Katowice, Jagiellońska 4, 41-200, Sosnowiec, Poland
| | - Jan Burczyk
- Department of Pharmacognosy and Phytochemistry, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, Katowice, Jagiellońska 4, 41-200, Sosnowiec, Poland
- Laboratory of Biotechnology, Puńcowska 74, 43-400, Cieszyn, Poland
| | - Przemysław Malec
- Department of Plant Physiology and Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387, Kraków, Poland.
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Rahikainen M. A recipe for death: Singlet oxygen and type II metacaspase mediate programmed cell death in Chlamydomonas. PLANT PHYSIOLOGY 2024; 194:2194-2196. [PMID: 38088195 PMCID: PMC10980386 DOI: 10.1093/plphys/kiad661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 12/04/2023] [Indexed: 04/01/2024]
Affiliation(s)
- Moona Rahikainen
- Assistant Features Editor, Plant Physiology, American Society of Plant Biologists
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, FI-00014 Helsinki, Finland
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Lambert L, de Carpentier F, André P, Marchand CH, Danon A. Type II metacaspase mediates light-dependent programmed cell death in Chlamydomonas reinhardtii. PLANT PHYSIOLOGY 2024; 194:2648-2662. [PMID: 37971939 PMCID: PMC10980519 DOI: 10.1093/plphys/kiad618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/12/2023] [Accepted: 10/22/2023] [Indexed: 11/19/2023]
Abstract
Among the crucial processes that preside over the destiny of cells from any type of organism are those involving their self-destruction. This process is well characterized and conceptually logical to understand in multicellular organisms; however, the levels of knowledge and comprehension of its existence are still quite enigmatic in unicellular organisms. We use Chlamydomonas (Chlamydomonas reinhardtii) to lay the foundation for understanding the mechanisms of programmed cell death (PCD) in a unicellular photosynthetic organism. In this paper, we show that while PCD induces the death of a proportion of cells, it allows the survival of the remaining population. A quantitative proteomic analysis aiming at unveiling the proteome of PCD in Chlamydomonas allowed us to identify key proteins that led to the discovery of essential mechanisms. We show that in Chlamydomonas, PCD relies on the light dependence of a photosynthetic organism to generate reactive oxygen species and induce cell death. Finally, we obtained and characterized mutants for the 2 metacaspase genes in Chlamydomonas and showed that a type II metacaspase is essential for PCD execution.
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Affiliation(s)
- Lou Lambert
- Institut de Biologie Paris Seine, UMR 7238, CNRS, Sorbonne Université, Paris 75005, France
| | - Félix de Carpentier
- Institut de Biologie Paris Seine, UMR 7238, CNRS, Sorbonne Université, Paris 75005, France
- Doctoral School of Plant Sciences, Université Paris-Saclay, Saint-Aubin 91190, France
| | - Phuc André
- Institut de Biologie Paris Seine, UMR 7238, CNRS, Sorbonne Université, Paris 75005, France
| | - Christophe H Marchand
- Institut de Biologie Paris Seine, UMR 7238, CNRS, Sorbonne Université, Paris 75005, France
- Institut de Biologie Physico-Chimique, Centre National de la Recherche Scientifique (CNRS), Paris F-75005, France
| | - Antoine Danon
- Institut de Biologie Paris Seine, UMR 7238, CNRS, Sorbonne Université, Paris 75005, France
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Bellido-Pedraza CM, Calatrava V, Llamas A, Fernandez E, Sanz-Luque E, Galvan A. Nitrous Oxide Emissions from Nitrite Are Highly Dependent on Nitrate Reductase in the Microalga Chlamydomonas reinhardtii. Int J Mol Sci 2022; 23:9412. [PMID: 36012676 PMCID: PMC9409008 DOI: 10.3390/ijms23169412] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/16/2022] [Accepted: 08/18/2022] [Indexed: 12/11/2022] Open
Abstract
Nitrous oxide (N2O) is a powerful greenhouse gas and an ozone-depleting compound whose synthesis and release have traditionally been ascribed to bacteria and fungi. Although plants and microalgae have been proposed as N2O producers in recent decades, the proteins involved in this process have been only recently unveiled. In the green microalga Chlamydomonas reinhardtii, flavodiiron proteins (FLVs) and cytochrome P450 (CYP55) are two nitric oxide (NO) reductases responsible for N2O synthesis in the chloroplast and mitochondria, respectively. However, the molecular mechanisms feeding these NO reductases are unknown. In this work, we use cavity ring-down spectroscopy to monitor N2O and CO2 in cultures of nitrite reductase mutants, which cannot grow on nitrate or nitrite and exhibit enhanced N2O emissions. We show that these mutants constitute a very useful tool to study the rates and kinetics of N2O release under different conditions and the metabolism of this greenhouse gas. Our results indicate that N2O production, which was higher in the light than in the dark, requires nitrate reductase as the major provider of NO as substrate. Finally, we show that the presence of nitrate reductase impacts CO2 emissions in both light and dark conditions, and we discuss the role of NO in the balance between CO2 fixation and release.
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Affiliation(s)
| | - Victoria Calatrava
- Department of Biochemistry and Molecular Biology, University of Cordoba, 14004 Cordoba, Spain
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Angel Llamas
- Department of Biochemistry and Molecular Biology, University of Cordoba, 14004 Cordoba, Spain
| | - Emilio Fernandez
- Department of Biochemistry and Molecular Biology, University of Cordoba, 14004 Cordoba, Spain
| | - Emanuel Sanz-Luque
- Department of Biochemistry and Molecular Biology, University of Cordoba, 14004 Cordoba, Spain
| | - Aurora Galvan
- Department of Biochemistry and Molecular Biology, University of Cordoba, 14004 Cordoba, Spain
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Kuo EY, Yang RY, Chin YY, Chien YL, Chen YC, Wei CY, Kao LJ, Chang YH, Li YJ, Chen TY, Lee TM. Multi-omics approaches and genetic engineering of metabolism for improved biorefinery and wastewater treatment in microalgae. Biotechnol J 2022; 17:e2100603. [PMID: 35467782 DOI: 10.1002/biot.202100603] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 03/12/2022] [Accepted: 04/01/2022] [Indexed: 11/06/2022]
Abstract
Microalgae, a group of photosynthetic microorganisms rich in diverse and novel bioactive metabolites, have been explored for the production of biofuels, high value-added compounds as food and feeds, and pharmaceutical chemicals as agents with therapeutic benefits. This article reviews the development of omics resources and genetic engineering techniques including gene transformation methodologies, mutagenesis, and genome-editing tools in microalgae biorefinery and wastewater treatment. The introduction of these enlisted techniques has simplified the understanding of complex metabolic pathways undergoing microalgal cells. The multiomics approach of the integrated omics datasets, big data analysis, and machine learning for the discovery of objective traits and genes responsible for metabolic pathways was reviewed. Recent advances and limitations of multiomics analysis and genetic bioengineering technology to facilitate the improvement of microalgae as the dual role of wastewater treatment and biorefinery feedstock production are discussed. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Eva YuHua Kuo
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, 804, Taiwan.,Frontier Center for Ocean Science and Technology, National Sun Yat-sen University, Kaohsiung, 804, Taiwan
| | - Ru-Yin Yang
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, 804, Taiwan
| | - Yuan Yu Chin
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, 804, Taiwan
| | - Yi-Lin Chien
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, 804, Taiwan.,Frontier Center for Ocean Science and Technology, National Sun Yat-sen University, Kaohsiung, 804, Taiwan
| | - Yu Chu Chen
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, 804, Taiwan
| | - Cheng-Yu Wei
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, 804, Taiwan
| | - Li-Jung Kao
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, 804, Taiwan
| | - Yi-Hua Chang
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, 804, Taiwan
| | - Yu-Jia Li
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, 804, Taiwan
| | - Te-Yuan Chen
- Doctoral Degree Program in Marine Biotechnology, National Sun Yat-sen University, Kaohsiung, 804, Taiwan
| | - Tse-Min Lee
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, 804, Taiwan.,Frontier Center for Ocean Science and Technology, National Sun Yat-sen University, Kaohsiung, 804, Taiwan.,Doctoral Degree Program in Marine Biotechnology, National Sun Yat-sen University, Kaohsiung, 804, Taiwan
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