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Monteiro LDFR, Giraldi LA, Winck FV. From Feasting to Fasting: The Arginine Pathway as a Metabolic Switch in Nitrogen-Deprived Chlamydomonas reinhardtii. Cells 2023; 12:1379. [PMID: 37408213 PMCID: PMC10216424 DOI: 10.3390/cells12101379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 07/07/2023] Open
Abstract
The metabolism of the model microalgae Chlamydomonas reinhardtii under nitrogen deprivation is of special interest due to its resulting increment of triacylglycerols (TAGs), that can be applied in biotechnological applications. However, this same condition impairs cell growth, which may limit the microalgae's large applications. Several studies have identified significant physiological and molecular changes that occur during the transition from an abundant to a low or absent nitrogen supply, explaining in detail the differences in the proteome, metabolome and transcriptome of the cells that may be responsible for and responsive to this condition. However, there are still some intriguing questions that reside in the core of the regulation of these cellular responses that make this process even more interesting and complex. In this scenario, we reviewed the main metabolic pathways that are involved in the response, mining and exploring, through a reanalysis of omics data from previously published datasets, the commonalities among the responses and unraveling unexplained or non-explored mechanisms of the possible regulatory aspects of the response. Proteomics, metabolomics and transcriptomics data were reanalysed using a common strategy, and an in silico gene promoter motif analysis was performed. Together, these results identified and suggested a strong association between the metabolism of amino acids, especially arginine, glutamate and ornithine pathways to the production of TAGs, via the de novo synthesis of lipids. Furthermore, our analysis and data mining indicate that signalling cascades orchestrated with the indirect participation of phosphorylation, nitrosylation and peroxidation events may be essential to the process. The amino acid pathways and the amount of arginine and ornithine available in the cells, at least transiently during nitrogen deprivation, may be in the core of the post-transcriptional, metabolic regulation of this complex phenomenon. Their further exploration is important to the discovery of novel advances in the understanding of microalgae lipids' production.
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Affiliation(s)
- Lucca de Filipe Rebocho Monteiro
- Laboratory of Regulatory Systems Biology, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba 13416-000, Brazil
- Department of Botany, Institute of Biosciences, University of São Paulo, São Paulo 05508-090, Brazil
| | - Laís Albuquerque Giraldi
- Laboratory of Regulatory Systems Biology, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba 13416-000, Brazil
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-000, Brazil
| | - Flavia Vischi Winck
- Laboratory of Regulatory Systems Biology, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba 13416-000, Brazil
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2
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Carbó M, Chaturvedi P, Álvarez A, Pineda-Cevallos D, Ghatak A, González PR, Cañal MJ, Weckwerth W, Valledor L. Ferroptosis is the key cellular process mediating Bisphenol A responses in Chlamydomonas and a promising target for enhancing microalgae-based bioremediation. J Hazard Mater 2023; 448:130997. [PMID: 36860062 DOI: 10.1016/j.jhazmat.2023.130997] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/31/2023] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
Microplastics are one of the major pollutants in aquatic environments. Among their components, Bisphenol A (BPA) is one of the most abundant and dangerous, leading to endocrine disorders deriving even in different types of cancer in mammals. However, despite this evidence, the xenobiotic effects of BPA over plantae and microalgae still need to be better understood at the molecular level. To fill this gap, we characterized the physiological and proteomic response of Chlamydomonas reinhardtii during long-term BPA exposure by analyzing physiological and biochemical parameters combined with proteomics. BPA imbalanced iron and redox homeostasis, disrupting cell function and triggering ferroptosis. Intriguingly, this microalgae defense against this pollutant is recovering at both molecular and physiological levels while starch accumulation at 72 h of BPA exposure. In this work, we addressed the molecular mechanisms involved in BPA exposure, demonstrating for the first time the induction of ferroptosis in a eukaryotic alga and how ROS detoxification mechanisms and other specific proteomic rearrangements reverted this situation. These results are of great significance not only for understanding the BPA toxicology or exploring the molecular mechanisms of ferroptosis in microalgae but also for defining novel target genes for microplastic bioremediation efficient strain development.
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Affiliation(s)
- María Carbó
- Department of Organisms and Systems Biology and University Institute of Biotechnology of Asturias (IUBA), University of Oviedo, Asturias, Spain
| | - Palak Chaturvedi
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Ana Álvarez
- Department of Organisms and Systems Biology and University Institute of Biotechnology of Asturias (IUBA), University of Oviedo, Asturias, Spain
| | | | - Arindam Ghatak
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | | | - María Jesús Cañal
- Department of Organisms and Systems Biology and University Institute of Biotechnology of Asturias (IUBA), University of Oviedo, Asturias, Spain
| | - Wolfram Weckwerth
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Luis Valledor
- Department of Organisms and Systems Biology and University Institute of Biotechnology of Asturias (IUBA), University of Oviedo, Asturias, Spain.
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3
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Wu D, Hou Y, Cheng J, Han T, Hao N, Zhang B, Fan X, Ji X, Chen F, Gong D, Wang L, McGinn P, Zhao L, Chen S. Transcriptome analysis of lipid metabolism in response to cerium stress in the oleaginous microalga Nannochloropsis oculata. Sci Total Environ 2022; 838:156420. [PMID: 35660445 DOI: 10.1016/j.scitotenv.2022.156420] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/28/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Nannochloropsis oculata can accumulate large amounts of lipids under rare earth element (REE) conditions. However, the lipid accumulation mechanism responsible for REE stress has not been elucidated. In this study, the effects of cerium (the most abundant REE) on the growth and lipid accumulation of N. oculata were investigated. The de novo transcriptome data of N. oculata under cerium conditions were subsequently collected and analyzed. The results showed that N. oculata exhibited good cerium-resistance ability, showed slightly decrease in biomass but significantly increase in lipid content (55.8 % dry cell weight) under 6.0 mg/L cerium condition. Meanwhile, about 83.4 % cerium was biological fixated. Through transcriptome analysis, we found that the inhibited photosynthesis and carbon fixation pathways coupled with the stress-sensitive expression of ribosome biogenesis genes acclimatized the cells to REE stress. The active glycolysis pathway accelerated carbon flux to pyruvate and acetyl-CoA, and the upregulation of glycerol kinase and phosphatidate cytidylyltransferase genes further induced lipid accumulation. In addition, cerium downregulated the acyl-CoA oxidase and triacylglycerol lipase genes, which inhibited the degradation of lipids. Therefore, different responses to cerium demonstrate how N. oculata cells adapt to REE stress, and this knowledge may be used to extend our understanding of triacylglycerol (TAG) and the synthesis of other important metabolites.
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Affiliation(s)
- Di Wu
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou 014010, China
| | - Yuyong Hou
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Jie Cheng
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou 014010, China
| | - Tong Han
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Nahui Hao
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Bingjie Zhang
- Department of Food Engineering, Anhui Science and Technology Trade School, Bengbu 233080, China
| | - Xiang Fan
- Department of Food Engineering, Anhui Science and Technology Trade School, Bengbu 233080, China
| | - Xiang Ji
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou 014010, China.
| | - Fangjian Chen
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin, China.
| | - Donghui Gong
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou 014010, China
| | - Lei Wang
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou 014010, China
| | - Patrick McGinn
- National Research Council Canada, 1200 Montreal Road, Building M-58, Ottawa, Ontario K1A 0R6, Canada
| | - Lei Zhao
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin, China.
| | - Shulin Chen
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
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López-hernández J, Kean-meng T, Asencio-alcudia G, Asyraf-kassim M, Alvarez-gonzález C, Márquez-rocha F. Sustainable Microalgae and Cyanobacteria Biotechnology. Applied Sciences 2022; 12:6887. [DOI: 10.3390/app12146887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Marine organisms are a valuable source of new compounds, many of which have remarkable biotechnological properties, such as microalgae and cyanobacteria, which have attracted special attention to develop new industrial production routes. These organisms are a source of many biologically active molecules in nature, including antioxidants, immunostimulants, antivirals, antibiotics, hemagglutinates, polyunsaturated fatty acids, peptides, proteins, biofuels, and pigments. The use of several technologies to improve biomass production, in the first step, industrial processes schemes have been addressed with different accomplishments. It is critical to consider all steps involved in producing a bioactive valuable compound, such as species and strain selection, nutrient supply required to support productivity, type of photobioreactor, downstream processes, namely extraction, recovery, and purification. In general, two product production schemes can be mentioned; one for large amounts of product, such as biodiesel or any other biofuel and the biomass for feeding purposes; the other for when the product will be used in the human health domain, such as antivirals, antibiotics, antioxidants, etc. Several applications for microalgae have been documented. In general, the usefulness of an application for each species of microalgae is determined by growth and product production. Furthermore, the use of OMICS technologies enabled the development of a new design for human therapeutic recombinant proteins, including strain selection based on previous proteomic profiles, gene cloning, and the development of expression networks. Microalgal expression systems have an advantage over traditional microbial, plant, and mammalian expression systems for new and sustainable microalga applications, for responsible production and consumption.
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Kato Y, Inabe K, Hidese R, Kondo A, Hasunuma T. Metabolomics-based engineering for biofuel and bio-based chemical production in microalgae and cyanobacteria: A review. Bioresour Technol 2022; 344:126196. [PMID: 34710610 DOI: 10.1016/j.biortech.2021.126196] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/18/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
Metabolomics, an essential tool in modern synthetic biology based on the design-build-test-learn platform, is useful for obtaining a detailed understanding of cellular metabolic mechanisms through comprehensive analyses of the metabolite pool size and its dynamic changes. Metabolomics is critical to the design of a rational metabolic engineering strategy by determining the rate-limiting reaction and assimilated carbon distribution in a biosynthetic pathway of interest. Microalgae and cyanobacteria are promising photosynthetic producers of biofuels and bio-based chemicals, with high potential for developing a bioeconomic society through bio-based carbon neutral manufacturing. Metabolomics technologies optimized for photosynthetic organisms have been developed and utilized in various microalgal and cyanobacterial species. This review provides a concise overview of recent achievements in photosynthetic metabolomics, emphasizing the importance of microalgal and cyanobacterial cell factories that satisfy industrial requirements.
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Affiliation(s)
- Yuichi Kato
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Kosuke Inabe
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Ryota Hidese
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; Graduate School of Science, Innovation and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Akihiko Kondo
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; Graduate School of Science, Innovation and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Tomohisa Hasunuma
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; Graduate School of Science, Innovation and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan.
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Bai F, Yu L, Shi J, Li-Beisson Y, Liu J. Long-chain acyl-CoA synthetases activate fatty acids for lipid synthesis, remodeling and energy production in Chlamydomonas. New Phytol 2022; 233:823-837. [PMID: 34665469 DOI: 10.1111/nph.17813] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/13/2021] [Indexed: 06/13/2023]
Abstract
Long-chain acyl-CoA synthetases (LACSs) play many roles in mammals, yeasts and plants, but knowledge on their functions in microalgae remains fragmented. Here via genetic, biochemical and physiological analyses, we unraveled the function and roles of LACSs in the model microalga Chlamydomonas reinhardtii. In vitro assays on purified recombinant proteins revealed that CrLACS1, CrLACS2 and CrLACS3 all exhibited bona fide LACS activities toward a broad range of free fatty acids. The Chlamydomonas mutants compromised in CrLACS1, CrLACS2 or CrLACS3 did not show any obvious phenotypes in lipid content or growth under nitrogen (N)-replete condition. But under N-deprivation, CrLACS1 or CrLACS2 suppression resulted in c. 50% less oil, yet with a higher amount of chloroplast lipids. By contrast, CrLACS3 suppression impaired oil remobilization and cell growth severely during N-recovery, supporting its role in fatty acid β-oxidation to provide energy and carbon sources for regrowth. Transcriptomics analysis suggested that the observed lipid phenotypes are likely not due to transcriptional reprogramming but rather a shift in metabolic adjustment. Taken together, this study provided solid experimental evidence for essential roles of the three Chlamydomonas LACS enzymes in lipid synthesis, remodeling and catabolism, and highlighted the importance of lipid homeostasis in cell growth under nutrient fluctuations.
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Affiliation(s)
- Fan Bai
- Laboratory for Algae Biotechnology and Innovation, College of Engineering, Peking University, Beijing, 100871, China
| | - Lihua Yu
- Laboratory for Algae Biotechnology and Innovation, College of Engineering, Peking University, Beijing, 100871, China
| | - Jianan Shi
- Laboratory for Algae Biotechnology and Innovation, College of Engineering, Peking University, Beijing, 100871, China
| | - Yonghua Li-Beisson
- CEA, CNRS, BIAM, Institut de Biosciences et Biotechnologies Aix-Marseille, CEA Cadarache, Aix Marseille Université, Saint Paul-Lez-Durance, 13108, France
| | - Jin Liu
- Laboratory for Algae Biotechnology and Innovation, College of Engineering, Peking University, Beijing, 100871, China
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7
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Pang H, Wang YN, Chi ZY, Xu YP, Li SY, Che J, Wang JH. Enhanced aquaculture effluent polishing by once and repetitive nutrients deprived seawater Chlorella sp. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102555] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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8
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Mochdia K, Tamaki S. Transcription Factor-Based Genetic Engineering in Microalgae. Plants (Basel) 2021; 10:plants10081602. [PMID: 34451646 PMCID: PMC8399792 DOI: 10.3390/plants10081602] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/16/2021] [Accepted: 07/30/2021] [Indexed: 11/16/2022]
Abstract
Sequence-specific DNA-binding transcription factors (TFs) are key components of gene regulatory networks. Advances in high-throughput sequencing have facilitated the rapid acquisition of whole genome assembly and TF repertoires in microalgal species. In this review, we summarize recent advances in gene discovery and functional analyses, especially for transcription factors in microalgal species. Specifically, we provide examples of the genome-scale identification of transcription factors in genome-sequenced microalgal species and showcase their application in the discovery of regulators involved in various cellular functions. Herein, we highlight TF-based genetic engineering as a promising framework for designing microalgal strains for microalgal-based bioproduction.
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Affiliation(s)
- Keiichi Mochdia
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan
- Kihara Institute for Biological Research, Yokohama City University, Totsuka-ku, Yokohama 244-0813, Japan
- RIKEN Baton Zone Program, Tsurumi-ku, Yokohama 230-0045, Japan;
- School of Information and Data Sciences, Nagasaki University, Bunkyo-machi, Nagasaki 852-8521, Japan
- Correspondence: ; Tel.: +81-045-503-9111
| | - Shun Tamaki
- RIKEN Baton Zone Program, Tsurumi-ku, Yokohama 230-0045, Japan;
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Kumari K, Samantaray S, Sahoo D, Tripathy BC. Nitrogen, phosphorus and high CO 2 modulate photosynthesis, biomass and lipid production in the green alga Chlorella vulgaris. Photosynth Res 2021; 148:17-32. [PMID: 33813714 DOI: 10.1007/s11120-021-00828-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 02/26/2021] [Indexed: 05/28/2023]
Abstract
Climate change could impact nutrient bioavailability in aquatic environment. To understand the interaction of nutrient bioavailability and elevated CO2, Chlorella vulgaris cells were grown in ambient air or 5% CO2 in different concentrations of nitrogen and phosphorus in a photobioreactor. The chlorophyll content, photosynthesis and respiration rates increased in 5% CO2 to support higher biomass production. The nutrient limitation in the growth media resulted in reduced photosynthetic rates of the algal cells and their PSI, PSII, and whole chain electron transport rates and biomass production. Conversely, their lipid content increased partly due to upregulation of expression of several lipid biosynthesis genes. The order of downregulation of photosynthesis and upregulation in lipid production due to nutrient limitation was in the order of N > P. The N-50 and 5% CO2 culture had only 10% reduction in biomass and 32% increase in lipids having 85% saturated fat required for efficient biofuel production. This growth condition is ideal for generation of biodiesel required to reduce the consumption of fossil fuel and combat global warming.
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Affiliation(s)
- Kanchan Kumari
- Department of Botany, University of Delhi, Delhi, 110007, India
| | | | - Dinabandhu Sahoo
- Department of Botany, University of Delhi, Delhi, 110007, India.
| | - Baishnab C Tripathy
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
- Department of Biotechnology, Sharda University, Knowledge Park 3, Greater Noida, 201306, Uttar Pradesh, India.
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Soós V, Shetty P, Maróti G, Incze N, Badics E, Bálint P, Ördög V, Balázs E. Biomolecule composition and draft genome of a novel, high-lipid producing Scenedesmaceae microalga. ALGAL RES 2021. [DOI: 10.1016/j.algal.2020.102181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Shao Y, Gu W, Qiu YA, Wang S, Peng Y, Zhu Y, Zhuang S. Lipids monitoring in Scenedesmus obliquus based on terahertz technology. Biotechnol Biofuels 2020; 13:161. [PMID: 32944077 PMCID: PMC7493189 DOI: 10.1186/s13068-020-01801-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 09/08/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Microalgae are considered as a source of low pollution and renewable fuel due to their ability to synthesize an abundance of lipids. Conventional methods for lipid quantification are time-consuming and chemically contaminated, while spectroscopic method combined with mathematical model is much more attractive due to its ability of qualitative and quantitative analysis of material composition, in this sense, terahertz technology provides not only timely and non-destructive testing without chemical pollution, but also provides information on the functional group vibration mode and structure of the measured components. Therefore, terahertz technology is utilized in our investigation and proposed for microalgae metabolism detection. RESULTS The aim of this study was to use terahertz spectroscopy to observe lipid content in Scenedesmus obliquus (S. obliquus). We collected the THz spectra of S. obliquus which were cultivated under nitrogen stress and terahertz spectroscopy was used to analyze changes in substance components (lipids, proteins, carbohydrates and β-carotene). The PLS algorithm was used to model the terahertz data to distinguish the different lipid content of S. obliquus under nitrogen stress. The correlation coefficient of the prediction results of the lipid characteristic band modeling was above 0.991, and the root mean square error was less than 0.132. It indicated that terahertz technology can be used to discriminate S. obliquus cells under different nitrogen stress effectively. The correlation between the terahertz characteristic peak (9.3 THz) and the total lipid content determined by gravimetry reaches 0.960. The final results were compared with the commonly used spectroscopic methods for lipid observation (Raman spectroscopy). CONCLUSIONS In this article, we demonstrated the effectiveness of terahertz spectroscopy to monitor changes in microalgae lipid content under nitrogen stress. Terahertz spectroscopy is more suitable for industrial production or ordinary laboratories which require intermediate result with low-frequency screening. When quantifying microalgae lipids, the constraint of terahertz spectroscopy is far less than that of Raman spectroscopy, and it is easier for operator to accurately quantify microalgae lipid. In addition, it is still in early stage for the study of microalgae using terahertz spectroscopy technology, there is still much potential for us to explore.
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Affiliation(s)
- Yongni Shao
- Terahertz Technology Innovation Research Institute, Terahertz Spectrum and Imaging Technology Cooperative Innovation Center, Shanghai Key Lab of Modern Optical System, University of Shanghai for Science and Technology, Shanghai, 200093 China
- Shanghai Institute of Intelligent Science and Technology, Tongji University, Shanghai, 200092 China
| | - Weimin Gu
- Terahertz Technology Innovation Research Institute, Terahertz Spectrum and Imaging Technology Cooperative Innovation Center, Shanghai Key Lab of Modern Optical System, University of Shanghai for Science and Technology, Shanghai, 200093 China
| | - Y ating Qiu
- Terahertz Technology Innovation Research Institute, Terahertz Spectrum and Imaging Technology Cooperative Innovation Center, Shanghai Key Lab of Modern Optical System, University of Shanghai for Science and Technology, Shanghai, 200093 China
| | - Shengfeng Wang
- Terahertz Technology Innovation Research Institute, Terahertz Spectrum and Imaging Technology Cooperative Innovation Center, Shanghai Key Lab of Modern Optical System, University of Shanghai for Science and Technology, Shanghai, 200093 China
| | - Yan Peng
- Terahertz Technology Innovation Research Institute, Terahertz Spectrum and Imaging Technology Cooperative Innovation Center, Shanghai Key Lab of Modern Optical System, University of Shanghai for Science and Technology, Shanghai, 200093 China
- Shanghai Institute of Intelligent Science and Technology, Tongji University, Shanghai, 200092 China
| | - YiMing Zhu
- Terahertz Technology Innovation Research Institute, Terahertz Spectrum and Imaging Technology Cooperative Innovation Center, Shanghai Key Lab of Modern Optical System, University of Shanghai for Science and Technology, Shanghai, 200093 China
- Shanghai Institute of Intelligent Science and Technology, Tongji University, Shanghai, 200092 China
| | - Songlin Zhuang
- Terahertz Technology Innovation Research Institute, Terahertz Spectrum and Imaging Technology Cooperative Innovation Center, Shanghai Key Lab of Modern Optical System, University of Shanghai for Science and Technology, Shanghai, 200093 China
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Almutairi AW. Effects of nitrogen and phosphorus limitations on fatty acid methyl esters and fuel properties of Dunaliella salina. Environ Sci Pollut Res Int 2020; 27:32296-32303. [PMID: 32242318 DOI: 10.1007/s11356-020-08531-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 03/20/2020] [Indexed: 06/11/2023]
Abstract
This study was designed to assess the synergistic effects of nitrogen (N) and phosphorus (P) concentrations on oil content, fatty acid profile, and predicted fuel properties of Dunaliella salina. Axenic D. salina cells were grown in F/2 growth medium of salinity 34 ppt containing 33.6 g.l-1 ultramarine synthetic sea salt. Growth dry weight, cell count, and their relationship were measured, and oils were extracted by soaking following Soxhlet extraction. Growth dry weight was markedly affected by N and P concentrations, with maximum growth dry weights of cultures grown at recommended N and P concentrations (control), half of the recommended N concentration (0.5 N) and (0.5 N/0.5P) being 0.911 g.l-1, 0.755 g.l-1, and 0.615 g.l-1, respectively. Oil content showed the reverse pattern, with cultures grown in the absence of phosphorus (0.0P), full N/P starvation (0.0 N/0.0P), and control resulting in maximum oil contents of 24.86%, 22.85%, and 5.88%, respectively. The majority of fatty acid methyl esters ranged between C14 and C22. Estimated fuel properties of algal cells grown under NP stress conditions were found to meet the American Society for Testing and Materials (ASTM) and European Committee for Standardization (EN) guidelines.
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Affiliation(s)
- Adel W Almutairi
- Biological Science Department, Rabigh- Faculty of Science and Arts, King Abdulaziz University, Jeddah, Saudi Arabia.
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Lee J, Yamaoka Y, Kong F, Cagnon C, Beyly-Adriano A, Jang S, Gao P, Kang BH, Li-Beisson Y, Lee Y. The phosphatidylethanolamine-binding protein DTH1 mediates degradation of lipid droplets in Chlamydomonas reinhardtii. Proc Natl Acad Sci U S A 2020; 117:23131-9. [PMID: 32868427 DOI: 10.1073/pnas.2005600117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Lipid droplets (LDs) are intracellular organelles found in a wide range of organisms and play important roles in stress tolerance. During nitrogen (N) starvation, Chlamydomonas reinhardtii stores large amounts of triacylglycerols (TAGs) inside LDs. When N is resupplied, the LDs disappear and the TAGs are degraded, presumably providing carbon and energy for regrowth. The mechanism by which cells degrade LDs is poorly understood. Here, we isolated a mutant (dth1-1, Delayed in TAG Hydrolysis 1) in which TAG degradation during recovery from N starvation was compromised. Consequently, the dth1-1 mutant grew poorly compared to its parental line during N recovery. Two additional independent loss-of-function mutants (dth1-2 and dth1-3) also exhibited delayed TAG remobilization. DTH1 transcript levels increased sevenfold upon N resupply, and DTH1 protein was localized to LDs. DTH1 contains a putative lipid-binding domain (DTH1LBD) with alpha helices predicted to be structurally similar to those in apolipoproteins E and A-I. Recombinant DTH1LBD bound specifically to phosphatidylethanolamine (PE), a major phospholipid coating the LD surface. Overexpression of DTH1LBD in Chlamydomonas phenocopied the dth1 mutant's defective TAG degradation, suggesting that the function of DTH1 depends on its ability to bind PE. Together, our results demonstrate that the lipid-binding DTH1 plays an essential role in LD degradation and provide insight into the molecular mechanism of protein anchorage to LDs at the LD surface in photosynthetic cells.
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Antal T, Petrova E, Slepnyova V, Kukarskikh G, Volgusheva A, Dubini A, Baizhumanov A, Tyystjärvi T, Gorelova O, Baulina O, Chivkunova O, Solovchenko A, Rubin A. Photosynthetic hydrogen production as acclimation mechanism in nutrient-deprived Chlamydomonas. ALGAL RES 2020; 49:101951. [DOI: 10.1016/j.algal.2020.101951] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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15
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Wood NJ, Baker A, Quinnell RJ, Camargo-Valero MA. A Simple and Non-destructive Method for Chlorophyll Quantification of Chlamydomonas Cultures Using Digital Image Analysis. Front Bioeng Biotechnol 2020; 8:746. [PMID: 32793564 PMCID: PMC7386287 DOI: 10.3389/fbioe.2020.00746] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 06/11/2020] [Indexed: 11/17/2022] Open
Abstract
Growing interest in the use of microalgae as a sustainable feedstock to support a green, circular, bio-economy has led to intensive research and development initiatives aimed at increasing algal biomass production covering a wide range of scales. At the heart of this lies a common need for rapid and accurate methods to measure algal biomass concentrations. Surrogate analytical techniques based on chlorophyll content use solvent extraction methods for chlorophyll quantification, but these methods are destructive, time consuming and require careful disposal of the resultant solvent waste. Alternative non-destructive methods based on chlorophyll fluorescence require expensive equipment and are less suitable for multiple sampling of small cultures which need to be maintained under axenic growth conditions. A simple, inexpensive and non-destructive method to estimate chlorophyll concentration of microalgal cultures in situ from digital photographs using the RGB color model is presented. Green pixel intensity and chlorophyll a, b and total chlorophyll concentration, measured by conventional means, follow a strong linear relationship (R2 = 0.985–0.988). In addition, the resulting standard curve was robust enough to accurately estimate chlorophyll concentration despite changes in sample volume, pH and low concentrations of bacterial contamination. In contrast, use of the same standard curve during nitrogen deprivation (causing the accumulation of neutral lipids) or in the presence of high quantities of bacterial contamination led to significant errors in chlorophyll estimation. The low requirement for equipment (i.e., a simple digital camera, available on smartphones) and widely available standard software for measuring pixel intensity make this method suitable for both laboratory and field-based work, particularly in situations where sample, qualified personnel and/or equipment is limited. By following the methods described here it should be possible to produce a standard curve for chlorophyll analysis in a wide range of testing conditions including different microalga cultures, culture vessel and photographic set up in any particular laboratory.
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Affiliation(s)
- Nicola J Wood
- Centre for Doctoral Training in Bioenergy, School of Chemical and Process Engineering, University of Leeds, Leeds, United Kingdom.,BioResource Systems Research Group, School of Civil Engineering, University of Leeds, Leeds, United Kingdom
| | - Alison Baker
- Centre for Plant Sciences and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Rupert J Quinnell
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Miller Alonso Camargo-Valero
- BioResource Systems Research Group, School of Civil Engineering, University of Leeds, Leeds, United Kingdom.,Departamento de Ingeniería Química, Universidad Nacional de Colombia, Manizales, Colombia
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David M, Lejeune C, Abreu S, Thibessard A, Leblond P, Chaminade P, Virolle MJ. Negative Correlation between Lipid Content and Antibiotic Activity in Streptomyces: General Rule and Exceptions. Antibiotics (Basel) 2020; 9:E280. [PMID: 32466356 PMCID: PMC7344866 DOI: 10.3390/antibiotics9060280] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/19/2020] [Accepted: 05/20/2020] [Indexed: 12/26/2022] Open
Abstract
Streptomycetes are well known antibiotic producers and are among the rare prokaryotes able to store carbon as lipids. Previous comparative studies of the weak antibiotic producer Streptomyces lividans with its ppk mutant and with Streptomyces coelicolor, which both produce antibiotics, suggested the existence of a negative correlation between total lipid content and the ability to produce antibiotics. To determine whether such a negative correlation can be generalized to other Streptomyces species, fifty-four strains were picked randomly and grown on modified R2YE medium, limited in phosphate, with glucose or glycerol as the main carbon source. The total lipid content and antibiotic activity against Micrococcus luteus were assessed for each strain. This study revealed that the ability to accumulate lipids was not evenly distributed among strains and that glycerol was more lipogenic than glucose and had a negative impact on antibiotic biosynthesis. Furthermore, a statistically significant negative Pearson correlation between lipid content and antibiotic activity could be established for most strains, but a few strains escape this general law. These exceptions are likely due to limits and biases linked to the type of test used to determine antibiotic activity, which relies exclusively on Micrococcus luteus sensitivity. They are characterized either by high lipid content and high antibiotic activity or by low lipid content and undetectable antibiotic activity against Micrococcus luteus. Lastly, the comparative genomic analysis of two strains with contrasting lipid content, and both named Streptomyces antibioticus (DSM 41,481 and DSM 40,868, which we found to be phylogenetically related to Streptomyces lavenduligriseus), indicated that some genetic differences in various pathways related to the generation/consumption of acetylCoA could be responsible for such a difference.
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Affiliation(s)
- Michelle David
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France; (M.D.); (C.L.)
| | - Clara Lejeune
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France; (M.D.); (C.L.)
| | - Sonia Abreu
- Lipides, Systèmes Analytiques et Biologiques, Université Paris-Saclay, 92296 Châtenay-Malabry, France; (S.A.); (P.C.)
| | | | - Pierre Leblond
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France; (A.T.); (P.L.)
| | - Pierre Chaminade
- Lipides, Systèmes Analytiques et Biologiques, Université Paris-Saclay, 92296 Châtenay-Malabry, France; (S.A.); (P.C.)
| | - Marie-Joelle Virolle
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France; (M.D.); (C.L.)
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Millan-Oropeza A, Henry C, Lejeune C, David M, Virolle MJ. Expression of genes of the Pho regulon is altered in Streptomyces coelicolor. Sci Rep 2020; 10:8492. [PMID: 32444655 PMCID: PMC7244524 DOI: 10.1038/s41598-020-65087-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 04/24/2020] [Indexed: 12/30/2022] Open
Abstract
Most currently used antibiotics originate from Streptomycetes and phosphate limitation is an important trigger of their biosynthesis. Understanding the molecular processes underpinning such regulation is of crucial importance to exploit the great metabolic diversity of these bacteria and get a better understanding of the role of these molecules in the physiology of the producing bacteria. To contribute to this field, a comparative proteomic analysis of two closely related model strains, Streptomyces lividans and Streptomyces coelicolor was carried out. These strains possess identical biosynthetic pathways directing the synthesis of three well-characterized antibiotics (CDA, RED and ACT) but only S. coelicolor expresses them at a high level. Previous studies established that the antibiotic producer, S. coelicolor, is characterized by an oxidative metabolism and a reduced triacylglycerol content compared to the none producer, S. lividans, characterized by a glycolytic metabolism. Our proteomic data support these findings and reveal that these drastically different metabolic features could, at least in part, due to the weaker abundance of proteins of the two component system PhoR/PhoP in S. coelicolor compared to S. lividans. In condition of phosphate limitation, PhoR/PhoP is known to control positively and negatively, respectively, phosphate and nitrogen assimilation and our study revealed that it might also control the expression of some genes of central carbon metabolism. The tuning down of the regulatory role of PhoR/PhoP in S. coelicolor is thus expected to be correlated with low and high phosphate and nitrogen availability, respectively and with changes in central carbon metabolic features. These changes are likely to be responsible for the observed differences between S. coelicolor and S. lividans concerning energetic metabolism, triacylglycerol biosynthesis and antibiotic production. Furthermore, a novel view of the contribution of the bio-active molecules produced in this context, to the regulation of the energetic metabolism of the producing bacteria, is proposed and discussed.
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Affiliation(s)
- Aaron Millan-Oropeza
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
- PAPPSO, Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Céline Henry
- PAPPSO, Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Clara Lejeune
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Michelle David
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Marie-Joelle Virolle
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
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18
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Takeuchi T, Sears BB, Lindeboom C, Lin YT, Fekaris N, Zienkiewicz K, Zienkiewicz A, Poliner E, Benning C. Chlamydomonas CHT7 Is Required for an Effective Quiescent State by Regulating Nutrient-Responsive Cell Cycle Gene Expression. Plant Cell 2020; 32:1240-1269. [PMID: 32001503 PMCID: PMC7145468 DOI: 10.1105/tpc.19.00628] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 01/07/2020] [Accepted: 01/27/2020] [Indexed: 06/10/2023]
Abstract
COMPROMISED HYDROLYSIS OF TRIACYLGLYCEROLS7 (CHT7) in Chlamydomonas (Chlamydomonas reinhardtii) was previously shown to affect the transcription of a subset of genes during nitrogen (N)-replete growth and following N refeeding. Here, we show that an extensive derepression of genes involved in DNA metabolism and cell cycle-related processes, as well as downregulation of genes encoding oxidoreductases and nutrient transporters, occurs in the cht7 mutant during N deprivation. Cellular mutant phenotypes are consistent with the observed transcriptome misregulation, as cht7 cells fail to properly arrest growth, nuclear replication, and cell division following N deprivation. Reduction in cht7 colony formation following N refeeding is explained by its compromised viability during N deprivation and by the occurrence of abortive divisions during N refeeding. Surprisingly, the largely unstructured C-terminal half of CHT7 with predicted protein binding domains, but not the canonical CXC DNA binding domain, is essential for the ability of CHT7 to form stable complexes and reverse the cellular phenotypes and transcription levels in the cht7 mutant. Hence, although lacking the presumed DNA binding domain, CHT7 modulates the expression of cell cycle genes in response to N availability, which is essential for establishing an effective quiescent state and the coordinated resumption of growth following N refeeding.
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Affiliation(s)
- Tomomi Takeuchi
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | - Barbara B Sears
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Chase Lindeboom
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Yang-Tsung Lin
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | - Nicholas Fekaris
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Krzysztof Zienkiewicz
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Centre of Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, 87-100 Toruń, Poland
| | - Agnieszka Zienkiewicz
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Centre of Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, 87-100 Toruń, Poland
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan 48824
| | - Eric Poliner
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Christoph Benning
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan 48824
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19
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Reza AM, Tavakoli J, Zhou Y, Qin J, Tang Y. Synthetic fluorescent probes to apprehend calcium signalling in lipid droplet accumulation in microalgae—an updated review. Sci China Chem 2020. [DOI: 10.1007/s11426-019-9664-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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20
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Akbar MA, Mohd Yusof NY, Tahir NI, Ahmad A, Usup G, Sahrani FK, Bunawan H. Biosynthesis of Saxitoxin in Marine Dinoflagellates: An Omics Perspective. Mar Drugs 2020; 18:md18020103. [PMID: 32033403 PMCID: PMC7073992 DOI: 10.3390/md18020103] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/09/2020] [Accepted: 01/09/2020] [Indexed: 02/07/2023] Open
Abstract
Saxitoxin is an alkaloid neurotoxin originally isolated from the clam Saxidomus giganteus in 1957. This group of neurotoxins is produced by several species of freshwater cyanobacteria and marine dinoflagellates. The saxitoxin biosynthesis pathway was described for the first time in the 1980s and, since then, it was studied in more than seven cyanobacterial genera, comprising 26 genes that form a cluster ranging from 25.7 kb to 35 kb in sequence length. Due to the complexity of the genomic landscape, saxitoxin biosynthesis in dinoflagellates remains unknown. In order to reveal and understand the dynamics of the activity in such impressive unicellular organisms with a complex genome, a strategy that can carefully engage them in a systems view is necessary. Advances in omics technology (the collective tools of biological sciences) facilitated high-throughput studies of the genome, transcriptome, proteome, and metabolome of dinoflagellates. The omics approach was utilized to address saxitoxin-producing dinoflagellates in response to environmental stresses to improve understanding of dinoflagellates gene–environment interactions. Therefore, in this review, the progress in understanding dinoflagellate saxitoxin biosynthesis using an omics approach is emphasized. Further potential applications of metabolomics and genomics to unravel novel insights into saxitoxin biosynthesis in dinoflagellates are also reviewed.
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Affiliation(s)
- Muhamad Afiq Akbar
- School of Bioscience and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia;
| | - Nurul Yuziana Mohd Yusof
- Department of Earth Science and Environment, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia; (N.Y.M.Y.); (F.K.S.)
| | - Noor Idayu Tahir
- Malaysian Palm Oil Board, No 6, Persiaran Institusi, Bandar Baru Bangi, Kajang 43000, Selangor, Malaysia;
| | - Asmat Ahmad
- University College Sabah Foundation, Jalan Sanzac, Kota Kinabalu 88100, Sabah, Malaysia; (A.A.); (G.U.)
| | - Gires Usup
- University College Sabah Foundation, Jalan Sanzac, Kota Kinabalu 88100, Sabah, Malaysia; (A.A.); (G.U.)
| | - Fathul Karim Sahrani
- Department of Earth Science and Environment, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia; (N.Y.M.Y.); (F.K.S.)
| | - Hamidun Bunawan
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia
- Correspondence: ; Tel.: +60-389-214-546
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21
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Zienkiewicz A, Zienkiewicz K, Poliner E, Pulman JA, Du ZY, Stefano G, Tsai CH, Horn P, Feussner I, Farre EM, Childs KL, Brandizzi F, Benning C. The Microalga Nannochloropsis during Transition from Quiescence to Autotrophy in Response to Nitrogen Availability. Plant Physiol 2020; 182:819-839. [PMID: 31740503 PMCID: PMC6997683 DOI: 10.1104/pp.19.00854] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 11/04/2019] [Indexed: 05/03/2023]
Abstract
The marine microalgae Nannochloropsis oceanica (CCMP1779) is a prolific producer of oil and is considered a viable and sustainable resource for biofuel feedstocks. Nitrogen (N) availability has a strong impact on the physiological status and metabolism of microalgal cells, but the exact nature of this response is poorly understood. To fill this gap we performed transcriptomic profiling combined with cellular and molecular analyses of N. oceanica CCMP1779 during the transition from quiescence to autotrophy. N deprivation-induced quiescence was accompanied by a strong reorganization of the photosynthetic apparatus and changes in the lipid homeostasis, leading to accumulation of triacylglycerol. Cell cycle activation and re-establishment of photosynthetic activity observed in response to resupply of the growth medium with N were accompanied by a rapid degradation of triacylglycerol stored in lipid droplets (LDs). Besides observing LD translocation into vacuoles, we also provide evidence for direct interaction between the LD surface protein (NoLDSP) and AUTOPHAGY-RELATED8 (NoATG8) protein and show a role of microlipophagy in LD turnover in N. oceanica CCMP1779. This knowledge is crucial not only for understanding the fundamental mechanisms controlling the cellular energy homeostasis in microalgal cells but also for development of efficient strategies to achieve higher algal biomass and better microalgal lipid productivity.
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Affiliation(s)
- Agnieszka Zienkiewicz
- Michigan State University-United States Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Great Lakes Bioenergy Center, Michigan State University, East Lansing, Michigan 48824
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, 87-100 Toruń, Poland
| | - Krzysztof Zienkiewicz
- Michigan State University-United States Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, 87-100 Toruń, Poland
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, 37073 Goettingen, Germany
| | - Eric Poliner
- Michigan State University-United States Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Cell and Molecular Biology Program, Michigan State University, East Lansing, Michigan 48824
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Jane A Pulman
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
- Center for Genomics-Enabled Plant Science, Michigan State University, East Lansing, Michigan 48824
| | - Zhi-Yan Du
- Michigan State University-United States Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | - Giovanni Stefano
- Michigan State University-United States Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | - Chia-Hong Tsai
- Michigan State University-United States Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Patrick Horn
- Michigan State University-United States Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | - Ivo Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, 37073 Goettingen, Germany
- Department of Plant Biochemistry, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, 37073 Goettingen, Germany
- Department of Plant Biochemistry, International Center for Advanced Studies of Energy Conversion (ICASEC), University of Goettingen, 37073 Goettingen, Germany
| | - Eva M Farre
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Kevin L Childs
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
- Center for Genomics-Enabled Plant Science, Michigan State University, East Lansing, Michigan 48824
| | - Federica Brandizzi
- Michigan State University-United States Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | - Christoph Benning
- Michigan State University-United States Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Great Lakes Bioenergy Center, Michigan State University, East Lansing, Michigan 48824
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
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22
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Kokabi K, Gorelova O, Zorin B, Didi-Cohen S, Itkin M, Malitsky S, Solovchenko A, Boussiba S, Khozin-Goldberg I. Lipidome Remodeling and Autophagic Respose in the Arachidonic-Acid-Rich Microalga Lobosphaera incisa Under Nitrogen and Phosphorous Deprivation. Front Plant Sci 2020; 11:614846. [PMID: 33329680 PMCID: PMC7728692 DOI: 10.3389/fpls.2020.614846] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 11/02/2020] [Indexed: 05/09/2023]
Abstract
The green microalga Lobosphaera incisa accumulates triacylglycerols (TAGs) with exceptionally high levels of long-chain polyunsaturated fatty acid (LC-PUFA) arachidonic acid (ARA) under nitrogen (N) deprivation. Phosphorous (P) deprivation induces milder changes in fatty acid composition, cell ultrastructure, and growth performance. We hypothesized that the resource-demanding biosynthesis and sequestration of ARA-rich TAG in lipid droplets (LDs) are associated with the enhancement of catabolic processes, including membrane lipid turnover and autophagic activity. Although this work focuses mainly on N deprivation, a comparative analysis of N and P deprivation responses is included. The results of lipidomic profiling showed a differential impact of N and P deprivation on the reorganization of glycerolipids. The formation of TAG under N deprivation was associated with the enhanced breakdown of chloroplast glycerolipids and the formation of lyso-lipids. N-deprived cells displayed a profound reorganization of cell ultrastructure, including internalization of cellular material into autophagic vacuoles, concomitant with the formation of LDs, while P-deprived cells showed better cellular ultrastructural integrity. The expression of the hallmark autophagy protein ATG8 and the major lipid droplet protein (MLDP) genes were coordinately upregulated, but to different extents under either N or P deprivation. The expression of the Δ5-desaturase gene, involved in the final step of ARA biosynthesis, was coordinated with ATG8 and MLDP, exclusively under N deprivation. Concanamycin A, the inhibitor of vacuolar proteolysis and autophagic flux, suppressed growth and enhanced levels of ATG8 and TAG in N-replete cells. The proportions of ARA in TAG decreased with a concomitant increase in oleic acid under both N-replete and N-deprived conditions. The photosynthetic apparatus's recovery from N deprivation was impaired in the presence of the inhibitor, along with the delayed LD degradation. The GFP-ATG8 processing assay showed the release of free GFP in N-replete and N-deprived cells, supporting the existence of autophagic flux. This study provides the first insight into the homeostatic role of autophagy in L. incisa and points to a possible metabolic link between autophagy and ARA-rich TAG biosynthesis.
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Affiliation(s)
- Kamilya Kokabi
- The Albert Katz International School for Desert Studies, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
- Microalgal Biotechnology Laboratory, The French Associates Institute for Agriculture and Biotechnology of Drylands, The J. Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion, Israel
| | - Olga Gorelova
- Department of Bioengineering, Faculty of Biology, Moscow State University, GSP-1, Moscow, Russia
| | - Boris Zorin
- Microalgal Biotechnology Laboratory, The French Associates Institute for Agriculture and Biotechnology of Drylands, The J. Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion, Israel
| | - Shoshana Didi-Cohen
- Microalgal Biotechnology Laboratory, The French Associates Institute for Agriculture and Biotechnology of Drylands, The J. Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion, Israel
| | - Maxim Itkin
- Metabolic Profiling Unit, Life Science Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Sergey Malitsky
- Metabolic Profiling Unit, Life Science Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Alexei Solovchenko
- Department of Bioengineering, Faculty of Biology, Moscow State University, GSP-1, Moscow, Russia
- Institute of Natural Sciences, Derzhavin Tambov State University, Tambov, Russia
- Peoples Friendship University of Russia (RUDN University), Moscow, Russia
| | - Sammy Boussiba
- Microalgal Biotechnology Laboratory, The French Associates Institute for Agriculture and Biotechnology of Drylands, The J. Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion, Israel
| | - Inna Khozin-Goldberg
- Microalgal Biotechnology Laboratory, The French Associates Institute for Agriculture and Biotechnology of Drylands, The J. Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion, Israel
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Colina F, Carbó M, Meijón M, Cañal MJ, Valledor L. Low UV-C stress modulates Chlamydomonas reinhardtii biomass composition and oxidative stress response through proteomic and metabolomic changes involving novel signalers and effectors. Biotechnol Biofuels 2020; 13:110. [PMID: 32577129 PMCID: PMC7305600 DOI: 10.1186/s13068-020-01750-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 06/11/2020] [Indexed: 05/06/2023]
Abstract
BACKGROUND The exposure of microalgae and plants to low UV-C radiation dosages can improve their biomass composition and stress tolerance. Despite UV-C sharing these effects with UV-A/B but at much lower dosages, UV-C sensing and signal mechanisms are still mostly unknown. Thus, we have described and integrated the proteometabolomic and physiological changes occurring in Chlamydomonas reinhardtii-a simple Plantae model-into the first 24 h after a short and low-intensity UV-C irradiation in order to reconstruct the microalgae response system to this stress. RESULTS The microalgae response was characterized by increased redox homeostasis, ROS scavenging and protein damage repair/avoidance elements. These processes were upregulated along with others related to the modulation of photosynthetic electron flux, carbon fixation and C/N metabolism. These changes, attributed to either direct UV-C-, ROS- or redox unbalances-associated damage, trigger a response process involving novel signaling intermediaries and effectors such as the translation modulator FAP204, a PP2A-like protein and a novel DYRK kinase. These elements were found linked to the modulation of Chlamydomonas biomass composition (starch accumulation) and proliferation, within an UV-C response probably modulated by different epigenetic factors. CONCLUSION Chosen multiomics integration approach was able to describe many fast changes, including biomass composition and ROS stress tolerance, as a response to a low-intensity UV-C stress. Moreover, the employed omics and systems biology approach placed many previously unidentified protein and metabolites at the center of these changes. These elements would be promising targets for the characterization of this stress response in microalgae and plants and the engineering of more productive microalgae strains.
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Affiliation(s)
- Francisco Colina
- Plant Physiology, Department of Organisms and Systems Biology and University Institute of Biotechnology of Asturias (IUBA), University of Oviedo, Oviedo, Spain
| | - María Carbó
- Plant Physiology, Department of Organisms and Systems Biology and University Institute of Biotechnology of Asturias (IUBA), University of Oviedo, Oviedo, Spain
| | - Mónica Meijón
- Plant Physiology, Department of Organisms and Systems Biology and University Institute of Biotechnology of Asturias (IUBA), University of Oviedo, Oviedo, Spain
| | - María Jesús Cañal
- Plant Physiology, Department of Organisms and Systems Biology and University Institute of Biotechnology of Asturias (IUBA), University of Oviedo, Oviedo, Spain
| | - Luis Valledor
- Plant Physiology, Department of Organisms and Systems Biology and University Institute of Biotechnology of Asturias (IUBA), University of Oviedo, Oviedo, Spain
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24
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Fei C, Wang T, Woldemicael A, He M, Zou S, Wang C. Nitrogen supplemented by symbiotic Rhizobium stimulates fatty-acid oxidation in Chlorella variabilis. ALGAL RES 2019; 44:101692. [DOI: 10.1016/j.algal.2019.101692] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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25
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Tran QG, Cho K, Kim U, Yun JH, Cho DH, Heo J, Park SB, Kim JW, Lee YJ, Ramanan R, Kim HS. Enhancement of β-carotene production by regulating the autophagy-carotenoid biosynthesis seesaw in Chlamydomonas reinhardtii. Bioresour Technol 2019; 292:121937. [PMID: 31408779 DOI: 10.1016/j.biortech.2019.121937] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/29/2019] [Accepted: 07/30/2019] [Indexed: 06/10/2023]
Abstract
This work aimed to demonstrate a new strategy for enhancing the production of carotenoids through the regulation of seesaw cross-talk between autophagy and carotenoid biosynthesis pathways in Chlamydomonas reinhardtii. Autophagy-related ATG1 and ATG8 genes were first silenced using artificial microRNA, which in turn reduced the mRNA expression of ATG1 and ATG8 by 84.4% and 74.3%, respectively. While ATG1 kinase controls early step in autophagy induction and ATG8 is an essential factor for the downstream formation of autophagosome membranes, the decreased expression of these genes led to a 2.34-fold increase in the amount of β-carotene content (i.e., 23.75 mg/g DCW). Furthermore, all mutants seemed to exhibit greater biodiesel properties than that of wild-type due to increased accumulation of saturated and monounsaturated fatty acids. These results support the role of autophagy in regulating the production of valuable metabolites, which could contribute to uplifting the economic outlook of nascent algal biorefinery.
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Affiliation(s)
- Quynh-Giao Tran
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science & Technology (UST), Daejeon 34113, Republic of Korea
| | - Kichul Cho
- Environmental Safety Group, Korea Institute of Science and Technology (KIST) Europe, Campus E 7.1, 66123 Saarbrücken, Germany
| | - Urim Kim
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science & Technology (UST), Daejeon 34113, Republic of Korea
| | - Jin-Ho Yun
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Dae-Hyun Cho
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Jina Heo
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science & Technology (UST), Daejeon 34113, Republic of Korea
| | - Su-Bin Park
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science & Technology (UST), Daejeon 34113, Republic of Korea
| | - Ji Won Kim
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science & Technology (UST), Daejeon 34113, Republic of Korea
| | - Yong Jae Lee
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Rishiram Ramanan
- Department of Environmental Science, Central University of Kerala, Kasaragod, Kerala, India
| | - Hee-Sik Kim
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science & Technology (UST), Daejeon 34113, Republic of Korea.
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26
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Ford MM, Smythers AL, McConnell EW, Lowery SC, Kolling DRJ, Hicks LM. Inhibition of TOR in Chlamydomonas reinhardtii Leads to Rapid Cysteine Oxidation Reflecting Sustained Physiological Changes. Cells 2019; 8:cells8101171. [PMID: 31569396 PMCID: PMC6829209 DOI: 10.3390/cells8101171] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/16/2019] [Accepted: 09/26/2019] [Indexed: 12/16/2022] Open
Abstract
The target of rapamycin (TOR) kinase is a master metabolic regulator with roles in nutritional sensing, protein translation, and autophagy. In Chlamydomonas reinhardtii, a unicellular green alga, TOR has been linked to the regulation of increased triacylglycerol (TAG) accumulation, suggesting that TOR or a downstream target(s) is responsible for the elusive “lipid switch” in control of increasing TAG accumulation under nutrient limitation. However, while TOR has been well characterized in mammalian systems, it is still poorly understood in photosynthetic systems, and little work has been done to show the role of oxidative signaling in TOR regulation. In this study, the TOR inhibitor AZD8055 was used to relate reversible thiol oxidation to the physiological changes seen under TOR inhibition, including increased TAG content. Using oxidized cysteine resin-assisted capture enrichment coupled with label-free quantitative proteomics, 401 proteins were determined to have significant changes in oxidation following TOR inhibition. These oxidative changes mirrored characterized physiological modifications, supporting the role of reversible thiol oxidation in TOR regulation of TAG production, protein translation, carbohydrate catabolism, and photosynthesis through the use of reversible thiol oxidation. The delineation of redox-controlled proteins under TOR inhibition provides a framework for further characterization of the TOR pathway in photosynthetic eukaryotes.
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Affiliation(s)
- Megan M Ford
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Amanda L Smythers
- Department of Chemistry, Marshall University, Huntington, WV 25755, USA.
| | - Evan W McConnell
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Sarah C Lowery
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | | | - Leslie M Hicks
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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Liu X, Wen J, Chen W, Du H. Physiological effects of nitrogen deficiency and recovery on the macroalga Gracilariopsis lemaneiformis (Rhodophyta). J Phycol 2019; 55:830-839. [PMID: 30916786 DOI: 10.1111/jpy.12862] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 03/05/2019] [Indexed: 05/07/2023]
Abstract
Algal metabolites are the most promising feedstocks for bio-energy production. Gracilariopsis lemaneiformis seems to be a good candidate red alga for polysaccharide production, especially relating to the agar production industry. Nitrogen deficiency is an efficient environmental pressure used to increase the accumulation of metabolites in algae. However, there are no studies on the physiological effects of G. lemaneiformis in response to nitrogen deficiency and its subsequent recovery. Here we integrated physiological data with molecular studies to explore the response strategy of G. lemaneiformis under nitrogen deficiency and recovery. Physiological measurements indicated that amino acids and protein biosynthesis were decreased, while endogenous NH4+ and soluble polysaccharides levels were increased under nitrogen stress. The expression of key genes involved in these pathways further suggested that G. lemaneiformis responded to nitrogen stress through up-regulation or down-regulation of genes related to nitrogen metabolism, and increased levels of endogenous NH4+ to complement the deficiency of exogenous nitrogen. Consistent with the highest accumulation of soluble polysaccharides, the gene encoding UDP-glucose pyrophosphorylase, a molecular marker used to evaluate agar content, was dramatically up-regulated more than 4-fold compared to the relative expression of actin after 4 d of nitrogen recovery. The present data provide important information on the mechanisms of nutrient balance in macroalgae.
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Affiliation(s)
- Xiaojuan Liu
- Guangdong Provincial Key Laboratory of Marine Biotechnology and STU-UNIVPM Joint Algal Research Center, College of Sciences, Shantou University, Shantou, Guangdong, 515063, China
| | - Jinyan Wen
- Guangdong Provincial Key Laboratory of Marine Biotechnology and STU-UNIVPM Joint Algal Research Center, College of Sciences, Shantou University, Shantou, Guangdong, 515063, China
| | - Weizhou Chen
- Guangdong Provincial Key Laboratory of Marine Biotechnology and STU-UNIVPM Joint Algal Research Center, College of Sciences, Shantou University, Shantou, Guangdong, 515063, China
| | - Hong Du
- Guangdong Provincial Key Laboratory of Marine Biotechnology and STU-UNIVPM Joint Algal Research Center, College of Sciences, Shantou University, Shantou, Guangdong, 515063, China
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28
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Colina F, Amaral J, Carbó M, Pinto G, Soares A, Cañal MJ, Valledor L. Genome-wide identification and characterization of CKIN/SnRK gene family in Chlamydomonas reinhardtii. Sci Rep 2019; 9:350. [PMID: 30674892 PMCID: PMC6344539 DOI: 10.1038/s41598-018-35625-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 11/09/2018] [Indexed: 12/29/2022] Open
Abstract
The SnRK (Snf1-Related protein Kinase) gene family plays an important role in energy sensing and stress-adaptive responses in plant systems. In this study, Chlamydomonas CKIN family (SnRK in Arabidopsis) was defined after a genome-wide analysis of all sequenced Chlorophytes. Twenty-two sequences were defined as plant SnRK orthologs in Chlamydomonas and classified into two subfamilies: CKIN1 and CKIN2. While CKIN1 subfamily is reduced to one conserved member and a close protein (CKIN1L), a large CKIN2 subfamily clusters both plant-like and algae specific CKIN2s. The responsiveness of these genes to abiotic stress situations was tested by RT-qPCR. Results showed that almost all elements were sensitive to osmotic stress while showing different degrees of sensibility to other abiotic stresses, as occurs in land plants, revealing their specialization and the family pleiotropy for some elements. The regulatory pathway of this family may differ from land plants since these sequences shows unique regulatory features and some of them are sensitive to ABA, despite conserved ABA receptors (PYR/PYL/RCAR) and regulatory domains are not present in this species. Core Chlorophytes and land plant showed divergent stress signalling, but SnRKs/CKINs share the same role in cell survival and stress response and adaption including the accumulation of specific biomolecules. This fact places the CKIN family as well-suited target for bioengineering-based studies in microalgae (accumulation of sugars, lipids, secondary metabolites), while promising new findings in stress biology and specially in the evolution of ABA-signalling mechanisms.
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Affiliation(s)
- Francisco Colina
- Plant Physiology, Department of Organisms and Systems Biology and University Institute of Biotechnology (IUBA), University of Oviedo, Oviedo, Spain
| | - Joana Amaral
- Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal
| | - María Carbó
- Plant Physiology, Department of Organisms and Systems Biology and University Institute of Biotechnology (IUBA), University of Oviedo, Oviedo, Spain
| | - Gloria Pinto
- Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal
| | - Amadeu Soares
- Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal
| | - María Jesús Cañal
- Plant Physiology, Department of Organisms and Systems Biology and University Institute of Biotechnology (IUBA), University of Oviedo, Oviedo, Spain
| | - Luis Valledor
- Plant Physiology, Department of Organisms and Systems Biology and University Institute of Biotechnology (IUBA), University of Oviedo, Oviedo, Spain.
- Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal.
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29
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Huang S, Jiang L, Zhuang X. Possible Roles of Membrane Trafficking Components for Lipid Droplet Dynamics in Higher Plants and Green Algae. Front Plant Sci 2019; 10:207. [PMID: 30858860 PMCID: PMC6397863 DOI: 10.3389/fpls.2019.00207] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 02/07/2019] [Indexed: 05/04/2023]
Abstract
Lipid droplets are ubiquitous dynamic organelles that contain neutral lipids surrounded by a phospholipid monolayer. They can store and supply lipids for energy metabolism and membrane synthesis. In addition, protein transport and lipid exchange often occur between LDs and various organelles to control lipid homeostasis in response to multiple stress responses and cellular signaling. In recent years, multiple membrane trafficking proteins have been identified through LD proteomics and genetic analyses. These membrane trafficking machineries are emerging as critical regulators to function in different LD-organelle interactions, e.g., for LD dynamics, biogenesis and turnover. In this review, we will summarize recent advances in regard to LD-related membrane trafficking proteins and discuss future investigations in higher plants and green algae.
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Affiliation(s)
- Shuxian Huang
- Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Liwen Jiang
- Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
- The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - Xiaohong Zhuang
- Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
- *Correspondence: Xiaohong Zhuang,
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30
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Werth EG, McConnell EW, Couso Lianez I, Perrine Z, Crespo JL, Umen JG, Hicks LM. Investigating the effect of target of rapamycin kinase inhibition on the Chlamydomonas reinhardtii phosphoproteome: from known homologs to new targets. New Phytol 2019; 221:247-260. [PMID: 30040123 DOI: 10.1111/nph.15339] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 06/11/2018] [Indexed: 05/20/2023]
Abstract
Target of rapamycin (TOR) kinase is a conserved regulator of cell growth whose activity is modulated in response to nutrients, energy and stress. Key proteins involved in the pathway are conserved in the model photosynthetic microalga Chlamydomonas reinhardtii, but the substrates of TOR kinase and downstream signaling network have not been elucidated. Our study provides a new resource for investigating the phosphorylation networks governed by the TOR kinase pathway in Chlamydomonas. We used quantitative phosphoproteomics to investigate the effects of inhibiting Chlamydomonas TOR kinase on dynamic protein phosphorylation. Wild-type and AZD-insensitive Chlamydomonas strains were treated with TOR-specific chemical inhibitors (rapamycin, AZD8055 and Torin1), after which differentially affected phosphosites were identified. Our quantitative phosphoproteomic dataset comprised 2547 unique phosphosites from 1432 different proteins. Inhibition of TOR kinase caused significant quantitative changes in phosphorylation at 258 phosphosites, from 219 unique phosphopeptides. Our results include Chlamydomonas homologs of TOR signaling-related proteins, including a site on RPS6 with a decrease in phosphorylation. Additionally, phosphosites on proteins involved in translation and carotenoid biosynthesis were identified. Follow-up experiments guided by these phosphoproteomic findings in lycopene beta/epsilon cyclase showed that carotenoid levels are affected by TORC1 inhibition and carotenoid production is under TOR control in algae.
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Affiliation(s)
- Emily G Werth
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Evan W McConnell
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Inmaculada Couso Lianez
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Sevilla, Avda. Américo Vespucio 49, 41092, Sevilla, Spain
| | - Zoee Perrine
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
| | - Jose L Crespo
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Sevilla, Avda. Américo Vespucio 49, 41092, Sevilla, Spain
| | - James G Umen
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
| | - Leslie M Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
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31
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Takeuchi T, Benning C. Nitrogen-dependent coordination of cell cycle, quiescence and TAG accumulation in Chlamydomonas. Biotechnol Biofuels 2019; 12:292. [PMID: 31890020 PMCID: PMC6927116 DOI: 10.1186/s13068-019-1635-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 12/12/2019] [Indexed: 05/07/2023]
Abstract
Microalgae hold great promises as sustainable cellular factories for the production of alternative fuels, feeds, and biopharmaceuticals for human health. While the biorefinery approach for fuels along with the coproduction of high-value compounds with industrial, therapeutic, or nutraceutical applications have the potential to make algal biofuels more economically viable, a number of challenges continue to hamper algal production systems at all levels. One such hurdle includes the metabolic trade-off often observed between the increased yields of desired products, such as triacylglycerols (TAG), and the growth of an organism. Initial genetic engineering strategies to improve lipid productivity in microalgae, which focused on overproducing the enzymes involved in fatty acid and TAG biosynthesis or inactivating competing carbon (C) metabolism, have seen some successes albeit at the cost of often greatly reduced biomass. Emergent approaches that aim at modifying the dynamics of entire metabolic pathways by engineering of pertinent transcription factors or signaling networks appear to have successfully achieved a balance between growth and neutral lipid accumulation. However, the biological knowledge of key signaling networks and molecular components linking these two processes is still incomplete in photosynthetic eukaryotes, making it difficult to optimize metabolic engineering strategies for microalgae. Here, we focus on nitrogen (N) starvation of the model green microalga, Chlamydomonas reinhardtii, to present the current understanding of the nutrient-dependent switch between proliferation and quiescence, and the drastic reprogramming of metabolism that results in the storage of C compounds following N starvation. We discuss the potential components mediating the transcriptional repression of cell cycle genes and the establishment of quiescence in Chlamydomonas, and highlight the importance of signaling pathways such as those governed by the target of rapamycin (TOR) and sucrose nonfermenting-related (SnRK) kinases in the coordination of metabolic status with cellular growth. A better understanding of how the cell division cycle is regulated in response to nutrient scarcity and of the signaling pathways linking cellular growth to energy and lipid homeostasis, is essential to improve the prospects of biofuels and biomass production in microalgae.
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Affiliation(s)
- Tomomi Takeuchi
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824 USA
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, MI 48824 USA
| | - Christoph Benning
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824 USA
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, MI 48824 USA
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824 USA
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Ji C, Mao X, Hao J, Wang X, Xue J, Cui H, Li R. Analysis of bZIP Transcription Factor Family and Their Expressions under Salt Stress in Chlamydomonas reinhardtii. Int J Mol Sci 2018; 19:E2800. [PMID: 30227676 DOI: 10.3390/ijms19092800] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 09/13/2018] [Accepted: 09/14/2018] [Indexed: 12/30/2022] Open
Abstract
The basic leucine-region zipper (bZIP) transcription factors (TFs) act as crucial regulators in various biological processes and stress responses in plants. Currently, bZIP family members and their functions remain elusive in the green unicellular algae Chlamydomonas reinhardtii, an important model organism for molecular investigation with genetic engineering aimed at increasing lipid yields for better biodiesel production. In this study, a total of 17 C. reinhardtii bZIP (CrebZIP) TFs containing typical bZIP structure were identified by a genome-wide analysis. Analysis of the CrebZIP protein physicochemical properties, phylogenetic tree, conserved domain, and secondary structure were conducted. CrebZIP gene structures and their chromosomal assignment were also analyzed. Physiological and photosynthetic characteristics of C. reinhardtii under salt stress were exhibited as lower cell growth and weaker photosynthesis, but increased lipid accumulation. Meanwhile, the expression profiles of six CrebZIP genes were induced to change significantly during salt stress, indicating that certain CrebZIPs may play important roles in mediating photosynthesis and lipid accumulation of microalgae in response to stresses. The present work provided a valuable foundation for functional dissection of CrebZIPs, benefiting the development of better strategies to engineer the regulatory network in microalgae for enhancing biofuel and biomass production.
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Nomaguchi T, Maeda Y, Liang Y, Yoshino T, Asahi T, Tanaka T. Comprehensive analysis of triacylglycerol lipases in the oleaginous diatom Fistulifera solaris JPCC DA0580 with transcriptomics under lipid degradation. J Biosci Bioeng 2018; 126:258-265. [DOI: 10.1016/j.jbiosc.2018.03.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 03/07/2018] [Accepted: 03/08/2018] [Indexed: 12/17/2022]
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Janssen JH, Kastenhofer J, de Hoop JA, Lamers PP, Wijffels RH, Barbosa MJ. Effect of nitrogen addition on lipid productivity of nitrogen starved Nannochloropsis gaditana. ALGAL RES 2018; 33:125-32. [DOI: 10.1016/j.algal.2018.05.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Papazi A, Korelidou A, Andronis E, Parasyri A, Stamatis N, Kotzabasis K. Bioenergetic reprogramming plasticity under nitrogen depletion by the unicellular green alga Scenedesmus obliquus. Planta 2018; 247:679-692. [PMID: 29170910 DOI: 10.1007/s00425-017-2816-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 11/16/2017] [Indexed: 06/07/2023]
Abstract
Simultaneous nitrogen depletion and 3,4-dichlorophenol addition induce a bioenergetic microalgal reprogramming, through strong Cyt b 6 f synthesis, that quench excess electrons from dichlorophenol's biodegradation to an overactivated photosynthetic electron flow and H 2 -productivity. Cellular energy management includes "rational" planning and operation of energy production and energy consumption units. Microalgae seem to have the ability to calculate their energy reserves and select the most profitable bioenergetic pathways. Under oxygenic mixotrophic conditions, microalgae invest the exogenously supplied carbon source (glucose) to biomass increase. If 3,4-dichlorophenol is added in the culture medium, then glucose is invested more to biodegradation rather than to growth. The biodegradation yield is enhanced in nitrogen-depleted conditions, because of an increase in the starch accumulation and a delay in the establishment of oxygen-depleted conditions in a closed system. In nitrogen-depleted conditions, starch cannot be invested in PSII-dependent and PSII-independent pathways for H2-production, mainly because of a strong decrease of the cytochrome b 6 f complex of the photosynthetic electron flow. For this reason, it seems more profitable for the microalga under these conditions to direct the metabolism to the synthesis of lipids as cellular energy reserves. Nitrogen-depleted conditions with exogenously supplied 3,4-dichlorophenol induce reprogramming of the microalgal bioenergetic strategy. Cytochrome b 6 f is strongly synthesized (mainly through catabolism of polyamines) to manage the electron bypass from the dichlorophenol biodegradation procedure to the photosynthetic electron flow (at the level of PQ pool) and consequently through cytochrome b 6 f and PSI to hydrogenase and H2-production. All the above showed that the selection of the appropriate cultivation conditions is the key for the manipulation of microalgal bioenergetic strategy that leads to different metabolic products and paves the way for a future microalgal "smart" biotechnology.
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Affiliation(s)
- Aikaterini Papazi
- Department of Biology, University of Crete, Voutes University Campus, 70013, Heraklion, Crete, Greece
| | - Anna Korelidou
- Department of Biology, University of Crete, Voutes University Campus, 70013, Heraklion, Crete, Greece
| | - Efthimios Andronis
- Department of Biology, University of Crete, Voutes University Campus, 70013, Heraklion, Crete, Greece
| | - Athina Parasyri
- Department of Biology, University of Crete, Voutes University Campus, 70013, Heraklion, Crete, Greece
| | - Nikolaos Stamatis
- Hellenic Agricultural Research Foundation "Demeter", Fisheries Research Institute, 64007, Nea Peramos, Kavala, Greece
| | - Kiriakos Kotzabasis
- Department of Biology, University of Crete, Voutes University Campus, 70013, Heraklion, Crete, Greece.
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Thiriet-Rupert S, Carrier G, Trottier C, Eveillard D, Schoefs B, Bougaran G, Cadoret JP, Chénais B, Saint-Jean B. Identification of transcription factors involved in the phenotype of a domesticated oleaginous microalgae strain of Tisochrysis lutea. ALGAL RES 2018. [DOI: 10.1016/j.algal.2017.12.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Escandón M, Meijón M, Valledor L, Pascual J, Pinto G, Cañal MJ. Metabolome Integrated Analysis of High-Temperature Response in Pinus radiata. Front Plant Sci 2018; 9:485. [PMID: 29719546 PMCID: PMC5914196 DOI: 10.3389/fpls.2018.00485] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 03/29/2018] [Indexed: 05/19/2023]
Abstract
The integrative omics approach is crucial to identify the molecular mechanisms underlying high-temperature response in non-model species. Based on future scenarios of heat increase, Pinus radiata plants were exposed to a temperature of 40°C for a period of 5 days, including recovered plants (30 days after last exposure to 40°C) in the analysis. The analysis of the metabolome using complementary mass spectrometry techniques (GC-MS and LC-Orbitrap-MS) allowed the reliable quantification of 2,287 metabolites. The analysis of identified metabolites and highlighter metabolic pathways across heat time exposure reveal the dynamism of the metabolome in relation to high-temperature response in P. radiata, identifying the existence of a turning point (on day 3) at which P. radiata plants changed from an initial stress response program (shorter-term response) to an acclimation one (longer-term response). Furthermore, the integration of metabolome and physiological measurements, which cover from the photosynthetic state to hormonal profile, suggests a complex metabolic pathway interaction network related to heat-stress response. Cytokinins (CKs), fatty acid metabolism and flavonoid and terpenoid biosynthesis were revealed as the most important pathways involved in heat-stress response in P. radiata, with zeatin riboside (ZR) and isopentenyl adenosine (iPA) as the key hormones coordinating these multiple and complex interactions. On the other hand, the integrative approach allowed elucidation of crucial metabolic mechanisms involved in heat response in P. radiata, as well as the identification of thermotolerance metabolic biomarkers (L-phenylalanine, hexadecanoic acid, and dihydromyricetin), crucial metabolites which can reschedule the metabolic strategy to adapt to high temperature.
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Affiliation(s)
- Mónica Escandón
- Plant Physiology, Department of Organisms and Systems Biology, Faculty of Biology, University of Oviedo, Oviedo, Spain
- *Correspondence: Mónica Escandón, ; María Jesús Cañal,
| | - Mónica Meijón
- Plant Physiology, Department of Organisms and Systems Biology, Faculty of Biology, University of Oviedo, Oviedo, Spain
- Plant Biotechnology Unit, University Institute of Biotechnology of Asturias (IUBA), Oviedo, Spain
| | - Luis Valledor
- Plant Physiology, Department of Organisms and Systems Biology, Faculty of Biology, University of Oviedo, Oviedo, Spain
- Plant Biotechnology Unit, University Institute of Biotechnology of Asturias (IUBA), Oviedo, Spain
| | - Jesús Pascual
- Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku, Finland
| | - Gloria Pinto
- Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal
| | - María Jesús Cañal
- Plant Physiology, Department of Organisms and Systems Biology, Faculty of Biology, University of Oviedo, Oviedo, Spain
- Plant Biotechnology Unit, University Institute of Biotechnology of Asturias (IUBA), Oviedo, Spain
- *Correspondence: Mónica Escandón, ; María Jesús Cañal,
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Roustan V, Weckwerth W. Quantitative Phosphoproteomic and System-Level Analysis of TOR Inhibition Unravel Distinct Organellar Acclimation in Chlamydomonas reinhardtii. Front Plant Sci 2018; 9:1590. [PMID: 30546371 PMCID: PMC6280106 DOI: 10.3389/fpls.2018.01590] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 10/15/2018] [Indexed: 05/13/2023]
Abstract
Rapamycin is an inhibitor of the evolutionary conserved Target of Rapamycin (TOR) kinase which promotes and coordinates translation with cell growth and division. In heterotrophic organisms, TOR regulation is based on intra- and extracellular stimuli such as amino acids level and insulin perception. However, how plant TOR pathways have evolved to integrate plastid endosymbiosis is a remaining question. Despite the close association of the TOR signaling with the coordination between protein turn-over and growth, proteome and phosphoproteome acclimation to a rapamycin treatment have not yet been thoroughly investigated in Chlamydomonas reinhardtii. In this study, we have used in vivo label-free phospho-proteomic analysis to profile both protein and phosphorylation changes at 0, 24, and 48 h in Chlamydomonas cells treated with rapamycin. Using multivariate statistics we highlight the impact of TOR inhibition on both the proteome and the phosphoproteome. Two-way ANOVA distinguished differential levels of proteins and phosphoproteins in response either to culture duration and rapamycin treatment or combined effects. Finally, protein-protein interaction networks and functional enrichment analysis underlined the relation between plastid and mitochondrial metabolism. Prominent changes of proteins involved in sulfur, cysteine, and methionine as well as nucleotide metabolism on the one hand, and changes in the TCA cycle on the other highlight the interplay of chloroplast and mitochondria metabolism. Furthermore, TOR inhibition revealed changes in the endomembrane trafficking system. Phosphoproteomics data, on the other hand, highlighted specific differentially regulated phosphorylation sites for calcium-regulated protein kinases as well as ATG7, S6K, and PP2C. To conclude we provide a first combined Chlamydomonas proteomics and phosphoproteomics dataset in response to TOR inhibition, which will support further investigations.
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Affiliation(s)
- Valentin Roustan
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
- *Correspondence: Wolfram Weckwerth,
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Hayashi T, Otaki R, Hirai K, Tsuzuki M, Sato N. Optimization of seawater-based triacylglycerol accumulation in a freshwater green alga, Chlorella kessleri , through simultaneous imposition of lowered-temperature and enhanced-light intensity. ALGAL RES 2017. [DOI: 10.1016/j.algal.2017.10.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Lauritano C, De Luca D, Ferrarini A, Avanzato C, Minio A, Esposito F, Ianora A. De novo transcriptome of the cosmopolitan dinoflagellate Amphidinium carterae to identify enzymes with biotechnological potential. Sci Rep 2017; 7:11701. [PMID: 28916825 PMCID: PMC5601461 DOI: 10.1038/s41598-017-12092-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 09/04/2017] [Indexed: 01/17/2023] Open
Abstract
Dinoflagellates are phytoplanktonic organisms found in both freshwater and marine habitats. They are often studied because related to harmful algal blooms but they are also known to produce bioactive compounds for the treatment of human pathologies. The aim of this study was to sequence the full transcriptome of the dinoflagellate Amphidinium carterae in both nitrogen-starved and -replete culturing conditions (1) to evaluate the response to nitrogen starvation at the transcriptional level, (2) to look for possible polyketide synthases (PKSs) in the studied clone (genes that may be involved in the synthesis of bioactive compounds), (3) if present, to evaluate if nutrient starvation can influence PKS expression, (4) to look for other possible enzymes of biotechnological interest and (5) to test strain cytotoxicity on human cell lines. Results showed an increase in nitrogen metabolism and stress response in nitrogen-starved cells and confirmed the presence of a type I β-ketosynthase. In addition, L-asparaginase (used for the treatment of Leukemia and for acrylamide reduction in food industries) and cellulase (useful for biofuel production and other industrial applications) have been identified for the first time in this species, giving new insights into possible biotechnological applications of dinoflagellates.
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Affiliation(s)
- Chiara Lauritano
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy.
| | - Daniele De Luca
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
| | - Alberto Ferrarini
- Università degli Studi di Verona, Ca' Vignal 1, Strada Le Grazie 15, 37134, Verona, Italy
| | - Carla Avanzato
- Università degli Studi di Verona, Ca' Vignal 1, Strada Le Grazie 15, 37134, Verona, Italy
| | - Andrea Minio
- Università degli Studi di Verona, Ca' Vignal 1, Strada Le Grazie 15, 37134, Verona, Italy
| | - Francesco Esposito
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
| | - Adrianna Ianora
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
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Jaeger D, Winkler A, Mussgnug JH, Kalinowski J, Goesmann A, Kruse O. Time-resolved transcriptome analysis and lipid pathway reconstruction of the oleaginous green microalga Monoraphidium neglectum reveal a model for triacylglycerol and lipid hyperaccumulation. Biotechnol Biofuels 2017; 10:197. [PMID: 28814974 PMCID: PMC5556983 DOI: 10.1186/s13068-017-0882-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 08/03/2017] [Indexed: 05/03/2023]
Abstract
BACKGROUND Oleaginous microalgae are promising production hosts for the sustainable generation of lipid-based bioproducts and as bioenergy carriers such as biodiesel. Transcriptomics of the lipid accumulation phase, triggered efficiently by nitrogen starvation, is a valuable approach for the identification of gene targets for metabolic engineering. RESULTS An explorative analysis of the detailed transcriptional response to different stages of nitrogen availability was performed in the oleaginous green alga Monoraphidium neglectum. Transcript data were correlated with metabolic data for cellular contents of starch and of different lipid fractions. A pronounced transcriptional down-regulation of photosynthesis became apparent in response to nitrogen starvation, whereas glucose catabolism was found to be up-regulated. An in-depth reconstruction and analysis of the pathways for glycerolipid, central carbon, and starch metabolism revealed that distinct transcriptional changes were generally found only for specific steps within a metabolic pathway. In addition to pathway analyses, the transcript data were also used to refine the current genome annotation. The transcriptome data were integrated into a database and complemented with data for other microalgae which were also subjected to nitrogen starvation. It is available at https://tdbmn.cebitec.uni-bielefeld.de. CONCLUSIONS Based on the transcriptional responses to different stages of nitrogen availability, a model for triacylglycerol and lipid hyperaccumulation is proposed, which involves transcriptional induction of thioesterases, differential regulation of lipases, and a re-routing of the central carbon metabolism. Over-expression of distinct thioesterases was identified to be a potential strategy to increase the oleaginous phenotype of M. neglectum, and furthermore specific lipases were identified as potential targets for future metabolic engineering approaches.
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Affiliation(s)
- Daniel Jaeger
- Algae Biotechnology and Bioenergy, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Anika Winkler
- Microbial Genomics and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Jan H. Mussgnug
- Algae Biotechnology and Bioenergy, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig-Universität, 35392 Gießen, Germany
| | - Olaf Kruse
- Algae Biotechnology and Bioenergy, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
- Algae Biotechnology and Bioenergy, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Universitaetsstrasse 27, 33615 Bielefeld, Germany
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Banerjee A, Banerjee C, Negi S, Chang JS, Shukla P. Improvements in algal lipid production: a systems biology and gene editing approach. Crit Rev Biotechnol 2017; 38:369-385. [DOI: 10.1080/07388551.2017.1356803] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Avik Banerjee
- Department of Environmental Science and Engineering, Indian Institute of Technology (Indian School of Mines), Dhanbad, India
| | - Chiranjib Banerjee
- Department of Environmental Science and Engineering, Indian Institute of Technology (Indian School of Mines), Dhanbad, India
| | | | - Jo-Shu Chang
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Pratyoosh Shukla
- Department of Microbiology, Enzyme Technology and Protein Bioinformatics Laboratory, Maharshi Dayanand University, Rohtak, India
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Escandón M, Valledor L, Pascual J, Pinto G, Cañal MJ, Meijón M. System-wide analysis of short-term response to high temperature in Pinus radiata. J Exp Bot 2017; 68:3629-3641. [PMID: 28645179 DOI: 10.1093/jxb/erx198] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 05/26/2017] [Indexed: 05/22/2023]
Abstract
Pinus radiata seedlings, the most widely planted pine species in the world, were exposed to temperatures within a range mimicking future scenarios based on current models of heat increase. The short-term heat response in P. radiata was studied in detail by exploring the metabolome, proteome and targeted transcriptome. The use of complementary mass spectrometry techniques, GC-MS and LC-Orbitrap-MS, together with novel bioinformatics tools allowed the reliable quantification of 2,075 metabolites and 901 protein groups. Integrative analyses of different functional levels and plant physiological status revealed a complex molecular interaction network of positive and negative correlations between proteins and metabolites involved in short-term heat response, including three main physiological functions as: 1) A hormone subnetwork, where fatty acids, flavonoids and hormones presented a key role; 2) An oxidoreductase subnetwork, including several dehydrogenase and peroxidase proteins; and 3) A heat shock protein subnetwork, with numerous proteins that contain a HSP20 domain, all of which were overexpressed at the transcriptional level. Integrated analysis pinpointed the basic mechanisms underlying the short-term physiological reaction of P. radiata during heat response. This approach was feasible in forest species and unmasked two novel candidate biomarkers of heat resistance, PHO1 and TRANSCRIPTION FACTOR APFI, and a MITOCHONDRIAL SMALL HEAT SHOCK PROTEIN, for use in future breeding programs.
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Affiliation(s)
- Mónica Escandón
- Plant Physiology, Department B.O.S., Faculty of Biology, University of Oviedo, Oviedo, Asturias, Spain
| | - Luis Valledor
- Plant Physiology, Department B.O.S., Faculty of Biology, University of Oviedo, Oviedo, Asturias, Spain
| | - Jesús Pascual
- Plant Physiology, Department B.O.S., Faculty of Biology, University of Oviedo, Oviedo, Asturias, Spain
| | - Gloria Pinto
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal
| | - María Jesús Cañal
- Plant Physiology, Department B.O.S., Faculty of Biology, University of Oviedo, Oviedo, Asturias, Spain
| | - Mónica Meijón
- Plant Physiology, Department B.O.S., Faculty of Biology, University of Oviedo, Oviedo, Asturias, Spain
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Pascual J, Cañal MJ, Escandón M, Meijón M, Weckwerth W, Valledor L. Integrated Physiological, Proteomic, and Metabolomic Analysis of Ultra Violet (UV) Stress Responses and Adaptation Mechanisms in Pinus radiata. Mol Cell Proteomics 2017; 16:485-501. [PMID: 28096192 DOI: 10.1074/mcp.m116.059436] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 10/06/2016] [Indexed: 12/22/2022] Open
Abstract
Globally expected changes in environmental conditions, especially the increase of UV irradiation, necessitate extending our knowledge of the mechanisms mediating tree species adaptation to this stress. This is crucial for designing new strategies to maintain future forest productivity. Studies focused on environmentally realistic dosages of UV irradiation in forest species are scarce. Pinus spp. are commercially relevant trees and not much is known about their adaptation to UV. In this work, UV treatment and recovery of Pinus radiata plants with dosages mimicking future scenarios, based on current models of UV radiation, were performed in a time-dependent manner. The combined metabolome and proteome analysis were complemented with measurements of + physiological parameters and gene expression. Sparse PLS analysis revealed complex molecular interaction networks of molecular and physiological data. Early responses prevented phototoxicity by reducing photosystem activity and the electron transfer chain together with the accumulation of photoprotectors and photorespiration. Apart from the reduction in photosynthesis as consequence of the direct UV damage on the photosystems, the primary metabolism was rearranged to deal with the oxidative stress while minimizing ROS production. New protein kinases and proteases related to signaling, coordination, and regulation of UV stress responses were revealed. All these processes demonstrate a complex molecular interaction network extending the current knowledge on UV-stress adaptation in pine.
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Affiliation(s)
- Jesús Pascual
- From the ‡Plant Physiology Lab, Organisms and Systems Biology, Faculty of Biology, University of Oviedo, Oviedo, Asturias, Spain
| | - María Jesús Cañal
- From the ‡Plant Physiology Lab, Organisms and Systems Biology, Faculty of Biology, University of Oviedo, Oviedo, Asturias, Spain
| | - Mónica Escandón
- From the ‡Plant Physiology Lab, Organisms and Systems Biology, Faculty of Biology, University of Oviedo, Oviedo, Asturias, Spain
| | - Mónica Meijón
- From the ‡Plant Physiology Lab, Organisms and Systems Biology, Faculty of Biology, University of Oviedo, Oviedo, Asturias, Spain
| | - Wolfram Weckwerth
- §Department of Ecogenomics and Systems Biology, Faculty of Life Sciences, University of Vienna, Vienna, Austria.,¶Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Luis Valledor
- From the ‡Plant Physiology Lab, Organisms and Systems Biology, Faculty of Biology, University of Oviedo, Oviedo, Asturias, Spain;
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Ghatak A, Chaturvedi P, Weckwerth W. Cereal Crop Proteomics: Systemic Analysis of Crop Drought Stress Responses Towards Marker-Assisted Selection Breeding. Front Plant Sci 2017; 8:757. [PMID: 28626463 PMCID: PMC5454074 DOI: 10.3389/fpls.2017.00757] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Sustainable crop production is the major challenge in the current global climate change scenario. Drought stress is one of the most critical abiotic factors which negatively impact crop productivity. In recent years, knowledge about molecular regulation has been generated to understand drought stress responses. For example, information obtained by transcriptome analysis has enhanced our knowledge and facilitated the identification of candidate genes which can be utilized for plant breeding. On the other hand, it becomes more and more evident that the translational and post-translational machinery plays a major role in stress adaptation, especially for immediate molecular processes during stress adaptation. Therefore, it is essential to measure protein levels and post-translational protein modifications to reveal information about stress inducible signal perception and transduction, translational activity and induced protein levels. This information cannot be revealed by genomic or transcriptomic analysis. Eventually, these processes will provide more direct insight into stress perception then genetic markers and might build a complementary basis for future marker-assisted selection of drought resistance. In this review, we survey the role of proteomic studies to illustrate their applications in crop stress adaptation analysis with respect to productivity. Cereal crops such as wheat, rice, maize, barley, sorghum and pearl millet are discussed in detail. We provide a comprehensive and comparative overview of all detected protein changes involved in drought stress in these crops and have summarized existing knowledge into a proposed scheme of drought response. Based on a recent proteome study of pearl millet under drought stress we compare our findings with wheat proteomes and another recent study which defined genetic marker in pearl millet.
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Affiliation(s)
- Arindam Ghatak
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
| | - Palak Chaturvedi
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
- Vienna Metabolomics Center, University of ViennaVienna, Austria
- *Correspondence: Wolfram Weckwerth
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Wang L, Sun X, Weiszmann J, Weckwerth W. System-Level and Granger Network Analysis of Integrated Proteomic and Metabolomic Dynamics Identifies Key Points of Grape Berry Development at the Interface of Primary and Secondary Metabolism. Front Plant Sci 2017; 8:1066. [PMID: 28713396 PMCID: PMC5491621 DOI: 10.3389/fpls.2017.01066] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 06/02/2017] [Indexed: 05/19/2023]
Abstract
Grapevine is a fruit crop with worldwide economic importance. The grape berry undergoes complex biochemical changes from fruit set until ripening. This ripening process and production processes define the wine quality. Thus, a thorough understanding of berry ripening is crucial for the prediction of wine quality. For a systemic analysis of grape berry development we applied mass spectrometry based platforms to analyse the metabolome and proteome of Early Campbell at 12 stages covering major developmental phases. Primary metabolites involved in central carbon metabolism, such as sugars, organic acids and amino acids together with various bioactive secondary metabolites like flavonols, flavan-3-ols and anthocyanins were annotated and quantified. At the same time, the proteomic analysis revealed the protein dynamics of the developing grape berries. Multivariate statistical analysis of the integrated metabolomic and proteomic dataset revealed the growth trajectory and corresponding metabolites and proteins contributing most to the specific developmental process. K-means clustering analysis revealed 12 highly specific clusters of co-regulated metabolites and proteins. Granger causality network analysis allowed for the identification of time-shift correlations between metabolite-metabolite, protein- protein and protein-metabolite pairs which is especially interesting for the understanding of developmental processes. The integration of metabolite and protein dynamics with their corresponding biochemical pathways revealed an energy-linked metabolism before veraison with high abundances of amino acids and accumulation of organic acids, followed by protein and secondary metabolite synthesis. Anthocyanins were strongly accumulated after veraison whereas other flavonoids were in higher abundance at early developmental stages and decreased during the grape berry developmental processes. A comparison of the anthocyanin profile of Early Campbell to other cultivars revealed similarities to Concord grape and indicates the strong effect of genetic background on metabolic partitioning in primary and secondary metabolism.
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Affiliation(s)
- Lei Wang
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
| | - Xiaoliang Sun
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
| | - Jakob Weiszmann
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
- Vienna Metabolomics Center, University of ViennaVienna, Austria
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
- Vienna Metabolomics Center, University of ViennaVienna, Austria
- *Correspondence: Wolfram Weckwerth
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Garibay-Hernández A, Barkla BJ, Vera-Estrella R, Martinez A, Pantoja O. Membrane Proteomic Insights into the Physiology and Taxonomy of an Oleaginous Green Microalga. Plant Physiol 2017; 173:390-416. [PMID: 27837088 PMCID: PMC5210721 DOI: 10.1104/pp.16.01240] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 11/03/2016] [Indexed: 05/22/2023]
Abstract
Ettlia oleoabundans is a nonsequenced oleaginous green microalga. Despite the significant biotechnological interest in producing value-added compounds from the acyl lipids of this microalga, a basic understanding of the physiology and biochemistry of oleaginous microalgae is lacking, especially under nitrogen deprivation conditions known to trigger lipid accumulation. Using an RNA sequencing-based proteomics approach together with manual annotation, we are able to provide, to our knowledge, the first membrane proteome of an oleaginous microalga. This approach allowed the identification of novel proteins in E. oleoabundans, including two photoprotection-related proteins, Photosystem II Subunit S and Maintenance of Photosystem II under High Light1, which were considered exclusive to higher photosynthetic organisms, as well as Retinitis Pigmentosa Type 2-Clathrin Light Chain, a membrane protein with a novel domain architecture. Free-flow zonal electrophoresis of microalgal membranes coupled to liquid chromatography-tandem mass spectrometry proved to be a useful technique for determining the intracellular location of proteins of interest. Carbon-flow compartmentalization in E. oleoabundans was modeled using this information. Molecular phylogenetic analyses of protein markers and 18S ribosomal DNA support the reclassification of E. oleoabundans within the trebouxiophycean microalgae, rather than with the Chlorophyceae class, in which it is currently classified, indicating that it may not be closely related to the model green alga Chlamydomonas reinhardtii A detailed survey of biological processes taking place in the membranes of nitrogen-deprived E. oleoabundans, including lipid metabolism, provides insights into the basic biology of this nonmodel organism.
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Affiliation(s)
- Adriana Garibay-Hernández
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210 Mexico (A.G.-H., R.V.-E., A.M., O.P.); and
- Southern Cross Plant Science, Southern Cross University, Lismore, 2480 New South Wales, Australia (B.J.B.)
| | - Bronwyn J Barkla
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210 Mexico (A.G.-H., R.V.-E., A.M., O.P.); and
- Southern Cross Plant Science, Southern Cross University, Lismore, 2480 New South Wales, Australia (B.J.B.)
| | - Rosario Vera-Estrella
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210 Mexico (A.G.-H., R.V.-E., A.M., O.P.); and
- Southern Cross Plant Science, Southern Cross University, Lismore, 2480 New South Wales, Australia (B.J.B.)
| | - Alfredo Martinez
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210 Mexico (A.G.-H., R.V.-E., A.M., O.P.); and
- Southern Cross Plant Science, Southern Cross University, Lismore, 2480 New South Wales, Australia (B.J.B.)
| | - Omar Pantoja
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210 Mexico (A.G.-H., R.V.-E., A.M., O.P.); and
- Southern Cross Plant Science, Southern Cross University, Lismore, 2480 New South Wales, Australia (B.J.B.)
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Roustan V, Bakhtiari S, Roustan PJ, Weckwerth W. Quantitative in vivo phosphoproteomics reveals reversible signaling processes during nitrogen starvation and recovery in the biofuel model organism Chlamydomonas reinhardtii. Biotechnol Biofuels 2017; 10:280. [PMID: 29209414 PMCID: PMC5704542 DOI: 10.1186/s13068-017-0949-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 11/01/2017] [Indexed: 05/22/2023]
Abstract
BACKGROUND Nitrogen deprivation and replenishment induces massive changes at the physiological and molecular level in the green alga Chlamydomonas reinhardtii, including reversible starch and lipid accumulation. Stress signal perception and acclimation involves transient protein phosphorylation. This study aims to provide the first experimental phosphoprotein dataset for the adaptation of C. reinhardtii during nitrogen depletion and recovery growth phases and its impact on lipid accumulation. RESULTS To decipher the signaling pathways involved in this dynamic process, we applied a label-free in vivo shotgun phosphoproteomics analysis on nitrogen-depleted and recovered samples. 1227 phosphopeptides belonging to 732 phosphoproteins were identified and quantified. 470 phosphopeptides showed a significant change across the experimental set-up. Multivariate statistics revealed the reversible phosphorylation process and the time/condition-dependent dynamic rearrangement of the phosphoproteome. Protein-protein interaction analysis of differentially regulated phosphoproteins identified protein kinases and phosphatases, such as DYRKP and an AtGRIK1 orthologue, called CDPKK2, as central players in the coordination of translational, photosynthetic, proteomic and metabolomic activity. Phosphorylation of RPS6, ATG13, and NNK1 proteins points toward a specific regulation of the TOR pathway under nitrogen deprivation. Differential phosphorylation pattern of several eukaryotic initiation factor proteins (EIF) suggests a major control on protein translation and turnover. CONCLUSION This work provides the first phosphoproteomics dataset obtained for Chlamydomonas responses to nitrogen availability, revealing multifactorial signaling pathways and their regulatory function for biofuel production. The reproducibility of the experimental set-up allows direct comparison with proteomics and metabolomics datasets and refines therefore the current model of Chlamydomonas acclimation to various nitrogen levels. Integration of physiological, proteomics, metabolomics, and phosphoproteomics data reveals three phases of acclimation to N availability: (i) a rapid response triggering starch accumulation as well as energy metabolism while chloroplast structure is conserved followed by (ii) chloroplast degradation combined with cell autophagy and lipid accumulation and finally (iii) chloroplast regeneration and cell growth activation after nitrogen replenishment. Plastid development seems to be further interconnected with primary metabolism and energy stress signaling in order to coordinate cellular mechanism to nitrogen availability stress.
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Affiliation(s)
- Valentin Roustan
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Shiva Bakhtiari
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Pierre-Jean Roustan
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
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49
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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50
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Garnier M, Bougaran G, Pavlovic M, Berard JB, Carrier G, Charrier A, Le Grand F, Lukomska E, Rouxel C, Schreiber N, Cadoret JP, Rogniaux H, Saint-Jean B. Use of a lipid rich strain reveals mechanisms of nitrogen limitation and carbon partitioning in the haptophyte Tisochrysis lutea. ALGAL RES 2016. [DOI: 10.1016/j.algal.2016.10.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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