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Dorrell RG, Zhang Y, Liang Y, Gueguen N, Nonoyama T, Croteau D, Penot-Raquin M, Adiba S, Bailleul B, Gros V, Pierella Karlusich JJ, Zweig N, Fernie AR, Jouhet J, Maréchal E, Bowler C. Complementary environmental analysis and functional characterization of lower glycolysis-gluconeogenesis in the diatom plastid. THE PLANT CELL 2024; 36:3584-3610. [PMID: 38842420 PMCID: PMC11371179 DOI: 10.1093/plcell/koae168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/14/2024] [Accepted: 05/30/2024] [Indexed: 06/07/2024]
Abstract
Organic carbon fixed in chloroplasts through the Calvin-Benson-Bassham Cycle can be diverted toward different metabolic fates, including cytoplasmic and mitochondrial respiration, gluconeogenesis, and synthesis of diverse plastid metabolites via the pyruvate hub. In plants, pyruvate is principally produced via cytoplasmic glycolysis, although a plastid-targeted lower glycolytic pathway is known to exist in non-photosynthetic tissue. Here, we characterized a lower plastid glycolysis-gluconeogenesis pathway enabling the direct interconversion of glyceraldehyde-3-phosphate and phospho-enol-pyruvate in diatoms, ecologically important marine algae distantly related to plants. We show that two reversible enzymes required to complete diatom plastid glycolysis-gluconeogenesis, Enolase and bis-phosphoglycerate mutase (PGAM), originated through duplications of mitochondria-targeted respiratory isoforms. Through CRISPR-Cas9 mutagenesis, integrative 'omic analyses, and measured kinetics of expressed enzymes in the diatom Phaeodactylum tricornutum, we present evidence that this pathway diverts plastid glyceraldehyde-3-phosphate into the pyruvate hub, and may also function in the gluconeogenic direction. Considering experimental data, we show that this pathway has different roles dependent in particular on day length and environmental temperature, and show that the cpEnolase and cpPGAM genes are expressed at elevated levels in high-latitude oceans where diatoms are abundant. Our data provide evolutionary, meta-genomic, and functional insights into a poorly understood yet evolutionarily recurrent plastid metabolic pathway.
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Affiliation(s)
- Richard G Dorrell
- Institut de Biologie de l’ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
- Laboratory of Computational and Quantitative Biology (LCQB), Institut de Biologie Paris-Seine (IBPS), CNRS, INSERM, Sorbonne Université, Paris 75005, France
| | - Youjun Zhang
- Department of Plant Metabolomics, Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
- Central Plant Metabolism Group, Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yue Liang
- Center of Deep Sea Research, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Mineral Resources, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Nolwenn Gueguen
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, University Grenoble Alpes, CEA, INRAE, IRIG, 38000 Grenoble, France
| | - Tomomi Nonoyama
- Institut de Biologie de l’ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Dany Croteau
- Institut de Biologie Physico-Chimique (IBPC), Université PSL, Paris 75005, France
| | - Mathias Penot-Raquin
- Institut de Biologie de l’ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
- Laboratory of Computational and Quantitative Biology (LCQB), Institut de Biologie Paris-Seine (IBPS), CNRS, INSERM, Sorbonne Université, Paris 75005, France
| | - Sandrine Adiba
- Institut de Biologie de l’ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Benjamin Bailleul
- Institut de Biologie Physico-Chimique (IBPC), Université PSL, Paris 75005, France
| | - Valérie Gros
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, University Grenoble Alpes, CEA, INRAE, IRIG, 38000 Grenoble, France
| | - Juan José Pierella Karlusich
- Institut de Biologie de l’ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Nathanaël Zweig
- Institut de Biologie de l’ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Alisdair R Fernie
- Department of Plant Metabolomics, Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
- Central Plant Metabolism Group, Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
| | - Juliette Jouhet
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, University Grenoble Alpes, CEA, INRAE, IRIG, 38000 Grenoble, France
| | - Eric Maréchal
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, University Grenoble Alpes, CEA, INRAE, IRIG, 38000 Grenoble, France
| | - Chris Bowler
- Institut de Biologie de l’ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
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Wang S, Zhou X, Wu S, Zhao M, Hu Z. Transcriptomic and metabolomic analyses revealed regulation mechanism of mixotrophic Cylindrotheca sp. glycerol utilization and biomass promotion. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:84. [PMID: 37208696 DOI: 10.1186/s13068-023-02338-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/08/2023] [Indexed: 05/21/2023]
Abstract
BACKGROUND Diatoms have been viewed as ideal cell factories for production of some high-value bioactive metabolites, such as fucoxanthin, but their applications are restrained by limited biomass yield. Mixotrophy, by using both CO2 and organic carbon source, is believed effective to crack the bottleneck of biomass accumulation and achieve a sustainable bioproduct supply. RESULTS Glycerol, among tested carbon sources, was proved as the sole that could significantly promote growth of Cylindrotheca sp. with illumination, a so-called growth pattern, mixotrophy. Biomass and fucoxanthin yields of Cylindrotheca sp., grown in medium with glycerol (2 g L-1), was increased by 52% and 29%, respectively, as compared to the autotrophic culture (control) without compromise in photosynthetic performance. As Cylindrotheca sp. was unable to use glycerol without light, a time-series transcriptomic analysis was carried out to elucidate the light regulation on glycerol utilization. Among the genes participating in glycerol utilization, GPDH1, TIM1 and GAPDH1, showed the highest dependence on light. Their expressions decreased dramatically when the alga was transferred from light into darkness. Despite the reduced glycerol uptake in the dark, expressions of genes associating with pyrimidine metabolism and DNA replication were upregulated when Cylindrotheca sp. was cultured mixotrophically. Comparative transcriptomic and metabolomic analyses revealed amino acids and aminoacyl-tRNA metabolisms were enhanced at different timepoints of diurnal cycles in mixotrophic Cylindrotheca sp., as compared to the control. CONCLUSIONS Conclusively, this study not only provides an alternative for large-scale cultivation of Cylindrotheca, but also pinpoints the limiting enzymes subject to further metabolic manipulation. Most importantly, the novel insights in this study should aid to understand the mechanism of biomass promotion in mixotrophic Cylindrotheca sp.
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Affiliation(s)
- Song Wang
- Guangdong Technology Research Center for Marine Algal Bioengineering; Guangdong Provincial Key Laboratory for Plant Epigenetics; Shenzhen Engineering Laboratory for Marine Algal Biotechnology; Longhua Innovation Institute for Biotechnology; College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Xiyi Zhou
- Guangdong Technology Research Center for Marine Algal Bioengineering; Guangdong Provincial Key Laboratory for Plant Epigenetics; Shenzhen Engineering Laboratory for Marine Algal Biotechnology; Longhua Innovation Institute for Biotechnology; College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Sha Wu
- Guangdong Technology Research Center for Marine Algal Bioengineering; Guangdong Provincial Key Laboratory for Plant Epigenetics; Shenzhen Engineering Laboratory for Marine Algal Biotechnology; Longhua Innovation Institute for Biotechnology; College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Mengkai Zhao
- Guangdong Technology Research Center for Marine Algal Bioengineering; Guangdong Provincial Key Laboratory for Plant Epigenetics; Shenzhen Engineering Laboratory for Marine Algal Biotechnology; Longhua Innovation Institute for Biotechnology; College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Zhangli Hu
- Guangdong Technology Research Center for Marine Algal Bioengineering; Guangdong Provincial Key Laboratory for Plant Epigenetics; Shenzhen Engineering Laboratory for Marine Algal Biotechnology; Longhua Innovation Institute for Biotechnology; College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China.
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Bo Y, Chu R, Sun D, Deng X, Zhou C, Yan X, Ruan R, Cheng P. Mixotrophic culture of bait microalgae for biomass and nutrients accumulation and their synergistic carbon metabolism. BIORESOURCE TECHNOLOGY 2023; 367:128301. [PMID: 36370937 DOI: 10.1016/j.biortech.2022.128301] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/04/2022] [Accepted: 11/05/2022] [Indexed: 06/16/2023]
Abstract
Microalgae cannot meet the bait demand for aquaculture due to light intensity limitation and other disadvantageous conditions. This research selected 6 mixotrophic microalgae, and the optimal strains and organic carbon were screened. The results showed that Thalassiosira pseudonana and Chlorella sp. are suitable for mixotrophic culture. The maximum cell density of Thalassiosira pseudonana was found to be 1.67 times than that of the photoautotrophic group when glycerol was added. The maximum cell density of Chlorella sp. with acetic acid was 1.69 times than that of the photoautotrophic group. When the concentration of acetic acid was 5.0 g·L-1 and the concentration of KNO3 was 0.2 g·L-1, the maximum biomass of Chlorella sp. could reach 3.54 × 107 cells·mL-1; the maximum biomass of Thalassiosira pseudonana was 5.53 × 106 cells·mL-1 with 10.0 g·L-1 glycerol and 0.2 g·L-1 KNO3. Metabolomic analysis further revealed that mixotrophic bait microalgae could promote the accumulation of lipids and amino acids.
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Affiliation(s)
- Yahui Bo
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Ruirui Chu
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Danni Sun
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Xiangyuan Deng
- College of Biotechnology, Jiangsu University of Science and Technology, 212100 Zhenjiang, China
| | - Chengxu Zhou
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Xiaojun Yan
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Roger Ruan
- Center for Biorefining, and Department of Bioproducts and Biosystems Engineering, University of Minnesota-Twin Cities, Saint Paul, MN 55108, USA
| | - Pengfei Cheng
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China.
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Krämer LC, Wasser D, Haitz F, Sabel B, Büchel C. Heterologous expression of HUP1 glucose transporter enables low-light mediated growth on glucose in Phaeodactylum tricornutum. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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Continuous Culture of Auxenochlorella protothecoides on Biodiesel Derived Glycerol under Mixotrophic and Heterotrophic Conditions: Growth Parameters and Biochemical Composition. Microorganisms 2022; 10:microorganisms10030541. [PMID: 35336116 PMCID: PMC8953379 DOI: 10.3390/microorganisms10030541] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 02/24/2022] [Accepted: 02/24/2022] [Indexed: 11/16/2022] Open
Abstract
As crude glycerol comprises a potential substrate for microalga fermentation and value added products’ biosynthesis, Auxenochlorella protothecoides was grown on it under heterotrophic and mixotrophic conditions and its growth kinetics were evaluated in a continuous system under steady state conditions. Increasing initial glycerol concentration (from 30 to 50 g/L) in the heterotrophic culture led to reduced biomass yield (Yx/S) and productivity (Px), but favored lipid accumulation. Under heterotrophic conditions, the microalga was found to grow better (biomass up to 7.888 g/L) and faster (higher growth rates), the system functioned more effectively (higher Px) and crude glycerol was exploited more efficiently. Heterotrophy also favored proteins synthesis (up to 53%), lipids (up to 9.8%), and carbohydrates (up to 44.6%) accumulation. However, different trophic modes had no significant impact on the consistency of proteins and lipids. Oleic acid was the most abundant fatty acid detected (55–61.2% of the total lipids). The algal biomass contained many essential and non-essential amino acids, especially arginine, glutamic acid, lysine, aspartic acid, leucine, and alanine. In all the experimental trials, the protein contents in the microalgal biomass increased with the increasing dilution rate (D), with a concomitant decrease in the lipids and carbohydrates fractions.
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Castillo T, Ramos D, García-Beltrán T, Brito-Bazan M, Galindo E. Mixotrophic cultivation of microalgae: An alternative to produce high-value metabolites. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108183] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Marella TK, Bhattacharjya R, Tiwari A. Impact of organic carbon acquisition on growth and functional biomolecule production in diatoms. Microb Cell Fact 2021; 20:135. [PMID: 34266439 PMCID: PMC8281487 DOI: 10.1186/s12934-021-01627-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/03/2021] [Indexed: 02/01/2023] Open
Abstract
Diatoms are unicellular photosynthetic protists which constitute one of the most successful microalgae contributing enormously to global primary productivity and nutrient cycles in marine and freshwater habitats. Though they possess the ability to biosynthesize high value compounds like eicosatetraenoic acid (EPA), fucoxanthin (Fx) and chrysolaminarin (Chrl) the major bottle neck in commercialization is their inability to attain high density growth. However, their unique potential of acquiring diverse carbon sources via varied mechanisms enables them to adapt and grow under phototrophic, mixotrophic as well as heterotrophic modes. Growth on organic carbon substrates promotes higher biomass, lipid, and carbohydrate productivity, which further triggers the yield of various biomolecules. Since, the current mass culture practices primarily employ open pond and tubular photobioreactors for phototrophic growth, they become cost intensive and economically non-viable. Therefore, in this review we attempt to explore and compare the mechanisms involved in organic carbon acquisition in diatoms and its implications on mixotrophic and heterotrophic growth and biomolecule production and validate how these strategies could pave a way for future exploration and establishment of sustainable diatom biorefineries for novel biomolecules.
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Affiliation(s)
- Thomas Kiran Marella
- Algae Biomass and Energy System R&D Center (ABES), University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, 305-8572, Japan
| | - Raya Bhattacharjya
- Diatom Research Laboratory, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India
| | - Archana Tiwari
- Diatom Research Laboratory, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India.
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Schada von Borzyskowski L, Bernhardsgrütter I, Erb TJ. Biochemical unity revisited: microbial central carbon metabolism holds new discoveries, multi-tasking pathways, and redundancies with a reason. Biol Chem 2021; 401:1429-1441. [PMID: 32990641 DOI: 10.1515/hsz-2020-0214] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 09/10/2020] [Indexed: 01/27/2023]
Abstract
For a long time, our understanding of metabolism has been dominated by the idea of biochemical unity, i.e., that the central reaction sequences in metabolism are universally conserved between all forms of life. However, biochemical research in the last decades has revealed a surprising diversity in the central carbon metabolism of different microorganisms. Here, we will embrace this biochemical diversity and explain how genetic redundancy and functional degeneracy cause the diversity observed in central metabolic pathways, such as glycolysis, autotrophic CO2 fixation, and acetyl-CoA assimilation. We conclude that this diversity is not the exception, but rather the standard in microbiology.
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Affiliation(s)
- Lennart Schada von Borzyskowski
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, D-35043Marburg, Germany
| | - Iria Bernhardsgrütter
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, D-35043Marburg, Germany
| | - Tobias J Erb
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, D-35043Marburg, Germany.,Center for Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, D-35043Marburg, Germany
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Mixotrophic cultivation of Thalassiosira pseudonana with pure and crude glycerol: Impact on lipid profile. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102194] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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10
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Wang X, Liu SF, Qin ZH, Balamurugan S, Li HY, Lin CSK. Sustainable and stepwise waste-based utilisation strategy for the production of biomass and biofuels by engineered microalgae. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 265:114854. [PMID: 32504890 DOI: 10.1016/j.envpol.2020.114854] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/04/2020] [Accepted: 05/20/2020] [Indexed: 05/08/2023]
Abstract
Waste streams have emerged as potential feedstocks for biofuel production via microbial bioconversion. Metabolic engineering of the microalga Phaeodactylum tricornutum in its lipid biosynthetic pathways has been conducted with an aim to improve lipid production. However, there has been only limited achievement in satisfying biofuel demands by utilising extracellular organic carbons from low-cost waste streams. Herein, we present a successive staged cultivation mode, based on a previously engineered strain that co-overexpresses two key triacylglycerol biosynthesis genes. We first optimised microalgal biomass and lipid production by using food waste hydrolysate and crude glycerol as the cultivation media. Food waste hydrolysate (5% v/v) is a low-cost organic carbon source for enhanced microalgal biomass production, and the resulting lipid concentration was 1.08-fold higher with food-waste hydrolysate than that of the defined medium. Additionally, the resultant lipid concentration after using crude glycerol (100 mM) was 1.24-fold higher than that using the defined medium. Two carbon feeding modes (hybrid and sequential) were also performed to investigate the potential of engineered P. tricornutum with preliminary mechanistic analyses. The biodiesel properties of lipids produced in the hybrid mode were evaluated for potential application prospects. Collectively, this study demonstrates a waste stream utilisation strategy for efficient and sustainable microalgal biofuel production.
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Affiliation(s)
- Xiang Wang
- Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institute, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Si-Fen Liu
- Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institute, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Zi-Hao Qin
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Srinivasan Balamurugan
- Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institute, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; Department of Biotechnology, Bharathidasan University, Tiruchirappalli, 620024, India
| | - Hong-Ye Li
- Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institute, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Carol Sze Ki Lin
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China.
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Xiao Y, Guo J, Zhu H, Muhammad A, Deng H, Hu Z, Wu Q. Inhibition of glucose assimilation in Auxenochlorella protothecoides by light. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:146. [PMID: 32831906 PMCID: PMC7437033 DOI: 10.1186/s13068-020-01787-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 08/12/2020] [Indexed: 05/06/2023]
Abstract
BACKGROUND The yield of microalgae biomass is the key to affect the accumulation of fatty acids. A few microalgae can assimilate organic carbon to improve biomass yield. In mixotrophic cultivation, microalgae can use organic carbon source and light energy simultaneously. The preference of the main energy source by microalgae determines the biomass yield. Auxenochlorella protothecoides is an oleaginous mixotrophic microalga that can efficiently assimilate glucose and accumulate a large amount of biomass and fatty acids. The current study focused on the effect of light on the growth and glucose assimilation of A. protothecoides. RESULTS In this study, we found that the uptake and metabolism of glucose in A. protothecoides could be inhibited by light, resulting in a reduction of biomass growth and lipid accumulation. We employed comparative proteomics to study the influence of light on the regulation of glucose assimilation in A. protothecoides. Proteomics revealed that proteins involving in gene translation and photosynthesis system were up-regulated in the light, such as ribulose-phosphate 3-epimerase and phosphoribulokinase. Calvin cycle-related proteins were also up-regulated, suggesting that light may inhibit glucose metabolism by enhancing the production of glyceraldehyde-3-phosphate (G3P) in the Calvin cycle. In addition, the redox homeostasis-related proteins such as thioredoxin reductase were up-regulated in the light, indicating that light may regulate glucose uptake by changing the redox balance. Moreover, the increase of NADH levels and redox potential of the medium under illumination might inhibit the activity of the glucose transport system and subsequently reduce glucose uptake. CONCLUSIONS A theoretical model of how glucose assimilation in A. protothecoides is negatively influenced by light was proposed, which will facilitate further studies on the complex mechanisms underlying the transition from autotrophy to heterotrophy for improving biomass accumulation.
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Affiliation(s)
- Yibo Xiao
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
- Key Laboratory of Optoelectronic Devices and Systems of the Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Jianying Guo
- Key Laboratory of Industrial Biocatalysis of the Ministry of Education and Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084 People’s Republic of China
| | - Huachang Zhu
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Anwar Muhammad
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
- Key Laboratory of Optoelectronic Devices and Systems of the Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Haiteng Deng
- Key Laboratory of Industrial Biocatalysis of the Ministry of Education and Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084 People’s Republic of China
| | - Zhangli Hu
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Longhua Innovation Institute for Biotechnology, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Qingyu Wu
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
- Key Laboratory of Industrial Biocatalysis of the Ministry of Education and Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084 People’s Republic of China
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Yang R, Wei D, Xie J. Diatoms as cell factories for high-value products: chrysolaminarin, eicosapentaenoic acid, and fucoxanthin. Crit Rev Biotechnol 2020; 40:993-1009. [DOI: 10.1080/07388551.2020.1805402] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Runqing Yang
- School of Food Science and Engineering, South China University of Technology, Guangzhou, People’s Republic of China
| | - Dong Wei
- School of Food Science and Engineering, South China University of Technology, Guangzhou, People’s Republic of China
| | - Jun Xie
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Chinese Academy of Fishery Sciences Pearl River Fisheries Research Institute, Guangzhou, People’s Republic of China
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Patel A, Karageorgou D, Rova E, Katapodis P, Rova U, Christakopoulos P, Matsakas L. An Overview of Potential Oleaginous Microorganisms and Their Role in Biodiesel and Omega-3 Fatty Acid-Based Industries. Microorganisms 2020; 8:E434. [PMID: 32204542 PMCID: PMC7143722 DOI: 10.3390/microorganisms8030434] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 03/16/2020] [Accepted: 03/18/2020] [Indexed: 12/17/2022] Open
Abstract
Microorganisms are known to be natural oil producers in their cellular compartments. Microorganisms that accumulate more than 20% w/w of lipids on a cell dry weight basis are considered as oleaginous microorganisms. These are capable of synthesizing vast majority of fatty acids from short hydrocarbonated chain (C6) to long hydrocarbonated chain (C36), which may be saturated (SFA), monounsaturated (MUFA), or polyunsaturated fatty acids (PUFA), depending on the presence and number of double bonds in hydrocarbonated chains. Depending on the fatty acid profile, the oils obtained from oleaginous microorganisms are utilized as feedstock for either biodiesel production or as nutraceuticals. Mainly microalgae, bacteria, and yeasts are involved in the production of biodiesel, whereas thraustochytrids, fungi, and some of the microalgae are well known to be producers of very long-chain PUFA (omega-3 fatty acids). In this review article, the type of oleaginous microorganisms and their expertise in the field of biodiesel or omega-3 fatty acids, advances in metabolic engineering tools for enhanced lipid accumulation, upstream and downstream processing of lipids, including purification of biodiesel and concentration of omega-3 fatty acids are reviewed.
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Affiliation(s)
- Alok Patel
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental, and Natural Resources Engineering, Luleå University of Technology, SE-971 87 Luleå, Sweden; (A.P.); (E.R.); (U.R.); (P.C.)
| | - Dimitra Karageorgou
- Laboratory of Biotechnology, Department of Biological Applications and Technologies, University of Ioannina, Ioannina 45110, Greece; (D.K.); (P.K.)
| | - Emma Rova
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental, and Natural Resources Engineering, Luleå University of Technology, SE-971 87 Luleå, Sweden; (A.P.); (E.R.); (U.R.); (P.C.)
| | - Petros Katapodis
- Laboratory of Biotechnology, Department of Biological Applications and Technologies, University of Ioannina, Ioannina 45110, Greece; (D.K.); (P.K.)
| | - Ulrika Rova
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental, and Natural Resources Engineering, Luleå University of Technology, SE-971 87 Luleå, Sweden; (A.P.); (E.R.); (U.R.); (P.C.)
| | - Paul Christakopoulos
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental, and Natural Resources Engineering, Luleå University of Technology, SE-971 87 Luleå, Sweden; (A.P.); (E.R.); (U.R.); (P.C.)
| | - Leonidas Matsakas
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental, and Natural Resources Engineering, Luleå University of Technology, SE-971 87 Luleå, Sweden; (A.P.); (E.R.); (U.R.); (P.C.)
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Ait-Mohamed O, Novák Vanclová AMG, Joli N, Liang Y, Zhao X, Genovesio A, Tirichine L, Bowler C, Dorrell RG. PhaeoNet: A Holistic RNAseq-Based Portrait of Transcriptional Coordination in the Model Diatom Phaeodactylum tricornutum. FRONTIERS IN PLANT SCIENCE 2020; 11:590949. [PMID: 33178253 PMCID: PMC7596299 DOI: 10.3389/fpls.2020.590949] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/15/2020] [Indexed: 05/04/2023]
Abstract
Transcriptional coordination is a fundamental component of prokaryotic and eukaryotic cell biology, underpinning the cell cycle, physiological transitions, and facilitating holistic responses to environmental stress, but its overall dynamics in eukaryotic algae remain poorly understood. Better understanding of transcriptional partitioning may provide key insights into the primary metabolism pathways of eukaryotic algae, which frequently depend on intricate metabolic associations between the chloroplasts and mitochondria that are not found in plants. Here, we exploit 187 publically available RNAseq datasets generated under varying nitrogen, iron and phosphate growth conditions to understand the co-regulatory principles underpinning transcription in the model diatom Phaeodactylum tricornutum. Using WGCNA (Weighted Gene Correlation Network Analysis), we identify 28 merged modules of co-expressed genes in the P. tricornutum genome, which show high connectivity and correlate well with previous microarray-based surveys of gene co-regulation in this species. We use combined functional, subcellular localization and evolutionary annotations to reveal the fundamental principles underpinning the transcriptional co-regulation of genes implicated in P. tricornutum chloroplast and mitochondrial metabolism, as well as the functions of diverse transcription factors underpinning this co-regulation. The resource is publically available as PhaeoNet, an advanced tool to understand diatom gene co-regulation.
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Affiliation(s)
- Ouardia Ait-Mohamed
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Anna M. G. Novák Vanclová
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Nathalie Joli
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Yue Liang
- Department of Oceanography, Dalhousie University, Halifax, NS, Canada
| | - Xue Zhao
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- Université de Nantes, CNRS, UFIP, UMR 6286, Nantes, France
| | - Auguste Genovesio
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Leila Tirichine
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- Université de Nantes, CNRS, UFIP, UMR 6286, Nantes, France
- *Correspondence: Leila Tirichine,
| | - Chris Bowler
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- Chris Bowler,
| | - Richard G. Dorrell
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
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15
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Cui Y, Thomas-Hall SR, Schenk PM. Phaeodactylum tricornutum microalgae as a rich source of omega-3 oil: Progress in lipid induction techniques towards industry adoption. Food Chem 2019; 297:124937. [DOI: 10.1016/j.foodchem.2019.06.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 06/01/2019] [Accepted: 06/02/2019] [Indexed: 10/26/2022]
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16
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Biosynthesis of Nutraceutical Fatty Acids by the Oleaginous Marine Microalgae Phaeodactylum tricornutum Utilizing Hydrolysates from Organosolv-Pretreated Birch and Spruce Biomass. Mar Drugs 2019; 17:md17020119. [PMID: 30781416 PMCID: PMC6410020 DOI: 10.3390/md17020119] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 01/20/2019] [Accepted: 02/13/2019] [Indexed: 11/17/2022] Open
Abstract
Polyunsaturated fatty acids (PUFAs) are essential for human function, however they have to be provided through the diet. As their production from fish oil is environmentally unsustainable, there is demand for new sources of PUFAs. The aim of the present work was to establish the microalgal platform to produce nutraceutical-value PUFAs from forest biomass. To this end, the growth of Phaeodactylum tricornutum on birch and spruce hydrolysates was compared to autotrophic cultivation and glucose synthetic media. Total lipid generated by P. tricornutum grown mixotrophically on glucose, birch, and spruce hydrolysates was 1.21, 1.26, and 1.29 g/L, respectively. The highest eicosapentaenoic acid (EPA) production (256 mg/L) and productivity (19.69 mg/L/d) were observed on spruce hydrolysates. These values were considerably higher than those obtained from the cultivation without glucose (79.80 mg/L and 6.14 mg/L/d, respectively) and also from the photoautotrophic cultivation (26.86 mg/L and 2.44 mg/L/d, respectively). To the best of our knowledge, this is the first report describing the use of forest biomass as raw material for EPA and docosapentaenoic acid (DHA) production.
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17
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Vavitsas K, Fabris M, Vickers CE. Terpenoid Metabolic Engineering in Photosynthetic Microorganisms. Genes (Basel) 2018; 9:E520. [PMID: 30360565 PMCID: PMC6266707 DOI: 10.3390/genes9110520] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/17/2018] [Accepted: 10/17/2018] [Indexed: 12/13/2022] Open
Abstract
Terpenoids are a group of natural products that have a variety of roles, both essential and non-essential, in metabolism and in biotic and abiotic interactions, as well as commercial applications such as pharmaceuticals, food additives, and chemical feedstocks. Economic viability for commercial applications is commonly not achievable by using natural source organisms or chemical synthesis. Engineered bio-production in suitable heterologous hosts is often required to achieve commercial viability. However, our poor understanding of regulatory mechanisms and other biochemical processes makes obtaining efficient conversion yields from feedstocks challenging. Moreover, production from carbon dioxide via photosynthesis would significantly increase the environmental and potentially the economic credentials of these processes by disintermediating biomass feedstocks. In this paper, we briefly review terpenoid metabolism, outline some recent advances in terpenoid metabolic engineering, and discuss why photosynthetic unicellular organisms-such as algae and cyanobacteria-might be preferred production platforms for the expression of some of the more challenging terpenoid pathways.
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Affiliation(s)
- Konstantinos Vavitsas
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia.
- CSIRO Synthetic Biology Future Science Platform, GPO Box 2583, Brisbane, QLD 4001, Australia.
| | - Michele Fabris
- Climate Change Cluster, University of Technology Sydney, 15 Broadway, Ultimo, NSW 2007, Australia.
- CSIRO Synthetic Biology Future Science Platform, GPO Box 2583, Brisbane, QLD 4001, Australia.
| | - Claudia E Vickers
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia.
- CSIRO Synthetic Biology Future Science Platform, GPO Box 2583, Brisbane, QLD 4001, Australia.
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18
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Villanova V, Fortunato AE, Singh D, Bo DD, Conte M, Obata T, Jouhet J, Fernie AR, Marechal E, Falciatore A, Pagliardini J, Le Monnier A, Poolman M, Curien G, Petroutsos D, Finazzi G. Investigating mixotrophic metabolism in the model diatom Phaeodactylum tricornutum. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0404. [PMID: 28717014 DOI: 10.1098/rstb.2016.0404] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2017] [Indexed: 12/14/2022] Open
Abstract
Diatoms are prominent marine microalgae, interesting not only from an ecological point of view, but also for their possible use in biotechnology applications. They can be cultivated in phototrophic conditions, using sunlight as the sole energy source. Some diatoms, however, can also grow in a mixotrophic mode, wherein both light and external reduced carbon contribute to biomass accumulation. In this study, we investigated the consequences of mixotrophy on the growth and metabolism of the pennate diatom Phaeodactylum tricornutum, using glycerol as the source of reduced carbon. Transcriptomics, metabolomics, metabolic modelling and physiological data combine to indicate that glycerol affects the central-carbon, carbon-storage and lipid metabolism of the diatom. In particular, provision of glycerol mimics typical responses of nitrogen limitation on lipid metabolism at the level of triacylglycerol accumulation and fatty acid composition. The presence of glycerol, despite provoking features reminiscent of nutrient limitation, neither diminishes photosynthetic activity nor cell growth, revealing essential aspects of the metabolic flexibility of these microalgae and suggesting possible biotechnological applications of mixotrophy.This article is part of the themed issue 'The peculiar carbon metabolism in diatoms'.
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Affiliation(s)
- Valeria Villanova
- Fermentalg SA, 33500 Libourne, France.,Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes (UGA), Centre National de la Recherche Scientifique (CNRS), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Institut National Recherche Agronomique (INRA), Institut de Biosciences et Biotechnologies de Grenoble (BIG), CEA Grenoble, F-38000 Grenoble, France
| | - Antonio Emidio Fortunato
- Laboratoire de Biologie Computationnelle et Quantitative, Sorbonne Universités, UPMC, Institut de Biologie Paris-Seine, CNRS, 15 rue de l'Ecole de Médecine, Paris 75006, France
| | - Dipali Singh
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Davide Dal Bo
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes (UGA), Centre National de la Recherche Scientifique (CNRS), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Institut National Recherche Agronomique (INRA), Institut de Biosciences et Biotechnologies de Grenoble (BIG), CEA Grenoble, F-38000 Grenoble, France
| | - Melissa Conte
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes (UGA), Centre National de la Recherche Scientifique (CNRS), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Institut National Recherche Agronomique (INRA), Institut de Biosciences et Biotechnologies de Grenoble (BIG), CEA Grenoble, F-38000 Grenoble, France
| | - Toshihiro Obata
- Max-Planck Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Golm-Potsdam, Germany
| | - Juliette Jouhet
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes (UGA), Centre National de la Recherche Scientifique (CNRS), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Institut National Recherche Agronomique (INRA), Institut de Biosciences et Biotechnologies de Grenoble (BIG), CEA Grenoble, F-38000 Grenoble, France
| | - Alisdair R Fernie
- Max-Planck Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Golm-Potsdam, Germany
| | - Eric Marechal
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes (UGA), Centre National de la Recherche Scientifique (CNRS), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Institut National Recherche Agronomique (INRA), Institut de Biosciences et Biotechnologies de Grenoble (BIG), CEA Grenoble, F-38000 Grenoble, France
| | - Angela Falciatore
- Laboratoire de Biologie Computationnelle et Quantitative, Sorbonne Universités, UPMC, Institut de Biologie Paris-Seine, CNRS, 15 rue de l'Ecole de Médecine, Paris 75006, France
| | | | | | - Mark Poolman
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Gilles Curien
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes (UGA), Centre National de la Recherche Scientifique (CNRS), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Institut National Recherche Agronomique (INRA), Institut de Biosciences et Biotechnologies de Grenoble (BIG), CEA Grenoble, F-38000 Grenoble, France
| | - Dimitris Petroutsos
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes (UGA), Centre National de la Recherche Scientifique (CNRS), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Institut National Recherche Agronomique (INRA), Institut de Biosciences et Biotechnologies de Grenoble (BIG), CEA Grenoble, F-38000 Grenoble, France
| | - Giovanni Finazzi
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes (UGA), Centre National de la Recherche Scientifique (CNRS), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Institut National Recherche Agronomique (INRA), Institut de Biosciences et Biotechnologies de Grenoble (BIG), CEA Grenoble, F-38000 Grenoble, France
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19
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Davis A, Abbriano R, Smith SR, Hildebrand M. Clarification of Photorespiratory Processes and the Role of Malic Enzyme in Diatoms. Protist 2016; 168:134-153. [PMID: 28104538 DOI: 10.1016/j.protis.2016.10.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 10/03/2016] [Accepted: 10/08/2016] [Indexed: 11/20/2022]
Abstract
Evidence suggests that diatom photorespiratory metabolism is distinct from other photosynthetic eukaryotes in that there may be at least two routes for the metabolism of the photorespiratory metabolite glycolate. One occurs primarily in the mitochondria and is similar to the C2 photorespiratory pathway, and the other processes glycolate through the peroxisomal glyoxylate cycle. Genomic analysis has identified the presence of key genes required for glycolate oxidation, the glyoxylate cycle, and malate metabolism, however, predictions of intracellular localization can be ambiguous and require verification. This knowledge gap leads to uncertainties surrounding how these individual pathways operate, either together or independently, to process photorespiratory intermediates under different environmental conditions. Here, we combine in silico sequence analysis, in vivo protein localization techniques and gene expression patterns to investigate key enzymes potentially involved in photorespiratory metabolism in the model diatom Thalassiosira pseudonana. We demonstrate the peroxisomal localization of isocitrate lyase and the mitochondrial localization of malic enzyme and a glycolate oxidase. Based on these analyses, we propose an updated model for photorespiratory metabolism in T. pseudonana, as well as a mechanism by which C2 photorespiratory metabolism and its associated pathways may operate during silicon starvation and growth arrest.
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Affiliation(s)
- Aubrey Davis
- Marine Biology Research Division, Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, U.S.A
| | - Raffaela Abbriano
- Marine Biology Research Division, Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, U.S.A
| | - Sarah R Smith
- Integrative Oceanography Division, Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, U.S.A.; J. Craig Venter Institute, La Jolla, CA, U.S.A
| | - Mark Hildebrand
- Marine Biology Research Division, Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, U.S.A..
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20
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Abstract
Marine diatoms have potential as a biotechnological production platform, especially for lipid-derived products, including biofuels. Here we introduce some features of diatom metabolism, particularly with respect to photosynthesis, photorespiration and lipid synthesis and their differences relative to other photosynthetic eukaryotes. Since structural metabolic modelling of other photosynthetic organisms has been shown to be capable of representing their metabolic capabilities realistically, we briefly review the main approaches to this type of modelling. We then propose that genome-scale modelling of the diatom Phaeodactylum tricornutum, in response to varying light intensity, could uncover the novel aspects of the metabolic potential of this organism.
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21
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Lima RN, Porto ALM. Recent Advances in Marine Enzymes for Biotechnological Processes. ADVANCES IN FOOD AND NUTRITION RESEARCH 2016; 78:153-92. [PMID: 27452170 DOI: 10.1016/bs.afnr.2016.06.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In the last decade, new trends in the food and pharmaceutical industries have increased concern for the quality and safety of products. The use of biocatalytic processes using marine enzymes has become an important and useful natural product for biotechnological applications. Bioprocesses using biocatalysts like marine enzymes (fungi, bacteria, plants, animals, algae, etc.) offer hyperthermostability, salt tolerance, barophilicity, cold adaptability, chemoselectivity, regioselectivity, and stereoselectivity. Currently, enzymatic methods are used to produce a large variety of products that humans consume, and the specific nature of the enzymes including processing under mild pH and temperature conditions result in fewer unwanted side-effects and by-products. This offers high selectivity in industrial processes. The marine habitat has been become increasingly studied because it represents a huge source potential biocatalysts. Enzymes include oxidoreductases, hydrolases, transferases, isomerases, ligases, and lyases that can be used in food and pharmaceutical applications. Finally, recent advances in biotechnological processes using enzymes of marine organisms (bacterial, fungi, algal, and sponges) are described and also our work on marine organisms from South America, especially marine-derived fungi and bacteria involved in biotransformations and biodegradation of organic compounds.
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Affiliation(s)
- R N Lima
- Laboratório de Química Orgânica e Biocatálise, Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil
| | - A L M Porto
- Laboratório de Química Orgânica e Biocatálise, Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil.
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22
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Kim J, Fabris M, Baart G, Kim MK, Goossens A, Vyverman W, Falkowski PG, Lun DS. Flux balance analysis of primary metabolism in the diatom Phaeodactylum tricornutum. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 85:161-176. [PMID: 26590126 DOI: 10.1111/tpj.13081] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Revised: 11/04/2015] [Accepted: 11/09/2015] [Indexed: 06/05/2023]
Abstract
Diatoms (Bacillarophyceae) are photosynthetic unicellular microalgae that have risen to ecological prominence in oceans over the past 30 million years. They are of interest as potential feedstocks for sustainable biofuels. Maximizing production of these feedstocks will require genetic modifications and an understanding of algal metabolism. These processes may benefit from genome-scale models, which predict intracellular fluxes and theoretical yields, as well as the viability of knockout and knock-in transformants. Here we present a genome-scale metabolic model of a fully sequenced and transformable diatom: Phaeodactylum tricornutum. The metabolic network was constructed using the P. tricornutum genome, biochemical literature, and online bioinformatic databases. Intracellular fluxes in P. tricornutum were calculated for autotrophic, mixotrophic and heterotrophic growth conditions, as well as knockout conditions that explore the in silico role of glycolytic enzymes in the mitochondrion. The flux distribution for lower glycolysis in the mitochondrion depended on which transporters for TCA cycle metabolites were included in the model. The growth rate predictions were validated against experimental data obtained using chemostats. Two published studies on this organism were used to validate model predictions for cyclic electron flow under autotrophic conditions, and fluxes through the phosphoketolase, glycine and serine synthesis pathways under mixotrophic conditions. Several gaps in annotation were also identified. The model also explored unusual features of diatom metabolism, such as the presence of lower glycolysis pathways in the mitochondrion, as well as differences between P. tricornutum and other photosynthetic organisms.
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Affiliation(s)
- Joomi Kim
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Michele Fabris
- Plant Functional Biology and Climate Change Cluster (C3), Faculty of Science University of Technology, Sydney, New South Wales, Australia
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Gent, Belgium
- Department of Biology, Laboratory of Protistology and Aquatic Ecology, Ghent University, B-9000, Gent, Belgium
| | - Gino Baart
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Gent, Belgium
- Department of Biology, Laboratory of Protistology and Aquatic Ecology, Ghent University, B-9000, Gent, Belgium
- Centre of Microbial and Plant Genetics Lab for Genetics and Genomics and Leuven Institute for Beer Research, Leuven University, Gaston Geenslaan 1, B-3001, Leuven, Belgium
| | - Min K Kim
- Center for Computational and Integrative Biology and Department of Computer Science, Rutgers University, Camden, NJ, 08102, USA
| | - Alain Goossens
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Gent, Belgium
| | - Wim Vyverman
- Department of Biology, Laboratory of Protistology and Aquatic Ecology, Ghent University, B-9000, Gent, Belgium
| | - Paul G Falkowski
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Desmond S Lun
- Center for Computational and Integrative Biology and Department of Computer Science, Rutgers University, Camden, NJ, 08102, USA
- Department of Plant Biology and Pathology, Rutgers University, New Brunswick, NJ, 08901, USA
- School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, South Australia, Australia
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23
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A Metabolic Probe-Enabled Strategy Reveals Uptake and Protein Targets of Polyunsaturated Aldehydes in the Diatom Phaeodactylum tricornutum. PLoS One 2015; 10:e0140927. [PMID: 26496085 PMCID: PMC4619725 DOI: 10.1371/journal.pone.0140927] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 10/01/2015] [Indexed: 01/12/2023] Open
Abstract
Diatoms are unicellular algae of crucial importance as they belong to the main primary producers in aquatic ecosystems. Several diatom species produce polyunsaturated aldehydes (PUAs) that have been made responsible for chemically mediated interactions in the plankton. PUA-effects include chemical defense by reducing the reproductive success of grazing copepods, allelochemical activity by interfering with the growth of competing phytoplankton and cell to cell signaling. We applied a PUA-derived molecular probe, based on the biologically highly active 2,4-decadienal, with the aim to reveal protein targets of PUAs and affected metabolic pathways. By using fluorescence microscopy, we observed a substantial uptake of the PUA probe into cells of the diatom Phaeodactylum tricornutum in comparison to the uptake of a structurally closely related control probe based on a saturated aldehyde. The specific uptake motivated a chemoproteomic approach to generate a qualitative inventory of proteins covalently targeted by the α,β,γ,δ-unsaturated aldehyde structure element. Activity-based protein profiling revealed selective covalent modification of target proteins by the PUA probe. Analysis of the labeled proteins gave insights into putative affected molecular functions and biological processes such as photosynthesis including ATP generation and catalytic activity in the Calvin cycle or the pentose phosphate pathway. The mechanism of action of PUAs involves covalent reactions with proteins that may result in protein dysfunction and interference of involved pathways.
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Pancha I, Chokshi K, Mishra S. Enhanced biofuel production potential with nutritional stress amelioration through optimization of carbon source and light intensity in Scenedesmus sp. CCNM 1077. BIORESOURCE TECHNOLOGY 2015; 179:565-572. [PMID: 25579231 DOI: 10.1016/j.biortech.2014.12.079] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 12/22/2014] [Accepted: 12/23/2014] [Indexed: 05/06/2023]
Abstract
Microalgal mixotrophic cultivation is one of the most potential ways to enhance biomass and biofuel production. In the present study, first of all ability of microalgae Scenedesmus sp. CCNM 1077 to utilize various carbon sources under mixotrophic growth condition was evaluated followed by optimization of glucose concentration and light intensity to obtain higher biomass, lipid and carbohydrate contents. Under optimized condition i.e. 4 g/L glucose and 150 μmol m(-2) s(-1) light intensity, Scenedesmus sp. CCNM 1077 produced 1.2g/L dry cell weight containing 23.62% total lipid and 42.68% carbohydrate. Addition of glucose shown nutritional stress ameliorating effects and around 70% carbohydrate and 25% total lipid content was found with only 21% reduction in dry cell weight under nitrogen starved condition. This study shows potential application of mixotrophically grown Scenedesmus sp. CCNM 1077 for bioethanol and biodiesel production feed stock.
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Affiliation(s)
- Imran Pancha
- Discipline of Salt & Marine Chemicals, CSIR - Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, India; Academy of Scientific & Innovative Research (AcSIR), CSIR - Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, India
| | - Kaumeel Chokshi
- Discipline of Salt & Marine Chemicals, CSIR - Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, India; Academy of Scientific & Innovative Research (AcSIR), CSIR - Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, India
| | - Sandhya Mishra
- Discipline of Salt & Marine Chemicals, CSIR - Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, India; Academy of Scientific & Innovative Research (AcSIR), CSIR - Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, India.
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