1
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Zeng L, Bi Y, Guo P, Bi Y, Wang T, Dong L, Wang F, Chen L, Zhang W. Metabolic Analysis of Schizochytrium Mutants With High DHA Content Achieved With ARTP Mutagenesis Combined With Iodoacetic Acid and Dehydroepiandrosterone Screening. Front Bioeng Biotechnol 2021; 9:738052. [PMID: 34869256 PMCID: PMC8637758 DOI: 10.3389/fbioe.2021.738052] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 10/04/2021] [Indexed: 11/13/2022] Open
Abstract
High DHA production cost caused by low DHA titer and productivity of the current Schizochytrium strains is a bottleneck for its application in competition with traditional fish-oil based approach. In this study, atmospheric and room-temperature plasma with iodoacetic acid and dehydroepiandrosterone screening led to three mutants, 6–8, 6–16 and 6–23 all with increased growth and DHA accumulations. A LC/MS metabolomic analysis revealed the increased metabolism in PPP and EMP as well as the decreased TCA cycle might be relevant to the increased growth and DHA biosynthesis in the mutants. Finally, the mutant 6–23, which achieved the highest growth and DHA accumulation among all mutants, was evaluated in a 5 L fermentor. The results showed that the DHA concentration and productivity in mutant 6–23 were 41.4 g/L and 430.7 mg/L/h in fermentation for 96 h, respectively, which is the highest reported so far in literature. The study provides a novel strain improvement strategy for DHA-producing Schizochytrium.
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Affiliation(s)
- Lei Zeng
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Yanqi Bi
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Pengfei Guo
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Yali Bi
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Tiantian Wang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Liang Dong
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Fangzhong Wang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China.,Center for Biosafety Research and Strategy, Tianjin University, Tianjin, China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China.,Center for Biosafety Research and Strategy, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
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2
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Hoys C, Romero-Losada AB, Del Río E, Guerrero MG, Romero-Campero FJ, García-González M. Unveiling the underlying molecular basis of astaxanthin accumulation in Haematococcus through integrative metabolomic-transcriptomic analysis. BIORESOURCE TECHNOLOGY 2021; 332:125150. [PMID: 33878543 DOI: 10.1016/j.biortech.2021.125150] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/04/2021] [Accepted: 04/05/2021] [Indexed: 06/12/2023]
Abstract
Astaxanthin is a valuable and highly demanded ketocarotenoid pigment, for which the chlorophycean microalga Haematococcus pluvialis is an outstanding natural source. Although information on astaxanthin accumulation in H. pluvialis has substantially advanced in recent years, its underlying molecular bases remain elusive. An integrative metabolic and transcriptomic analysis has been performed for vegetative Haematococcus cells, grown both under N sufficiency (green palmelloid cells) and under moderate N limitation, allowing concurrent active cell growth and astaxanthin synthesis (reddish palmelloid cells). Transcriptional activation was noticeable in reddish cells of key enzymes participating in glycolysis, pentose phosphate cycle and pyruvate metabolism, determining the adequate provision of glyceraldehyde 3 phosphate and pyruvate, precursors of carotenoids and fatty acids. Moreover, for the first time, transcriptional regulators potentially involved in controlling astaxanthin accumulation have been identified, a knowledge enabling optimization of commercial astaxanthin production by Haematococcus through systems metabolic engineering.
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Affiliation(s)
- Cristina Hoys
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla-Consejo Superior de Investigaciones Científicas, Centro de Investigaciones Científicas Isla de la Cartuja, Avda. Américo Vespucio, 49, 41092 Sevilla, Spain
| | - Ana B Romero-Losada
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla-Consejo Superior de Investigaciones Científicas, Centro de Investigaciones Científicas Isla de la Cartuja, Avda. Américo Vespucio, 49, 41092 Sevilla, Spain; Department of Computer Science and Artificial Intelligence (University of Sevilla), Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | - Esperanza Del Río
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla-Consejo Superior de Investigaciones Científicas, Centro de Investigaciones Científicas Isla de la Cartuja, Avda. Américo Vespucio, 49, 41092 Sevilla, Spain
| | - Miguel G Guerrero
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla-Consejo Superior de Investigaciones Científicas, Centro de Investigaciones Científicas Isla de la Cartuja, Avda. Américo Vespucio, 49, 41092 Sevilla, Spain; AlgaEnergy S.A, Avda. de Europa 19, 28108 Alcobendas, Madrid, Spain
| | - Francisco J Romero-Campero
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla-Consejo Superior de Investigaciones Científicas, Centro de Investigaciones Científicas Isla de la Cartuja, Avda. Américo Vespucio, 49, 41092 Sevilla, Spain; Department of Computer Science and Artificial Intelligence (University of Sevilla), Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | - Mercedes García-González
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla-Consejo Superior de Investigaciones Científicas, Centro de Investigaciones Científicas Isla de la Cartuja, Avda. Américo Vespucio, 49, 41092 Sevilla, Spain.
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3
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Chakdar H, Hasan M, Pabbi S, Nevalainen H, Shukla P. High-throughput proteomics and metabolomic studies guide re-engineering of metabolic pathways in eukaryotic microalgae: A review. BIORESOURCE TECHNOLOGY 2021; 321:124495. [PMID: 33307484 DOI: 10.1016/j.biortech.2020.124495] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/24/2020] [Accepted: 11/28/2020] [Indexed: 06/12/2023]
Abstract
Eukaryotic microalgae are a rich source of commercially important metabolites including lipids, pigments, sugars, amino acids and enzymes. However, their inherent genetic potential is usually not enough to support high level production of metabolites of interest. In order to move on from the traditional approach of improving product yields by modification of the cultivation conditions, understanding the metabolic pathways leading to the synthesis of the bioproducts of interest is crucial. Identification of new targets for strain engineering has been greatly facilitated by the rapid development of high-throughput sequencing and spectroscopic techniques discussed in this review. Despite the availability of high throughput analytical tools, examples of gathering and application of proteomic and metabolomic data for metabolic engineering of microalgae are few and mainly limited to lipid production. The present review highlights the application of contemporary proteomic and metabolomic techniques in eukaryotic microalgae for redesigning pathways for enhanced production of algal metabolites.
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Affiliation(s)
- Hillol Chakdar
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Maunath Bhanjan, Uttar Pradesh 275103, India
| | - Mafruha Hasan
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Sunil Pabbi
- Centre for Conservation and Utilisation of Blue Green Algae (CCUBGA), Division of Microbiology, ICAR - Indian Agricultural Research Institute, New Delhi 110 012
| | - Helena Nevalainen
- Department of Molecular Sciences, Macquarie University, NSW 2109, Australia; Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, NSW 2109, Australia
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak 124001, Haryana, India; School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
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4
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Oyebamiji OO, Boeing WJ, Holguin FO, Ilori O, Amund O. Green microalgae cultured in textile wastewater for biomass generation and biodetoxification of heavy metals and chromogenic substances. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.biteb.2019.100247] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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5
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Multiomics resolution of molecular events during a day in the life of Chlamydomonas. Proc Natl Acad Sci U S A 2019; 116:2374-2383. [PMID: 30659148 PMCID: PMC6369806 DOI: 10.1073/pnas.1815238116] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The unicellular green alga Chlamydomonas reinhardtii displays metabolic flexibility in response to a changing environment. We analyzed expression patterns of its three genomes in cells grown under light-dark cycles. Nearly 85% of transcribed genes show differential expression, with different sets of transcripts being up-regulated over the course of the day to coordinate cellular growth before undergoing cell division. Parallel measurements of select metabolites and pigments, physiological parameters, and a subset of proteins allow us to infer metabolic events and to evaluate the impact of the transcriptome on the proteome. Among the findings are the observations that Chlamydomonas exhibits lower respiratory activity at night compared with the day; multiple fermentation pathways, some oxygen-sensitive, are expressed at night in aerated cultures; we propose that the ferredoxin, FDX9, is potentially the electron donor to hydrogenases. The light stress-responsive genes PSBS, LHCSR1, and LHCSR3 show an acute response to lights-on at dawn under abrupt dark-to-light transitions, while LHCSR3 genes also exhibit a later, second burst in expression in the middle of the day dependent on light intensity. Each response to light (acute and sustained) can be selectively activated under specific conditions. Our expression dataset, complemented with coexpression networks and metabolite profiling, should constitute an excellent resource for the algal and plant communities.
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6
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Xie Y, Sen B, Wang G. Mining terpenoids production and biosynthetic pathway in thraustochytrids. BIORESOURCE TECHNOLOGY 2017; 244:1269-1280. [PMID: 28549813 DOI: 10.1016/j.biortech.2017.05.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 04/28/2017] [Accepted: 05/01/2017] [Indexed: 05/26/2023]
Abstract
Terpenoids are major bioactive compounds produced by microalgae and other eukaryotic microorganisms. Mining metabolic potential of marine microalgae for commercial production of terpenoids suggest thraustochytrids as one of the promising cell factories. The identification of potential thraustochytrid strains and relevant laboratory scale bioprocesses has been pursued largely. Further investigations in the improvement of terpenoids biosynthesis expect relevant molecular mechanisms to be understood directing metabolic engineering of the pathways. In this review, fermentative and mechanistic studies to identify key enzymes and pathways that are associated to terpenoids biosynthesis in thraustochytrids are discussed. Exploration of biosynthesis mechanisms in other model organisms facilitated identification of potential molecular targets for engineering terpenoids biosynthetic pathway in thraustochytrids. In addition, the preliminary genetic manipulation and in silico analysis in this review provides a platform for system-level metabolic engineering towards thraustochytrid strains improvement. Overall, the review contributes comprehensive information to allow better terpenoids productivity in thraustochytrids.
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Affiliation(s)
- Yunxuan Xie
- Center for Marine Environmental Ecology, School of Environmental Science & Engineering, Tianjin University, Tianjin 300072, China
| | - Biswarup Sen
- Center for Marine Environmental Ecology, School of Environmental Science & Engineering, Tianjin University, Tianjin 300072, China
| | - Guangyi Wang
- Center for Marine Environmental Ecology, School of Environmental Science & Engineering, Tianjin University, Tianjin 300072, China.
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7
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Lu N, Chen JH, Wei D, Chen F, Chen G. Global Metabolic Regulation of the Snow Alga Chlamydomonas nivalis in Response to Nitrate or Phosphate Deprivation by a Metabolome Profile Analysis. Int J Mol Sci 2016; 17:ijms17050694. [PMID: 27171077 PMCID: PMC4881520 DOI: 10.3390/ijms17050694] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 04/29/2016] [Accepted: 04/29/2016] [Indexed: 01/27/2023] Open
Abstract
In the present work, Chlamydomonas nivalis, a model species of snow algae, was used to illustrate the metabolic regulation mechanism of microalgae under nutrient deprivation stress. The seed culture was inoculated into the medium without nitrate or phosphate to reveal the cell responses by a metabolome profile analysis using gas chromatography time-of-flight mass spectrometry (GC/TOF-MS). One hundred and seventy-one of the identified metabolites clustered into five groups by the orthogonal partial least squares discriminant analysis (OPLS-DA) model. Among them, thirty of the metabolites in the nitrate-deprived group and thirty-nine of the metabolites in the phosphate-deprived group were selected and identified as “responding biomarkers” by this metabolomic approach. A significant change in the abundance of biomarkers indicated that the enhanced biosynthesis of carbohydrates and fatty acids coupled with the decreased biosynthesis of amino acids, N-compounds and organic acids in all the stress groups. The up- or down-regulation of these biomarkers in the metabolic network provides new insights into the global metabolic regulation and internal relationships within amino acid and fatty acid synthesis, glycolysis, the tricarboxylic acid cycle (TCA) and the Calvin cycle in the snow alga under nitrate or phosphate deprivation stress.
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Affiliation(s)
- Na Lu
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China.
| | - Jun-Hui Chen
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China.
| | - Dong Wei
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China.
| | - Feng Chen
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China.
- Institute for Food and Bioresource Engineering, College of Engineering, Peking University, Beijing 100871, China.
| | - Gu Chen
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China.
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8
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Gimpel JA, Henríquez V, Mayfield SP. In Metabolic Engineering of Eukaryotic Microalgae: Potential and Challenges Come with Great Diversity. Front Microbiol 2015; 6:1376. [PMID: 26696985 PMCID: PMC4678203 DOI: 10.3389/fmicb.2015.01376] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 11/20/2015] [Indexed: 12/03/2022] Open
Abstract
The great phylogenetic diversity of microalgae is corresponded by a wide arrange of interesting and useful metabolites. Nonetheless metabolic engineering in microalgae has been limited, since specific transformation tools must be developed for each species for either the nuclear or chloroplast genomes. Microalgae as production platforms for metabolites offer several advantages over plants and other microorganisms, like the ability of GMO containment and reduced costs in culture media, respectively. Currently, microalgae have proved particularly well suited for the commercial production of omega-3 fatty acids and carotenoids. Therefore most metabolic engineering strategies have been developed for these metabolites. Microalgal biofuels have also drawn great attention recently, resulting in efforts for improving the production of hydrogen and photosynthates, particularly triacylglycerides. Metabolic pathways of microalgae have also been manipulated in order to improve photosynthetic growth under specific conditions and for achieving trophic conversion. Although these pathways are not strictly related to secondary metabolites, the synthetic biology approaches could potentially be translated to this field and will also be discussed.
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Affiliation(s)
- Javier A Gimpel
- Chemical and Biotechnology Engineering Department, Centre for Biotechnology and Bioengineering, Universidad de Chile Santiago, Chile
| | - Vitalia Henríquez
- Instituto de Biología, Pontificia Universidad Católica de Valparaíso Valparaiso, Chile
| | - Stephen P Mayfield
- Division of Biological Sciences, California Center for Algae Biotechnology, University of California, San Diego La Jolla, CA, USA
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9
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Plucinak TM, Horken KM, Jiang W, Fostvedt J, Nguyen ST, Weeks DP. Improved and versatile viral 2A platforms for dependable and inducible high-level expression of dicistronic nuclear genes in Chlamydomonas reinhardtii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 82:717-729. [PMID: 25846675 DOI: 10.1111/tpj.12844] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 03/20/2015] [Accepted: 03/25/2015] [Indexed: 06/04/2023]
Abstract
A significantly improved viral 2A peptide system for dependable high-level expression of dicistronic genes in Chlamydomonas reinhardtii has been developed. Data are presented demonstrating that use of an especially proficient 'extended FMDV 2A' coding region allows production of two independent protein products from a dicistronic gene with almost complete efficiency. Importantly, results are also presented that demonstrate the utility of this 2A system for efficient high-level expression of foreign genes in C. reinhardtii, which has not previously been reliably achievable in this algal model system. To expand the versatility of the 2A expression system, a number of commonly used selectable marker proteins were assessed for their compatibility with the extended FMDV 2A peptide. Additional experiments demonstrate the feasibility and utility of 2A-containing dicistronic systems that rely on a strong conditional promoter for transcriptional control and a low-expression marker gene for selection. This strategy allows easy and efficient delivery of genes of interest whose expression levels require regulation either to mitigate potential toxicity or allow differential expression under controlled experimental conditions. Finally, as an additional practical demonstration of the utility of the extended FMDV 2A system, confocal fluorescence microscopy is used to demonstrate that native and foreign proteins of interest bearing post-translational remnants of the extended FMDV 2A peptide localize correctly to various cellular compartments, including a striking demonstration of the almost exclusive localization of the Rubisco small subunit protein to the pyrenoid of the C. reinhardtii chloroplast in cells maintained under ambient CO2 concentrations.
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Affiliation(s)
- Thomas M Plucinak
- Department of Biochemistry, University of Nebraska, Lincoln, NE, 68588-0664, USA
| | - Kempton M Horken
- Department of Biochemistry, University of Nebraska, Lincoln, NE, 68588-0664, USA
| | - Wenzhi Jiang
- Department of Biochemistry, University of Nebraska, Lincoln, NE, 68588-0664, USA
| | - Jessica Fostvedt
- Department of Biochemistry, University of Nebraska, Lincoln, NE, 68588-0664, USA
| | - Sanh Tan Nguyen
- Department of Biochemistry, University of Nebraska, Lincoln, NE, 68588-0664, USA
| | - Donald P Weeks
- Department of Biochemistry, University of Nebraska, Lincoln, NE, 68588-0664, USA
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10
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Sarkar D, Shimizu K. An overview on biofuel and biochemical production by photosynthetic microorganisms with understanding of the metabolism and by metabolic engineering together with efficient cultivation and downstream processing. BIORESOUR BIOPROCESS 2015. [DOI: 10.1186/s40643-015-0045-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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11
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Chaiboonchoe A, Dohai BS, Cai H, Nelson DR, Jijakli K, Salehi-Ashtiani K. Microalgal Metabolic Network Model Refinement through High-Throughput Functional Metabolic Profiling. Front Bioeng Biotechnol 2014; 2:68. [PMID: 25540776 PMCID: PMC4261833 DOI: 10.3389/fbioe.2014.00068] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 11/24/2014] [Indexed: 12/19/2022] Open
Abstract
Metabolic modeling provides the means to define metabolic processes at a systems level; however, genome-scale metabolic models often remain incomplete in their description of metabolic networks and may include reactions that are experimentally unverified. This shortcoming is exacerbated in reconstructed models of newly isolated algal species, as there may be little to no biochemical evidence available for the metabolism of such isolates. The phenotype microarray (PM) technology (Biolog, Hayward, CA, USA) provides an efficient, high-throughput method to functionally define cellular metabolic activities in response to a large array of entry metabolites. The platform can experimentally verify many of the unverified reactions in a network model as well as identify missing or new reactions in the reconstructed metabolic model. The PM technology has been used for metabolic phenotyping of non-photosynthetic bacteria and fungi, but it has not been reported for the phenotyping of microalgae. Here, we introduce the use of PM assays in a systematic way to the study of microalgae, applying it specifically to the green microalgal model species Chlamydomonas reinhardtii. The results obtained in this study validate a number of existing annotated metabolic reactions and identify a number of novel and unexpected metabolites. The obtained information was used to expand and refine the existing COBRA-based C. reinhardtii metabolic network model iRC1080. Over 254 reactions were added to the network, and the effects of these additions on flux distribution within the network are described. The novel reactions include the support of metabolism by a number of d-amino acids, l-dipeptides, and l-tripeptides as nitrogen sources, as well as support of cellular respiration by cysteamine-S-phosphate as a phosphorus source. The protocol developed here can be used as a foundation to functionally profile other microalgae such as known microalgae mutants and novel isolates.
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Affiliation(s)
- Amphun Chaiboonchoe
- Division of Science and Math, New York University Abu Dhabi , Abu Dhabi , UAE ; Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi Institute , Abu Dhabi , UAE
| | - Bushra Saeed Dohai
- Division of Science and Math, New York University Abu Dhabi , Abu Dhabi , UAE ; Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi Institute , Abu Dhabi , UAE
| | - Hong Cai
- Division of Science and Math, New York University Abu Dhabi , Abu Dhabi , UAE ; Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi Institute , Abu Dhabi , UAE
| | - David R Nelson
- Division of Science and Math, New York University Abu Dhabi , Abu Dhabi , UAE ; Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi Institute , Abu Dhabi , UAE
| | - Kenan Jijakli
- Division of Science and Math, New York University Abu Dhabi , Abu Dhabi , UAE ; Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi Institute , Abu Dhabi , UAE ; Engineering Division, Biofinery , Manhattan, KS , USA
| | - Kourosh Salehi-Ashtiani
- Division of Science and Math, New York University Abu Dhabi , Abu Dhabi , UAE ; Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi Institute , Abu Dhabi , UAE
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12
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Hemme D, Veyel D, Mühlhaus T, Sommer F, Jüppner J, Unger AK, Sandmann M, Fehrle I, Schönfelder S, Steup M, Geimer S, Kopka J, Giavalisco P, Schroda M. Systems-wide analysis of acclimation responses to long-term heat stress and recovery in the photosynthetic model organism Chlamydomonas reinhardtii. THE PLANT CELL 2014; 26:4270-97. [PMID: 25415976 PMCID: PMC4277220 DOI: 10.1105/tpc.114.130997] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 10/13/2014] [Accepted: 10/24/2014] [Indexed: 05/19/2023]
Abstract
We applied a top-down systems biology approach to understand how Chlamydomonas reinhardtii acclimates to long-term heat stress (HS) and recovers from it. For this, we shifted cells from 25 to 42°C for 24 h and back to 25°C for ≥8 h and monitored abundances of 1856 proteins/protein groups, 99 polar and 185 lipophilic metabolites, and cytological and photosynthesis parameters. Our data indicate that acclimation of Chlamydomonas to long-term HS consists of a temporally ordered, orchestrated implementation of response elements at various system levels. These comprise (1) cell cycle arrest; (2) catabolism of larger molecules to generate compounds with roles in stress protection; (3) accumulation of molecular chaperones to restore protein homeostasis together with compatible solutes; (4) redirection of photosynthetic energy and reducing power from the Calvin cycle to the de novo synthesis of saturated fatty acids to replace polyunsaturated ones in membrane lipids, which are deposited in lipid bodies; and (5) when sinks for photosynthetic energy and reducing power are depleted, resumption of Calvin cycle activity associated with increased photorespiration, accumulation of reactive oxygen species scavengers, and throttling of linear electron flow by antenna uncoupling. During recovery from HS, cells appear to focus on processes allowing rapid resumption of growth rather than restoring pre-HS conditions.
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Affiliation(s)
- Dorothea Hemme
- Molekulare Biotechnologie and Systembiologie, TU Kaiserslautern, D-67663 Kaiserslautern, Germany Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | - Daniel Veyel
- Molekulare Biotechnologie and Systembiologie, TU Kaiserslautern, D-67663 Kaiserslautern, Germany Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | - Timo Mühlhaus
- Molekulare Biotechnologie and Systembiologie, TU Kaiserslautern, D-67663 Kaiserslautern, Germany Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | - Frederik Sommer
- Molekulare Biotechnologie and Systembiologie, TU Kaiserslautern, D-67663 Kaiserslautern, Germany Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | - Jessica Jüppner
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | - Ann-Katrin Unger
- Zellbiologie/Elektronenmikroskopie, Universität Bayreuth, D-95440 Bayreuth, Germany
| | - Michael Sandmann
- Institut für Biochemie und Biologie, Universität Potsdam, D-14476 Potsdam-Golm, Germany
| | - Ines Fehrle
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | - Stephanie Schönfelder
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | - Martin Steup
- Institut für Biochemie und Biologie, Universität Potsdam, D-14476 Potsdam-Golm, Germany
| | - Stefan Geimer
- Zellbiologie/Elektronenmikroskopie, Universität Bayreuth, D-95440 Bayreuth, Germany
| | - Joachim Kopka
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | - Patrick Giavalisco
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | - Michael Schroda
- Molekulare Biotechnologie and Systembiologie, TU Kaiserslautern, D-67663 Kaiserslautern, Germany Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
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Polle JEW, Neofotis P, Huang A, Chang W, Sury K, Wiech EM. Carbon partitioning in green algae (chlorophyta) and the enolase enzyme. Metabolites 2014; 4:612-28. [PMID: 25093929 PMCID: PMC4192683 DOI: 10.3390/metabo4030612] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 07/25/2014] [Accepted: 07/28/2014] [Indexed: 02/08/2023] Open
Abstract
The exact mechanisms underlying the distribution of fixed carbon within photoautotrophic cells, also referred to as carbon partitioning, and the subcellular localization of many enzymes involved in carbon metabolism are still unknown. In contrast to the majority of investigated green algae, higher plants have multiple isoforms of the glycolytic enolase enzyme, which are differentially regulated in higher plants. Here we report on the number of gene copies coding for the enolase in several genomes of species spanning the major classes of green algae. Our genomic analysis of several green algae revealed the presence of only one gene coding for a glycolytic enolase [EC 4.2.1.11]. Our predicted cytosolic localization would require export of organic carbon from the plastid to provide substrate for the enolase and subsequent re-import of organic carbon back into the plastids. Further, our comparative sequence study of the enolase and its 3D-structure prediction may suggest that the N-terminal extension found in green algal enolases could be involved in regulation of the enolase activity. In summary, we propose that the enolase represents one of the crucial regulatory bottlenecks in carbon partitioning in green algae.
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Affiliation(s)
- Jürgen E W Polle
- Department of Biology, Brooklyn College of the City University of New York, 2900 Bedford Avenue 200NE, Brooklyn, NY 11210, USA.
| | - Peter Neofotis
- Department of Biology, Brooklyn College of the City University of New York, 2900 Bedford Avenue 200NE, Brooklyn, NY 11210, USA.
| | - Andy Huang
- Department of Biology, Brooklyn College of the City University of New York, 2900 Bedford Avenue 200NE, Brooklyn, NY 11210, USA.
| | - William Chang
- Department of Biology, Brooklyn College of the City University of New York, 2900 Bedford Avenue 200NE, Brooklyn, NY 11210, USA.
| | - Kiran Sury
- Department of Biology, Brooklyn College of the City University of New York, 2900 Bedford Avenue 200NE, Brooklyn, NY 11210, USA.
| | - Eliza M Wiech
- Department of Biology, Brooklyn College of the City University of New York, 2900 Bedford Avenue 200NE, Brooklyn, NY 11210, USA.
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