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Zhang Z, Li Y, Wen S, Yang S, Zhu H, Zhou H. Metabolomics Reveals the Impact of Overexpression of Cytosolic Fructose-1,6-Bisphosphatase on Photosynthesis and Growth in Nannochloropsis gaditana. Int J Mol Sci 2024; 25:6800. [PMID: 38928505 PMCID: PMC11204352 DOI: 10.3390/ijms25126800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 06/18/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
Nannochloropsis gaditana, a microalga known for its photosynthetic efficiency, serves as a cell factory, producing valuable biomolecules such as proteins, lipids, and pigments. These components make it an ideal candidate for biofuel production and pharmaceutical applications. In this study, we genetically engineered N. gaditana to overexpress the enzyme fructose-1,6-bisphosphatase (cyFBPase) using the Hsp promoter, aiming to enhance sugar metabolism and biomass accumulation. The modified algal strain, termed NgFBP, exhibited a 1.34-fold increase in cyFBPase activity under photoautotrophic conditions. This modification led to a doubling of biomass production and an increase in eicosapentaenoic acid (EPA) content in fatty acids to 20.78-23.08%. Additionally, the genetic alteration activated the pathways related to glycine, protoporphyrin, thioglucosides, pantothenic acid, CoA, and glycerophospholipids. This shift in carbon allocation towards chloroplast development significantly enhanced photosynthesis and growth. The outcomes of this study not only improve our understanding of photosynthesis and carbon allocation in N. gaditana but also suggest new biotechnological methods to optimize biomass yield and compound production in microalgae.
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Affiliation(s)
- Zhengying Zhang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361000, China; (Z.Z.); (Y.L.); (S.W.); (S.Y.)
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361000, China;
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen 361000, China
| | - Yanyan Li
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361000, China; (Z.Z.); (Y.L.); (S.W.); (S.Y.)
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361000, China;
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen 361000, China
| | - Shuting Wen
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361000, China; (Z.Z.); (Y.L.); (S.W.); (S.Y.)
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361000, China;
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen 361000, China
| | - Shu Yang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361000, China; (Z.Z.); (Y.L.); (S.W.); (S.Y.)
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361000, China;
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen 361000, China
| | - Hongmei Zhu
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361000, China;
| | - Hantao Zhou
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361000, China; (Z.Z.); (Y.L.); (S.W.); (S.Y.)
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361000, China;
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen 361000, China
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2
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Canini D, Ceschi E, Perozeni F. Toward the Exploitation of Sustainable Green Factory: Biotechnology Use of Nannochloropsis spp. BIOLOGY 2024; 13:292. [PMID: 38785776 PMCID: PMC11117969 DOI: 10.3390/biology13050292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 04/19/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024]
Abstract
Securing food, energy, and raw materials for a growing population is one of the most significant challenges of our century. Algae play a central role as an alternative to plants. Wastewater and flue gas can secure nutrients and CO2 for carbon fixation. Unfortunately, algae domestication is necessary to enhance biomass production and reduce cultivation costs. Nannochloropsis spp. have increased in popularity among microalgae due to their ability to accumulate high amounts of lipids, including PUFAs. Recently, the interest in the use of Nannochloropsis spp. as a green bio-factory for producing high-value products increased proportionally to the advances of synthetic biology and genetic tools in these species. In this review, we summarized the state of the art of current nuclear genetic manipulation techniques and a few examples of their application. The industrial use of Nannochloropsis spp. has not been feasible yet, but genetic tools can finally lead to exploiting this full-of-potential microalga.
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Affiliation(s)
| | | | - Federico Perozeni
- Department of Biotechnology, University of Verona, 37134 Verona, Italy; (D.C.); (E.C.)
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3
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Du Z, Bhat WW, Poliner E, Johnson S, Bertucci C, Farre E, Hamberger B. Engineering Nannochloropsis oceanica for the production of diterpenoid compounds. MLIFE 2023; 2:428-437. [PMID: 38818264 PMCID: PMC10989085 DOI: 10.1002/mlf2.12097] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 08/24/2023] [Accepted: 10/04/2023] [Indexed: 06/01/2024]
Abstract
Photosynthetic microalgae like Nannochloropsis hold enormous potential as sustainable, light-driven biofactories for the production of high-value natural products such as terpenoids. Nannochloropsis oceanica is distinguished as a particularly robust host with extensive genomic and transgenic resources available. Its capacity to grow in wastewater, brackish, and sea waters, coupled with advances in microalgal metabolic engineering, genome editing, and synthetic biology, provides an excellent opportunity. In the present work, we demonstrate how N. oceanica can be engineered to produce the diterpene casbene-an important intermediate in the biosynthesis of pharmacologically relevant macrocyclic diterpenoids. Casbene accumulated after stably expressing and targeting the casbene synthase from Daphne genkwa (DgTPS1) to the algal chloroplast. The engineered strains yielded production titers of up to 0.12 mg g-1 total dry cell weight (DCW) casbene. Heterologous overexpression and chloroplast targeting of two upstream rate-limiting enzymes in the 2-C-methyl- d-erythritol 4-phosphate pathway, Coleus forskohlii 1-deoxy- d-xylulose-5-phosphate synthase and geranylgeranyl diphosphate synthase genes, further enhanced the yield of casbene to a titer up to 1.80 mg g-1 DCW. The results presented here form a basis for further development and production of complex plant diterpenoids in microalgae.
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Affiliation(s)
- Zhi‐Yan Du
- Department of Molecular Biosciences and BioengineeringUniversity of Hawaii at ManoaHonoluluHawaiiUSA
| | - Wajid W. Bhat
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMichiganUSA
| | - Eric Poliner
- Department of Plant BiologyMichigan State UniversityEast LansingMichiganUSA
| | - Sean Johnson
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMichiganUSA
- Present address:
New England Biolabs Inc.240 County RoadIpswich01938MAUSA
| | - Conor Bertucci
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMichiganUSA
| | - Eva Farre
- Department of Plant BiologyMichigan State UniversityEast LansingMichiganUSA
| | - Bjoern Hamberger
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMichiganUSA
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Xu W, Lin Y, Wang Y, Li Y, Zhu H, Zhou H. Phenotypic Analysis and Molecular Characterization of Enlarged Cell Size Mutant in Nannochloropsis oceanica. Int J Mol Sci 2023; 24:13595. [PMID: 37686401 PMCID: PMC10487731 DOI: 10.3390/ijms241713595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 08/22/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
The cell cycle is the fundamental cellular process of eukaryotes. Although cell-cycle-related genes have been identified in microalgae, their cell cycle progression differs from species to species. Cell enlargement in microalgae is an essential biological trait. At the same time, there are various causes of cell enlargement, such as environmental factors, especially gene mutations. In this study, we first determined the phenotypic and biochemical characteristics of a previously obtained enlarged-cell-size mutant of Nannochloropsis oceanica, which was designated ECS. Whole-genome sequencing analysis of the insertion sites of ECS indicated that the insertion fragment is integrated inside the 5'-UTR of U/P-type cyclin CYCU;1 and significantly decreases the gene expression of this cyclin. In addition, the transcriptome showed that CYCU;1 is a highly expressed cyclin. Furthermore, cell cycle analysis and RT-qPCR of cell-cycle-related genes showed that ECS maintains a high proportion of 4C cells and a low proportion of 1C cells, and the expression level of CYCU;1 in wild-type (WT) cells is significantly increased at the end of the light phase and the beginning of the dark phase. This means that CYCU;1 is involved in cell division in the dark phase. Our results explain the reason for the larger ECS size. Mutation of CYCU;1 leads to the failure of ECS to fully complete cell division in the dark phase, resulting in an enlargement of the cell size and a decrease in cell density, which is helpful to understand the function of CYCU;1 in the Nannochloropsis cell cycle.
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Affiliation(s)
- Weinan Xu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361000, China; (W.X.); (Y.L.); (Y.W.); (Y.L.)
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361000, China;
| | - Yihua Lin
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361000, China; (W.X.); (Y.L.); (Y.W.); (Y.L.)
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361000, China;
| | - Yu Wang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361000, China; (W.X.); (Y.L.); (Y.W.); (Y.L.)
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361000, China;
| | - Yanyan Li
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361000, China; (W.X.); (Y.L.); (Y.W.); (Y.L.)
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361000, China;
| | - Hongmei Zhu
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361000, China;
| | - Hantao Zhou
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361000, China; (W.X.); (Y.L.); (Y.W.); (Y.L.)
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361000, China;
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Gao B, Xu M, Shan D, Zhang C, Yang Y, Dong Z, Zhang H, Han B, Huang L, Zhang C. The genomes of Vischeria oleaginous microalgae shed light on the molecular basis of hyper-accumulation of lipids. BMC Biol 2023; 21:133. [PMID: 37280620 DOI: 10.1186/s12915-023-01618-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 05/09/2023] [Indexed: 06/08/2023] Open
Abstract
BACKGROUND With the urgent need to reduce carbon emissions, and the dwindling reserves of easily exploitable fossil fuel, microalgae-based biofuels that can be used for transport systems and CO2 abatement have attracted great attention worldwide in recent years. One useful characteristic of microalgae is their ability to accumulate high levels of lipid content, in particular under conditions of nitrogen deprivation, with numerous species identified so far. However, a trade-off between levels of lipid accumulation and biomass productivity hinders the commercial applicability of lipids from microalgae. Here, we sequenced the genomes of Vischeria sp. CAUP H4302 and Vischeria stellata SAG 33.83, which can accumulate high content of lipids rich in nutraceutical fatty acids and with excellent biomass yield in nitrogen-limiting culture. RESULTS A whole-genome duplication (WGD) event was revealed in V. sp. CAUP H4302, which is a rare event in unicellular microalgae. Comparative genomic analyses showed that a battery of genes encoding pivotal enzymes involved in fatty acids and triacylglycerol biosynthesis, storage polysaccharide hydrolysis, and nitrogen and amino acid-related metabolisms are expanded in the genus Vischeria or only in V. sp. CAUP H4302. The most highlighted is the expansion of cyanate lyase genes in the genus Vischeria, which may enhance their detoxification ability against the toxic cyanate by decomposing cyanate to NH3 and CO2, especially under nitrogen-limiting conditions, resulting in better growth performance and sustained accumulation of biomass under the aforementioned stress conditions. CONCLUSIONS This study presents a WGD event in microalgae, providing new insights into the genetic and regulatory mechanism underpinning hyper-accumulation of lipids and offering potentially valuable targets for future improvements in oleaginous microalgae by metabolic engineering.
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Affiliation(s)
- Baoyan Gao
- Department of Ecology & Research Center for Hydrobiology, Jinan University, Guangzhou, 510632, China
| | - Meng Xu
- Department of Ecology & Research Center for Hydrobiology, Jinan University, Guangzhou, 510632, China
| | - Dai Shan
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Chi Zhang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Yulan Yang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | | | - Hu Zhang
- Department of Ecology & Research Center for Hydrobiology, Jinan University, Guangzhou, 510632, China
| | - Boping Han
- Department of Ecology & Research Center for Hydrobiology, Jinan University, Guangzhou, 510632, China.
| | - Luodong Huang
- Department of Ecology & Research Center for Hydrobiology, Jinan University, Guangzhou, 510632, China.
| | - Chengwu Zhang
- Department of Ecology & Research Center for Hydrobiology, Jinan University, Guangzhou, 510632, China.
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Yang J, Liu J, Pan Y, Maréchal E, Amato A, Liu M, Gong Y, Li Y, Hu H. PDAT regulates PE as transient carbon sink alternative to triacylglycerol in Nannochloropsis. PLANT PHYSIOLOGY 2022; 189:1345-1362. [PMID: 35385114 PMCID: PMC9237688 DOI: 10.1093/plphys/kiac160] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 03/14/2022] [Indexed: 05/21/2023]
Abstract
Triacylglycerols (TAGs) are the main storage lipids in photosynthetic organisms under stress. In the oleaginous alga Nannochloropsis oceanica, while multiple acyl CoA:diacylglycerol (DAG) acyltransferases (NoDGATs) are involved in TAG production, the role of the unique phospholipid:DAG acyltransferase (NoPDAT) remains unknown. Here, we performed a functional complementation assay in TAG-deficient yeast (Saccharomyces cerevisiae) and an in vitro assay to probe the acyltransferase activity of NoPDAT. Subcellular localization, overexpression, and knockdown (KD) experiments were also conducted to elucidate the role of NoPDAT in N. oceanica. NoPDAT, residing at the outermost plastid membrane, does not phylogenetically fall into the clades of algae or plants and uses phosphatidylethanolamine (PE) and phosphatidylglycerol with 16:0, 16:1, and 18:1 at position sn-2 as acyl-donors in vivo. NoPDAT KD, not triggering any compensatory mechanism via DGATs, led to an ∼30% decrease of TAG content, accompanied by a vast accumulation of PEs rich in 16:0, 16:1, and 18:1 fatty acids (referred to as "LU-PE") that was positively associated with CO2 availability. We conclude that the NoPDAT pathway is parallel to and independent of the NoDGAT pathway for oil production. LU-PE can serve as an alternative carbon sink for photosynthetically assimilated carbon in N. oceanica when PDAT-mediated TAG biosynthesis is compromised or under stress in the presence of high CO2 levels.
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Affiliation(s)
| | | | - Yufang Pan
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Eric Maréchal
- Laboratoire de Physiologie Cellulaire Végétale, Université Grenoble Alpes, CEA, CNRS, INRA, IRIG‐LPCV, 38054 Grenoble Cedex 9, France
| | - Alberto Amato
- Laboratoire de Physiologie Cellulaire Végétale, Université Grenoble Alpes, CEA, CNRS, INRA, IRIG‐LPCV, 38054 Grenoble Cedex 9, France
| | - Meijing Liu
- Laboratory for Algae Biotechnology and Innovation, College of Engineering, Peking University, Beijing 100871, China
| | - Yangmin Gong
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Yantao Li
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science and University of Maryland Baltimore County, Baltimore, Maryland 21202, USA
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7
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Wei L, Liu B, Liu D, Xu Z, Wang R, Zhang W. Identification and expression analysis of genome-wide long noncoding RNA responsive CO 2 fluctuated environment in marine microalga Nannochloropsis oceanica. MARINE POLLUTION BULLETIN 2022; 176:113419. [PMID: 35152114 DOI: 10.1016/j.marpolbul.2022.113419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 01/27/2022] [Accepted: 01/30/2022] [Indexed: 06/14/2023]
Abstract
Long non-coding RNAs (lncRNAs) have been demonstrated to participate in plant growth and development as well as response to different biotic and abiotic stresses. However, the knowledge of lncRNA was limited in microalgae. In this study, by RNA deep sequencing, 134 lncRNAs were identified in marine Nannochloropsis oceanica in response to carbon dioxide fluctuation. Among them, there were 51 lncRNAs displayed differentially expressed between low and high CO2 treatments, including 33 upregulation and 18 downregulation lncRNAs. Cellulose metabolic process, glucan metabolic process, polysaccharide metabolic process, and transmembrane transporter activity were functionally enriched. Multiple potential target genes of lncRNA and lncRNA-mRNA co-located gene network were analyzed. Subsequent analysis had demonstrated that lncRNAs would participate in many biological molecular processes, including gene expression, transcriptional regulation, protein expression and epigenetic regulation. In addition, alternative splicing events were firstly analyzed in response to CO2 fluctuation. There were 2051 alternative splicing (AS events) identified, which might be associated with lncRNA. These observations will provide a novel insight into lncRNA function in Nannochloropsis and provide a series of targets for lncRNA-based gene editing in future.
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Affiliation(s)
- Li Wei
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou 571158, China.
| | - Bingqing Liu
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou 571158, China
| | - Danmei Liu
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou 571158, China
| | - Zhengru Xu
- College of Foreign Language, Hainan Normal University, Haikou 571157, China
| | - Ruiping Wang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou 571158, China
| | - Wenfei Zhang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou 571158, China.
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8
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Manipulation of triacylglycerol biosynthesis in Nannochloropsis oceanica by overexpressing an Arabidopsis thaliana diacylglycerol acyltransferase gene. ALGAL RES 2022. [DOI: 10.1016/j.algal.2021.102590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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9
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Kselíková V, Singh A, Bialevich V, Čížková M, Bišová K. Improving microalgae for biotechnology - From genetics to synthetic biology - Moving forward but not there yet. Biotechnol Adv 2021; 58:107885. [PMID: 34906670 DOI: 10.1016/j.biotechadv.2021.107885] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/28/2021] [Accepted: 12/07/2021] [Indexed: 12/28/2022]
Abstract
Microalgae are a diverse group of photosynthetic organisms that can be exploited for the production of different compounds, ranging from crude biomass and biofuels to high value-added biochemicals and synthetic proteins. Traditionally, algal biotechnology relies on bioprospecting to identify new highly productive strains and more recently, on forward genetics to further enhance productivity. However, it has become clear that further improvements in algal productivity for biotechnology is impossible without combining traditional tools with the arising molecular genetics toolkit. We review recent advantages in developing high throughput screening methods, preparing genome-wide mutant libraries, and establishing genome editing techniques. We discuss how algae can be improved in terms of photosynthetic efficiency, biofuel and high value-added compound production. Finally, we critically evaluate developments over recent years and explore future potential in the field.
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Affiliation(s)
- Veronika Kselíková
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Laboratory of Cell Cycles of Algae, 379 81 Třeboň, Czech Republic; Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic
| | - Anjali Singh
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Laboratory of Cell Cycles of Algae, 379 81 Třeboň, Czech Republic
| | - Vitali Bialevich
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Laboratory of Cell Cycles of Algae, 379 81 Třeboň, Czech Republic
| | - Mária Čížková
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Laboratory of Cell Cycles of Algae, 379 81 Třeboň, Czech Republic
| | - Kateřina Bišová
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Laboratory of Cell Cycles of Algae, 379 81 Třeboň, Czech Republic.
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Yang HP, Wenzel M, Hauser DA, Nelson JM, Xu X, Eliáš M, Li FW. Monodopsis and Vischeria Genomes Shed New Light on the Biology of Eustigmatophyte Algae. Genome Biol Evol 2021; 13:6402010. [PMID: 34665222 PMCID: PMC8570151 DOI: 10.1093/gbe/evab233] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2021] [Indexed: 11/12/2022] Open
Abstract
Members of eustigmatophyte algae, especially Nannochloropsis and Microchloropsis, have been tapped for biofuel production owing to their exceptionally high lipid content. Although extensive genomic, transcriptomic, and synthetic biology toolkits have been made available for Nannochloropsis and Microchloropsis, very little is known about other eustigmatophytes. Here we present three near-chromosomal and gapless genome assemblies of Monodopsis strains C73 and C141 (60 Mb) and Vischeria strain C74 (106 Mb), which are the sister groups to Nannochloropsis and Microchloropsis in the order Eustigmatales. These genomes contain unusually high percentages of simple repeats, ranging from 12% to 21% of the total assembly size. Unlike Nannochloropsis and Microchloropsis, long interspersed nuclear element repeats are abundant in Monodopsis and Vischeria and might constitute the centromeric regions. We found that both mevalonate and nonmevalonate pathways for terpenoid biosynthesis are present in Monodopsis and Vischeria, which is different from Nannochloropsis and Microchloropsis that have only the latter. Our analysis further revealed extensive spliced leader trans-splicing in Monodopsis and Vischeria at 36-61% of genes. Altogether, the high-quality genomes of Monodopsis and Vischeria not only serve as the much-needed outgroups to advance Nannochloropsis and Microchloropsis research, but also shed new light on the biology and evolution of eustigmatophyte algae.
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Affiliation(s)
| | - Marius Wenzel
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | | | | | - Xia Xu
- Boyce Thompson Institute, Ithaca, New York, USA
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, New York, USA.,Plant Biology Section, Cornell University, USA
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11
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Investigating the Viral Suppressor HC-Pro Inhibiting Small RNA Methylation through Functional Comparison of HEN1 in Angiosperm and Bryophyte. Viruses 2021; 13:v13091837. [PMID: 34578418 PMCID: PMC8473176 DOI: 10.3390/v13091837] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/09/2021] [Accepted: 09/09/2021] [Indexed: 12/27/2022] Open
Abstract
In plants, HEN1-facilitated methylation at 3′ end ribose is a critical step of small-RNA (sRNA) biogenesis. A mutant of well-studied Arabidopsis HEN1 (AtHEN1), hen1-1, showed a defective developmental phenotype, indicating the importance of sRNA methylation. Moreover, Marchantia polymorpha has been identified to have a HEN1 ortholog gene (MpHEN1); however, its function remained unfathomed. Our in vivo and in vitro data have shown MpHEN1 activity being comparable with AtHEN1, and their substrate specificity towards duplex microRNA (miRNA) remained consistent. Furthermore, the phylogenetic tree and multiple alignment highlighted the conserved molecular evolution of the HEN1 family in plants. The P1/HC-Pro of the turnip mosaic virus (TuMV) is a known RNA silencing suppressor and inhibits HEN1 methylation of sRNAs. Here, we report that the HC-Pro physically binds with AtHEN1 through FRNK motif, inhibiting HEN1’s methylation activity. Moreover, the in vitro EMSA data indicates GST-HC-Pro of TuMV lacks sRNA duplex-binding ability. Surprisingly, the HC-Pro also inhibits MpHEN1 activity in a dosage-dependent manner, suggesting the possibility of interaction between HC-Pro and MpHEN1 as well. Further investigations on understanding interaction mechanisms of HEN1 and various HC-Pros can advance the knowledge of viral suppressors.
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12
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Mochdia K, Tamaki S. Transcription Factor-Based Genetic Engineering in Microalgae. PLANTS 2021; 10:plants10081602. [PMID: 34451646 PMCID: PMC8399792 DOI: 10.3390/plants10081602] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/16/2021] [Accepted: 07/30/2021] [Indexed: 11/16/2022]
Abstract
Sequence-specific DNA-binding transcription factors (TFs) are key components of gene regulatory networks. Advances in high-throughput sequencing have facilitated the rapid acquisition of whole genome assembly and TF repertoires in microalgal species. In this review, we summarize recent advances in gene discovery and functional analyses, especially for transcription factors in microalgal species. Specifically, we provide examples of the genome-scale identification of transcription factors in genome-sequenced microalgal species and showcase their application in the discovery of regulators involved in various cellular functions. Herein, we highlight TF-based genetic engineering as a promising framework for designing microalgal strains for microalgal-based bioproduction.
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Affiliation(s)
- Keiichi Mochdia
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan
- Kihara Institute for Biological Research, Yokohama City University, Totsuka-ku, Yokohama 244-0813, Japan
- RIKEN Baton Zone Program, Tsurumi-ku, Yokohama 230-0045, Japan;
- School of Information and Data Sciences, Nagasaki University, Bunkyo-machi, Nagasaki 852-8521, Japan
- Correspondence: ; Tel.: +81-045-503-9111
| | - Shun Tamaki
- RIKEN Baton Zone Program, Tsurumi-ku, Yokohama 230-0045, Japan;
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13
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Niu L, He H, Zhang Y, Yang J, Zhao Q, Xing G, Zhong X, Yang X. Efficient identification of genomic insertions and flanking regions through whole-genome sequencing in three transgenic soybean events. Transgenic Res 2021; 30:1-9. [PMID: 33393017 DOI: 10.1007/s11248-020-00225-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 11/25/2020] [Indexed: 10/22/2022]
Abstract
Genomic insertions and flanking regions of transgenes in host genomes constitute a critical component of precise molecular characterization and event-specific detection, which are required in the development and assessment for regulatory approval of genetically modified (GM) crops. Previously, we reported three transgenic soybean events harboring the inverted repeats of the soybean mosaic virus NIb (nuclear inclusion b) gene, exhibiting significantly enhanced resistance to multiple Potyvirus strains. To facilitate safety assessment and event-specific detection, we identified the transgene insertion sites and flanking sequences of the events L120, L122, and L123 using whole-genome sequencing. More than 14.48 Gb sequence data (13 × coverage) were generated using the Illumina HiSeq Xten platform for each event. The sequence reads corresponding to boundaries of inserted T-DNA, and associated native flanking sequences were identified by bioinformatic comparison with the soybean reference genome (Wm82.a2.v1) and the transformation vector sequence. The results indicated that two T-DNA insertions occurred in L120, on Chr07 and Chr13, while L122 and L123 showed single insertions, on Chr02 and Chr06, respectively. Based on the flanking sequences of the inserted T-DNA, the event-specific detection for each event was established using specific PCR primers, and PCR amplification followed by sequencing of PCR products further confirmed the putative insertion loci and flanking regions in the transgenic lines. Our results demonstrate the efficacy and robustness of whole-genome sequencing in identifying the genomic insertions and flanking regions in GM crops. Moreover, the characterization of insertion loci and the establishment of event-specific detection will facilitate the application and development of broad-spectrum virus-resistant transgenic soybean cultivars.
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Affiliation(s)
- Lu Niu
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Hongli He
- School of Life Science, Jilin Normal University, Siping, 136000, China
| | - Yuanyu Zhang
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Jing Yang
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Qianqian Zhao
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Guojie Xing
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Xiaofang Zhong
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China.
| | - Xiangdong Yang
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China.
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14
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Feng JJ, He CY, Jiang SH, Zhang T, Yu LY. Saccharomycomorpha psychra n. g., n. sp., a Novel Member of Glissmonadida (Cercozoa) Isolated from Arctic and Antarctica. J Eukaryot Microbiol 2021; 68:e12840. [PMID: 33448091 DOI: 10.1111/jeu.12840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 12/14/2020] [Accepted: 01/06/2021] [Indexed: 12/01/2022]
Abstract
A novel genus and species within the order Glissmonadida (Cercozoa, Rhizaria), Saccharomycomorpha psychra n. g., n. sp., is described from lichen in the Ny-Ålesund region (High Arctic) and moss in the Fildes peninsula of King George Island (Maritime Antarctica). Cells were spherical and did not appear to present flagella in organic-rich Potato Dextrose Agar medium where they were able to feed osmotrophically. Molecular phylogenetic analyses based on 18S rRNA gene sequence demonstrated that Saccharomycomorpha psychra belong to "clade T" within the order Glissmonadida (Cercozoa, Rhizaria). All three investigated strains could grow at 4 °C and had an optimum growth temperature of 12 °C, 20 °C, and 20 °C, while a maximum growth temperature of 20 °C, 20 °C, and 25 °C, respectively. In conclusion, we established the phenotypic identity of "clade T," which until now was exclusively detected by environmental sequences, and erect a new family Saccharomycomorphidae for "clade T." Nomenclatural, morphological and ecological aspects of this novel species are discussed.
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Affiliation(s)
- Jian-Ju Feng
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Chen-Yang He
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Shu-Hua Jiang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tao Zhang
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Li-Yan Yu
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
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15
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Gong Y, Kang NK, Kim YU, Wang Z, Wei L, Xin Y, Shen C, Wang Q, You W, Lim JM, Jeong SW, Park YI, Oh HM, Pan K, Poliner E, Yang G, Li-Beisson Y, Li Y, Hu Q, Poetsch A, Farre EM, Chang YK, Jeong WJ, Jeong BR, Xu J. The NanDeSyn database for Nannochloropsis systems and synthetic biology. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:1736-1745. [PMID: 33103271 DOI: 10.1111/tpj.15025] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 09/10/2020] [Accepted: 09/23/2020] [Indexed: 06/11/2023]
Abstract
Nannochloropsis species, unicellular industrial oleaginous microalgae, are model organisms for microalgal systems and synthetic biology. To facilitate community-based annotation and mining of the rapidly accumulating functional genomics resources, we have initiated an international consortium and present a comprehensive multi-omics resource database named Nannochloropsis Design and Synthesis (NanDeSyn; http://nandesyn.single-cell.cn). Via the Tripal toolkit, it features user-friendly interfaces hosting genomic resources with gene annotations and transcriptomic and proteomic data for six Nannochloropsis species, including two updated genomes of Nannochloropsis oceanica IMET1 and Nannochloropsis salina CCMP1776. Toolboxes for search, Blast, synteny view, enrichment analysis, metabolic pathway analysis, a genome browser, etc. are also included. In addition, functional validation of genes is indicated based on phenotypes of mutants and relevant bibliography. Furthermore, epigenomic resources are also incorporated, especially for sequencing of small RNAs including microRNAs and circular RNAs. Such comprehensive and integrated landscapes of Nannochloropsis genomics and epigenomics will promote and accelerate community efforts in systems and synthetic biology of these industrially important microalgae.
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Affiliation(s)
- Yanhai Gong
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Nam K Kang
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, 61801, USA
| | - Young U Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
| | - Zengbin Wang
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Li Wei
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Yi Xin
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Chen Shen
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Qintao Wang
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Wuxin You
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- Department of Plant Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Jong-Min Lim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Suk-Won Jeong
- Department of Biological Sciences, Chungnam National University, Daejeon, 34134, Korea
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon, 34134, Korea
| | - Hee-Mock Oh
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Korea
| | - Kehou Pan
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- Laboratory of Applied Microalgae, College of Fisheries, Ocean University of China, Qingdao, 266003, China
| | - Eric Poliner
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
| | - Guanpin Yang
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, China
- Institutes of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong, 266003, China
| | - Yonghua Li-Beisson
- Aix Marseille Univ, CEA, CNRS, Institut de Biosciences et Biotechnologies Aix-Marseille, CEA Cadarache, 13108, Saint Paul-Lez-Durance, France
| | - Yantao Li
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, University of Maryland, Baltimore County, Baltimore, MD, 21202, USA
| | - Qiang Hu
- Center for Microalgal Biotechnology and Biofuels, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Ansgar Poetsch
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- Department of Plant Biochemistry, Ruhr University Bochum, Bochum, Germany
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, China
| | - Eva M Farre
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Yong K Chang
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
| | - Won-Joong Jeong
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Byeong-Ryool Jeong
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Korea
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
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16
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Microalgae of the genus Nannochloropsis: Chemical composition and functional implications for human nutrition. J Funct Foods 2020. [DOI: 10.1016/j.jff.2020.103919] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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17
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Ng I, Keskin BB, Tan S. A Critical Review of Genome Editing and Synthetic Biology Applications in Metabolic Engineering of Microalgae and Cyanobacteria. Biotechnol J 2020; 15:e1900228. [DOI: 10.1002/biot.201900228] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 02/07/2020] [Indexed: 12/13/2022]
Affiliation(s)
- I‐Son Ng
- Department of Chemical EngineeringNational Cheng Kung University Tainan 701 Taiwan
| | - Batuhan Birol Keskin
- Department of Chemical EngineeringNational Cheng Kung University Tainan 701 Taiwan
| | - Shih‐I Tan
- Department of Chemical EngineeringNational Cheng Kung University Tainan 701 Taiwan
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18
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Absolute Quantification of the Central Carbon Metabolome in Eight Commonly Applied Prokaryotic and Eukaryotic Model Systems. Metabolites 2020; 10:metabo10020074. [PMID: 32093075 PMCID: PMC7073941 DOI: 10.3390/metabo10020074] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/14/2020] [Accepted: 02/17/2020] [Indexed: 02/07/2023] Open
Abstract
Absolute quantification of intracellular metabolite pools is a prerequisite for modeling and in-depth biological interpretation of metabolomics data. It is the final step of an elaborate metabolomics workflow, with challenges associated with all steps—from sampling to quantifying the physicochemically diverse metabolite pool. Chromatographic separation combined with mass spectrometric (MS) detection is the superior platform for high coverage, selective, and sensitive detection of metabolites. Herein, we apply our quantitative MS-metabolomics workflow to measure and present the central carbon metabolome of a panel of commonly applied biological model systems. The workflow includes three chromatographic methods combined with isotope dilution tandem mass spectrometry to allow for absolute quantification of 68 metabolites of glycolysis, the pentose phosphate pathway, the tricarboxylic acid cycle, and the amino acid and (deoxy) nucleoside pools. The biological model systems; Bacillus subtilis, Saccharomyces cerevisiae, two microalgal species, and four human cell lines were all cultured in commonly applied culture media and sampled in exponential growth phase. Both literature and databases are scarce with comprehensive metabolite datasets, and existing entries range over several orders of magnitude. The workflow and metabolite panel presented herein can be employed to expand the list of reference metabolomes, as encouraged by the metabolomics community, in a continued effort to develop and refine high-quality quantitative metabolomics workflows.
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