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Alothman A, Emwas AH, Singh U, Jaremko M, Agusti S. Metabolomics-based analysis of the diatom Cheatoceros tenuissimus combining NMR and GC-MS techniques. MethodsX 2024; 12:102695. [PMID: 38595808 PMCID: PMC11001764 DOI: 10.1016/j.mex.2024.102695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 04/02/2024] [Indexed: 04/11/2024] Open
Abstract
Metabolomics, a recent addition to omics sciences, studies small molecules across plants, animals, humans, and marine organisms. Nuclear magnetic resonance (NMR) and gas chromatography-mass spectrometry (GC-MS) are widely used in those studies, including microalgae metabolomics. NMR is non-destructive and highly reproducible but has limited sensitivity, which could be supplemented by joining GC-MS analysis. Extracting metabolites from macromolecules requires optimization for trustworthy results. Different extraction methods yield distinct profiles, emphasizing the need for optimization. The results indicated that the optimized extraction procedure successfully identified NMR and GC-MS-based metabolites in MeOH, CHCl3, and H2O extraction solvents. The findings represented the spectral information related to carbohydrates, organic molecules, and amino acids from the water-soluble metabolites fraction and a series of fatty acid chains, lipids, and sterols from the lipid fraction. Our study underscores the benefit of combining NMR and GC-MS techniques to comprehensively understand microalgae metabolomes, including high and low metabolite concentrations and abundances.•In this study, we focused on optimizing the extraction procedure and combining NMR and GC-MS techniques to overcome the low NMR sensitivity and the different detected range limits of NMR and GC-MS.•We explored metabolome diversity in a tropical strain of the small cells' diatom Cheatoceros tenuissimus.
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Affiliation(s)
- Afrah Alothman
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental and Science and Engineering, Marine Science Program, Thuwal, 23955-6900, Saudi Arabia
| | - Abdul-Hamid Emwas
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, 23955-6900, Saudi Arabia
| | - Upendra Singh
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental and Science and Engineering, Thuwal, 23955-6900, Saudi Arabia
| | - Mariusz Jaremko
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental and Science and Engineering, Thuwal, 23955-6900, Saudi Arabia
| | - Susana Agusti
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental and Science and Engineering, Marine Science Program, Thuwal, 23955-6900, Saudi Arabia
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Hongo Y, Hano T, Yamaguchi H, Tomaru Y. Transcriptional responses of the marine diatom Chaetoceros tenuissimus to phosphate deficiency. Gene 2023; 884:147695. [PMID: 37549856 DOI: 10.1016/j.gene.2023.147695] [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: 06/07/2023] [Revised: 07/25/2023] [Accepted: 08/04/2023] [Indexed: 08/09/2023]
Abstract
The planktonic diatom Chaetoceros tenuissimus sometimes forms blooms in coastal surface waters where dissolved inorganic phosphorus (P) is typically deficient. To understand the molecular mechanisms for survival under P-deficient conditions, we compared whole transcripts and metabolites with P-sufficient conditions using stationary growth cells. Under P-deficient conditions, cell numbers and photosynthetic activities decreased as cells entered the stationary growth phase, with downregulation of transcripts related to the Calvin cycle and glycolysis/gluconeogenesis. Therefore, metabolites varied across nutritional conditions. Alkaline phosphatase, phosphodiesterase, phytase, phosphate transporter, and transcription factor genes were drastically upregulated under dissolved inorganic P deficiency. Genes related to phospholipid degradation and nonphospholipid synthesis were also upregulated. These results indicate that C. tenuissimus rearranges its membrane composition from phospholipids to nonphospholipids to conserve phosphate. To endure in P-deficient conditions, C. tenuissimus modifies its gene responses, suggesting a potential survival strategy in nature.
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Affiliation(s)
- Yuki Hongo
- Fisheries Resources Institute, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648, Japan.
| | - Takeshi Hano
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima 739-0452, Japan
| | - Haruo Yamaguchi
- Faculty of Agriculture and Marine Science, Kochi University, 200 Otsu, Monobe, Nankoku, Kochi 783-8502, Japan
| | - Yuji Tomaru
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima 739-0452, Japan
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Ando M, Sugiyama K, Kubo K, Horii S, Hano T, Tomaru Y, Takeyama H. Single-Cell Level Raman Molecular Profiling Reveals the Classification of Growth Phases of Chaetoceros tenuissimus. J Phys Chem B 2023. [PMID: 37243612 DOI: 10.1021/acs.jpcb.3c02152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Harmful algal blooms (HABs) are a natural phenomenon caused by outbreaks of algae, resulting in serious problems for aquatic ecosystems and the coastal environment. Chaetoceros tenuissimus (C. tenuissimus) is one of the diatoms responsible for HABs. The growth curve of C. tenuissimus can be observed from beginning to end of HABs: therefore, detailed analysis is necessary to characterize each growth phase of C. tenuissimus. It is important to examine the phenotype of each diatom cell individually, as they display heterogeneity even in the same growth phase. Raman spectroscopy is a label-free technique to elucidate biomolecular profiles and spatial information at the cellular level. Multivariate data analysis (MVA) is an efficient method for the analysis of complicated Raman spectra, to identify molecular features. Here, we utilized Raman microspectroscopy to identify the molecular information of each diatom cell, at the single-cell level. The MVA, together with a support vector machine, which is a machine learning technique, allowed the classification of proliferating and nonproliferating cells. The classification includes polyunsaturated fatty acids such as linoleic acid, eicosapentaenoic acid, and docosahexaenoic acid. This study indicated that Raman spectroscopy is an appropriate technique to examine C. tenuissimus at the single-cell level, providing relevant data to assess the correlation between the molecular details obtained from the Raman analysis, at each growth phase.
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Affiliation(s)
- Masahiro Ando
- Research Organization for Nano and Life Innovation, Waseda University, 513 Wasedatsurumaki-Cho, Shinjuku-Ku,Tokyo 169-0041, Japan
| | - Kaori Sugiyama
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-Ku, Tokyo 169-8555, Japan
| | - Koya Kubo
- Department of Advanced Science Engineering, Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-Ku, Tokyo 169-8555, Japan
- Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-Ku, Tokyo 169-8555, Japan
| | - Shumpei Horii
- Department of Advanced Science Engineering, Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-Ku, Tokyo 169-8555, Japan
- Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-Ku, Tokyo 169-8555, Japan
| | - Takeshi Hano
- Environment Conservation Division, National Research and Development Agency, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima 739-0452, Japan
| | - Yuji Tomaru
- Environment Conservation Division, National Research and Development Agency, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima 739-0452, Japan
| | - Haruko Takeyama
- Research Organization for Nano and Life Innovation, Waseda University, 513 Wasedatsurumaki-Cho, Shinjuku-Ku,Tokyo 169-0041, Japan
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-Ku, Tokyo 169-8555, Japan
- Department of Advanced Science Engineering, Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-Ku, Tokyo 169-8555, Japan
- Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-Ku, Tokyo 169-8555, Japan
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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Hano T, Tomaru Y. Chronological age-related metabolome responses in the dinoflagellate Karenia mikimotoi, can predict future bloom demise. Commun Biol 2023; 6:273. [PMID: 36922623 PMCID: PMC10017670 DOI: 10.1038/s42003-023-04646-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 03/01/2023] [Indexed: 03/18/2023] Open
Abstract
Karenia mikimotoi is a common harmful algal bloom (HAB)-forming dinoflagellate and has caused severe financial loss in aquaculture. There are limited metabolomic studies on dinoflagellate biology. Here, we examined alterations in metabolic profiles over the growth curve of K. mikimotoi under nitrogen or phosphorus deficiency and further explored a key criterion for the diagnosis of late stationary phase to identify when the dinoflagellate cells will enter bloom demise. The results demonstrate the differential expression of metabolites for coping with chronological aging or nutrient deprivation. Furthermore, an increase in the glucose to glycine ratio in the late stationary phase was indicative of dinoflagellate cells entering bloom demise; this was also detected in the cultured diatom, Chaetoceros tenuissimus, indicating that this may be the general criterion for phytoplankton species. Our findings provide insights regarding chronological aging and the criterion for the prediction of phytoplankton bloom demise.
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Affiliation(s)
- Takeshi Hano
- Environment Conservation Division, Fisheries Technology Institute, National Research and Development Agency, Japan Fisheries Research and Education Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima, 739-0452, Japan.
| | - Yuji Tomaru
- Environment Conservation Division, Fisheries Technology Institute, National Research and Development Agency, Japan Fisheries Research and Education Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima, 739-0452, Japan
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Recent Progress in the Study of Peroxiredoxin in the Harmful Algal Bloom Species Chattonella marina. Antioxidants (Basel) 2021; 10:antiox10020162. [PMID: 33499182 PMCID: PMC7911785 DOI: 10.3390/antiox10020162] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 01/17/2021] [Accepted: 01/19/2021] [Indexed: 02/06/2023] Open
Abstract
Peroxiredoxin (Prx) is a relatively recently discovered antioxidant enzyme family that scavenges peroxides and is known to be present in organisms from biological taxa ranging from bacteria to multicellular eukaryotes, including photosynthetic organisms. Although there have been many studies of the Prx family in higher plants, green algae, and cyanobacteria, few studies have concerned raphidophytes and dinoflagellates, which are among the eukaryotic algae that cause harmful algal blooms (HABs). In our proteomic study using 2-D electrophoresis, we found a highly expressed 2-Cys peroxiredoxin (2-CysPrx) in the raphidophyte Chattonella marina var. antiqua, a species that induces mass mortality of aquacultured fish. The abundance of the C. marina 2-CysPrx enzyme was highest in the exponential growth phase, during which photosynthetic activity was high, and it then decreased by about a factor of two during the late stationary growth phase. This pattern suggested that 2-CysPrx is a key enzyme involved in the maintenance of high photosynthesis activity. In addition, the fact that the depression of photosynthesis by excessively high irradiance was more severe in the 2-CysPrx low-expression strain (wild type) than in the normal-expression strain (wild type) of C. marina suggested that 2-CysPrx played a critical role in protecting the cell from oxidative stress caused by exposure to excessively high irradiance. In the field of HAB research, estimates of growth potential have been desired to predict the population dynamics of HABs for mitigating damage to fisheries. Therefore, omics approaches have recently begun to be applied to elucidate the physiology of the growth of HAB species. In this review, we describe the progress we have made using a molecular physiological approach to identify the roles of 2-CysPrx and other antioxidant enzymes in mitigating environmental stress associated with strong light and high temperatures and resultant oxidative stress. We also describe results of a survey of expressed Prx genes and their growth-phase-dependent behavior in C. marina using RNA-seq analysis. Finally, we speculate about the function of these genes and the ecological significance of 2-CysPrx, such as its involvement in circadian rhythms and the toxicity of C. marina to fish.
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Azizan A, Maulidiani M, R. R, Shaari K, Ismail IS, Nagao N, Abas F. Mass Spectrometry-Based Metabolomics Combined with Quantitative Analysis of the Microalgal Diatom ( Chaetoceros calcitrans). Mar Drugs 2020; 18:md18080403. [PMID: 32751412 PMCID: PMC7459737 DOI: 10.3390/md18080403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/07/2020] [Accepted: 04/14/2020] [Indexed: 11/16/2022] Open
Abstract
Although many metabolomics studies of higher land plant species have been conducted, similar studies of lower nonland plant species, which include microalgae, are still developing. The present study represents an attempt to characterize the metabolic profile of a microalgal diatom Chaetoceros calcitrans, by applying high-resolution mass spectrometry detection, via Q-ExactiveTM Plus Orbitrap mass spectrometry. The results showed that 54 metabolites of various classes were tentatively identified. Experimentally, the chloroform and acetone extracts were clearly distinguished from other solvent extracts in chemometric regression analysis using PLS, showing the differences in the C. calcitrans metabolome between the groups. In addition, specific metabolites were evaluated, which supported the finding of antioxidant and anti-inflammatory activities. This study also provides data on the quantitative analysis of four carotenoids based on the identification results. Therefore, these findings could serve as a reliable tool for identifying and quantifying the metabolome that could reflect the metabolic activities of C. calcitrans.
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Affiliation(s)
- Awanis Azizan
- Laboratory of Natural Products, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (A.A.); (M.M.); (K.S.); (I.S.I.)
| | - M. Maulidiani
- Laboratory of Natural Products, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (A.A.); (M.M.); (K.S.); (I.S.I.)
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Kuala Nerus 21030, Terengganu, Malaysia
| | - Rudiyanto R.
- Faculty of Fisheries and Food Science, Universiti Malaysia Terengganu, Kuala Nerus 21030, Terengganu, Malaysia;
| | - Khozirah Shaari
- Laboratory of Natural Products, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (A.A.); (M.M.); (K.S.); (I.S.I.)
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Intan Safinar Ismail
- Laboratory of Natural Products, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (A.A.); (M.M.); (K.S.); (I.S.I.)
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Norio Nagao
- Laboratory of Marine Biotechnology, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia;
| | - Faridah Abas
- Laboratory of Natural Products, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (A.A.); (M.M.); (K.S.); (I.S.I.)
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Correspondence: ; Tel.: +603-97698343
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A Metabolomics Exploration of the Sexual Phase in the Marine Diatom Pseudo-nitzschia multistriata. Mar Drugs 2020; 18:md18060313. [PMID: 32545923 PMCID: PMC7345340 DOI: 10.3390/md18060313] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/11/2020] [Accepted: 06/12/2020] [Indexed: 12/31/2022] Open
Abstract
Pseudo-nitzschia multistriata is a planktonic marine diatom with a diplontic life cycle comprising a short sexual phase, during which gametes are produced following the encounter of two diploid cells of opposite mating type (MT). Gene expression studies have highlighted the presence of substantial changes occurring at the onset of sexual reproduction. Herein, we have hypothesized that the amount and nature of cellular metabolites varies along the mating process. To capture the metabolome of Pseudo-nitzschia multistriata at different harvesting times in an unbiased manner, we undertook an untargeted metabolomics approach based on liquid chromatography-tandem mass spectrometry. Using three different extraction steps, the method revealed pronounced differences in the metabolic profiles between control cells in the vegetative phase (MT+ and MT-) and mixed strains of opposite MTs (cross) undergoing sexual reproduction. Of the 2408 high-quality features obtained, 70 known metabolites could be identified based on in-house libraries and online databases; additional 46 features could be classified by molecular networking of tandem mass spectra. The reduction of phytol detected in the cross can be linked to the general downregulation of photosynthesis during sexual reproduction observed elsewhere. Moreover, the role of highly regulated compounds such as 7-dehydrodesmosterol, whose changes in abundance were the highest in the experiment, oleamide, ectoine, or trigonelline is discussed.
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