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Iman MN, Haslam DE, Liang L, Guo K, Joshipura K, Pérez CM, Clish C, Tucker KL, Manson JE, Bhupathiraju SN, Fukusaki E, Lasky-Su J, Putri SP. Multidisciplinary approach combining food metabolomics and epidemiology identifies meglutol as an important bioactive metabolite in tempe, an Indonesian fermented food. Food Chem 2024; 446:138744. [PMID: 38432131 DOI: 10.1016/j.foodchem.2024.138744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 02/09/2024] [Accepted: 02/10/2024] [Indexed: 03/05/2024]
Abstract
This study introduces a multidisciplinary approach to investigate bioactive food metabolites often overlooked due to their low concentrations. We integrated an in-house food metabolite library (n = 494), a human metabolite library (n = 891) from epidemiological studies, and metabolite pharmacological databases to screen for food metabolites with potential bioactivity. We identified six potential metabolites, including meglutol (3-hydroxy-3-methylglutarate), an understudied low-density lipoprotein (LDL)-lowering compound. We further focused on meglutol as a case study to showcase the range of characterizations achievable with this approach. Green pea tempe was identified to contain the highest meglutol concentration (21.8 ± 4.6 mg/100 g). Furthermore, we identified a significant cross-sectional association between plasma meglutol (per 1-standard deviation) and lower LDL cholesterol in two Hispanic adult cohorts (n = 1,628) (β [standard error]: -5.5 (1.6) mg/dl, P = 0.0005). These findings highlight how multidisciplinary metabolomics can serve as a systematic tool for discovering and enhancing bioactive metabolites in food, such as meglutol, with potential applications in personalized dietary approaches for disease prevention.
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Affiliation(s)
- Marvin N Iman
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Japan
| | - Danielle E Haslam
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Liming Liang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Kai Guo
- Center for Clinical Research and Health Promotion, Graduate School of Public Health, University of Puerto Rico Medical Sciences Campus, Puerto Rico, USA
| | - Kaumudi Joshipura
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Center for Clinical Research and Health Promotion, Graduate School of Public Health, University of Puerto Rico Medical Sciences Campus, Puerto Rico, USA
| | - Cynthia M Pérez
- Department of Biostatistics and Epidemiology, Graduate School of Public Health, University of Puerto Rico Medical Sciences Campus, Puerto Rico, USA
| | - Clary Clish
- Broad Institute of Massachusetts Institute of Technology and Harvard, USA
| | - Katherine L Tucker
- Department of Biomedical and Nutritional Sciences, University of Massachusetts Lowell, USA
| | - JoAnn E Manson
- Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Shilpa N Bhupathiraju
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Japan; Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Japan; Osaka University-Shimadzu Omics Innovation Research Laboratories, Osaka University, Japan
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Sastia P Putri
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Japan; Osaka University-Shimadzu Omics Innovation Research Laboratories, Osaka University, Japan.
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Onishi K, Furuno M, Mori A, Fukusaki E. New insights into the characteristic flavor components of traditional sour beers such as Lambic and Flanders Red Ale beers. J Biosci Bioeng 2024:S1389-1723(24)00111-7. [PMID: 38653595 DOI: 10.1016/j.jbiosc.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 03/10/2024] [Accepted: 04/05/2024] [Indexed: 04/25/2024]
Abstract
In recent years, the demand for beers with a variety of flavors has increased considerably owing to the diversification of consumer preferences. Sour beer is characterized by a sour taste unlike normal beer flavor, and previous studies on sour beer have been primarily focused on addressing issues, such as inconsistent product quality and long production time, and on the associated microorganisms. Scientific knowledge regarding the characteristic flavor of sour beer and flavor components is limited. Therefore, in this study, we aimed to clarify the characteristic sensory attributes of sour beer and the component profiles that explain these attributes. Component analysis was performed on 10 traditional sour beers (eight Flanders Red Ales and two Lambics), using untargeted gas chromatography-mass spectrometry with liquid-liquid extraction, liquid chromatography-mass spectrometry targeting amines and anionic compounds. Further, sensory evaluation was conducted by well-trained panelists via quantitative descriptive analysis. Orthogonal partial least squares regression analysis was also conducted to investigate candidate flavor components. Thus, 261 components were identified and our methods could explain the flavor attributes of the examined samples. Comprehensive component profiling data also showed that differences in fermentation method, barrel aging duration, and blending ratio affected beer flavor. Further, Lambics were found to be characterized by citrus and phenolic aroma, while Flanders Red Ales were characterized by solvent-like aroma, sourness complexity, full bodied, graininess, astringency, and bitterness. These findings may serve as a basis for addressing issues related to sour beer production and may facilitate process design for obtaining targeted sour beer flavors.
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Affiliation(s)
- Kyoya Onishi
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masahiro Furuno
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Asuka Mori
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiative, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Osaka University Shimadzu Omics Innovation Research Laboratories, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
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3
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Murakami Y, Ikuta S, Fukuda W, Akasaka N, Maruyama JI, Shinma S, Fukusaki E, Fujiwara S. Identification and enzymatic properties of arginine decarboxylase from Aspergillus oryzae. Appl Environ Microbiol 2024:e0029424. [PMID: 38624200 DOI: 10.1128/aem.00294-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 03/23/2024] [Indexed: 04/17/2024] Open
Abstract
Aspergillus oryzae spores, when sprinkled onto steamed rice and allowed to propagate, are referred to as rice "koji." Agmatine, a natural polyamine derived from arginine through the action of arginine decarboxylase (ADC), is abundantly produced by solid state-cultivated rice koji of A. oryzae RIB40 under low pH conditions, despite the apparent absence of ADC orthologs in its genome. Mass spectrometry imaging revealed that agmatine was accumulated inside rice koji at low pH conditions, where arginine was distributed. ADC activity was predominantly observed in substrate mycelia and minimally in aerial mycelia. Natural ADC was isolated from solid state-cultivated A. oryzae rice koji containing substrate mycelia, using ammonium sulfate fractionation, ion exchange, and gel-filtration chromatography. The purified protein was subjected to sodium dodecyl sulfate poly-acrylamide gel electrophoresis (SDS-PAGE), and the detected peptide band was digested for identification by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The gene AO090102000327 of strain RIB40 was identified, previously annotated as phosphatidylserine decarboxylase (PSD), and encoded a 483-amino acid peptide. Recombinant protein encoded by AO090102000327 was expressed in Escherichia coli cells cultivated at 20°C, resulting in the detection of 49 kDa and 5 kDa peptides. The protein exhibited pyruvoyl-dependent decarboxylase activity, favoring arginine over ornithine and showing no activity with phosphatidylserine. The gene was designated Ao-adc1. Ao-ADC1 expression in rice koji at pH 4-6 was confirmed through western blotting using the anti-Ao-ADC1 serum. These findings indicate that Ao-adc1 encodes arginine decarboxylase involved in agmatine production.IMPORTANCEGene AO090102000327 in A. oryzae RIB40, previously annotated as a PSD, falls into a distinct clade when examining the phylogenetic distribution of PSDs. Contrary to the initial PSD annotation, our analysis indicates that the protein encoded by AO090102000327 is expressed in the substrate mycelia area of solid state-cultivated A. oryzae rice koji and functions as an arginine decarboxylase (ADC). The clade to which Ao-ADC1 belongs includes three other Ao-ADC1 paralogs (AO090103000445, AO090701000800, and AO090701000802) that presumably encode ADC rather than PSDs. Regarding PSD, AO090012000733 and AO090005001124 were speculated to be nonmitochondrial and mitochondrial PSDs in A. oryzae RIB40, respectively.
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Affiliation(s)
- Yui Murakami
- Department of Biosciences, Graduate School of Science and Technology, Kwansei-Gakuin University, Gakuen-Uegahara, Sanda, Hyogo, Japan
| | - Soichiro Ikuta
- Department of Biosciences, School of Biological and Environmental Sciences, Kwansei-Gakuin University, Gakuen-Uegahara, Sanda, Hyogo, Japan
| | - Wakao Fukuda
- Department of Biosciences, School of Biological and Environmental Sciences, Kwansei-Gakuin University, Gakuen-Uegahara, Sanda, Hyogo, Japan
| | - Naoki Akasaka
- Department of Biosciences, Graduate School of Science and Technology, Kwansei-Gakuin University, Gakuen-Uegahara, Sanda, Hyogo, Japan
- Laboratory for Circular Bioeconomy Development, Office of Society-Academia Collaboration for Innovation, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, Japan
| | - Jun-Ichi Maruyama
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Shuichi Shinma
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
- Osaka University Shimadzu Analytical Innovation Laboratory, Osaka University, Suita,, Osaka, Japan
- Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, Japan
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
- Osaka University Shimadzu Analytical Innovation Laboratory, Osaka University, Suita,, Osaka, Japan
- Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, Japan
| | - Shinsuke Fujiwara
- Department of Biosciences, Graduate School of Science and Technology, Kwansei-Gakuin University, Gakuen-Uegahara, Sanda, Hyogo, Japan
- Department of Biosciences, School of Biological and Environmental Sciences, Kwansei-Gakuin University, Gakuen-Uegahara, Sanda, Hyogo, Japan
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Yunindanova MB, Putri SP, Novarianto H, Fukusaki E. Characteristics of kopyor coconut (Cocos nucifera L.) using sensory analysis and metabolomics-based approach. J Biosci Bioeng 2024:S1389-1723(24)00078-1. [PMID: 38614830 DOI: 10.1016/j.jbiosc.2024.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 02/14/2024] [Accepted: 02/21/2024] [Indexed: 04/15/2024]
Abstract
Kopyor is a coconut with unique characteristics from Indonesia, one of the largest coconut producers in the world. Kopyor is an edible mature coconut with soft endosperm. Although this fruit is one of the most popular coconuts in the world, there are limited studies on its properties, including its sensory attributes and metabolite profiles. This study investigates the characteristics of kopyor using sensory evaluation, a widely targeted metabolomics approach, and multivariate analysis. The liquid (water) and solid (flesh) endosperms were collected as the samples. The results showed that kopyor has characteristics that distinguish it from normal mature and young coconuts. Kopyor water has a milky, creamy, nutty, bitter, and astringent taste with an oily aftertaste and mouthfeel. Kopyor flesh is soft and moist and gives a sandy mouth feel. This study analyzed the sensory attributes of the kopyor endosperm for the first time and compared it with those of normal mature and young coconuts. A gas chromatography mass spectrometry analysis showed that kopyor contained wider variety of metabolites than normal coconuts of the same age. Based on the differential analysis and orthogonal projections to latent structures-regression, kopyor water was characterized by the accumulation of flavor-related metabolites, such as amino acids and organic acids, which contributed to its sensory complexity. This study solidified the effects of maturation and endosperm type on metabolite accumulation in kopyor endosperm. This pioneering information will lead to the future use of kopyor and other unique coconuts worldwide for food, contributing to the sustainability of the coconut industry.
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Affiliation(s)
- Mercy Bientri Yunindanova
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Study Program of Agrotechnology, Faculty of Agriculture, Universitas Sebelas Maret, Jl. Ir Sutami No. 36A, Jebres, Surakarta City, Central Java 57126, Indonesia
| | - Sastia Prama Putri
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Hengky Novarianto
- National Research and Innovation Agency (BRIN), Jl. Pingkan Matindas No. 92, Dendengan Dalam, Kec. Tikala, Kota Manado, Sulawesi Utara 95127, Indonesia
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Osaka University Shimadzu Omics Innovation Research Laboratories, International Center for Biotechnology, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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Tamada Y, Asai T, Kubodera T, Akashi T, Fukusaki E, Shimma S. Rice grain structural characteristics of sake rice cultivar Hakutsurunishiki for daiginjo-shu brewing. Biosci Biotechnol Biochem 2024; 88:445-452. [PMID: 38326278 DOI: 10.1093/bbb/zbae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 01/02/2024] [Indexed: 02/09/2024]
Abstract
Hakutsurunishiki is a sake rice cultivar bred using Yamadabo (seed parent) and Wataribune 2 (pollen parent), equivalent to a Yamadanishiki sibling. This study evaluated the structural characteristics of the Hakutsurunishiki rice grain that contribute to the brewing characteristics of daiginjo-shu, via a comparison with Yamadanishiki. Hakutsurunishiki brown rice was a little heavy and had a large white core. Observing a cross-section of white rice after soaking revealed that the rice grain structure of Hakutsurunishiki was different from that of Yamadanishiki. Hakutsurunishiki white rice showed fewer voids than Yamadanishiki, promoting a slower water absorption rate. Glucose distribution in rice koji obtained by mass spectrometry imaging showed that Hakutsurunishiki rice koji, like Yamadanishiki, is tsuki-haze type, suggesting that its grain structure is suitable for making rice koji for daiginjo-shu. With these observations, we were able to clarify the structural characteristics of Hakutsurunishiki rice grain.
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Affiliation(s)
- Yoshihiro Tamada
- H akutsuru Sake Brewing Co., Ltd., Kobe, Hyogo, Japan
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
| | - Takuya Asai
- H akutsuru Sake Brewing Co., Ltd., Kobe, Hyogo, Japan
| | | | | | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
- Osaka University Shimadzu Omics Innovation Research Laboratory, Osaka University, Suita, Osaka, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan
| | - Shuichi Shimma
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
- Osaka University Shimadzu Omics Innovation Research Laboratory, Osaka University, Suita, Osaka, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan
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Kurogi K, Sakakibara Y, Hashiguchi T, Kakuta Y, Kanekiyo M, Teramoto T, Fukushima T, Bamba T, Matsumoto J, Fukusaki E, Kataoka H, Suiko M. A new type of sulfation reaction: C-sulfonation for α,β-unsaturated carbonyl groups by a novel sulfotransferase SULT7A1. PNAS Nexus 2024; 3:pgae097. [PMID: 38487162 PMCID: PMC10939482 DOI: 10.1093/pnasnexus/pgae097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 02/20/2024] [Indexed: 03/17/2024]
Abstract
Cytosolic sulfotransferases (SULTs) are cytosolic enzymes that catalyze the transfer of sulfonate group to key endogenous compounds, altering the physiological functions of their substrates. SULT enzymes catalyze the O-sulfonation of hydroxy groups or N-sulfonation of amino groups of substrate compounds. In this study, we report the discovery of C-sulfonation of α,β-unsaturated carbonyl groups mediated by a new SULT enzyme, SULT7A1, and human SULT1C4. Enzymatic assays revealed that SULT7A1 is capable of transferring the sulfonate group from 3'-phosphoadenosine 5'-phosphosulfate to the α-carbon of α,β-unsaturated carbonyl-containing compounds, including cyclopentenone prostaglandins as representative endogenous substrates. Structural analyses of SULT7A1 suggest that the C-sulfonation reaction is catalyzed by a novel mechanism mediated by His and Cys residues in the active site. Ligand-activity assays demonstrated that sulfonated 15-deoxy prostaglandin J2 exhibits antagonist activity against the prostaglandin receptor EP2 and the prostacyclin receptor IP. Modification of α,β-unsaturated carbonyl groups via the new prostaglandin-sulfonating enzyme, SULT7A1, may regulate the physiological function of prostaglandins in the gut. Discovery of C-sulfonation of α,β-unsaturated carbonyl groups will broaden the spectrum of potential substrates and physiological functions of SULTs.
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Affiliation(s)
- Katsuhisa Kurogi
- Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan
| | - Yoichi Sakakibara
- Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan
| | - Takuyu Hashiguchi
- Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan
| | - Yoshimitsu Kakuta
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Miho Kanekiyo
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Takamasa Teramoto
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Tsuyoshi Fukushima
- Department of Pathology, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Takeshi Bamba
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Jin Matsumoto
- Department of Applied Chemistry, Faculty of Engineering, University of Miyazaki, Miyazaki 889-2192, Japan
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita 565-0871, Japan
| | - Hiroaki Kataoka
- Department of Pathology, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Masahito Suiko
- Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan
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Wada K, Uebayashi K, Toya Y, Putri SP, Matsuda F, Fukusaki E, C Liao J, Shimizu H. Effects of n-butanol production on metabolism and the photosystem in Synecococcus elongatus PCC 7942 based on metabolic flux and target proteome analyses. J GEN APPL MICROBIOL 2024; 69:185-195. [PMID: 36935115 DOI: 10.2323/jgam.2023.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023]
Abstract
Although n-butanol (BuOH) is an ideal fuel because of its superior physical properties, it has toxicity to microbes. Previously, a Synechococcus elongatus PCC 7942 derivative strain that produces BuOH from CO2 was developed by introducing six heterologous genes (BUOH-SE strain). To identify the bottleneck in BuOH production, the effects of BuOH production and its toxicity on central metabolism and the photosystem were investigated. Parental (WT) and BUOH-SE strains were cultured under autotrophic conditions. Consistent with the results of a previous study, BuOH production was observed only in the BUOH-SE strain. Isotopically non-stationary 13C-metabolic flux analysis revealed that the CO2 fixation rate was much larger than the BuOH production rate in the BUOH-SE strain (1.70 vs 0.03 mmol gDCW-1 h-1), implying that the carbon flow for BuOH biosynthesis was less affected by the entire flux distribution. No large difference was observed in the flux of metabolism between the WT and BUOH-SE strains. Contrastingly, in the photosystem, the chlorophyll content and maximum O2 evolution rate per dry cell weight of the BUOH-SE strain were decreased to 81% and 43% of the WT strain, respectively. Target proteome analysis revealed that the amounts of some proteins related to antennae (ApcA, ApcD, ApcE, and CpcC), photosystem II (PsbB, PsbU, and Psb28-2), and cytochrome b6f complex (PetB and PetC) in photosystems decreased in the BUOH-SE strain. The activation of photosynthesis would be a novel approach for further enhancing BuOH production in S. elongatus PCC 7942.
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Affiliation(s)
- Keisuke Wada
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University
| | - Kiyoka Uebayashi
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University
| | - Yoshihiro Toya
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University
| | - Sastia Prama Putri
- Department of Biotechnology, Graduate School of Engineering, Osaka University
| | - Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University
| | - James C Liao
- Department of Chemical and Biomolocular Engineering, University of California
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University
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Nagao H, Nishizawa H, Fukuda S, Fujishima Y, Kita S, Maeda N, Bamba T, Fukusaki E, Shimomura I. Correlation between plasma glutamate and adiponectin in patients with type 2 diabetes. Endocr J 2024; 71:55-63. [PMID: 38030259 DOI: 10.1507/endocrj.ej23-0506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/01/2023] Open
Abstract
Visceral fat accumulation is a major determinant of type 2 diabetes mellitus and cardiovascular diseases. Recent studies have reported that glutamate is the most elevated amino acid in the plasma amino acid profile in patients with obesity and/or visceral fat accumulation. Here, we show the relationship between plasma glutamate and the clinical features of patients with type 2 diabetes. The study subjects were 62 (28 men and 34 women) Japanese patients with type 2 diabetes. Blood profiles, including glutamate and adiponectin (APN) levels and estimated visceral fat area (eVFA), were measured. We also evaluated the plasma amino acid levels in mice with or without obesity by GC/MS analysis. In patients with type 2 diabetes, plasma glutamate was positively correlated with BMI, eVFA, and fasting insulin but negatively correlated with APN and duration of diabetes. Additionally, multiple regression analysis revealed that plasma glutamate was a significant determinant of APN. The plasma glutamate level was most significantly increased in obese mice compared to control mice, and it was negatively correlated with APN. These results suggest that the level of plasma glutamate could be a strong indicator of adipocyte dysfunction in patients with type 2 diabetes.
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Affiliation(s)
- Hirofumi Nagao
- Department of Metabolism and Atherosclerosis, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Hitoshi Nishizawa
- Department of Metabolism and Atherosclerosis, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Shiro Fukuda
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Yuya Fujishima
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Shunbun Kita
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
- Department of Adipose Management, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Norikazu Maeda
- Department of Metabolism and Atherosclerosis, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
- Department of Endocrinology, Metabolism and Diabetes, Kindai University Faculty of Medicine, Osaka 589-8511, Japan
| | - Takeshi Bamba
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka 565-0871, Japan
- Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, Fukuoka 812-8582, Japan
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka 565-0871, Japan
| | - Iichiro Shimomura
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
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9
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Malikul Ikram MM, Putri SP, Fukusaki E. Chitosan-based coating enriched with melezitose alters primary metabolites in fresh-cut pineapple during storage. J Biosci Bioeng 2023; 136:374-382. [PMID: 37689569 DOI: 10.1016/j.jbiosc.2023.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/25/2023] [Accepted: 08/06/2023] [Indexed: 09/11/2023]
Abstract
Demand for minimally processed fresh fruit is increasing due to its convenience. However, the distribution of fresh-cut fruits is limited because of their short shelf life. Pineapple, a popular tropical fruit, sold in fresh-cut form has a shelf life of approximately 5-7 days at 4 °C. Chitosan, an edible coating, is commonly used to prolong the shelf life of food products. Similarly, the sugar melezitose has been reported to change during pineapple ripening and may play a role in regulating the shelf life of pineapple. However, the direct effects of this sugar have yet to be studied. The objective of this study was to investigate the effect of chitosan coating with melezitose to prolong the shelf life of fresh-cut pineapple. Full-ripe Bogor pineapples from Okinawa, Japan, were cut into cubes and soaked in either chitosan 1.25%, melezitose 5 mg/L, or chitosan+melezitose and stored for 5 days under dark conditions (23.6 ± 0.5 °C; relative humidity, 40.0 ± 10.4%). None of the treatments significantly altered the weight loss or color changes in the fresh-cut fruit. However, treatment significantly altered the primary metabolites, namely quinic acid, sucrose, and xylitol based on orthogonal projection to latent structures data with the screening from p-value score. Moreover, cell-wall metabolism is possibly affected in pineapple cut fruit treated by chitosan-melezitose as shown from metabolite sets enrichment analysis. This study showed that chitosan added with melezitose might have potential to prolong the shelf-life of fresh-cut pineapple, providing a basis for further post-harvest studies of the whole pineapple fruit.
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Affiliation(s)
- Muhammad Maulana Malikul Ikram
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Sastia Prama Putri
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan.
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan; Osaka University-Shimadzu Omics Innovation Research Laboratories, Osaka University, Suita, Osaka, Japan
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Amalia F, Irifune T, Takegami T, Yusianto, Sumirat U, Putri SP, Fukusaki E. Identification of potential quality markers in Indonesia's Arabica specialty coffee using GC/MS-based metabolomics approach. Metabolomics 2023; 19:90. [PMID: 37880543 PMCID: PMC10600306 DOI: 10.1007/s11306-023-02051-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 09/08/2023] [Indexed: 10/27/2023]
Abstract
INTRODUCTION The cupping test is a widely used method for quality assessment of Arabica coffee. However, the cupping test is limited by the low number of certified panelists and the low throughput. Therefore, an analytical-based quality assessment may be a promising tool to complement the cupping test. A present, there is no report investigating quality marker candidates, focusing only on "specialty" grade Arabica coffee from Indonesia. OBJECTIVE This study identified the potential quality marker(s) in Arabica Specialty coffee at different stages (green beans, roasted beans, and brewed coffee. METHODS The metabolite profiles of ten different Arabica specialty-grade coffees were analyzed with different cup scores using gas chromatography-mass spectrometry (GC/MS). From the ten samples, green coffee beans, roasted coffee beans, and brewed coffee were selected. In addition, an orthogonal projection to latent structure (OPLS) regression analysis was conducted to obtain a potential quality marker based on the variable importance in projection (VIP). The potential quality marker(s) were validated by GC/MS metabolome profiling and OPLS analysis of different sets of samples consisting of 35 Arabica specialty-grade coffee samples. RESULTS In Arabica coffee samples, the OPLS model of the three stages showed galactinol to have a high VIP score. Galactinol showed a consistent positive correlation with cup scores at all stages of coffee production (green beans, roasted beans, and brewed coffee). The correlation suggests galactinol is a potential quality marker after further validation using different samples. CONCLUSION GC/MS combined with OPLS regression analysis suggested galactinol as a quality marker and provide an early screening method for Arabica coffee quality that complements the cupping test performed by certified panelists.
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Affiliation(s)
- Fitri Amalia
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Tomoya Irifune
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Tetsuji Takegami
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yusianto
- Indonesian Coffee and Cocoa Research Institute, Jl. PB. Sudirman 90, Jember, East Java, 68118, Indonesia
| | - Ucu Sumirat
- Indonesian Coffee and Cocoa Research Institute, Jl. PB. Sudirman 90, Jember, East Java, 68118, Indonesia
| | - Sastia Prama Putri
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.
- Industrial Biotechnology Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Industrial Biotechnology Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Osaka University Shimadzu Omics Innovation Research Laboratories, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
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11
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Iman MN, Irdiani R, Rahmawati D, Fukusaki E, Putri SP. Improvement of the functional value of green soybean (edamame) using germination and tempe fermentation: A comparative metabolomics study. J Biosci Bioeng 2023; 136:205-212. [PMID: 37331843 DOI: 10.1016/j.jbiosc.2023.05.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/17/2023] [Accepted: 05/26/2023] [Indexed: 06/20/2023]
Abstract
Green soybean, also known as edamame, is a legume with high nutritional and functional value. Despite its growing popularity and potential health benefits, the functionality of green soybean has not been thoroughly studied. Previous research on the functionality of green soybean has largely focused on a limited number of specific, well-studied, bioactive metabolites, without comprehensively investigating the metabolome of this legume. Additionally, very few studies have explored the improvement of the functional value of green soybean. This study aimed to investigate the metabolome profile of green soybean, identify bioactive metabolites, and to further explore the potential improvement of the identified bioactive metabolites using germination and tempe fermentation. A total of 80 metabolites were annotated from green soybean using GC-MS and HPLC-PDA-MS. Among them, 16 important bioactive metabolites were identified: soy isoflavones daidzin, glycitin, genistin, malonyl daidzin, malonyl genistin, malonyl glycitin, acetyl daidzin, acetyl genistin, acetyl glycitin, daidzein, glycitein, and genistein, as well as other metabolites including 3,4-dihydroxybenzoic acid, 3-hydroxyanthranillic acid, 3-hydroxy-3-methylglutaric acid (meglutol), and 4-aminobutyric acid (GABA). Germination and tempe fermentation techniques were employed to potentially improve the concentrations of these bioactive metabolites. While showing improvements in amino acid contents, germination process did not improve bioactive metabolites significantly. In contrast, tempe fermentation was found to significantly increase the concentrations of daidzein, genistein, glycitein, acetyl genistin, acetyl daidzin, 3-hydroxyanthranillic acid, and meglutol (>2-fold increase with p < 0.05) while also improving amino acid levels. This study highlights the potentials of germination and fermentation to improve the functionality of legumes, particularly green soybean.
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Affiliation(s)
- Marvin Nathanael Iman
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Rafidha Irdiani
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Della Rahmawati
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan; Department of Food Technology, Faculty of Life Science and Technology, Swiss German University, Tangerang, Banten, Indonesia
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan; Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka 565-0871, Japan; Osaka University-Shimadzu Omics Innovation Research Laboratories, Osaka University, Suita, Osaka 565-0871, Japan
| | - Sastia Prama Putri
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan; Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka 565-0871, Japan.
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Ikuta S, Fukusaki E, Shimma S. Visualization of azoxystrobin penetration in wheat leaves using mass microscopy imaging. J Pestic Sci 2023; 48:29-34. [PMID: 37361488 PMCID: PMC10288002 DOI: 10.1584/jpestics.d22-063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 02/02/2023] [Indexed: 06/28/2023]
Abstract
Fungicides must penetrate the internal tissues of plants to kill pathogenic fungi. Mass spectrometers have been used to confirm this penetration, but conventional mass spectrometric methods cannot distinguish the fungicides in different internal tissues owing to the extraction steps. However, matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) can detect the penetration of fungicides into leaf sections through direct analysis of the sample surfaces. Therefore, the objective of this study was to establish a method for visualizing fungicide penetration in wheat leaf cross sections using MALDI-MSI. The penetration of azoxystrobin from the epidermal to the internal tissue of the leaves was observed. Moreover, azoxystrobin accumulates in the cells around the vascular bundle. This study suggests that MSI can be useful for the evaluation of fungicide penetration in plant leaves.
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Affiliation(s)
- Soichiro Ikuta
- Department of Biotechnology, Graduate School of Engineering, Osaka University
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University
- Osaka University Shimadzu Omics Innovation Research Laboratory, Osaka University
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University
| | - Shuichi Shimma
- Department of Biotechnology, Graduate School of Engineering, Osaka University
- Osaka University Shimadzu Omics Innovation Research Laboratory, Osaka University
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University
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Hoffmann K, Halmschlag B, Briel S, Sieben M, Putri S, Fukusaki E, Blank LM, Büchs J. Online measurement of the viscosity in shake flasks enables monitoring of γ-PGA production in depolymerase knockout mutants of Bacillus subtilis with the phosphate-starvation inducible promoter P pst. Biotechnol Prog 2023; 39:e3293. [PMID: 36081345 DOI: 10.1002/btpr.3293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/26/2022] [Accepted: 08/11/2022] [Indexed: 11/10/2022]
Abstract
Poly-γ-glutamic acid (γ-PGA) is a biopolymer with a wide range of applications, mainly produced using Bacillus strains. The formation and concomitant secretion of γ-PGA increases the culture broth viscosity, while enzymatic depolymerisation and degradation of γ-PGA decreases the culture broth viscosity. In this study, the recently published ViMOS (Viscosity Monitoring Online System) is applied for optical online measurements of broth viscosity in eight parallel shake flasks. It is shown that the ViMOS is suitable to monitor γ-PGA production and degradation online in shake flasks. This online monitoring enables the detailed analysis of the Ppst promoter and γ-PGA depolymerase knockout mutants in genetically modified Bacillus subtilis 168. The Ppst promoter becomes active under phosphate starvation. The different single depolymerase knockout mutants are ∆ggt, ∆pgdS, ∆cwlO and a triple knockout mutant. An increase in γ-PGA yield in gγ-PGA /gglucose of 190% could be achieved with the triple knockout mutant compared to the Ppst reference strain. The single cwlO knockout also increased γ-PGA production, while the other single knockouts of ggt and pgdS showed no impact. Partial depolymerisation of γ-PGA occurred despite the triple knockout. The online measured data are confirmed with offline measurements. The online viscosity system directly reflects γ-PGA synthesis, γ-PGA depolymerisation, and changes in the molecular weight. Thus, the ViMOS has great potential to rapidly gain detailed and reliable information about new strains and cultivation conditions. The broadened knowledge will facilitate the further optimization of γ-PGA production.
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Affiliation(s)
- Kyra Hoffmann
- AVT - Biochemical Engineering, RWTH Aachen University, Aachen, Germany
| | - Birthe Halmschlag
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Aachen, Germany
| | - Simon Briel
- AVT - Biochemical Engineering, RWTH Aachen University, Aachen, Germany
| | - Michaela Sieben
- AVT - Biochemical Engineering, RWTH Aachen University, Aachen, Germany
| | - Sastia Putri
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
| | - Lars M Blank
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Aachen, Germany
| | - Jochen Büchs
- AVT - Biochemical Engineering, RWTH Aachen University, Aachen, Germany
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Sakanaka A, Katakami N, Furuno M, Nishizawa H, Omori K, Taya N, Ishikawa A, Mayumi S, Inoue M, Tanaka Isomura E, Amano A, Shimomura I, Fukusaki E, Kuboniwa M. Salivary metabolic signatures of carotid atherosclerosis in patients with type 2 diabetes hospitalized for treatment. Front Mol Biosci 2022; 9:1074285. [PMID: 36619162 PMCID: PMC9815705 DOI: 10.3389/fmolb.2022.1074285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Atherosclerosis is a life-threatening disease associated with morbidity and mortality in patients with type 2 diabetes (T2D). This study aimed to characterize a salivary signature of atherosclerosis based on evaluation of carotid intima-media thickness (IMT) to develop a non-invasive predictive tool for diagnosis and disease follow-up. Metabolites in saliva and plasma samples collected at admission and after treatment from 25 T2D patients hospitalized for 2 weeks to undergo medical treatment for diabetes were comprehensively profiled using metabolomic profiling with gas chromatography-mass spectrometry. Orthogonal partial least squares analysis, used to explore the relationships of IMT with clinical markers and plasma and salivary metabolites, showed that the top predictors for IMT included salivary allantoin and 1,5-anhydroglucitol (1,5-AG) at both the baseline examination at admission and after treatment. Furthermore, though treatment induced alterations in salivary levels of allantoin and 1,5-AG, it did not modify the association between IMT and these metabolites (p interaction > 0.05), and models with these metabolites combined yielded satisfactory diagnostic accuracy for the high IMT group even after treatment (area under curve = 0.819). Collectively, this salivary metabolite combination may be useful for non-invasive identification of T2D patients with a higher atherosclerotic burden in clinical settings.
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Affiliation(s)
- Akito Sakanaka
- Department of Preventive Dentistry, Osaka University Graduate School of Dentistry, Suita, Japan
| | - Naoto Katakami
- Department of Metabolic Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Masahiro Furuno
- Department of Biotechnology, Osaka University Graduate School of Engineering, Suita, Japan
| | - Hitoshi Nishizawa
- Department of Metabolic Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Kazuo Omori
- Department of Metabolic Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Naohiro Taya
- Department of Metabolic Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Asuka Ishikawa
- Department of Preventive Dentistry, Osaka University Graduate School of Dentistry, Suita, Japan
| | - Shota Mayumi
- Department of Preventive Dentistry, Osaka University Graduate School of Dentistry, Suita, Japan
| | - Moe Inoue
- Department of Preventive Dentistry, Osaka University Graduate School of Dentistry, Suita, Japan
| | - Emiko Tanaka Isomura
- First Department of Oral and Maxillofacial Surgery, Osaka University Graduate School of Dentistry, Suita, Japan
| | - Atsuo Amano
- Department of Preventive Dentistry, Osaka University Graduate School of Dentistry, Suita, Japan
| | - Iichiro Shimomura
- Department of Metabolic Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Eiichiro Fukusaki
- Department of Biotechnology, Osaka University Graduate School of Engineering, Suita, Japan
| | - Masae Kuboniwa
- Department of Preventive Dentistry, Osaka University Graduate School of Dentistry, Suita, Japan,*Correspondence: Masae Kuboniwa,
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Pitchapa R, Dissook S, Putri SP, Fukusaki E, Shimma S. MALDI Mass Spectrometry Imaging Reveals the Existence of an N-Acyl-homoserine Lactone Quorum Sensing System in Pseudomonas putida Biofilms. Metabolites 2022; 12:1148. [PMID: 36422288 PMCID: PMC9697013 DOI: 10.3390/metabo12111148] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 02/28/2024] Open
Abstract
Quorum sensing (QS) is generally used to describe the process involving the release and recognition of signaling molecules, such as N-acyl-homoserine lactones, by bacteria to coordinate their response to population density and biofilm development. However, detailed information on the heterogeneity of QS metabolites in biofilms remains largely unknown. Here, we describe the utilization of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) to follow the production of specific metabolites, including QS metabolites, during Pseudomonas putida biofilm development. To do so, a method to grow an agar-based biofilm was first established, and MALDI-MSI was used to detect and visualize the distribution of QS metabolites in biofilms at different cultivation times. This study demonstrated that N-acyl-homoserine lactones are homogeneously produced in the early stages of P. putida biofilm formation. In contrast, the spatial distribution of quinolones and pyochelin correlated with the swarming motility of P. putida in mature biofilms. These two metabolites are involved in the production of extracellular polymeric substances and iron chelators. Our study thus contributes to establishing the specific temporal regulation and spatial distribution of N-acyl-homoserine lactone-related metabolites and quinolone and pyochelin in P. putida biofilms.
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Affiliation(s)
- Rattanaburi Pitchapa
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 5650871, Osaka, Japan
| | - Sivamoke Dissook
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 5650871, Osaka, Japan
| | - Sastia Prama Putri
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 5650871, Osaka, Japan
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 5650871, Osaka, Japan
- Osaka University Shimadzu Analytical Innovation Laboratory, Osaka University, 2-1 Yamadaoka, Suita 5650871, Osaka, Japan
| | - Shuichi Shimma
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 5650871, Osaka, Japan
- Osaka University Shimadzu Analytical Innovation Laboratory, Osaka University, 2-1 Yamadaoka, Suita 5650871, Osaka, Japan
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Iman MN, Herawati E, Fukusaki E, Putri SP. Metabolomics-driven strain improvement: A mini review. Front Mol Biosci 2022; 9:1057709. [PMID: 36438656 PMCID: PMC9681786 DOI: 10.3389/fmolb.2022.1057709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 10/28/2022] [Indexed: 07/22/2023] Open
Abstract
In recent years, mass spectrometry-based metabolomics has been established as a powerful and versatile technique for studying cellular metabolism by comprehensive analysis of metabolites in the cell. Although there are many scientific reports on the use of metabolomics for the elucidation of mechanism and physiological changes occurring in the cell, there are surprisingly very few reports on its use for the identification of rate-limiting steps in a synthetic biological system that can lead to the actual improvement of the host organism. In this mini review, we discuss different strategies for improving strain performance using metabolomics data and compare the application of metabolomics-driven strain improvement techniques in different host microorganisms. Finally, we highlight several success stories on the use of metabolomics-driven strain improvement strategies, which led to significant bioproductivity improvements.
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Affiliation(s)
- Marvin Nathanael Iman
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Elisa Herawati
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Sebelas Maret, Surakarta, Indonesia
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Sastia Prama Putri
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka, Japan
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Ikuta S, Shinohara N, Fukusaki E, Shimma S. Mass spectrometry imaging enables visualization of the localization of glutamate decarboxylase activity in germinating legume seeds. J Biosci Bioeng 2022; 134:356-361. [PMID: 36008275 DOI: 10.1016/j.jbiosc.2022.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/09/2022] [Accepted: 07/12/2022] [Indexed: 11/29/2022]
Abstract
Visualizing the distribution of enzymes is vital for understanding physiological phenomena. Enzyme histochemistry is a technique used to investigate the localization of enzyme activity. However, the target is restricted to enzymes with easy-to-design artificial substrates that can develop color through reactions. Mass spectrometry imaging (MSI)-based enzyme histochemistry has been developed as a novel method to visualize enzyme localization. It can be applied to enzyme histochemistry as it detects products from the supplied substrate using enzymes present on the tissue sections. However, enzyme histochemistry using MSI has not been applied to plant tissue samples yet. Glutamate decarboxylase (GAD, EC: 4.1.1.15) is an enzyme that catalyzes the decarboxylation reaction of l-glutamic acid to produce γ-aminobutyric acid (GABA). GABA biosynthesis is important both in the field of food chemistry and plant physiology. This study focused on GAD during the legume germination process and successfully visualized GAD activity in legume seeds using MSI for the first time. Furthermore, the localization of GAD activity in the embryonic axis of germinated soybean seeds and alfalfa seeds could be visualized.
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Affiliation(s)
- Soichiro Ikuta
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Naho Shinohara
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Osaka University Shimadzu Omics Innovation Research Laboratory, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shuichi Shimma
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Osaka University Shimadzu Omics Innovation Research Laboratory, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
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Sato A, Putri SP, Astuti DI, Fukusaki E. Metabolome analysis to investigate the effect of controlled fermentation on taste-related metabolites in terasi. Metabolomics 2022; 18:44. [PMID: 35760928 DOI: 10.1007/s11306-022-01902-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 05/25/2022] [Indexed: 10/17/2022]
Abstract
INTRODUCTION Terasi is a fermented shrimp paste unique to Indonesia and is used in dishes to add umami and saltiness. In a previous study, the controlled fermentation of terasi was optimized using starters containing three bacterial isolates: Staphylococcus saprophyticus, Bacillus subtilis, and Lactobacillus murinus. However, the influence of controlled fermentation using these starters on the metabolites in terasi has not yet been studied. OBJECTIVES Therefore, this study aimed to investigate the effect of controlled fermentation on taste-related metabolites in terasi using a metabolomics approach. RESULTS Non-targeted analysis indicated that amino acids contributed to variations during fermentation. Subsequently, targeted analysis of amino acids revealed that terasi subjected to controlled fermentation using a starter with a 2:1:2 ratio of S. saprophyticus, B. subtilis, and L. murinus, respectively, resulted in a product containing D-amino acids, such as D-Asp, D-Gln, and D-Leu that was unique when compared to other terasi products prepared using controlled fermentation. Genetic analysis of isolates from the terasi produced using controlled fermentation was also carried out, and this is the first study to suggest that Staphylococcus spp. has the potential to produce D-amino acids. CONCLUSION In conclusion, the ratio of bacterial species in starter cultures used in controlled fermentation influenced the amino acid profile of the product and starters with a higher ratio of Staphylococcus spp. may result in the production of D-amino acids.
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Affiliation(s)
- Arisa Sato
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Sastia Prama Putri
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.
- School of Life Sciences and Technology, Institut Technology Bandung, Jl. Ganesha No.10, Lb. Siliwangi, Coblong, Kota Bandung, Jawa Barat, 40132, Indonesia.
- Osaka University-Shimadzu Omics Innovation Research Laboratories, Osaka University, Osaka, 565 0871, Japan.
| | - Dea Indriani Astuti
- School of Life Sciences and Technology, Institut Technology Bandung, Jl. Ganesha No.10, Lb. Siliwangi, Coblong, Kota Bandung, Jawa Barat, 40132, Indonesia
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, 565 0871, Japan
- Osaka University-Shimadzu Omics Innovation Research Laboratories, Osaka University, Osaka, 565 0871, Japan
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Kitani Y, Putri SP, Fukusaki E. Investigation of the effect of processing on the component changes of single-origin chocolate during the bean-to-bar process. J Biosci Bioeng 2022; 134:138-143. [PMID: 35753972 DOI: 10.1016/j.jbiosc.2022.05.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 05/23/2022] [Accepted: 05/27/2022] [Indexed: 11/28/2022]
Abstract
Chocolate is one of the most popular sweets in the world. In recent years, the bean-to-bar process for chocolate production has attracted global attention. Bean-to-bar is a method of managing the whole production process from cocoa beans to chocolate bars, including single-origin chocolate (SOC). Many manufacturers aim to produce high-quality chocolate to maximize the flavor of cocoa beans. However, chocolate compounds are very complex due to many processes, and there are a limited number of studies on the SOC produced from the bean-to-bar process. Therefore, understanding the effects of processing is important for the growth of the chocolate industry. The objective of this study was to investigate the processing effect on the component changes of SOC during the bean-to-bar process. In this study, the component changes during the bean-to-bar process were monitored using gas chromatography/mass spectrometry (GC/MS). Then, the characteristics of SOC from five regions in Indonesia were further investigated. Lastly, the component profiles were combined with the data obtained from sensory evaluation. Our results showed that the influence of the manufacturing process was greater than that of the difference in the cocoa production area. Moreover, 1-pentanol, raffinose, and heptanoic acid were correlated with sweetness and dairy flavor, whereas glutamic acid, tartaric acid, 3-methyl-2-butanone, mannitol, and ethyl cinnamate were correlated with bitterness, astringency, and cocoa flavor, which were shown to be affected by fermentation, roasting, and sugar addition. This information might provide a basis for improving the chocolate production process and its quality related to the component profiles.
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Affiliation(s)
- Yuka Kitani
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Sastia Prama Putri
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka 565-0871, Japan.
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka 565-0871, Japan; Osaka University-Shimadzu Omics Innovation Research Laboratories, Osaka University, Osaka 565-0871, Japan
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20
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Hanifah A, Firmanto H, Putri SP, Fukusaki E. Unique metabolite profiles of Indonesian cocoa beans from different origins and their correlation with temperature. J Biosci Bioeng 2022; 134:125-132. [PMID: 35654674 DOI: 10.1016/j.jbiosc.2022.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 04/14/2022] [Accepted: 05/02/2022] [Indexed: 12/27/2022]
Abstract
Chocolate flavors vary depending on the origin of the cocoa beans used. Differences in soil, microorganisms, and environmental factors contribute to the formation of flavor precursors in cocoa beans. During cocoa bean fermentation, environmental temperature has been shown to alter metabolite concentrations. However, the correlation between the metabolite profile of cocoa beans and the temperature of their region of origin has not been fully defined. In this study, the metabolite profiles of Indonesian cocoa beans of various origins were evaluated using gas chromatography/mass spectrometry-based analysis, and were found to differ depending on the origin of the bean. Subsequently, the correlation between metabolite profile and environmental temperature of the origin was assessed using orthogonal projection to latent structure regression (OPLS-R) analysis. The analysis revealed that seven metabolites were associated with temperature: γ-aminobutyric acid (GABA), ethanolamine, glycerol, isocitric acid + citric acid, succinic acid, malic acid, and saccharic acid. The findings of this study will be valuable to chocolate industries for the production of single-origin chocolates.
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Affiliation(s)
- Abu Hanifah
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hendy Firmanto
- Indonesian Coffee and Cocoa Research Institute, Jl. PB. Sudirman 90, Jember, Jawa Timur 68118, Indonesia
| | - Sastia Prama Putri
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka 565-0871, Japan.
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka 565-0871, Japan; Osaka University-Shimadzu Omics Innovation Research Laboratories, Osaka University, Osaka 565-0871, Japan
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21
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Wisman AP, Minami M, Tamada Y, Hirohata S, Gomi K, Fukusaki E, Shimma S. Visualization of dipeptidyl peptidase B enzymatic reaction in rice koji using mass spectrometry imaging. J Biosci Bioeng 2022; 134:133-137. [PMID: 35643851 DOI: 10.1016/j.jbiosc.2022.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/02/2022] [Accepted: 05/05/2022] [Indexed: 10/18/2022]
Abstract
Enzyme histochemistry via mass spectrometry imaging (MSI) has garnered attention as a straightforward approach for visualizing enzymatic reactions. While several studies in the medical and physiological fields have shown its promising application potential, its applicability to agricultural or food studies has not yet been demonstrated. Rice koji, known as an enzyme source for various fermented products, is a suitable model for demonstrating the applicability of this method to food-related materials. In this study, the enzymatic reaction of dipeptidyl peptidase B (DppB) in rice koji was visualized using MSI for the first time. The method was optimized and applied to investigate the effects of rice variety, polishing ratio, and cultivation time on the location of the DppB reaction. The DppB enzymatic reaction was found to occur in different locations in each of the two rice varieties, Yamadanishiki and Hakutsurunishiki. The polishing ratio also affected the distribution of the DppB enzymatic reactions. Furthermore, a time-course investigation of rice koji cultivation revealed that while the location of the reaction was largely associated with mycelial penetration, the structure and features of the rice grain may also affect the location of the enzymatic reaction. In summary, these results demonstrate the applicability of enzyme histochemistry by MSI to food-related materials.
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Affiliation(s)
- Adinda Putri Wisman
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 5650871, Japan
| | - Makiho Minami
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 5650871, Japan
| | - Yoshihiro Tamada
- Hakutsuru Sake Brewing Co., Ltd., 4-5-5 Sumiyoshi Minamimachi, Higashinada-ku, Kobe, Hyogo 6580041, Japan
| | - Shuji Hirohata
- Hakutsuru Sake Brewing Co., Ltd., 4-5-5 Sumiyoshi Minamimachi, Higashinada-ku, Kobe, Hyogo 6580041, Japan
| | - Katsuya Gomi
- Department of Bioindustrial Informatics and Genomics, Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 9808572, Japan; Laboratory of Fermentation Microbiology, Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 9808572, Japan
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 5650871, Japan; Osaka University Shimadzu Omics Innovation Research Laboratory, Osaka University, 2-1 Yamadaoka, Suita, Osaka 5650871, Japan; Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, Osaka 5650871, Japan
| | - Shuichi Shimma
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 5650871, Japan; Osaka University Shimadzu Omics Innovation Research Laboratory, Osaka University, 2-1 Yamadaoka, Suita, Osaka 5650871, Japan; Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, Osaka 5650871, Japan.
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22
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Mori A, Taniguchi M, Kuboniwa M, Amano A, Fukusaki E. Profiling volatile compounds from culture supernatants of periodontal bacteria using gas chromatography/mass spectrometry/olfactometry analysis with a monolithic silica gel adsorption device. J Biosci Bioeng 2022; 134:77-83. [PMID: 35484014 DOI: 10.1016/j.jbiosc.2022.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/31/2022] [Accepted: 04/06/2022] [Indexed: 11/26/2022]
Abstract
Halitosis is formed mainly by the volatile compounds produced by periodontal bacteria. Three volatile sulfur compounds (VSCs), hydrogen sulfide, methanethiol, and dimethyl sulfide, have attracted attention as major components of halitosis. However, these compounds cannot account for all odors. In this study, we profiled volatile compounds from the culture supernatants of periodontal bacteria using gas chromatography/mass spectrometry/olfactometry analysis with a monolithic silica gel adsorption device to investigate the potential odorous compounds. Periodontal bacteria have been found to produce volatile compounds belonging to various classes, such as alcohols, ketones, fatty acids, and aromatic compounds, in addition to VSCs. In addition, VSCs different from hydrogen sulfide and methanethiol, which are considered important causative compounds, may also influence to halitosis.
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Affiliation(s)
- Asuka Mori
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Moyu Taniguchi
- Osaka University Shimadzu Omics Innovation Research Laboratories, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masae Kuboniwa
- Department of Preventive Dentistry, Graduate School of Dentistry, Osaka University, 1-8 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Atsuo Amano
- Department of Preventive Dentistry, Graduate School of Dentistry, Osaka University, 1-8 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Osaka University Shimadzu Omics Innovation Research Laboratories, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiative, Osaka University, 1-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
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23
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Ohtake T, Kawase N, Pontrelli S, Nitta K, Laviña WA, Shen CR, Putri SP, Liao JC, Fukusaki E. Metabolomics-Driven Identification of the Rate-Limiting Steps in 1-Propanol Production. Front Microbiol 2022; 13:871624. [PMID: 35495658 PMCID: PMC9048197 DOI: 10.3389/fmicb.2022.871624] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 03/17/2022] [Indexed: 11/13/2022] Open
Abstract
The concerted effort for bioproduction of higher alcohols and other commodity chemicals has yielded a consortium of metabolic engineering techniques to identify targets to enhance performance of engineered microbial strains. Here, we demonstrate the use of metabolomics as a tool to systematically identify targets for improved production phenotypes in Escherichia coli. Gas chromatography/mass spectrometry (GC/MS) and ion-pair LC-MS/MS were performed to investigate metabolic perturbations in various 1-propanol producing strains. Two initial strains were compared that differ in the expression of the citramalate and threonine pathways, which hold a synergistic relationship to maximize production yields. While this results in increased productivity, no change in titer was observed when the threonine pathway was overexpressed beyond native levels. Metabolomics revealed accumulation of upstream byproducts, norvaline and 2-aminobutyrate, both of which are derived from 2-ketobutyrate (2KB). Eliminating the competing pathway by gene knockouts or improving flux through overexpression of glycolysis gene effectively increased the intracellular 2KB pool. However, the increase in 2KB intracellular concentration yielded decreased production titers, indicating toxicity caused by 2KB and an insufficient turnover rate of 2KB to 1-propanol. Optimization of alcohol dehydrogenase YqhD activity using an ribosome binding site (RBS) library improved 1-propanol titer (g/L) and yield (g/g of glucose) by 38 and 29% in 72 h compared to the base strain, respectively. This study demonstrates the use of metabolomics as a powerful tool to aid systematic strain improvement for metabolically engineered organisms.
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Affiliation(s)
- Toshiyuki Ohtake
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan
| | - Naoki Kawase
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan
| | - Sammy Pontrelli
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, United States
- Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland
| | - Katsuaki Nitta
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan
| | - Walter A. Laviña
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan
- Microbiology Division, Institute of Biological Sciences, University of the Philippines Los Baños, Los Baños, Philippines
| | - Claire R. Shen
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Sastia P. Putri
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan
- Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Osaka University Shimadzu Omics Innovation Research Laboratories, Osaka University, Suita, Japan
- *Correspondence: Sastia P. Putri,
| | - James C. Liao
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, United States
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan
- Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Osaka University Shimadzu Omics Innovation Research Laboratories, Osaka University, Suita, Japan
- Eiichiro Fukusaki,
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24
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Batubara I, SaadatulHusna S, Mohamad Rafi MR, Sumaryada T, Uchiyama S, Juliandi B, Sastia Prama Putri SPP, Fukusaki E. A Combination of UV-Vis Spectroscopy and Chemometrics for Detection of Sappanwood (Caesalpinia sappan) Adulteration from Three Dyes. SAINS MALAYS 2022. [DOI: 10.17576/jsm-2022-5103-11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Sappan wood (Caesalpinia sappan) is very well known as a natural dye for traditional food and beverage in many countries. Recently, there are many reports of sappan wood adulteration by adding synthetic or natural dyes to obtain quality color and better appearance. In this study, UV-Vis absorption spectra coupled with chemometrics were used to develop rapid detection of sappan wood raw material adulteration (authentication) from three dyes, i.e., sudan III, commercial textile dyes, and red yeast rice. Absorption spectra of 13 sappan wood raw material and adulterated sappan wood with the three dyes in two different concentrations which resulted about 78 adulterated samples were measured with UV-Vis spectrophotometer at a wavelength range of 200-800 nm. A principal component analysis followed by discriminant analysis was used to construct a model for the authentication of sappan wood from the three dyes used in this study. The combination of both methods was successfully classified sappan wood as non-adulterated and adulterated with the dyes. Cross-validation results of the authentication model of sappan wood from sudan III, commercial textile dyes, and red yeast rice were 94.12%, 94.12%, and 92.16% correctly classified into their groups, respectively.
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Parijadi AAR, Yamamoto K, Ikram MMM, Dwivany FM, Wikantika K, Putri SP, Fukusaki E. Metabolome Analysis of Banana (Musa acuminata) Treated With Chitosan Coating and Low Temperature Reveals Different Mechanisms Modulating Delayed Ripening. Front Sustain Food Syst 2022. [DOI: 10.3389/fsufs.2022.835978] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Banana (Musa acuminata) is one of the most important crop plants consumed in many countries. However, the commercial value decreases during storage and transportation. To maintain fruit quality, postharvest technologies have been developed. Storage at low temperature is a common method to prolong the shelf life of food products, especially during transportation and distribution. Another emerging approach is the use of chitosan biopolymer as an edible coating, which can extend the shelf life of fruit by preventing moisture and aroma loss, and inhibiting oxygen penetration into the plant tissue. Gas chromatography-mass spectrometry metabolite profiling of the banana ripening process was performed to clarify the global metabolism changes in banana after chitosan coating or storage at low temperature. Both postharvest treatments were effective in delaying banana ripening. Interestingly, principal component analysis and orthogonal projection to latent structure regression analysis revealed significant differences of both treatments in the metabolite changes, indicating that the mechanism of prolonging the banana shelf life may be different. Chitosan (1.25% w/v) treatment stored for 11 days resulted in a distinct accumulation of 1-aminocyclopropane-1-carboxylic acid metabolite, an important precursor of ethylene that is responsible for the climacteric fruit ripening process. Low temperature (LT, 14 ± 1°C) treatment stored for 9 days resulted in higher levels of putrescine, a polyamine that responds to plant stress, at the end of ripening days. The findings clarify how chitosan delays fruit ripening and provides a deeper understanding of how storage at low temperature affects banana metabolism. The results may aid in more effective development of banana postharvest strategies.
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Putri SLE, Suantika G, Situmorang ML, Putri SP, Fukusaki E. Metabolomics approach to elucidate the importance of count size in commercial penaeid shrimps: white leg shrimp (Litopenaeus vannamei) and black tiger shrimp (Penaeus monodon). J Biosci Bioeng 2022; 133:459-466. [DOI: 10.1016/j.jbiosc.2022.01.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 01/05/2022] [Accepted: 01/21/2022] [Indexed: 02/06/2023]
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27
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Putri SP, Ikram MMM, Sato A, Dahlan HA, Rahmawati D, Ohto Y, Fukusaki E. Application of gas chromatography-mass spectrometry-based metabolomics in food science and technology. J Biosci Bioeng 2022; 133:425-435. [DOI: 10.1016/j.jbiosc.2022.01.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 01/21/2022] [Accepted: 01/21/2022] [Indexed: 12/23/2022]
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28
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Helmi H, Astuti DI, Putri SP, Sato A, Laviña WA, Fukusaki E, Aditiawati P. Dynamic Changes in the Bacterial Community and Metabolic Profile during Fermentation of Low-Salt Shrimp Paste (Terasi). Metabolites 2022; 12:metabo12020118. [PMID: 35208193 PMCID: PMC8874951 DOI: 10.3390/metabo12020118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/19/2022] [Accepted: 01/19/2022] [Indexed: 11/24/2022] Open
Abstract
Low-salt shrimp paste, or terasi, is an Indonesian fermented food made from planktonic shrimp mixed with a low concentration of salt. Since high daily intake of sodium is deemed unhealthy, reduction of salt content in shrimp paste production is desired. Until now, there is no reported investigation on the bacterial population and metabolite composition of terasi during fermentation. In this study, the bacterial community of terasi was assessed using high-throughput sequencing of the 16S rRNA V3–V4 region. From this analysis, Tetragenococcus, Aloicoccus, Alkalibacillus, Atopostipes, and Alkalibacterium were found to be the dominant bacterial genus in low-salt shrimp paste. GC/MS-based metabolite profiling was also conducted to monitor the metabolite changes during shrimp paste fermentation. Results showed that acetylated amino acids increased, while glutamine levels decreased, during the fermentation of low-salt shrimp paste. At the start of shrimp paste fermentation, Tetragenococcus predominated with histamine and cadaverine accumulation. At the end of fermentation, there was an increase in 4-hydroxyphenyl acetic acid and indole-3-acetic acid levels, as well as the predominance of Atopostipes. Moreover, we found that aspartic acid increased during fermentation. Based on our findings, we recommend that fermentation of low-salt shrimp paste be done for 7 to 21 days, in order to produce shrimp paste that has high nutritional content and reduced health risk.
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Affiliation(s)
- Henny Helmi
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jalan Ganesha No.10, Bandung 40132, Indonesia; (H.H.); (D.I.A.); (S.P.P.)
- Department of Biology, Bangka Belitung University, Kampus Terpadu Balunijuk, Jalan Raya Balunijuk, Merawang, Bangka 33172, Indonesia
| | - Dea Indriani Astuti
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jalan Ganesha No.10, Bandung 40132, Indonesia; (H.H.); (D.I.A.); (S.P.P.)
| | - Sastia Prama Putri
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jalan Ganesha No.10, Bandung 40132, Indonesia; (H.H.); (D.I.A.); (S.P.P.)
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; (A.S.); (E.F.)
- Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka 565-0871, Japan
| | - Arisa Sato
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; (A.S.); (E.F.)
| | - Walter A. Laviña
- Microbiology Division, Institute of Biological Sciences, University of the Philippines Los Baños, Los Baños, Laguna 4031, Philippines;
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; (A.S.); (E.F.)
- Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka 565-0871, Japan
- Osaka University-Shimadzu Omics Innovation Research Laboratories, Osaka University, Osaka 565-0871, Japan
| | - Pingkan Aditiawati
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jalan Ganesha No.10, Bandung 40132, Indonesia; (H.H.); (D.I.A.); (S.P.P.)
- Correspondence: ; Tel.: +62-22-251-1575 or +62-22-250-0258
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29
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Taya N, Katakami N, Omori K, Arakawa S, Hosoe S, Watanabe H, Takahara M, Miyashita K, Nishizawa H, Matsuoka T, Furuno M, Bamba T, Iida J, Fukusaki E, Shimomura I. Evaluation of change in metabolome caused by comprehensive diabetes treatment: A prospective observational study of diabetes inpatients with gas chromatography/mass spectrometry-based non-target metabolomic analysis. J Diabetes Investig 2021; 12:2232-2241. [PMID: 34032389 PMCID: PMC8668060 DOI: 10.1111/jdi.13600] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 04/17/2021] [Accepted: 05/20/2021] [Indexed: 11/28/2022] Open
Abstract
AIMS/INTRODUCTION Diabetes patients develop a variety of metabolic abnormalities in addition to hyperglycemia. However, details regarding change in various metabolites after comprehensive diabetes treatment remain unknown. This study aimed to identify the short-term change in metabolome in inpatients who were subject to comprehensive diabetes treatment, using gas chromatography/mass spectrometry-based non-target metabolomics techniques. MATERIALS AND METHODS Participants of the present study were randomly recruited from the patients with type 2 diabetes hospitalized due to problems with glycemic control (n = 31) and volunteers without diabetes (n = 30), both of whom were aged between 20 and 75 years. A metabolomic analysis of fasting plasma samples on the 2nd (pre-treatment) and 16th hospital (post-treatment) day with gas chromatography/mass spectrometry using a multiple reaction monitoring mode was carried out. RESULTS A principal component analysis showed that metabolome of fasting plasma was different between individuals with and without diabetes. The metabolome of fasting plasma in diabetes patients after treatment was different from that of pre-treatment, as well as individuals without diabetes. Many amino acids (proline, glycine, serine, threonine, methionine, pyroglutamic acid, glutamine and lysine) were significantly increased by >10% after administering the inpatient diabetes treatment. A hierarchical clustering analysis showed that in the case of patients with markedly decreased monosaccharide levels and increased 1,5-anhydroglucitol, the levels of amino acids increased more significantly. CONCLUSIONS After a 2-week comprehensive treatment, the plasma levels of various amino acids increased in conjunction with the reduction in monosaccharide levels in poorly controlled type 2 diabetes patients.
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Affiliation(s)
- Naohiro Taya
- Department of Metabolic MedicineOsaka University Graduate School of MedicineOsakaJapan
| | - Naoto Katakami
- Department of Metabolic MedicineOsaka University Graduate School of MedicineOsakaJapan
- Department of Metabolism and AtherosclerosisOsaka University Graduate School of MedicineOsakaJapan
| | - Kazuo Omori
- Department of Metabolic MedicineOsaka University Graduate School of MedicineOsakaJapan
| | - Shoya Arakawa
- Laboratory of Bioresource EngineeringDepartment of BiotechnologyGraduate School of EngineeringOsaka UniversityOsakaJapan
| | - Shigero Hosoe
- Department of Metabolic MedicineOsaka University Graduate School of MedicineOsakaJapan
| | - Hirotaka Watanabe
- Department of Metabolic MedicineOsaka University Graduate School of MedicineOsakaJapan
| | - Mitsuyoshi Takahara
- Department of Metabolic MedicineOsaka University Graduate School of MedicineOsakaJapan
- Department of Diabetes Care MedicineGraduate School of MedicineOsaka UniversityOsakaJapan
| | - Kazuyuki Miyashita
- Department of Metabolic MedicineOsaka University Graduate School of MedicineOsakaJapan
| | - Hitoshi Nishizawa
- Department of Metabolic MedicineOsaka University Graduate School of MedicineOsakaJapan
| | - Taka‐Aki Matsuoka
- Department of Metabolic MedicineOsaka University Graduate School of MedicineOsakaJapan
| | - Masahiro Furuno
- Laboratory of Bioresource EngineeringDepartment of BiotechnologyGraduate School of EngineeringOsaka UniversityOsakaJapan
| | - Takeshi Bamba
- Division of MetabolomicsResearch Center for Transomics MedicineMedical Institute of BioregulationKyushu UniversityFukuokaJapan
| | - Junko Iida
- Shimadzu CorporationKyotoJapan
- Osaka University Shimadzu Omics Innovation Research LaboratoriesGraduate School of EngineeringOsaka UniversityOsakaJapan
| | - Eiichiro Fukusaki
- Laboratory of Bioresource EngineeringDepartment of BiotechnologyGraduate School of EngineeringOsaka UniversityOsakaJapan
| | - Iichiro Shimomura
- Department of Metabolic MedicineOsaka University Graduate School of MedicineOsakaJapan
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Rahmawati D, Astawan M, Putri SP, Fukusaki E. Gas chromatography-mass spectrometry-based metabolite profiling and sensory profile of Indonesian fermented food (tempe) from various legumes. J Biosci Bioeng 2021; 132:487-495. [PMID: 34465490 DOI: 10.1016/j.jbiosc.2021.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 07/02/2021] [Accepted: 07/05/2021] [Indexed: 12/21/2022]
Abstract
Tempe is an Indonesian fermented food prepared from soybean or other non-soy legumes. Non-soy legumes based tempes have been reported to have a nutritional profile different from that of soybean-based tempe. However, a comprehensive study of the metabolite and sensory profiles of legume tempes has not been conducted. This study investigated the metabolite profile of legumes before and after fermentation using a metabolomic approach and its relation to the sensory profile. Four different legumes, namely red kidney bean, soybean, cowpea bean, and jack bean, and four kinds of tempe prepared from the abovementioned legumes were subjected to gas chromatography-mass spectrometry (GC-MS) analysis. These tempe samples were fermented in two different production places, Japan and Indonesia. In total, 83 metabolites were annotated from all samples. Principal component analysis (PCA) showed that the samples were separated based on their type (legume and tempe) along PC1 with a 36.3% variance, in which sugars and amino acids significantly contributed to the separation. In addition, samples were separated along PC2 with a 17.2% variance based on the different production places. The combination of 75% soybean and 25% red kidney bean (75S:25R) could increase the concentrations of amino acids that were initially low in soybean tempe. The 75S:25R tempe showed no significant differences in taste and texture preference compared to the 100% soybean tempe, based on sensory result. These findings provide evidence that metabolomics could be used to identify the differences between tempes from different legumes.
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Affiliation(s)
- Della Rahmawati
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Department of Food Technology, Faculty of Life Science and Technology, Swiss German University, Tangerang, Banten 15143, Indonesia
| | - Made Astawan
- Department of Food Science and Technology, Faculty of Agricultural Engineering and Technology, IPB University, Jl. Raya Dramaga, Bogor, Jawa Barat 16680, Indonesia
| | - Sastia Prama Putri
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Industrial Biotechnology Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Industrial Biotechnology Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Osaka University Shimadzu Omics Innovation Research Laboratories, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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Sato M, Ikram MMM, Pranamuda H, Agusta W, Putri SP, Fukusaki E. Characterization of five Indonesian mangoes using gas chromatography-mass spectrometry-based metabolic profiling and sensory evaluation. J Biosci Bioeng 2021; 132:613-620. [PMID: 34656425 DOI: 10.1016/j.jbiosc.2021.09.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 08/30/2021] [Accepted: 09/07/2021] [Indexed: 01/13/2023]
Abstract
Indonesia is one of the world's leading mango producers and grows many cultivars. However, only a few cultivars have been commercialized, perhaps because of limited information on consumer preferences that meet the market demands. Here, non-targeted gas chromatography-mass spectrometry (GC-MS)-based metabolome analysis was used to characterize five Indonesian mango cultivars considering their taste characteristics. A total of 95 components (47 annotated and 48 unknown metabolites) were identified. Cultivars with a higher general impression score (Arumanis 143 and Gedong) in principal component analysis (PCA) accumulated more sugars and sweetening components, such as glycine and lyxose. Meanwhile, cultivars with a lower general impression score in PCA (Lalijiwo and Cengkir Indramayu) accumulated more aspartic acid, isocitric acid, and citric acid, which increase sourness; methionine, which is a precursor of sulfur-containing volatile aroma components; and phenylalanine, which contributes to bitterness. Furthermore, orthogonal projection to latent structures discriminant analysis revealed that nicotinic acid, glutamic acid, aspartic acid, glycine, and ribose characterized higher or lower general impression cultivars. In addition, metabolic profiling of eight mango cultivars, including five Indonesian and three overseas cultivars, suggested that taste was more influential than differences in cultivars, production areas, and cultivation conditions by its hydrophilic primary metabolomics. These findings will serve as fundamental data for future mango industry development considering the association between the unique taste of each cultivar and its metabolites as well as the consumer preferences for Indonesian mango.
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Affiliation(s)
- Miwa Sato
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Miyazaki Agricultural Research Institute, 5805 Shimonaka, Sadowara-cho, Miyazaki 880-0212, Japan
| | - Muhammad Maulana Malikul Ikram
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hardaning Pranamuda
- Center of Technology for Agroindustry, Gedung 610-612, LAPTIAB-BPPT, PUSPIPTEK, Serpong, Banten 15314, Indonesia
| | - Waqif Agusta
- Center of Technology for Agroindustry, Gedung 610-612, LAPTIAB-BPPT, PUSPIPTEK, Serpong, Banten 15314, Indonesia
| | - Sastia Prama Putri
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan.
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan; Osaka University-Shimadzu Omics Innovation Research Laboratories, Osaka University, Suita, Osaka, Japan
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Yamamoto K, Taniguchi M, Nakahara T, Ito Y, Sasano R, Fukusaki E. Metabolomic investigation of differences in components and taste between hon-mirin and mirin-like-seasoning. J Biosci Bioeng 2021; 132:599-605. [PMID: 34607774 DOI: 10.1016/j.jbiosc.2021.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 08/14/2021] [Accepted: 08/24/2021] [Indexed: 10/20/2022]
Abstract
Hon-mirin (HM) is a traditional Japanese brewed seasoning used to confer sweetness and koku. Mirin-like-seasoning (MLS) is a less-expensive alternative to HM because it is not subjected to liquor tax in Japan. In this study, components and taste qualities of HM and MLS were compared by gas chromatography/mass spectrometry (GC/MS)-based metabolomics and a sensory evaluation. GC/MS analyses of foods with high sugar content are limited by contamination of the ion source and difficulty in detecting other compounds. To resolve this issue, solid-phase analytical derivatization (SPAD), in which the extraction and derivatization of analytes can be conducted in a single step, was applied as a novel sample preparation method in this study. The effect of sugar was removed by the specific absorption, derivatization, and elution of ionic compounds, such as amino acids and organic acids, with ion-exchange solid-phases. The SPAD method application enabled the detection of 15 amino acids and 14 organic acids using ion-exchange solid-phases by performing GC/MS analysis twice. These ionic compounds were not detected in mirin using conventional sample preparation. HM samples had a higher amino acid content and a lower sugar content than those of MLS samples. Furthermore, differences in sweetness and koku between HM and MLS were observed in a sensory evaluation. This is the first GC/MS-based metabolomics analysis of mirin using the SPAD method; our results provide insight into the differences between HM and MLS.
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Affiliation(s)
- Kana Yamamoto
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Moyu Taniguchi
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takeharu Nakahara
- Research and Development Division, Kikkoman Corporation, 338 Noda, Noda, Chiba 278-0037, Japan
| | - Yusuke Ito
- Research and Development Division, Kikkoman Corporation, 338 Noda, Noda, Chiba 278-0037, Japan
| | - Ryoichi Sasano
- AiSTI SCIENCE CO., Ltd., 120-6 Kuroda, Wakayama, Wakayama 640-8341, Japan
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
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Ikram MMM, Mizuno R, Putri SP, Fukusaki E. Comparative metabolomics and sensory evaluation of pineapple (Ananas comosus) reveal the importance of ripening stage compared to cultivar. J Biosci Bioeng 2021; 132:592-598. [PMID: 34593317 DOI: 10.1016/j.jbiosc.2021.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/17/2021] [Accepted: 08/23/2021] [Indexed: 12/31/2022]
Abstract
The pineapple ripening stage is determined at the time of harvest and can be classified into the C0 to C4 stage based on its peel color. C1 and C4 pineapples are the most commonly exported products with high demand. Pineapple also has many cultivars with different tastes and appearances. However, there are limited studies regarding the metabolite and taste profiles of pineapple from different cultivars and ripening stages using a metabolomics approach. Therefore, the objective of this study was to investigate the metabolite and sensory profiles of pineapple from different cultivars and different ripening stages. Three cultivars of pineapple (Red Spanish, Smooth Cayenne, and Queen) and C1, C3, and C4 stages from Indonesia, Japan, the Philippines, and Taiwan, respectively, were analyzed by gas chromatography/mass spectrometry (GC/MS). The data obtained from GC/MS analysis were combined with the data obtained from sensory evaluation, which showed that sourness and firmness contributed to C1 fruits with metabolites correlated to isocitric acid+citric acid, malic acid, ascorbic acid, and quinic acid, while sweetness, juiciness, and high acceptability contributed to C4 fruits with metabolites that correlated were asparagine, serine, glycine, threonic acid, sucrose, and 5-hydroxytryptamine. GC/MS analysis using different pineapple cultivars also showed characteristic metabolites for each cultivar. Prediction of the sensory profile was performed by investigating the relative intensity of taste-related metabolites. This information can provide a basis for improving pineapple taste quality related to metabolites, depending on the cultivar and ripening stage.
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Affiliation(s)
- Muhammad Maulana Malikul Ikram
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Reo Mizuno
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Sastia Prama Putri
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan.
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan; Osaka University-Shimadzu Omics Innovation Research Laboratories, Osaka University, Suita, Osaka, Japan
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Sakanaka A, Kuboniwa M, Katakami N, Furuno M, Nishizawa H, Omori K, Taya N, Ishikawa A, Mayumi S, Tanaka Isomura E, Shimomura I, Fukusaki E, Amano A. Saliva and Plasma Reflect Metabolism Altered by Diabetes and Periodontitis. Front Mol Biosci 2021; 8:742002. [PMID: 34589520 PMCID: PMC8473679 DOI: 10.3389/fmolb.2021.742002] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/25/2021] [Indexed: 12/28/2022] Open
Abstract
Periodontitis is an inflammatory disorder caused by disintegration of the balance between the periodontal microbiome and host response. While growing evidence suggests links between periodontitis and various metabolic disorders including type 2 diabetes (T2D), non-alcoholic liver disease, and cardiovascular disease (CVD), which often coexist in individuals with abdominal obesity, factors linking periodontal inflammation to common metabolic alterations remain to be fully elucidated. More detailed characterization of metabolomic profiles associated with multiple oral and cardiometabolic traits may provide better understanding of the complexity of oral-systemic crosstalk and its underlying mechanism. We performed comprehensive profiling of plasma and salivary metabolomes using untargeted gas chromatography/mass spectrometry to investigate multivariate covariation with clinical markers of oral and systemic health in 31 T2D patients with metabolic comorbidities and 30 control subjects. Orthogonal partial least squares (OPLS) results enabled more accurate characterization of associations among 11 oral and 25 systemic clinical outcomes, and 143 salivary and 78 plasma metabolites. In particular, metabolites that reflect cardiometabolic changes were identified in both plasma and saliva, with plasma and salivary ratios of (mannose + allose):1,5-anhydroglucitol achieving areas under the curve of 0.99 and 0.92, respectively, for T2D diagnosis. Additionally, OPLS analysis of periodontal inflamed surface area (PISA) as the numerical response variable revealed shared and unique responses of metabolomic and clinical markers to PISA between healthy and T2D groups. When combined with linear regression models, we found a significant correlation between PISA and multiple metabolites in both groups, including threonate, cadaverine and hydrocinnamate in saliva, as well as lactate and pentadecanoic acid in plasma, of which plasma lactate showed a predominant trend in the healthy group. Unique metabolites associated with PISA in the T2D group included plasma phosphate and salivary malate, while those in the healthy group included plasma gluconate and salivary adenosine. Remarkably, higher PISA was correlated with altered hepatic lipid metabolism in both groups, including higher levels of triglycerides, aspartate aminotransferase and alanine aminotransferase, leading to increased risk of cardiometabolic disease based on a score summarizing levels of CVD-related biomarkers. These findings revealed the potential utility of saliva for evaluating the risk of metabolic disorders without need for a blood test, and provide evidence that disrupted liver lipid metabolism may underlie the link between periodontitis and cardiometabolic disease.
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Affiliation(s)
- Akito Sakanaka
- Department of Preventive Dentistry, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Masae Kuboniwa
- Department of Preventive Dentistry, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Naoto Katakami
- Department of Metabolic Medicine, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Masahiro Furuno
- Department of Biotechnology, Osaka University Graduate School of Engineering, Osaka, Japan
| | - Hitoshi Nishizawa
- Department of Metabolic Medicine, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Kazuo Omori
- Department of Metabolic Medicine, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Naohiro Taya
- Department of Metabolic Medicine, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Asuka Ishikawa
- Department of Preventive Dentistry, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Shota Mayumi
- Department of Preventive Dentistry, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Emiko Tanaka Isomura
- First Department of Oral and Maxillofacial Surgery, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Iichiro Shimomura
- Department of Metabolic Medicine, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Eiichiro Fukusaki
- Department of Biotechnology, Osaka University Graduate School of Engineering, Osaka, Japan
| | - Atsuo Amano
- Department of Preventive Dentistry, Osaka University Graduate School of Dentistry, Osaka, Japan
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Amalia F, Aditiawati P, Yusianto, Putri SP, Fukusaki E. Gas chromatography/mass spectrometry-based metabolite profiling of coffee beans obtained from different altitudes and origins with various postharvest processing. Metabolomics 2021; 17:69. [PMID: 34254180 DOI: 10.1007/s11306-021-01817-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 07/02/2021] [Indexed: 11/29/2022]
Abstract
INTRODUCTION Coffee is a popular beverage because of its pleasant aroma and distinctive flavor. The flavor of coffee results from chemical transformations influenced by various intrinsic and extrinsic factors, including altitude, geographical origin, and postharvest processing. Despite is the importance of grading coffee quality, there is no report on the dominant factor that influences the metabolomic profile of green coffee beans and the correlated metabolites for each factor. OBJECTIVE This study investigated the total metabolite profile of coffees from different altitudes and coffees subjected to different postharvest processing. METHOD Arabica green coffee beans obtained from different geographical origins and different altitudes (400 and 800 m) and produced by different postharvest processes (dry, honey, and washed process) were used in this study. Coffee samples obtained from altitudes of 400-1600 m above sea level from various origins that were produced by the washed method were used for further study with regard to altitudes. Samples were subjected to gas chromatography/mass spectrometry (GC/MS) analysis and visualized using principal component analysis (PCA) and orthogonal partial least squares (OPLS) regression analysis. RESULTS The PCA results showed sample separation based on postharvest processing in PC1 and sample separation based on altitude in PC2. A clear separation between samples from different altitudes was observed if the samples were subjected to the same postharvest processing method, and the samples were of the same origin. Based on this result, OPLS analysis was conducted using coffee samples obtained from various altitudes with the same postharvest processing. An OPLS model using altitude as a response variable and 79 metabolites annotated from the GC/MS analysis as an explanatory variable was constructed with good R2 and Q2 values. CONCLUSION Postharvest processing was found to be the dominant factor affecting coffee metabolite composition; this was followed by geographical origin and altitude. The metabolites glutamic acid and galactinol were associated with the washed and honey process, while glycine, lysine, sorbose, fructose, glyceric acid, and glycolic acid were associated with the dry process. Two metabolites with high variable influence on projection scores in the OPLS model for altitude were inositol and serotonin, which showed positive and negative correlations, respectively. This is the first study to report characteristic coffee metabolites obtained from different altitudes.
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Affiliation(s)
- Fitri Amalia
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Pingkan Aditiawati
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No.10, Lb. Siliwangi, Coblong, Kota Bandung, Jawa Barat, 40132, Indonesia
| | - Yusianto
- Indonesian Coffee and Cocoa Research Institute, Jl. PB. Sudirman 90, Jember, Indonesia
| | - Sastia Prama Putri
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No.10, Lb. Siliwangi, Coblong, Kota Bandung, Jawa Barat, 40132, Indonesia.
- Industrial Biotechnology Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Industrial Biotechnology Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Osaka University Shimadzu Omics Innovation Research Laboratories, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
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Takeo E, Sugiura Y, Ohnishi Y, Kishima H, Fukusaki E, Shimma S. Mass Spectrometric Enzyme Histochemistry for Choline Acetyltransferase Reveals De Novo Acetylcholine Synthesis in Rodent Brain and Spinal Cord. ACS Chem Neurosci 2021; 12:2079-2087. [PMID: 34078081 DOI: 10.1021/acschemneuro.0c00720] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Choline acetyltransferase (ChAT), responsible for the synthesis of acetylcholine, plays an important role in neurotransmission. However, no method to visualize the ChAT activity in tissues has been reported to date. In this study, mass spectrometry imaging (MSI) was used to visualize ChAT activity in situ, which is difficult with conventional enzyme histochemistry. By using choline chloride-trimethyl-d9 (choline-d9) as a substrate and simultaneously supplying an inhibitor of cholinesterase to tissues, we succeeded in directly visualizing the ChAT activity in the rodent brain and spinal cord. The findings revealed heterogeneous ChAT activity in the striatum of the mouse brain and in the spinal lower motor neurons that connect the anterior horn to the ventral root. Furthermore, extending the developed method to spinal cord injury (SCI) model mice revealed the site-specific effect of primary and secondary injury on ChAT activity. This study shows that the MSI-based enzyme histochemistry of ChAT could be a useful tool for studying cholinergic neurons.
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Affiliation(s)
- Emi Takeo
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yuki Sugiura
- Department of Biochemistry, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Yuichiro Ohnishi
- Department of Neurosurgery, Graduate school of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Haruhiko Kishima
- Department of Neurosurgery, Graduate school of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shuichi Shimma
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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Ohto Y, Putri SP, Suantika G, Fukusaki E. Investigation of the characteristics of different shrimps by species and habitat using gas chromatography/mass spectrometry based metabolomics. J Biosci Bioeng 2021; 132:258-264. [PMID: 34127378 DOI: 10.1016/j.jbiosc.2021.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 04/19/2021] [Accepted: 04/20/2021] [Indexed: 11/18/2022]
Abstract
Approximately 6.5 million tons of shrimp are consumed annually worldwide. The price of shrimp is greatly influenced by species and habitat (e.g., farmed vs wild-caught). In recent years, false labeling has become a problem in the shrimp industry. False labeling can include species, habitat (whether farmed or wild-caught). This problem is motivated by the potential for economic benefit, and significantly reduces the consumer reliability of food. As a first step in establishing a detection method, we took a metabolomics approach to elucidate phenotypic diversity by assessing genetic differences and environmental factors. Metabolites identified by gas chromatography/mass spectrometry (GC/MS) analysis were subjected to multivariate analysis to identify metabolites that correlated with shrimp species and habitat. The characteristics based on species and habitat were observed respectively. For species, the classification approximately tended to be based on taxonomy. It suggests that species different have strong effect on metabolite profiles. In particular, the difference between Panaediae and Pandalidae was significantly observed, and some fatty acids such as palmitoleic acid and elaidic acid are abundant in Pandalidae. Among Pandalidae, Japanese tiger shrimp was characterized by metabolites related to purine metabolism. For habitat, farmed shrimp had a high amino acid content, and wild caught shrimp had a high fatty acid content. Habitat-based separation was observed in Indonesian black tiger shrimp samples, indicating that metabolites such as glycolic acid, phosphate, and pentadecanoic acid are characteristic components of natural black tiger shrimp.
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Affiliation(s)
- Yukina Ohto
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Sastia P Putri
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Gede Suantika
- School of Life Sciences and Technology, Bandung Institute of Technology, Bandung, Jawa Barat 40132, Indonesia
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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Mohamad Rafi MR, Bayu Nurcahyo BN, Wahyuni WT, Arif Z, Septaningsih DA, Sastia Prama Putri SPP, Fukusaki E. Feasibility of UV-Vis Spectral Fingerprinting Combined with Chemometrics for Rapid Detection of Phyllanthus niruri Adulteration with Leucaena leucocephala. SAINS MALAYS 2021. [DOI: 10.17576/jsm-2021-5004-10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Phyllanthus niruri is widely used in Indonesia as immunostimulant. The morphology of Leucaena leucocephala leaves is similar to that of P. niruri leaves. L. leucocephala is easy to find and collect because it is widely distributed in the world. Therefore, it is likely P. niruri could be adulterated with L. leucocephala. Therefore, identification and authentication of P. niruri is important to ensure the raw materials used are original without any substitution or mixture with other similar plants causing inconsistencies in their efficacy. In this paper, we described feasibility used of UV-Vis spectral fingerprinting and chemometrics for rapid method for the identification and detection of P. niruri leaves adulterated with L. leucocephala leaves. UV-Vis spectra of samples measured in the interval of 200-800 nm and signal smoothing followed by standard normal variate were used for pre-processing the spectral data. Principal component analysis (PCA)with the absorbance data from the pre-processed UV-Vis spectra in the range of 250-700 nm as variables could distinguish P. niruri from L. leucocephala. PCA followed by discriminant analysis (DA) could successfully classified P. niruri mixed with 5, 25, and 50% L. luecocephala into their respective groups (96.81%). We also employed soft independent modelling of class analogy (SIMCA) for authentication of P. niruri and found that 88.3% of the samples were also correctly classified into their respective groups. A combination of UV-Vis spectroscopy with chemometrics, such as PCA-DA and SIMCA, were used for the first time for the identification and detection of P. niruri adulterated with L. leucocephala.
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Arakawa S, Furuno M, Fukusaki E. Minimization of adverse effects of blank matrices from various apparatuses in the downsizing of gas chromatography-mass spectrometry-based metabolomics. J Biosci Bioeng 2021; 132:102-107. [PMID: 33879405 DOI: 10.1016/j.jbiosc.2021.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 02/23/2021] [Accepted: 03/10/2021] [Indexed: 10/21/2022]
Abstract
The ability to reduce sample volume required for gas chromatography-mass spectrometry (GC/MS) metabolome analyses is limited by the effects of blank matrices. In this study, a GC/MS metabolome analytical method requiring only 5 μL of plasma obtained by fingertip puncture, was developed, while minimizing the adverse effects of blank matrices. The applicability of the newly developed method was investigated using mice tail venous blood. Removing the effects of blank matrices greatly affected the detection repeatability for trace amounts. The newly developed method has higher metabolite coverage and higher sensitivity than those of the conventional method. This study is the first to demonstrate that comparable, or improved, metabolome profile data can be obtained with one-tenth the plasma volume required for the conventional method.
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Affiliation(s)
- Shoya Arakawa
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masahiro Furuno
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
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Hayashi Y, Komatsu T, Iwashita K, Fukusaki E. 1H-NMR metabolomics-based classification of Japanese sake and comparative metabolome analysis by gas chromatography-mass spectrometry. J Biosci Bioeng 2021; 131:557-564. [PMID: 33593699 DOI: 10.1016/j.jbiosc.2020.12.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 12/03/2020] [Accepted: 12/11/2020] [Indexed: 11/25/2022]
Abstract
Six categories of Japanese sake have been established by the National Tax Agency of Japan. In this system, the rice polishing ratio and the addition of alcohol are the main criteria for classification. The most common nuclear magnetic resonance (NMR) spectrometry method is 1H-NMR, and has higher throughput than gas chromatography-mass spectrometry (GC-MS) or liquid chromatography-mass spectrometry (LC-MS) analysis due to its short measurement time, easy sample preparation, and high reproducibility. However, owing to the production of dominant ethanol signals, metabolome analyses have not been used for classifying Japanese sake using 1H-NMR. In this study, a technique to selectively suppress ethanol signals was used to classify Japanese sake by 1H-NMR, and a model was constructed to predict the rice polishing ratio. The results were compared to those obtained by GC-MS. The suppression of ethanol signals enabled the detection of trace components by 1H-NMR. In a principal component analysis (PCA) score plot of 1H-NMR spectra with ethanol signal suppression, PC1 was associated with both the addition of alcohol and the rice polishing ratio. Additionally, the separation of samples observed was similar when PCA score plots of 1H-NMR and GC-MS data were compared. Similarly, to predict the rice polishing ratio using partial least squares regression analysis, a model was constructed using 1H-NMR data, and showed nearly similar values for precision and predictive performance with the model constructed using GC-MS data. These results suggest that metabolomic analyses of Japanese sake based on 1H-NMR spectral patterns may be useful for classification.
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Affiliation(s)
- Yuji Hayashi
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takanori Komatsu
- Application Group, Marketing Division, JEOL Resonance Inc., 1-2 Musashino 3- Chome Akishima, Tokyo 196-8558, Japan
| | - Kazuhiro Iwashita
- National Research Institute of Brewing, 3-7-1, Kagamiyama, Higashihiroshima, Hiroshima 739-0046, Japan
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
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Terada H, Kuroda I, Uzu H, Ohira M, Yoshikawa K, Furuno M, Fukusaki E, Tanaka N. Reduction of the extra-column band dispersion by a slow transport and splitting of a sample band in isocratic reversed-phase liquid chromatography. J Chromatogr A 2021; 1641:461996. [PMID: 33640804 DOI: 10.1016/j.chroma.2021.461996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 02/05/2021] [Accepted: 02/08/2021] [Indexed: 11/26/2022]
Abstract
Sample introduction method was studied to reduce the extra-column effect in reversed-phase HPLC. Slow transport of a sample band (SToSB) in the pre-column space followed by the introduction of the band into the column at a near-optimum flow rate resulted in larger plate counts for a 1.0 mmID, 5 cm long column as much as 1.4-1.6 times for solutes with a retention factor (k) of 0.5-1.8 compared to a conventional elution method. Further reduction of the extra-column effect was possible by orthogonally splitting the sample band (SplSB) by flow switching during its slow transport followed by the introduction of the leading part of the band into the column. In this case, increased plate counts of up to 2-3 times for solutes with k of 0.5-1.8 were observed for a 1.0 mmID, 5 cm column. The sample introduction method, SToSB in the injector and the pre-column tube of a few μL, was found to reduce the extra-column band variance by 0.4-0.5 μL2 for an UHPLC system with the extra-column volume (Vextra) of ca. 4.6 μL and the system variance (σextra2) of 1.1 μL2 at flow rate of 100 μL/min, while SToSB and subsequent SplSB were found to be more effective, reducing σextra2 by about 0.8 μL2. With an UHPLC instrument with Vextra of about 10 μL and σextra2 of ca. 3.6 μL2 at flow rate of 300 μL/min, 1.4-2.1 times as many plate counts were observed with SToSB and SplSB compared to the normal elution method for early-eluting solutes with k=0.25-1.7 for a column, 2.1 mmID, 5 cm long. With this UHPLC instrument, SToSB and/or SplSB resulted in the reduction of σextra2 by 1.2-2.2 μL2.
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Affiliation(s)
- Hidetoshi Terada
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Osaka University Shimadzu Omics Innovation Research Laboratories, Osaka University, Suita, Osaka, 565-0871, Japan; Shimadzu Corporation, 1 Nishinokyo Kuwabara-cho, Nakagyo-ku, Kyoto 604-8511, Japan
| | - Ikuma Kuroda
- GL Sciences Inc., 237-2 Sayamagahara, Iruma, Saitama 358-0032, Japan
| | - Hideyuki Uzu
- GL Sciences Inc., 237-2 Sayamagahara, Iruma, Saitama 358-0032, Japan
| | - Masayoshi Ohira
- GL Sciences Inc., 237-2 Sayamagahara, Iruma, Saitama 358-0032, Japan
| | - Kohei Yoshikawa
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masahiro Furuno
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Osaka University Shimadzu Omics Innovation Research Laboratories, Osaka University, Suita, Osaka, 565-0871, Japan.
| | - Nobuo Tanaka
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; GL Sciences Inc., 237-2 Sayamagahara, Iruma, Saitama 358-0032, Japan.
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Nitta K, Breitling R, Takano E, Putri SP, Fukusaki E. Investigation of the effects of actinorhodin biosynthetic gene cluster expression and a rpoB point mutation on the metabolome of Streptomyces coelicolor M1146. J Biosci Bioeng 2021; 131:525-536. [PMID: 33549493 DOI: 10.1016/j.jbiosc.2021.01.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 01/12/2021] [Accepted: 01/13/2021] [Indexed: 02/07/2023]
Abstract
The previously reported Streptomyces coelicolor M1146 is commonly used as a host strain for engineering of secondary metabolite production. In this study, absolute quantification of intracellular and extracellular metabolites of M1146 was performed in mid-log phase and stationary phase to observe major metabolites and the changes that occurred during growth. Decreased levels of central carbon metabolites (glycolysis, TCA cycle, and pentose phosphate pathway) and increased levels of amino acids were observed in stationary phase compared to mid-log phase. Furthermore, comparative metabolome analyses of M1146 upon expression of the actinorhodin biosynthetic gene cluster (M1146+ACT), a point mutation on the rpoB gene encoding RNA polymerase beta-subunit (M1152), and both expression of actinorhodin biosynthetic gene cluster and a rpoB point mutation (M1152+ACT) were performed. M1146+ACT showed higher levels of important cofactors, such as ATP, NADPH, and FMN while M1152 led to higher levels of intracellular S-adenosyl-methionine, acyl-CoAs, and extracellular nucleosides compared to M1146. M1152+ACT exhibited the highest levels of actinorhodin with elevated bases, nucleosides, and nucleotides, such as intracellular PRPP (phosphoribosyl phosphate), ATP, along with extracellular inosine, uridine, and guanine compared to the other three strains, which were considered to be combined effects of actinorhodin gene cluster expression and a rpoB point mutation. Metabolites analysis by means of absolute quantification demonstrated changes in precursors of secondary metabolites before and after phosphate depletion in M1146. Comparative metabolome analysis provided further insights into the effects of actinorhodin gene cluster expression along with a rpoB point mutation on the metabolome of S. coelicolor.
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Affiliation(s)
- Katsuaki Nitta
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Rainer Breitling
- Manchester Institute of Biotechnology, Manchester Synthetic Biology Research Centre SYNBIOCHEM, Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Eriko Takano
- Manchester Institute of Biotechnology, Manchester Synthetic Biology Research Centre SYNBIOCHEM, Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Sastia P Putri
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
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Putri SLE, Suantika G, Situmorang ML, Christina J, Nikijuluw C, Putri SP, Fukusaki E. Shrimp count size: GC/MS-based metabolomics approach and quantitative descriptive analysis (QDA) reveal the importance of size in white leg shrimp (Litopenaeus vannamei). Metabolomics 2021; 17:19. [PMID: 33515101 DOI: 10.1007/s11306-020-01766-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 12/26/2020] [Indexed: 11/25/2022]
Abstract
INTRODUCTION "Count size" is a term used to represent the number of shrimps in one pound or kilogram that applies globally in the shrimp industry. Based on shrimp body weight, count sizes range over the smallest (> 70) up to the largest size (U15) of shrimp. Large shrimps are considered highly palatable; therefore, they are priced higher than the small shrimps. However, the pricing of shrimp has not been based on scientific findings since there have been no studies reporting the correlation between shrimp quality and shrimp size. OBJECTIVE In this study, we aimed to investigate the importance of shrimp size in terms of metabolite profile and sensory properties. METHODS Nine groups of Litopenaeus vannamei, categorized based on their body weight similarity, were collected from various sampling sites regardless of the difference in days of culture (count size 16/20, 21/25, 26/30, 41/50, and 51/60). Gas chromatography/mass spectrometry (GC/MS)-based metabolomics analysis was employed to characterize their metabolite profiles. Furthermore, a robust PLS regression model was constructed to predict the shrimp size using metabolome data. Following this, the difference in sensory attributes among commercial shrimp count sizes 21/25-41/50 was confirmed using quantitative descriptive analysis (QDA). RESULTS Small shrimp (> 70-51/60) had higher accumulation of proteinogenic and non-proteinogenic amino acids, sugars, and organic acids compared to large shrimps (41/50-16/20). The QDA of commercial count sizes (21/25-41/50) performed by trained panelists showed that sweetness, juiciness, crispness, and red color attributes increased with an increase in shrimp size. Based on the PLS model, proline as a sweet-tasting metabolite also showed an increased level along with the shrimp size. CONCLUSIONS These findings demonstrate the importance of shrimp count size with regard to shrimp quality.
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Affiliation(s)
- Safira Latifa Erlangga Putri
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Gede Suantika
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jalan Ganesha No. 10, Bandung, 40132, Indonesia
| | - Magdalena Lenny Situmorang
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jalan Ganesha No. 10, Bandung, 40132, Indonesia
| | - Josephine Christina
- Department of Food Science and Nutrition, School of Life Sciences, Indonesia International Institute for Life Sciences, Jl. Pulomas Barat No.Kav. 88, Jakarta, 13210, Indonesia
| | - Corazon Nikijuluw
- Department of Food Technology, School of Life Sciences, Indonesia International Institute for Life Sciences, Jl. Pulomas Barat No. Kav. 88, Jakarta, 13210, Indonesia
| | - Sastia Prama Putri
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
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Dissook S, Putri SP, Fukusaki E. Metabolomic Analysis of Response to Nitrogen-Limiting Conditions in Yarrowia spp. Metabolites 2020; 11:metabo11010016. [PMID: 33383744 PMCID: PMC7823547 DOI: 10.3390/metabo11010016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/16/2020] [Accepted: 12/24/2020] [Indexed: 11/26/2022] Open
Abstract
Yarrowia is a yeast genus that has been used as a model oleaginous taxon for a wide array of studies. However, information regarding metabolite changes within Yarrowia spp. under different environmental conditions is still limited. Among various factors affecting Yarrowia metabolism, nitrogen-limiting conditions have a profound effect on the metabolic state of yeast. In this study, a time-course LC-MS/MS-based metabolome analysis of Y. lipolytica was performed to determine the optimal cultivation time and carbon-to-nitrogen ratio for studying the effects of nitrogen-limiting conditions on Yarrowia; we found that cultivation time of 36 h and carbon-to-nitrogen ratio of 4:1 and 5:0 was suitable for studying the effects of nitrogen-limiting conditions on Yarrowia and these conditions were applied to six strains of Yarrowia. These six strains of Yarrowia showed similar responses to nitrogen-limiting conditions; however, each strain had a unique metabolomic profile. Purine and pyrimidine metabolism were the most highly affected biological pathways in nitrogen-limiting conditions, indicating that these conditions affect energy availability within cells. This stress leads to a shift in cells to the utilization of a less ATP-dependent biological pathway. This information will be beneficial for the development of Yarrowia strains for further scientific and industrial applications.
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Nitta K, Carratore FD, Breitling R, Takano E, Putri SP, Fukusaki E. Multi-Omics Analysis of the Effect of cAMP on Actinorhodin Production in Streptomyces coelicolor. Front Bioeng Biotechnol 2020; 8:595552. [PMID: 33251203 PMCID: PMC7674942 DOI: 10.3389/fbioe.2020.595552] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 10/08/2020] [Indexed: 12/16/2022] Open
Abstract
Cyclic adenosine monophosphate (cAMP) has been known to play an important role in regulating morphological development and antibiotic production in Streptomyces coelicolor. However, the functional connection between cAMP levels and antibiotic production and the mechanism by which cAMP regulates antibiotic production remain unclear. In this study, metabolomics- and transcriptomics-based multi-omics analysis was applied to S. coelicolor strains that either produce the secondary metabolite actinorhodin (Act) or lack most secondary metabolite biosynthesis pathways including Act. Comparative multi-omics analysis of the two strains revealed that intracellular and extracellular cAMP abundance was strongly correlated with actinorhodin production. Notably, supplementation of cAMP improved cell growth and antibiotic production. Further multi-omics analysis of cAMP-supplemented S. coelicolor cultures showed an increase of guanine and the expression level of purine metabolism genes. Based on this phenomenon, supplementation with 7-methylguanine, a competitive inhibitor of reactions utilizing guanine, with or without additional cAMP supplementation, was performed. This experiment revealed that the reactions inhibited by 7-methylguanine are mediating the positive effect on growth and antibiotic production, which may occur downstream of cAMP supplementation.
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Affiliation(s)
- Katsuaki Nitta
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Francesco Del Carratore
- Department of Chemistry, Manchester Synthetic Biology Research Centre SYNBIOCHEM, Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Rainer Breitling
- Department of Chemistry, Manchester Synthetic Biology Research Centre SYNBIOCHEM, Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Eriko Takano
- Department of Chemistry, Manchester Synthetic Biology Research Centre SYNBIOCHEM, Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Sastia P Putri
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka, Japan
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Kanazawa S, Noda A, Ito A, Hashimoto K, Kunisawa A, Nakanishi T, Kajihara S, Mukai N, Iida J, Fukusaki E, Matsuda F. Fake metabolomics chromatogram generation for facilitating deep learning of peak-picking neural networks. J Biosci Bioeng 2020; 131:207-212. [PMID: 33051155 DOI: 10.1016/j.jbiosc.2020.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/14/2020] [Accepted: 09/21/2020] [Indexed: 10/23/2022]
Abstract
Finding peaks in chromatograms and determining their start and end points (peak picking) is a core task in chromatography based biotechnology. Construction of peak-picking neural networks by deep learning was, however, hampered from the preparation of exact peak-picked or "labeled" chromatograms since the exact start and end points were often unclear in overlapping peaks in real chromatograms. We present a design of a fake chromatogram generator, along with a method for deep learning of peak-picking neural networks. Fake chromatograms were generated by generation of fake peaks, random sampling of peak positions from feature distributions, and merging with real blank sample chromatograms. Information on the exact start and end points, as labeled on the fake chromatograms, were effective for training and evaluating peak-picking neural networks. The peak-picking neural networks constructed herein outperformed conventional peak-picking software and showed comparable performance with that of experienced operators for processing the widely targeted metabolome data. Results of this study indicate that generation of fake chromatograms would be crucial for developing peak-picking neural networks and a key technology for further improvement of peak picking neural networks.
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Affiliation(s)
- Shinji Kanazawa
- Shimadzu Corporation, 3-9-4 Hikaridai, Seika-cho, Soraku-gun, Kyoto 619-0237, Japan; Osaka University Shimadzu Omics Innovation Research Laboratories, Osaka University, 2-1 Yamada-oka, Osaka 565-0871, Japan; Graduate School of Information Science and Technology, Osaka University, 2-1, Yamada-oka, Osaka 565-0871, Japan.
| | - Akira Noda
- Shimadzu Corporation, 3-9-4 Hikaridai, Seika-cho, Soraku-gun, Kyoto 619-0237, Japan.
| | - Arisa Ito
- Osaka University Shimadzu Omics Innovation Research Laboratories, Osaka University, 2-1 Yamada-oka, Osaka 565-0871, Japan.
| | - Kyoko Hashimoto
- Osaka University Shimadzu Omics Innovation Research Laboratories, Osaka University, 2-1 Yamada-oka, Osaka 565-0871, Japan.
| | - Akihiro Kunisawa
- Shimadzu Corporation, 3-9-4 Hikaridai, Seika-cho, Soraku-gun, Kyoto 619-0237, Japan.
| | - Tsuyoshi Nakanishi
- Shimadzu Corporation, 3-9-4 Hikaridai, Seika-cho, Soraku-gun, Kyoto 619-0237, Japan.
| | - Shigeki Kajihara
- Shimadzu Corporation, 3-9-4 Hikaridai, Seika-cho, Soraku-gun, Kyoto 619-0237, Japan.
| | - Norio Mukai
- Shimadzu Corporation, 3-9-4 Hikaridai, Seika-cho, Soraku-gun, Kyoto 619-0237, Japan.
| | - Junko Iida
- Shimadzu Corporation, 3-9-4 Hikaridai, Seika-cho, Soraku-gun, Kyoto 619-0237, Japan; Osaka University Shimadzu Omics Innovation Research Laboratories, Osaka University, 2-1 Yamada-oka, Osaka 565-0871, Japan.
| | - Eiichiro Fukusaki
- Graduate School of Engineering, Osaka University, 1-5 Yamada-oka, Osaka 565-0871, Japan.
| | - Fumio Matsuda
- Graduate School of Information Science and Technology, Osaka University, 2-1, Yamada-oka, Osaka 565-0871, Japan.
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Nojima Y, Takeda Y, Maeda Y, Bamba T, Fukusaki E, Itoh MN, Mizuguchi K, Kumanogoh A. Metabolomic analysis of fibrotic mice combined with public RNA-Seq human lung data reveal potential diagnostic biomarker candidates for lung fibrosis. FEBS Open Bio 2020; 10:2427-2436. [PMID: 32961634 PMCID: PMC7609803 DOI: 10.1002/2211-5463.12982] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 08/06/2020] [Accepted: 09/15/2020] [Indexed: 01/22/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a severe lung disease with poor survival that warrants early and precise diagnosis for timely therapeutic intervention. Despite accumulating genomic, transcriptomic, proteomic, and lipidomic data on IPF, evidence from water‐soluble metabolomics is limited. To identify biomarkers for IPF from water‐soluble metabolomic data, we measured the levels of various metabolites in bronchoalveolar lavage fluid (BALF) and serum samples from a bleomycin‐induced murine pulmonary fibrotic model using gas chromatography/mass spectrometry. Thirty‐two of 73 BALF metabolites and 29 of 74 serum metabolites were annotated. We observed that the levels of proline and methionine were higher in BALF but lower in serum than those in the control. Furthermore, analysis of public RNA‐Seq data from the lungs of patients with IPF revealed that proline‐ and methionine‐related genes were significantly upregulated compared to those in the lungs of healthy controls. These results suggest that proline and methionine may be potential biomarkers for IPF and may help to deepen our understanding of the pathophysiology of the disease. Based on our results, we propose a model capable of recapitulating the proline and methionine metabolism of fibrotic lungs, thereby providing better means for studying the disease and developing novel therapeutic strategies for IPF.
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Affiliation(s)
- Yosui Nojima
- Laboratory of BioinformaticsArtificial Intelligence Center for Health and Biomedical Research (ArCHER)National Institutes of Biomedical Innovation, Health and NutritionOsakaJapan
| | - Yoshito Takeda
- Department of Respiratory Medicine and Clinical ImmunologyOsaka University Graduate School of MedicineJapan
| | - Yohei Maeda
- Department of Respiratory Medicine and Clinical ImmunologyOsaka University Graduate School of MedicineJapan
| | - Takeshi Bamba
- Department of BiotechnologyGraduate School of EngineeringOsaka UniversityJapan
- Division of MetabolomicsMedical Institute of BioregulationKyushu UniversityFukuokaJapan
| | - Eiichiro Fukusaki
- Department of BiotechnologyGraduate School of EngineeringOsaka UniversityJapan
| | - Mari N. Itoh
- Laboratory of BioinformaticsArtificial Intelligence Center for Health and Biomedical Research (ArCHER)National Institutes of Biomedical Innovation, Health and NutritionOsakaJapan
| | - Kenji Mizuguchi
- Laboratory of BioinformaticsArtificial Intelligence Center for Health and Biomedical Research (ArCHER)National Institutes of Biomedical Innovation, Health and NutritionOsakaJapan
- Institute for Protein ResearchOsaka UniversityJapan
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical ImmunologyOsaka University Graduate School of MedicineJapan
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Sato A, Astuti DI, Putri SP, Fukusaki E. Quality Improvement of Semi-Wet Terasi by Optimizing the Starter Culture Ratio of Controlled Fermentation. HAYATI J Biosci 2020. [DOI: 10.4308/hjb.27.4.320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Terasi is a traditional fermented shrimp paste used in Indonesian dish as condiments. Due to its affordability, the paste is widely consumed among the general population, and thus has a great impact in Indonesia. Currently, small-scale or home industry is common for terasi production, and natural fermentation process is the traditional method. Fermentation process is considered complete when desired aromatic odors are obtained. However, this makes the fermentation process subjective, because the decision is solely dependent on the producer. Additionally, natural fermentation poses a higher risk for contamination of microbial pathogens. As a result, the quality of the final product varies greatly from region to region. Therefore, it is necessary to improve the quality of terasi by means of controlled fermentation. Hence, the objective of the research is to optimize the controlled fermentation condition of terasi by determining the most optimal ratio of mixed starter culture. Optimal fermentation conditions were determined by analyzing the effect of the various starter inoculum on the inner microbial community, and results indicated that mixed culture of Staphylococcus saprophyticus, Bacillus subtilis, and Lactobacillus murinus with ratio of 2:1:2 was the most effective for suppressing the growth of unwanted microorganisms. The difference in the microbial composition also resulted to a change in the metabolite profile of terasi.
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Omori K, Katakami N, Arakawa S, Yamamoto Y, Ninomiya H, Takahara M, Matsuoka TA, Tsugawa H, Furuno M, Bamba T, Fukusaki E, Shimomura I. Identification of Plasma Inositol and Indoxyl Sulfate as Novel Biomarker Candidates for Atherosclerosis in Patients with Type 2 Diabetes. -Findings from Metabolome Analysis Using GC/MS. J Atheroscler Thromb 2020; 27:1053-1067. [PMID: 31983701 PMCID: PMC7585911 DOI: 10.5551/jat.52506] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 12/08/2019] [Indexed: 12/29/2022] Open
Abstract
AIM An identification of the high-risk group of atherosclerotic cardiovascular disease (CVD) is important in the management of patients with diabetes. Metabolomics is a potential tool for the discovery of new biomarkers. With this background, we aimed to identify metabolites associated with atherosclerosis in patients with type 2 diabetes mellitus (T2DM). METHODS A total of 176 patients with T2DM who have never had a CVD event and 40 who were survivors of coronary artery disease (CAD) events were enrolled. Non-targeted metabolome analysis of fasting plasma samples was performed using gas chromatography coupled with mass spectrometry (GC/MS) highly optimized for multiple measurement of blood samples. First, metabolites were screened by analyzing the association with the established markers of subclinical atherosclerosis (i.e., carotid maximal intima-media thickness (max-IMT) and flow-mediated vasodilation (FMD)) in the non-CVD subjects. Then, the associations between the metabolites detected and the history of CAD were investigated. RESULT A total of 65 annotated metabolites were detected. Non-parametric univariate analysis identified inositol and indoxyl sulfate as significantly (p<0.05) associated with both max-IMT and FMD. These metabolites were also significantly associated with CAD. Moreover, inositol remained to be associated with CAD even after adjustments for traditional coronary risk factors. CONCLUSIONS We identified novel biomarker candidates for atherosclerosis in Japanese patients with T2DM using GC/MS-based non-targeted metabolomics.
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Affiliation(s)
- Kazuo Omori
- Department of Metabolic Medicine, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Naoto Katakami
- Department of Metabolic Medicine, Osaka University Graduate School of Medicine, Osaka, Japan
- Department of Metabolism and Atherosclerosis, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Shoya Arakawa
- Laboratory of Bioresource Engineering, Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Yuichi Yamamoto
- Department of Metabolic Medicine, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Hiroyo Ninomiya
- Department of Metabolic Medicine, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Mitsuyoshi Takahara
- Department of Metabolic Medicine, Osaka University Graduate School of Medicine, Osaka, Japan
- Department of Diabetes Care Medicine, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Taka-aki Matsuoka
- Department of Metabolic Medicine, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Hiroshi Tsugawa
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - Masahiro Furuno
- Laboratory of Bioresource Engineering, Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Takeshi Bamba
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Eiichiro Fukusaki
- Laboratory of Bioresource Engineering, Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Iichiro Shimomura
- Department of Metabolic Medicine, Osaka University Graduate School of Medicine, Osaka, Japan
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Putri Wisman A, Tamada Y, Hirohata S, Fukusaki E, Shimma S. Metabolic Visualization Reveals the Distinct Distribution of Sugars and Amino Acids in Rice Koji. Mass Spectrom (Tokyo) 2020; 9:A0089. [PMID: 32944490 PMCID: PMC7471875 DOI: 10.5702/massspectrometry.a0089] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 07/13/2020] [Indexed: 11/23/2022] Open
Abstract
The compounds inside rice koji have been thoroughly investigated as an essential material in making many food-related products, including sake. However, these studies focused only on quantitative aspects, leaving features that can still be uncovered if seen from a new perspective. Visualization of the metabolites inside rice koji may as well be the new angle needed to retrieve more information regarding rice koji making. Here we utilized mass spectrometry imaging (MSI) to visualize the distribution of sugars, sugar alcohols, and amino acids inside rice koji. Imaging results revealed that several sugars alcohols and amino acids were shown to have characteristic distribution near the edges or surface of rice koji. Furthermore, the distribution appears to be correlated with the different structure of rice koji. This study is the first report of using MSI to visualize sugars, sugar alcohols, and amino acids in rice koji.
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Affiliation(s)
- Adinda Putri Wisman
- Department of Biotechnology, Graduate School of Engineering, Osaka University
| | | | | | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University.,Osaka University Shimadzu Analytical Innovation Laboratory, Osaka University
| | - Shuichi Shimma
- Department of Biotechnology, Graduate School of Engineering, Osaka University.,Osaka University Shimadzu Analytical Innovation Laboratory, Osaka University
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