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Maciel F, Madureira L, Geada P, Teixeira JA, Silva J, Vicente AA. The potential of Pavlovophyceae species as a source of valuable carotenoids and polyunsaturated fatty acids for human consumption. Biotechnol Adv 2024; 74:108381. [PMID: 38777244 DOI: 10.1016/j.biotechadv.2024.108381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 05/17/2024] [Accepted: 05/17/2024] [Indexed: 05/25/2024]
Abstract
Microalgae are a group of microorganisms, mostly photoautotrophs with high CO2 fixation capacity, that have gained increased attention in the last decades due to their ability to produce a wide range of valuable metabolites, such as carotenoids and polyunsaturated fatty acids, for application in food/feed, pharmaceutical, and cosmeceutical industries. Their increasing relevance has highlighted the importance of identifying and culturing new bioactive-rich microalgae species, as well as of a thorough understanding of the growth conditions to optimize the biomass production and master the biochemical composition according to the desired application. Thus, this review intends to describe the main cell processes behind the production of carotenoids and polyunsaturated fatty acids, in order to understand the possible main triggers responsible for the accumulation of those biocompounds. Their economic value and the biological relevance for human consumption are also summarized. In addition, an extensive review of the impact of culture conditions on microalgae growth performance and their biochemical composition is presented, focusing mainly on the studies involving Pavlovophyceae species. A complementary description of the biochemical composition of these microalgae is also presented, highlighting their potential applications as a promising bioresource of compounds for large-scale production and human and animal consumption.
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Affiliation(s)
- Filipe Maciel
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal; LABBELS -Associate Laboratory, Braga/Guimarães, Portugal.
| | - Leandro Madureira
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal.
| | - Pedro Geada
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal; LABBELS -Associate Laboratory, Braga/Guimarães, Portugal.
| | - José António Teixeira
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal; LABBELS -Associate Laboratory, Braga/Guimarães, Portugal.
| | - Joana Silva
- ALLMICROALGAE, Natural Products S.A., R&D Department, Rua 25 de Abril 19, 2445-287 Pataias, Portugal.
| | - António Augusto Vicente
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal; LABBELS -Associate Laboratory, Braga/Guimarães, Portugal.
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Peter EK, Jaeger C, Lisec J, Peters RS, Mourot R, Rossel PE, Tranter M, Anesio AM, Benning LG. Endometabolic profiling of pigmented glacier ice algae: the impact of sample processing. Metabolomics 2024; 20:98. [PMID: 39123092 PMCID: PMC11315761 DOI: 10.1007/s11306-024-02147-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 06/24/2024] [Indexed: 08/12/2024]
Abstract
INTRODUCTION Glacier ice algae, mainly Ancylonema alaskanum and Ancylonema nordenskiöldi, bloom on Greenland Ice Sheet bare ice surfaces. They significantly decrease surface albedo due to their purple-brown pigmentation, thus increasing melt. Little is known about their metabolic adaptation and factors controlling algal growth dynamics and pigment formation. A challenge in obtaining such data is the necessity of melting samples, which delays preservation and introduces bias to metabolomic analysis. There is a need to evaluate the physiological response of algae to melting and establish consistent sample processing strategies for metabolomics of ice microbial communities. OBJECTIVES To address the impact of sample melting procedure on metabolic characterization and establish a processing and analytical workflow for endometabolic profiling of glacier ice algae. METHODS We employed untargeted, high-resolution mass spectrometry and tested the effect of sample melt temperature (10, 15, 20 °C) and processing delay (up to 49 h) on the metabolome and lipidome, and complemented this approach with cell counts (FlowCam), photophysiological analysis (PAM) and diversity characterization. RESULTS AND CONCLUSION We putatively identified 804 metabolites, with glycerolipids, glycerophospholipids and fatty acyls being the most prominent superclasses (> 50% of identified metabolites). Among the polar metabolome, carbohydrates and amino acid-derivatives were the most abundant. We show that 8% of the metabolome is affected by melt duration, with a pronounced decrease in betaine membrane lipids and pigment precursors, and an increase in phospholipids. Controlled fast melting at 10 °C resulted in the highest consistency, and is our recommendation for future supraglacial metabolomics studies.
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Affiliation(s)
- Elisa K Peter
- German Research Centre for Geosciences - GFZ, 14473, Potsdam, Germany.
- Department of Earth Sciences, Freie Universität Berlin, 12249, Berlin, Germany.
| | - Carsten Jaeger
- Bundesanstalt für Materialforschung und -prüfung (BAM), 12489, Berlin, Germany
| | - Jan Lisec
- Bundesanstalt für Materialforschung und -prüfung (BAM), 12489, Berlin, Germany
| | - R Sven Peters
- German Research Centre for Geosciences - GFZ, 14473, Potsdam, Germany
| | - Rey Mourot
- German Research Centre for Geosciences - GFZ, 14473, Potsdam, Germany
- Department of Earth Sciences, Freie Universität Berlin, 12249, Berlin, Germany
| | - Pamela E Rossel
- German Research Centre for Geosciences - GFZ, 14473, Potsdam, Germany
| | - Martyn Tranter
- Department of Environmental Science, Aarhus University, 4000, Roskilde, Denmark
| | - Alexandre M Anesio
- Department of Environmental Science, Aarhus University, 4000, Roskilde, Denmark
| | - Liane G Benning
- German Research Centre for Geosciences - GFZ, 14473, Potsdam, Germany.
- Department of Earth Sciences, Freie Universität Berlin, 12249, Berlin, Germany.
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Wang N, Sheng Q, Zhu H, Wang J, Qiu J, Cui M, Zhou Y, Deng X, Deng Y, Wang L. Enhancing the effectiveness of Polymyxin E with a Fisetin Nanoemulsion against a Colistin-resistant Salmonella typhimurium infection. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 130:155768. [PMID: 38815408 DOI: 10.1016/j.phymed.2024.155768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 05/13/2024] [Accepted: 05/21/2024] [Indexed: 06/01/2024]
Abstract
BACKGROUND Polymyxin E is widely recognized as a last resort for treating multidrug-resistant gram-negative bacteria. Unfortunately, the effectiveness of polymyxin E is significantly reduced when treating life-threatening bacterial infections due to plasmid-mediated polymyxin E resistance. The synergistic effect of applying a polymyxin E adjuvant is a promising strategy for overcoming the growing threat of antibiotic-resistant pathogens. PURPOSE To evaluate the synergistic effect of fisetin and polymyxin E on S. typhimurium infections in vivo and further elucidate the underlying mechanism of this effect. METHODS The effect of combining fisetin and polymyxin E to treat mobilized colistin resistance-1-positive (MCR-1-positive) gram-negative bacteria in vitro was examined using various methods, such as checkerboard assays, growth curves and time‒kill curves. To elucidate the mechanism by which fisetin affects MCR-1, we employed ultraviolet (UV) absorption spectroscopy, thin layer chromatography (TLC), and western blot analysis to investigate its effect at the protein level. Subsequently, molecular dynamics simulations (MDS) and metabolomics analysis were utilized to determine the site of interaction between fisetin and MCR-1 as well as the potential pathways and mechanisms involved. A new nanoemulsion of fisetin was produced using high-pressure homogenization, and its stability was tested. Finally, two animal models of S. typhimurium HYM2 infection were established to evaluate the synergistic effect of polymyxin E and fisetin in vivo. RESULTS Our study revealed that fisetin exhibited a synergistic effect when combined with polymyxin E against MCR-1-positive S. typhimurium. The TLC results demonstrated that fisetin could inhibit the phosphoethanolamine (PEA) transfer of the MCR-1 protein, thereby restoring the activity of polymyxin E in strains against MCR-1. The MDS analysis indicated robust and immediate binding between fisetin and the MCR-1 protein, with both hydrophobic and polar effects playing significant roles in determining the binding energy of the former. Metabolomic studies demonstrated that the addition of fisetin significantly modulated bacterial metabolites. Moreover, it effectively inhibited the activity of ABC transporters in bacteria, thereby mitigating bacterial drug resistance and enhancing the therapeutic efficacy of polymyxin E. Furthermore, in mouse and chick models of infection, intragastric administration of the fisetin nanoemulsion together with polymyxin E resulted in significant therapeutic benefits, including increased survival rates, reduced bacterial colonization, and decreased levels of inflammatory factors. CONCLUSION Fisetin, an MCR-1 inhibitor and a promising synergistic partner of polymyxin E, has significant potential for clinical application in the treatment of S. typhimurium infections, particularly those resulting extensively from drug-resistant MCR-1-positive strains.
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Affiliation(s)
- Nan Wang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, Jilin, PR China
| | - Qiushuang Sheng
- Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, Jinlin, PR China
| | - Haoyu Zhu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, Jilin, PR China
| | - Jianfeng Wang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, Jilin, PR China
| | - Jiazhang Qiu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, Jilin, PR China
| | - Minhe Cui
- Jilin Mushuo Breeding Co., Ltd, Changchun 130052, Jilin, PR China
| | - Yonglin Zhou
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, Jilin, PR China
| | - Xuming Deng
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, Jilin, PR China
| | - Yanhong Deng
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, Jilin, PR China.
| | - Lin Wang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, Jilin, PR China.
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Wood PL, Le A, Palazzolo DL. Comparative Lipidomics of Oral Commensal and Opportunistic Bacteria. Metabolites 2024; 14:240. [PMID: 38668368 PMCID: PMC11052126 DOI: 10.3390/metabo14040240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/15/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024] Open
Abstract
The oral cavity contains a vast array of microbes that contribute to the balance between oral health and disease. In addition, oral bacteria can gain access to the circulation and contribute to other diseases and chronic conditions. There are a limited number of publications available regarding the comparative lipidomics of oral bacteria and fungi involved in the construction of oral biofilms, hence our decision to study the lipidomics of representative oral bacteria and a fungus. We performed high-resolution mass spectrometric analyses (<2.0 ppm mass error) of the lipidomes from five Gram-positive commensal bacteria: Streptococcus oralis, Streptococcus intermedius, Streptococcus mitis, Streptococcus sanguinis, and Streptococcus gordonii; five Gram-positive opportunistic bacteria: Streptococcus mutans, Staphylococcus epidermis, Streptococcus acidominimus, Actinomyces viscosus, and Nanosynbacter lyticus; seven Gram-negative opportunistic bacteria: Porphyromonas gingivalis. Prevotella brevis, Proteus vulgaris, Fusobacterium nucleatum, Veillonella parvula, Treponema denticola, and Alkermansia muciniphila; and one fungus: Candida albicans. Our mass spectrometric analytical platform allowed for a detailed evaluation of the many structural modifications made by microbes for the three major lipid scaffolds: glycerol, sphingosine and fatty acyls of hydroxy fatty acids (FAHFAs).
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Affiliation(s)
- Paul L. Wood
- Metabolomics Unit, College of Veterinary Medicine, Lincoln Memorial University, 6965 Cumberland Gap Pkwy., Harrogate, TN 37752, USA
| | - Annie Le
- Clinical Training Program, DeBusk College of Osteopathic Medicine, Lincoln Memorial University, 6965 Cumberland Gap Pkwy., Harrogate, TN 37752, USA
| | - Dominic L. Palazzolo
- Department of Physiology, DeBusk College of Osteopathic Medicine, Lincoln Memorial University, 6965 Cumberland Gap Pkwy., Harrogate, TN 37752, USA;
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Santos GBM, de Abreu FAP, da Silva GS, Guedes JAC, Lira SM, Dionísio AP, Pontes DF, Zocolo GJ. UPLC-QTOF-MS E based metabolomics and chemometrics study of the pitaya processing. Food Res Int 2024; 178:113957. [PMID: 38309877 DOI: 10.1016/j.foodres.2024.113957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/20/2023] [Accepted: 01/02/2024] [Indexed: 02/05/2024]
Abstract
The search for knowledge related to the Pitaya (Hylocereus polyrhizus [F.A.C. Weber] Britton & Rose, family Cactaceae) is commonly due to its beneficial health properties e aesthetic values. But process to obtain pitaya pulp is a first and important step in providing information for the subsequent use of this fruit as colorant, for example. Therefore, the effects of the pulping process on the metabolomic and chemometric profile of non-volatile compounds of pitaya were assessed for the first time. The differences in metabolic fingerprints using UPLC-QTOF-MSE and multivariate modeling (PCA and OPLS-DA) was performed in the following treatments: treatment A, which consists of pelled pitaya and no ascorbic acid addition during pulping; treatment B, use of unpelled pitaya added of ascorbic acid during pulping; and control, unpelled pitaya and no ascorbic acid addition during pulping. For the metabolomic analysis, UPLC-QTOF-MSE shows an efficient method for the simultaneous determination of 35 non-volatile pitaya metabolites, including isorhamnetin glucosyl rhamnosyl isomers, phyllocactin isomers, 2'-O-apiosyl-phylocactin and 4'-O-malonyl-betanin. In addition, the chemometric analysis efficiently distinguished the metabolic compounds of each treatment applied and shows that the use of unpelled pitaya added of ascorbic acid during pulping has an interesting chemical profile due to the preservation or formation of compounds, such as those derived from betalain, and higher yields, which is desirable for the food industry.
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Affiliation(s)
| | | | | | | | - Sandra Machado Lira
- Department of Nutrition, State University of Ceara, 60714-903 Fortaleza, CE, Brazil
| | - Ana Paula Dionísio
- Embrapa Agroindústria Tropical, Dra Sara Mesquita St., 2270, 60511-110 Fortaleza, CE, Brazil
| | | | - Guilherme Julião Zocolo
- Embrapa Agroindústria Tropical, Dra Sara Mesquita St., 2270, 60511-110 Fortaleza, CE, Brazil.
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Feng C, Zheng W, Han L, Wang JK, Zha XP, Xiao Q, He ZJ, Kang JC. AaLaeA targets AaFla1 to mediate the production of antitumor compound in Alternaria alstroemeria. J Basic Microbiol 2024; 64:68-80. [PMID: 37717245 DOI: 10.1002/jobm.202300319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/25/2023] [Accepted: 09/05/2023] [Indexed: 09/19/2023]
Abstract
Endophytic fungi are an important source of novel antitumor substances. Previously, we isolated an endophytic fungus, Alternaria alstroemeria, from the medicinal plant Artemisia artemisia, whose crude extracts strongly inhibited A549 tumor cells. We obtained a transformant, namely AaLaeAOE26 , which completely loses its antitumor activity due to overexpression of the global regulator AaLaeA. Re-sequencing analysis of the genome revealed that the insertion site was in the noncoding region and did not destroy any other genes. Metabolomics analysis revealed that the level of secondary antitumor metabolic substances was significantly lower in AaLaeAOE26 compared with the wild strain, in particular flavonoids were more downregulated according to the metabolomics analysis. A further comparative transcriptome analysis revealed that a gene encoding FAD-binding domain protein (Fla1) was significantly downregulated. On the other hand, overexpression of AaFla1 led to significant enhancement of antitumor activity against A549 with a sevenfold higher inhibition ratio than the wild strain. At the same time, we also found a significant increase in the accumulation of antitumor metabolites including quercetin, gitogenin, rhodioloside, liensinine, ginsenoside Rg2 and cinobufagin. Our data suggest that the global regulator AaLaeA negatively affects the production of antitumor compounds via controlling the transcription of AaFla1 in endophytic A. alstroemeria.
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Affiliation(s)
- Can Feng
- College of Pharmacy, Guizhou University, Guiyang, People's Republic of China
- Southwest Biomedical Resources of the Ministry of Education, Guizhou University, Guiyang, People's Republic of China
| | - Wen Zheng
- Southwest Biomedical Resources of the Ministry of Education, Guizhou University, Guiyang, People's Republic of China
| | - Long Han
- Southwest Biomedical Resources of the Ministry of Education, Guizhou University, Guiyang, People's Republic of China
| | - Jian-Kang Wang
- Southwest Biomedical Resources of the Ministry of Education, Guizhou University, Guiyang, People's Republic of China
| | - Xing-Ping Zha
- Southwest Biomedical Resources of the Ministry of Education, Guizhou University, Guiyang, People's Republic of China
| | - Qing Xiao
- Southwest Biomedical Resources of the Ministry of Education, Guizhou University, Guiyang, People's Republic of China
| | - Zhang-Jiang He
- College of Pharmacy, Guizhou University, Guiyang, People's Republic of China
- Southwest Biomedical Resources of the Ministry of Education, Guizhou University, Guiyang, People's Republic of China
| | - Ji-Chuan Kang
- College of Pharmacy, Guizhou University, Guiyang, People's Republic of China
- Southwest Biomedical Resources of the Ministry of Education, Guizhou University, Guiyang, People's Republic of China
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Ke X, Wu Z, Liu Y, Liang Y, Du M, Li Y. Isolation, Antimicrobial Effect and Metabolite Analysis of Bacillus amyloliquefaciens ZJLMBA1908 against Citrus Canker Caused by Xanthomonas citri subsp. citri. Microorganisms 2023; 11:2928. [PMID: 38138073 PMCID: PMC10746125 DOI: 10.3390/microorganisms11122928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/30/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
Citrus canker caused by Xanthomonas citri subsp. citri is a devastating bacterial disease with severe implications for the citrus industry. Microorganisms possessing biocontrol capabilities against X. citri subsp. citri offer a highly promising strategy for healthy citrus management. In the present study, a broad-spectrum antagonist strain ZJLMBA1908 with potent antibacterial activity against X. citri subsp. citri was isolated from symptomatic lemon leaves, and identified as Bacillus amyloliquefaciens. Cell-free supernatant (CFS) of strain ZJLMBA1908 also exhibited remarkable antimicrobial activity, especially suppressing the growth of X. citri subsp. citri and Nigrospora oryzae, with inhibition rates of 27.71% and 63.75%, respectively. The antibacterial crude extract (CE) derived from the CFS displayed effective activity against X. citri subsp. citri. A preventive treatment using the CE significantly reduced the severity and incidence of citrus canker in a highly susceptible citrus host. Additionally, the CE maintained activity in the presence of protease and under a wide range of temperature and pH treatments. Applying high-performance liquid chromatography (HPLC) to separate and purify the CE resulted in the discovery of one highly potent anti-X. citri subsp. citri subfraction, namely CE3, which could completely inhibit the growth of X. citri subsp. citri. Liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS) analysis revealed that CE3 mainly consisted of palmitic acid, surfactin C15, phytosphingosine and dihydrosphingosine. Taken together, the results contribute to the possible biocontrol mechanisms of B. amyloliquefaciens ZJLMBA1908, as well as providing a promising new candidate strain as a biological control agent for controlling citrus canker.
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Affiliation(s)
| | | | | | | | | | - Ya Li
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang 524088, China; (X.K.); (Z.W.); (Y.L.); (Y.L.); (M.D.)
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Choueiry F, Xu R, Meyrath K, Zhu J. Database-assisted, globally optimized targeted secondary electrospray ionization high resolution mass spectrometry (dGOT-SESI-HRMS) and spectral stitching enhanced volatilomics analysis of bacterial metabolites. Analyst 2023; 148:5673-5683. [PMID: 37819163 PMCID: PMC10841745 DOI: 10.1039/d3an01487h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Secondary electrospray ionization high-resolution mass spectrometry (SESI-HRMS) is an innovative analytical technique for the rapid and non-invasive analysis of volatile organic compounds (VOCs). However, compound annotation and ion suppression in the SESI source has hindered feature detection, stability and reproducibility of SESI-HRMS in untargeted volatilomics. To address this, we have developed and optimized a novel pseudo-targeted approach, database-assisted globally optimized targeted (dGOT)-SESI-HRMS using the microbial-VOC (mVOC) database, and spectral stitching methods to enhance metabolite detection in headspace of anaerobic bacterial cultures. Headspace volatiles from representative bacteria strains were assessed using full scan with data dependent acquisition (DDA), conventional globally optimized targeted (GOT) method, and spectral stitching supported dGOT experiments based on a MS peaks list derived from mVOC. Our results indicate that spectral stitching supported dGOT-SESI-HRMS can proportionally fragment peaks with respect to different analysis windows, with a total of 109 VOCs fragmented from 306 targeted compounds. Of the collected spectra, 88 features were confirmed as culture derived volatiles with respect to media blanks. Annotation was also achieved with a total of 25 unique volatiles referenced to standard databases allowing for biological interpretation. Principal component analysis (PCA) summarizing the headspace volatile demonstrated improved separation of clusters when data was acquired using the dGOT method. Collectively, our dGOT-SESI-HRMS method afforded robust capability of capturing unique VOC profiles from different bacterial strains and culture conditions when compared to conventional GOT and DDA modes, suggesting the newly developed approach can serve as a more reliable analytical method for the sensitive monitoring of gut microbial metabolism.
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Affiliation(s)
- Fouad Choueiry
- Department of Human Sciences, The Ohio State University, USA.
- James Comprehensive Cancer Center, The Ohio State University, 400 W 12th Ave, Columbus, OH 43210, USA
| | - Rui Xu
- Department of Human Sciences, The Ohio State University, USA.
| | - Kelly Meyrath
- Department of Human Sciences, The Ohio State University, USA.
| | - Jiangjiang Zhu
- Department of Human Sciences, The Ohio State University, USA.
- James Comprehensive Cancer Center, The Ohio State University, 400 W 12th Ave, Columbus, OH 43210, USA
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Roussel A, Mériot V, Jauffrais T, Berteaux-Lecellier V, Lebouvier N. OMICS Approaches to Assess Dinoflagellate Responses to Chemical Stressors. BIOLOGY 2023; 12:1234. [PMID: 37759633 PMCID: PMC10525455 DOI: 10.3390/biology12091234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/13/2023] [Accepted: 07/18/2023] [Indexed: 09/29/2023]
Abstract
Dinoflagellates are important primary producers known to form Harmful Algae Blooms (HABs). In water, nutrient availability, pH, salinity and anthropogenic contamination constitute chemical stressors for them. The emergence of OMICs approaches propelled our understanding of dinoflagellates' responses to stressors. However, in dinoflagellates, these approaches are still biased, as transcriptomic approaches are largely conducted compared to proteomic and metabolomic approaches. Furthermore, integrated OMICs approaches are just emerging. Here, we report recent contributions of the different OMICs approaches to the investigation of dinoflagellates' responses to chemical stressors and discuss the current challenges we need to face to push studies further despite the lack of genomic resources available for dinoflagellates.
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Affiliation(s)
- Alice Roussel
- ISEA, EA7484, Campus de Nouville, Université de la Nouvelle Calédonie, Noumea 98851, New Caledonia; (A.R.); (V.M.)
| | - Vincent Mériot
- ISEA, EA7484, Campus de Nouville, Université de la Nouvelle Calédonie, Noumea 98851, New Caledonia; (A.R.); (V.M.)
- Ifremer, IRD, CNRS, Univ. de la Réunion, Univ. de la Nouvelle Calédonie, UMR 9220 ENTROPIE, 101 Promenade Roger Laroque, Noumea 98897, New Caledonia;
| | - Thierry Jauffrais
- Ifremer, IRD, CNRS, Univ. de la Réunion, Univ. de la Nouvelle Calédonie, UMR 9220 ENTROPIE, 101 Promenade Roger Laroque, Noumea 98897, New Caledonia;
| | - Véronique Berteaux-Lecellier
- CNRS, Ifremer, IRD, Univ. de la Réunion, Univ. de la Nouvelle Calédonie, UMR 9220 ENTROPIE, 101 Promenade Roger Laroque, Noumea 98897, New Caledonia;
| | - Nicolas Lebouvier
- ISEA, EA7484, Campus de Nouville, Université de la Nouvelle Calédonie, Noumea 98851, New Caledonia; (A.R.); (V.M.)
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Sakai R, Goto-Inoue N, Yamashita H, Aimoto N, Kitai Y, Maruyama T. Smart utilization of betaine lipids in the giant clam Tridacna crocea. iScience 2023; 26:107250. [PMID: 37485344 PMCID: PMC10362313 DOI: 10.1016/j.isci.2023.107250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 05/14/2023] [Accepted: 06/26/2023] [Indexed: 07/25/2023] Open
Abstract
The giant clam Tridacna crocea thrives in poorly nourished coral reef water by forming a holobiont with zooxanthellae and utilizing photosynthetic products of the symbiont. However, detailed metabolic crosstalk between clams and symbionts is elusive. Here, we discovered that the nonphosphorous microalgal betaine lipid DGCC (diacylglycerylcarboxy-hydroxymethylcholine) and its deacylated derivative GCC are present in all tissues and organs, including algae-free sperm and eggs, and are metabolized. Colocalization of DGCC and PC (phosphatidylcholine) evidenced by MS imaging suggested that DGCC functions as a PC substitute. The high content of GCC in digestive diverticula (DD) suggests that the algal DGCC was digested in DD for further utilization. Lipidomics analysis showing the organ-specific distribution pattern of DGCC species suggests active utilization of DGCC as membrane lipids in the clam. Thus, the utilization of zooxanthellal DGCC in animal cells is a unique evolutionary outcome in phosphorous-deficient coral reef waters.
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Affiliation(s)
- Ryuichi Sakai
- Faculty and Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho, Hakodate 041-8611, Japan
| | - Naoko Goto-Inoue
- Department of Marine Science and Resources, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-0880, Japan
| | - Hiroshi Yamashita
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 148 Fukai-Ohta, Ishigaki, Okinawa 907-0451, Japan
| | - Naoya Aimoto
- Faculty and Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho, Hakodate 041-8611, Japan
| | - Yuto Kitai
- Faculty and Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho, Hakodate 041-8611, Japan
| | - Tadashi Maruyama
- School of Marine Biosciences, Kitasato University, 1-15-1, Kitazato, Minami, Sagamihara, Kanagawa 252-0374, Japan
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11
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Xie X, Chen L, Chen T, Yang F, Wang Z, Hu Y, Lu J, Lu X, Li Q, Zhang X, Ma M, Wang L, Hu C, Xu G. Profiling and annotation of carbonyl compounds in Baijiu Daqu by chlorine isotope labeling-assisted ultrahigh-performance liquid chromatography-high resolution mass spectrometry. J Chromatogr A 2023; 1703:464110. [PMID: 37262933 DOI: 10.1016/j.chroma.2023.464110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/03/2023]
Abstract
Carbonyl compounds are among the most important flavor substances that affect the taste of Baijiu. However, high coverage analysis of carbonyl compounds is obstructed due to the poor ionization efficiency of these compounds. Here we report a chlorine isotope labeling-assisted ultrahigh-performance liquid chromatography-high resolution mass spectrometry-based method (CIL-UHPLCHRMS) for profiling and annotation of carbonyl compounds in sauce flavored-Baijiu Daqu. 4-Chloro-2-hydrazinylpyridine was demonstrated to be a good labeling reagent that could achieve highly sensitive profiling and high-coverage screening of carbonyl compounds in the absence of heavy isotope labeling reagents. In the analysis of eight carbonyl standards representing different carbonyl categories, l-(-)-fucose, 2-carboxybenzaldehyde, 2-hydroxyacetophenone and heptan-2-one could be ionized only after labeling and MS signals were significantly increased for other 4 standards with an enhancement factor ranging from 181-fold for 3-methoxysalicylaldehyde to 3141-fold for tridecan-2-one. The annotation was achieved based on multidimensional information including MS1, predicted tR, in silico MS/MS and manually annotated fragments. In total, 487 carbonyl compounds were detected in Baijiu Daqu, among which, 314 (64.5%) of them were positively or putatively identified. The outcome of the linearity (with a linear range of 2, 3 orders of magnitude), precision (less than 10%), and limit of detection (varied from 0.07 to 0.10 nM) indicated that the method was adequate for profiling carbonyl compounds in complex biological samples. The established method was successfully applied to study carbonyl compounds in Baijiu Daqu with different colors and different seasons. Taken collectively, the present work provides an effective, simple and economic strategy for comprehensive analysis of carbonyl compounds in complex matrix samples.
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Affiliation(s)
- Xiaoyu Xie
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; Key Laboratory of Phytochemical R&D of Hunan Province, Hunan Normal University, Changsha 410081, China
| | - Liangqiang Chen
- Kweichow Moutai Co., Ltd, Renhuai, Guizhou 564501, China; Kweichow Moutai Group, Renhuai, Guizhou 564501, China
| | - Tiantian Chen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Fan Yang
- Kweichow Moutai Co., Ltd, Renhuai, Guizhou 564501, China; Kweichow Moutai Group, Renhuai, Guizhou 564501, China
| | - Zixuan Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yang Hu
- Kweichow Moutai Co., Ltd, Renhuai, Guizhou 564501, China; Kweichow Moutai Group, Renhuai, Guizhou 564501, China
| | - Jianjun Lu
- Kweichow Moutai Co., Ltd, Renhuai, Guizhou 564501, China; Kweichow Moutai Group, Renhuai, Guizhou 564501, China
| | - Xin Lu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, China
| | - Qi Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, China
| | - Xiuqiong Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Ming Ma
- Key Laboratory of Phytochemical R&D of Hunan Province, Hunan Normal University, Changsha 410081, China
| | - Li Wang
- Kweichow Moutai Co., Ltd, Renhuai, Guizhou 564501, China; Kweichow Moutai Group, Renhuai, Guizhou 564501, China.
| | - Chunxiu Hu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, China.
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, China
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12
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Sajid S, Salas LH, Rafiq M, Lund T, Jørgensen MG, Honoré B, Christensen LP, Hansen PR, Franzyk H, Mirza O, Prabhala BK. Physiological response in E. coli to YdgR overexpression depends on whether the protein has an intact function. Biochem Biophys Res Commun 2023; 661:42-49. [PMID: 37087797 DOI: 10.1016/j.bbrc.2023.04.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/13/2023] [Accepted: 04/14/2023] [Indexed: 04/25/2023]
Abstract
Membrane transport proteins are essential for the transport of a wide variety of molecules across the cell membrane to maintain cellular homeostasis. Generally, these transport proteins can be overexpressed in a suitable host (bacteria, yeast, or mammalian cells), and it is well documented that overexpression of membrane proteins alters the global metabolomic and proteomic profiles of the host cells. In the present study, we investigated the physiological consequences of overexpression of a membrane transport protein YdgR that belongs to the POT/PTR family from E. coli by using the lab strain BL21 (DE3)pLysS in its functional and attenuated mutant YdgR-E33Q. We found significant differences between the omics (metabolomics and proteomics) profiles of the cells expressing functional YdgR as compared to cells expressing attenuated YdgR, e.g., upregulation of several uncharacterized y-proteins and enzymes involved in the metabolism of peptides and amino acids. Furthermore, molecular network analysis suggested a relatively higher presence of proline-containing tripeptides in cells expressing functional YdgR. We envisage that an in-depth investigation of physiological alterations due to protein over-expression may be used for the deorphanization of the y-gene transportome.
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Affiliation(s)
- Salvia Sajid
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark; Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, København Ø, Denmark
| | - Lilia Hernandez Salas
- Department of Science and Environment, Roskilde University, Universitetsvej 1, 10.1, DK-4000, Roskilde, Denmark
| | - Maria Rafiq
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, København Ø, Denmark
| | - Torben Lund
- Department of Science and Environment, Roskilde University, Universitetsvej 1, 10.1, DK-4000, Roskilde, Denmark
| | - Mikkel Girke Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Bent Honoré
- Department of Biomedicine, Aarhus University, Nordre Ringgade 1, 8000, Aarhus C, Denmark
| | - Lars Porskjær Christensen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Paul Robert Hansen
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, København Ø, Denmark
| | - Henrik Franzyk
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, København Ø, Denmark
| | - Osman Mirza
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, København Ø, Denmark
| | - Bala Krishna Prabhala
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark.
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13
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Ni Z, Wölk M, Jukes G, Mendivelso Espinosa K, Ahrends R, Aimo L, Alvarez-Jarreta J, Andrews S, Andrews R, Bridge A, Clair GC, Conroy MJ, Fahy E, Gaud C, Goracci L, Hartler J, Hoffmann N, Kopczyinki D, Korf A, Lopez-Clavijo AF, Malik A, Ackerman JM, Molenaar MR, O'Donovan C, Pluskal T, Shevchenko A, Slenter D, Siuzdak G, Kutmon M, Tsugawa H, Willighagen EL, Xia J, O'Donnell VB, Fedorova M. Guiding the choice of informatics software and tools for lipidomics research applications. Nat Methods 2023; 20:193-204. [PMID: 36543939 PMCID: PMC10263382 DOI: 10.1038/s41592-022-01710-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 11/02/2022] [Indexed: 12/24/2022]
Abstract
Progress in mass spectrometry lipidomics has led to a rapid proliferation of studies across biology and biomedicine. These generate extremely large raw datasets requiring sophisticated solutions to support automated data processing. To address this, numerous software tools have been developed and tailored for specific tasks. However, for researchers, deciding which approach best suits their application relies on ad hoc testing, which is inefficient and time consuming. Here we first review the data processing pipeline, summarizing the scope of available tools. Next, to support researchers, LIPID MAPS provides an interactive online portal listing open-access tools with a graphical user interface. This guides users towards appropriate solutions within major areas in data processing, including (1) lipid-oriented databases, (2) mass spectrometry data repositories, (3) analysis of targeted lipidomics datasets, (4) lipid identification and (5) quantification from untargeted lipidomics datasets, (6) statistical analysis and visualization, and (7) data integration solutions. Detailed descriptions of functions and requirements are provided to guide customized data analysis workflows.
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Affiliation(s)
- Zhixu Ni
- Center of Membrane Biochemistry and Lipid Research, Faculty of Medicine Carl Gustav Carus of TU Dresden, Dresden, Germany
| | - Michele Wölk
- Center of Membrane Biochemistry and Lipid Research, Faculty of Medicine Carl Gustav Carus of TU Dresden, Dresden, Germany
| | - Geoff Jukes
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK
| | | | - Robert Ahrends
- Department of Analytical Chemistry, University of Vienna, Vienna, Austria
| | - Lucila Aimo
- Swiss-Prot group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland
| | - Jorge Alvarez-Jarreta
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Simon Andrews
- Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Robert Andrews
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK
| | - Alan Bridge
- Swiss-Prot group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland
| | - Geremy C Clair
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Matthew J Conroy
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK
| | - Eoin Fahy
- Department of Bioengineering, University of California, San Diego, CA, USA
| | - Caroline Gaud
- Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Laura Goracci
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Jürgen Hartler
- Institute of Pharmaceutical Sciences, University of Graz, Graz, Austria
- Field of Excellence BioHealthe-University of Graz, Graz, Austria
| | - Nils Hoffmann
- Center for Biotechnology, University of Bielefeld, Bielefeld, Germany
| | - Dominik Kopczyinki
- Department of Analytical Chemistry, University of Vienna, Vienna, Austria
| | - Ansgar Korf
- Bruker Daltonics GmbH & Co. KG, Bremen, Germany
| | | | - Adnan Malik
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Martijn R Molenaar
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Claire O'Donovan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Tomáš Pluskal
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Denise Slenter
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
| | - Gary Siuzdak
- Scripps Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, La Jolla, CA, USA
| | - Martina Kutmon
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
- Maastricht Centre for Systems Biology, Maastricht University, Maastricht, The Netherlands
| | - Hiroshi Tsugawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Egon L Willighagen
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
| | - Jianguo Xia
- Institute of Parasitology, McGill University, Montreal, Canada
| | - Valerie B O'Donnell
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK.
| | - Maria Fedorova
- Center of Membrane Biochemistry and Lipid Research, Faculty of Medicine Carl Gustav Carus of TU Dresden, Dresden, Germany.
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14
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Lu Y, Eiriksson FF, Thorsteinsdóttir M, Cronberg N, Simonsen HT. Lipidomes of Icelandic bryophytes and screening of high contents of polyunsaturated fatty acids by using lipidomics approach. PHYTOCHEMISTRY 2023; 206:113560. [PMID: 36528120 DOI: 10.1016/j.phytochem.2022.113560] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/08/2022] [Accepted: 12/10/2022] [Indexed: 06/17/2023]
Abstract
Bryophytes (mosses, liverworts, and hornworts) have interested researchers because of their high chemical diversity and their potential uses in pharmaceutical, food, and cosmetic industries. Specifically, long-chain polyunsaturated fatty acids (l-PUFA) such as arachidonic acid (AA) and eicosapentaenoic acid (EPA) are commonly found in bryophytes, but not in vascular plants. Bryophytes accumulate PUFAs in cold or even freezing temperature to keep the cell fluidity. Iceland has a long history of bryophyte vegetation. These bryophytes are highly adapted to the harsh environment in Iceland and therefore are expected to produce high amounts of PUFAs. However, despite the fact that hundreds of mosses and liverworts have been found in Iceland, their lipid profiles largely remain unknown. In this study, we performed untargeted lipidomics by using UPLC-ESI-QTOF-MS as a rapid screening strategy to examine the lipid compositions of 39 local bryophyte species in Iceland and aimed to find high AA and EPA producers. A total of 280 lipid molecular species from 15 lipid classes were quantified with isotope-labeled internal standards. AA and EPA were abundantly distributed in the phospholipids (mainly PC and PE) and glycerolipids (MGDG and DGDG) in six moss species, namely Racomotrium lanuginosum, R. ericoides, Bryum psedotriquetrium, Plagiomnium ellipticum, Hylocomium splendens, and Rhytidiadelphus triquetrus. Two of the six species (B. psedotriquetrium and H. splendens) also accumulated high concentrations of PUFA-containing-triacylglycerols.
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Affiliation(s)
- Yi Lu
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark; ArcticMass, Reykjavik, Iceland.
| | - Finnur Freyr Eiriksson
- ArcticMass, Reykjavik, Iceland; Faculty of Pharmaceutical Sciences, University of Iceland, Reykjavik, Iceland
| | - Margrét Thorsteinsdóttir
- ArcticMass, Reykjavik, Iceland; Faculty of Pharmaceutical Sciences, University of Iceland, Reykjavik, Iceland
| | - Nils Cronberg
- Department of Biology, Lund University, Lund, Sweden
| | - Henrik Toft Simonsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark; Université Jean Monnet Saint-Etienne, CNRS, LBVpam UMR 5079, Saint-Étienne, France.
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15
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Computational mass spectrometry accelerates C = C position-resolved untargeted lipidomics using oxygen attachment dissociation. Commun Chem 2022; 5:162. [PMID: 36698019 PMCID: PMC9814143 DOI: 10.1038/s42004-022-00778-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/14/2022] [Indexed: 12/23/2022] Open
Abstract
Mass spectrometry-based untargeted lipidomics has revealed the lipidome atlas of living organisms at the molecular species level. Despite the double bond (C = C) position being a crucial factor in biological system, the C = C defined structures have not yet been characterized comprehensively. Here, we present an approach for C = C position-resolved untargeted lipidomics using a combination of oxygen attachment dissociation and computational mass spectrometry to increase the annotation rate. We validated the accuracy of our platform as per the authentic standards of 85 lipids and the biogenic standards of 52 molecules containing polyunsaturated fatty acids (PUFAs) from the cultured cells fed with various fatty acid-enriched media. By analyzing human and mice-derived samples, we characterized 648 unique lipids with the C = C position-resolved level encompassing 24 lipid subclasses defined by LIPIDMAPS. Our platform also illuminated the unique profiles of tissue-specific lipids containing n-3 and/or n-6 very long-chain PUFAs (carbon [Formula: see text] 28 and double bonds [Formula: see text] 4) in the eye, testis, and brain of the mouse.
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16
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Lu Y, Eiriksson FF, Thorsteinsdóttir M, Simonsen HT. Lipidomic analysis of moss species Bryum pseudotriquetrum and Physcomitrium patens under cold stress. PLANT-ENVIRONMENT INTERACTIONS (HOBOKEN, N.J.) 2022; 3:254-263. [PMID: 37284430 PMCID: PMC10168071 DOI: 10.1002/pei3.10095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 11/06/2022] [Accepted: 11/22/2022] [Indexed: 06/08/2023]
Abstract
Bryophytes, which lack lignin for protection, support themselves in harsh environments by producing various chemicals. In response to cold stress, lipids play a crucial role in cell adaptation and energy storage. Specifically, bryophytes survive at low temperatures by producing very long-chain polyunsaturated fatty acids (vl-PUFAs). The in-depth understanding of the lipid response to cold stress of bryophytes was studied by performing lipid profiling using ultra-high-performance liquid chromatography-quadrupole time of flight mass spectrometry (UHPLC-QTOF-MS). Two moss species (Bryum pseudotriquetrum and Physcomitrium patens) cultivated at 23°C and at 10°C were included in this study. Relative quantitative lipid concentrations were compared and the potential lipid biomarkers were identified by multivariate statistical analysis in each species. In B. pseudotriquetrum, it was observed that the phospholipids and glycolipids increased under cold stress, while storage lipids decreased. The accumulation of the lipids with high unsaturation degrees mostly appears in phospholipids and glycolipids for both mosses. The results also indicate that two unusual lipid classes in plants, sulfonolipids and phosphatidylmethanol are biosynthesized by the bryophytes. This has not been seen previously and show that bryophytes have a very diverse chemistry and substantially different from other plant groups.
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Affiliation(s)
- Yi Lu
- Department of Biotechnology and BiomedicineTechnical University of DenmarkKongens LyngbyDenmark
- ArcticMassReykjavikIceland
| | - Finnur Freyr Eiriksson
- ArcticMassReykjavikIceland
- Faculty of Pharmaceutical SciencesUniversity of IcelandReykjavikIceland
| | - Margrét Thorsteinsdóttir
- ArcticMassReykjavikIceland
- Faculty of Pharmaceutical SciencesUniversity of IcelandReykjavikIceland
| | - Henrik Toft Simonsen
- Department of Biotechnology and BiomedicineTechnical University of DenmarkKongens LyngbyDenmark
- Laboratoire Biotechnologies Végétales plantes aromatiques et médicinales, Faculté des sciencesUniversité Jean MonnetSaint‐Étienne Cédex 2France
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17
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Zhou L, Lu L, Chen C, Zhou T, Wu Q, Wen F, Chen J, Pritchard HW, Peng C, Pei J, Yan J. Comparative changes in sugars and lipids show evidence of a critical node for regeneration in safflower seeds during aging. FRONTIERS IN PLANT SCIENCE 2022; 13:1020478. [PMID: 36388552 PMCID: PMC9661361 DOI: 10.3389/fpls.2022.1020478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
During seed aging, there is a critical node (CN) where the population viability drops sharply. Exploring the specific locations of the CN in different species of plants is crucial for understanding the biological storage properties of seeds and refining seed life span management. Safflower, a bulk oil crop that relies on seeds for propagation, has a short seed life. However, at present, its biological characteristics during storage are not clear, especially the changes in metabolic capability and cell structures. Such knowledge is needed to improve the management of safflower seed life span and effective preservation in gene banks. Here, the seed survival curve of oilseed safflower under the controlled deterioration conditions of 60% relative humidity and 50°C was detected. The seed population showed an inverted S shape for the fall in germination. In the first 12 days of aging, germination remained above 86%. Prior to the CN at approximately day 10 (C10), when viability was in the "plateau" interval, seed vigor reduced at the same imbibition time point. Further analysis of the changes in sugar concentration found that the sucrose content decreased slowly with aging and the content of raffinose and two monosaccharides decreased abruptly at C10. Differentially metabolized lipids, namely lysophospholipids [lyso-phosphatidylcholine (LPC) and lyso-phosphatidylethanolamines (LPE)] and PMeOH, increased at day 3 of aging (C3). Fatty acid content increased by C6, and the content of phospholipids [phosphatidylcholines (PC), phosphatidylethanolamines (PE), and phosphatidylinositols (PI) and glycolipids [digalactosyl diacylglycerol, monogalactosyl diacylglycerol, and sulphoquinovosyl diglycerides (SQDG)] decreased significantly from C10. In addition, the activities of raffinose hydrolase alpha-galactosidase and the glyoxylate key enzyme isocitrate lyase decreased with seed aging. Confocal microscopy and transmission electron microscopy revealed shrinkage of the seed plasma membrane at C10 and the later fragmentation. Seedling phenotypic indicators and 2,3,5-triphenyltetrazolium chloride activity assays also verified that there were significant changes in seeds quality at the CN. In summary, the time point C10 is a CN during seed population aging. Before the CN, sugar and lipid metabolism, especially fatty acid metabolism into sugar, can make up for the energy consumed by aging. After this point, the seeds were irreversibly damaged, and their viability was greatly and rapidly reduced as the cell structure became increasingly destroyed.
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Affiliation(s)
- Lanyu Zhou
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Lijie Lu
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Chao Chen
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Tao Zhou
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Qinghua Wu
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Feiyan Wen
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jiang Chen
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Hugh W. Pritchard
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Wakehurst, Ardingly, United Kingdom
- Chinese Academy of Sciences, Kunming Institute of Botany, Kunming Yunnan, China
| | - Cheng Peng
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jin Pei
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jie Yan
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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18
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Wase N, Gutiérrez JM, Rucavado A, Fox JW. Longitudinal Metabolomics and Lipidomics Analyses Reveal Alterations Associated with Envenoming by Bothrops asper and Daboia russelii in an Experimental Murine Model. Toxins (Basel) 2022; 14:657. [PMID: 36287926 PMCID: PMC9610966 DOI: 10.3390/toxins14100657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/18/2022] [Accepted: 09/20/2022] [Indexed: 12/26/2023] Open
Abstract
Longitudinal metabolomics and lipidomics analyses were carried out on the blood plasma of mice injected intramuscularly with venoms of the viperid species Bothrops asper or Daboia russelii. Blood samples were collected 1, 3, 6, and 24 h after venom injection, and a control group of non-envenomed mice was included. Significant perturbations in metabolomics and lipidomics were observed at 1, 3, and 6 h, while values returned close to those of control mice by 24 h, hence reflecting a transient pattern of metabolic disturbance. Both venoms induced significant changes in amino acids, as well as in several purines and pyrimidines, and in some metabolites of the tricarboxylic acid cycle. KEGG analysis of metabolic pathways that showed those with the greatest change included aminoacyl tRNA synthesis and amino acid biosynthesis and metabolism pathways. With regard to lipid metabolism, there was an increase in triglycerides and some acyl carnitines and a concomitant drop in the levels of some phospholipids. In addition, envenomed mice had higher levels of cortisol, heme, and some oxidative stress markers. The overall pattern of metabolic changes in envenomed mice bears similarities with the patterns described in several traumatic injuries, thus underscoring a metabolic response/adaptation to the injurious action of the venoms.
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Affiliation(s)
- Nishikant Wase
- School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - José María Gutiérrez
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José 11501, Costa Rica
| | - Alexandra Rucavado
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José 11501, Costa Rica
| | - Jay W. Fox
- School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
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19
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Moreira AS, Gonçalves J, Conde TA, Couto D, Melo T, Maia IB, Pereira H, Silva J, Domingues MR, Nunes C. Chrysotila pseudoroscoffensis as a source of high-value polar lipids with antioxidant activity: A lipidomic approach. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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20
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Choueiry F, Zhu J. Secondary electrospray ionization-high resolution mass spectrometry (SESI-HRMS) fingerprinting enabled treatment monitoring of pulmonary carcinoma cells in real time. Anal Chim Acta 2022; 1189:339230. [PMID: 34815037 PMCID: PMC8613447 DOI: 10.1016/j.aca.2021.339230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/05/2021] [Accepted: 10/28/2021] [Indexed: 01/04/2023]
Abstract
Lung cancer is one of the leading causes of cancer related deaths in the United States. A novel volatile analysis platform is needed to complement current diagnostic techniques and better elucidate chemical signatures of lung cancer and subsequent treatments. A systems biology bottom-up approach using cell culture volatilomics was employed to identify pathological volatile fingerprints of lung cancer in real time. An advanced secondary electrospray ionization (SESI) source, named SuperSESI was used in this study and directly attached to a Thermo Q-Exactive high-resolution mass spectrometer (HRMS). We performed a series of experiments to determine if our optimized SESI-HRMS platform can distinguish between cancer types by sampling their in vitro volatilome profiles. We detected 60 significant volatile organic compound (VOC) features in positive mode that were deemed of cancer cell origin. The cell derived features were used for subsequent analyses to distinguish between our two studied lung cancer types, non-small cell lung cancer (NSCLC) and small cell lung cancer (SCLC). Partial least squares-discriminant analysis (PLS-DA) model revealed a good separation of the two cancer types, suggesting unique chemical composition of their headspace profiles. A receiver operating characteristic (ROC) curve using 10 prominent features was used to predict disease type, with an area under the curve (AUC) of 0.811. Cultures were also treated with cisplatin to determine the feasibility of classifying drug treatment from expelled gases. A PLS-DA model revealed independent clustering based on their headspace profiles. An ROC curve using the top features driving separation of PLS-DA model suggested good accuracy with an AUC of 1. It is thus possible to benefit from the advantages of this platform to distinguish the unique volatile fingerprints of cancers to uncover potential biomarkers for cancer type differentiation and treatment monitoring.
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Affiliation(s)
- Fouad Choueiry
- Department of Human Sciences, The Ohio State University; Columbus, OH 43210
| | - Jiangjiang Zhu
- Department of Human Sciences, The Ohio State University; Columbus, OH 43210, James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210
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21
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Jarmusch SA, van der Hooft JJJ, Dorrestein PC, Jarmusch AK. Advancements in capturing and mining mass spectrometry data are transforming natural products research. Nat Prod Rep 2021; 38:2066-2082. [PMID: 34612288 PMCID: PMC8667781 DOI: 10.1039/d1np00040c] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Covering: 2016 up to 2021Mass spectrometry (MS) is an essential technology in natural products research with MS fragmentation (MS/MS) approaches becoming a key tool. Recent advancements in MS yield dense metabolomics datasets which have been, conventionally, used by individual labs for individual projects; however, a shift is brewing. The movement towards open MS data (and other structural characterization data) and accessible data mining tools is emerging in natural products research. Over the past 5 years, this movement has rapidly expanded and evolved with no slowdown in sight; the capabilities of today vastly exceed those of 5 years ago. Herein, we address the analysis of individual datasets, a situation we are calling the '2021 status quo', and the emergent framework to systematically capture sample information (metadata) and perform repository-scale analyses. We evaluate public data deposition, discuss the challenges of working in the repository scale, highlight the challenges of metadata capture and provide illustrative examples of the power of utilizing repository data and the tools that enable it. We conclude that the advancements in MS data collection must be met with advancements in how we utilize data; therefore, we argue that open data and data mining is the next evolution in obtaining the maximum potential in natural products research.
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Affiliation(s)
- Scott A Jarmusch
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, DK-2800 Kongens Lyngby, Denmark.
| | | | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093-0751, USA
| | - Alan K Jarmusch
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093-0751, USA
- Immunity, Inflammation, and Disease Laboratory, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
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22
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Villaseñor A, Godzien J, Barker-Tejeda TC, Gonzalez-Riano C, López-López Á, Dudzik D, Gradillas A, Barbas C. Analytical approaches for studying oxygenated lipids in the search of potential biomarkers by LC-MS. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116367] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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23
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da Silva KM, Iturrospe E, Bars C, Knapen D, Van Cruchten S, Covaci A, van Nuijs ALN. Mass Spectrometry-Based Zebrafish Toxicometabolomics: A Review of Analytical and Data Quality Challenges. Metabolites 2021; 11:metabo11090635. [PMID: 34564451 PMCID: PMC8467701 DOI: 10.3390/metabo11090635] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 12/17/2022] Open
Abstract
Metabolomics has achieved great progress over the last 20 years, and it is currently considered a mature research field. As a result, the number of applications in toxicology, biomarker, and drug discovery has also increased. Toxicometabolomics has emerged as a powerful strategy to provide complementary information to study molecular-level toxic effects, which can be combined with a wide range of toxicological assessments and models. The zebrafish model has gained importance in recent decades as a bridging tool between in vitro assays and mammalian in vivo studies in the field of toxicology. Furthermore, as this vertebrate model is a low-cost system and features highly conserved metabolic pathways found in humans and mammalian models, it is a promising tool for toxicometabolomics. This short review aims to introduce zebrafish researchers interested in understanding the effects of chemical exposure using metabolomics to the challenges and possibilities of the field, with a special focus on toxicometabolomics-based mass spectrometry. The overall goal is to provide insights into analytical strategies to generate and identify high-quality metabolomic experiments focusing on quality management systems (QMS) and the importance of data reporting and sharing.
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Affiliation(s)
- Katyeny Manuela da Silva
- Toxicological Center, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, Campus Drie Eiken, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; (E.I.); (A.C.)
- Correspondence: (K.M.d.S.); (A.L.N.v.N.)
| | - Elias Iturrospe
- Toxicological Center, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, Campus Drie Eiken, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; (E.I.); (A.C.)
- Department of In Vitro Toxicology and Dermato-Cosmetology, Faculty of Medicine and Pharmacy, Campus Jette, Free University of Brussels, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Chloe Bars
- Comparative Perinatal Development, Department of Veterinary Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, Campus Drie Eiken, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; (C.B.); (S.V.C.)
| | - Dries Knapen
- Zebrafishlab, Veterinary Physiology and Biochemistry, Department of Veterinary Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, Campus Drie Eiken, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium;
| | - Steven Van Cruchten
- Comparative Perinatal Development, Department of Veterinary Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, Campus Drie Eiken, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; (C.B.); (S.V.C.)
| | - Adrian Covaci
- Toxicological Center, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, Campus Drie Eiken, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; (E.I.); (A.C.)
| | - Alexander L. N. van Nuijs
- Toxicological Center, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, Campus Drie Eiken, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; (E.I.); (A.C.)
- Correspondence: (K.M.d.S.); (A.L.N.v.N.)
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24
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Non-targeted analysis of vulgarisins by using collisional dissociation mass spectrometry for the discovery of analogues from Prunella vulgaris. Anal Bioanal Chem 2021; 413:6513-6521. [PMID: 34476524 DOI: 10.1007/s00216-021-03615-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/20/2021] [Accepted: 08/10/2021] [Indexed: 01/09/2023]
Abstract
Vulgarisins are members of diterpenoids with rare 5/6/4/5 ring skeleton from Prunella vulgaris Linn. (P. vulgaris). Their molecular scaffolds comprise different hydroxylation and degree of esterification. Vulgarisins have attracted many attentions in the fields of food and medicine for their potent bioactivities. Firstly, four reference compounds were analyzed by higher-energy collisional dissociation mass spectrometry (HCD MS/MS) and the fragmentation patterns for molecular scaffold were summarized. And then, a high-performance liquid chromatography/electrospray ionization/high-resolution mass spectrometry (HPLC-ESI-HR-MS) method was adopted to investigate the P. vulgaris extracts. Finally, the proposed analysis results were successfully applied to facilitate the discovery of the vulgarisins analogues from P. vulgaris. For the four reference compounds, the sodium adduct was the predominate ion in full scan. A specific fragmentation pathway of [M+Na]+ ions leads to produce diagnostic ions of vulgarisins at m/z 325 under HCD, which was formed through consecutive-side chains lost. Twenty-three diterpenoids, including 18 vulgarisins analogues, were identified or tentatively characterized in the botanical extracts of P. vulgaris based on their elemental constituents and characteristic fragment ion profiles. Two new vulgarisins analogues in the plant were isolated and their structures were illustrated based on extensive spectroscopic analysis using 1D and 2D nuclear magnetic resonance (NMR) spectroscopy. The HCD MS/MS method, including the profiles of the diagnostic ions induced by characteristic fragmentation, is an effective technique for the discovery of vulgarisins analogues in P. vulgaris. The expected fragmentation pattern knowledge will also facilitate the analysis of other natural products.
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25
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Shen H, Zhang Y, Schramm KW. Analytical aspects of meet-in-metabolite analysis for molecular pathway reconstitution from exposure to adverse outcome. Mol Aspects Med 2021; 87:101006. [PMID: 34304900 DOI: 10.1016/j.mam.2021.101006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 06/05/2021] [Accepted: 07/20/2021] [Indexed: 12/22/2022]
Abstract
To explore the etiology of diseases is one of the major goals in epidemiological study. Meet-in-metabolite analysis reconstitutes biomonitoring-based adverse outcome (AO) pathways from environmental exposure to a disease, in which the chemical exposome-related metabolism responses are transmitted to incur the AO-related metabolism phenotypes. However, the ongoing data-dependent acquisition of non-targeted biomonitoring by high-resolution mass spectrometry (HRMS) is biased against the low abundance molecules, which forms the major of molecular internal exposome, i.e., the totality of trace levels of environmental pollutants and/or their metabolites in human samples. The recent development of data-independent acquisition protocols for HRMS screening has opened new opportunities to enhance unbiased measurement of the extremely low abundance molecules, which can encompass a wide range of analytes and has been applied in metabolomics, DNA, and protein adductomics. In addition, computational MS for small molecules is urgently required for the top-down exposome databases. Although a holistic analysis of the exposome and endogenous metabolites is plausible, multiple and flexible strategies, instead of "putting one thing above all" are proposed.
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Affiliation(s)
- Heqing Shen
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, 361102, Xiamen, PR China.
| | - Yike Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, 361102, Xiamen, PR China
| | - Karl-Werner Schramm
- Helmholtz Zentrum München, Molecular EXposomics, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.
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26
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Diray-Arce J, Conti MG, Petrova B, Kanarek N, Angelidou A, Levy O. Integrative Metabolomics to Identify Molecular Signatures of Responses to Vaccines and Infections. Metabolites 2020; 10:E492. [PMID: 33266347 PMCID: PMC7760881 DOI: 10.3390/metabo10120492] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/24/2020] [Accepted: 11/30/2020] [Indexed: 12/16/2022] Open
Abstract
Approaches to the identification of metabolites have progressed from early biochemical pathway evaluation to modern high-dimensional metabolomics, a powerful tool to identify and characterize biomarkers of health and disease. In addition to its relevance to classic metabolic diseases, metabolomics has been key to the emergence of immunometabolism, an important area of study, as leukocytes generate and are impacted by key metabolites important to innate and adaptive immunity. Herein, we discuss the metabolomic signatures and pathways perturbed by the activation of the human immune system during infection and vaccination. For example, infection induces changes in lipid (e.g., free fatty acids, sphingolipids, and lysophosphatidylcholines) and amino acid pathways (e.g., tryptophan, serine, and threonine), while vaccination can trigger changes in carbohydrate and bile acid pathways. Amino acid, carbohydrate, lipid, and nucleotide metabolism is relevant to immunity and is perturbed by both infections and vaccinations. Metabolomics holds substantial promise to provide fresh insight into the molecular mechanisms underlying the host immune response. Its integration with other systems biology platforms will enhance studies of human health and disease.
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Affiliation(s)
- Joann Diray-Arce
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children’s Hospital, Boston, MA 02115, USA; (M.G.C.); (A.A.)
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; (B.P.); (N.K.)
| | - Maria Giulia Conti
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children’s Hospital, Boston, MA 02115, USA; (M.G.C.); (A.A.)
- Department of Maternal and Child Health, Sapienza University of Rome, 5, 00185 Rome, Italy
| | - Boryana Petrova
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; (B.P.); (N.K.)
- Department of Pathology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Naama Kanarek
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; (B.P.); (N.K.)
- Department of Pathology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Asimenia Angelidou
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children’s Hospital, Boston, MA 02115, USA; (M.G.C.); (A.A.)
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; (B.P.); (N.K.)
- Department of Neonatology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Ofer Levy
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children’s Hospital, Boston, MA 02115, USA; (M.G.C.); (A.A.)
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; (B.P.); (N.K.)
- Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA
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27
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Xu T, Hu C, Xuan Q, Xu G. Recent advances in analytical strategies for mass spectrometry-based lipidomics. Anal Chim Acta 2020; 1137:156-169. [PMID: 33153599 PMCID: PMC7525665 DOI: 10.1016/j.aca.2020.09.060] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 12/20/2022]
Abstract
Lipids are vital biological molecules and play multiple roles in cellular function of mammalian organisms such as cellular membrane anchoring, signal transduction, material trafficking and energy storage. Driven by the biological significance of lipids, lipidomics has become an emerging science in the field of omics. Lipidome in biological systems consists of hundreds of thousands of individual lipid molecules that possess complex structures, multiple categories, and diverse physicochemical properties assembled by different combinations of polar headgroups and hydrophobic fatty acyl chains. Such structural complexity poses a huge challenge for comprehensive lipidome analysis. Thanks to the great innovations in chromatographic separation techniques and the continuous advances in mass spectrometric detection tools, analytical strategies for lipidomics have been highly diversified so that the depth and breadth of lipidomics have been greatly enhanced. This review will present the current state of mass spectrometry-based analytical strategies including untargeted, targeted and pseudotargeted lipidomics. Recent typical applications of lipidomics in biomarker discovery, pathogenic mechanism and therapeutic strategy are summarized, and the challenges facing to the field of lipidomics are also discussed.
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Affiliation(s)
- Tianrun Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunxiu Hu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiuhui Xuan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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28
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Miralles A, Bruy T, Wolcott K, Scherz MD, Begerow D, Beszteri B, Bonkowski M, Felden J, Gemeinholzer B, Glaw F, Glöckner FO, Hawlitschek O, Kostadinov I, Nattkemper TW, Printzen C, Renz J, Rybalka N, Stadler M, Weibulat T, Wilke T, Renner SS, Vences M. Repositories for Taxonomic Data: Where We Are and What is Missing. Syst Biol 2020; 69:1231-1253. [PMID: 32298457 PMCID: PMC7584136 DOI: 10.1093/sysbio/syaa026] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 02/20/2020] [Accepted: 03/24/2020] [Indexed: 12/05/2022] Open
Abstract
Natural history collections are leading successful large-scale projects of specimen digitization (images, metadata, DNA barcodes), thereby transforming taxonomy into a big data science. Yet, little effort has been directed towards safeguarding and subsequently mobilizing the considerable amount of original data generated during the process of naming 15,000-20,000 species every year. From the perspective of alpha-taxonomists, we provide a review of the properties and diversity of taxonomic data, assess their volume and use, and establish criteria for optimizing data repositories. We surveyed 4113 alpha-taxonomic studies in representative journals for 2002, 2010, and 2018, and found an increasing yet comparatively limited use of molecular data in species diagnosis and description. In 2018, of the 2661 papers published in specialized taxonomic journals, molecular data were widely used in mycology (94%), regularly in vertebrates (53%), but rarely in botany (15%) and entomology (10%). Images play an important role in taxonomic research on all taxa, with photographs used in >80% and drawings in 58% of the surveyed papers. The use of omics (high-throughput) approaches or 3D documentation is still rare. Improved archiving strategies for metabarcoding consensus reads, genome and transcriptome assemblies, and chemical and metabolomic data could help to mobilize the wealth of high-throughput data for alpha-taxonomy. Because long-term-ideally perpetual-data storage is of particular importance for taxonomy, energy footprint reduction via less storage-demanding formats is a priority if their information content suffices for the purpose of taxonomic studies. Whereas taxonomic assignments are quasifacts for most biological disciplines, they remain hypotheses pertaining to evolutionary relatedness of individuals for alpha-taxonomy. For this reason, an improved reuse of taxonomic data, including machine-learning-based species identification and delimitation pipelines, requires a cyberspecimen approach-linking data via unique specimen identifiers, and thereby making them findable, accessible, interoperable, and reusable for taxonomic research. This poses both qualitative challenges to adapt the existing infrastructure of data centers to a specimen-centered concept and quantitative challenges to host and connect an estimated $ \le $2 million images produced per year by alpha-taxonomic studies, plus many millions of images from digitization campaigns. Of the 30,000-40,000 taxonomists globally, many are thought to be nonprofessionals, and capturing the data for online storage and reuse therefore requires low-complexity submission workflows and cost-free repository use. Expert taxonomists are the main stakeholders able to identify and formalize the needs of the discipline; their expertise is needed to implement the envisioned virtual collections of cyberspecimens. [Big data; cyberspecimen; new species; omics; repositories; specimen identifier; taxonomy; taxonomic data.].
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Affiliation(s)
- Aurélien Miralles
- Departement Origins and Evolution, Institut Systématique, Evolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP50, 75005 Paris, France
- Systematic Botany and Mycology, University of Munich (LMU), Menzingerstraße 67, 80638 Munich, Germany
| | - Teddy Bruy
- Departement Origins and Evolution, Institut Systématique, Evolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP50, 75005 Paris, France
- Systematic Botany and Mycology, University of Munich (LMU), Menzingerstraße 67, 80638 Munich, Germany
| | - Katherine Wolcott
- Systematic Botany and Mycology, University of Munich (LMU), Menzingerstraße 67, 80638 Munich, Germany
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Mark D Scherz
- Department of Herpetology, Zoologische Staatssammlung München (ZSM-SNSB), Münchhausenstraße 21, 81247 München, Germany
- Department of Biology, Universität Konstanz, Universitätstraße 10, 78464 Konstanz, Germany
| | - Dominik Begerow
- Department of Geobotany, Ruhr-University Bochum, Universitätsstraße 150, 44780 Bochum, Germany
| | - Bank Beszteri
- Department of Phycology, Faculty of Biology, University of Duisburg-Essen, Universitätsstraße 2, 45141 Essen, Germany
| | - Michael Bonkowski
- Department of Terrestrial Ecology, Center of Excellence in Plant Sciences (CEPLAS), Terrestrial Ecology, Institute of Zoology, University of Cologne, 50674 Köln, Germany
| | - Janine Felden
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Leobenerstraße 8, 28359 Bremen, Germany
- Alfred Wegener Institute - Helmholtz Center for Polar- and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Birgit Gemeinholzer
- Department of Systematic Botany, Justus Liebig University Gießen, Heinrich-Buff Ring 38, 35392 Giessen, Germany
| | - Frank Glaw
- Department of Herpetology, Zoologische Staatssammlung München (ZSM-SNSB), Münchhausenstraße 21, 81247 München, Germany
| | - Frank Oliver Glöckner
- Alfred Wegener Institute - Helmholtz Center for Polar- and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Oliver Hawlitschek
- Department of Herpetology, Zoologische Staatssammlung München (ZSM-SNSB), Münchhausenstraße 21, 81247 München, Germany
- Department of Scientific Infrastructure, Centrum für Naturkunde (CeNak), Universität Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Ivaylo Kostadinov
- GFBio - Gesellschaft für Biologische Daten e.V., c/o Research II, Campus Ring 1, 28759 Bremen, Germany
| | - Tim W Nattkemper
- Biodata Mining Group, Center of Biotechnology (CeBiTec), Bielefeld University, PO Box 100131, 33501 Bielefeld, Germany
| | - Christian Printzen
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, 60325 Frankfurt/Main, Germany
| | - Jasmin Renz
- Zooplankton Research Group, DZMB – Senckenberg am Meer, Martin-Luther-King Platz 3, 20146 Hamburg, Germany
| | - Nataliya Rybalka
- Department of Experimental Phycology and Culture Collection of Algae, University Göttingen, Nikolausberger-Weg 18, 37073 Göttingen, Germany
| | - Marc Stadler
- Department Microbial Drugs, Helmholtz Centre for Infection Research (HZI), and German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Tanja Weibulat
- GFBio - Gesellschaft für Biologische Daten e.V., c/o Research II, Campus Ring 1, 28759 Bremen, Germany
| | - Thomas Wilke
- Department of Animal Ecology and Systematics, Justus Liebig University Gießen, Heinrich-Buff Ring 26, 35392 Giessen, Germany
| | - Susanne S Renner
- Systematic Botany and Mycology, University of Munich (LMU), Menzingerstraße 67, 80638 Munich, Germany
| | - Miguel Vences
- Department of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, Mendelssohnstraße 4, 38106 Braunschweig, Germany
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29
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Tian H, Zhou Z, Shui G, Lam SM. Extensive Profiling of Polyphenols from two Trollius Species Using a Combination of Untargeted and Targeted Approaches. Metabolites 2020; 10:metabo10030119. [PMID: 32210165 PMCID: PMC7143900 DOI: 10.3390/metabo10030119] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/15/2020] [Accepted: 03/20/2020] [Indexed: 12/13/2022] Open
Abstract
Various species of globeflowers, belonging to the genus Trollius, have been extensively used in traditional Chinese medicine due to their anti-inflammatory, antimicrobial, and antiviral properties, which are mainly attributed to their high polyphenol content. Differences in polyphenol composition, and abundances, will lead to varying treatment efficacies of globeflowers. Herein, we employ a combination of targeted and untargeted mass spectrometry (MS) approaches to characterize and quantify a comprehensive array of polyphenols, mainly including flavonoids and phenolic acids in two globeflower species commonly used in Chinese medicine, Trollius chinensis Bunge and Trollius ledebouri Reichb. In addition, free radical scavenging activity was investigated to evaluate the association between polyphenol composition and antioxidation capacity. Liquid chromatography (LC)-based separation and multiple-reaction-monitoring (MRM) transitions were optimized using a library of 78 polyphenol reference compounds to achieve absolute quantification on triple quadrupoles MS (QqQ). The analytical method was further expanded via high-resolution MS to provide relative quantitation of an additional 104 endogenous polyphenols in globeflowers not included in our reference library. Our results revealed stark differences in polyphenol content between T. chinensis and T. ledebouri, emphasizing the need for systematic characterization of polyphenol composition to ensure treatment efficacy and consistency in standardizing the use of globeflowers in Chinese medicine.
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Affiliation(s)
- He Tian
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China;
| | - Zhiyang Zhou
- Lipidall Technologies Company Limited, Changzhou 213022, China;
| | - Guanghou Shui
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China;
- Correspondence: (G.S.); (S.M.L.); Tel.: +86-106-480-8831 (G.S.); +86-106-480-6670 (S.M.L.)
| | - Sin Man Lam
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China;
- Lipidall Technologies Company Limited, Changzhou 213022, China;
- Correspondence: (G.S.); (S.M.L.); Tel.: +86-106-480-8831 (G.S.); +86-106-480-6670 (S.M.L.)
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Marcellin-Gros R, Piganeau G, Stien D. Metabolomic Insights into Marine Phytoplankton Diversity. Mar Drugs 2020; 18:E78. [PMID: 31991720 PMCID: PMC7074452 DOI: 10.3390/md18020078] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 01/10/2020] [Accepted: 01/22/2020] [Indexed: 02/08/2023] Open
Abstract
The democratization of sequencing technologies fostered a leap in our knowledge of the diversity of marine phytoplanktonic microalgae, revealing many previously unknown species and lineages. The evolutionary history of the diversification of microalgae can be inferred from the analysis of their genome sequences. However, the link between the DNA sequence and the associated phenotype is notoriously difficult to assess, all the more so for marine phytoplanktonic microalgae for which the lab culture and, thus, biological experimentation is very tedious. Here, we explore the potential of a high-throughput untargeted metabolomic approach to explore the phenotypic-genotypic gap in 12 marine microalgae encompassing 1.2 billion years of evolution. We identified species- and lineage-specific metabolites. We also provide evidence of a very good correlation between the molecular divergence, inferred from the DNA sequences, and the metabolomic divergence, inferred from the complete metabolomic profiles. These results provide novel insights into the potential of chemotaxonomy in marine phytoplankton and support the hypothesis of a metabolomic clock, suggesting that DNA and metabolomic profiles co-evolve.
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Affiliation(s)
- Rémy Marcellin-Gros
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologie Microbiennes, LBBM, Observatoire Océanologique, 66650 Banyuls-sur-Mer, France;
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, Observatoire Océanologique, 66650 Banyuls-sur-Mer, France
| | - Gwenaël Piganeau
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, Observatoire Océanologique, 66650 Banyuls-sur-Mer, France
| | - Didier Stien
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologie Microbiennes, LBBM, Observatoire Océanologique, 66650 Banyuls-sur-Mer, France;
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Naoe S, Tsugawa H, Takahashi M, Ikeda K, Arita M. Characterization of Lipid Profiles after Dietary Intake of Polyunsaturated Fatty Acids Using Integrated Untargeted and Targeted Lipidomics. Metabolites 2019; 9:E241. [PMID: 31640217 PMCID: PMC6836067 DOI: 10.3390/metabo9100241] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/17/2019] [Accepted: 10/17/2019] [Indexed: 12/25/2022] Open
Abstract
Illuminating the comprehensive lipid profiles after dietary supplementation of polyunsaturated fatty acids (PUFAs) is crucial to revealing the tissue distribution of PUFAs in living organisms, as well as to providing novel insights into lipid metabolism. Here, we performed lipidomic analyses on mouse plasma and nine tissues, including the liver, kidney, brain, white adipose, heart, lung, small intestine, skeletal muscle, and spleen, with the dietary intake conditions of arachidonic acid (ARA), eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA) as the ethyl ester form. We incorporated targeted and untargeted approaches for profiling oxylipins and complex lipids such as glycerol (phospho) lipids, sphingolipids, and sterols, respectively, which led to the characterization of 1026 lipid molecules from the mouse tissues. The lipidomic analysis indicated that the intake of PUFAs strongly impacted the lipid profiles of metabolic organs such as the liver and kidney, while causing less impact on the brain. Moreover, we revealed a unique lipid modulation in most tissues, where phospholipids containing linoleic acid were significantly decreased in mice on the ARA-supplemented diet, and bis(monoacylglycero)phosphate (BMP) selectively incorporated DHA over ARA and EPA. We comprehensively studied the lipid profiles after dietary intake of PUFAs, which gives insight into lipid metabolism and nutrition research on PUFA supplementation.
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Affiliation(s)
- Satoko Naoe
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.
| | - Hiroshi Tsugawa
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.
- Metabolome informatics research team, RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan.
| | - Mikiko Takahashi
- Metabolome informatics research team, RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan.
| | - Kazutaka Ikeda
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.
- Cellular and Molecular Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan.
| | - Makoto Arita
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.
- Cellular and Molecular Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan.
- Division of Physiological Chemistry and Metabolism, Graduate School of Pharmaceutical Sciences, Keio University, Minato-ku, Tokyo 105-8512, Japan.
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