1
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Kinmonth-Schultz H, Walker SM, Bingol K, Hoyt DW, Kim YM, Markillie LM, Mitchell HD, Nicora CD, Taylor R, Ward JK. Oligosaccharide production and signaling correlate with delayed flowering in an Arabidopsis genotype grown and selected in high [CO2]. PLoS One 2023; 18:e0287943. [PMID: 38153952 PMCID: PMC10754469 DOI: 10.1371/journal.pone.0287943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 12/05/2023] [Indexed: 12/30/2023] Open
Abstract
Since industrialization began, atmospheric CO2 ([CO2]) has increased from 270 to 415 ppm and is projected to reach 800-1000 ppm this century. Some Arabidopsis thaliana (Arabidopsis) genotypes delayed flowering in elevated [CO2] relative to current [CO2], while others showed no change or accelerations. To predict genotype-specific flowering behaviors, we must understand the mechanisms driving flowering response to rising [CO2]. [CO2] changes alter photosynthesis and carbohydrates in plants. Plants sense carbohydrate levels, and exogenous carbohydrate application influences flowering time and flowering transcript levels. We asked how organismal changes in carbohydrates and transcription correlate with changes in flowering time under elevated [CO2]. We used a genotype (SG) of Arabidopsis that was selected for high fitness at elevated [CO2] (700 ppm). SG delays flowering under elevated [CO2] (700 ppm) relative to current [CO2] (400 ppm). We compared SG to a closely related control genotype (CG) that shows no [CO2]-induced flowering change. We compared metabolomic and transcriptomic profiles in these genotypes at current and elevated [CO2] to assess correlations with flowering in these conditions. While both genotypes altered carbohydrates in response to elevated [CO2], SG had higher levels of sucrose than CG and showed a stronger increase in glucose and fructose in elevated [CO2]. Both genotypes demonstrated transcriptional changes, with CG increasing genes related to fructose 1,6-bisphosphate breakdown, amino acid synthesis, and secondary metabolites; and SG decreasing genes related to starch and sugar metabolism, but increasing genes involved in oligosaccharide production and sugar modifications. Genes associated with flowering regulation within the photoperiod, vernalization, and meristem identity pathways were altered in these genotypes. Elevated [CO2] may alter carbohydrates to influence transcription in both genotypes and delayed flowering in SG. Changes in the oligosaccharide pool may contribute to delayed flowering in SG. This work extends the literature exploring genotypic-specific flowering responses to elevated [CO2].
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Affiliation(s)
- Hannah Kinmonth-Schultz
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, United States of America
- Departiment of Biology, Tennessee Technological University, Cookeville, TN, United States of America
| | - Stephen Michael Walker
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, United States of America
| | - Kerem Bingol
- Department of Energy, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States of America
| | - David W. Hoyt
- Department of Energy, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States of America
| | - Young-Mo Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States of America
| | - Lye Meng Markillie
- Department of Energy, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States of America
| | - Hugh D. Mitchell
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States of America
| | - Carrie D. Nicora
- Department of Energy, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States of America
| | - Ronald Taylor
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States of America
| | - Joy K. Ward
- Department of Biology, College of Arts and Sciences, Case Western Reserve University, Cleveland, OH, United States of America
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2
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Wang G, Zhao Z, Ke J, Engel Y, Shi YM, Robinson D, Bingol K, Zhang Z, Bowen B, Louie K, Wang B, Evans R, Miyamoto Y, Cheng K, Kosina S, De Raad M, Silva L, Luhrs A, Lubbe A, Hoyt DW, Francavilla C, Otani H, Deutsch S, Washton NM, Rubin EM, Mouncey NJ, Visel A, Northen T, Cheng JF, Bode HB, Yoshikuni Y. CRAGE enables rapid activation of biosynthetic gene clusters in undomesticated bacteria. Nat Microbiol 2019; 4:2498-2510. [PMID: 31611640 DOI: 10.1038/s41564-019-0573-8] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 08/27/2019] [Indexed: 12/11/2022]
Abstract
It is generally believed that exchange of secondary metabolite biosynthetic gene clusters (BGCs) among closely related bacteria is an important driver of BGC evolution and diversification. Applying this idea may help researchers efficiently connect many BGCs to their products and characterize the products' roles in various environments. However, existing genetic tools support only a small fraction of these efforts. Here, we present the development of chassis-independent recombinase-assisted genome engineering (CRAGE), which enables single-step integration of large, complex BGC constructs directly into the chromosomes of diverse bacteria with high accuracy and efficiency. To demonstrate the efficacy of CRAGE, we expressed three known and six previously identified but experimentally elusive non-ribosomal peptide synthetase (NRPS) and NRPS-polyketide synthase (PKS) hybrid BGCs from Photorhabdus luminescens in 25 diverse γ-Proteobacteria species. Successful activation of six BGCs identified 22 products for which diversity and yield were greater when the BGCs were expressed in strains closely related to the native strain than when they were expressed in either native or more distantly related strains. Activation of these BGCs demonstrates the feasibility of exploiting their underlying catalytic activity and plasticity, and provides evidence that systematic approaches based on CRAGE will be useful for discovering and identifying previously uncharacterized metabolites.
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Affiliation(s)
- Gaoyan Wang
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Zhiying Zhao
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Jing Ke
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Yvonne Engel
- Molecular Biotechnology, Department of Biosciences and Buchmann Institute for Molecular Life Sciences, Goethe Universität Frankfurt, Frankfurt am Main, Germany
| | - Yi-Ming Shi
- Molecular Biotechnology, Department of Biosciences and Buchmann Institute for Molecular Life Sciences, Goethe Universität Frankfurt, Frankfurt am Main, Germany
| | - David Robinson
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Kerem Bingol
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Zheyun Zhang
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Benjamin Bowen
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Katherine Louie
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Bing Wang
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Robert Evans
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Yu Miyamoto
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Kelly Cheng
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Suzanne Kosina
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Markus De Raad
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Leslie Silva
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | | | | | - David W Hoyt
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | | | - Hiroshi Otani
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Samuel Deutsch
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nancy M Washton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Edward M Rubin
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Nigel J Mouncey
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Axel Visel
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Trent Northen
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jan-Fang Cheng
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Helge B Bode
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA. .,LOEWE Centre for Translational Biodiversity Genomics, Frankfurt, Germany.
| | - Yasuo Yoshikuni
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA. .,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, IL, USA. .,Global Institution for Collaborative Research and Education, Hokkaido University, Hokkaido, Japan.
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3
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Bingol K. Recent Advances in Targeted and Untargeted Metabolomics by NMR and MS/NMR Methods. High Throughput 2018; 7:E9. [PMID: 29670016 PMCID: PMC6023270 DOI: 10.3390/ht7020009] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 04/09/2018] [Accepted: 04/13/2018] [Indexed: 12/23/2022] Open
Abstract
Metabolomics has made significant progress in multiple fronts in the last 18 months. This minireview aimed to give an overview of these advancements in the light of their contribution to targeted and untargeted metabolomics. New computational approaches have emerged to overcome the manual absolute quantitation step of metabolites in one-dimensional (1D) ¹H nuclear magnetic resonance (NMR) spectra. This provides more consistency between inter-laboratory comparisons. Integration of two-dimensional (2D) NMR metabolomics databases under a unified web server allowed for very accurate identification of the metabolites that have been catalogued in these databases. For the remaining uncatalogued and unknown metabolites, new cheminformatics approaches have been developed by combining NMR and mass spectrometry (MS). These hybrid MS/NMR approaches accelerated the identification of unknowns in untargeted studies, and now they are allowing for profiling ever larger number of metabolites in application studies.
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Affiliation(s)
- Kerem Bingol
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA.
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4
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Boiteau RM, Hoyt DW, Nicora CD, Kinmonth-Schultz HA, Ward JK, Bingol K. Structure Elucidation of Unknown Metabolites in Metabolomics by Combined NMR and MS/MS Prediction. Metabolites 2018; 8:metabo8010008. [PMID: 29342073 PMCID: PMC5875998 DOI: 10.3390/metabo8010008] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 01/13/2018] [Accepted: 01/13/2018] [Indexed: 11/16/2022] Open
Abstract
We introduce a cheminformatics approach that combines highly selective and orthogonal structure elucidation parameters; accurate mass, MS/MS (MS²), and NMR into a single analysis platform to accurately identify unknown metabolites in untargeted studies. The approach starts with an unknown LC-MS feature, and then combines the experimental MS/MS and NMR information of the unknown to effectively filter out the false positive candidate structures based on their predicted MS/MS and NMR spectra. We demonstrate the approach on a model mixture, and then we identify an uncatalogued secondary metabolite in Arabidopsis thaliana. The NMR/MS² approach is well suited to the discovery of new metabolites in plant extracts, microbes, soils, dissolved organic matter, food extracts, biofuels, and biomedical samples, facilitating the identification of metabolites that are not present in experimental NMR and MS metabolomics databases.
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Affiliation(s)
- Rene M Boiteau
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA.
| | - David W Hoyt
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA.
| | - Carrie D Nicora
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA.
| | | | - Joy K Ward
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA.
| | - Kerem Bingol
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA.
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5
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Bingol K, Li DW, Zhang B, Brüschweiler R. Comprehensive Metabolite Identification Strategy Using Multiple Two-Dimensional NMR Spectra of a Complex Mixture Implemented in the COLMARm Web Server. Anal Chem 2016; 88:12411-12418. [PMID: 28193069 DOI: 10.1021/acs.analchem.6b03724] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Identification of metabolites in complex mixtures represents a key step in metabolomics. A new strategy is introduced, which is implemented in a new public web server, COLMARm, that permits the coanalysis of up to three two-dimensional (2D) NMR spectra, namely, 13C-1H HSQC (heteronuclear single quantum coherence spectroscopy), 1H-1H TOCSY (total correlation spectroscopy), and 13C-1H HSQC-TOCSY, for the comprehensive, accurate, and efficient performance of this task. The highly versatile and interactive nature of COLMARm permits its application to a wide range of metabolomics samples independent of the magnetic field. Database query is performed using the HSQC spectrum, and the top metabolite hits are then validated against the TOCSY-type experiment(s) by superimposing the expected cross-peaks on the mixture spectrum. In this way the user can directly accept or reject candidate metabolites by taking advantage of the complementary spectral information offered by these experiments and their different sensitivities. The power of COLMARm is demonstrated for a human serum sample uncovering the existence of 14 metabolites that hitherto were not identified by NMR.
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Affiliation(s)
- Kerem Bingol
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory , Richland, Washington 99354, United States
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6
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Walker LR, Hoyt DW, Walker SM, Ward JK, Nicora CD, Bingol K. Unambiguous metabolite identification in high-throughput metabolomics by hybrid 1D 1 H NMR/ESI MS 1 approach. Magn Reson Chem 2016; 54:998-1003. [PMID: 27539910 DOI: 10.1002/mrc.4503] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 07/08/2016] [Accepted: 08/15/2016] [Indexed: 06/06/2023]
Affiliation(s)
- Lawrence R Walker
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - David W Hoyt
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - S Michael Walker
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA
| | - Joy K Ward
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA
| | - Carrie D Nicora
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Kerem Bingol
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
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7
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Bingol K, Brüschweiler R. Knowns and unknowns in metabolomics identified by multidimensional NMR and hybrid MS/NMR methods. Curr Opin Biotechnol 2016; 43:17-24. [PMID: 27552705 DOI: 10.1016/j.copbio.2016.07.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 07/26/2016] [Accepted: 07/28/2016] [Indexed: 01/10/2023]
Abstract
Metabolomics continues to make rapid progress through the development of new and better methods and their applications to gain insight into the metabolism of a wide range of different biological systems from a systems biology perspective. Customization of NMR databases and search tools allows the faster and more accurate identification of known metabolites, whereas the identification of unknowns, without a need for extensive purification, requires new strategies to integrate NMR with mass spectrometry, cheminformatics, and computational methods. For some applications, the use of covalent and non-covalent attachments in the form of labeled tags or nanoparticles can significantly reduce the complexity of these tasks.
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Affiliation(s)
- Kerem Bingol
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Rafael Brüschweiler
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH 43210, United States; Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, United States; Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, United States.
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8
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Abstract
PURPOSE OF REVIEW This review describes some of the advances made over the past year in NMR-based metabolomics for the elucidation of known and unknown compounds, including new ways of how to combine this information with high-resolution mass spectrometry. RECENT FINDINGS A new method allows the back-calculation of mass spectra from NMR spectra that have been queried against databases improving the accuracy of the identified compounds by validation and consistency analysis. For the de-novo characterization of unknown compounds, an algorithm has been introduced that predicts all viable NMR spectra from accurate masses allowing, by comparison with experimental NMR data, the determination of the structures of new metabolites in complex mixtures. SUMMARY Recent advances in NMR and mass spectrometry-based metabolomics and their synergistic use promises to significantly improve metabolomics sample characterization both in terms of identification and quantitation, and accelerate metabolite discovery.
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Affiliation(s)
| | - Rafael Brüschweiler
- Department of Chemistry and Biochemistry
- Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio, USA
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9
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Zhang B, Xie M, Bruschweiler-Li L, Bingol K, Brüschweiler R. Use of Charged Nanoparticles in NMR-Based Metabolomics for Spectral Simplification and Improved Metabolite Identification. Anal Chem 2015; 87:7211-7. [PMID: 26087125 DOI: 10.1021/acs.analchem.5b01142] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Metabolomics aims at a complete characterization of all metabolites in biological samples in terms of both their identities and concentrations. Because changes of metabolites and their concentrations are a direct reflection of cellular activity, it allows for a better understanding of cellular processes and function to be obtained. Although NMR spectroscopy is routinely applied to complex biological mixtures without purification, overlapping NMR peaks often pose a challenge for the comprehensive and accurate identification of the underlying metabolites. To address this problem, we present a novel nanoparticle-based strategy that differentiates between metabolites based on their electric charge. By adding electrically charged silica nanoparticles to the solution NMR sample, metabolites of opposite charge bind to the nanoparticles and their NMR signals are weakened or entirely suppressed due to peak broadening caused by the slow rotational tumbling of the nanometer-sized nanoparticles. Comparison of the edited with the original spectrum significantly facilitates analysis and reduces ambiguities in the identification of metabolites. This method makes NMR directly sensitive to the detection of molecular charges at constant pH, as demonstrated here both for model mixtures and human urine. The simplicity of the approach should make it useful for a wide range of metabolomics applications.
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Affiliation(s)
- Bo Zhang
- †Department of Chemistry and Biochemistry, ‡Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Mouzhe Xie
- †Department of Chemistry and Biochemistry, ‡Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Lei Bruschweiler-Li
- †Department of Chemistry and Biochemistry, ‡Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Kerem Bingol
- †Department of Chemistry and Biochemistry, ‡Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Rafael Brüschweiler
- †Department of Chemistry and Biochemistry, ‡Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, United States
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Bingol K, Brüschweiler R. NMR/MS Translator for the Enhanced Simultaneous Analysis of Metabolomics Mixtures by NMR Spectroscopy and Mass Spectrometry: Application to Human Urine. J Proteome Res 2015; 14:2642-8. [PMID: 25881480 DOI: 10.1021/acs.jproteome.5b00184] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A novel metabolite identification strategy is presented for the combined NMR/MS analysis of complex metabolite mixtures. The approach first identifies metabolite candidates from 1D or 2D NMR spectra by NMR database query, which is followed by the determination of the masses (m/z) of their possible ions, adducts, fragments, and characteristic isotope distributions. The expected m/z ratios are then compared with the MS(1) spectrum for the direct assignment of those signals of the mass spectrum that contain information about the same metabolites as the NMR spectra. In this way, the mass spectrum can be assigned with very high confidence, and it provides at the same time validation of the NMR-derived metabolites. The method was first demonstrated on a model mixture, and it was then applied to human urine collected from a pool of healthy individuals. A number of metabolites could be detected that had not been reported previously, further extending the list of known urine metabolites. The new analysis approach, which is termed NMR/MS Translator, is fully automated and takes only a few seconds on a computer workstation. NMR/MS Translator synergistically uses the power of NMR and MS, enhancing the accuracy and efficiency of the identification of those metabolites compiled in databases.
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Affiliation(s)
- Kerem Bingol
- †Department of Chemistry and Biochemistry, ‡Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Rafael Brüschweiler
- †Department of Chemistry and Biochemistry, ‡Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, United States
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11
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Bingol K, Bruschweiler-Li L, Yu C, Somogyi A, Zhang F, Brüschweiler R. Metabolomics beyond spectroscopic databases: a combined MS/NMR strategy for the rapid identification of new metabolites in complex mixtures. Anal Chem 2015; 87:3864-70. [PMID: 25674812 PMCID: PMC5035699 DOI: 10.1021/ac504633z] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A novel strategy is introduced that combines high-resolution mass spectrometry (MS) with NMR for the identification of unknown components in complex metabolite mixtures encountered in metabolomics. The approach first identifies the chemical formulas of the mixture components from accurate masses by MS and then generates all feasible structures (structural manifold) that are consistent with these chemical formulas. Next, NMR spectra of each member of the structural manifold are predicted and compared with the experimental NMR spectra in order to identify the molecular structures that match the information obtained from both the MS and NMR techniques. This combined MS/NMR approach was applied to Escherichia coli extract, where the approach correctly identified a wide range of different types of metabolites, including amino acids, nucleic acids, polyamines, nucleosides, and carbohydrate conjugates. This makes this approach, which is termed SUMMIT MS/NMR, well suited for high-throughput applications for the discovery of new metabolites in biological and biomedical mixtures, overcoming the need of experimental MS and NMR metabolite databases.
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Affiliation(s)
- Kerem Bingol
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Lei Bruschweiler-Li
- Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Cao Yu
- Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Arpad Somogyi
- Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Fengli Zhang
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | - Rafael Brüschweiler
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, United States
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
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12
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Bingol K, Li DW, Bruschweiler-Li L, Cabrera OA, Megraw T, Zhang F, Brüschweiler R. Unified and isomer-specific NMR metabolomics database for the accurate analysis of (13)C-(1)H HSQC spectra. ACS Chem Biol 2015; 10:452-9. [PMID: 25333826 PMCID: PMC4340359 DOI: 10.1021/cb5006382] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
A new
metabolomics database and query algorithm for the analysis
of 13C–1H HSQC spectra is introduced,
which unifies NMR spectroscopic information on 555 metabolites from
both the Biological Magnetic Resonance Data Bank (BMRB) and Human
Metabolome Database (HMDB). The new database, termed Complex Mixture
Analysis by NMR (COLMAR) 13C–1H HSQC
database, can be queried via an interactive, easy to use web interface
at http://spin.ccic.ohio-state.edu/index.php/hsqc/index. Our new HSQC database separately treats slowly exchanging isomers
that belong to the same metabolite, which permits improved query in
cases where lowly populated isomers are below the HSQC detection limit.
The performance of our new database and query web server compares
favorably with the one of existing web servers, especially for spectra
of samples of high complexity, including metabolite mixtures from
the model organisms Drosophila melanogaster and Escherichia coli. For such samples, our web server has on
average a 37% higher accuracy (true positive rate) and a 82% lower
false positive rate, which makes it a useful tool for the rapid and
accurate identification of metabolites from 13C–1H HSQC spectra at natural abundance. This information can
be combined and validated with NMR data from 2D TOCSY-type spectra
that provide connectivity information not present in HSQC spectra.
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Affiliation(s)
| | | | | | - Oscar A. Cabrera
- Department
of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, Florida 32306, United States
| | - Timothy Megraw
- Department
of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, Florida 32306, United States
| | - Fengli Zhang
- National
High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | - Rafael Brüschweiler
- National
High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
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13
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Bingol K, Bruschweiler-Li L, Li DW, Brüschweiler R. Customized metabolomics database for the analysis of NMR ¹H-¹H TOCSY and ¹³C-¹H HSQC-TOCSY spectra of complex mixtures. Anal Chem 2014; 86:5494-501. [PMID: 24773139 PMCID: PMC4051244 DOI: 10.1021/ac500979g] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
![]()
A customized metabolomics NMR database,
termed 1H(13C)-TOCCATA, is introduced, which
contains complete 1H and 13C chemical shift
information on individual spin
systems and isomeric states of common metabolites. Since this information
directly corresponds to cross sections of 2D 1H–1H TOCSY and 2D 13C–1H HSQC-TOCSY
spectra, it allows the straightforward and unambiguous identification
of metabolites of complex metabolic mixtures at 13C natural
abundance from these types of experiments. The 1H(13C)-TOCCATA database, which is complementary to the previously
introduced TOCCATA database for the analysis of uniformly 13C-labeled compounds, currently contains 455 metabolites, and it can
be used through a publicly accessible web portal. We demonstrate its
performance by applying it to 2D 1H–1H TOCSY and 2D 13C–1H HSQC-TOCSY spectra
of a cell lysate from E. coli, which
yields a substantial improvement over other databases, as well as
1D NMR-based approaches, in the number of compounds that can be correctly
identified with high confidence.
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Affiliation(s)
- Kerem Bingol
- Department of Chemistry and Biochemistry, The Ohio State University , Columbus, Ohio 43210, United States
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Affiliation(s)
- Kerem Bingol
- Department of Chemistry and Biochemistry, The Ohio State University , Columbus, Ohio 43210
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Bingol K, Zhang F, Bruschweiler-Li L, Brüschweiler R. Quantitative analysis of metabolic mixtures by two-dimensional 13C constant-time TOCSY NMR spectroscopy. Anal Chem 2013; 85:6414-20. [PMID: 23773204 PMCID: PMC4447502 DOI: 10.1021/ac400913m] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An increasing number of organisms can be fully (13)C-labeled, which has the advantage that their metabolomes can be studied by high-resolution two-dimensional (2D) NMR (13)C-(13)C constant-time (CT) total correlation spectroscopy (TOCSY) experiments. Individual metabolites can be identified via database searching or, in the case of novel compounds, through the reconstruction of their backbone-carbon topology. Determination of quantitative metabolite concentrations is another key task. Because strong peak overlaps in one-dimensional (1D) NMR spectra prevent straightforward quantification through 1D peak integrals, we demonstrate here the direct use of (13)C-(13)C CT-TOCSY spectra for metabolite quantification. This is accomplished through the quantum mechanical treatment of the TOCSY magnetization transfer at short and long-mixing times or by the use of analytical approximations, which are solely based on the knowledge of the carbon-backbone topologies. The methods are demonstrated for carbohydrate and amino acid mixtures.
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Affiliation(s)
- Kerem Bingol
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310
| | - Fengli Zhang
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310
| | - Lei Bruschweiler-Li
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306
| | - Rafael Brüschweiler
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306
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Bingol K, Zhang F, Bruschweiler-Li L, Brüschweiler R. TOCCATA: a customized carbon total correlation spectroscopy NMR metabolomics database. Anal Chem 2012; 84:9395-401. [PMID: 23016498 DOI: 10.1021/ac302197e] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A customized metabolomics NMR database, TOCCATA, is introduced, which uses (13)C chemical shift information for the reliable identification of metabolites, their spin systems, and isomeric states. TOCCATA, whose information was derived from the BMRB and HMDB databases and the literature, currently contains 463 compounds and 801 spin systems, and it can be used through a publicly accessible web server. TOCCATA allows the identification of metabolites in the submillimolar concentration range from (13)C-(13)C total correlation spectroscopy experiments of complex mixtures, which is demonstrated for an Escherichia coli cell lysate, a carbohydrate mixture, and an amino acid mixture, all of which were uniformly (13)C-labeled.
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Affiliation(s)
- Kerem Bingol
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, United States
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Abstract
The complex metabolic makeup of a biological system, such as a cell, is a key determinant of its biological state providing unique insights into its function. Here we characterize the metabolome of a cell by a novel homonuclear (13)C 2D NMR approach applied to a nonfractionated uniformly (13)C-enriched lysate of E. coli cells and determine de novo their carbon backbone topologies that constitute the "topolome". A protocol was developed, which first identifies traces in a constant-time (13)C-(13)C TOCSY NMR spectrum that are unique for individual mixture components and then assembles for each trace the corresponding carbon-bond topology network by consensus clustering. This led to the determination of 112 topologies of unique metabolites from a single sample. The topolome is dominated by carbon topologies of carbohydrates (34.8%) and amino acids (45.5%) that can constitute building blocks of more complex structures.
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Affiliation(s)
- Kerem Bingol
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
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Abstract
Identification and quantification of analytes in complex solution-state mixtures are critical procedures in many areas of chemistry, biology, and molecular medicine. Nuclear magnetic resonance (NMR) is a unique tool for this purpose providing a wealth of atomic-detail information without requiring extensive fractionation of the samples. We present three new multidimensional-NMR based approaches that are geared toward the analysis of mixtures with high complexity at natural (13)C abundance, including approaches that are encountered in metabolomics. Common to all three approaches is the concept of the extraction of one-dimensional (1D) consensus spectral traces or 2D consensus planes followed by clustering, which significantly improves the capability to identify mixture components that are affected by strong spectral overlap. The methods are demonstrated for covariance (1)H-(1)H TOCSY and (13)C-(1)H HSQC-TOCSY spectra and triple-rank correlation spectra constructed from pairs of (13)C-(1)H HSQC and (13)C-(1)H HSQC-TOCSY spectra. All methods are first demonstrated for an eight-compound metabolite model mixture before being applied to an extract from E. coli cell lysate.
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Affiliation(s)
- Kerem Bingol
- Institute of Molecular Biophysics, Department of Chemistry & Biochemistry and National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32306, USA
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Abstract
Higher-rank correlation spectroscopy is introduced as an alternative to 3D Fourier-transform (FT) NMR spectroscopy for resonance assignment and molecular structure determination. The method combines standard 2D FT spectra that share a common frequency dimension, such as a 2D (13)C-(1)H HSQC and a 2D (1)H-(1)H TOCSY spectrum, and constructs higher-rank correlation spectra with ultra-high spectral resolution. Spectral overlap along a common dimension, in particular the (1)H dimension, is addressed by a spectral filtering method, which identifies mismatches between the 1(st) and 2(nd) moments of cross-peak profiles. The method, which provides a substantial speed-up over traditional 3D FT spectroscopy while effectively suppressing false peaks, is demonstrated for the triple-rank (13)C-(1)H HSQC-TOCSY spectrum of a cyclic decapeptide with different mixing times. Higher-rank correlation spectroscopy is usefully applicable to the analysis of a wide range of NMR spectra of synthetic and natural products.
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Affiliation(s)
- Kerem Bingol
- Department of Chemistry & Biochemistry and National High Magnetic Field Laboratory Florida State University, Tallahassee, FL 32306
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