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Microbial Metabolomics: From Methods to Translational Applications. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021. [PMID: 33791977 DOI: 10.1007/978-3-030-51652-9_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Most microbe-associated infectious diseases severely affect human health. However, clinical diagnosis of pathogenic diseases remains challenging due to the lack of specific and highly reliable methods. To better understand the diagnosis, pathogenesis, and treatment of these diseases, systems biology-driven metabolomics goes beyond the annotated phenotype and better targets the functions than conventional approaches. As a novel strategy for analysis of metabolomes in microbes, microbial metabolomics has been recently used to study many diseases, such as obesity, urinary tract infection (UTI), and hepatitis C. In this chapter, we attempt to introduce various microbial metabolomics methods to better interpret the microbial metabolism underlying a diversity of infectious diseases and inspire scientists to pay more attention to microbial metabolomics, enabling broadly and efficiently its translational applications to infectious diseases, from molecular diagnosis to therapeutic discovery.
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2
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Functional metabolomics innovates therapeutic discovery of traditional Chinese medicine derived functional compounds. Pharmacol Ther 2021; 224:107824. [PMID: 33667524 DOI: 10.1016/j.pharmthera.2021.107824] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/11/2021] [Accepted: 02/22/2021] [Indexed: 12/12/2022]
Abstract
Traditional Chinese medicines (TCMs) produce chemically diverse functional compounds that are importantly chemical resource for facilitating new drug discovery and development against a diversity of diseases. However, modern exploration of TCM derived functional compounds is significantly hindered by the inefficient elucidation of pharmacological functions over past decades, because conventional research methods are incapable of efficiently elucidating therapeutic potential of TCM conferred by multiple functional compounds. Functional metabolomics has the priority-capacity to characterize systems therapeutic actions of TCM by precisely capturing molecular interactions between disease response metabolite biomarkers (DRMB) and functional compounds (secondary metabolites), which underline pharmacological efficiency and associated therapeutic mechanisms. In this critical review, we innovatively summarize systems therapeutic feature of TCM derived functional compounds from a functional-metabolism perspective, then systems metabolic targets (SMT) identified by functional metabolomics method are strategically proposed to better understanding of therapeutic discovery of TCM derived functional compounds. In addition, we propose the perspective strategy as Spatial Temporal Operative Real Metabolomics (STORM) to considerably improve analytical capacity of functional metabolomics method by selectively incorporating the cutting edge technologies of mass spectrometry imaging, isotope-metabolic fluxomics, synthetic and biosynthetic chemistry, which could considerably enhance the precision and resolution of elucidating pharmacological efficiency and associated therapeutic mechanisms of TCM derived functional compounds. Collectively, such critical review is expected to provide novel perspective-strategy that could significantly improve modern exploration and exploitation of TCM derived functional compounds that further promote new drug discovery and development against the complex diseases.
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Hu L, Liu J, Zhang W, Wang T, Zhang N, Lee YH, Lu H. FUNCTIONAL METABOLOMICS DECIPHER BIOCHEMICAL FUNCTIONS AND ASSOCIATED MECHANISMS UNDERLIE SMALL-MOLECULE METABOLISM. MASS SPECTROMETRY REVIEWS 2020; 39:417-433. [PMID: 31682024 DOI: 10.1002/mas.21611] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 10/08/2019] [Accepted: 10/10/2019] [Indexed: 06/10/2023]
Abstract
Metabolism is the collection of biochemical reactions enabled by chemically diverse metabolites, which facilitate different physiological processes to exchange substances and synthesize energy in diverse living organisms. Metabolomics has emerged as a cutting-edge method to qualify and quantify the metabolites in different biological matrixes, and it has the extraordinary capacity to interrogate the biological significance that underlies metabolic modification and modulation. Liquid chromatography combined with mass spectrometry (LC/MS), as a robust platform for metabolomics analysis, has increased in popularity over the past 10 years due to its excellent sensitivity, throughput, and versatility. However, metabolomics investigation currently provides us with only phenotype data without revealing the biochemical functions and associated mechanisms. This limitation indeed weakens the core value of metabolomics data in a broad spectrum of the life sciences. In recent years, the scientific community has actively explored the functional features of metabolomics and translated this cutting-edge approach to be used to solve key multifaceted questions, such as disease pathogenesis, the therapeutic discovery of drugs, nutritional issues, agricultural problems, environmental toxicology, and microbial evolution. Here, we are the first to briefly review the history and applicable progression of LC/MS-based metabolomics, with an emphasis on the applications of metabolic phenotyping. Furthermore, we specifically highlight the next era of LC/MS-based metabolomics to target functional metabolomes, through which we can answer phenotype-related questions to elucidate biochemical functions and associated mechanisms implicated in dysregulated metabolism. Finally, we propose many strategies to enhance the research capacity of functional metabolomics by enabling the combination of contemporary omics technologies and cutting-edge biochemical techniques. The main purpose of this review is to improve the understanding of LC/MS-based metabolomics, extending beyond the conventional metabolic phenotype toward biochemical functions and associated mechanisms, to enhance research capability and to enlarge the applicable scope of functional metabolomics in small-molecule metabolism in different living organisms.
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Affiliation(s)
- Longlong Hu
- Laboratory for Functional Metabolomics Science, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jingjing Liu
- Laboratory for Functional Metabolomics Science, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wenhua Zhang
- Laboratory for Functional Metabolomics Science, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
- Department of Pharmacognosy, College of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, 150040, China
| | - Tianyu Wang
- Laboratory for Functional Metabolomics Science, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ning Zhang
- Department of Pharmacognosy, College of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, 150040, China
- Department of Pharmaceutical Analysis, College of Jiamusi, Heilongjiang University of Chinese Medicine, Harbin, 121000, China
| | - Yie Hou Lee
- Translational 'Omics and Biomarkers Group, KK Research Centre, KK Women's and Children's Hospital, Singapore, 229899, Singapore
- OBGYN-Academic Clinical Program, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Haitao Lu
- Laboratory for Functional Metabolomics Science, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
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Creydt M, Fischer M. Food Phenotyping: Recording and Processing of Non-Targeted Liquid Chromatography Mass Spectrometry Data for Verifying Food Authenticity. Molecules 2020; 25:E3972. [PMID: 32878155 PMCID: PMC7504784 DOI: 10.3390/molecules25173972] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 12/11/2022] Open
Abstract
Experiments based on metabolomics represent powerful approaches to the experimental verification of the integrity of food. In particular, high-resolution non-targeted analyses, which are carried out by means of liquid chromatography-mass spectrometry systems (LC-MS), offer a variety of options. However, an enormous amount of data is recorded, which must be processed in a correspondingly complex manner. The evaluation of LC-MS based non-targeted data is not entirely trivial and a wide variety of strategies have been developed that can be used in this regard. In this paper, an overview of the mandatory steps regarding data acquisition is given first, followed by a presentation of the required preprocessing steps for data evaluation. Then some multivariate analysis methods are discussed, which have proven to be particularly suitable in this context in recent years. The publication closes with information on the identification of marker compounds.
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Affiliation(s)
- Marina Creydt
- Hamburg School of Food Science-Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany;
- Center for Hybrid Nanostructures (CHyN), Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Markus Fischer
- Hamburg School of Food Science-Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany;
- Center for Hybrid Nanostructures (CHyN), Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
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5
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Fu L, Zhang J, Si T. Recent advances in high-throughput mass spectrometry that accelerates enzyme engineering for biofuel research. ACTA ACUST UNITED AC 2020. [DOI: 10.1186/s42500-020-0011-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
AbstractEnzymes play indispensable roles in producing biofuels, a sustainable and renewable source of transportation fuels. Lacking rational design rules, the development of industrially relevant enzyme catalysts relies heavily on high-throughput screening. However, few universal methods exist to rapidly characterize large-scale enzyme libraries. Therefore, assay development is necessary on an ad hoc basis to link enzyme properties to spectrophotometric signals and often requires the use of surrogate, optically active substrates. On the other hand, mass spectrometry (MS) performs label-free enzyme assays that utilize native substrates and is therefore generally applicable. But the analytical speed of MS is considered rate limiting, mainly due to the use of time-consuming chromatographic separation in traditional MS analysis. Thanks to new instrumentation and sample preparation methods, direct analyte introduction into a mass spectrometer without a prior chromatographic step can be achieved by laser, microfluidics, and acoustics, so that each sample can be analyzed within seconds. Here we review recent advances in MS platforms that improve the throughput of enzyme library screening and discuss how these advances can potentially facilitate biofuel research by providing high sensitivity, selectivity and quantitation that are difficult to obtain using traditional assays. We also highlight the limitations of current MS assays in studying biofuel-related enzymes and propose possible solutions.
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6
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Kai H, Kinoshita K, Harada H, Uesawa Y, Maeda A, Suzuki R, Okada Y, Takahashi K, Matsuno K. Establishment of a Direct-Injection Electron Ionization-Mass Spectrometry Metabolomics Method and Its Application to Lichen Profiling. Anal Chem 2017; 89:6408-6414. [DOI: 10.1021/acs.analchem.7b00077] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hisahiro Kai
- Department of Pharmaceutical Health Sciences, School of Pharmaceutical
Sciences, Kyushu University of Health and Welfare, 1714-1 Yoshino-machi, Nobeoka, Miyazaki 882-8508, Japan
| | - Kaoru Kinoshita
- Department of Pharmacognosy and Phytochemistry, Meiji Pharmaceutical University, 2-522-1 Noshio, Kiyose, Tokyo 204-8588, Japan
| | - Hiroshi Harada
- Natural History Museum and Institute, Chiba, 955-2 Aoba-cho, Chuo-ku, Chiba 260-8682, Japan
| | - Yoshihiro Uesawa
- Department of Clinical Pharmaceutics, Meiji Pharmaceutical University, 2-522-1, Noshio, Kiyose, Tokyo 204-8588, Japan
| | - Akihiro Maeda
- Department of Pharmaceutical Health Sciences, School of Pharmaceutical
Sciences, Kyushu University of Health and Welfare, 1714-1 Yoshino-machi, Nobeoka, Miyazaki 882-8508, Japan
| | - Ryuichiro Suzuki
- Department of Pharmaceutical
Sciences, Faculty of Pharmacy and Pharmaceutical Sciences, Josai University, 1-1 Keyakidai, Sakado, Saitama 350-0295, Japan
| | - Yoshihito Okada
- Department
of Natural Medicine and Phytochemistry, Meiji Pharmaceutical University, 2-522-1 Noshio, Kiyose, Tokyo 204-8588, Japan
| | - Kunio Takahashi
- Department of Pharmacognosy and Phytochemistry, Meiji Pharmaceutical University, 2-522-1 Noshio, Kiyose, Tokyo 204-8588, Japan
| | - Koji Matsuno
- Department of Pharmaceutical Health Sciences, School of Pharmaceutical
Sciences, Kyushu University of Health and Welfare, 1714-1 Yoshino-machi, Nobeoka, Miyazaki 882-8508, Japan
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7
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Nie W, Yan L, Lee YH, Guha C, Kurland IJ, Lu H. Advanced mass spectrometry-based multi-omics technologies for exploring the pathogenesis of hepatocellular carcinoma. MASS SPECTROMETRY REVIEWS 2016; 35:331-349. [PMID: 24890331 DOI: 10.1002/mas.21439] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Revised: 04/17/2014] [Accepted: 04/17/2014] [Indexed: 06/03/2023]
Abstract
Hepatocellular carcinoma (HCC) is one of the primary hepatic malignancies and is the third most common cause of cancer related death worldwide. Although a wealth of knowledge has been gained concerning the initiation and progression of HCC over the last half century, efforts to improve our understanding of its pathogenesis at a molecular level are still greatly needed, to enable clinicians to enhance the standards of the current diagnosis and treatment of HCC. In the post-genome era, advanced mass spectrometry driven multi-omics technologies (e.g., profiling of DNA damage adducts, RNA modification profiling, proteomics, and metabolomics) stand at the interface between chemistry and biology, and have yielded valuable outcomes from the study of a diversity of complicated diseases. Particularly, these technologies are being broadly used to dissect various biological aspects of HCC with the purpose of biomarker discovery, interrogating pathogenesis as well as for therapeutic discovery. This proof of knowledge-based critical review aims at exploring the selected applications of those defined omics technologies in the HCC niche with an emphasis on translational applications driven by advanced mass spectrometry, toward the specific clinical use for HCC patients. This approach will enable the biomedical community, through both basic research and the clinical sciences, to enhance the applicability of mass spectrometry-based omics technologies in dissecting the pathogenesis of HCC and could lead to novel therapeutic discoveries for HCC.
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Affiliation(s)
- Wenna Nie
- Chongqing University Innovative Drug Research Centre, School of Chemistry and Chemical Engineering, Chongqing, 401331, PR China
| | - Leyu Yan
- Chongqing University Innovative Drug Research Centre, School of Chemistry and Chemical Engineering, Chongqing, 401331, PR China
| | - Yie H Lee
- Interdisciplinary Research Group in Infectious Diseases, Singapore-MIT Alliance for Research & Technology, Singapore, 138602, Singapore
| | - Chandan Guha
- Department of Radiation Oncology, Montefiore Medical Center, New York, New York, 10461
- Department of Medicine, Albert Einstein College of Medicine, New York, New York, 10461
| | - Irwin J Kurland
- Stable Isotope and Metabolomics Core Facility, Diabetes Research and Training Center, Department of Medicine, Albert Einstein College of Medicine, New York, New York, 10461
| | - Haitao Lu
- Chongqing University Innovative Drug Research Centre, School of Chemistry and Chemical Engineering, Chongqing, 401331, PR China
- Tissue Repair and Regeneration Program, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, 4059, Australia
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Siderophore biosynthesis coordinately modulated the virulence-associated interactive metabolome of uropathogenic Escherichia coli and human urine. Sci Rep 2016; 6:24099. [PMID: 27076285 PMCID: PMC4831015 DOI: 10.1038/srep24099] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/22/2016] [Indexed: 02/06/2023] Open
Abstract
Uropathogenic Escherichia coli (UPEC) growth in women’s bladders during urinary tract infection (UTI) incurs substantial chemical exchange, termed the “interactive metabolome”, which primarily accounts for the metabolic costs (utilized metabolome) and metabolic donations (excreted metabolome) between UPEC and human urine. Here, we attempted to identify the individualized interactive metabolome between UPEC and human urine. We were able to distinguish UPEC from non-UPEC by employing a combination of metabolomics and genetics. Our results revealed that the interactive metabolome between UPEC and human urine was markedly different from that between non-UPEC and human urine, and that UPEC triggered much stronger perturbations in the interactive metabolome in human urine. Furthermore, siderophore biosynthesis coordinately modulated the individualized interactive metabolome, which we found to be a critical component of UPEC virulence. The individualized virulence-associated interactive metabolome contained 31 different metabolites and 17 central metabolic pathways that were annotated to host these different metabolites, including energetic metabolism, amino acid metabolism, and gut microbe metabolism. Changes in the activities of these pathways mechanistically pinpointed the virulent capability of siderophore biosynthesis. Together, our findings provide novel insights into UPEC virulence, and we propose that siderophores are potential targets for further discovery of drugs to treat UPEC-induced UTI.
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9
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Su Q, Guan T, He Y, Lv H. Siderophore Biosynthesis Governs the Virulence of Uropathogenic Escherichia coli by Coordinately Modulating the Differential Metabolism. J Proteome Res 2016; 15:1323-32. [DOI: 10.1021/acs.jproteome.6b00061] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Qiao Su
- The Laboratory
for Functional
Omics and Innovative Chinese Medicine, Innovative Drug Research Center, Chongqing University, Chongqing 401331, P.R. China
| | - Tianbing Guan
- The Laboratory
for Functional
Omics and Innovative Chinese Medicine, Innovative Drug Research Center, Chongqing University, Chongqing 401331, P.R. China
| | - Yan He
- The Laboratory
for Functional
Omics and Innovative Chinese Medicine, Innovative Drug Research Center, Chongqing University, Chongqing 401331, P.R. China
| | - Haitao Lv
- The Laboratory
for Functional
Omics and Innovative Chinese Medicine, Innovative Drug Research Center, Chongqing University, Chongqing 401331, P.R. China
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10
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A comparative LC-MS based profiling approach to analyze lipid composition in tissue culture systems. Methods Mol Biol 2015; 1232:103-13. [PMID: 25331131 DOI: 10.1007/978-1-4939-1752-5_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Although lipids participate in many cellular processes both as signaling and structural molecules, our understanding of the roles of individual lipids as well as global changes in lipid composition are limited. Here we describe an LC-MS based method to identify lipids that change in a biological process. This method describes the isolation of lipids from tissue culture cells, sample preparation for LC-MS, the LC-MS run, and the subsequent data processing steps to compare the global lipid profiles and identify species that are enhanced or depleted. Identifying lipids that change is the first step towards functional studies to unravel their roles.
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11
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Turi CE, Finley J, Shipley PR, Murch SJ, Brown PN. Metabolomics for phytochemical discovery: development of statistical approaches using a cranberry model system. JOURNAL OF NATURAL PRODUCTS 2015; 78:953-966. [PMID: 25751407 DOI: 10.1021/np500667z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Metabolomics is the qualitative and quantitative analysis of all of the small molecules in a biological sample at a specific time and influence. Technologies for metabolomics analysis have developed rapidly as new analytical tools for chemical separations, mass spectrometry, and NMR spectroscopy have emerged. Plants have one of the largest metabolomes, and it is estimated that the average plant leaf can contain upward of 30 000 phytochemicals. In the past decade, over 1200 papers on plant metabolomics have been published. A standard metabolomics data set contains vast amounts of information and can either investigate or generate hypotheses. The key factors in using plant metabolomics data most effectively are the experimental design, authentic standard availability, extract standardization, and statistical analysis. Using cranberry (Vaccinium macrocarpon) as a model system, this review will discuss and demonstrate strategies and tools for analysis and interpretation of metabolomics data sets including eliminating false discoveries and determining significance, metabolite clustering, and logical algorithms for discovery of new metabolites and pathways. Together these metabolomics tools represent an entirely new pipeline for phytochemical discovery.
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Affiliation(s)
- Christina E Turi
- †Department of Chemistry, University of British Columbia, 3247 University Way, Kelowna, British Columbia, Canada, V1V 1V7
| | - Jamie Finley
- ‡Natural Health Products and Food Research Group, British Columbia Institute of Technology, 4355 Mathissi Place, Burnaby, British Columbia, Canada, V5G 3H2
| | - Paul R Shipley
- †Department of Chemistry, University of British Columbia, 3247 University Way, Kelowna, British Columbia, Canada, V1V 1V7
| | - Susan J Murch
- †Department of Chemistry, University of British Columbia, 3247 University Way, Kelowna, British Columbia, Canada, V1V 1V7
| | - Paula N Brown
- ‡Natural Health Products and Food Research Group, British Columbia Institute of Technology, 4355 Mathissi Place, Burnaby, British Columbia, Canada, V5G 3H2
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12
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Tamir S, Paddock ML, Darash-Yahana-Baram M, Holt SH, Sohn YS, Agranat L, Michaeli D, Stofleth JT, Lipper CH, Morcos F, Cabantchik IZ, Onuchic JN, Jennings PA, Mittler R, Nechushtai R. Structure-function analysis of NEET proteins uncovers their role as key regulators of iron and ROS homeostasis in health and disease. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:1294-315. [PMID: 25448035 DOI: 10.1016/j.bbamcr.2014.10.014] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 10/01/2014] [Accepted: 10/16/2014] [Indexed: 12/31/2022]
Abstract
A novel family of 2Fe-2S proteins, the NEET family, was discovered during the last decade in numerous organisms, including archea, bacteria, algae, plant and human; suggesting an evolutionary-conserved function, potentially mediated by their CDGSH Iron-Sulfur Domain. In human, three NEET members encoded by the CISD1-3 genes were identified. The structures of CISD1 (mitoNEET, mNT), CISD2 (NAF-1), and the plant At-NEET uncovered a homodimer with a unique "NEET fold", as well as two distinct domains: a beta-cap and a 2Fe-2S cluster-binding domain. The 2Fe-2S clusters of NEET proteins were found to be coordinated by a novel 3Cys:1His structure that is relatively labile compared to other 2Fe-2S proteins and is the reason of the NEETs' clusters could be transferred to apo-acceptor protein(s) or mitochondria. Positioned at the protein surface, the NEET's 2Fe-2S's coordinating His is exposed to protonation upon changes in its environment, potentially suggesting a sensing function for this residue. Studies in different model systems demonstrated a role for NAF-1 and mNT in the regulation of cellular iron, calcium and ROS homeostasis, and uncovered a key role for NEET proteins in critical processes, such as cancer cell proliferation and tumor growth, lipid and glucose homeostasis in obesity and diabetes, control of autophagy, longevity in mice, and senescence in plants. Abnormal regulation of NEET proteins was consequently found to result in multiple health conditions, and aberrant splicing of NAF-1 was found to be a causative of the neurological genetic disorder Wolfram Syndrome 2. Here we review the discovery of NEET proteins, their structural, biochemical and biophysical characterization, and their most recent structure-function analyses. We additionally highlight future avenues of research focused on NEET proteins and propose an essential role for NEETs in health and disease. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
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Affiliation(s)
- Sagi Tamir
- The Alexander Silberman Life Science Institute and the Wolfson Centre for Applied Structural Biology, Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 91904, Israel
| | - Mark L Paddock
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA
| | - Merav Darash-Yahana-Baram
- The Alexander Silberman Life Science Institute and the Wolfson Centre for Applied Structural Biology, Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 91904, Israel
| | - Sarah H Holt
- Department of Biology, University of North Texas, Denton, TX 76203, USA
| | - Yang Sung Sohn
- The Alexander Silberman Life Science Institute and the Wolfson Centre for Applied Structural Biology, Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 91904, Israel
| | - Lily Agranat
- The Alexander Silberman Life Science Institute and the Wolfson Centre for Applied Structural Biology, Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 91904, Israel
| | - Dorit Michaeli
- The Alexander Silberman Life Science Institute and the Wolfson Centre for Applied Structural Biology, Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 91904, Israel
| | - Jason T Stofleth
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA
| | - Colin H Lipper
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA
| | - Faruck Morcos
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77050, USA; Department of Physics and Astronomy, Rice University, Houston, TX 77050, USA; Department of Chemistry, Rice University, Houston, TX 77050, USA; Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77050, USA
| | - Ioav Z Cabantchik
- The Alexander Silberman Life Science Institute and the Wolfson Centre for Applied Structural Biology, Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 91904, Israel
| | - Jose' N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77050, USA; Department of Physics and Astronomy, Rice University, Houston, TX 77050, USA; Department of Chemistry, Rice University, Houston, TX 77050, USA; Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77050, USA
| | - Patricia A Jennings
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA
| | - Ron Mittler
- Department of Biology, University of North Texas, Denton, TX 76203, USA
| | - Rachel Nechushtai
- The Alexander Silberman Life Science Institute and the Wolfson Centre for Applied Structural Biology, Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 91904, Israel.
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13
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Fukushima A, Kusano M. A network perspective on nitrogen metabolism from model to crop plants using integrated 'omics' approaches. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:5619-30. [PMID: 25129130 DOI: 10.1093/jxb/eru322] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Nitrogen (N), as an essential element in amino acids, nucleotides, and proteins, is a key factor in plant growth and development. Omics approaches such as metabolomics and transcriptomics have become a promising way to inspect complex network interactions in N metabolism and can be used for monitoring the uptake and regulation, translocation, and remobilization of N. In this review, the authors highlight recent progress in omics approaches, including transcript profiling using microarrays and deep sequencing, and show recent technical developments in metabolite profiling for N studies. Further, network analysis studies including network inference methods with correlations, information-theoretic measures, and a network concept to examine gene expression clusters in relation to N regulatory systems in plants are introduced, and integrating network inference methods and integrated networks using multiple omics data are discussed. Finally, this review summarizes recent omics application examples using metabolite and/or transcript profiling analysis to elucidate the regulation of N metabolism and signalling and the coordination of N and carbon metabolism in model plants (Arabidopsis and rice), crops (tomato, maize, and legumes), and trees (Populus).
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Affiliation(s)
- Atsushi Fukushima
- RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehirocho, Tsurumi, Yokohama 230-0045, Japan JST, National Bioscience Database Center (NBDC), 5-3, Yonbancho, Chiyoda, Tokyo 102-0081, Japan
| | - Miyako Kusano
- RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehirocho, Tsurumi, Yokohama 230-0045, Japan Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan Japan Science and Technology Agency (JST), Precursory Research for Embryonic Science and Technology (PRESTO), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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14
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Beisken S, Earll M, Baxter C, Portwood D, Ament Z, Kende A, Hodgman C, Seymour G, Smith R, Fraser P, Seymour M, Salek RM, Steinbeck C. Metabolic differences in ripening of Solanum lycopersicum 'Ailsa Craig' and three monogenic mutants. Sci Data 2014; 1:140029. [PMID: 25977786 PMCID: PMC4322568 DOI: 10.1038/sdata.2014.29] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 08/06/2014] [Indexed: 12/02/2022] Open
Abstract
Application of mass spectrometry enables the detection of metabolic differences between groups of related organisms. Differences in the metabolic fingerprints of wild-type Solanum lycopersicum and three monogenic mutants, ripening inhibitor (rin), non-ripening (nor) and Colourless non-ripening (Cnr), of tomato are captured with regard to ripening behaviour. A high-resolution tandem mass spectrometry system coupled to liquid chromatography produced a time series of the ripening behaviour at discrete intervals with a focus on changes post-anthesis. Internal standards and quality controls were used to ensure system stability. The raw data of the samples and reference compounds including study protocols have been deposited in the open metabolomics database MetaboLights via the metadata annotation tool Isatab to enable efficient re-use of the datasets, such as in metabolomics cross-study comparisons or data fusion exercises.
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Affiliation(s)
- Stephan Beisken
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus , Hinxton, Cambridge CB10 2HA, UK
| | - Mark Earll
- Syngenta Jealott's Hill International Research Centre , Bracknell, Berkshire RG42 6EY, UK
| | - Charles Baxter
- Syngenta Jealott's Hill International Research Centre , Bracknell, Berkshire RG42 6EY, UK
| | - David Portwood
- Syngenta Jealott's Hill International Research Centre , Bracknell, Berkshire RG42 6EY, UK
| | - Zsuzsanna Ament
- Syngenta Jealott's Hill International Research Centre , Bracknell, Berkshire RG42 6EY, UK
| | - Aniko Kende
- Syngenta Jealott's Hill International Research Centre , Bracknell, Berkshire RG42 6EY, UK
| | - Charlie Hodgman
- Centre for Plant Integrative Biology, University of Nottingham , Loughborough, Leicestershire LE12 5RD, UK
| | - Graham Seymour
- Centre for Plant Integrative Biology, University of Nottingham , Loughborough, Leicestershire LE12 5RD, UK
| | - Rebecca Smith
- Centre for Plant Integrative Biology, University of Nottingham , Loughborough, Leicestershire LE12 5RD, UK
| | - Paul Fraser
- School of Biological Sciences, Royal Holloway, University of London, Egham Hill , Egham, Surrey TW20 0EX, UK
| | - Mark Seymour
- Syngenta Jealott's Hill International Research Centre , Bracknell, Berkshire RG42 6EY, UK
| | - Reza M Salek
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus , Hinxton, Cambridge CB10 2HA, UK
| | - Christoph Steinbeck
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus , Hinxton, Cambridge CB10 2HA, UK
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15
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MS-based metabolomics facilitates the discovery of in vivo functional small molecules with a diversity of biological contexts. Future Med Chem 2014; 5:1953-65. [PMID: 24175746 DOI: 10.4155/fmc.13.148] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
In vivo small molecules as necessary intermediates are involved in numerous critical metabolic pathways and biological processes associated with many essential biological functions and events. There is growing evidence that MS-based metabolomics is emerging as a powerful tool to facilitate the discovery of functional small molecules that can better our understanding of development, infection, nutrition, disease, toxicity, drug therapeutics, gene modifications and host-pathogen interaction from metabolic perspectives. However, further progress must still be made in MS-based metabolomics because of the shortcomings in the current technologies and knowledge. This technique-driven review aims to explore the discovery of in vivo functional small molecules facilitated by MS-based metabolomics and to highlight the analytic capabilities and promising applications of this discovery strategy. Moreover, the biological significance of the discovery of in vivo functional small molecules with different biological contexts is also interrogated at a metabolic perspective.
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16
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Wang J, Christison TT, Misuno K, Lopez L, Huhmer AF, Huang Y, Hu S. Metabolomic Profiling of Anionic Metabolites in Head and Neck Cancer Cells by Capillary Ion Chromatography with Orbitrap Mass Spectrometry. Anal Chem 2014; 86:5116-24. [DOI: 10.1021/ac500951v] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Junhua Wang
- Thermo Fisher
Scientific, Inc., 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Terri T. Christison
- Thermo Fisher
Scientific, Inc., 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Kaori Misuno
- School
of Dentistry and Jonsson Comprehensive Cancer Center, University of California, Los Angeles, 10833 Le Conte Avenue, Los
Angeles, California 90095, United States
| | - Linda Lopez
- Thermo Fisher
Scientific, Inc., 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Andreas F. Huhmer
- Thermo Fisher
Scientific, Inc., 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Yingying Huang
- Thermo Fisher
Scientific, Inc., 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Shen Hu
- School
of Dentistry and Jonsson Comprehensive Cancer Center, University of California, Los Angeles, 10833 Le Conte Avenue, Los
Angeles, California 90095, United States
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17
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Xu YJ, Wang C, Ho WE, Ong CN. Recent developments and applications of metabolomics in microbiological investigations. Trends Analyt Chem 2014. [DOI: 10.1016/j.trac.2013.12.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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18
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Kell DB, Goodacre R. Metabolomics and systems pharmacology: why and how to model the human metabolic network for drug discovery. Drug Discov Today 2014; 19:171-82. [PMID: 23892182 PMCID: PMC3989035 DOI: 10.1016/j.drudis.2013.07.014] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 07/03/2013] [Accepted: 07/16/2013] [Indexed: 02/06/2023]
Abstract
Metabolism represents the 'sharp end' of systems biology, because changes in metabolite concentrations are necessarily amplified relative to changes in the transcriptome, proteome and enzyme activities, which can be modulated by drugs. To understand such behaviour, we therefore need (and increasingly have) reliable consensus (community) models of the human metabolic network that include the important transporters. Small molecule 'drug' transporters are in fact metabolite transporters, because drugs bear structural similarities to metabolites known from the network reconstructions and from measurements of the metabolome. Recon2 represents the present state-of-the-art human metabolic network reconstruction; it can predict inter alia: (i) the effects of inborn errors of metabolism; (ii) which metabolites are exometabolites, and (iii) how metabolism varies between tissues and cellular compartments. However, even these qualitative network models are not yet complete. As our understanding improves so do we recognise more clearly the need for a systems (poly)pharmacology.
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Affiliation(s)
- Douglas B Kell
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
| | - Royston Goodacre
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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19
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Zhou W, Liotta LA, Petricoin EF. Cancer metabolism and mass spectrometry-based proteomics. Cancer Lett 2013; 356:176-83. [PMID: 24262660 DOI: 10.1016/j.canlet.2013.11.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 10/25/2013] [Accepted: 11/11/2013] [Indexed: 12/17/2022]
Abstract
Cancer metabolism has been extensively investigated by various tools, and the fact of diverse metabolic reprogramming in cancer cells has been gradually unveiled. In this review, we discuss some contributions in cancer metabolism by general proteomic analysis and post-translational modification analysis using mass spectrometry (MS) technique. Instead of following one or several metabolic enzymes/pathways, the current MS approach can quickly identify a large number of proteins and compare their expression levels in different samples, providing a potentially comprehensive picture of cancer metabolism. The MS analyses from pancreatic cancer cells support a hypothesis that hypoxia promotes cells in solid tumor to reprogram metabolic pathways in order to minimize the oxygen consumption. The oxidative stress in pancreatic cancer cells is lower than that in normal duct cells, and the cancer cells adaptively express less antioxidant proteins, contrary to claims that oxidative stress is higher in cancer cells. Separately, the MS analyses confirm that pyruvate kinase isoform 2 (PKM2) can be detected in both cancer and normal cells, disagreeing with report that tumor cells express exclusively PKM2. In addition, MS analyses from pancreatic cancer cells demonstrate that lactate dehydrogenase-B is significantly upregulated in pancreatic cancer cells, whereas previous reports show that lactate dehydrogenase-A is overexpressed and is responsible for lactate production in cancer cells. Lastly, the result from MS analysis suggests that the glutaminolysis in pancreatic cancer cells is different from that observed in glioblastoma cells.
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Affiliation(s)
- Weidong Zhou
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA 20110, USA.
| | - Lance A Liotta
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA 20110, USA
| | - Emanuel F Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA 20110, USA
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20
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Abstract
Metabolism has a decisive role in many fundamental biological processes, including organism development and tissue homeostasis. Here we describe a protocol for fast and reliable (13)C-isotope-based in vivo metabolic profiling. This protocol covers the loading of isotope precursor; extraction, preparation and quantification of the labeled lipid metabolites (e.g., the prenyl lipid CoQ10) by the means of HPLC-MS; and its analysis in zebrafish embryos. This protocol can be applied to different types of experimental settings, including tissue-specific metabolic analyses or dynamic metabolic changes that occur during vertebrate embryogenesis. The protocol takes 5-7 d to complete, requiring minimal equipment and analytical expertise, and it represents a unique alternative to the existing ex vivo (e.g., cell lines) isotope-based metabolic methods. This procedure represents a valuable approach for researchers interested in studying the effect of gene manipulation on lipid metabolism in zebrafish and in understanding the genetic conditions that result in metabolism dysfunction.
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