51
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Esteves AM, Graça G, Peyriga L, Torcato IM, Borges N, Portais JC, Santos H. Combined transcriptomics-metabolomics profiling of the heat shock response in the hyperthermophilic archaeon Pyrococcus furiosus. Extremophiles 2018; 23:101-118. [PMID: 30430272 DOI: 10.1007/s00792-018-1065-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/28/2018] [Indexed: 12/25/2022]
Abstract
Pyrococcus furiosus is a remarkable archaeon able to grow at temperatures around 100 °C. To gain insight into how this model hyperthermophile copes with heat stress, we compared transcriptomic and metabolomic data of cells subjected to a temperature shift from 90 °C to 97 °C. In this study, we used RNA-sequencing to characterize the global variation in gene expression levels, while nuclear magnetic resonance (NMR) and targeted ion exchange liquid chromatography-mass spectrometry (LC-MS) were used to determine changes in metabolite levels. Of the 552 differentially expressed genes in response to heat shock conditions, 257 were upregulated and 295 were downregulated. In particular, there was a significant downregulation of genes for synthesis and transport of amino acids. At the metabolite level, 37 compounds were quantified. The level of di-myo-inositol phosphate, a canonical heat stress solute among marine hyperthermophiles, increased considerably (5.4-fold) at elevated temperature. Also, the levels of mannosylglycerate, UDP-N-acetylglucosamine (UDPGlcNac) and UDP-N-acetylgalactosamine were enhanced. The increase in the pool of UDPGlcNac was concurrent with an increase in the transcript levels of the respective biosynthetic genes. This work provides the first metabolomic analysis of the heat shock response of a hyperthermophile.
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Affiliation(s)
- Ana M Esteves
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-127, Oeiras, Portugal
| | - Gonçalo Graça
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-127, Oeiras, Portugal
| | - Lindsay Peyriga
- LISBP, Université de Toulouse, CNRS, INRA, INSA, 31077, Toulouse, France.,MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, 31077, Toulouse, France
| | - Inês M Torcato
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-127, Oeiras, Portugal
| | - Nuno Borges
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-127, Oeiras, Portugal
| | - Jean-Charles Portais
- LISBP, Université de Toulouse, CNRS, INRA, INSA, 31077, Toulouse, France.,MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, 31077, Toulouse, France.,Université Paul Sabatier, Université de Toulouse, 31062, Toulouse, France
| | - Helena Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-127, Oeiras, Portugal.
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52
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Antireflection Surfaces for Biological Analysis Using Laser Desorption Ionization Mass Spectrometry. RESEARCH 2018; 2018:5439729. [PMID: 31549031 PMCID: PMC6750120 DOI: 10.1155/2018/5439729] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 10/16/2018] [Indexed: 12/14/2022]
Abstract
Laser desorption ionization mass spectrometry (LDI-MS) is a primary tool for biological analysis. Its success relies on the use of chemical matrices that facilitate soft desorption and ionization of the biomolecules, which, however, also limits its application for metabolomics study due to the chemical interference by the matrix compounds. The requirement for sample pretreatment is also undesirable for direct sampling analysis or tissue imaging. In this study, antireflection (AR) metal surfaces were investigated as sample substrates for matrix-free LDI-MS. They were prepared through ultrafast laser processing, with high light-to-heat energy conversion efficiency. The morphology and micro/nanostructures on the metal surfaces could be adjusted and optimized by tuning the laser fabrication process. The super-high UV absorption at 97% enabled highly efficient thermal desorption and ionization of analytes. The analytical performance for the matrix-free LDI was explored by analyzing a variety of biological compounds, including carbohydrates, drugs, metabolites, and amino acids. Its applicability for direct analysis of complex biological samples was also demonstrated by direct analysis of metabolites in yeast cells.
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53
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Quenching for Microalgal Metabolomics: A Case Study on the Unicellular Eukaryotic Green Alga Chlamydomonas reinhardtii. Metabolites 2018; 8:metabo8040072. [PMID: 30384421 PMCID: PMC6315863 DOI: 10.3390/metabo8040072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 10/25/2018] [Accepted: 10/29/2018] [Indexed: 11/30/2022] Open
Abstract
Capturing a valid snapshot of the metabolome requires rapid quenching of enzyme activities. This is a crucial step in order to halt the constant flux of metabolism and high turnover rate of metabolites. Quenching with cold aqueous methanol is treated as a gold standard so far, however, reliability of metabolomics data obtained is in question due to potential problems connected to leakage of intracellular metabolites. Therefore, we investigated the influence of various parameters such as quenching solvents, methanol concentration, inclusion of buffer additives, quenching time and solvent to sample ratio on intracellular metabolite leakage from Chlamydomonas reinhardtii. We measured the recovery of twelve metabolite classes using gas chromatography mass spectrometry (GC-MS) in all possible fractions and established mass balance to trace the fate of metabolites during quenching treatments. Our data demonstrate significant loss of intracellular metabolites with the use of the conventional 60% methanol, and that an increase in methanol concentration or quenching time also resulted in higher leakage. Inclusion of various buffer additives showed 70 mM HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid) to be suitable. In summary, we recommend quenching with 60% aqueous methanol supplemented with 70 mM HEPES (−40 °C) at 1:1 sample to quenching solvent ratio, as it resulted in higher recoveries for intracellular metabolites with subsequent reduction in the metabolite leakage for all metabolite classes.
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54
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Zheng X, Yu J, Cairns TC, Zhang L, Zhang Z, Zhang Q, Zheng P, Sun J, Ma Y. Comprehensive Improvement of Sample Preparation Methodologies Facilitates Dynamic Metabolomics of Aspergillus niger. Biotechnol J 2018; 14:e1800315. [PMID: 30144348 DOI: 10.1002/biot.201800315] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/27/2018] [Indexed: 12/23/2022]
Abstract
Metabolomics is an essential discipline in industrial biotechnology. Sample preparation approaches dramatically influence data quality and, ultimately, interpretation and conclusions from metabolomic experiments. However, standardized protocols for highly reproducible metabolic datasets are limited, especially for the fungal cell factory Aspergillus niger. Here, an improved liquid chromatography-tandem mass spectrometry-based pipeline for A. niger metabolomics is developed. It is found that fast filtration with liquid nitrogen is more suitable for cell quenching, causing minimal disruption to cell integrity, and improved intracellular metabolite recovery when compared to cold methanol quenching approaches. Seven solutions are evaluated for intracellular metabolite extraction, and found acetonitrile/water (1:1, v/v) at -20 °C, combined with boiling ethanol extraction protocols, showed unbiased metabolite profiling. This improved methodology is applied to unveil the dynamic metabolite profile of one citrate over-producing A. niger isolate under citrate fermentation. Citrate precursors, especially pyruvate, oxaloacetate, and malate, are maintained at a relatively high intracellular level, which can be necessary for high citrate synthesis flux. Glutamine shows a similar trend compared to citrate production, suggesting glutamine may be involved in intracellular pH homeostasis. Taken together, this study delivers a highly standardized and improved metabolomics methodology and paves the way for systems metabolic engineering in biotechnologically important fungi.
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Affiliation(s)
- Xiaomei Zheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Jiandong Yu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Timothy C Cairns
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Lihui Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Zhidan Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Qiongqiong Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Ping Zheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jibin Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanhe Ma
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
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55
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Krzyszczyk P, Acevedo A, Davidoff EJ, Timmins LM, Marrero-Berrios I, Patel M, White C, Lowe C, Sherba JJ, Hartmanshenn C, O'Neill KM, Balter ML, Fritz ZR, Androulakis IP, Schloss RS, Yarmush ML. The growing role of precision and personalized medicine for cancer treatment. TECHNOLOGY 2018; 6:79-100. [PMID: 30713991 PMCID: PMC6352312 DOI: 10.1142/s2339547818300020] [Citation(s) in RCA: 196] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Cancer is a devastating disease that takes the lives of hundreds of thousands of people every year. Due to disease heterogeneity, standard treatments, such as chemotherapy or radiation, are effective in only a subset of the patient population. Tumors can have different underlying genetic causes and may express different proteins in one patient versus another. This inherent variability of cancer lends itself to the growing field of precision and personalized medicine (PPM). There are many ongoing efforts to acquire PPM data in order to characterize molecular differences between tumors. Some PPM products are already available to link these differences to an effective drug. It is clear that PPM cancer treatments can result in immense patient benefits, and companies and regulatory agencies have begun to recognize this. However, broader changes to the healthcare and insurance systems must be addressed if PPM is to become part of standard cancer care.
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Affiliation(s)
- Paulina Krzyszczyk
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ 08854, USA
| | - Alison Acevedo
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ 08854, USA
| | - Erika J Davidoff
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ 08854, USA
| | - Lauren M Timmins
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ 08854, USA
| | - Ileana Marrero-Berrios
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ 08854, USA
| | - Misaal Patel
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ 08854, USA
| | - Corina White
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ 08854, USA
| | - Christopher Lowe
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ 08854, USA
| | - Joseph J Sherba
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ 08854, USA
| | - Clara Hartmanshenn
- Department of Chemical & Biochemical Engineering, Rutgers University, 98 Brett Road, Piscataway, NJ 08854, USA
| | - Kate M O'Neill
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ 08854, USA
| | - Max L Balter
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ 08854, USA
| | - Zachary R Fritz
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ 08854, USA
| | - Ioannis P Androulakis
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ 08854, USA
- Department of Chemical & Biochemical Engineering, Rutgers University, 98 Brett Road, Piscataway, NJ 08854, USA
| | - Rene S Schloss
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ 08854, USA
| | - Martin L Yarmush
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ 08854, USA
- Department of Chemical & Biochemical Engineering, Rutgers University, 98 Brett Road, Piscataway, NJ 08854, USA
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56
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Schmidt M, Tran-Nguyen D, Chizek P. Influence of boric acid on energy metabolism and stress tolerance of Candida albicans. J Trace Elem Med Biol 2018; 49:140-145. [PMID: 29895364 DOI: 10.1016/j.jtemb.2018.05.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 05/08/2018] [Accepted: 05/17/2018] [Indexed: 10/16/2022]
Abstract
Boron presents at physiological pH in the form of boric acid (BA), a molecule that has both positive and negative effects on biological processes. In medicine, BA is used as a topical treatment for vaginal yeast infections by Candida species because of its well-documented but poorly understood effect on inhibition of growth in general and of invasive, hyphal growth in particular. The present study examines the influence of BA on carbohydrate energy metabolism of this common human pathogen. Starting from previous findings about an inhibition of key NAD-dependent enzymes by BA in vitro, we confirmed that such an inhibition occurs in permeabilized C. albicans cells. Cultures growing even with moderate concentrations of BA experience mitochondrial failure, increase ethanol production from glucose and decrease the deposition of carbohydrate stores in the form of glycogen. Cells growing on the non-fermentable, FAD-generating carbon source lactate have a higher BA tolerance, which suggests that the toxicity of BA is rooted in an inhibition of NAD-dependent reactions and the increased production of ethanol. Boric acid exposure sensitizes C. albicans selectively to the toxic effects of ethanol. This additive effect suggests that the endogenously produced ethanol increases the load on ethanol resistance mechanisms. Lastly, combination studies showed no interactions of BA with common antifungal drugs, meaning that addition of BA to topical formulations can provide an additive antifungal effect regardless of the chosen active ingredient.
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Affiliation(s)
- Martin Schmidt
- Des Moines University, 3200 Grand Avenue, Des Moines, IA 50312, USA.
| | | | - Patrick Chizek
- Des Moines University, 3200 Grand Avenue, Des Moines, IA 50312, USA.
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57
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Misra BB, Langefeld CD, Olivier M, Cox LA. Integrated Omics: Tools, Advances, and Future Approaches. J Mol Endocrinol 2018; 62:JME-18-0055. [PMID: 30006342 DOI: 10.1530/jme-18-0055] [Citation(s) in RCA: 220] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 07/02/2018] [Accepted: 07/12/2018] [Indexed: 12/13/2022]
Abstract
With the rapid adoption of high-throughput omic approaches to analyze biological samples such as genomics, transcriptomics, proteomics, and metabolomics, each analysis can generate tera- to peta-byte sized data files on a daily basis. These data file sizes, together with differences in nomenclature among these data types, make the integration of these multi-dimensional omics data into biologically meaningful context challenging. Variously named as integrated omics, multi-omics, poly-omics, trans-omics, pan-omics, or shortened to just 'omics', the challenges include differences in data cleaning, normalization, biomolecule identification, data dimensionality reduction, biological contextualization, statistical validation, data storage and handling, sharing, and data archiving. The ultimate goal is towards the holistic realization of a 'systems biology' understanding of the biological question in hand. Commonly used approaches in these efforts are currently limited by the 3 i's - integration, interpretation, and insights. Post integration, these very large datasets aim to yield unprecedented views of cellular systems at exquisite resolution for transformative insights into processes, events, and diseases through various computational and informatics frameworks. With the continued reduction in costs and processing time for sample analyses, and increasing types of omics datasets generated such as glycomics, lipidomics, microbiomics, and phenomics, an increasing number of scientists in this interdisciplinary domain of bioinformatics face these challenges. We discuss recent approaches, existing tools, and potential caveats in the integration of omics datasets for development of standardized analytical pipelines that could be adopted by the global omics research community.
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Affiliation(s)
- Biswapriya B Misra
- B Misra, Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, United States
| | - Carl D Langefeld
- C Langefeld, Biostatistical Sciences, Wake Forest University School of Medicine, Winston-Salem, United States
| | - Michael Olivier
- M Olivier, Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, United States
| | - Laura A Cox
- L Cox, Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, United States
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58
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Abstract
PURPOSE OF THE REVIEW This review presents the analytical techniques, processing and analytical steps used in metabolomics phenotyping studies, as well as the main results from epidemiological studies on the associations between metabolites and high blood pressure. RECENT FINDINGS A variety of metabolomic approaches have been applied to a range of epidemiological studies to uncover the pathophysiology of high blood pressure. Several pathways have been suggested in relation to blood pressure including the possible role of the gut microflora, inflammatory, oxidative stress, and lipid pathways. Metabolic changes have also been identified associated with blood pressure lowering effects of diets high in fruits and vegetables and low in meat intake. However, the current body of literature on metabolic profiling and blood pressure is still in its infancy, not fully consistent and requires careful interpretation. Metabolic phenotyping is a promising approach to uncover metabolic pathways associated with high blood pressure and throw light into the complex pathophysiology of hypertension.
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Affiliation(s)
- Ioanna Tzoulaki
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK.
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK.
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece.
| | - Aikaterini Iliou
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Athens, Athens, Greece
| | - Emmanuel Mikros
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Athens, Athens, Greece
| | - Paul Elliott
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- Health Data Research UK (HDR-UK), London, UK
- Dementia Research Institute at Imperial College London, London, UK
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59
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Kang YP, Ward NP, DeNicola GM. Recent advances in cancer metabolism: a technological perspective. Exp Mol Med 2018; 50:1-16. [PMID: 29657324 PMCID: PMC5938018 DOI: 10.1038/s12276-018-0027-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 12/12/2017] [Indexed: 01/28/2023] Open
Abstract
Cancer cells are highly dependent on metabolic pathways to sustain both their proliferation and adaption to harsh microenvironments. Thus, understanding the metabolic reprogramming that occurs in tumors can provide critical insights for the development of therapies targeting metabolism. In this review, we will discuss recent advancements in metabolomics and other multidisciplinary techniques that have led to the discovery of novel metabolic pathways and mechanisms in diverse cancer types. Researchers now have access to a rapidly growing number of tools for probing the metabolic abnormalities associated with tumor growth. Unrestrained growth puts special demands on cancer cells, and scientists have known for nearly a century that tumor metabolism differs considerably from healthy tissue metabolism. Gina DeNicola and colleagues at the Moffitt Cancer Center and Research Institute, Tampa, USA, have reviewed the technological tools available for monitoring the molecules that power cell growth and survival. These include mass spectrometry, which can generate an extremely detailed census of cellular metabolites in a single experiment. The authors also highlight techniques that can help ‘trap’ short-lived or unstable chemical intermediates for analysis. Other chemical labeling and tracing techniques can illuminate activity of selected metabolic processes in living tumor cells or even in patients, findings that could reveal therapeutic vulnerabilities.
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Affiliation(s)
- Yun Pyo Kang
- Department of Cancer Imaging and Metabolism, Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Nathan P Ward
- Department of Cancer Imaging and Metabolism, Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Gina M DeNicola
- Department of Cancer Imaging and Metabolism, Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA.
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60
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Alcalde E, Fraser PD. Extending our tools and resources in the non-conventional industrial yeast Xanthophyllomyces dendrorhous through the application of metabolite profiling methodologies. Metabolomics 2018; 14:30. [PMID: 29479298 PMCID: PMC5809543 DOI: 10.1007/s11306-017-1313-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 12/22/2017] [Indexed: 11/30/2022]
Abstract
INTRODUCTION Xanthophyllomyces dendrorhous is a non-conventional industrial yeast. It has the unique ability among yeasts to produce geranylgeranyl pyrophosphate derived terpenoids such as carotenoids and in particular the high value pigment astaxanthin. OBJECTIVE In order to fully exploit the industrial potential of Xanthophyllomyces using modern industrial biotechnology approaches the further development of "omic" resources in this organism are required to build on the now sequenced and annotated genome. To contribute to this goal, the present study has developed and implemented an efficient metabolite profiling system comprised of, quenching, extraction and associated GC-MS and UPLC analysis. METHOD Four quenching methods and five extraction methods compatible with GC-MS and UPLC profiling were tested and validated by analysing steady state metabolite changes of Xanthophyllomyces cultivated at laboratory scale in liquid shake culture at lag, exponential and early and late stationary phases. RESULTS A customised Automated Mass Spectral Deconvolution and Identification System (AMDIS) library has been created for Xanthophyllomyces, over 400 compounds are present in the library of which 78 are detected and quantified routinely in polar and non-polar derived extracts. A preliminary biochemical network has been constructed. Over a standardised laboratory growth cycle, changes in metabolite levels have been determined to create reference point for future strain improvement approaches and the initial biochemical network construction. Correlation analysis has illustrated that astaxanthin formation correlates positively with different sectors of intermediary metabolism (e.g. the TCA cycle intermediates and amino acid formation), "short" saturated fatty acids and β-carotene, while other metabolites are reduced in response to astaxanthin production. These sectors of intermediary metabolism offer potential future targets for the manipulation resulting in the generation of strains with improved titres of given terpenoids. DISCUSSION In summary a robust metabolite profiling system for Xanthophyllomyces is in place to further our understanding and potential exploitation of this underutilised industrial yeast.
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Affiliation(s)
- Eugenio Alcalde
- School Biological Sciences, Royal Holloway, University London, Egham Hill, Egham, Surrey TW20OEX UK
| | - Paul D. Fraser
- School Biological Sciences, Royal Holloway, University London, Egham Hill, Egham, Surrey TW20OEX UK
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61
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Cambiaghi A, Ferrario M, Masseroli M. Analysis of metabolomic data: tools, current strategies and future challenges for omics data integration. Brief Bioinform 2017; 18:498-510. [PMID: 27075479 DOI: 10.1093/bib/bbw031] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Indexed: 11/13/2022] Open
Abstract
Metabolomics is a rapidly growing field consisting of the analysis of a large number of metabolites at a system scale. The two major goals of metabolomics are the identification of the metabolites characterizing each organism state and the measurement of their dynamics under different situations (e.g. pathological conditions, environmental factors). Knowledge about metabolites is crucial for the understanding of most cellular phenomena, but this information alone is not sufficient to gain a comprehensive view of all the biological processes involved. Integrated approaches combining metabolomics with transcriptomics and proteomics are thus required to obtain much deeper insights than any of these techniques alone. Although this information is available, multilevel integration of different 'omics' data is still a challenge. The handling, processing, analysis and integration of these data require specialized mathematical, statistical and bioinformatics tools, and several technical problems hampering a rapid progress in the field exist. Here, we review four main tools for number of users or provided features (MetaCoreTM, MetaboAnalyst, InCroMAP and 3Omics) out of the several available for metabolomic data analysis and integration with other 'omics' data, highlighting their strong and weak aspects; a number of related issues affecting data analysis and integration are also identified and discussed. Overall, we provide an objective description of how some of the main currently available software packages work, which may help the experimental practitioner in the choice of a robust pipeline for metabolomic data analysis and integration.
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62
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Microdosing, isotopic labeling, radiotracers and metabolomics: relevance in drug discovery, development and safety. Bioanalysis 2017; 9:1913-1933. [PMID: 29171759 DOI: 10.4155/bio-2017-0137] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
This review discusses the use of stable (13C, 2D) or radioactive isotopes (14C, 11C, 18F, 131I, 64Cu, 68Ga) incorporated into the molecular structure of new drug entities for the purpose of pharmacokinetic or -dynamic studies. Metabolite in safety testing requires the administration of pharmacologically active doses. In such studies, radiotracers find application mainly in preclinical animal investigations, whereby LC-MS/MS is used to identify metabolite structure and drug-related effects. In contrast, first-in-human metabolite studies have to be carried out at nonpharmacological doses not exceeding 100 μg (microdose), which is generally too low for metabolite detection by LC-MS/MS. This short-coming can be overcome by specific radio- or isotopic labeling of the drug of interest and measurements using accelerator mass spectroscopy, single-photon emission computed tomography and positron emission tomography. Such combined radioisotope-based approaches permit Phase 0, first-in-human metabolite study.
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63
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Pinu FR, Villas-Boas SG, Aggio R. Analysis of Intracellular Metabolites from Microorganisms: Quenching and Extraction Protocols. Metabolites 2017; 7:E53. [PMID: 29065530 PMCID: PMC5746733 DOI: 10.3390/metabo7040053] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 10/11/2017] [Accepted: 10/21/2017] [Indexed: 11/17/2022] Open
Abstract
Sample preparation is one of the most important steps in metabolome analysis. The challenges of determining microbial metabolome have been well discussed within the research community and many improvements have already been achieved in last decade. The analysis of intracellular metabolites is particularly challenging. Environmental perturbations may considerably affect microbial metabolism, which results in intracellular metabolites being rapidly degraded or metabolized by enzymatic reactions. Therefore, quenching or the complete stop of cell metabolism is a pre-requisite for accurate intracellular metabolite analysis. After quenching, metabolites need to be extracted from the intracellular compartment. The choice of the most suitable metabolite extraction method/s is another crucial step. The literature indicates that specific classes of metabolites are better extracted by different extraction protocols. In this review, we discuss the technical aspects and advancements of quenching and extraction of intracellular metabolite analysis from microbial cells.
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Affiliation(s)
- Farhana R Pinu
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland 1142, New Zealand.
| | - Silas G Villas-Boas
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1010, New Zealand.
| | - Raphael Aggio
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Crown Street, Liverpool L693BX, UK.
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64
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Rosebrock AP, Caudy AA. Metabolite Extraction from Saccharomyces cerevisiae for Liquid Chromatography-Mass Spectrometry. Cold Spring Harb Protoc 2017; 2017:pdb.prot089086. [PMID: 28864564 DOI: 10.1101/pdb.prot089086] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Prior to mass spectrometric analysis, cellular small molecules must be extracted and separated from interfering components such as salts and culture medium. To ensure minimal perturbation of metabolism, yeast cells grown in liquid culture are rapidly harvested by filtration as described here. Simultaneous quenching of metabolism and extraction is afforded by immediate immersion in low-temperature organic solvent. Samples prepared using this method are suitable for a range of downstream liquid chromatography-mass spectrometry analyses and are stable in solvent for >1 yr at -80°C.
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Affiliation(s)
- Adam P Rosebrock
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S3E1, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S3E1, Canada
| | - Amy A Caudy
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S3E1, Canada; .,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S3E1, Canada
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65
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Wordofa GG, Kristensen M, Schrübbers L, McCloskey D, Forster J, Schneider K. Quantifying the Metabolome of Pseudomonas taiwanensis VLB120: Evaluation of Hot and Cold Combined Quenching/Extraction Approaches. Anal Chem 2017; 89:8738-8747. [PMID: 28727413 DOI: 10.1021/acs.analchem.7b00793] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Absolute quantification of free intracellular metabolites is a valuable tool in both pathway discovery and metabolic engineering. In this study, we conducted a comprehensive examination of different hot and cold combined quenching/extraction approaches to extract and quantify intracellular metabolites of Pseudomonas taiwanensis (P. taiwanensis) VLB120 to provide a useful reference data set of absolute intracellular metabolite concentrations. The suitability of commonly used metabolomics tools including a pressure driven fast filtration system followed by combined quenching/extraction techniques (such as cold methanol/acetonitrile/water, hot water, and boiling ethanol/water, as well as cold ethanol/water) were tested and evaluated for P. taiwanensis VLB120 metabolome analysis. In total 94 out of 107 detected intracellular metabolites were quantified using an isotope-ratio-based approach. The quantified metabolites include amino acids, nucleotides, central carbon metabolism intermediates, redox cofactors, and others. The acquired data demonstrate that the pressure driven fast filtration approach followed by boiling ethanol quenching/extraction is the most adequate technique for P. taiwanensis VLB120 metabolome analysis based on quenching efficiency, extraction yields of metabolites, and experimental reproducibility.
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Affiliation(s)
- Gossa G Wordofa
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark , DK-2800 Lyngby, Denmark
| | - Mette Kristensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark , DK-2800 Lyngby, Denmark
| | - Lars Schrübbers
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark , DK-2800 Lyngby, Denmark
| | - Douglas McCloskey
- Department of Bioengineering, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093-0412, United States
| | - Jochen Forster
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark , DK-2800 Lyngby, Denmark
| | - Konstantin Schneider
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark , DK-2800 Lyngby, Denmark
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66
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Extracellular Microbial Metabolomics: The State of the Art. Metabolites 2017; 7:metabo7030043. [PMID: 28829385 PMCID: PMC5618328 DOI: 10.3390/metabo7030043] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 08/21/2017] [Accepted: 08/22/2017] [Indexed: 02/04/2023] Open
Abstract
Microorganisms produce and secrete many primary and secondary metabolites to the surrounding environment during their growth. Therefore, extracellular metabolites provide important information about the changes in microbial metabolism due to different environmental cues. The determination of these metabolites is also comparatively easier than the extraction and analysis of intracellular metabolites as there is no need for cell rupture. Many analytical methods are already available and have been used for the analysis of extracellular metabolites from microorganisms over the last two decades. Here, we review the applications and benefits of extracellular metabolite analysis. We also discuss different sample preparation protocols available in the literature for both types (e.g., metabolites in solution and in gas) of extracellular microbial metabolites. Lastly, we evaluate the authenticity of using extracellular metabolomics data in the metabolic modelling of different industrially important microorganisms.
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67
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Dudzik D, Barbas-Bernardos C, García A, Barbas C. Quality assurance procedures for mass spectrometry untargeted metabolomics. a review. J Pharm Biomed Anal 2017; 147:149-173. [PMID: 28823764 DOI: 10.1016/j.jpba.2017.07.044] [Citation(s) in RCA: 206] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 07/28/2017] [Accepted: 07/29/2017] [Indexed: 12/16/2022]
Abstract
Untargeted metabolomics, as a global approach, has already proven its great potential and capabilities for the investigation of health and disease, as well as the wide applicability for other research areas. Although great progress has been made on the feasibility of metabolomics experiments, there are still some challenges that should be faced and that includes all sources of fluctuations and bias affecting every step involved in multiplatform untargeted metabolomics studies. The identification and reduction of the main sources of unwanted variation regarding the pre-analytical, analytical and post-analytical phase of metabolomics experiments is essential to ensure high data quality. Nowadays, there is still a lack of information regarding harmonized guidelines for quality assurance as those available for targeted analysis. In this review, sources of variations to be considered and minimized along with methodologies and strategies for monitoring and improvement the quality of the results are discussed. The given information is based on evidences from different groups among our own experiences and recommendations for each stage of the metabolomics workflow. The comprehensive overview with tools presented here might serve other researchers interested in monitoring, controlling and improving the reliability of their findings by implementation of good experimental quality practices in the untargeted metabolomics study.
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Affiliation(s)
- Danuta Dudzik
- Center for Metabolomics and Bioanalysis (CEMBIO), Faculty of Pharmacy, San Pablo CEU University, Boadilla del Monte, ES-28668, Madrid, Spain.
| | - Cecilia Barbas-Bernardos
- Center for Metabolomics and Bioanalysis (CEMBIO), Faculty of Pharmacy, San Pablo CEU University, Boadilla del Monte, ES-28668, Madrid, Spain.
| | - Antonia García
- Center for Metabolomics and Bioanalysis (CEMBIO), Faculty of Pharmacy, San Pablo CEU University, Boadilla del Monte, ES-28668, Madrid, Spain.
| | - Coral Barbas
- Center for Metabolomics and Bioanalysis (CEMBIO), Faculty of Pharmacy, San Pablo CEU University, Boadilla del Monte, ES-28668, Madrid, Spain.
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68
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Datta S, Timson DJ, Annapure US. Antioxidant properties and global metabolite screening of the probiotic yeast Saccharomyces cerevisiae var. boulardii. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2017; 97:3039-3049. [PMID: 27868205 DOI: 10.1002/jsfa.8147] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 10/31/2016] [Accepted: 11/16/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND Saccharomyces cerevisiae var. boulardii is the only yeast species with probiotic properties. It is considered to have therapeutic significance in gastrointestinal disorders. In the present study, a comparative physiological study between this yeast and Saccharomyces cerevisiae (BY4742) was performed by evaluating two prominent traits of probiotic species, responses to different stress conditions and antioxidant capacity. A global metabolite profile was also developed aiming to identify which therapeutically important secondary metabolites are produced. RESULTS Saccharomyces cerevisiae var. boulardii showed no significant difference in growth patterns but greater stress tolerance compared to S. cerevisiae. It also demonstrated a six- to 10-fold greater antioxidant potential (judged by the 1,1-diphenyl-2-picrylhydrazyl assay), with a 70-fold higher total phenolic content and a 20-fold higher total flavonoid content in the extracellular fraction. These features were clearly differentiated by principal component analysis and further indicated by metabolite profiling. The extracellular fraction of the S. cerevisiae var. boulardii cultures was found to be rich in polyphenolic metabolites: vanillic acid, cinnamic acid, phenyl ethyl alcohol (rose oil), erythromycin, amphetamine and vitamin B6 , which results in the antioxidant capacity of this strain. CONCLUSION The present study presents a new perspective for differentiating the two genetically related strains of yeast, S. cerevisiae and S. cerevisiae var. boulardii by assessing their metabolome fingerprints. In addition to the correlation of the phenotypic properties with the secretory metabolites of these two yeasts, the present study also emphasizes the potential to exploit S. cerevisiae var. boulardii in the industrial production of these metabolites. © 2016 Society of Chemical Industry.
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Affiliation(s)
- Suprama Datta
- Food Engineering and Technology Department, Institute of Chemical Technology (ICT), Matunga, Mumbai, 400 019, India
- School of Biological Sciences, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast, BT9 7BL, UK
| | - David J Timson
- School of Biological Sciences, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast, BT9 7BL, UK
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Huxley Building, Lewes Road, Brighton, Sussex, BN2 4GJ, UK
| | - Uday S Annapure
- Food Engineering and Technology Department, Institute of Chemical Technology (ICT), Matunga, Mumbai, 400 019, India
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Lüddecke J, Francois L, Spät P, Watzer B, Chilczuk T, Poschet G, Hell R, Radlwimmer B, Forchhammer K. P II Protein-Derived FRET Sensors for Quantification and Live-Cell Imaging of 2-Oxoglutarate. Sci Rep 2017; 7:1437. [PMID: 28469248 PMCID: PMC5431102 DOI: 10.1038/s41598-017-01440-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 03/30/2017] [Indexed: 12/21/2022] Open
Abstract
The citric acid cycle intermediate 2-oxoglutarate (2-OG, a.k.a. alpha-ketoglutarate) links the carbon and nitrogen metabolic pathways and can provide information on the metabolic status of cells. In recent years, it has become exceedingly clear that 2-OG also acts as a master regulator of diverse biologic processes in all domains of life. Consequently, there is a great demand for time-resolved data on 2-OG fluctuations that can’t be adequately addressed using established methods like mass spectrometry-based metabolomics analysis. Therefore, we set out to develop a novel intramolecular 2-OG FRET sensor based on the signal transduction protein PII from Synechococcus elongatus PCC 7942. We created two variants of the sensor, with a dynamic range for 2-OG from 0.1 µM to 0.1 mM or from 10 µM to 10 mM. As proof of concept, we applied the sensors to determine in situ glutamine:2-oxoglutarate aminotransferase (GOGAT) activity in Synechococcus elongatus PCC 7942 cells and measured 2-OG concentrations in cell extracts from Escherichia coli in vitro. Finally, we could show the sensors’ functionality in living human cell lines, demonstrating their potential in the context of mechanistic studies and drug screening.
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Affiliation(s)
- Jan Lüddecke
- Interfaculty Institute for Microbiology and Infection Medicine, Division Organismic Interactions, University of Tübingen, Tübingen, Germany
| | - Liliana Francois
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Philipp Spät
- Interfaculty Institute for Microbiology and Infection Medicine, Division Organismic Interactions, University of Tübingen, Tübingen, Germany
| | - Björn Watzer
- Interfaculty Institute for Microbiology and Infection Medicine, Division Organismic Interactions, University of Tübingen, Tübingen, Germany
| | - Tomasz Chilczuk
- Interfaculty Institute for Microbiology and Infection Medicine, Division Organismic Interactions, University of Tübingen, Tübingen, Germany
| | - Gernot Poschet
- Centre for Organismal Studies Heidelberg, Rupprecht-Karls-Universität Heidelberg, Heidelberg, Germany
| | - Rüdiger Hell
- Centre for Organismal Studies Heidelberg, Rupprecht-Karls-Universität Heidelberg, Heidelberg, Germany
| | - Bernhard Radlwimmer
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Karl Forchhammer
- Interfaculty Institute for Microbiology and Infection Medicine, Division Organismic Interactions, University of Tübingen, Tübingen, Germany.
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70
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Marshall DD, Powers R. Beyond the paradigm: Combining mass spectrometry and nuclear magnetic resonance for metabolomics. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2017; 100:1-16. [PMID: 28552170 PMCID: PMC5448308 DOI: 10.1016/j.pnmrs.2017.01.001] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Revised: 01/04/2017] [Accepted: 01/08/2017] [Indexed: 05/02/2023]
Abstract
Metabolomics is undergoing tremendous growth and is being employed to solve a diversity of biological problems from environmental issues to the identification of biomarkers for human diseases. Nuclear magnetic resonance (NMR) and mass spectrometry (MS) are the analytical tools that are routinely, but separately, used to obtain metabolomics data sets due to their versatility, accessibility, and unique strengths. NMR requires minimal sample handling without the need for chromatography, is easily quantitative, and provides multiple means of metabolite identification, but is limited to detecting the most abundant metabolites (⩾1μM). Conversely, mass spectrometry has the ability to measure metabolites at very low concentrations (femtomolar to attomolar) and has a higher resolution (∼103-104) and dynamic range (∼103-104), but quantitation is a challenge and sample complexity may limit metabolite detection because of ion suppression. Consequently, liquid chromatography (LC) or gas chromatography (GC) is commonly employed in conjunction with MS, but this may lead to other sources of error. As a result, NMR and mass spectrometry are highly complementary, and combining the two techniques is likely to improve the overall quality of a study and enhance the coverage of the metabolome. While the majority of metabolomic studies use a single analytical source, there is a growing appreciation of the inherent value of combining NMR and MS for metabolomics. An overview of the current state of utilizing both NMR and MS for metabolomics will be presented.
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Affiliation(s)
- Darrell D Marshall
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, United States
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, United States.
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71
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Abstract
Metabolism is highly complex and involves thousands of different connected reactions; it is therefore necessary to use mathematical models for holistic studies. The use of mathematical models in biology is referred to as systems biology. In this review, the principles of systems biology are described, and two different types of mathematical models used for studying metabolism are discussed: kinetic models and genome-scale metabolic models. The use of different omics technologies, including transcriptomics, proteomics, metabolomics, and fluxomics, for studying metabolism is presented. Finally, the application of systems biology for analyzing global regulatory structures, engineering the metabolism of cell factories, and analyzing human diseases is discussed.
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Affiliation(s)
- Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE41128 Gothenburg, Sweden; .,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800 Lyngby, Denmark.,Science for Life Laboratory, Royal Institute of Technology, SE17121 Stockholm, Sweden
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72
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Tian J, Zhang S, Li H. Changes in intracellular metabolism underlying the adaptation of Saccharomyces cerevisiae strains to ethanol stress. ANN MICROBIOL 2017. [DOI: 10.1007/s13213-016-1251-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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73
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Pluskal T, Yanagida M. Metabolomic Analysis of Schizosaccharomyces pombe: Sample Preparation, Detection, and Data Interpretation. Cold Spring Harb Protoc 2016; 2016:2016/12/pdb.top079921. [PMID: 27934694 DOI: 10.1101/pdb.top079921] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Metabolomics is a modern field of chemical biology that strives to simultaneously quantify hundreds of cellular metabolites. Techniques for metabolomic analysis in Schizosaccharomyces pombe have only recently been developed. Here we introduce methods that provide a complete workflow for metabolomic analysis in S. pombe Based on available literature, we estimate the yeast metabolome to comprise on the order of several thousand different metabolites. We discuss the feasibility of extraction and detection of such a large number of metabolites, and the influences of various parameters on the results. Among the parameters addressed are cell cultivation conditions, metabolite extraction techniques, and detection and quantification methods. Further, we provide recommendations on data management and data processing for metabolomic experiments, and describe possible pitfalls regarding the interpretation of metabolomic data. Finally, we briefly discuss potential future developments of this technique.
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Affiliation(s)
- Tomáš Pluskal
- G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Kunigami, Okinawa 904-0495, Japan
| | - Mitsuhiro Yanagida
- G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Kunigami, Okinawa 904-0495, Japan
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74
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Metabolomic profiling of the astaxanthin accumulation process induced by high light in Haematococcus pluvialis. ALGAL RES 2016. [DOI: 10.1016/j.algal.2016.09.019] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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75
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Affiliation(s)
- Jennifer Pfizenmaier
- University of Stuttgart; Institute of Biochemical Engineering; Allmandring 31 70569 Stuttgart Germany
| | - Ralf Takors
- University of Stuttgart; Institute of Biochemical Engineering; Allmandring 31 70569 Stuttgart Germany
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76
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Payet LA, Leroux M, Willison JC, Kihara A, Pelosi L, Pierrel F. Mechanistic Details of Early Steps in Coenzyme Q Biosynthesis Pathway in Yeast. Cell Chem Biol 2016; 23:1241-1250. [PMID: 27693056 DOI: 10.1016/j.chembiol.2016.08.008] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 07/20/2016] [Accepted: 08/01/2016] [Indexed: 11/17/2022]
Abstract
Coenzyme Q (Q) is a redox lipid that is central for the energetic metabolism of eukaryotes. The biosynthesis of Q from the aromatic precursor 4-hydroxybenzoic acid (4-HB) is understood fairly well. However, biosynthetic details of how 4-HB is produced from tyrosine remain elusive. Here, we provide key insights into this long-standing biosynthetic problem by uncovering molecular details of the first and last reactions of the pathway in the yeast Saccharomyces cerevisiae, namely the deamination of tyrosine to 4-hydroxyphenylpyruvate by Aro8 and Aro9, and the oxidation of 4-hydroxybenzaldehyde to 4-HB by Hfd1. Inactivation of the HFD1 gene in yeast resulted in Q deficiency, which was rescued by the human enzyme ALDH3A1. This suggests that a similar pathway operates in animals, including humans, and led us to propose that patients with genetically unassigned Q deficiency should be screened for mutations in aldehyde dehydrogenase genes, especially ALDH3A1.
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Affiliation(s)
- Laurie-Anne Payet
- Université Grenoble Alpes, Laboratoire Technologies de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble (TIMC-IMAG), 38000 Grenoble, France; Centre National de Recherche Scientifique (CNRS), TIMC-IMAG, 38000 Grenoble, France
| | - Mélanie Leroux
- CEA-Grenoble, DRF-BIG-CBM, UMR5249, 38000 Grenoble, France
| | | | - Akio Kihara
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12-jo, Nishi 6-chome, Kita-ku, Sapporo 060-0812, Japan
| | - Ludovic Pelosi
- Université Grenoble Alpes, Laboratoire Technologies de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble (TIMC-IMAG), 38000 Grenoble, France; Centre National de Recherche Scientifique (CNRS), TIMC-IMAG, 38000 Grenoble, France
| | - Fabien Pierrel
- Université Grenoble Alpes, Laboratoire Technologies de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble (TIMC-IMAG), 38000 Grenoble, France; Centre National de Recherche Scientifique (CNRS), TIMC-IMAG, 38000 Grenoble, France.
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77
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Jorge TF, Rodrigues JA, Caldana C, Schmidt R, van Dongen JT, Thomas-Oates J, António C. Mass spectrometry-based plant metabolomics: Metabolite responses to abiotic stress. MASS SPECTROMETRY REVIEWS 2016; 35:620-49. [PMID: 25589422 DOI: 10.1002/mas.21449] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 10/02/2014] [Accepted: 10/14/2014] [Indexed: 05/08/2023]
Abstract
Metabolomics is one omics approach that can be used to acquire comprehensive information on the composition of a metabolite pool to provide a functional screen of the cellular state. Studies of the plant metabolome include analysis of a wide range of chemical species with diverse physical properties, from ionic inorganic compounds to biochemically derived hydrophilic carbohydrates, organic and amino acids, and a range of hydrophobic lipid-related compounds. This complexitiy brings huge challenges to the analytical technologies employed in current plant metabolomics programs, and powerful analytical tools are required for the separation and characterization of this extremely high compound diversity present in biological sample matrices. The use of mass spectrometry (MS)-based analytical platforms to profile stress-responsive metabolites that allow some plants to adapt to adverse environmental conditions is fundamental in current plant biotechnology research programs for the understanding and development of stress-tolerant plants. In this review, we describe recent applications of metabolomics and emphasize its increasing application to study plant responses to environmental (stress-) factors, including drought, salt, low oxygen caused by waterlogging or flooding of the soil, temperature, light and oxidative stress (or a combination of them). Advances in understanding the global changes occurring in plant metabolism under specific abiotic stress conditions are fundamental to enhance plant fitness and increase stress tolerance. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 35:620-649, 2016.
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Affiliation(s)
- Tiago F Jorge
- Plant Metabolomics Laboratory, Instituto de Tecnologia Química e Biológica António Xavier-Universidade Nova de Lisboa (ITQB-UNL), Avenida República, 2780-157, Oeiras, Portugal
| | - João A Rodrigues
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
| | - Camila Caldana
- Max-Planck-partner group at the Brazilian Bioethanol Science and Technology Laboratory/CNPEM, 13083-970, Campinas-SP, Brazil
| | - Romy Schmidt
- Institute of Biology I, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Joost T van Dongen
- Institute of Biology I, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Jane Thomas-Oates
- Jane Thomas-Oates, Centre of Excellence in Mass Spectrometry, and Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Carla António
- Plant Metabolomics Laboratory, Instituto de Tecnologia Química e Biológica António Xavier-Universidade Nova de Lisboa (ITQB-UNL), Avenida República, 2780-157, Oeiras, Portugal
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78
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Ortmayr K, Causon TJ, Hann S, Koellensperger G. Increasing selectivity and coverage in LC-MS based metabolome analysis. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2016.06.011] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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79
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Lunetti P, Damiano F, De Benedetto G, Siculella L, Pennetta A, Muto L, Paradies E, Marobbio CMT, Dolce V, Capobianco L. Characterization of Human and Yeast Mitochondrial Glycine Carriers with Implications for Heme Biosynthesis and Anemia. J Biol Chem 2016; 291:19746-59. [PMID: 27476175 DOI: 10.1074/jbc.m116.736876] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Indexed: 01/19/2023] Open
Abstract
Heme is an essential molecule in many biological processes, such as transport and storage of oxygen and electron transfer as well as a structural component of hemoproteins. Defects of heme biosynthesis in developing erythroblasts have profound medical implications, as represented by sideroblastic anemia. The synthesis of heme requires the uptake of glycine into the mitochondrial matrix where glycine is condensed with succinyl coenzyme A to yield δ-aminolevulinic acid. Herein we describe the biochemical and molecular characterization of yeast Hem25p and human SLC25A38, providing evidence that they are mitochondrial carriers for glycine. In particular, the hem25Δ mutant manifests a defect in the biosynthesis of δ-aminolevulinic acid and displays reduced levels of downstream heme and mitochondrial cytochromes. The observed defects are rescued by complementation with yeast HEM25 or human SLC25A38 genes. Our results identify new proteins in the heme biosynthetic pathway and demonstrate that Hem25p and its human orthologue SLC25A38 are the main mitochondrial glycine transporters required for heme synthesis, providing definitive evidence of their previously proposed glycine transport function. Furthermore, our work may suggest new therapeutic approaches for the treatment of congenital sideroblastic anemia.
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Affiliation(s)
- Paola Lunetti
- From the Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy
| | - Fabrizio Damiano
- From the Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy
| | - Giuseppe De Benedetto
- Laboratory of Analytical and Isotopic Mass Spectrometry, Department of Cultural Heritage, University of Salento, 73100 Lecce, Italy
| | - Luisa Siculella
- From the Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy
| | - Antonio Pennetta
- Laboratory of Analytical and Isotopic Mass Spectrometry, Department of Cultural Heritage, University of Salento, 73100 Lecce, Italy
| | - Luigina Muto
- Department of Pharmacy, Health, and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende (Cosenza), Italy
| | - Eleonora Paradies
- Consiglio Nazionale delle Ricerche, Institute of Biomembranes and Bioenergetics, 70125 Bari, Italy, and
| | - Carlo Marya Thomas Marobbio
- Department of Biosciences, Biotechnology, and Pharmacological Sciences, University of Bari, 70125 Bari, Italy
| | - Vincenza Dolce
- Department of Pharmacy, Health, and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende (Cosenza), Italy
| | - Loredana Capobianco
- From the Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy
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80
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Vrabl P, Artmann DJ, Schinagl CW, Burgstaller W. Rapid sample processing for intracellular metabolite studies in Penicillium ochrochloron CBS 123.824: the FiltRes-device combines cold filtration of methanol quenched biomass with resuspension in extraction solution. SPRINGERPLUS 2016; 5:966. [PMID: 27429876 PMCID: PMC4932030 DOI: 10.1186/s40064-016-2649-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Accepted: 06/23/2016] [Indexed: 11/10/2022]
Abstract
Background Many issues concerning sample processing for intracellular metabolite studies in filamentous fungi still need to be solved, e.g. how to reduce the contact time of the biomass to the quenching solution in order to minimize metabolite leakage. Since the required time to separate the biomass from the quenching solution determines the contact time, speeding up this step is thus of utmost interest. Recently, separation approaches based on cold-filtration were introduced as promising alternative to cold-centrifugation, which exhibit considerably reduced contact times. In previous works we were unable to obtain a compact pellet from cold methanol quenched samples of the filamentous fungus Penicillium ochrochloron CBS 123.824 via centrifugation. Therefore our aim was to establish for this organism a separation technique based on cold-filtration to determine intracellular levels of a selected set of nucleotides. Results We developed a cold-filtration based technique as part of our effort to revise the entire sample processing method and analytical procedure. The Filtration-Resuspension (FiltRes) device combined in a single apparatus (1) a rapid cold-filtration and (2) a rapid resuspension of the biomass in hot extraction solution. Unique to this is the injection of the extraction solution from below the membrane filter (FiltRes-principle). This caused the mycelial cake to detach completely from the filter membrane and to float upwards so that the biomass could easily be transferred into preheated tubes for metabolite extraction. The total contact time of glucose-limited chemostat mycelium to the quenching solution could be reduced to 15.7 ± 2.5 s, whereby each washing step added another 10–15 s. We evaluated critical steps like filtration time, temperature profile, reproducibility of results, and using the energy charge (EC) as a criterion, effectiveness of enzyme destruction during the transition in sample temperature from cold to hot. As control we used total broth samples quenched in hot ethanol. Averaged over all samples an EC of 0.93 ± 0.020 was determined with the FiltRes-principle compared to 0.89 ± 0.049 with heat stopped total broth samples. Conclusions We concluded that for P. ochrochloron this technique is a reliable sample processing method for intracellular metabolite analysis, which might offer also other possible applications. Electronic supplementary material The online version of this article (doi:10.1186/s40064-016-2649-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pamela Vrabl
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria
| | - Desiree J Artmann
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria
| | - Christoph W Schinagl
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria
| | - Wolfgang Burgstaller
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria
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81
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Kurczy ME, Forsberg EM, Thorgersen MP, Poole FL, Benton HP, Ivanisevic J, Tran ML, Wall JD, Elias DA, Adams MWW, Siuzdak G. Global Isotope Metabolomics Reveals Adaptive Strategies for Nitrogen Assimilation. ACS Chem Biol 2016; 11:1677-85. [PMID: 27045776 DOI: 10.1021/acschembio.6b00082] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nitrogen cycling is a microbial metabolic process essential for global ecological/agricultural balance. To investigate the link between the well-established ammonium and the alternative nitrate assimilation metabolic pathways, global isotope metabolomics was employed to examine three nitrate reducing bacteria using (15)NO3 as a nitrogen source. In contrast to a control (Pseudomonas stutzeri RCH2), the results show that two of the isolates from Oak Ridge, Tennessee (Pseudomonas N2A2 and N2E2) utilize nitrate and ammonia for assimilation concurrently with differential labeling observed across multiple classes of metabolites including amino acids and nucleotides. The data reveal that the N2A2 and N2E2 strains conserve nitrogen-containing metabolites, indicating that the nitrate assimilation pathway is a conservation mechanism for the assimilation of nitrogen. Co-utilization of nitrate and ammonia is likely an adaption to manage higher levels of nitrite since the denitrification pathways utilized by the N2A2 and N2E2 strains from the Oak Ridge site are predisposed to the accumulation of the toxic nitrite. The use of global isotope metabolomics allowed for this adaptive strategy to be investigated, which would otherwise not have been possible to decipher.
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Affiliation(s)
- Michael E. Kurczy
- Scripps
Center for Metabolomics, The Scripps Research Institute, 10550 North
Torrey Pines Road, La Jolla, California 92037, United States
| | - Erica M. Forsberg
- Scripps
Center for Metabolomics, The Scripps Research Institute, 10550 North
Torrey Pines Road, La Jolla, California 92037, United States
| | - Michael P. Thorgersen
- Department
of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - Farris L. Poole
- Department
of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - H. Paul Benton
- Scripps
Center for Metabolomics, The Scripps Research Institute, 10550 North
Torrey Pines Road, La Jolla, California 92037, United States
| | - Julijana Ivanisevic
- Metabolomics
Platform, Faculty of Biology and Medicine, University of Lausanne, Rue du Bugnon 19, 1011 Lausanne, Switzerland
| | - Minerva L. Tran
- Scripps
Center for Metabolomics, The Scripps Research Institute, 10550 North
Torrey Pines Road, La Jolla, California 92037, United States
| | - Judy D. Wall
- Department
of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Dwayne A. Elias
- Biosciences
Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Michael W. W. Adams
- Department
of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - Gary Siuzdak
- Scripps
Center for Metabolomics, The Scripps Research Institute, 10550 North
Torrey Pines Road, La Jolla, California 92037, United States
- Departments
of Chemistry, Molecular, and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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82
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Busti S, Mapelli V, Tripodi F, Sanvito R, Magni F, Coccetti P, Rocchetti M, Nielsen J, Alberghina L, Vanoni M. Respiratory metabolism and calorie restriction relieve persistent endoplasmic reticulum stress induced by calcium shortage in yeast. Sci Rep 2016; 6:27942. [PMID: 27305947 PMCID: PMC4910072 DOI: 10.1038/srep27942] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 05/27/2016] [Indexed: 11/26/2022] Open
Abstract
Calcium homeostasis is crucial to eukaryotic cell survival. By acting as an enzyme cofactor and a second messenger in several signal transduction pathways, the calcium ion controls many essential biological processes. Inside the endoplasmic reticulum (ER) calcium concentration is carefully regulated to safeguard the correct folding and processing of secretory proteins. By using the model organism Saccharomyces cerevisiae we show that calcium shortage leads to a slowdown of cell growth and metabolism. Accumulation of unfolded proteins within the calcium-depleted lumen of the endoplasmic reticulum (ER stress) triggers the unfolded protein response (UPR) and generates a state of oxidative stress that decreases cell viability. These effects are severe during growth on rapidly fermentable carbon sources and can be mitigated by decreasing the protein synthesis rate or by inducing cellular respiration. Calcium homeostasis, protein biosynthesis and the unfolded protein response are tightly intertwined and the consequences of facing calcium starvation are determined by whether cellular energy production is balanced with demands for anabolic functions. Our findings confirm that the connections linking disturbance of ER calcium equilibrium to ER stress and UPR signaling are evolutionary conserved and highlight the crucial role of metabolism in modulating the effects induced by calcium shortage.
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Affiliation(s)
- Stefano Busti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
- SYSBIO, Centre of Systems Biology, Milan, Italy
| | - Valeria Mapelli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
- Department of Biology and Biological Engineering, Division of Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden
| | - Farida Tripodi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
- SYSBIO, Centre of Systems Biology, Milan, Italy
| | - Rossella Sanvito
- Department of Health Sciences, University of Milano-Bicocca, Milan, Italy
| | - Fulvio Magni
- Department of Health Sciences, University of Milano-Bicocca, Milan, Italy
| | - Paola Coccetti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
- SYSBIO, Centre of Systems Biology, Milan, Italy
| | - Marcella Rocchetti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Lilia Alberghina
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
- SYSBIO, Centre of Systems Biology, Milan, Italy
| | - Marco Vanoni
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
- SYSBIO, Centre of Systems Biology, Milan, Italy
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83
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Feng B, Guo Z, Zhang W, Pan Y, Zhao Y. Metabolome response to temperature-induced virulence gene expression in two genotypes of pathogenic Vibrio parahaemolyticus. BMC Microbiol 2016; 16:75. [PMID: 27113578 PMCID: PMC4845332 DOI: 10.1186/s12866-016-0688-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Accepted: 04/14/2016] [Indexed: 04/03/2023] Open
Abstract
BACKGROUND Vibrio parahaemolyticus is a main causative agent of serious human seafood-borne gastroenteritis disease. Many researchers have investigated its pathogenesis by observing the alteration of its virulence factors in different conditions. It was previously known that culture conditions will influence the gene expression and the metabolic profile of V. parahaemolyticus, but little attention has been paid on the relationship between them. In this study, for the first time, the metabolomics response in relation to the expression of two major virulence genes, tdh and trh, induced at three temperatures (4, 25 and 37 °C) was examined in two genotypes of pathogenic Vibrio parahaemolyticus (ATCC33846 (tdh+/trh-/tlh+) and ATCC17802 (tdh-/trh+/tlh+)). RESULTS Reverse transcription real-time PCR (RT-qPCR) analysis illustrated that the expression levels of tdh and trh induced at 25 °C in V. parahaemolyticus were significantly higher than those induced at 4 and 37 °C. Principal components analysis (PCA) based on the UPLC & Q-TOF MS data presented clearly distinct groups among the samples treated by different temperatures. Metabolic profiling demonstrated that 179 of 1,033 kinds of identified metabolites in ATCC33846 changed significantly (p <0.01) upon culturing at different temperatures, meanwhile 101 of 930 kinds of metabolites changed (p <0.01) in ATCC17802. Pearson's correlation analysis highlighted the correlation between metabolites and virulence gene expression levels. At the threshold of | r | = 1, p <0.01, 12 kinds of metabolites showed extremely significant correlations with tdh expression, and 4 kinds of metabolites significantly correlated with trh expression. It is interesting that 3D, 7D, 11D-Phytanic acid showed the same trend with pyrophosphate, whose derivative could activate the degradation of phytanic acid. Several metabolites could be sorted into the same class by the method of chemical taxonomy, by assuming that they are involved in the same metabolic pathways. CONCLUSIONS This research can help to find biomarkers to monitor virulence gene expression, and can further help laboratory and clinical research of V. parahaemolyticus from the perspective of metabolomics.
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Affiliation(s)
- Bo Feng
- College of Food Science and Technology, Shanghai Ocean University, No. 999 Hu Cheng Huan Road, Shanghai, China
| | - Zhuoran Guo
- College of Food Science and Technology, Shanghai Ocean University, No. 999 Hu Cheng Huan Road, Shanghai, China
| | - Weijia Zhang
- College of Food Science and Technology, Shanghai Ocean University, No. 999 Hu Cheng Huan Road, Shanghai, China
- Shanghai Engineering Research Center of Aquatic-Product Processing & Preservation, Shanghai, China
- Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai, China
| | - Yingjie Pan
- College of Food Science and Technology, Shanghai Ocean University, No. 999 Hu Cheng Huan Road, Shanghai, China
- Shanghai Engineering Research Center of Aquatic-Product Processing & Preservation, Shanghai, China
- Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai, China
| | - Yong Zhao
- College of Food Science and Technology, Shanghai Ocean University, No. 999 Hu Cheng Huan Road, Shanghai, China.
- Shanghai Engineering Research Center of Aquatic-Product Processing & Preservation, Shanghai, China.
- Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai, China.
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84
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Liu M, Zhong C, Zhang YM, Xu ZM, Qiao CS, Jia SR. Metabolic Investigation in Gluconacetobacter xylinus and Its Bacterial Cellulose Production under a Direct Current Electric Field. Front Microbiol 2016; 7:331. [PMID: 27014248 PMCID: PMC4794480 DOI: 10.3389/fmicb.2016.00331] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 03/02/2016] [Indexed: 01/05/2023] Open
Abstract
The effects of a direct current (DC) electric field on the growth and metabolism of Gluconacetobacter xylinus were investigated in static culture. When a DC electric field at 10 mA was applied using platinum electrodes to the culture broth, bacterial cellulose (BC) production was promoted in 12 h but was inhibited in the last 12 h as compared to the control (without DC electric field). At the cathode, the presence of the hydrogen generated a strong reductive environment that is beneficial to cell growth. As compared to the control, the activities of glycolysis and tricarboxylic acid cycle, as well as BC productivity were observed to be slightly higher in the first 12 h. However, due to the absence of sufficient oxygen, lactic acid was accumulated from pyruvic acid at 18 h, which was not in favor of BC production. At the anode, DC inhibited cell growth in 6 h when compared to the control. The metabolic activity in G. xylinus was inhibited through the suppression of the tricarboxylic acid cycle and glycolysis. At 18-24 h, cell density was observed to decrease, which might be due to the electrolysis of water that significantly dropped the pH of cultural broth far beyond the optimal range. Meanwhile, metabolites for self-protection were accumulated, for instance proline, glutamic acid, gluconic acid, and fatty acids. Notably, the accumulation of gluconic acid and lactic acid made it a really tough acid stress to cells at the anode and finally led to depression of cell growth.
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Affiliation(s)
- Miao Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology Tianjin, China
| | - Cheng Zhong
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and TechnologyTianjin, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin UniversityTianjin, China
| | - Yu Ming Zhang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology Tianjin, China
| | - Ze Ming Xu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology Tianjin, China
| | - Chang Sheng Qiao
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology Tianjin, China
| | - Shi Ru Jia
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology Tianjin, China
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85
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Cardenas J, Da Silva NA. Engineering cofactor and transport mechanisms in Saccharomyces cerevisiae for enhanced acetyl-CoA and polyketide biosynthesis. Metab Eng 2016; 36:80-89. [PMID: 26969250 DOI: 10.1016/j.ymben.2016.02.009] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Revised: 02/04/2016] [Accepted: 02/23/2016] [Indexed: 01/01/2023]
Abstract
Synthesis of polyketides at high titer and yield is important for producing pharmaceuticals and biorenewable chemical precursors. In this work, we engineered cofactor and transport pathways in Saccharomyces cerevisiae to increase acetyl-CoA, an important polyketide building block. The highly regulated yeast pyruvate dehydrogenase bypass pathway was supplemented by overexpressing a modified Escherichia coli pyruvate dehydrogenase complex (PDHm) that accepts NADP(+) for acetyl-CoA production. After 24h of cultivation, a 3.7-fold increase in NADPH/NADP(+) ratio was observed relative to the base strain, and a 2.2-fold increase relative to introduction of the native E. coli PDH. Both E. coli pathways increased acetyl-CoA levels approximately 2-fold relative to the yeast base strain. Combining PDHm with a ZWF1 deletion to block the major yeast NADPH biosynthesis pathway resulted in a 12-fold NADPH boost and a 2.2-fold increase in acetyl-CoA. At 48h, only this coupled approach showed increased acetyl-CoA levels, 3.0-fold higher than that of the base strain. The impact on polyketide synthesis was evaluated in a S. cerevisiae strain expressing the Gerbera hybrida 2-pyrone synthase (2-PS) for the production of the polyketide triacetic acid lactone (TAL). Titers of TAL relative to the base strain improved only 30% with the native E. coli PDH, but 3.0-fold with PDHm and 4.4-fold with PDHm in the Δzwf1 strain. Carbon was further routed toward TAL production by reducing mitochondrial transport of pyruvate and acetyl-CoA; deletions in genes POR2, MPC2, PDA1, or YAT2 each increased titer 2-3-fold over the base strain (up to 0.8g/L), and in combination to 1.4g/L. Combining the two approaches (NADPH-generating acetyl-CoA pathway plus reduced metabolite flux into the mitochondria) resulted in a final TAL titer of 1.6g/L, a 6.4-fold increase over the non-engineered yeast strain, and 35% of theoretical yield (0.16g/g glucose), the highest reported to date. These biological driving forces present new avenues for improving high-yield production of acetyl-CoA derived compounds.
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Affiliation(s)
- Javier Cardenas
- Department of Chemical Engineering and Materials Science, University of California, Irvine, CA 92697-2575, USA
| | - Nancy A Da Silva
- Department of Chemical Engineering and Materials Science, University of California, Irvine, CA 92697-2575, USA.
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86
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Scott RA, Lindow SE. Transcriptional control of quorum sensing and associated metabolic interactions inPseudomonas syringaestrain B728a. Mol Microbiol 2016; 99:1080-98. [DOI: 10.1111/mmi.13289] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 12/02/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Russell A. Scott
- Department of Plant and Microbial Biology; University of California; 111 Koshland Hall Berkeley CA 94720-3102 USA
| | - Steven E. Lindow
- Department of Plant and Microbial Biology; University of California; 111 Koshland Hall Berkeley CA 94720-3102 USA
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87
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Fan TWM, Lane AN. Applications of NMR spectroscopy to systems biochemistry. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2016; 92-93:18-53. [PMID: 26952191 PMCID: PMC4850081 DOI: 10.1016/j.pnmrs.2016.01.005] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 01/26/2016] [Accepted: 01/28/2016] [Indexed: 05/05/2023]
Abstract
The past decades of advancements in NMR have made it a very powerful tool for metabolic research. Despite its limitations in sensitivity relative to mass spectrometric techniques, NMR has a number of unparalleled advantages for metabolic studies, most notably the rigor and versatility in structure elucidation, isotope-filtered selection of molecules, and analysis of positional isotopomer distributions in complex mixtures afforded by multinuclear and multidimensional experiments. In addition, NMR has the capacity for spatially selective in vivo imaging and dynamical analysis of metabolism in tissues of living organisms. In conjunction with the use of stable isotope tracers, NMR is a method of choice for exploring the dynamics and compartmentation of metabolic pathways and networks, for which our current understanding is grossly insufficient. In this review, we describe how various direct and isotope-edited 1D and 2D NMR methods can be employed to profile metabolites and their isotopomer distributions by stable isotope-resolved metabolomic (SIRM) analysis. We also highlight the importance of sample preparation methods including rapid cryoquenching, efficient extraction, and chemoselective derivatization to facilitate robust and reproducible NMR-based metabolomic analysis. We further illustrate how NMR has been applied in vitro, ex vivo, or in vivo in various stable isotope tracer-based metabolic studies, to gain systematic and novel metabolic insights in different biological systems, including human subjects. The pathway and network knowledge generated from NMR- and MS-based tracing of isotopically enriched substrates will be invaluable for directing functional analysis of other 'omics data to achieve understanding of regulation of biochemical systems, as demonstrated in a case study. Future developments in NMR technologies and reagents to enhance both detection sensitivity and resolution should further empower NMR in systems biochemical research.
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Affiliation(s)
- Teresa W-M Fan
- Department of Toxicology and Cancer Biology, University of Kentucky, 789 S. Limestone St., Lexington, KY 40536, United States.
| | - Andrew N Lane
- Department of Toxicology and Cancer Biology, University of Kentucky, 789 S. Limestone St., Lexington, KY 40536, United States.
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Schinagl CW, Vrabl P, Burgstaller W. Adapting High-Resolution Respirometry to Glucose-Limited Steady State Mycelium of the Filamentous Fungus Penicillium ochrochloron: Method Development and Standardisation. PLoS One 2016; 11:e0146878. [PMID: 26771937 PMCID: PMC4714917 DOI: 10.1371/journal.pone.0146878] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 12/24/2015] [Indexed: 11/29/2022] Open
Abstract
Fungal electron transport systems (ETS) are branched, involving alternative NADH dehydrogenases and an alternative terminal oxidase. These alternative respiratory enzymes were reported to play a role in pathogenesis, production of antibiotics and excretion of organic acids. The activity of these alternative respiratory enzymes strongly depends on environmental conditions. Functional analysis of fungal ETS under highly standardised conditions for cultivation, sample processing and respirometric assay are still lacking. We developed a highly standardised protocol to explore in vivo the ETS—and in particular the alternative oxidase—in Penicillium ochrochloron. This included cultivation in glucose-limited chemostat (to achieve a defined and reproducible physiological state), direct transfer without any manipulation of a broth sample to the respirometer (to maintain the physiological state in the respirometer as close as possible to that in the chemostat), and high-resolution respirometry (small sample volume and high measuring accuracy). This protocol was aimed at avoiding any changes in the physiological phenotype due to the high phenotypic plasticity of filamentous fungi. A stable oxygen consumption (< 5% change in 20 minutes) was only possible with glucose limited chemostat mycelium and a direct transfer of a broth sample into the respirometer. Steady state respiration was 29% below its maximum respiratory capacity. Additionally to a rotenone-sensitive complex I and most probably a functioning complex III, the ETS of P. ochrochloron also contained a cyanide-sensitive terminal oxidase (complex IV). Activity of alternative oxidase was present constitutively. The degree of inhibition strongly depended on the sequence of inhibitor addition. This suggested, as postulated for plants, that the alternative terminal oxidase was in dynamic equilibrium with complex IV—independent of the rate of electron flux. This means that the onset of activity does not depend on a complete saturation or inhibition of the cytochrome pathway.
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Affiliation(s)
| | - Pamela Vrabl
- University of Innsbruck, Institute of Microbiology, Innsbruck, Austria
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89
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Casadei L, Valerio M. (1)H NMR Metabolomic Footprinting Analysis for the In Vitro Screening of Potential Chemopreventive Agents. Methods Mol Biol 2016; 1379:89-97. [PMID: 26608292 DOI: 10.1007/978-1-4939-3191-0_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Metabolomics is the quantification and analysis of the concentration profiles of low-molecular-weight compounds present in biological samples. In particular metabolic footprinting analysis, based on the monitoring of metabolites consumed from and secreted into the growth medium, is a valuable tool for the study of pharmacological and toxicological effects of drugs. Mass spectrometry and nuclear magnetic resonance (NMR) are the two main complementary techniques used in this field. Although less sensitive, NMR gives a direct fingerprint of the system, and the spectra obtained contain metabolic information that can be distilled by chemometric techniques. In this chapter, we present how metabolomic footprinting can be used to assess in vitro a potential chemopreventive molecule as metformin.
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Affiliation(s)
- Luca Casadei
- Department of Chemistry, "Sapienza" University of Rome, Piazzale Aldo More 5, 00185, Rome, Italy.
| | - Mariacristina Valerio
- Department of Chemistry, "Sapienza" University of Rome, Piazzale Aldo More 5, 00185, Rome, Italy.
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90
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Shen Y, Fatemeh T, Tang L, Cai Z. Quantitative metabolic network profiling of Escherichia coli: An overview of analytical methods for measurement of intracellular metabolites. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2015.07.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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91
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Kim J, Stewart B, Weiss R. Extraction and Quantification of Tryptophan and Kynurenine from Cultured Cells and Media Using a High Performance Liquid Chromatography (HPLC) System Equipped with an Ultra-sensitive Diode Array Detector. Bio Protoc 2016; 6:e1781. [DOI: 10.21769/bioprotoc.1781] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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92
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A capillary zone electrophoresis method for adenine nucleotides analysis in Saccharomyces cerevisiae. J Chromatogr B Analyt Technol Biomed Life Sci 2015; 1008:156-163. [PMID: 26655107 DOI: 10.1016/j.jchromb.2015.11.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 11/19/2015] [Accepted: 11/21/2015] [Indexed: 02/04/2023]
Abstract
Adenosine triphosphate and its metabolites are involved in the cellular metabolism process in Saccharomyces cerevisiae. It is very important to simultaneously determine the relative contents of ATP and its metabolites in yeast. In this study, an effective capillary zone electrophoresis method with high selectivity was established. The calibration curves were linear in the concentration range from 1 to 20mg/L (ATP and cAMP) and 2 to 40mg/L (ADP and AMP) with excellent correlation coefficients (r(2))>0.999. The recovery of ATP, ADP, AMP, and cAMP were 99.4%, 94.7%, 100.3% and 99.6%, respectively. Simple sample preparation and easy detection of ATP and its metabolites make this method suitable for the study of changes in the four adenine nucleotides levels caused by caloric restriction in yeast. It is expected that the current method may contribute to further energy metabolism and related investigations of yeast.
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93
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Cui FX, Zhang RM, Liu HQ, Wang YF, Li H. Metabolic responses to Lactobacillus plantarum contamination or bacteriophage treatment in Saccharomyces cerevisiae using a GC–MS-based metabolomics approach. World J Microbiol Biotechnol 2015; 31:2003-13. [DOI: 10.1007/s11274-015-1949-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 09/15/2015] [Indexed: 12/01/2022]
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Strucko T, Magdenoska O, Mortensen UH. Benchmarking two commonly used Saccharomyces cerevisiae strains for heterologous vanillin-β-glucoside production. Metab Eng Commun 2015; 2:99-108. [PMID: 34150513 PMCID: PMC8193238 DOI: 10.1016/j.meteno.2015.09.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 07/29/2015] [Accepted: 09/03/2015] [Indexed: 11/26/2022] Open
Abstract
The yeast Saccharomyces cerevisiae is a widely used eukaryotic model organism and a key cell factory for production of biofuels and wide range of chemicals. From the broad palette of available yeast strains, the most popular are those derived from laboratory strain S288c and the industrially relevant CEN.PK strain series. Importantly, in recent years these two strains have been subjected to comparative "-omics" analyzes pointing out significant genotypic and phenotypic differences. It is therefore possible that the two strains differ significantly with respect to their potential as cell factories for production of specific compounds. To examine this possibility, we have reconstructed a de novo vanillin-β-glucoside pathway in an identical manner in S288c and CEN.PK strains. Characterization of the two resulting strains in two standard conditions revealed that the S288c background strain produced up to 10-fold higher amounts of vanillin-β-glucoside compared to CEN.PK. This study demonstrates that yeast strain background may play a major role in the outcome of newly developed cell factories for production of a given product.
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Affiliation(s)
- Tomas Strucko
- Department of Systems Biology, Technical University of Denmark, 2800Kgs Lyngby, Denmark
| | - Olivera Magdenoska
- Department of Systems Biology, Technical University of Denmark, 2800Kgs Lyngby, Denmark
| | - Uffe H Mortensen
- Department of Systems Biology, Technical University of Denmark, 2800Kgs Lyngby, Denmark
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95
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Jäpelt KB, Christensen JH, Villas-Bôas SG. Metabolic fingerprinting of Lactobacillus paracasei: the optimal quenching strategy. Microb Cell Fact 2015; 14:132. [PMID: 26337225 PMCID: PMC4559878 DOI: 10.1186/s12934-015-0322-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 08/21/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Quenching in cold buffered methanol at -40 °C has long been the preferred method for sub-second inactivation of cell metabolism during metabolic fingerprinting. However, methanol is known to cause intracellular metabolite leakage of microbial cells, making the distinction between intra- and extracellular metabolites in microbial systems challenging. In this paper, we tested three quenching protocols proposed for microbial cultures: fast filtration, cold buffered methanol and cold glycerol saline. RESULTS Our results clearly showed that cold glycerol saline quenching resulted in the best recovery of intracellular metabolites in Lactobacillus paracasei subsp. paracasei (L. paracasei). Membrane integrity assayed by propidium iodide revealed that approximately 100 % [Corrected] of the L. paracasei cell membranes were damaged by contact with the cold buffered methanol solution, whilst cold glycerol saline quenching led to minimal cell damage. Due to the nature of the L. paracasei culture, fast filtration took several minutes, which is far from ideal for metabolites with high intracellular turnover rates. CONCLUSION The implementation of a reliable, reproducible quenching method is essential within the metabolomics community. Cold glycerol saline prevented leakage of intracellular metabolites, and, thus, allowed more accurate determinations of intracellular metabolite levels.
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Affiliation(s)
- Kristina B Jäpelt
- Analytical Chemistry Group, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Copenhagen, Denmark. .,Chr. Hansen A/S, Hoersholm, Denmark.
| | - Jan H Christensen
- Analytical Chemistry Group, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Copenhagen, Denmark.
| | - Silas G Villas-Bôas
- The Metabolomics Lab, School of Biological Sciences, University of Auckland, Auckland, New Zealand.
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96
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Liu M, Zhong C, Wu XY, Wei YQ, Bo T, Han PP, Jia SR. Metabolomic profiling coupled with metabolic network reveals differences in Gluconacetobacter xylinus from static and agitated cultures. Biochem Eng J 2015. [DOI: 10.1016/j.bej.2015.05.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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97
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Calderón-Santiago M, Priego-Capote F, de Castro MDL. Enhancing detection coverage in untargeted metabolomics analysis by solid-phase extraction on-line coupled to LC-MS/MS. Electrophoresis 2015; 36:2179-2187. [DOI: 10.1002/elps.201500060] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 06/03/2015] [Accepted: 06/05/2015] [Indexed: 12/14/2022]
Affiliation(s)
- Mónica Calderón-Santiago
- Department of Analytical Chemistry, Annex Marie Curie Building, Campus of Rabanales; University of Córdoba; Córdoba Spain
- Maimónides Institute of Biomedical Research (IMIBIC), Reina Sofía University Hospital; University of Córdoba; Córdoba Spain
| | - Feliciano Priego-Capote
- Department of Analytical Chemistry, Annex Marie Curie Building, Campus of Rabanales; University of Córdoba; Córdoba Spain
- Maimónides Institute of Biomedical Research (IMIBIC), Reina Sofía University Hospital; University of Córdoba; Córdoba Spain
| | - María D. Luque de Castro
- Department of Analytical Chemistry, Annex Marie Curie Building, Campus of Rabanales; University of Córdoba; Córdoba Spain
- Maimónides Institute of Biomedical Research (IMIBIC), Reina Sofía University Hospital; University of Córdoba; Córdoba Spain
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98
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Todor H, Gooding J, Ilkayeva OR, Schmid AK. Dynamic Metabolite Profiling in an Archaeon Connects Transcriptional Regulation to Metabolic Consequences. PLoS One 2015; 10:e0135693. [PMID: 26284786 PMCID: PMC4540570 DOI: 10.1371/journal.pone.0135693] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 07/24/2015] [Indexed: 02/04/2023] Open
Abstract
Previous work demonstrated that the TrmB transcription factor is responsible for regulating the expression of many enzyme-coding genes in the hypersaline-adapted archaeon Halobacterium salinarum via a direct interaction with a cis-regulatory sequence in their promoters. This interaction is abolished in the presence of glucose. Although much is known about the effects of TrmB at the transcriptional level, it remains unclear whether and to what extent changes in mRNA levels directly affect metabolite levels. In order to address this question, here we performed a high-resolution metabolite profiling time course during a change in nutrients using a combination of targeted and untargeted methods in wild-type and ΔtrmB strain backgrounds. We found that TrmB-mediated transcriptional changes resulted in widespread and significant changes to metabolite levels across the metabolic network. Additionally, the pattern of growth complementation using various purines suggests that the mis-regulation of gluconeogenesis in the ΔtrmB mutant strain in the absence of glucose results in low phosphoribosylpyrophosphate (PRPP) levels. We confirmed these low PRPP levels using a quantitative mass spectrometric technique and found that they are associated with a metabolic block in de novo purine synthesis, which is partially responsible for the growth defect of the ΔtrmB mutant strain in the absence of glucose. In conclusion, we show how transcriptional regulation of metabolism affects metabolite levels and ultimately, phenotypes.
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Affiliation(s)
- Horia Todor
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Jessica Gooding
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Departments of Pharmacology and Cancer Biology and Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Olga R. Ilkayeva
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Departments of Pharmacology and Cancer Biology and Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Amy K. Schmid
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- University Program in Genetics and Genomics, Duke University, Durham, North Carolina, United States of America
- Center for Systems Biology, Duke University, Durham, North Carolina, United States of America
- * E-mail:
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99
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Russmayer H, Troyer C, Neubauer S, Steiger MG, Gasser B, Hann S, Koellensperger G, Sauer M, Mattanovich D. Metabolomics sampling of Pichia pastoris revisited: rapid filtration prevents metabolite loss during quenching. FEMS Yeast Res 2015; 15:fov049. [PMID: 26091839 DOI: 10.1093/femsyr/fov049] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/12/2015] [Indexed: 01/28/2023] Open
Abstract
Metabolomics can be defined as the quantitative assessment of a large number of metabolites of a biological system. A prerequisite for the accurate determination of intracellular metabolite concentrations is a reliable and reproducible sample preparation method, which needs to be optimized for each organism individually. Here, we compare the performance of rapid filtration and centrifugation after quenching of Pichia pastoris cells in cold methanol. During incubation in the quenching solution, metabolites are lost from the cells with a half-life of 70-180 min. Metabolites with lower molecular weights showed lower half-lifes compared to metabolites with higher molecular weight. Rapid filtration within 2 min after quenching leads to only minor losses below 2%, and is thus the preferred method for cell separation.
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Affiliation(s)
- Hannes Russmayer
- Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria
| | - Christina Troyer
- Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria Department of Chemistry, Division of Analytical Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Stefan Neubauer
- Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria Department of Chemistry, Division of Analytical Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Matthias G Steiger
- Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria
| | - Brigitte Gasser
- Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria
| | - Stephan Hann
- Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria Department of Chemistry, Division of Analytical Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Gunda Koellensperger
- Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria Institute of Analytical Chemistry, University of Vienna, Waehringer Str. 42, 1090 Vienna, Austria
| | - Michael Sauer
- Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria
| | - Diethard Mattanovich
- Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria
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100
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Jäpelt KB, Nielsen NJ, Wiese S, Christensen JH. Metabolic fingerprinting of Lactobacillus paracasei: a multi-criteria evaluation of methods for extraction of intracellular metabolites. Anal Bioanal Chem 2015; 407:6095-104. [DOI: 10.1007/s00216-015-8783-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 05/06/2015] [Accepted: 05/13/2015] [Indexed: 11/29/2022]
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