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Metabolic Feedback Inhibition Influences Metabolite Secretion by the Human Gut Symbiont Bacteroides thetaiotaomicron. mSystems 2020; 5:5/5/e00252-20. [PMID: 32873608 PMCID: PMC7470985 DOI: 10.1128/msystems.00252-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteroides is a highly abundant taxon in the human gut, and Bacteroides thetaiotaomicron (B. theta) is a ubiquitous human symbiont that colonizes the host early in development and persists throughout its life span. The phenotypic plasticity of keystone organisms such as B. theta is important to understand in order to predict phenotype(s) and metabolic interactions under changing nutrient conditions such as those that occur in complex gut communities. Our study shows B. theta prioritizes energy conservation and suppresses secretion of “overflow metabolites” such as organic acids and amino acids when concentrations of acetate are high. Secreted metabolites, especially amino acids, can be a source of nutrients or signals for the host or other microbes in the community. Our study suggests that when metabolically stressed by acetate, B. theta stops sharing with its ecological partners. Microbial metabolism and trophic interactions between microbes give rise to complex multispecies communities in microbe-host systems. Bacteroides thetaiotaomicron (B. theta) is a human gut symbiont thought to play an important role in maintaining host health. Untargeted nuclear magnetic resonance metabolomics revealed B. theta secretes specific organic acids and amino acids in defined minimal medium. Physiological concentrations of acetate and formate found in the human intestinal tract were shown to cause dose-dependent changes in secretion of metabolites known to play roles in host nutrition and pathogenesis. While secretion fluxes varied, biomass yield was unchanged, suggesting feedback inhibition does not affect metabolic bioenergetics but instead redirects carbon and energy to CO2 and H2. Flux balance analysis modeling showed increased flux through CO2-producing reactions under glucose-limiting growth conditions. The metabolic dynamics observed for B. theta, a keystone symbiont organism, underscores the need for metabolic modeling to complement genomic predictions of microbial metabolism to infer mechanisms of microbe-microbe and microbe-host interactions. IMPORTANCEBacteroides is a highly abundant taxon in the human gut, and Bacteroides thetaiotaomicron (B. theta) is a ubiquitous human symbiont that colonizes the host early in development and persists throughout its life span. The phenotypic plasticity of keystone organisms such as B. theta is important to understand in order to predict phenotype(s) and metabolic interactions under changing nutrient conditions such as those that occur in complex gut communities. Our study shows B. theta prioritizes energy conservation and suppresses secretion of “overflow metabolites” such as organic acids and amino acids when concentrations of acetate are high. Secreted metabolites, especially amino acids, can be a source of nutrients or signals for the host or other microbes in the community. Our study suggests that when metabolically stressed by acetate, B. theta stops sharing with its ecological partners.
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Maity S, Gundampati RK, Suresh Kumar TK. NMR Methods to Characterize Protein-Ligand Interactions. Nat Prod Commun 2019. [DOI: 10.1177/1934578x19849296] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Structural information pertaining to the interactions between biological macromolecules and ligands is of potential significance for understanding of molecular mechanisms in key biological processes. Recently, nuclear magnetic resonance (NMR) spectroscopic techniques has come of age and has widened its scope to characterize binding interactions of small molecules with biological macromolecules especially, proteins. NMR spectroscopy-based techniques are versatile due to their ability to examine weak binding interactions and for rapid screening the binding affinities of ligands with proteins at atomic resolution. In this review, we provide a broad overview of some of the important NMR approaches to investigate interactions of small organic molecules with proteins.
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Affiliation(s)
- Sanhita Maity
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, USA
| | - Ravi Kumar Gundampati
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, USA
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Abstract
Drug discovery is an extremely difficult and challenging endeavor with a very high failure rate. The task of identifying a drug that is safe, selective, and effective is a daunting proposition because disease biology is complex and highly variable across patients. Metabolomics enables the discovery of disease biomarkers, which provides insights into the molecular and metabolic basis of disease and may be used to assess treatment prognosis and outcome. In this regard, metabolomics has evolved to become an important component of the drug discovery process to resolve efficacy and toxicity issues and as a tool for precision medicine. A detailed description of an experimental protocol is presented that outlines the application of NMR metabolomics to the drug discovery pipeline. This includes (1) target identification by understanding the metabolic dysregulation in diseases, (2) predicting the mechanism of action of newly discovered or existing drug therapies, (3) and using metabolomics to screen a chemical lead to assess biological activity. Unlike other OMICS approaches, the metabolome is "fragile" and may be negatively impacted by improper sample collection, storage, and extraction procedures. Similarly, biologically irrelevant conclusions may result from incorrect data collection, preprocessing or processing procedures, or the erroneous use of univariate and multivariate statistical methods. These critical concerns are also addressed in the protocol.
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Bhinderwala F, Lei S, Woods J, Rose J, Marshall DD, Riekeberg E, Leite ADL, Morton M, Dodds ED, Franco R, Powers R. Metabolomics Analyses from Tissues in Parkinson's Disease. Methods Mol Biol 2019; 1996:217-257. [PMID: 31127560 DOI: 10.1007/978-1-4939-9488-5_19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Metabolomics has been successfully applied to study neurological and neurodegenerative disorders including Parkinson's disease for (1) the identification of potential biomarkers of onset and disease progression; (2) the identification of novel mechanisms of disease progression; and (3) the assessment of treatment prognosis and outcome. Reproducible and efficient extraction of metabolites is imperative to the success of any metabolomics investigation. Unlike other omics techniques, the composition of the metabolome can be negatively impacted by the preparation, processing, and handling of these samples. The proper choice of data collection, preprocessing, and processing protocols is similarly important to the design of an effective metabolomics experiment. Likewise, the correct application of univariate and multivariate statistical methods is essential for providing biologically relevant insights. In this chapter, we have outlined a detailed metabolomics workflow that addresses all of these issues. A step-by-step protocol from the preparation of neuronal cells and metabolomic tissue samples to their metabolic analyses using nuclear magnetic resonance, mass spectrometry, and chemometrics is presented.
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Affiliation(s)
- Fatema Bhinderwala
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Shulei Lei
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jade Woods
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jordan Rose
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA.,Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Darrell D Marshall
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Eli Riekeberg
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Aline De Lima Leite
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA.,Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Martha Morton
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA.,Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Eric D Dodds
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA.,Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Rodrigo Franco
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA. .,Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE, USA.
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA. .,Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE, USA. .,Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE, USA.
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Vu T, Riekeberg E, Qiu Y, Powers R. Comparing normalization methods and the impact of noise. Metabolomics 2018; 14:108. [PMID: 30830388 PMCID: PMC6638559 DOI: 10.1007/s11306-018-1400-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 07/23/2018] [Indexed: 10/28/2022]
Abstract
INTRODUCTION Failure to properly account for normal systematic variations in OMICS datasets may result in misleading biological conclusions. Accordingly, normalization is a necessary step in the proper preprocessing of OMICS datasets. In this regards, an optimal normalization method will effectively reduce unwanted biases and increase the accuracy of downstream quantitative analyses. But, it is currently unclear which normalization method is best since each algorithm addresses systematic noise in different ways. OBJECTIVE Determine an optimal choice of a normalization method for the preprocessing of metabolomics datasets. METHODS Nine MVAPACK normalization algorithms were compared with simulated and experimental NMR spectra modified with added Gaussian noise and random dilution factors. Methods were evaluated based on an ability to recover the intensities of the true spectral peaks and the reproducibility of true classifying features from orthogonal projections to latent structures-discriminant analysis model (OPLS-DA). RESULTS Most normalization methods (except histogram matching) performed equally well at modest levels of signal variance. Only probabilistic quotient (PQ) and constant sum (CS) maintained the highest level of peak recovery (> 67%) and correlation with true loadings (> 0.6) at maximal noise. CONCLUSION PQ and CS performed the best at recovering peak intensities and reproducing the true classifying features for an OPLS-DA model regardless of spectral noise level. Our findings suggest that performance is largely determined by the level of noise in the dataset, while the effect of dilution factors was negligible. A minimal allowable noise level of 20% was also identified for a valid NMR metabolomics dataset.
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Affiliation(s)
- Thao Vu
- Department of Statistics, University of Nebraska-Lincoln, Lincoln, NE, 68583-0963, USA
| | - Eli Riekeberg
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588-0304, USA
| | - Yumou Qiu
- Department of Statistics, University of Nebraska-Lincoln, Lincoln, NE, 68583-0963, USA
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588-0304, USA.
- Nebraska Center for Integrated Biomolecular Communication, Lincoln, NE, 68588-0304, USA.
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Gardner SG, Marshall DD, Daum RS, Powers R, Somerville GA. Metabolic Mitigation of Staphylococcus aureus Vancomycin Intermediate-Level Susceptibility. Antimicrob Agents Chemother 2018; 62:e01608-17. [PMID: 29109158 PMCID: PMC5740343 DOI: 10.1128/aac.01608-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 10/28/2017] [Indexed: 11/20/2022] Open
Abstract
Staphylococcus aureus is a major human pathogen whose infections are increasingly difficult to treat due to increased antibiotic resistance, including resistance to vancomycin. Vancomycin-intermediate S. aureus (VISA) strains develop resistance to vancomycin through adaptive changes that are incompletely understood. Central to this adaptation are metabolic changes that permit growth in the presence of vancomycin. To define the metabolic changes associated with adaptive resistance to vancomycin in S. aureus, the metabolomes of a vancomycin-sensitive and VISA strain pair isolated from the same patient shortly after vancomycin therapy began and following vancomycin treatment failure were analyzed. The metabolic adaptations included increases in acetogenesis, carbon flow through the pentose phosphate pathway, wall teichoic acid and peptidoglycan precursor biosynthesis, purine biosynthesis, and decreased tricarboxylic acid (TCA) cycle activity. The significance of these metabolic pathways for vancomycin-intermediate susceptibility was determined by assessing the synergistic potential of human-use-approved inhibitors of these pathways in combination with vancomycin against VISA strains. Importantly, inhibitors of amino sugar and purine biosynthesis acted synergistically with vancomycin to kill a diverse set of VISA strains, suggesting that combinatorial therapy could augment the efficacy of vancomycin even in patients infected with VISA strains.
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Affiliation(s)
- Stewart G Gardner
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Darrell D Marshall
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Robert S Daum
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Institute for Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Greg A Somerville
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
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Bernier M, Catazaro J, Singh NS, Wnorowski A, Boguszewska-Czubara A, Jozwiak K, Powers R, Wainer IW. GPR55 receptor antagonist decreases glycolytic activity in PANC-1 pancreatic cancer cell line and tumor xenografts. Int J Cancer 2017; 141:2131-2142. [PMID: 28741686 DOI: 10.1002/ijc.30904] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 06/28/2017] [Accepted: 07/14/2017] [Indexed: 01/09/2023]
Abstract
The Warburg effect is a predominant metabolic pathway in cancer cells characterized by enhanced glucose uptake and its conversion to l-lactate and is associated with upregulated expression of HIF-1α and activation of the EGFR-MEK-ERK, Wnt-β-catenin, and PI3K-AKT signaling pathways. (R,R')-4'-methoxy-1-naphthylfenoterol ((R,R')-MNF) significantly reduces proliferation, survival, and motility of PANC-1 pancreatic cancer cells through inhibition of the GPR55 receptor. We examined (R,R')-MNF's effect on glycolysis in PANC-1 cells and tumors. Global NMR metabolomics was used to elucidate differences in the metabolome between untreated and (R,R')-MNF-treated cells. LC/MS analysis was used to quantify intracellular concentrations of β-hydroxybutyrate, carnitine, and l-lactate. Changes in target protein expression were determined by Western blot analysis. Data was also obtained from mouse PANC-1 tumor xenografts after administration of (R,R')-MNF. Metabolomics data indicate that (R,R')-MNF altered fatty acid metabolism, energy metabolism, and amino acid metabolism and increased intracellular concentrations of β-hydroxybutyrate and carnitine while reducing l-lactate content. The cellular content of phosphoinositide-dependent kinase-1 and hexokinase 2 was reduced consistent with diminished PI3K-AKT signaling and glucose metabolism. The presence of the GLUT8 transporter was established and found to be attenuated by (R,R')-MNF. Mice treated with (R,R')-MNF had significant accumulation of l-lactate in tumor tissue relative to vehicle-treated mice, together with reduced levels of the selective l-lactate transporter MCT4. Lower intratumoral levels of EGFR, pyruvate kinase M2, β-catenin, hexokinase 2, and p-glycoprotein were also observed. The data suggest that (R,R')-MNF reduces glycolysis in PANC-1 cells and tumors through reduced expression and function at multiple controlling sites in the glycolytic pathway.
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Affiliation(s)
- Michel Bernier
- Translational Gerontology Branch, Intramural Research Program of the National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224
| | - Jonathan Catazaro
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588-0304
| | - Nagendra S Singh
- Laboratory of Clinical Investigation, Intramural Research Program of the National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224
| | - Artur Wnorowski
- Department of Biopharmacy, Medical University of Lublin, Lublin, 20-093, Poland
| | | | - Krzysztof Jozwiak
- Department of Biopharmacy, Medical University of Lublin, Lublin, 20-093, Poland
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588-0304
| | - Irving W Wainer
- Laboratory of Clinical Investigation, Intramural Research Program of the National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224.,Mitchell Woods Pharmaceuticals, Shelton, CT, 06484
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8
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Metabolic Investigations of the Molecular Mechanisms Associated with Parkinson's Disease. Metabolites 2017; 7:metabo7020022. [PMID: 28538683 PMCID: PMC5487993 DOI: 10.3390/metabo7020022] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 05/16/2017] [Accepted: 05/16/2017] [Indexed: 12/20/2022] Open
Abstract
Parkinson’s disease (PD) is a neurodegenerative disorder characterized by fibrillar cytoplasmic aggregates of α-synuclein (i.e., Lewy bodies) and the associated loss of dopaminergic cells in the substantia nigra. Mutations in genes such as α-synuclein (SNCA) account for only 10% of PD occurrences. Exposure to environmental toxicants including pesticides and metals (e.g., paraquat (PQ) and manganese (Mn)) is also recognized as an important PD risk factor. Thus, aging, genetic alterations, and environmental factors all contribute to the etiology of PD. In fact, both genetic and environmental factors are thought to interact in the promotion of idiopathic PD, but the mechanisms involved are still unclear. In this study, we summarize our findings to date regarding the toxic synergistic effect between α-synuclein and paraquat treatment. We identified an essential role for central carbon (glucose) metabolism in dopaminergic cell death induced by paraquat treatment that is enhanced by the overexpression of α-synuclein. PQ “hijacks” the pentose phosphate pathway (PPP) to increase NADPH reducing equivalents and stimulate paraquat redox cycling, oxidative stress, and cell death. PQ also stimulated an increase in glucose uptake, the translocation of glucose transporters to the plasma membrane, and AMP-activated protein kinase (AMPK) activation. The overexpression of α-synuclein further stimulated an increase in glucose uptake and AMPK activity, but impaired glucose metabolism, likely directing additional carbon to the PPP to supply paraquat redox cycling.
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Marshall DD, Halouska S, Zinniel DK, Fenton RJ, Kenealy K, Chahal HK, Rathnaiah G, Barletta RG, Powers R. Assessment of Metabolic Changes in Mycobacterium smegmatis Wild-Type and alr Mutant Strains: Evidence of a New Pathway of d-Alanine Biosynthesis. J Proteome Res 2017; 16:1270-1279. [PMID: 28121156 DOI: 10.1021/acs.jproteome.6b00871] [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: 01/10/2023]
Abstract
In mycobacteria, d-alanine is an essential precursor for peptidoglycan biosynthesis. The only confirmed enzymatic pathway to form d-alanine is through the racemization of l-alanine by alanine racemase (Alr, EC 5.1.1.1). Nevertheless, the essentiality of Alr in Mycobacterium tuberculosis and Mycobacterium smegmatis for cell survivability in the absence of d-alanine has been a point of controversy with contradictory results reported in the literature. To address this issue, we examined the effects of alr inactivation on the cellular metabolism of M. smegmatis. The M. smegmatis alr insertion mutant TAM23 exhibited essentially identical growth to wild-type mc2155 in the absence of d-alanine. NMR metabolomics revealed drastically distinct phenotypes between mc2155 and TAM23. A metabolic switch was observed for TAM23 as a function of supplemented d-alanine. In the absence of d-alanine, the metabolic response directed carbon through an unidentified transaminase to provide the essential d-alanine required for survival. The process is reversed when d-alanine is available, in which the d-alanine is directed to peptidoglycan biosynthesis. Our results provide further support for the hypothesis that Alr is not an essential function of M. smegmatis and that specific Alr inhibitors will have no bactericidal action.
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Affiliation(s)
- Darrell D Marshall
- Department of Chemistry, University of Nebraska-Lincoln , Lincoln, Nebraska 68588-0304, United States
| | - Steven Halouska
- Department of Chemistry, University of Nebraska-Lincoln , Lincoln, Nebraska 68588-0304, United States
| | - Denise K Zinniel
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln , Lincoln, Nebraska 68583-0905, United States
| | - Robert J Fenton
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln , Lincoln, Nebraska 68583-0905, United States
| | - Katie Kenealy
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln , Lincoln, Nebraska 68583-0905, United States
| | - Harpreet K Chahal
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln , Lincoln, Nebraska 68583-0905, United States
| | - Govardhan Rathnaiah
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln , Lincoln, Nebraska 68583-0905, United States
| | - Raúl G Barletta
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln , Lincoln, Nebraska 68583-0905, United States.,Center for Redox Biology, University of Nebraska-Lincoln , Lincoln, Nebraska 68588-0662, United States
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln , Lincoln, Nebraska 68588-0304, United States.,Center for Redox Biology, University of Nebraska-Lincoln , Lincoln, Nebraska 68588-0662, United States
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Marshall DD, Sadykov MR, Thomas VC, Bayles KW, Powers R. Redox Imbalance Underlies the Fitness Defect Associated with Inactivation of the Pta-AckA Pathway in Staphylococcus aureus. J Proteome Res 2016; 15:1205-12. [PMID: 26975873 DOI: 10.1021/acs.jproteome.5b01089] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The phosphotransacetylase-acetate kinase (Pta-AckA) pathway is thought to be a vital ATP generating pathway for Staphylococcus aureus. Disruption of the Pta-AckA pathway during overflow metabolism causes significant reduction in growth rate and viability, albeit not due to intracellular ATP depletion. Here, we demonstrate that toxicity associated with inactivation of the Pta-AckA pathway resulted from an altered intracellular redox environment. Growth of the pta and ackA mutants under anaerobic conditions partially restored cell viability. NMR metabolomics analyses and (13)C6-glucose metabolism tracing experiments revealed the activity of multiple pathways that promote redox (NADH/NAD(+)) turnover to be enhanced in the pta and ackA mutants during anaerobic growth. Restoration of redox homeostasis in the pta mutant by overexpressing l- lactate dehydrogenase partially restored its viability under aerobic conditions. Together, our findings suggest that during overflow metabolism, the Pta-AckA pathway plays a critical role in preventing cell viability defects by promoting intracellular redox homeostasis.
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Affiliation(s)
- Darrell D Marshall
- Department of Chemistry, University of Nebraska-Lincoln , Lincoln, Nebraska 68588, United States
| | - Marat R Sadykov
- Department of Pathology and Microbiology, University of Nebraska Medical Center , Omaha, Nebraska 68198, United States
| | - Vinai C Thomas
- Department of Pathology and Microbiology, University of Nebraska Medical Center , Omaha, Nebraska 68198, United States
| | - Kenneth W Bayles
- Department of Pathology and Microbiology, University of Nebraska Medical Center , Omaha, Nebraska 68198, United States
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln , Lincoln, Nebraska 68588, United States
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Worley B, Sisco NJ, Powers R. Statistical removal of background signals from high-throughput (1)H NMR line-broadening ligand-affinity screens. JOURNAL OF BIOMOLECULAR NMR 2015; 63:53-58. [PMID: 26156049 PMCID: PMC4577452 DOI: 10.1007/s10858-015-9962-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 06/30/2015] [Indexed: 06/04/2023]
Abstract
NMR ligand-affinity screens are vital to drug discovery, are routinely used to screen fragment-based libraries, and used to verify chemical leads from high-throughput assays and virtual screens. NMR ligand-affinity screens are also a highly informative first step towards identifying functional epitopes of unknown proteins, as well as elucidating the biochemical functions of protein-ligand interaction at their binding interfaces. While simple one-dimensional (1)H NMR experiments are capable of indicating binding through a change in ligand line shape, they are plagued by broad, ill-defined background signals from protein (1)H resonances. We present an uncomplicated method for subtraction of protein background in high-throughput ligand-based affinity screens, and show that its performance is maximized when phase-scatter correction is applied prior to subtraction.
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Affiliation(s)
- Bradley Worley
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588-0304, USA
| | - Nicholas J Sisco
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588-0304, USA
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ, 85287, USA
- Magnetic Resonance Research Center, Arizona State University, Tempe, AZ, 85287, USA
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588-0304, USA.
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Binczyk F, Tarnawski R, Polanska J. Strategies for optimizing the phase correction algorithms in Nuclear Magnetic Resonance spectroscopy. Biomed Eng Online 2015; 14 Suppl 2:S5. [PMID: 26329486 PMCID: PMC4648061 DOI: 10.1186/1475-925x-14-s2-s5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nuclear Magnetic Resonance (NMR) spectroscopy is a popular medical diagnostic
technique. NMR is also the favourite tool of chemists/biochemists to elucidate the
molecular structure of small or big molecules; it is also a widely used tool in
material science, in food science etc. In the case of medical diagnosis it allows for
determining a metabolic composition of analysed tissue which may support the
identification of tumour cells. Precession signal, that is a crucial part of MR
phenomenon, contains distortions that must be filtered out before signal analysis.
One of such distortions is phase error. Five popular algorithms: Automics, Shanon's entropy minimization, Ernst's method,
Dispa and eDispa are presented and discussed. A novel adaptive tuning algorithm for
Automics method was developed and numerically optimal solutions to automatic tuning
of the other four algorithms were proposed. To validate the performance of the
proposed techniques, two experiments were performed - the first one was done with the
use of in silico generated data. For all presented methods, the fine tuning
strategies significantly increased the correction accuracy. The highest improvement
was observed for Automics algorithm, independently of noise level, with relative
phase error dropping by average from 10.25% to 2.40% for low noise level and from
12.45% to 2.66% for high noise level. The second validation experiment, done with the
use of phantom data, confirmed the in silico results. The obtained accuracy
of the estimation of metabolite concentration was at 99.5%.
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Staphylococcus aureus metabolic adaptations during the transition from a daptomycin susceptibility phenotype to a daptomycin nonsusceptibility phenotype. Antimicrob Agents Chemother 2015; 59:4226-38. [PMID: 25963986 DOI: 10.1128/aac.00160-15] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 04/29/2015] [Indexed: 02/07/2023] Open
Abstract
Staphylococcus aureus is a major cause of nosocomial and community-acquired infections. The success of S. aureus as a pathogen is due in part to its many virulence determinants and resistance to antimicrobials. In particular, methicillin-resistant S. aureus has emerged as a major cause of infections and led to increased use of the antibiotics vancomycin and daptomycin, which has increased the isolation of vancomycin-intermediate S. aureus and daptomycin-nonsusceptible S. aureus strains. The most common mechanism by which S. aureus acquires intermediate resistance to antibiotics is by adapting its physiology and metabolism to permit growth in the presence of these antibiotics, a process known as adaptive resistance. To better understand the physiological and metabolic changes associated with adaptive resistance, six daptomycin-susceptible and -nonsusceptible isogenic strain pairs were examined for changes in growth, competitive fitness, and metabolic alterations. Interestingly, daptomycin nonsusceptibility coincides with a slightly delayed transition to the postexponential growth phase and alterations in metabolism. Specifically, daptomycin-nonsusceptible strains have decreased tricarboxylic acid cycle activity, which correlates with increased synthesis of pyrimidines and purines and increased carbon flow to pathways associated with wall teichoic acid and peptidoglycan biosynthesis. Importantly, these data provided an opportunity to alter the daptomycin nonsusceptibility phenotype by manipulating bacterial metabolism, a first step in developing compounds that target metabolic pathways that can be used in combination with daptomycin to reduce treatment failures.
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Marshall DD, Lei S, Worley B, Huang Y, Garcia-Garcia A, Franco R, Dodds ED, Powers R. Combining DI-ESI-MS and NMR datasets for metabolic profiling. Metabolomics 2015; 11:391-402. [PMID: 25774104 PMCID: PMC4354777 DOI: 10.1007/s11306-014-0704-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Metabolomics datasets are commonly acquired by either mass spectrometry (MS) or nuclear magnetic resonance spectroscopy (NMR), despite their fundamental complementarity. In fact, combining MS and NMR datasets greatly improves the coverage of the metabolome and enhances the accuracy of metabolite identification, providing a detailed and high-throughput analysis of metabolic changes due to disease, drug treatment, or a variety of other environmental stimuli. Ideally, a single metabolomics sample would be simultaneously used for both MS and NMR analyses, minimizing the potential for variability between the two datasets. This necessitates the optimization of sample preparation, data collection and data handling protocols to effectively integrate direct-infusion MS data with one-dimensional (1D) 1H NMR spectra. To achieve this goal, we report for the first time the optimization of (i) metabolomics sample preparation for dual analysis by NMR and MS, (ii) high throughput, positive-ion direct infusion electrospray ionization mass spectrometry (DI-ESI-MS) for the analysis of complex metabolite mixtures, and (iii) data handling protocols to simultaneously analyze DI-ESI-MS and 1D 1H NMR spectral data using multiblock bilinear factorizations, namely multiblock principal component analysis (MB-PCA) and multiblock partial least squares (MB-PLS). Finally, we demonstrate the combined use of backscaled loadings, accurate mass measurements and tandem MS experiments to identify metabolites significantly contributing to class separation in MB-PLS-DA scores. We show that integration of NMR and DI-ESI-MS datasets yields a substantial improvement in the analysis of neurotoxin involvement in dopaminergic cell death.
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Affiliation(s)
- Darrell D. Marshall
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE
68588-0304
| | - Shulei Lei
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE
68588-0304
| | - Bradley Worley
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE
68588-0304
| | - Yuting Huang
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE
68588-0304
| | - Aracely Garcia-Garcia
- Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE
68583-0905
- School of Veterinary Medicine and Biomedical Sciences, University of
Nebraska-Lincoln, Lincoln, NE 68583-0905
| | - Rodrigo Franco
- Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE
68583-0905
- School of Veterinary Medicine and Biomedical Sciences, University of
Nebraska-Lincoln, Lincoln, NE 68583-0905
| | - Eric D. Dodds
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE
68588-0304
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE
68588-0304
- Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE
68583-0905
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Larive CK, Barding GA, Dinges MM. NMR spectroscopy for metabolomics and metabolic profiling. Anal Chem 2014; 87:133-46. [PMID: 25375201 DOI: 10.1021/ac504075g] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Cynthia K Larive
- Department of Chemistry, University of California-Riverside , Riverside, California 92521, United States
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17
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Abstract
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Data
handling in the field of NMR metabolomics has historically
been reliant on either in-house mathematical routines or long chains
of expensive commercial software. Thus, while the relatively simple
biochemical protocols of metabolomics maintain a low barrier to entry,
new practitioners of metabolomics experiments are forced to either
purchase expensive software packages or craft their own data handling
solutions from scratch. This inevitably complicates the standardization
and communication of data handling protocols in the field. We report
a newly developed open-source platform for complete NMR metabolomics
data handling, MVAPACK, and describe its application on an example
metabolic fingerprinting data set.
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Affiliation(s)
- Bradley Worley
- Department
of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0304, United States
| | - Robert Powers
- Department
of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0304, United States
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