Metabolomics and its application to studying metal toxicity

Metallomics

Volumn 3, Issue 11, 2011, Pages 1142-1152

  Booth, Sean C ^a   Workentine, Matthew L ^a   Weljie, Aalim M ^a   Turner, Raymond J ^a  

^a UNIVERSITY OF CALGARY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CRITICAL EVALUATION; DISEASE STATE; ENVIRONMENTAL SYSTEMS; METABOLOMICS; METAL TOXICITY; METALLOMICS; PHYSIOLOGICAL RESPONSE; TOXIC METALS;

PHYSIOLOGICAL MODELS; PHYSIOLOGY; TOXICITY;

METALS;

CADMIUM; CARBON 13; COPPER; MERCURY; TOXIN;

ARABIDOPSIS; BIOFILM; BIOINFORMATICS; CAENORHABDITIS ELEGANS; CELL METABOLISM; CHROMATOGRAPHY; ENVIRONMENTAL ASPECTS AND RELATED PHENOMENA; ENVIRONMENTAL MONITORING; HUMAN; INFORMATION PROCESSING; MASS SPECTROMETRY; METABOLITE; METABOLOMICS; MICROORGANISM; NONHUMAN; PLANKTON; PRIORITY JOURNAL; PROTON NUCLEAR MAGNETIC RESONANCE; REVIEW; RICE; STATISTICAL ANALYSIS; SYSTEMS BIOLOGY; TOMATO;

ANIMALS; BACTERIA; COMPUTATIONAL BIOLOGY; ENVIRONMENTAL POLLUTANTS; HUMANS; METABOLOMICS; METALS; METALS, HEAVY; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PLANTS; POISONING;

EID: 80455137211     PISSN: 17565901     EISSN: 1756591X     Source Type: Journal    
DOI: 10.1039/c1mt00070e     Document Type: Review

References (84)

1. D. A. Fell Beyond genomics. Trends in Genetics 2001 17 680 682
2. O. Fiehn Metabolomics-The link between genotypes and phenotypes Plant Mol. Biol. 2002 48 155 171
3. M. R. Mashego K. Rumbold M. Mey E. Vandamme W. Soetaert J. J. Heijnen Microbial metabolomics: past, present and future methodologies Biotechnol. Lett. 2006 29 1 16
4. D. Ryan K. Robards Metabolomics: The greatest omics of them all? Anal. Chem. 2006 78 7954 7958 (Pubitemid 44871759)
5. I. M. Keseler C. Bonavides-Martínez J. Collado-Vides S. Gama-Castro R. P. Gunsalus D. A. Johnson M. Krummenacker L. M. Nolan S. Paley I. T. Paulsen M. Peralta-Gil A. Santos-Zavaleta A. G. Shearer P. D. Karp EcoCyc: A comprehensive view of Escherichia coli biology Nucleic Acids Res. 2009 37 D464 D470
6. I. Nobeli H. Ponstingl E. B. Krissinel J. M. Thornton A structure-based anatomy of the E. coli metabolome J. Mol. Biol. 2003 334 697 719 (Pubitemid 37433886)
7. M. Robert T. Soga M. Tomita E. Coli metabolomics: capturing the complexity of a "simple" model Topics in Current Genetics 2007 18 189 234
8. M. J. v. d. Werf K. M. Overkamp B. Muilwijk L. Coulier T. Hankemeier Microbial metabolomics: Toward a platform with full metabolome coverage Anal. Biochem. 2007 370 17 25 (Pubitemid 47404495)
9. X. H. Wu H. L. Yu Z. Y. Ba J. Y. Chen H. G. Sun B. Z. Han Sampling methods for NMR-based metabolomics of Staphylococcus aureus Biotechnol. J. 2010 5 75 84
10. M. J. Van Der Werff K. M. Overkamp B. Muilwijk M. M. Koek B. J. C. Van Der Werff-Van Der Vat R. H. Jellema L. Coulier T. Hankemeier Comprehensive analysis of the metabolome of Pseudomonas putida S12 grown on different carbon sources Mol. BioSyst. 2008 4 315 327 (Pubitemid 351422587)
11. C. L. Winder W. B. Dunn S. Schuler D. Broadhurst R. Jarvis G. M. Stephens R. Goodacre Global metabolic profiling of Escherichia coli cultures: An evaluation of methods for quenching and extraction of intracellular metabolites Anal. Chem. 2008 80 2939 2948 (Pubitemid 351556459)
12. W. M. van Gulik Fast sampling for quantitative microbial metabolomics Curr. Opin. Biotechnol. 2010 21 27 34
13. R. Prasad Maharjan T. Ferenci Global metabolite analysis: The influence of extraction methodology on metabolome profiles of Escherichia coli Anal. Biochem. 2003 313 145 154 (Pubitemid 36268829)
14. W. B. Dunn N. J. C. Bailey H. E. Johnson Measuring the metabolome: Current analytical technologies Analyst 2005 130 606 625 (Pubitemid 40685888)
15. M. M. Koek B. Muilwijk M. J. Van Der Werf T. Hankemeier Microbial metabolomics with gas chromatography/mass spectrometry Anal. Chem. 2006 78 1272 1281 (Pubitemid 43271861)
16. A. M. Weljie J. Newton P. Mercier E. Carlson C. M. Slupsky Targeted Profiling: Quantitative Analysis of 1H NMR Metabolomics Data Anal. Chem. 2006 78 4430 4442
17. W. De Koning K. Van Dam A method for the determination of changes of glycolytic metabolites in yeast on a subsecond time scale using extraction at neutral pH Anal. Biochem. 1992 204 118 123
18. L. M. Raamsdonk B. Teusink D. Broadhurst N. Zhang A. Hayes M. C. Walsh J. A. Berden K. M. Brindle D. B. Kell J. J. Rowland H. V. Westerhoff K. Van Dam S. G. Oliver A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations Nat. Biotechnol. 2001 19 45 50 (Pubitemid 32051955)
19. W. Weckwerth M. E. Loureiro K. Wenzel O. Fiehn Differential metabolic networks unravel the effects of silent plant phenotypes Proc. Natl. Acad. Sci. U. S. A. 2004 101 7809 7814 (Pubitemid 38658110)
20. P. J. Turnbaugh J. I. Gordon An Invitation to the marriage of metagenomics and metabolomics Cell 2008 134 708 713
21. S. Vaidyanathan Profiling microbial metabolomes: what do we stand to gain? Metabolomics 2005 1 17 28
22. J. Lemire P. Kumar R. Mailloux K. Cossar V. D. Appanna Metabolic adaptation and oxaloacetate homeostasis in P. fluorescens exposed to aluminum toxicity J. Basic Microbiol. 2008 48 252 259
23. J. J. Harrison H. Ceri J. Yerly M. Rabiei Y. Hu R. Martinuzzi R. J. Turner Metal ions may suppress or enhance cellular differentiation in Candida albicans and Candida tropicalis biofilms Appl. Environ. Microbiol. 2007 73 4940 4949 (Pubitemid 47237243)
24. S. C. Booth M. L. Workentine J. Wen R. Shaykhutdinov H. J. Vogel H. Ceri R. J. Turner A. M. Weljie Differences in Metabolism between the Biofilm and Planktonic Response to Metal Stress J. Proteome Res. 2011 3190 10.1021/pr2002353
25. A. P. White A. M. Weljie D. Apel P. Zhang R. Shaykhutdinov H. J. Vogel M. G. Surette A global metabolic shift is linked to Salmonella multicellular development PLoS ONE 2010 5
26. J. J. Harrison H. Ceri R. J. Turner Multimetal resistance and tolerance microbial biofilms Nat. Rev. Microbiol. 2007 5 928 938 (Pubitemid 350131181)
27. M. L. Workentine J. J. Harrison P. U. Stenroos H. Ceri R. J. Turner Pseudomonas fluorescens' view of the periodic table Environ. Microbiol. 2008 10 238 50
28. B. Álvarez-Sánchez F. Priego-Capote M. D. L. d. Castro Metabolomics analysis II. Preparation of biological samples prior to detection TrAC, Trends Anal. Chem. 2010 29 120 127
29. B. Álvarez-Sánchez F. Priego-Capote M. D. Luque de Castro Metabolomics analysis I. Selection of biological samples and practical aspects preceding sample preparation TrAC, Trends Anal. Chem. 2010 29 111 119
30. M. R. Viant Recent developments in environmental metabolomics Mol. BioSyst. 2008 4 980 986
31. J. G. Bundy H. C. Keun J. K. Sidhu D. J. Spurgeon C. Svendsen P. Kille A. J. Morgan Metabolic profile biomarkers of metal contamination in a sentinel terrestrial species are applicable across multiple sites Environ. Sci. Technol. 2007 41 4458 4464 (Pubitemid 46981743)
32. M. L. Reaves J. D. Rabinowitz Metabolomics in systems microbiology Curr. Opin. Biotechnol. 2011 22 17 25
33. M. R. Mashego L. Wu J. C. Van Dam C. Ras J. L. Vinke W. A. Van Winden W. M. Van Gulik J. J. Heijnen MIRACLE: Mass Isotopomer Ratio Analysis of U-13C-Labeled Extracts. A New Method for Accurate Quantification of Changes in Concentrations of Intracellular Metabolites Biotechnol. Bioeng. 2004 85 620 628 (Pubitemid 38270494)
34. B. D. Bennett J. Yuan E. H. Kimball J. D. Rabinowitz Absolute quantitation of intracellular metabolite concentrations by an isotope ratio-based approach Nat. Protoc. 2008 3 1299 1311
35. S. G. Villas-Bôas P. Bruheim Cold glycerol-saline: The promising quenching solution for accurate intracellular metabolite analysis of microbial cells Anal. Biochem. 2007 370 87 97 (Pubitemid 47404490)
36. J. L. Spratlin N. J. Serkova S. G. Eckhardt Clinical applications of metabolomics in oncology: A review Clin. Cancer Res. 2009 15 431 440
37. D. S. Wishart Quantitative metabolomics using NMR TrAC, Trends Anal. Chem. 2008 27 228 237
38. S. C. Brown G. Kruppa J. L. Dasseux Metabolomics applications of FT-ICR mass spectrometry Mass Spectrom. Rev. 2005 24 223 231 (Pubitemid 40328975)
39. J. Hummel, J. Selbig, D. Walther, J. Kopka. 2007, vol. 18, pp 75-95
40. J. Hummel N. Strehmel J. Selbig D. Walther J. Kopka Decision tree supported substructure prediction of metabolites from GC-MS profiles Metabolomics 2010 6 322 333
41. Á. Cuadros-Inostroza C. Caldana H. Redestig M. Kusano J. Lisec H. Peña-Cortés L. Willmitzer M. A. Hannah TargetSearch-a Bioconductor package for the efficient preprocessing of GC-MS metabolite profiling data BMC Bioinformatics 2009 10
42. C. D. Broeckling I. R. Reddy A. L. Duran X. Zhao L. W. Sumner MET-IDEA: Data extraction tool for mass spectrometry-based metabolomics Anal. Chem. 2006 78 4334 4341
43. K. Hiller J. Hangebrauk C. Jäger J. Spura K. Schreiber D. Schomburg Metabolite detector: Comprehensive analysis tool for targeted and nontargeted GC/MS based metabolome analysis Anal. Chem. 2009 81 3429 3439
44. A. V. Antonov S. Dietmann P. Wong H. W. Mewes TICL-a web tool for network-based interpretation of compound lists inferred by high-throughput metabolomics FEBS J. 2009 276 2084 2094
45. M. Kanehisa S. Goto KEGG: Kyoto Encyclopedia of Genes and Genomes Nucleic Acids Res. 2000 28 27 30 (Pubitemid 30047706)
46. L. Cottret D. Wildridge F. Vinson M. P. Barrett H. Charles M. F. Sagot F. Jourdan MetExplore: A web server to link metabolomic experiments and genome-scale metabolic networks Nucleic Acids Res. 2010 38 W132 W137
47. M. E. Smoot K. Ono J. Ruscheinski P. L. Wang T. Ideker Cytoscape 2.8: New features for data integration and network visualization Bioinformatics 2011 27 431 432
48. J. G. Bundy M. P. Davey M. R. Viant Environmental metabolomics: A critical review and future perspectives Metabolomics 2009 5 3 21
49. C. Y. Lin M. R. Viant R. S. Tjeerdema Metabolomics: Methodologies and applications in the environmental sciences J. Pestic. Sci. 2006 31 245 251 (Pubitemid 44285772)
50. J. E. Sarry L. Kuhn C. Ducruix A. Lafaye C. Junot V. Hugouvieux A. Jourdain O. Bastien J. B. Fievet D. Vailhen B. Amekraz C. Moulin E. Ezan J. Garin J. Bourguignon The early responses of Arabidopsis thaliana cells to cadmium exposure explored by protein and metabolite profiling analyses Proteomics 2006 6 2180 2198
51. H. Hédiji W. Djebali C. Cabasson M. Maucourt P. Baldet A. Bertrand L. Boulila Zoghlami C. Deborde A. Moing R. Brouquisse W. Chaïbi P. Gallusci Effects of long-term cadmium exposure on growth and metabolomic profile of tomato plants Ecotoxicol. Environ. Saf. 2010 73 1965 1974
52. X. Sun J. Zhang H. Zhang Y. Ni Q. Zhang J. Chen Y. Guan The responses of Arabidopsis thaliana to cadmium exposure explored via metabolite profiling Chemosphere 2010 78 840 845
53. X. Liu C. Yang L. Zhang L. Li S. Liu J. Yu L. You D. Zhou C. Xia J. Zhao H. Wu Metabolic profiling of cadmium-induced effects in one pioneer intertidal halophyte Suaeda salsa by NMR-based metabolomics Ecotoxicology 2011 1 10
54. L. B. Zoghlami W. Djebali Z. Abbes H. Hediji M. Maucourt A. Moing R. Brouquisse W. Chaïbi Metabolite modifications in Solanum lycopersicum roots and leaves under cadmium stress African Journal of Biotechnology 2011 10 567 579
55. V. Tremaroli M. L. Workentine A. M. Weljie H. J. Vogel H. Ceri C. Viti E. Tatti P. Zhang A. P. Hynes R. J. Turner D. Zannoni Metabolomic investigation of the bacterial response to a metal challenge Appl. Environ. Microbiol. 2009 75 719 728
56. M. L. Workentine J. J. Harrison A. M. Weljie V. A. Tran P. U. Stenroos V. Tremaroli H. J. Vogel H. Ceri R. J. Turner Phenotypic and metabolic profiling of colony morphology variants evolved from Pseudomonas fluorescens biofilms Environ. Microbiol. 2010 12 1565 1577
57. X. Liu L. Zhang L. You M. Cong J. Zhao H. Wu C. Li D. Liu J. Yu Toxicological responses to acute mercury exposure for three species of Manila clam Ruditapes philippinarum by NMR-based metabolomics Environ. Toxicol. Pharmacol. 2011 31 323 332
58. X. Liu L. Zhang L. You J. Yu J. Zhao L. Li Q. Wang F. Li C. Li D. Liu H. Wu Differential toxicological effects induced by mercury in gills from three pedigrees of Manila clam Ruditapes philippinarum by NMR-based metabolomics Ecotoxicology 2011 20 177 186
59. H. Wu W. X. Wang Tissue-specific toxicological effects of cadmium in green mussels (Perna viridis): Nuclear magnetic resonance-based metabolomics study Environ. Toxicol. Chem. 2011 30 806 812
60. L. Zhang X. Liu L. You D. Zhou H. Wu L. Li J. Zhao J. Feng J. Yu Metabolic responses in gills of Manila clam Ruditapes philippinarum exposed to copper using NMR-based metabolomics Marine Environmental Research
61. J. G. Bundy D. J. Spurgeon C. Svendsen P. K. Hankard J. M. Weeks D. Osborn J. C. Lindon J. K. Nicholson Environmental metabonomics: Applying combination biomarker analysis in earthworms at a metal contaminated site Ecotoxicology 2004 13 797 806 (Pubitemid 40380955)
62. J. G. Bundy J. K. Sidhu F. Rana D. J. Spurgeon C. Svendsen J. F. Wren S. R. Stürzenbaum A. J. Morgan P. Kille 'Systems toxicology' approach identifies coordinated metabolic responses to copper in a terrestrial non-model invertebrate, the earthworm Lumbricus rubellus BMC Biology 2008 6
63. Q. Guo J. K. Sidhu T. M. D. Ebbels F. Rana D. J. Spurgeon C. Svendsen S. R. Stürzenbaum P. Kille A. J. Morgan J. G. Bundy Validation of metabolomics for toxic mechanism of action screening with the earthworm Lumbricus rubellus Metabolomics 2009 5 72 83
64. J. L. Griffin L. A. Walker R. F. Shore J. K. Nicholson Metabolic profiling of chronic cadmium exposure the rat. Chem. Res. Toxicol. 2001 14 1428 1434 (Pubitemid 32988408)
65. Y. Sugiura M. Kashiba K. Maruyama K. Hoshikawa R. Sasaki K. Saito H. Kimura N. Goda M. Suematsu Cadmium exposure alters metabolomics of sulfur-containing amino acids in rat testes. Antioxid. Redox Signaling 2005 7 781 787 (Pubitemid 40563219)
66. H. Wu X. Zhang X. Li Z. Li P. Liao W. Li Y. Wu F. Pei Investigation on acute biochemical effects of Ce(NO3)3 on (43) liver and kidney tissues by MAS 1H NMR spectroscopic-based metabonomic approach. J. Rare Earths 2006 24 357 363 (Pubitemid 44312607)
67. R. Lei C. Wu B. Yang H. Ma C. Shi Q. Wang Y. Yuan M. Liao Integrated metabolomic analysis of the nano-sized copper particle-induced hepatotoxicity and nephrotoxicity in rats: A rapid vivo screening method for nanotoxicity. Toxicol. Appl. Pharmacol. 2008 232 292 301
68. P. Liao L. Wei H. Wu W. Li Y. Wu X. Li J. Ni F. Pei Biochemical effects of gadolinium chloride in rats liver and kidney studied by 1H NMR metabolomics J. Rare Earths 2009 27 280 287
69. J. L. Griffin L. Walker R. F. Shore J. K. Nicholson High-resolution magic angle spinning 1H-NMR spectroscopy studies on the renal biochemistry in the bank vole (Clethrionomys glareolus) and the effects of arsenic (As3+) toxicity Xenobiotica 2001 31 377 385 (Pubitemid 32679314)
70. Q. Bu G. Yan P. Deng F. Peng H. Lin Y. Xu Z. Cao T. Zhou A. Xue Y. Wang X. Cen Y. L. Zhao NMR-based metabonomic study of the sub-acute toxicity of titanium dioxide nanoparticles in rats after oral administration Nanotechnology 2010 21 12 125105
71. E. M. Santos J. S. Ball T. D. Williams H. Wu F. Ortega R. Van Aerle I. Katsiadaki F. Falciani M. R. Viant J. K. Chipman C. R. Tyler Identifying health impacts of exposure to copper using transcriptomics and metabolomics in a fish model Environ. Sci. Technol. 2010 44 820 826
72. S. L. Hughes J. G. Bundy E. J. Want P. Kille S. R. Stürzenbaum The metabolomic responses of Caenorhabditis elegans to cadmium are largely independent of metallothionein status, but dominated by changes in cystathionine and phytochelatins J. Proteome Res. 2009 8 3512 3519
73. H. C. Poynton N. S. Taylor J. Hicks K. Colson S. Chan C. Clark L. Scanlan A. V. Loguinov C. Vulpe M. R. Viant Metabolomics of microliter hemolymph samples enables an improved understanding of the combined metabolic and transcriptional responses of Daphnia magna to cadmium Environ. Sci. Technol. 2011 45 3710 3717
74. N. S. Taylor R. J. M. Weber A. D. Southam T. G. Payne O. Hrydziuszko T. N. Arvanitis M. R. Viant A new approach to toxicity testing in Daphnia magna: Application of high throughput FT-ICR mass spectrometry metabolomics Metabolomics 2009 5 44 58
75. S. Dubey P. Misra S. Dwivedi S. Chatterjee S. K. Bag S. Mantri M. H. Asif A. Rai S. Kumar M. Shri P. Tripathi R. D. Tripathi P. K. Trivedi D. Chakrabarty R. Tuli Transcriptomic and metabolomic shifts in rice roots in response to Cr (VI) stress BMC Genomics 2010 11 1 648
76. G. Otting Protein NMR using paramagnetic ions Annual Review of Biophysics 2010 39 1 387 405
77. M. J. Simpson J. R. McKelvie Environmental metabolomics: New insights into earthworm ecotoxicity and contaminant bioavailability in soil Anal. Bioanal. Chem. 2009 394 137 149
78. N. J. C. Bailey M. Oven E. Holmes J. K. Nicholson M. H. Zenk Metabolomic analysis of the consequences of cadmium exposure in Silene cucubalus cell cultures via 1H NMR spectroscopy and chemometrics Phytochemistry 2003 62 851 858 (Pubitemid 36262388)
79. L. Sanità Di Toppi R. Gabbrielli Response to cadmium in higher plants Environ. Exp. Bot. 1999 41 105 130 (Pubitemid 29194798)
80. C. L. Winder W. B. Dunn R. Goodacre TARDIS-based microbial metabolomics: time and relative differences in systems Trends in Microbiology 2011 1 8
81. J. G. Bundy T. L. Willey R. S. Castell D. J. Ellar K. M. Brindle Discrimination of pathogenic clinical isolates and laboratory strains of Bacillus cereus by NMR-based metabolomic profiling FEMS Microbiol. Lett. 2005 242 127 136 (Pubitemid 40038429)
82. C. M. Slupsky A. Cheypesh D. V. Chao H. Fu K. N. Rankin T. J. Marrie P. Lacy Streptococcus pneumoniae and Staphylococcus aureus pneumonia induce distinct metabolic responses J. Proteome Res. 2009 8 3029 3036
83. C. M. Slupsky K. N. Rankin H. Fu D. Chang B. H. Rowe P. G. P. Charles A. McGeer D. Low R. Long D. Kunimoto M. B. Sawyer R. N. Fedorak D. J. Adamko E. J. Saude S. L. Shah T. J. Marrie Pneumococcal pneumonia: Potential for diagnosis through a urinary metabolic profile J. Proteome Res. 2009 8 5550 5558
84. W. Zhang F. Li L. Nie Integrating multiple 'omics' analysis for microbial biology: Application and methodologies Microbiology 2010 156 287 301