Advertisement

Metallomics: The Science of Biometals and Biometalloids

  • Wolfgang Maret
Chapter
Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 1055)

Abstract

Metallomics, a discipline integrating sciences that address the biometals and biometalloids, provides new opportunities for discoveries. As part of a systems biology approach, it draws attention to the importance of many chemical elements in biochemistry. Traditionally, biochemistry has treated life as organic chemistry, separating it from inorganic chemistry, considered a field reserved for investigating the inanimate world. However, inorganic chemistry is part of the chemistry of life, and metallomics contributes by showing the importance of a neglected fifth branch of building blocks in biochemistry. Metallomics adds chemical elements/metals to the four building blocks of biomolecules and the fields of their studies: carbohydrates (glycome), lipids (lipidome), proteins (proteome), and nucleotides (genome). The realization that non-essential elements are present in organisms in addition to essential elements represents a certain paradigm shift in our thinking, as it stipulates inquiries into the functional implications of virtually all the natural elements. This article discusses opportunities arising from metallomics for a better understanding of human biology and health. It looks at a biological periodic system of the elements as a sum of metallomes and focuses on the major roles of metals in about 30–40% of all proteins, the metalloproteomes. It emphasizes the importance of zinc and iron biology and discusses why it is important to investigate non-essential metal ions, what bioinformatics approaches can contribute to understanding metalloproteins, and why metallomics has a bright future in the many dimensions it covers.

Keywords

Biometals Biometalloids Bioinformatics 

Abbreviations

AAS

Atomic absorption spectroscopy

BMP

Basic metabolic panel

CMP

Comprehensive metabolic panel

ICP-MS

Inductively coupled plasma mass spectrometry

MRI

Magnetic resonance imaging

SMA

Sequential multiple analysis

References

  1. Andreini C, Bertini I, Rosato A (2006) Metalloproteomes: a bioinformatic approach. Acc Chem Res 42:1471–1479CrossRefGoogle Scholar
  2. Andreini C, Banci L, Rosato A (2016) Exploiting bacterial operons to illuminate human iron-sulfur proteins. J Proteome Res 15:1308–1322CrossRefPubMedGoogle Scholar
  3. Andreini C, Bertini I, Cavallaro G et al (2011) A simple protocol for the comparative analysis of the structure and occurrence of biochemical pathways across superkingdoms. J Chem Inf Model 51:730–738CrossRefPubMedGoogle Scholar
  4. Baker M (2013) The ‘omes puzzle. Nature 494:416–419CrossRefPubMedGoogle Scholar
  5. Blockhuys S, Celauro E, Hildesjö C et al (2017) Defining the human copper proteome and analysis of its expression variation in cancers. Metallomics 9:112–123CrossRefPubMedGoogle Scholar
  6. Bourassa D, Gleber S-C, Vogt S et al (2014) 3D imaging of transition metals in the zebrafish embryo by X-ray fluorescence microtomography. Metallomics 6:1648–1655CrossRefPubMedPubMedCentralGoogle Scholar
  7. Colvin RA, Holmes WR, Fontaine CP et al (2010) Cytosolic zinc buffering and muffling: their role in intracellular zinc homeostasis. Metallomics 2:306–317CrossRefGoogle Scholar
  8. Costello RB, Elin RJ, Rosanoff A et al (2016) Perspective: the case for an evidence-based reference interval for serum magnesium: the time has come. Adv Nutr 7:977–993CrossRefPubMedPubMedCentralGoogle Scholar
  9. Lide DR (ed) (1998) CRC Handbook of Chemistry and Physics, 79th edn. CRC Press, Boca RatonGoogle Scholar
  10. Cvetkovic A, Menon AL, Thorgersen MP et al (2010) Microbial metalloproteomes are largely uncharacterized. Nature 466:779–784CrossRefPubMedGoogle Scholar
  11. De Samber B, Evens R, De Schamphelaere G et al (2008) A combination of synchrotron and laboratory X-ray techniques for studying tissue-specific trace level metal distributions in Daphnia magna. JAAS 23:829–839Google Scholar
  12. Drinker KR, Collier ES (1926) The significance of zinc in the living organism. J Industr Hygiene 8:257–269Google Scholar
  13. Emsley J (1998) The elements, 3rd edn. Clarendon Press, OxfordGoogle Scholar
  14. Foster AW, Osman D, Robinson NJ (2014) Metal preferences and metallation. J Biol Chem 289:28095–28103CrossRefPubMedPubMedCentralGoogle Scholar
  15. Freeland-Graves JH, Mousa TY, Kim S (2016) International variability in diet and requirements of manganese: causes and consequences. J Trace Elem Med Biol 38:24–32CrossRefPubMedGoogle Scholar
  16. Gladyshev VN, Zhang Y (2013) Comparative genomics analysis of the metallomes. In: Metallomics and the cell, Banci L, (Guest ed.) vol 12 of Metal Ions in Life Sciences, A. Sigel, H. Sigel, R. K. O. Sigel (eds). Springer Science + Business Media B.V., Dordrecht, pp 529–580Google Scholar
  17. Haraguchi H (2004) Metallomics as integrated biometal science. JAAS 19:5–14Google Scholar
  18. Haraguchi H, Ishii A, Hasegawa T et al (2008) Metallomics study on all-elements analysis of salmon egg cells and fractionation analysis of metal in cell cytoplasm. Pure Appl Chem 80:2595–2608CrossRefGoogle Scholar
  19. Haraguchi H (2017) Metallomics: the history in the last decade and the future outlook. Metallomics 9:1001–1013CrossRefPubMedGoogle Scholar
  20. Hogstrand C, Maret W (2016) Genetics of human zinc deficiencies. In: eLS. John Wiley & Sons, Ltd, Chichester.  https://doi.org/10.1002/9780470015901.a0026346 CrossRefGoogle Scholar
  21. Iyengar GV, Kollmer WE, Bowen HJM (1978) The elemental composition of human tissues and body fluids. Weinheim, Verlag ChemieGoogle Scholar
  22. Keilin D, Mann T (1939) Carbonic Anydrase. Nature 144:442–443CrossRefGoogle Scholar
  23. Kretsinger RH, Barry CD (1975) The predicted structure of the calcium-binding component of troponin. Biochim Biophys Acta 405:40–52CrossRefPubMedGoogle Scholar
  24. Krężel A, Maret W (2017) The functions of metamorphic metallothioneins in zinc and copper metabolism. Int J Mol Sci 18:1237CrossRefPubMedCentralGoogle Scholar
  25. Lahner B, Gong J, Mahmoudian M et al (2003) Genomic scale profiling of nutrient and trace elements in Arabidopsis thaliana. Nat Biotechnol 21:1215–1221CrossRefPubMedGoogle Scholar
  26. Lane TW, Morel FMM (2000) A biological function for cadmium in marine diatoms. Proc Natl Acad Sci U S A 97:4627–4631CrossRefPubMedPubMedCentralGoogle Scholar
  27. Leyssens L, Vinck B, Van Der Straeten C et al (2017) Cobalt toxicity in humans-a review of the potential sources and systemic health effects. Toxicology 387:43–56CrossRefPubMedGoogle Scholar
  28. Li Y-F, Chen C, Qu Y et al (2008) Metallomics, elementomics, and analytical techniques. Pure Appl Chem 80:2577–2594CrossRefGoogle Scholar
  29. Ljungdahl LG, Andreesen JR (1975) Tungsten, a component of active formate dehydrogenase from Clostridium thermoaceticum. FEBS Lett 54:279–282CrossRefPubMedGoogle Scholar
  30. Lobinski R, Becker JS, Haraguchi H et al (2010) Metallomics: guidelines for terminology and critical evaluation of analytical chemistry approaches (IUPAC technical report). Pure Appl Chem 82:493–504CrossRefGoogle Scholar
  31. Lu J, Holmgren A (2009) Selenoproteins. J Biol Chem 284:723–727CrossRefPubMedGoogle Scholar
  32. Maret W (2004) Exploring the zinc proteome. JAAS 19:15–19CrossRefGoogle Scholar
  33. Maret W (2008) Zinc proteomics and the annotation of the human zinc proteome. Pure Appl Chem 80:2679–2687CrossRefGoogle Scholar
  34. Maret W, Li Y (2009) Coordination dynamics of zinc in proteins. Chem Rev 109:4682–4707CrossRefPubMedGoogle Scholar
  35. Maret W (2010) Metalloproteomics, metalloproteomes, and the annotation of metalloproteins. Metallomics 2:117–125CrossRefGoogle Scholar
  36. Maret W (2013) Zinc and the Zinc Proteome. In Metallomics and the cell, Banci L, (Guest ed.) vol. 12 of Metal ions in life sciences, A. Sigel, H. Sigel, R. K. O. Sigel (eds). Springer Science + Business Media B.V., Dordrecht, pp 479–501Google Scholar
  37. Maret W, Moulis J-M (2013) The bioinorganic chemistry of cadmium in the context of its toxicity. In Cadmium: from toxicity to essentiality, vol. 11 of Metal ions in life sciences, A. Sigel, H. Sigel, R. K. O. Sigel (eds). Springer Science + Business Media B.V., Dordrecht, pp 1–29Google Scholar
  38. Maret W (2014) Molecular aspects of zinc signals. In: Fukada T, Kambe T (eds) Zinc signals in cellular functions and disorders. Springer, Tokyo, pp 7–26Google Scholar
  39. Maret W, Wedd AG (eds) (2014) Binding, Transport and Storage of Metal Ions in Biological Cells. Royal Society of Chemistry, CambridgeGoogle Scholar
  40. Maret W, Caruso JA, Contag CH et al (2015) In: Nriagu JO, Skaar EP (eds) Trace Metals and Infectious Diseases. MIT Press, Cambridge, pp 341–401Google Scholar
  41. Maret W (2016a) Metallomics, a primer to integrated biometal sciences. Imperial College Press, LondonCrossRefGoogle Scholar
  42. Maret W (2016b) The metals in the biological periodic system of the elements: concepts and conjectures. Int J Mol Sci 17:66CrossRefPubMedCentralGoogle Scholar
  43. Maret W (2017) The bioinorganic chemistry of lead in the context of its toxicity. In Lead – its effects on environment and health, vol 17 of Metal Ions in Life Sciences, A. Sigel, H. Sigel, R. K. O. Sigel (eds), W. de Gruyter, Berlin, pp 1–20Google Scholar
  44. McCall AS, Cummings CF, Bhave G et al (2014) Bromine is an essential trace element for assembly of collagen IV scaffolds in tissue development and architecture. Cell 157:1380–1392CrossRefPubMedPubMedCentralGoogle Scholar
  45. Menghini V (1747) De Ferreorum particulerum sede in sanguis. Commentar. Bononiens (Bologna)ii, p 475Google Scholar
  46. Mertz W (1993) Chromium in human nutrition. J Nutr 123:626–633CrossRefPubMedGoogle Scholar
  47. Miller J, McLachlan AD, Klug A (1985) Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes. EMBO J 4:1609–1624PubMedPubMedCentralCrossRefGoogle Scholar
  48. Nielsen FH (2014a) Should bioactive trace elements not recognized as essential, but with beneficial health effects, have intake recommendations. J Trace Elem Med Biol 28:406–408CrossRefPubMedGoogle Scholar
  49. Nielsen FH (2014b) Update on the possible nutritional importance of silicon. J Trace Elem Med Biol 28:379–382CrossRefPubMedGoogle Scholar
  50. Nielsen FH (2014c) Update on human health effects of boron. J Trace Elem Med Biol 28:383–387CrossRefPubMedGoogle Scholar
  51. Pol A, Barends TRM, Dietl A et al (2014) Rare earth metals are essential for methanotrophic life in volcanic mudpots. Env Microbiol 16:255–264CrossRefGoogle Scholar
  52. Prasad AS, Halsted JA, Nadimi M (1961) Syndrome of iron deficiency anemia, hepatosplenomegaly, hypogonadism, dwarfism and geophagia. Am J Med 31:532–546CrossRefPubMedGoogle Scholar
  53. Ramalho J, Ramalho M, Jay M et al (2016) Gadolinium toxicity and treatment. Magn Reson Imaging 34:1394–1398CrossRefPubMedGoogle Scholar
  54. Raulin J (1869) Etudes chimiques sur la végétation. Ann Sci Nat Bot Biol Veg 11:92–299Google Scholar
  55. Ridgway A, Webb R (2015) The materials bonanza. New Sci 225:35–41CrossRefGoogle Scholar
  56. Salt DE (2004) Update on ionomics. Plant Physiol 136:2451–2456CrossRefPubMedPubMedCentralGoogle Scholar
  57. Szpunar J (2004) Metallomics: a new frontier in analytical chemistry. Anal Bioanal Chem 378:54–56CrossRefPubMedGoogle Scholar
  58. Vallee BL, Auld DS (1989) Short and long spacer sequences and other structural features of zinc binding sites in zinc enzymes. FEBS Lett 257:138–140CrossRefPubMedGoogle Scholar
  59. Vincent JB (2014) Is chromium pharmacologically relevant? J Trace Elem Med Biol 28:397–405CrossRefPubMedGoogle Scholar
  60. WHO (1996) Trace elements in human nutrition and health. World Health Organization, Geneva, pp 258–259Google Scholar
  61. Williams RJP (2001) Chemical selection of elements by cells. Coord Chem Rev 216:583–595CrossRefGoogle Scholar
  62. Yasuda H, Yonashiro T, Yoshida K et al (2006) Relationship between body mass index and minerals in male Japanese adults. Biomed Res Trace Elem 17:316–321Google Scholar
  63. Zhang P, Georgiou CA, Brusic V (2017) Elemental metabolomics. Brief Bioinform.  https://doi.org/10.1093/bib/bbw131

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Metal Metabolism Group, Departments of Biochemistry and Nutritional Sciences, School of Life Course Sciences, Faculty of Life Sciences and Medicine, King’s College LondonLondonUK

Personalised recommendations