Metallomics and the Cell

This volume, edited by Lucia Banci, is probably the first real book on metallomics. The table of contents looks very promising, and judging from those bits that I am able to access, I’d love to say that is is a great book... But honestly I can’t. The days when I could persuade the library to purchase (for me) a book, however expensive, are long gone. At the Springer website, eBook is priced at €142.79 and hardcover costs €181.85. You can buy them slightly cheaper from Amazon ($175.82 and $227.05, respectively.)

The book is dedicated to Ivano Bertini, who sadly passed away last year. I was lucky enough to meet the man himself on a few occasions. Ivano was a formidable scientist and one of the most colourful figures of bioinorganic chemistry and structural biology.

Metallomics and the Cell
Metal Ions in Life Sciences, vol. 12
Lucia Banci, Editor

1. Banci, L. and Bertini, I. Metallomics and the cell: some definitions and general comments, pp. 1—13.
2. Penner-Hahn, J.E. Technologies for detecting metals in single cells, pp. 15—40.
3. Clausen, M.J.V. and Poulsen, H. Sodium/potassium homeostasis in the cell, pp. 41—67.
4. Romani, A.M.P. Magnesium homeostasis in mammalian cells, pp. 69—118.
5. Brini, M., Calì, T., Ottolini, D. and Carafoli, E. Intracellular calcium homeostasis and signaling, pp. 119—168.
6. Roth, J., Ponzoni, S. and Aschner, M. Manganese homeostasis and transport, pp. 169—201.
7. Andrews, S., Norton, I., Salunkhe, A.S., Goodluck, H., Aly, W.S.M., Mourad-Agha, H. and Cornelis, P. Control of iron metabolism in bacteria, pp. 203—239.
8. Dlouhy, A.C. and Outten, C.E. The iron metallome in eukaryotic organisms, pp. 241—278.
9. Benson, D.R. and Rivera, M. Heme uptake and metabolism in bacteria, pp. 279—332.
10. Cracan, V. and Banerjee, R. Cobalt and corrinoid transport and biochemistry, pp. 333—374.
11. Sydor, A.M. and Zamble, D.B. Nickel metallomics: general themes guiding nickel homeostasis, pp. 375—416.
12. Rensing, C. and McDevitt, S.F. The copper metallome in prokaryotic cells, 417—450.
13. Vest, K.E., Hashemi, H.F. and Cobine, P.A. The copper metallome in eukaryotic cells, pp. 451—478.
14. Maret, W. Zinc and the zinc proteome, pp. 479—501.
15. Mendel, R.R. Metabolism of molybdenum, pp. 503—528.
16. Gladyshev, V.N. and Zhang, Y. Comparative genomics analysis of the metallomes, pp. 529—580.

Metalloproteomics

“Metalloproteomics” is a relatively new and not that widely known term. Today (20 October 2009), PubMed search produces only 13 hits. (The search for “metallomics” gives only twice as many hits.) The earliest use of the term is by Alfredo Sanz-Medel and by Scott et al. — incidentally, both papers were published online 23 December 2004.

Metalloproteomics by Eugene Permyakov (Wiley-Interscience, 2009) gives us a definition of the term:

Metalloproteomics is a proteomics of metal-binding proteins.

That’s easy, right? But wait. Check out the table of contents. It looks to me like another bioinorganic chemistry book, and a rather pricey one. It mostly deals with metalloproteins, but there are also Chapter 15, Interactions of metal cations with nucleic acids, and Chapter 16, “Nonphysiologic” metals. Nothing here is specifically proteomic or metallomic. I suppose that Chapter 3, Experimental methods used for studies of the binding of metal cations could be of some relevance to metalloproteomics. Then again, maybe not: how come that mass spectrometry, the most obvious proteomics technique, is not mentioned at all? And why metal cations only? Some metalloproteins contain vanadate. Maybe I am jumping to conclusions here (without even reading the book!), but this title is simply misleading.

Wine metallomics

I suppose everybody who follows this blog is acquainted with the theory linking the lead posoning and decline of Roman Empire. But sure that was a long time ago? Bad news, everybody: the wine we drink now still has the metals we really needn’t. According to this paper,

The THQ <target hazard quotient> values were determined as ranges from previously reported ranges of metal ion concentrations and were frequently concerningly high. Apart from the wines selected from Italy, Brazil and Argentina, all other wines exhibited THQ values significantly greater than one indicating levels of risk. The levels of vanadium, copper and manganese had the highest impact on THQ measures. Typical potential maximum THQ values ranged from 50 to 200 with Hungarian and Slovakian wines reaching 300. THQ values for a sample of red and white wines were high for both having values ranging from 30 to 80 for females based on a 250 mL glass per day.

Well, I’ll stick to Italian (post-Roman) wine then.

Stories of chronomes and metallomes

I do not understand what principle is used by PubMed to indicate which papers are “related” to the one you are looking at. Take, for instance, the recent paper “Epigenetics: an important challenge for ICP-MS in metallomics studies” — among “Related Articles”, the top one is entitled “Chronoastrobiology: proposal, nine conferences, heliogeomagnetics, transyears, near-weeks, near-decades, phylogenetic and ontogenetic memories”. (Is that a real title? Yes it is.) True, the abstract, though truncated, makes an intriguing reading, but has it anything to do with metallomics (or epigenetics, for that matter)? The only passage related to any ome or omics is the following:

Structures in time are called chronomes; their mapping in us and around us is called chronomics. The scientific study of chronomes is chronobiology.

Well, I don’t know, Webster’s definition of chronobiology makes more sense to me and it does not use the dodgy concept of “chronome”. As for today, 27 March 2009, PubMed citations for chronome (61) and chronomics (39) visibly outnumber metallome (8) and metallomics (20), while there is none that combines any of the first pair of terms with any of the second pair of terms.

The Royal Society of Chemistry News

By some amazing coincidence, the same day as I have resuscitated this blog, the Royal Society of Chemistry has published the first issue of Metallomics, “a new journal covering the research fields related to biometals”. Good news is that the first issue is free. Check the “enhanced HTML articles” (for instance, this one) which provide “chemical ontology terms” which are nothing else but ChEBI ontology terms, with links to ChEBI.

On a lighter, but still metal-related note, the article on RSC blog entitled Gold saved! lists a winner and four more solutions to “The Italian Job problem”. Cool.

The definition of metallome

Just in case anyone wonders what the title of this blog means, here’s the definition of metallome from Wikipedia.