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Comparative Genomics Analysis of the Metallomes

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Metallomics and the Cell

Part of the book series: Metal Ions in Life Sciences ((MILS,volume 12))

Abstract

Biological trace metals are needed in small quantities, but used by all living organisms. They are employed in key cellular functions in a variety of biological processes, resulting in the various degree of dependence of organisms on metals. Most effort in the field has been placed on experimental studies of metal utilization pathways and metal-dependent proteins. On the other hand, systemic level analyses of metalloproteomes (or metallomes) have been limited for most metals. In this chapter, we focus on the recent advances in comparative genomics, which provides many insights into evolution and function of metal utilization. These studies suggested that iron and zinc are widely used in biology (presumably by all organisms), whereas some other metals such as copper, molybdenum, nickel, and cobalt, show scattered occurrence in various groups of organisms. For these metals, most user proteins are well characterized and their dependence on a specific element is evolutionarily conserved. We also discuss evolutionary dynamics of the dependence of user proteins on different metals. Overall, comparative genomics analysis of metallomes provides a foundation for the systemic level understanding of metal utilization as well as for investigating the general features, functions, and evolutionary dynamics of metal use in the three domains of life.

Please cite as: Met. Ions Life Sci. 12 (2013) 529–580

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Abbreviations

5,6-LAM:

D-lysine 5,6-aminomutase

ABC:

ATP-binding cassette

AO:

aldehyde oxidase

AOR:

aldehyde:ferredoxin oxidoreductase

CoA:

coenzyme A

CODH:

carbon monoxide dehydrogenase

CODH/ACS:

acetyl-coenzyme A decarbonylase/synthase

CoM:

coenzyme M

COX:

cytochrome c oxidase

cPMP:

cyclic pyranopterin monophosphate

Ctr:

Cu transporter

CuAO:

Cu amine oxidase

Cu-Zn SOD:

Cu-Zn superoxide dismutase

Cys:

cysteine

DBM:

dopamine β-monooxygenase

DDH/GDH:

diol/glycerol dehydratase

DMSOR:

dimethylsulfoxide reductase

EAL:

ethanolamine ammonia lyase

ECM:

ethylmalonyl-CoA mutase

EPR:

electron paramagnetic resonance

GAO:

galactose oxidase

GlxI:

glyoxalase I

GM:

glutamate mutase

GTP:

guanosine 5¢-triphosphate

ICM:

isobutyryl-CoA mutase

L-dopa:

L-dihydroxyphenylalanine

mARC:

mitochondrial amidoxime-reducing component

MCM:

methylmalonyl-CoA mutase

MCO:

multicopper oxidase

MCP:

Moco carrier protein

MCR:

methyl-coenzyme M reductase

MetH:

methionine synthase

MGD:

molybdopterin guanine dinucleotide

MGM:

methyleneglutarate mutase

MoBP:

Moco-binding protein

Moco:

Mo cofactor

Mop:

Mo-binding protein

MPT:

molybdopterin

Mtr:

methyltetrahydromethanopterin:CoM methyltransferase

N2OR:

nitrous oxide reductase

NADH:

nicotinamide adenine dinucleotide (reduced)

NCBI:

National Center for Biotechnology Information

Ndh2:

NADH dehydrogenase 2

NHase:

nitrile hydratase

NiR:

nitrite reductase

NMR:

nuclear magnetic resonance

NR:

nitrate reductase

PAM:

peptidylglycine R-amidating monooxygenase

PDB:

Protein Data Bank

PHM:

peptidylglycine R-hydroxylating monooxygenase

pMMO:

particulate methane monooxygenase

RNR II:

B12-dependent ribonucleotide reductase

SO:

sulfite oxidase

SOD:

superoxide dismutase

SodN:

Ni-containing superoxide dismutase

TRP:

tyrosinase-related proteins

Wco:

tunftsen cofactor

XDH:

xanthine dehydrogenase

XO:

xanthine oxidase

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Acknowledgments

This work was supported, in whole or in part, by National Institutes of Health Grants GM061603 and CA080946 (to V. N. G.), and by the National Natural Science Foundation of China under NO. 31171233 (to Y. Z.).

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  1. Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, New Research Building, 77 Av. Pasteur, Boston, MA, 02115, USA

    Vadim N. Gladyshev

  2. Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 294 Tai Yuan Road, Shanghai, 200031, China

    Yan Zhang

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    Lucia Banci

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Gladyshev, V.N., Zhang, Y. (2013). Comparative Genomics Analysis of the Metallomes. In: Banci, L. (eds) Metallomics and the Cell. Metal Ions in Life Sciences, vol 12. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-5561-1_16

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