Biological trace elements are needed in small quantities but are used by all living organisms. A growing list of trace elementdependent proteins and trace element utilization pathways highlights the importance of these elements for life. In this minireview, we focus on recent advances in comparative genomics of trace elements and explore the evolutionary dynamics of the dependence of user proteins on these elements. Many zinc protein families evolved representatives that lack this metal, whereas selenocysteine in proteins is dynamically exchanged with cysteine. Several other elements, such as molybdenum and nickel, have a limited number of user protein families, but they are strictly dependent on these metals. Comparative genomics of trace elements provides a foundation for investigating the fundamental properties, functions, and evolutionary dynamics of trace element dependence in biology.All organisms require a regular supply of nutrients. The major biological elements, carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur, are present in large quantities and are the main constituents of nucleic acids, proteins, lipids, cell walls, and mechanical structures (1, 2). There are also chemical elements, most of which are metals, that are present in small quantities (known as biological trace elements), including cobalt, copper, iron, manganese, molybdenum, nickel, zinc, selenium, and several other elements. The roles of trace elements primarily involve providing proteins with unique catalytic, structural, electron transfer, and other properties. They are used in numerous pathways, and all organisms utilize at least some of these elements (3-5). Their deficiency or mutations in genes that handle these elements often result in abnormal development, metabolic abnormalities, and even death (6 -8).Among trace elements, some such as zinc and iron appear to be used by all organisms (9 -11). Although organisms that survive under iron limitation have been reported (12, 13), it is unclear if they do not use this metal under iron-sufficient conditions. The number of proteins that utilize zinc or iron is large. For instance, Ͼ300 enzyme families require zinc for proper function (14). Metals are used by a wide range of proteins in the form of metal ions (e.g. manganese, copper, and nickel) or complex metal-containing cofactors (e.g. molybdopterin in the case of molybdenum and vitamin B 12 in the case of cobalt) (15-17). Selenium is used mainly in the form of selenocysteine (Sec) 2 residues in proteins (18).From the many studies on the functions of trace elements, metalloproteins emerged as one of the most diverse sets of proteins (19). Some protein families are strictly dependent on certain metals for their function (e.g. copper in cytochrome c oxidase and nickel in urease), whereas other families include both metal-dependent and metal-independent forms or evolved to use alternative metals (e.g. glyoxalase I binds nickel in Escherichia coli but zinc in humans and yeast) (20). In addition, orthologs of selenoproteins exist ...