Comparative genomics of trace element dependence in biology

Abstract

Biological trace elements are needed in small quantities but are used by all living organisms. A growing list of trace element-dependent 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.

FIGURE 1.

Schematic diagram illustrating searches for zinc-dependent and zinc-independent forms of protein families. Zinc-binding proteins with PDB-annotated zinc ligands were used as queries.

FIGURE 2.

Multiple sequence alignments of representative zinc-binding protein families that also have zinc-independent forms. In each protein family, residues involved in zinc binding are highlighted in red. Other conserved residues are highlighted in black or gray.

FIGURE 3.

Multiple alignment of three groups of the tyrosinase family. Only CuB-binding sites are shown. Three His residues involved in metal binding are shown in a red background. A conserved His that is detected only in tyrosinases and that might also be involved in copper binding is highlighted in green.

FIGURE 4.

Analyses of evolutionary trends of selenoproteins. A, a strategy to identify events of conversion between Sec- and Cys-containing forms in protein families. B, a strategy to identify selenoprotein loss events in sister species. See text for details.