BACKGROUND:
Nickel (Ni) and
cobalt (Co) are trace elements required for a variety of
biological processes. Ni is directly coordinated by proteins, whereas Co is mainly used as a component of
vitamin B12. Although a number of Ni and Co-dependent
enzymes have been characterized, systematic evolutionary analyses of
utilization of these
metals are limited. RESULTS: We carried out comparative genomic analyses to examine occurrence and evolutionary dynamics of the use of Ni and Co at the level of (i) transport systems, and (ii) metalloproteomes. Our data show that both
metals are widely used in
bacteria and
archaea. Cbi/NikMNQO is the most common
prokaryotic Ni/Co transporter, while Ni-dependent
urease and Ni-Fe
hydrogenase, and B12-dependent
methionine synthase (MetH),
ribonucleotide reductase and
methylmalonyl-CoA mutase are the most widespread
metalloproteins for Ni and Co, respectively. Occurrence of other
metalloenzymes showed a mosaic distribution and a new B12-dependent
protein family was predicted.
Deltaproteobacteria and
Methanosarcina generally have larger Ni- and Co-dependent
proteomes. On the other
hand,
utilization of these two
metals is limited in eukaryotes, and very few of these organisms utilize both of them. The Ni-utilizing eukaryotes are mostly
fungi (except
saccharomycotina) and plants, whereas most B12-utilizing organisms are animals. The NiCoT transporter family is the most widespread eukaryotic Ni transporter, and eukaryotic
urease and MetH are the most common Ni- and B12-dependent
enzymes, respectively. Finally, investigation of environmental and other conditions and identity of organisms that show dependence on Ni or Co revealed that host-associated organisms (particularly
obligate intracellular parasites and
endosymbionts) have a tendency for loss of Ni/Co
utilization. CONCLUSION: Our data provide information on the evolutionary dynamics of Ni and Co
utilization and highlight widespread use of these
metals in the three domains of life, yet only a limited number of user proteins.
