Phylogenomic analysis of Cation Diffusion Facilitator proteins uncovers Ni/Co transporters

• Published in: Metallomics 2013-12, Vol.5 (12), p.1634-1643
• Main Authors: Cubillas, Ciro, Vinuesa, Pablo, Tabche, Maria Luisa, García-de los Santos, Alejandro
• Format: Article
• Language: English
• ISSN: 1756-5901; 1756-591X
• DOI: 10.1039/c3mt00204g

The ubiquitous Cation Diffusion Facilitator proteins (CDF) play a key role in maintaining the cellular homeostasis of essential metal ions. Previous neighbor-joining phylogenetic analysis classified CDF proteins into three substrate-defined groups: Zn 2+ , Fe 2+ /Zn 2+ and Mn 2+ . These studies were unable to discern substrate-defined clades for Ni 2+ , Co 2+ , Cd 2+ and Cu 2+ transporters, despite their existence in this family. In this study we improved the accuracy of this previous functional classification using a phylogenomic approach based on a thorough maximum-likelihood phylogeny and the inclusion of recently characterized CDF transporters. The inference of CDF protein function predicted novel clades for Zn 2+ , Fe 2+ , Cd 2+ and Mn 2+ . The Ni 2+ /Co 2+ and Co 2+ substrate specificities of two clades containing uncharacterized proteins were defined through the functional characterization of nepA and cepA metal inducible genes which independently conferred Ni 2+ and Co 2+ resistances to Rhizobium etli CFN42 and increased, respectively, Ni 2+ /Co 2+ and Co 2+ resistances to Escherichia coli . Neither NepA nor CepA confer Zn 2+ , Fe 2+ and Mn 2+ resistances. The ability of NepA to confer Ni 2+ /Co 2+ resistance is dependent on clade-specific residues Asn 88 and Arg 197 whose mutations produce a non-functional protein. An improved functional classification of the CDF family of proteins enables the discovery of Ni 2+ /Co 2+ and Co 2+ transporters.