Phylogenetic and functional analysis of the Cation Diffusion Facilitator (CDF) family: improved signature and prediction of substrate specificity

• DOI: 10.1186/1471-2164-8-107
• Publication Date: 2007-04-30T15:55:30Z
• Authors: Barbara Montanini; Damien Blaudez; Sylvain Jeandroz; Dale Sanders; Michel Chalot
• Keywords: 0301 basic medicine; 570; [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics; Iron; Molecular Sequence Data; QH426-470; [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy; Bacterial Physiological Phenomena; Substrate Specificity; 03 medical and health sciences; PHYLOGENETIC;SUBSTRATE; Cations; Metals, Heavy; [SDV.BID.SPT] Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy; Genetics; Humans; Synthetic Define; Cation Transport Proteins; Conserved Sequence; Phylogeny; Plant Proteins; Manganese; Sequence Homology, Amino Acid; 500; Metal Specificity; Biological Transport; Phylogenetics and taxonomy; Cobalt; Conserve Glycine Residue; Archaea; 3. Good health; Zinc; Cation Diffusion Facilitator; Eukaryotic Cells; Sequence Alignment; TP248.13-248.65; Biotechnology; Research Article; Cadmium

Abstract

Background The Cation Diffusion Facilitator (CDF) family is a ubiquitous family of heavy metal transporters. Much interest in this family has focused on implications for human health and bioremediation. In this work a broad phylogenetic study has been undertaken which, considered in the context of the functional characteristics of some fully characterised CDF transporters, has aimed at identifying molecular determinants of substrate selectivity and at suggesting metal specificity for newly identified CDF transporters.

Results Representative CDF members from all three kingdoms of life (Archaea, Eubacteria, Eukaryotes) were retrieved from genomic databases. Protein sequence alignment has allowed detection of a modified signature that can be used to identify new hypothetical CDF members. Phylogenetic reconstruction has classified the majority of CDF family members into three groups, each containing characterised members that share the same specificity towards the principally-transported metal, i.e. Zn, Fe/Zn or Mn. The metal selectivity of newly identified CDF transporters can be inferred by their position in one of these groups. The function of some conserved amino acids was assessed by site-directed mutagenesis in the poplar Zn2+ transporter PtdMTP1 and compared with similar experiments performed in prokaryotic members. An essential structural role can be assigned to a widely conserved glycine residue, while aspartate and histidine residues, highly conserved in putative transmembrane domains, might be involved in metal transport. The potential role of group-conserved amino acid residues in metal specificity is discussed.

Conclusion In the present study phylogenetic and functional analyses have allowed the identification of three major substrate-specific CDF groups. The metal selectivity of newly identified CDF transporters can be inferred by their position in one of these groups. The modified signature sequence proposed in this work can be used to identify new hypothetical CDF members.