Corresponding Author: Kavita Shah E-mail: kshah.iesdbhu@sify.com, kavitashah@bhu.ac.in J P P JOURNAL OF PROTEINS AND PROTEOMICS 2(2), July-December 2011, pp. 99-113 PHYLOGENETIC RELATIONSHIPS IN ZnT SUPERFAMILY OF ZINC ION TRANSPORTERS IN SILICO Kavita Shah 1 , Avinash Chandra Rai 2 and Vinita Singh 3 1 Environmental Biochemistry and Bioinformatics, Institute of Environment and Sustainable Development Banaras Hindu University, Varanasi 221 005, India 2 Department of Biochemistry, Faculty of Science, Banaras Hindu University, Varanasi 221 005, India 3 Bioinformatics Division, Mahila Mahavidyalaya, Banaras Hindu University, Varanasi 221 005, India Abstract: The Zinc transporter (ZnT superfamily) facilitates Zn-transport into intracellular vesicles in life forms. Existing database has been enriched with the identification of new Zn-transporters important for therapeutic and intra-channel metal binding capacity. The present work uses a consensus sequence approach to identify extra-membrane metal-binding motif in Zn transporter protein family. Molecular phylogeny among members of ZnT superfamily proteins was analyzed. In all 166 representative sequences covering all known members of ZnT protein subfamilies (subgroups Znt1-Znt10) from bacteria, archaea and eukarya were selected and used to obtain ten consensus sequences, each representing a specific ZnT subgroup (1-10). Using bioinformatics tools a phylogenetic tree was constructed to explore the evolutionary link between the various ZnT subgroup considering members from lower and higher life forms. The unrooted phylogenetic tree obtained by Clustal W and NJ method revealed the existence of three clearly separated clades, which were segregated early in the evolution of this superfamily. Consensus sequence analysis using Weblogo revealed motifs of (HX)n type that evolved to bind the Zn ions effectively, enabling Zn transport. No significant similarity among members of Znt1 and Znt10 or Znt2 and Znt10 suggest that gene duplication event in the ZnT superfamily gene probably occurred in the later phase of evolution when individual specificities of the distinguished ZnT subgroups were already formed. Keywords: Bioinformatics; Consensus sequence; Motif; Phylogeny; Zinc-transporter. Introduction Zinc is an essential trace element required for the structural stability of a variety of proteins involved in transcription and protein trafficking as well as for the catalytic activity of metalloenzymes. More than 300 metalloenzymes of six major functional classes require zinc as a key structural component or as a cofactor (Vallee and Auld, 1990; Vallee and Falchuk, 1993; Berg and Shi, 1996), which include pancreatic carboxypeptidases, alkaline phosphatase, various dehydrogenases and superoxide dismutase (Frausto da Silva, 1991). In mammals, zinc is absorbed through the brush border of small intestinal mucosa from diet and transported through blood to the tissues and cells where zinc is needed (Reyes, 1996). Moreover, zinc is an element requisite for zinc containing DNA binding proteins. Human genes encoding C2H2 zinc-finger proteins amount to more than 3-4% of the total (Kowalski et al., 2002; Mackay et al., 1998). Zinc can potentially modulate cellular signal recognition, second messenger metabolism and the function of protein kinase and protein phosphatase (Reyes, 1996). Consequently, the disturbance of zinc homeostasis causes a variety of severe detrimental effects on animals, including humans. The understanding of zinc transport and its regulation in plants has increased with the identification of both Zrt-Irt-like proteins and Cation Diffusion Facilitator family genes in many plant species. Recently, 86 ZIP members were