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Genomic and Proteomic Properties of the Genes involved for Zinc Transportation in Firmicutes

Author Affiliations

  • 1Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, INDIA

Int. Res. J. Biological Sci., Volume 2, Issue (12), Pages 90-101, December,10 (2013)

Abstract

Two types of zinc transport systems known as high affinity and low affinity on the basis of zinc availability in medium have been identified in bacteria. Genes responsible for the high affinity uptake system of zinc are ycdH, ycdI, yceA and for low affinity uptake system are yciA, yciB, yciC in firmicutes. From phylogenetic tree analysis of genes responsible for high affinity zinc uptake, Bacillus is the earliest to have evolved among the 4 genuses. Amino acids composition and the Gravy’s score analysis shows that ycdH, ycdI, and yciC genes are hydrophilic amino acid rich, suggesting that they can either form a transport channel for zinc entry or can bind to zinc cation for transport, and yceA is hydrophobic amino acid rich showing its function in membrane composition. Also, all the three genes of both high affinity and low affinity uptake system are AT rich. The relationship between GC content and amino acid groups based on polarity and charge, depicts that the gene ycd Hand ycdI shows similar trend but different from yceA, whereas yciA, yciB, and yciC shows similar trend in all the groups except acidic and basic polar and aromatics in yciC. For high affinity genes, a hierarchical clustering based on amino acid frequencies of the proteins encoded by the genes, the GC3 content and RSCU values of these genes, shows that all the organisms under a particular genus falls under same cluster, supporting their taxonomical lineage. ENc plot shows that all the genes involved in high affinity system for zinc uptake are under mutational bias except few ycdI and yceA from Listeria whereas the genes involved in low affinity zinc uptake system are under selectional bias except few yciA genes. Correspondence analysis shows that ycdH and ycdI follows similar pattern and yceA follows pattern which is opposite to both ycdH and ycdI whereas yciA and yciC follows similar pattern but yciB is different.CAI values predicts that the degree of expression of the genes for high affinity system from Bacillus and Paenibacillus to be high but from Enterococcus and Listeria to be low and expression of low affinity genes is high, except from Staphylococcus and few sub-species of Bacillus subtilis.

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