5th International Young Scientist Congress (IYSC-2019).  International E-publication: Publish Projects, Dissertation, Theses, Books, Souvenir, Conference Proceeding with ISBN.  International E-Bulletin: Information/News regarding: Academics and Research

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)


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.


  1. Mishra P.C., Dash A.K., and Pradhan K., Metals in Environmental segments at Hirakud of Odisha, India, ISCA Journal of Biological Sciences,1(1), 7-23 (2012)
  2. Mohammed M.B., Mohammed S.S. and Adewumi A.A.J., Assessment of Zn Bioavailability in Dumpsites of Kaduna Metropolis,Nigeria, Research Journal of Recent Sciences,1(12), 21-24, December (2012)
  3. Francis A.R., and Masilamai D., Removal of Zinc (II) by Non Living Biomass of Agaricus Bisporus, Research Journal of Recent Sciences1(9), 13-17, September (2012)
  4. Blencowe DK, and Morby AP Zn(II) metabolism in prokaryotes, FEMS Microbiol Rev, 27291–311, (2003)
  5. Gaballa A, and Helmann J D., Identification of a zinc-specific metalloregulatory protein, Zur, controlling zinc transport operons in Bacillus subtilis, J. Bacteriol, 180, 5815-5821, (1998)
  6. Gaballa A, and Helmann J D, A peroxide-induced zinc uptake system plays an important role in protection against oxidative stress in Bacillus subtilis, Mol. Microbiol, 45, 997-1005, (2002)
  7. El Yacoubi B, Bonnett S, Anderson JN, Swairjo MA, Iwata-Reuyl D, and de Crécy-Lagard V, Discovery of a new prokaryotic type I GTP cyclohydrolase family, J Biol Chem, 281(49), 37586-93, (2006)
  8. http://subtiwiki.uni-goettingen.de/wiki/index.php/YciB (2013)
  9. Gaballa A, Wang T, Rick W. Ye, and Helmann J D, Functional Analysis of the Bacillus subtilis Zur Regulon,  \n , 184(23), 6508–6514 (2002)
  10. Hollenstein K, Dawson RJ, and Locher K.P., Structure and mechanism of ABC transporter proteins, Curr. Opin. Struct. Biol , 17 (4), 412–8 (2007)
  11. Felsenstein J., PHYLIP: Phylogeny interference package (version 3.69) Department of Genome Sciences and Department of Biology, University of Washington, Washington, USA), 164-166 (1989)
  12. Swofford D. L., Olsen G. J., Waddell P. J. and Hillis D. M., Phylogenetic inference, In D M Hillis, C Moritz & B K Mable (Eds.), Molecular systematics, Sunderland, USA: Sinauer Associates, Inc., Publishers, 2nd edn, 407-514 (1996)
  13. Mondal S. K., Shit S. and Kundu S., A comparative computational study of the ‘rbcL’ gene in plants and in the three prokaryotic families-Archaea, cyanobacteria and proteobacteria, IJBT, 12, 58-66 (2013)
  14. Saldanha A. J., Java Treeview-extensible visualization of microarray data. BIOINFORMATICS APPLICATIONS NOTE, 20(17), 3246–3248 (2004)
  15. dKaufman L & Rousseeuw P J, Finding groups in data : An introduction to cluster analysis, (John Wiley and Sons, Inc., New Jersey, USA), (1990)
  16. Fu C, Xiong J and Miao W, Genome-wide identification and characterization of cytochrome P450 monooxygenase genes in the ciliate Tetrahymena thermophila, BMC Genomics,10, 208, (2009)
  17. Meng Z, Wei L and Xia L, Analysis of synonymous codon usage in chloroplast genome of Populus alba, J for Res19, 293-297, (2008)
  18. Sharp P M and Li W H, The codon adaptation index-A measure of directional synonymous codon usage bias, and its potential applications, Nucleic Acids Res,15, 1281-1295, (1987)
  19. Kumar S, Lingaiah K, Ramachandra N.B., and Nair M V., Genetic variations among Ecologically diverse species of Anurans at the level of Genus based on ISSR Marker, International Research Journal of Biological Sciences 1(7), 11-19, November (2012)
  20. Dwivedi VD, Sharma T, Mishra S.K., and Pandey A.K., Insights to Sequence Information of Lactoylglutathione Lyase Enzyme from Different Source Organisms, International Research Journal of Biological Sciences,1(6), 38-42, October (2012)
  21. Sharma A., and Sharma P., Genetic and Phytochemical analysis of Cluster bean Cyamopsis tetragonaloba (L.) Taub) by RAPD and HPLC, Research Journal of Recent Sciences,2(2), 1-9, February (2013)
  22. Maithri S.K., Ramesh K.V., and Muntanga D, Theoretical structure prediction of TcaA from Photorhabdus luminescens and aminopeptidase receptor from Helicoverpa armigera, Research Journal of Recent Sciences,2(2), 40-49, February (2013)
  23. Bhattacharya A, Power J.B., and Davey M. R., Genetic Manipulation of Gibberellin (GA) Oxidase Genes in Nicotiana sylvestris using constitutive promoter to modify Plant Architecture, Research Journal of Recent Sciences,1(5), 1-7, May (2012)
  24. Maithri S.K., Ramesh K.V., Dieudonné M, and Deshmukh S., Molecular Modeling and Docking Studies of PirB Fusion Protein from Photorhabdus Luminescens, International Research Journal of Biological Sciences,1(8), 7-18, December (2012)
  25. Kamaraj M., Jansi L., Sivaraj R., Sama K., Salam H.A. and Rajiv P., Gas Chromatographic and UV-VIS spectrometric analysis of Bisphenol-A degradation in garden soil collected from Coimbatore district,Tamil Nadu, India, International Research Journal of Biological Sciences,1(8), 54-60, December (2012)
  26. Sharp P.M., Tuohy T.M.F. and Mosurski K.R., Codon usage in yeast: Cluster analysis clearly differentiates highly and lowly expressed genes, Nucleic Acids Res,14, 5125-5143, (1986)