Comparative functional genomics approach for the annotation of proteins in Unclassified Halophilic archaeon DL31

N Sardeshmukh,E Nakkeeran,S Sanmukh

doi:10.1038/npre.2012.6784.1

Abstract

AbstractThe structure, function and sub-cellular location prediction for the unknown proteins from Unclassified Halophilic archaeon DL31 were carried out for characterization of the proteins in their respective families. The 991 genes for hypothetical proteins in Halophilic archaeon DL31 chromosome were predicted by the application of computational methods and Bioinformatics web tools. The structure predictions for 206 unknown proteins were possible whereas functions were predicted in 825 protein sequences. The function prediction for the proteins were done by using Bioinformatics web tools like CDD-BLAST, INTERPROSCAN and PFAM by searching protein databases for the presence of conserved domains. The Sub-cellular location predictions were done for all the unknown proteins by using CELLO v 2.5 server. While tertiary structures were constructed using PS2 Server- Protein Structure Prediction server. This study revealed structural, functional and Sub-cellular localization of unknown proteins in Unclassified Halophilic archaeon DL31chromosome.

Highlights

Studies based on culturing showed a decrease in prokaryotic diversity recovered on plates as salt concentration increased (Rodríguez-Valera et al, 1981; 1985; 1988).At salinity up to 15%, most isolates were those, which are commonly found in seawater
Many alkaliphiles are halophilic as well, and many useful enzymes applied in the detergent industry, the textile industry, and other processes were derived from bacteria growing in saline alkaline lakes and are already explored for the production of commercially valuable enzymes, in particular, proteases and amylases
PHA production by halophilic Archaea and Bacteria, with a focus on Haloferax mediterranei, which shows the highest potential of an archaeal source for industrial applications, and the characterization of enzymes involved in synthesis of PHA

Summary

INTRODUCTION

Studies based on culturing showed a decrease in prokaryotic diversity recovered on plates as salt concentration increased (Rodríguez-Valera et al, 1981; 1985; 1988).At salinity up to 15%, most isolates were those, which are commonly found in seawater. In comparison to other groups of extremophilic microorganisms such as the thermophiles and the alkaliphiles, the halophiles of all three domains have been relatively little exploited in biotechnological processes, with notable exceptions of β-carotene from Dunaliella, bacteriorhodopsin from Halobacterium, and ectoine from Halomonas (Oren, 2010). Halophilic enzymes (typical for Archaea and Salinibacter and for exoenzymes of any halophile) are characterized by an excess of acidic amino acids and subsequent negative surface charge This peculiarity allows effective competition for hydration water and enables function in solutions of low water activity PHA production by halophilic Archaea and Bacteria, with a focus on Haloferax mediterranei, which shows the highest potential of an archaeal source for industrial applications, and the characterization of enzymes involved in synthesis of PHA. The present paper reports the functional properties along with their structural and sub-cellular localization of unknown proteins present in chromosome of Halophilic archaeon DL31which will prove to be helpful for identifying novel enzymes and protein candidates with possible applications in the near future

MATERIALS AND METHODS

RESULTS AND DISCUSSION

CONCLUSION