Title

Study of codon bias perspective of fungal xylanase gene by multivariate analysis

Authors

Smriti Shrivastava, Raju Poddar, Pratyoosh Shukla*, Kunal Mukhopadhyay

Affiliation

Department of Biotechnology, Birla Institute of Technology (Deemed University), Mesra, Ranchi, India

Email

pshukla@bitmesra.ac.in

Article Type

Hypothesis

Date

Received February 1, 2009; revised March 2, 2009; accepted March 8, 2009; published July 27, 2009

Abstract

Fungal xylanases has important applications in food, baking, pulp and paper industries in addition to various other industries. Xylanases are produced extensively by both bacterial and fungal sources and has tremendous potential of being active at extremes of temperature and pH. In the present study an effort has been made to explore the codon bias perspective of this potential enzyme using bioinformatics tools. Multivariate analysis has been used as a tool to study codon bias perspectives of xylanases. It was further observed that the codon usage of xylanases genes from different fungal sources is not similar and to reveal this phenomenon the relative synonymous codon usage (RSCU) and base composition variation in fungal xylanase genes were also studied. The codon biasing data like GC content at third position (GC3S), effective codon number (NC), codon adaptive
index (CAI) were further analyzed with statistical softwares like Sigma1plot 9.0 and Systat 11.0. Furthermore, study of translation selection was also performed to verify the influences of codon usage variation among the 94 xylanase genes. In the present study xylanase gene from 12 organisms were analyzed and codon usages of all xylanases from each organism were compared separately. Analysis indicates biased codon among all 12 fungi taken for study with Aspergillus nidulans, Chaetomium globosum, Aspergillus terreus and Aspergillus clavatus showing maximum biasing. NC plot and correspondence analysis on relative synonymous codon usage indicate that mutation bias and translation selection influences codon usage variation in fungal xylanase gene. To reveal the relative synonymous codon usage and base composition variation in xylanase, 94 genes from 12 fungi were used as model system.

Keywords

relative synonymous codon usage, correspondence analysis, translation selection, multivariate statistical analysis, xylanases.

Citation

Shrivastava et al, Bioinformation 3(10): 425-429 (2009)

Edited by

P. Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.