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 (GC(3S)), effective codon number (N(C)), 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. N(C) 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.
Highlights
The analysis of codon usage patterns can be traced back to when the first molecular sequence databases were being collated [1]
Amino acid usage varies between proteins and this variation has been shown to correlate with the properties of the proteins [3]
The program has some principal components analysis (PCA) methods implemented for comparative purposes
Summary
The analysis of codon usage patterns can be traced back to when the first molecular sequence databases were being collated [1]. In order to evaluate codon and amino acid usage variation, multivariate analysis options are available. To investigate major trends in codon usage variation among genes, correspondence analysis on RSCU values have been used widely [10]; [11]; [12]. NC, the effective number of codons used by a gene, is generally used to measure the bias of synonymous codons and independent of amino acid compositions and codon number [14]. Our analysis showed that the codon usage pattern of almost all xylanase gene were very similar and among all fungi Aspergillus nidulans, Chaetomium globosum, Aspergillus terreus and Aspergillus clavatus were maximum biased. The relative synonymous codon usage had been determined to study the overall codon usage variation among the xylanase gene. The parameters RSCU, GC3S (frequency of G+C at synonymous third position of codon), A3S (frequency of A at synonymous third position of codon), T3S (frequency of T at synonymous third position of codon), G3S (frequency of G at synonymous third position of codon), C3S (frequency of C at synonymous third position of codon) were determined and correspondence analysis were carried out by program codonW v1.3 (available at http://www.molbiol.ox.ac.uk/cu)
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