Optimization of the Clustal X program for the alignment of multicopper oxidase bacterial sequences and their presence in the Bacillus genus

Abstract

Bioinformatic methods for the alignment of amino acid sequences and function prediction have to be robust, principally in conserved regions bound to enzymatic activity. In order to optimize amino acid sequence alignment in multicopper oxidase conserved sites of a collection of 103 bacterial sequences, modification were made in the weight values in different matrices for amino acid residues from the Clustal X 1.83 program. The results obtained with modified Clustal X program allowed us to identify different multicopper oxidase activity according to the groups from the relationship diagram, identifying two well differentiated groups within the Bacillus genus. This analysis allowed infers multicopper oxidase activity in Bacillus thuringiensis similar to that presented by Bacillus halodurans, but distinct with respect to other laccase type bacterial oxidases. Specific oligonucleotides were designed to amplify through polymerase chain reaction (PCR) the gene that codifies for the B. thuringiensis laccase, finding that this sequence is present in only 6 out of 32 sero varieties of B. thuringiensis analyzed.

Key words: Bacterial laccases, protein matrices, conserved motifs, multicopper oxidase.