Bioinformatics Analyses of Endo-1,4-beta-xylanase from Bacillus sp. SS3.4

Abstract

Various types of microorganisms particularly bacteria and fungi are capable of producing xylanolytic enzymes that degrade xylan into simple sugars to be used as their carbon sources. Xylanolytic enzymes, particularly endo-1,4-β-xylanase, has been extensively used in various industrial sectors, including biofuel, livestock, paper, and food. Previously, Bacillus sp. SS3.4 was observed to have xylanolytic activities on wheat bran, suggesting its capability of producing xylanolytic enzymes, endo-1,4-β-xylanase included. With great numbers of data available in nucleotide and protein sequence databases, bioinformatics analyses of protein structure for function prediction have become attractive to supplement wet laboratory experiments to reduce time and money consumption. Therefore, in this study, bioinformatics analyses were performed on Bacillus sp. endo-1,4-β-xylanase sequence in order to further evaluate the enzyme’s function by exploring its protein structure in comparison to other known bacterial endo-1,4-β-xylanase. In this study, Bacillus sp. endo-1,4-β-xylanase sequence was identified from its whole genome sequence. The sequence was then analyzed by using BLAST to perform a homology search for identifying the protein, MUSCLE to perform multiple sequence alignment for comparing with other enzyme sequences, PHYLOGENY-FR to display its relatedness among Bacillus, Aspergillus niger and Trichoderma reesei, and SWISS-MODEL to generate its three-dimensional structure. Results from BLAST confirmed that the identified sequence was endo-1,4-β-xylanase, with greater relatedness to Bacillus velezensis and Bacillus amyloliquefaciens endo- 1,4-β-xylanase. While results from MUSCLE and SWISS-MODEL suggested that the endo-1,4-β-xylanase belongs to the Glycosyl Hydrolase 11 (GH11) family bearing the distinct shape of a jelly roll with well-conserved binding and catalytic residues. These results strongly suggest that Bacillus sp. endo-1,4-β-xylanase is potentially capable of degrading xylan with highly similar mechanism as with other endo-1,4-β-xylanase.
 Keywords: Bacillus, bioinformatics analysis, endo-1,4-