In silico analysis of cysteine cathepsins identified from the transcriptome profile of blunt snout bream (Megalobrama amblycephala)

Abstract

Cysteine cathepsins are described as lysosomal proteases with housekeeping and highly specialised functions in many organisms. In this study, cysteine cathepsins were identified from the transcriptome profile of blunt snout bream (Megalobrama amblycephala). A total of 41 cysteine cathepsin-like sequences were found and divided into groups of cathepsin (Cts): B, C, F, H, K, L, S, and Z. Twenty-nine of these sequences contained coding sequences, encoding 92-473 amino acids, which exhibited the highest (78%-95%) homology to the counterparts from zebrafish (Danio rerio). Multiple sequence alignment of the amino acids showed highly conserved domains among the cysteine cathepsins of M. amblycephala to its homologs. The putative proteins, including maCtsb1, maCtsc1, maCtsf2, maCtsh1, maCtsk5, maCtsl5, maCtss1, and maCtsz5 were characterised and structured using in silico methods. Additionally, codon usage of full length open reading frame sequences of these cathepsins was analysed. This study provided basic information for further studies on the specific functions of cysteine cathepsins of M. amblycephala in the future.

Keywords

• cysteine cathepsin
• blunt snout bream
• in silico
• homology modelling
• codon usage