Analysis of the phylogenetic sequence relationships between plant alpha amylases

Abstract

Enzymes are highly valuable in the industry, such industries are food, beverage industry and the biofuel sector. Amylases are very important in starch processing such as liquefaction, hydrolysis and saccharification. Alpha amylase has liquefying ability by hydrolysing the glycosidic bonds at internal positions. This paper aims to present a brief overview of the sequence comparison between plant alpha amylases. The protein sequences were obtained from the NCBI, aligned using the clustal W tool and the phylogenetic trees were constructed using the Mega 7.0 tool. The proteins can be classified into three distinct families; one, two and three. Each family has some peculiar features, family one amylases are proteins of about 450 amino acids long with signal peptides at their N-terminus, family two proteins are similar in size to those of family one but are cytosolic with no targeting peptide. In contrast, family three amylase are proteins targeted to the chloroplast with transit peptides at their N-terminus, however, they are 900 amino acids long. In addition, the last family of protein has an additional domain that is yet to be fully characterized. Across the three families, there is a high homology and thus conservation of the catalytic domain which is at the C-terminus. This implied that the proteins are evolutionary related and perform similar functions. The unknown domain in family three amylases is also conserved across members of this family. The domain may be a starch binding domain that is required for the family three amylases to digest storage starch in the plastid.

Keywords: Alpha amylases, Cytosol, Plastid, Family one, Unknown domain