Evolution of β-amylase: Patterns of variation and conservation in subfamily sequences in relation to parsimony mechanisms

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Abstract
Soybean and sweet potato beta-amylases are structured as alpha/beta barrels and the same kind of folding may account for all known beta-amylases. We provide a comprehensive analysis of both protein and DNA (coding region) sequences of beta-amylases. The aim of the study is to contribute to the knowledge of the evolutionary molecular relationships among all known beta-amylases. Our approach combines the identification of the putative eightfold structural core formed by beta-strands with a complete multi-alignment analysis of all known sequences. Comparing putative beta-amylase (alpha/beta)8 cores from plants and microorganisms, two differentiated versions of residues at the packing sites, and a unique set of eight identical residues at the C-terminal catalytical site are observed, indicating early evolutionary divergence and absence of localized three-dimensional evolution, respectively. A new analytical approach has been developed in order to work out conserved motifs for beta-amylases, mostly related with the enzyme activity. This approach appears useful as a new routine to find sets of motifs (each set being known as a fingerprint) in protein families. We demonstrate that the evolutionary mechanism for beta-amylases is a combination of parsimonious divergence at three distinguishable rates in relation to the functional signatures, the barrel scaffold, and alpha-helix-containing loops.