Phylogeny of structural domains of plant serine β-lactamase family proteins

Abstract

Bacterial serine β-lactamases (βL) constitute a class of penicillin-binding proteins that hydrolyze β-lactams and prevent the inhibition of enzymes involved in peptidoglycan synthesis. Genes homologous to βL have been discovered in Protozoa, Metazoa and Plantae; however, the function of the non-bacterial genes remains elusive. Structural and phylogenetic analysis has revealed important hints related to the function. The non-bacterial protein structure includes a conservative three-motif amino acid sequence signature characteristic of the active center of βLs. In addition, plant βL homologue represents a multimodular enzyme containing an ABC1 domain at the N-terminal part of the polypeptide chain. Characterization of the diversity of βL homologues provides guidelines for experimental investigations on the protein function. Four distinct alloparalogous lineages of the protein have been identified in metazoan βL homologues. In this study, the diversity of plant βL homologue was characterized by assessing the phylogeny of functional domains. Sequence collection from genomic and assembled EST databases resulted in a set of 57 sequences with at least partial coverage of the structural domains. A phylogenetic diversity was estimated at the ABC1 domain and at three regions corresponding to the active-site motifs SXXK, [SY]X[NT], [K / H] [T / S]G within the βL domain. Protein sequence parsimony analysis revealed the presence of at least four distinct phylogenetic clusters in each region of the catalytic motifs of the βL domain, suggesting a structural and functional diversity of the protein family in plants. Sequences of the ABC1 domain are closely related among the multimodular proteins homologous to βL and constitute a distinct phylogenetic group within the ABC1 protein family in plants. Keywords: serine β-lactamase, LACTB, ABC1, sequence alignment, structural domain, phylogeny