Prediction of lipase-specific foldase-dependence in bacterial lipase subfamilies I.1 and I.2.

Abstract

Background: Most bacterial lipases in subfamily I.1/I.2 depend on a specific chaperone protein, lipase-specific foldase (Lif), for folding into their active form. In contrast, several Lif-independent lipases have been reported in subfamily I.1. Lif-independent lipases have the potential to be industrially useful owing to their ease of heterologous expression; however, no method has been reported to predict Lif-dependence for an arbitrary lipase. In this study, we comprehensively estimated the Lif-dependence of subfamily I.1/I.2.

Results: To estimate Lif-dependence, we comprehensively analyzed the presence or absence of Lif genes in the genomes of bacteria from which the lipases were derived and integrated the results with those of phylogenetic analysis. We identified a range of lipases from the Pseudomonas fragi/Proteus vulgaris clade, which contained all known Lif-independent lipases and were enriched for lipases that did not coexist with Lif. Sequences and structural features conserved in the P. fragi/P. vulgaris clade and other lipases were identified, and the residues involved in Lif-dependence were inferred. Furthermore, we identified the Pseudoalteromonas shioyasakiensis clade, which is phylogenetically distinct from the P. fragi/P. vulgaris clade, as having no Lif in the genome of the bacterium from which the lipase was derived. The P. shioyasakiensis clade lipase, PliLip, was heterologously expressed in Escherichia coli in an active form, independent of Lif.

Conclusions: In this study, we developed a method to predict Lif-dependence in any lipase belonging to subfamily I.1/I.2 and comprehensively extracted putative Lif-independent lipases from public databases. This study contributes to expand the diversity of industrially available Lif-independent lipases and provides fundamental insights into the evolution of lipases and Lif.