Identification of prospective PETases across prokaryotes using an in silico approach

Plastics count as one of the most potent threats to the habitats and survival of global flora and fauna. Reports keep accumulating globally about the ever-exploding load of plastic wastes, but the need and economics of multiple industrial and household processes compel the production of more plastic materials. It has always been imperative to look for natural sources of degradation of plastic. The identification of plastic-degrading microbes, therefore, remains a major focus of the microbial fraternity. While the discoveries of Ideonella sakaiensis or later, Rhizobacter gummiphilus were more out of providence, the structure determination of the enzyme responsible for PET degradation does provide a fillip to efforts towards the identification of more such prokaryotic entities.

In this work, a comprehensive profiling of prokaryotic sequences has been undertaken to look for the presence of similar plastic-degradation abilities across the kingdom. The identification of twenty-seven such 'hits' across different bacterial species led us to believe in the natural diversity of plastic-degradation enzymes. Moreover, there seems to be conservation of the structural motif that renders such ability, as has been observed from the constructed models and analysis of their interfaces. Docking of BHET, one of the key products of PET, against these 27 entities showed considerable interactions with the above and pointed towards the possible roles of these bacteria as natural plastic degradation models. Eight of these proteins have very close similarity in binding interactions and surface properties to the PETase from I. sakaiensis and were shortlisted as prospective candidates.

Of these eight, three PETases from Halopseudomonas pertucinogena, Halopseudomonas bauzanensis and Ketobacter sp. revealed significant similarity in structure and conformational stability to the PETase from I. sakaiensis, as was evident from the analysis of their molecular dynamics parameters. Principal Component Analysis and the free energy landscape during binding to BHET also validated the hypothesis, and these three PETases could be immediately explored for possible plastic degradation activity.