The Bacteroidetes Aequorivita sp. and Kaistella jeonii Produce Promiscuous Esterases With PET-Hydrolyzing Activity

Hongli Zhang; Pablo Perez-Garcia; Robert F Dierkes; Violetta Applegate; Julia Schumacher; Cynthia Maria Chibani; Stefanie Sternagel; Lena Preuss; Sebastian Weigert; Christel Schmeisser; Dominik Danso; Juergen Pleiss; Alexandre Almeida; Birte Höcker; Steven J Hallam; Ruth A Schmitz; Sander H J Smits; Jennifer Chow; Wolfgang R Streit

doi:10.3389/fmicb.2021.803896

The Bacteroidetes Aequorivita sp. and Kaistella jeonii Produce Promiscuous Esterases With PET-Hydrolyzing Activity

Front Microbiol. 2022 Jan 5:12:803896. doi: 10.3389/fmicb.2021.803896. eCollection 2021.

Authors

Hongli Zhang¹, Pablo Perez-Garcia^{1

2}, Robert F Dierkes¹, Violetta Applegate³, Julia Schumacher³, Cynthia Maria Chibani², Stefanie Sternagel⁴, Lena Preuss¹, Sebastian Weigert⁵, Christel Schmeisser¹, Dominik Danso¹, Juergen Pleiss⁶, Alexandre Almeida^{7

8}, Birte Höcker⁵, Steven J Hallam^{4

9

10

11

12}, Ruth A Schmitz², Sander H J Smits^{3

13}, Jennifer Chow¹, Wolfgang R Streit¹

Affiliations

¹ Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany.
² Molecular Microbiology, Institute for General Microbiology, Kiel University, Kiel, Germany.
³ Center for Structural Studies, Heinrich-Heine-University, Düsseldorf, Germany.
⁴ Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada.
⁵ Department of Biochemistry, University of Bayreuth, Bayreuth, Germany.
⁶ Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany.
⁷ European Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingdom.
⁸ Wellcome Sanger Institute, Hinxton, United Kingdom.
⁹ Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, Canada.
¹⁰ Genome Science and Technology Program, University of British Columbia, Vancouver, BC, Canada.
¹¹ Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada.
¹² ECOSCOPE Training Program, University of British Columbia, Vancouver, BC, Canada.
¹³ Institute of Biochemistry, Heinrich-Heine-University, Düsseldorf, Germany.

Abstract

Certain members of the Actinobacteria and Proteobacteria are known to degrade polyethylene terephthalate (PET). Here, we describe the first functional PET-active enzymes from the Bacteroidetes phylum. Using a PETase-specific Hidden-Markov-Model- (HMM-) based search algorithm, we identified several PETase candidates from Flavobacteriaceae and Porphyromonadaceae. Among them, two promiscuous and cold-active esterases derived from Aequorivita sp. (PET27) and Kaistella jeonii (PET30) showed depolymerizing activity on polycaprolactone (PCL), amorphous PET foil and on the polyester polyurethane Impranil^® DLN. PET27 is a 37.8 kDa enzyme that released an average of 174.4 nmol terephthalic acid (TPA) after 120 h at 30°C from a 7 mg PET foil platelet in a 200 μl reaction volume, 38-times more than PET30 (37.4 kDa) released under the same conditions. The crystal structure of PET30 without its C-terminal Por-domain (PET30ΔPorC) was solved at 2.1 Å and displays high structural similarity to the IsPETase. PET30 shows a Phe-Met-Tyr substrate binding motif, which seems to be a unique feature, as IsPETase, LCC and PET2 all contain Tyr-Met-Trp binding residues, while PET27 possesses a Phe-Met-Trp motif that is identical to Cut190. Microscopic analyses showed that K. jeonii cells are indeed able to bind on and colonize PET surfaces after a few days of incubation. Homologs of PET27 and PET30 were detected in metagenomes, predominantly aquatic habitats, encompassing a wide range of different global climate zones and suggesting a hitherto unknown influence of this bacterial phylum on man-made polymer degradation.

Keywords: Bacteroidetes; Flavobacteriaceae; PET degradation; PETase; metagenomic screening; metagenomics; polyethylene terephthalate (PET).