Genomic and structural insights into the high-efficiency poly(3-hydroxybutyrate) biodegradation in Terrabacter sp. AAH1

Abstract

The freshwater isolate Terrabacter sp. AAH1 exhibits highly efficient poly(3-hydroxybutyrate) (PHB) biodegradation, achieving 98.02 ± 0.08% weight loss within 12 days. Scanning electron microscopy and Fourier-transform infrared spectroscopy demonstrated that this rapid disintegration is driven by extensive surface erosion and the hydrolytic cleavage of ester bonds. Comparative genomic analysis across related taxa revealed that while putative PHB depolymerase genes are present in a subset of Terrabacter and allied genera, strain AAH1 is distinguished by its candidate degradation phenotype. The strain’s genomic architecture is predicted to integrate a secreted putative PHB depolymerase with a predict metabolic suite for the degradation of PHB via 3-HB oxidation, SCOT-mediated acetoacetate activation, and β-oxidation-like pathway converging on the TCA cycle. In silico structural modeling and molecular docking further supported a hypothetical compartmentalized degradation system, in which the Sec-type secreted putative depolymerase Te_EPD is proposed to initiate extracellular PHB hydrolysis, while Te_YbfF, Te_AES1, and Te_AES2 predicted to lack signal peptides are tentatively assigned putative intracellular roles. Among the four candidates, Te_EPD exhibited a predicted binding affinity of –4.9 kcal/mol for the PHB trimer via a conserved Ser–Asp–His (S–D–H) catalytic triad, and was uniquely classified within the extracellular short-chain-length PHA depolymerase type 1 (e_dPHAscl_type1) family based on domain annotation and sequence motif analysis. By proposing a putative association between specific genomic features and macroscopic polymer degradation, this study suggests that Terrabacter sp. AAH1 may represent a candidate biocatalyst warranting further investigation for potential applications in bioplastic waste management.