The “Motif‐to‐Market” framework is proposed, using the M5 motif as a fingerprint to curate functional PETases for efficiency and stability, with distinct pathways for industrial and marine applications.
Abstract
The persistence of PET plastic has triggered a global microbial response. A recent work used AI, structural biology, and experiments to reveal widespread PET‐degrading enzymes (PETases). Analysis of 415 marine metagenomes found the M5 functional motif—catalytic triad, substrate clamps, and disulfide bonds—in nearly 80% of samples, from surface to abyss, peaking at 1000–2000 m depths where microplastics accumulate. These enzymes, from
Pseudomonadales
and
Halopseudomonas
, break PET into monomers in the lab; in vivo microcosms showed 2.7% degradation of PET films over 85 days in seawater. This 2.7% figure represents total mass loss, including abiotic contributions not separately quantified. Metagenomes indicate gene presence, not activity, and natural degradation remains catastrophically slow, with weak correlation between PETase abundance and plastic concentration (
R
2
= 0.09) and no deep‐sea activity evidence. We propose the “Motif‐to‐Market” framework: (1) Discovery—using the M5 motif as a fingerprint to curate functional PETases; (2) Deconstruction—creating a mechanistic blueprint; (3) Design—engineering enzymes for efficiency and stability, with distinct pathways for industrial (thermostable) and marine (cold‐active, salt‐tolerant) applications; (4) Deployment—applying them to recycling, bioremediation, and wastewater treatment. Despite slow rates and economic challenges, this roadmap offers a path toward a circular plastic economy.
A targeted mining workflow is developed that screens exclusively plastic-associated datasets through multi-step bioinformatic filtering—integrating catalytic-motif screening, disulfide-topology validation, structural-similarity scoring, and phylogenetic profiling—to recover high-confidence PETase candidates, resulting in a thermostable enzyme that depolymerizes PET across a broad temperature range.
Konstantinos Rigkos, Dimitra S Bezantakou, Kyriakos Antoniadis et al.· bioRxiv· 0 citations
ABSTRACT Polyethylene terephthalate (PET) waste represents a major environmental challenge due to limited recycling solutions. Thermophilic bacteria from geothermal environments harbor diverse enzymatic machinery adapted to extreme conditions, offering promising biocatalysts for plastic degradation; however, biological resources from Peru and other South American countries remain scarce. We characterized four bacterial strains isolated from two geothermal sites in Cajamarca, Peru, screened for PET hydrolysis at 50°C. Whole‐genome sequencing using hybrid assembly achieved near‐complete circular genomes. GTDB‐Tk classification identified three species: Neobacillus thermocopriae (strain 19A), Bacillus licheniformis (strains 16P and BI2), and Brevibacillus agri (strain BI8). Quantitative assays revealed that strain 16P achieved the highest mass loss (0.598%), followed by strain BI8 (0.449%). ATR‐FTIR analysis of the incubated sheets showed a significant reduction of the ester carbonyl index in strains 16P, 19A, and BI8 relative to both non‐incubated PET and an abiotic control, whereas strain BI2 did not differ from the controls, indicating preferential modification of ester bonds at the sheet surface. Genome mining and structure‐based homology searches identified multiple candidate enzymes similar to validated PETases and carboxylesterases, including PETase46‐like homologs in strains BI8 and 16P and a terephthalate‐active carboxylesterase homolog in strain 16P. Molecular docking supported the conservation of catalytic geometry and substrate‐binding sites in these candidates. This work represents one of the first systematic genomic and structural characterizations of putative PET‐hydrolases in Peruvian geothermal bacteria, expanding knowledge of extremophile diversity and advancing thermostable enzymes for sustainable plastic waste management.
Marco A Rivera-Jacinto, Claudia Rodríguez-Ulloa, Sara R Briones-Ramírez et al.· MicrobiologyOpen· 0 citations
A metagenomic analysis of soil and rhizosphere samples from the Antarctic vascular plants Deschampsia antarctica and Colobanthus quitensis is conducted, as sources of microbial enzymes with potential PET-hydrolytic activity, demonstrating the diversity of PET-hydrolase-like genes within Antarctic rhizosphere and soil microbiomes.
Valentín Berrios-Farías, Sergio Guajardo-Leiva, Jorge Gallardo-Cerda et al.· Frontiers in Microbiology· 0 citations
Plastic pollution is a global environmental challenge of increasing severity. Global plastic production reached approximately 413.8 million metric tonnes in 2023, yet global assessments, including those by Geyer et al., suggest that fewer than 10% of post-consumer plastics are effectively recycled. Here we present a theoretical Plastic-to-Fertilizer (P2F) framework that proposes an engineered four-member microbial consortium capable of partially depolymerizing mixed plastic waste, including polyethylene terephthalate (PET), high-density polyethylene (HDPE), polystyrene (PS), and polypropylene (PP), and channeling selected plastic-derived carbon intermediates toward biosynthesis of agronomically beneficial compounds, including organic acids, amino acids, and humic-like macromolecules (HLMs). The proposed consortium comprises an engineered Pseudomonas putida KT2440 chassis expressing heterologous PETase and MHETase [mono(2-hydroxyethyl) terephthalate hydrolase] for PET depolymerization and harboring a native styrene catabolic pathway for PS intermediates; Bacillus subtilis 168 providing CotA laccase-mediated polyolefin surface oxidation; Aspergillus niger serving as a biofilm scaffold and oxidative enzyme source; and a biocontained Azotobacter vinelandii strain with a conditionally active, speculative nitrogen-fixation module. A theoretical mathematical framework encompassing Langmuir-adsorption-based surface degradation kinetics, substrate-specific Haldane-Andrews growth models, and enzyme synergy quantification is presented alongside a corrected stoichiometric mass balance for the P2F metabolic funnel. Techno-economic projections are presented as illustrative scenarios only, given the current technology readiness level (TRL 1–2). Key biological constraints are explicitly acknowledged throughout: HDPE and PP are highly crystalline polymers requiring mandatory abiotic pre-treatment before enzymatic action is feasible; PS depolymerization to metabolisable intermediates requires abiotic pre-treatment as no biological route has been demonstrated for bulk PS; heterologous nitrogen fixation is technically challenging and is framed as a speculative high-risk long-term aspiration rather than a functional module; and all stoichiometric yields are theoretical upper bounds. This paper provides a conceptual foundation, a corrected mathematical framework, and a five-phase experimental roadmap intended to guide empirical validation.
Krishnaraj Narayanan· Frontiers in Microbiology· 0 citations
Xylella fastidiosa is a xylem-limited phytopathogenic bacterium responsible for severe diseases in many economically important crops. Despite its impact, its metabolism remains poorly characterized due to fastidious growth and the limited availability of defined culture media. Here, we reconstruct the first pangenome-based genome-scale metabolic model for X. fastidiosa, integrating conserved metabolic functions from 18 strains across five subspecies. The resulting consensus model, iXfcore, is manually curated and used to explore the species' metabolic capabilities. Model simulations predict minimal nutritional requirements that guide us in the formulation of defined media to assess biofilm formation in vitro, supporting the utility of the resulting predictions. Network analysis also identifies a previously undescribed model-predicted candidate pathway for acetate assimilation, consistent with genomic evidence but requiring further empirical validation. In addition, the model predicts the overproduction of polyamines, compounds linked to virulence in other phytopathogens. Experimental analyses confirm polyamine production in multiple X. fastidiosa strains in vitro, providing the first evidence of polyamine detection in culture supernatants of this phytopathogen. Overall, iXfcore provides a systems-level framework to investigate X. fastidiosa metabolism, generate testable hypotheses on its physiology and putative virulence-associated traits, and support future strain-specific models and studies of host-pathogen metabolic interactions.
Paola Corbín-Agustí, Miguel Álvarez-Herrera, M. Román-Écija et al.· Microbiology Research· 0 citations
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.
Sunho Park, Ji Hyuk Ko, Chaeyeon Yang et al.· Frontiers in Microbiology· 0 citations