Micro-nano plastics (MNPs), emerging contaminants resulting from the fragmentation of larger plastic debris, pose a serious threat to ecosystems and human health due to their small size, widespread distribution, and potential for bioaccumulation and toxicity. The comprehensive review explores the current landscape of bioremediation as a sustainable approach for mitigating MNP pollution, emphasizing microbial degradation, enzymatic pathways, and biofilm-mediated interactions. A PRISMA-based systematic review approach was used to filter more than 5,243 peer-reviewed publications from PubMed, Web of Science, and Scopus databases. Based on inclusion criteria including relevance to microbial, enzymatic, or algal degradation of MNPs, experimental validation, and ecological consequences, 20 high-quality research published between 2020 and 2024 were selected for a detailed review. The findings highlight capable microbial strains such as Pseudomonas, Bacillus, and Ideonella sakaiensis, and enzymes such as PETase (polyethylene terephthalate hydrolase) and MHETase (mono(2-hydroxyethyl) terephthalic acid hydrolase) capable of depolymerizing various plastic polymers including PET (polyethylene terephthalate), PE (polyethylene), and PS (polystyrene) at micro-scales and nano-scales. Despite these advancements, significant challenges remain, including limited degradation efficiency, lack of standard testing protocols for MNP biodegradation, and uncertainties regarding ecological safety and long-term effects of intermediate degradation products. The review also identifies significant gaps in field-scale applications, synergistic consortia modeling, and bioinformatics integration for gene-editing approaches to enhance plastic-degrading capabilities. Emerging opportunities include the use of metagenomics, synthetic biology, and nanobiocatalysts to improve the specificity and performance of bioremediation systems. Further research contains interdisciplinary collaborations, standardized environmental risk assessments, and regulatory frameworks to support safe and scalable implementation. The review provides a consolidated platform for scientists, environmental engineers, and policymakers to harness bioremediation technologies in addressing the pressing issue of micro-nano plastic pollution.

Regulation of terephthalic acid metabolism drives the enhancement of PET degradation in Ideonella sakaiensis.

The global rise in plastic production has resulted in extensive environmental accumulation and fragmentation into microplastics and nanoplastics. These persistent particles are now found in aquatic, terrestrial, and atmospheric ecosystems, posing ecotoxicological risks by transporting toxic chemicals, disrupting microbial communities, and entering the food chain, with potential human health impacts. Biodegradation by microorganisms has therefore gained attention as a sustainable remediation strategy. This review examines the role of microorganisms in degrading plastic and microplastics, focusing on enzymatic mechanisms, biotechnological applications, and associated risks. Bacteria such as Ideonella sakaiensis, Pseudomonas, Bacillus, and Rhodococcus exhibit strong degradative abilities via PETase, MHETase, cutinases, and oxidases, often enhanced by biofilm formation. Fungi, including Aspergillus and Penicillium, as well as microalgae, contribute through the production of extracellular enzymes and synergistic interactions. Environmental conditions—such as temperature, pH, salinity, and oxygen levels—directly influence microbial activity and enzyme performance. Biotechnological approaches have improved degradation efficiency through microbial consortia, genetic engineering, and omics-based discovery of novel enzymes. Laboratory-scale applications, including bioreactors and nanoparticle-assisted systems, have achieved higher degradation rates compared to single strains. However, major limitations persist, including microbial stability in natural environments, scalability, and the toxicity of degradation intermediates such as terephthalate and ethylene glycol. Overall, microbial biodegradation offers a promising alternative to conventional treatments but requires careful evaluation of ecological safety and economic feasibility. This review emphasizes the importance of interdisciplinary strategies combining microbiology, biotechnology, and environmental toxicology to advance plastic biodegradation and support sustainable waste management.

Simple SummaryExploring new polyethylene terephthalate (PET)-degrading enzymes is essential for improving the efficiency of PET degradation. Bis(2-hydroxyethyl) terephthalate (BHET) is a key intermediate in the enzymatic depolymerization of PET. In this study, we investigated, for the first time, the BHET degradation activity and thermal stability of the esterase Gs. Our results indicate that Gs exhibits excellent BHET degradation activity; however, it lacks thermal stability during BHET hydrolysis. We performed a comparative structural analysis of the key amino acids involved in the catalysis of BHET and p-nitrophenyl butyrate (pNPB) by Gs using molecular docking. Gs not only demonstrates strong BHET degradation activity but also degrades the PET model substrate bis(benzyloxyethyl) terephthalate (3PET) and PET nanoparticles. Moreover, the combination of Gs and the mono-2-hydroxyethyl terephthalate (MHET) hydrolase, MHETase, can completely hydrolyze BHET. Finally, considering the structural similarity between LCC-ICCG and Gs, this study presents a novel approach to expanding the search for efficient biocatalysts for the degradation of PET plastic.The continuous increase in demand for polyethylene terephthalate (PET) has drawn global attention to the significant environmental pollution caused by the degradation of PET plastics. Exploring new PET-degrading enzymes is essential for enhancing the degradation efficiency of PET, and esterases and lipases with plastic degradation capabilities have become a focal point of research. In this study, we utilized the ultra-efficient mutant FASTase of the PET-degrading enzyme IsPETase, derived from Ideonella sakaiensis, as a positive control, based on the similarity in enzyme activity and substrate. We investigated the PET model substrate degradation activities of the esterase Gs and lipase GI, both derived from Bacillus spp., as well as the lipase CAI derived from Pseudomonas spp. The results indicated that Gs exhibited excellent bis(2-hydroxyethyl) terephthalate (BHET) degradation activity; however, Gs demonstrated a lack of thermal stability when hydrolyzing BHET. Molecular docking analyses were conducted to identify the key amino acids involved in the degradation of BHET by Gs from a structural perspective. At the same time, GI and CAI showed no BHET degradation activity. The combination of Gs and the mono-2-hydroxyethyl terephthalate (MHET) hydrolase, MHETase, can completely hydrolyze BHET, and Gs also exhibited degradation activity against the PET model substrate bis(benzyloxyethyl) terephthalate and PET nanoparticles. Given the structural similarity between PET hydrolase LCC-ICCG and Gs, this study provides new enzyme resources for advancing the efficient biological enzymatic degradation of PET plastics.

The extensive use of pharmaceutical plastics, such as multilayer blister packs and medical packaging, has contributed to persistent plastic pollution due to improper disposal and limited recycling options. This study investigated the biodegradation potential of native bacterial strains isolated from local landfill soil and wastewater sludge. Pseudomonas aeruginosa, Ideonella sakaiensis, and Bacillus subtilis were identified as key strains with selective degradation capacities for polyethylene (PE), PET, and polypropylene (PP), respectively. When combined in a bacterial consortium, these strains showed significantly higher degradation rates compared to individual cultures. Experimental analysis included weight loss measurements, enzyme activity assays, scanning electron microscopy to confirm surface erosion, and CO₂ evolution tests under semi-natural soil microcosm conditions. The results demonstrate that native bacterial consortia can break down pharmaceutical plastics efficiently, producing measurable mineralization and structural damage. This finding suggests that local bacterial communities could be used as a viable biotechnological alternative to supplement traditional plastic waste management strategies, particularly for pharmaceutical packaging. Further research should focus on scaling up this approach through long-term field tests and pilot bioreactor applications to validate its effectiveness under real conditions.

Plastic is a synthetic polymer that consists of high molecular weight. Plastic is prepared from organic compounds first derived from natural gas or renewable sources. There are different types of plastics: Polypropylene (PP), Polyethylene (PE), Polyethylene Terephthalate (PET), etc... The polymeric material takes long time for decompose leading to long term accumulation in landfills and oceans. To overcome the problem, researchers have researched the biodegradation of plastic by Enzymes, including bacteria and fungi, have been identified for their ability to degrade plastics under specific conditions. Recently in biotechnology, a Plastic eating enzyme was identified i.e PETase (polyethylene terepthalate hydrolase) from Ideonella sakaiensis in Japan. This review explores the mechanisms and potential applications of biodegradation of plastic waste and some factors that affect the biodegradation of plastic.

Polyethylene terephthalate (PET), a widely used synthetic polymer in daily life, has become a major source of post-consumer waste due to its complex molecular structure and resistance to natural degradation, which has posed a significant threat to the global ecological environment and human health. Current PET-processing methods include physical, chemical, and biological approaches, however each have their limitations. Given that numerous microbial strains exhibit a remarkable capacity to degrade plastic materials, microbial degradation of PET has emerged as a highly promising alternative. This approach not only offers the possibility of converting waste into valuable resources but also contributes to the advancement of a circular economy. Therefore in this review, it is mainly focused on the cutting-edge microbial technologies and the key role of specific microbial strains such as Ideonella sakaiensis 201-F6, which can efficiently degrade and assimilate PET. Particularly noteworthy are the catalytic enzymes related to the metabolism of PET, which have been emphasized as a sustainable and eco-friendly strategy for plastic recycling within the framework of a circular economy. Furthermore, the study also elucidates the innovative utilization of degraded plastic materials as feedstock for the production of high-value chemicals, highlighting a sustainable path forward in the management of plastic waste.

Ideonella and Thermobifida were the most promising bacterial candidates for degrading plastic polymers. A comparative pan- and phylogenomic analysis of 33 Ideonella and Thermobifida strains was done to determine their plastic degradation potential, niche adaptation and speciation. Our study disclosed that more accessory genes in the strains showed phenotypic plasticity, according to the BPGA data. Pan and core genes were employed for the phylogenetic reconstruction. Pathway enrichment analyses scrutinized the functional roles of the core and adaptive-associated genes. KEGG annotation revealed that most genes were associated with the metabolism of amino acids and carbohydrates. The detailed COG analysis disclosed that approximately 40% of the pan genes performed metabolic functions. The unique gene pool consisted of genes chiefly involved in "general function prediction" and "amino acid transport and metabolism". Our in silico study revealed that these strains could assist in agronomic applications in the future since they devour nitrogen compounds and their central metabolic pathways are involved in amino acid metabolism. The rational selection of strains of Ideonella is far more effective at depolymerising plastics than Thermobifida. A greater number of unique genes, 1701 and 692, were identified for Ideonella sakaiensis 201-F6 and Thermobifida alba DSM-43795, respectively. Furthermore, we examined the singletons involved in xenobiotic catabolism. The unique singleton data were used to construct a supertree. To characterize the conserved patterns, we used SMART and MEME to identify domain and transmembrane regions in the unique protein sequences. Therefore, our study unraveled the genomic insights into the ecology-driven speciation of Ideonella and Thermobifida.

Polyethylene terephthalate (PET), a widely used plastic, is a significant environmental pollutant due to its persistence. While the PET-degrading enzyme PETase from Ideonella sakaiensis offers promising solutions, its limited activity at higher temperatures hinders its practical application. This study aimed to enhance the PETase performance through protein engineering. We introduced multiple amino acid substitutions to the wild-type I. sakaiensis PETase to improve its thermostability, substrate binding, and catalytic activity. Several potential mutant IsPETases were generated using computational design and evaluated in silico. The selected mutant was then produced in E. coli BL21(DE3). Finally, the catalytic activity of the purified mutant IsPETase was examined in vitro using p-nitrophenyl butyrate and PET substrates. IsPETaseMT has been confirmed to be catalytically active and more thermostable with a maximum temperature reaching 60 °C and the T m value increasing up to 15.3 °C compared to the wild-type PETase, IsPETaseWT. IsPETaseMT also showed better degradation toward the PET plastic film in comparison to IsPETaseWT. Thus, these findings demonstrate successful protein engineering to create a more robust PETase for potential plastic waste management applications.

Plastic poses a significant environmental impact due to its chemical resilience, leading to prolonged and degradation times and resulting in widespread adverse effects on global flora and fauna. Cutinases are essential enzymes in the biodegradation process of synthetic polymers like polyethylene terephthalate (PET), which recognized organisms can break down. Here, we used molecular dynamics and binding free energy calculations to explore the interaction of nine synthetic polymers, including PET, with Cutinase from Fusarium oxysporum (FoCut). According to our findings, the polymers poly(ethylene terephthalate) (PET), poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) (PHBH), poly(butylene succinate) (PBS), poly(butylene adipate-co-terephthalate) (PBAT) and poly(ε-caprolactone) (PCL) can bind to the Cutinase enzyme from F. oxysporum, indicating potential biodegradation activity for these polymers. PET exhibited the highest binding affinity (− 34.26 kcal/mol). Besides PET, the polymers PHBH, PBS, PBAT, and PCL also demonstrated significant affinities for the FoCut enzyme, with binding values of − 18.44, − 29.71, − 22.78, and − 22.26 kcal/mol, respectively. Additionally, analysis of the phylogenetic tree of cutinases produced by different organisms demonstrated that even though the organisms belong to different kingdoms, the cutinase from F. oxysporum (FoCut) showed biological similarity in its activity in degrading polymers with the cutinase enzyme from the bacterium Kineococcus radiotolerans and the fungus Moniliophthora roreri. Furthermore, the phylogenetic analysis demonstrated that the PETase enzyme has a very high similarity with the bacterial cutinase enzyme than with the fungal cutinase, therefore demonstrating that the PETase enzyme from Ideonella sakaiensis can easily be a modified bacterial cutinase enzyme that created a unique feature in biodegrading only the pet polymer through an evolutionary process due to its environment and its biochemical need for carbon. Our data demonstrate that bacterial cutinase enzymes have the same common ancestor as the PETase enzyme. Therefore, cutinases and PETase are interconnected through their biological similarity in biodegrading polymers. We demonstrated that important conserved regions, such as the Ser-Asp-His catalytic triad, exist in the enzyme’s catalytic site and that all Cut enzymes from different organisms have the same region to couple with the polymer structures.

Polyethylene terephthalate (PET) has been widely used in plastic products, leading to massive PET waste accumulation in ecosystems worldwide. Efforts to find greener processes for dealing with post-consumer PET waste led to the discovery of PET-degrading enzymes such as Ideonella sakaiensis PETase (IsPETase). In silico studies have provided valuable contributions to this field, shedding light on the catalytic mechanisms and substrate interactions in many PET hydrolase enzymes. However, most of these studies have often relied on short PET oligomers, failing to replicate catalytic-relevant interactions and true substrate motions occurring during contact with a PET-degrading enzyme. A comprehensive atomistic study of PET in both its crystalline (cPET) and amorphous (aPET) states, along with investigation of the adsorption of PET-degrading enzymes onto solid PET, would greatly advance our understanding of mechanisms driving PET biodegradation. In this study, we developed large-scale computational models of cPET, comprising thousands of monomers, and conducted molecular dynamics simulations to follow the transformation of cPET into aPET. Next, these models were validated by comparison with experimentally determined data. We then studied the adsorption of IsPETase on the assembled PET models, investigated the main phenomena that differentiate the two adsorption processes, and explored them from a catalytic perspective. The results and computational PET models provided herein are envisioned to aid in the development of innovative strategies for PET waste biodegradation.

Computational analysis reveals temperature-induced stabilization of FAST-PETase.

Polyethylene terephthalate (PET) plastic is one of the most widely used plastic primarily due to its flexibility, endurance, and low cost. However, the plastics one-time use nature and long degradation time have led to massive waste accumulation, damaging our ecosystem, health, and biodiversity. While previous degradation methods are ineffective due to their high cost and low efficiency, the discovery of two enzymes PETase and MHETase in the bacteria Ideonella sakaiensis to degrade PET and mono(2-hydroxyethyl), a reaction intermediate in PET degradation, respectively, sparked the idea of a sustainable approach to degradation. Ever since, many approaches, including directed evolution, rational protein engineering, and computational redesign strategies, have optimized PETase in terms of its thermostability, catalytic activity, and more. This study proposes the incorporation of newly developed machine learning-based computational tools, including MutCompute, AlphaFold, and DiffDock, into a holistic protein engineering process to predict optimal PETase mutations. Here, in-silico experiments using machine learning tools as well as molecular dynamics simulation and interactions analysis screened for large amounts of PETase mutants in a time and cost-saving manner. Degradation assay coupled with mass analysis and high-performance liquid chromatography techniques then experimentally characterized PETase and its chosen mutants; thus, further screening found the most viable PETase mutant. Using various strategies, the project directly tackles one of the major global issues sustainability by bio-recycling PET. The research also aims to pave the way for introducing a new, imitable process for the more effective and resource-efficient engineering of all proteins.

Boosting extracellular FastPETase production in E. coli: A combined approach of cognate chaperones co-expression and vesicle nucleating peptide tag fusion.

Exploit and elucidate chaperone assisted PET hydrolase for upcycling plastics

β-sheet Engineering of IsPETase for PET Depolymerization

The discovery of novel plastic degrading enzymes commonly relies on comparing features of the primary sequence to those of known plastic degrading enzymes. However, this approach cannot always guarantee success. This is exemplified by the different degradation rates of the two polymers poly(ethylene terephthalate) (PET) and polybutylene succinate (PBS) by two hydrolases: IsPETase from Ideonella sakaiensis and AdCut from Acidovorax delafieldii. Despite the enzymes showing a very high sequence identity of 82%, IsPETase shows significant hydrolysis activity for both polymers, whereas AdCut only shows significant hydrolysis activity for PBS. By solving the structure of AdCut using X-ray crystallography, and using this as the basis for computer simulations, comparisons are made between the differences in the calculated binding geometries and the catalytic results obtained from biochemical experiments. The results reveal that the low activity of AdCut toward PET can be explained by the low sampling of the productive conformation observed in the simulations. While the active site serine in IsPETase can closely encounter the PET carbonyl carbon, in AdCut it cannot: a feature that can be attributed to the shape of the catalytic binding pocket. These results yield an important insight into the design requirements for novel plastic degrading enzymes, as well as showing that computational methods can be used as a valuable tool in understanding the molecular basis for different hydrolysis activities in homologous polyesterase enzymes.

Discovered in 2016, the enzyme PETase, secreted by bacterial Ideonella Sakaiensis 201-F6, has an excellent hydrolytic activity toward poly(ethylene terephthalate) (PET) at room temperature, while it decreases at higher temperatures due to the low thermostability. Many variants have been engineered to overcome this limitation, which hinders industrial application. In this work, we systematically compare PETase wild-type (WT) and four mutants (DuraPETase, ThermoPETase, FastPETase, and HotPETase) using standard molecular dynamics (MD) simulations and unbinding free energy calculations. In particular, we analyze the enzymes' structural characteristics and binding to a tetrameric PET chain (PET4) under two temperature conditions: T1─300 K and T2─350 K. Our results indicate that (i) PET4 forms stable complexes with the five enzymes at room temperature (∼300 K) and (ii) most of the interactions are localized close to the active site of the protein, where the W185 and Y87 residues interact with the aromatic rings of the substrate. Specifically, (iii) the W185 side-chain explores different conformations in each variant (a phenomenon known in the literature as "W185 wobbling"). This suggests that the binding pocket retains structural plasticity and flexibility among the variants, facilitating substrate recognition and localization events at moderate temperatures. Moreover, (iv) PET4 establishes aromatic interactions with the catalytic H237 residue, stabilizing the catalytic triad composed of residues S160-H237-D206, and helping the system achieve an effective configuration for the hydrolysis reaction. Conversely, (v) the binding affinity decreases at a higher temperature (∼350 K), retaining moderate interactions only for HotPETase. Finally, (vi) MD simulations of complexes formed with poly(ethylene-2,5-furan dicarboxylate) (PEF) show no persistent interactions, suggesting that these enzymes are not yet optimized for binding this alternative semiaromatic plastic polymer. Our study offers valuable insights into the structural stability of these enzymes and the molecular determinants driving PET binding onto their surfaces, sheds light on the mechanistic steps that precede the onset of hydrolysis, and provides a foundation for future enzyme optimization.

Understanding all parameters contributing to enzyme activity is crucial in enzyme catalysis. For enzymatic PET degradation, this involves examining the formation of the enzyme-PET complex. In IsPETase (WT), a PET-degrading enzyme from Ideonella sakaiensis, mutating two non-catalytic residues (DM) significantly enhances activity. Such mutations, depending on their position in the tertiary structure, fine-tune enzyme function. However, detailed molecular insights into these mutations' structure-function relationship for PET degradation are lacking. This study characterizes IsPETase's catalytic ability compared to WT TfCut2 using molecular dynamics simulations and quantum mechanical methods. We explore the conformational landscape of the enzyme-PET complex and quantify residue-wise interaction energy. Notably, aromatic and hydrophobic residues Tyr, Trp, and Ile in the catalytic subsite S1, and aromatic Phe and polar Asn in the anchoring subsite S3, crucially optimize PET binding. These residues enhance PET specificity over non-aromatic plastics. Our findings suggest that the balance between binding at subsite S1 and subsite S3, which is influenced by cooperative mutations, underlies catalytic activity. This balance shows a positive correlation with experimentally obtained kcat/Km values: WT TfCut2<WT IsPETase≪DM IsPETase.

Engineering dual-functional and thermophilic BMHETase for efficient degradation of polyethylene terephthalate