{"title":"Rosa damascena-derived exosome-like nanovesicles inhibit Salmonella enterica via membrane disruption, oxidative stress, and virulence suppression.","authors":"Subhashini Brahadeeswaran, Ramasamy Tamizhselvi","doi":"10.1007/s11274-026-05274-5","DOIUrl":"10.1007/s11274-026-05274-5","url":null,"abstract":"<p><p>Plant-derived exosome-like nanoparticles (P-DENs) have emerged as promising bio-nanocarriers with antimicrobial potential. In this study, we isolated and characterized exosome-like nanovesicles from Rosa damascena and evaluated their antibacterial efficacy against Salmonella enterica, a significant foodborne pathogen. Rosa damascena-derived exosomes-like nanovesicles (R-DENs) exhibited 8.9 × 10<sup>9</sup> particles/mL in nanoparticle tracking analysis. Growth assays revealed significant inhibition of bacterial proliferation (63.52%). Propidium iodide (PI) staining in flow cytometry demonstrated concentration-dependent bacterial cell death (65.78%), while scanning electron microscopy (SEM) visualized distinct ultrastructural damage to the bacterial envelope, confirming membrane disruption as a primary antibacterial mechanism. Consistent with these effects, R-DENs markedly reduced biofilm formation (69.88%) and suppressed exopolysaccharide (EPS) production (69.10%). Elevated intracellular reactive oxygen species (ROS) levels (up to 65.37%) further indicated oxidative stress as a major antibacterial contributor. Moreover, R-DENs treatment impaired bacterial adhesion (77.88%) and invasion (67.37%) in L929 fibroblasts, correlating with attenuation of pathogenicity. Gene expression analysis confirmed significant downregulation of biofilm- and virulence-associated genes (fimA, csgD, bcsA, rsmA, and rpoS), linking the phenotypic changes to molecular interference with pathogenic pathways. Collectively, these findings demonstrate that R-DENs exert multifaceted antibacterial activity through membrane disruption, biofilm and EPS inhibition, ROS generation, and suppression of virulence traits, underscoring their potential as natural, biocompatible nanotherapeutics against drug-resistant bacterial infections.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"42 10","pages":""},"PeriodicalIF":4.7,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149018130","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Development of a lactose-complemented antibiotic-free host-vector platform for stable enzyme expression in Limosilactobacillus fermentum 217 - 82.","authors":"Ruize Xu, Junlin Li, Fangyu Guo, Weiyan Wang, Chen Yang, Zhenshang Xu, Ting Wang","doi":"10.1007/s11274-026-05266-5","DOIUrl":"10.1007/s11274-026-05266-5","url":null,"abstract":"<p><p>Food-grade microbial bioprocessing requires genetically stable and antibiotic-free host-vector systems that are compatible with food-related applications. However, the use of Limosilactobacillus fermentum as a biomanufacturing chassis is limited by inefficient DNA delivery and the lack of strain-adapted food-grade selection strategies. In this study, a proof-of-concept, lactose-complemented antibiotic-free host-vector framework was established in L. fermentum 217 - 82. An efficient electrotransformation protocol was first established as an enabling step for host engineering, yielding a transformation efficiency of 7.50 × 10⁵ CFU/µg DNA. The genes lacM and lacLM were individually targeted to validate their involvement in lactose utilization, and subsequent gene inactivation experiments confirmed their utility as effective markers for metabolic complementation. Antibiotic-free shuttle vectors were constructed by combining lacZα-assisted plasmid screening in E. coli with host-specific lacM/lacLM-mediated lactose complementation in L. fermentum. The resulting recombinant strains maintained plasmid stability during serial passage and supported functional heterologous expression of cis-proline 4-hydroxylase. Functional validation using cis-proline 4-hydroxylase confirmed that the platform supported whole-cell L-proline-to-hydroxyproline bioconversion, with hydroxyproline production reaching 147.62 µg/mL. These findings demonstrate the feasibility of integrating lactose-dependent selection, stable antibiotic-free plasmid maintenance, functional heterologous enzyme expression, and whole-cell bioconversion within a strain-adapted host-vector framework in L. fermentum 217 - 82. Although broader applicability remains to be validated using additional heterologous proteins and process conditions, the established framework provides a methodological basis for the future development of more generally applicable antibiotic-free expression platforms in L. fermentum.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"42 10","pages":""},"PeriodicalIF":4.7,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149018170","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mateusz Maździarz, Katarzyna Bilska, Katarzyna Krawczyk, Patryk Wiśniewski, Paulina Staniszewska, Tomasz Kulik
{"title":"ZymoR: Bridging plant pathology and automated bioinformatics for fungicide resistance profiling in Zymoseptoria tritici.","authors":"Mateusz Maździarz, Katarzyna Bilska, Katarzyna Krawczyk, Patryk Wiśniewski, Paulina Staniszewska, Tomasz Kulik","doi":"10.1007/s11274-026-05287-0","DOIUrl":"10.1007/s11274-026-05287-0","url":null,"abstract":"<p><p>Zymoseptoria tritici, the causal agent of Septoria tritici blotch (STB), is one of the most destructive fungal pathogens of wheat worldwide. The extensive use of fungicides has driven the emergence of diverse resistance mechanisms involving multiple target-site genes, as well as non-target-site resistance. High-throughput sequencing (HTS) technologies now enable large-scale detection of resistance-associated genetic variation, yet routine implementation of HTS-based monitoring remains constrained by the lack of standardized analytical workflows and tools that translate sequence data into biologically meaningful resistance information. Here, we present ZymoR, a dedicated bioinformatics platform for automated molecular surveillance of fungicide resistance in Z. tritici. ZymoR integrates sequence quality assessment, mutation detection and CYP51 haplotype classification within a single user-friendly workflow. The platform incorporates a curated and expandable database of resistance-associated variants across the principal fungicide target genes, enabling standardized annotation of known resistance markers while facilitating the identification of previously undescribed variants. Unlike conventional variant-calling pipelines, ZymoR links detected genetic variation to standardized nomenclature and resistance-associated metadata, substantially reducing the bioinformatic expertise required for data interpretation. The ZymoR package was made available as an open-source tool via GitHub at https://github.com/Mordziarz/ZymoR .</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"42 10","pages":""},"PeriodicalIF":4.7,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13593640/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149017441","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Lan Chen, Wang Ke, Hongxin Su, Zixuan Wang, Yufei Mao, Zhongzeng Su, Linke Zhang, Yan Guo, Xiaohui Hong, Hui Ye, Ruizhe Feng, Lingyi Luo, Fuyong Lin, Tianpei Huang
{"title":"Formulation-dependent sugar regulation enhances biofilm-mediated stability and bioactivity of Bacillus thuringiensis formulations.","authors":"Lan Chen, Wang Ke, Hongxin Su, Zixuan Wang, Yufei Mao, Zhongzeng Su, Linke Zhang, Yan Guo, Xiaohui Hong, Hui Ye, Ruizhe Feng, Lingyi Luo, Fuyong Lin, Tianpei Huang","doi":"10.1007/s11274-026-05280-7","DOIUrl":"10.1007/s11274-026-05280-7","url":null,"abstract":"<p><p>Sugars are important carbon sources involved in microbial growth and functional regulation. However, how sugars with different structural characteristics regulate microbial pesticide performance in complex formulation systems remains unclear. In this study, Bacillus thuringiensis (Bt) formulations were used to systematically evaluate the effects of different sugars on functional traits. The results showed pronounced type-dependent regulatory effects. Sugars with distinct structural features modulated biofilm formation by affecting cell adhesion and extracellular polysaccharide production. An optimized sugar combination increased biofilm yield by approximately tenfold. Certain sugars further enhanced UV tolerance and insecticidal activity. For example, pectin increased the survival rate of suspension concentrates by 5.3-fold after 4 h of UV exposure, while glucose, glycerol, and maltose improved insecticidal activity by 2.72-3.91-fold. Further analysis indicated that sugar structural characteristics are critical determinants of their regulatory effects, influencing bacterial surface interactions and the microenvironment. This biofilm-centered mechanism showed consistency across different formulation types. Overall, this study provides new insights into the development of stable and efficient Bt-based biopesticides.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"42 10","pages":""},"PeriodicalIF":4.7,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149018132","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
W Monroy-Martínez, J C González-Hernández, M C Chávez-Parga
{"title":"Beyond monoculture limits: a critical review of yeast co-cultures for xylitol production from lignocellulosic biomass : Yeast co-cultures for xylitol production.","authors":"W Monroy-Martínez, J C González-Hernández, M C Chávez-Parga","doi":"10.1007/s11274-026-05268-3","DOIUrl":"10.1007/s11274-026-05268-3","url":null,"abstract":"<p><p>The biotechnological production of xylitol from lignocellulosic biomass residues offers a sustainable alternative to traditional chemical synthesis; however, its industrial implementation is limited by the metabolic constraints of conventional microbial monocultures. This review examines the limitations of monocultures, highlighting how redox cofactor imbalances, glucose-induced catabolic repression, and the toxicity of furanic inhibitors and organic acids in crude hydrolysates create energetic and metabolic challenges that reduce yields and volumetric productivity. To overcome these biological limitations, it is necessary to shift toward co-culture engineering based on the principle of division of labor (DoL). Key synergistic mechanisms, including in situ detoxification, parallel utilization of pentose and hexose mixtures, and metabolite exchange (cross-feeding), which distribute metabolic functions among specialized strains, expanding metabolic diversity and optimizing carbon valorization, are analyzed. Implementing control strategies that maintain coordinated fluxes is critical to positioning consortia as a viable and profitable platform for xylitol production.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"42 10","pages":""},"PeriodicalIF":4.7,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149018129","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yuehang Zhu, Shuoshuo Wu, Jun Li, Baowei Hu, Guixin Chu, Rui Tao
{"title":"Asynchronous recovery of canonical ammonia oxidizers and comammox drives post-drought N<sub>2</sub>O emissions in contrasting soils.","authors":"Yuehang Zhu, Shuoshuo Wu, Jun Li, Baowei Hu, Guixin Chu, Rui Tao","doi":"10.1007/s11274-026-05260-x","DOIUrl":"10.1007/s11274-026-05260-x","url":null,"abstract":"<p><p>Intensifying drought regimes driven by global climate change pose a severe threat to soil nitrogen cycling stability. While the metabolic responses of microbes to stress are documented, the mechanisms linking the differential resilience of nitrifying guilds to post-drought nitrous oxide (N<sub>2</sub>O) pulses remain elusive. Here, we investigated the recovery dynamics of ammonia-oxidizing archaea (AOA), bacteria (AOB), and comammox Nitrospira alongside temporal N<sub>2</sub>O emission pulses in contrasting acidic and alkaline soils following common drought and extreme drought. Treatment effects and community structural divergence were evaluated using permutational multivariate analysis of variance (PERMANOVA). Post-drought response patterns differed among guilds: AOA and AOB exhibited marked population fluctuations, signaling a resilience-based recovery, whereas comammox Nitrospira demonstrated greater abundance stability, maintaining stable abundance in both soils throughout the 60-day incubation. Community reassembly was primarily governed by soil pH, which acted as a divergent environmental filter; specifically, acidic conditions favored the dominance of AOA and comammox, whereas alkaline conditions selectively promoted AOB proliferation. Critically, N<sub>2</sub>O emissions correlated with recovery patterns among the specific nitrifier guilds. Random forest modeling demonstrated that comammox was the primary driver of emissions during the rapid \"early recovery\" phase of rewetting, while the delayed resurgence of AOA and AOB sustained N<sub>2</sub>O production in the later stages, revealing the asynchronous recovery of these guilds modulated the temporal duration of nitrification-derived N<sub>2</sub>O fluxes. This study highlights how the temporal niche differentiation of nitrifiers regulates the magnitude and duration of nitrogen losses following extreme drought events.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"42 10","pages":""},"PeriodicalIF":4.7,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149018173","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nguyen Thi Tam Thu, Le Thi Nhi-Cong, Tran Thi Huyen Nga, Pham Kien Cuong, Le Minh Tri
{"title":"Polyhydroxyalkanoate synthesis ability of the salt-tolerant bacterial strain Salinicola lusitanus BTNC26 isolated from the coastal zone in Vietnam and its application in food packaging film production.","authors":"Nguyen Thi Tam Thu, Le Thi Nhi-Cong, Tran Thi Huyen Nga, Pham Kien Cuong, Le Minh Tri","doi":"10.1007/s11274-026-05273-6","DOIUrl":"10.1007/s11274-026-05273-6","url":null,"abstract":"<p><p>Recently, polyhydroxyalkanoates (PHAs) have attracted increasing attention as biodegradable alternatives to conventional petroleum-based plastics. This study aimed to identify bacterial strains synthesizing poly(3-hydroxybutyrate) (PHB) from coastal areas of Vietnam. Strain BTNC26, isolated as a PHA producer, was identified as Salinicola lusitanus BTNC26 via 16S rRNA gene sequencing (GenBank: PZ087081). Optimization of carbon (glucose) and nitrogen (yeast extract) sources, pH (7), temperature (30 °C), and NaCl (5%) enhanced cell growth and PHA accumulation. Under these conditions, biopolymer yield reached 73.07% after 96 h. FTIR, GC-MS, and NMR analyses confirmed that the extracted polymer was PHB: FTIR showed a carbonyl peak at 1710.52 cm⁻<sup>1</sup>; <sup>1</sup>H/<sup>13</sup>C NMR revealed resonances at 169.14 (C = O), 67.62 (-CH-), 40.80 (-CH₂-), and 19.76 ppm (-CH₃); GC-MS displayed the 3-hydroxybutyric acid methyl ester molecular ion. Scale-up fermentation (200 mL to 100 L) with 10 g/L glucose supplementation yielded PHB concentrations of 4.76, 4.23, 3.98, and 3.59 g/L at 200 mL, 1 L, 5 L, and 100 L, respectively. Composite films prepared from extracted PHB blended with PBAT, CaCO₃, PEG, and glycerol formed thin, strong, and flexible films. Their biodegradability was confirmed by laboratory seawater degradation assays. These findings highlight the potential of the halophilic bacterium S. lusitanus for PHB production and biodegradable plastic applications in marine environments, and provide a basis for further scale-up and industrial development.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"42 10","pages":""},"PeriodicalIF":4.7,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149018196","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Maria Claudia Gatto, Flora Cozzolino, Laura Vitale, Fortunato Palma Esposito, Paola Cicatiello, Donatella de Pascale, Maria Monti
{"title":"Multi-omics insights into bacterial and fungal bioremediation of Potentially Toxic Elements (PTEs): a critical overview of their applications.","authors":"Maria Claudia Gatto, Flora Cozzolino, Laura Vitale, Fortunato Palma Esposito, Paola Cicatiello, Donatella de Pascale, Maria Monti","doi":"10.1007/s11274-026-05253-w","DOIUrl":"10.1007/s11274-026-05253-w","url":null,"abstract":"<p><p>Potentially toxic elements (PTEs) are persistent contaminants of terrestrial and aquatic ecosystems and heavy metals and metalloids represent a major environmental and health concern. Microbial bioremediation exploits the ability of bacteria, fungi, and microbial communities to modulate PTE fate through processes including biosorption, bioaccumulation, redox transformation, biomineralization, precipitation, chelation, and extracellular sequestration. This review examines the major advances of the last decade in the application of genomics, transcriptomics, proteomics, and metabolomics and their integration, to investigate molecular mechanisms of microbial adaptation to PTE contamination, supporting the selection of suitable microorganisms or microbial communities and the development of more effective bioremediation strategies. Genomic and metagenomic analyses enable the identification of genes and gene families associated with PTE resistance and adaptation, revealing both metal-specific and more general responses according to the presence of operons and/or cluster genes. Transcriptomic and proteomic approaches are applied to validate genetic potentialities, identifying mechanisms and protein mediators for transport, detoxification, redox homeostasis, and metal interactions. Metabolomics complements these approaches by characterizing metabolites involved in microbial responses, including organic acids, siderophores, biosurfactants, and extracellular polymeric substance-associated compounds. The review also discusses the advantages, limitations, and complementarity of the different omics approaches, emphasizing their impact in feasibility to move from ex situ to in situ applications. Finally, the review also addresses how omics layers could be combined across the phases of a real bioremediation project (screening, implementation, monitoring), highlighting integrated multi-omics approaches as powerful tools for developing and optimizing effective bioremediation strategies.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"42 10","pages":""},"PeriodicalIF":4.7,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13593802/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149018194","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mohtasim Fuad, Muhammad Fazle Rabbee, Zimam Mahmud, Kwang-Hyun Baek
{"title":"Role of extended-spectrum β-lactamase (ESBL) genes in the dissemination of β-lactam resistance within aquatic environments: mechanisms, persistence, and one health implications.","authors":"Mohtasim Fuad, Muhammad Fazle Rabbee, Zimam Mahmud, Kwang-Hyun Baek","doi":"10.1007/s11274-026-05258-5","DOIUrl":"10.1007/s11274-026-05258-5","url":null,"abstract":"<p><p>Antimicrobial resistance of pathogenic bacteria has rapidly increased over the past 20 years, creating a major global health threat. Extended-spectrum β-lactamases (ESBLs) are major drivers of resistance to β-lactam antibiotics, hydrolyzing broad-spectrum cephalosporines and monobactams. ESBL-producing Enterobacteriaceae are widespread across aquatic environments. While previous reviews have broadly described clinical ESBL epidemiology, a comprehensive synthesis explicitly linking aquatic microenvironmental niches, mobile genetic element dynamics, and environmental selection mechanisms remains lacking. This review addresses this gap by critically evaluating how aquatic environments function as active evolutionary reactors rather than mere passive sinks. The dissemination of these ESBL genes depends on conjugative plasmids, insertion sequences, and transposons. Specifically, insertion sequence ISEcp1 mobilizes and enhances the expression of blaCTX-M genes through transposition and strong promoter activity, while IS26 promotes the capture, rearrangement and accumulation of multi-drug resistance determinants within plasmids and transposons. ESBL genes persist in both intracellular and extracellular forms within sediments, biofilms, and microplastic-associated habitats. This review describes the prevalence, mobility, dissemination mechanisms, and environmental-clinical connectivity of ESBL determinants in aquatic systems.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"42 10","pages":""},"PeriodicalIF":4.7,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149018152","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Structural analysis of Sphingobium yanoikuyae P4 carboxylesterase reveals conformational and catalytic determinants for PET biodegradation.","authors":"Sunidhi Bhatt, Yusuf Akhter, Subhankar Chatterjee","doi":"10.1007/s11274-026-05276-3","DOIUrl":"10.1007/s11274-026-05276-3","url":null,"abstract":"<p><p>The accumulation of poorly biodegradable polyethylene terephthalate (PET) in the environment has become an emerging ecological and health problem, with a strong need to develop environmentally friendly, biobased degradation methods. This in silico study demonstrates the structural and mechanistic characterization of a carboxylesterase from the phthalate-degrading Sphingobium yanoikuyae P4 for its potential to catalyze the hydrolysis of PET. Sequence analysis of the amino acid residues revealed the conserved α/β-hydrolase fold and the sequence motifs GXSXG and GGX, typical of PET-active enzymes, with evolutionary conservation of the active-site residues. Structural similarity to known PET hydrolases, such as a carboxylesterase from Thermobifida fusca and lipase from Streptomyces exfoliatus, suggested the conservation of the catalytic scaffold. The defined PET backbone oligomer and the hydrolysis intermediates BHET and MHET docked at the same catalytic site with the scissile ester in an ideal conformation for the nucleophilic attack of the Ser215-His418-Glu332 catalytic triad and also stabilized by the Gly217 oxyanion hole. Further, the molecular dynamics simulation for 500 ns supported the stability of the catalytic core of the enzyme-substrate complex, and MM/PBSA revealed a binding free energy of -14.03 kcal/mol, which was strongly affected by van der Waals interactions. Free-energy landscape and principal-component analyses found a flexible, low-energy dominant state in which the loop is mobile, and DFT single-point calculations showed that the catalytic center is electronically well-defined and preorganized. Collectively, these analyses indicate that S. yanoikuyae P4 carboxylesterase possesses the structural and mechanistic prerequisites for PET hydrolysis, providing a candidate scaffold for further experimental and protein-engineering studies.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"42 10","pages":""},"PeriodicalIF":4.7,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149017465","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}