Bioresources and Bioprocessing最新文献

{"title":"Engineered phenylalanine hydroxylase coupled with an effective cofactor synthesis and regeneration system for high-yield production of 5-hydroxytryptophan.","authors":"Yulin Ai, Yusong Huang, Hongru Zhao, Bingmei Su, Juan Lin","doi":"10.1186/s40643-025-00846-z","DOIUrl":"10.1186/s40643-025-00846-z","url":null,"abstract":"<p><p>5-Hydroxytryptophan (5-HTP) is widely used as a natural remedy for sleep disorders. In terms of biosafety, bio-derived 5-HTP is preferred over chemically synthesized 5-HTP. However, the low titer of 5-HTP in the reported microbiological methods (< 10 g/L) limits the industrialization of 5-HTP biosynthesis. In the present study, a Trp-accumulating E. coli strain TRP1 was constructed by blocking the degradation path (ΔtnaA), branching paths (ΔpheA, ΔtyrA) and repression system (ΔtrpR, ΔtrpL). Next, the hydroxylation module employing a phenylalanine hydroxylase mutant XcPAH^W179F (XC2) coupled with an MH4 regenerating system (CvPCD-EcFolM system) was screened to convert L-Trp into 5-HTP. Protein engineering was performed on hydroxylase XC2 based on the molecular dynamics simulation of the enzyme-substrate complex, and the strain TRP1-XC4 harboring the triple-mutant XcPAH^{L98I/A129K/W179F} (XC4) was able to produce 319.4 mg/L 5-HTP. Genome editing was carried out focused on accelerating product efflux (strengthening YddG) and increasing MH4 supply (strengthening FolM, FolE and FolX), resulting in a strain TRP5-XC4 to produce 13.9 g/L 5-HTP in 5 L fed-batch fermentation with a space-time yield of 0.29 g/L/h, which is the highest production and productivity record for 5-HTP biosynthesis. This study successfully provided an engineered strain and an efficient green method for the industrial synthesis of 5-HTP.</p>","PeriodicalId":9067,"journal":{"name":"Bioresources and Bioprocessing","volume":"12 1","pages":"15"},"PeriodicalIF":4.3,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143565951","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":"Membrane fractionation of hydrolysates of the water-soluble protein from tuna fish meal obtained by subcritical water and enzymatic treatments. Comparison of physical and chemical properties.","authors":"Pedro Barea, Alba Ester Illera, Helena Candela, Rodrigo Melgosa, José Manuel Benito, Sagrario Beltrán, María Teresa Sanz","doi":"10.1186/s40643-025-00850-3","DOIUrl":"10.1186/s40643-025-00850-3","url":null,"abstract":"<p><p>Two different hydrolysates of the water-soluble protein (WSP) fraction from tuna fish meal were obtained by subcritical water-CO₂ (subW-CO₂) and Alcalase^® treatments. Hydrolysates showed different chemical composition regarding their free amino acid (FAA) profile and molecular weight distribution of the peptides generated. Consequently, different strategies were proposed by using a stirred dead-end filtration system equipped with flat sheet membranes. Two nanofiltration (NF) consecutive steps were proposed for fractionation of subW-CO₂ hydrolysates with polyamide membranes (800-600 Da and 300-150 Da) yielding a first retentate where 79% of the protein fraction was retained, while 92% of FAA were retained in the second step with a purity index of 29%. Alcalase^® hydrolysates were fractionated by ultrafiltration (UF, 10 kDa) followed by NF (1-1.1 kDa) with polyethersulfone membranes obtaining a first retentate with more than 65% of protein fraction retention with a purity index of 50%. A relatively wide molecular weight distribution was observed in all streams, with high antioxidant and iron-chelating capacities in the retentate fractions.</p>","PeriodicalId":9067,"journal":{"name":"Bioresources and Bioprocessing","volume":"12 1","pages":"16"},"PeriodicalIF":4.3,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143565967","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":"Unraveling the multiple interactions between phages, microbes and flavor in the fermentation of strong-flavor Baijiu.","authors":"Huadong Zhang, Hongxia Zhang, Hai Du, Yan Zhang, Menghui Zhang, Xiaowei Yu, Yan Xu","doi":"10.1186/s40643-025-00852-1","DOIUrl":"10.1186/s40643-025-00852-1","url":null,"abstract":"<p><p>The fermentation process of strong-flavor Baijiu represents a complex and unique ecosystem, characterized by the involvement of various microorganisms that drive intricate biochemical reactions, ultimately contributing to the distinct flavor profile of the Baijiu. Viruses may affect the succession of microorganisms and thus affect the style and quality of the product. However, the interaction between viruses and microorganisms during the fermentation of Baijiu is still unclear. Here we combined viral metagenomics and amplicon sequencing, physicochemical analysis, and GC-MS detection with temporal sampling to study the dynamics of viral and microbial communities, physicochemical properties, and flavor compounds during strong-flavor Baijiu fermentation. Viral metagenomic analysis revealed 513 viral operational taxonomic units (vOTUs), encompassing 34 viral families. Principal coordinates analysis (PCoA) demonstrated significant differences in vOTUs at different fermentation stages. Notably, the microbial community exhibited distinct succession patterns at various fermentation stages; it changed rapidly during the initial five days, with similarities observed between days 10 and 20. Volatile profile analysis identified 38 flavor components in fermented grains, comprising 16 ester compounds, 11 alcohols, and 8 acids, with the majority formed between days 10 and 30. The Spearman's rank correlation analysis revealed that Peduoviridae exhibited a negative correlation with Gluconobacter. Genomoviridae showed a negative correlation with Issatchenkia, Penicillium, and Monascus. These findings highlight the potential for complex interactions between viruses and microbial communities during Baijiu fermentation, underscoring the importance of considering viral communities in studies of the microbial ecology of fermented foods.</p>","PeriodicalId":9067,"journal":{"name":"Bioresources and Bioprocessing","volume":"12 1","pages":"14"},"PeriodicalIF":4.3,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11883080/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143555873","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}

{"title":"Comparative evaluation of free radical scavenging activity and total metabolite profiles among 30 macrofungi species.","authors":"Tetiana Krupodorova, Victor Barshteyn, Yusufjon Gafforov, Milena Rašeta, Tetiana Zaichenko, Yaroslav Blume","doi":"10.1186/s40643-025-00841-4","DOIUrl":"10.1186/s40643-025-00841-4","url":null,"abstract":"&lt;p&gt;&lt;p&gt;The high antioxidant content of mushrooms such as polyphenols, polysaccharides, carotenoids, ergothioneine, glutathione, vitamins, and other compounds, has sparked interest in their potential use in preventive and therapeutic medicine. Therefore, this study aimed to evaluate the antioxidant potential of various macrofungi by measuring 1,1-diphenyl-2-picryl-hydrazyl (DPPH) radical scavenging activity and quantifying two classes of compounds: phenolics (TPC) and polysaccharides, both endo- (IPS) and exopolysaccharides (EPS). Species-specific abilities to produce mycelium, polysaccharides, and polyphenols were observed under submerged cultivation without agitation over 14 days. Mycelium productivity (P&lt;sub&gt;M&lt;/sub&gt;) ranged significantly from 292 ± 11 to 1110 ± 37 mg·L⁻&lt;sup&gt;1&lt;/sup&gt;·day⁻&lt;sup&gt;1&lt;/sup&gt;, with the highest values observed in Ophiocordyceps sinensis (1110 ± 37 mg·L⁻&lt;sup&gt;1&lt;/sup&gt; ·day⁻&lt;sup&gt;1&lt;/sup&gt;), Pleurotus djamor (1090 ± 14 mg·L⁻&lt;sup&gt;1&lt;/sup&gt;·day⁻&lt;sup&gt;1&lt;/sup&gt;), and Cordyceps militaris (1080 ± 90 mg· L⁻&lt;sup&gt;1&lt;/sup&gt;·day⁻&lt;sup&gt;1&lt;/sup&gt;). The DPPH inhibition values of the extracts varied from 4.30 ± 0.20 to 87.9 ± 0.80%, while TPC ranged from 0.35 ± 0.10 to 34.6 ± 0.80 mg GAE/g d.w. Lentinula edodes was the best source of produced IPS (10.3 ± 0.35 g·L&lt;sup&gt;-1&lt;/sup&gt;), while Hypsizygus marmoreus exhibited the highest EPS content (2.24 ± 0.30 g·L&lt;sup&gt;-1&lt;/sup&gt;). Overall, IPS levels across species were higher, ranging from 1.56 to 10.3 g·L&lt;sup&gt;-1&lt;/sup&gt;. In half of the fungal species, the mycelium exhibited superior antioxidant activity compared to culture broth. However, in the majority (66.7%), TPC was higher in the culture broth than in the fungal mycelium. Distinct scavenging abilities and metabolite profiles were observed among different isolates. Notably, the mycelium of Fomitopsis pinicola and L. edodes showed the highest DPPH inhibition and TPC. The antioxidant activity and TPC varied depending on the culture medium, and solvents used. The highest DPPH inhibition (90%) and TPC (38.5 ± 0.40 mg GAE/g d.w.) were observed in the methanol (MeOH) extract of F. pinicola mycelium grown in Sabouraud dextrose medium. Similarly, MeOH and ethyl acetate (EtOAc) extracts demonstrated strong DPPH inhibition (over 87%), while the maximum TPC (40.0 ± 0.60 mg GAE/g d.w.) was detected in the water (H&lt;sub&gt;2&lt;/sub&gt;O) extract of L. edodes mycelium cultivated in glucose-peptone-yeast medium. A positive correlation was found between TPC and antioxidant activity, with Pearson's coefficient of 0.6615 for fungal mycelium, 0.1192 for culture broth, and 0.8924 and 0.7143 for F. pinicola and L. edodes, respectively. Both fungal mycelium and culture broth exhibit significant potential as natural antioxidants. These can be applied in nutraceuticals, food products, and nutritional supplements, offering diverse health benefits. Additionally, this study is a pioneering exploration of Auriporia aurea, Hohenbuehelia myxotricha, Lepista luscina, Oxyporus obducens, and Pseudospong","PeriodicalId":9067,"journal":{"name":"Bioresources and Bioprocessing","volume":"12 1","pages":"13"},"PeriodicalIF":4.3,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11845661/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143466421","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}

{"title":"Enhancing thermostability of Moloney murine leukemia virus reverse transcriptase through greedy combination of multiple mutant residues.","authors":"Youhui Yang, Jie Zhang, Zhong Li, Hao Qi","doi":"10.1186/s40643-025-00845-0","DOIUrl":"10.1186/s40643-025-00845-0","url":null,"abstract":"<p><p>Reverse transcription is crucial in bioengineering and biomedical fields, particularly for genome sequencing and virus diagnosis. Enhancing the thermostability of reverse transcriptase can significantly improve its efficiency and accuracy by enabling it to function at higher temperatures, thereby reducing RNA secondary structures and minimizing interference from contaminating enzymes, particularly in clinical samples. Here, using a combinatorial strategy, a variant of Moloney Murine Leukemia Virus reverse transcriptase (MMLV RT) with improved activity across a wide temperature range (30-50 °C) was identified and maintained 100% activity after incubation at 50 °C for 10 min. Eleven hot-spot residues were mutated in various combinations, and the mutant proteins were rapidly expressed in a cell-free system for reverse transcription activity testing. Variant M5, which carries five mutated residues (E47K/E280R/T284R/L413G/D631V), exhibited enhanced thermostability and activity compared to any variant with a single residue mutation. Using purified recombinant protein for precise characterization, the melting temperature (Tm) of M5 increased by 4.7 °C when assembled with a nucleotide template-primer (T/P). Consequently, the half-life of M5 at 50 °C extended to approximately 60 min, in contrast to less than 4 min for the wild type. These findings demonstrate that the epistasis of combining multiple mutant residues holds excellent potential for significantly enhancing enzyme activity, even with existing knowledge. This heat-stable MMLV RT variant M5 may potentially improve efficiency and accuracy in molecular biology research and clinical diagnostics.</p>","PeriodicalId":9067,"journal":{"name":"Bioresources and Bioprocessing","volume":"12 1","pages":"12"},"PeriodicalIF":4.3,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11842686/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143466426","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}

{"title":"Antibacterial and physicomechanical properties of cellulosic nonwovens functionalized with chitosan: a study on interaction effects of influencing factors and assessment methods.","authors":"Esubalew Kasaw Gebeyehu, Rekha Shresth, Tonmoy Saha, Jenni Tienaho, Ulla Jauhiainen, Ali Amin Tarhini, Ali Reza Tehrani-Bagha","doi":"10.1186/s40643-025-00843-2","DOIUrl":"10.1186/s40643-025-00843-2","url":null,"abstract":"<p><p>The growing demand for antimicrobial textiles and environmental concerns over synthetic agents have driven interest in biobased agents like chitosan, an eco-friendly alternative reported with variable effectiveness on textiles. This research investigates the effects of chitosan's molecular weight, concentration, treatment method, and their interaction effects on the antibacterial and physicomechanical properties of cellulosic nonwovens. The role of culture medium dynamics in antibacterial testing was also examined. Chitosan with low (30 kDa), medium (250 kDa) and high (2100 kDa) molecular weights at concentrations of 1 to 15 g/L was applied using pad-dry and dip-dry methods, with dip coating resulting in higher chitosan deposition. Antibacterial activity against Escherichia coli (E. coli) was assessed using three methods: agar diffusion, a luminescent bacterial biosensor assay, and log reduction of colony-forming units (CFU/mL) in a time-kill test. While the first two test methods showed no antibacterial effect, CFU/mL revealed significant activity with interaction effects showing that the dip-coated, 30 kDa chitosan above a concentration of 5 g/L achieved complete bacterial reduction. The enhanced antibacterial performance of chitosan-coated cellulosic substrates, compared to chitosan in a culture medium, highlighted the role of cellulosic nonwoven in boosting antibacterial effectiveness, likely through improved contact and interaction with bacterial cells. The study demonstrated that chitosan-treated cellulosic nonwovens, particularly with dip-dry coating altered tensile strength and increased the bending resistance and bending stiffness.</p>","PeriodicalId":9067,"journal":{"name":"Bioresources and Bioprocessing","volume":"12 1","pages":"11"},"PeriodicalIF":4.3,"publicationDate":"2025-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11829891/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143424967","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}

{"title":"Environmental friendly warp yarn coating from feather wastes with enhanced toughness and tenacity via thiol-ene click chemistry grafting modification.","authors":"Xing Pan, Daen Qin, Kaili Song, Aixue Dong","doi":"10.1186/s40643-025-00838-z","DOIUrl":"10.1186/s40643-025-00838-z","url":null,"abstract":"<p><p>The development of biodegradable and environmental friendly wrap sizing agent is beneficial for reducing the impact of textile desizing effluent on environment. In this work, green and biodegradable keratin sizing agent with enhanced toughness and tenacity was prepared by adjusting side chain tails structure via thiol-ene click chemistry grafting modification for warp yarn slashing against film thermal-embrittlement and fracture during weaving. Feather keratin from waste feather has become an attractive target to replace petroleum-based Poly (vinyl alcohol) sizes due to its easy film-forming ability, excellent adhesive property, biodegradability and low cost. However, keratin yarn coating showed brittleness and easily peeled off from weaving yarn which highly restrict its application. Thus, polymer branched side chain tails with a structure that similar to the wrap yarn was grafted onto keratin molecular chain by utilizing its distinctive thio group as anchor point by means of click chemistry. The results showed that grafting modification could obviously improve the adhesiveness of keratin sizing by the principle of similarity compatibility. The sizing performance, desizing performance as well as its degradability were comprehensively studied. Successful utilization of modified keratin sizes will bring opportunities for the green and sustainable development of textile industry.</p>","PeriodicalId":9067,"journal":{"name":"Bioresources and Bioprocessing","volume":"12 1","pages":"10"},"PeriodicalIF":4.3,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11825430/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143405688","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}

{"title":"Tea leaf exosome-like nanoparticles (TELNs) improve oleic acid-induced lipid metabolism by regulating miRNAs in HepG-2 cells.","authors":"Xuanhao Lei, Haonan Li, Sibei Chen, Bing Li, Huili Xia, Jun Li, Feng Guan, Jian Ge","doi":"10.1186/s40643-025-00844-1","DOIUrl":"10.1186/s40643-025-00844-1","url":null,"abstract":"<p><p>Tea is a widely consumed beverage globally, but the tea industry faces a significant waste management challenge. In this study, we developed tea leaf exosome-like nanoparticles (TELNs) with an average size of 274 ± 24.7 nm and a zeta potential of -20.6 ± 0.78 mV, using polyethylene glycol (PEG) 6000 precipitation followed by ultracentrifugation. Structural analysis confirmed that TELNs are composed of lipids, proteins, and RNAs. In vitro assays on HepG-2 cells revealed that TELNs are non-toxic at concentrations up to 300 µg/mL and can be efficiently internalized. TELNs exhibited significant antioxidant capacity and were able to significantly ameliorate H₂O₂-induced oxidative stress, increase the viability and reduce the accumulation of ROS in Hepg-2 cells. Notably, TELNs significantly alleviated OA-induced lipid metabolic disorders and hepatocellular injury. Further molecular analysis revealed that TELNs downregulated the expression of miR-21-5p, miR-17-3p, and miR-107, leading to the upregulation of their target genes PPARα, CYP7A1, and CPT-1A, which contributed to the improvement of lipid metabolism. This study is the first to demonstrate the lipid metabolism regulation potential of TELNs, providing new insights into their underlying mechanisms and helping to develop new therapeutic strategies for lipid metabolism-related diseases. Furthermore, it expands the scope of tea use and helps to reuse tea residues.</p>","PeriodicalId":9067,"journal":{"name":"Bioresources and Bioprocessing","volume":"12 1","pages":"9"},"PeriodicalIF":4.3,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11810870/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143390081","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}

{"title":"Production of HMF-derivatives from wine residues using Saccharomyces cerevisiae as whole-cell biocatalyst.","authors":"Joana T Cunha, Aloia Romaní, Lucília Domingues","doi":"10.1186/s40643-025-00840-5","DOIUrl":"10.1186/s40643-025-00840-5","url":null,"abstract":"<p><strong>Background: </strong>There is an urgent need to develop bioprocesses independent of fossil resources to address resource depletion and mitigate environmental harm. Transitioning to a bio-based economy requires prioritizing chemical production processes that utilize renewable resources, ensuring sustainability and environmental responsibility. 5-Hydroxymethylfurfural (HMF) and its derivatives are promising building blocks, ranked among the top 12 bio-based molecules derived from biomass. This study investigates the potential of wine residues as substrates for HMF production and explores the yeast Saccharomyces cerevisiae, a robust industrial microbial cell factory, as a whole-cell biocatalyst for converting HMF into high-value compounds, offering an alternative to chemical synthesis.</p><p><strong>Findings: </strong>Several S. cerevisiae strains were compared for their ability to convert HMF, demonstrating varying capacities for oxidation or reduction. For the first time, HMF derivatives with potential industrial applications were produced using an HMF-rich hydrolysate obtained from sustainable processing of wine-growing waste, such as grape pomace and must surplus. The selected yeast strain was engineered to express the oxidoreductase enzyme of HMF/Furfural from Cupriavidua basilensis strain HMF14, resulting in a 15-fold increase in the accumulation of oxidized derivatives such as 2,5-furandicarboxylic acid (FDCA).</p><p><strong>Conclusions: </strong>These findings highlight the potential of leveraging wine residues and engineered S. cerevisiae strains to develop sustainable bioprocesses for producing valuable HMF derivatives, thereby contributing to the advancement of bio-based chemical production.</p>","PeriodicalId":9067,"journal":{"name":"Bioresources and Bioprocessing","volume":"12 1","pages":"8"},"PeriodicalIF":4.3,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11785874/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143063594","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}

{"title":"Mining versatile feruloyl esterases: phylogenetic classification, structural features, and deep learning model.","authors":"Liang Guo, Yuxin Dong, Deyong Zhang, Xinrong Pan, Xinjie Jin, Xinyu Yan, Yin Lu","doi":"10.1186/s40643-024-00835-8","DOIUrl":"10.1186/s40643-024-00835-8","url":null,"abstract":"<p><p>Feruloyl esterases (FEs, EC 3.1.1.73) play a crucial role in biological synthesis and metabolism. However, the identification of versatile FEs, capable of catalyzing a wide range of substrates, remains a challenge. In this study, we obtained 2085 FE sequences from the BRENDA database and initiated with an enzyme similarity network analysis, revealing three main clusters (1-3). Notably, both cluster 1 and cluster 3 included the characterized FEs, which exhibited significant differences in sequence length. Subsequent phylogenetic analysis of these clusters unveiled a correlation between phylogenetic classification and substrate promiscuity, and enzymes with broad substrate scope tended to locate within specific branches of the phylogenetic tree. Further, molecular dynamics simulations and dynamical cross-correlation matrix analysis were employed to explore structural dynamics differences between promiscuous and substrate-specific FEs. Finally, to expand the repertoire of versatile FEs, we employed deep learning models to predict potentially promiscuous enzymes and identified 38 and 75 potential versatile FEs from cluster 1 and cluster 3 with a probability score exceeding 90%. Our findings underscore the utility of integrating phylogenetic and structural features with deep learning approaches for mining versatile FEs, shedding light on unexplored enzymatic diversity and expanding the repertoire of biocatalysts for synthetic applications.</p>","PeriodicalId":9067,"journal":{"name":"Bioresources and Bioprocessing","volume":"12 1","pages":"7"},"PeriodicalIF":4.3,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11780051/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143058022","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}