Bioresources and Bioprocessing最新文献_第2页

Computational-guided discovery of UDP-glycosyltransferases for lauryl glucoside production using engineered E. coli. 利用工程大肠杆菌，在计算指导下发现用于生产月桂基葡糖苷的 UDP-糖基转移酶。

IF 4.3 3区生物学

Bioresources and Bioprocessing Pub Date : 2024-10-26 DOI: 10.1186/s40643-024-00820-1

Kasimaporn Promubon, Kritsada Tathiya, Aussara Panya, Wasu Pathom-Aree, Pachara Sattayawat

{"title":"Computational-guided discovery of UDP-glycosyltransferases for lauryl glucoside production using engineered E. coli.","authors":"Kasimaporn Promubon, Kritsada Tathiya, Aussara Panya, Wasu Pathom-Aree, Pachara Sattayawat","doi":"10.1186/s40643-024-00820-1","DOIUrl":"10.1186/s40643-024-00820-1","url":null,"abstract":"Defining suitable enzymes for reaction steps in novel synthetic pathways is crucial for developing microbial cell factories for non-natural products. Here, we developed a computational workflow to identify C12 alcohol-active UDP-glycosyltransferases. The workflow involved three steps: (1) assembling initial candidates of putative UDP-glycosyltransferases, (2) refining selection by examining conserved regions, and (3) 3D structure prediction and molecular docking. Genomic sequences from Candida, Pichia, Rhizopus, and Thermotoga, known for lauryl glucoside synthesis via whole-cell biocatalysis, were screened. Out of 240 predicted glycosyltransferases, 8 candidates annotated as glycosyltransferases were selected after filtering out those with signal peptides and identifying conserved UDP-glycosyltransferase regions. These proteins underwent 3D structure prediction and molecular docking with 1-dodecanol. RO3G, a candidate from Rhizopus delemar RA 99-880 with a relatively high ChemPLP fitness score, was selected and expressed in Escherichia coli BL21 (DE3). It was further characterized using a feeding experiment with 1-dodecanol. Results confirmed that the RO3G-expressing strain could convert 1-dodecanol to lauryl glucoside, as quantified by HPLC and identified by targeted LC-MS. Monitoring the growth and fermentation profiles of the engineered strain revealed that RO3G expression did not affect cell growth. Interestingly, acetate, a major fermentation product, was reduced in the RO3G-expressing strain compared to the GFP-expressing strain, suggesting a redirection of flux from acetate to other pathways. Overall, this work presents a successful workflow for discovering UDP-glycosyltransferase enzymes with confirmed activity toward 1-dodecanol for lauryl glucoside production.","PeriodicalId":9067,"journal":{"name":"Bioresources and Bioprocessing","volume":"11 1","pages":"103"},"PeriodicalIF":4.3,"publicationDate":"2024-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11561197/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142614605","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}

引用次数: 0

Identification of metabolites from the gut microbiota in hypertension via network pharmacology and molecular docking. 通过网络药理学和分子对接鉴定高血压肠道微生物群的代谢物。

IF 4.3 3区生物学

Bioresources and Bioprocessing Pub Date : 2024-10-21 DOI: 10.1186/s40643-024-00815-y

Wenjie Zhang, Yinming Zhang, Jun Li, Jiawei Tang, Ji Wu, Zicong Xie, Xuanchun Huang, Shiyi Tao, Tiantian Xue

{"title":"Identification of metabolites from the gut microbiota in hypertension via network pharmacology and molecular docking.","authors":"Wenjie Zhang, Yinming Zhang, Jun Li, Jiawei Tang, Ji Wu, Zicong Xie, Xuanchun Huang, Shiyi Tao, Tiantian Xue","doi":"10.1186/s40643-024-00815-y","DOIUrl":"10.1186/s40643-024-00815-y","url":null,"abstract":"Hypertension is the most prevalent cardiovascular disease, affecting one-third of adults. All antihypertensive drugs have potential side effects. Gut metabolites influence hypertension. The objective of this study was to identify antihypertensive gut metabolites through network pharmacology and molecular docking techniques and to validate their antihypertensive mechanisms via in vitro experiments. A total of 10 core antihypertensive targets and 18 gut metabolites that act on hypertension were identified. Four groups of protein metabolites, namely, CXCL8-baicalein, CXCL8-baicalin, CYP1A1-urolithin A, and PTGS2-equol, which have binding energies of - 7.7, - 8.5, - 7.2, and - 8.8 kcal-mol-1, respectively, were found to have relatively high affinities. Based on its drug-likeness properties in silico and toxicological properties, equol was identified as a potential antihypertensive metabolite. On the basis of the results of network pharmacology and molecular docking, equol may exert antihypertensive effects by regulating the IL-17 signaling pathway and PTGS2. A phenylephrine-induced H9c2 cell model was subsequently utilized to verify that equol inhibits cell hypertrophy (P < 0.05) by inhibiting the IL-17 signaling pathway and PTGS2 (P < 0.05). This study demonstrated that equol has the potential to be developed as a novel therapeutic agent for the treatment of hypertension.","PeriodicalId":9067,"journal":{"name":"Bioresources and Bioprocessing","volume":"11 1","pages":"102"},"PeriodicalIF":4.3,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11493893/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142457722","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}

引用次数: 0

Retraction Note: Microwave-ultrasonic assisted extraction of lignin to synthesize new nano micellar organometallic surfactants for refining oily wastewater. 撤回声明：微波-超声波辅助萃取木质素以合成用于含油废水精炼的新型纳米胶束有机金属表面活性剂。

IF 4.3 3区生物学

Bioresources and Bioprocessing Pub Date : 2024-10-18 DOI: 10.1186/s40643-024-00819-8

M H Alhalafi, S A Rizk, E S Al-Malki, A M Algohary

引用次数: 0

Engineering a high-sugar tolerant strain of Saccharomyces cerevisiae for efficient trehalose production using a cell surface display approach. 利用细胞表面展示法培育高糖耐受性酿酒酵母菌株，以高效生产曲哈糖。

IF 4.3 3区生物学

Bioresources and Bioprocessing Pub Date : 2024-10-18 DOI: 10.1186/s40643-024-00816-x

Kan Tulsook, Piyada Bussadee, Jantima Arnthong, Wuttichai Mhuantong, Panida U-Thai, Srisakul Trakarnpaiboon, Verawat Champreda, Surisa Suwannarangsee

{"title":"Engineering a high-sugar tolerant strain of Saccharomyces cerevisiae for efficient trehalose production using a cell surface display approach.","authors":"Kan Tulsook, Piyada Bussadee, Jantima Arnthong, Wuttichai Mhuantong, Panida U-Thai, Srisakul Trakarnpaiboon, Verawat Champreda, Surisa Suwannarangsee","doi":"10.1186/s40643-024-00816-x","DOIUrl":"10.1186/s40643-024-00816-x","url":null,"abstract":"Trehalose production via a one-step enzymatic route using trehalose synthase (TreS) holds significant promise for industrial-scale applications due to its simplicity and utilization of low-cost substrates. However, the development of a robust whole-cell biocatalyst expressing TreS remains crucial for enabling practical and economically viable production. In this study, a high-sugar tolerant strain of S. cerevisiae was screened and employed as a host cell for the cell surface display of TreS from Acidiplasma aeolicum. The resultant strain, S. cerevisiae I3A, exhibited remarkable surface displayed TreS activity of 3358 U/g CDW and achieved approximately 64% trehalose yield (10.8 g/L/h productivity) from maltose. Interestingly, no glucose by-product was observed during trehalose production. The S. cerevisiae I3A cells exhibited reusability for up to 12 cycles leading to potential cost reduction of trehalose products. Therefore, our study demonstrated the development of a high-sugar tolerant S. cerevisiae strain expressing TreS on its surface as a whole-cell biocatalyst for efficient and economical trehalose production with potential applications in the food and pharmaceutical industries.","PeriodicalId":9067,"journal":{"name":"Bioresources and Bioprocessing","volume":"11 1","pages":"101"},"PeriodicalIF":4.3,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11489382/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142457721","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}

引用次数: 0

Highly efficient synthesis of the chiral ACE inhibitor intermediate (R)-2-hydroxy-4-phenylbutyrate ethyl ester via engineered bi-enzyme coupled systems. 通过工程化双酶偶联系统高效合成手性 ACE 抑制剂中间体 (R)-2- 羟基-4-苯基丁酸乙酯。

IF 4.3 3区生物学

Bioresources and Bioprocessing Pub Date : 2024-10-15 DOI: 10.1186/s40643-024-00814-z

Yanmei Dai, Jinmei Wang, Zijuan Tao, Liangli Luo, Changshun Huang, Bo Liu, Hanbing Shi, Lan Tang, Zhimin Ou

{"title":"Highly efficient synthesis of the chiral ACE inhibitor intermediate (R)-2-hydroxy-4-phenylbutyrate ethyl ester via engineered bi-enzyme coupled systems.","authors":"Yanmei Dai, Jinmei Wang, Zijuan Tao, Liangli Luo, Changshun Huang, Bo Liu, Hanbing Shi, Lan Tang, Zhimin Ou","doi":"10.1186/s40643-024-00814-z","DOIUrl":"https://doi.org/10.1186/s40643-024-00814-z","url":null,"abstract":"(R)-2-Hydroxy-4-phenylbutyric acid ethyl ester ((R)-HPBE) is an essential chiral intermediate in the synthesis of angiotensin-converting enzyme (ACE) inhibitors. Its production involves the highly selective asymmetric reduction of ethyl 2-oxo-4-phenylbutyrate (OPBE), catalyzed by carbonyl reductase (CpCR), with efficient cofactor regeneration playing a crucial role. In this study, an in-situ coenzyme regeneration system was developed by coupling carbonyl reductase (CpCR) with glucose dehydrogenase (GDH), resulting in the construction of five recombinant strains capable of NADPH regeneration. Among these, the recombinant strain E. coli BL21-pETDuet-1-GDH-L-CpCR, where CpCR is fused to the C-terminus of GDH, demonstrated the highest catalytic activity. This strain exhibited an enzyme activity of 69.78 U/mg and achieved a conversion rate of 98.3%, with an enantiomeric excess (ee) of 99.9% during the conversion of 30 mM OPBE to (R)-HPBE. High-density fermentation further enhanced enzyme yield, achieving an enzyme activity of 1960 U/mL in the fermentation broth, which is 16.2 times higher than the volumetric activity obtained from shake flask fermentation. Additionally, the implementation of a substrate feeding strategy enabled continuous processing, allowing the strain to efficiently convert a final OPBE concentration of 920 mM, producing 912 mM of (R)-HPBE. These findings highlight the system's improved catalytic efficiency, stability, and scalability, making it highly suitable for industrial-scale biocatalytic production.","PeriodicalId":9067,"journal":{"name":"Bioresources and Bioprocessing","volume":"11 1","pages":"99"},"PeriodicalIF":4.3,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11473482/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142485893","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}

引用次数: 0

Correction: Engineering of fast-growing Vibrio natriegens for biosynthesis of poly(3-hydroxybutyrate-co-lactate). 更正：对快速生长的纳氏弧菌进行生物合成聚（3-羟基丁酸-乳酸）工程学研究。

IF 4.3 3区生物学

Bioresources and Bioprocessing Pub Date : 2024-10-14 DOI: 10.1186/s40643-024-00811-2

Xinye Sun, Yanzhe Shang, Binghao Zhang, Pengye Guo, Yuanchan Luo, Hui Wu

引用次数: 0

Correction: Enhancement of lactate fraction in poly(lactate-co-3-hydroxybutyrate) biosynthesized by metabolically engineered E. coli. 更正：提高代谢工程大肠杆菌生物合成的聚（乳酸-3-羟基丁酸）中的乳酸含量。

IF 4.3 3区生物学

Bioresources and Bioprocessing Pub Date : 2024-10-12 DOI: 10.1186/s40643-024-00810-3

Binghao Zhang, Pengye Guo, Xinye Sun, Yanzhe Shang, Yuanchan Luo, Hui Wu

引用次数: 0

Stirring the hydrogen and butanol production from Enset fiber via simultaneous saccharification and fermentation (SSF) process. 通过同步糖化和发酵（SSF）工艺，搅拌利用恩塞特纤维生产氢气和丁醇。

IF 4.3 3区生物学

Bioresources and Bioprocessing Pub Date : 2024-10-10 DOI: 10.1186/s40643-024-00809-w

Nebyat Seid, Lea Wießner, Habibu Aliyu, Anke Neumann

{"title":"Stirring the hydrogen and butanol production from Enset fiber via simultaneous saccharification and fermentation (SSF) process.","authors":"Nebyat Seid, Lea Wießner, Habibu Aliyu, Anke Neumann","doi":"10.1186/s40643-024-00809-w","DOIUrl":"10.1186/s40643-024-00809-w","url":null,"abstract":"Enset fiber is a promising feedstock for biofuel production with the potential to reduce carbon emissions and improve the sustainability of the energy system. This study aimed to maximize hydrogen and butanol production from Enset fiber through simultaneous saccharification and fermentation (SSF) process in bottles as well as in bioreactor. The SSF process in bottles resulted in a higher butanol concentration of 11.36 g/L with a yield of 0.23 g/g and a productivity of 0.16 g/(L h) at the optimal process parameters of 5% (w/v) substrate loading, 16 FPU/g cellulase loading, and 100 rpm agitation speed from pretreated Enset fiber. Moreover, a comparable result to the bottle experiment was observed in the bioreactor with pH-uncontrolled SSF process, although with a decreased in butanol productivity to 0.095 g/(L h). However, using the pre-hydrolysis simultaneous saccharification and fermentation (PSSF) process in the bioreactor with a 7% (w/v) substrate loading led to the highest butanol concentration of 12.84 g/L with a productivity of 0.104 g/(L h). Furthermore, optimizing the SSF process parameters to favor hydrogen resulted in an increased hydrogen yield of 198.27 mL/g-Enset fiber at atmospheric pressure, an initial pH of 8.0, and 37 °C. In general, stirring the SSF process to shift the product ratio to either hydrogen or butanol was possible by adjusting temperature and pressure. At 37 °C and atmospheric pressure, the process resulted in an e-mol yield of 12% for hydrogen and 38% for butanol. Alternatively, at 30 °C and 0.55 bar overpressure, the process achieved a yield of 6% e-mol of hydrogen and 48% e-mol of butanol. This is the first study to produce hydrogen and butanol from Enset fiber using the SSF process and contributes to the development of a circular bioeconomy.","PeriodicalId":9067,"journal":{"name":"Bioresources and Bioprocessing","volume":"11 1","pages":"96"},"PeriodicalIF":4.3,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11466926/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142399303","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}

引用次数: 0

A combination of calcium hydroxide and sodium hydrosulphate controls pathogens causing environmental mastitis in recycled manure solids. 氢氧化钙和硫氢化钠的组合可控制回收粪便固体中导致环境乳腺炎的病原体。

IF 4.3 3区生物学

Bioresources and Bioprocessing Pub Date : 2024-10-08 DOI: 10.1186/s40643-024-00812-1

Selladurai Praveen, Mukund A Kataktalware, Priyanka Meena, Maharajan Lavanya, Priyanka Patoliya, Sakthivel Jeyakumar, Menon Rekha Ravindra, Mamta Chauhan, K P Ramesha, G Letha Devi, John P Kastelic, Arindam Dhali

{"title":"A combination of calcium hydroxide and sodium hydrosulphate controls pathogens causing environmental mastitis in recycled manure solids.","authors":"Selladurai Praveen, Mukund A Kataktalware, Priyanka Meena, Maharajan Lavanya, Priyanka Patoliya, Sakthivel Jeyakumar, Menon Rekha Ravindra, Mamta Chauhan, K P Ramesha, G Letha Devi, John P Kastelic, Arindam Dhali","doi":"10.1186/s40643-024-00812-1","DOIUrl":"10.1186/s40643-024-00812-1","url":null,"abstract":"Recycled manure solids (RMS) are dried cow dung processed using a manure dewatering machine and subsequently sun-dried to ~ 20% moisture. Benefits of RMS include abundant availability, low cost, and eco-friendliness, but its use as bedding material for cows is hindered by a moisture content that promotes microbial growth. This in vitro study evaluated impacts of calcium hydroxide (CH; 5 and 7.5%) and sodium hydrosulphate (SHS; 6 and 8%), independently and in combinations, at various depths of RMS, on physicochemical and microbial properties. The CH-treated groups had increased pH and reduced moisture on Day 0. Incorporating 7.5% CH + 6% SHS at 15-20 cm, and 7.5% CH + 8% SHS at all depths, effectively suppressed Escherichia coli and Klebsiella spp. Furthermore, a combination of 7.5% CH + 8% SHS at 20 cm inhibited coliform growth, whereas 7.5% CH with 6% SHS inhibited Streptococcus spp. In conclusion, a combination of 7.5% CH with either 6 or 8% SHS at a depth of 15 cm in RMS was particularly effective in controlling environmental mastitis-causing pathogens, specifically E. coli and Klebsiella spp.","PeriodicalId":9067,"journal":{"name":"Bioresources and Bioprocessing","volume":"11 1","pages":"95"},"PeriodicalIF":4.3,"publicationDate":"2024-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11461433/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142387842","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}

引用次数: 0

Characterization of argonaute nucleases from mesophilic bacteria Pseudobutyrivibrio ruminis. 嗜中性细菌鲁米弧菌的箭状核酸酶的特征。

IF 4.3 3区生物学

Bioresources and Bioprocessing Pub Date : 2024-10-07 DOI: 10.1186/s40643-024-00797-x

Xiaoyi Xu, Hao Yang, Huarong Dong, Xiao Li, Qian Liu, Yan Feng

{"title":"Characterization of argonaute nucleases from mesophilic bacteria Pseudobutyrivibrio ruminis.","authors":"Xiaoyi Xu, Hao Yang, Huarong Dong, Xiao Li, Qian Liu, Yan Feng","doi":"10.1186/s40643-024-00797-x","DOIUrl":"10.1186/s40643-024-00797-x","url":null,"abstract":"Mesophilic Argonautes (Agos) from microbial resources have received significant attention due to their potential applications in genome editing and molecular diagnostics. This study characterizes a novel Ago from Pseudobutyrivibrio ruminis (PrAgo), which can cleave single-stranded DNA using guide DNA (gDNA). PrAgo, functioning as a multi-turnover enzyme, effectively cleaves DNA using 5'-phosphate gDNA, 14-30 nucleotides in length, in the presence of both Mn2+ and Mg2+ ions. PrAgo demonstrates DNA cleavage activity over a broad pH range (pH 4-12), with optimal activity at pH 11. As a mesophilic enzyme, PrAgo cleaves efficiently DNA at temperatures ranging from 25 to 65 °C, particularly at 65 °C. PrAgo does not show strong preferences for the 5'-nucleotide in gDNA. It shows high tolerance for single-base mismatches, except at positions 13 and 15 of gDNA. Continuous double-nucleotide mismatches at positions 10-16 of gDNA significantly reduce cleavage activity. Furthermore, PrAgo mediates DNA-guided DNA cleavage of AT-rich double stranded DNA at 65 °C. Additionally, molecular dynamic simulations suggest that interactions between the PAZ domain and different nucleic acids strongly influence cleavage efficiency. These findings expand our understanding of Protokaryotic Agos and their potential applications in biotechnology.","PeriodicalId":9067,"journal":{"name":"Bioresources and Bioprocessing","volume":"11 1","pages":"94"},"PeriodicalIF":4.3,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11458871/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142379981","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}

引用次数: 0