Pub Date : 2025-01-16DOI: 10.1016/j.bej.2025.109641
Rui Zhang , Hong Pan , Lihui Xu , Xueqiang Fu , Meng Wang , Hongtao Xu , Qun Yang , Yong Shen , Hong Zhao
The basic mechanical properties of traditional hydrogels and their limited range of application conditions restrict their further use in many fields. A self-healing hydrogel, MC-Cys-MEK, with enhanced mechanical performance and mild application conditions., was synthesized using natural biomass raw materials—methylcellulose. Modified methylcellulose (MC-Cys) was prepared by reacting methylcellulose (MC) with cysteine through the Steglich esterification reaction. Subsequently, based on the reversible thiol-yne double conjugate addition reaction, the novel self-healing hydrogel, MC-Cys-MEK, was synthesized from MC-Cys and MEK (3-butyne-2-one).The covalent bonds and reversible hydrogen bonds formed between the molecules work synergistically to enhance the mechanical properties of the cellulose hydrogel. This hydrogel can self-heal at room temperature under neutral to weak alkaline conditions (pH 7–8), with a maximum tensile strength of 1.540 MPa, which is double that of the MC hydrogel (0.626 MPa). Consequently, this hydrogel presents broader applications in the biomedical and tissue engineering fields.
{"title":"Preparation and properties of MC-Cys-MEK Self -healing Hydrogel with improved mechanical Performence","authors":"Rui Zhang , Hong Pan , Lihui Xu , Xueqiang Fu , Meng Wang , Hongtao Xu , Qun Yang , Yong Shen , Hong Zhao","doi":"10.1016/j.bej.2025.109641","DOIUrl":"10.1016/j.bej.2025.109641","url":null,"abstract":"<div><div>The basic mechanical properties of traditional hydrogels and their limited range of application conditions restrict their further use in many fields. A self-healing hydrogel, MC-Cys-MEK, with enhanced mechanical performance and mild application conditions., was synthesized using natural biomass raw materials—methylcellulose. Modified methylcellulose (MC-Cys) was prepared by reacting methylcellulose (MC) with cysteine through the Steglich esterification reaction. Subsequently, based on the reversible thiol-yne double conjugate addition reaction, the novel self-healing hydrogel, MC-Cys-MEK, was synthesized from MC-Cys and MEK (3-butyne-2-one).The covalent bonds and reversible hydrogen bonds formed between the molecules work synergistically to enhance the mechanical properties of the cellulose hydrogel. This hydrogel can self-heal at room temperature under neutral to weak alkaline conditions (pH 7–8), with a maximum tensile strength of 1.540 MPa, which is double that of the MC hydrogel (0.626 MPa). Consequently, this hydrogel presents broader applications in the biomedical and tissue engineering fields.</div></div>","PeriodicalId":8766,"journal":{"name":"Biochemical Engineering Journal","volume":"216 ","pages":"Article 109641"},"PeriodicalIF":3.7,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143167653","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}
Pub Date : 2025-01-15DOI: 10.1016/j.bej.2025.109637
Sebastián Espinel-Ríos , José Montaño López , José L. Avalos
This work presents an omics-driven modeling pipeline that integrates machine-learning tools to facilitate the dynamic modeling of multiscale biological systems. Random forests and permutation feature importance are proposed to mine omics datasets, guiding feature selection and dimensionality reduction for dynamic modeling. Continuous and differentiable machine-learning functions can be trained to link the reduced omics feature set to key components of the dynamic model, resulting in a hybrid model. As proof of concept, we apply this framework to a high-dimensional proteomics dataset of Saccharomyces cerevisiae. After identifying key intracellular proteins that correlate with cell growth, targeted dynamic experiments are designed, and key model parameters are captured as functions of the selected proteins using Gaussian processes. This approach captures the dynamic behavior of yeast strains under varying proteome profiles while estimating the uncertainty in the hybrid model’s predictions. The outlined modeling framework is adaptable to other scenarios, such as integrating additional layers of omics data for more advanced multiscale biological systems, or employing alternative machine-learning methods to handle larger datasets. Overall, this study outlines a strategy for leveraging omics data to inform multiscale dynamic modeling in systems biology and bioprocess engineering.
{"title":"Omics-driven hybrid dynamic modeling of bioprocesses with uncertainty estimation","authors":"Sebastián Espinel-Ríos , José Montaño López , José L. Avalos","doi":"10.1016/j.bej.2025.109637","DOIUrl":"10.1016/j.bej.2025.109637","url":null,"abstract":"<div><div>This work presents an omics-driven modeling pipeline that integrates machine-learning tools to facilitate the dynamic modeling of multiscale biological systems. Random forests and permutation feature importance are proposed to mine omics datasets, guiding feature selection and dimensionality reduction for dynamic modeling. Continuous and differentiable machine-learning functions can be trained to link the reduced omics feature set to key components of the dynamic model, resulting in a hybrid model. As proof of concept, we apply this framework to a high-dimensional proteomics dataset of <em>Saccharomyces cerevisiae</em>. After identifying key intracellular proteins that correlate with cell growth, targeted dynamic experiments are designed, and key model parameters are captured as functions of the selected proteins using Gaussian processes. This approach captures the dynamic behavior of yeast strains under varying proteome profiles while estimating the uncertainty in the hybrid model’s predictions. The outlined modeling framework is adaptable to other scenarios, such as integrating additional layers of omics data for more advanced multiscale biological systems, or employing alternative machine-learning methods to handle larger datasets. Overall, this study outlines a strategy for leveraging omics data to inform multiscale dynamic modeling in systems biology and bioprocess engineering.</div></div>","PeriodicalId":8766,"journal":{"name":"Biochemical Engineering Journal","volume":"216 ","pages":"Article 109637"},"PeriodicalIF":3.7,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143167654","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}
Pub Date : 2025-01-14DOI: 10.1016/j.bej.2025.109638
Virmal S. Jain, Deepti Sahasrabuddhe, Avinash Vellore Sunder, Pramod P. Wangikar
Cyanobacteria have emerged as attractive hosts for the sustainable photosynthetic conversion of CO2 to biofuels, especially ethanol. However, the low ethanol titers and productivity achieved so far have limited the industrial translation of the process. Conventional model cyanobacterial host strains exhibit slow growth and large pool of storage molecules which may limit the production of heterogeneous products like ethanol. In this context, we have isolated and characterized a set of fast-growing Synechococcus elongatus strains, of which IITB1(PCC11801) and IITB6 have been promising for metabolic engineering. Here, we engineered the ethanologenic pathway in IITB6 and optimized gene expression levels by screening combinations of native cyanobacterial promoters of varying strength. Expression of pyruvate decarboxylase and NADPH-dependent alcohol dehydrogenase under low-strength promoters coupled with cultivation in 5X concentrated BG-11 medium gave 1.3 g/L ethanol in 4 days, twice that of the previously reported shake-flask titer from pdc-adh-expressed recombinant cyanobacterial strains. This work opens avenues for developing S. elongatus IITB6 as an efficient host for ethanol production.
{"title":"Engineering Synechococcus elongatus IITB6 as a highly efficient ethanol bioproduction host","authors":"Virmal S. Jain, Deepti Sahasrabuddhe, Avinash Vellore Sunder, Pramod P. Wangikar","doi":"10.1016/j.bej.2025.109638","DOIUrl":"10.1016/j.bej.2025.109638","url":null,"abstract":"<div><div>Cyanobacteria have emerged as attractive hosts for the sustainable photosynthetic conversion of CO<sub>2</sub> to biofuels, especially ethanol. However, the low ethanol titers and productivity achieved so far have limited the industrial translation of the process. Conventional model cyanobacterial host strains exhibit slow growth and large pool of storage molecules which may limit the production of heterogeneous products like ethanol. In this context, we have isolated and characterized a set of fast-growing <em>Synechococcus elongatus</em> strains, of which IITB1(PCC11801) and IITB6 have been promising for metabolic engineering. Here, we engineered the ethanologenic pathway in IITB6 and optimized gene expression levels by screening combinations of native cyanobacterial promoters of varying strength. Expression of pyruvate decarboxylase and NADPH-dependent alcohol dehydrogenase under low-strength promoters coupled with cultivation in 5X concentrated BG-11 medium gave 1.3 g/L ethanol in 4 days, twice that of the previously reported shake-flask titer from <em>pdc-adh</em>-expressed recombinant cyanobacterial strains. This work opens avenues for developing <em>S. elongatus</em> IITB6 as an efficient host for ethanol production.</div></div>","PeriodicalId":8766,"journal":{"name":"Biochemical Engineering Journal","volume":"215 ","pages":"Article 109638"},"PeriodicalIF":3.7,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143104074","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}
Pub Date : 2025-01-14DOI: 10.1016/j.bej.2025.109640
Shaofeng Chen , Weide Xiong , Xiaoyu Lin , Xuejun Wu , Chuanyi Yao , Yinghua Lu , Xueping Ling
Phospholipase D (PLD) has a unique phosphatidyl catalytic site and is capable of synthesizing a variety of active phospholipids, such as phosphatidylserine, for use in the food industry. However, the microbial production of PLD is limited by its cytotoxicity. In this study, the constructed trehalase-deficient strains by CRISPR-Cas9 showed increased intracellular trehalose content and high performance in PLD production. Molecular dynamics (MD) simulations suggested that trehalose could stabilize the natural conformation of PLD, increase its solubility and expression. High PLD production (47.63 U/mL) was achieved in the recombinant strain E. coli BW25113 ΔtreA ΔtreC ΔtreF using an optimized culture strategy, with an efficiency of 5.95 U/mL/h—the highest level reported in shake flask cultures to date. Our results showed that the accumulated endogenous trehalose improved the salt tolerance of cells to alleviate PLD cytotoxicity and promote continuous PLD expression. Thus, the trehalase-deficient Escherichia coli expression system shows great potential for application in industrial PLD production.
{"title":"Improved performance of toxic Streptomyces phospholipase D expression by combinatorial optimization in the trehalase-deficient Escherichia coli","authors":"Shaofeng Chen , Weide Xiong , Xiaoyu Lin , Xuejun Wu , Chuanyi Yao , Yinghua Lu , Xueping Ling","doi":"10.1016/j.bej.2025.109640","DOIUrl":"10.1016/j.bej.2025.109640","url":null,"abstract":"<div><div>Phospholipase D (PLD) has a unique phosphatidyl catalytic site and is capable of synthesizing a variety of active phospholipids, such as phosphatidylserine, for use in the food industry. However, the microbial production of PLD is limited by its cytotoxicity. In this study, the constructed trehalase-deficient strains by CRISPR-Cas9 showed increased intracellular trehalose content and high performance in PLD production. Molecular dynamics (MD) simulations suggested that trehalose could stabilize the natural conformation of PLD, increase its solubility and expression. High PLD production (47.63 U/mL) was achieved in the recombinant strain <em>E. coli</em> BW25113 <em>ΔtreA ΔtreC ΔtreF</em> using an optimized culture strategy, with an efficiency of 5.95 U/mL/h—the highest level reported in shake flask cultures to date. Our results showed that the accumulated endogenous trehalose improved the salt tolerance of cells to alleviate PLD cytotoxicity and promote continuous PLD expression. Thus, the trehalase-deficient <em>Escherichia coli</em> expression system shows great potential for application in industrial PLD production.</div></div>","PeriodicalId":8766,"journal":{"name":"Biochemical Engineering Journal","volume":"215 ","pages":"Article 109640"},"PeriodicalIF":3.7,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143102921","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}
Pub Date : 2025-01-13DOI: 10.1016/j.bej.2025.109633
Ramalingam Kayalvizhi, Samuel Jacob
Amidst advancements underway in exploiting lignocellulosic biomass efficiently, there is a noticeable dearth of scientific data concerning the utilization of de-oiled rice bran (DRB), an agro-industrial residue of the rice bran oil processing industry for the production of commercially valuable chemicals. The biochemical analysis of DRB biomass revealed that its holocellulosic content was 39.09 % w/w. A combined pretreatment and saccharification strategy was employed with mono and co-culture of two fungal species namely white rot fungi and Aspergillus niger sequentially followed by mild acid treatment (1 % (v/v) H2SO4) to extract maximum sugar from DRB biomass. This comprehensive treatment resulted in a total sugar yield of 518.3 mg/g of DRB and the maximum delignification and saccharification achieved were 75.4 % (w/w) and 78.5 % (w/w) respectively. At 96 h of batch fermentation, Pichia fermentans NCIM 3638 with detoxified DRB hydrolysate achieved a maximum xylitol yield and concentration of 0.48 g/g of xylose and 23.56 g/L and was confirmed through HPLC analysis. The produced xylitol was crystallized with maximum yield of 73.22 %. Further, an unstructured kinetic model was employed to study the feasibility of xylitol production. This work validates that DRB biomass possesses significant promise as a highly efficient feedstock for the bioproduction of xylitol.
{"title":"Process strategies for enhanced sugar recovery from de-oiled rice bran for xylitol production using Pichia fermentans NCIM 3638","authors":"Ramalingam Kayalvizhi, Samuel Jacob","doi":"10.1016/j.bej.2025.109633","DOIUrl":"10.1016/j.bej.2025.109633","url":null,"abstract":"<div><div>Amidst advancements underway in exploiting lignocellulosic biomass efficiently, there is a noticeable dearth of scientific data concerning the utilization of de-oiled rice bran (DRB), an agro-industrial residue of the rice bran oil processing industry for the production of commercially valuable chemicals. The biochemical analysis of DRB biomass revealed that its holocellulosic content was 39.09 % w/w. A combined pretreatment and saccharification strategy was employed with mono and co-culture of two fungal species namely white rot fungi and <em>Aspergillus niger</em> sequentially followed by mild acid treatment (1 % (v/v) H<sub>2</sub>SO<sub>4</sub>) to extract maximum sugar from DRB biomass. This comprehensive treatment resulted in a total sugar yield of 518.3 mg/g of DRB and the maximum delignification and saccharification achieved were 75.4 % (w/w) and 78.5 % (w/w) respectively. At 96 h of batch fermentation, <em>Pichia fermentans</em> NCIM 3638 with detoxified DRB hydrolysate achieved a maximum xylitol yield and concentration of 0.48 g/g of xylose and 23.56 g/L and was confirmed through HPLC analysis. The produced xylitol was crystallized with maximum yield of 73.22 %. Further, an unstructured kinetic model was employed to study the feasibility of xylitol production. This work validates that DRB biomass possesses significant promise as a highly efficient feedstock for the bioproduction of xylitol.</div></div>","PeriodicalId":8766,"journal":{"name":"Biochemical Engineering Journal","volume":"215 ","pages":"Article 109633"},"PeriodicalIF":3.7,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143104037","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}
Pub Date : 2025-01-13DOI: 10.1016/j.bej.2025.109636
Rufei Liu , Xiaoyue Li , Tao Liu , Huiyan Jing , Jie Liu , Zhihan Zhang , Ziyi Yang , Yanping Liu
Producing chemicals from waste can be considered as a sustainable method to valorize residues. In this study, the effects of alkyl polyglycoside 06 (APG06) pretreatment on volatile fatty acid (VFA) production from food waste were determined by evaluating organic degradation, microbial reactions, enzyme activity, and functional enzyme species. When the dosage of APG06 was 9.45 g/L, the VFA production was the highest, reaching 16.7 g/L, with the main components of acetic acid and butyric acid. Total carbohydrate, and the concentrations of soluble protein and NH4+-N were obtained 1.8 times, 1.2 times and 1.1 times of increment with APG06 addition. After adding APG06, acetate kinase and butyrate kinase activity was increased by 48 % and 140 %, respectively. Enterococcus and Terrisporobacter were enriched as the dominant genera with adding APG06, reaching 40 % and 12 %. In the metabolic pathway, glucose-6-phosphate isomerase, phosphoglycerate mutase and pyruvate dehydrogenase were significantly improved, increasing by 224 %,78 % and 115 %, respectively, leading to the 59 % increment on the total abundance of functional enzymes. The addition of APG06 mainly enhanced glucose isomerization and pyruvate metabolism steps, thus promoted the production of VFAs. The addition of APG06 not only optimizes microbial reactions and enzyme activities, but also promotes the enrichment of specific microbial populations, thereby enhancing the entire biodegradation process and providing new ideas for waste resource utilization, especially in bioenergy production.
{"title":"Alkyl polyglycoside addition could enhance the volatile fatty acids production from anaerobic digestion of food waste","authors":"Rufei Liu , Xiaoyue Li , Tao Liu , Huiyan Jing , Jie Liu , Zhihan Zhang , Ziyi Yang , Yanping Liu","doi":"10.1016/j.bej.2025.109636","DOIUrl":"10.1016/j.bej.2025.109636","url":null,"abstract":"<div><div>Producing chemicals from waste can be considered as a sustainable method to valorize residues. In this study, the effects of alkyl polyglycoside 06 (APG06) pretreatment on volatile fatty acid (VFA) production from food waste were determined by evaluating organic degradation, microbial reactions, enzyme activity, and functional enzyme species. When the dosage of APG06 was 9.45 g/L, the VFA production was the highest, reaching 16.7 g/L, with the main components of acetic acid and butyric acid. Total carbohydrate, and the concentrations of soluble protein and NH<sub>4</sub><sup>+</sup>-N were obtained 1.8 times, 1.2 times and 1.1 times of increment with APG06 addition. After adding APG06, acetate kinase and butyrate kinase activity was increased by 48 % and 140 %, respectively. <em>Enterococcus</em> and <em>Terrisporobacter</em> were enriched as the dominant genera with adding APG06, reaching 40 % and 12 %. In the metabolic pathway, glucose-6-phosphate isomerase, phosphoglycerate mutase and pyruvate dehydrogenase were significantly improved, increasing by 224 %,78 % and 115 %, respectively, leading to the 59 % increment on the total abundance of functional enzymes. The addition of APG06 mainly enhanced glucose isomerization and pyruvate metabolism steps, thus promoted the production of VFAs. The addition of APG06 not only optimizes microbial reactions and enzyme activities, but also promotes the enrichment of specific microbial populations, thereby enhancing the entire biodegradation process and providing new ideas for waste resource utilization, especially in bioenergy production.</div></div>","PeriodicalId":8766,"journal":{"name":"Biochemical Engineering Journal","volume":"215 ","pages":"Article 109636"},"PeriodicalIF":3.7,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143102920","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}
Pub Date : 2025-01-10DOI: 10.1016/j.bej.2025.109635
Can Zi , Huajie Liu , Jiangwei He , Xiuhu Dang , Xiaobang Liu , Jianchang Li
A combination of computational fluid dynamics (CFD) and population balance model (PBM) was used to study gas-liquid mixing in a fermenter. Numerical simulations assessed how heat exchange structure and tracer injection location affect mixing time. Results show that global mixing time is mainly influenced by the flow field, especially overall circulation strength in the core region. For the upper tracer injection point, global mixing time in Models 1–4 decreases as overall circulation improves with increased spacing of heat exchange tube bundles. Improper heat exchanger structures can increase global mixing time by up to 60 %. The effect of heat exchange structures on local mixing time at the upper injection point is similar to that on global mixing time. However, local mixing time is nearly 40 % shorter, making it unsuitable for reflecting the mixing performance in large-scale fermenters. The tracer injection location significantly affects mixing efficiency, with Model 1 showing an 18 % decrease at lower injection point, while Models 2–4 experience a 7∼14 % increase. This research offers valuable insights for designing and optimizing fermenters.
{"title":"Simulation analysis the impact of heat exchange structure on mixing time in fermenter","authors":"Can Zi , Huajie Liu , Jiangwei He , Xiuhu Dang , Xiaobang Liu , Jianchang Li","doi":"10.1016/j.bej.2025.109635","DOIUrl":"10.1016/j.bej.2025.109635","url":null,"abstract":"<div><div>A combination of computational fluid dynamics (CFD) and population balance model (PBM) was used to study gas-liquid mixing in a fermenter. Numerical simulations assessed how heat exchange structure and tracer injection location affect mixing time. Results show that global mixing time is mainly influenced by the flow field, especially overall circulation strength in the core region. For the upper tracer injection point, global mixing time in Models 1–4 decreases as overall circulation improves with increased spacing of heat exchange tube bundles. Improper heat exchanger structures can increase global mixing time by up to 60 %. The effect of heat exchange structures on local mixing time at the upper injection point is similar to that on global mixing time. However, local mixing time is nearly 40 % shorter, making it unsuitable for reflecting the mixing performance in large-scale fermenters. The tracer injection location significantly affects mixing efficiency, with Model 1 showing an 18 % decrease at lower injection point, while Models 2–4 experience a 7∼14 % increase. This research offers valuable insights for designing and optimizing fermenters.</div></div>","PeriodicalId":8766,"journal":{"name":"Biochemical Engineering Journal","volume":"215 ","pages":"Article 109635"},"PeriodicalIF":3.7,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143102912","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}
Pub Date : 2025-01-10DOI: 10.1016/j.bej.2025.109634
Eduardo Luís Menezes de Almeida , Wendel Batista da Silveira
Lipid production by oleaginous yeasts from lignocellulosic biomasses is a sustainable alternative to produce oleochemicals; nevertheless, the pretreatment of these biomasses releases yeast inhibitors, including acetic acid. Papiliotrema laurentii UFV-1 converts lignocelulose-derived sugars into high lipid contents; however, wild strains are sensitive to acetic acid. Previously, our group selected an acetic acid-tolerant strain of P. laurentii (ATS) by Adaptive Laboratory Evolution and identified mutations that might contribute to its tolerance. Here, we combined transcriptome, metabolic modeling and protein-protein interaction analyses to deepen our understanding about acetic acid stress targets and adaptive responses in P. laurentii. Acetic acid stress promoted global expression changes; most of them related to transcription, translation, and ribosome biogenesis. Under acetic acid stress, the sensitive strain induced DNA mismatch repair and meiosis, while the tolerant strain negatively regulated autophagy and cell cycle. The tolerant strain induced processes related to increasing intracellular pH, detoxification, and proton efflux. Importantly, ATS presented a remarkable NAD(P)H pool in the metabolic modeling analysis, which might support the reducing power required by tolerance mechanisms. Meanwhile, the sensitive strain induced genes related to cell wall biogenesis, consistent with its morphological changes described in our previous study. The pathways described as tolerant-related might be used in metabolic engineering strategies to improve the tolerance of P. laurentii to weak acids, boosting its application in lignocellulosic biorefineries.
{"title":"Insights into the response and tolerance mechanisms of Papiliotrema laurentii to acetic acid stress by RNA-seq and genome-scale metabolic modeling analysis","authors":"Eduardo Luís Menezes de Almeida , Wendel Batista da Silveira","doi":"10.1016/j.bej.2025.109634","DOIUrl":"10.1016/j.bej.2025.109634","url":null,"abstract":"<div><div>Lipid production by oleaginous yeasts from lignocellulosic biomasses is a sustainable alternative to produce oleochemicals; nevertheless, the pretreatment of these biomasses releases yeast inhibitors, including acetic acid. <em>Papiliotrema laurentii</em> UFV-1 converts lignocelulose-derived sugars into high lipid contents; however, wild strains are sensitive to acetic acid. Previously, our group selected an acetic acid-tolerant strain of <em>P. laurentii</em> (ATS) by Adaptive Laboratory Evolution and identified mutations that might contribute to its tolerance. Here, we combined transcriptome, metabolic modeling and protein-protein interaction analyses to deepen our understanding about acetic acid stress targets and adaptive responses in <em>P. laurentii</em>. Acetic acid stress promoted global expression changes; most of them related to transcription, translation, and ribosome biogenesis. Under acetic acid stress, the sensitive strain induced DNA mismatch repair and meiosis, while the tolerant strain negatively regulated autophagy and cell cycle. The tolerant strain induced processes related to increasing intracellular pH, detoxification, and proton efflux. Importantly, ATS presented a remarkable NAD(P)H pool in the metabolic modeling analysis, which might support the reducing power required by tolerance mechanisms. Meanwhile, the sensitive strain induced genes related to cell wall biogenesis, consistent with its morphological changes described in our previous study. The pathways described as tolerant-related might be used in metabolic engineering strategies to improve the tolerance of <em>P. laurentii</em> to weak acids, boosting its application in lignocellulosic biorefineries.</div></div>","PeriodicalId":8766,"journal":{"name":"Biochemical Engineering Journal","volume":"215 ","pages":"Article 109634"},"PeriodicalIF":3.7,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143102922","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}
Pub Date : 2025-01-10DOI: 10.1016/j.bej.2025.109632
Zhen Zhang , Weixin Cai , Ruijuan Ma , Shih-Hsin Ho , Youping Xie , Jianfeng Chen
The versatile trophic adaptability of Chlorella sorokiniana has garnered significant attention, establishing it as a promising alga for efficient lutein production. In this study, the lutein production characteristics of C. sorokiniana FZU60 were compared under autotrophic, mixotrophic, and heterotrophic conditions. The results demonstrated that glucose supplementation promoted algal cell growth but concurrently reduced lutein content. In contrast, light induction was essential for enhancing lutein synthesis. Consequently, two-stage trophic strategies were developed to simultaneously facilitate cell growth and lutein synthesis. It was determined that optimal lutein production could be achieved by employing the heterotrophy-mixotrophy strategy in conjunction with white light at 500 μmol/m2/s during the second stage (mixotrophic stage). Furthermore, combining the heterotrophy-mixotrophy strategy with fed-batch operation further enhanced the efficacy of lutein production in FZU60. The resulting lutein productivity demonstrated a remarkable 365.1 % improvement over the heterotrophy strategy (Strategy I) and an 80.8 % increase over the mixotrophy strategy (Strategy III), when both were coupled with fed-batch operation. These findings were subsequently validated in a 5 L fermenter where FZU60 exhibited exceptional lutein content, yield, and productivity reaching 6.14 mg/g, 285.02 mg/L, and 44.95 mg/L/d, respectively. Overall, this study successfully develops an effective cultivation strategy to address the inherent conflict between cell growth and lutein synthesis in algal cells, thereby demonstrating considerable potential as an industrial pathway for efficient lutein production.
{"title":"Two-stage trophic strategy coupled with fed-batch operation for simultaneous enhancement of cell growth and lutein synthesis in Chlorella sorokiniana","authors":"Zhen Zhang , Weixin Cai , Ruijuan Ma , Shih-Hsin Ho , Youping Xie , Jianfeng Chen","doi":"10.1016/j.bej.2025.109632","DOIUrl":"10.1016/j.bej.2025.109632","url":null,"abstract":"<div><div>The versatile trophic adaptability of <em>Chlorella sorokiniana</em> has garnered significant attention, establishing it as a promising alga for efficient lutein production. In this study, the lutein production characteristics of <em>C</em>. <em>sorokiniana</em> FZU60 were compared under autotrophic, mixotrophic, and heterotrophic conditions. The results demonstrated that glucose supplementation promoted algal cell growth but concurrently reduced lutein content. In contrast, light induction was essential for enhancing lutein synthesis. Consequently, two-stage trophic strategies were developed to simultaneously facilitate cell growth and lutein synthesis. It was determined that optimal lutein production could be achieved by employing the heterotrophy-mixotrophy strategy in conjunction with white light at 500 μmol/m<sup>2</sup>/s during the second stage (mixotrophic stage). Furthermore, combining the heterotrophy-mixotrophy strategy with fed-batch operation further enhanced the efficacy of lutein production in FZU60. The resulting lutein productivity demonstrated a remarkable 365.1 % improvement over the heterotrophy strategy (Strategy I) and an 80.8 % increase over the mixotrophy strategy (Strategy III), when both were coupled with fed-batch operation. These findings were subsequently validated in a 5 L fermenter where FZU60 exhibited exceptional lutein content, yield, and productivity reaching 6.14 mg/g, 285.02 mg/L, and 44.95 mg/L/d, respectively. Overall, this study successfully develops an effective cultivation strategy to address the inherent conflict between cell growth and lutein synthesis in algal cells, thereby demonstrating considerable potential as an industrial pathway for efficient lutein production.</div></div>","PeriodicalId":8766,"journal":{"name":"Biochemical Engineering Journal","volume":"215 ","pages":"Article 109632"},"PeriodicalIF":3.7,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143171497","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}
Pub Date : 2025-01-07DOI: 10.1016/j.bej.2025.109631
Min Li , Nuerla Ailijiang , Muzhapaer Mijiti , Yiping Wu , Yixian Wu , Xiaoxiao Luo , Junxuan Ma
Wastewater with a low COD/TIN ratio has low organic content and is difficult to treat at low-temperature conditions. To strengthen nitrogen removal performance at low temperature, this study adopted an up flow anaerobic-aerobic coupling system and applied low-frequency and low-voltage sinusoidal alternating current (LFV-AC) in an intermittent power supply mode. 5 Hz LFV-AC stimulation removed 80.6 % NH4+-N, which was 24.4 % greater than that of the control group. Using 10 Hz, 38.6 % more total inorganic nitrogen was removed than that in the control group. The results of the study show that intermittent LFV-AC stimulation can effectively increase the activity of denitrogenation-related enzyme genes and enhance their adaptability to low-temperature environments in biofilm reactors. Electrostimulation selectively enriched denitrifying bacteria (Thiothrix, Reyranella, Hydrogenophaga, Pseudomonas, etc.) and heterotrophic nitrifying and aerobic denitrifying bacteria Delftia associated with denitrification. However, LFV-AC with varying parameters exhibited distinct effects on the enrichment of denitrifying functional genes, resulting in differential accumulation of NO3--N concentrations. This further confirms the effectiveness of intermittent LFV-AC electrical stimulation in the treatment of low COD/TIN wastewater in biofilm reactors and provides an important reference for LFV-AC treatment of nitrogen-containing wastewater.
{"title":"Enhanced nitrogen removal at low temperature using low frequency-low voltage alternating electric current","authors":"Min Li , Nuerla Ailijiang , Muzhapaer Mijiti , Yiping Wu , Yixian Wu , Xiaoxiao Luo , Junxuan Ma","doi":"10.1016/j.bej.2025.109631","DOIUrl":"10.1016/j.bej.2025.109631","url":null,"abstract":"<div><div>Wastewater with a low COD/TIN ratio has low organic content and is difficult to treat at low-temperature conditions. To strengthen nitrogen removal performance at low temperature, this study adopted an up flow anaerobic-aerobic coupling system and applied low-frequency and low-voltage sinusoidal alternating current (LFV-AC) in an intermittent power supply mode. 5 Hz LFV-AC stimulation removed 80.6 % NH<sub>4</sub><sup>+</sup>-N, which was 24.4 % greater than that of the control group. Using 10 Hz, 38.6 % more total inorganic nitrogen was removed than that in the control group. The results of the study show that intermittent LFV-AC stimulation can effectively increase the activity of denitrogenation-related enzyme genes and enhance their adaptability to low-temperature environments in biofilm reactors. Electrostimulation selectively enriched denitrifying bacteria (<em>Thiothrix, Reyranella, Hydrogenophaga, Pseudomonas, etc</em>.) and heterotrophic nitrifying and aerobic denitrifying bacteria <em>Delftia</em> associated with denitrification. However, LFV-AC with varying parameters exhibited distinct effects on the enrichment of denitrifying functional genes, resulting in differential accumulation of NO<sub>3</sub><sup>-</sup>-N concentrations. This further confirms the effectiveness of intermittent LFV-AC electrical stimulation in the treatment of low COD/TIN wastewater in biofilm reactors and provides an important reference for LFV-AC treatment of nitrogen-containing wastewater.</div></div>","PeriodicalId":8766,"journal":{"name":"Biochemical Engineering Journal","volume":"215 ","pages":"Article 109631"},"PeriodicalIF":3.7,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143102910","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}
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