Biotechnology and Bioengineering最新文献

{"title":"Manganese Peroxidase Participates in the Liquid–Solid–Gas Triphase Regulation on Microbial Degradation of Lignocellulose in Solid-State Fermentation","authors":"Lei Zhu, Juan Ding, Wenjing Xue, Shu Zhou, Longyu Wang, Ailiang Jiang, Mingwen Zhao, Qin He, Ang Ren","doi":"10.1002/bit.28927","DOIUrl":"https://doi.org/10.1002/bit.28927","url":null,"abstract":"The three-phase structure of solid-state fermentation (SSF) directly affects substrate degradation and fermentation efficiency. However, the mechanism of three-phase regulation on lignocellulose utilization and microbial metabolism is still unclear. Based on comparative transcriptome analysis, a lignocellulose degrading enzyme, manganese peroxidase (GlMnP), which was significantly affected by water stress meanwhile related to triphase utilization, was screened to reveal the mechanism using <i>Ganoderma lucidum</i> as the reference strain. The results showed that GlMnP directly participates in lignocellulose degradation by positively regulating the activity of carboxymethylcellulase (CMCase), filter paper (FPAse), and laccase (LACase) enzymes, and indirectly participates in lignocellulose degradation by negatively regulating the redox levels in microorganisms. In addition, GlMnP can also control microbial glycolysis rate to enhance lignocellulose utilization. The results indicated that GlMnP participates in the liquid–solid–gas triphase regulation on lignocellulose degradation by <i>G. lucidum</i> in SSF.","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"43 1","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142981671","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Engineering Gene and Protein Switches for Regulation of Lineage-Specifying Transcription Factors","authors":"Ana P. Teixeira, Nik Franko, Martin Fussenegger","doi":"10.1002/bit.28920","DOIUrl":"https://doi.org/10.1002/bit.28920","url":null,"abstract":"Human pluripotent stem cells (hPSCs) can be differentiated in vitro to an increasing number of mature cell types, presenting significant promise for addressing a wide range of diseases and studying human development. One approach to further enhance stem cell differentiation methods would be to coordinate multiple inducible gene or protein switches to operate simultaneously within the same cell, with minimal cross-interference, to precisely regulate a network of lineage-specifying transcription factors (TFs) to guide cell fate decisions. Therefore, in this study, we designed and tested various mammalian gene and protein switches responsive to clinically safe small-molecule inhibitors of viral proteases. First, we leveraged hepatitis C virus and human rhinovirus proteases to control the activity of chimeric transcription factors, enabling gene expression activation exclusively in the presence of protease inhibitors and achieving high fold-inductions in hPSC lines. Second, we built single-chain protein switches regulating the activity of three differentiation-related pancreatic TFs, MafA, Pdx1, and Ngn3, each engineered with a protease cleavage site within its structure and having the corresponding protease fused at one terminus. While variants lacking the protease retained most of the unmodified TF activity, the attachment of the protease significantly decreased the activity, which could be rescued upon addition of the corresponding protease inhibitor. We confirmed the functionality of these protein switches for simultaneously controlling the activity of three TFs with a common input molecule, as well as the orthogonality of each protease-based system to independently regulate two TFs. Finally, we validated these very compact systems for precisely controlling TF activity in hPSCs. Our results suggest that they will be valuable tools for research in both developmental biology and regenerative medicine.","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"11 1","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142968456","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Heterologous Expression and Optimization of Fermentation Conditions for Recombinant Ikarugamycin Production","authors":"Julia K. Evers, Anna Glöckle, Monique Wiegand, Sebastian Schuler, Manuel Einsiedler, Tobias A. M. Gulder","doi":"10.1002/bit.28919","DOIUrl":"https://doi.org/10.1002/bit.28919","url":null,"abstract":"Ikarugamycin is a member of the natural product family of the polycyclic tetramate macrolactams (PoTeMs). The compound exhibits a diverse range of biological activities, including antimicrobial, antiprotozoal, anti-leukemic, and anti-inflammatory properties. In addition, it interferes with several crucial cellular functions, such as oxidized low-density lipoprotein uptake in macrophages, Nef-induced CD4 cell surface downregulation, and mechanisms of endocytosis. It is, therefore, used as a tool compound to study diverse biological processes. However, ikarugamycin commercial prices are very high, with up to 1300 € per 1 mg, thus limiting its application. We, therefore, set out to develop a high-yielding recombinant production platform of ikarugamycin by screening different expression vectors, recombinant host strains, and cultivation conditions. Overall, this has led to overproduction levels of more than 100 mg/L, which, together with a straightforward purification protocol, establishes biotechnological access to affordable ikarugamycin enabling its increased use in biomedical research in the future.","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"16 1","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142962642","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biotechnology and Bioengineering: Volume 122, Number 2, February 2025","authors":"","doi":"10.1002/bit.28742","DOIUrl":"10.1002/bit.28742","url":null,"abstract":"","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"122 2","pages":"243-246"},"PeriodicalIF":3.5,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bit.28742","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142940433","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Effect of Accessibility of Insoluble Substrate on the Overall Kinetics of Enzymatic Degradation","authors":"Zdeněk Petrášek, Bernd Nidetzky","doi":"10.1002/bit.28921","DOIUrl":"https://doi.org/10.1002/bit.28921","url":null,"abstract":"The enzymatic reaction kinetics on cellulose and other solid substrates is limited by the access of the enzyme to the reactive substrate sites. We introduce a general model in which the reaction rate is determined by the active surface area, and the resulting kinetics consequently reflects the evolving relationship between the exposed substrate surface and the remaining substrate volume. Two factors influencing the overall surface-to-volume ratio are considered: the shape of the substrate particles, characterized by a single numerical parameter related to its dimensionality, and the distribution of the particle sizes. The model is formulated in a form of simple analytical equations, enabling fast and efficient application to experimental data, and facilitating its incorporation into more detailed and complex models. The application of the introduced formalism exploring its potential to account for the observed reaction rate is demonstrated on two examples: the derivation of particle size distribution from experimentally determined reaction kinetics, and the prediction of reaction slowdown from experimental particle size distribution.","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"29 1","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142935059","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-Scale Community Model-Guided Development of Bacterial Coculture for Lignocellulose Bioconversion","authors":"Pritam Kundu, Amit Ghosh","doi":"10.1002/bit.28918","DOIUrl":"https://doi.org/10.1002/bit.28918","url":null,"abstract":"Microbial communities have shown promising potential in degrading complex biopolymers, producing value-added products through collaborative metabolic functionality. Hence, developing synthetic microbial consortia has become a predominant technique for various biotechnological applications. However, diverse microbial entities in a consortium can engage in distinct biochemical interactions that pose challenges in developing mutualistic communities. Therefore, a systems-level understanding of the inter-microbial metabolic interactions, growth compatibility, and metabolic synergisms is essential for developing effective synthetic consortia. This study demonstrated a genome-scale community modeling approach to assess the inter-microbial interaction pattern and screen metabolically compatible bacterial pairs for designing the lignocellulolytic coculture system. Here, we have investigated the pairwise growth and biochemical synergisms among six termite gut bacterial isolates by implementing flux-based parameters, i.e., pairwise growth support index (PGSI) and metabolic assistance (PMA). Assessment of the PGSI and PMA helps screen nine beneficial bacterial pairs that were validated by designing a coculture experiment with lignocellulosic substrates. For the cocultured bacterial pairs, the experimentally measured enzymatic synergisms (DES) showed good coherence with model-derived biochemical compatibility (PMA), which explains the fidelity of the in silico predictions. The highest degree of enzymatic synergisms has been observed in <i>C. denverensis</i> P3 and <i>Brevibacterium</i> sp P5 coculture, where the total cellulase activity has been increased by 53%. Hence, the flux-based assessment of inter-microbial interactions and metabolic compatibility helps select the best bacterial coculture system with enhanced lignocellulolytic functionality. The flux-based parameters (PGSI and PMA) in the proposed community modeling strategy will help optimize the composition of microbial consortia for developing synthetic microcosms for bioremediation, bioengineering, and biomedical applications.","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"43 1","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142929716","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Novel, Site-Specific N-Linked Glycosylation Model Provides Mechanistic Insights Into the Process-Condition Dependent Distinct Fab and Fc Glycosylation of an IgG1 Monoclonal Antibody Produced by CHO VRC01 Cells","authors":"Jayanth Venkatarama Reddy, Thomas Leibiger, Sumit Kumar Singh, Kelvin H. Lee, Eleftherios Papoutsakis, Marianthi Ierapetritou","doi":"10.1002/bit.28916","DOIUrl":"https://doi.org/10.1002/bit.28916","url":null,"abstract":"The CHO VRC01 cell line produces an anti-HIV IgG1 monoclonal antibody containing N-linked glycans on both the Fab (variable) and Fc (constant) regions. Site-specific glycan analysis was used to measure the complex effects of cell culture process conditions on Fab and Fc glycosylation. Experimental data revealed major differences in glycan fractions across the two sites. Bioreactor pH was found to influence fucosylation, galactosylation, and sialylation in the Fab region and galactosylation in the Fc region. To understand the complex effects of process conditions on site-specific N-linked glycosylation, a kinetic model of site-specific N-linked glycosylation was developed. The model parameters provided mechanistic insights into the differences in glycan fractions observed in the Fc and Fab regions. Enzyme activities calculated from the model provided insights into the effect of bioreactor pH on site-specific N-linked glycosylation. Model predictions were experimentally tested by measuring glycosyltransferase-enzyme mRNA-levels and intracellular nucleotide sugar concentrations. The model was used to demonstrate the effect of increasing galactosyltransferase activity on site-specific N-linked glycan fractions. Experiments involving galactose and MnCl₂ supplementation were used to test model predictions. The model is capable of providing insights into experimentally measured data and also of making predictions that can be used to design media supplementation strategies.","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"7 1","pages":""},"PeriodicalIF":3.8,"publicationDate":"2024-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142905038","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Predictions to Increase Lasso Peptide Production in the Heterologous Host Streptomyces coelicolor M1152","authors":"Valeria Razmilic, Juan A. Asenjo, Irene Martínez","doi":"10.1002/bit.28917","DOIUrl":"https://doi.org/10.1002/bit.28917","url":null,"abstract":"Production of specialized metabolites are restricted to the metabolic capabilities of the organisms. Genome‐scale models (GEM)s are useful to study the whole metabolism and to find metabolic engineering targets to increase the yield of a target compound. In this work we use a modified model of <jats:italic>Streptomyces coelicolor</jats:italic> M145 to simulate the production of lagmysin A (LP4) and the novel lagmysin B (LP2) lasso peptide, in the heterologous host <jats:italic>Streptomyces coelicolor</jats:italic> M1152. Overexpression targets were identified using the flux scanning based on enforced objective flux (FSEOF) algorithm and flux variability analysis (FVA), considering growth in minimum and in complex medium. Thirteen reactions were found as candidate metabolic engineering targets for both lasso peptides considering both settings. We propose the overexpression of enzymes of the glycolysis pathway (GAPD, PGK, PGM and ENO) and leucine biosynthesis (IPPS, IPPMIb, IPPMIa, IPMD and OMCDC) to enhance the production of either lagmysin A or B.","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"327 1","pages":""},"PeriodicalIF":3.8,"publicationDate":"2024-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142901714","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CFD‐Based Determination of Optimal Design and Operating Conditions of a Fermentation Reactor Using Bayesian Optimization","authors":"Hongbum Choi, Kosan Roh, Jay H. Lee","doi":"10.1002/bit.28912","DOIUrl":"https://doi.org/10.1002/bit.28912","url":null,"abstract":"The efficiency of fermentation reactors is significantly impacted by gas dispersion and concentration distribution, which are influenced by the reactor's design and operating conditions. As the process scales up, optimizing these parameters becomes crucial due to the pronounced concentration gradients that can arise. This study integrates the kinetics of the fermentation process with hydrodynamic analysis using Bayesian optimization to efficiently determine the optimal reactor design and operating conditions. By utilizing computational fluid dynamics (CFD) simulations, the study provides a comprehensive assessment of distributions ranging from gas supply to cell growth. The results demonstrate that a combination of wide baffle width, narrow impeller gap, slow gas flow rate, and high agitation speed significantly enhances reactor performance by improving gas distribution and minimizing stagnant zones. These findings underscore the importance of considering both kinetic and hydrodynamic factors to achieve more precise and scalable fermentation processes, offering valuable insights for industrial applications.","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"154 1","pages":""},"PeriodicalIF":3.8,"publicationDate":"2024-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142887941","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"H2 Consumption by Various Acetogenic Bacteria Follows First‐Order Kinetics up to H2 Saturation","authors":"Laura Muñoz‐Duarte, Susmit Chakraborty, Louise Vinther Grøn, Maria Florencia Bambace, Jacopo Catalano, Jo Philips","doi":"10.1002/bit.28904","DOIUrl":"https://doi.org/10.1002/bit.28904","url":null,"abstract":"Acetogenic bacteria play an important role in various biotechnological processes, because of their chemolithoautotrophic metabolism converting carbon dioxide with molecular hydrogen (H<jats:sub>2</jats:sub>) as electron donor into acetate. As the main factor limiting acetogenesis is often H<jats:sub>2</jats:sub>, insights into the H<jats:sub>2</jats:sub> consumption kinetics of acetogens are required to assess their potential in biotechnological processes. In this study, initial H<jats:sub>2</jats:sub> consumption rates at a range of different initial H<jats:sub>2</jats:sub> concentrations were measured for three different acetogens. Interestingly, for all three strains, H<jats:sub>2</jats:sub> consumption was found to follow first‐order kinetics, i.e. the H<jats:sub>2</jats:sub> consumption rate increased linearly with the dissolved H<jats:sub>2</jats:sub> concentration, up to almost saturated H<jats:sub>2</jats:sub> levels (600 µM). This is in contrast with Monod kinetics and low half‐saturation concentrations, which have commonly been assumed for acetogens. The obtained biomass specific first‐order rate coefficients (<jats:italic>k</jats:italic><jats:sub>1</jats:sub><jats:sup>X</jats:sup>) were further validated by comparison with values obtained by fitting first‐order kinetics on previous time‐course experimental results. The latter method was also used to determine the <jats:italic>k</jats:italic><jats:sub>1</jats:sub><jats:sup>X</jats:sup> value of five additional acetogens strains. Biomass specific first‐order rate coefficients were found to vary up to six‐fold, with the highest <jats:italic>k</jats:italic><jats:sub>1</jats:sub><jats:sup>X</jats:sup> for <jats:italic>Acetobacterium wieringae</jats:italic> and the lowest for <jats:italic>Sporomusa sphaeroides</jats:italic>. Overall, our results demonstrate the importance of the dissolved H<jats:sub>2</jats:sub> concentration to understand the rate of acetogenesis in biotechnological systems.","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"48 1","pages":""},"PeriodicalIF":3.8,"publicationDate":"2024-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142887942","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}