Biotechnology for Biofuels最新文献

{"title":"Biofuel production: exploring renewable energy solutions for a greener future","authors":"R. El-Araby","doi":"10.1186/s13068-024-02571-9","DOIUrl":"10.1186/s13068-024-02571-9","url":null,"abstract":"<div><p>Biofuel production has emerged as a leading contender in the quest for renewable energy solutions, offering a promising path toward a greener future. This comprehensive state-of-the-art review delves into the current landscape of biofuel production, exploring its potential as a viable alternative to conventional fossil fuels. This study extensively examines various feedstock options, encompassing diverse sources such as plants, algae, and agricultural waste, and investigates the technological advancements driving biofuel production processes. This review highlights the environmental benefits of biofuels, emphasizing their capacity to significantly reduce greenhouse gas emissions compared to those of fossil fuels. Additionally, this study elucidates the role of biofuels in enhancing energy security by decreasing reliance on finite fossil fuel reserves, thereby mitigating vulnerabilities to geopolitical tensions and price fluctuations. The economic prospects associated with biofuel production are also elucidated, encompassing job creation, rural development, and the potential for additional revenue streams for farmers and landowners engaged in biofuel feedstock cultivation. While highlighting the promise of biofuels, the review also addresses the challenges and considerations surrounding their production. Potential issues such as land use competition, resource availability, and sustainability implications are critically evaluated. Responsible implementation, including proper land-use planning, resource management, and adherence to sustainability criteria, is emphasized as critical for the long-term viability of biofuel production. Moreover, the review underscores the importance of ongoing research and development efforts aimed at enhancing biofuel production efficiency, feedstock productivity, and conversion processes. Technological advancements hold the key to increasing biofuel yields, reducing production costs, and improving overall sustainability. This review uniquely synthesizes the latest advancements across the entire spectrum of biofuel production, from feedstock selection to end-use applications. It addresses critical research gaps by providing a comprehensive analysis of emerging technologies, sustainability metrics, and economic viability of various biofuel pathways. Unlike previous reviews, this work offers an integrated perspective on the interplay between technological innovation, environmental impact, and socio-economic factors in biofuel development, thereby providing a holistic framework for future research and policy directions in renewable energy.</p></div>","PeriodicalId":494,"journal":{"name":"Biotechnology for Biofuels","volume":"17 1","pages":""},"PeriodicalIF":6.1,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://biotechnologyforbiofuels.biomedcentral.com/counter/pdf/10.1186/s13068-024-02571-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142443271","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Elucidating Thermothielavioides terrestris secretome changes for improved saccharification of mild steam-pretreated spruce","authors":"Fabio Caputo,&nbsp;Romanos Siaperas,&nbsp;Camila Dias,&nbsp;Efstratios Nikolaivits,&nbsp;Lisbeth Olsson","doi":"10.1186/s13068-024-02569-3","DOIUrl":"10.1186/s13068-024-02569-3","url":null,"abstract":"<div><h3>Background</h3><p>The efficient use of softwood in biorefineries is hampered by its recalcitrance to enzymatic saccharification. In the present study, the fungus <i>Thermothielavioides terrestris</i> LPH172 was cultivated on three steam-pretreated spruce materials (STEX_180°C/auto, STEX_210°C/auto, and STEX_210°C/H2SO4), characterized by different hemicellulose content and structure, as well as on untreated biomass. The aim of the study was to map substrate-induced changes in the secretome of <i>T. terrestris</i> grown on differently treated spruce materials and to evaluate the hydrolytic efficiency of the secretome as supplement for a commercial enzyme mixture.</p><h3>Results</h3><p>The cultivation of <i>T. terrestris</i> was monitored by endo-cellulase, endo-xylanase, endo-mannanase, laccase, and peroxidase activity measurements. Proteomic analysis was performed on the secretomes induced by the spruce materials to map the differences in enzyme production. Growth of <i>T. terrestris</i> on STEX_180°C/auto and STEX_210°C/auto induced higher expression level of mannanases and mannosidases of the GH5_7 CAZy family compared to cultivation on the other materials. Cultivation on untreated biomass led to overexpression of GH47, GH76, and several hemicellulose debranching enzymes compared to the cultivation on the pretreated materials. <i>T. terrestris</i> grown on untreated, STEX_180°C/auto and STEX_210°C/auto induced three arabinofuranosidases of the GH43 and GH62 families; while growth on STEX_210°C/H2SO4 induced a GH51 arabinofuranosidase and a GH115 glucuronidase. All secretomes contained five lytic polysaccharide monooxygenases of the AA9 family. Supplementation of Celluclast® + Novozym188 with the secretome obtained by growing the fungus grown on STEX_180°C/auto achieved a twofold higher release of mannose from spruce steam-pretreated with acetic acid as catalyst, compared to the commercial enzyme cocktail alone.</p><h3>Conclusions</h3><p>Minor changes in the structure and composition of spruce affect the composition of fungal secretomes, with differences in some classes explaining an increased hydrolytic efficiency. As demonstrated here, saccharification of spruce biomass with commercial enzyme cocktails can be further enhanced by supplementation with tailor-made secretomes.</p></div>","PeriodicalId":494,"journal":{"name":"Biotechnology for Biofuels","volume":"17 1","pages":""},"PeriodicalIF":6.1,"publicationDate":"2024-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://biotechnologyforbiofuels.biomedcentral.com/counter/pdf/10.1186/s13068-024-02569-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142378709","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The overexpression of the switchgrass (Panicum virgatum L.) genes PvTOC1-N or PvLHY-K affects circadian rhythm and hormone metabolism in transgenic Arabidopsis seedlings","authors":"Shumeng Zhang,&nbsp;Jiayang Ma,&nbsp;Weiwei Wang,&nbsp;Chao Zhang,&nbsp;Fengli Sun,&nbsp;Yajun Xi","doi":"10.1186/s13068-024-02574-6","DOIUrl":"10.1186/s13068-024-02574-6","url":null,"abstract":"<div><p>Switchgrass (<i>Panicum virgatum</i> L.) is a perennial C4 warm-season grass known for its high-biomass yield and wide environmental adaptability, making it an ideal bioenergy crop. Despite its potential, switchgrass seedlings grow slowly, often losing out to weeds in field conditions and producing limited biomass in the first year of planting. Furthermore, during the reproductive growth stage, the above-ground biomass rapidly increases in lignin content, creating a significant saccharification barrier. Previous studies have identified rhythm-related genes <i>TOC1</i> and <i>LHY</i> as crucial to the slow seedling development in switchgrass, yet the precise regulatory functions of these genes remain largely unexplored. In this study, the genes <i>TOC1</i> and <i>LHY</i> were characterized within the tetraploid genome of switchgrass. Gene expression analysis revealed that <i>PvTOC1</i> and <i>PvLHY</i> exhibit circadian patterns under normal growth conditions, with opposing expression levels over time. <i>PvTOC1</i> genes were predominantly expressed in florets, vascular bundles, and seeds, while <i>PvLHY</i> genes showed higher expression in stems, leaf sheaths, and nodes. Overexpression of <i>PvTOC1</i> from the N chromosome group (<i>PvTOC1-N</i>) or <i>PvLHY</i> from the K chromosome group (<i>PvLHY-K</i>) in <i>Arabidopsis thaliana</i> led to alterations in circadian rhythm and hormone metabolism, resulting in shorter roots, delayed flowering, and decreased resistance to oxidative stress. These transgenic lines exhibited reduced sensitivity to hormones and hormone inhibitors, and displayed altered gene expression in the biosynthesis and signal transduction pathways of abscisic acid (ABA), gibberellin (GA), 3-indoleacetic acid (IAA), and strigolactone (SL). These findings highlight roles of <i>PvTOC1-N</i> and <i>PvLHY-K</i> in plant development and offer a theoretical foundation for genetic improvements in switchgrass and other crops.</p></div>","PeriodicalId":494,"journal":{"name":"Biotechnology for Biofuels","volume":"17 1","pages":""},"PeriodicalIF":6.1,"publicationDate":"2024-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://biotechnologyforbiofuels.biomedcentral.com/counter/pdf/10.1186/s13068-024-02574-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142373793","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Efficient enhancement of the antimicrobial activity of Chlamydomonas reinhardtii extract by transgene expression and molecular modification using ionizing radiation","authors":"Shubham Kumar Dubey,&nbsp;Seung Sik Lee,&nbsp;Jin-Hong Kim","doi":"10.1186/s13068-024-02575-5","DOIUrl":"10.1186/s13068-024-02575-5","url":null,"abstract":"<div><h3>Background</h3><p>Ionizing radiation has been used for mutagenesis or material modification. The potential to use microalgae as a platform for antimicrobial production has been reported, but little work has been done to advance it beyond characterization to biotechnology. This study explored two different applications of ionizing radiation as a metabolic remodeler and a molecular modifier to enhance the antimicrobial activity of total protein and solvent extracts of <i>Chlamydomonas reinhardtii</i> cells.</p><h3>Results</h3><p>First, highly efficient transgenic <i>C. reinhardtii</i> strains expressing the plant-derived antimicrobial peptides, AtPR1 or AtTHI2.1, were developed using the radiation-inducible promoter, <i>CrRPA70Ap</i>. Low transgene expression was significantly improved through X-irradiation (12–50 Gy), with peak activity observed within 2 h. Protein extracts from these strains after X-irradiation showed enhanced antimicrobial activity against the prokaryotic bacterium, <i>Pseudomonas syringae</i>, and the eukaryotic fungus, <i>Cryptococcus neoformans</i>. In addition, X-irradiation (12 Gy) increased the growth and biomass of the transgenic strains. Second, <i>C. reinhardtii</i> cell extracts in ethanol were γ-irradiated (5–20 kGy), leading to molecular modifications and increased antimicrobial activity against the phytopathogenic bacteria, <i>P. syringae</i> and <i>Burkholderia glumae</i>, in a dose-dependent manner. These changes were associated with alterations in fatty acid composition. When both transgenic expression of antimicrobial peptides and molecular modification of bioactive substances were applied, the antimicrobial activity of <i>C. reinhardtii</i> cell extracts was further enhanced to some extent.</p><h3>Conclusion</h3><p>Overall, these findings suggest that ionizing radiation can significantly enhance the antimicrobial potential of <i>C. reinhardtii</i> through efficient transgene expression and molecular modification of bioactive substances, making it a valuable source of natural antimicrobial agents. Ionizing radiation can act not only as a metabolic remodeler of transgene expression in microalgae but also as a molecular modifier of the bioactive substances.</p></div>","PeriodicalId":494,"journal":{"name":"Biotechnology for Biofuels","volume":"17 1","pages":""},"PeriodicalIF":6.1,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://biotechnologyforbiofuels.biomedcentral.com/counter/pdf/10.1186/s13068-024-02575-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142359789","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Process scale-up simulation and techno-economic assessment of ethanol fermentation from cheese whey","authors":"Mattia Colacicco,&nbsp;Claudia De Micco,&nbsp;Stefano Macrelli,&nbsp;Gennaro Agrimi,&nbsp;Matty Janssen,&nbsp;Maurizio Bettiga,&nbsp;Isabella Pisano","doi":"10.1186/s13068-024-02567-5","DOIUrl":"10.1186/s13068-024-02567-5","url":null,"abstract":"<div><h3>Background</h3><p>Production of cheese whey in the EU exceeded 55 million tons in 2022, resulting in lactose-rich effluents that pose significant environmental challenges. To address this issue, the present study investigated cheese-whey treatment via membrane filtration and the utilization of its components as fermentation feedstock. A simulation model was developed for an industrial-scale facility located in Italy’s Apulia region, designed to process 539 m³/day of untreated cheese-whey. The model integrated experimental data from ethanolic fermentation using a selected strain of <i>Kluyveromyces marxianus</i> in lactose-supplemented media, along with relevant published data.</p><h3>Results</h3><p>The simulation was divided into three different sections. The first section focused on cheese-whey pretreatment through membrane filtration, enabling the recovery of 56%_w/w whey protein concentrate, process water recirculation, and lactose concentration. In the second section, the recovered lactose was directed towards fermentation and downstream anhydrous ethanol production. The third section encompassed anaerobic digestion of organic residue, sludge handling, and combined heat and power production. Moreover, three different scenarios were produced based on ethanol yield on lactose (Y_E/L), biomass yield on lactose, and final lactose concentration in the medium. A techno-economic assessment based on the collected data was performed as well as a sensitivity analysis focused on economic parameters, encompassing considerations on cheese-whey by assessing its economical impact as a credit for the simulated facility, dictated by a gate fee, or as a cost by considering it a raw material. The techno-economic analysis revealed different minimum ethanol selling prices across the three scenarios. The best performance was obtained in the scenario presenting a Y_E/L = 0.45 g/g, with a minimum selling price of 1.43 €/kg. Finally, sensitivity analysis highlighted the model’s dependence on the price or credit associated with cheese-whey handling.</p><h3>Conclusions</h3><p>This work highlighted the importance of policy implementation in this kind of study, demonstrating how a gate fee approach applied to cheese-whey procurement positively impacted the final minimum selling price for ethanol across all scenarios. Additionally, considerations should be made about the implementation of the simulated process as a plug-in addition in to existing processes dealing with dairy products or handling multiple biomasses to produce ethanol.</p></div>","PeriodicalId":494,"journal":{"name":"Biotechnology for Biofuels","volume":"17 1","pages":""},"PeriodicalIF":6.1,"publicationDate":"2024-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://biotechnologyforbiofuels.biomedcentral.com/counter/pdf/10.1186/s13068-024-02567-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142329419","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microwave-assisted organic acids and green hydrogen production during mixed culture fermentation","authors":"Maximilian Barth,&nbsp;Magdalena Werner,&nbsp;Pascal Otto,&nbsp;Benjamin Richwien,&nbsp;Samira Bahramsari,&nbsp;Maximilian Krause,&nbsp;Benjamin Schwan,&nbsp;Christian Abendroth","doi":"10.1186/s13068-024-02573-7","DOIUrl":"10.1186/s13068-024-02573-7","url":null,"abstract":"<div><h3>Background</h3><p>The integration of anaerobic digestion into bio-based industries can create synergies that help render anaerobic digestion self-sustaining. Two-stage digesters with separate acidification stages allow for the production of green hydrogen and short-chain fatty acids, which are promising industrial products. Heat shocks can be used to foster the production of these products, the practical applicability of this treatment is often not addressed sufficiently, and the presented work therefore aims to close this gap.</p><h3>Methods</h3><p>Batch experiments were conducted in 5 L double-walled tank reactors incubated at 37 °C. Short microwave heat shocks of 25 min duration and exposure times of 5–10 min at 80 °C were performed and compared to oven heat shocks. Pairwise experimental group differences for gas production and chemical parameters were determined using ANOVA and post–hoc tests. High-throughput 16S rRNA gene amplicon sequencing was performed to analyse taxonomic profiles.</p><h3>Results</h3><p>After heat–shocking the entire seed sludge, the highest hydrogen productivity was observed at a substrate load of 50 g/l with 1.09 mol H₂/mol hexose. With 1.01 mol H₂/mol hexose, microwave-assisted treatment was not significantly different from oven-based treatments. This study emphasised the better repeatability of heat shocks with microwave-assisted experiments, revealing low variation coefficients averaging 29%. The pre-treatment with microwaves results in a high predictability and a stronger microbial community shift to <i>Clostridia</i> compared to the treatment with the oven. The pre-treatment of heat shocks supported the formation of butyric acid up to 10.8 g/l on average, with a peak of 24.01 g/l at a butyric/acetic acid ratio of 2.0.</p><h3>Conclusion</h3><p>The results support the suitability of using heat shock for the entire seed sludge rather than just a small inoculum, making the process more relevant for industrial applications. The performed microwave-based treatment has proven to be a promising alternative to oven-based treatments, which ultimately may facilitate their implementation into industrial systems. This approach becomes economically sustainable with high-temperature heat pumps with a coefficient of performance (COP) of 4.3.</p><h3>Graphical abstract</h3>\u0000<div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":494,"journal":{"name":"Biotechnology for Biofuels","volume":"17 1","pages":""},"PeriodicalIF":6.1,"publicationDate":"2024-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://biotechnologyforbiofuels.biomedcentral.com/counter/pdf/10.1186/s13068-024-02573-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142329389","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Divergent roles of ADP-ribosylation factor GTPase-activating proteins in lignocellulose utilization of Trichoderma guizhouense NJAU4742","authors":"Tuo Li,&nbsp;Qin Wang,&nbsp;Yang Liu,&nbsp;Jiaguo Wang,&nbsp;Han Zhu,&nbsp;Linhua Cao,&nbsp;Dongyang Liu,&nbsp;Qirong Shen","doi":"10.1186/s13068-024-02570-w","DOIUrl":"10.1186/s13068-024-02570-w","url":null,"abstract":"<div><h3>Background</h3><p>The ability of lignocellulose degradation for filamentous fungi is always attributed to their efficient CAZymes system with broader applications in bioenergy development. ADP-ribosylation factor GTPase-activating proteins (Arf-GAPs), pivotal in fungal morphogenesis, lack comprehensive studies on their regulatory mechanisms in lignocellulose utilization.</p><h3>Results</h3><p>Here, the orthologs (<i>Tg</i>Glo3 and <i>Tg</i>Gcs1) of Arf-GAPs in <i>S. cerevisiae</i> were characterized in <i>Trichoderma guizhouense</i> NJAU4742. The results indicated that overexpression of <i>Tggcs1</i> (OE-<i>Tggcs1</i>) enhanced the lignocellulose utilization, whereas increased expression of <i>Tgglo3</i> (OE-<i>Tgglo3</i>) elicited antithetical responses. On the fourth day of fermentation with rice straw as the sole carbon source, the activities of endoglucanase, cellobiohydrolase, xylanase, and filter paper of the wild-type strain (WT) reached 8.20 U mL⁻¹, 4.42 U mL⁻¹, 14.10 U mL⁻¹, and 3.56 U mL⁻¹, respectively. Compared to WT, the four enzymes activities of OE-<i>Tggcs1</i> increased by 7.93%, 6.11%, 9.08%, and 12.92%, respectively, while those decreased to varying degrees of OE-<i>Tgglo3</i>. During the nutritional growth, OE-<i>Tgglo3</i> resulted in the hyphal morphology characterized by sparsity and constriction, while OE-<i>Tggcs1</i> led to a notable increase in vacuole volume. In addition, OE-<i>Tggcs1</i> exhibited higher transport efficiencies for glucose and cellobiose thereby sustaining robust cellular metabolic rates. Further investigations revealed that <i>Tgglo3</i> and <i>Tggcs1</i> differentially regulated the transcription level of a dynamin-like GTPase gene (<i>Tggtp</i>), eliciting distinct redox states and apoptotic reaction, thus orchestrating the cellular response to lignocellulose utilization.</p><h3>Conclusions</h3><p>Overall, these findings underscored the significance of <i>Tg</i>Arf-GAPs as pivotal regulators in lignocellulose utilization and provided initial insights into their differential modulation of downstream targets.</p></div>","PeriodicalId":494,"journal":{"name":"Biotechnology for Biofuels","volume":"17 1","pages":""},"PeriodicalIF":6.1,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://biotechnologyforbiofuels.biomedcentral.com/counter/pdf/10.1186/s13068-024-02570-w","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142253567","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Engineering Escherichia coli for utilization of PET degraded ethylene glycol as sole feedstock","authors":"Junxi Chi,&nbsp;Pengju Wang,&nbsp;Yidan Ma,&nbsp;Xingmiao Zhu,&nbsp;Leilei Zhu,&nbsp;Ming Chen,&nbsp;Changhao Bi,&nbsp;Xueli Zhang","doi":"10.1186/s13068-024-02568-4","DOIUrl":"10.1186/s13068-024-02568-4","url":null,"abstract":"<div><p>From both economic and environmental perspectives, ethylene glycol, the principal constituent in the degradation of PET, emerges as an optimal feedstock for microbial cell factories. Traditional methods for constructing <i>Escherichia coli</i> chassis cells capable of utilizing ethylene glycol as a non-sugar feedstock typically involve overexpressing the genes <i>fucO</i> and <i>aldA</i>. However, these approaches have not succeeded in enabling the exclusive use of ethylene glycol as the sole source of carbon and energy for growth. Through ultraviolet radiation-induced mutagenesis and subsequent laboratory adaptive evolution, an EG02 strain emerged from <i>E. coli</i> MG1655 capable of utilizing ethylene glycol as its sole carbon and energy source, demonstrating an uptake rate of 8.1 ± 1.3 mmol/gDW h. Comparative transcriptome analysis guided reverse metabolic engineering, successfully enabling four wild-type <i>E. coli</i> strains to metabolize ethylene glycol exclusively. This was achieved through overexpression of the <i>gcl</i>, <i>hyi</i>, <i>glxR</i>, and <i>glxK</i> genes. Notably, the engineered <i>E. coli</i> chassis cells efficiently metabolized the 87 mM ethylene glycol found in PET enzymatic degradation products following 72 h of fermentation. This work presents a practical solution for recycling ethylene glycol from PET waste degradation products, demonstrating that simply adding M9 salts can effectively convert them into viable raw materials for <i>E. coli</i> cell factories. Our findings also emphasize the significant roles of genes associated with the glycolate and glyoxylate degradation I pathway in the metabolic utilization of ethylene glycol, an aspect frequently overlooked in previous research.</p></div>","PeriodicalId":494,"journal":{"name":"Biotechnology for Biofuels","volume":"17 1","pages":""},"PeriodicalIF":6.1,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://biotechnologyforbiofuels.biomedcentral.com/counter/pdf/10.1186/s13068-024-02568-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142206069","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Discovery of alkaline laccases from basidiomycete fungi through machine learning-based approach","authors":"Xing Wan,&nbsp;Sazzad Shahrear,&nbsp;Shea Wen Chew,&nbsp;Francisco Vilaplana,&nbsp;Miia R. Mäkelä","doi":"10.1186/s13068-024-02566-6","DOIUrl":"10.1186/s13068-024-02566-6","url":null,"abstract":"<div><h3>Background</h3><p>Laccases can oxidize a broad spectrum of substrates, offering promising applications in various sectors, such as bioremediation, biomass fractionation in future biorefineries, and synthesis of biochemicals and biopolymers. However, laccase discovery and optimization with a desirable pH optimum remains a challenge due to the labor-intensive and time-consuming nature of the traditional laboratory methods.</p><h3>Results</h3><p>This study presents a machine learning (ML)-integrated approach for predicting pH optima of basidiomycete fungal laccases, utilizing a small, curated dataset against a vast metagenomic data. Comparative computational analyses unveiled the structural and pH-dependent solubility differences between acidic and neutral-alkaline laccases, helping us understand the molecular bases of enzyme pH optimum. The pH profiling of the two ML-predicted alkaline laccase candidates from the basidiomycete fungus <i>Lepista nuda</i> further validated our computational approach, showing the accuracy of this comprehensive method.</p><h3>Conclusions</h3><p>This study uncovers the efficacy of ML in the prediction of enzyme pH optimum from minimal datasets, marking a significant step towards harnessing computational tools for systematic screening of enzymes for biotechnology applications.</p><h3>Graphical Abstract</h3>\u0000<div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":494,"journal":{"name":"Biotechnology for Biofuels","volume":"17 1","pages":""},"PeriodicalIF":6.1,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://biotechnologyforbiofuels.biomedcentral.com/counter/pdf/10.1186/s13068-024-02566-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142169810","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Clostridium autoethanogenum alters cofactor synthesis, redox metabolism, and lysine-acetylation in response to elevated H2:CO feedstock ratios for enhancing carbon capture efficiency","authors":"Megan E. Davin,&nbsp;R. Adam Thompson,&nbsp;Richard J. Giannone,&nbsp;Lucas W. Mendelson,&nbsp;Dana L. Carper,&nbsp;Madhavi Z. Martin,&nbsp;Michael E. Martin,&nbsp;Nancy L. Engle,&nbsp;Timothy J. Tschaplinski,&nbsp;Steven D. Brown,&nbsp;Robert L. Hettich","doi":"10.1186/s13068-024-02554-w","DOIUrl":"10.1186/s13068-024-02554-w","url":null,"abstract":"<div><h3>Background</h3><p><i>Clostridium autoethanogenum</i> is an acetogenic bacterium that autotrophically converts carbon monoxide (CO) and carbon dioxide (CO₂) gases into bioproducts and fuels via the Wood–Ljungdahl pathway (WLP). To facilitate overall carbon capture efficiency, the reaction stoichiometry requires supplementation of hydrogen at an increased ratio of H₂:CO to maximize CO₂ utilization; however, the molecular details and thus the ability to understand the mechanism of this supplementation are largely unknown.</p><h3>Results</h3><p>In order to elucidate the microbial physiology and fermentation where at least 75% of the carbon in ethanol comes from CO₂, we established controlled chemostats that facilitated a novel and high (11:1) H₂:CO uptake ratio. We compared and contrasted proteomic and metabolomics profiles to replicate continuous stirred tank reactors (CSTRs) at the same growth rate from a lower (5:1) H₂:CO condition where ~ 50% of the carbon in ethanol is derived from CO₂. Our hypothesis was that major changes would be observed in the hydrogenases and/or redox-related proteins and the WLP to compensate for the elevated hydrogen feed gas. Our analyses did reveal protein abundance differences between the two conditions largely related to reduction–oxidation (redox) pathways and cofactor biosynthesis, but the changes were more minor than we would have expected. While the Wood–Ljungdahl pathway proteins remained consistent across the conditions, other post-translational regulatory processes, such as lysine-acetylation, were observed and appeared to be more important for fine-tuning this carbon metabolism pathway. Metabolomic analyses showed that the increase in H₂:CO ratio drives the organism to higher carbon dioxide utilization resulting in lower carbon storages and accumulated fatty acid metabolite levels.</p><h3>Conclusions</h3><p>This research delves into the intricate dynamics of carbon fixation in <i>C. autoethanogenum</i>, examining the influence of highly elevated H₂:CO ratios on metabolic processes and product outcomes. The study underscores the significance of optimizing gas feed composition for enhanced industrial efficiency, shedding light on potential mechanisms, such as post-translational modifications (PTMs), to fine-tune enzymatic activities and improve desired product yields.</p></div>","PeriodicalId":494,"journal":{"name":"Biotechnology for Biofuels","volume":"17 1","pages":""},"PeriodicalIF":6.1,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://biotechnologyforbiofuels.biomedcentral.com/counter/pdf/10.1186/s13068-024-02554-w","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142123085","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}