Biotechnology advances最新文献

{"title":"Bacterial 5′ UTR: A treasure-trove for post-transcriptional regulation","authors":"Ya-Jun Liu ,&nbsp;Xiaoqing Wang ,&nbsp;Yuman Sun ,&nbsp;Yingang Feng","doi":"10.1016/j.biotechadv.2024.108478","DOIUrl":"10.1016/j.biotechadv.2024.108478","url":null,"abstract":"<div><div>In bacteria, where gene transcription and translation occur concurrently, post-transcriptional regulation is acknowledged to be effective and precise. The 5′ untranslated regions (5′ UTRs) typically harbor diverse post-transcriptional regulatory elements, like riboswitches, RNA thermometers, small RNAs, and upstream open reading frames, that serve to modulate transcription termination, translation initiation, and mRNA stability. Consequently, exploring 5′ UTR-derived regulatory elements is vital for synthetic biology and metabolic engineering. Over the past few years, the investigation of successive mechanisms has facilitated the development of various genetic tools from bacterial 5′ UTRs. This review consolidates current understanding of 5′ UTR regulatory functions, presents recent progress in 5′ UTR-element design and screening, updates the tools and regulatory strategies developed, and highlights the challenges and necessity of establishing reliable bioinformatic analysis methods and non-model bacterial chassis in the future.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"78 ","pages":"Article 108478"},"PeriodicalIF":12.1,"publicationDate":"2024-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142646927","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Synthetic biology approaches to improve tolerance of inhibitors in lignocellulosic hydrolysates","authors":"Linyue Tian ,&nbsp;Tianqi Qi ,&nbsp;Fenghui Zhang ,&nbsp;Vinh G. Tran ,&nbsp;Jifeng Yuan ,&nbsp;Yuanpeng Wang ,&nbsp;Ning He ,&nbsp;Mingfeng Cao","doi":"10.1016/j.biotechadv.2024.108477","DOIUrl":"10.1016/j.biotechadv.2024.108477","url":null,"abstract":"<div><div>Increasing attention is being focused on using lignocellulose for valuable products. Microbial decomposition can convert lignocellulose into renewable biofuels and other high-value bioproducts, contributing to sustainable development. However, the presence of inhibitors in lignocellulosic hydrolysates can negatively affect microorganisms during fermentation. Improving microbial tolerance to these hydrolysates is a major focus in metabolic engineering. Traditional detoxification methods increase costs, so there is a need for cheap and efficient cell-based detoxification strategies. Synthetic biology approaches offer several strategies for improving microbial tolerance, including redox balancing, membrane engineering, omics-guided technologies, expression of protectants and transcription factors, irrational engineering, cell flocculation, and other novel technologies. Advances in molecular biology, high-throughput sequencing, and artificial intelligence (AI) allow for precise strain modification and efficient industrial production. Developing AI-based computational models to guide synthetic biology efforts and creating large-scale heterologous libraries with automation and high-throughput technologies will be important for future research.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"78 ","pages":"Article 108477"},"PeriodicalIF":12.1,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142646932","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fusarium as a promising fungal genus with potential application in bioremediation for pollutants mitigation: A review","authors":"Carmen Sánchez","doi":"10.1016/j.biotechadv.2024.108476","DOIUrl":"10.1016/j.biotechadv.2024.108476","url":null,"abstract":"<div><div><em>Fusarium</em> is genetically diverse and widely distributed geographically. It is one of the genera with more endophytes (which cause no damage to the host plants). This review highlights the capability of <em>Fusarium</em> species to degrade environmental pollutants and describes the biodegradation pathways of some of the emerging environmental contaminants. Some <em>Fusarium</em> species use metabolic strategies enabling them to efficiently mineralize high concentrations of toxic environmental pollutants. These fungi can degrade hydrocarbons, pesticides, herbicides, dyes, pharmaceutical compounds, explosives, plastics, and plastic additives, among other pollutants, and possess high metal biosorption capabilities. According to data from consulted reports, <em>Fusarium</em> strains showed a percentage of biodegradation of a variety of contaminants ranging between 30 % and 100 % for different tested concentrations (from 1 mg to 10 g/L) in a time range between 10 h and 90 d. Enzymes such as esterase, cutinase, laccase, lignin peroxidase, manganese peroxidase, dehydrogenase, lipase, dioxygenase, and phosphoesterase were detected during the pollutant biodegradation process. <em>Fusarium oxysporum</em>, <em>Fusarium solani</em>, and <em>Fusarium culmorum</em> are the most studied species of this genus. Owing to their metabolic versatility, these fungal species and their enzymes represent promising tools for bioremediation applications to mitigate the adverse effects of environmental pollution.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"77 ","pages":"Article 108476"},"PeriodicalIF":12.1,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142614093","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metabolic engineering of Corynebacterium glutamicum: Unlocking its potential as a key cell factory platform for organic acid production","authors":"Ming-Hou Li ,&nbsp;Han Li ,&nbsp;Xue Zhang ,&nbsp;Yu-Chen Liang ,&nbsp;Cheng Li ,&nbsp;Meng-Lin Sun ,&nbsp;Kai Li ,&nbsp;Chen-Guang Liu ,&nbsp;Anthony J. Sinskey","doi":"10.1016/j.biotechadv.2024.108475","DOIUrl":"10.1016/j.biotechadv.2024.108475","url":null,"abstract":"<div><div><em>Corynebacterium glutamicum</em>, a well-studied industrial model microorganism, has garnered widespread attention due to its ability for producing amino acids with a long history. In recent years, research efforts have been increasingly focused on exploring its potential for producing various organic acids beyond amino acids. Organic acids, which are characterized by their acidic functional groups, have diverse applications across industries such as food, agriculture, pharmaceuticals, and biobased materials. Leveraging advancements in metabolic engineering and synthetic biology, the metabolic pathways of <em>C. glutamicum</em> have been broadened to facilitate the production of numerous high-value organic acids. This review summarizes the recent progress in metabolic engineering for the production of both amino acids and other organic acids by <em>C. glutamicum</em>. Notably, these acids include, amino acids (lysine, isoleucine, and phenylalanine), TCA cycle-derived organic acids (succinic acid, α-ketoglutaric acid), aromatic organic acids (protocatechuate, 4-amino-3-hydroxybenzoic acid, anthranilate, and para-coumaric acid), and other organic acids (itaconic acid and cis, cis-muconic acid).</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"77 ","pages":"Article 108475"},"PeriodicalIF":12.1,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142614098","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbial electrosynthesis technology for CO2 mitigation, biomethane production, and ex-situ biogas upgrading","authors":"Tae Hyun Chung ,&nbsp;Simran Kaur Dhillon ,&nbsp;Chungheon Shin ,&nbsp;Deepak Pant ,&nbsp;Bipro Ranjan Dhar","doi":"10.1016/j.biotechadv.2024.108474","DOIUrl":"10.1016/j.biotechadv.2024.108474","url":null,"abstract":"<div><div>Currently, global annual CO₂ emissions from fossil fuel consumption are extremely high, surpassing tens of billions of tons, yet our capacity to capture and utilize CO₂ remains below a small fraction of the amount generated. Microbial electrosynthesis (MES) systems, an integration of microbial metabolism with electrochemistry, have emerged as a highly efficient and promising bio-based carbon-capture-and-utilization technology over other conventional techniques. MES is a unique technology for lowering the atmospheric CO₂ as well as CO₂ in the biogas, and also simultaneously convert them to renewable bioenergy, such as biomethane. As such, MES techniques could be applied for biogas upgrading to generate high purity biomethane, which has the potential to meet natural gas standards. This article offers a detailed overview and assessment of the latest advancements in MES for biomethane production and biogas upgrading, in terms of selecting optimal methane production pathways and associated electron transfer processes, different electrode materials and types, inoculum sources and microbial communities, ion-exchange membrane, externally applied energy level, operating temperature and pH, mode of operation, CO₂ delivery method, selection of inorganic carbon source and its concentration, start-up time, and system pressure. It also highlights the current MES challenges associated with upscaling, design and configuration, long-term stability, energy demand, techno-economics, achieving net negative carbon emission, and other operational issues. Moreover, we provide a summary of current and future opportunities to integrate MES with other unique biosystems, such as methanotrophic bioreactors, and incorporate quorum sensing, 3D printing, and machine learning to further develop MES as a better biomethane-producer and biogas upgrading technique.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"77 ","pages":"Article 108474"},"PeriodicalIF":12.1,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142614109","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biotechnological applications of purine and pyrimidine deaminases","authors":"Jon Del Arco ,&nbsp;Javier Acosta ,&nbsp;Jesús Fernández-Lucas","doi":"10.1016/j.biotechadv.2024.108473","DOIUrl":"10.1016/j.biotechadv.2024.108473","url":null,"abstract":"<div><div>Deaminases, ubiquitous enzymes found in all living organisms from bacteria to humans, serve diverse and crucial functions. Notably, purine and pyrimidine deaminases, while biologically essential for regulating nucleotide pools, exhibit exceptional versatility in biotechnology. This review systematically consolidates current knowledge on deaminases, showcasing their potential uses and relevance in the field of biotechnology. Thus, their transformative impact on pharmaceutical manufacturing is highlighted as catalysts for the synthesis of nucleic acid derivatives. Additionally, the role of deaminases in food bioprocessing and production is also explored, particularly in purine content reduction and caffeine production, showcasing their versatility in this field. The review also delves into most promising biomedical applications including deaminase-based GDEPT and genome and transcriptome editing by deaminase-based systems. All in all, illustrated with practical examples, we underscore the role of purine and pyrimidine deaminases in advancing sustainable and efficient biotechnological practices. Finally, the review highlights future challenges and prospects in deaminase-based biotechnological processes, encompassing both industrial and medical perspectives.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"77 ","pages":"Article 108473"},"PeriodicalIF":12.1,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142590090","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":"Harnessing Raman spectroscopy for cell therapy bioprocessing","authors":"Marta H.G. Costa ,&nbsp;Inês Carrondo ,&nbsp;Inês A. Isidro ,&nbsp;Margarida Serra","doi":"10.1016/j.biotechadv.2024.108472","DOIUrl":"10.1016/j.biotechadv.2024.108472","url":null,"abstract":"<div><div>Cell therapy manufacturing requires precise monitoring of critical parameters to ensure product quality, consistency and to facilitate the implementation of cost-effective processes. While conventional analytical methods offer limited real-time insights, integration of process analytical technology tools such as Raman spectroscopy in bioprocessing has the potential to drive efficiency and reliability during the manufacture of cell-based therapies while meeting stringent regulatory requirements. The non-destructive nature of Raman spectroscopy, combined with its ability to be integrated on-line with scalable platforms, allows for continuous data acquisition, enabling real-time correlations between process parameters and critical quality attributes.</div><div>Herein, we review the role of Raman spectroscopy in cell therapy bioprocessing and discuss how simultaneous measurement of distinct parameters and attributes, such as cell density, viability, metabolites and cell identity biomarkers can streamline on-line monitoring and facilitate adaptive process control. This, in turn, enhances productivity and mitigates process-related risks. We focus on recent advances integrating Raman spectroscopy across various manufacturing stages, from optimizing culture media feeds to monitoring bioprocess dynamics, covering downstream applications such as detection of co-isolated contaminating cells, cryopreservation, and quality control of the drug product. Finally, we discuss the potential of Raman spectroscopy to revolutionize current practices and accelerate the development of advanced therapy medicinal products.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"77 ","pages":"Article 108472"},"PeriodicalIF":12.1,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142567634","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":"Implications of glycosylation for the development of selected cytokines and their derivatives for medical use","authors":"Giulia Scapin ,&nbsp;Ece Cagdas ,&nbsp;Lise Marie Grav ,&nbsp;Nathan E Lewis ,&nbsp;Steffen Goletz ,&nbsp;Lise Hafkenscheid","doi":"10.1016/j.biotechadv.2024.108467","DOIUrl":"10.1016/j.biotechadv.2024.108467","url":null,"abstract":"<div><div>Cytokines are important regulators of immune responses, making them attractive targets for autoimmune diseases and cancer therapeutics. Yet, the significance of cytokine glycosylation remains underestimated. Many cytokines carry <em>N</em>- and <em>O</em>-glycans and some even undergo <em>C</em>-mannosylation. Recombinant cytokines produced in heterologous host cells may lack glycans or exhibit a different glycosylation pattern such as varying levels of galactosylation, sialylation, fucosylation or xylose addition compared to their human counterparts, potentially impacting critical immune interactions.</div><div>We focused on cytokines that are currently utilized or designed in advanced therapeutic formats, including immunocytokines, fusokines, engager cytokines, and genetically engineered ‘supercytokines.’ Despite the innovative designs of these cytokine derivatives, their glycosylation patterns have not been extensively studied. By examining the glycosylation of the human native cytokines, G-CSF and GM-CSF, interferons β and γ, TNF-α and interleukins-2, −3 -4, −6, −7, −9, −12, −13, −15, −17A, −21, and − 22, we aim to assess its potential impact on their therapeutic derivatives. Understanding the glycosylation of the native cytokines could provide critical insights into the safety, efficacy, and functionality of these next-generation cytokine therapies, affecting factors such as stability, bioactivity, antigenicity, and half-life. This knowledge can guide the choice of optimal expression hosts for production and advance the development of effective cytokine-based therapeutics and synthetic immunology drugs.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"77 ","pages":"Article 108467"},"PeriodicalIF":12.1,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142494479","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":"Constructed wetland microbial fuel cell as enhancing pollutants treatment technology to produce green energy","authors":"Iryna Rusyn ,&nbsp;Julio César Gómora-Hernández","doi":"10.1016/j.biotechadv.2024.108468","DOIUrl":"10.1016/j.biotechadv.2024.108468","url":null,"abstract":"<div><div>The persistent challenge of water pollution, exacerbated by slow progress in ecofriendly technologies and accumulating pollutants, underscores the need for innovative solutions. Constructed Wetland Microbial Fuel Cell (CW-MFC) emerges as an intriguing environmental technology capable of adressing this issue by eliminating contaminants from wastewater while simultaneously producing green energy as an additional bonus. In recent years, CW-MFC technology has gained attention due to its sustainability and promising prospects for a circular waste-free industry. However, due to various technological and biological challenges, it has not yet achieved wide-scale application. This review examines the current state of CW-MFC technology and identifies both biotic and abiotic strategies for optimization through operational and structural improvements affecting biocomponents. Our review highlights several key findings: (1) Plants play an important role in reducing the system's inner resistance through mechanisms such as radial oxygen loss, evapotranspiration, and high photosynthetic flow, which facilitate electroactive bacteria and affect redox potential. (2) Plant characteristics such as root porosity, phloem and aerenchyma development, chlorophyll content, and plant biomass are key indicators of CW-MFC performance and significantly impact both pollutant removal and energy harvesting. (3) We expand the criteria for selecting suitable plants to include mesophytes and C3 pollutant-tolerant species, in addition to traditional aquatic and C4 plants. Additionally, the review presents several technical approaches that enhance CW-MFC efficiency: (1) design optimization, (2) use of novel materials, and (3) application of external electrical fields, aeration, light, and temperature adjustments. CW-MFCs are capable of nearly complete elimination of a wide range of contaminants, including organic matter (84 % ± 10), total nitrogen (80 % ± 7) and phosphorus (79 % ± 18) compounds, metals (86 % ± 10), pharmaceuticals (87 % ± 7), dyes (90 % ± 8), and other complex pollutants, while generating green energy. We hope our findings will be useful in optimizing CW-MFC design and providing insights for researchers aiming to advance the technology and facilitate its future scaling.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"77 ","pages":"Article 108468"},"PeriodicalIF":12.1,"publicationDate":"2024-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142494480","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring the versatility of Porphyridium sp.: A comprehensive review of cultivation, bio-product extraction, purification, and characterization techniques","authors":"Anh Quynh Nguyen ,&nbsp;Maedeh Mohammadi ,&nbsp;Mahsa Alian ,&nbsp;Gangatharan Muralitharan ,&nbsp;Vikas Singh Chauhan ,&nbsp;Venkatesh Balan","doi":"10.1016/j.biotechadv.2024.108471","DOIUrl":"10.1016/j.biotechadv.2024.108471","url":null,"abstract":"<div><div>Interest in red microalgae of the <em>Porphyridium</em> genus has surged due to their richness in phycobiliproteins, polyunsaturated fatty acids, and sulfated polysaccharides. These biomasses and their derivatives find applications across food, feed, nutraceutical, pharmaceutical, and cosmetic industries. A deeper understanding of their properties and extraction methods is essential to optimize downstream processing. This paper comprehensively reviews <em>Porphyridium</em> sp., focusing on cultivation techniques, bioproduct extraction, purification, and characterization. It delves into protein, lipid, and polysaccharide extraction, considering the influence of culture conditions on biomass yield. Various methods like chromatography, electrophoresis, and membrane-based techniques for cell lysis and bioproduct recovery are explored, highlighting their pros and cons. By offering diverse insights, this review aims to inspire innovative research and industry progress in red microalgae biotechnology, contributing to sustainable solutions across sectors.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"77 ","pages":"Article 108471"},"PeriodicalIF":12.1,"publicationDate":"2024-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142494492","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}