Frontiers in Synthetic Biology最新文献

{"title":"A comprehensive review of Microfluidic approaches in cell-free synthetic biology","authors":"Amogh Kumar Baranwal, Sebastian J. Maerkl","doi":"10.3389/fsybi.2024.1397533","DOIUrl":"https://doi.org/10.3389/fsybi.2024.1397533","url":null,"abstract":"Cell-free synthetic biology has gained increasing popularity owing to its ability to elucidate biological functions in isolation from intricate cellular environments and the capacity to build increasingly complex biochemical systems in vitro. But cell-free transcription—translation systems are often only available in small volumes which has been a major challenge in the field. Microfluidic technologies helped address this challenge by enabling miniaturization and implementation of robust multi-step workflows. In this review, we highlight microfluidic technologies which have been applied to cell-free applications and discuss various ways in which they have advanced the boundaries of cell-free synthetic biology.","PeriodicalId":492179,"journal":{"name":"Frontiers in Synthetic Biology","volume":"55 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141007862","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biosurfactants as templates to inspire new environmental and health applications","authors":"Toriana N. Vigil, Samantha Felton, William E. Fahy, Mason A. Kinkeade, Alexandra M. Visek, Abigail R. Janiga, Sarah G. Jacob, Bryan W. Berger","doi":"10.3389/fsybi.2024.1303423","DOIUrl":"https://doi.org/10.3389/fsybi.2024.1303423","url":null,"abstract":"Life exists at an interface. One of the key characteristics of biological cells is compartmentalization, which is facilitated by lipids that create a water-impenetrable barrier to control transport of materials across the hydrophilic-hydrophobic interface. Microbial systems utilize a rich diversity of surfactants beyond lipids to adapt to an environmental niche, modify the properties of an interface, facilitate solubilization of nutrients for metabolism and as antimicrobials. As such, they are a fascinating class of biomolecules to study in terms of how effectiveness in an application or niche environment depends on sequence, structure and chemical properties. Moreover, there is increasing appreciation of the negative health and environmental impacts petrochemical-based surfactants can have, such as soil erosion and toxicity to plants and aquatic life, as well as the carbon footprint and associated greenhouse gas emissions associated with petrochemical surfactant manufacturing. In this review, we discuss the properties of biosurfactants and applications, and highlight key glycolipid-, protein- and peptide-based surfactants described in literature as examples of biosurfactants with unique potential and applications. As society looks towards the transition to a circular bioeconomy, we are excited by the potential of synthetic biology to develop new materials such as biosurfactants to facilitate this important transition.","PeriodicalId":492179,"journal":{"name":"Frontiers in Synthetic Biology","volume":"12 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140712510","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Escherichia coli adapts metabolically to 6- and 7-fluoroindole, enabling proteome-wide fluorotryptophan substitution","authors":"Christin Treiber-Kleinke, A. Berger, Lorenz Adrian, N. Budisa, Beate Koksch","doi":"10.3389/fsybi.2023.1345634","DOIUrl":"https://doi.org/10.3389/fsybi.2023.1345634","url":null,"abstract":"Nature has scarcely evolved a biochemistry around fluorine. However, modern science has shown that fluorinated organic molecules are suitable building blocks for biopolymers, from peptides and proteins up to entire organisms. Here, we conducted adaptive laboratory evolution (ALE) experiments to introduce organofluorine into living microorganisms. By cultivating Escherichia coli with fluorinated indole analogs, we successfully evolved microbial cells capable of utilizing either 6-fluoroindole or 7-fluoroindole for growth. Our improved ALE protocols enabled us to overcome previous challenges and adaptation was achieved, enabling a former growth inhibiting unnatural molecule to become a substrate for the cell’s protein synthesis machinery to the extent that the entire proteome underwent Trp to F-Trp substitution. In the ALE experiments, we supplied fluoroindoles to Trp-auxotrophic E. coli bacteria, exerting strong selective pressure that led to microbial adaptation. Within the cells, these indoles were converted into the corresponding amino acids (6- and 7-fluorotryptophan) and globally incorporated into the proteome at tryptophan sites. This study is a first step and establishes a strong foundation for further exploration of the mechanisms underlying fluorine-based life and how a former antimetabolite can become a vital nutrient.","PeriodicalId":492179,"journal":{"name":"Frontiers in Synthetic Biology","volume":" 30","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139619596","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Influence of three different manure treatments on antimicrobial resistance genes and mobile genetic elements","authors":"D. Flores-Orozco, David B. Levin, Ayush Kumar, R. Sparling, N. Cicek","doi":"10.3389/fsybi.2023.1301879","DOIUrl":"https://doi.org/10.3389/fsybi.2023.1301879","url":null,"abstract":"There is a growing concern about the potential dissemination of antimicrobial resistance into agricultural fields due to the application of manure as crop fertilizer. While reducing the usage of antibiotics in livestock production stands as the first alternative to prevent this problem, there is evidence that this may not be enough to eliminate antimicrobial resistance elements already present in manure microbiomes. This study employed a metagenomic approach to investigate the impact of common manure treatments, including aerobic storage, mesophilic anaerobic digestion (MAD), and solid-liquid separation, on the presence and abundance of antimicrobial resistance genes (ARGs), bactericides, and heavy metal resistance genes (BacMet), and mobile genetic elements (MGEs) in manure from three different farms, including one operating in an antibiotic-free environment. The results indicated that MAD was the best method to reduce the numbers of ARGs, BacMet, and MGEs, achieving reduction rates greater than 40%, 89%, and 68%, respectively. Manure storage significantly reduced BacMet levels (over 30%) and MGEs (28%) but had no significant effect on total ARG levels. Solids recovered through solid-liquid separation exhibited elevated levels of ARGs, BacMet, and MGEs, while the liquid fraction displayed levels similar to untreated manures. Correlation and co-occurrence modeling analyses indicated that changes in microbial communities, particularly fluctuations in aerobic and facultative communities belonging to Bacillota, Actinomycetota, and Pseudomonadota phyla, played a significant role in driving changes in ARGs, BacMet, and MGEs. The results also showed the presence of toxin-antitoxin and transposon systems near different ARGs. Overall, the results confirmed that genes conferring resistance to various antimicrobials and MGE capable of mobilizing them are widely spread in dairy farms; that even under the absence of antibiotics, the use of heavy metals and disinfectants may promote the maintenance of ARGs and MGEs, and; that treatment such as anaerobic digestion could reduce the risk of the spread of antimicrobial resistance.","PeriodicalId":492179,"journal":{"name":"Frontiers in Synthetic Biology","volume":"9 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138603579","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Seven governing principles in biology","authors":"Tae Seok Moon","doi":"10.3389/fsybi.2023.1296513","DOIUrl":"https://doi.org/10.3389/fsybi.2023.1296513","url":null,"abstract":"In physical science such as physics and chemistry, there are governing principles that are universal and applicable to all relevant systems, including energy conservation, entropy increase, uncertainty principle in quantum mechanics, and chemical equilibrium. However, what are governing principles in biology that are unique to all living systems? After collecting opinions and thoughts from diverse scientists and engineers all over the world, I summarize seven governing principles or laws in biology: central dogma, evolution, biological robustness, regeneration, reproduction, development, and causality. Some of these are not necessarily unique in biological systems from a reductionist’s point of view (e.g., causality), and others are applicable predominantly to eukaryotes (e.g., reproduction and development). Notably, many engineering systems have mimicked biological systems to enhance their performance. In this perspective article, I discuss these principles to better understand the rules of life and help construct improved engineering systems that we can use and control in an ethical, safe, and rational way.","PeriodicalId":492179,"journal":{"name":"Frontiers in Synthetic Biology","volume":"22 10","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135820816","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Synthetic biology encompasses metagenomics, ecosystems, and biodiversity sustainability within its scope","authors":"David B. Levin, Nediljko Budisa","doi":"10.3389/fsybi.2023.1255472","DOIUrl":"https://doi.org/10.3389/fsybi.2023.1255472","url":null,"abstract":"We envision the convergence of synthetic biology (SynBio) and metagenomics as a significant development for the engineering of complex biological systems. The entire biosphere with its diverse life forms can also be considered as a reservoir for evolutionary innovations and a source of modules for SynBio. Metagenomics, which is a large part of biodiversity, should be considered as an important source of modules. The abstraction hierarchy of amalgamating SynBio and metagenomics (“synthetic metagenomics”) entails the standardized integration of parts, devices, circuits, and modules into functional chassis. These principles transcend the boundaries of single cell design and apply to the engineering of biodiversity sustainability in multicellular entities, their interconnections, and their dynamics in communities and whole ecosystems. Examples include applications in environmental sustainability, such as analysis of antimicrobial resistance in waste management, bioremediation of oil spills, and degradation of plastics. Future research and experimental interventions will ultimately provide a strong link between bioengineering, metagenomics, microbial consortia, ecosystems, and biodiversity sustainability under the umbrella of synthetic biology.","PeriodicalId":492179,"journal":{"name":"Frontiers in Synthetic Biology","volume":"33 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135786184","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolving a mitigation of the stress response pathway to change the basic chemistry of life","authors":"Isabella Tolle, Stefan Oehm, Michael Georg Hoesl, Christin Treiber-Kleinke, Lauri Peil, Mihaela Bozukova, Suki Albers, Abdul-Rahman Adamu Bukari, Torsten Semmler, Juri Rappsilber, Zoya Ignatova, Aleeza C. Gerstein, Nediljko Budisa","doi":"10.3389/fsybi.2023.1248065","DOIUrl":"https://doi.org/10.3389/fsybi.2023.1248065","url":null,"abstract":"Despite billions of years of evolution, there have been only minor changes in the number and types of proteinogenic amino acids and the standard genetic code with codon assignments across the three domains of life. The rigidity of the genetic code sets it apart from other aspects of organismal evolution, giving rise to key questions about its origins and the constraints it places on innovation in translation. Through adaptive laboratory evolution (ALE) in Escherichia coli , we aimed to replace tryptophan (Trp) in the genetic code with an analogue L-β-(thieno[3,2-b]pyrrolyl)alanine ([3,2]Tpa). This required Escherichia coli to recruit thienopyrrole instead of indole and allowed reassignment of UGG codons. Crossing the stress response system emerged as a major obstacle for ancestral growth in the presence of [3,2]Tp and Trp limitation. During ALE, a pivotal innovation was the deactivation of the master regulon RpoS, which allowed growth solely in the presence of [3,2]Tp in minimal medium. Notably, knocking out the rpoS gene in the ancestral strain also facilitated growth on [3,2]Tp. Our findings suggest that regulatory constraints, not just a rigid translation mechanism, guard Life’s canonical amino acid repertoire. This knowledge will not only facilitate the design of more effective synthetic amino acid incorporation systems but may also shed light on a general biological mechanism trapping organismal configurations in a status quo .","PeriodicalId":492179,"journal":{"name":"Frontiers in Synthetic Biology","volume":"22 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134984098","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}