Journal of Industrial Microbiology & Biotechnology最新文献

{"title":"Correction to: CRISPRi screen for enhancing heterologous α-amylase yield in Bacillus subtilis.","authors":"","doi":"10.1093/jimb/kuad003","DOIUrl":"https://doi.org/10.1093/jimb/kuad003","url":null,"abstract":"Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark 2 Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark” instead of: “1 Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, 1172 Copenhagen, Denmark 2 Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, 1172 Copenhagen, Denmark”. This is a correction to: Adrian Sven Geissler, Annaleigh Ohrt Fehler, Line Dahl Poulsen, Enrique González-Tortuero, Thomas Beuchert Kallehauge, Ferhat Alkan, Christian Anthon, Stefan Ernst Seemann, Michael Dolberg Rasmussen, Anne Breüner, Carsten Hjort, Jeppe Vinther, Jan Gorodkin, CRISPRi screen for enhancing heterologous α-amylase yield in Bacillus subtilis , Journal of Industrial Microbiology and Biotechnology , kuac028, https://doi.org/ 10.1093/jimb/kuac028","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":"50 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2023-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10124125/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9702429","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Improvement of the stability and catalytic efficiency of heparan sulfate N-sulfotransferase for preparing N-sulfated heparosan.","authors":"Xintong Xi, Litao Hu, Hao Huang, Yang Wang, Ruirui Xu, Guocheng Du, Jian Chen, Zhen Kang","doi":"10.1093/jimb/kuad012","DOIUrl":"10.1093/jimb/kuad012","url":null,"abstract":"<p><p>The chemo-enzymatic and enzymatic synthesis of heparan sulfate and heparin are considered as an attractive alternative to the extraction of heparin from animal tissues. Sulfation of the hydroxyl group at position 2 of the deacetylated glucosamine is a prerequisite for subsequent enzymatic modifications. In this study, multiple strategies, including truncation mutagenesis based on B-factor values, site-directed mutagenesis guided by multiple sequence alignment, and structural analysis were performed to improve the stability and activity of human N-sulfotransferase. Eventually, a combined variant Mut02 (MBP-hNST-NΔ599-602/S637P/S741P/E839P/L842P/K779N/R782V) was successfully constructed, whose half-life at 37°C and catalytic activity were increased by 105-fold and 1.35-fold, respectively. After efficient overexpression using the Escherichia coli expression system, the variant Mut02 was applied to N-sulfation of the chemically deacetylated heparosan. The N-sulfation content reached around 82.87% which was nearly 1.88-fold higher than that of the wild-type. The variant Mut02 with high stability and catalytic efficiency has great potential for heparin biomanufacturing.</p>","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":"50 1","pages":""},"PeriodicalIF":3.2,"publicationDate":"2023-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/21/ec/kuad012.PMC10291996.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9706234","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Optimizing the strain engineering process for industrial-scale production of bio-based molecules.","authors":"Eric Abbate,&nbsp;Jennifer Andrion,&nbsp;Amanda Apel,&nbsp;Matthew Biggs,&nbsp;Julie Chaves,&nbsp;Kristi Cheung,&nbsp;Anthony Ciesla,&nbsp;Alia Clark-ElSayed,&nbsp;Michael Clay,&nbsp;Riarose Contridas,&nbsp;Richard Fox,&nbsp;Glenn Hein,&nbsp;Dan Held,&nbsp;Andrew Horwitz,&nbsp;Stefan Jenkins,&nbsp;Karolina Kalbarczyk,&nbsp;Nandini Krishnamurthy,&nbsp;Mona Mirsiaghi,&nbsp;Katherine Noon,&nbsp;Mike Rowe,&nbsp;Tyson Shepherd,&nbsp;Katia Tarasava,&nbsp;Theodore M Tarasow,&nbsp;Drew Thacker,&nbsp;Gladys Villa,&nbsp;Krishna Yerramsetty","doi":"10.1093/jimb/kuad025","DOIUrl":"10.1093/jimb/kuad025","url":null,"abstract":"<p><p>Biomanufacturing could contribute as much as ${$}$30 trillion to the global economy by 2030. However, the success of the growing bioeconomy depends on our ability to manufacture high-performing strains in a time- and cost-effective manner. The Design-Build-Test-Learn (DBTL) framework has proven to be an effective strain engineering approach. Significant improvements have been made in genome engineering, genotyping, and phenotyping throughput over the last couple of decades that have greatly accelerated the DBTL cycles. However, to achieve a radical reduction in strain development time and cost, we need to look at the strain engineering process through a lens of optimizing the whole cycle, as opposed to simply increasing throughput at each stage. We propose an approach that integrates all 4 stages of the DBTL cycle and takes advantage of the advances in computational design, high-throughput genome engineering, and phenotyping methods, as well as machine learning tools for making predictions about strain scale-up performance. In this perspective, we discuss the challenges of industrial strain engineering, outline the best approaches to overcoming these challenges, and showcase examples of successful strain engineering projects for production of heterologous proteins, amino acids, and small molecules, as well as improving tolerance, fitness, and de-risking the scale-up of industrial strains.</p>","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2023-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10548853/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10128135","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Improved 13C metabolic flux analysis in Escherichia coli metabolism: application of a high-resolution MS (GC-EI-QTOF) for comprehensive assessment of MS/MS fragments.","authors":"Chris Richter, Eva Grafahrend-Belau, Jörg Ziegler, Manish L Raorane, Björn H Junker","doi":"10.1093/jimb/kuad039","DOIUrl":"10.1093/jimb/kuad039","url":null,"abstract":"<p><p>Gas chromatography-tandem mass spectrometry with electron ionization (GC-EI-MS/MS) provides rich information on stable-isotope labeling for 13C-metabolic flux analysis (13C-MFA). To pave the way for the routine application of tandem MS data for metabolic flux quantification, we aimed to compile a comprehensive library of GC-EI-MS/MS fragments of tert-butyldimethylsilyl (TBDMS) derivatized proteinogenic amino acids. First, we established an analytical workflow that combines high-resolution gas chromatography-quadrupole time-of-flight mass spectrometry and fully 13C-labeled biomass to identify and structurally elucidate tandem MS amino acid fragments. Application of the high-mass accuracy MS procedure resulted into the identification of 129 validated precursor-product ion pairs of 13 amino acids with 30 fragments being accepted for 13C-MFA. The practical benefit of the novel tandem MS data was demonstrated by a proof-of-concept study, which confirmed the importance of the compiled library for high-resolution 13C-MFA.</p><p><strong>One sentence summary: </strong>An analytical workflow that combines high-resolution mass spectrometry (MS) and fully 13C-labeled biomass to identify and structurally elucidate tandem MS amino acid fragments, which provide positional information and therefore offering significant advantages over traditional MS to improve 13C-metabolic flux analysis.</p>","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2023-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10716738/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"92154743","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Antifungal activity and mechanism of action of natural product derivates as potential environmental disinfectants.","authors":"Norma Patricia Silva-Beltrán, Stephanie A Boon, M Khalid Ijaz, Julie McKinney, Charles P Gerba","doi":"10.1093/jimb/kuad036","DOIUrl":"10.1093/jimb/kuad036","url":null,"abstract":"<p><p>There have been a considerable number of antifungal studies that evaluated natural products (NPs), such as medicinal plants and their secondary metabolites, (phenolic compounds, alkaloids), essential oils, and propolis extracts. These studies have investigated natural antifungal substances for use as food preservatives, medicinal agents, or in agriculture as green pesticides because they represent an option of safe, low-impact, and environmentally friendly antifungal compounds; however, few have studied these NPs as an alternative to disinfection/sanitation for indoor air or environmental surfaces. This review summarizes recent studies on NPs as potential fungal disinfectants in different environments and provides information on the mechanisms of inactivation of these products by fungi. The explored mechanisms show that these NPs can interfere with ATP synthesis and Ca++ and K+ ion flow, mainly damaging the cell membrane and cell wall of fungi, respectively. Another mechanism is the reactive oxygen species effect that damages mitochondria and membranes. Inhibition of the overexpression of the efflux pump is another mechanism that involves damage to fungal proteins. Many NPs appear to have potential as indoor environmental disinfectants.</p><p><strong>One-sentence summary: </strong>This review shows the latest advances in natural antifungals applied to different indoor environments. Fungi have generated increased tolerance to the mechanisms of traditional antifungals, so this review also explores the various mechanisms of action of various natural products to facilitate the implementation of technology.</p>","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2023-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10710307/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89718608","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cytochromes P450 involved in bacterial RiPP biosyntheses.","authors":"Sylvia Kunakom,&nbsp;Hiroshi Otani,&nbsp;Daniel W Udwary,&nbsp;Drew T Doering,&nbsp;Nigel J Mouncey","doi":"10.1093/jimb/kuad005","DOIUrl":"https://doi.org/10.1093/jimb/kuad005","url":null,"abstract":"<p><p>Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a large class of secondary metabolites that have garnered scientific attention due to their complex scaffolds with potential roles in medicine, agriculture, and chemical ecology. RiPPs derive from the cleavage of ribosomally synthesized proteins and additional modifications, catalyzed by various enzymes to alter the peptide backbone or side chains. Of these enzymes, cytochromes P450 (P450s) are a superfamily of heme-thiolate proteins involved in many metabolic pathways, including RiPP biosyntheses. In this review, we focus our discussion on P450 involved in RiPP pathways and the unique chemical transformations they mediate. Previous studies have revealed a wealth of P450s distributed across all domains of life. While the number of characterized P450s involved in RiPP biosyntheses is relatively small, they catalyze various enzymatic reactions such as C-C or C-N bond formation. Formation of some RiPPs is catalyzed by more than one P450, enabling structural diversity. With the continuous improvement of the bioinformatic tools for RiPP prediction and advancement in synthetic biology techniques, it is expected that further cytochrome P450-mediated RiPP biosynthetic pathways will be discovered.</p><p><strong>Summary: </strong>The presence of genes encoding P450s in gene clusters for ribosomally synthesized and post-translationally modified peptides expand structural and functional diversity of these secondary metabolites, and here, we review the current state of this knowledge.</p>","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":"50 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2023-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/b1/fa/kuad005.PMC10124130.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9954485","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to: Fungi as a commercial source of eumelanin: current understanding & prospects.","authors":"","doi":"10.1093/jimb/kuad032","DOIUrl":"10.1093/jimb/kuad032","url":null,"abstract":"","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":"50 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2023-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/68/a3/kuad032.PMC10569374.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41203293","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Lessons from assembling a microbial natural product and pre-fractionated extract library in an academic laboratory.","authors":"Michael A Cook, Daniel Pallant, Linda Ejim, Arlene D Sutherland, Xiaodong Wang, Jarrod W Johnson, Susan McCusker, Xuefei Chen, Maya George, Sommer Chou, Kalinka Koteva, Wenliang Wang, Christian Hobson, Dirk Hackenberger, Nicholas Waglechner, Obi Ejim, Tracey Campbell, Ricardo Medina, Lesley T MacNeil, Gerard D Wright","doi":"10.1093/jimb/kuad042","DOIUrl":"10.1093/jimb/kuad042","url":null,"abstract":"<p><p>Microbial natural products are specialized metabolites that are sources of many bioactive compounds including antibiotics, antifungals, antiparasitics, anticancer agents, and probes of biology. The assembly of libraries of producers of natural products has traditionally been the province of the pharmaceutical industry. This sector has gathered significant historical collections of bacteria and fungi to identify new drug leads with outstanding outcomes-upwards of 60% of drug scaffolds originate from such libraries. Despite this success, the repeated rediscovery of known compounds and the resultant diminishing chemical novelty contributed to a pivot from this source of bioactive compounds toward more tractable synthetic compounds in the drug industry. The advent of advanced mass spectrometry tools, along with rapid whole genome sequencing and in silico identification of biosynthetic gene clusters that encode the machinery necessary for the synthesis of specialized metabolites, offers the opportunity to revisit microbial natural product libraries with renewed vigor. Assembling a suitable library of microbes and extracts for screening requires the investment of resources and the development of methods that have customarily been the proprietary purview of large pharmaceutical companies. Here, we report a perspective on our efforts to assemble a library of natural product-producing microbes and the establishment of methods to extract and fractionate bioactive compounds using resources available to most academic labs. We validate the library and approach through a series of screens for antimicrobial and cytotoxic agents. This work serves as a blueprint for establishing libraries of microbial natural product producers and bioactive extract fractions suitable for screens of bioactive compounds.</p><p><strong>One-sentence summary: </strong>Natural products are key to discovery of novel antimicrobial agents: Here, we describe our experience and lessons learned in constructing a microbial natural product and pre-fractionated extract library.</p>","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2023-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10724011/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138487744","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Abolishing storage lipids induces protein misfolding and stress responses in Yarrowia lipolytica.","authors":"Simone Zaghen, Oliver Konzock, Jing Fu, Eduard J Kerkhoven","doi":"10.1093/jimb/kuad031","DOIUrl":"10.1093/jimb/kuad031","url":null,"abstract":"<p><p>Yarrowia lipolytica naturally saves excess carbon as storage lipids. Engineering efforts allow redirecting the high precursor flux required for lipid synthesis toward added-value chemicals such as polyketides, flavonoids, and terpenoids. To redirect precursor flux from storage lipids to other products, four genes involved in triacylglycerol and sterol ester synthesis (DGA1, DGA2, LRO1, and ARE1) can be deleted. To elucidate the effect of the deletions on cell physiology and regulation, we performed chemostat cultivations under carbon and nitrogen limitations, followed by transcriptome analysis. We found that storage lipid-free cells show an enrichment of the unfolded protein response, and several biological processes related to protein refolding and degradation are enriched. Additionally, storage lipid-free cells show an altered lipid class distribution with an abundance of potentially cytotoxic free fatty acids under nitrogen limitation. Our findings not only highlight the importance of lipid metabolism on cell physiology and proteostasis, but can also aid the development of improved chassy strains of Y. lipolytica for commodity chemical production.</p>","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2023-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10563384/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41138947","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Monitoring biofilm growth and dispersal in real-time with impedance biosensors.","authors":"Matthew McGlennen,&nbsp;Markus Dieser,&nbsp;Christine M Foreman,&nbsp;Stephan Warnat","doi":"10.1093/jimb/kuad022","DOIUrl":"https://doi.org/10.1093/jimb/kuad022","url":null,"abstract":"<p><p>Microbial biofilm contamination is a widespread problem that requires precise and prompt detection techniques to effectively control its growth. Microfabricated electrochemical impedance spectroscopy (EIS) biosensors offer promise as a tool for early biofilm detection and monitoring of elimination. This study utilized a custom flow cell system with integrated sensors to make real-time impedance measurements of biofilm growth under flow conditions, which were correlated with confocal laser scanning microscopy (CLSM) imaging. Biofilm growth on EIS biosensors in basic aqueous growth media (tryptic soy broth, TSB) and an oil-water emulsion (metalworking fluid, MWF) attenuated in a sigmoidal decay pattern, which lead to an ∼22-25% decrease in impedance after 24 Hrs. Subsequent treatment of established biofilms increased the impedance by ∼14% and ∼41% in TSB and MWF, respectively. In the presence of furanone C-30, a quorum-sensing inhibitor (QSI), impedance remained unchanged from the initial time point for 18 Hrs in TSB and 72 Hrs in MWF. Biofilm changes enumerated from CLSM imaging corroborated impedance measurements, with treatment significantly reducing biofilm. Overall, these results support the application of microfabricated EIS biosensors for evaluating the growth and dispersal of biofilm in situ and demonstrate potential for use in industrial settings.</p><p><strong>One-sentence summary: </strong>This study demonstrates the use of microfabricated electrochemical impedance spectroscopy (EIS) biosensors for real-time monitoring and treatment evaluation of biofilm growth, offering valuable insights for biofilm control in industrial settings.</p>","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":"50 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2023-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10485796/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10251927","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}