Journal of Industrial Microbiology & Biotechnology最新文献

{"title":"Molecular evolution of nucleoside deoxyribosyl transferase to enhance the activity toward 2'-fluoro-2'-deoxynucleoside.","authors":"Su-Been Yang, Yeon-Jin Yoo, Kanghyun Choi, Byungkyun Kim, Si-Sun Choi, Seung-Hoon Kang, Eung-Soo Kim","doi":"10.1093/jimb/kuaf005","DOIUrl":"10.1093/jimb/kuaf005","url":null,"abstract":"<p><p>Nucleoside deoxyribosyl transferase (NDT) is an enzyme that catalyzes the transfer of purine and pyrimidine bases between 2'-deoxyribonucleosides and is widely used for synthesizing nucleoside analogs in various biotechnological applications. While NDT exhibits high activity toward natural nucleosides, its activity toward unnatural nucleoside analogs is significantly lower. Previously, the NDT mutant named fNDT(L59Q) was identified displaying 4.4-fold higher activity toward 2'-fluoro-2'-deoxyuridine (2FDU). In this study, molecular evolution strategies using error-prone PCR were employed to further generate mutant enzymes with enhanced activity toward 2FDU. After two rounds of mutational screening, two mutant clones that exhibited high activity against 2FDU were identified as fNDT-i1 (V52A) and fNDT-i2 (L28I), respectively. A double mutant, fNDT-i4, was subsequently constructed by combining the V52A and L28I mutations. Whole-cell-based activity measurements showed that fNDT-i4 exhibited 4.0- and 20.6-fold higher activity at 40°C and 50°C, respectively, compared to the wild-type NDT. The detailed characterization of the purified enzymes conducted under various conditions, including temperature, pH, thermal stability, and enzyme kinetics experiments, showed that fNDT-i1 and fNDT-i4 exhibited 3.1- and 3.7-fold higher catalytic efficiency, respectively than wild-type NDT. The L59Q mutation was identified as a key factor in improving the thermal stability, whereas the V52A and L28I mutations were critical for improving substrate affinity and reaction efficiency. These findings provide the potential of fNDT-i1 and fNDT-i4 as highly efficient biocatalysts for developing industrially relevant nucleoside analog synthesis.</p><p><strong>One-sentence summary: </strong>The nucleoside deoxyribosyl transferase mutant were engineered to enhance biological activity and physical resistance for production of fluorinated deoxynucleoside as a raw material of oligonucleotide therapeutics.</p>","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11892431/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143501903","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":"Adoption of a novel medium for the industrial (3000 L) production of Serendipita indica employing a nutrient limitation strategy using insoluble carbon and phosphate sources.","authors":"Jubair Al Rashid, Md Abuhena, Md Dilshad Karim, Lutfur Rahman, Jingjing Wang, Zhiyong Huang","doi":"10.1093/jimb/kuaf009","DOIUrl":"https://doi.org/10.1093/jimb/kuaf009","url":null,"abstract":"<p><p>The use of the endophytic fungus Serendipita indica has rapidly increased due to its wide range of host species, ability to foster plant-growth, and ability to confer tolerance to a number of stresses. However, its industrial-scale production is still in its infancy due to its low-biomass yield and prolonged cultivation time. Thus far, Hill-Kafer medium has traditionally been used for S. indica cultivation, resulting in lower yields and excessively long incubation times. Here, we adopted a simple insoluble carbon and phosphate input medium for rapidly generating high biomass. We developed and optimized the SIF1 medium, achieving maximum biomass production (424.5 ± 1.9 g/L), significantly outperforming Hill-Kafer medium. Statistical optimization of SIF1 identified optimal levels (15 g/L oats, 7.5 g/L tricalcium phosphate, 95-hr incubation). Validated results in the laboratory (FUS-10 L: 484.4 ± 4.7), pilot (300 L: 496.5 ± 7 g/L), and industrial (3000L: 492.4 ± 7.1 g/L) bioreactors proved the efficacy of SIF1. Compared to Hill-Kafer (54.8 ± 3.7 g/L), SIF1 showed nine-fold higher biomass productivity and reduced cultivation time by approximately 6 days. Based on our findings, it appears that SF1 will be a highly efficient medium for producing S. indica on an industrial scale and expanding its use.</p><p><strong>One-sentence summary: </strong>This study presents a rapid industrial production strategy for the beneficial fungus Serendipita indica, providing a scalable solution for wider applications and contributing to global food security and environmental sustainability.</p>","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":"52 ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12010874/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143969704","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":"Purple non-sulfur bacteria for biotechnological applications.","authors":"Hailee M Morrison, Arpita Bose","doi":"10.1093/jimb/kuae052","DOIUrl":"10.1093/jimb/kuae052","url":null,"abstract":"<p><p>In this review, we focus on how purple non-sulfur bacteria can be leveraged for sustainable bioproduction to support the circular economy. We discuss the state of the field with respect to the use of purple bacteria for energy production, their role in wastewater treatment, as a fertilizer, and as a chassis for bioplastic production. We explore their ability to serve as single-cell protein and production platforms for fine chemicals from waste materials. We also introduce more Avant-Garde technologies that leverage the unique metabolisms of purple bacteria, including microbial electrosynthesis and co-culture. These technologies will be pivotal in our efforts to mitigate climate change and circularize the economy in the next two decades.</p><p><strong>One-sentence summary: </strong>Purple non-sulfur bacteria are utilized for a range of biotechnological applications, including the production of bio-energy, single cell protein, fertilizer, bioplastics, fine chemicals, in wastewater treatment and in novel applications like co-cultures and microbial electrosynthesis.</p>","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11730080/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142895168","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":"Control of industrially relevant microbial isolates by antimicrobial agents: Implications for sugar factories.","authors":"Gillian O Bruni, Evan Terrell, K Thomas Klasson, Yunci Qi","doi":"10.1093/jimb/kuaf001","DOIUrl":"10.1093/jimb/kuaf001","url":null,"abstract":"<p><p>Microbial isolates from sugar crop processing facilities were tested for sensitivity to several industrial antimicrobial agents to determine optimal dosing. Hydritreat 2216 showed broad-spectrum activity against all bacterial isolates as well as Saccharomyces cerevisiae. Sodium hypochlorite showed broad-spectrum activity against all isolates, but at much higher effective concentrations. Hops BetaStab XL was effective against Gram-positive isolates. Magna Cide D minimum inhibitory concentration was lowest for S. cerevisiae and Zymomonas mobilis but was less effective against Gram-positive bacterial strains. Based on laboratory experiments, factory losses of sucrose from a single microbial species in the absence of antimicrobials could range from 0.13 to 0.52 kg of sucrose per tonne of cane. Additional improvements in sugar yield are anticipated from agents with broad-spectrum activity. A cost analysis was conducted considering sucrose savings due to antimicrobial application to provide estimates for break-even costs, which ranged from approximately $0.50 to $2.00/L for a given antimicrobial agent.</p><p><strong>One-sentence summary: </strong>Application of antimicrobial agents at minimal inhibitory doses for microbes results in optimal inhibition of microbial growth and sucrose consumption.</p>","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11744779/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142950107","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":"Development of Modular Expression Across Phylogenetically Distinct Diazotrophs","authors":"Shawn Kulakowski, Alex Rivier, Rita Kuo, Sonya Mengel, Thomas Eng","doi":"10.1093/jimb/kuae033","DOIUrl":"https://doi.org/10.1093/jimb/kuae033","url":null,"abstract":"Diazotrophic bacteria can reduce atmospheric nitrogen into ammonia enabling bioavailability of the essential element. Many diazotrophs closely associate with plant roots increasing nitrogen availability, acting as plant growth promoters. These associations have the potential to reduce the need for costly synthetic fertilizers if they could be engineered for agricultural applications. However, despite the importance of diazotrophic bacteria, genetic tools are poorly developed in a limited number of species, in turn narrowing the crops and root microbiomes that can be targeted. Here we report optimized protocols and plasmids to manipulate phylogenetically diverse diazotrophs with the goal of enabling synthetic biology and genetic engineering. Three broad-host-range plasmids can be used across multiple diazotrophs, with the identification of one specific plasmid (containing origin of replication RK2 and a kanamycin resistance marker) showing the highest degree of compatibility across bacteria tested. We then demonstrated modular expression by testing seven promoters and eleven ribosomal binding sites using proxy fluorescent proteins. Finally, we tested four small molecule inducible systems to report expression in three diazotrophs and demonstrated genome editing in Klebsiella michiganensis M5al.","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":"4 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142205949","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Simultaneous enumeration of yeast and bacterial cells in the context of industrial bioprocesses","authors":"Carolina Teixeira Martins, Ana Paula Jacobus, Renilson Conceição, Douglas Fernandes Barbin, Helena Bolini, Andreas Karoly Gombert","doi":"10.1093/jimb/kuae029","DOIUrl":"https://doi.org/10.1093/jimb/kuae029","url":null,"abstract":"In scenarios where yeast and bacterial cells coexist, it is of interest to simultaneously quantify the concentrations of both cell types, since traditional methods used to determine these concentrations individually take more time and resources. Here, we compared different methods for quantifying the fuel ethanol Saccharomyces cerevisiae PE-2 yeast strain and cells from the probiotic Lactiplantibacillus plantarum strain in microbial suspensions. Individual suspensions were prepared, mixed in 1:1 or 100:1 yeast-to-bacteria ratios, covering the range typically encountered in sugarcane biorefineries, and analyzed using bright field microscopy, manual and automatic Spread-plate and Drop-plate counting, flow cytometry (at 1:1 and 100:1 ratios), and a Coulter Counter (at 1:1 and 100:1 ratios). We observed that for yeast cell counts in the mixture (1:1 and 100:1 ratios), flow cytometry, the Coulter Counter, and both Spread-plate options (manual and automatic CFU counting) yielded statistically similar results, while the Drop-plate and microscopy-based methods gave statistically different results. For bacterial cell quantification, the microscopy-based method, Drop-plate, and both Spread-plate plating options and flow cytometry (1:1 ratio) produced no significantly different results (p &amp;gt; .05). In contrast, the Coulter Counter (1:1 ratio) and flow cytometry (100:1 ratio) presented results statistically different (p &amp;lt; .05). Additionally, quantifying bacterial cells in a mixed suspension at a 100:1 ratio wasn't possible due to an overlap between yeast cell debris and bacterial cells. We conclude that each method has limitations, advantages, and disadvantages. One-Sentence Summary This study compares methods for simultaneously quantifying yeast and bacterial cells in a mixed sample, highlighting that in different cell proportions, some methods cannot quantify both cell types and present distinct advantages and limitations regarding time, cost, and precision.","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":"57 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142205852","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multi-modular metabolic engineering and efflux engineering for enhanced lycopene production in recombinant Saccharomyces cerevisiae","authors":"Guangxi Huang, Jiarong Li, Jingyuan Lin, Changqing Duan, Guoliang Yan","doi":"10.1093/jimb/kuae015","DOIUrl":"https://doi.org/10.1093/jimb/kuae015","url":null,"abstract":"Lycopene has been widely used in the food industry and medical field due to its antioxidant, anti-cancer, and anti-inflammatory properties. However, achieving efficient manufacture of lycopene using chassis cells on an industrial scale remains a major challenge. Herein, we attempted to integrate multiple metabolic engineering strategies to establish an efficient and balanced lycopene biosynthetic system in Saccharomyces cerevisiae. First, the lycopene synthesis pathway was modularized to sequentially enhance the metabolic flux of the Mevalonate pathway, the acetyl-CoA supply module, and lycopene exogenous enzymatic module. The modular operation enabled the efficient conversion of acetyl-CoA to downstream pathway of lycopene synthesis, resulting in a 3.1-fold increase of lycopene yield. Second, we introduced acetate as an exogenous carbon source and utilized an acetate-repressible promoter to replace the natural ERG9 promoter. This approach not only enhanced the supply of acetyl-CoA but also concurrently diminished the flux towards the competitive ergosterol pathway. As a result, a further 42.3% increase in lycopene production was observed. Third, we optimized NADPH supply and mitigated cytotoxicity by overexpressing ABC transporters to promote lycopene efflux. The obtained strain YLY-PDR11 showed a 12.7-fold increase in extracellular lycopene level compared to the control strain. Finally, the total lycopene yield reached 343.7mg/L, which was 4.3 times higher than that of the initial strain YLY-04. Our results demonstrate that combining multi-modular metabolic engineering with efflux engineering is an effective approach to improve the production of lycopene. This strategy can also be applied to the overproduction of other desirable isoprenoid compounds with similar synthesis and storage patterns in S. cerevisiae.","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":"414 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140584408","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Application of the surface engineered recombinant Escherichia coli to the industrial battery waste solution for lithium recovery","authors":"Jaehoon Jeong, Vidhya Selvamani, Murali kannan Maruthamuthu, Kulandaisamy Arulsamy, Soon Ho Hong","doi":"10.1093/jimb/kuae012","DOIUrl":"https://doi.org/10.1093/jimb/kuae012","url":null,"abstract":"Escherichia coli were engineered to selectively adsorb and recover lithium from the environment by employing bacterial cell surface display strategy. Lithium binding peptide LBP1 was integrated to the Escherichia coli membrane protein OmpC. The effect of environmental conditions on the adsorption of lithium by recombinant strain was evaluated, and lithium particles on cellular surface was analysed by FE-SEM and XRD. To elevate the lithium adsorption, dimeric, trimeric and tetrameric repeats of the LBP1 peptide was constructed and displayed on the surface of E. coli. The constructed recombinant E. coli displaying LBP1 trimer was applied to real industrial lithium battery wastewater to recover lithium.","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":"35 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140584320","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Harnessing regulatory networks in Actinobacteria for natural product discovery","authors":"Hannah E Augustijn, Anna M Roseboom, Marnix H Medema, Gilles P van Wezel","doi":"10.1093/jimb/kuae011","DOIUrl":"https://doi.org/10.1093/jimb/kuae011","url":null,"abstract":"Microbes typically live in complex habitats where they need to rapidly adapt to continuously changing growth conditions. To do so, they produce an astonishing array of natural products with diverse structures and functions. Actinobacteria stand out for their prolific production of bioactive molecules, including antibiotics, anticancer agents, antifungals, and immunosuppressants. Attention has been directed especially towards the identification of the compounds they produce and the mining of the large diversity of biosynthetic gene clusters (BGCs) in their genomes. However, the current return on investment in random screening for bioactive compounds is low, while it is hard to predict which of the millions of BGCs should be prioritized. Moreover, many of the BGCs for yet undiscovered natural products are silent or cryptic under laboratory growth conditions. To identify ways to prioritize and activate these BGCs, knowledge regarding the way their expression is controlled is crucial. Intricate regulatory networks control global gene expression in Actinobacteria, governed by a staggering number of up to 1000 transcription factors per strain. This review highlights recent advances in experimental and computational methods for characterizing and predicting transcription factor binding sites and their applications to guide natural product discovery. We propose that regulation-guided genome mining approaches will open new avenues toward eliciting the expression of BGCs, as well as prioritizing subsets of BGCs for expression using synthetic biology approaches. One-Sentence Summary This review provides insights into advances in experimental and computational methods aimed at predicting transcription factor binding sites and their applications to guide natural product discovery.","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":"22 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140584317","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"One-pot chemoenzymatic syntheses of non-canonical amino acids.","authors":"Tsung-Han Chao, Xiangyu Wu, Hans Renata","doi":"10.1093/jimb/kuae005","DOIUrl":"10.1093/jimb/kuae005","url":null,"abstract":"<p><p>Despite their prevalent use in drug discovery and protein biochemistry, non-canonical amino acids are still challenging to synthesize through purely chemical means. In recent years, biocatalysis has emerged as a transformative paradigm for small-molecule synthesis. One strategy to further empower biocatalysis is to use it in combination with modern chemical reactions and take advantage of the strengths of each method to enable access to challenging structural motifs that were previously unattainable using each method alone. In this Mini-Review, we highlight several recent case studies that feature the synergistic use of chemical and enzymatic transformations in one pot to synthesize novel non-canonical amino acids.</p><p><strong>One-sentence summary: </strong>This Mini-Review highlights several recent case studies that feature the synergistic use of chemical and enzymatic transformations in one pot to synthesize novel non-canonical amino acids.</p>","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10853765/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139564289","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}