Journal of Industrial Microbiology & Biotechnology最新文献

{"title":"Development of lactic acid production from coffee grounds hydrolysate by fermentation with Lacticaseibacillus rhamnosus.","authors":"Łukasz Wysocki, Patrycja Adamczuk, Paula Bardadyn, Anna Gabor, Karolina Jelonek, Monika Kudelska, Maksymilian Kukuć, Adrianna Piasek, Marta Pietras, Monika Słomka, Zoja Trojan, Wiktoria Tybulczuk, Anna Sobiepanek, Joanna Żylińska-Urban, Joanna Cieśla","doi":"10.1093/jimb/kuae032","DOIUrl":"10.1093/jimb/kuae032","url":null,"abstract":"<p><p>Spent coffee grounds (SCG) are commercial waste that are still rich in numerous valuable ingredients and can be further processed into useful products such as coffee oil, antioxidant extract, lactic acid, and lignin. The challenge and innovation is to develop the SCG processing technology, maximizing the use of raw material and minimizing the use of other resources within the sequential process. The presented research is focused on the aspect of biotechnological production of lactic acid from SCG by using the Lacticaseibacillus rhamnosus strain isolated from the environment. Thanks to the optimization of the processes of acid hydrolysis, neutralization, enzymatic hydrolysis of SCG, and fermentation, the obtained concentration of lactic acid was increased after 72 hr of culture from the initial 4.60 g/l to 48.6 g/l. In addition, the whole process has been improved, taking into account the dependence on other processes within the complete SCG biorefinery, economy, energy, and waste aspects. Costly enzymatic hydrolysis was completely eliminated, and it was proven that supplementation of SCG hydrolysate with expensive yeast extract can be replaced by cheap waste from the agri-food industry.</p><p><strong>One-sentence summary: </strong>A process for efficient lactic acid production from spent coffee grounds using the Lacticaseibacillus rhamnosus strain was developed and optimized, including nutrient solution preparation, supplementation and fermentation.</p>","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11399779/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142125953","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":"Engineered biosynthesis of plant heteroyohimbine and corynantheine alkaloids in Saccharomyces cerevisiae.","authors":"Moriel J Dror, Joshua Misa, Danielle A Yee, Angela M Chu, Rachel K Yu, Bradley B Chan, Lauren S Aoyama, Anjali P Chaparala, Sarah E O'Connor, Yi Tang","doi":"10.1093/jimb/kuad047","DOIUrl":"10.1093/jimb/kuad047","url":null,"abstract":"<p><p>Monoterpene indole alkaloids (MIAs) are a class of natural products comprised of thousands of structurally unique bioactive compounds with significant therapeutic values. Due to difficulties associated with isolation from native plant species and organic synthesis of these structurally complex molecules, microbial production of MIAs using engineered hosts are highly desired. In this work, we report the engineering of fully integrated Saccharomyces cerevisiae strains that allow de novo access to strictosidine, the universal precursor to thousands of MIAs at 30-40 mg/L. The optimization efforts were based on a previously reported yeast strain that is engineered to produce high titers of the monoterpene precursor geraniol through compartmentalization of mevalonate pathway in the mitochondria. Our approaches here included the use of CRISPR-dCas9 interference to identify mitochondria diphosphate transporters that negatively impact the titer of the monoterpene, followed by genetic inactivation; the overexpression of transcriptional regulators that increase cellular respiration and mitochondria biogenesis. Strain construction included the strategic integration of genes encoding both MIA biosynthetic and accessory enzymes into the genome under a variety of constitutive and inducible promoters. Following successful de novo production of strictosidine, complex alkaloids belonging to heteroyohimbine and corynantheine families were reconstituted in the host with introduction of additional downstream enzymes. We demonstrate that the serpentine/alstonine pair can be produced at ∼5 mg/L titer, while corynantheidine, the precursor to mitragynine can be produced at ∼1 mg/L titer. Feeding of halogenated tryptamine led to the biosynthesis of analogs of alkaloids in both families. Collectively, our yeast strain represents an excellent starting point to further engineer biosynthetic bottlenecks in this pathway and to access additional MIAs and analogs through microbial fermentation.</p><p><strong>One sentence summary: </strong>An Saccharomyces cerevisiae-based microbial platform was developed for the biosynthesis of monoterpene indole alkaloids, including the universal precursor strictosidine and further modified heteroyohimbine and corynantheidine alkaloids.</p>","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10995622/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138885046","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":"Exploring the frontiers of therapeutic breadth of antifungal peptides: A new avenue in antifungal drugs.","authors":"Ihtisham Ul Haq, Sajida Maryam, Divine Y Shyntum, Taj A Khan, Fan Li","doi":"10.1093/jimb/kuae018","DOIUrl":"10.1093/jimb/kuae018","url":null,"abstract":"<p><p>The growing prevalence of fungal infections alongside rising resistance to antifungal drugs poses a significant challenge to public health safety. At the close of the 2000s, major pharmaceutical firms began to scale back on antimicrobial research due to repeated setbacks and diminished economic gains, leaving only smaller companies and research labs to pursue new antifungal solutions. Among various natural sources explored for novel antifungal compounds, antifungal peptides (AFPs) emerge as particularly promising. Despite their potential, AFPs receive less focus than their antibacterial counterparts. These peptides have been sourced extensively from nature, including plants, animals, insects, and especially bacteria and fungi. Furthermore, with advancements in recombinant biotechnology and computational biology, AFPs can also be synthesized in lab settings, facilitating peptide production. AFPs are noted for their wide-ranging efficacy, in vitro and in vivo safety, and ability to combat biofilms. They are distinguished by their high specificity, minimal toxicity to cells, and reduced likelihood of resistance development. This review aims to comprehensively cover AFPs, including their sources-both natural and synthetic-their antifungal and biofilm-fighting capabilities in laboratory and real-world settings, their action mechanisms, and the current status of AFP research.</p><p><strong>One-sentence summary: </strong>This comprehensive review of AFPs will be helpful for further research in antifungal research.</p>","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11119867/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140861537","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":"Discovery and adaptation of microbes that degrade oxidized low-density polyethylene films.","authors":"Amit K Jha, Daniella V Martinez, Estevan J Martinez, Jay E Salinas, Michael S Kent, Oleg Davydovich","doi":"10.1093/jimb/kuae050","DOIUrl":"10.1093/jimb/kuae050","url":null,"abstract":"<p><p>There is a growing interest in developing a methodology for effectively cleaving carbon-carbon (C-C) bonds in polymer backbones through bioconversion processes that utilize microorganisms and their enzymes. This upsurge of interest is driven by the goal of achieving a circular economy. Polyolefin post-consumer plastics are a substantial source of carbon, but the recycling potential is severely limited. Upcycling routes are needed for converting polyolefin post-consumer plastics into value-added products while concurrently mitigating adverse environmental effects. These materials contain carbon-based chemicals that can, in principle, serve as the feedstock for microbial metabolism. Some microbes have been reported to grow on polyolefin plastics, but the rate of biodegradation is insufficient for industrial processes. In this study, low-density polyethylene (LDPE) films were subjected to two mild ozone-based oxidation treatments, which facilitated biodegradation. The degree of oxidation was determined by Fourier transform infrared spectroscopy via analysis of the carbonyl index (1,710/1,460 cm-1), which ranged from 0.3 to 2.0, and also via analysis of the carboxylic acid content. Following oxidation of the films, studies were conducted to investigate the ability of a panel of polyvinyl alcohol-degrading microbes to degrade the oxidized films. A defined minimal medium was used to cultivate and assess microbial growth on the oxidized films. Following 45 days of cultivation, the most effective strains were further cultivated up to three additional generations on the oxidized film substrates to improve their ability to degrade the oxidized LDPE films. After these enrichments, we identified a strain from the third generation of Pseudomonas sp. Rh926 that exhibited significant cell growth and reduced the oxidized LDPE film mass by 25% in 30 days, demonstrating an enhanced capacity for degrading the oxidized LDPE films.</p><p><strong>One-sentence summary: </strong>Discovery and adaptation techniques were used to enhance the metabolic capability of microorganisms for increased biodegradation of ozone-oxidized LDPE films as a step toward a future upcycling process.</p>","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11664187/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142807491","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: Characterization and catalytic investigation of fungal single-module nonribosomal peptide synthetase in terpene-amino acid meroterpenoid biosynthesis.","authors":"","doi":"10.1093/jimb/kuae002","DOIUrl":"10.1093/jimb/kuae002","url":null,"abstract":"","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":"51 ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10845890/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139485729","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":"Evolution and screening of Trichoderma reesei mutants for secreted protein production at elevated temperature.","authors":"Elizabeth Bodie, Zhongqiang Chen, Kirstin Crotty, Cherry Lin, Chuanbin Liu, Sergio Sunux, Michael Ward","doi":"10.1093/jimb/kuae038","DOIUrl":"10.1093/jimb/kuae038","url":null,"abstract":"<p><p>The filamentous fungus Trichoderma reesei is a mesophilic ascomycete commercially used to produce industrial enzymes for a variety of applications. Strain improvement efforts over many years have resulted not only in more productive hosts, but also in undesirable traits such as the need for lower temperatures to achieve maximum protein secretion rates. Lower fermentation temperatures increase the need for cooling resulting in higher manufacturing costs. We used a droplet-based evolution strategy to increase the protein secretion temperature of a highly productive T. reesei whole cellulase strain from 25°C to 28°C by first isolating an improved mutant and subsequently tracing the causative high-temperature mutation to one gene designated gef1. An industrial host with a gef1 deletion was found to be capable of improved productivity at higher temperature under industrially relevant fermentation conditions.</p><p><strong>One-sentence summary: </strong>High-temperature droplet-based evolution resulted in the identification of a mutation in Trichoderma reesei gef1 enabling high productivity at elevated temperatures.</p>","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11566232/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142467553","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":"Phytopathological management through bacteriophages: enhancing food security amidst climate change.","authors":"Ihtisham Ul Haq, Mehtab Khan, Imran Khan","doi":"10.1093/jimb/kuae031","DOIUrl":"10.1093/jimb/kuae031","url":null,"abstract":"<p><p>The increasing global population and climate change pose significant challenges to agriculture, particularly in managing plant diseases caused by phytopathogens. Traditional methods, including chemical pesticides and antibiotics, have become less effective due to pathogen resistance and environmental concerns. Phage therapy emerges as a promising alternative, offering a sustainable and precise approach to controlling plant bacterial diseases without harming beneficial soil microorganisms. This review explores the potential of bacteriophages as biocontrol agents, highlighting their specificity, rapid multiplication, and minimal environmental impact. We discuss the historical context, current applications, and prospects of phage therapy in agriculture, emphasizing its role in enhancing crop yield and quality. Additionally, the paper examines the integration of phage therapy with modern agricultural practices and the development phage cocktails and genetically engineered phages to combat resistant pathogens. The findings suggest that phage therapy could revolutionize phytopathological management, contributing to global food security and sustainable agricultural practices.</p><p><strong>One-sentence summary: </strong>The burden of plant diseases and phage-based phytopathological treatment.</p>","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11388930/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142108120","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":"Discovery and Structure Elucidation of Glycosyl and 5-Hydroxy Migrastatins from Dung Beetle Gut Kitasatospora sp.","authors":"Ji Hyeon Im, Seoyoung Oh, Eun Seo Bae, Soohyun Um, Sang Kook Lee, Yeon Hee Ban, Dong-Chan Oh","doi":"10.1093/jimb/kuad046","DOIUrl":"https://doi.org/10.1093/jimb/kuad046","url":null,"abstract":"Two new macrocyclic secondary metabolites, glycosyl-migrastatin (1) and 5-hydroxy-migrastatin (2), were isolated from a gut bacterium Kitasatospora sp. JL24 in dung beetle Onthophagus lenzii. Based on a comprehensive analysis of the NMR, MS, and UV spectroscopic data, the planar structures of 1 and 2 were successfully identified as new candidates for migrastatin. Compound 1 was the first glycosylated member of the migrastatin family. The absolute configuration of the sugar moiety was determined to be d-glucose through the analysis of coupling constants and ROESY correlations, followed by chromatographic chemical derivatization and comparison with authentic d- and l-glucose. Compound 2, identified as 5-hydroxy-migrastatin possessing an additional hydroxy group with a previously unreported chiral center, was assigned using Mosher's method through 19F NMR chemical shifts and confirmed with the modified Mosher's method. Genomic analysis of Kitasatospora sp. strain JL24 revealed a putative biosynthetic pathway involving an acyltransferase-less type I polyketide synthase biosynthetic gene cluster.","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":"1 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2023-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138686947","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":"Computer-Aided, Resistance Gene-Guided Genome Mining for Proteasome and HMG-CoA Reductase Inhibitors","authors":"Cory B Jenkinson, Adam R Podgorny, Cuncong Zhong, Berl R Oakley","doi":"10.1093/jimb/kuad045","DOIUrl":"https://doi.org/10.1093/jimb/kuad045","url":null,"abstract":"Secondary metabolites (SMs) are biologically active small molecules, many of which are medically valuable. Fungal genomes contain vast numbers of SM biosynthetic gene clusters (BGCs) with unknown products, suggesting that huge numbers of valuable SMs remain to be discovered. It is challenging, however, to identify SM BGCs, among the millions present in fungi, that produce useful compounds. One solution is resistance gene-guided genome mining, which takes advantage of the fact that some BGCs contain a gene encoding a resistant version of the protein targeted by the compound produced by the BGC. The bioinformatic signature of such BGCs is that they contain an allele of an essential gene with no SM biosynthetic function, and there is a second allele elsewhere in the genome. We have developed a computer-assisted approach to resistance gene-guided genome mining that allows users to query large databases for BGCs that putatively make compounds that have targets of therapeutic interest. Working with the MycoCosm genome database, we have applied this approach to look for SM BGCs that target the proteasome β6 subunit, the target of the proteasome inhibitor fellutamide B, or HMG-CoA reductase, the target of cholesterol reducing therapeutics such as lovastatin. Our approach proved effective, finding known fellutamide and lovastatin BGCs as well as fellutamide- and lovastatin-related BGCs with variations in the SM genes that suggest they may produce structural variants of fellutamides and lovastatin. Gratifyingly, we also found BGCs that are not closely related to lovastatin BGCs but putatively produce novel HMG-CoA reductase inhibitors.","PeriodicalId":16092,"journal":{"name":"Journal of Industrial Microbiology & Biotechnology","volume":"11 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2023-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138554763","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":"Characterization and catalytic investigation of fungal single-module nonribosomal peptide synthetase in terpene-amino acid meroterpenoid biosynthesis.","authors":"Cheng-Chung Tseng, Li-Xun Chen, Chi-Fang Lee, Zhijay Tu, Chun-Hung Lin, Hsiao-Ching Lin","doi":"10.1093/jimb/kuad043","DOIUrl":"10.1093/jimb/kuad043","url":null,"abstract":"<p><p>Hybrid natural products are compounds that originate from diverse biosynthetic pathways and undergo a conjugation process, which enables them to expand their chemical diversity and biological functionality. Terpene-amino acid meroterpenoids have garnered increasing attention in recent years, driven by the discovery of noteworthy examples such as the anthelmintic CJ-12662, the insecticidal paeciloxazine, and aculene A (1). In the biosynthesis of terpene-amino acid natural products, single-module nonribosomal peptide synthetases (NRPSs) have been identified to be involved in the esterification step, catalyzing the fusion of modified terpene and amino acid components. Despite prior investigations into these NRPSs through gene deletion or in vivo experiments, the enzymatic basis and mechanistic insights underlying this family of single-module NRPSs remain unclear. In this study, we performed biochemical characterization of AneB by in vitro characterization, molecular docking, and site-directed mutagenesis. The enzyme reaction analyses, performed with L-proline and daucane/nordaucane sesquiterpene substrates, revealed that AneB specifically esterifies the C10-OH of aculenes with L-proline. Notably, in contrast to ThmA in CJ-12662 biosynthesis, which exclusively recognizes oxygenated amorpha-4,11-diene sesquiterpenes for L-tryptophan transfer, AneB demonstrates broad substrate selectivity, including oxygenated amorpha-4,11-diene and 2-phenylethanol, resulting in the production of diverse unnatural prolyl compounds. Furthermore, site-directed mutagenesis experiments indicated the involvement of H794 and D798 in the esterification catalyzed by AneB. Lastly, domain swapping between AneB and ThmA unveiled that the A‒T domains of ThmA can be effectively harnessed by the C domain of AneB for L-tryptophan transfer, thus highlighting the potential of the C domain of AneB for generating various terpene-amino acid meroterpenoid derivatives.</p><p><strong>One-sentence summary: </strong>The enzymatic basis and mechanistic insights into AneB, a single-module NRPS, highlight its capacity to generate various terpene-amino acid meroterpenoid derivatives.</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/PMC10720950/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138482450","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}