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Using design of experiments to guide genetic optimization of engineered metabolic pathways J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2024-03-14 Seonyun Moon, Anna Saboe, Michael J Smanski
Design of Experiments (DoE) is a term used to describe the application statistical approaches to interrogate the impact of many variables on the performance of a multivariate system. It is commonly used for process optimization in fields such as chemical engineering and material science. Recent advances in the ability to quantitatively control the expression of genes in biological systems opens up
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CRISPR-aided genome engineering for secondary metabolite biosynthesis in Streptomyces J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2024-03-02 Yongjae Lee, Soonkyu Hwang, Woori Kim, Ji Hun Kim, Bernhard O Palsson, Byung-Kwan Cho
The demand for discovering novel microbial secondary metabolites is growing to address the limitations in bioactivities such as antibacterial, antifungal, anticancer, anthelmintic, and immunosuppressive functions. Among microbes, the genus Streptomyces holds particular significance for secondary metabolite discovery. Each Streptomyces species typically encodes approximately 30 secondary metabolite
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Expanding the synthetic biology toolbox of Cupriavidus necator for establishing fatty acid production J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2024-02-17 Shivangi Mishra, Paul M Perkovich, Wayne P Mitchell, Maya Venkataraman, Brian Pfleger
The Gram-negative beta-proteobacterium Cupriavidus necator is a chemolithotroph that can convert CO2 into biomass. C. necator has been engineered to produce a variety of high-value chemicals in the past. However, there is still a lack of a well-characterized toolbox for gene expression and genome engineering. Development and optimization of biosynthetic pathways in metabolically engineered microorganisms
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Cultivation of recombinant Aspergillus niger strains on dairy whey as a carbohydrate source J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2024-02-01 Teagan C Crament, Kayline Arendsen, Shaunita H Rose, Trudy Jansen
Agricultural waste valorisation provides a sustainable solution to waste management and combining waste utilisation with commodity production allows for responsible production processes. Recombinant Aspergillus niger D15 strains expressing fungal endoglucanases (Trichoderma reesei eg1 and eg2 and Aspergillus carneus aceg) were evaluated for the ability to utilise lactose as a carbon source to determine
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Transcriptional and translational flux optimization at the key regulatory node for enhanced production of naringenin using acetate in engineered Escherichia coli J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2024-01-29 Dong Hwan Kim, Hyun Gyu Hwang, Dae-yeol Ye, Gyoo Yeol Jung
As a key molecular scaffold for various flavonoids, naringenin is a value-added chemical with broad pharmaceutical applicability. For efficient production of naringenin from acetate, it is crucial to precisely regulate the carbon flux of the OAA-PEP regulatory node through appropriate pckA expression control, as excessive overexpression of pckA can cause extensive loss of OAA and metabolic imbalance
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One-Pot Chemoenzymatic Syntheses of Non-Canonical Amino Acids J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2024-01-25 Tsung-Han Chao, Xiangyu Wu, Hans Renata
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
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Development of platensimycin, platencin, and platensilin overproducers by biosynthetic pathway engineering and fermentation medium optimization J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2024-01-24 Lucas L Fluegel, Ming-Rong Deng, Ping Su, Edward Kalkreuter, Dong Yang, Jeffrey D Rudolf, Liao-Bin Dong, Ben Shen
The platensimycin (PTM), platencin (PTN), and platensilin (PTL) family of natural products continues to inspire the discovery of new chemistry, enzymology, and medicine. Engineered production of this emerging family of natural products however remains laborious due to the lack of practical systems to manipulate their biosynthesis in the native producing Streptomyces platensis species. Here we report
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Secretory expression of amylosucrase in Bacillus licheniformis through twin-arginine translocation pathway J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2024-01-23 Caizhe Wang, Dandan Niu, Nokuthula Peace Mchunu, Meng Zhang, Suren Singh, Zhengxiang Wang
Amylosucrase (EC 2.4.1.4) is a versatile enzyme with significant potential in biotechnology and food production. To facilitate its efficient preparation, a novel expression strategy was implemented in Bacillus licheniformis for the secretory expression of Neisseria polysaccharea amylosucrase (NpAS). The host strain B. licheniformis CBBD302 underwent genetic modification through the deletion of sacB
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A discussion and evaluation of statistical procedures used by JIMB authors when comparing means J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2024-01-11 K Thomas Klasson
Out of the 166 articles published in Journal of Industrial Microbiology and Biotechnology (JIMB) in 2019–2020 (not including special issues or review articles), 51 of them used a statistical test to compare two or more means. The most popular test was the (Standard) t-test, which often was used to compare several pairs of means. Other statistical procedures used included Fisher's Least Significant
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Engineered Biosynthesis of Plant Heteroyohimbine and Corynantheine Alkaloids in Saccharomyces cerevisiae J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-12-23 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
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
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Discovery and Structure Elucidation of Glycosyl and 5-Hydroxy Migrastatins from Dung Beetle Gut Kitasatospora sp. J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-12-12 Ji Hyeon Im, Seoyoung Oh, Eun Seo Bae, Soohyun Um, Sang Kook Lee, Yeon Hee Ban, Dong-Chan Oh
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
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Computer-Aided, Resistance Gene-Guided Genome Mining for Proteasome and HMG-CoA Reductase Inhibitors J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-12-07 Cory B Jenkinson, Adam R Podgorny, Cuncong Zhong, Berl R Oakley
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
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Bacterial natural product discovery by heterologous expression J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-12-04 Adjo E Kadjo, Alessandra S Eustáquio
Natural products have found important applications in the pharmaceutical and agricultural sectors. In bacteria, the genes that encode the biosynthesis of natural products are often colocalized in the genome, forming biosynthetic gene clusters. It has been predicted that only 3% of natural products encoded in bacterial genomes have been discovered thus far, in part because gene clusters may be poorly
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Characterization and Catalytic Investigation of Fungal Single-Module Nonribosomal Peptide Synthetase in Terpene-Amino Acid Meroterpenoid Biosynthesis J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-12-01 Cheng-Chung Tseng, Li-Xun Chen, Chi-Fang Lee, Zhijay Tu, Chun-Hung Lin, Hsiao-Ching Lin
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
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Genomic, phenotypic and clinical safety of Limosilactobacillus reuteri ATCC PTA 4659 J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-11-17 Malin Sendelius, Jakob Axelsson, Peidi Liu, Stefan Roos
Evaluating the safety of probiotic microorganisms is an important part of the development of probiotic products. In this study, we have performed a systematic safety assessment of Limosilactobacillus reuteri ATCC PTA 4659 based on genome analysis, antibiotic susceptibility testing, phenotypic characterization, and a human clinical safety study. Genome sequence analysis showed that the strain is free
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Improved 13C metabolic flux analysis in Escherichia coli metabolism: application of a high resolution MS (GC-EI-QTOF) for comprehensive assessment MS/MS fragments J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-11-14 Chris Richter, Eva Grafahrend-Belau, Jörg Ziegler, Manish L Raorane, Björn H Junker
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
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Antifungal activity and mechanism of action of natural product derivates as potential environmental disinfectants J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-11-12 Norma Patricia Silva-Beltrán, Stephanie A Boon, M Khalid Ijaz, Julie McKinney, Charles P Gerba
There have been a considerable number of antifungal studies that evaluated natural products, such as medicinal plants, and their secondary metabolites, (phenolic compounds, alkaloids), essential oils, as well as 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
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Recent progress in unraveling the biosynthesis of natural sunscreens mycosporine-like amino acids J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-11-11 Manyun Chen, Yujia Jiang, Yousong Ding
Exposure to ultraviolet (UV) rays is a known risk factor for skin cancer, which can be notably mitigated through the application of sun care products. However, escalating concerns regarding the adverse health and environmental impacts of synthetic anti-UV chemicals underscore a pressing need for the development of biodegradable and eco-friendly sunscreen ingredients. Mycosporine-like amino acids (MAAs)
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Characterization of the off-flavor from Pichia pastoris GS115 during the over-expression of a α-L-rhamnosidase. J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-11-06 YuXuan Yao,ShengLan Zheng,ShiLin Chi,Feng Chen,Ning Cai,ZhenZhen Cai,Zhipeng Li,Hui Ni
The off-flavor of Pichia pastoris strains is a negative characteristic of proteins overexpressed with this yeast. In the present study, the P. pastoris GS115 overexpressing a α-L-rhamnosidase was taken as the example to characterize the off-flavor via sensory evaluation, gas chromatography-mass spectrometer (GC-MS), gas chromatography-olfaction (GC-O), and omission test. The result showed the off-flavor
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Mechanistic aspects of IPTG (isopropylthio-β-galactoside) transport across the cytoplasmic membrane of Escherichia coli – a rate limiting step in the induction of recombinant protein expression J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-10-18 Rodrigo G Simas, Adalberto Pessoa Junior, Paul F Long
Coupling transcription of a cloned gene to the lac operon with induction by isopropylthio-β-galactoside (IPTG) has been a favoured approach for recombinant protein expression using Escherichia coli as a heterologous host for more than six decades. Despite a wealth of experimental data gleaned over this period, a quantitative relationship between extracellular IPTG concentration and consequent levels
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Abolishing storage lipids induces protein misfolding and stress responses in Yarrowia lipolytica J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-09-24 Simone Zaghen, Oliver Konzock, Jing Fu, Eduard J Kerkhoven
Yarrowia lipolytica naturally saves carbon excess as storage lipids. Engineering efforts allow redirecting the high precursor flux required for lipid synthesis towards 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, ARE1) can be
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Reducing the virulence of Pseudomonas aeruginosa by using multiple quorum quenching enzymes J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-09-19 Mst Afroza Khatun, Md Anarul Hoque, Mattheos Koffas, Yan Feng
The emergence of multidrug-resistant Pseudomonas aeruginosa in healthcare settings poses a tremendous challenge to traditional antibiotic therapy. P. aeruginosa utilizes quorum sensing (QS) to coordinate the production of virulence factors and the formation of drug-resistant biofilms. QS is mediated by signal compounds produced by P. aeruginosa as well as signal molecules produced by other non-pseudomonad
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Metabolic engineering and optimization of Escherichia coli co-culture for the de novo synthesis of genkwanin J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-09-18 Thuan Huy Nguyen, Vinay Bharadwaj Tatipamula, Nguyen Thanh Trung, Nguyen Van Giang
Genkwanin has various significant roles in nutrition, biomedicine, and pharmaceutical biology. Previously, this compound has been chiefly produced by plant-originated extraction or chemical synthesis. However, due to increasing concern and demand for safe food and environmental issues, the biotechnological production of genkwanin and other bioactive compounds based on safe, cheap, and renewable substrates
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Co-feeding enhances the yield of methyl ketones J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-09-12 Anita L Ziegler, Carolin Grütering, Leon Poduschnick, Alexander Mitsos, Lars M Blank
The biotechnological production of methyl ketones is a sustainable alternative to the fossil-derived chemical production. To date, the best host for microbial production of methyl ketones is a genetically engineered Pseudomonas taiwanensis VLB120 ∆6 pProd strain, achieving yields of 101mgg−1 on glucose in batch cultivations. For competitiveness with the petrochemical production pathway, however, higher
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Biosynthesis, enzymology, and future of eunicellane diterpenoids J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-09-07 Zining Li, Jeffrey D Rudolf
Eunicellane diterpenoids are a remarkable family of terpene natural products and have been of high interest for over five decades. Widely distributed in soft corals and rare in plants, eunicellanes were also recently identified from actinobacteria. These terpenoids have foundational 6/10-bicyclic frameworks that are frequently oxidized into structures containing transannular ether bridges. Interest
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Streptomyces lividans 66 produces a protease inhibitor via a tRNA-utilizing enzyme interacting with a C-minus NRPS J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-09-06 César Aguilar, Karina Verdel-Aranda, Hilda E Ramos-Aboites, Cuauhtémoc Licona-Cassani, Francisco Barona-Gómez
Small peptide aldehydes (SPAs) with protease inhibitory activity are naturally occurring compounds shown to be synthesized by nonribosomal peptide synthetases (NRPS). SPAs are widely used in biotechnology and have been utilized as therapeutic agents. They are also physiologically relevant and have been postulated to regulate the development of their producing microorganisms. Previously, we identified
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Perkinsus marinus in bioreactor: Growth and a cost-reduced growth medium J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-09-06 Caitlin Murphy, José A Fernández Robledo, G Peter Van Walsum
Perkinsus marinus (Perkinsea) is an osmotrophic facultative intracellular marine protozoan responsible for ‘Dermo’ disease in the eastern oyster, Crassostrea virginica. In 1993, three laboratories developed the in vitro culture of P. marinus in the absence of host cells. Two of the culture media and conditions went through several optimization reiterations, with one becoming the standard for the small-scale
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Optimizing the strain engineering process for industrial scale production of bio-based molecules J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-09-01 Eric Abbate, Jennifer Andrion, Amanda Apel, Matthew Biggs, Julie Chaves, Kristi Cheung, Anthony Ciesla, Alia Clark-ElSayed, Michael Clay, Riarose Contridas, Richard Fox, Glenn Hein, Dan Held, Andrew Horwitz, Stefan Jenkins, Karolina Kalbarczyk, Nandini Krishnamurthy, Mona Mirsiaghi, Katherine Noon, Mike Rowe, Tyson Shepherd, Katia Tarasava, Theodore M Tarasow, Drew Thacker, Gladys Villa, Krishna Yerramsetty
Biomanufacturing could contribute as much as $30 trillion to the global economy by 2030. But 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
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Production of S-methyl-methionine using engineered Saccharomyces cerevisiae sake K6 J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-09-01 Jun-Min Lee, Min-Ho Park, Bu-Soo Park, Min-Kyu Oh
S-methyl-methionine (SMM), also known as vitamin U, is an important food supplement produced by various plants. In this study, we attempted to produce it in an engineered microorganism, Saccharomyces cerevisiae, by introducing an MMT gene encoding a Methionine S-methyltransferase from Arabidopsis thaliana. The S. cerevisiae Sake K6 strain which is a Generally Recognized as Safe (GRAS) strain, was chosen
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Diversity and taxonomic distribution of bacterial biosynthetic gene clusters predicted to produce compounds with therapeutically relevant bioactivities J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-08-29 Max L Beck, Siyeon Song, Isra E Shuster, Aarzu Miharia, Allison S Walker
Bacteria have long been a source of natural products with diverse bioactivities that have been developed into therapeutics to treat human disease. Historically, researchers have focused on a few taxa of bacteria, mainly Streptomyces and other actinomycetes. This strategy was initially highly successful and resulted in the golden era of antibiotic discovery. The golden era ended when the most common
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Small Molecule Inducers of Actinobacteria Natural Product Biosynthesis J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-08-17 Amir Y Alwali, Elizabeth I Parkinson
Actinobacteria are a large and diverse group of bacteria that are known to produce a wide range of secondary metabolites, many of which have important biological activities, including antibiotics, anti-cancer agents, and immunosuppressants. The biosynthesis of these compounds is often highly regulated with many natural products being produced at very low levels in laboratory settings. Environmental
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Utilizing a divalent metal ion transporter to control biogenic nanoparticle synthesis J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-08-15 Manasi Subhash Gangan, Kyle L Naughton, James Q Boedicker
Biogenic synthesis of inorganic nanomaterials has been demonstrated for both wild and engineered bacterial strains. In many systems the nucleation and growth of nanomaterials is poorly controlled and requires concentrations of heavy metals toxic to living cells. Here we utilized the tools of synthetic biology to engineer a strain of Escherichia coli capable of synthesizing cadmium sulfide nanoparticles
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Transcriptomics analysis and fed-batch regulation of high astaxanthin producing Phaffia rhodozyma/Xanthophyllomyces dendrorhous obtained through adaptive laboratory evolution J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-08-12 Liang Yang, Hao-Yi Yang, Li You, Hui Ni, Ze-Dong Jiang, Xi-Ping Du, Yan-Bing Zhu, Ming-Jing Zheng, Li-Jun Li, Rui Lin, Zhi-Peng Li, Qing-Biao Li
Astaxanthin has high utilization value in functional food because of its strong antioxidant capacity. However, the astaxanthin content of Phaffia rhodozyma is relatively low. Adaptive laboratory evolution is an excellent method to obtain high-yield strains. TiO2 is a good inducer of oxidative stress. In this study, different concentrations of TiO2 were used to domesticate P. rhodozyma. Results showed
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A common inducer molecule enhances sugar utilization by Shewanella oneidensis MR-1 J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-08-02 Megan C Gruenberg, Michaela A TerAvest
Shewanella oneidensis MR-1 is an electroactive bacterium that is a promising host for bioelectrochemical technologies, which makes it a common target for genetic engineering, including gene deletions and expression of heterologous pathways. Expression of heterologous genes and gene knockdown via CRISPRi in S. oneidensis are both frequently induced by β-D-1-thiogalactopyranoside (IPTG), a commonly used
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Micrococcus spp. as a promising source for drug discovery: A review J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-07-14 Daniela Tizabi, Russell T Hill
Historically, bacteria of the phylum Actinobacteria have been a very prominent source of bioactive compounds for drug discovery. Among the actinobacterial genera, Micrococcus has not generally been prioritized in the search for novel drugs. The bacteria in this genus are known to have very small genomes (generally < 3 Mb). Actinobacteria with small genomes seldom contain the well-characterized biosynthetic
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Diverse enzymatic chemistry for propionate side chain cleavages in tetrapyrrole biosynthesis J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-07-09 Richiro Ushimaru, Jiaqi Lyu, Ikuro Abe
Tetrapyrroles represent a unique class of natural products that possess diverse chemical architectures and exhibit a broad range of biological functions. Accordingly, they attract keen attention from the natural product community. Many metal-chelating tetrapyrroles serve as enzyme cofactors essential for life, while certain organisms produce metal-free porphyrin metabolites with biological activities
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Fungi as a commercial source of eumelanin: current understanding & prospects J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-06-17 William Beeson, Kyle Gabriel, Christopher Cornelison
Melanins represent a diverse collection of pigments with a variety of structures and functions. One class of melanin, eumelanin, is recognizable to most as the source of the dark black color found in cephalopod ink. Sepia officinalis is the most well-known and sought-after source of non-synthetic eumelanin, but its harvest is limited by the availability of cuttlefish, and its extraction from an animal
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Improvement of the stability and catalytic efficiency of heparan sulfate N-sulfotransferase for preparing N-sulfated heparosan J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-06-16 Xintong Xi, Litao Hu, Hao Huang, Yang Wang, Ruirui Xu, Guocheng Du, Jian Chen, Zhen Kang
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 the 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
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Biosensor Development for Single-Cell Detection of Glucuronate J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-06-16 Jennifer Kaczmarek Nash, Kristala L J Prather
Recent work in biosensors has shown promise to enable high throughput searches through large genetic libraries. However, just as physiological limitations and lack of in-depth mechanistic knowledge can prevent us from achieving high titers in microbial systems, similar roadblocks can appear in the application of biosensors. Here, we characterized a previously developed transcription-factor (ExuR) based
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Repurposing of waste PET by microbial biotransformation to functionalized materials for additive manufacturing J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-05-30 Bhagya S Kolitha, Sandhya K Jayasekara, Rina Tannenbaum, Iwona M Jasiuk, Lahiru N Jayakody
Plastic waste is an outstanding environmental thread. Poly (ethylene terephthalate) (PET) is one of the most abundantly produced single-use plastics worldwide, while its recycling rates are low. In parallel, additive manufacturing is a rapidly evolving technology with wide-ranging applications. Thus, there is a need for a broad spectrum of polymers to meet the demands of this growing industry and address
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Strategic nutrient sourcing for biomanufacturing intensification J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-05-28 Kimia Noroozi Fashkhami, Laura R Jarboe
The successful design of economically viable bioprocesses can help to abate global dependence on petroleum, increase supply chain resilience, and add value to agriculture. Specifically, bioprocessing provides the opportunity to replace petrochemical production methods with biological methods and to develop novel bioproducts. Even though a vast range of chemicals can be biomanufactured, the constraints
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Versatile microbial communities rapidly assimilate ammonium hydroxide-treated plastic waste J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-04-16 Laura G Schaerer, Emily Wood, Sulihat Aloba, Emily Byrne, M Aamir Bashir, Kaushik Baruah, Elizabeth Schumann, Libby Umlor, Ruochen Wu, Hyeonseok Lee, Christopher J Orme, Aaron D Wilson, Jeffrey A Lacey, Rebecca G Ong, Stephen M Techtmann
Waste plastic presently accumulates in landfills or the environment. While natural microbial metabolisms can degrade plastic polymers, biodegradation of plastic is very slow. This study demonstrates that chemical deconstruction of polyethylene terephthalate (PET) with ammonium hydroxide can replace the rate limiting step (depolymerization) and by producing plastic-derived terephthalic acid and terephthalic
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Enhanced β-carotene production in Yarrowia lipolytica through the metabolic and fermentation engineering J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-04-14 Yiwen Jing, Jingnan Wang, Haiyan Gao, Yujia Jiang, Wankui Jiang, Min Jiang, Fengxue Xin, Wenming Zhang
β-Carotene is a kind of high-value tetraterpene compound, which shows various applications in medical, agricultural and industrial areas owing to its antioxidant, anti-tumor and anti-inflammatory activities. In this study, Yarrowia lipolytica was successfully metabolically modified through the construction and optimization of β-carotene biosynthetic pathway for β-carotene production. The β-carotene
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A novel image-based method for simultaneous counting of Lactobacillus and Saccharomyces in mixed culture fermentation. J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-02-17 Cecelia Williamson,Kevin Kennedy,Sayak Bhattacharya,Samir Patel,Jennifer Perry,Jason Bolton,Lewis Brian Perkins,Leo Li-Ying Chan
Mixed microorganism cultures are prevalent in the food industry. A variety of microbiological mixtures have been used in these unique fermenting processes to create distinctive flavor profiles and potential health benefits. Mixed cultures are typically not well characterized, which may be due to the lack of simple measurement tools. Image-based cytometry systems have been employed to automatically
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Cytochromes P450 involved in Bacterial RiPP Biosyntheses J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-03-18 Sylvia Kunakom, Hiroshi Otani, Daniel W Udwary, Drew T Doering, Nigel J Mouncey
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 the additional modifications, catalyzed by various enzymes to alter the
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Effect of nitrogen management in cultivation on the stability and microbial community of post-harvest Monoraphidium sp. algae biomass J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-03-17 Bradley D Wahlen, Lynn M Wendt, Chelsea C St. Germain, Sarah M Traynor, Caitlin Barboza, Thomas Dempster, Henri Gerken, John McGowen, Yaqi You
Seasonal variation in algae biomass productivity is a significant obstacle to the economical production of fuels and chemicals from algae biomass. Long-term storage is necessary to guarantee a constant supply to a conversion facility and harvested microalgae biomass (20% solids) is subject to degradation immediately upon harvesting as a result of aerobic instability. Ensiling has been successfully
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Analyzing CRISPR screens in non-conventional microbes J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-03-17 Varun Trivedi, Adithya Ramesh, Ian Wheeldon
The multifaceted nature of CRISPR screens has propelled advancements in the field of functional genomics. Pooled CRISPR screens involve creating programmed genetic perturbations across multiple genomic sites in a pool of host cells subjected to a challenge, empowering researchers to identify genetic causes of desirable phenotypes. These genome-wide screens have been widely used in mammalian cells to
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Determining mating type and ploidy in Rhodotorula toruloides and its effect on growth on sugars from lignocellulosic biomass. J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-02-17 Daiane Dias Lopes,Bruce S Dien,Ronald E Hector,Vijay Singh,Stephanie R Thompson,Patricia J Slininger,Kyria Boundy-Mills,Sujit S Jagtap,Christopher V Rao
Rhodotorula toruloides is being developed for the use in industrial biotechnology processes because of its favorable physiology. This includes its ability to produce and store large amounts of lipids in the form of intracellular lipid bodies. Nineteen strains were characterized for mating type, ploidy, robustness for growth, and accumulation of lipids on inhibitory switchgrass hydrolysate (SGH). Mating
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Correction to: Fungi as a commercial source of eumelanin: current understanding & prospects. J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-02-17
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Diverse mechanisms of bioproduction heterogeneity in fermentation and their control strategies. J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-02-17 Xinyue Mu,Fuzhong Zhang
Microbial bioproduction often faces challenges related to populational heterogeneity, where cells exhibit varying biosynthesis capabilities. Bioproduction heterogeneity can stem from genetic and non-genetic factors, resulting in decreased titer, yield, stability, and reproducibility. Consequently, understanding and controlling bioproduction heterogeneity are crucial for enhancing the economic competitiveness
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Monitoring biofilm growth and dispersal in real-time with impedance biosensors. J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-02-17 Matthew McGlennen,Markus Dieser,Christine M Foreman,Stephan Warnat
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
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Correction to: CRISPRi screen for enhancing heterologous α-amylase yield in Bacillus subtilis. J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-02-17
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Enhancing the production of a heterologous Trametes laccase (LacA) by replacement of the major cellulase CBH1 in Trichoderma reesei J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-01-24 Jiaxin Zhang, Yu Hong, Kehang Li, Yu Sun, Cheng Yao, Jianya Ling, Yaohua Zhong
The laccases from white-rot fungi exhibit high redox potential in treating phenolic compounds. However, their application in commercial purposes has been limited because of the relatively low productivity by the native hosts. Here, the laccase A-encoding gene lacA of Trametes sp. AH28-2 was overexpressed under the control of the strong promoter of cbh1 (Pcbh1), the gene encoding the endogenous cellobiohydrolase
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Natural promoters and promoter engineering strategies for metabolic regulation in Saccharomyces cerevisiae J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-01-12 Shifan He, Zhanwei Zhang, Wenyu Lu
Saccharomyces cerevisiae is currently one of the most important foreign gene expression systems. S. cerevisiae is an excellent host for high-value metabolite cell factories due to its advantages of simplicity, safety, and nontoxicity. A promoter, as one of the basic elements of gene transcription, plays an important role in regulating gene expression and optimizing metabolic pathways. Promoters control
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The effect of CO2 concentration on yeast fermentation: rates, metabolic products, and yeast stress indicators J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2023-01-12 Mario Guadalupe-Daqui, Renee M Goodrich-Schneider, Paul J Sarnoski, John C Carriglio, Charles A Sims, Brian J Pearson, Andrew J MacIntosh
This research aimed to assess how the partial removal of carbon dioxide affects fermentations to provide a better understanding of how the manipulation of carbon dioxide concentration can be used to optimize industrial fermentations. To achieve this, fermentation kinetics, fermentation metabolic products, and yeast stress indicators were analyzed throughout ongoing brewing fermentations conducted under
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Improvement of rimocidin production in Streptomyces rimosus M527 by reporter-guided mutation selection J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2022-12-22 Yujie Jiang, Jinyao Zhang, Xinyi Huang, Zheng Ma, Yongyong Zhang, Andreas Bechthold, Xiaoping Yu
In this study, we employed a reporter-guided mutation selection (RGMS) strategy to improve the rimocidin production of Streptomyces rimosus M527, which is based on a single-reporter plasmid pAN and atmospheric and room temperature plasma (ARTP). In plasmid pAN, PrimA, a native promoter of the loading module of rimocidin biosynthesis (RimA) was chosen as target, and the kanamycin resistance gene (neo)
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CRISPRi screen for enhancing heterologous α-amylase yield in Bacillus subtilis J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2022-12-21 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
Enhancing yield during bacterial enzyme production could have positive economic and environmental impacts. For cell factories, such improvements in yields could potentially be obtained by fine-tuning the metabolic processes and their regulatory mechanisms for gene candidates. In pursuit of such candidates, we performed RNA-sequencing of two α-amylase producing Bacillus strains and predict hundreds
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A Multi-plex Protein Expression System for Production of Complex Enzyme Formulations in Trichoderma reesei J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2022-12-14 Venkataramanan Subramanian, Samuel J Farmer, Kelsey L Heiland, Kyle T Moore, Todd A Vander Wall, Weiman Sun, Yogesh B Chaudhari, Michael E Himmel, Stephen R Decker
Historically, heterologous protein production has been challenging using the hyper-cellulolytic fungus, Trichoderma reesei. T. reesei is known for poor transformation efficiency, low homologous recombination frequency, and marginal screening systems for identification of successful transformants. In this work, we have applied the 2A-peptide multi-gene expression system to co-express four enzymes, which
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De novo Synthesis of 2-phenylethanol from Glucose by Metabolically Engineered Escherichia coli J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2022-11-12 Guanglu Wang, Mengyuan Wang, Jinchu Yang, Qian Li, Nianqing Zhu, Lanxi Liu, Xianmei Hu, Xuepeng Yang
2-Phenylethanol (2- PE) is an aromatic alcohol with wide applications, but there is still no efficient microbial cell factory for 2-PE based on Escherichia coli. In this study, we constructed a metabolically engineered E. coli capable of de novo synthesis of 2-PE from glucose. Firstly, the heterologous styrene-derived and Ehrlich pathways were individually constructed in an L-Phe producer. The results
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The growth and metabolome of Saccharomyces uvarum in wine fermentations is strongly influenced by the route of nitrogen assimilation J. Ind. Microbiol. Biotechnol. (IF 3.4) Pub Date : 2022-11-12 Angela Coral-Medina, John P Morrissey, Carole Camarasa
Nitrogen is a critical nutrient in beverage fermentations, influencing fermentation performance and formation of compounds that affect organoleptic properties of the product. Traditionally, most commercial wine fermentations rely on Saccharomyces cerevisiae but the potential of alternative yeasts is increasingly recognised because of the possibility to deliver innovative products and process improvements