Review
Biotechnology & Applied Microbiology
Enrico Orsi, Jules Beekwilder, Gerrit Eggink, Serve W. M. Kengen, Ruud A. Weusthuis
Summary: Microbial cell factories play a crucial role in industrial biotechnology, and microbial strain engineering through the DBTL concept has been successful in improving competitiveness. New-to-industry microorganisms like Rhodobacter sphaeroides are being investigated as novel cell factories, showcasing potential for bio-based product synthesis.
BIOTECHNOLOGY AND BIOENGINEERING
(2021)
Review
Biotechnology & Applied Microbiology
Jinyi Qian, Yuzhou Wang, Zijian Hu, Tianqiong Shi, Yuetong Wang, Chao Ye, He Huang
Summary: Bacillus sp. is a safe genus with a clear genetic background that can efficiently utilize cheap carbon sources and secrete useful substances. It has been extensively studied and applied in systems and synthetic biology, but still faces some challenges.
BIOTECHNOLOGY ADVANCES
(2023)
Review
Biotechnology & Applied Microbiology
Marlene Baptista, Lucilia Domingues
Summary: This review summarizes the production of bioethanol and value-added chemicals by Kluyveromyces marxianus from different lignocellulosic biomasses, as well as the metabolic engineering, process optimization strategies and cell mechanisms developed to cope with lignocellulosic-derived inhibitors. Bioethanol represents 71% of the reports, while xylitol represents 17% of the reports. K. marxianus also shows potential in producing lactic acid and volatile compounds from lignocellulosic biomass.
BIOTECHNOLOGY ADVANCES
(2022)
Review
Biotechnology & Applied Microbiology
Meijie Li, Peng Ning, Yi Sun, Jie Luo, Jianming Yang
Summary: Rhodopseudomonas palustris is a versatile bacterium with the ability to use a variety of carbon sources and degrade organic compounds. It has traditionally been used in wastewater treatment and bioremediation, and also finds applications in agriculture and aquaculture. Recently, it has been engineered as a microbial cell factory for the production of valuable chemicals, especially hydrogen through photofermentation.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Chemistry, Applied
Liting Zhao, Zhongbao Ma, Jian Yin, Guiyang Shi, Zhongyang Ding
Summary: This review discusses recent biotechnological approaches to oligo/polysaccharide synthesis, involving in vitro enzymatic synthesis and cell factory synthesis. The important factors in nucleotide sugar production are explored, along with strategies like metabolic flux rebuilding and regulation, enzyme engineering, and route design. Research challenges and prospects are also outlined and discussed.
CARBOHYDRATE POLYMERS
(2021)
Review
Biochemical Research Methods
Lei Qin, Xia Liu, Ke Xu, Chun Li
Summary: Enhancing the yield of target products is the main objective in constructing and optimizing microbial cell factories. Applying biosensor-based intelligence to these strains is a crucial approach for solving engineering challenges such as metabolic flux imbalance and accumulation of toxic intermediates. Genetically encoded biosensors, created through rational design, directed evolution, or machine learning, have been rapidly developed for detection of both metabolites and environmental signals. Besides being a rapid detection method for high-throughput screening, biosensors are increasingly utilized for directed evolution of strains and dynamic regulation of metabolic pathways. The implementation of biosensor-based intelligence will play a significant role in the construction of microbial cell factories.
CURRENT OPINION IN BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Angela Kranz, Tino Polen, Christian Kotulla, Annette Arndt, Graziella Bosco, Michael Bussmann, Ava Chattopadhyay, Annette Cramer, Cedric-Farhad Davoudi, Ursula Degner, Ramon Diesveld, Raphael Freiherr von Boeselager, Kim Gaertner, Cornelia Gaetgens, Tobias Georgi, Christian Geraths, Sabine Haas, Antonia Heyer, Max Huennefeld, Takeru Ishige, Armin Kabus, Nicolai Kallscheuer, Larissa Kever, Simon Klaffl, Britta Kleine, Martina Kocan, Abigail Koch-Koerfges, Kim J. Kraxner, Andreas Krug, Aileen Krueger, Andreas Kueberl, Mohamed Labib, Christian Lange, Christina Mack, Tomoya Maeda, Regina Mahr, Stephan Majda, Andrea Michel, Xenia Morosov, Olga Mueller, Arun M. Nanda, Jens Nickel, Jennifer Pahlke, Eugen Pfeifer, Laura Platzen, Paul Ramp, Doris Rittmann, Steffen Schaffer, Sandra Scheele, Stephanie Spelberg, Julia Schulte, Jens-Eric Schweitzer, Georg Sindelar, Ulrike Sorger-Herrmann, Markus Spelberg, Corinna Stansen, Apilaasha Tharmasothirajan, Jan van Ooyen, Philana van Summeren-Wesenhagen, Michael Vogt, Sabrina Witthoff, Lingfeng Zhu, Bernhard J. Eikmanns, Marco Oldiges, Georg Schaumann, Meike Baumgart, Melanie Brocker, Lothar Eggeling, Roland Freudl, Julia Frunzke, Jan Marienhagen, Volker F. Wendisch, Michael Bott
Summary: Corynebacterium glutamicum is a major host for amino acid production and has been extensively studied in microbial biotechnology. This study presents a large compendium of transcriptional profiles, allowing researchers to investigate gene expression changes under different environmental conditions or genetic modifications. The compendium provides valuable insights into the understanding of C. glutamicum as a microbial cell factory.
Review
Agricultural Engineering
Zhihan Yang, Donald Delano Leero, Chengtai Yin, Lei Yang, Liying Zhu, Zhengming Zhu, Ling Jiang
Summary: This review highlights the progress in using Clostridia as cell factories for the sustainable production of chemicals and biofuels. The focus is on using agro-industrial wastes as feedstocks and analyzing the metabolic and process engineering efforts, as well as discussing the challenges associated with their utilization.
BIORESOURCE TECHNOLOGY
(2022)
Article
Agricultural Engineering
Thai Le, Sunghoon Park
Summary: 2-Hydroxybutyric acid (2-HBA) production was achieved in recombinant Escherichia coli through overexpression of key genes and disruption of degradation pathways, resulting in a high yield of 650 mM in 33 hours. This study presents an efficient microbial cell factory for the bioconversion of threonine to 2-HBA.
BIORESOURCE TECHNOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Chao Shou, Yu-Cong Zheng, Jing-Ru Zhan, Chun-Xiu Li, Jian-He Xu
Summary: A new method has been developed for microbial synthesis of plant-based (-)-menthol, with significantly increased production by replacing inefficient enzymes from Mentha piperita. This lays a reliable foundation for the microbial synthesis of (-)-menthol.
Review
Biotechnology & Applied Microbiology
Diep Thi Ngoc Nguyen, Ok Kyung Lee, Thu Thi Nguyen, Eun Yeol Lee
Summary: The review highlights recent advances in Type II methanotrophs related to multi-omics studies and metabolic engineering. It also discusses representative examples and prospects of metabolic engineering strategies for the production of suitable products.
BIOTECHNOLOGY ADVANCES
(2021)
Review
Biotechnology & Applied Microbiology
Jinho Yeom, Jong Seong Park, Seung-Woon Jung, Sumin Lee, Hyukjin Kwon, Seung Min Yoo
Summary: In this paper, the current high-throughput genetic engineering tools for gene regulation are reviewed, and a variety of technological approaches used in constructing microbial cell factories are introduced. The representative applications of these tools are also presented.
CRITICAL REVIEWS IN BIOTECHNOLOGY
(2023)
Article
Agricultural Engineering
Liangzi He, Yue Zhao, Xinyu Zhao, Yan Wang, Qiuling Dang
Summary: This study investigated the effects of microbial and environmental factors on potentially active phosphorus in factory compost. The results showed that chicken manure had higher available phosphorus throughout the composting process compared to kitchen waste, and also exhibited higher microbial diversity. Certain bacteria were identified as the core bacteria involved in bioavailable phosphorus conversion in both composts. Moisture and pH were identified as key environmental factors influencing bioavailable phosphorus.
BIORESOURCE TECHNOLOGY
(2023)
Article
Engineering, Environmental
Anh Duc Nguyen, Tin Hoang Trung Chau, Eun Yeol Lee
Summary: The study developed a novel cell factory platform for highly efficient biosynthesis of chemicals from methane and xylose, successfully synthesizing various chemicals including sunscreen material, 2,3-butanediol, acetoin, and 3-hydroxybutyric acid. This provides a new direction for sustainable production of chemicals from abundant methane and renewable xylose.
CHEMICAL ENGINEERING JOURNAL
(2021)
Article
Biotechnology & Applied Microbiology
Yerin Jin, Sora Yu, Jing-Jing Liu, Eun Ju Yun, Jae Won Lee, Yong-Su Jin, Kyoung Heon Kim
Summary: In this study, the probiotic yeast S. boulardii was engineered to produce health-beneficial neoagarooligosaccharides (NAOSs) by expressing an endo-type beta-agarase, BpGH16A, derived from a human gut bacterium Bacteroides plebeius. The results suggest that engineered S. boulardii can be considered a microbial cell factory for producing useful substances in the human gut, with successful production of health-benefiting NeoDP4 from agarose.
MICROBIAL CELL FACTORIES
(2021)
Article
Environmental Sciences
William Palmer-Brown, Paula Leticia de Melo Souza, Cormac D. Murphy
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2019)
Article
Multidisciplinary Sciences
William Palmer-Brown, Raul Miranda-CasoLuengo, Kenneth H. Wolfe, Kevin P. Byrne, Cormac D. Murphy
SCIENTIFIC REPORTS
(2019)
Review
Chemistry, Organic
Diana Gimenez, Aoife Phelan, Cormac D. Murphy, Steven L. Cobb
Summary: F-19 NMR is widely used in the field of chemical biology for synthesizing new fluorinated probes, monitoring protein interactions, structural analysis, etc. It remains relevant for investigating the biosynthesis and biodegradation of fluorinated organic compounds.
BEILSTEIN JOURNAL OF ORGANIC CHEMISTRY
(2021)
Article
Mycology
Mohd Faheem Khan, Cormac D. Murphy
Summary: This study investigated the transition of fungi from planktonic to biofilm growth, identifying 3-hydroxytyrosol as a potential new signaling molecule regulating biofilm growth in C. elegans.
Article
Chemistry, Organic
Diana Gimenez, Aoife Phelan, Cormac D. Murphy, Steven L. Cobb
Summary: The synthesis of fengycin A analogues with enhanced antifungal properties and chemical stability under acidic and basic conditions is reported. The analogues show that the fengycin core structure can be modified and simplified without loss of antifungal activity.
Article
Biotechnology & Applied Microbiology
Mohd Faheem Khan, Cormac D. Murphy
Summary: Cunninghamella spp. fungi were used to model the metabolism of fluorinated pyrethroid pesticides, generating mammalian-equivalent metabolites of transfluthrin and beta-cyfluthrin. The fungi were found to be able to replicate the biotransformation process of fluorinated pesticides in a manner similar to mammalian metabolism.
Article
Biotechnology & Applied Microbiology
Mohd Faheem Khan, Cormac D. Murphy
Summary: The study demonstrates that common environmental bacteria can use fluoxetine as a sole carbon and energy source, leading to metabolites that impact aquatic life. Further investigations into the degradation pathway reveal the formation of trifluoroacetate and fluoride ion as final products. These findings suggest the importance of understanding the environmental impact of pharmaceuticals like fluoxetine.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Environmental Sciences
Liam J. Reynolds, Laura Sala-Comorera, Mohd Faheem Khan, Niamh A. Martin, Megan Whitty, Jayne H. Stephens, Tristan M. Nolan, Eadaoin Joyce, Nicola F. Fletcher, Cormac D. Murphy, Wim G. Meijer
Summary: Wastewater surveillance is a cost-effective tool for monitoring SARS-CoV-2 transmission in a community. This study demonstrates the usefulness of coprostanol as a population biomarker for wastewater surveillance studies, as it exhibits the lowest variation in wastewater samples and shows strong correlations with COVID-19 cases when levels are normalized to coprostanol.
Article
Environmental Sciences
Mohd Faheem Khan, Cormac D. Murphy
Summary: This study reports the biotransformation of 6:2 FTOH by Cunninghamella elegans and identifies 5:3 FTCA as the main product. It also confirms the essential role of cytochrome P450 enzymes in this process.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2023)
Article
Engineering, Environmental
Mohd Faheem Khan, Suvrat Chowdhary, Beate Koksch, Cormac D. Murphy
Summary: The degradation of peptides with fluorinated amino acids was studied, and the degree of degradation depended on the enzyme and extent of fluorination. The microbial consortium from garden soil can degrade the peptides and release fluoride ions. Serratia liquefaciens bacterium was identified as the organism that can enzymatically defluorinate MfeGly.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2023)
Article
Mycology
Carina Hof, Mohd Faheem Khan, Cormac D. Murphy
Summary: This study found that the filamentous fungus Cunninghamella echinulata produces lower concentrations of 2-phenylethanol when grown as a biofilm. Exogenously added 2-phenylethanol inhibits biofilm growth and causes detachment, suggesting its role in regulating biofilm growth.
Review
Biotechnology & Applied Microbiology
Mohd Faheem Khan, Carina Hof, Patricie Niemcova, Cormac D. Murphy
Summary: This review provides an overview of recent advances in fungal metabolism of drugs and pollutants, and discusses the potential of fungi in bioremediation and biocatalysis.
WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY
(2023)
Article
Environmental Sciences
Mohd Faheem Khan, Jhimli Paul Guin, Ravindranathan K. Thampi, James A. Sullivan, Cormac D. Murphy
Summary: This paper investigates the degradation of perfluorooctanoic acid (PFOA) using a photocatalyst (bismuth oxyiodide, BiOI) and a fungal biocatalyst (Cunninghamella elegans). Both the photocatalyst and biocatalyst can degrade 35-40% of 100 ppm PFOA individually, with 20-30% defluorination. However, a combination of the two treatments results in a higher degradation rate of 90% and defluorination rate of 60%. The study also identifies the products formed during the degradation process and reveals the mechanism of PFOA biodegradation.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Mohd Faheem Khan, Cormac D. Murphy
Summary: Cunninghamella elegans, a microbial model of mammalian drug metabolism, contains three cytochrome P450 reductase genes, which can convert drugs into nitroreduced metabolites and are sensitive to oxygen.
BIOCHEMISTRY AND BIOPHYSICS REPORTS
(2022)
Article
Microbiology
Mohd Faheem Khan, Dua Saleem, Cormac D. Murphy
Summary: The study identified two molecules, tyrosol and tryptophol, in C. blakesleeana cultures that had a significant impact on biofilm growth compared to other species. These molecules inhibited biofilm growth and promoted planktonic culture growth, indicating their potential role in biofilm regulation.
Article
Chemistry, Organic
Faiza Diaba, Gisela Trenchs
Summary: The first violet light-mediated synthesis of gamma- and delta-lactams from N-alkenyl trichloroacetamides is reported in this paper. The reactions are conducted in tetrahydrofuran or 2-methyltetrahydrofuran as the sole solvent without catalysts or additives, under non-anhydrous conditions in an air atmosphere where the solvent serves as the radical initiator.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2024)
Article
Chemistry, Organic
Feroze Hussain, Sajjad Ahmed, Ashiq Hussain Padder, Qazi Naveed Ahmed
Summary: This study reports a novel and efficient one-pot synthesis method for mixed phosphorotrithioates, which does not require supplementary additives and shows broad applicability.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2024)
Article
Chemistry, Organic
Hyunjin Oh, Ikyon Kim
Summary: A new 1,2,4-triazole-pyrrolo[1,2-a]pyrazine hybrid system, 6-acylpyrrolo[1,2-a][1,2,4]triazolo[5,1-c]pyrazine, was synthesized using a catalyst-free method. This method involved sequential exposure of pyrrole-2-carbonitrile-derived substrates to DMF-DMA and acyl hydrazide, resulting in the formation of acylated pyrazine and 1,2,4-triazole rings, enabling the installation of various substituents at specific positions on the core skeleton.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2024)
Article
Chemistry, Organic
Ming Yan, Si-fan Wang, Yong-po Zhang, Jin-zhong Zhao, Zhuo Tang, Guang-xun Li
Summary: Here we developed an efficient photocatalytic approach for the convenient preparation of sulfinamides. The reaction allows for the gram-scale preparation of sulfinamides and the one-pot synthesis of various sulfonyl amides.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2024)
Article
Chemistry, Organic
Farzaneh Bandehali-Naeini, Zahra Tanbakouchian, Noushin Farajinia-Lehi, Nicolas Mayer, Morteza Shiri, Martin Breugst
Summary: Two tandem catalytic systems were developed for the synthesis of novel 3,4-disubstituted maleimides using the same Ugi adducts. Different maleimide structures can be synthesized using either Pd or Cu catalysis.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2024)
Article
Chemistry, Organic
Tanya Raghava, Anjan Chattopadhyay, Subhadeep Banerjee, Nivedita Sarkar
Summary: Amine substitution of two ortho fluorine atoms of tetrafluoroterephthalonitrile through SNAr chemistry is easily achievable. But further fluorine substitution is only possible under forcing conditions, yielding valuable fluorophores for bioimaging.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2024)
Review
Chemistry, Organic
Anju Chadha, Santosh Kumar Padhi, Selvaraj Stella, Sowmyalakshmi Venkataraman, Thangavelu Saravanan
Summary: Alcohol dehydrogenases are enzymes that use cofactors for oxidation or reduction reactions of alcohols or carbonyl compounds. They are utilized in green chemistry and have applications in the production of pharmaceuticals. Recombinant enzymes have solved the challenge of producing purified enzymes in large quantities. Engineered alcohol dehydrogenases have been used in asymmetric synthesis in industry. Various methods have been established for regenerating expensive cofactors to make the enzymatic process more efficient and economically viable.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2024)
