Article
Food Science & Technology
Huabiao Miao, Xia Xiang, Nanyu Han, Qian Wu, Zunxi Huang
Summary: This study aimed to improve the thermostability of the serine protease PB92 from Bacillus alcalophilus to meet the high-temperature requirements of biotechnological treatments. Mutations were introduced at eight sites, and 21 mutants were constructed, among which 15 mutants showed increased half-life values at 65 degrees C. Six complex mutants with improved thermal stability were identified based on enzyme activity and thermostability scores, and structural analysis suggested that the increased stability might be due to additional hydrophobic interactions and reduced flexibility. Overall, the N18L/R143L/S97A, N18L/R143L/S99L, and N18L/R143L/G100A mutants showed 4-fold increase in thermal stability, indicating potential industrial applications.
Article
Biotechnology & Applied Microbiology
Guangqi Li, Xuan Zhou, Zhihong Li, Yunpeng Liu, Dongyang Liu, Youzhi Miao, Qun Wan, Ruifu Zhang
Summary: This study characterized and engineered a thermophilic GH10 family xylanase XynAF1 to improve its thermostability, resulting in a 6-fold increase in stability through rational design and saturation mutagenesis. The high-resolution X-ray crystallographic structure of XynAF1 revealed a rigid skeleton contributing to its hyperthermophilic characteristics. The study provides a promising biocatalyst for high-temperature biotechnological applications.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Review
Biotechnology & Applied Microbiology
Zarina Iqbal, Saima Sadaf
Summary: Generating functional protein variants with novel or improved characteristics can be achieved through rational design and directed evolution. In laboratory evolution, new tools and methods are needed to create genetic diversity and identify variants with desired traits. Building large libraries of target molecules and protocols to alter their properties has been a challenge in directed evolution experiments.
BIOTECHNOLOGY AND BIOENGINEERING
(2022)
Article
Biochemistry & Molecular Biology
Satoru Watanabe, Masahiro Ito, Takanori Kigawa
Summary: DiRect is a novel PCR-based mutagenesis method that achieves high quality product (>99% substitution) without the use of recombinant DNA technology. It has been successfully applied in the study of an industrially relevant enzyme, showing simplicity, efficiency, and potential scalability in site-directed mutagenesis.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Yawen Zhou, Linshu Jiao, Juan Shen, Huibing Chi, Zhaoxin Lu, Huawei Liu, Fengxia Lu, Ping Zhu
Summary: In this study, smart libraries were constructed using semi-rational design to improve the catalytic activity of type II L-asparaginase from Bacillus licheniformis. Mutants with significantly enhanced catalytic efficiency were obtained through saturation mutations and combinatorial mutations. The quintuple mutant ILRAC showed the highest specific activity and k(cat)/K-m, and also exhibited improved pH stability and thermal stability. Structural alignment and molecular dynamic simulation revealed that the stability and substrate binding of ILRAC contributed to its enhanced thermal stability and enzymatic activity. This study presents a novel semi-rational approach to enhance the enzymatic activity of type II L-asparaginase and provides insights for industrial applications.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Agriculture, Multidisciplinary
Zhihua Nie, Pi Liu, Yu Wang, Xuan Guo, Zijian Tan, Jie Shen, Zijing Tang, Jianping Lin, Jibin Sun, Ping Zheng, Leilei Zhu
Summary: This study focused on protein engineering of the mechanosensitive glutamate exporter MscCG2 to improve glutamate excretion efficiency, using directed evolution and computer-assisted design. The engineered variants showed increased levels of glutamate excretion and enhanced efflux of 4-fluoroglutamate, with structural analysis revealing changes in the size of MscCG2 portals and inner channel. These findings demonstrate the potential of protein engineering in enhancing bioproduction through improved secretion efficiency of exporters.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Review
Biotechnology & Applied Microbiology
Haoran Yu, Shuang Ma, Yiwen Li, Paul A. Dalby
Summary: Directed evolution is a powerful strategy to engineer protein properties, and hot spot prediction is crucial for producing smart libraries. Selection of hot spots based on sequence and structure allows for efficient generation of proteins with desired properties.
BIOTECHNOLOGY ADVANCES
(2022)
Article
Chemistry, Physical
Xiaowen Wu, Yingying Jiang, Zengyu Wang, Xiaobin Yu, Zhoutong Sun, Wei Luo
Summary: This study improved the thermal stability of a formate dehydrogenase from Lodderomyces elongisporus through semi-rational design, resulting in a mutant with enhanced thermal stability and unchanged specific activity. The mutant exhibited good stability in alkaline environment and improved operational stability in catalytic reactions.
MOLECULAR CATALYSIS
(2022)
Review
Agricultural Engineering
Aravind Madhavan, K. B. Arun, Parameswaran Binod, Ranjna Sirohi, Ayon Tarafdar, R. Reshmy, Mukesh Kumar Awasthi, Raveendran Sindhu
Summary: Enzyme engineering plays a crucial role in improving the efficiency and stability of enzymes in industrial processes. Protein engineers focus on studying the design and application of enzyme engineering to tailor industrially important enzymes for versatile production of biochemicals.
BIORESOURCE TECHNOLOGY
(2021)
Review
Chemistry, Organic
Beatriz de Pina Mariz, Sara Carvalho, Iris L. Batalha, Ana Sofia Pina
Summary: Enzymes are protein catalysts widely used in natural and industrial processes, with the global enzymes market projected to reach $10.5 billion in 2024. The development of artificial enzymes, created through computational design and directed evolution, aims to expand catalytic power and create novel catalysts with promising activity. The combination of these technologies is opening new opportunities in pharmaceutical, chemical, biofuels, and food industries, contributing to a more sustainable development.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2021)
Article
Engineering, Chemical
Wan-Wen Ting, Sefli Sri Wahyu Effendi, Ruei-En Hu, I-Son Ng
Summary: The study aims to enhance protein production and catalytic efficiency of MlCA through directed evolution in genetically Escherichia coli. The CRISPRi-based DEPEND-2.0 system effectively inhibits cell growth, and structural prediction and codon design improve enzyme activity and protein expression. The developed MlCA variant shows high durability and catalytic activity.
JOURNAL OF THE TAIWAN INSTITUTE OF CHEMICAL ENGINEERS
(2023)
Article
Chemistry, Physical
Ridha Zerdoumi, Alan Savan, Marshal Amalraj, Emmanuel Batsa Tetteh, Florian Lourens, Olga A. Krysiak, Joao R. C. Junqueira, Alfred Ludwig, Wolfgang Schuhmann
Summary: Alloying dissimilar elements is an effective strategy for enhancing the electrocatalytic properties of multi-metal materials, by modifying electronic and geometric effects. This research investigates the interplay between these parameters using the quaternary PdAgCuFe thin-film system, and establishes a correlation between valence electron density and catalytic activity.
ADVANCED ENERGY MATERIALS
(2023)
Article
Biochemistry & Molecular Biology
Soroosh Pouyan, Milad Lagzian, Mohammad Hossein Sangtarash
Summary: This study characterized a new alpha-amylase from Bacillus cereus GL96 and used an in-silico approach to redesign the enzyme for improved thermal stability. The engineered enzyme showed higher stability and activity at elevated temperatures compared to the wild-type enzyme. Specifically, the D162K mutation resulted in the best performance, with increased optimum temperature and improved stability. This mutant enzyme holds promise for further investigation and industrial applications.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Chemistry, Physical
Zexing Wen, Zhi-Min Zhang, Liang Zhong, Jiaqian Fan, Min Li, Yuanhong Ma, Yang Zhou, Wei Zhang, Bin Guo, Bo Chen, Jian-Bo Wang
Summary: Plant glycosyltransferase MiCGT was engineered by directed evolution to catalyze the glycosylation of flavonoids for pharmaceutical applications, resulting in mutants with enhanced selectivity and activity towards seven different flavonoids. The best quadruple mutant VFAH showed strict 3-O glycosylation selectivity and a 120-fold activity enhancement towards the model substrate quercetin.
Article
Chemistry, Applied
Julian L. Wissner, Jona T. Schelle, Wendy Escobedo-Hinojosa, Andreas Vogel, Bernhard Hauer
Summary: By engineering Toluene dioxygenase (TDO) from Pseudomonas putida F1, successful oxyfunctionalization of bicyclic substrates was achieved with introduced mutations improving product formation rate and selectivity. The most active TDO variants were successfully applied to the oxyfunctionalization of two substrates, producing high yield and enantioselectivity products.
ADVANCED SYNTHESIS & CATALYSIS
(2021)
Article
Biotechnology & Applied Microbiology
Andres Costa, Belen Corallo, Vanesa Amarelle, Silvina Stewart, Dinorah Pan, Susana Tiscornia, Elena Fabiano
Summary: A strain of Paenibacillus sp. UY79 isolated from wild peanut was found to exhibit antagonistic activity against various fungi and oomycetes. It produces volatile compounds that can inhibit the growth of these pathogens. Furthermore, it does not affect the symbiotic association or growth promotion of alfalfa plants when co-inoculated with rhizobia. This strain shows great potential as a biofungicide.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Microbiology
Diego M. Roldan, Andres Costa, Stanislava Kralova, Hans-Juergen Busse, Vanesa Amarelle, Elena Fabiano, Rodolfo Javier Menes
Summary: Based on the study of strain UY79(T), it is considered to be a novel species of the genus Paenibacillus and is named Paenibacillus farraposensis sp. nov.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Steven A. van der Hoek, Matej Rusnak, Guokun Wang, Lyubomir Dimitrov Stanchev, Luana de Fatima Alves, Mathew M. Jessop-Fabre, Kalaivani Paramasivan, Irene Hjorth Jacobsen, Nikolaus Sonnenschein, Jose L. Martinez, Behrooz Darbani, Douglas B. Kell, Irina Borodina
Summary: Ergothioneine is a rare sulfur-containing amino acid with potent antioxidant properties. Engineered yeast strains can be used to produce high levels of ergothioneine using glucose as the carbon source. Metabolic engineering and medium optimization are effective strategies to improve ergothioneine production.
METABOLIC ENGINEERING
(2022)
Article
Virology
Franziska Hufsky, Denis Beslic, Dimitri Boeckaerts, Sebastian Duchene, Enrique Gonzalez-Tortuero, Andreas J. Gruber, Jiarong Guo, Daan Jansen, John Juma, Kunaphas Kongkitimanon, Antoni Luque, Muriel Ritsch, Gabriel Lencioni Lovate, Luca Nishimura, Celia Pas, Esteban Domingo, Emma Hodcroft, Philippe Lemey, Matthew B. Sullivan, Friedemann Weber, Fernando Gonzalez-Candelas, Sarah Krautwurst, Alba Perez-Cataluna, Walter Randazzo, Gloria Sanchez, Manja Marz
Summary: The International Virus Bioinformatics Meeting 2022 aimed to promote discussions, collaborations, and inspire new research directions, with 380 participants joining online. The event featured eight invited talks, 18 contributed talks, and three virtual poster sessions, providing insights into the latest research in virus bioinformatics.
Article
Infectious Diseases
Gilberto G. Gaspar, Gustavo Tamasco, Nathalia Abichabki, Ana Flavia T. Scaranello, Maria Auxiliadora-Martins, Renata Pocente, Leonardo N. Andrade, Maria-Eugenia Guazzaroni, Rafael Silva-Rocha, Valdes R. Bollela
Summary: We studied an outbreak of polymyxin B (PB)- and carbapenem-resistant Klebsiella pneumoniae during the COVID-19 pandemic and found that all isolates showed resistance to multiple drugs, with one particular subtype spreading in the ICU. This outbreak was related to the collapse of the local healthcare system and resulted in high mortality rates.
Article
Infectious Diseases
Joao Vitor Wagner Ordine, Gabrielle Messias De Souza, Gustavo Tamasco, Stela Virgilio, Ana Flavia Tonelli Fernandes, Rafael Silva-Rocha, Maria-Eugenia Guazzaroni
Summary: Land-use conversion and antibiotic overuse promote the expansion of the soil resistome, which can be influenced by different land practices. This study profiled the resistome and microbiota of soils under different land practices in Sao Paulo, Brazil. The analysis revealed differences in community structures and dynamics correlated with land practices, as well as variations in the abundance and diversity of antibiotic resistance genes and virulence factors. Overall, this highlights the importance of monitoring antimicrobial resistance in the environment, particularly in soils undergoing land-use transformations.
Article
Biochemistry & Molecular Biology
Celia Jakob, Gabriel L. Lovate, Daniel Desiro, Lara Giessler, Redmond P. Smyth, Roland Marquet, Kevin Lamkiewicz, Manja Marz, Martin Schwemmle, Hardin Bolte
Summary: A study shows that the vRNA-vRNA interactions detected in influenza virus particles using the SPLASH method may not be critical for genome packaging.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Vanesa Amarelle, Diego M. Roldan, Elena Fabiano, Maria-Eugenia Guazzaroni
Summary: One major limitation of function-driven metagenomics is the ability of the host to express the metagenomic DNA correctly. The use of alternative hosts is an appropriate approach to favor the identification of enzymatic activities in function-driven metagenomics.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Biochemical Research Methods
Guilherme Marcelino Viana de Siqueira, Maria-Eugenia Guazzaroni
Summary: In this study, the effects of different terminators on the output of a reporter construct in two bacterial species were investigated using the SEVA scaffold. By replacing the conventional T1 and T0 terminators with broad-host metagenomic terminators, a significant improvement in signal was observed in Pseudomonas putida KT2440 but not in Escherichia coli DH10B. These findings suggest that replacing the default set of terminators in the SEVA specification can be a useful strategy for optimizing circuit expression in P. putida.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Virology
Franziska Hufsky, Ana B. Abecasis, Artem Babaian, Sebastian Beck, Liam Brierley, Simon Dellicour, Christian Eggeling, Santiago F. Elena, Udo Gieraths, Anh D. Ha, Will Harvey, Terry C. Jones, Kevin Lamkiewicz, Gabriel L. Lovate, Dominik Luecking, Martin Machyna, Luca Nishimura, Maximilian K. Nocke, Bernard Y. Renard, Shoichi Sakaguchi, Lygeri Sakellaridi, Jannes Spangenberg, Maria Tarradas-Alemany, Sandra Triebel, Yulia Vakulenko, Rajitha Yasas Wijesekara, Fernando Gonzalez-Candelas, Sarah Krautwurst, Alba Perez-Cataluna, Walter Randazzo, Gloria Sanchez, Manja Marz
Summary: The 2023 International Virus Bioinformatics Meeting held in Valencia, Spain was a significant event for researchers and scientists worldwide interested in virus bioinformatics. With the primary objective of fostering discussions and collaborations, it provided a platform for sharing insights, research findings, and novel ideas related to virus bioinformatics research.
Article
Chemistry, Physical
Julia Pereira Narcizo, Lucca Bonjy Kikuti Mancilio, Matheus Pedrino, Maria-Eugenia Guazzaroni, Adalgisa Rodrigues de Andrade, Valeria Reginatto
Summary: A new pyoverdine-producing Pseudomonas aeruginosa strain, EL14, was isolated from an MFC biofilm oxidizing glycerol. EL14 showed electrogenic ability and produced 1,3-propanediol as a by-product. The yield of 1,3-propanediol was enhanced under MFC conditions compared to fermentation, indicating the potential of EL14 in converting biodiesel by-products into valuable chemicals.
Article
Microbiology
Jonata Bortolucci, Maria-Eugenia Guazzaroni, Teresa Schoch, Peter Duerre, Valeria Reginatto
Summary: Biotechnological processes in biorefineries offer attractive alternatives for converting biomasses into bioproducts, biofuels, and bioenergy. This study focused on the overexpression of genes involved in 1,3-PDO synthesis in C. beijerinckii Br21, leading to increased 1,3-PDO productivity. In addition to contributing to a better understanding of glycerol conversion pathways, this study also expanded the genetic tools available for this bacterium, which is highly relevant in biotechnological applications.
Article
Multidisciplinary Sciences
Luana de Fatima Alves, Jonata Bortolucci, Valeria Reginatto, Maria-Eugenia Guazzaroni, Solange I. Mussatto
Summary: Innovations in obtaining products from lignocellulosic biomass have focused on improving microorganisms and enzymes for degrading these materials. To complete the process, microorganisms must ferment sugars and withstand various stresses. In this study, we engineered Saccharomyces cerevisiae strains to enhance acid and oxidative stress resistance by introducing a gene (hu) and using different promoters. The strains showed improved survival rates at low pH and increased tolerance to high concentrations of H2O2.