Article
Food Science & Technology
Yongpeng Guo, Yanan Wang, Yu Tang, Qiugang Ma, Cheng Ji, Lihong Zhao
Summary: This study investigates the detoxification potential of dye-decolorizing peroxidase BsDyP from Bacillus subtilis 168 on the mycotoxin Zearalenone (ZEN) commonly found in food. Computational and experimental analyses suggest that BsDyP can bind ZEN and oxidize it using H2O2 as an electron acceptor. Addition of ABTS as a redox mediator further enhances ZEN degradation, and the transformation product shows reduced estrogenicity. The application of a bi-enzyme system achieves a significant degradation percentage of ZEN in contaminated corn steep liquor. These findings suggest the potential use of BsDyP as a biocatalyst for detoxification of ZEN in food and feed.
Article
Biotechnology & Applied Microbiology
Martino Adamo, Sophie Comtet-Marre, Enrico Buttner, Harald Kellner, Patricia Luis, Laurent Vallon, Rocio Prego, Martin Hofrichter, Mariangela Girlanda, Pierre Peyret, Roland Marmeisse
Summary: Fungal dye-decolorizing peroxidases (DyPs) have diverse roles in fungal biology, with one distinct clade of DyPs showing unique characteristics and being predominantly found in white-rot and other saprotrophic Basidiomycota species. This suggests a specific role of DyPs from this clade in biochemical lignin modification, highlighting the potential significance of further studying DyPs from different clades with novel catalytic properties.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Celica Cagide, Juan Jose Marizcurrena, Diego Valles, Beatriz Alvarez, Susana Castro-Sowinski
Summary: In this study, a dyp gene encoding a class B DyP enzyme was identified in an Antarctic cold-tolerant microbe. The recombinant protein showed high activity at low temperatures and exhibited characteristics of psychrophilic enzymes. It also demonstrated the ability to decolorize dyes and modify kraft lignin, suggesting its potential applications in bioremediation and the cellulose and biofuel industries.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Materials Science, Paper & Wood
Vu Dinh Giap, Do Huu Nghi, Le Huu Cuong, Dang Thu Quynh
Summary: Lignin peroxidase LsLiP can effectively degrade dyes in textile wastewater and biodegrade lignin from pulp and paper industry wastewater and agricultural waste. Purification and enzymatic activity analysis showed that LsLiP can efficiently remove various dyes and also modify the structure of lignin.
Article
Biotechnology & Applied Microbiology
Yaru Zhang, Jing Ren, Quan Wang, Shuxiang Wang, Shuna Li, Hongya Li
Summary: The study showed that Bacillus amyloliquefaciens BaDyP can efficiently degrade CV dye, with degradation products undergoing N-demethylation and cleavage of chromophore structure; BaDyP also exhibited high decolorization efficiency, making it suitable as a biocatalyst for dye treatment in wastewater.
BIOCHEMICAL ENGINEERING JOURNAL
(2021)
Article
Biotechnology & Applied Microbiology
Jing Ren, Jingjing Huo, Quan Wang, Ze Liu, Shuna Li, Shuxiang Wang, Weiting Guo, Hongya Li
Summary: In this paper, dopamine-modified, chitosan-coated, halloysite nanotube porous microspheres were used as a matrix to immobilize dye-decolorizing peroxidase from Bacillus amyloliquefaciens. The immobilized enzyme showed better stability, high loading capacity, and excellent decolorization ability, demonstrating its feasibility for the bioremediation of dyeing wastewater.
BIOCHEMICAL ENGINEERING JOURNAL
(2022)
Article
Biotechnology & Applied Microbiology
Van Hong Thi Pham, Jaisoo Kim, Soonwoong Chang, Woojin Chung
Summary: The study demonstrates that Bacillus velezensis strain React3 isolated from soil has the potential to efficiently remove methylene blue from water under optimal conditions.
FERMENTATION-BASEL
(2022)
Article
Chemistry, Multidisciplinary
Oezlem Kalkan, Sravya Kantamneni, Lea Brings, Huijong Han, Richard Bean, Adrian P. Mancuso, Faisal H. M. Koua
Summary: By expressing DdDyP peroxidase in enriched medium at low temperature without adding heme supplement, native heme can be correctly incorporated into the protein, resulting in a stable protein with a strong Soret peak. The native structure of DdDyP was determined, revealing the geometry of its active site and its implications for DyP catalysis.
FRONTIERS IN CHEMISTRY
(2023)
Article
Microbiology
Jing Ren, Xiaodan Li, Weitao Zhang, Zhuofan Li, Quan Wang, Shuna Li, Shuxiang Wang, Hongya Li
Summary: In this study, a dye-decolorizing peroxidase from Bacillus amyloliquefaciens MN-13 was used for the bioremediation of pulp and paper mill effluent. The enzyme showed high efficiency in degrading lignin and reducing pollutants load, COD, color, and toxicity of the effluent.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Amrita Rai, Johann P. Klare, Patrick Y. A. Reinke, Felix Englmaier, Joerg Fohrer, Roman Fedorov, Manuel H. Taft, Igor Chizhov, Ute Curth, Oliver Plettenburg, Dietmar J. Manstein
Summary: A novel cytoplasmic dye-decolorizing peroxidase from Dictyostelium discoideum was investigated, showing unique structure and active sites for efficient oxidation of various substrates. The enzyme exists as a stable dimer in solution, contributing to the stabilization of the dimer interface. Further structural analysis revealed the conformation of active sites and substrate-binding pockets in the enzyme.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biotechnology & Applied Microbiology
Qian Pi, Zhubing Zhu, Lei Tang
Summary: A new superfamily of heme-containing peroxidases, DyPs, has been discovered to efficiently decolorize various dyes, especially anthraquinone dyes. Using TfuDyP, it was found that the attack site on RB19 was identified and the incomplete degradation products of RB19 inhibited the growth of Bacillus subtilis. These findings provide a novel understanding of DyPs catalysis to anthraquinone dyes.
BIOPROCESS AND BIOSYSTEMS ENGINEERING
(2022)
Article
Environmental Sciences
Mingchen Xia, Han Zhou, Charles Amanze, Lan Hu, Li Shen, Runlan Yu, Yuandong Liu, Miao Chen, Jiaokun Li, Xueling Wu, Guanzhou Qiu, Weimin Zeng
Summary: The bacterial strain Bacillus subtilis ZHX3 was identified as a high bioflocculant producer, capable of producing the bioflocculant MBF-ZHX3 with excellent flocculation performance. The bioflocculant was composed mainly of polysaccharides and proteins, with potential applications in wastewater treatment as a more effective and environmentally friendly alternative to polyacrylamide.
Article
Biotechnology & Applied Microbiology
Zahra Choolaei, Robert Flick, Anna N. Khusnutdinova, Elizabeth A. Edwards, Alexander F. Yakunin
Summary: Efficient lignin biotransformation requires the activity of different oxidative enzymes. This study identified the bacterial multi-copper oxidase laccase CotA(Bsu) from Bacillus subtilis as having the highest activity against soluble substrates. Site-directed mutagenesis of CotA(Bsu) revealed critical residues for activity and a lignin-agarose plate screen confirmed the results, showing increased activity towards kraft lignin for certain mutant variants. X-ray photoelectron spectroscopy analysis of low sulfonate kraft lignin after incubation with CotA(Bsu) indicated a reduction in C-C/C=C bonds and an increase in C-O/C=O bonds. Product analyses suggested radical intermediates followed by radical coupling in the oxidation of lignin by laccases.
JOURNAL OF BIOTECHNOLOGY
(2021)
Article
Plant Sciences
O. V. Lastochkina, S. R. Garipova, L. I. Pusenkova, D. Yu. Garshina, An. Kh. Baymiev, I. S. Koryakov
Summary: The influence of endophytic bacteria Bacillus subtilis (strain 10-4) on the growth, tolerance, and lignin deposition in the roots of Pisum sativum L. seedlings under sodium chloride salinity conditions was studied. The impact of salinity reduced seedling germination energy, viability, root and shoot length, wet and dry weight, and increased proline content and lipid peroxidation level. Pretreatment with strain 10-4 had a positive effect on seedlings in normal conditions and protected them from salinity, improving germination energy, seed viability, root length, and dry mass accumulation under saline conditions. Strain 10-4 also promoted the formation of lateral roots and reduced stress-induced lipid peroxidation and proline content, indicating protection against oxidative and osmotic damage under saline conditions. Furthermore, the strain played an important role in lignification and strengthening of the cell walls, reducing the toxic effect of sodium chloride salinity and providing protection for pea plants.
RUSSIAN JOURNAL OF PLANT PHYSIOLOGY
(2023)
Article
Microbiology
Dilara Maslennikova, Igor Koryakov, Ruslan Yuldashev, Irina Avtushenko, Albina Yakupova, Oksana Lastochkina
Summary: Pre-sowing seed treatment with Bacillus subtilis 10-4 (BS), a growth-promoting endophyte, improves the resistance of wheat to cadmium stress by enhancing seed germination, biomass accumulation, photosynthetic pigments content, reducing oxidative stress and cadmium ions accumulation, and enhancing the integrity and barrier properties of the cell wall.
Article
Biotechnology & Applied Microbiology
Seung Soo Lee, Jaehyun Park, Yu Been Heo, Han Min Woo
ENZYME AND MICROBIAL TECHNOLOGY
(2020)
Article
Biotechnology & Applied Microbiology
Hyun Jeong Lee, Jigyeong Son, Sang Jun Sim, Han Min Woo
PLANT BIOTECHNOLOGY JOURNAL
(2020)
Article
Agriculture, Multidisciplinary
Hyun Jeong Lee, Jong-il Choi, Han Min Woo
Summary: This study developed a biocontainment system using genetically modified cyanobacteria to produce alpha-farnesene, by deleting gene clusters related to the beta-carboxysome and the carbon concentrating mechanism. The production of alpha-farnesene was dependent on CO2 concentration in the photobioreactor, with potential applications in next generation bio-solar cell factories.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Article
Biochemical Research Methods
Mieun Lee, Han Min Woo
ACS SYNTHETIC BIOLOGY
(2020)
Article
Chemistry, Multidisciplinary
Yoojin Lee, Hye Jeong Cho, Jong-il Choi, Han Min Woo
Summary: The study successfully constructed a hybrid EMP pathway in an industrial bacterium by replacing the first phase of the EMP with NOG, establishing a metabolic link between carbon and phosphorus metabolism. This redesigned pathway reduced CO2 emissions by 10% and increased acetyl-CoA levels by 19% compared to the wild type, providing an efficient microbial platform for sustainable biochemical production.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2021)
Article
Biochemical Research Methods
Dong Hun Kang, Sung Cheon Ko, Yu Been Heo, Hyun Jeong Lee, Han Min Woo
Summary: Efficient and versatile DNA assembly frameworks have had a significant impact on promoting synthetic biology. However, the traditional MoClo system for multiple DNA assemblies in a biofoundry workflow has limitations in terms of simplicity and feasibility. In this study, a robot-assisted MoClo (RoboMoClo) system was proposed to accelerate synthetic biology projects with multiple gene expressions. The RoboMoClo framework combines hierarchical gene assembly and iterative gene assembly strategies, and requires fewer destination vectors. The application of RoboMoClo in an industrial bacterium, C. glutamicum, demonstrated its potential in laboratory automation for synthetic biology.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Jaehyun Park, Dong Hun Kang, Han Min Woo
Summary: Engineering Corynebacterium glutamicum enabled the production and secretion of hydrophobic squalene without the need for in situ extractions, resulting in increased total squalene production. By promoting extraction and formulating bio-squalene nanoemulsions, creaming effects were analyzed for cosmetic applications. Combining metabolic pathway engineering and facilitated secretion in microbial cells shows promise for sustainable production of hydrophobic chemicals.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2021)
Article
Biochemical Research Methods
Dong Jae Kim, Jiwoo Kim, Dong Hyun Lee, Jongwuk Lee, Han Min Woo
Summary: Controlling translational elongation is crucial for protein synthesis efficiency. A new deep learning model, DeepTESR, is presented to predict the degree of translational elongation short ramp (TESR) based on mRNA sequence. The model showed superior performance in predicting TESR scores compared to conventional machine learning models. Experimental validation demonstrated a moderate correlation between predictions and heterologous protein expression. Furthermore, analysis of Escherichia coli coding sequences revealed conserved TESRs. DeepTESR can be used to predict TESR degree for gene expression control and elucidate translational control mechanisms with ribosome profiling.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biochemical Research Methods
Sung Cheon Ko, Mingu Cho, Hyun Jeong Lee, Han Min Woo
Summary: Lab automation has played an important role in the advancement of synthetic biology applications, and biofoundry facilities have enabled automated high-throughput experiments. However, the procedures before experiments in biofoundry applications are uncertain. We have developed the Python-based software Biofoundry Palette, which provides precise information for before-experiment units in the biofoundry workflow, to help reduce human errors and improve the success rate of synthetic biology applications.
ACS SYNTHETIC BIOLOGY
(2022)
Correction
Agriculture, Multidisciplinary
Jaehyun Park, Han Min Woo
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Agriculture, Multidisciplinary
Jaehyun Park, Han Min Woo
Summary: Corynebacterium glutamicum has been engineered for co-production of L-lysine and heterologous squalene, and metabolic fluxes were controlled by regulating the concentration of pyruvate, an intermediate in the central metabolism. In situ extraction with oil overlay showed high efficiency in co-production.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Plant Sciences
Mieun Lee, Yu Been Heo, Han Min Woo
Summary: Base editing enables precise gene editing without donor DNA or double-stranded breaks. However, the uracil DNA glycosylase inhibitor (UGI) fused with the cytidine deaminase-Cas nickase cannot inhibit the archaic Type IV uracil DNA glycosylase in cyanobacteria. To overcome this limitation, dCas12a-assisted gene repression of the udg gene allowed base editing with high mutation frequencies in cyanobacteria.
Article
Microbiology
Yu Been Heo, Gue-Ho Hwang, Seok Won Kang, Sangsu Bae, Han Min Woo
Summary: Genome editing technology is a powerful tool for programming microbial cell factories, but there is a risk of off-target effects. To address this issue, we developed high-fidelity cytosine base editors for precise gene editing and successfully created mutant strains to enhance succinate production. However, whole-genome sequencing revealed mutations in each strain. To reduce off-target effects, we employed high-fidelity editors and achieved more efficient and precise gene editing.
MICROBIOLOGY SPECTRUM
(2022)
Article
Biochemistry & Molecular Biology
Sung Cheon Ko, Han Min Woo
Summary: This study reports a method for bacterial RNA repression using the CRISPR-dCas13a system. By using programmable crRNAs, trans-acting and cis-acting sRNAs can be repressed, altering the regulatory mechanisms and stress-related phenotypes in bacteria. This system can be used for discovering novel sRNAs and fine-tuning bacterial RNA repression in both scientific and industrial applications.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Sung Cheon Ko, Han Min Woo
ACS SYNTHETIC BIOLOGY
(2020)
