Article
Biotechnology & Applied Microbiology
Jamin C. Wood, R. Axayacatl Gonzalez-Garcia, Dara Daygon, Gert Talbo, Manuel R. Plan, Esteban Marcellin, Bernardino Virdis
Summary: Formate metabolism in E. limosum, a promising energy carrier, is poorly understood, but this study presents the first steady-state dataset for formatotrophic growth. The research reveals that E. limosum has a high specific uptake rate of formate, but most carbon is converted to CO2. Protein differential expression and intracellular metabolomics indicate that the bacteria upregulates phosphotransacetylase (Pta) to produce acetate but also accumulates pyruvate due to cellular energy limitation and upregulates pyruvate formate ligase (Pfl) to convert formate to pyruvate. This protein-level metabolic control is unusual for an acetogen.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Microbiology
James Millard, Alexander Agius, Ying Zhang, Philippe Soucaille, Nigel Peter Minton
Summary: Targeted mutations in Eubacterium limosum were achieved using an inducible counter-selective system combined with a non-replicative integrating mutagenesis vector. This system allowed for precise gene deletions, including genes involved in histidine biosynthesis, methanol metabolism, and L-carnitine demethylation. The desired mutants could be obtained with only one induction step after the initial selection of transformant colonies. This approach enables quick and efficient gene editing of E. limosum.
Article
Agricultural Engineering
Hyunsoo Kang, Byeonghyeok Park, Soyoung Oh, Duleepa Pathiraja, Ji-Yeon Kim, Seunghyeon Jung, Jiyeong Jeong, Minseok Cha, Zee-Yong Park, In-Geol Choi, In Seop Chang
Summary: Through in silico prediction and in vivo assessment, we have successfully improved the rates of carbon monoxide conversion to acetate by Eubacterium limosum KIST612 strain.
BIORESOURCE TECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Lars Westphal, Dennis Litty, Volker Mueller
Summary: ATP synthases are essential for cellular bioenergetics and are structurally and functionally conserved in all life forms. A unique diversity in ion-binding site size and number exists in the c subunit of ancestral microbes, the archaea. Recent research on a Na+-dependent archaeal ATP synthase with a V-type c subunit in the mesophilic bacterium E. coli revealed insights into ATP synthesis and hydrolysis, functional coupling of F-1 and F-O domains, and the importance of specific amino acid residues in maintaining enzyme activity.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
(2021)
Article
Biotechnology & Applied Microbiology
Dennis Litty, Volker Mueller
Summary: Eubacterium limosum KIST612 primarily produces butyrate from acetate and glucose, with limited production observed from carbon monoxide, hydrogen, CO2, or formate. Interestingly, butyrate formation was also seen when using glucose or methanol as substrates during the stationary growth phase.
MICROBIAL BIOTECHNOLOGY
(2021)
Article
Microbiology
Guillaume Pregnon, Nigel P. Minton, Philippe Soucaille
Summary: E. limosum B2, an acetogen capable of producing butyrate and acetate from methanol, was subjected to adaptive laboratory evolution on methanol mineral medium. The evolved populations showed a significant increase in growth rate and exhibited changes in protein and methylome profiles, indicating the involvement of epigenetic regulation in metabolic improvements.
Article
Biochemical Research Methods
Chaoxian Bai, Gilles P. van Wezel
Summary: Streptomyces, a genus of Gram-positive bacteria, is a valuable producer of natural products with significant benefits for human health, agriculture, and biotechnology. Researchers have developed the CUBIC system, which allows efficient and inducible gene knockdown in Streptomyces, demonstrating its versatility and reliability.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Microbiology
Patrick A. Sanford, Katherine G. Miller, Kathryn O. Hoyt, Benjamin M. Woolston
Summary: Researchers developed a rapid and simple gene deletion protocol to eliminate biofilm formation in the gas-fermenting microbe Eubacterium limosum, which improves its handling and genetic engineering. This study provides important methods and strategies to address the challenges in bioprocessing and genetic engineering of this organism.
FEMS MICROBIOLOGY LETTERS
(2023)
Article
Biotechnology & Applied Microbiology
Ugochi Jennifer Nwaokorie, Kristina Reinmets, Lorena Azevedo de Lima, Pratik Rajendra Pawar, Kurshedaktar Majibullah Shaikh, Audrey Harris, Michael Kopke, Kaspar Valgepea
Summary: Gas fermentation is a sustainable approach to produce fuels and chemicals using gas-fermenting microbes. Acetogens that use the Wood-Ljungdahl pathway are the most advanced biocatalysts for gas fermentation, but our understanding of the genes involved in the C-1-fixing gene cluster is incomplete. This study investigates the role of two genes, hp and nbp, in gas-fermenting acetogen Clostridium autoethanogenum.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Article
Biochemical Research Methods
Hyun-Woo Je, Chang-Hun Ji, Jun-Yong Kim, Hahk-Soo Kang
Summary: The CRISPR/Cas9 system faces toxicity issues in Streptomyces genome engineering due to overexpression of the Cas9 protein. The CaExTun platform has been developed to optimize Cas9 expression for reduced toxicity while maintaining sufficient DSB activity. This tool enables rapid optimization of the CRISPR/Cas9 system in a species-specific manner, facilitating genome engineering efforts in Streptomyces.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Plant Sciences
Wenwen Kong, Mingliang Wang, Lijuan Huang, Feiyan Wu, Jinyuan Tao, Beixin Mo, Yu Yu
Summary: CRISPR/Cas9-dependent genome editing has been successfully applied to various plant species for fundamental studies and crop improvement, enabling random or targeted insertions, deletions, and base changes. To simplify the screening process for edited transformants, a dsRED2 cassette driven by CaMV 35S was introduced into the Cas9 vector, providing a visible protein for easy genetic screening without the need for instruments. Moreover, the use of the WUS promoter to drive the expression of Cas9 improved editing efficiency and enabled homozygous mutagenesis of target genes in Arabidopsis, making this system potentially applicable to other crops.
Article
Multidisciplinary Sciences
Arvind Sharma, Michael N. Pham, Jeremiah B. Reyes, Randeep Chana, Won C. Yim, Chan C. Heu, Donghun Kim, Duverney Chaverra-Rodriguez, Jason L. Rasgon, Robert A. Harrell, Andrew B. Nuss, Monika Gulia-Nuss
Summary: Ticks have the ability to transmit various debilitating pathogens, but research on ticks has been lacking compared to other arthropod vectors due to challenges in applying genetic and molecular tools. This study reports a successful embryo injection protocol for the black-legged tick and demonstrates the use of CRISPR-Cas9 for genome editing. The results provide innovative tools for tick research.
Article
Biochemical Research Methods
Ivana Cengic, Ines C. Candas, Nigel P. Minton, Elton P. Hudson
Summary: This study presents a riboswitch-inducible CRISPR/Cas9 system on a single replicative vector for precise and markerless genome editing in the model cyanobacterium Synechocystis sp. PCC 6803. The system allows for efficient editing of various genomic targets and reliable segregation of mutants. Additionally, a vector curing system is introduced for markerless mutants.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biochemical Research Methods
Ivana Cengic, Ines C. Canadas, Nigel P. Minton, Elton P. Hudson
Summary: In this study, a theophylline-responsive riboswitch-induced CRISPR/Cas9 system was developed for precise and markerless genome editing in cyanobacterium. This single-vector system enables multiplexed editing and allows for the generation of markerless mutants.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biochemical Research Methods
Surbhi Jain, Guanhua Xun, Shireen Abesteh, Sherri Ho, Manasi Lingamaneni, Teresa A. Martin, Ipek Tasan, Che Yang, Huimin Zhao
Summary: Using engineered anti-CRISPR protein AcrIIA4 in combination with a ligand-inducible destabilization domain, the specificity of the CRISPR/Cas9 system in mammalian cells has been significantly improved. Additionally, a new inducible promoter system AcrOFF, regulated by the FDA-approved ligand trimethoprim, allows for control over the CRISPR system activity.
ACS SYNTHETIC BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Bit-Na Kim, Wooil Choi, Byung-Kwan Cho, Jiho Min
Summary: The vacuole in Saccharomyces cerevisiae, similar to lysosomes, has been found to have various functions including antimicrobial, detection of toxic substances and pathogens, melanin reduction and antioxidant activity, and potential as drug carriers in cancer treatment. Genetic manipulation and expression control mechanisms have led to the creation of novel vacuole systems. The ability to control the size of vacuoles and research in nanomedicine further expands the applications of vacuoles.
MOLECULAR & CELLULAR TOXICOLOGY
(2023)
Article
Agricultural Engineering
Sanjay K. S. Patel, Vipin C. Kalia, Jung -Kul Lee
Summary: In this study, enzyme-based rice straw hydrolysate was used to produce dark-fermentative biogas, which was then integrated with biogas derived from anaerobic digestion to generate methanol via methanotrophs. The integration of these two sources resulted in the production of 13.8 mmol/L of methanol. In addition, under repeated batch mode, 64.6 mmol/L of methanol was produced. This is the first report on the integration of biogas derived from anaerobic digestion and dark-fermentative biogas to produce biomethanol. These findings could contribute to the development of a sustainable biowaste-based circular economy for biofuel production.
BIORESOURCE TECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Jongoh Shin, Jiyun Bae, Hyeonsik Lee, Seulgi Kang, Sangrak Jin, Yoseb Song, Suhyung Cho, Byung-Kwan Cho
Summary: Acetogenic bacteria have potential in sustainable bioconversion of carbon oxides into biochemicals. Through genome-scale CRISPR interference screening, we identified the fitness contributions of 96% of the genes in E. limosum, revealing the essentiality of certain pathways for autotrophic acetogenesis. We also discovered repression target genes that improved autotrophic growth rates and acetoin production.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Microbiology
Donghui Choe, Uigi Kim, Soonkyu Hwang, Sang Woo Seo, Donghyuk Kim, Suhyung Cho, Bernhard Palsson, Byung-Kwan Cho
Summary: Transposon mutagenesis is an efficient method for exploring gene essentiality in bacteria. However, there are discrepancies between the essential gene sets determined by transposon mutagenesis and single-gene knockout methods. This study identified false negatives and false positives in essential gene discovery using Tn-Seq, which should be considered to avoid misinterpretation of results.
Article
Chemistry, Multidisciplinary
Afia Tasnim Rahman, Jongoh Shin, Chang-Hee Whang, Wonsik Jung, Dohyun Yoo, Changjin Seo, Byung-Kwan Cho, Sangyong Jon
Summary: This study reports a nanomedicine composed of bilirubin-attached low-molecular-weight, water-soluble chitosan nanoparticles that can promote restoration of intestinal barrier, mucosal immunity, and gut microbiome homeostasis, thereby exhibiting robust therapeutic efficacy.
Article
Thermodynamics
Hobin Son, Haijun Jeong, Ikhyun Ryu, Kwan-Soo Lee, Dong Rip Kim
Summary: This study experimentally investigates frost growth behavior at ultra-low temperatures on vertical plates under buoyancy-assisting and buoyancy-opposing flows. Different frost growth behaviors were observed due to the combined effects of frost gravity and drag force. A higher-density and lower-thickness frost layer was formed in the opposing flow due to the formation of unique frost walls. The frost wall not only delayed frost growth on downstream plates but also promoted condensation phenomena. Correlation equations were suggested to predict ultra-low temperature frosting behaviors with an error within 10%.
INTERNATIONAL JOURNAL OF HEAT AND MASS TRANSFER
(2023)
Article
Thermodynamics
Jae Woo Sim, Haeyeon Lee, Sungwon Jo, Sanghyun Oh, Sungil Kim, Dong Rip Kim
Summary: Spray drying process, widely used in industrial applications, is highly energy-consuming. Efforts have been made to optimize the operating conditions or utilize heat from exhaust air to reduce energy consumption while securing the yield. However, high temperature processing may degrade the quality of dried materials. Therefore, further strategies are needed for yield enhancement in low temperature environments.
CASE STUDIES IN THERMAL ENGINEERING
(2023)
Article
Biochemistry & Molecular Biology
Yunyoung Cho, Ji Hun Kim, Wooil Choi, Dae-Young Park, Byung-Kwan Cho, Yang-Hoon Kim, Jiho Min
Summary: In this study, the researchers developed a new drug delivery system called reassembled vacuoles (ReV) by removing vacuolar enzymes and reassembling the vacuolar membrane. ReV demonstrated improved structural stability, a more uniform size, and enhanced release of the loaded antibiotic polymyxin B (PMB) compared to natural vacuoles. The study highlights the potential of ReV as a drug delivery system, providing opportunities for targeted and efficient drug release.
Article
Engineering, Environmental
Ju Hyeong Kim, Min Kim, Jeong Hoo Hong, Yun Chan Kang
Summary: A bifunctional oxygen electrocatalyst for Zn-air batteries was synthesized by forming a unique structured composite of cobalt hydroxy selenide (Co(OH)Se) and nitrogen-doped carbon (C) using a novel water vapor-assisted heat-treatment and an anion-exchange technique. The composite exhibited excellent electrocatalytic activities for both the oxygen reduction reaction (ORR) and oxygen evolution reaction (OER), resulting in improved cycle stability and rate capability of the ZAB. This study expands the range of electrocatalyst design and synthesis by demonstrating the potential use of multi-anionic Co(OH)Se and presenting a technique for complexing transition metal compounds and carbon matrices.
CHEMICAL ENGINEERING JOURNAL
(2023)
Review
Environmental Sciences
Vipin Chandra Kalia, Sanjay K. S. Patel, Jung-Kul Lee
Summary: Bacteria causing infectious diseases use biofilms as a common lifestyle, which makes antibiotics ineffective. Quorum sensing and c-di-GMP are signaling mechanisms that regulate bacterial biofilm formation. The research aims to provide methods for inhibiting biofilm formation and disrupting mature biofilms to aid in the treatment of infectious diseases.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2023)
Article
Biotechnology & Applied Microbiology
Sanjay K. S. Patel, Rahul K. Gupta, In-Won Kim, Jung-Kul Lee
Summary: This study successfully applied a bio-friendly inorganic protein hybrid-based enzyme immobilization system using partially purified Coriolus versicolor laccase (CvLac) to enhance sugar production for biofuels. CvLac immobilized through inorganic protein hybrids showed significantly improved enzyme activity and stability. The synthesized hybrid nanoflowers exhibited a high residual activity and improved biomass hydrolysis, resulting in enhanced hydrogen and ethanol production.
ENZYME AND MICROBIAL TECHNOLOGY
(2023)
Article
Thermodynamics
Haijun Jeong, Hobin Son, Sungjoon Byun, Seounghwan Hyeon, Kwan-Soo Lee, Dong Rip Kim
Summary: An experimental study was conducted to investigate the phase change on a cryogenic cooling surface under forced convection conditions. Measurements were taken for the mass and surface temperature of frost, as well as the heat flux at the cooling surface. The study explored the heat and mass transfer analogy under cryogenic conditions. By using the modified analogy, the estimated mass differed by up to 8% from the experimentally measured mass under various conditions. The density and thermal conductivity of frost at cryogenic temperatures were derived through regression analysis, and the calculated values differed from the measured values by up to 9% and 11%, respectively. A model was developed based on the presented frost density and thermal conductivity correlations to predict heat and mass transfer and improve thermal performance on the cooling surfaces of various cryogenic devices.
INTERNATIONAL JOURNAL OF HEAT AND MASS TRANSFER
(2023)
Article
Biochemistry & Molecular Biology
Thi Thuy Nguyen, Le Minh Bui, Ji-Young Byun, Byung-Kwan Cho, Sun Chang Kim
Summary: This study explores the potential of a genome-reduced Escherichia coli as a host for pDNA production. By removing approximately 23% of the genome and increasing the abundance of NADPH, it was found that pDNA production capabilities were enhanced three-fold compared to the widely employed DH5 ff strain. Furthermore, the genome-reduced strain exhibited heightened sensitivity to various antibiotics, bolstering its potential for industrial pDNA production.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Polymer Science
Sanjay K. S. Patel, Rahul K. Gupta, In-Won Kim, Jung-Kul Lee
Summary: This study examines the influence of Cu and Fe nanoparticles on the growth of methanotrophs and the development of a polymeric-matrix-based encapsulation system for methanol production. The results show that the presence of nanoparticles and the use of simulated biogas feed greatly enhance methanol production, and the encapsulation system improves the stability and reusability of methanotrophs.
Article
Microbiology
Jaeyoung Yu, Woo-Ri Shin, Ji Hun Kim, Soo Youn Lee, Byung-Kwan Cho, Yang-Hoon Kim, Jiho Min
Summary: This study demonstrates the benefits of temperature control in enhancing CO2 recycling and the synthesis of organic acids in engineered bacterial strains. Lowering the culture temperature effectively suppresses inclusion body formation, resulting in decreased CO2 emissions and increased pyruvate accumulation.
MICROBIOLOGY SPECTRUM
(2023)
