Article
Microbiology
Mohamed Yahia Eljonaid, Hisao Tomita, Fumiyoshi Okazaki, Yutaka Tamaru
Summary: The cellulolytic system of Clostridium cellulovorans consists of a cellulosome and non-complexed enzymes which effectively degrade cellulosic biomass to produce glucose and cellobiose. The addition of new culture medium and L-cysteine can enhance the degradation efficiency.
Article
Biochemical Research Methods
Loredana Tarraran, Chiara Gandini, Anna Luganini, Roberto Mazzoli
Summary: Engineering synthetic scaffoldins derived from C. cellulovorans cellulosome components successfully introduced them into L. lactis, with a focus on their potential cell-surface anchoring capabilities. Among the engineered scaffoldins, only those carrying three EngE SLH modules were able to bind to the surface of L. lactis, despite the absence of the conserved TRAE motif typically involved in binding with secondary cell wall polysaccharides. These synthetic scaffoldins could potentially be used for assembling secreted or surface-displayed designer cellulosomes in L. lactis.
BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Marlene Duarte, Victor D. Alves, Marcia Correia, Catarina Caseiro, Luis M. A. Ferreira, Maria Joao Romao, Ana Luisa Carvalho, Shabir Najmudin, Edward A. Bayer, Carlos M. G. A. Fontes, Pedro Bule
Summary: The cellulosome is a complex multi-enzyme structure secreted by anaerobic microorganisms for efficient degradation of lignocellulosic substrates. It consists of catalytic and non-catalytic components that are assembled through protein-protein interactions. The structure of an adaptor scaffoldin-borne ScaH Doc in complex with the Coh from anchoring scaffoldin ScaE was described, revealing a dual-binding mode interaction and identifying key residues for Coh recognition. Rational protein engineering was used to improve the affinity between the two modules, showing the potential for tailored Coh-Doc interactions in bioengineering applications.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Biotechnology & Applied Microbiology
Wen-Zhu Tang, Dan-Dan Jiang, Yi-Xuan Fan, Quan Zhang, Li-Cheng Liu, Fu-Li Li, Zi-Yong Liu
Summary: Clostridium cellulovorans, an anaerobic butyrate-producing bacterium, can secrete various extracellular enzymes to degrade plant-based cellulose. However, it still secretes a large amount of protein in the broth when glucose is used as the carbon source. The metabolism and regulation of protein secretion need further investigation.
FERMENTATION-BASEL
(2023)
Article
Chemistry, Physical
Penghui Li, Xin Wang, Chunchun Zhang, Dingguo Xu
Summary: This study investigates the processive binding mechanism of cellulase family 9 (Cel9G) to polysaccharides. The simulations reveal that the binding of the cellulose chain exhibits several local minima, which are influenced by the CH/pi interactions between sugar rings and aromatic residues. Y520 is found to be critical for processive binding, and the straight-line morphology of the substrate is observed after the formation of the slide mode. The study proposes a four-step catalytic cycle for Cel9G.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Immunology
Luis F. Soto, Ana C. Romani, Gabriel Jimenez-Avalos, Yshoner Silva, Carla M. Ordinola-Ramirez, Rainer M. Lopez Lapa, David Requena
Summary: This study computationally screened the whole proteome of Clostridium perfringens and identified highly immunogenic proteins, domains, and epitopes. They found potential recombinant vaccine candidates, a potential sub-unit vaccine, and designed a multi-epitope protein. These findings are important for the development of safe and effective vaccines against C. perfringens infection.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Sean R. McIntyre, Paola A. Saenz-Cavazos, Elwin Hunter-Sellars, Daryl R. Williams
Summary: This paper examines the significance of diffusion processes in the transfer hydrogenation reaction of levulinic acid to gamma-valerolactone using MIL-88B, MIL-100, and ZIF8@Pd monolithic catalysts. The Fe-based catalysts showed similar conversions to the ZIF-8 supported Pd, but with lower aqueous stability. By calculating diffusion constants and mass transfer coefficients, it was found that ZIF-8 had better mass transport performance compared to MIL-100.
FRONTIERS IN CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Shi-Hai Mao, Hong-Hai Zhang, Guang-Chao Zhuang, Xiao-Jun Li, Qiao Liu, Zhen Zhou, Wei-Lei Wang, Chun-Yang Li, Ke-Yu Lu, Xi-Ting Liu, Andrew Montgomery, Samantha B. Joye, Yu-Zhong Zhang, Gui-Peng Yang
Summary: This study investigated methane sources and fates in the East China Sea and estimated the global rates of aerobic methane oxidation (MOx) in shallow waters using machine-learning models. The results showed that methane is produced during methylphosphonate decomposition and sedimentary release. High MOx rates were observed in productive coastal waters and were correlated with methanotrophic activity and biomass. The study estimated that aerobic methanotrophy can consume around half of the methane annually in near-shore waters, significantly reducing global methane emissions.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Yasar Kemal Recepoglu, Ozguer Arar, Asli Yuksel
Summary: Biosorption using phosphorylated hazelnut shell waste (FHS) is a promising method for lithium removal and recovery. This study investigated the performance of a continuous-flow packed-bed column system using FHS for ultra-low level lithium removal. The results showed that the lihium biosorption capacity of the FHS column was unaffected by the bed height, but decreased with increasing flow rate.
JOURNAL OF CHROMATOGRAPHY A
(2024)
Article
Biotechnology & Applied Microbiology
Yukai Suo, Wenyi Li, Liqiong Wan, Linshuang Luo, Shuang Liu, Shiwen Qin, Jufang Wang
Summary: Lignocellulosic biomass is a rich and renewable feedstock for biobased butyric acid production. However, the presence of furan derivatives from the pretreatment of lignocellulose severely inhibits the growth of the best strain for producing butyric acid, Clostridium tyrobutyricum. This study investigated the tolerance mechanism of C. tyrobutyricum to furan derivatives and found that upregulation of genes related to membrane transport, heat shock proteins, and transcriptional regulation occurs under furan derivative stress. Additionally, it was discovered that C. tyrobutyricum is unable to rapidly convert furan derivatives to low-toxicity alcohols, leading to its low tolerance. These findings provide insights into the development of furan derivative-tolerant strains for enhanced bioconversion of lignocellulosic biomass to butyric acid.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Microbiology
Shunsuke Ichikawa, Yoichiro Tsuge, Shuichi Karita
Summary: Constituents from membrane vesicles of C. thermocellum and B. subtilis can enhance the growth rate of C. thermocellum, leading to improved efficiency of cellulosic biomass utilization.
Article
Agricultural Engineering
Hao Tang, Yuan-Qiu Li, Ming-Jun Wang, Chao-Bing Luo
Summary: This study investigates the mechanisms behind efficient lignocellulosic biomass degradation by Cyrtotrachelus buqueti through transcriptome and microbiome analysis. The gut secretory protein and gut microbiota both show efficiency in degrading cellulose, hemicellulose, and lignin. The composition and abundance of bacteria in different gut regions play a crucial role in lignocellulosic biomass degradation.
INDUSTRIAL CROPS AND PRODUCTS
(2023)
Article
Plant Sciences
Congpeng Wang, Naixu Liu, Zhao Geng, Meijing Ji, Shumin Wang, Yamei Zhuang, Dian Wang, Guo He, Shutang Zhao, Gongke Zhou, Guohua Chai
Summary: This study generated transgenic poplar lines with edited PdBRI1 genes and investigated the influence of brassinosteroid (BR) signaling on wood development. By analyzing the transcriptome and proteome, the study revealed a dual role of BRs in procambial cell division and xylem differentiation.
HORTICULTURE RESEARCH
(2022)
Article
Multidisciplinary Sciences
Yang Shu, Jinqi Zhang, Wei Li, Pengwu Zhao, Qiyue Zhang, Mei Zhou
Summary: The study found that Larix and Quercus forests have high combustibility values and can be established as fire-resistant forests to reduce the risk of forest fires.
Article
Chemistry, Analytical
Balazs Bobaly, Alex Keresztfalvi, Thomas Graeber, Maria Anna Schwarz
Summary: The use of reversed phase liquid chromatography at mild or elevated temperatures is common for therapeutic protein analysis. Utilizing ultra-short columns and fast gradients can minimize on-column degradation under superheated conditions and achieve informative separations efficiently.
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS
(2021)
Article
Multidisciplinary Sciences
Tatsuya Yoshida, Rinako Ujiie, Alan H. Savitzky, Teppei Jono, Takato Inoue, Naoko Yoshinaga, Shunsuke Aburaya, Wataru Aoki, Hirohiko Takeuchi, Li Ding, Qin Chen, Chengquan Cao, Tein-Shun Tsai, Anslem de Silva, Dharshani Mahaulpatha, Tao Thien Nguyen, Yezhong Tang, Naoki Mori, Akira Mori
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Microbiology
Keisuke Motone, Toshiyuki Takagi, Shunsuke Aburaya, Natsuko Miura, Wataru Aoki, Mitsuyoshi Ueda
Article
Multidisciplinary Sciences
Takahiro Tsuji, Hiroaki Ozasa, Wataru Aoki, Shunsuke Aburaya, Tomoko Yamamoto Funazo, Koh Furugaki, Yasushi Yoshimura, Masatoshi Yamazoe, Hitomi Ajimizu, Yuto Yasuda, Takashi Nomizo, Hironori Yoshida, Yuichi Sakamori, Hiroaki Wake, Mitsuyoshi Ueda, Young Hak Kim, Toyohiro Hirai
NATURE COMMUNICATIONS
(2020)
Article
Biotechnology & Applied Microbiology
Yukio Watanabe, Kouichi Kuroda, Yuki Tatemichi, Takeharu Nakahara, Wataru Aoki, Mitsuyoshi Ueda
Article
Multidisciplinary Sciences
Shunsuke Aburaya, Yuji Yamauchi, Takashi Hashimoto, Hiroyoshi Minakuchi, Wataru Aoki, Mitsuyoshi Ueda
SCIENTIFIC REPORTS
(2020)
Article
Biotechnology & Applied Microbiology
Yuki Tatemichi, Kouichi Kuroda, Takeharu Nakahara, Mitsuyoshi Ueda
Article
Multidisciplinary Sciences
Yuishin Kosaka, Wataru Aoki, Megumi Mori, Shunsuke Aburaya, Yuta Ohtani, Hiroyoshi Minakuchi, Mitsuyoshi Ueda
Article
Biology
Makoto Hibi, Dai Fukuda, Chihiro Kenchu, Masutoshi Nojiri, Ryotaro Hara, Michiki Takeuchi, Shunsuke Aburaya, Wataru Aoki, Kimihiko Mizutani, Yoshihiko Yasohara, Mitsuyoshi Ueda, Bunzo Mikami, Satomi Takahashi, Jun Ogawa
Summary: The study identified a novel three-component monooxygenase system in Rhodococcus wratislaviensis, which catalyzes the activation of an inert C-H bond. This system shows potential importance as a biocatalyst for industrial applications.
COMMUNICATIONS BIOLOGY
(2021)
Article
Cell Biology
Yuki Yoshimura, Reina Hirayama, Natsuko Miura, Ryotaro Utsumi, Kouichi Kuroda, Mitsuyoshi Ueda, Michihiko Kataoka
Summary: Glycolytic enzymes in Saccharomyces cerevisiae reorganize to form cytoplasmic foci under hypoxia, with enolase responding the fastest. Small-scale hypoxic culture systems have been shown to regulate oxygen concentration and accelerate foci formation. Screening with this method revealed that an AMPK inhibitor delayed the formation of foci in glycolytic enzymes.
CELL BIOLOGY INTERNATIONAL
(2021)
Article
Biochemistry & Molecular Biology
Ryota Yamamoto, Genki Sato, Takamitsu Amai, Mitsuyoshi Ueda, Kouichi Kuroda
Summary: In this study, a novel technology for inducing chromatin loosening in target regions of Saccharomyces cerevisiae was established through nucleosomal histone acetylation. The system successfully increased euchromatic DNA at the target locus, suggesting the potential of inducing euchromatic state in a target locus using this developed method.
Article
Biochemistry & Molecular Biology
Wataru Aiba, Takamitsu Amai, Mitsuyoshi Ueda, Kouichi Kuroda
Summary: This study successfully increased the efficiency of precise genome editing by creating a donor DNA/guide RNA hybrid duplex. Compared to editing with separately introduced gRNA and donor DNA, the HDR-mediated editing efficiency using this hybrid duplex technique was improved by 1.8-fold.
Review
Microbiology
Genki Sato, Kouichi Kuroda
Summary: Modification of the yeast Saccharomyces cerevisiae genome using the CRISPR-Cas9 system has great potential in biological research and biotechnology. Overcoming the limitations of the conventional system, this review focuses on developments in reducing unintended editing and inducing desired changes in the target region's epigenetic state. Moreover, the expansion of the CRISPR-Cas9 system to edit genomes within intracellular organelles like mitochondria is discussed, highlighting the key role of yeast cells in driving advancements in genome editing.
Article
Biochemistry & Molecular Biology
Yuki Tatemichi, Takeharu Nakahara, Mitsuyoshi Ueda, Kouichi Kuroda
Summary: The study successfully assembled 17 scattered nif-related genes from Azotobacter vinelandii into synthetic gene clusters and expressed them in Escherichia coli, demonstrating nitrogenase activity under anaerobic and microaerobic conditions. This provides a promising strategy for developing biological nitrogen fixation methods.
BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Takamitsu Amai, Tomoka Tsuji, Mitsuyoshi Ueda, Kouichi Kuroda
Summary: A mito-CRISPR system has been developed to specifically generate rho degrees cells in yeast, providing a concise technology for deleting mtDNA in yeast.
BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Kazuki Ikeda, Masatomo Takahashi, Shunsuke Aburaya, Daiki Harada, Maki Ikeda, Yume Kitagawa, Yuki Soma, Yoshihiro Izumi, Takeshi Bamba, Mitsuhiro Furuse
Summary: HMB is an intermediate in leucine metabolism and has effects on skeletal muscle function. Administration of HMB in mice led to increased metabolites and changes in body weight, with an increase in gastrocnemius muscle relative weight.
BIOCHEMISTRY AND BIOPHYSICS REPORTS
(2021)
