Article
Chemistry, Medicinal
Sree Kavya Penneru, Moumita Saharay, Marimuthu Krishnan
Summary: Bacterial cellulase enzymes are potential candidates for the efficient production of bioethanol from cellulosic biomass. CelS is a microbial enzyme that cleaves cellulose into cellobiose. This study investigates the mechanism of substrate dynamics and product expulsion in CelS through molecular dynamics simulations.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Agronomy
Le Gao, Qiuhui Chen, Haofan Dong, Zhaokun Zhang, Tongtong Bao, Lixian Wang, Fan Yang, Xin Wu
Summary: There is a high level of conservation of tryptophans within the active site architecture of the cellulase family, but the function of the four tryptophans in the catalytic domain of Cel7A is unclear. By mutating these tryptophan residues, it was found that they played a critical role in substrate binding and catalytic activity. The study also showed that using cellulose analogs for cellulase screening may lead to overestimation of activity compared to natural substrates.
GLOBAL CHANGE BIOLOGY BIOENERGY
(2023)
Article
Biotechnology & Applied Microbiology
Venkataramanan Subramanian, Samuel J. Farmer, Kelsey L. Heiland, Kyle T. Moore, Todd A. Vander Wall, Weiman Sun, Yogesh B. Chaudhari, Michael E. Himmel, Stephen R. Decker
Summary: Heterologous protein production in Trichoderma reesei is challenging due to low transformation efficiency and screening systems. The 2A-peptide multi-gene expression system was successfully used to co-express four proteins, including cellulases and a marker protein. The functionality of the cellulases was confirmed, and the reliability of the screening technique was validated by the level of eGFP fluorescence.
JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Yuanyuan Xia, Meng Yin, Lukasz Peplowski, Zhongyi Cheng, Zhemin Zhou
Summary: A mutant of nitrile hydratase with improved activity towards 3-cyanopyridine has been identified, showing potential for industrial production of nicotinamide.
Article
Biochemistry & Molecular Biology
Akihiko Nakamura, Takashi Kanazawa, Tadaomi Furuta, Minoru Sakurai, Markku Saloheimo, Masahiro Samejima, Anu Koivula, Kiyohiko Igarashi
Summary: The Trp38 residue in TrCel7A plays a key role in processively loading the reducing-end of cellulose chain into the catalytic tunnel, while Trp40 is important for recruiting cellulose chain ends on the substrate surface. The mutation W38A disrupts the smooth gradient of binding energy and leads to increased activity towards amorphous cellulose but decreased activity towards crystalline cellulose.
JOURNAL OF APPLIED GLYCOSCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Keisuke Kojima, Naoki Sunagawa, Nils Egil Mikkelsen, Henrik Hansson, Saeid Karkehabadi, Masahiro Samejima, Mats Sandgren, Kiyohiko Igarashi
Summary: In this study, two xylan enzymes were compared to gain insights into their structures and catalytic mechanisms. The results showed that the two enzymes exhibited different degradation efficiencies and specificities towards xylooligosaccharides of different lengths. Additionally, it was found that wood-decaying fungi and molds use different enzymes for xylan degradation, possibly due to their distinct environmental niches.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Keisuke Kojima, Naoki Sunagawa, Yoshihisa Yoshimi, Theodora Tryfona, Masahiro Samejima, Paul Dupree, Kiyohiko Igarashi
Summary: This study compares the activity of two types of xylanases in degrading acetylated and deacetylated xylan. The results suggest that the degradability of xylan by GH11 xylanases is highly dependent on the extent of acetyl group substitution. Additionally, the study found a potential coevolution relationship between GH11 xylanases and CE1 AXEs.
JOURNAL OF APPLIED GLYCOSCIENCE
(2022)
Article
Materials Science, Paper & Wood
Kaisa Marjamaa, Jenni Rahikainen, Marika Karjalainen, Natalia Maiorova, Ulla Holopainen-Mantila, Matthieu Molinier, Nina Aro, Heli Nygren, Atte Mikkelson, Anu Koivula, Kristiina Kruus
Summary: This study investigated the parameters affecting the efficiency of LPMO in oxidative modification of cotton linters and softwood kraft fibres. The results showed that temperature and pH affected the stability and efficacy of the enzyme. The oxidative enzymatic treatment facilitated fibre dissolution and degradation of fibre surface structures, preventing swelling.
Article
Biochemistry & Molecular Biology
Genta Kamiya, Nobuo Kitada, Tadaomi Furuta, Takashi Hirano, Shojiro A. Maki, Sung-Bae Kim
Summary: A unique combinatorial bioluminescence imaging system was developed to determine molecular events in mammalian cells. This system utilizes various colors and BL intensity patterns by using reporter luciferases and novel coelenterazine analogues. The synthesized substrates showed unique specificity and BL intensity patterns with marine luciferases, enabling the identification of different reporters and ligand-specific fold intensities in mammalian cells.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Ellen Tanudjaja, Naomi Hoshi, Kaneyoshi Yamamoto, Kunio Ihara, Tadaomi Furuta, Masaru Tsujii, Yasuhiro Ishimaru, Nobuyuki Uozumi
Summary: Escherichia coli K-12 has two versions of potassium ion (K+) transporters, TrkG and TrkH. TrkG requires Na+ for K+ uptake, while TrkH is not affected by Na+. An aspartic acid near a critical glycine in TrkG may regulate its Na+-dependent activation. TrkG can complement the loss of TrkH-mediated K+ uptake, but TrkH supports cell growth more than TrkG. The transcription of trkG in E. coli is downregulated but not completely silenced by the silencing factor H-NS.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Materials Science, Biomaterials
Mariko Kojima, Satoshi Abe, Tadaomi Furuta, Duy Phuoc Tran, Kunio Hirata, Keitaro Yamashita, Yuki Hishikawa, Akio Kitao, Takafumi Ueno
Summary: Protein crystals can serve as porous scaffolds for capturing exogenous molecules. Fixing target proteins in the pores of scaffold protein crystals has been challenging due to limited strategies to control protein-protein interactions. This study successfully fixes a miniprotein within a polyhedra crystal scaffold, revealing the potential of modulating intermolecular interactions for trapping various protein conformations.
BIOMATERIALS SCIENCE
(2023)
Article
Biochemical Research Methods
Yuki Ohmuro-Matsuyama, Hayato Matsui, Masaki Kanai, Tadaomi Furuta
Summary: This study found that adding oligopeptides with charged residues to the C-terminus of picALuc significantly enhanced its luminescence by up to 50-fold, indicating an increased enzymatic activity. This enhancement was observed in both bacterial and mammalian expression systems.
BIOTECHNOLOGY JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Ayumu Kobayashi, Masamune Nakamura, Masaru Tsujii, Kohei Makino, Tatsuya Nagayama, Kensuke Nakamura, Kei Nanatani, Kera Kota, Yuki Furuuchi, Shunsuke Kayamori, Tadaomi Furuta, Iwane Suzuki, Yoshihiro Hayakawa, Ellen Tanudjaja, Yasuhiro Ishimaru, Nobuyuki Uozumi
Summary: Two two-component regulatory systems (TCSs), Rre2-Hik12 and Rre8-Hik14, were found to be involved in biofilm formation in Synechocystis sp. PCC 6803. Rre2 and Rre8 regulated c-di-GMP production, with Rre2 having DGC activity regardless of its phosphorylation status and Rre8 requiring phosphorylation for DGC activity.
MOLECULAR MICROBIOLOGY
(2023)
Article
Chemistry, Analytical
Sung-Bae Kim, Tadaomi Furuta, Genta Kamiya, Nobuo Kitada, Ramasamy Paulmurugan, Shojiro A. Maki
Summary: In this study, we developed bright and highly sensitive single-chain molecular strain probe templates with luciferase reporters for imaging protein-protein interactions (PPIs). By utilizing the concept of molecular strains and rapamycin-triggered intramolecular PPIs, the ligand-sensing properties of the templates were maximized. The highest fold intensities were achieved with RLuc86SG and ALuc49, with tunable colors to blue, green, and yellow.
Article
Chemistry, Multidisciplinary
Basudev Maity, Jiaxin Tian, Tadaomi Furuta, Satoshi Abe, Takafumi Ueno
Summary: Water behavior on protein surfaces affects protein structure and function. Antifreeze proteins (AFPs) have been extensively studied in the field of biological cytotechnology. They can inhibit ice microcrystal growth through the formation of unique water cluster networks influenced by protein surface morphology and hydrophobicity. However, there is limited information about the atomic-level process of semi-clathrate formation and the structural units of water-clathrate networks.
CRYSTAL GROWTH & DESIGN
(2023)
Article
Biochemistry & Molecular Biology
Yuki Ohmuro-Matsuyama, Hayato Matsui, Masaki Kanai, Tadaomi Furuta
Summary: Researchers developed a bright luciferase, picALuc, and identified important residues and regions for its catalysis and bioluminescence through mutational analyses. These findings provide important insights into the bioluminescence mechanism of picALuc and copepod luciferases and have potential applications for sustained observations.
Article
Biochemistry & Molecular Biology
Haruka Kono, Satoshi Hara, Tadaomi Furuta, Hiroshi Ichinose
Summary: In this study, the binding profile of quinonoid-form dihydrobiopterin (qBH2) to quinonoid dihydropteridine reductase (QDPR) was analyzed using in vitro and in silico methods. It was found that qBH2 and quinonoid-form dihydrofolate (qDHF) could be potential physiological substrates for QDPR, suggesting that QDPR may have a bifunctional role. These findings provide important insights into biopterin and folate metabolism and have implications for drug development.
JOURNAL OF BIOCHEMISTRY
(2023)
Article
Chemistry, Analytical
Sung-Bae Kim, Tadaomi Furuta, Nobuo Kitada, Shojiro A. A. Maki
Summary: A series of new artificial luciferases (ALucs) were created by compensating missing peptide blocks in the alignment of existing ALuc sequences. These new ALucs formed an independent branch genetically isolated from other natural marine luciferases and showed bioluminescent properties in living mammalian cells. The success of this study can provide new insights into engineering and functionalizing marine luciferases for various applications in bioassays and molecular imaging.
Article
Chemistry, Analytical
Sung-Bae Kim, Genta Kamiya, Tadaomi Furuta, Nobuo Kitada, Shojiro A. Maki
Summary: Synthetic coelenterazine (CTZ) indicators were developed to quantitatively study human and bovine serum albumins (HSA and BSA) with high specificity. The CTZ indicators emit luminescence with specific modifications, and their colors and peak positions can determine the origins and mixing levels of albumins. The study also found that serum albumins catalyze the CTZ indicators and this catalytic reaction can be efficiently inhibited by specific inhibitors.
Article
Biochemistry & Molecular Biology
Sung-Bae Kim, Tadaomi Furuta, Yuki Ohmuro-Matsuyama, Nobuo Kitada, Ryo Nishihara, Shojiro A. Maki
Summary: In this study, a near-infrared bioluminescence (BL) imaging system was developed using copepod luciferases ALuc30 and its miniaturized version picALuc. The system was characterized and analyzed with different coelenterazine analogues and Cy5. The results showed that picALuc-based system enhances BL intensities in the red and NIR region, while both ALuc30- and picALuc-based systems exhibit unique spectral bands in the NIR region with a Cy5-conjugated coelenterazine analogue.
PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES
(2023)