Article
Chemistry, Multidisciplinary
Kohtaro Hirao, Immacolata Speciale, Anna Notaro, Yoshiyuki Manabe, Yoshiaki Teramoto, Takaaki Sato, Haruyuki Atomi, Antonio Molinaro, Yoshihiro Ueda, Cristina De Castro, Koichi Fukase
Summary: This study describes the isolation, structural determination, and chemical synthesis of the N-glycan from the hyperthermophilic archaeon Thermococcus kodakarensis, revealing a unique structure including myo-inositol not found in previously characterized N-glycans. The synthesis of this glycan was successfully achieved through diastereoselective phosphorylation and phosphodiester construction by S(N)2 coupling. This research is expected to provide insights into the primitive function of glycan modification at the molecular level by considering the early divergence of hyperthermophilic organisms in evolution.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Microbiology
Kelly M. Zatopek, Brett W. Burkhart, Richard D. Morgan, Alexandra M. Gehring, Kristin A. Scott, Thomas J. Santangelo, Andrew F. Gardner
Summary: This study reveals that deletion of either one or both of the R-M enzymes in T. kodakarensis strains results in slower growth but significantly enhanced competency compared to strains with intact R-M systems. This suggests that both TkoI and TkoII play a role in maintaining genomic integrity and likely protect against viral or plasmid-based DNA transfers. Further analysis using Pacific Biosciences single molecule real-time (SMRT) sequencing and in vitro biochemical characterization demonstrate the specific recognition sites and activities of the TkoI and TkoII enzymes in the restriction modification system of T. kodakarensis.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Yu Su, Yuta Michimori, Haruyuki Atomi
Summary: The hyperthermophilic archaeon Thermococcus kodakarensis uses amino acids as a carbon and energy source. Two Class I aminotransferases, TK0548 and TK2268, are responsible for the conversion of specific amino acids. Genetic examination reveals their importance in amino acid metabolism.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Jian-Qiang Jin, Takaaki Sato, Shin-Ichi Hachisuka, Haruyuki Atomi
Summary: Based on genetic analyses, the study shows that the lipoate-protein ligase (Lpl) in T. kodakarensis is not only involved in lipoate salvage, but also in de novo protein lipoylation. The results also reveal the broad substrate specificity of Lpl and the strict substrate specificity of the lipoyl synthase LipS in this organism.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Microbiology
Ren-Chao Zheng, Xia-Feng Lu, Hiroya Tomita, Shin-ichi Hachisuka, Yu-Guo Zheng, Haruyuki Atomi
Summary: Members of Thermococcales contain genes encoding putative aminotransferase class III enzymes, with the TK1211 protein from Thermococcus kodakarensis exhibiting racemase activity towards Leu and Met. The TK1211 protein functions as a Leu racemase in vivo, as demonstrated by growth experiments with mutant strains on different Leu isomers. This study expands our understanding of the various activities of aminotransferase class III proteins across different subgroups.
JOURNAL OF BACTERIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Paul Villain, Violette da Cunha, Etienne Villain, Patrick Forterre, Jacques Oberto, Ryan Catchpole, Tamara Basta
Summary: Research shows that expressing bacterial gyrase from Thermotoga maritima in the archaeon Thermococcus kodakarensis can induce negative supercoiling and impact gene expression and chromosomal topology. However, this artificially introduced supercoiling activity did not significantly affect the growth rate of the archaeon.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Microbiology
Travis J. Sanders, Fahad Ullah, Alexandra M. Gehring, Brett W. Burkhart, Robert L. Vickerman, Sudili Fernando, Andrew F. Gardner, Asa Ben-Hur, Thomas J. Santangelo
Summary: Histone proteins compact and organize DNA to impact gene expression. Research shows that the chromatin structure in Archaea plays a crucial role in regulating gene expression, with changes in chromatin landscape significantly affecting gene expression.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biology
Nils-Kare Birkeland, Boyke Bunk, Cathrin Sproeer, Hans-Peter Klenk, Peter Schoenheit
Summary: Hyperthermophiles are microorganisms that thrive in high temperature environments. A new strain of starch-degrading archaeon, Thermococcus bergensis, was isolated and characterized in this study.
Article
Biochemistry & Molecular Biology
Miyako Shiraishi, Michihi Hidaka, Shigenori Iwai
Summary: This study explored the biochemical properties of EndoV in the hyperthermophilic archaeon Thermococcus kodakarensis and found that it has a strong preference for RNA and selectively acts on inosine. These findings suggest a potential role of archaeal EndoV in the regulation of inosine-containing RNA.
BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Danyun Zeng, Ainur Abzhanova, Benjamin P. Brown, Nicholas J. Reiter
Summary: RNase P is a crucial RNA-protein endonuclease for processing ptRNA. The functional RNase P holoenzyme consists of a single P RNA and a P protein. Studies have shown that at 45 degrees Celsius, the diffusion coefficients and rotational correlation times of RNase P protein monomers and dimers correlate well with calculated diffusion coefficients from crystallographic data.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Nisar Ahmed Shakir, Mehwish Aslam, Tahira Bibi, Naeem Rashid
Summary: TK-GLK is an extremely thermostable enzyme that is dependent on ADP and shows activities of glucokinase, glucosamine kinase, and glucose 6-phosphatase. Its thermostability is significantly increased in the presence of ammonium sulfate.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Genetics & Heredity
Mai Wu, Guangyu Ma, Yushan Lin, Philippe Oger, Peng Cao, Likui Zhang
Summary: This study reveals the biochemical characteristics of EndoQ from Thermococcus gammatolerans and the roles of its conserved residues in DNA cleavage. The enzyme is highly efficient in cleaving DNA with deaminated bases, especially uracil-containing DNA. It displays the maximum activity at high temperature and neutral to slightly alkaline pH, and it is extremely thermostable. Mutational analysis identifies essential and catalytic residues in the enzyme.
Article
Genetics & Heredity
Lei Wang, Tan Lin, Philippe Oger, Yong Gong, Likui Zhang
Summary: This study provides the first biochemical characterization of a thermophilic euryarchaeal MIG, enhancing our understanding of archaeal MIG function.
Article
Multidisciplinary Sciences
Sarah Kamel, Miriam C. Walczak, Felix Kaspar, Sarah Westarp, Peter Neubauer, Anke Kurreck
Summary: Catalytically active inclusion bodies (CatIBs) produced in Escherichia coli are an interesting strategy for enzyme immobilization, with potential applications as stable and reusable catalysts. Research on naturally formed CatIBs, such as the thermostable TkAMPpase, has shown that they exhibit higher specific activity compared to heat-induced aggregates, with differences in substrate preference. This highlights the potential of recombinant thermostable enzymes as naturally formed CatIBs for biocatalysis applications.
SCIENTIFIC REPORTS
(2021)
Article
Microbiology
Thomas Klaus, Sabrina Ninck, Andreas Albersmeier, Tobias Busche, Daniel Wibberg, Jianbing Jiang, Alexander G. Elcheninov, Kseniya S. Zayulina, Farnusch Kaschani, Christopher Braesen, Herman S. Overkleeft, Joern Kalinowski, Ilya V. Kublanov, Markus Kaiser, Bettina Siebers
Summary: This study is the first to apply activity-based protein profiling (ABPP) in Archaea, identifying two novel proteins with xylanase activity in extremophilic organisms. This expands the applicability of ABPP for glycoside hydrolase identification in hyperthermophiles.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Mariko Nagata, Sonoko Ishino, Takeshi Yamagami, Yoshizumi Ishino
BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY
(2019)
Article
Microbiology
Ying Liu, David Brandt, Sonoko Ishino, Yoshizumi Ishino, Eugene V. Koonin, Joern Kalinowski, Mart Krupovic, David Prangishvili
ENVIRONMENTAL MICROBIOLOGY
(2019)
Article
Biochemistry & Molecular Biology
Natsuki Takashima, Sonoko Ishino, Keisuke Oki, Mika Takafuji, Takeshi Yamagami, Ryotaro Matsuo, Kouta Mayanagi, Yoshizumi Ishino
Article
Multidisciplinary Sciences
Kei Maruyama, Hirotatsu Imai, Momoko Kawamura, Sonoko Ishino, Yoshizumi Ishino, Kosuke Ito, Toshio Uchiumi
SCIENTIFIC REPORTS
(2019)
Review
Biochemistry & Molecular Biology
Yoshizumi Ishino
BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY
(2020)
Article
Biochemistry & Molecular Biology
Keisuke Oki, Takeshi Yamagami, Mariko Nagata, Kouta Mayanagi, Tsuyoshi Shirai, Naruhiko Adachi, Tomoyuki Numata, Sonoko Ishino, Yoshizumi Ishino
Summary: This study demonstrated how PolD in the hyperthermophilic archaeon Thermococcus kodakarensis connects primase to the archaeal replisome before interacting with PCNA, with the conserved hydrophobic motif at the C-terminus of the DP2 subunit of PolD playing a critical role in this process. The interaction of PolD with primase is through association with GINS, and cryo-EM analysis revealed a highly flexible PolD-primase complex.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Chiaki Yaeshima, Natsumi Murata, Sonoko Ishino, Ikuko Sagawa, Kosuke Ito, Toshio Uchiumi
Summary: Ribosome dimerization is an event that suppresses protein synthesis in bacteria during the stationary phase. While the protein factors responsible for ribosome dimerization in bacteria are well characterized, little is known about the corresponding factors in archaeal and eukaryotic cells. In this study, a protein (PF0560) was identified that dimerizes the 30S ribosomal subunit in the archaeon Pyrococcus furiosus. This protein had a pronounced effect on the sedimentation pattern of the 30S subunit, indicating the formation of 30S dimers. Furthermore, the protein suppressed the formation of functional 70S ribosomes. These findings suggest that PF0560 is a novel dimerization factor involved in the regulation of translation in archaea.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Keisuke Oki, Mariko Nagata, Takeshi Yamagami, Tomoyuki Numata, Sonoko Ishino, Takuji Oyama, Yoshizumi Ishino
Summary: This study demonstrates the molecular mechanism by which the CMG-like helicase cooperates with the PolD DNA polymerase in the archaeon T. kodakarensis, facilitating DNA replication. The direct interaction between PolD and the CMG helicase is critical for synchronizing strand unwinding and nascent strand synthesis, providing a functional machinery for effective replication fork progression. The assembly of helicase and replicase identified in this study is conserved in eukaryotes, suggesting a similar mechanism of DNA replication across different domains of life.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biology
Aya Fujikane, Atsuhiko Sakamoto, Ryosuke Fujikane, Akinori Nishi, Yoshizumi Ishino, Kenji Hiromatsu, Shigeki Nabeshima
Summary: Traditional herbal medicine maoto contains two components, Ephedrae Herba (EH) and Cinnamomi Cortex (CC), which can interact with the G protein of respiratory syncytial virus (RSV), blocking viral entry into mammalian cells.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biology
Kouta Mayanagi, Keisuke Oki, Naoyuki Miyazaki, Sonoko Ishino, Takeshi Yamagami, Kosuke Morikawa, Kenji Iwasaki, Daisuke Kohda, Tsuyoshi Shirai, Yoshizumi Ishino
Article
Biotechnology & Applied Microbiology
Takashi Kushida, Issay Narumi, Sonoko Ishino, Yoshizumi Ishino, Shinsuke Fujiwara, Tadayuki Imanaka, Hiroki Higashibata
MICROBES AND ENVIRONMENTS
(2019)
Article
Biochemistry & Molecular Biology
Yoji Igarashi, Daisuke Mori, Susumu Mitsuyama, Kazutoshi Yoshitake, Hiroaki Ono, Tsuyoshi Watanabe, Yukiko Taniuchi, Tomoko Sakami, Akira Kuwata, Takanori Kobayashi, Yoshizumi Ishino, Shugo Watabe, Takashi Gojobori, Shuichi Asakawa
Article
Biochemistry & Molecular Biology
Soojung Hahn, Gyuri Kim, Sang-Man Jin, Jae Hyeon Kim
Summary: This study utilized three-dimensional intestinal organoids to investigate the effects of metformin on inflammatory bowel disease (IBD) and found that metformin can enhance intestinal barrier function and reduce levels of inflammatory cytokines.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
V. V. Sudarev, M. S. Gette, S. V. Bazhenov, O. M. Tilinova, E. V. Zinovev, I. V. Manukhov, A. I. Kuklin, Yu. L. Ryzhykau, A. V. Vlasov
Summary: This study investigated the self-assembly processes of ferritin-based protein complexes and obtained structurally characterized oligomeric states. These results provide new potential and opportunities for the application of ferritin in various fields.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Yalda Sabaghi, Farnaz Pourfarzad, Leila Zolghadr, Azita Bahrami, Tahereh Shojazadeh, Alireza Farasat, Nematollah Gheibi
Summary: p-Coumaric acid (p-CA) is a plant compound with anti-cancer activities. This study designed a nano-liposomal carrier containing p-CA to enhance its effectiveness against melanoma cells. The findings showed that the liposomal form of p-CA had a greater impact on the cells. Kinetic modeling indicated that the best fitting model was zero-order.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
M. D. Nazmul Hasan, Md Mahfuzur Rahman, Al Asmaul Husna, Nobuhiro Nozaki, Osamu Yamato, Naoki Miura
Summary: This study investigated the expression of ncRNAs other than miRNAs in different histologic subtypes of canine mammary gland tumors (MGT). Three aberrantly expressed ncRNAs were identified as potential biomarkers for differentiating MGT subtypes. YRNA and tRFs expression levels were found to be decreased in metastatic compared to primary MGT cell lines.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Seine A. Shintani
Summary: In this study, the researchers used signal analysis to study the instantaneous amplitude and phase of sarcomeric oscillations in skeletal muscle. They identified two types of oscillations, sarcomeric oscillations and sarcosynced oscillations, and visualized their behavior during propagating waves. The researchers discovered the presence of sarcomeric defect holes and sarcomeric collision holes, which are important indicators for understanding the oscillation properties of sarcomeres. This finding has important implications for improving our understanding of muscle function and its regulatory mechanisms.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Shuanglin Zhang, Yuzhong Jia, Guolan Ma, Yanyan Yang, Zhenzhen Cao, Antao Luo, Zefu Zhang, Shihan Li, Jie Wen, Hanfeng Liu, Jihua Ma
Summary: Bupleurum is an antiarrhythmic agent that may exert its effects by inhibiting L-type calcium channels.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Tomotaka Ohkubo, Yasuhiko Matsumoto, Hiroaki Sasaki, Kaoru Kinoshita, Yuki Ogasawara, Takashi Sugita
Summary: This study found that Citrobacter koseri inhibits the growth of Staphylococcus epidermidis, disrupting the balance between S. epidermidis and Staphylococcus aureus, and exacerbating inflammation in atopic dermatitis.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Toshifumi Asano, Philipp Sasse, Takao Nakata
Summary: A Cre recombination-based fluorescent reporter system was developed to monitor cell-cell fusion. The system successfully detected the formation of multinuclear myotubes and placental syncytiotrophoblast. This tool could facilitate the study of cell-to-cell fusion.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Ke Shi, Yunlong Shan, Xiao Sun, Kuida Chen, Qiong Luo, Qiang Xu
Summary: This study found that low expression of TP53INP2 is associated with poor survival in colorectal cancer (CRC) patients. As the malignancy of CRC progresses, TP53INP2 expression gradually decreases. Knockdown of TP53INP2 promotes CRC cell proliferation and tumor growth. Mechanistically, TP53INP2 deficiency decreases phosphorylation of beta-catenin, leading to increased accumulation and enhanced nuclear translocation and transcriptional activity. Additionally, TP53INP2 sequesters TIM50, inhibiting its activation of beta-catenin. In conclusion, downregulation of TP53INP2 promotes CRC progression by activating beta-catenin.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Martina Rossi, Fabio Tomaselli, Alejandro Hochkoeppler
Summary: Oligomeric enzymes are known for their higher catalytic rates compared to monomeric enzymes, but the extent of additivity in their activity is still not well understood. This study used tetrameric rabbit lactate dehydrogenase as a model to examine the kinetics of its catalytic action. Surprisingly, when the concentration of the limiting reactant exceeded that of a single subunit, there was a significant slowdown in the enzyme's conformational rearrangements.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Amin Sahraei, Mohammad Javad Shamsoddini, Fakhrossadat Mohammadi, Leila Hassani
Summary: This study explored the inhibitory effects of gallium curcumin, indium curcumin, and vanadyl curcumin on the amyloid fibrillation of hen egg white lysozyme, as well as the binding interactions of these metal complexes with the enzyme. The results showed that indium curcumin and vanadyl curcumin exhibited higher binding affinities and stronger inhibitory effects on amyloid fibrillation compared to gallium curcumin.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Takahiro Sasaki, Yoshiki Kuse, Shinsuke Nakamura, Masamitsu Shimazawa
Summary: PGRN deficiency plays a significant role in cardiac remodeling and arrhythmias post-myocardial infarction (MI), potentially by promoting metabolic abnormalities in macrophages.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Hongwei Zhao, Yiqiang Li, Yibo Zhang, Chi Zhang
Summary: Electrical brain stimulation technology is commonly used to treat brain neurological disorders, but it can cause side effects. This study investigated the impact of electric fields on nerve fibers and revealed the possible origin of side effects. The findings provide guidance for selecting electrical parameters in clinical stimulation therapy.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Julia S. Scott, Lake-Ee Quek, Andrew J. Hoy, Johannes V. Swinnen, Zeyad D. Nassar, Lisa M. Butler
Summary: The fatty acid elongation enzyme ELOVL5 plays a critical role in promoting metastasis in prostate cancer. Knocking down ELOVL5 leads to the accumulation of malonyl-CoA, which inhibits fatty acid oxidation in mitochondria. This study highlights the importance of fatty acid elongation in regulating cell viability and provides a potential target for prostate cancer treatment.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Zan Zhou, Wen-jun Jiang, Li Li, Jun-qiang Si
Summary: This study investigates the effect of noise exposure on cognitive function in mice and explores the underlying molecular mechanisms. The findings suggest that noise exposure leads to increased inflammation, increased phosphorylation of Tau protein, and decreased levels of postsynaptic density protein, resulting in cognitive impairment.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)