Article
Biochemistry & Molecular Biology
Yu-Ri Lee, Se Hee Kim, Afif Ben-Mahmoud, Oc-Hee Kim, Tae-Ik Choi, Kang-Han Lee, Bonsu Ku, Juneyong Eum, Yun Kee, Sangkyu Lee, Jihoon Cha, DongJu Won, Seung-Tae Lee, Jong Rak Choi, Joon Soo Lee, Heung Dong Kim, Hyung-Goo Kim, Joshua L. Bonkowsky, Hoon-Chul Kang, Cheol-Hee Kim
Summary: This study established the first EIF2B3 animal model for VWM disease in vertebrates and provided novel insights into VWM pathogenesis. Using the eif2b3 mutant zebrafish model, the study demonstrated the pathogenicity of reported mutations in EIF2B3 and identified a novel variant in a 19-month-old female patient.
HUMAN MOLECULAR GENETICS
(2021)
Article
Genetics & Heredity
Inna Slynko, Stephanie Nguyen, Eline M. C. Hamilton, Lisanne E. Wisse, Iwan J. P. de Esch, Chris de Graaf, John B. Bruning, Christopher G. Proud, Truus E. M. Abbink, Marjo S. van der Knaap
Summary: This study analyzed 97 missense mutations in vanishing white matter disease (VWM) and found that over 50% of mutations have (ultra-)severe phenotypic effects. Approximately 60% of mutations affect the ε-subunit containing the catalytic domain, while about 36% affect subunit interfaces, mostly with severe effects.
MOLECULAR GENETICS & GENOMIC MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Maria K. Mateyak, Dongming He, Pragati Sharma, Terri Goss Kinzy
Summary: Phosphorylation of eEF1A affects its function, and mutation analysis confirms the importance of several phosphorylation sites, with the S289D mutant's activity being influenced by eEF1B alpha.
Review
Genetics & Heredity
Prakash Amruth Raj Chukka, Stacey D. Wetmore, Nehal Thakor
Summary: Translational control plays a crucial role in dictating gene expression and altering physiological processes in eukaryotic cells. eIF5B plays a significant role in this process, especially in the survival and drug resistance of cancer cells.
FRONTIERS IN GENETICS
(2021)
Article
Genetics & Heredity
Parith Wongkittichote, Soe Soe Mar, Robert C. McKinstry, Hoanh Nguyen
Summary: This article presents a case of CACH/VWM and emphasizes the importance of genetic testing in patients with leukodystrophies.
FRONTIERS IN GENETICS
(2022)
Review
Biochemistry & Molecular Biology
Daniel Friedrich, Assen Marintchev, Haribabu Arthanari
Summary: In this review, the authors examine the versatility and functionality of HEAT domains in the regulation of mRNA translation initiation. They describe the basic structural architecture of HEAT domains and their involvement in various cellular processes. The focus is on proteins in the translation initiation system that feature HEAT domains, highlighting their remarkably flexible interactions and the functional importance of these domains.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Oncology
Chengzhi Xu, Yupeng Shen, Yong Shi, Ming Zhang, Liang Zhou
Summary: This study reveals the role of EIF3B in head and neck squamous cell carcinoma (HNSCC) and identifies its promotion of CEBPB translation and IL6R expression. These findings provide important insights into the molecular basis and pathogenesis of HNSCC.
CANCER CELL INTERNATIONAL
(2022)
Article
Biotechnology & Applied Microbiology
Shaoran Song, Jie Liu, Miao Zhang, Xiaoqian Gao, Wei Sun, Peijun Liu, Yaochun Wang, Juan Li
Summary: The expression of the EIF3 gene family is associated with prognosis in breast cancer and may serve as a therapeutic target.
Article
Biochemistry & Molecular Biology
Patrick Senechal, Francis Robert, Regina Cencic, Akiko Yanagiya, Jennifer Chu, Nahum Sonenberg, Marilene Paquet, Jerry Pelletier
Summary: The translation initiation factor eIF4F is crucial for cap-dependent protein synthesis initiation. Different subunits of eIF4F have varying roles in development and tumorigenesis, with some being essential for viability and tumor onset, while others have non-essential functions. This study highlights the complex roles of different eIF4F subunits in gene expression regulation during embryogenesis and tumor development.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Su Wu, Gerhard Wagner
Summary: eIF4F plays diverse roles in human cancers, with overexpression of EIF4G1 being more selective than EIF4E, serving as a prognostic indicator in cancer patients. This expression imbalance affects housekeeping pathways and cancer-related pathways, leading to cap-independent initiation due to eIF4G1 hyperphosphorylation. These findings provide a novel model of dysregulated eIF4F function and highlight the clinical relevance of cap-(in)dependent initiation in cancer.
Article
Oncology
Angela Rubio, Gavin D. Garland, Aristeidis Sfakianos, Robert F. Harvey, Anne E. Willis
Summary: Abnormalities in RNA binding proteins within the canonical translation factor machinery are associated with tumorigenesis and can be targeted for therapeutic purposes.
SEMINARS IN CANCER BIOLOGY
(2022)
Article
Chemistry, Medicinal
Xintao Gao, Yonglong Jin, Wenyong Zhu, Xiaochen Wu, Jing Wang, Chuanlong Guo
Summary: eIF4E is a central regulator in cancer cell growth, but there are currently no clinically available eIF4E inhibitors. Interfering with eIF4E/eIF4G interactions may provide a new strategy for designing eIF4E inhibitors.
JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Paul Powell, Usha Bhardwaj, Dixie Goss
Summary: This study identifies secondary structures that selectively interact with eIF3 and explores its role in translation initiation of BYDV. The findings propose a new model for BYDV translation initiation and expand the known functionality of eIF3.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Radiology, Nuclear Medicine & Medical Imaging
Menno D. Stellingwerff, Murtadha L. Al-Saady, Tim van de Brug, Frederik Barkhof, Petra J. W. Pouwels, Marjo S. van der Knaap
Summary: According to the study, there are variations in the nature and progression of cerebral white matter abnormalities in patients with vanishing white matter (VWM) based on their age at onset. Patients with later onset have slower white matter decay, but exhibit more significant white matter atrophy and gliosis.
Article
Multidisciplinary Sciences
Muminjon Djumagulov, Natalia Demeshkina, Lasse Jenner, Alexey Rozov, Marat Yusupov, Gulnara Yusupova
Summary: Translation of the genetic code into proteins in eukaryotes is facilitated by eEF2 and tRNA modifications, whose specific functions in translocation accuracy are not fully understood. A high-resolution X-ray structure of the eukaryotic 80S ribosome in a translocation-intermediate state reveals the network of stabilization of codon-anticodon interactions involving diphthamide and wybutosine, emphasizing the role of eEF2 as a 'pawl' in defining translocation directionality. This model demonstrates the large-scale molecular reorganizations of eukaryotic specific elements to maintain mRNA reading frame during translocation.
Article
Cell Biology
Kazue Terasawa, Yuji Kato, Yuta Ikami, Kensaku Sakamoto, Kazumasa Ohtake, Seisuke Kusano, Yuri Tomabechi, Mutsuko Kukimoto-Niino, Mikako Shirouzu, Jun-Lin Guan, Toshihide Kobayashi, Takanori Iwata, Tetsuro Watabe, Shigeyuki Yokoyama, Miki Hara-Yokoyama
Summary: This study demonstrated the direct homophilic interaction of mouse LAMP2A molecules and highlighted the importance of side A-specific homophilic interaction for the functional aspects of LAMP2A.
Article
Biophysics
Fahu He, Kanako Kuwasako, Masayuki Takizawa, Mari Takahashi, Kengo Tsuda, Takashi Nagata, Satoru Watanabe, Akiko Tanaka, Naohiro Kobayashi, Takanori Kigawa, Peter Guntert, Mikako Shirouzu, Shigeyuki Yokoyama, Yutaka Muto
Summary: Matrin-3 is a multifunctional protein with DNA-binding and RNA-binding activities, which are associated with nuclear matrix formation, transcriptional regulation, and mRNA metabolism. Pathogenic mutations in its disordered region cause ALS and FTD, linked to its RNA-binding activity mediated by the RRM domains.
BIOMOLECULAR NMR ASSIGNMENTS
(2022)
Article
Oncology
Yuta Ikami, Kazue Terasawa, Kensaku Sakamoto, Kazumasa Ohtake, Hiroyuki Harada, Tetsuro Watabe, Shigeyuki Yokoyama, Miki Hara-Yokoyama
Summary: This study reveals the direct interaction between Hsc70 and LAMP2A in chaperone-mediated autophagy (CMA), as well as the significance of the two-domain architecture of the lumenal domains of LAMP2A in this interaction.
EXPERIMENTAL CELL RESEARCH
(2022)
Article
Multidisciplinary Sciences
Toshiaki Hosaka, Takashi Nomura, Minoru Kubo, Takanori Nakane, Luo Fangjia, Shun-ichi Sekine, Takuhiro Ito, Kazutaka Murayama, Kentaro Ihara, Haruhiko Ehara, Kazuhiro Kashiwagi, Kazushige Katsura, Ryogo Akasaka, Tamao Hisano, Tomoyuki Tanaka, Rie Tanaka, Toshi Arima, Ayumi Yamashita, Michihiro Sugahara, Hisashi Naitow, Yoshinori Matsuura, Susumu Yoshizawa, Kensuke Tono, Shigeki Owada, Osamu Nureki, Tomomi Kimura-Someya, So Iwata, Eriko Nango, Mikako Shirouzu
Summary: Time-resolved serial femtosecond crystallography was used to study the structural changes and ion transfer mechanisms in anion-pumping rhodopsins. The study revealed the conformational alterations during ion transfer and ion release, as well as the halide binding site for ion transfer.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Tomoya Fujita, Takeshi Yokoyama, Mikako Shirouzu, Hideki Taguchi, Takuhiro Ito, Shintaro Iwasaki
Summary: In this study, ribosome pause sites in Escherichia coli were surveyed using monosome and disome profiling strategies. Compared to eukaryotes, ribosome collisions in bacteria showed remarkable differences, and the identified pause sites were biochemically validated and showed puromycin resistance.
Article
Engineering, Biomedical
Eiji Kobayashi, Aishun Jin, Hiroshi Hamana, Kiyomi Shitaoka, Kazuto Tajiri, Seisuke Kusano, Shigeyuki Yokoyama, Tatsuhiko Ozawa, Tsutomu Obata, Atsushi Muraguchi, Hiroyuki Kishi
Summary: By analyzing T cells at the single-cell level on a microwell array, researchers discovered that T-cell activation can occur via both trans and cis interactions, and successfully cloned tumor-antigen-specific TCRs.
NATURE BIOMEDICAL ENGINEERING
(2022)
Article
Biophysics
Kanako Kuwasako, Sakura Suzuki, Nobukazu Nameki, Masayuki Takizawa, Mari Takahashi, Kengo Tsuda, Takashi Nagata, Satoru Watanabe, Akiko Tanaka, Naohiro Kobayashi, Takanori Kigawa, Peter Guentert, Mikako Shirouzu, Shigeyuki Yokoyama, Yutaka Muto
Summary: The structure and sequence characteristics of the KH domain of mtRbfA were studied, and differences were found compared to RbfA, which may be related to its function in ribosome biogenesis.
BIOMOLECULAR NMR ASSIGNMENTS
(2022)
Article
Biology
Eriko Matsuura-Suzuki, Tadahiro Shimazu, Mari Takahashi, Kaoru Kotoshiba, Takehiro Suzuki, Kazuhiro Kashiwagi, Yoshihiro Sohtome, Mai Akakabe, Mikiko Sodeoka, Naoshi Dohmae, Takuhiro Ito, Yoichi Shinkai, Shintaro Iwasaki, Qing Zhang
Summary: In this study, it was discovered that human METTL18 acts as a histidine methyltransferase for the ribosomal protein RPL3. The methylation of RPL3 at His245 position slows ribosome traversal on Tyr codons, allowing proper protein folding and preventing cellular aggregation of Tyr-rich proteins.
Article
Biochemistry & Molecular Biology
K. Dhanalakshmi, Seiki Kuramitsu, Shigeyuki Yokoyama, Kumarevel Thirumananseri, Karthe Ponnuraj
Summary: This study reports the crystal structure of arginase from Thermus thermophilus (TtArginase), and compares it with other homologous structures. The results show that TtArginase is more stable compared to its mesophilic counterpart, Bacillus subtilis arginase (BsArginase). Additionally, the study reveals the critical role of metal ions in both the catalytic function and maintenance of proper active site geometry. These findings are important for optimizing the enzymatic action of arginase in various conditions.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
K. Dhanalakshmi, Seiki Kuramitsu, Shigeyuki Yokoyama, Thirumananseri Kumarevel, Karthe Ponnuraj
Summary: The crystal structure of pyrrolidone carboxyl peptidase from Thermus thermophilus (TtPCP) was solved and refined at 1.9 angstrom resolution using the molecular replacement method. Comparing TtPCP with its structural homologs, it was found that the putative thermal stability of TtPCP may be attributed to more intra and inter-molecular hydrogen bonds, hydrophobic and ion pair interactions. This structural information of TtPCP can contribute to understanding the intrinsic stability of thermophilic proteins and can be useful for protein engineering.
BIOPHYSICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Mutsuko Kukimoto-Niino, Kentaro Ihara, Chiemi Mishima-Tsumagari, Mio Inoue, Yoshinori Fukui, Shigeyuki Yokoyama, Mikako Shirouzu
Summary: This study reveals the crystal structures of the catalytic DHR2 domain of mouse DOCK10, complexed with either Cdc42 or Rac1, and uncovers the unique dual activation mechanism of DOCK10.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Tatsuo Yanagisawa, Eiko Seki, Hiroaki Tanabe, Yoshifumi Fujii, Kensaku Sakamoto, Shigeyuki Yokoyama
Summary: Pairs of pyrrolysyl-tRNA synthetase (PylRS) and tRNA(Pyl) from Methanosarcina mazei and Methanosarcina barkeri are used for site-specific incorporations of non-canonical amino acids into proteins. Mutations in Methanomethylophilus alvus PylRS allow efficient binding with N-e-((((E)-cyclooct-2-en-1-yl)oxy)carbonyl)-L-lysine (TCO*Lys) but not with N-e-(p-ethynylbenzyloxycarbonyl)-L-lysine (pEtZLys).
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biology
Mingming Chen, Naoyoshi Kumakura, Hironori Saito, Ryan Muller, Madoka Nishimoto, Mari Mito, Pamela Gan, Nicholas T. Ingolia, Ken Shirasu, Takuhiro Ito, Yuichi Shichino, Shintaro Iwasaki
Summary: A parasitic fungus has been found to overcome the toxicity of antimicrobial compounds produced by plants through a specific amino acid substitution. This study reveals the molecular mechanisms of fungal resistance against plant defense mechanisms.
Article
Immunology
Seisuke Kusano, Sho Ueda, Daisuke Oryoji, Aya Toyoumi, Akiko Hashimoto-Tane, Hiroyuki Kishi, Hiroshi Hamana, Atsushi Muraguchi, Hui Jin, Hisashi Arase, Hiroko Miyadera, Reiko Kishikawa, Yasunobu Yoshikai, Hisakata Yamada, Ken Yamamoto, Yasuharu Nishimura, Takashi Saito, Takehiko Sasazuki, Shigeyuki Yokoyama
Summary: Cry j 1 is a major allergen in Japanese cedar pollens. The NF region of Cry j 1 peptide plays a role in enhancing T-cell activation. Mutation of Ser and Lys in the NF region to Glu reduces the affinity for HLA-DP5, antigen presentation, and T-cell activation.
INTERNATIONAL IMMUNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Tomoya Fujita, Takeshi Yokoyama, Mikako Shirouzu, Hideki Taguchi, Takuhiro Ito, Shintaro Iwasaki
Summary: This study investigated ribosome pause sites in Escherichia coli using different ribosome profiling strategies, revealing remarkable differences compared to eukaryotes. The identified pause sites were biochemically validated and provided a useful resource for ribosome stalling sites in bacteria.
Article
Biochemistry & Molecular Biology
Ankita Chadda, Alexander G. Kozlov, Binh Nguyen, Timothy M. Lohman, Eric A. Galburt
Summary: In this study, it was found that the DNA damage response in Mycobacterium tuberculosis differs from well-studied model bacteria. The DNA repair helicase UvrD1 in Mtb is activated through a redox-dependent process and is closely associated with the homo-dimeric Ku protein. Additionally, Ku protein is shown to stimulate the helicase activity of UvrD1.
JOURNAL OF MOLECULAR BIOLOGY
(2024)