Article
Biochemistry & Molecular Biology
Jialin Yao, Yingfeng Tu, Congcong Shen, Qiao Zhou, Hengyi Xiao, Da Jia, Qingxiang Sun
Summary: The majority of long non-coding RNAs and a small fraction of messenger RNAs localize in the cell nucleus to exert their functions. A study found that the nuclear localization of SIRLOIN RNA is mediated by a complex of hnRNPK and Imp alpha 1, with the nuclear import receptors functioning as drivers/regulators and hnRNPK acting as an adaptor.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2021)
Article
Multidisciplinary Sciences
Lyra Chang, James Campbell, Idris O. Raji, Shiva K. R. Guduru, Prasanna Kandel, Michelle Nguyen, Steven Liu, Kevin Tran, Navneet K. Venugopal, Bethany C. Taylor, Matthew Holt, Nicolas L. Young, Errol L. G. Samuel, Prashi Jain, Conrad Santini, Banumathi Sankaran, Kevin R. MacKenzie, Damian W. Young
Summary: Despite the established roles of the epigenetic factor UHRF1 in oncogenesis, no UHRF1-targeting therapeutics have been reported to date. In this study, a novel scaffold for targeting the isolated UHRF1 tandem Tudor domain (TTD) was identified using fragment-based ligand discovery. 2,4-lutidine was found to potentially evolve into more potent inhibitors for UHRF1 and provides a starting point for developing potent chemical probes against UHRF1.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Chao-Hua Jiang, Mengping Wei, Chen Zhang, Yun Stone Shi
Summary: Long-term potentiation (LTP) is a crucial cellular mechanism for learning and memory, with the amino-terminal domain (ATD) of GluA1 interacting with neuroplastin-65 (Np65) playing a key role in anchoring AMPARs at the postsynaptic membrane during LTP.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Xiawei Huang, Hongmiao Hu, Alexandre Webster, Fan Zou, Jiamu Du, Katalin Fejes Toth, Alexei A. Aravin, Sisi Li, Dinshaw J. Patek, Ravi Sachidanandam
Summary: PIWI proteins use piRNAs to repress transposons and protect genomic integrity of gametes, ensuring fertility. Post-translational modification of Aub with sDMA is essential for piRNA biogenesis and transposon silencing. Krimper facilitates piRNA generation through its Tudor domains that bind Aub and Ago3 in different modification and piRNA-loading states.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Xiaolei Chen, Zhongmei Yang, Wenfeng Wang, Kaiyue Qian, Mingjie Liu, Junchao Wang, Mingzhu Wang
Summary: This study elucidated the binding mechanisms of RBM45's N-terminal tandem RRM domains with DNA, including specific RNA/ssDNA sequences and critical residues. These findings help to uncover the physiological functions and pathological significance of RBM45.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Pooppadi Maxin Sayeesh, Mayumi Iguchi, Yusuke Suemoto, Jin Inoue, Kohsuke Inomata, Teppei Ikeya, Yutaka Ito
Summary: Drk, a homologue of human GRB2 in Drosophila, receives signals from outside the cells through the interaction of its SH2 domain with the phospho-tyrosine residues in the intracellular regions of receptor tyrosine kinases (RTKs) and transduces the signals downstream through the association of its N- and C-terminal SH3 domains with proline-rich motifs (PRMs) in Son of Sevenless (Sos) or Daughter of Sevenless (Dos). The affinity of the SH3 domains towards Sos and Dos was assessed using NMR titration experiments, revealing that Sos-S1 binds to Drk-NSH3 with the highest affinity and that the two Sos-derived PRMs favor NSH3 for binding, while the two Dos-derived PRMs show similar affinity for both NSH3 and CSH3. Docking simulations based on chemical shift perturbations caused by Sos and Dos-derived peptides were also performed to further understand the interactions of Drk with Sos/Dos.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Michel Choudalakis, Goran Kungulovski, Rebekka Mauser, Pavel Bashtrykov, Albert Jeltsch
Summary: This study found that the Tandem-Tudor domain (TTD) of human UHRF1 can bind not only H3K9me2/3 histones, but also H3 peptides and mononucleosomes containing K9me2/3 and additional K4me1. The binding of TTD to H3K4me1-K9me2/3 was stronger than the binding to H3K9me2/3 alone, and the interaction between R207 and the methyl group of H3K4me1 and the H-bond capacity of H3K4 played a crucial role in the read-out mechanism. These findings highlight the important physiological function of UHRF1-TTD binding to H3K4me1-K9me2/3 double marks in a cellular context.
Article
Multidisciplinary Sciences
Sachiko Fujiwara, Thanh Phuong Nguyen, Kyoko Furuse, Yugo Fukazawa, Tetsuhisa Otani, Mikio Furuse
Summary: The interaction of claudins with ZO proteins is not a prerequisite for tight junction formation at the most apical part of cell-cell contacts.
ANNALS OF THE NEW YORK ACADEMY OF SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Michel Choudalakis, Goran Kungulovski, Rebekka Mauser, Pavel Bashtrykov, Albert Jeltsch
Summary: UHRF1 is a crucial chromatin protein involved in DNA methylation maintenance, mammalian development, and gene regulation. The study focused on the Tandem-Tudor domain (TTD) of UHRF1, which is responsible for binding to H3K9me2/3 histones and determining UHRF1 localization in cells. Unexpectedly, the research discovered stronger binding of TTD to H3 peptides and mononucleosomes containing K9me2/3 with additional K4me1. Mutant analysis revealed a novel mechanism where TTD interacts with the methyl group of H3K4me1 and counts the H-bond capacity of H3K4 in an H3K9me2/3 context. The study also identified the specific binding of UHRF1-TTD to enhancers and promoters of cell-type-specific genes marked by H3K4me1-K9me2/3, as well as its downregulation effect on these genes. These findings highlight the physiological importance of UHRF1-TTD binding to H3K4me1-K9me2/3 double marks in a cellular context.
Article
Biochemistry & Molecular Biology
Mahmudul Hasan, Daniel G. S. Capelluto
Summary: This study determined the concurrence of the PH-FYVE module with the polyD motif in Phafin2 protein using bioinformatics tools and resources. It was found that the polyD motif only evolved in Phafin2 and PH- or both PH-FYVE-containing proteins in animals.
Article
Neurosciences
Atsushi Shimohata, Dilip Rai, Takumi Akagi, Sumiko Usui, Ikuo Ogiwara, Makoto Kaneda
Summary: In this study, the subcellular localization of mGluR6 CTD mutants in 293T cells was investigated using immunocytochemistry, immunoprecipitation, and flow cytometry. The results showed that mGluR6 mutants with 15- and 20-amino acid deletions from the C terminus localized to the ER and were deficient at the cell surface. Introducing an alanine substitution at basic residues within the CTD rescued the surface deficiency of mGluR6 mutants.
MOLECULAR AND CELLULAR NEUROSCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Xiaokang Zhang, Chao Wang, Linlu Qi, Shiwei Wang, Yitong Chen, Zhiwei Kong, Saijie Li, Xin Zhang, Zhengguang Zhang, Junfeng Liu, Dongli Wang
Summary: Clathrin-mediated endocytosis (CME) is crucial for physiological processes in eukaryotic cells. In fungi, the Pan1/End3/Sla1 complex regulates the transition between early and late stages of CME. This study uncovers the detailed interaction mechanism between MoEnd3 and MoSla1 in the pathogenic fungus Magnaporthe oryzae, revealing the synergistic effect of EH domains in improving affinity and specificity.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Medha, Priyanka, Parul Bhatt, Sadhna Sharma, Monika Sharma
Summary: This study investigates the role of the unique C-terminal of Mycobacterium tuberculosis's (Mtb) PE6/Rv0335c protein in causing host mitochondrial perturbations and apoptosis. The experiments confirm that the deletion of the C-terminal domain significantly reduces mitochondrial perturbations and apoptosis, while not affecting the protein's localization to mitochondria. Additionally, the study shows that the protein increases intracellular calcium influx, with the C-terminal deletion having minimal effect on calcium influx. These findings suggest that Rv0335c may mimic eukaryotic Bcl2 proteins, leading to host mitochondrial perturbations and apoptosis.
Article
Biochemistry & Molecular Biology
Marie Sofie Moller, Souad El Bouaballati, Bernard Henrissat, Birte Svensson
Summary: The study shows that a bacterium Saccharophagus degradans produces an endo-beta-mannanase with three phylogenetically distinct family 10 CBMs. Among these, only the C-terminal CBM10-3 binds strongly to microcrystalline cellulose. The different CBMs in the enzyme play specific roles in polysaccharide binding, with CBM10-3 being crucial.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Immunology
Yuewen Ding, Zheye Zhou, Jinyu Chen, Yu Peng, Haitao Wang, Wei Qiu, Wei Xie, Jun Zhang, Honghao Wang
Summary: The study established a novel mouse model of anti-NMDAR encephalitis by actively immunizing against NMDARs with a peptide targeting the ATD of GluN1. Immunized mice showed significant memory loss and decreased surface NMDAR cluster density in hippocampal neurons, similar to effects observed in patients with anti-NMDAR encephalitis. These findings may contribute to further research on the pathogenesis of anti-NMDAR encephalitis and the development of new therapies for this disease.
JOURNAL OF NEUROINFLAMMATION
(2021)
Review
Biochemistry & Molecular Biology
Hideharu Hashimoto, Xing Zhang, Paula M. Vertino, Xiaodong Cheng
JOURNAL OF BIOLOGICAL CHEMISTRY
(2015)
Article
Biochemistry & Molecular Biology
Hideharu Hashimoto, June E. Pais, Nan Dai, Ivan R. Correa, Xing Zhang, Yu Zheng, Xiaodong Cheng
NUCLEIC ACIDS RESEARCH
(2015)
Article
Multidisciplinary Sciences
Leila K. Myrick, Pan-Yue Deng, Hideharu Hashimoto, Young Mi Oh, Yongcheol Cho, Mickael J. Poidevin, Joshua A. Suhl, Jeannie Visootsak, Valeria Cavalli, Peng Jin, Xiaodong Cheng, Stephen T. Warren, Vitaly A. Klyachko
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2015)
Article
Biochemistry & Molecular Biology
Hideharu Hashimoto, Xing Zhang, Yu Zheng, Geoffrey G. Wilson, Xiaodong Cheng
NUCLEIC ACIDS RESEARCH
(2016)
Article
Biochemistry & Molecular Biology
Hideharu Hashimoto, Dongxue Wang, Alyse N. Steves, Peng Jin, Robert M. Blumenthal, Xing Zhang, Xiaodong Cheng
NUCLEIC ACIDS RESEARCH
(2016)
Article
Biochemistry & Molecular Biology
Dongxue Wang, Hideharu Hashimoto, Xing Zhang, Benjamin G. Barwick, Sagar Lonial, Lawrence H. Boise, Paula M. Vertino, Xiaodong Cheng
NUCLEIC ACIDS RESEARCH
(2017)
Article
Biochemistry & Molecular Biology
Hideharu Hashimoto, Dongxue Wang, John R. Horton, Xing Zhang, Victor G. Corces, Xiaodong Cheng
Article
Multidisciplinary Sciences
Hideharu Hashimoto, June E. Pais, Xing Zhang, Lana Saleh, Zheng-Qing Fu, Nan Dai, Ivan R. Correa, Yu Zheng, Xiaodong Cheng
Article
Biochemistry & Molecular Biology
Yiwei Liu, Yusuf Olatunde Olanrewaju, Yu Zheng, Hideharu Hashimoto, Robert M. Blumenthal, Xing Zhang, Xiaodong Cheng
NUCLEIC ACIDS RESEARCH
(2014)
Article
Biochemistry & Molecular Biology
Ren Ren, Swanand Hardikar, John R. Horton, Yue Lu, Yang Zeng, Anup K. Singh, Kevin Lin, Luis Della Coletta, Jianjun Shen, Celine Shuet Lin Kong, Hideharu Hashimoto, Xing Zhang, Taiping Chen, Xiaodong Cheng
NUCLEIC ACIDS RESEARCH
(2019)
Article
Biochemistry & Molecular Biology
Bartlomiej J. Blus, Hideharu Hashimoto, Hyuk-Soo Seo, Aleksandra Krolak, Erik W. Debler
Article
Biochemistry & Molecular Biology
Hideharu Hashimoto, Lucie Kafkova, Ashleigh Raczkowski, Kelsey D. Jordan, Laurie K. Read, Erik W. Debler
JOURNAL OF MOLECULAR BIOLOGY
(2020)
Article
Multidisciplinary Sciences
Marina Farkas, Hideharu Hashimoto, Yingtao Bi, Ramana V. Davuluri, Lois Resnick-Silverman, James J. Manfredi, Erik W. Debler, Steven B. McMahon
Summary: The tumor suppressor p53 is a master regulator of cellular stress response pathways, including cell cycle arrest and apoptosis. The authors identify molecular mechanisms of p53 binding to high- and low-affinity p53 response elements in the genome, linked to cell cycle arrest and pro-apoptotic genes, respectively.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Hideharu Hashimoto, Daniel H. Ramirez, Ophelie Lautier, Natalie Pawlak, Gunter Blobel, Benoit Palancade, Erik W. Debler
Summary: The study reports the retention of unspliced pre-mRNA by ScPml39 protein in Saccharomyces cerevisiae prior to export through nuclear pore complexes. The crystal structure of ScPml39 was determined, revealing its structural orthologs and providing insights into its function and mechanism.
SCIENTIFIC REPORTS
(2022)