Article
Biochemistry & Molecular Biology
Artem Bonchuk, Konstantin Boyko, Anna Fedotova, Alena Nikolaeva, Sofya Lushchekina, Anastasia Khrustaleva, Vladimir Popov, Pavel Georgiev
Summary: In arthropods, ZAD-C2H2 proteins form homodimers in Drosophila melanogaster, with only certain ZADs able to heterodimerize. The rapid evolutionary acquisition of interaction specificity in ZAD-C2H2 proteins is mediated by the more energy-favorable formation of homodimers compared to heterodimers. Specific homodimerization is crucial for the architectural role of ZAD-C2H2 proteins in genome organization.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Microbiology
Chiara Aloise, Jelle G. Schipper, Arno van Vliet, Judith Oymans, Tim Donselaar, Daniel L. Hurdiss, Raoul J. de Groot, Frank J. M. van Kuppeveld
Summary: The nucleocapsid protein N of SARS-CoV-2 acts as an antagonist of the innate antiviral defense and inhibits type I interferon responses. It blocks PKR-mediated ISR activation through its N2b domain and sequesters dsRNA to prevent activation of PKR and RIG-I-like receptors.
Article
Biochemistry & Molecular Biology
Michael Morse, Jana Sefcikova, Ioulia Rouzina, Penny J. Beuning, Mark C. Williams
Summary: The SARS-CoV-2 nucleocapsid (N) protein plays a crucial role in binding and packaging the viral genome into the viral particle. It consists of two domains, with the N-terminal domain primarily involved in RNA binding and the C-terminal domain primarily involved in dimerization/oligomerization. The study used an optical tweezers system to observe the binding and packaging function of the protein at a single molecule level in real time.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Florian Altegoer, Tessa E. F. Quax, Paul Weiland, Phillip Nussbaum, Pietro Giammarinaro, Megha Patro, Zhengqun Li, Dieter Oesterhelt, Martin Grininger, Sonja-Verena Albers, Gert Bange
Summary: Signal transduction via phosphorylated CheY is conserved in bacteria and archaea. In this study, the authors employ structural biochemistry combined with cell biology to delineate the mechanism of CheY recognition by the adaptor protein CheF.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Megija Sede, Jekabs Fridmanis, Martins Otikovs, Jan Johansson, Anna Rising, Nina Kronqvist, Kristaps Jaudzems
Summary: The N-terminal domain of spider silk proteins plays a crucial role in storage and fiber formation. It has high solubility and pH-dependent assembly. Although the residues involved may differ, the pH dependency is conserved among different silk types. The N-terminal domain of tubuliform spidroin lacks key residues for dimerization. The structure and mutant studies suggest that tubuliform spidroin N-terminal domain assembles through elimination of intramolecular repulsive charge interactions.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Qiuling Wang
Summary: The FHA domain is a common protein module that mediates protein-protein interactions by targeting motifs containing phosphothreonine. This review provides a comprehensive overview of FHA domain-containing proteins in plants and summarizes the research progress in this field. The regulatory subunit of protein phosphatase 1 (PP1) in plants, particularly AT5G47790 and its homologs, may play an important role.
PLANT MOLECULAR BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Nina L. Jacobsen, Magnus Bloch, Peter S. Millard, Sarah F. Ruidiaz, Jonas D. Elsborg, Wouter Boomsma, Ruth Hendus-Altenburger, Rasmus Hartmann-Petersen, Birthe B. Kragelund
Summary: This study found that Schizosaccharomyces pombe Dss1 is phosphorylated by casein kinase 2 at three threonine sites in its linker region. The phosphorylation does not affect its ubiquitin binding ability, but slightly destabilizes the C-terminal alpha-helix and directly interacts with the forkhead-associated domain of the RING-FHA E3-ubiquitin ligase defective in mitosis 1 (Dma1). These phosphorylation sites are absent in human Dss1.
Article
Biochemistry & Molecular Biology
Matthew Day, Sarah Parry-Morris, Jack Houghton-Gisby, Antony W. Oliver, Laurence H. Pearl
Summary: CHK1 is a protein kinase that phosphorylates multiple targets downstream of activated ATR, and its interaction with CLASPIN is essential for its activation by ATR. The crystal structure of CHK1 bound to a high-affinity motif from CLASPIN reveals the mechanism of how CLASPIN functions as a scaffold for CHK1 activation.
Article
Multidisciplinary Sciences
Andrea Piserchio, Eta A. Isiorho, Kimberly Long, Amanda L. Bohanon, Eric A. Kumar, Nathan Will, David Jeruzalmi, Kevin N. Dalby, Ranajeet Ghose
Summary: Translation is a regulated process that maintains protein quality and adapts to energy/nutrient availability. eEF-2K, a key regulator of translation, phosphorylates eEF-2 to suppress the elongation phase of protein synthesis. Its activation requires calmodulin binding and phosphorylation at a specific site. The crystal structure of the eEF-2K and calmodulin complex reveals the atomic details of this activation mechanism.
Article
Biochemistry & Molecular Biology
Jiyeon Leem, Jae-Sung Kim, Jeong Su Oh
Summary: Effective DNA damage sensing and repair are crucial for cellular survival due to the threats of DNA double-strand breaks (DSBs). However, DSB repair is mainly repressed during mitosis. In this study, we discovered that oocytes can repair DSBs during meiosis I through microtubule-dependent chromosomal recruitment of the CIP2A-MDC1-TOPBP1 complex from spindle poles. This pole-to-chromosome relocation of the complex is regulated by PLK1 but not by ATM activity.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Biochemistry & Molecular Biology
Amita R. Sahoo, Matthias Buck
Summary: This review focuses on the interaction between Eph receptors and ephrin ligands in regulating various processes from embryonic development to tissue homeostasis. It also highlights the importance of the transmembrane domain of Eph receptors in signal transduction and introduces techniques such as NMR and molecular modeling used to study them. Additionally, the use of transmembrane peptides to manipulate Eph receptor signaling is discussed, along with future directions for research in this field.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Osamu Sato, Tsuyoshi Sakai, Young-yeon Choo, Reiko Ikebe, Tomonobu M. Watanabe, Mitsuo Ikebe
Summary: Myo19 is a protein that can move and transport mitochondria within cells by binding to actin filaments. This study reveals, for the first time at the cellular and molecular levels, the role of Myo19 in mitochondrial dynamics. It provides important insights into the understanding of mitochondrial function and the mechanisms associated with disease development.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biology
Sensen Zhang, Jun Zhou, Yuebin Zhang, Tianya Liu, Perrine Friedel, Wei Zhuo, Suma Somasekharan, Kasturi Roy, Laixing Zhang, Yang Liu, Xianbin Meng, Haiteng Deng, Wenwen Zeng, Guohui Li, Biff Forbush, Maojun Yang
Summary: In this study, the cryo-electron microscopy structures of the two neuronal cation-chloride cotransporters human NKCC1 and mouse KCC2 were presented, identifying essential residues for ion transport. The study proposes mechanisms by which phosphorylation regulates the activity of these cation-chloride cotransporters.
COMMUNICATIONS BIOLOGY
(2021)
Article
Gastroenterology & Hepatology
Guangli Wang, Chan Fan, Hui Wang, Chengyi Jia, Xiaoting Li, Jianru Yang, Tao Zhang, Song Gao, Xun Min, Jian Huang
Summary: This study reveals a novel regulatory role of the FHA domain protein TagH in controlling the hemolytic activity of Vibrio cholerae, in addition to regulating the T6SS. TagH negatively regulates HlyA expression at the transcriptional and post-translational levels, and the phosphopeptide binding sites of the FHA domain play a crucial role in the regulation of hemolytic activity. Deletion of tagH enhances the intestinal pathogenicity and extraintestinal invasion ability of V. cholerae, which mostly rely on the expression of HlyA.
Article
Chemistry, Physical
Ayan Majumder, John E. Straub
Summary: This study establishes an effective computational protocol for calculating equilibrium association constants for transmembrane homodimer formation. By simulating a set of transmembrane protein homodimers using metadynamics, the method is found to be accurate and computationally efficient, providing a standard for future simulation studies.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Multidisciplinary Sciences
Shukun Luo, Bruna G. Coutinho, Prikshat Dadhwal, Yasuhiro Oda, Jiahong Ren, Amy L. Schaefer, E. Peter Greenberg, Caroline S. Harwood, Liang Tong
Summary: Some plant-associated proteobacteria have LuxR family transcription factors known as PipR subfamily members that play important roles in interactions with plant hosts and bacterial virulence of plants. The ethanolamine derivative, HEHEAA, was identified as an effective effector of PipR-mediated gene regulation in the plant endophyte Pseudomonas GM79. Crystallization of a HEHEAA-responsive SBP revealed the molecular basis of PipR system responses to plant factors, showing that different PipR-associated SBPs bind different effectors.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Endocrinology & Metabolism
Aiyun Yuan, Xiangyan Tang, Jing Li
Summary: Translation:
The centrosome apparatus is crucial for spindle assembly and chromosome segregation during mitotic divisions, and a variety of post-translational modifications have been implicated in centrosome modulation, including the emerging O-linked N-acetylglucosamine (O-GlcNAc) modification. O-GlcNAc couples glucose metabolism with signal transduction and forms a yin-yang relationship with phosphorylation, playing a significant role in centrosome dynamics. More molecular details regarding the role of O-GlcNAc in centrosome biology are expected to be unveiled in the future.
FRONTIERS IN ENDOCRINOLOGY
(2021)
Article
Oncology
Yan-Fang Chen, Guang-Can Shao, Jie Li, An-Qi Yang, Jing Li, Xin-Shan Ye
Summary: The O-GlcNAcylation of Blimp-1 in lymphocytes inhibits the migration and invasion of breast cancer cells, making it a potential new target for the treatment of metastatic breast cancer.
MOLECULAR CANCER RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Yingxin Shi, Sheng Yan, Guang-Can Shao, Jinglong Wang, Yong-Ping Jian, Bo Liu, Yanqiu Yuan, Ke Qin, Shanshan Nai, Xiahe Huang, Yingchun Wang, Zhenghui Chen, Xing Chen, Meng-Qiu Dong, Yiqun Geng, Zhi-Xiang Xu, Jing Li
Summary: This study demonstrates that O-GlcNAcylation regulates the expression and stability of ULK1 in HPV-positive HNSCCs. O-GlcNAcylation of ULK1 at Ser409Ser410 antagonizes its phosphorylation at Ser423, leading to the upregulation of autophagy. Furthermore, O-GlcNAcylation enhances the association of ULK1 with the autophagy-related protein STX17, promoting the fusion between autophagosomes and lysosomes.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Review
Biochemistry & Molecular Biology
Xuefei Zhu, Xiang-Yang Zheng, Peng Gong, Xingzhi Xu
Summary: This article discusses the role of CLASPIN ubiquitination in the regulation of the ATR-CHK1 signaling pathway and its importance for genome integrity and cell survival. Specifically, the degradation and deubiquitination of CLASPIN play a crucial role in the activation and inactivation of the signaling pathway. Research in this area is progressing rapidly and provides promising opportunities for chemotherapeutic targets.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2022)
Article
Chemistry, Multidisciplinary
Jie Wu, Cong Lei, Xilong Li, Xueyang Dong, Ke Qin, Weiyao Hong, Jing Li, Yuntao Zhu, Xing Chen
Summary: Protein O-GlcNAcylation is a widespread posttranslational modification in both animals and plants. This study developed a chemoproteomic strategy based on metabolic glycan labeling for profiling O-GlcNAcylated proteins in Arabidopsis. By using this method, 645 candidate O-GlcNAcylated proteins were identified in Arabidopsis seedlings, and their O-GlcNAc modification was validated. This work provides a valuable resource for investigating the functional role of O-GlcNAc in Arabidopsis.
ISRAEL JOURNAL OF CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Shuailin Hao, Ya Wang, Yuqin Zhao, Wen Gao, Wei Cui, Youhang Li, Jian Cui, Yu Liu, Lixiu Lin, Xingzhi Xu, Hailong Wang
Summary: Protein reversible post-translational modification (PTM) plays a crucial role in cellular processes. Lysine crotonylation (Kcr), a newly identified PTM, is found to be involved in replication stress response. The modification of histone H2A at lysine 119 (H2AK119) by crotonylation and ubiquitination specifically regulates transcription-replication conflicts (TRCs), protecting genome stability under replication stress.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Sheng Yan, Bin Peng, Shifeng Kan, Guangcan Shao, Zhikai Xiahou, Xiangyan Tang, Yong-Xiang Chen, Meng-Qiu Dong, Xiao Liu, Xingzhi Xu, Jing Li
Summary: This article investigates the impact of O-GlcNAc transferase (OGT) on PLK1, and finds that OGT can modify PLK1 through O-GlcNAcylation. Further research reveals that the T291A and T291N mutations increase the stability of PLK1 and lead to chromosome segregation defects and uterine carcinoma. The findings suggest that OGT exerts its mitotic function partially through O-GlcNAcylation of PLK1, which may contribute to tumorigenesis by elevating O-GlcNAc levels.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Medicine, Research & Experimental
Ningda Xu, Yi Cai, Jiarui Li, Tianchang Tao, Caifei Liu, Yan Shen, Xiaoxin Li, Leiliang Zhang, Mingwei Zhao, Xuan Shi, Jing Li, Lvzhen Huang
Summary: Using whole-exome sequencing, we identified a candidate disease-causing DNA variant, SNX31, in a Chinese family with familial exudative vitreoretinopathy (FEVR). The SNX31 mutation led to retinal vasculature underdevelopment and phenotypes similar to FEVR-like changes in a mouse model. This study expands our understanding of the molecular pathogenesis of FEVR and may contribute to the development of diagnostic and preventive methods for FEVR.
Review
Pharmacology & Pharmacy
Ying Tian, Tao Zhang, Jing Li, Yong Tao
Summary: This article reviews the applications of exosomes in treating ophthalmic diseases. Exosomes, as delivery vectors, can effectively deliver drugs and therapeutic genes and avoid unnecessary immune responses. However, exosome-based therapies also come with potential ocular risks.
ADVANCED DRUG DELIVERY REVIEWS
(2023)
Review
Biochemistry & Molecular Biology
Donghui Xia, Xuefei Zhu, Ying Wang, Peng Gong, Hong-Shu Su, Xingzhi Xu
Summary: DNA replication forks are tightly regulated to ensure accurate duplication of genetic information. Replication stress responses stabilize stalled replication forks and repair pathways further contribute to fork stabilization. The signaling network, regulated by post-translational modifications such as ubiquitination, plays a key role in the regulation of replication fork progression and stability. Targeting replication fork stability and the ubiquitination system may have therapeutic implications for cancer treatment.
BIOSCIENCE REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Jie Li, Xiangxiang Liu, Bin Peng, Tingting Feng, Wen Zhou, Li Meng, Shanshan Zhao, Xiyuan Zheng, Chen Wu, Shian Wu, Xing Chen, Xingzhi Xu, Jianwei Sun, Jing Li
Summary: The study reveals that O-GlcNAc glycosylation promotes nuclear localization and chromatin association of PARG, enhances its recruitment to DNA damage sites, and inhibits the ADP-ribosylation of DDB1, stabilizing DDB1 and degrading its downstream target c-Myc. Additionally, the O-GlcNAc-deficient mutant PARG-S26A promotes hepatocellular carcinoma (HCC) in mouse xenograft models.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Yuqin Zhao, Kaiping Hou, Youhang Li, Shuailin Hao, Yu Liu, Yinan Na, Chao Li, Jian Cui, Xingzhi Xu, Xiaohua Wu, Hailong Wang
Summary: HELQ has opposing activities in regulating DNA end resection at double strand breaks (DSBs) and stalled forks, and plays a crucial role in maintaining genome stability.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Ophthalmology
Ningda Xu, Yue Liu, Shanshan Nai, Yong Tao, Yuehe Ding, Lemei Jia, Qizhi Geng, Jie Li, Yujing Bai, Gong-Hong Wei, Meng-Qiu Dong, Linyi Luo, Mingwei Zhao, Xingzhi Xu, Xiao-Xin Li, Jing Li, Lvzhen Huang
Summary: The study suggests that ubiquitin-protein ligase E3D (UBE3D) may be associated with DNA damage response and the pathogenesis of age-related macular degeneration (AMD). The findings demonstrate that UBE3D affects homologous recombination and heterochromatin de-condensation upon DNA damage through interactions with PCNA and KAP1, respectively. The study also shows that UBE3D depletion reduces blue light-induced eye damage in a mouse model. These results provide potential directions for the treatment of AMD.
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Yan-Fang Chen, Jing-Jing Zhu, Jing Li, Xin-Shan Ye
Summary: O-GlcNAcylation is an important post-translational modification that affects various processes in cancer cells. This study focused on the O-GlcNAcylation of liver glycogen phosphorylase (PYGL), uncovering the critical role of Ser430 O-GlcNAcylation in PYGL activity regulation.