Article
Multidisciplinary Sciences
Marcin Makowski, Victor G. Almendro-Vedia, Marco M. Domingues, Octavio L. Franco, Ivan Lopez-Montero, Manuel N. Melo, Nuno C. Santos
Summary: The designed AMP EcDBS1R4 kills Escherichia coli by membrane hyperpolarization and can interact with the phospholipid cardiolipin. It alters the membrane environment, impairing the interaction between cardiolipin and the peripheral stalk that binds the F-1 and F-O domains. This mechanism may inspire new research on the mode of action and design of other AMPs.
Article
Biochemistry & Molecular Biology
Yumeng Cui, Xiaojie Wu, Jie Jin, Weiling Man, Jie Li, Xiang Li, Yanghua Li, He Yao, Rongbin Zhong, Shiyun Chen, Jiahui Wu, Tianhao Zhu, Yanli Lin, Junjie Xu, Youliang Wang
Summary: In this study, circHERC1 was found to be significantly upregulated in lung cancer tissues and cells, and its ectopic expression promoted proliferation, invasion, and metastasis while inhibiting apoptosis of lung cancer cells both in vitro and in vivo. Mechanistic studies revealed that circHERC1 acted as a competitive endogenous RNA of miR-142-3p to relieve the suppressive effect on its target HMGB1, thus activating the MAPK/ERK and NF-kappa B pathways and promoting migration and invasion. Additionally, circHERC1 was found to sequester FOXO1 in the cytoplasm, regulating AKT activity and BIM transcription, which led to increased cell proliferation and decreased apoptosis.
Article
Biochemistry & Molecular Biology
David Sychantha, Caitlyn M. Rotondo, Kamaleddin H. M. E. Tehrani, Nathaniel Martin, Gerard D. Wright
Summary: Class B metallo-beta-lactamases (MBLs) are enzymes that confer antibiotic resistance in bacteria by catalyzing the hydrolysis of beta-lactam antibiotics with the help of Zn2+ cofactors. Aspergillomarasmine A (AMA) is a natural inhibitor of class B1 MBLs which selectively removes one catalytic Zn2+ cofactor, causing inactivation of enzymes like NDM-1. The mechanism of action of AMA involves encouraging dissociation of Zn2+ from MBLs, leading to their rapid degradation and improved efficacy as a beta-lactam potentiator, although some MBLs with higher metal affinity show greater tolerance to AMA.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Hao Xiao, Le Tan, Zhixue Tan, Yewei Zhang, Wenyuan Chen, Xiaowu Li, Jingdong Song, Lingpeng Cheng, Hongrong Liu
Summary: This study reveals the structure of the neck-tail complex of siphophage lambda and demonstrates the presence of conserved domains in the tail tips, which play important roles in tail assembly, receptor binding, cell adsorption, and DNA retention/release.
Article
Biology
Vivek Susvirkar, Alex C. Faesen
Summary: The Shieldin complex inhibits end resection at DNA double-strand breaks (DSBs) and acts as a pro-non homologous end joining (NHEJ) factor. The assembly and recruitment of Shieldin to DSBs are not well understood. SHLD3 in Shieldin binds a dimer of REV7, where the interaction with the first REV7 is the rate-limiting step in Shieldin assembly and DNA-DSB recruitment.
COMMUNICATIONS BIOLOGY
(2023)
Article
Immunology
Humayun Sharif, L. Robert Hollingsworth, Andrew R. Griswold, Jeffrey C. Hsiao, Qinghui Wang, Daniel A. Bachovchin, Hao Wu
Summary: CARD8 senses danger signals and forms an inflammasome, which can be activated by DPP8/9 inhibitors promoting CARD8 NT degradation and weakening ternary complex stability.
Article
Biochemistry & Molecular Biology
Xi Liu, Laixing Zhang, Yu Xiu, Teng Gao, Ling Huang, Yongchao Xie, Lingguang Yang, Wenhe Wang, Peiyi Wang, Yi Zhang, Maojun Yang, Yue Feng
Summary: The study reveals that AcrIF14 interacts with the Csy complex to prevent the hybridization of target DNA to crRNA and enables the Csy complex to interact with non-sequence-specific dsDNA. The PAM recognition loop of the Cas8f subunit and electropositive patches within the N-terminal domain of AcrIF14 are crucial for this interaction, different from the mechanism of AcrIF9.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Luciano G. Dolce, Yevheniia Nesterenko, Leon Walther, Felix Weis, Eva Kowalinski
Summary: The cryo-EM structure of Trypanosoma brucei RESC1-RESC2, a central hub module of the RESC complex, has been revealed. The structure shows that RESC1 and RESC2 form an obligatory domain-swapped dimer, and only RESC2 selectively binds 5'-triphosphate-nucleosides, which are a defining characteristic of gRNAs. This suggests that RESC2 acts as the protective 5'-end binding site for gRNAs within the RESC complex.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Multidisciplinary
Gabriele Giachin, Matthew Jessop, Romain Bouverot, Samira Acajjaoui, Melissa Saidi, Anais Chretien, Maria Bacia-Verloop, Luca Signor, Philippe J. Mas, Adrien Favier, Eve Borel Meneroud, Michael Hons, Darren J. Hart, Eaazhisai Kandiah, Elisabetta Boeri Erba, Alain Buisson, Gordon Leonard, Irina Gutsche, Montserrat Soler-Lopez
Summary: ECSIT functions as the bridging node of the MCIA core complex, inducing the transformation of ACAD9 from a FAO enzyme to an MCIA factor, providing a unique molecular mechanism for coordinating the regulation of the FAO and OXPHOS pathways.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Multidisciplinary
Juan A. Valdez-Moreira, Daniel M. Beagan, Hao Yang, Joshua Telser, Brian M. Hoffman, Maren Pink, Veronica Carta, Jeremy M. Smith
Summary: The study characterized a thermally stable iron(III) oxo complex and analyzed its structure, spectroscopic, and computational properties. The complex has an unusually short iron-oxygen bond length and is able to perform hydrocarbon oxidations.
ACS CENTRAL SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Huili Yang, Yadong Xue, Bing Li, Yanan Lin, Haochuan Li, Zhanyong Guo, Weihua Li, Zhiyuan Fu, Dong Ding, Jihua Tang
Summary: This study identified a chimeric mitochondrial gene (ATP6C) as the factor causing CMS in maize, and discovered its mechanism of action involving reduction in the quantity and activity of assembled F1Fo-ATP synthase, accumulation of excess protons in the mitochondrial inner membrane space, triggering ROS burst, premature programmed cell death of tapetal cells, and pollen abortion.
Article
Biochemistry & Molecular Biology
Xi Liu, Laixing Zhang, Yu Xiu, Teng Gao, Ling Huang, Yongchao Xie, Lingguang Yang, Wenhe Wang, Peiyi Wang, Yi Zhang, Maojun Yang, Yue Feng
Summary: The study reveals how AcrIF14 interacts with the Csy complex, blocking target DNA from binding to crRNA and enabling the Csy complex to interact with non-sequence-specific dsDNA. The PAM recognition loop of the Cas8f subunit and electropositive patches in the N-terminal domain of AcrIF14 are essential for this interaction, different from the mechanism of AcrIF9.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Jian Li, Jiangqing Dong, Weitao Wang, Daqi Yu, Xinyu Fan, Yan Chit Hui, Clare S. K. Lee, Wai Hei Lam, Nathan Alary, Yang Yang, Yingyi Zhang, Qian Zhao, Chun-Long Chen, Bik-Kwoon Tye, Shangyu Dang, Yuanliang Zhai
Summary: In eukaryotes, the assembly and activation of the MCM2-7 double hexamer (DH) is required for DNA replication initiation. The mechanism for the initial melting of DNA strands is unknown. This study presents the cryo-electron microscopy structure of the human MCM-DH, revealing that it untwists and stretches the DNA strands to create an initial open structure (IOS) at the hexamer junction. The disruption of IOS inhibits DH formation and replication initiation. The mapping of hMCM-DH footprints suggests that IOSs are distributed across the genome, aligning with initiation zones for stochastic origin firing.
Editorial Material
Biochemistry & Molecular Biology
Sharon R. Garrott, Morgan E. DeSantis
Summary: In this study, Chaaban and Carter employ cryo-electron microscopy and innovative data processing techniques to reveal the high-resolution structure of the dynein-dynactin-BICDR1 complex assembled on microtubules. The structure uncovers novel stoichiometry and offers new insights into the function and mechanism of dynein.
TRENDS IN BIOCHEMICAL SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Sven M. Lange, Marina Nelen, Philip Cohen, Yogesh Kulathu
Summary: IRAK3 is a negative regulator of innate immune signaling, associated with asthma and cancer. By analyzing asthma-related mutations, a conserved surface on IRAK3 was found that may interact with IRAK4, proposing a model for the negative regulation of IRAK4 by IRAK3.
Article
Fisheries
Shuyang Ma, Caihong Fu, Jianchao Li, Peng Sun, Yang Liu, Zhenjiang Ye, Yoshiro Watanabe, Yongjun Tian
Summary: This study used variable coefficients generalized additive models to reveal the non-stationary effects of density dependence, fishing pressure, and climatic conditions on the population dynamics of Japanese sardine. The results indicated that the dynamics of Japanese sardine from 1976 to 2018 could be divided into four periods: the 1980s with high abundance sustained by suitable climatic conditions, the 1990s with population collapse due to negative density-dependent effects and degrading climatic conditions, the 2000s with restricted population increase caused by negative triple effects, particularly high fishing pressure, and the 2010s with population recovery facilitated by favorable climatic conditions and low fishing pressure.
FISH AND FISHERIES
(2023)
Article
Plant Sciences
Jianchao Li, Kaiyi Wu, Ying Zhong, Jiangying Kuang, Nana Huang, Xin Guo, Hang Du, Chong Guo, Rongrong Li, Xiaomin Zhu, Tianyu Zhang, Liping Gong, Lisong Sheng, Rong Sun
Summary: Si-Ni-San (SNS), a famous Chinese herbal formula, has therapeutic effects on obesity by improving lipid accumulation through the AMPK signaling pathway.
JOURNAL OF ETHNOPHARMACOLOGY
(2023)
Review
Plant Sciences
Xin Guo, Rongrong Li, Nana Huang, Tianyu Zhang, Jianchao Li, Liping Gong, Rong Sun
Summary: This study evaluated the clinical effect and safety of Shouhui Tongbian Capsules (SHTB) in treating constipation through a systematic review and meta-analysis. The results showed that SHTB was more effective than the control group in improving the total effective rate, clinical symptom score, gastrointestinal peptide index, and reducing adverse reactions and recurrence rate.
Article
Biodiversity Conservation
Huilin Guo, Chi Zhang, Mi Duan, Jianchao Li, Wenchao Zhang, Yongjun Tian
Summary: This article reports on the high-density discovery of gray rockcod larvae in high latitudes in the Southern Ocean and reveals their early life characteristics through otolith microstructure analysis. Compared to populations in lower latitudes, the gray rockcod in the Amundsen Sea polynyas showed later hatch times, smaller hatch sizes, and faster growth rates. Therefore, it is speculated that the Amundsen Sea polynyas may be potential spawning grounds for gray rockcod.
Article
Engineering, Electrical & Electronic
Di Mou, Liqiang Yuan, Jia Li, Nie Hou, Jianchao Li, Yunwei Li, Zhengming Zhao
Summary: This article proposes a novel four-degree-of-freedom (4-DOFs) modulation scheme for the hybrid dual active bridge (HDAB) converter, which improves efficiency by utilizing the respective structural characteristics of the half bridge and full bridge. The steady-state model of the HDAB converter with the 4-DOF modulation scheme is established, and the optimal O4-DOF modulation scheme is obtained using the particle swarm optimization (PSO) algorithm. Compared to the conventional phase shift modulation (PSM) scheme, the proposed O4-DOFs modulation scheme significantly improves converter efficiency. The theoretical analysis is verified through an experimental platform with specific input and output parameters.
IEEE JOURNAL OF EMERGING AND SELECTED TOPICS IN POWER ELECTRONICS
(2023)
Review
Oceanography
Zihui Gao, Shuyang Ma, Jianchao Li, Peng Sun, Yang Liu, Qinwang Xing, Qingsong He, Yongjun Tian
Summary: This study explores the long-term variations and regime shifts of eight large marine ecosystems in the Arctic, focusing on the comparison between ecosystems in the Atlantic and Pacific sectors. The results suggest that the fish abundance in the Atlantic sector showed an increasing trend before the 1970s/1980s and decreased subsequently, while the Pacific sector showed an increasing trend before the 1990s. Most of the ecosystems were regulated by Atlantic Multi-decadal Oscillation, with exceptions in the Greenland Sea and West Bering Sea LMEs.
PROGRESS IN OCEANOGRAPHY
(2023)
Article
Multidisciplinary Sciences
Amit Kumar Gaurav, Marjia Afrin, Xian Yang, Arpita Saha, S. K. Abdus Sayeed, Xuehua Pan, Zeyang Ji, Kam-Bo Wong, Mingjie Zhang, Yanxiang Zhao, Bibo Li
Summary: Trypanosoma brucei is a protozoan parasite that causes human African trypanosomiasis. TbRAP1, a telomere protein, has been shown to silence VSG genes by binding to dsDNA. However, the mechanism by which TbRAP1 allows the expression of a single active VSG gene was unknown. In this study, the researchers unexpectedly discovered an RNA Recognition Motif (RRM) in TbRAP1, which is unprecedented for RAP1 homologs. They found that TbRAP1 RRM, assisted by a specific patch, can recognize and bind to the 3'UTR sequences of VSG genes. Mutating the conserved residues in RRM abolished RNA binding activity, significantly decreased the level of active VSG RNA, and derepressed silent VSG genes. Their findings suggest a monoallelic expression mechanism for VSG genes, in which the abundant RNA of the active VSG gene antagonizes TbRAP1's silencing effect.
NATURE COMMUNICATIONS
(2023)
Article
Cell Biology
Qixu Cai, Xiumin Chen, Shihan Zhu, Roger A. Nicoll, Mingjie Zhang
Summary: Calcium calmodulin-dependent kinase II (CaMKII) is crucial for synaptic transmission and plasticity. The length of the unstructured linker between the kinase domain and the oligomerizing hub plays a crucial role in determining the ability of CaMKII to rescue defects in synaptic transmission and long-term potentiation. The phase separation capacity of CaMKII with GluN2B is critical for its cellular functions in the brain.
Article
Biology
Zeyu Shen, Bowen Jia, Yang Xu, Jonas Wessen, Tanmoy Pal, Hue Sun Chan, Shengwang Du, Mingjie Zhang, Rohit Pappu
Summary: Formation of membraneless organelles or biological condensates via phase separation expands the cellular organelle repertoire. In this study, an adaptive single-molecule imaging method was developed to track individual molecules in various biological condensates. The method enables measurements of concentrations, motion behavior, and molecular exchanges between condensed and dilute phases. The findings offer insights into the molecular mechanisms underlying the assembly and dynamics of biological condensates.
Article
Biology
Xudong Chen, Bowen Jia, Shihan Zhu, Mingjie Zhang
Summary: The volume and electric strength of an excitatory synapse are correlated with the area of its postsynaptic density (PSD). The molecular mechanism underlying the communication between the PSD assembly and spine actin cytoskeleton is poorly understood. This study discovers that PSD condensates can promote actin polymerization and bundling, and the Homer scaffold protein and a positively charged actin-binding surface of the Homer EVH1 domain are essential for this process. The communication between PSD and spine cytoskeleton may be modulated by targeting the phase separation of the PSD condensates.
Article
Multidisciplinary Sciences
Meng Zhang, Aili Cao, Lin Lin, Ying Chen, Yuan Shang, Chao Wang, Mingjie Zhang, Jinwei Zhu
Summary: The truncated guanylate kinase (GK) domain of MAGI2 interacts with its adjacent PDZ0 domain to form a supramodule capable of recognizing phosphoproteins. Identification of a phosphorylation-dependent binding motif for PDZ0-GK leads to the discovery of previously unknown binding partners. The structure and function of the MAGI2-target complex is explored using an inhibitory peptide derived from the consensus motif, revealing the action mechanism of cryptic MAGI GKs and broadening our understanding of target recognition rules of phosphoprotein binding modules.
Article
Multidisciplinary Sciences
Ran He, Guanhao Chen, Zhiwei Li, Jianchao Li
Summary: In this study, it was found that the N-terminal coil structure of Rpgrip1l is made up of two parallel dimers. Overexpression of these dimers significantly shortened the length of primary cilia, and this effect was dependent on the formation of dimers. It was also observed that the N-terminal structure of Rpgrip1 in mouse and human differed significantly from Rpgrip1l. Furthermore, disease-related mutations were found to alter the dimeric states of Rpgrip1l or Rpgrip1, possibly explaining the mechanisms behind the associated pathologies.
Review
Biochemistry & Molecular Biology
Jianchao Li
Summary: As an emerging concept, liquid-liquid phase separation (LLPS) in biological systems has provided insights into the formation mechanisms of membrane-less compartments. In the inner ear hair cells, LLPS-based biomolecular condensate assembly is crucial for the development and maintenance of stereocilia. This review summarizes recent findings on the molecular basis of LLPS in Usher syndrome-related gene-encoding proteins and their binding partners, offering a better understanding of this inherited disease that causes deaf-blindness.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Marine & Freshwater Biology
Rui Wu, Qinghuan Zhu, Satoshi Katayama, Yongjun Tian, Jianchao Li, Kunihiro Fujiwara, Yoji Narimatsu
Summary: This study tracked the early life stages of Pacific cod and found that early growth had a lasting effect on subsequent growth, but had minimal impact on body size at each stage, which was primarily influenced by growth during that stage.
MARINE LIFE SCIENCE & TECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Dayong Shen, Qiang Chen, Jianchao Li, Shuang Wang, He Song, Feng Wang
Summary: This study investigated the clinical role of HOTAIR in patients with carotid artery stenosis (CAS) and its mechanism in vascular smooth muscle cells (VSMCs). The results showed that HOTAIR was significantly upregulated in CAS patients and could discriminate between patients and healthy individuals. Overexpression of HOTAIR increased the viability and migration of VSMCs, while silencing HOTAIR restricted abnormal activities of VSMCs. Furthermore, a targeted relationship between HOTAIR and miR-148b-3p was confirmed, and the levels of miR-148b-3p in VSMCs were regulated by HOTAIR. Therefore, HOTAIR may serve as a diagnostic biomarker for CAS patients and play a role in regulating the activity of VSMCs.
CRITICAL REVIEWS IN EUKARYOTIC GENE EXPRESSION
(2023)
