Article
Multidisciplinary Sciences
John Sedat, Angus McDonald, Hu Cang, Joseph Lucas, Muthuvel Arigovindan, Zvi Kam, Cornelis Murre, Michael Elbaum
Summary: Cryoelectron tomography of the cell nucleus using scanning transmission electron microscopy and deconvolution processing technology has revealed a large-scale chromosome structure. This study further investigates and analyzes these structures, proposing a unified architecture for interphase chromosomes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Meijing Li, Ishita Tripathi-Giesgen, Brenda A. Schulman, Wolfgang Baumeister, Florian Wilfling
Summary: Selective macroautophagy is a process in which cytosolic material is enclosed in a double membrane organelle and transported to a lytic compartment for degradation. This study used cryo-electron tomography to observe the formation of phagophores around damaged Salmonella-containing vacuoles (SCVs). Host cells generated multiple phagophores at the site of SCVs and established contact with the endoplasmic reticulum for membrane formation and expansion.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Anna Bieber, Cristina Capitanio, Philipp S. Erdmann, Fabian Fiedler, Florian Beck, Chia-Wei Lee, Delong Li, Gerhard Hummer, Brenda A. Schulman, Wolfgang Baumeister, Florian Wilfling
Summary: By combining different research methods, we directly revealed the structural progression of autophagosome biogenesis and organelle interactome within yeast cells. These findings have important implications for understanding the contribution of different membrane sources during autophagy and the forces shaping and driving phagophores.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Biochemistry & Molecular Biology
Miguel Ricardo Leung, Tzviya Zeev-Ben-Mordehai
Summary: The different oligomeric forms of acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) have defined cellular and subcellular distributions. While crystal structures of AChE and BChE have been available for many years, structures of the physiologically relevant cholinesterase tetramer were only recently solved by cryo-electron microscopy (cryo-EM). The next frontier in cholinesterase structural biology is to image membrane-anchored ChE oligomers directly in their native environment - the cell.
JOURNAL OF NEUROCHEMISTRY
(2021)
Article
Biochemical Research Methods
Xuefeng Du, Haohan Wang, Zhenxi Zhu, Xiangrui Zeng, Yi-Wei Chang, Jing Zhang, Eric Xing, Min Xu
Summary: In this study, a Hybrid Active Learning (HAL) framework is proposed to alleviate the labeling burden by querying a large pool of unlabeled subtomograms. HAL framework utilizes uncertainty sampling and a discriminator to optimize subtomogram selection, achieving comparable testing performance with less labeled resources.
Article
Multidisciplinary Sciences
Kayo Nozawa, Yoshimasa Takizawa, Leonidas Pierrakeas, Chizuru Sogawa-Fujiwara, Kazumi Saikusa, Satoko Akashi, Ed Luk, Hitoshi Kurumizaka
Summary: The canonical nucleosome is the major packaging unit of eukaryotic chromatin, and the H3-H4 octasome is a nucleosome-like particle with alternative histone stoichiometry. The structure of the H3-H4 octasome is flexible.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Xiulian Yu, Tao Ni, George Munson, Peijun Zhang, Robert J. C. Gilbert
Summary: In this study, the structure of Perforin-2 in different conformations was determined using multiple techniques. The mechanism of pore formation in acidification conditions was found to be related to the conformational transition of the pre-pores, and it was observed that PFN2 pores mainly exist as incomplete arc structures on membranes.
Article
Biochemistry & Molecular Biology
Xiulian Yu, Tao Ni, George Munson, Peijun Zhang, Robert J. C. Gilbert
Summary: This study investigated the conformational transition of PFN2 from pre-pore to pore structures. The complete pre-pore rings found in isolation could convert into pores with different conformations. On membranes, however, the assembled PFN2 pre-pores showed various degrees of completeness, while the pores were mainly incomplete arc structures. It was also found that both assemblies utilized the P2 beta-hairpin for binding to the lipid membrane surface. These findings provide insights into the molecular mechanism of PFN2 in forming pores on targeted membranes.
Article
Biology
Elena Farah Lehmann, Marton Liziczai, Katarzyna Drozdzyk, Patrick Altermatt, Cassiano Langini, Vania Manolova, Hanna Sundstrom, Franz Durrenberger, Raimund Dutzler, Cristina Manatschal
Summary: The regulatory mechanism of iron homeostasis in humans involves the interaction between ferroportin (FPN) and hepcidin, and dysregulation leads to various pathological conditions. Vamifeport, a clinical-stage FPN inhibitor, competes with hepcidin for FPN binding. Cryo-electron microscopy structures reveal the conformational changes of FPN and the binding site of Vamifeport. This study provides insights into the structural and pharmacological aspects of FPN.
Article
Neurosciences
Vladan Lucic
Summary: This article reviews the importance of electron microscopy in the study of neuronal synapse structures and discusses the use of image processing software methods. Special attention is given to the application of recent cryo-electron microscopy and tomography methods in molecular level analysis.
CURRENT OPINION IN NEUROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Yibo Jin, Paul K. Fyfe, Scott Gardner, Stephan Wilmes, Doryen Bubeck, Ignacio Moraga
Summary: IL-27 is an important cytokine that induces immunosuppressive responses. The study reveals the structure of the IL-27 receptor recognition complex and provides insights into the mechanism of IL-27 signaling. These findings contribute to a better understanding of IL-27's function and regulation.
Article
Biochemical Research Methods
Jie E. Yang, Matthew R. Larson, Bryan S. Sibert, Joseph Y. Kim, Daniel Parrell, Juan C. Sanchez, Victoria Pappas, Anil Kumar, Kai Cai, Keith Thompson, Elizabeth R. Wright
Summary: In this paper, robust tools for montage parallel array cryo-tomography (MPACT) tailored for vitrified specimens are presented, which can image large fields of view while preserving high-resolution structural information. The combination of multiple techniques in MPACT supports studies that contextually define the three-dimensional architecture of cells, and it provides flexibility and efficient data processing and analysis.
Review
Biophysics
Ye Hong, Yutong Song, Zheyuan Zhang, Sai Li
Summary: The recent advancement in cryo-electron tomography (cryo-ET) techniques has revolutionized the resolution of cryo-ET. Efforts have also been made to improve the identification of targets in cellular context and the throughput of cryo-focused ion beam (FIB) milling. These developments have led to an increase in in situ discoveries about virus assembly and virus-cell interactions within infected hosts.
ANNUAL REVIEW OF BIOPHYSICS
(2023)
Article
Multidisciplinary Sciences
Shujun Cai, Yumei Wu, Andres Guillen-Samander, William Hancock-Cerutti, Jun Liu, Pietro De Camilli
Summary: Researchers have found in situ evidence for the bridge-like lipid transport mechanism of VPS13 at membrane contact sites using AlphaFold predictions and cryo-electron tomography.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Engineering, Environmental
Wangbiao Guo, Lingchong Feng, Zhenyi Wang, Jiansheng Guo, Donghyun Park, Brittany L. Carroll, Xing Zhang, Jun Liu, Jun Cheng
Summary: This study uses a multidisciplinary approach to analyze the wild-type Chlorella pyrenoidosa and a nuclear-irradiated mutant. The mutant shows increased volume in subcellular organelles, overexpression of rubisco, and enlarged membrane width in the thylakoid, indicating enhanced carbon fixation and chlorophyll synthesis. This research provides detailed insights into how subcellular organelles collaborate to support macroscopic traits in microalgae.
CHEMICAL ENGINEERING JOURNAL
(2022)
Article
Biology
Danyang Zhang, Yan Zhang, Jun Ma, Chunmei Zhu, Tongxin Niu, Wenbo Chen, Xiaoyun Pang, Yujia Zhai, Fei Sun
Review
Biochemistry & Molecular Biology
Xiaojun Huang, Lei Zhang, Zuoling Wen, Hui Chen, Shuoguo Li, Gang Ji, Chang-cheng Yin, Fei Sun
PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY
(2020)
Article
Multidisciplinary Sciences
Yang Shi, Yueyong Xin, Chao Wang, Robert E. Blankenship, Fei Sun, Xiaoling Xu
Article
Biology
Jiuwei Lu, Chun Chan, Leiye Yu, Jun Fan, Fei Sun, Yujia Zhai
COMMUNICATIONS BIOLOGY
(2020)
Article
Multidisciplinary Sciences
Yan Zhang, Xiaoyun Pang, Jian Li, Jiashu Xu, Victor W. Hsu, Fei Sun
Summary: By using cryoelectron microscopy, researchers have revealed the protein lattice formed by SNX1, which helps to understand how it functions in generating transport carriers. Comparing the structure of SNX1 with that of an endosomal coat complex formed by retromer coupled to a SNX provides insights into the molecular organization of SNX and the intermediary stages of assembly leading to the formation of the complex on the membrane.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Biochemistry & Molecular Biology
Xiaojun Huang, Lei Zhang, Zuoling Wen, Hui Chen, Shuoguo Li, Gang Ji, Chang-Cheng Yin, Fei Sun
Summary: Cryo-electron microscopy (cryoEM) has become a key method in structural biology. This study introduced a new supporting substrate, the amorphous nickel-titanium alloy (ANTA) film, for cryoEM sample preparation, which showed advantages in electron conductivity and interaction with proteins compared to conventional carbon film, leading to improved particle distribution and reconstruction resolution in experiments.
PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY
(2021)
Article
Biology
Nick Y. Larsen, Xixia Li, Xueke Tan, Gang Ji, Jing Lin, Grazyna Rajkowska, Jesper Moller, Ninna Vihrs, Jon Sporring, Fei Sun, Jens R. Nyengaard
Summary: The study utilized deep learning and 3D reconstruction techniques to reveal the columnar organization of cortical pyramidal cells, showcasing the potential of this method for characterizing cells in various tissues.
COMMUNICATIONS BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Hongcheng Fan, Bo Wang, Yan Zhang, Yun Zhu, Bo Song, Haijin Xu, Yujia Zhai, Mingqiang Qiao, Fei Sun
Summary: The amphiphilic low-molecular-weight protein hydrophobin (HFBI) can self-assemble into a crystalline monolayer film, which is used as a support film in cryo-EM to protect specimens and overcome the preferred orientation problem. By adjusting the buffer pH, the distribution of particle orientations can be regulated. This support film has been successfully applied to determine high-resolution structures of various specimens in cryo-EM.
NATURE COMMUNICATIONS
(2021)
Article
Cell Biology
Linhua Tai, Yun Zhu, He Ren, Xiaojun Huang, Chuanmao Zhang, Fei Sun
Summary: The nuclear pore complex (NPC) is a large protein complex in eukaryotes that regulates the transport of molecules between the nucleus and cytoplasm. By using cryo-electron microscopy and AlphaFold2, researchers determined the structure of the outer rings of the Xenopus laevis NPC and identified the composition and interactions of its components. This detailed structural information represents a significant advancement in understanding the assembly of the NPC.
Article
Multidisciplinary Sciences
Li Qin, Ling-hui Tang, Jia-shu Xu, Xian-hui Zhang, Yun Zhu, Chun-rui Zhang, Mei-hua Wang, Xue-lei Liu, Fei Li, Fei Sun, Min Su, Yujia Zhai, Yu-hang Chen
Summary: This study describes the structure of ALMT12/QUAC1 in soybeans, revealing it to be a symmetrical dimer that forms a T-shaped pore across the membrane. The currents mediated by ALMT12/QUAC1 display rapid activation/deactivation kinetics and a bell-shaped voltage dependency. The study uncovers a domain-twisting mechanism for malate-mediated activation.
Article
Cell Biology
Chao Zhai, Nan Zhang, Xi-Xia Li, Xi Chen, Fei Sun, Meng-Qiu Dong
Summary: This study investigated the changes in distribution of vitellogenins (Vtg) in C. elegans as it ages. The levels of Vtg increase significantly with age, and inhibiting their production extends lifespan. Additionally, the study found that mislocalized yolk organelles in post-reproductive worms also increase in size, potentially worsening aging pathologies.
Article
Biochemical Research Methods
Shuoguo Li, Ziyan Wang, Xing Jia, Tongxin Niu, Jianguo Zhang, Guoliang Yin, Xiaoyun Zhang, Yun Zhu, Gang Ji, Fei Sun
Summary: This study presents a precise cryogenic fabrication system, ELI-TriScope, which accurately and efficiently prepares target cryo-lamellae for cryo-electron tomography. It enables the discovery of new in situ structural features of cellular macromolecular machines.
Correction
Biochemical Research Methods
Shuoguo Li, Ziyan Wang, Xing Jia, Tongxin Niu, Jianguo Zhang, Guoliang Yin, Xiaoyun Zhang, Yun Zhu, Gang Ji, Fei Sun
Article
Biology
Shuoguo Li, Xing Jia, Tongxin Niu, Xiaoyun Zhang, Chen Qi, Wei Xu, Hongyu Deng, Fei Sun, Gang Ji
Summary: A cryo-correlative light and electron microscopy (cryo-CLEM) system named HOPE-SIM has been developed to efficiently target cryo-FIB for cryo-ET studies by incorporating a 3D structured illumination fluorescence microscopy (SIM) system and an upgraded high-vacuum stage. With the 3D super resolution of cryo-SIM and cryo-CLEM software 3D-View, the correlation precision of the targeting region of interest can reach 110 nm, sufficient for subsequent cryo-lamella fabrication. The HOPE-SIM system has been successfully utilized to prepare cryo-lamellae targeting mitochondria, centrosomes of HeLa cells, and herpesvirus assembly compartments of infected BHK-21 cells, demonstrating its high potential for future in situ cryo-ET workflows.
COMMUNICATIONS BIOLOGY
(2023)
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)
