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
Biochemistry & Molecular Biology
Noemi Zimmermann, Akira Noga, Jagan Mohan Obbineni, Takashi Ishikawa
Summary: Using in situ cryo-electron tomography, subtomogram averaging, and classification, we analyzed three states of the axonemal outer dynein arm (ODA) during the power stroke cycle, which include the prepower stroke, postpower stroke, and intermediate state conformations. Our analysis revealed differences in the orientation and position of the dynein head compared to published in vitro atomic structures. Additionally, we found that in the absence of ATP, dynein linkers interact with the AAA3/AAA4 domains, suggesting that they are directed by interactions with the adjacent microtubule doublet B-tubule. Our findings provide insight into the conformational changes of ODA during force generation.
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
Biotechnology & Applied Microbiology
Danielle L. Sexton, Gao Chen, Fadime Kara Murdoch, Ameena Hashimi, Frank E. Loffler, Elitza Tocheva
Summary: In this study, the morphological and ultrastructural features of Dehalococcoides mccartyi (Dhc) and Dehalogenimonas spp. (Dhgm) bacteria, which respire organohalogen compounds, were revealed using cryo-electron tomography. The results provided insights into the overall cellular shape, cell envelope architecture, cytoskeletal filaments, enzymatic complexes involved in reductive dehalogenation, and the structure of extracellular vesicles.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
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
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)
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)
Review
Biochemistry & Molecular Biology
Eeva-Liisa Eskelinen
Summary: The generation of autophagosomes is a long-standing question in the field of autophagy. Recent studies using cryo-electron tomography and detailed analysis of image data have revealed new information on the membrane dynamics of autophagosome biogenesis, including the shape and dimensions of omegasomes, phagophores, and autophagosomes, and their relationships with surrounding organelles. An important prediction from these findings is that 60-80% of the autophagosome membrane area is obtained through direct lipid transfer or lipid synthesis. Cryo-electron tomography is expected to provide new directions for autophagy research in the future.
Article
Multidisciplinary Sciences
Nils Marechal, Banyuhay P. Serrano, Xinyan Zhang, Charles J. Weitz
Summary: Thyroid hormones play vital roles in metabolism, development, and growth, but the process of their formation is still poorly understood. By analyzing the cryo-EM structure of native bovine thyroglobulin, scientists have identified local structural rearrangements during the formation of nascent thyroid hormones, providing insights into the mechanisms underlying hormone formation and stabilization.
NATURE COMMUNICATIONS
(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
Biology
Irene Carlon-Andres, Tomas Malinauskas, Sergi Padilla-Parra
Summary: The study by Irene Carlon-Andres et al. used single-molecule spectroscopy and two-photon FRET-FLIM to characterize the dynamics of HIV-1 envelope glycoprotein trimer. Their results suggest that Env-Env interactions are maturation-dependent and disrupted by CD4 and neutralizing antibodies, providing insights into HIV-1 entry and immune evasion mechanisms.
COMMUNICATIONS BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Linhua Tai, Guoliang Zhu, Minnan Yang, Lei Cao, Xiaorui Xing, Guoliang Yin, Chun Chan, Chengfeng Qin, Zihe Rao, Xiangxi Wang, Fei Sun, Yun Zhu
Summary: By utilizing cryo-electron tomography, researchers observed prefusion and postfusion spikes in beta-propiolactone-inactivated SARS-CoV-2 virions, and successfully solved the in situ structure of the postfusion spike at nanometer resolution. The study provided detailed information on the fusion core, glycosylation sites, and transmembrane domain location, shedding light on the mechanism of fusion pore formation through spike oligomerization patterns on the viral membrane.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Immunology
Cuicui Zhao, Da Lu, Qian Zhao, Chongjiao Ren, Huangtao Zhang, Jiaqi Zhai, Jiaxin Gou, Shilin Zhu, Yaqi Zhang, Xinqi Gong
Summary: This review provides an overview of the data processing workflow and reconstruction steps in cryo-ET, as well as classical mathematical models and deep learning methods. It also discusses current limitations and future prospects, and offers software and methods to experts in various fields, helping them understand the latest research trends in cryo-ET.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Biology
Sven Klumpe, Herman K. H. Fung, Sara K. Goetz, Ievgeniia Zagoriy, Bernhard Hampoelz, Xiaojie Zhang, Philipp S. Erdmann, Janina Baumbach, Christoph W. Mueller, Martin Beck, Juergen M. Plitzko, Julia Mahamid
Summary: Lamella micromachining by cryo-FIB at low temperature has become a widely used method for cellular cryo-electron tomography. The improved stability of new-generation cryo-FIB instruments now allows for automated operations. The SerialFIB software tool enables the creation of automated and customizable cryo-FIB preparation protocols, laying the foundation for further development of advanced cryogenic imaging and sample preparation protocols.
