Article
Multidisciplinary Sciences
Stella Y. Sun, Av Segev-Zarko, Muyuan Chen, Grigore D. Pintilie, Michael F. Schmid, Steven J. Ludtke, John C. Boothroyd, Wah Chiu
Summary: This study used cryogenic electron tomography to determine the molecular structures of subpellicular microtubules (SPMTs) and conoid fibrils (CFs) in Toxoplasma gondii. The SPMTs have an intralumenal spiral lining and the CFs have an altered pitch during conoid protrusion. This highlights the versatility of tubulin to form different assemblies in one organism.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Martin Obr, Wim J. H. Hagen, Robert A. Dick, Lingbo Yu, Abhay Kotecha, Florian K. M. Schur
Summary: This study assessed the performance of recently introduced hardware for cryo-electron tomography and subtomogram averaging, and compared two different systems. The results demonstrate the potential of the new generation of energy filters and direct electron detectors for structural determination, and the effects of using different processing pipelines.
JOURNAL OF STRUCTURAL BIOLOGY
(2022)
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
Computer Science, Interdisciplinary Applications
E. Moebel, C. Kervrann
Summary: This paper presents a weakly supervised subtomogram classification method based on transfer learning, using a deep neural network to learn a clustering friendly representation capable of capturing 3D shapes in the presence of noise and artifacts. By applying k-means clustering to a learning-based representation, real subtomograms can be classified satisfactorily according to structural similarity without manual annotation.
COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE
(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
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
Biochemistry & Molecular Biology
Salim Sazzed, Peter Scheible, Jing He, Willy Wriggers
Summary: In this paper, a dynamic programming-based framework, named Spaghetti Tracer, is developed to characterize the structural arrangement of filaments in subcellular components. The framework performs well under experimental noise conditions according to the tests on simulated tomograms.
Review
Biochemistry & Molecular Biology
Paula P. Navarro
Summary: This article reviews the hardware and software developments in quantitative cryo-electron tomography, discusses its importance and limitations in biological research. Quantitative cryo-electron tomography can be used to visualize the three-dimensional structure of biological systems, helping us understand changes in cellular structure and function.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Yixin Huang, Yu Zhang, Tao Ni
Summary: Cryo-electron tomography and subtomogram averaging are rapidly evolving imaging techniques that provide unprecedented structural information about biological events at high resolution in their native contexts. This review highlights the current technology development enabling high-resolution structural study in situ, emphasizing the use of a priori information of biological samples to assess the quality of subtomogram averaging pipeline. Examples of the applications of these techniques to understanding viruses and principles of macromolecule assembly using different biological systems are provided, offering structural information at various resolutions and contexts.
JOURNAL OF STRUCTURAL BIOLOGY
(2023)
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
Microbiology
Lavinia Gambelli, Rob Mesman, Wouter Versantvoort, Christoph A. Diebolder, Andreas Engel, Wiel Evers, Mike S. M. Jetten, Martin Pabst, Bertram Daum, Laura van Niftrik
Summary: The study revealed that the S-layer protein mela_00855 of Methylomirabilis bacteria determines their polygonal cell shape, with a hexagonal symmetry. The S-layer consists of multiple rigid sheets that partially overlap, potentially giving rise to the unique polygonal cell shape.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Matthew Croxford, Michael Elbaum, Muthuvel Arigovindan, Zvi Kam, David Agard, Elizabeth Villa, John Sedat
Summary: Entropy-regularized deconvolution (ER-DC) was applied to cryo-electron tomography (cryo-ET) data to address limitations in signal-to-noise ratio and Z resolution, with assessment conducted through Fourier analysis and subtomogram analysis (STA).
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Computer Science, Interdisciplinary Applications
Yu Hao, Xiaohua Wan, Rui Yan, Zhiyong Liu, Jintao Li, Shihua Zhang, Xuefeng Cui, Fa Zhang
Summary: This study presents a precise macromolecule localization and classification method called VP-Detector, which utilizes a 3D multiscale dense convolutional neural network and weighted focal loss to achieve high accuracy particle detection and classification under challenging conditions such as low signal-to-noise ratio, missing wedge artifacts, and diverse macromolecule shapes and sizes. Experimental results demonstrate that VP-Detector outperforms other state-of-the-art methods, and it can replace manual particle picking in real-world tomograms.
COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE
(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)
Editorial Material
Microbiology
Jan Bohning, Tanmay A. M. Bharat
Summary: This month's article explores how the combination of cryo-electron tomography and cross-linking mass spectrometry has been instrumental in elucidating the mechanisms of transcription-coupled translation in bacteria.
NATURE REVIEWS MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Jan Bohning, Tanmay A. M. Bharat, Sean M. Collins
Summary: Cryoelectron tomography and subtomogram averaging enable direct visualization and study of biological macromolecules in their native cellular environment. However, limitations such as low signal-to-noise ratios, low particle abundance, and low throughput have restricted the obtainable structural information. This study demonstrates the potential of a compressed sensing approach to enhance the visualization and resolution of tomograms, addressing these limitations.
Article
Biochemistry & Molecular Biology
Matthew Herdman, Andriko von Kugelgen, Danguole Kureisaite-Ciziene, Ramona Duman, Kamel El Omari, Elspeth F. Garman, Andreas Kjaer, Dimitrios Kolokouris, Jan Lowe, Armin Wagner, Phillip J. Stansfeld, Tanmay A. M. Bharat
Summary: In this study, the role of metal ions in the formation of Caulobacter crescentus S-layer was investigated. It was found that calcium ions facilitate S-layer lattice formation and cell-surface binding, and that bound metal ions are crucial for the S-layer lattice. The positions of metal ions in the S-layer were also mapped using advanced imaging techniques. These findings contribute to the understanding of S-layer formation and have implications for synthetic biology.
Article
Multidisciplinary Sciences
Susanne Krause, Sabrina Gfrerer, Andriko von Kuegelgen, Carsten Reuse, Nina Dombrowski, Laura Villanueva, Boyke Bunk, Cathrin Sproeer, Thomas R. Neu, Ute Kuhlicke, Kerstin Schmidt-Hohagen, Karsten Hiller, Tanmay A. M. Bharat, Reinhard Rachel, Anja Spang, Johannes Gescher
Summary: This study reports a stable co-culture of a member of the Micrarchaeota and its host, and sheds light on this symbiosis through multi-omic and physiological analyses.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Andriko von Kugegen, Sofie van Dorst, Vikram Alva, Tanmay A. M. Bharat
Summary: Deinococcus radiodurans is a bacterium that is extremely tolerant to various environmental stresses. A study investigated the cell envelope structure and stabilization mechanisms of D. radiodurans, and discovered the role of the OM protein SlpA in connecting the outer membrane to the peptidoglycan layer. The study also found that similar OM-PG connector proteins are widespread in phylogenetically deep-branching Gram-negative bacteria. The results provide insights into the cell surface organization and hyperstability of D. radiodurans and related bacteria.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Editorial Material
Biochemical Research Methods
Olivia E. R. Smith, Tanmay A. M. Bharat
Summary: DeepPiCt, a deep learning approach, enables segmentation and identification of macromolecules in the cellular jungle of electron cryotomography data.
Article
Multidisciplinary Sciences
Jan Bohning, Mnar Ghrayeb, Conrado Pedebos, Daniel K. Abbas, Syma Khalid, Liraz Chai, Tanmay A. M. Bharat
Summary: Fibres formed by the protein TasA in Bacillus subtilis biofilms are assembled from globular monomers through donor-strand exchange and form bundles. This study provides insights into the structure and assembly of TasA fibres, which are important for the formation of B. subtilis biofilms.
NATURE COMMUNICATIONS
(2022)
Article
Biology
Jasenko Zivanov, Joaquin Oton, Zunlong Ke, Andriko von Kuegelgen, Euan Pyle, Kun Qu, Dustin Morado, Daniel Castano-Diez, Giulia Zanetti, Tanmay A. M. Bharat, John A. G. Briggs, Sjors H. W. Scheres
Summary: We propose a new approach for determining macromolecular structures from cryo-ET data. Unlike existing methods, our approach optimizes a regularized likelihood target that approximates a function of the 2D experimental images. Additionally, we optimize tilt-series alignments, beam-induced motions, defoci, and higher-order optical aberrations using the increased signal-to-noise ratio in the averaged structure.
Article
Chemistry, Physical
Tim K. Esser, Jan Bohning, Paul Fremdling, Tanmay Bharat, Joseph Gault, Stephan Rauschenbach
Summary: An increasing number of studies are combining mass spectrometry with imaging techniques such as cryo-EM to investigate biomolecular function. Native electrospray ion-beam deposition can provide a direct link between native MS and cryo-EM. However, there are still many aspects of this workflow that need to be understood and optimized.
FARADAY DISCUSSIONS
(2022)
Article
Multidisciplinary Sciences
Tim K. Esser, Jan Bohning, Paul Fremdling, Mark T. Agasid, Adam Costin, Kyle Fort, Albert Konijnenberg, Joshua D. Gilbert, Alan Bahm, Alexander Makarov, Carol V. Robinson, Justin L. P. Benesch, Lindsay Baker, Tanmay A. M. Bharat, Joseph Gault, Stephan Rauschenbach
Summary: Despite advances in cryo-EM and SPA, sample heterogeneity remains a challenge. The study demonstrates the potential of native ES-IBD as an alternative approach for preparing high-purity samples. This method has the potential to increase the scope and throughput of cryo-EM for protein structure determination.
