Article
Biotechnology & Applied Microbiology
Derek M. Bickhart, Mikhail Kolmogorov, Elizabeth Tseng, Daniel M. Portik, Anton Korobeynikov, Ivan Tolstoganov, Gherman Uritskiy, Ivan Liachko, Shawn T. Sullivan, Sung Bong Shin, Alvah Zorea, Victoria Pascal Andreu, Kevin Panke-Buisse, Marnix H. Medema, Itzhak Mizrahi, Pavel A. Pevzner, Timothy P. L. Smith
Summary: This study demonstrates that deep sequencing combined with haplotype phasing can address the challenge of identifying closely related organisms in microbial communities. The resolution of closely related microbes improves the identification of biosynthetic gene clusters and the assignment of mobile genetic elements to host genomes.
NATURE BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Rebecca Conners, Rayen Ignacia Leon-Quezada, Mathew McLaren, Nicholas J. Bennett, Bertram Daum, Jasna Rakonjac, Vicki A. M. Gold
Summary: Phages, viruses that infect bacteria, are prevalent in every ecosystem on Earth and have various applications in molecular biology and biotechnology. The structure and mechanisms of infection and assembly of filamentous phages, particularly the Ff phages, have been largely unknown. In this study, the researchers used cryo-electron microscopy and a highly efficient system to produce short Ff-derived nanorods, successfully determining the structure of a filamentous virus including the tips. By combining the structure with mutagenesis, they identified important phage domains involved in bacterial attack and release of new viral progeny, leading to the proposal of new models for the phage lifecycle.
NATURE COMMUNICATIONS
(2023)
Article
Microbiology
Charles Bou-Nader, Frauke Muecksch, Janae B. Brown, Jackson M. Gordon, Ashley York, Chen Peng, Rodolfo Ghirlando, Michael F. Summers, Paul D. Bieniasz, Jinwei Zhang
Summary: The HIV-1 virion structural polyprotein Gag is directed to assembly sites by its N-terminal matrix domain, which also binds to host tRNAs. The co-crystal structure of the HIV-1 MA-tRNA(Lys3) complex reveals a specialized interface that facilitates binding in solution and living cells. Mutations disrupting this interaction cause Gag redistribution and reduced HIV-1 replication, indicating the virus's reliance on host tRNAs for subcellular localization control.
CELL HOST & MICROBE
(2021)
Article
Multidisciplinary Sciences
Pietro Fontana, Ying Dong, Xiong Pi, Alexander B. Tong, Corey W. Hecksel, Longfei Wang, Tian-Min Fu, Carlos Bustamante, Hao Wu
Summary: This study determined the near-complete structure of the cytoplasmic ring of the nuclear pore complex (NPC) using cryo-electron microscopy and AlphaFold prediction. Molecular interactions and the binding modes of Nup358, the largest NPC subunit, were also predicted. The findings shed light on the formation and function of the NPC.
Article
Chemistry, Multidisciplinary
Haodan Guo, Yanyan Fang, Hong-Bo Cheng, Jinpeng Wu, Yan Lei, Shumao Wang, Xiangrong Li, Yuhua Dai, Wanchun Xiang, Ding-Jiang Xue, Yuan Lin, Anders Hagfeldt
Summary: Defects in perovskite films can be effectively passivated by using a cholesterol derivative self-assembly strategy to construct crosslinked and compact membranes. These membranes act as protective layers, improving the performance and stability of perovskite solar cells (PSCs).
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Multidisciplinary Sciences
Min Zhang, Anna Jungblut, Franziska Kunert, Luis Hauptmann, Thomas Hoffmann, Olga Kolesnikova, Felix Metzner, Manuela Moldt, Felix Weis, Frank DiMaio, Karl-Peter Hopfner, Sebastian Eustermann
Summary: In this study, the authors reveal the structural mechanism for ATP-dependent chromatin remodeling of hexasomes by the INO80 complex. They demonstrate how INO80 recognizes noncanonical DNA and histone features of hexasomes that emerge from the loss of H2A-H2B. The researchers also find that the loss of H2A-H2B grants remodelers access to a different, yet unexplored layer of energy-driven chromatin regulation.
Article
Agriculture, Dairy & Animal Science
M. Huang, H. Zhang, Z. P. Wu, X. P. Wang, D. S. Li, S. J. Liu, S. M. Zheng, L. J. Yang, B. B. Liu, G. X. Li, Y. C. Jiang, H. Chen, J. Ren
Summary: The study reveals a significant genetic association between Pudong White pigs and European Large White pigs, suggesting that the European lineage in Pudong White pigs originated from Large White pigs and introgressed into the breed via hybridization with East Chinese pigs in China. This research provides valuable insights for the conservation of this unique Chinese indigenous pig population.
Article
Genetics & Heredity
Minhui Zhuang, Jian Zhao, Jing Wu, Shilong Fu, Ping Han, Xiaofeng Song
Summary: This study revealed the expression profile of circRNAs in ovarian serous cystadenocarcinoma tissues, showing that the differential expression of circRNAs may be associated with the occurrence of ovarian serous cystadenocarcinoma. A complex circRNA-miRNA interaction network was constructed, demonstrating the potential functions of certain circRNAs for future diagnosis and treatment.
BMC MEDICAL GENOMICS
(2021)
Article
Multidisciplinary Sciences
Yingke Liang, Alicia Plourde, Stephanie A. Bueler, Jun Liu, Peter Brzezinski, Siavash Vahidi, John L. Rubinstein
Summary: Oxidative phosphorylation is a promising target for treating Mycobacterium tuberculosis and other mycobacteria infections. The structure of the mycobacterial electron transport chain reveals the presence of several important components, including the orphan protein MSMEG_2064, acyl phosphati-dylinositol dimannoside, menaquinone, and a purine nucleoside triphosphate. These findings provide insights into the function and structure of the enzyme.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
A. Manuel Liaci, Barbara Steigenberger, Paulo Cesar Telles de Souza, Sem Tamara, Mariska Grollers-Mulderij, Patrick Ogrissek, Siewert J. Marrink, Richard A. Scheltema, Friedrich Forster
Summary: Human SPC has two functional paralogs with distinct proteolytic subunits, and its structure plays a key role in the specificity for SPs based on the length of their hydrophobic segments.
Article
Nanoscience & Nanotechnology
Baoping Zhang, Qinfen Gu, Cheng Wang, Qili Gao, Jiaxin Guo, Pak Wai Wong, Chain Tsuan Liu, Alicia Kyoungjin An
Summary: This study presents a self-assembled flexible porphyrin Ti3C2Tx MXene Janus membrane for dual-functional enabled photothermal desalination, demonstrating efficient water pumping, heat localization, vapor generation, and salt resistance. The interaction and charge redistribution between MXene and porphyrin lead to a stable hydrophobic/hydrophilic Janus structure with synergistically enhanced photothermal conversion, providing an effective strategy for seawater desalination using MXene membranes.
ACS APPLIED MATERIALS & INTERFACES
(2021)
Article
Biochemistry & Molecular Biology
Marcin Jaciuk, David Scherf, Karol Kaszuba, Monika Gaik, Alexander Rau, Anna Koscielniak, Roscislaw Krutyholowa, Michal Rawski, Paulina Indyka, Andrea Graziadei, Andrzej Chramiec-Glabik, Anna Biela, Dominika Dobosz, Ting-Yu Lin, Nour-el-Hana Abbassi, Alexander Hammermeister, Juri Rappsilber, Jan Kosinski, Raffael Schaffrath, Sebastian Glatt
Summary: The Elongator complex is responsible for modifying tRNAs in eukaryotes by adding a carboxymethyl group to wobble uridines. This modification is crucial for maintaining cellular proteome integrity and protecting against neurodegenerative diseases.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Pharmacology & Pharmacy
Melissa Alegria-Arcos, Tabata Barbosa, Felipe Sepulveda, German Combariza, Janneth Gonzalez, Carmen Gil, Ana Martinez, David Ramirez
Summary: The COVID-19 pandemic has accelerated the development of drugs/vaccines by integrating scientists globally. In this study, researchers collected information on the interactions between proteins from SARS-CoV-2 and humans, as well as information on protein-drug interactions from public databases. By representing this data as networks, they were able to gain insights into the interactions between proteins from both organisms. Through data analysis, they identified important proteins and drugs from a network pharmacology perspective, suggesting potential therapeutic options for COVID-19. This study also revealed the potential importance of human proteins in drug repurposing campaigns.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Plant Sciences
Takehiko Kanazawa, Ryuichi Nishihama, Takashi Ueda
Summary: Eukaryotic cells possess endomembrane organelles that require a tightly regulated membrane trafficking system for transportation and localization. This study discovered that a mutation in a COPI subunit affects the morphology of oil bodies in Marchantia polymorpha, suggesting the involvement of cell wall biosynthesis in shaping these organelles.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
Chenchen Mi, Li Zhang, Guoqiang Huang, Guangcan Shao, Fan Yang, Xin You, Meng-Qiu Dong, Shan Sun, Sen-Fang Sui
Summary: This study presents cryo-EM structures of yeast TRAPPII in apo and Ypt32-bound states, revealing a dimeric architecture assembled by two triangle-shaped monomers. The Ypt32-bound monomer captures the closed conformation and interacts with core TRAPP/TRAPPI, Trs120, and Trs31. These structures provide insights into the assembly of TRAPPII and the mechanism of Ypt31/Ypt32 activation by TRAPPII.
Review
Biochemistry & Molecular Biology
Euan Pyle, Giulia Zanetti
Summary: Cryo-ET with STA has achieved subnanometer resolution thanks to improvements in microscope hardware and data processing strategies, along with an increase in the number and quality of software packages available for processing cryo-ET data.
BIOCHEMICAL JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Aaron M. N. Joiner, Ben P. Phillips, Kumar Yugandhar, Ethan J. Sanford, Marcus B. Smolka, Haiyuan Yu, Elizabeth A. Miller, J. Christopher Fromme
Summary: The study revealed the regulation of Rab1 activation by the TRAPPIII complex, with the Trs85 subunit serving as a membrane anchor for the entire complex via its amphipathic helix. These findings provide a structural understanding of Rab activation on organelle and vesicle membranes.
Article
Multidisciplinary Sciences
Yan Huang, Haidi Yin, Baiying Li, Qian Wu, Yang Liu, Kristina Poljak, Julija Maldutyte, Xiao Tang, Mo Wang, Zhixiao Wu, Elizabeth A. Miller, Liwen Jiang, Zhong-Ping Yao, Yusong Guo
Summary: The study utilized an in vitro assay and quantitative mass spectrometry analysis to reveal cargo proteins enriched in transport vesicles through specific sorting machinery. It identified novel factors regulating vesicular trafficking and specific cargo clients of cellular factors, demonstrating the robustness and power of this approach for uncovering molecular mechanisms in protein transport.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Michaela J. Conley, Judith M. Short, Andrew M. Burns, James Streetley, Joshua Hutchings, Saskia E. Bakker, B. Joanne Power, Hussain Jaffery, Joanne Haney, Giulia Zanetti, Pablo R. Murcia, Murray Stewart, Rachel Fearns, Swetha Vijayakrishnan, David Bhella
Summary: The study found that the envelope-associated proteins and glycoproteins of RSV filamentous virions exhibit extensive helical ordering, with a helical lattice of M-dimers forming an endoskeleton below the viral envelope. The clustered pairs of envelope glycoproteins, coordinated by the M-layer, may have implications for the conformation of fusion glycoprotein epitopes. The presence of N-RNA rings packaged within RSV virions in authentic virus infections provides molecular insight into the organization of the virion and the mechanism of its assembly.
Article
Multidisciplinary Sciences
Natalia Gomez-Navarro, Julija Maldutyte, Kristina Poljak, Sew-Yeu Peak-Chew, Jonathon Orme, Brittany J. Bisnett, Caitlin H. Lamb, Michael Boyce, Davide Gianni, Elizabeth A. Miller
Summary: This study explores the possibility of selectively inhibiting protein secretion by perturbing protein-protein interactions involved in capture into transport vesicles. The researchers discovered a specific small molecule that can disrupt the function of the SEC24 protein, leading to decreased secretion of specific proteins.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Biochemistry & Molecular Biology
Sander E. Van Der Verren, Giulia Zanetti
Summary: Sar1, a small GTPase protein of the ARF family, plays a role in cargo concentration and membrane deformation by associating with the endoplasmic reticulum membrane and recruiting COPII components. The regulation of Sar1's GTP hydrolysis and its role in coat assembly, as well as the mechanism of Sar1-induced membrane deformation and scission, are still not fully understood, especially in higher organisms with a wider range of secreted cargoes. This review focuses on these aspects and highlights the additional specialization in higher eukaryotes, along with the outstanding questions regarding the orchestration of Sar1 functions.
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
Multidisciplinary Sciences
Michael R. R. Wozny, Andrea Di Luca, Dustin R. R. Morado, Andrea Picco, Rasha Khaddaj, Pablo Campomanes, Lazar Ivanovic, Patrick C. C. Hoffmann, Elizabeth A. A. Miller, Stefano Vanni, Wanda Kukulski
Summary: The endoplasmic reticulum and mitochondria play crucial roles in eukaryotic membrane biogenesis through lipid exchange at membrane contact sites. However, the mechanisms underlying this process are not well understood. In this study, researchers used integrative structural biology techniques to investigate the molecular organization of the endoplasmic reticulum-mitochondria encounter structure (ERMES) in yeast cells. They found that ERMES forms discrete bridge-like complexes at contact sites, consisting of synaptotagmin-like mitochondrial lipid binding protein domains. This study provides important insights into the supramolecular architecture and lipid transfer mechanisms involved in inter-organelle communication.
Article
Cell Biology
Sergej Limar, Carolin Koerner, Fernando Martinez-Montanes, Viktoriya G. Stancheva, Verena N. Wolf, Stefan Walter, Elizabeth A. Miller, Christer S. Ejsing, Vanesa Viviana Galassi, Florian Froehlich
Summary: Limar et al. discovered that the yeast protein Svf1 localizes to the cis Golgi apparatus and is involved in the transport of ceramides between the ER and the Golgi. Svf1 binds ceramides and plays a role in maintaining appropriate levels of complex sphingolipids. This study provides insights into the mechanism of ceramide transport in yeast cells and its significance in sphingolipid metabolism.
JOURNAL OF CELL BIOLOGY
(2023)
Article
Chemistry, Physical
Euan Pyle, Joshua Hutchings, Giulia Zanetti
Summary: This article presents a time-efficient and accurate strategy for picking and cleaning membrane-associated particles and provides a step-by-step guide and necessary scripts for users to carry out these strategies.
FARADAY DISCUSSIONS
(2022)