Article
Multidisciplinary Sciences
Masahiro Naganuma, Hisashi Tadakuma, Yukihide Tomari
Summary: By utilizing single-molecule imaging, this study found that the terminal structures of long dsRNAs and the presence or absence of Loqs-PD do not fundamentally alter Dcr-2's cleavage mode between processive and distributive, but simply impact the likelihood of Dcr-2 undergoing the cleavage reaction. These results provide a refined model for the regulation of the dicing reaction by Dcr-2.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Stefan Niekamp, Nico Stuurman, Nan Zhang, Ronald D. Vale
Summary: The study reveals that during motility, the motor protein dynein exhibits variability in the movement between its domains, with the AAA ring and MTBDs not always stepping simultaneously and taking differently sized steps. This variability results in a large number of unexpected conformational states of dynein during motility. The flexibility between major dynein domains is found to be critical for dynein motility.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Microbiology
Vadim Dubinsky, Iris Dotan, Uri Gophna
Summary: We reconstructed bacterial genomes from specific sites within the human intestines and found that strains at these sites are genetically distinct yet interrelated and derived from a single founder population. Organ-specific metagenomic information can provide valuable insights into gastrointestinal diseases, such as inflammatory bowel disease. This study used metagenomic data obtained from colonoscopy aspirates to reconstruct the genomes of common gut bacteria and revealed site-specific evolution as well as the absence of site-specific adaptations in accessory genes.
Article
Multidisciplinary Sciences
Daniel Ramirez Montero, Humberto Sanchez, Edo van Veen, Theo van Laar, Belen Solano, John F. X. Diffley, Nynke H. Dekker
Summary: In this study, the authors examined the single-molecule motion of fully reconstituted and activated CMG helicases. They found that CMG can move on DNA through both unidirectional translocation and diffusion, with a preference for the former in the presence of ATP and the latter in the absence of ATP. They also demonstrated that nucleotide binding can halt the diffusive motion of CMG. These findings support a mechanism in which nucleotide binding allows newly assembled CMG to engage with the DNA, halting diffusion and facilitating DNA melting for replication initiation.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Silvia Hormeno, Oliver J. Wilkinson, Clara Aicart-Ramos, Sahiti Kuppa, Edwin Antony, Mark S. Dillingham, Fernando Moreno-Herrero
Summary: Human DNA helicase B (HELB) plays important regulatory roles in DNA replication and recombination. It interacts with Replication Protein A (RPA) and RPA-single-stranded DNA (ssDNA) filaments to exhibit ATP hydrolysis translocation and helicase activities, and its ability to clear RPA from ssDNA allows other proteins to access these intermediates.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Multidisciplinary
Zhenhui Liu, Sheetal Parida, Shaoguang Wu, Cynthia L. Sears, Dipali Sharma, Ishan Barman
Summary: Investigating the molecular and morphological changes of cancer cells in response to external stimuli is crucial for understanding tumor progression. Label-free optical imaging techniques can visualize the morphology and determine biomolecular changes. In this study, using breast cancer cells as a model system, label-free Raman microspectroscopy and quantitative phase microscopy were used to detect biomolecular and morphological changes in single cells exposed to Bacteroides fragilis toxin.
Article
Biology
Martin Rieu, Jessica Valle-Orero, Bertrand Ducos, Jean-Francois Allemand, Vincent Croquette
Summary: The researchers introduced a single-molecule manipulation method called kinetic locking based on magnetic tweezers, which enables direct detection of biomolecular binding without the use of fluorescent probes. By measuring the dynamic interactions of E. coli RecQ helicase with its DNA substrate, they demonstrated the potential of this method for studying DNA-DNA and DNA-protein interactions while avoiding the need for labeling. This fluorescence-free micro-manipulation technique allows functional characterization of DNA/RNA processing proteins, without interference from labels.
COMMUNICATIONS BIOLOGY
(2021)
Article
Physics, Multidisciplinary
Weishuai Di, Kai Xue, Jun Cai, Zhenshu Zhu, Zihan Li, Hui Fu, Hai Lei, Wenbing Hu, Chun Tang, Wei Wang, Yi Cao
Summary: In this study, the binding strength and mechanism of cation-pi interactions in aqueous media were investigated using single-molecule force spectroscopy and nuclear magnetic resonance measurement. The results showed that the interaction strength is linearly dependent on the cation concentrations, with the order of Li+ < NH4+ < Na+ < K+. This order is different from the strength of cation-p interactions in gas phase and may be attributed to the differential dehydration ability of the cations. Overall, this method provides a unique perspective to study cation-pi interactions under physiologically relevant conditions.
PHYSICAL REVIEW LETTERS
(2023)
Article
Biochemistry & Molecular Biology
Markus B. Tomek, Bettina Janesch, Matthias L. Braun, Manfred Taschner, Rudolf Figl, Clemens Gruenwald-Gruber, Michael J. Coyne, Markus Blaukopf, Friedrich Altmann, Paul Kosma, Hanspeter Kaehlig, Laurie E. Comstock, Christina Schaeffer
Summary: Various members of the Bacteroidetes phylum possess general protein O-glycosylation systems that are crucial for processes such as host colonization and pathogenesis. The FucT family, widely encoded in Bacteroidetes protein O-glycosylation genetic loci, shows similar functions in different species and exhibits flexibility in transferring l-fucose.
Article
Chemistry, Multidisciplinary
Ken-ichi Shinohara, Yuu Makida, Takashi Oohashi, Ryoga Hori
Summary: In this study, the observation of a molecule walking along a synthetic helical polymer chain is reported. The movement is driven by van der Waals interactions and the tapping effect of an atomic force microscopy tip. The phenomenon is recorded using a fast-scanning atomic force microscope and simulated through molecular dynamics calculations. Based on these findings, the principle of a polymer molecular motor is proposed.
Article
Immunology
Bruno Perichon, Julian Lichtl-Hafele, Emma Bergsten, Vincent Delage, Patrick Trieu-Cuot, Philippe Sansonetti, Iradj Sobhani, Shaynoor Dramsi
Summary: This study indicates that the prevalence and levels of bacteria associated with colorectal cancer vary during cancer development. Only the pathobiont B. fragilis was detected in early-stage adenoma patients.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Zhiqing Zhang, Noemie Danne, Bonno Meddens, Iddo Heller, Erwin J. G. Peterman
Summary: The study investigates the mechanism of motor turnarounds in intraflagellar transport using a dual-color imaging system. It reveals that turnarounds are actually single-motor switching between opposite-direction IFT trains, not independent movements. The analysis shows that kinesin-2 and IFTdynein motors have different diffusion times and coefficients, providing important insights into motor cooperation in intracellular transport.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Cell Biology
Subhas Chandra Bera, Mona Seifert, Robert N. Kirchdoerfer, Pauline van Nies, Yibulayin Wubulikasimu, Salina Quack, Flavia S. Papini, Jamie J. Arnold, Bruno Canard, Craig E. Cameron, Martin Depken, David Dulin
Summary: The study uncovers the presence of at least three distinct conformations of the core RNA polymerase of coronaviruses and reveals the use of a thermal ratchet mechanism for the transition between pre- and post-translocated states. By utilizing high-throughput magnetic-tweezers approach, researchers were able to directly observe deep backtracking phenomenon of coronavirus polymerase, shedding light on the replication process of coronaviruses.
Article
Chemistry, Multidisciplinary
Teng Wang, Jiaojiao Hu, Yanan Li, Lulu Bi, Lijuan Guo, Xinshuo Jia, Xia Zhang, Dan Li, Xi-Miao Hou, Mauro Modesti, Xu-Guang Xi, Cong Liu, Bo Sun
Summary: The study reveals that Bloom syndrome protein (BLM) possesses the intrinsic ability for phase separation and can co-phase separate with single-stranded DNA (ssDNA) to form co-condensates. ATP enhances BLM's condensation capability on ssDNA and promotes ssDNA compression against a resistive force. BLM can also condense replication protein A (RPA)- or RAD51-coated ssDNA by dismantling these ssDNA-binding proteins.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biochemistry & Molecular Biology
Chaoyou Xue, Lucia Molnarova, Justin B. Steinfeld, Weixing Zhao, Chujian Ma, Mario Spirek, Kyle Kaniecki, Youngho Kwon, Ondrej Belan, Katerina Krejci, Simon J. Boulton, Patrick Sung, Eric C. Greene, Lumir Krejci
Summary: RECQ5 is identified as an ATP-dependent single-stranded DNA motor protein that can translocate on various nucleoprotein complexes and dismantle RAD51-ssDNA filaments. Protein-protein interaction with RAD51 is crucial for RECQ5's functions, but its substrate specificity and ability to remove certain mutant RAD51 proteins suggest a complex regulatory role in genome maintenance.
NUCLEIC ACIDS RESEARCH
(2021)
