Article
Biochemistry & Molecular Biology
Evgeniia Prokhorova, Thomas Agnew, Anne R. Wondisford, Michael Tellier, Nicole Kaminski, Danique Beijer, James Holder, Josephine Groslambert, Marcin J. Suskiewicz, Kang Zhu, Julia M. Reber, Sarah C. Krassnig, Luca Palazzo, Shona Murphy, Michael L. Nielsen, Aswin Mangerich, Dragana Ahel, Jonathan Baets, Roderick J. O'Sullivan, Ivan Ahel
Summary: ARH3 and PARG play different roles in vivo, with ARH3 showing tolerance to MARylation and PARG demonstrating toxicity towards PARylation. There is a synthetic lethal interaction between the two enzymes, and loss of ARH3 can lead to resistance to PARP inhibitors.
Article
Multidisciplinary Sciences
Zhaoxia Cui, Yuan Liu, Jianbo Yuan, Xiaojun Zhang, Tomer Ventura, Ka Yan Ma, Shuai Sun, Chengwen Song, Dongliang Zhan, Yanan Yang, Hourong Liu, Guangyi Fan, Qingle Cai, Jing Du, Jing Qin, Chengcheng Shi, Shijie Hao, Quinn P. Fitzgibbon, Gregory G. Smith, Jianhai Xiang, Tin-Yam Chan, Min Hui, Chenchang Bao, Fuhua Li, Ka Hou Chu
Summary: The study presents a chromosome-level genome and transcriptome data for the Chinese mitten crab, shedding light on the biology of Brachyurans. The research reveals the expansion of specific gene families in crabs, and highlights the importance of down-regulation of Hox genes during brachyurization development.
NATURE COMMUNICATIONS
(2021)
Article
Cell Biology
Grant A. King, Rahel Wettstein, Joseph M. Varberg, Keerthana Chetlapalli, Madison E. Walsh, Ludovic C. J. Gillet, Claudia Hernandez-Armenta, Pedro Beltrao, Ruedi Aebersold, Sue L. Jaspersen, Joao Matos, Elcin Unal
Summary: King and Wettstein et al. have discovered that nuclear pore complexes undergo two distinct remodeling events during budding yeast meiosis. This study provides insights into the organization of the nuclear basket and reveals a conserved aspect of NPC plasticity.
JOURNAL OF CELL BIOLOGY
(2022)
Article
Biology
Theres Friesacher, Haritha P. Reddy, Harald Bernsteiner, J. Carlo Combista, Boris Shalomov, Amal K. Bera, Eva-Maria Zangerl-Plessl, Nathan Dascal, Anna Stary-Weinzinger
Summary: This study investigates the impact of a selectivity filter mutation on the structure and function of GIRK2 channels through molecular dynamics simulations and electrophysiological experiments. It reveals an allosteric connection between the selectivity filter and a crucial activator binding site, providing insights into the mechanism of neurological disorders.
COMMUNICATIONS BIOLOGY
(2022)
Review
Multidisciplinary Sciences
Wenping Wu, Jimin Zheng, Zongchao Jia
Summary: The mitochondrial uniporter is a Ca2+-selective ion-conducting channel in the inner mitochondrial membrane composed of MCU, MCUb, EMRE, MICU1, and MICU2. Recent structural studies have provided insights into the component structures and their spatial relationship, contributing to a better understanding of mitochondrial Ca2+ uptake and regulation. Further research in this area could lead to advancements in studying mitochondrial Ca2+ permeation and related diseases.
Article
Biochemistry & Molecular Biology
Christian Sirko, Matthew J. Novello, Peter B. Stathopulos
Summary: Stromal interaction molecule 1 (STIM1) is a calcium sensing protein that regulates store-operated calcium entry. S-Glutathionylation of STIM1 at Cys49 or Cys56 induces conformational changes and thermodynamic destabilization. This modification or mutation of Cys56 reduces the binding affinity to calcium ions.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Chemistry, Physical
Sharon Ruthstein, Lukas Hofmann
Summary: The use of electron para-magnetic resonance (EPR) spectroscopy has had a significant impact in the field of structural biology in the last 20 years. EPR spectroscopy provides the advantage of being able to detect minor conformational changes in biomolecules or macromolecular complexes, regardless of their size or complexity, or their environment. This article focuses on the application of EPR spectroscopy in studying transmembrane transport and transcription mechanisms, and discusses experimental and analytical considerations in two specific biological reaction mechanisms.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Cell Biology
Martijn Wehrens, Anne E. de Leeuw, Maya Wright-Clark, Joep E. C. Eding, Cornelis J. Boogerd, Bas Molenaar, Petra H. van der Kraak, Diederik W. D. Kuster, Jolanda van der Velden, Michelle Michels, Aryan Vink, Eva van Rooij
Summary: Functional links between genes and cell size relevant for HCM were identified using scRNA-seq on patients' samples. The study provides valuable insights into molecular events involved in HCM and may contribute to the development of enhanced therapies.
Article
Biology
Benjamin Garcia-Ramirez, Israel Mares-Mejia, Annia Rodriguez-Hernandez, Patricia Cano-Sanchez, Alfredo Torres-Larios, Enrique Ortega, Adela Rodriguez-Romero
Summary: Allergies have become a growing health problem, and allergens play a major role in triggering allergic reactions. This study reports the crystal structures of murine IgE antibody in complex with an allergen, revealing specific interactions and high affinity between the antibody and allergen. Additionally, experiments with allergen mutants suggest that this antibody may be a promising tool for allergy diagnosis and research applications.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biology
Zeng Wang, Changjun Peng, Wei Wu, Chaochao Yan, Yunyun Lv, Jia-Tang Li
Summary: Based on the analysis of three de novo-assembled genomes of limbless lizards from different lineages, this study demonstrates the crucial role of divergence of conserved non-coding elements (CNEs) in limb development. It is found that these CNEs are associated with genes essential for limb initiation and outgrowth as well as regulatory signals in the early stage of limb development. Moreover, the study highlights the significance of insertions and deletions (InDels) in the CNEs, which are lineage-specific in limbless squamates and affect the regulatory function of the CNEs.
SCIENCE CHINA-LIFE SCIENCES
(2023)
Article
Plant Sciences
Huibo Zhang, Xiaofeng Shen, Sijie Sun, Ying Li, Shu Wang, Jianhe Wei, Baolin Guo, Chao Sun
Summary: This study investigated the biosynthesis mechanism of the anti-cancer agent camptothecin through the use of multiomics methods. Key genes and proteins were identified, providing important insights for future development of cancer therapies and synthetic biology approaches.
PHYSIOLOGIA PLANTARUM
(2023)
Article
Biology
Tao Deng, Xiaokang Lu, Shiqi Wang, Lawrence J. Flynn, Danhui Sun, Wen He, Shanqin Chen
Summary: A new species of giant rhino, Paraceratherium linxiaense, has been reported from northwestern China with an age of 26.5Ma. Morphological and phylogenetic analysis show that it is a highly derived species of the genus Paraceratherium, with close ties to Paraceratherium lepidum and Paraceratherium bugtiense, suggesting a possible range expansion from Central Asia via the Tibetan region.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Dan Zeng, Ximing Guo
Summary: This study investigates the growth of the eastern oyster Crassostrea virginica at molecular levels by sequencing and comparing the mantle transcriptomes of large and small oysters. The results reveal differentially expressed genes related to shell formation and growth, and identify novel candidate genes and markers associated with these processes. The study also suggests the importance of both transcriptional modulation and functional polymorphism in determining growth.
MARINE BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Xing Guo, Dongming Fang, Sunil Kumar Sahu, Shuai Yang, Xuanmin Guang, Ryan Folk, Stephen A. Smith, Andre S. Chanderbali, Sisi Chen, Min Liu, Ting Yang, Shouzhou Zhang, Xin Liu, Xun Xu, Pamela S. Soltis, Douglas E. Soltis, Huan Liu
Summary: Chloranthales are the last major mesangiosperm lineage without a nuclear genome assembly, but a high-quality genome assembly of Chloranthus spicatus has now been achieved, providing insights into the evolutionary relationships and genome evolution of mesangiosperms. This study sheds light on the unique characteristics of Chloranthales and magnoliids compared to other angiosperms, and contributes to a better understanding of angiosperm diversification and phylogeny.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Yuan Yuan, Yaolei Zhang, Peijun Zhang, Chang Liu, Jiahao Wang, Haiyu Gao, A. Rus Hoelzel, Inge Seim, Meiqi Lv, Mingli Lin, Lijun Dong, Haoyang Gao, Zixin Yang, Francesco Caruso, Wenzhi Lin, Rute R. da Fonseca, Ding Wang, Xianyan Wang, Marianne H. Rasmussen, Mingming Liu, Jinsong Zheng, Liyuan Zhao, Paula F. Campos, Hui Kang, Maria Iversen, Yue Song, Xinyu Guo, Jiao Guo, Yating Qin, Shanshan Pan, Qiwu Xu, Lingfeng Meng, A. Yunga, Shanshan Liu, Simon Ming-Yuen Lee, Xin Liu, Xun Xu, Huanming Yang, Guangyi Fan, Kun Wang, Songhai Li
Summary: The study generated high-quality genome assemblies of 17 marine mammals, revealing unique and convergent genomic variations associated with the transition to aquatic life in marine mammal lineages. The research advances understanding of the timing, pattern, and molecular changes associated with the evolution of mammalian lineages adapting to aquatic life.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Biochemistry & Molecular Biology
Gabriela Bernal Astrain, Maya Nikolova, Matthew J. Smith
Summary: RAS small GTPases are important signaling regulators in cancer development. While most research has focused on three well-known oncogenes (HRAS, KRAS, and NRAS), the full RAS subfamily consists of 35 related GTPases with diverse functions. In this study, we highlight a poorly characterized group of 17 RAS GTPases that are down-regulated in cancer and may function as tumor suppressors. These GTPases are clustered into two families, 'distal-RAS' (D-RAS) and 'CaaX-Less RAS' (CL-RAS), and their roles in cellular function, regulation, and interaction with effector proteins remain largely unknown. The evidence suggests that these GTPases may collectively regulate cellular proliferation.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2022)
Article
Multidisciplinary Sciences
Stanislau Yatskevich, Kyle W. Muir, Dom Bellini, Ziguo Zhang, Jing Yang, Thomas Tischer, Masa Predin, Tom Dendooven, Stephen H. McLaughlin, David Barford
Summary: This study reveals that CCAN can bind to CENP-A(Nuc) and form a robust structure around the linker DNA, enabling kinetochores to withstand forces exerted by the mitotic spindle.
Article
Oncology
Owen J. Chen, Ester Castellsague, Mohamed Moustafa-Kamal, Javad Nadaf, Barbara Rivera, Somayyeh Fahiminiya, Yilin Wang, Isabelle Gamache, Caterina Pacifico, Lai Jiang, Jian Carrot-Zhang, Leora Witkowski, Albert M. Berghuis, Stefan Schoenberger, Dominik Schneider, Morten Hillmer, Susanne Bens, Reiner Siebert, Colin J. R. Stewart, Ziguo Zhang, William C. H. Chao, Celia M. T. Greenwood, David Barford, Marc Tischkowitz, Jacek Majewski, William D. Foulkes, Jose G. Teodoro
Summary: Two germline CDC20 missense variants that segregate with cancer in two families compromise the spindle assembly checkpoint and lead to aberrant mitotic progression, which could predispose cells to transformation.
Article
Multidisciplinary Sciences
Marilyn Goudreault, Valerie Gagne, Chang Hwa Jo, Swati Singh, Ryan C. Killoran, Anne-Claude Gingras, Matthew J. Smith
Summary: Goudreault et al. investigate the role of Afadin as a genuine effector of RAS GTPases, showing its association with cell polarity through Scribble protein. AFDN is essential for cell-cell contacts and has broad specificity for RAS and RAP GTPases. The study also reveals the interaction between the first PDZ domain of SCRIB and the FHA domain of AFDN, and demonstrates the importance of AFDN and SCRIB in MAPK and PI3K activation kinetics and cell motility.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Andreas Boland, Jean-Francois Cote, David Barford
Summary: DOCK proteins are a type of guanine nucleotide exchange factors (GEFs) that activate CDC42 and RAC1 to regulate cellular processes. They have a catalytic DHR2 domain and a DHR1 domain that targets them to plasma membranes. Different subfamilies of DOCK GEFs activate CDC42 and RAC1 with specificities and are regulated by accessory signaling domains and ELMO proteins. Structural studies have provided insights into the mechanism of DOCK proteins, which are involved in various diseases and need to be further understood for targeted therapy.
Article
Biochemistry & Molecular Biology
Tamara Sijacki, Pablo Alcon, Zhuo A. Chen, Stephen H. McLaughlin, Shabih Shakeel, Juri Rappsilber, Lori A. Passmore
Summary: This study reveals that phosphorylation of FANCI by the ATR DNA damage kinase primes the FANCD2-FANCI clamp for ubiquitination, facilitating the initiation of DNA cross-link repair.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Elyse S. Fischer, Conny W. H. Yu, Johannes F. Hevler, Stephen H. McLaughlin, Sarah L. Maslen, Albert J. R. Heck, Stefan M. Freund, David Barford
Summary: This study reveals the complex interaction network required for the formation of the MCC during mitosis. The assembly of MCC is initiated by Mad1 on unattached kinetochores and facilitated by a phosphorylation-dependent scaffold for the binding of Cdc20 and Mad2. This research is of great importance for a better understanding of the regulatory mechanisms of cell division.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Clinton A. Gabel, Zhuang Li, Andrew G. DeMarco, Ziguo Zhang, Jing Yang, Mark C. Hall, David Barford, Leifu Chang
Summary: This study investigates the structure and function of the human augmin complex. The authors utilized cryo-EM, computational methods, and CLMS to elucidate the molecular architecture of augmin. They found that augmin has a highly flexible structure and plays a role in regulating the assembly of the mitotic spindle.
NATURE COMMUNICATIONS
(2022)
Article
Microbiology
Tim Nierhaus, Stephen H. McLaughlin, Frank Burmann, Danguole Kureisaite-Ciziene, Sarah L. Maslen, J. Mark Skehel, Conny W. H. Yu, Stefan M. Freund, Louise F. H. Funke, Jason W. Chin, Jan Lowe
Summary: FtsA and FtsN form double filaments to regulate peptidoglycan synthesis during bacterial cell division; FtsZ forms the Z-ring as a cytoplasmic scaffold; FtsA anchors the Z-ring to the membrane.
NATURE MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Viviane Tran, Sarah Nahle, Amelie Robert, Ines Desanlis, Ryan Killoran, Sophie Ehresmann, Marie-Pier Thibault, David Barford, Kodi S. Ravichandran, Martin Sauvageau, Matthew J. Smith, Marie Kmita, Jean-Francois Cote
Summary: Myoblast fusion is essential for development of multinucleated myofibers. Expression of an open conformation of Elmo2 promotes myoblast fusion and has the potential to improve muscle diseases.
NATURE COMMUNICATIONS
(2022)
Review
Biochemistry & Molecular Biology
Jun Yu, David O. Morgan, Andreas Boland
Summary: Sister chromatid segregation is a crucial step in mitosis, and its regulation involves the activation of separase, a cysteine protease that cleaves the cohesin protein ring. This process is tightly controlled in all eukaryotic cells. This mini-review focuses on the regulation of separase, particularly its inhibition by securin and CDK1-cyclin B, highlighting the different mechanisms by which these inhibitors block separase activity.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2023)
Article
Multidisciplinary Sciences
Tom Dendooven, Ziguo Zhang, Jing Yang, Stephen H. McLaughlin, Johannes Schwab, Sjors H. W. Scheres, Stanislau Yatskevich, David Barford
Summary: The point centromere of budding yeast controls the assembly of large kinetochore complex for chromatid segregation. The kinetochore complex consists of the inner kinetochore (CCAN) and the outer kinetochore KNL1-MIS12-NDC80 (KMN) network. The cryo-electron microscopy structure reveals the assembly of the yeast inner kinetochore onto the centromere-specific CENP-A nucleosomes with unwrapped DNA ends. The CCAN protomers bind the free DNA duplexes and are connected through CBF3. A model is presented for the assembly of the inner kinetochore onto a point centromere and its organization of the outer kinetochore for chromosome attachment to the mitotic spindle.
