Article
Plant Sciences
Hira Khan, Takashi Ochi
Summary: Non-homologous end joining (NHEJ) is important for repairing DNA double-strand breaks in plants, but the molecular mechanism of plant NHEJ is still unclear. This study discovered a previously unidentified plant ortholog of PAXX, which has a similar structure to human PAXX but functions similar to human XLF by interacting with Ku70/80 and XRCC4. This suggests that plant PAXX combines the roles of mammalian PAXX and XLF, indicating a functional redundancy between PAXX and XLF in plants.
Article
Biochemistry & Molecular Biology
Helene Bordelet, Rafael Costa, Clementine Brocas, Jordane Depagne, Xavier Veaute, Didier Busso, Amandine Batte, Raphael Guerois, Stephane Marcand, Karine Dubrana
Summary: Heterochromatin proteins, particularly the SIR complex, play a crucial role in regulating DNA repair pathways in yeast, with a focus on NHEJ. Sir3 interacts with the Sae2 protein to impair MRX complex functions, ultimately promoting NHEJ by limiting DNA resection and delaying MRX removal from DSB ends.
Article
Multidisciplinary Sciences
Metztli Cisneros-Aguirre, Felicia Wednesday Lopezcolorado, Linda Jillianne Tsai, Ragini Bhargava, Jeremy M. Stark
Summary: DNAPKcs is required for blunt DNA break end joining when XLF is weakened, but its influence is not enhanced with loss of XLF for homologous recombination and radiation resistance.
NATURE COMMUNICATIONS
(2022)
Article
Biology
Changkun Hu, Taylor Bugbee, Rachel Palinski, Ibukun A. Akinyemi, Michael T. McIntosh, Thomas MacCarthy, Sumita Bhaduri-McIntosh, Nicholas Wallace, Wolf-Dietrich Heyer
Summary: The E6 protein of beta-human papillomavirus (HPV8) delays DNA double strand break (DSB) repair and promotes an alternative DSB repair pathway known as alternative end joining (Alt-EJ). HPV8 E6 also inhibits the normal DSB repair mechanism by binding to p300. This study fills the knowledge gap of how DSB is repaired in cells with HPV8 E6 and highlights the mutagenic consequences of HPV8 E6 mediated p300 destabilization. It supports the hypothesis that beta-HPV promotes cancer formation by increasing genomic instability.
Article
Biochemistry & Molecular Biology
Raquel Gago-Fuentes, Valentyn Oksenych
Summary: NHEJ factors XLF, DNA-PKcs, and PAXX play crucial roles in maintaining neural stem and progenitor cell populations and neurodevelopment in mammals, particularly evident in double knockout models.
Article
Genetics & Heredity
Alex Vogt, Yuan He
Summary: DNA double-stranded breaks (DSBs) are difficult to repair and the molecular mechanisms involved are not well understood. Recent advances in cryo-Electron Microscopy have allowed for the visualization of key steps in the nonhomologous end joining (NHEJ) repair pathway, including the sequential assembly of repair factors and end-bridging mediated by protein-protein complexes. This article examines the structural evidence for these models and discusses new discoveries in NHEJ repair mechanisms.
Article
Cell Biology
Marta Llorens-Agost, Michael Ensminger, Hang Phuong Le, Anugrah Gawai, Jie Liu, Andres Cruz-Garcia, Sarita Bhetawal, Richard D. Wood, Wolf-Dietrich Heyer, Markus Loebrich
Summary: BRCA2-deficient cells are vulnerable to inactivation of DNA repair pathways for DSBs, which can be exploited clinically. RAD52 and BRCA2 regulate the TMEJ process by blocking the POL theta function, ensuring proper repair of DSBs in mitosis.
NATURE CELL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Robin Oz, Jing L. Wang, Raphael Guerois, Gaurav Goyal, Sriram Kk, Virginie Ropars, Rajhans Sharma, Firat Koca, Jean-Baptiste Charbonnier, Mauro Modesti, Terence R. Strick, Fredrik Westerlund
Summary: In this study, single-molecule techniques were used to characterize the dynamics of prokaryotic DNA repair by non-homologous end-joining (NHEJ). The findings suggest differences in the mechanisms of bacterial NHEJ compared to human NHEJ, with bacterial Ku playing a significant role in the process. The study also proposes evolutionary similarities between bacterial and eukaryotic NHEJ mechanisms.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Cell Biology
Jenny Kaur Singh, Haico van Attikum
Summary: Zinc-Finger proteins are a highly abundant group of proteins in the human genome, with the ability to bind various substrates beyond just DNA. They play crucial roles in biological processes such as transcription regulation and cell migration, and have emerged as key players in orchestrating the repair of DNA double-strand breaks for genome stability and human disease prevention.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2021)
Review
Oncology
Mohsen Valikhani, Elahe Rahimian, Seyed Esmaeil Ahmadi, Rouzbeh Chegeni, Majid Safa
Summary: Chromosomal translocations are the main cause of hematologic malignancies, resulting from aberrant DNA double-strand break repair. Defective NHEJ, HR, or A-EJ pathways may drive hematopoietic cells towards tumorigenesis. Targeting these repair pathways can potentially sensitize cancer cells, especially resistant clones, to radiation or chemotherapy agents.
EXPERIMENTAL HEMATOLOGY & ONCOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Richard L. Frock, Cheyenne Sadeghi, Jodie Meng, Jing L. Wang
Summary: Humans have evolved multiple DNA double-strand break repair pathways, with NHEJ and A-EJ functioning in different cell cycle phases. While NHEJ is primarily utilized for covalent rejoining of DNA ends, A-EJ can also repair DSBs in the absence of NHEJ.
Article
Immunology
My-Phuc Vo-Ho, Hong-Dao Pham-Thi, Thuy-Vy Nguyen
Summary: Infection with Helicobacter pylori, a risk factor for gastric cancer, can cause genomic instability in infected cells by increasing DNA double-stranded breaks and disrupting DNA repair systems. This study investigates the impact of H. pylori on the efficacy of non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks.
MICROBIAL PATHOGENESIS
(2023)
Article
Multidisciplinary Sciences
Jenny Kaur Singh, Rebecca Smith, Magdalena B. Rother, Anton J. L. de Groot, Wouter W. Wiegant, Kees Vreeken, Ostiane D'Augustin, Robbert Q. Kim, Haibin Qian, Przemek M. Krawczyk, Roman Gonzalez-Prieto, Alfred C. O. Vertegaal, Meindert Lamers, Sebastien Huet, Haico van Attikum
Summary: The study reveals that PARP1-driven chromatin expansion facilitates the recruitment of ZNF384, which subsequently recruits Ku70/Ku80 to promote cNHEJ. This plays a crucial role in repairing DSBs and maintaining genome stability.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Nhung Pham, Zhenxin Yan, Yang Yu, Mosammat Faria Afreen, Anna Malkova, James E. Haber, Grzegorz Ira
Summary: The research demonstrates that mutagenic break-induced replication (BIR) is suppressed at two-ended DNA double-strand breaks (DSBs) by proteins coordinating the usage of two ends of a DSB. Key proteins involved in this suppression include ssDNA annealing proteins Rad52 and Rad59, D-loop unwinding helicase Mph1, and the Mre11-Rad50-Xrs2 complex promoting synchronous resection of DSB ends. Sir2 also plays a role in silencing heterochromatic repair templates to prevent BIR.
Article
Biochemistry & Molecular Biology
Chuxuan Li, Hanwen Zhu, Shikai Jin, Leora M. Maksoud, Nikhil Jain, Ji Sun, Yang Gao
Summary: DNA polymerase theta (Pol theta) plays a crucial role in the microhomology-mediated end joining (MMEJ) pathway for repairing DNA double-strand breaks. This study presents cryo-electron microscope structures of Lates calcarifer Pol theta, revealing its interactions with long and short DNA substrates and its similarity to high-fidelity A-family polymerases. Computational simulations and mutagenesis studies suggest that unique insertion loops of Pol theta stabilize short DNA binding and assemble the active site for MMEJ repair. These findings provide a structural basis for understanding Pol theta-mediated MMEJ.
NUCLEIC ACIDS RESEARCH
(2023)
Editorial Material
Biochemistry & Molecular Biology
Takashi Ochi
Summary: This study presents the crystal structures of coiled-coil bundles from SAS-6 and reveals the asymmetric interaction between two coiled-coil domains, providing new insights into the establishment of centriole polarity.
Article
Biochemistry & Molecular Biology
Herman K. H. Fung, Shelley Grimes, Alexis Huet, Robert L. Duda, Maria Chechik, Joseph Gault, Carol Robinson, Roger W. Hendrix, Paul J. Jardine, James F. Conway, Christoph G. Baumann, Alfred A. Antson
Summary: Many cellular processes rely on substrate rotation or translocation by a multi-subunit, ring-type NTPase. Researchers have reconstituted a cos packaging system and provided a detailed description of its biochemical and structural properties, revealing similarities and differences in its mechanism and regulation.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Multidisciplinary
Di Wu, Carol Robinson
Summary: Oligomerization and glycosylation play important roles in the stability and efficacy of therapeutic glycoproteins, but the interplay between these two attributes is often difficult to define. In this study, a native top-down mass spectrometry approach was used to assess the glycosylation status of therapeutic cytokine and hormone assemblies and to relate interfacial glycan occupancy to complex stability. The study found that interfacial O-glycan stabilizes tumor necrosis factor-alpha trimer, while interferon-beta 1a dimerization is independent of glycosylation. Furthermore, a unique distribution of N-glycans on the follicle-stimulating hormone alpha subunit was discovered, and the interfacial N-glycan was found to interact extensively with the beta subunit to regulate dimer assembly.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Medicinal
Lisbeth R. Kjolbye, Lars Sorensen, Jun Yan, Nils A. Berglund, Jesper Ferkinghoff-Borg, Carol V. Robinson, Birgit Schiott
Summary: This study used molecular dynamics simulations and native mass spectrometry to investigate the interaction between PI(4,5)P-2 lipids and GCGR, revealing differential affinities of the lipids to different conformations of GCGR. Furthermore, the study uncovered the role of a conserved binding site in stabilizing the inactive conformation of GCGR in class B GPCRs.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Biochemistry & Molecular Biology
Noah J. Goff, Manon Breniere, Christopher J. Buehl, Abinadabe J. de Melo, Hana Huskova, Takashi Ochi, Tom L. Blundell, Weifeng Mao, Kefei Yu, Mauro Modesti, Katheryn Meek
Summary: Studies show that inactive Lig4 can promote DNA repair by enhancing the activity of DNA ligase III, with repair products showing both alternative end-joining utilizing micro-homology and joints without micro-homology.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Multidisciplinary
Di Wu, Manman Guo, Carol V. Robinson
Summary: Understanding the impact of genetic variations and post-translational modifications on protein interactions is made possible by using native mass spectrometry (MS). In this study, we characterized the proteoforms of plasma serine protease inhibitors and found that different fucosylation linkages have opposing effects on protein interactions.
Article
Chemistry, Multidisciplinary
Tarick J. El-Baba, Corinne A. Lutomski, Sean A. Burnap, Jani R. Bolla, Lindsay A. Baker, Andrew J. Baldwin, Weston B. Struwe, Carol V. Robinson
Summary: In this study, the impact of glycans on mediating ACE2 dimerization and interactions with Spike was investigated. The researchers found that glycans play a regulatory role in ACE2 dimerization and that positive cooperativity drives ACE2 to complex with multiple Spike trimers. These findings are important for developing strategies to neutralize the virus.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Correction
Biochemistry & Molecular Biology
Rei Matsuoka, Roman Fudim, Sukkyeong Jung, Chenou Zhang, Andre Bazzone, Yurie Chatzikyriakidou, Carol V. Robinson, Norimichi Nomura, So Iwata, Michael Landreh, Laura Orellana, Oliver Beckstein, David Drew
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Review
Pharmacology & Pharmacy
Hsin-Yung Yen, Ali Jazayeri, Carol Robinson
Summary: GPCRs are important drug targets due to their involvement in physiological processes. Mass spectrometry techniques, such as HDX-MS and native-MS, provide opportunities to investigate GPCR pharmacology and discover new drugs. This review highlights the potential of MS techniques for in-depth investigations of GPCR biology.
PHARMACOLOGICAL REVIEWS
(2023)
Article
Plant Sciences
Hira Khan, Takashi Ochi
Summary: Non-homologous end joining (NHEJ) is important for repairing DNA double-strand breaks in plants, but the molecular mechanism of plant NHEJ is still unclear. This study discovered a previously unidentified plant ortholog of PAXX, which has a similar structure to human PAXX but functions similar to human XLF by interacting with Ku70/80 and XRCC4. This suggests that plant PAXX combines the roles of mammalian PAXX and XLF, indicating a functional redundancy between PAXX and XLF in plants.
Article
Multidisciplinary Sciences
Benjamin J. Hardy, Alvaro Martin Hermosilla, Dinesh K. Chinthapalli, Carol V. Robinson, J. L. Ross Anderson, Paul Curnow
Summary: In this study, a minimal diheme membrane cytochrome was computationally designed and produced in live bacteria. The synthetic construct mimics a four-helix bundle found in respiratory complexes and has no sequence homology to natural polypeptides. This artificial membrane metalloprotein has the potential to function as an electron transfer module in both synthetic protocells and living systems.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Gabriela Dias Noske, Yun Song, Rafaela Sachetto Fernandes, Rod Chalk, Haitem Elmassoudi, Lizbe Koekemoer, C. David J. Owen, Tarick V. El-Baba, Carol Robinson, Glaucius Oliva, Andre Schutzer Godoy
Summary: The main protease of SARS-CoV-2, M-pro, is responsible for cleaving the viral polyprotein and is crucial for enzyme dimerization and activity. N-terminal cleavage is not critical for dimerization, and different types of inhibitors can affect the oligomeric states. This study provides insights into the maturation process of M-pro and how it can be targeted by inhibitors.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Kenneth R. R. Durbin, Matthew T. T. Robey, Lilien N. N. Voong, Ryan T. T. Fellers, Corinne A. A. Lutomski, Tarick J. J. El-Baba, Carol V. V. Robinson, Neil L. L. Kelleher
Summary: Native mass spectrometry has become an important technique for determining the composition of protein complexes. However, there is a lack of software tools for comprehensive analysis of native mass spectrometry data. In this study, we introduce ProSight Native as an informatics platform that can determine the complete composition of protein complexes. We demonstrated its features by successfully determining the composition of a homotetrameric membrane complex and a heterodimer complex with associated ligands.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Multidisciplinary Sciences
Hongmiao Hu, Anne-Marie M. van Roon, George E. Ghanim, Bilal Ahsan, Abraham O. Oluwole, Sew-Yeu Peak-Chew, Carol V. Robinson, Thi Hoang Duong Nguyen
Summary: Shelterin and nucleosomes interact at mammalian telomeres, but the mechanism is not yet understood. Cryo-electron microscopy was used to study the structure of a human telomeric nucleosome bound to the shelterin factor TRF1. The study revealed that TRF1 binds to unwrapped nucleosomal DNA ends by engaging both the DNA and the histone octamer, resulting in a shift in the nucleosomal DNA. Phosphorylation of TRF1 and a noncanonical DNA binding surface on TRF1 were found to be crucial for its association with telomeric nucleosomes. These findings provide important insights into shelterin-chromatin interactions and its roles at telomeres.
Article
Multidisciplinary Sciences
Luke Smithers, Oksana Degtjarik, Dietmar Weichert, Chia-Ying Huang, Coilin Boland, Katherine Bowen, Abraham Oluwole, Corinne Lutomski, Carol V. Robinson, Eoin M. Scanlan, Meitian Wang, Vincent Olieric, Moran Shalev-Benami, Martin Caffrey
Summary: This study investigates the structural changes of the enzyme apolipoprotein N-acyltransferase (Lnt) during its reaction. The study confirms the ping-pong mechanism of Lnt and explains the molecular basis for its ability to bind different substrates.