Article
Biology
Annika Breidenstein, Josy ter Beek, Ronnie P-A Berntsson
Summary: Type 4 secretion systems are protein machineries that aid in the transfer of antibiotic resistance and other virulence factors. The relaxase TraI from the pKM101 plasmid was studied and its crystal structure revealed its DNA-binding mechanism. The study also showed the conformational change of the thumb subdomain upon DNA binding. The behavior of the TraI relaxase from pKM101 was found to be similar to its homologs from R388 and F plasmids.
LIFE SCIENCE ALLIANCE
(2023)
Article
Biochemistry & Molecular Biology
Dalibor Kosek, Ivana Grabundzija, Haotian Lei, Ilija Bilic, Huaibin Wang, Yukun Jin, Graham F. Peaslee, Alison B. Hickman, Fred Dyda
Summary: Helitrons are widespread eukaryotic DNA transposons that contribute to genome variability and evolution through replicative rolling-circle mechanism. The cryo-electron microscopy structure of a Helitron transposase reveals its multidomain architecture and function, and shows unexpected architectural similarity to Tral, a bacterial relaxase. The HUH active site of Helitron transposase suggests a mechanism for strand cleavage and ligation reactions.
Article
Biology
Barbara Stekas, Steve Yeo, Alice Troitskaia, Masayoshi Honda, Sei Sho, Maria Spies, Yann R. Chemla
Summary: Helicases use NTP hydrolysis to move along and unwind single-stranded nucleic acids in cells, often working in conjunction with other nucleic acid-associated proteins. By studying the interaction between XPD helicase and RPA2, it has been discovered that helicases can switch between different processive states, with transient RPA2 interactions stabilizing the more processive state. This finding sheds light on how accessory proteins regulate helicase activity.
Article
Multidisciplinary Sciences
Jiawei Ding, Xiangting Li, Jiangchuan Shen, Yiling Zhao, Shuchen Zhong, Luhua Lai, Hengyao Niu, Zhi Qi
Summary: The authors investigated the behavior of the RPA protein in DNA replication and repair using single molecule DNA Curtains and Markov chain modeling. They discovered that the interaction between RPA and Rad52 regulates the accessibility of ssDNA, facilitating the loading of Rad51 recombinase. This study provides insights into the bimolecular dynamics of RPA on ssDNA and its crucial role in DNA metabolic pathways.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Julia A. M. Bakx, Andreas S. Biebricher, Graeme A. King, Panagiotis Christodoulis, Kata Sarlos, Anna H. Bizard, Ian D. Hickson, Gijs J. L. Wuite, Erwin J. G. Peterman
Summary: Topoisomerase IIIa is a type 1A topoisomerase that forms a complex with RMI1 and RMI2 called TRR in human cells. In this study, the authors used optical tweezers and fluorescence microscopy to investigate the catalytic steps of TRR. They found that TRR forms an open gate in single-stranded DNA and can bind a second single-stranded or double-stranded DNA molecule, leading to catenation. Interestingly, double-stranded DNA binding increases the gate size and the helicase BLM affects the flexibility of the gate. These findings suggest that TRR-mediated transfer of double-stranded DNA may be more important than previously believed.
NATURE COMMUNICATIONS
(2022)
Review
Biochemistry & Molecular Biology
Jun-Tao Guo, Fareeha Malik
Summary: Single-stranded DNA binding proteins (SSBs) play critical roles in maintaining genome stability and transcriptional regulation, and machine learning-based approaches have been developed for predicting SSBs from double-stranded DNA binding proteins (DSBs).
Article
Multidisciplinary Sciences
Agathe Couturier, Chloe Virolle, Kelly Goldlust, Annick Berne-Dedieu, Audrey Reuter, Sophie Nolivos, Yoshiharu Yamaichi, Sarah Bigot, Christian Lesterlin
Summary: Conjugation is a contact-dependent mechanism for the transfer of plasmid DNA between bacterial cells. Live-cell microscopy was used to visualize the intracellular dynamics of conjugation, revealing a molecular strategy for the sequential production of factors involved in establishing, maintaining, and disseminating the plasmid.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Sahiti Kuppa, Jaigeeth Deveryshetty, Rahul Chadda, Jenna R. Mattice, Nilisha Pokhrel, Vikas Kaushik, Angela Patterson, Nalini Dhingra, Sushil Pangeni, Marisa K. Sadauskas, Sajad Shiekh, Hamza Balci, Taekjip Ha, Xiaolan Zhao, Brian Bothner, Edwin Antony
Summary: The chaperone-like protein Rtt105 plays a crucial role in regulating DNA metabolism by preventing untimely protein interactions with RPA and stabilizing RPA-ssDNA filaments at DNA lesion sites.
NATURE COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Ana R. Cardoso, Monica Lopes-Marques, Manuela Oliveira, Antonio Amorim, Maria J. Prata, Luisa Azevedo
Summary: The study found that the highest degree of conservation in CHD proteins is observed in Group II (CHD3, CHD4, and CHD5), with pathological variations often occurring in conserved amino acid residues. The parallel analysis of both orthologous and paralogous proteins revealed patterns of flexibility and interchangeability between amino acid positions. This added complexity should be taken into consideration when evaluating the impact of novel mutations in terms of evolutionary conservation.
Article
Chemistry, Physical
Xun Gong, Nicholas Renegar, Retsef Levi, Michael S. Strano
Summary: Nanoparticle corona phase design allows for molecular recognition for sensing applications. In this study, the largest DNA-SWCNT PL response library was generated and machine learning techniques were utilized to understand the dependence of molecular recognition and DNA sequence.
NPJ COMPUTATIONAL MATERIALS
(2022)
Article
Biochemical Research Methods
Jian Zhang, Sina Ghadermarzi, Akila Katuwawala, Lukasz Kurgan
Summary: Efforts to elucidate protein-DNA interactions at the molecular level rely on accurate predictions of DNA-binding residues in protein sequences. DNAgenie, a new predictor utilizing a custom-designed machine learning architecture, outperforms current methods in predicting residue-level interactions with A-DNA, B-DNA, and single-stranded DNA, reducing cross-predictions and generating promising leads for potential DNA-binding proteins.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Kelsey S. Whinn, Zhi-Qiang Xu, Slobodan Jergic, Nischal Sharma, Lisanne M. Spenkelink, Nicholas E. Dixon, Antoine M. van Oijen, Harshad Ghodke
Summary: The accessory helicase Rep in Escherichia coli removes DNA-binding proteins that act as roadblocks to the replication fork, ensuring the smooth progress of genome duplication.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Ananya Acharya, Kristina Kasaciunaite, Martin Goese, Vera Kissling, Raphael Guerois, Ralf Seidel, Petr Cejka
Summary: The study shows that RPA collaborates with Dna2 in DNA double-strand break repair. While RPA is known to recruit Dna2 to single-stranded DNA, it was found that the RPA subunit Rfa1 can also enhance Dna2 nuclease activity. Additionally, different domains of Rfa1 regulate Dna2 recruitment and its nuclease and helicase activities.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Andrea Huskova, Dhurvas Chandrasekaran Dinesh, Pavel Srb, Evzen Boura, Vaclav Veverka, Jan Silhan
Summary: Covalent DNA interstrand crosslinks are toxic DNA damage lesions that block replication and cause genomic instability. NEIL3, a DNA glycosylase, plays a key role in repairing these lesions. By studying the structure of NEIL3 and its interaction with DNA, we have revealed the mechanism underlying its repair process.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Plant Sciences
Sayuri Ando, Mika Nomoto, Hidekazu Iwakawa, Simon Vial-Pradel, Lilan Luo, Michiko Sasabe, Iwai Ohbayashi, Kotaro T. Yamamoto, Yasuomi Tada, Munetaka Sugiyama, Yasunori Machida, Shoko Kojima, Chiyoko Machida
Summary: Arabidopsis ASYMMETRIC LEAVES2 (AS2) is crucial for the formation of flat symmetric leaves. AS2 represses the expression of ETTIN/AUXIN RESPONSE FACTOR3 (ETT/ARF3) gene. The formation of AS2 bodies is tightly linked to the morphology and functions of the nucleolus.
Article
Genetics & Heredity
Kip E. Guja, Joel F. Schildbach
Article
Genetics & Heredity
Katherine E. L. Cox, Joel F. Schildbach
Article
Biochemistry & Molecular Biology
Andrew R. Buller, Michael F. Freeman, Joel F. Schildbach, Craig A. Townsend
Article
Biophysics
Casey W. Hemmis, Nathan T. Wright, Ananya Majumdar, Joel F. Schildbach
BIOMOLECULAR NMR ASSIGNMENTS
(2014)
Article
Microbiology
Casey W. Hemmis, Mehmet Berkmen, Markus Eser, Joel F. Schildbach
JOURNAL OF BACTERIOLOGY
(2011)
Article
Biochemistry & Molecular Biology
Andrew R. Buller, Jason W. Labonte, Michael F. Freeman, Nathan T. Wright, Joel F. Schildbach, Craig A. Townsend
JOURNAL OF MOLECULAR BIOLOGY
(2012)
Article
Biochemistry & Molecular Biology
Nicholas J. Clark, Madushi Raththagala, Nathan T. Wright, Elizabeth A. Buenger, Joel F. Schildbach, Susan Krueger, Joseph E. Curtis
JOURNAL OF MOLECULAR MODELING
(2014)
Article
Biochemistry & Molecular Biology
Lubomir Dostal, Sichen Shao, Joel F. Schildbach
NUCLEIC ACIDS RESEARCH
(2011)
Article
Biochemistry & Molecular Biology
Fabian Lorenzo-Diaz, Lubomir Dostal, Miquel Coll, Joel F. Schildbach, Margarita Menendez, Manuel Espinosa
NUCLEIC ACIDS RESEARCH
(2011)
Review
Biology
Ellen L. Zechner, Silvia Lang, Joel F. Schildbach
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2012)
Review
Genetics & Heredity
Casey W. Hemmis, Joel F. Schildbach
Article
Multidisciplinary Sciences
Steven G. Cresawn, Welkin H. Pope, Deborah Jacobs-Sera, Charles A. Bowman, Daniel A. Russell, Rebekah M. Dedrick, Tamarah Adair, Kirk R. Anders, Sarah Ball, David Bollivar, Caroline Breitenberger, Sandra H. Burnett, Kristen Butela, Deanna Byrnes, Sarah Carzo, Kathleen A. Cornely, Trevor Cross, Richard L. Daniels, David Dunbar, Ann M. Findley, Chris R. Gissendanner, Urszula P. Golebiewska, Grant A. Hartzog, J. Robert Hatherill, Lee E. Hughes, Chernoh S. Jalloh, Carla De Los Santos, Kevin Ekanem, Sphindile L. Khambule, Rodney A. King, Christina King-Smith, Karen Klyczek, Greg P. Krukonis, Christian Laing, Jonathan S. Lapin, A. Javier Lopez, Sipho M. Mkhwanazi, Sally D. Molloy, Deborah Moran, Vanisha Munsamy, Eddie Pacey, Ruth Plymale, Marianne Poxleitner, Nathan Reyna, Joel F. Schildbach, Joseph Stukey, Sarah E. Taylor, Vassie C. Ware, Amanda L. Wellmann, Daniel Westholm, Donna Wodarski, Michelle Zajko, Thabiso S. Zikalala, Roger W. Hendrix, Graham F. Hatfull
Article
Multidisciplinary Sciences
Andrew R. Buller, Michael F. Freeman, Nathan T. Wright, Joel F. Schildbach, Craig A. Townsend
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2012)
Article
Biochemistry & Molecular Biology
Nathan T. Wright, Madushi Raththagala, Casey W. Hemmis, Sheldon Edwards, Joseph E. Curtis, Susan Krueger, Joel F. Schildbach
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2012)
Article
Biochemistry & Molecular Biology
Christian J. Gruber, Silvia Lang, Vinod K. H. Rajendra, Monika Nuk, Sandra Raffl, Joel F. Schildbach, Ellen L. Zechner
FRONTIERS IN MOLECULAR BIOSCIENCES
(2016)