Article
Microbiology
Peter B. Bohall, Stephen D. Bell
Summary: The loss of putative repair polymerases PolB2 and/or PolB3 in the crenarchaeon Sulfolobus islandicus leads to a modest growth advantage and insensitivity to hydrogen peroxide. However, cells lacking PolB3 show enhanced sensitivity to the DNA damaging agent 4-NQO, suggesting that these non-essential DNA polymerases may influence DNA repair pathway choice in hyperthermophilic aerobes.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Xu Feng, Baochang Zhang, Zhe Gao, Ruyi Xu, Xiaotong Liu, Sonoko Ishino, Mingxia Feng, Yulong Shen, Yoshizumi Ishino, Qunxin She
Summary: In this work, we discovered that Sulfolobus islandicus Dpo2, a B-family DNA polymerase once predicted to be inactive, is a functional DNA polymerase involved in translesion synthesis. S. islandicus Dpo2 belongs to a large group of B-family DNA polymerases (PolB2) that exists in many archaea and some bacteria, and they carry variations in conserved amino acids in the functional domains responsible for polymerization and proofreading. Contrary to predictions, this prokaryotic B-family DNA polymerase not only replicates undamaged DNA accurately, but also efficiently extends mismatched and DNA lesion-containing substrates. Based on our findings, we propose that this enzyme functions as an extender polymerase, representing the first prokaryotic enzyme of this type. Our data also suggests that this PolB2 enzyme serves as a functional counterpart of the eukaryotic DNA polymerase Pol zeta, which is dedicated to DNA damage repair.
Article
Microbiology
Xu Feng, Baochang Zhang, Zhe Gao, Ruyi Xu, Xiaotong Liu, Sonoko Ishino, Mingxia Feng, Yulong Shen, Yoshizumi Ishino, Qunxin She
Summary: The study reveals that Sulfolobus islandicus Dpo2, previously predicted to be inactive, is actually a functional DNA polymerase involved in translesion synthesis. Dpo2 replicates undamaged DNA with high fidelity and efficiently extends mismatched and DNA lesion-containing substrates, highlighting its importance in DNA damage repair.
Article
Chemistry, Analytical
Jian Zhang, Xiangning Han, Ye Wang, Xiaofeng Mu, Chao Shi, Yong Li, Cuiping Ma
Summary: In this study, a staggered strand exchange amplification (SSEA) method was developed to detect Staphylococcus aureus with high specificity and efficiency at a constant temperature. The sensitivity of SSEA was 20 times that of the traditional method. An all-in-one SSEA platform was established by incorporating magnetic bead-based DNA extraction, which further enhanced the sensitivity of SSEA by two orders of magnitude. The SSEA platform showed high specificity and the ability to detect S. aureus in meat samples within 1 hour without a bacterial enrichment step, making it a promising tool for the food safety industry.
Review
Biotechnology & Applied Microbiology
Aleksandra A. Kuznetsova, Nikita A. Kuznetsov
Summary: DNA-dependent DNA polymerases have been extensively studied and are widely used in biotechnological and diagnostic applications. Understanding their mechanisms and improving their properties are crucial for developing new enzymes for various applications.
BIOENGINEERING-BASEL
(2023)
Article
Microbiology
Felix Grunberger, Robert Reichelt, Ingrid Waege, Verena Ned, Korbinian Bronner, Marcell Kaljanac, Nina Weber, Zubeir El Ahmad, Lena Knauss, M. Gregor Madej, Christine Ziegler, Dina Grohmann, Winfried Hausner
Summary: Although copper is essential for cellular life, higher concentrations can be toxic. The study analyzed the transcriptome response of Pyrococcus furiosus to increased copper levels and highlighted the crucial role of the copper-sensing regulator CopR in detoxification.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Mai Wu, Tan Lin, Kunming Dong, Yong Gong, Xipeng Liu, Likui Zhang
Summary: This study characterizes a family IV uracil DNA glycosylase (Sis-UDGIV) from the hyperthermophilic crenarchaeon Sulfolobus islandicus REY15A and investigates the roles of nine conserved residues in uracil excision and four conserved cysteine residues in maintaining protein conformation and stability. The results provide insights into the biochemical function and DNA-binding specificity of archaeal family IV UDGs.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Multidisciplinary Sciences
Joaquin Ezpeleta, Ignacio Garcia Labari, Gabriela Vanina Villanova, Pilar Bulacio, Sofia Lavista-Llanos, Victoria Posner, Flavia Krsticevic, Silvia Arranz, Elizabeth Tapia
Summary: This study demonstrates the use of NS-watermark barcodes in a proof of concept where amplicons from two different species are tagged and sequenced simultaneously. The NS-watermark barcodes show accuracy comparable to high-accuracy Illumina sequencing and have potential for future large-scale sequencing applications.
SCIENTIFIC REPORTS
(2022)
Article
Chemistry, Analytical
Michihiko Nakano, Masafumi Inaba, Junya Suehiro
Summary: This study introduces a rapid and cost-effective method for amplicon detection, where amplicons are attached to magnetic microbeads, suspended in deionized water, and agglomerated in a circular pattern on a hydrophilic surface under a magnetic field, making them visible to the naked eye.
Article
Biochemistry & Molecular Biology
Sun Ju Lee, Sang-Yong Park, Kwang-Ho Lee, Min-Woo Lee, Chae-Yeon Yu, Jaeyoung Maeng, Hyeong-Dong Kim, Suhng Wook Kim
Summary: We developed a method using Escherichia coli that expresses thermostable Taq DNA polymerase directly in the PCR without purification. EcoliTaq showed activity comparable to that of commercial DNA polymerase and remained stable for 3 months. It proved to be useful as a DNA polymerase in hot-start PCR by effectively minimizing non-specific amplification.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Astronomy & Astrophysics
Lorenzo Carre, Ghislaine Henneke, Etienne Henry, Didier Flament, Eric Girard, Franzetti Bruno
Summary: The presence of stable liquid water oceans beneath the ice crust of moons within the Solar System is of great interest for astrobiology. Subglacial oceans may have hydrothermal processes similar to terrestrial hydrothermal vents, making extremophilic deep life on Earth a possible model for extraterrestrial life. However, the comparison between extraterrestrial abysses and their terrestrial counterparts may be limited due to potential differences in hydrostatic pressure. This study investigates the effects of high hydrostatic pressure on DNA synthesis catalyzed by DNA polymerases.
Article
Microbiology
Xu Feng, Baochang Zhang, Ruyi Xu, Zhe Gao, Xiaotong Liu, Guanhua Yuan, Sonoko Ishino, Mingxia Feng, Yulong Shen, Yoshizumi Ishino, Qunxin She
Summary: ABasic sites are common DNA lesions requiring specialized DNA polymerases for replication. In archaea, the coordinated actions of Dpo2 and Dpo4 are essential for efficient lesion bypass, with Dpo2 bridging the activity gap between Dpo4 and Dpo1 in translesion DNA synthesis.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Hiroka Miyabayashi, Hiroyuki D. Sakai, Norio Kurosawa
Summary: The subunits PBP1 and PBP2 greatly influence the activity of DNA polymerase PolB1, with PBP1 deletion leading to sensitivity to various types of DNA damage and increased mutation rate, while PBP2 is crucial for the replication process.
Article
Multidisciplinary Sciences
Jiaojiao Gong, Guanghui Zhang, Wangguo Wang, Liping Liang, Qianyun Li, Menghao Liu, Liang Xue, Guanghui Tang
Summary: The study proposed a non-genotyping method for detecting 13 types of high-risk HPV in a single reaction by combining isothermal recombinase polymerase amplification (RPA) with CRISPR-Cas12a technology. The result could be achieved in 35 minutes with high sensitivity (500 copies per reaction), representing significant advances for the application of the RPA-Cas12a system and holding great potential to address key challenges in HPV diagnostics.
SCIENTIFIC REPORTS
(2021)
Article
Genetics & Heredity
Mai Wu, Likui Zhang, Kunming Dong, Yong Gong, Xipeng Liu
Summary: Sis-UDGV is a bi-functional enzyme that can excise uracil from DNA and cleave AP sites, suggesting its involvement in AP site repair. It displays high activity and substrate preference at specific temperature and pH ranges. Mutational analyses revealed essential residues for catalytic activity. This is the first report of a bi-functional Family V UDG from Archaea with glycosylase/AP lyase activity.
Article
Multidisciplinary Sciences
Ludovic Sauguet, Pierre Raia, Ghislaine Henneke, Marc Delarue
NATURE COMMUNICATIONS
(2016)
Article
Biochemistry & Molecular Biology
Celine Ralec, Etienne Henry, Melanie Lemor, Tom Killelea, Ghislaine Henneke
NUCLEIC ACIDS RESEARCH
(2017)
Article
Genetics & Heredity
Tiphaine Birien, Axel Thiel, Ghislaine Henneke, Didier Flament, Yann Moalic, Mohamed Jebbar
Article
Biochemical Research Methods
Tom Killelea, Christine Saint-Pierre, Celine Ralec, Didier Gasparutto, Ghislaine Henneke
Article
Biochemistry & Molecular Biology
Jerome Gouge, Celine Ralec, Ghislaine Henneke, Marc Delarue
JOURNAL OF MOLECULAR BIOLOGY
(2012)
Article
Biochemistry & Molecular Biology
Tomas T. Richardson, Louise Gilroy, Yoshizumi Ishino, Bernard A. Connolly, Ghislaine Henneke
NUCLEIC ACIDS RESEARCH
(2013)
Article
Multidisciplinary Sciences
Pierre-Francois Pluchon, Thomas Fouqueau, Christophe Creze, Sebastien Laurent, Julien Briffotaux, Gaelle Hogrel, Adeline Palud, Ghislaine Henneke, Anne Godfroy, Winfried Hausner, Michael Thomm, Jacques Nicolas, Didier Flament
Article
Multidisciplinary Sciences
Giuseppe Cannone, Silvia Visentin, Adeline Palud, Ghislaine Henneke, Laura Spagnolo
SCIENTIFIC REPORTS
(2017)
Article
Microbiology
Melissa Castillo-Lizardo, Ghislaine Henneke, Enrique Viguera
FRONTIERS IN MICROBIOLOGY
(2014)
Article
Biochemistry & Molecular Biology
Melanie Lemor, Ziqing Kong, Etienne Henry, Raphael Brizard, Sebastien Laurent, Audrey Bosse, Ghislaine Henneke
JOURNAL OF MOLECULAR BIOLOGY
(2018)
Article
Biochemistry & Molecular Biology
Pierre Raia, Marta Carroni, Etienne Henry, Gerard Pehau-Arnaudet, Sebastien Brule, Pierre Beguin, Ghislaine Henneke, Erik Lindahl, Marc Delarue, Ludovic Sauguet
Article
Biochemistry & Molecular Biology
Matilde Clarissa Malfatti, Ghislaine Henneke, Sathya Balachander, Kyung Duk Koh, Gary Newnam, Ryo Uehara, Robert J. Crouch, Francesca Storici, Gianluca Tell
JOURNAL OF BIOLOGICAL CHEMISTRY
(2019)
Article
Biology
Tom Killelea, Adeline Palud, Farida Akcha, Melanie Lemor, Stephane L'haridon, Anne Godfroy, Ghislaine Henneke
Article
Multidisciplinary Sciences
ClEment Madru, Ghislaine Henneke, Pierre Raia, Ines Hugonneau-Beaufet, Gerard Pehau-Arnaudet, Patrick England, Erik Lindahl, Marc Delarue, Marta Carroni, Ludovic Sauguet
NATURE COMMUNICATIONS
(2020)