Article
Biology
Deepak Bhat, Samuel Hauf, Charles Plessy, Yohei Yokobayashi, Simone Pigolotti, Armita Nourmohammad
Summary: In this study, a new method was proposed to infer the dynamics of Replisomes from DNA abundance distribution. The method was applied to measure the DNA abundance distribution in Escherichia coli populations growing at different temperatures. The results showed that the speed of Replisomes increases with temperature and exhibits wave-like variations along the genome, which correlates with the variation of mutation rate. This study provides insights into the replication dynamics of bacteria.
Article
Multidisciplinary Sciences
Karel Naiman, Eduard Campillo-Funollet, Adam T. Watson, Alice Budden, Izumi Miyabe, Antony M. Carr
Summary: Replication forks restarted by homologous recombination utilize Pol delta to synthesize both strands without maturing to a delta/epsilon configuration, while the template for the lagging strand remains as a gap filled in by Pol delta later. These restarted forks are able to progress through barriers that arrest canonical forks, demonstrating stability of the 3' single strand during increased resection.
NATURE COMMUNICATIONS
(2021)
Article
Hematology
Yusuke Okamoto, Masako Abe, Anfeng Mu, Yasuko Tempaku, Colette B. Rogers, Ayako L. Mochizuki, Yoko Katsuki, Masato T. Kanemaki, Akifumi Takaori-Kondo, Alexandra Sobeck, Anja-Katrin Bielinsky, Minoru Takata
Summary: Fanconi anemia (FA) is a hereditary disorder caused by mutations in any 1 of 22 FA genes. Recent studies have shown that the DNA/RNA helicase SLFN11 plays a role in cell death sensitivity to chemotherapeutic treatments in cancer cells. The depletion of SLFN11 has been shown to improve cell survival in FA patient-derived cells, suggesting a potential link between SLFN11 and FA pathophysiology.
Article
Multidisciplinary Sciences
Ann-Marie K. Shorrocks, Samuel E. Jones, Kaima Tsukada, Carl A. Morrow, Zoulikha Belblidia, Johanna Shen, Iolanda Vendrell, Roman Fischer, Benedikt M. Kessler, Andrew N. Blackford
Summary: The study reveals that the BTR complex contains multiple conserved motifs that interact cooperatively with the single-stranded DNA-binding protein RPA, facilitating BLM recruitment to stalled replication forks for promoting their restart after replication stress.
NATURE COMMUNICATIONS
(2021)
Article
Biotechnology & Applied Microbiology
Michael A. Boemo
Summary: This paper introduces a new software, DNAscent v2, for high-throughput, single-molecule detection of DNA replication dynamics with fast and accurate detection of the thymidine analogue BrdU. The software excels in accuracy, speed, and versatility across different experimental protocols.
Article
Biochemistry & Molecular Biology
Liu He, Rebecca Lever, Andrew Cubbon, Muhammad Tehseen, Tabitha Jenkins, Alice O. Nottingham, Anya Horton, Hannah Betts, Martin Fisher, Samir M. Hamdan, Panos Soultanas, Edward L. Bolt
Summary: DNA strand breaks are repaired by DNA synthesis using a homologous DNA template. The DNA polymerase delta (Pol delta) catalyzes this DNA synthesis but can cause genome instability. However, the human protein HelQ inhibits DNA synthesis by Pol delta and promotes DNA strand annealing during repair. This mechanism involves the interaction between Pol delta and its POLD3 subunit with the intrinsically disordered region of HelQ.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Kazutoshi Kasho, Gorazd Stojkovic, Cristina Velazquez-Ruiz, Maria Isabel Martinez-Jimenez, Mara Doimo, Timothee Laurent, Andreas Berner, Aldo E. Perez-Rivera, Louise Jenninger, Luis Blanco, Sjoerd Wanrooij
Summary: PrimPol interacts with PolDIP2 to enhance its processivity, increasing primer-template and dNTP binding affinities, and thereby enhancing nucleotide incorporation efficiency. This mechanism, involving a unique arginine cluster in PolDIP2, may be critical for PrimPol's function in tolerating DNA lesions at physiological nucleotide concentrations.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Alexander T. Duckworth, Tricia A. Windgassen, James L. Keck
Summary: Bacteria use DNA replication restart mechanisms to reload replisomes onto abandoned replication forks when encountering barriers, to prevent incomplete DNA replication and lethality. The Escherichia coli PriA DNA helicase plays a crucial role in this process by recognizing and remodeling replication forks, with a conserved sequence motif potentially serving as an autoregulatory element. Multiple PriA molecules may work in tandem to enhance DNA unwinding processivity, showing unexpected similarities with other DNA helicases.
Article
Biochemistry & Molecular Biology
Grazia Pellicano, Mohammed Al Mamun, Dolores Jurado-Santiago, Sara Villa-Hernandez, Xingyu Yin, Michele Giannattasio, Michael C. Lanz, Marcus B. Smolka, Joseph Yeeles, Katsuhiko Shirahige, Miguel Garcia-Diaz, Rodrigo Bermejo
Summary: DNA polymerase e (Pole) plays a key role in nascent strand resection, which can be prevented and stalled replication forks stabilized through checkpoint kinase regulation.
Article
Biochemistry & Molecular Biology
Kang Liu, Joshua D. Graves, Fang-Tsyr Lin, Weei-Chin Lin
Summary: TopBP1 regulates the activation of ATR/Chk1 in a biphasic, concentration-dependent manner, with excessive accumulation hindering the checkpoint response and leading to genomic instability. Moderate depletion of TopBP1 enhances checkpoint response after replicative stress in cancer cells, suggesting TopBP1 overexpression as a new mechanism contributing to genomic instability during tumorigenesis.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Cell Biology
Andrew Dolson, Safia Mahabub Sauty, Kholoud Shaban, Krassimir Yankulov
Summary: Dbf4-Dependent Kinase (DDK) plays an essential role in DNA replication and repair, although some of its activities are not essential for viability. Recent studies have shown that DDK also plays a key role in regulating genome-wide origin firing and replication-coupled chromatin assembly.
Article
Multidisciplinary Sciences
Isabel E. Wassing, Emily Graham, Xanita Saayman, Lucia Rampazzo, Christine Ralf, Andrew Bassett, Fumiko Esashi
Summary: The study reveals a previously unknown function of RAD51 in promoting genomic stability during mitosis by protecting under-replicated DNA, promoting mitotic DNA synthesis (MiDAS), and successful chromosome segregation.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Swagata Halder, Aurore Sanchez, Lepakshi Ranjha, Giordano Reginato, Ilaria Ceppi, Ananya Acharya, Roopesh Anand, Petr Cejka
Summary: RAD51 and BRCA2 play critical roles in DNA repair and protection. RAD51 binds to single-stranded DNA for its recombination function, but binding to double-stranded DNA is inhibitory. Surprisingly, we found that the protective function of RAD51 actually depends on its binding to double-stranded DNA. The BRC4 repeat of BRCA2 disrupts RAD51 binding to double-stranded DNA and impairs its protective function. However, the C-terminal RAD51-binding segment (TR2) of BRCA2 overcomes the inhibitory effect of BRC4 and stabilizes RAD51 binding to double-stranded DNA, promoting DNA protection.
Article
Biology
Thomas J. Etheridge, Desiree Villahermosa, Eduard Campillo-Funollet, Alex David Herbert, Anja Irmisch, Adam T. Watson, Hung Q. Dang, Mark A. Osborne, Antony W. Oliver, Antony M. Carr, Johanne M. Murray
Summary: The Smc5/6 complex is associated with chromatin in unchallenged cells through the non-SMC protein Nse6, involving at least two Nse6-dependent sub-pathways. Mutations in core subunits of the Smc5/6 complex affect chromatin association, with disruption of single-stranded DNA binding activity leading to elevated levels of chromosomal rearrangements during replication restart.
Article
Infectious Diseases
Christopher Campion, Godefroid Charbon, Thomas T. Thomsen, Peter E. Nielsen, Anders Lobner-Olesen
Summary: The study showed that NrdA-PNA specifically inhibited the growth of E. coli and NrdA protein translation, as well as reducing DNA synthesis rate, leading to incomplete chromosomal replication, double-stranded DNA breaks, and cell death. The results suggest that targeting the NrdAB RNR subunits with antisense PNAs could be a promising approach for developing microbial agents, while also providing insights into bacterial responses to RNR-targeting antimicrobials.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2021)
Review
Microbiology
Peixuan Guo, Hiroyuki Noji, Christopher M. Yengo, Zhengyi Zhao, Ian Grainge
MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS
(2016)
Article
Multidisciplinary Sciences
Andrew N. Keller, Yue Xin, Stephanie Boer, Jonathan Reinhardt, Rachel Baker, Lidia K. Arciszewska, Peter J. Lewis, David J. Sherratt, Jan Lowe, Ian Grainge
SCIENTIFIC REPORTS
(2016)
Article
Biochemistry & Molecular Biology
Georgia M. Weaver, Karla A. Mettrick, Tayla-Ann Corocher, Adam Graham, Ian Grainge
MOLECULAR MICROBIOLOGY
(2019)
Article
Microbiology
Emanuele Conte, Linda Mende, Ian Grainge, Sean D. Colloms
FRONTIERS IN MICROBIOLOGY
(2019)
Review
Biochemistry & Molecular Biology
Phillip Balalovski, Ian Grainge
MOLECULAR MICROBIOLOGY
(2020)
Article
Environmental Sciences
Shiv Bolan, Balaji Seshadri, Ian Grainge, Nicholas J. Talley, Ravi Naidu
Summary: This study investigated the impact of gut microbes on the bioaccessibility of lead in soil, finding that gut microbes can decrease the bioaccessibility of lead, particularly at low pH values. Additionally, the study revealed that lead adsorption by gut microbes increased at higher pH levels, with Escherichia coli adsorbing more lead than Lactobacillus species.
Article
Engineering, Environmental
Geetika Bhagwat, Qiyun Zhu, Wayne O'Connor, Suresh Subashchandrabose, Ian Grainge, Rob Knight, Thava Palanisami
Summary: This study investigates the interaction between different types of plastics and marine biofilm-forming microorganisms using whole-genome sequencing, revealing unique microbial profiles on microplastic surfaces that may pose potential risks to the marine food chain and aquaculture industries. Additionally, the plastic-microbiome is involved in diverse processes such as xenobiotic compound degradation and carbon cycling.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2021)
Article
Engineering, Environmental
Geetika Bhagwat, Maddison Carbery, Thi Kim Anh Tran, Ian Grainge, Wayne O'Connor, Thava Palanisami
Summary: This study investigated the contaminant profiles and bacterial communities in plastic-associated inorganic and organic matter from 10 year-aged plastic. It revealed high concentrations of metal(loid)s, PAHs, and PFAS in the PIOM present on long-term aged high-density polyethylene plastic. Metagenomic analysis showed different bacterial compositions in the PIOM based on habitat type, potentially including pathogenic taxa.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2021)
Article
Engineering, Environmental
Geetika Bhagwat, Thi Kim Anh Tran, Dane Lamb, Kala Senathirajah, Ian Grainge, Wayne O'Connor, Albert Juhasz, Thava Palanisami
Summary: This study compared the adsorption capacity of naturally aged, biofilm-covered microplastic fibers (BMFs) for perfluorooctane sulfonate (PFOS) and lead (Pb) at environmentally relevant concentrations. Results showed that aged MFs exhibited higher surface areas due to biomass accumulation and had higher concentrations of adsorbed Pb and PFOS, with variations among polymer types. The increased contaminant adsorption was linked with altered surface area and hydrophobic/hydrophilic characteristics of the samples.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2021)
Article
Multidisciplinary Sciences
Shiv Bolan, Balaji Seshadri, Simon Keely, Anitha Kunhikrishnan, Jessica Bruce, Ian Grainge, Nicholas J. Talley, Ravi Naidu
Summary: In this study, it was found that the intestinal permeability of metal(loid)s was significantly reduced in the presence of gut microbes or chelating agents. Chelating agents reduce ML absorption by forming complexes, while gut bacteria may protect the intestinal barrier or sequester MLs indirectly. Both gut microbes and chelating agents can be used to decrease the intestinal permeability of MLs, thereby mitigating their toxicity.
SCIENTIFIC REPORTS
(2021)
Article
Microbiology
Geetika Bhagwat, Wayne O'Connor, Ian Grainge, Thava Palanisami
Summary: The study found that marine conditioning of PET and PLA samples for 24 hours resulted in an increase of approximately 11% and 31% in average surface roughness, with coccoid-shaped bacterial cells attaching to the surfaces and accumulation of salt precipitates revealed through EDS analysis. The increase in surface roughness due to conditioning is linked to a material's hydrophilicity, leading to easier attachment of bacteria on the surfaces. Further research on CFs could provide important insights into the interaction between plastics and microbes with implications for medical, industrial, and environmental research.
FRONTIERS IN MICROBIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Helena Chan, Ahmed M. T. Mohamed, Ian Grainge, Christopher D. A. Rodrigues
Summary: The article summarizes and discusses the important roles of SpoIIIE and FtsK in bacterial cytokinesis, particularly their coordination with chromosome segregation.
TRENDS IN MICROBIOLOGY
(2022)
Article
Microbiology
Belinda Loh, Xiaoqing Wang, Xiaoting Hua, Junhan Luo, Tanye Wen, Liwei Zhang, Long Ma, Prasanth Manohar, Ramesh Nachimuthu, Ian Grainge, Yunsong Yu, Sebastian Leptihn
Summary: Pseudomonas aeruginosa is a major public health concern due to drug-resistant strains increasing mortality in hospital-acquired infections. The isolation and complete genome sequences of four lytic bacteriophages that target clinical multidrug-resistant P. aeruginosa strains are reported.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2021)
Article
Environmental Sciences
Shiv Bolan, Balaji Seshadri, Anitha Kunhikrishnan, Ian Grainge, Nicholas J. Talley, Nanthi Bolan, Ravi Naidu
Summary: Specific gut microbes play a crucial role in maintaining gut health and resisting toxic elements, and the toxicity of these elements towards microbes is determined by their speciation and bioavailability.
