Article
Multidisciplinary Sciences
Anna Knoppel, Oscar Brostrom, Konrad Gras, Johan Elf, David Fange
Summary: Escherichia coli coordinates replication and division cycles by initiating replication at a narrow range of cell sizes. The conversion of DnaA between its active ATP-bound state and inactive ADP-bound state is more important for initiation size control than the total free concentration of DnaA. Disruption of the regulatory inactivation of DnaA mechanism has a radical impact on replication initiation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Mareike Berger, Pieter Rein ten Wolde
Summary: The study investigates the replication initiation cycles of Escherichia coli at different growth rates and reveals that both the titration mechanism and the activation switch play crucial roles in driving stable replication cycles.
NATURE COMMUNICATIONS
(2022)
Review
Biochemistry & Molecular Biology
Kazutoshi Kasho, Shogo Ozaki, Tsutomu Katayama
Summary: This review summarizes the mechanisms of timely binding and dissociation of nucleoid proteins IHF and Fis in chromosomal DNA replication initiation in Escherichia coli. The timely stabilization of IHF binding at oriC and the timely regulation of DnaA activity via DARS2 and datA are crucial for the timing control of replication initiation. IHF and Fis play specific roles in the regulation of replication initiation and proposed mechanisms for the regulation of timely IHF binding and dissociation at DARS2 and datA are discussed in this review.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Pawel Jaworski, Dorota Zyla-Uklejewicz, Malgorzata Nowaczyk-Cieszewska, Rafal Donczew, Thorsten Mielke, Christoph Weigel, Anna Zawilak-Pawlik
Summary: This study reveals the structure of Helicobacter pylori oriC, with the DnaA trio being crucial for DNA unwinding and an observed interplay between DNA unwinding and DnaA binding during replication. This research also identifies a new class of ATP-DnaA boxes in oriC, suggesting a potential new regulatory pathway for orisome assembly in H. pylori.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Godefroid Charbon, Belen Mendoza-Chamizo, Christopher Campion, Xiaobo Li, Peter Ruhdal Jensen, Jakob Frimodt-Moller, Anders Lobner-Olesen
Summary: Research has shown that in E. coli cells depleted of ATP, the initiator protein DnaA is degraded, leading to a block in chromosome replication initiation.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Charles Winterhalter, Daniel Stevens, Stepan Fenyk, Simone Pelliciari, Elie Marchand, Panos Soultanas, Aravindan Ilangovan, Heath Murray
Summary: This study reports both positive and negative mechanisms for directing helicase recruitment in the model organism Bacillus subtilis. By characterizing the initiation protein DnaD, distinct protein interfaces required for helicase loading were identified. The role of the repressor protein SirA in inhibiting helicase recruitment was also discovered, advancing our understanding of DNA replication initiation in B. subtilis.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Microbiology
Digvijay Patil, Dan Xun, Markus Schueritz, Shivani Bansal, Amrita Cheema, Elliott Crooke, Rahul Saxena
Summary: The study found that in Escherichia coli, regulation of Lpp protein expression levels and mutations in DnaA and fis genes can affect cell growth, indicating a close link between the physiological state of the cell membrane and growth.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Jin Young Kang, Tatiana V. Mishanina, Yu Bao, James Chen, Eliza Llewellyn, James Liu, Seth A. Darst, Robert Landick
Summary: Transcriptional pausing is an important mechanism for regulating cellular RNA synthesis. The interactions between DNA, RNA, and RNA polymerase can cause reversible conformational changes, leading to the formation of ePECs. The existence of multiple ePEC conformations has broad implications for transcriptional regulation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Ryusei Yoshida, Shogo Ozaki, Hironori Kawakami, Tsutomu Katayama
Summary: This study describes the unwinding mechanisms of the DUE in the replication origin oriC of Escherichia coli, which are promoted by DnaA, IHF, and the structural homolog HU. IHF and HU promote DUE unwinding by promoting the binding of R1/R5M-bound DnaAs to ssDUE. Notably, HU binds the R1-R5M interspace stimulated by ATP-DnaA and ssDUE, suggesting a model of DUE unwinding triggered by DnaA interactions and stabilized by HU binding.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Ganesh K. Maurya, Reema Chaudhary, Neha Pandey, Hari S. Misra
Summary: Deinococcus radiodurans harbors a multipartite ploid genome system with two chromosomes and two plasmids, but how these elements are maintained and inherited is not well understood. The pleiotropic protein PprA has been shown to regulate the ploidy of the chromosomes and inhibit the activity of the initiator protein drDnaA, which suggests that PprA plays a role as a checkpoint regulator for DNA replication initiation in D. radiodurans.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Genetics & Heredity
Weiwei Zhu, Lingjun Xi, Jiaxin Qiao, Dongdong Du, Yao Wang, Morigen
Summary: Regulation of the cell cycle process is crucial for maintaining the stability and accuracy of genetic material in bacteria under various stresses. The small RNA DsrA has various targets and helps bacteria adapt to different environments, but its involvement in the cell cycle has been poorly understood. Through flow cytometry analysis, we observed that deleting dsrA promoted replication initiation, while overexpressing DsrA inhibited replication initiation in Escherichia coli. The absence of the chaperone protein Hfq, the DNA replication negative regulator protein Dps, or the transcription factor OxyR abolished the inhibitory effect of DsrA on replication initiation.
Article
Biochemistry & Molecular Biology
Ibrahim S. Al'Abri, Daniel J. Haller, Zidan Li, Nathan Crook
Summary: Directed evolution is a powerful method for engineering biology without detailed sequence-function relationships. To address the evolution of multigene pathways, the Inducible Directed Evolution (IDE) approach was developed and successfully applied in accelerating tagatose catabolism and improving utilization of melezitose in E. coli.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Fiona Jenkinson, Kang Wei Tan, Barbara Schopf, Miguel M. Santos, Philip Zegerman
Summary: In eukaryotes, cyclin-dependent kinase (CDK) inhibits helicase loading factors to ensure the exact duplication of the genome. CDK activates origin firing by phosphorylating Sld2 and Sld3, forming a transient intermediate called the pre-initiation complex (pre-IC). In yeast, the CDK phosphorylations of Sld3 and Sld2 are rapidly turned over by the phosphatases PP2A and PP4 during S phase. This dephosphorylation is important for genome-wide origin firing, pre-IC formation, and maintaining Sld3 dephosphorylation in G1 phase. PP2ARts1 specifically targets Sld3 and its dephosphorylation is critical for replication and cell viability.
Article
Multidisciplinary Sciences
Avik Mukherjee, Jade Ealy, Yanqing Huang, Nina Catherine Benites, Mark Polk, Markus Basan
Summary: Utilizing a combination of experiments and computer simulations, researchers have found that the emergence and persistence of coexistence of multiple ecotypes in Escherichia coli long-term evolution experiment can be explained by two interacting trade-offs rooted in biochemical constraints. Faster growth enabled by higher fermentation and obligate acetate excretion results in longer lag times when utilizing acetate after glucose is depleted, creating an ecological niche for a slower-growing ecotype specialized in switching to acetate. These findings highlight the importance of trade-offs in the evolution of complex microbial communities.
NATURE COMMUNICATIONS
(2023)
Article
Biology
Farah Shahid, Youssef Saeed Alghamdi, Mutaib Mashraqi, Mohsin Khurshid, Usman Ali Ashfaq
Summary: Shigella sonnei is a major cause of diarrhea, and antibiotic therapy is crucial for reducing the prevalence and fatality rate of infections. This study utilized subtractive genomics to identify potential drug targets for S. sonnei, and suggested several phytochemicals as potential antibacterial drugs.
SAUDI JOURNAL OF BIOLOGICAL SCIENCES
(2022)
Article
Microbiology
Saki Taniguchi, Kazutoshi Kasho, Shogo Ozaki, Tsutomu Katayama
FRONTIERS IN MICROBIOLOGY
(2019)
Article
Cell Biology
Hironori Kawakami, Ryuya Muraoka, Eiji Ohashi, Kenta Kawabata, Shota Kanamoto, Takeaki Chichibu, Toshiki Tsurimoto, Tsutomu Katayama
Article
Chemistry, Multidisciplinary
Jan Jamroskovic, Mara Doimo, Karam Chand, Ikenna Obi, Rajendra Kumar, Kristoffer Brannstrom, Mattias Hedenstrom, Rabindra Nath Das, Almaz Akhunzianov, Marco Deiana, Kazutoshi Kasho, Sebastian Sulis Sato, Parham L. Pourbozorgi, James E. Mason, Paolo Medini, Daniel Ohlund, Sjoerd Wanrooij, Erik Chorell, Nasim Sabouri
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2020)
Article
Biochemistry & Molecular Biology
Chihiro Hayashi, Erika Miyazaki, Shogo Ozaki, Yoshito Abe, Tsutomu Katayama
JOURNAL OF BIOLOGICAL CHEMISTRY
(2020)
Article
Thermodynamics
S. Seo, H. Kawakami, F. Miksik, N. Takata, K. Thu, T. Miyazaki
Summary: Adsorption cycles using different adsorbent-adsorbate pairs were studied for adsorption cooling and heat transformer applications. The study evaluated the specific cooling energy, coefficient of performance, and the impact of thermal mass ratios on the performance of the cycles. Results showed that the thermal mass had a significant impact on the cycles, with some pairs offering better performance at higher regeneration temperatures.
INTERNATIONAL JOURNAL OF REFRIGERATION
(2021)
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
Biochemistry & Molecular Biology
Kazutoshi Kasho, Lukas Krasauskas, Vytautas Smirnovas, Gorazd Stojkovic, Ludmilla A. Morozova-Roche, Sjoerd Wanrooij
Summary: The study demonstrates that PolDIP2 interacts with Tau and inhibits Tau aggregation and amyloid fibril growth in vitro, suggesting it as a potential regulator for future Tau-targeting therapeutics.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Kenya Miyoshi, Yuka Tatsumoto, Shogo Ozaki, Tsutomu Katayama
Summary: In Escherichia coli, the replication initiator DnaA oscillates between ATP- and ADP-bound states in a cell cycle-dependent manner, playing a key regulatory role in chromosome replication. The binding of ATP-DnaA and ADP-DnaA to DARS2 has different effects on chromosome replication at different stages.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Yukari Sakiyama, Mariko Nagata, Ryusei Yoshida, Kazutoshi Kasho, Shogo Ozaki, Tsutomu Katayama
Summary: Unwinding of the replication origin and loading of DNA helicases are crucial steps in chromosomal replication. In Escherichia coli, the Left/Right-DnaA subcomplexes promote unwinding of the duplex unwinding element (DUE), while the role of the Right-DnaA subcomplex is unclear. The AT-cluster element is important for efficient loading of the DnaB helicase.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Shogo Ozaki, Dengyu Wang, Yasutaka Wakasugi, Naoto Itani, Tsutomu Katayama
Summary: In this study, the researchers demonstrated the important role of DciA in maintaining DNA replication forks using the model bacterium Caulobacter crescentus. They found that DciA promotes loading of DnaB onto single-stranded DNA through conformational changes in the DnaB hexamer, ensuring proper progression of the replication fork.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Ryusei Yoshida, Shogo Ozaki, Hironori Kawakami, Tsutomu Katayama
Summary: This study describes the unwinding mechanisms of the DUE in the replication origin oriC of Escherichia coli, which are promoted by DnaA, IHF, and the structural homolog HU. IHF and HU promote DUE unwinding by promoting the binding of R1/R5M-bound DnaAs to ssDUE. Notably, HU binds the R1-R5M interspace stimulated by ATP-DnaA and ssDUE, suggesting a model of DUE unwinding triggered by DnaA interactions and stabilized by HU binding.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Biochemistry & Molecular Biology
Kazutoshi Kasho, Shogo Ozaki, Tsutomu Katayama
Summary: This review summarizes the mechanisms of timely binding and dissociation of nucleoid proteins IHF and Fis in chromosomal DNA replication initiation in Escherichia coli. The timely stabilization of IHF binding at oriC and the timely regulation of DnaA activity via DARS2 and datA are crucial for the timing control of replication initiation. IHF and Fis play specific roles in the regulation of replication initiation and proposed mechanisms for the regulation of timely IHF binding and dissociation at DARS2 and datA are discussed in this review.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)