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
Chemistry, Analytical
Haoran Li, Yubo Wang, Yaohua Li, Wei Wang
Summary: This study presents a new label-free bacterial viability assay based on optical tweezers technology, which quantifies bacterial viability by monitoring bacterial nanomotion in the optical traps. The assay is characterized by short time consumption, simple sample preparations, and no cytotoxicity, making it a reliable method for assessing bacterial viability at the single-cell level.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Haoran Li, Yubo Wang, Yaohua Li, Wei Wang
Summary: The new method successfully quantifies bacterial viability at a single-cell level using optical tweezers, holding potential in antibiotic susceptibility testing, drug screening, and rapid diagnostics.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Manli Xiang, Kaijiang Xia, Bingyi Chen, Zhiteng Luo, Ying Yu, Lili Jiang, Huihao Zhou
Summary: Tryptophanyl-tRNA synthetase (TrpRS) plays a crucial role in protein translation by linking tryptophan to tRNA(Trp). In this study, an 'open-closed' asymmetric structure of bacterial TrpRS was captured, providing evidence for the half-of-the-sites reactivity of bacterial TrpRS. Fragment screening against the asymmetric TrpRS led to the identification of 19 hits, 8 of which were successfully cocrystallized. These findings enhance our understanding of the catalytic mechanism of TrpRS and aid in the discovery of bacterial TrpRS inhibitors with therapeutic potential.
NUCLEIC ACIDS RESEARCH
(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
Multidisciplinary Sciences
Yi Yang, Mytien Nguyen, Varnica Khetrapal, Nicole D. Sonnert, Anjelica L. Martin, Haiwei Chen, Martin A. Kriegel, Noah W. Palm
Summary: This study reveals that within-host evolution of gut commensal bacteria plays a critical role in bacterial translocation and initiation of inflammation. Gut microbiota strains can adapt and evolve, affecting their propensity to elicit inflammatory diseases. The changes in bacterial behavior are associated with genetic mutations, altered microbial gene expression programs, and remodelled cell wall structures.
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
Microbiology
Henry P. P. Oswin, Allen E. E. Haddrell, Cordelia Hughes, Mara Otero-Fernandez, Richard J. J. Thomas, Jonathan P. P. Reid
Summary: Using CELEBS, researchers found that the decay of Escherichia coli in airborne droplets is influenced by factors such as residence time and oxygen concentration. The presence of oxygen facilitates the formation of reactive oxygen species, leading to bacterial death.
MICROBIOLOGY SPECTRUM
(2023)
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
Environmental Sciences
Xiang Xiao, En-Jing He, Xue-Rong Lu, Li-Jun Wu, Yang-Yang Fan, Han-Qing Yu
Summary: The study shows that silver nanoparticles possess strong antibacterial ability, leading to the majority of bacteria entering a viable but non-culturable state. Environmental factors such as Cl- and illumination can affect the solubility of nanoparticles and thereby impact the survival state of bacteria.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Biochemistry & Molecular Biology
Alexander Doan, Soniya Chatterjee, Roopa Kothapalli, Zaki Khan, Shaanit Sen, Noemi Kedei, Jyoti K. Jha, Dhruba K. Chattoraj, Revathy Ramachandran
Summary: The study demonstrates that Lrp binds to crtS DNA and possibly contacts RctB, enhancing the binding between RctB and crtS. The crtS-Lrp complex controls the initiation of replication by modulating RctB binding to ori2.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Ecology
Qinqin Wang, Shaodong Wei, Ana Filipa Silva, Jonas Stenlokke Madsen
Summary: The rise of beta-lactam resistance due to the transfer of plasmid-encoded beta-lactamases is a global health crisis. Expressing beta-lactamase on plasmids enhances its activity and promotes the transfer of plasmids to non-producers, expanding the potential recipient pool. Cooperative plasmids are more competitive in the presence of a beta-lactam antibiotic, while plasmid-free non-producers are more competitive than those burdened with a plasmid. This suggests that cooperative antibiotic resistance benefits the fitness of horizontally transmitting replicons like conjugative plasmids.
Article
Biology
Eric Mandela, Christopher J. Stubenrauch, David Ryoo, Hyea Hwang, Eli J. Cohen, Von L. Torres, Pankaj Deo, Chaille T. Webb, Cheng Huang, Ralf B. Schittenhelm, Morgan Beeby, J. C. Gumbart, Trevor Lithgow, Iain D. Hay
Summary: The cell envelope of Gram-negative bacteria is composed of two membranes and plays a crucial role in spatial constraints and load-bearing forces. This study focuses on the mechanism behind spatial constraints in Escherichia coli, specifically the role of the coiled-coil lipoprotein Lpp. The findings demonstrate that E. coli can accommodate elongated Lpp through various factors and genetic adaptations, highlighting the importance of maintaining spatial constraints in bacterial cell envelopes.
Article
Environmental Sciences
Xiangpeng Zeng, Yu Cao, Lanning Wang, Min Wang, Qiang Wang, Qingxiang Yang
Summary: This study reveals that multidrug resistant (MDR) bacterial strains have a higher viability and different gene expression patterns compared to susceptible strains under hexavalent chromium (Cr(VI) stress. The MDR strain showed higher bacteriostatic rates and lower levels of reactive oxygen species compared to the susceptible strain. Moreover, the MDR strain also exhibited higher expression levels of antibiotic resistance genes and other related genes.
ENVIRONMENTAL POLLUTION
(2023)
Article
Multidisciplinary Sciences
Jeongjoon Choi, Matias Schmukler, Eduardo A. Groisman
Summary: Horizontal gene transfer drives bacterial evolution, and H-NS proteolysis is a mechanism essential for derepressing foreign genes and colonization of mammalian hosts.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
David Magnan, Mohan C. Joshi, Anna K. Barker, Bryan J. Visser, David Bates
Article
Genetics & Heredity
Jessica M. Moore, David Magnan, Ana K. Mojica, Mara Angelica Bravo Nunez, David Bates, Susan M. Rosenberg, P. J. Hastings
Review
Microbiology
David Magnan, David Bates
JOURNAL OF BACTERIOLOGY
(2015)
Article
Microbiology
Mark Lies, Bryan J. Visser, Mohan C. Joshi, David Magnan, David Bates
FRONTIERS IN MICROBIOLOGY
(2015)
Editorial Material
Biology
David Bates, B. Montgomery Pettitt, Gregory R. Buck, Lynn Zechiedrich
PHYSICS OF LIFE REVIEWS
(2016)
Article
Multidisciplinary Sciences
Jun Xia, Li-Tzu Chen, Qian Mei, Chien-Hui Ma, Jennifer A. Halliday, Hsin-Yu Lin, David Magnan, John P. Pribis, Devon M. Fitzgerald, Holly M. Hamilton, Megan Richters, Ralf B. Nehring, Xi Shen, Lei Li, David Bates, P. J. Hastings, Christophe Herman, Makkuni Jayaram, Susan M. Rosenberg
Review
Microbiology
Nancy Kleckner, Jay K. Fisher, Mathieu Stouf, Martin A. White, David Bates, Guillaume Witz
CURRENT OPINION IN MICROBIOLOGY
(2014)
Article
Microbiology
Joshua Cambridge, Alexandra Blinkova, David Magnan, David Bates, James R. Walker
JOURNAL OF BACTERIOLOGY
(2014)
Article
Genetics & Heredity
Mohan C. Joshi, David Magnan, Timothy P. Montminy, Mark Lies, Nicholas Stepankiw, David Bates
Article
Biology
Chandan Shee, Ben D. Cox, Franklin Gu, Elizabeth M. Luengas, Mohan C. Joshi, Li-Ya Chiu, David Magnan, Jennifer A. Halliday, Ryan L. Frisch, Janet L. Gibson, Ralf Bernd Nehring, Huong G. Do, Marcos Hernandez, Lei Li, Christophe Herman, P. J. Hastings, David Bates, Reuben S. Harris, Kyle M. Miller, Susan M. Rosenberg
Article
Biochemistry & Molecular Biology
Jun Xia, Li-Ya Chiu, Ralf B. Nehring, Maria Angelica Bravo Nunez, Qian Mei, Mercedes Perez, Yin Zhai, Devon M. Fitzgerald, John P. Pribis, Yumeng Wang, Chenyue W. Hu, Reid T. Powell, Sandra A. LaBonte, Ali Jalali, Meztli L. Matadamas Guzman, Alfred M. Lentzsch, Adam T. Szafran, Mohan C. Joshi, Megan Richters, Janet L. Gibson, Ryan L. Frisch, P. J. Hastings, David Bates, Christine Queitsch, Susan G. Hilsenbeck, Cristian Coarfa, James C. Hu, Deborah A. Siegele, Kenneth L. Scott, Han Liang, Michael A. Mancini, Christophe Herman, Kyle M. Miller, Susan M. Rosenberg
Article
Biochemistry & Molecular Biology
John P. Pribis, Libertad Garcia-Villada, Yin Zhai, Ohad Lewin-Epstein, Anthony Z. Wang, Jingjing Liu, Jun Xia, Qian Mei, Devon M. Fitzgerald, Julia Bos, Robert H. Austin, Christophe Herman, David Bates, Lilach Hadany, P. J. Hastings, Susan M. Rosenberg
Article
Genetics & Heredity
Megan S. Behrmann, Himasha M. Perera, Joy M. Hoang, Trisha A. Venkat, Bryan J. Visser, David Bates, Michael A. Trakselis
Summary: This study investigates the effects of specific mutations in the helicase on bacterial growth, fitness, and cellular morphology to understand how helicase regulation mechanisms impact an organism's ability to survive and maintain a stable genome. The findings suggest a dynamic model for helicase regulation involving both excluded strand interactions and conformational states, highlighting the importance of helicase dysregulation in genomic stability and viability.
Article
Biochemistry & Molecular Biology
Bryan J. Visser, Sonum Sharma, Po J. Chen, Anna B. McMullin, Maia L. Bates, David Bates
Summary: DNA supercoiling is a key regulator of DNA metabolic processes, but a reliable genomic assay for supercoiling is lacking. In this study, a high-resolution method (Psora-seq) is presented to measure whole-genome supercoiling, and it is applied in Escherichia coli to observe a supercoiling landscape that is well correlated to transcription. The results indicate that transcription is the major determinant of chromosome supercoiling, while DNA replication also strongly influences supercoiling.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biology
Po Jui Chen, Anna B. McMullin, Bryan J. Visser, Qian Mei, Susan M. Rosenberg, David Bates
Summary: In bacteria, sister replisomes are functionally interdependent and remain colocalized throughout replication. Our study reveals the crucial role of physical association between sister replisomes in ensuring an efficient and uninterrupted replication program.