Article
Multidisciplinary Sciences
Jung-Un Park, Amy Wei-Lun Tsai, Eshan Mehrotra, Michael T. Petassi, Shan-Chi Hsieh, Ailong Ke, Joseph E. Peters, Elizabeth H. Kellogg
Summary: CRISPR-associated transposition systems allow integration of a single DNA cargo directed by guide RNA in one orientation at a fixed distance from a programmable target sequence. Cryo-EM was used to characterize the transposition regulator TnsC, revealing the mechanism behind transposase polarity information transfer. Mechanistic findings include polymerization of ATP-bound TnsC helical filaments, TniQ capping the TnsC filament, and transposase-driven disassembly for element delivery only to unused protospacers. These findings provide a foundation for engineering CRISPR-associated transposition systems for research and therapeutic applications.
Article
Biochemistry & Molecular Biology
Shan-Chi Hsieh, Joseph E. Peters
Summary: The CRISPR-Cas defense systems have been coopted for guide RNA-directed transposition by bacterial transposons. Cyanobacterial genomes contain various Tn7-like elements, including guide RNA-directed transposons and CRISPR-Cas based systems. A type I-D CRISPR-Cas system was discovered, which showed flexibility in guide RNA length requirements and had naturally fused transposase proteins. These findings provide new possibilities for future gene editing work. In addition, the analysis revealed a broader understanding of the evolution of Tn7-like elements, including extensive swapping of targeting systems among cyanobacteria.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biology
Sonia Castanheira, Francisco Garcia-del Portillo
Summary: Cell shape is genetically inherited and controlled by a universal system of peptidoglycan synthases guided by cytoskeletal scaffolds. This study reveals the existence of two elongasomes that generate rod-shaped morphology in the same bacterium, Salmonella. These elongasomes can be purified independently, respond to different environmental cues, and are directed by distinct peptidoglycan synthases.
COMMUNICATIONS BIOLOGY
(2023)
Article
Cell Biology
Vladimir Baytshtok, Xue Fei, Tsai-Ting Shih, Robert A. Grant, Justin C. Santos, Tania A. Baker, Robert T. Sauer
Summary: At low temperatures, protein degradation by the AAA+ HslUV protease is slow due to residues in the intermediate domain of the HslU(6) unfoldase blocking the axial channel, preventing substrate binding and degradation until heat-induced melting of this autoinhibitory plug activates HslUV proteolysis through a model supported by biochemical experiments with wild-type and mutant enzymes.
Article
Microbiology
Masato Kawamura, Ryota Ito, Yurina Tamura, Mio Takahashi, Miho Umenai, Yuriko Chiba, Takumi Sato, Shigeru Fujimura
Summary: This study is the first to demonstrate that mutations in the chromosomal-ampC attenuator region are responsible for the emergence of cefazolin resistance in Escherichia coli strains. The resistance was maintained even after culturing E. coli without cefazolin. This study highlights one of the key factors contributing to the increase in the number of cefazolin-resistant E. coli strains, which can pose a considerable challenge for treating common infections, such as urinary tract infections.
MICROBIOLOGY SPECTRUM
(2022)
Article
Gastroenterology & Hepatology
Nadege Bossuet, Cecile Guyonnet, Camille Chagneau, Min Tang-Fichaux, Marie Penary, Dorian Loubet, Priscilla Branchu, Eric Oswald, Jean-Philippe Nougayrede
Summary: Up to 25% of healthy human feces-derived E. coli strains carry the pks genomic island, which is responsible for synthesizing colibactin, a genotoxic compound implicated in colorectal cancer. However, the expression conditions of colibactin in the gut remain poorly understood. In this study, it is demonstrated that colibactin production is highest under anoxic conditions and decreases with increased oxygen concentration. The positive regulation of colibactin production and genotoxicity by the aerobic respiration control (ArcA) in response to oxygen availability suggests that the pks biosynthetic pathway is adapted for the anoxic intestinal lumen and hypoxic infected or tumor tissue.
Article
Biochemistry & Molecular Biology
Carlos K. Gurnani Serrano, Matthias Winkle, Alessandra M. Martorana, Jacob Biboy, Niccolo More, Patrick Moynihan, Manuel Banzhaf, Waldemar Vollmer, Alessandra Polissi
Summary: In this study, it was shown that the morphological defects and lysis associated with a ldtF mutant with impaired LPS transport can be alleviated by the loss of the OM-anchored lipoprotein ActS. ActS was found to be an inactive member of LytM-type peptidoglycan endopeptidases, capable of activating several periplasmic peptidoglycan amidases. Additionally, ActS was shown to preferentially activate AmiC and its function is linked to cell envelope stress.
MOLECULAR MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Yu-Hsuan Chen, Han-Hsiun Chen, Won-Jing Wang, Hsin-Yi Chen, Wei-Syun Huang, Chien-Han Kao, Sin-Rong Lee, Nai Yang Yeat, Ruei-Liang Yan, Shu-Jou Chan, Kuen-Phon Wu, Ruey-Hwa Chen
Summary: Activation of tumor-intrinsic innate immunity is crucial for improving immunotherapy. The deubiquitinating enzyme TRABID is found to play a suppressive role in anti-tumor immunity by regulating mitotic cell division and activating the cGAS/STING pathway. TRABID inhibition induces micronuclei and protects cGAS from autophagy, thus promoting anti-tumor immune responses.
NATURE COMMUNICATIONS
(2023)
Article
Physics, Fluids & Plasmas
Debarshi Mitra, Shreerang Pande, Apratim Chatterji
Summary: The entropic repulsion between DNA ring polymers under confinement plays a crucial role in the spatial segregation of bacterial DNA before cell division. Additionally, the introduction of internal loops enhances this repulsion and induces entropy-driven spatial organization of polymer segments. By designing different polymer architectures and investigating their segregation under confinement, we identify the structures that lead to higher success rates of segregation and establish the mechanism behind the localization of specific polymer segments.
Article
Biochemistry & Molecular Biology
Debika Ojha, Malgorzata M. Jaszczur, Adhirath Sikand, John P. McDonald, Andrew Robinson, Antoine M. van Oijen, Chi H. Mak, Fabien Pinaud, Michael M. Cox, Roger Woodgate, Myron F. Goodman
Summary: Homologs of mutagenic DNA polymerase V are encoded by pathogens and mobile elements. These polymerases can be transferred horizontally into different cells but require activation by host factors.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Jeongjoon Choi, Hubert Salvail, Eduardo A. Groisman
Summary: The study reveals that in Salmonella enterica serovar Typhimurium, the RNA chaperone CspC is essential for activating the master virulence regulator PhoP in mildly acidic pH conditions, while CspE is not necessary. This activation is mediated by the virulence gene ugtL and enhances translation by disrupting mRNA secondary structure.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Microbiology
Kate R. Fortney, Sara N. Smith, Julia J. van Rensburg, Julie A. Brothwell, Jessi J. Gardner, Barry P. Katz, Nagib Ahsan, Adam S. Duerfeldt, Harry L. T. Mobley, Stanley M. Spinola
Summary: This study suggests that chemical activation of the CpxRA system may be a viable strategy for treating infections caused by uropathogenic Escherichia coli (UPEC). The most potent compound significantly reduced bacterial recovery in the urine and downregulated multiple proteins involved in UPEC virulence.
MICROBIOLOGY SPECTRUM
(2022)
Article
Multidisciplinary Sciences
B. T. Fabunmi, A. C. Adegaye, S. T. Ogunjo
Summary: This study aims to characterize and understand the expression pattern, catalytic structure, and modulatory role of unidentified molecular entities following treatment with glyphosate shock. The study identified two upregulated genes and twenty-eight downregulated genes after glyphosate shock. Additionally, the study discovered the differential expression of unidentified proteins after glyphosate treatment. The results provide valuable insights for the development of new antibiotics.
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
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
Murli Manohar, Hyong Woo Choi, Patricia Manosalva, Caroline A. Austin, Joseph E. Peters, Daniel F. Klessig
MOLECULAR PLANT-MICROBE INTERACTIONS
(2017)
Article
Multidisciplinary Sciences
Joseph E. Peters, Kira S. Makarova, Sergey Shmakov, Eugene V. Koonin
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2017)
Article
Multidisciplinary Sciences
Calvin K. Lee, Jaime de Anda, Amy E. Baker, Rachel R. Bennett, Yun Luo, Ernest Y. Lee, Joshua A. Keefe, Joshua S. Helali, Jie Ma, Kun Zhao, Ramin Golestanian, George A. O'Toole, Gerard C. L. Wong
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2018)
Article
Chemistry, Analytical
T. C. Hinkley, S. Garing, S. Singh, A-L M. Le Ny, K. P. Nichols, J. E. Peters, J. N. Talbert, S. R. Nugen
Article
Multidisciplinary Sciences
Troy C. Hinkley, Sangita Singh, Spencer Garing, Anne-Laure M. Le Ny, Kevin P. Nichols, Joseph E. Peters, Joey N. Talbert, Sam R. Nugen
SCIENTIFIC REPORTS
(2018)
Article
Microbiology
Jason M. Peters, Byoung-Mo Koo, Ramiro Patino, Gary E. Heussler, Cameron C. Hearne, Jiuxin Qu, Yuki F. Inclan, John S. Hawkins, Candy H. S. Lu, Melanie R. Silvis, M. Michael Harden, Hendrik Osadnik, Joseph E. Peters, Joanne N. Engel, Rachel J. Dutton, Alan D. Grossman, Carol A. Gross, Oren S. Rosenberg
NATURE MICROBIOLOGY
(2019)
Review
Microbiology
Guilhem Faure, Sergey A. Shmakov, Winston X. Yan, David R. Cheng, David A. Scott, Joseph E. Peters, Kira S. Makarova, Eugene Koonin
NATURE REVIEWS MICROBIOLOGY
(2019)
Review
Biochemistry & Molecular Biology
Joseph E. Peters
MOLECULAR MICROBIOLOGY
(2019)
Article
Chemistry, Analytical
Troy C. Hinkley, Spencer Garing, Paras Jain, John Williford, Anne-Laure M. Le Ny, Kevin P. Nichols, Joseph E. Peters, Joey N. Talbert, Sam R. Nugen
Article
Biotechnology & Applied Microbiology
Yun Luo, Mari Valkonen, Raymond E. Jackson, Jonathan M. Palmer, Aditya Bhalla, Igor Nikolaev, Markku Saloheimo, Michael Ward
BIOTECHNOLOGY FOR BIOFUELS
(2020)
Article
Biochemistry & Molecular Biology
Michael T. Petassi, Shan-Chi Hsieh, Joseph E. Peters
Article
Multidisciplinary Sciences
Jung-Un Park, Amy Wei-Lun Tsai, Eshan Mehrotra, Michael T. Petassi, Shan-Chi Hsieh, Ailong Ke, Joseph E. Peters, Elizabeth H. Kellogg
Summary: CRISPR-associated transposition systems allow integration of a single DNA cargo directed by guide RNA in one orientation at a fixed distance from a programmable target sequence. Cryo-EM was used to characterize the transposition regulator TnsC, revealing the mechanism behind transposase polarity information transfer. Mechanistic findings include polymerization of ATP-bound TnsC helical filaments, TniQ capping the TnsC filament, and transposase-driven disassembly for element delivery only to unused protospacers. These findings provide a foundation for engineering CRISPR-associated transposition systems for research and therapeutic applications.
Article
Biochemistry & Molecular Biology
Yao Shen, Josue Gomez-Blanco, Michael T. Petassi, Joseph E. Peters, Joaquin Ortega, Alba Guarne
Summary: Tn7 transposable elements have a unique target-site selection mechanism and precise insertions. The TnsC adaptor plays a key role in coordinating target-site selection and preventing insertions at sites containing a Tn7 element. A recent study reveals how TnsC recognizes pre-distorted DNA substrates to control sequence-specific transposon insertion.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Jung-Un Park, Amy Wei-Lun Tsai, Tiffany H. Chen, Joseph E. Peters, Elizabeth H. Kellogg
Summary: This study reveals the conformation and mechanistic relationships of the transposase component TnsB in CRISPR-associated transposons, providing insights into its role in transposon integration. The structural information presented here will guide future work in modifying these systems as programmable gene integration tools.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Shan-Chi Hsieh, Joseph E. Peters
Summary: The CRISPR-Cas defense systems have been coopted for guide RNA-directed transposition by bacterial transposons. Cyanobacterial genomes contain various Tn7-like elements, including guide RNA-directed transposons and CRISPR-Cas based systems. A type I-D CRISPR-Cas system was discovered, which showed flexibility in guide RNA length requirements and had naturally fused transposase proteins. These findings provide new possibilities for future gene editing work. In addition, the analysis revealed a broader understanding of the evolution of Tn7-like elements, including extensive swapping of targeting systems among cyanobacteria.
NUCLEIC ACIDS RESEARCH
(2023)