Article
Multidisciplinary Sciences
Viktor Mamontov, Alexander Martynov, Natalia Morozova, Anton Bukatin, Dmitry B. Staroverov, Konstantin A. Lukyanov, Yaroslav Ispolatov, Ekaterina Semenova, Konstantin Severinov
Summary: This study demonstrates that plasmids can persist for multiple generations in certain Escherichia coli cell lineages under continuous targeting by the type I-E CRISPR-Cas system. The researchers propose that this complex dynamic process provides long-term benefits for bacterial populations by maintaining mobile genetic elements in some cells, leading to phenotypic diversification and rapid changes in the population structure to meet the demands of a changing environment.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Immunology
Xinhua Luo, Zhe Yin, Lijun Zeng, Lingfei Hu, Xiaoyuan Jiang, Ying Jing, Fangzhou Chen, Dongguo Wang, Yajun Song, Huiying Yang, Dongsheng Zhou
Summary: In this study, a detailed genetic dissection of the bla (NDM)-carrying genetic elements and their related mobile genetic elements in Enterobacteriaceae revealed the presence of numerous resistance genes and complex structures. The analysis identified eight novel mobile elements, including ICEs, IMEs, composite transposons, and an integron.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Meng Liu, Jialin Liu, Guitian Liu, Hui Wang, Xiaoli Wang, Zixin Deng, Yongqun He, Hong-Yu Ou
Summary: This study developed an Integrative and Conjugative Element Ontology (ICEO) to represent the gene components, functional modules, and other information of bacterial integrative and conjugative elements (ICEs). ICEO can facilitate the representation, integration, and computer-assisted queries of systematic ICE knowledge.
Article
Biochemistry & Molecular Biology
Boris Shaskolskiy, Dmitry Kravtsov, Ilya Kandinov, Ekaterina Dementieva, Dmitry Gryadunov
Summary: Chromosomal rearrangements and mobile elements were studied in N. gonorrhoeae and N. meningitidis, revealing a stronger correlation between gene order changes and phylogenetic proximity in N. meningitidis. Multiple mobile elements were identified to be involved in chromosomal rearrangements.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Engineering, Environmental
Hu Li, Qiu-Ping Luo, Qiang Pu, Xiao-Ru Yang, Xin-Li An, Dong Zhu, Jian-Qiang Su
Summary: Globally distributed earthworms can affect the compositions of soil compounds, microbial community structures, and antibiotic resistance genes (ARGs). However, little is known about how earthworms impact the dissemination of ARGs in soil.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
Article
Chemistry, Physical
Eric R. Homer, Oliver K. Johnson, Darcey Britton, James E. Patterson, Eric T. Sevy, Gregory B. Thompson
Summary: Observations of microstructural coarsening and grain boundary motion at cryogenic temperatures have posed challenges to the expected Arrhenius behavior. However, this study demonstrates that classical equations can account for these anomalies and show that non-Arrhenius behavior can arise from thermally activated processes. The phenomenon occurs when the intrinsic barrier energies of the processes become small, allowing activation at cryogenic temperatures.
NPJ COMPUTATIONAL MATERIALS
(2022)
Review
Pharmacology & Pharmacy
Qingquan Chen, Tejas Dharmaraj, Pamela C. Cai, Elizabeth B. Burgener, Naomi L. Haddock, Andy J. Spakowitz, Paul L. Bollyky
Summary: Bacteriophages can have complex effects on bacterial responses to antibiotics, promoting susceptibility to antibiotics or contributing to antimicrobial resistance and tolerance. Some bacteriophages facilitate the transfer of antibiotic resistance genes between bacteria, while chronic infection by filamentous phages can promote bacterial tolerance and hinder the effectiveness of antibiotics.
Review
Environmental Sciences
Shengnan Li, Xue Li, Haixing Chang, Nianbing Zhong, Nanqi Ren, Shih-Hsin Ho
Summary: With the increasing use of antibiotics, antibiotic resistance gene (ARG) prevalence is on the rise in aquatic environments. Microalgal-bacterial consortia have shown potential in minimizing the transmission of antibiotic resistance and removing ARGs. However, the mechanism of ARG migration in these consortia has not been extensively studied. This review provides valuable information on the migration of ARGs and factors influencing gene transfer, offering insights for the development of innovative techniques for ARG removal by microalgal-bacterial consortia.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Microbiology
Teolincacihuatl Ayala Nunez, Gabriela N. Cerbino, Maria Florencia Rapisardi, Cecilia Quiroga, Daniela Centron
Summary: In this study, we evaluated the occurrence of integrase genes, integron systems, and their genetic surroundings in the genus Shewanella. We identified 22 integrase gene types, including 17 newly described ones, indicating multiple lateral genetic transfer events. Our findings suggest that integrase genes and mobile integrons may contribute to the development of multidrug resistance in Shewanella strains.
Review
Microbiology
Alexandra J. Weisberg, Jeff H. Chang
Summary: Mobile genetic elements (MGEs) play a key role in the evolution of bacteria and the traits that impact host and ecosystem health. This article synthesizes recent findings on MGEs using a hierarchical and modular system framework, highlighting their emergent properties of flexibility, robustness, and genetic capacity that impact bacterial evolution. Some traits of MGEs can be stored, shared, and diversified across different MGEs, bacterial taxa, and time, contributing to functionality maintenance and trait diversification. The study of MGEs has long been challenging, but the implementation of new technologies and strategies allows for their analysis in new and powerful ways.
ANNUAL REVIEW OF MICROBIOLOGY
(2023)
Article
Engineering, Environmental
Cheng Wang, Ruiwen Hu, P. J. Strong, Wei Zhuang, Weiming Huang, Zhiwen Luo, Qingyun Yan, Zhili He, Longfei Shu
Summary: The majority of antibiotic resistance genes are shared across different root-associated compartments and disseminated continuously along the soil-root continuum. This dissemination is independent of the root-associated microbiota but may be facilitated by various mobile genetic elements. Multiple-drug resistant pathogens are consistently present across different compartments, suggesting the potential dissemination of antibiotic pathogens along the soil-root continuum.
JOURNAL OF HAZARDOUS MATERIALS
(2021)
Article
Microbiology
Janine Zara Bowring, Yue Su, Ahlam Alsaadi, Sine L. Svenningsen, Julian Parkhill, Hanne Ingmer
Summary: Bacteriophage-mediated transduction is a major mechanism for horizontal gene transfer in bacterial pathogens, and understanding this process is crucial for combating virulence and antibiotic resistance.
MICROBIOLOGY SPECTRUM
(2022)
Article
Evolutionary Biology
Alexandra J. Weisberg, Joel L. Sachs, Jeff H. Chang
Summary: The chromosome architecture of Bradyrhizobium bacteria is largely conserved despite variations in genome composition and location of attachment sites recognized by integrases of symICEs. Simulated nonnative chromosome-symICE combinations are predicted to result in lethal deletions or disruptions to architecture. The findings suggest compatibility between chromosomes and symICEs.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Biotechnology & Applied Microbiology
Connor L. Brown, James Mullet, Fadi Hindi, James E. Stoll, Suraj Gupta, Minyoung Choi, Ishi Keenum, Peter Vikesland, Amy Pruden, Liqing Zhang
Summary: This study provides a comprehensive analysis of bacterial mobile genetic elements (MGEs) and presents a database, mobileOG-db, containing over 6,000 protein families for the annotation and analysis of MGEs. The database offers a multilevel classification scheme, allowing for the annotation of plasmids, phages, integrative elements, and transposable elements.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
William J. Jowsey, Calum R. P. Morris, Drew A. Hall, John T. Sullivan, Robert D. Fagerlund, Karina Y. Eto, Paul D. Solomon, Joel P. Mackay, Charles S. Bond, Joshua P. Ramsay, Clive W. Ronson
Summary: Horizontal gene transfer in bacteria is tightly regulated by the DUF2285 domain, which is involved in both transcriptional activation and antiactivation. The DUF2285 domain interacts with other domains to control the initiation of gene transfer.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Genetics & Heredity
Rodrigo Ibarra-Chavez, Aisling Brady, John Chen, Jose R. Penades, Andreas F. Haag
Summary: Phage-inducible chromosomal islands (PICIs) are highly mobile genetic elements that disseminate virulence and toxin genes among bacterial populations. Recent research has shown that PICIs promote bacterial diversity and protect the bacterial population from phage attack.
Article
Multidisciplinary Sciences
Francisca Gallego del Sol, Nuria Quiles-Puchalt, Aisling Brady, Jose R. Penades, Alberto Marina
Summary: This study provides insights into the mechanism of the arbitrium system by elucidating the structure of an additional AimR and confirming the role of AimP-induced conformational restriction. The findings shed light on the specificity of the peptide and its cross-regulation with other biological processes.
NATURE COMMUNICATIONS
(2022)
Article
Microbiology
Nasser Alqurainy, Laura Miguel-Romero, Jorge Moura de Sousa, John Chen, Eduardo P. C. Rocha, Alfred Fillol-Salom, Jose R. Penades
Summary: Phage satellites are genetic elements that interfere with phage packaging by producing small capsids and exclusively packaging themselves. A new family of phage-inducible chromosomal islands (cf-PICIs) encodes all the proteins required for this process and only requires phage tails to generate particles. These cf-PICIs are not parasitic and have evolved independently in both gram-positive and gram-negative bacteria.
CELL HOST & MICROBE
(2023)
Article
Microbiology
Andreas F. Haag, Lassi Liljeroos, Paolo Donato, Clarissa Pozzi, Tarcisio Brignoli, Matthew J. Bottomley, Fabio Bagnoli, Isabel Delany
Summary: Vaccination and phage therapy are potential strategies to prevent or combat Staphylococcus aureus infections. In this study, a high-throughput qRT-PCR assay was used to identify highly expressed staphylococcal genes, lukE and lukD, which encode detoxified recombinant proteins. Immunization with these proteins conferred protection against staphylococcal skin infection in mice. This approach of studying in vivo gene expression can guide the selection and design of effective vaccine antigens.
MICROBIOLOGY SPECTRUM
(2023)
Article
Microbiology
Carla Sanz-Frasquet, J. Rafael Ciges-Tomas, Christian Alite, Jose R. Penades, Alberto Marina
Summary: This study reveals how Stl interacts with different types of dUTPases through structural specificity to regulate the life cycle of SaPI and helper phage.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biochemistry & Molecular Biology
Jorge A. Moura de Sousa, Alfred Fillol-Salom, Jose R. Penades, Eduardo P. C. Rocha
Summary: We developed SatelliteFinder to identify satellites in bacterial genomes, detecting a vast number of them, with some found in novel taxa. The gene repertoires and genomic organizations of satellites are variable but relatively conserved. The independent evolution of hijacking modules suggests that phage satellites have ancient, diverse origins.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Sergio Arredondo-Alonso, George Blundell-Hunter, Zuyi Fu, Rebecca A. Gladstone, Alfred Fillol-Salom, Jessica Loraine, Elaine Cloutman-Green, Pal J. Johnsen, Orjan Samuelsen, Anna K. Poentinen, Francois Cleon, Susana Chavez-Bueno, Miguel A. De la Cruz, Miguel A. Ares, Manivanh Vongsouvath, Agnieszka Chmielarczyk, Carolyne Horner, Nigel Klein, Alan McNally, Joice N. Reis, Jose R. Penades, Nicholas R. Thomson, Jukka Corander, Peter W. Taylor, Alex J. McCarthy
Summary: Escherichia coli is a leading cause of invasive bacterial infections in humans. The study reveals the distribution, evolution, and functions of the K1 capsule, a potent capsule type, in E. coli. The findings emphasize the importance of assessing virulence factors in population levels to predict and control bacterial infections.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Melissa Su Juan Chee, Ester Serrano, Yin Ning Chiang, Joshua Harling-Lee, Rebecca Man, Rodrigo Bacigalupe, J. Ross Fitzgerald, Jose R. Penades, John Chen
Summary: We report a versatile and complex mechanism of gene transfer called lateral transduction in staphylococcal pathogenicity islands (SaPIs), which enables them to mobilize large sections of the bacterial chromosome and transfer additional virulence genes. The activated SaPIs form concatamers in the bacterial chromosome by switching between parallel genomic tracks in replication bubbles. This research reveals previously unknown roles of pathogenicity islands in bacterial virulence.
Article
Multidisciplinary Sciences
Mohammed A. Thabet, Jose R. Penades, Andreas F. Haag
Summary: Bacteriophages play a significant role in the dissemination of bacterial virulence, pathogenicity, and antimicrobial resistance. A study has discovered the unexpected involvement of the bacterial protease ClpX in the activation of bacteriophages.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Rodrigo Ibarra-Chavez, Julien Reboud, Jose R. Penades, Jonathan M. Cooper
Summary: Phage-inducible chromosomal islands (PICIs) are genetic constructs that repurpose phage components to mobilize and spread. They have been used as antibacterial drones and a user-friendly diagnostic system based on PICI transduction has been developed for selective enrichment and detection of Escherichia coli and Staphylococcus aureus. This approach enables visual sensing of viable pathogens only, extending diagnostic sensing mechanisms beyond conventional strategies.