Phosphorothioate (PT) modification by the dnd gene cluster is the first identified DNA backbone modification and constitute an epigenetic system with multiple functions, including antioxidant ability, restriction modification, and virus resistance. Despite these advantages for hosting dnd systems, they are surprisingly distributed sporadically among contemporary prokaryotic genomes. To address this ecological paradox, we systematically investigate the occurrence and phylogeny of dnd systems, and they are suggested to have originated in ancient Cyanobacteria after the Great Oxygenation Event. Interestingly, the occurrence of dnd systems and prophages is significantly negatively correlated. Further, we experimentally confirm that PT modification activates the filamentous phage SW1 by altering the binding affinity of repressor and the transcription level of its encoding gene. Competition assays, concurrent epigenomic and transcriptomic sequencing subsequently show that PT modification affects the expression of a variety of metabolic genes, which reduces the competitive fitness of the marine bacterium Shewanella piezotolerans WP3. Our findings strongly suggest that a series of negative effects on microorganisms caused by dnd systems limit horizontal gene transfer, thus leading to their sporadic distribution. Overall, our study reveals putative evolutionary scenario of the dnd system and provides novel insights into the physiological and ecological influences of PT modification.
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http://dx.doi.org/10.1038/s41467-021-26636-7 | DOI Listing |
bioRxiv
November 2024
Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA.
Errors in multiple sequence alignments (MSAs) are known to bias many comparative evolutionary methods. In the context of natural selection analyses, specifically codon evolutionary models, excessive rates of false positives result. A characteristic signature of error-driven findings is unrealistically high estimates of dN/dS (e.
View Article and Find Full Text PDFEur J Pharm Sci
January 2025
Department of Pharmaceutical Technology and Biopharmacy, Institute of Pharmaceutical Sciences, University of Graz, Universitätsplatz 1, 8010, Graz, Austria. Electronic address:
Cationic nanostructured lipid carriers (cNLCs) represent promising non-viral carriers for nucleic acids, such as miRNAs, forming stable self-assembled miRNA complexes due to electrostatic interactions. Prepared by high-pressure homogenization, cNLC formulations, both with and without Nile Red dye demonstrated stable particle sizes in the range of 100-120 nm and positive surface charges (>30 mV), which are necessary for effective cellular uptake. The miRNA complexes formed at mass ratios of 1:2.
View Article and Find Full Text PDFSci Rep
November 2024
ImVitro, AI Team, Paris, France.
The use of time lapse systems (TLS) in In Vitro Fertilization (IVF) labs to record developing embryos has paved the way for deep-learning based computer vision algorithms to assist embryologists in their morphokinetic evaluation. Today, most of the literature has characterized algorithms that predict pregnancy, ploidy or blastocyst quality, leaving to the side the task of identifying key morphokinetic events. Using a dataset of N = 1909 embryos collected from multiple clinics equipped with EMBRYOSCOPE/EMBRYOSCOPE+ (Vitrolife), GERI (Genea Biomedx) or MIRI (Esco Medical), this study proposes a novel deep-learning architecture to automatically detect 11 kinetic events (from 1-cell to blastocyst).
View Article and Find Full Text PDFMicrobiol Spectr
November 2024
College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.
Archaea play a significant role in natural ecosystems and the human body. Archaeal viruses exert a considerable influence on the structure and composition of archaeal communities and their associated ecological environments. The present study revealed the complete genomes of 38 archaeal head-tailed proviruses through comprehensive data mining.
View Article and Find Full Text PDFNat Microbiol
December 2024
Department of Burn and Plastic Surgery, Shenzhen Key Laboratory of Microbiology in Genomic Modification and Editing and Application, Shenzhen Institute of Translational Medicine, Medical Innovation Technology Transformation Center of Shenzhen Second People's Hospital, Shenzhen University Medical School, The First Affiliated Hospital of Shenzhen University, Shenzhen, China.
DNA degradation (Dnd) is a widespread bacterial antiphage defence system that relies on DNA phosphorothioate (PT) modification for self/non-self discrimination and subsequent degradation of unmodified DNA. Phages employ counterstrategies to evade host immunity, but anti-Dnd immunity has not been characterized. Here we report an immune evasion protein encoded by the Salmonella phage JSS1 that contributes to subverting Dnd and other defence systems.
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