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DNA Bacteriophages01:26

DNA Bacteriophages

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Bacteriophages, or phages, are viruses that specifically infect bacteria, utilizing their genetic material to hijack host cellular machinery for replication. DNA bacteriophages employ single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) genomes. These phages exhibit diverse replication strategies and host interactions, influencing their ecological roles and applications in biotechnology and medicine.ssDNA BacteriophagesssDNA phages, with their small genomes, utilize unique strategies to...
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Bacteriophages, also known as phages, are specialized viruses that infect bacteria. A key characteristic of phages is their distinctive “head-tail” morphology. A phage begins the infection process (i.e., lytic cycle) by attaching to the outside of a bacterial cell. Attachment is accomplished via proteins in the phage tail that bind to specific receptor proteins on the outer surface of the bacterium. The tail injects the phage’s DNA genome into the bacterial cytoplasm. In the...
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In contrast to the lytic cycle, phages infecting bacteria via the lysogenic cycle do not immediately kill their host cell. Instead, they combine their genome with the host genome, allowing the bacteria to replicate the phage DNA along with the bacterial genome. The incorporated copy of the phage genome is called the prophage. Some prophages can re-activate and enter the lytic cycle. This often occurs in response to a perturbation, such as DNA damage, but can also transpire in the absence of...
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Erwin Chargaff’s rules on DNA equivalence paved the way for the discovery of base pairing in DNA. Chargaff’s rules state that in a double-stranded DNA molecule,
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The histone proteins have a flexible N-terminal tail extending out from the nucleosome. These histone tails are often subjected to post-translational modifications such as acetylation, methylation, phosphorylation, and ubiquitination. Particular combinations of these modifications form “histone codes” that influence the chromatin folding and tissue-specific gene expression.
Acetylation
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DNA Methylation: Bisulphite Modification and Analysis
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Type II Restriction of Bacteriophage DNA With 5hmdU-Derived Base Modifications.

Kiersten Flodman1, Rebecca Tsai1, Michael Y Xu1

  • 1New England Biolabs, Inc., Ipswich, MA, United States.

Frontiers in Microbiology
|April 16, 2019
PubMed
Summary

Bacteriophages use modified thymidine bases to resist bacterial restriction enzymes. This study reveals specific DNA sequences targeted by these modifications, aiding in mapping and cloning phage DNA.

Keywords:
5hmdU-derived nucleotide modificationDelftia phi W-14Pseudomonas bacteriophage (phage) M6Salmonella phage ViIType II restriction and modificationphage therapy

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Area of Science:

  • Molecular Biology
  • Genomics
  • Microbiology

Background:

  • Bacteriophages (phages) employ base modifications to evade bacterial defense systems like endonuclease restriction.
  • Thymidine (T) modifications, including 5-methyldeoxyuridine (5mdU), are crucial for phage genome protection.

Purpose of the Study:

  • To evaluate the Type II restriction resistance of three thymidine-modified phage genomes: Pseudomonas phage M6 (5-N-edU), Salmonella phage ViI (5-N-eOmdU), and Delftia phage phi W-14 (putT).
  • To identify conserved DNA sequences targeted by these modifications and assess the efficacy of DNA methyltransferases (MTases) in conferring resistance.

Main Methods:

  • Testing >200 commercially available Type II restriction endonucleases (REases) against modified phage genomic DNAs (gDNA).
  • Analyzing resistant sites to identify conserved dinucleotide sequences (TG or TC).
  • Assessing the ability of various DNA methyltransferases (MTases) to modify phage DNA and confer resistance.

Main Results:

  • Pseudomonas phage M6, Salmonella phage ViI, and Delftia phage phi W-14 gDNAs showed resistance to 48.4%, 71.0%, and 68.8% of Type II REases, respectively.
  • Conserved TG or TC dinucleotide sequences were identified as targets for base modification.
  • Certain MTases demonstrated the ability to fully or partially modify phage DNA, enhancing resistance to REase cleavage.

Conclusions:

  • Hypermodified thymidine in phage genomes provides significant resistance to host-encoded restriction systems.
  • The findings offer guidance for using REases to map and clone phage DNA containing hypermodified thymidine.
  • This research expands understanding of phage-host interactions and DNA modification strategies.