pyrimidinones and 7-deazaguanine

In the constant evolutionary battle against mobile genetic elements (MGEs), bacteria have developed several defense mechanisms, some of which target the incoming, foreign nucleic acids e.g. restriction-modification (R-M) or CRISPR-Cas systems. Some of these MGEs, including bacteriophages, have in turn evolved different strategies to evade these hurdles. It was recently shown that the siphophage CAjan and 180 other viruses use 7-deazaguanine modifications in their DNA to evade bacterial R-M systems. Among others, phage CAjan genome contains a gene coding for a DNA-modifying homolog of a tRNA-deazapurine modification enzyme, together with four 7-cyano-7-deazaguanine synthesis genes. Using the CRISPR-Cas9 genome editing tool combined with the Nanopore Sequencing (ONT) we showed that the 7-deazaguanine modification in the CAjan genome is dependent on phage-encoded genes. The modification is also site-specific and is found mainly in two separate DNA sequence contexts: GA and GGC. Homology modeling of the modifying enzyme DpdA provides insight into its probable DNA binding surface and general mode of DNA recognition.

Topics: Bacteriophages; Base Sequence; CRISPR-Cas Systems; DNA; DNA Restriction-Modification Enzymes; Escherichia coli; Gene Editing; Guanine; Humans; Nanopore Sequencing; Nucleotide Motifs; Pyrimidinones; Pyrroles; Siphoviridae

Genome modifications are central components of the continuous arms race between viruses and their hosts. The archaeosine base (G

Topics: Archaeal Viruses; Bacteriophages; DNA; DNA Restriction Enzymes; Guanine; Pyrimidinones; Pyrroles

QueF (MW = 19.4 kDa) is a recently characterized nitrile oxidoreductase which catalyzes the NADPH-dependent reduction of 7-cyano-7-deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine, a late step in the biosynthesis of the modified tRNA nucleoside queuosine. Initial crystals of homododecameric Bacillus subtilis QueF diffracted poorly to 8.0 A. A three-dimensional model based on homology with the tunnel-fold enzyme GTP cyclohydrolase I suggested catalysis at intersubunit interfaces and a potential role for substrate binding in quaternary structure stabilization. Guided by this insight, a second crystal form was grown that was strictly dependent on the presence of preQ0. This crystal form diffracted to 2.25 A resolution.

Topics: Bacillus subtilis; Catalysis; Computational Biology; Crystallization; Crystallography, X-Ray; GTP Cyclohydrolase; Guanine; Models, Chemical; Models, Molecular; NADP; Nucleoside Q; Oxidoreductases; Protein Conformation; Protein Isoforms; Protein Structure, Tertiary; Pyrimidinones; Pyrroles; RNA Processing, Post-Transcriptional; RNA, Transfer; X-Ray Diffraction