archaeosine and 7-deazaguanine

The discovery of ∼20-kb gene clusters containing a family of paralogs of tRNA guanosine transglycosylase genes, called tgtA5, alongside 7-cyano-7-deazaguanine (preQ0) synthesis and DNA metabolism genes, led to the hypothesis that 7-deazaguanine derivatives are inserted in DNA. This was established by detecting 2'-deoxy-preQ0 and 2'-deoxy-7-amido-7-deazaguanosine in enzymatic hydrolysates of DNA extracted from the pathogenic, Gram-negative bacteria Salmonella enterica serovar Montevideo. These modifications were absent in the closely related S. enterica serovar Typhimurium LT2 and from a mutant of S Montevideo, each lacking the gene cluster. This led us to rename the genes of the S. Montevideo cluster as dpdA-K for 7-deazapurine in DNA. Similar gene clusters were analyzed in ∼150 phylogenetically diverse bacteria, and the modifications were detected in DNA from other organisms containing these clusters, including Kineococcus radiotolerans, Comamonas testosteroni, and Sphingopyxis alaskensis Comparative genomic analysis shows that, in Enterobacteriaceae, the cluster is a genomic island integrated at the leuX locus, and the phylogenetic analysis of the TgtA5 family is consistent with widespread horizontal gene transfer. Comparison of transformation efficiencies of modified or unmodified plasmids into isogenic S. Montevideo strains containing or lacking the cluster strongly suggests a restriction-modification role for the cluster in Enterobacteriaceae. Another preQ0 derivative, 2'-deoxy-7-formamidino-7-deazaguanosine, was found in the Escherichia coli bacteriophage 9 g, as predicted from the presence of homologs of genes involved in the synthesis of the archaeosine tRNA modification. These results illustrate a deep and unexpected evolutionary connection between DNA and tRNA metabolism.

Topics: Amino Acid Sequence; Bacterial Proteins; Coliphages; Deoxyguanosine; DNA, Bacterial; Gene Transfer, Horizontal; Genomic Islands; Guanine; Guanosine; Molecular Sequence Data; Multigene Family; Mutation; Phylogeny; Purines; RNA, Transfer; Salmonella enterica; Salmonella typhimurium

The G15-C48 Levitt base pair, located at a crucial position in the core of canonical tRNAs, assumes a reverse Watson-Crick (RWC) geometry. By means of bioinformatics analysis and quantum mechanics calculations we show here that such a geometry is moderately more stable than an alternative bifurcated trans geometry, involving the guanine Watson-Crick face and the cytosine keto group, which we have also found in known RNA structures. However we also demonstrate that the RWC geometry can take advantage of additional stabilizing effects such as metal binding or post-transcriptional chemical modification. One of the few strong metal binding sites characterized for cytosolic tRNAs is localized on G15, and a domain-specific complex modification known as archaeosine is widespread at position 15 in archaeal tRNAs. We have found that both the bound Mg2+ ion and the archaeosine modification induce an analogous electron density redistribution, which results in an effective stabilization of the RWC geometry. Metal binding and chemical modification thus play an interchangeable role in stabilizing the G15-C48 correct geometry. Interestingly, these different but convergent strategies are selectively adopted in the different life domains.

Topics: Archaeal Proteins; Base Pairing; Binding Sites; Computer Simulation; Enzyme Stability; Guanine; Guanosine; Magnesium; Models, Molecular; Nucleic Acid Conformation; Pentosyltransferases; RNA, Archaeal; RNA, Transfer; Sequence Analysis, RNA; Thermodynamics