Abstract
A novel siphovirus, vB_PagS_MED16 (MED16) was isolated in Lithuania using Pantoea agglomerans strain BSL for the phage propagation. The double-stranded DNA genome of MED16 (46,103 bp) contains 73 predicted open reading frames (ORFs) encoding proteins, but no tRNA. Our comparative sequence analysis revealed that 26 of these ORFs code for unique proteins that have no reliable identity when compared to database entries. Based on phylogenetic analysis, MED16 represents a new genus with siphovirus morphology. In total, 35 MED16 ORFs were given a putative functional annotation, including those coding for the proteins responsible for virion morphogenesis, phage–host interactions, and DNA metabolism. In addition, a gene encoding a preQ0 DNA deoxyribosyltransferase (DpdA) is present in the genome of MED16 and the LC–MS/MS analysis indicates 2′-deoxy-7-amido-7-deazaguanosine (dADG)-modified phage DNA, which, to our knowledge, has never been experimentally validated in genomes of Pantoea phages. Thus, the data presented in this study provide new information on Pantoea-infecting viruses and offer novel insights into the diversity of DNA modifications in bacteriophages.
Highlights
Introduction distributed under the terms andBacteriophages, the viruses that infect bacteria, are the most abundant biological entities in the biosphere [1]
We report the experimental identification of hypermodified guanosine nucleotides in the DNA of two Pantoea agglomerans-infecting phages: vB_PagS_MED16 and vB_PagS_Vid5 (Vid5) [22]
Transmission electron microscopy (TEM) analysis revealed that MED16 is a siphovirus that corresponds to the B1 morphotype in Bradley’s classification [23,24]
Summary
Bacteriophages, the viruses that infect bacteria, are the most abundant biological entities in the biosphere [1]. Phages are widespread in a variety of environments and play a major role in modulating the abundance of bacterial populations. Bacteria have developed mechanisms of defending themselves from phages, such as the conditions of the Creative Commons. Phages have evolved counter measures to escape these defenses, and one of the most widespread strategies is to modify their DNA [4,5,6]. Bacteriophages contain the greatest diversity of known naturally occurring modified DNA bases compared with any group of cellular organisms [7,8,9,10]. Noncanonical deoxyribonucleosides have been reported for all four bases of phage genomic
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