The Sequence of Two Bacteriophages with Hypermodified Bases Reveals Novel Phage-Host Interactions

Kropinski, Andrew M.; Turner, Dann; Nash, John H. E.; Ackermann, Hans-Wolfgang; Lingohr, Erika J.; Warren, R. A. J.; Ehrlich, Kenneth C.; Ehrlich, Melanie

doi:10.3390/v10050217

Cited by 5 publications

(3 citation statements)

References 78 publications

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“…An examination of the literature for DfrE thymidylate synthase demonstrated it conferred resistance to trimethoprim in E. coli when cloned into a high copy plasmid [46]. However, the majority of the literature surrounding phage encoding thymidylate synthases characterize this enzyme as important in DNA synthesis [56] with recent literature showing these enzymes are present in phages which synthesize modified DNA bases during replication [57]. Therefore, it is not clear if the elderly-associated faecal viruses examined in this study confer trimethoprim resistance to their host bacteria; however, any potential trimethoprim resistance conferred through these phages is likely a secondary consequence of the phage's natural replication strategy.…”

Section: Discussionmentioning

confidence: 99%

Viral Dark Matter in the Gut Virome of Elderly Humans

Stockdale

Ryan

McCann

et al. 2018

Preprint

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The human virome is an area of increasing interest with relation to human health and disease. It has been demonstrated to alter in concert with the bacterial microbiome in early life and was also found to be different in patients with certain diseases such as inflammatory bowel disease. However, all virome analyses are hampered by a lack of annotated representative database sequences, often referred to as the ‘viral dark matter’. Here we provide the first description of the gut DNA virome in elderly individuals (>65 years old) as well as the description of novel bacteriophages not present in current reference databases. Diversity analysis comparing elderly persons from different residence locations (community living vs long term care facilities) did not reveal any difference in their virome diversity profiles despite the reported differences at the bacteriome level. An abundance of Microviridae of the subfamily Gokushovirinae were present in the faeces of elderly individuals. Several novel members of the order Caudovirales were also characterized and annotated. Assignment of host bacteria to detected viral genomes was attempted using a combination of CRISPR spacers, tRNA genes and a probabilistic approach. Further characterization of the viral dark matter is necessary for developing tools and expanding databases to study the human virome. This study focused on the virome of an aging human cohort with the goal of illuminating part of the viral dark matter.

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Section: Discussionmentioning

confidence: 99%

Viral Dark Matter in the Gut Virome of Elderly Humans

Stockdale

Ryan

McCann

et al. 2018

Preprint

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“…The whole genome sequences of bacteria revealed an abundance of lysogenic phage sequences in the genomes of many bacterial species [23]. Interestingly, some phage genes originated in bacterial cells, and these phage-introduced genes (called auxiliary metabolic genes) in host cells can modulate host cell metabolism during infection [24][25][26]. Therefore, phages have served as vectors of horizontal gene transfer and drivers of bacterial evolution.…”

Section: Introductionmentioning

confidence: 99%

The analysis of the function, diversity, and evolution of the Bacillus phage genome

et al. 2023

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Background Phages play a pivotal role in the evolution of microbial populations. The interactions between phages and their hosts are complex and may vary in response to host physiology and environmental conditions. Here, we have selected the genomes of some representative Bacillus prophages and lysosomes from the NCBI database for evolutionary analysis. We explored their evolutionary relationships and analyzed the protein information encoded by hundreds of Bacillus phages. Results We obtained the following conclusions: First, Bacillus phages carried some known functional gene fragments and a large number of unknown functional gene fragments, which might have an important impact on Bacillus populations, such as the formation of spores and biofilms and the transmission of virulence factors. Secondly, the Bacillus phage genome showed diversity, with a clear genome boundary between Bacillus prophages and Bacillus lytic phages. Furthermore, genetic mutations, sequence losses, duplications, and host-switching have occurred during the evolution of the Bacillus phage, resulting in low genome similarity between the Bacillus phages. Finally, the lysis module played an important influence on the process of Bacillus phage cross-species infestation. Conclusions This study systematically described their protein function, diversity, and genome evolution, and the results of this study provide a basis for evolutionary diversity, horizontal gene transfer and co-evolution with the host in Bacillus phages.

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“…Collectively, bacteriophages contain the greatest diversity of known naturally occurring modified DNA bases compared with any group of cellular organisms [ 7 , 8 , 9 , 10 ]. Non-canonical deoxyribonucleosides have been reported for all four bases of phage genomic DNAs, for example, 5-methyl-2′-deoxycytidine (m5dC) in Xanthomonas phage XP12 [ 11 , 12 ], 2′-deoxy-7-formamidimide-7-deazaguanosine (dG + ) in Enterobacteria phage 9g [ 13 , 14 ], N 6 -methyl-2′-deoxyadenosine (m6dA) in Escherichia phage T2 [ 15 ], and 5-putrescinylthymidine (α-putT) in Pseudomonas phage phi W-14 [ 16 , 17 ].…”

Section: Introductionmentioning

confidence: 99%

Pantoea Bacteriophage vB_PagS_MED16—A Siphovirus Containing a 2′-Deoxy-7-amido-7-deazaguanosine-Modified DNA

Šimoliūnienė

Žukauskienė

Truncaitė

et al. 2021

IJMS

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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.

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The Sequence of Two Bacteriophages with Hypermodified Bases Reveals Novel Phage-Host Interactions

Cited by 5 publications

References 78 publications

Viral Dark Matter in the Gut Virome of Elderly Humans

Viral Dark Matter in the Gut Virome of Elderly Humans

The analysis of the function, diversity, and evolution of the Bacillus phage genome

Pantoea Bacteriophage vB_PagS_MED16—A Siphovirus Containing a 2′-Deoxy-7-amido-7-deazaguanosine-Modified DNA

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