Two novel temperate bacteriophages co-existing in Aeromonas sp. ARM81 – characterization of their genomes, proteomes and DNA methyltransferases

Abstract

Aeromonas species are causative agents of a wide spectrum of diseases in animals and humans. Although these bacteria are commonly found in various environments, little is known about their phages. Thus far, only one temperate Aeromonas phage has been characterized. Whole-genome sequencing of an Aeromonas sp. strain ARM81 revealed the presence of two prophage clusters. One of them is integrated into the chromosome and the other was maintained as an extrachromosomal, linear plasmid-like prophage encoding a protelomerase. Both prophages were artificially and spontaneously inducible. We separately isolated both phages and compared their genomes with other known viruses. The novel phages show no similarity to the previously characterized Aeromonas phages and might represent new evolutionary lineages of viruses infecting Aeromonadaceae. Apart from the comparative genomic analyses of these phages, complemented with their structural and molecular characterization, a functional analysis of four DNA methyltransferases encoded by these viruses was conducted. One of the investigated N6-adenine-modifying enzymes shares sequence specificity with a Dam-like methyltransferase of its bacterial host, while another one is non-specific, as it catalyzes adenine methylation in various sequence contexts. The presented results shed new light on the diversity of Aeromonas temperate phages.

Phage-Encoded LuxR-Type Receptors Responsive to Host-Produced Bacterial Quorum-Sensing Autoinducers

“…Furthermore, PCR amplification of the putative phage origin and primase gene required for replication ( repA ), ligation of the product to an antibiotic resistance cassette followed by introduction and selection in E. coli , shows that the ligated product can be maintained as a plasmid. This final result demonstrates that the luxR -containing contig encodes a functional replication gene for a plasmid-like element, which is the reported state in which ΦARM81ld exists when it lysogenizes its Aeromonas host (6). Lastly, the contig carrying this putative phage luxR gene is comparable in length to the genome of phage ΦARM81ld (46.8 kb in A. popoffii vs. 47.6 kb in ΦARM81ld) and can be aligned along its entire length to the complete ΦARM81Id genome (60.1% pairwise identify; Figure 1C).…”

“…ARM81 (accession: KT898133.1). This phage is called ΦARM81ld (6) (Figure 1A) and the gene designated p37 encodes a putative LuxR-type transcription factor. While we were unable to obtain Aeromonas sp .…”

“…Consistent with this idea, we found that, as is the case for Aeromonas sp . ARM81 (6), lysis of A. popoffii is induced by the DNA damaging agent mitomycin C (MMC). Specifically, a precipitous decline in OD 600 over time occurs following MMC addition (Figure S2A).…”

Characterization of Sinorhizobium sp. LM21 Prophages and Virus-Encoded DNA Methyltransferases in the Light of Comparative Genomic Analyses of the Sinorhizobial Virome

“…ARM81 phages. Genes encoding ARM81mr_p29 of ФARM81mr and ARM81ld_p31 of the linear plasmid-prophage ФARM81ld (both have 34% identity with Phi2LM21_p23) are localized in a replication module (the same as Phi2LM21_p23) or in the vicinity of the plasmid partitioning system, respectively [ 51 ]. The location of these MTase genes adjacent to the replication/segregation module may suggest the relevance of the methyltransferase activity at this stage of the virus reproductive cycle.…”

Novel Bacteriophages Capable of Disrupting Biofilms From Clinical Strains of Aeromonas hydrophila

“…Bacteriophages, although discovered before antibiotics, have recently emerged as adjuncts and alternatives to antibiotics (Golkar et al, 2014). While temperate (Beilstein and Dreiseikelmann, 2008;Dziewit and Radlinska, 2016) and lytic (Chow and Rouf, 1983;Merino et al, 1990a,b;Shen et al, 2012;Jun et al, 2013;Anand et al, 2016;Wang et al, 2016;Le et al, 2018;Yuan et al, 2018) bacteriophages against A. hydrophila have been previously reported, these were isolated using environmental and fish pathogenic isolates of A. hydrophila. In the instances where host range was tested, their activity did not extend to clinical strains of A. hydrophila (Wang et al, 2016), that is, strains which were isolated from hospital patients suffering from A. hydrophila infections.…”