First genome sequences of Achromobacter phages reveal new members of the N4 family

Wittmann, Johannes; Dreiseikelmann, Brigitte; Rohde, Manfred; Meier‐Kolthoff, Jan P.; Bunk, Boyke; Rohde, Christine

doi:10.1186/1743-422x-11-14

Cited by 49 publications

(62 citation statements)

References 76 publications

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“…10,[17][18][19] However, a survey of recent studies comparing codon usage by phages and their hosts revealed a mixture of studies where the presence of tRNA genes corresponds to codons overly expressed by the phage compared to its host 10,[20][21][22][23] and studies where that is not the case. [24][25][26][27] In phage PVP-SE1, only 11 of the codons associated with its 24 tRNA genes were present at a frequency higher than in its Salmonella hosts.…”

Section: Codon Versus Amino Acid Usagementioning

confidence: 99%

Testing hypotheses for the presence of tRNA genes in mycobacteriophage genomes

et al. 2016

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The presence of tRNA genes in bacteriophages has been explained on the basis of codon usage (tRNA genes are retained in the phage genome if they correspond to codons more common in the phage than in its host) or amino acid usage (independent of codon, the amino acid corresponding to the retained tRNA gene is more common in the phage genome than in the bacterial host). The existence of a large database of sequenced mycobacteriophages, isolated on the common host Mycobacterium smegmatis, allows us to test the above hypotheses as well as explore other hypotheses for the presence of tRNA genes. Our analyses suggest that amino acid rather than codon usage better explains the presence of tRNA genes in mycobacteriophages. However, closely related phages that differ in the presence of tRNA genes in their genomes are capable of lysing the common bacterial host and do not differ in codon or amino acid usage. This suggests that the benefits of having tRNA genes may be associated with either growth in the host or the ability to infect more hosts (i.e., host range) rather than simply infecting a particular host.

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Section: Codon Versus Amino Acid Usagementioning

confidence: 99%

Testing hypotheses for the presence of tRNA genes in mycobacteriophage genomes

et al. 2016

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“…DNA was precipitated with ethanol by adding 300 l of 3 M sodium acetate (Roth). SMRTbell template libraries were prepared according to instructions from Pacific Biosciences, Menlo Park, CA, USA, following the procedure and checklist for low-input 10-kb template preparation and sequencing by using C2-C2 chemistry as described previously (14).…”

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Paenibacilluslarvae-Directed Bacteriophage HB10c2 and Its Application in American Foulbrood-Affected Honey Bee Larvae

Beims

Wittmann

Bunk

et al. 2015

Appl Environ Microbiol

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dPaenibacillus larvae is the causative agent of American foulbrood (AFB), the most serious honey bee brood bacterial disease. We isolated and characterized P. larvae-directed bacteriophages and developed criteria for safe phage therapy. Whole-genome analysis of a highly lytic virus of the family Siphoviridae (HB10c2) provided a detailed safety profile and uncovered its lysogenic nature and a putative beta-lactamase-like protein. To rate its antagonistic activity against the pathogens targeted and to specify potentially harmful effects on the bee population and the environment, P. larvae genotypes ERIC I to IV, representatives of the bee gut microbiota, and a broad panel of members of the order Bacillales were analyzed for phage HB10c2-induced lysis. Breeding assays with infected bee larvae revealed that the in vitro phage activity observed was not predictive of the real-life scenario and therapeutic efficacy. On the basis of the disclosed P. larvae-bacteriophage coevolution, we discuss the future prospects of AFB phage therapy.

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“…Subsequent studies have described the isolation and characterization of additional N4-like phages that infect a variety of bacterial species, including Vibrio, Pseudomonas, Salmonella, and Achromobacter spp. (17)(18)(19)(20)(21)(22)(23). With the exception of Enterobacter phage EcP1 (NC_019485), which has a relatively small capsid and genome, all N4-like phages characterized to date share morphologies, genome sizes, and genomic architectures similar to those of coliphage N4 (24).…”

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Novel N4 Bacteriophages Prevail in the Cold Biosphere

Zhan

Buchan

Chen

2015

Appl Environ Microbiol

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bColiphage N4 is a lytic bacteriophage discovered nearly half a century ago, and it was considered to be a "genetic orphan" until very recently, when several additional N4-like phages were discovered to infect nonenteric bacterial hosts. Interest in this genus of phages is stimulated by their unique genetic features and propagation strategies. To better understand the ecology of N4-like phages, we investigated the diversity and geographic patterns of N4-like phages by examining 56 Chesapeake Bay viral communities, using a PCR-clone library approach targeting a diagnostic N4-like DNA polymerase gene. Many new lineages of N4-like phages were found in the bay, and their genotypes shift from the lower to the upper bay. Interestingly, signature sequences of N4-like phages were recovered only from winter month samples, when water temperatures were below 4°C. An analysis of existing metagenomic libraries from various aquatic environments supports the hypothesis that N4-like phages are most prolific in colder waters. In particular, a high number of N4-like phages were detected in Organic Lake, Antarctica, a cold and hypersaline system. The prevalence of N4-like phages in the cold biosphere suggests these viruses possess yet-to-be-determined mechanisms that facilitate lytic infections under cold conditions. A s the most abundant microbial form, viruses play important roles in shaping host population structures, mediating genetic exchange between hosts, and modulating trophic transfer in marine food webs (1-3). Marine viral metagenomic studies suggest that viruses encompass the largest genetic repertoire in the ocean (4, 5), yet the functions of ϳ70% of the putative genes identified in viral metagenomic studies remain unknown (6). Recently, several novel phages infecting dominant marine bacteria have been isolated from the ocean (7,8). Both cultivation techniques and molecular approaches suggest that a great many marine viruses await discovery.Bacteriophage N4 was first isolated from sewer waters using Escherichia coli as a host nearly half a century ago (9) and remained a "genetic orphan" for decades, as no other genetically similar phages were characterized. Phage N4 has several unique features with regard to its morphology, physiology, and genome that have made it a focus of study. It has a 70-nm isocahedral capsid, and its genome size is 70 kb. More remarkably, N4 is the only known phage that does not rely on host RNA polymerase for early transcription (10, 11). Instead, it contains a DNA-dependent virionencapsidated RNA polymerase (vRNAP), which is coinjected with viral DNA into its host and initiates transcription (12). The phage also exhibits a lysis-inhibited infection cycle and an extremely large burst size (ca. 3,000 phages per cell), suggestive of a novel mechanism of cell lysis regulation (13,14).The recent renewed interest in the ecology of N4 was prompted by the isolation from a coastal estuary of two new N4-like phages, which infect bacteria of the marine Roseobacter lineage (15). Roseobacters are a widely ...

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First genome sequences of Achromobacter phages reveal new members of the N4 family

Cited by 49 publications

References 76 publications

Testing hypotheses for the presence of tRNA genes in mycobacteriophage genomes

Testing hypotheses for the presence of tRNA genes in mycobacteriophage genomes

Paenibacilluslarvae-Directed Bacteriophage HB10c2 and Its Application in American Foulbrood-Affected Honey Bee Larvae

Novel N4 Bacteriophages Prevail in the Cold Biosphere

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