Genomic Diversity of Type B3 Bacteriophages of Caulobacter crescentus

Ash, Kurt T.; Drake, Kristina M.; Gibbs, Whitney S.; Ely, Bert

doi:10.1007/s00284-017-1248-4

Cited by 14 publications

(6 citation statements)

References 27 publications

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“…This exceptionally small plaque size produced by Kronos counters the typical inverse relationship of plaque size to genome size among caulophages. For example, giant caulophages that possess larger genomes such as phiCbk (205 kbp) and Colossus (297 kbp) produce small plaques (1 mm) [3,14]. In contrast, caulophages with small genomes (40-50 kbp) and small capsid sizes (< 60 nm), such as Lullwater [20] produce variable-sized larger plaques (1-3.5 mm).…”

Section: Phage Isolation and Characterizationmentioning

confidence: 99%

The Isolation and Characterization of Kronos, a Novel Caulobacter Rhizosphere Phage that is Similar to Lambdoid Phages

Berrios

Ely

2019

Curr Microbiol

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Despite their ubiquity, relatively few bacteriophages have been characterized. Here, we set out to explore Caulobacter bacteriophages (caulophages) in the rhizosphere and characterized Kronos, the first caulophage isolated from the rhizosphere. Kronos is a member of the Siphoviridae family since it has a long flexible tail. In addition, an analysis of the Kronos genome indicated that many of the predicted proteins were distantly-related to those of bacteriophages in the lambdoid family. Consistent with this observation, we were able to demonstrate the presence of cos sites that are similar to those found at ends of lambdoid phage genomes. Moreover, Kronos displayed a relatively rare head and tail morphology compared to other caulophages but was similar to that of the lambdoid phages. Taken together, these data indicate that Kronos is distantly related to lambdoid phages and may represent a new Siphoviridae genus.

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Section: Phage Isolation and Characterizationmentioning

confidence: 99%

The Isolation and Characterization of Kronos, a Novel Caulobacter Rhizosphere Phage that is Similar to Lambdoid Phages

Berrios

Ely

2019

Curr Microbiol

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“…Sequencing produced a circular assembly with a length of 104,206 bp. The large genome is consistent with its B3 morphotype [ 25 ], and the extremely prolate capsid of an enlarged size is able to carry a larger genome than its icosahedral counterpart. The first 10,992 bp were determined to be a direct terminal repeat (DTR), with a 434.36 ± 68.26× sequencing coverage that was approximately 2-fold greater than that of the rest of the genome (230.88 ± 28.14×) ( Figure 3 A).…”

Section: Resultsmentioning

confidence: 99%

“…Plaques of phage RXM are clear and round, with a well-defined boundary ranging from 1.5 to 1.8 mm in diameter ( Figure 1 A). TEM inspection revealed that RXM displays a unique Siphoviridae B3 morphotype [ 25 ], with a prolate capsid (111.50 ± 1.48 nm long and 56.02 ± 3.06 nm wide) and a long flexible tail (220.57 ± 3.88 nm long). Intriguingly, TEM showed that virions often adhere to each other through their heads ( Figure 1 B; see also Supplementary Figure S1A and S1B ).…”

Section: Resultsmentioning

confidence: 99%

A Novel Phage Infecting the Marine Photoheterotrophic Bacterium Citromicrobium bathyomarinum

Shao

Wei

et al. 2022

Viruses

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This study isolated and characterized a new phage infecting the marine photoheterotrophic bacterium Citromicrobium bathyomarinum, which fills the gap in research on phages targeting this ecologically important species. The phage vB_CbaS-RXM (RXM) has a dsDNA genome with a length of 104,206 bp and G+C content of 61.64%. The taxonomic analysis found a close evolutionary relationship between RXM, Erythrobacter phage vB_EliS-L02, and Sphingobium phage Lacusarx, and we propose that RXM represents a new species of the Lacusarxvirus genus. A one-step growth curve revealed a burst size of 75 plaque-forming units (PFUs) per cell in a 3-hour infection cycle. The lysis profile of RXM showed an intraspecific lethal rate of 26.3% against 38 citromicrobial strains. RXM contains 15 auxiliary metabolic genes (AMGs) related to diverse cellular processes, such as putative metabolic innovation and hijacking of host nucleotide metabolism to enhance its biosynthetic capacity. An in-depth analysis showed that phage functional genes strongly rely on the host for translation, while the translation of unique phage genes with less host dependency may be complemented by phage tRNA. Overall, our study investigated the infection kinetics, genetic traits, taxonomy, and predicted roles of AMGs and tRNA genes of this new phage, which contributes to a better understanding of phage diversity and phage–bacterium interactions.

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“…Predicted functions are only available for genes 71 and 95; AAA ATPase and ThyX respectively. The RcD homologs of RcZahn 37-41 are in the same order in RcZahn and are in the highly conserved region on the left side of the genome (RcD genes [10][11][12][13][14]. Another gene encoding an ADP ribosyltransferase is present in RcZahn (gene 101) and in 6 of the 8 RcD phages but is absent from RcMcDreamy and RcSalem.…”

Section: Rcd Clustermentioning

confidence: 99%

Genomic diversity of bacteriophages infecting Rhodobacter capsulatus and their relatedness to its gene transfer agent RcGTA

et al. 2021

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The diversity of bacteriophages is likely unparalleled in the biome due to the immense variety of hosts and the multitude of viruses that infect them. Recent efforts have led to description at the genomic level of numerous bacteriophages that infect the Actinobacteria, but relatively little is known about those infecting other prokaryotic phyla, such as the purple non-sulfur photosynthetic α-proteobacterium Rhodobacter capsulatus. This species is a common inhabitant of freshwater ecosystems and has been an important model system for the study of photosynthesis. Additionally, it is notable for its utilization of a unique form of horizontal gene transfer via a bacteriophage-like element known as the gene transfer agent (RcGTA). Only three bacteriophages of R. capsulatus had been sequenced prior to this report. Isolation and characterization at the genomic level of 26 new bacteriophages infecting this host advances the understanding of bacteriophage diversity and the origins of RcGTA. These newly discovered isolates can be grouped along with three that were previously sequenced to form six clusters with four remaining as single representatives. These bacteriophages share genes with RcGTA that seem to be related to host recognition. One isolate was found to cause lysis of a marine bacterium when exposed to high-titer lysate. Although some clusters are more highly represented in the sequenced genomes, it is evident that many more bacteriophage types that infect R. capsulatus are likely to be found in the future.

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Genomic Diversity of Type B3 Bacteriophages of Caulobacter crescentus

Cited by 14 publications

References 27 publications

The Isolation and Characterization of Kronos, a Novel Caulobacter Rhizosphere Phage that is Similar to Lambdoid Phages

The Isolation and Characterization of Kronos, a Novel Caulobacter Rhizosphere Phage that is Similar to Lambdoid Phages

A Novel Phage Infecting the Marine Photoheterotrophic Bacterium Citromicrobium bathyomarinum

Genomic diversity of bacteriophages infecting Rhodobacter capsulatus and their relatedness to its gene transfer agent RcGTA

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