Complete Genome Sequence of Bacteriophage EC6, Capable of Lysing Escherichia coli O157:H7

Tiwari, Birendra R.; Kim, Jungmin

doi:10.1128/genomea.00085-12

Cited by 7 publications

(6 citation statements)

References 12 publications

(8 reference statements)

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“…Both SUSP1 and SUSP2 are members of the family Myoviridae and form clear plaques (see Fig. S6); possess genomes of 90.8 and 88.7 kb, respectively; and are most closely related to Escherichia phage EC6 (21), Citrobacter phage Moogle (22), and other Felix O1-like viruses (see Table S1). Because both SUSP1 and SUSP2 share <90% whole-genome homology with all other published phage sequences and encode a substantial number of hypothetical proteins with unknown biological functions, we considered the possibility that these phages actively produce some type of DNA-protecting factor(s) during infection.…”

Section: Resultsmentioning

confidence: 99%

Novel “Superspreader” Bacteriophages Promote Horizontal Gene Transfer by Transformation

Keen

Bliskovsky

Malagón

et al. 2017

mBio

120

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Bacteriophages infect an estimated 1023 to 1025 bacterial cells each second, many of which carry physiologically relevant plasmids (e.g., those encoding antibiotic resistance). However, even though phage-plasmid interactions occur on a massive scale and have potentially significant evolutionary, ecological, and biomedical implications, plasmid fate upon phage infection and lysis has not been investigated to date. Here we show that a subset of the natural lytic phage population, which we dub “superspreaders,” releases substantial amounts of intact, transformable plasmid DNA upon lysis, thereby promoting horizontal gene transfer by transformation. Two novel Escherichia coli phage superspreaders, SUSP1 and SUSP2, liberated four evolutionarily distinct plasmids with equal efficiency, including two close relatives of prominent antibiotic resistance vectors in natural environments. SUSP2 also mediated the extensive lateral transfer of antibiotic resistance in unbiased communities of soil bacteria from Maryland and Wyoming. Furthermore, the addition of SUSP2 to cocultures of kanamycin-resistant E. coli and kanamycin-sensitive Bacillus sp. bacteria resulted in roughly 1,000-fold more kanamycin-resistant Bacillus sp. bacteria than arose in phage-free controls. Unlike many other lytic phages, neither SUSP1 nor SUSP2 encodes homologs to known hydrolytic endonucleases, suggesting a simple potential mechanism underlying the superspreading phenotype. Consistent with this model, the deletion of endonuclease IV and the nucleoid-disrupting protein ndd from coliphage T4, a phage known to extensively degrade chromosomal DNA, significantly increased its ability to promote plasmid transformation. Taken together, our results suggest that phage superspreaders may play key roles in microbial evolution and ecology but should be avoided in phage therapy and other medical applications.

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Section: Resultsmentioning

confidence: 99%

Novel “Superspreader” Bacteriophages Promote Horizontal Gene Transfer by Transformation

Keen

Bliskovsky

Malagón

et al. 2017

mBio

120

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“…strain CcI3) to 9.04 Mbp for a broad host range Elaeagnus strain (EAN1pec) [ 23 ]. In recent years, several more Frankia strains have been sequenced [ 24 – 31 ]. Analysis of these genomes confirmed that the Frankia genome size correlates positively to host specificity and biogeography ranges [ 22 , 23 ].…”

Section: Introductionmentioning

confidence: 99%

“…Analysis of these genomes confirmed that the Frankia genome size correlates positively to host specificity and biogeography ranges [ 22 , 23 ]. Presently, genome sequences are available for all four Frankia lineages: Cluster 1 “medium and narrow host range” strains CcI3, ACN14a, CcI6, BMG5.23, Thr, and QA3 [ 23 , 26 , 29 – 31 ]; Cluster 2 “uncultured” Frankia datiscae Dg1 [ 25 ]; Cluster 3 “broad host range” strains EAN1pec, EUN1f, BMG5.12 and BCU110501 [ 23 , 24 , 27 ]; and Cluster 4 “atypical” strains EuI1c, CN3 and DC12 [ 22 , 24 ]. Atypical Frankia strains used in this study are unable to fix nitrogen, and two (strains CN3 and DC12) are unable to re-infect their host plant.…”

Section: Introductionmentioning

confidence: 99%

The ins and outs of metal homeostasis by the root nodule actinobacterium Frankia

Furnholm

Tisa

2014

BMC Genomics

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BackgroundFrankia are actinobacteria that form a symbiotic nitrogen-fixing association with actinorhizal plants, and play a significant role in actinorhizal plant colonization of metal contaminated areas. Many Frankia strains are known to be resistant to several toxic metals and metalloids including Pb2+, Al+3, SeO2, Cu2+, AsO4, and Zn2+. With the availability of eight Frankia genome databases, comparative genomics approaches employing phylogeny, amino acid composition analysis, and synteny were used to identify metal homeostasis mechanisms in eight Frankia strains. Characterized genes from the literature and a meta-analysis of 18 heavy metal gene microarray studies were used for comparison.ResultsUnlike most bacteria, Frankia utilize all of the essential trace elements (Ni, Co, Cu, Se, Mo, B, Zn, Fe, and Mn) and have a comparatively high percentage of metalloproteins, particularly in the more metal resistant strains. Cation diffusion facilitators, being one of the few known metal resistance mechanisms found in the Frankia genomes, were strong candidates for general divalent metal resistance in all of the Frankia strains. Gene duplication and amino acid substitutions that enhanced the metal affinity of CopA and CopCD proteins may be responsible for the copper resistance found in some Frankia strains. CopA and a new potential metal transporter, DUF347, may be involved in the particularly high lead tolerance in Frankia. Selenite resistance involved an alternate sulfur importer (CysPUWA) that prevents sulfur starvation, and reductases to produce elemental selenium. The pattern of arsenate, but not arsenite, resistance was achieved by Frankia using the novel arsenite exporter (AqpS) previously identified in the nitrogen-fixing plant symbiont Sinorhizobium meliloti. Based on the presence of multiple tellurite resistance factors, a new metal resistance (tellurite) was identified and confirmed in Frankia.ConclusionsEach strain had a unique combination of metal import, binding, modification, and export genes that explain differences in patterns of metal resistance between strains. Frankia has achieved similar levels of metal and metalloid resistance as bacteria from highly metal-contaminated sites. From a bioremediation standpoint, it is important to understand mechanisms that allow the endosymbiont to survive and infect actinorhizal plants in metal contaminated soils.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-1092) contains supplementary material, which is available to authorized users.

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“…Since many of the genomes of Felix01-related phages have already been examined in detail and published, herein is provided only a brief overview of VpaE1 genome. Bacteriophage VpaE1 has a linear ds DNA genome of 88,403 bp that is similar in size to those of other Felix01-related viruses whose genome sizes range between 84 and 93 kb [ 19 , 23 , 24 , 27 , 29 , 32 , 33 , 35 ]. As is the case with other virulent phages, the VpaE1 genome has an average mol% G+C content of 38.9%, which differs significantly from that of the host (~50%).…”

Section: Resultsmentioning

confidence: 99%

“…Felix01 has long been considered as a singleton within the family Myoviridae [ 22 ]. However, during the last few years, a dozen of its close relatives, active mainly against E. coli [ 23 , 24 , 25 , 26 , 27 ] or Salmonella [ 28 , 29 , 30 , 31 , 32 ] have been isolated and sequenced. In addition, more distant Felix01 relatives that infect Erwinia [ 33 ], Citrobacter [ 34 ] or Pseudomonas [ 35 ] have been described.…”

Section: Introductionmentioning

confidence: 99%

Incomplete LPS Core-Specific Felix01-Like Virus vB_EcoM_VpaE1

Šimoliūnas

Vilkaitytė

Kalinienė

et al. 2015

Viruses

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Bacteriophages represent a valuable source for studying the mechanisms underlying virus-host interactions. A better understanding of the host-specificity of viruses at the molecular level can promote various phage applications, including bacterial diagnostics, antimicrobial therapeutics, and improve methods in molecular biology. In this study, we describe the isolation and characterization of a novel coliphage, vB_EcoM_VpaE1, which has different host specificity than its relatives. Morphology studies, coupled with the results of genomic and proteomic analyses, indicate that vB_EcoM_VpaE1 belongs to the newly proposed genus Felix01likevirus in the family Myoviridae. The genus Felix01likevirus comprises a group of highly similar phages that infect O-antigen-expressing Salmonella and Escherichia coli (E. coli) strains. Phage vB_EcoM_VpaE1 differs from the rest of Felix01-like viruses, since it infects O-antigen-deficient E. coli strains with an incomplete core lipopolysaccharide (LPS). We show that vB_EcoM_VpaE1 can infect mutants of E. coli that contain various truncations in their LPS, and can even recognize LPS that is truncated down to the inner-core oligosaccharide, showing potential for the control of rough E. coli strains, which usually emerge as resistant mutants upon infection by O-Ag-specific phages. Furthermore, VpaE1 can replicate in a wide temperature range from 9 to 49 °C, suggesting that this virus is well adapted to harsh environmental conditions. Since the structural proteins of such phages tend to be rather robust, the receptor-recognizing proteins of VpaE1 are an attractive tool for application in glycan analysis, bacterial diagnostics and antimicrobial therapeutics.

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Complete Genome Sequence of Bacteriophage EC6, Capable of Lysing Escherichia coli O157:H7

Cited by 7 publications

References 12 publications

Novel “Superspreader” Bacteriophages Promote Horizontal Gene Transfer by Transformation

Novel “Superspreader” Bacteriophages Promote Horizontal Gene Transfer by Transformation

The ins and outs of metal homeostasis by the root nodule actinobacterium Frankia

Incomplete LPS Core-Specific Felix01-Like Virus vB_EcoM_VpaE1

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