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Putative type 1 thymidylate synthase and dihydrofolate reductase as signature genes of a novel Bastille-like group of phages in the subfamily Spounavirinae.

Asare PT, Jeong TY, Ryu S, Klumpp J, Loessner MJ, Merrill BD, Kim KP - BMC Genomics (2015)

Bottom Line: More importantly, type 1 thymidylate synthase (TS1) and dihydrofolate reductase (DHFR) genes were shown to be unique for the members of the proposed Bastille-like phage group, and are suitable as molecular markers.We confirm the creation of a new genus--the "Bastille-like group"--in Spounavirinae, and propose that the presence of TS1- and DHFR-encoding genes could serve as signatures for the new Bastille-like group.In addition, the presence of metallo-beta-lactamase and/or SpoIIIE homologs in all members of Bastille-like group phages makes questionable their suitability for use in biocontrol.

View Article: PubMed Central - PubMed

Affiliation: Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do, 561-756, Korea. paul20104real@gmail.com.

ABSTRACT

Background: Spounavirinae viruses have received an increasing interest as tools for the control of harmful bacteria due to their relatively broad host range and strictly virulent phenotype.

Results: In this study, we collected and analyzed the complete genome sequences of 61 published phages, either ICTV-classified or candidate members of the Spounavirinae subfamily of the Myoviridae. A set of comparative analyses identified a distinct, recently proposed Bastille-like phage group within the Spounavirinae. More importantly, type 1 thymidylate synthase (TS1) and dihydrofolate reductase (DHFR) genes were shown to be unique for the members of the proposed Bastille-like phage group, and are suitable as molecular markers. We also show that the members of this group encode beta-lactamase and/or sporulation-related SpoIIIE homologs, possibly questioning their suitability as biocontrol agents.

Conclusions: We confirm the creation of a new genus--the "Bastille-like group"--in Spounavirinae, and propose that the presence of TS1- and DHFR-encoding genes could serve as signatures for the new Bastille-like group. In addition, the presence of metallo-beta-lactamase and/or SpoIIIE homologs in all members of Bastille-like group phages makes questionable their suitability for use in biocontrol.

No MeSH data available.


Related in: MedlinePlus

Nucleotide (a) and amino acid sequence (b) dot plot analysis of 26 Bastille-like group phages in Spounavirinae. Dot plots were generated using Gepard [9] and whole amino acid sequence of phages were retrieved from Phamerator [33]
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Fig2: Nucleotide (a) and amino acid sequence (b) dot plot analysis of 26 Bastille-like group phages in Spounavirinae. Dot plots were generated using Gepard [9] and whole amino acid sequence of phages were retrieved from Phamerator [33]

Mentions: Whole genome nucleotide (Additional file 1: Figure S1A) and amino acid sequence (Additional file 1: Figure S1B) dot plot analysis of the 61 phages also revealed 3 clusters and singletons similar to the CLANS analysis result. More detailed analysis showed that similarity at amino acid level was clearly more obvious than at nucleotide level among Bastille-like group phages (Fig. 2). Similar results were reported previously [13].Fig. 2


Putative type 1 thymidylate synthase and dihydrofolate reductase as signature genes of a novel Bastille-like group of phages in the subfamily Spounavirinae.

Asare PT, Jeong TY, Ryu S, Klumpp J, Loessner MJ, Merrill BD, Kim KP - BMC Genomics (2015)

Nucleotide (a) and amino acid sequence (b) dot plot analysis of 26 Bastille-like group phages in Spounavirinae. Dot plots were generated using Gepard [9] and whole amino acid sequence of phages were retrieved from Phamerator [33]
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4528723&req=5

Fig2: Nucleotide (a) and amino acid sequence (b) dot plot analysis of 26 Bastille-like group phages in Spounavirinae. Dot plots were generated using Gepard [9] and whole amino acid sequence of phages were retrieved from Phamerator [33]
Mentions: Whole genome nucleotide (Additional file 1: Figure S1A) and amino acid sequence (Additional file 1: Figure S1B) dot plot analysis of the 61 phages also revealed 3 clusters and singletons similar to the CLANS analysis result. More detailed analysis showed that similarity at amino acid level was clearly more obvious than at nucleotide level among Bastille-like group phages (Fig. 2). Similar results were reported previously [13].Fig. 2

Bottom Line: More importantly, type 1 thymidylate synthase (TS1) and dihydrofolate reductase (DHFR) genes were shown to be unique for the members of the proposed Bastille-like phage group, and are suitable as molecular markers.We confirm the creation of a new genus--the "Bastille-like group"--in Spounavirinae, and propose that the presence of TS1- and DHFR-encoding genes could serve as signatures for the new Bastille-like group.In addition, the presence of metallo-beta-lactamase and/or SpoIIIE homologs in all members of Bastille-like group phages makes questionable their suitability for use in biocontrol.

View Article: PubMed Central - PubMed

Affiliation: Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do, 561-756, Korea. paul20104real@gmail.com.

ABSTRACT

Background: Spounavirinae viruses have received an increasing interest as tools for the control of harmful bacteria due to their relatively broad host range and strictly virulent phenotype.

Results: In this study, we collected and analyzed the complete genome sequences of 61 published phages, either ICTV-classified or candidate members of the Spounavirinae subfamily of the Myoviridae. A set of comparative analyses identified a distinct, recently proposed Bastille-like phage group within the Spounavirinae. More importantly, type 1 thymidylate synthase (TS1) and dihydrofolate reductase (DHFR) genes were shown to be unique for the members of the proposed Bastille-like phage group, and are suitable as molecular markers. We also show that the members of this group encode beta-lactamase and/or sporulation-related SpoIIIE homologs, possibly questioning their suitability as biocontrol agents.

Conclusions: We confirm the creation of a new genus--the "Bastille-like group"--in Spounavirinae, and propose that the presence of TS1- and DHFR-encoding genes could serve as signatures for the new Bastille-like group. In addition, the presence of metallo-beta-lactamase and/or SpoIIIE homologs in all members of Bastille-like group phages makes questionable their suitability for use in biocontrol.

No MeSH data available.


Related in: MedlinePlus