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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

Gene arrangement of TS, DHFR, SpoIIIE and beta-lactamase genes in phage genomes. a Bastille-like group; b Singleton; c Twort-like group; d SPO1-like group. Gene location is not to the scale. Numbers found in (A) represent gene designation number in each genome
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Fig7: Gene arrangement of TS, DHFR, SpoIIIE and beta-lactamase genes in phage genomes. a Bastille-like group; b Singleton; c Twort-like group; d SPO1-like group. Gene location is not to the scale. Numbers found in (A) represent gene designation number in each genome

Mentions: B4 gp21 encoded a putative DHFR, however, the gene size (71 amino acids long) as annotated in the published genome was much smaller than the average size (164.9 amino acids) of DHFR proteins from other members of the Bastille-like phages. When the B4 genome was compared with B5S due to their high similarity [24], both phages share 100 % nucleotide identity in the DHFR region. We further observed that the difference in DHFR gene sizes was due to the choice of start codon (ATG and TTG for B4 and B5S, respectively) used in predicting the ORFs in both cases. Accordingly, the open reading frame of B4 DHFR was modified and used for preparing Fig. 7 The new gp21 of phage B4 shares a minimum global identity and E-value of 47.3 % and 2.71 × 10−51, respectively, to the DHFR in the other Bastille-like phages.Fig. 7


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)

Gene arrangement of TS, DHFR, SpoIIIE and beta-lactamase genes in phage genomes. a Bastille-like group; b Singleton; c Twort-like group; d SPO1-like group. Gene location is not to the scale. Numbers found in (A) represent gene designation number in each genome
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig7: Gene arrangement of TS, DHFR, SpoIIIE and beta-lactamase genes in phage genomes. a Bastille-like group; b Singleton; c Twort-like group; d SPO1-like group. Gene location is not to the scale. Numbers found in (A) represent gene designation number in each genome
Mentions: B4 gp21 encoded a putative DHFR, however, the gene size (71 amino acids long) as annotated in the published genome was much smaller than the average size (164.9 amino acids) of DHFR proteins from other members of the Bastille-like phages. When the B4 genome was compared with B5S due to their high similarity [24], both phages share 100 % nucleotide identity in the DHFR region. We further observed that the difference in DHFR gene sizes was due to the choice of start codon (ATG and TTG for B4 and B5S, respectively) used in predicting the ORFs in both cases. Accordingly, the open reading frame of B4 DHFR was modified and used for preparing Fig. 7 The new gp21 of phage B4 shares a minimum global identity and E-value of 47.3 % and 2.71 × 10−51, respectively, to the DHFR in the other Bastille-like phages.Fig. 7

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