Characterization of Paenibacillus larvae bacteriophages and their genomic relationships to firmicute bacteriophages

Abstract

BackgroundPaenibacillus larvae is a Firmicute bacterium that causes American Foulbrood, a lethal disease in honeybees and is a major source of global agricultural losses. Although P. larvae phages were isolated prior to 2013, no full genome sequences of P. larvae bacteriophages were published or analyzed. This report includes an in-depth analysis of the structure, genomes, and relatedness of P. larvae myoviruses Abouo, Davis, Emery, Jimmer1, Jimmer2, and siphovirus phiIBB_Pl23 to each other and to other known phages.ResultsP. larvae phages Abouo, Davies, Emery, Jimmer1, and Jimmer2 are myoviruses with ~50 kbp genomes. The six P. larvae phages form three distinct groups by dotplot analysis. An annotated linear genome map of these six phages displays important identifiable genes and demonstrates the relationship between phages. Sixty phage assembly or structural protein genes and 133 regulatory or other non-structural protein genes were identifiable among the six P. larvae phages. Jimmer1, Jimmer2, and Davies formed stable lysogens resistant to superinfection by genetically similar phages. The correlation between tape measure protein gene length and phage tail length allowed identification of co-isolated phages Emery and Abouo in electron micrographs. A Phamerator database was assembled with the P. larvae phage genomes and 107 genomes of Firmicute-infecting phages, including 71 Bacillus phages. Phamerator identified conserved domains in 1,501 of 6,181 phamilies (only 24.3%) encoded by genes in the database and revealed that P. larvae phage genomes shared at least one phamily with 72 of the 107 other phages. The phamily relationship of large terminase proteins was used to indicate putative DNA packaging strategies. Analyses from CoreGenes, Phamerator, and electron micrograph measurements indicated Jimmer1, Jimmer2, Abouo and Davies were related to phages phiC2, EJ-1, KC5a, and AQ113, which are small-genome myoviruses that infect Streptococcus, Lactobacillus, and Clostridium, respectively.ConclusionsThis paper represents the first comparison of phage genomes in the Paenibacillus genus and the first organization of P. larvae phages based on sequence and structure. This analysis provides an important contribution to the field of bacteriophage genomics by serving as a foundation on which to build an understanding of the natural predators of P. larvae.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-745) contains supplementary material, which is available to authorized users.

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

“…Compared to the complete P. larvae genomes sequenced so far (44 to 45% GϩC content [32]), the GϩC content of the phage genome is lower and similar to that of other Paenibacillus phage genomes (33,34). Sequence analysis with tRNAscan-SE v.1.21 (35) did not reveal any genes for tRNAs in the genome, which is also consistent with other Paenibacillus phage genomes analyzed.…”

“…Downstream of the cluster for structural genes, we identified a lysis cluster consisting of three genes that encode two putative holins and an endolysin. Comparison with other Paenibacillus phages showed that they indeed also harbor either a gene for N-acetylmuramoyl L-alanine amidase, e.g., phage Emery, or a gene for an endo-beta-N-acetylglucosamidase, e.g., phage Davies (33). In particular, endolysins of phages with Gram-positive hosts often act as endopeptidases or amidases and exhibit highly specific activity (39).…”

“…Terminases are highly conserved, and phylogenetic analyses with other terminases with different known DNA packaging strategies can give first hints about the mechanisms that are used for packaging (36). Recently, Merrill et al performed a phylogenetic analysis of all of the terminases from all known P. larvae phages (33). The phages that belong to the family Myoviridae seem to use a headful packaging system, whereas siphovirus phiIBB_Pl23 likely has 3= cohesive ends.…”

Bacillus safensisFO-36b andBacillus pumilusSAFR-032: A Whole Genome Comparison of Two Spacecraft Assembly Facility Isolates

“…The SPP1 is a 44-kb virulent Bacillus subtilis phage, well-known for its ability to mediate generalized transduction, a widespread mechanism for the transfer of any gene from one bacterium to another [70]. The second insertion is homologous to Brevibacillus phage Jimmer 1, which is one of several myoviruses that specifically target Paenibacillus larvae, a Firmicute bacterium, as a host [71].…”

Phage on the stage

“…22 For example, phages that kill Paenibacillus, a serious problem in the honeybee industry, have been found. 23 Unique endolysins that kill bacteria could play a major role in human and animal health and in food safety. 24 This list goes on.…”