Identification and characterization of a novel Geobacillus thermoglucosidasius bacteriophage, GVE3

Abstract

The study of extremophilicphages may reveal new phage families as well as different mechanisms of infection, propagation and lysis to those found in phages from temperate environments. We describe a novel siphovirus, GVE3, that infects the thermophileGeobacillusthermoglucosidasius. The genome size is 141298 bp(G+C 29.6%) making it the largest Geobacillusspp infecting phage known.GVE3 appears to be most closely related to the recently described Bacillus anthracis phage vB_BanS_Tsamsa, rather thanGeobacillus infecting phages described thus far.Tetranucleotide usage deviation analysis supports this relationship, showing that the GVE3 genome sequence correlates best with B. anthracis and Bacillus cereus genome sequences, rather than Geobacillusspp genome sequences.2

Bacteriophages of Thermophilic ‘Bacillus Group’ Bacteria—A Review

“…The presence of a GVE3-encoded pyrimidine nucleoside phosphorylase suggests an obligatory requirement for its activity: upon GVE3 genome integration the host relies on the bacteriophage enzyme. There is an alternative explanation: if the enzyme is not essential for either the GVE3 or the host, since the mutation in the pyrimidine nucleoside phosphorylase-coding gene is non-lethal, this may suggest that GVE3 is a specialized transducing thermophage [ 62 ]. Interestingly, the genome size is 141,298 bp comprising the largest known among the bacteriophages that infect Geobacillus sp., and has a unique DNA sequence, with no close relatives.…”

“…A large number of 202 putative ORFs were bioinformatically detected and, out of those, putative functions to 62 of them were assigned. As observed in a number of other members of the Siphoviridae , the GVE3 genome displays the functional clusters [ 62 ]. Remarkably, GVE3 resembles GBK2 in that it is apparently most closely related to the mesophilic B. anthracis bacteriophage vB_BanS_Tsamsa, rather than the Geobacillus -infecting bacteriophages.…”

“…Tetranucleotide usage deviation analysis confirms this finding, indicating that the GVE3 genome sequence correlates mostly with B. anthracis and B. cereus sequences, rather than Geobacillus sp. sequences [ 62 , 63 ], which again points to widespread genetic recombination among meso- and thermophilic ‘ Bacillus group’ bacteriophages. The analysis also suggests that there exist a different ‘natural’ host, unidentified Geobacillus sp., with tetranucleotide usage deviation patterns more similar to the two Bacillus species that might be the “natural” hosts for GVE3.…”

“…Similar findings have been shown for GBK2 [ 64 ]. The GVE3 genome sequence has a much lower G+C content (29.6%) than its host G. thermoglucosidasius (44%) [ 62 ], which is also observed for most bacteriophage–host pairs. It is suggested that its base composition bias might have resulted from a competition for metabolic resources and/or reflects an adaptation to thermophily [ 65 ].…”

“…The large genome segment, DNA replication, modification and repair, contains tens of genes, not all of them with assigned functions. These make the GVE3 enzymatic machinery remarkably independent, including three subunits diverging hosts DNA polymerase to the bacteriophage replication and three DNA modification methyltransferases, protecting the genome from restriction, among others [ 62 ].…”