Complete nucleotide sequence of the Salmonella enterica, serovar Typhimurium LT2 bacteriophage SP6.

摘要

The SP6 genome is transcribed in a temporal manner yielding a total of 10 discrete RNA species. This finding suggests that there are discrete sequences present along the SP6 genome that serve as specific signals for transcription initiation and termination. Few genes and transcriptional elements have been previously reported for SP6, including but not limited to the proteins that encode SP6 DNA polymerase, SP6 RNA polymerase, primase, and the SP6 tail protein. In 1989, one SP6 RNA polymerase terminator sequence was identified, although termination efficiency was not fully characterized. The intricate organization and regulation of the entire SP6 genome remain unknown. In order to systematically analyze the bacteriophage SP6 genome, identify additional SP6 genes and genetic signals, and continue SP6 RNA polymerase terminator efficiency studies, the bacteriophage SP6 genome was sequenced. Bacteriophage SP6 is a bacterial virus specific for Salmonella Typhimurium LT2. By methods of shotgun sequencing and sequence analysis, the SP6 genome has been found to be 43,769 by in length, totaling 52 genes. A detailed physical map of the SP6 genome has been constructed and the bacteriophage SP6 genome has been compared to coliphage T7 and the T-odd group of related phages. The results of this study reveal ten putative SP6 promoter sequences and seven putative rho independent terminator sites (including the previously identified terminator sequence) within the SP6 genome. In addition, an apparent prophage of the recently sequenced genome of Pseudomonas putida KT2440 was identified that corresponded to a 40 kb segment of the SP6 genome. In vitro transcription analysis revealed that transcription termination in this system is less than 100% efficient (∼50--60%). Based on these observations, determination of the complete nucleotide sequence of bacteriophage SP6 provides critical information for more inclusive comparisons and observations of the SP6 genome to other phage and prophage sequences. Additionally, this study improves the knowledge base of the SP6 RNA polymerase terminator sequence efficiency and thus lends itself to further study for a more enhanced understanding of bacteriophage genetics and evolution.