Sequence, genome organization, annotation and proteomics of the thermophilic, 47.7-kb Geobacillus stearothermophilus bacteriophage TP-84 and its classification in the new Tp84virus genus
Piotr Skowron , Andrew M. Kropinski , Joanna Żebrowska , Kasjan Szemiako , Edyta Czajkowska , Natalia Maciejewska , Malgorzata Skowron , Joanna Monika Łoś , Marcin Łoś , Agnieszka Żylicz-Stachula , Łukasz Janus
AbstractBacteriophage TP-84 is a well-characterized bacteriophage of historical interest. It is a member of the Siphoviridae, and infects a number of thermophilic Geobacillus (Bacillus) stearothermophilus strains. Its’ 47.7-kbp double-stranded DNA genome revealed the presence of 81 coding sequences (CDSs) coding for polypeptides of 4 kDa or larger. Interestingly, all CDSs are oriented in the same direction, pointing to a dominant transcription direction of one DNA strand. Based on a homology search, a hypothetical function could be assigned to 31 CDSs. No RNA or DNA polymerase-coding genes were found on the bacteriophage genome indicating that TP-84 relies on the host’s transcriptional and replication enzymes. The TP84 genome is tightly packed with CDSs, typically spaced by several-to-tens of bp or often overlapping. The genome contains five putative promoter-like sequences showing similarity to the host promoter consensus sequence and allowing for a 2-bp mismatch. In addition, ten putative rho-independent terminators were detected. Because the genome sequence shows essentially no similarity to any previously characterised bacteriophage, TP-84 should be considered a new species in an undefined genus within the Siphoviridae family. Thus a taxonomic proposal of a new Tp84virus genus has been accepted by the International Committee on Taxonomy of Viruses. The bioinformatics genome analysis was verified by confirmation of 33 TP-84 proteins, which included: a) cloning of a selected CDS in Escherichia coli, coding for a DNA single-stranded binding protein (SSB; gene TP84_63), b) purification and functional assays of the recombinant TP-84 SSB, which has been shown to improve PCR reactions, c) mass spectrometric (MS) analysis of TP-84 bacteriophage capsid proteins, d) purification of TP-84 endolysin activity, e) MS analysis of the host cells from infection time course.
|Journal series||PLoS ONE, ISSN 1932-6203, (A 40 pkt)|
|Publication size in sheets||1.1|
|ASJC Classification||; ;|
|License||Journal (articles only); published final; ; with publication|
|Score||= 40.0, 28-02-2020, ArticleFromJournal|
|Publication indicators||= 1; : 2017 = 1.111; : 2018 = 2.776 (2) - 2018=3.337 (5)|
|Citation count*||4 (2020-05-22)|
* presented citation count is obtained through Internet information analysis and it is close to the number calculated by the Publish or Perish system.