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

Abstract

Bacteriophage 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.
Author Piotr Skowron (FCh / DMBt / LGE)
Piotr Skowron,,
- Laboratory of Genetic Engineering
, Andrew M. Kropinski
Andrew M. Kropinski,,
-
, Joanna Żebrowska (FCh / DMBt / LGE)
Joanna Żebrowska,,
- Laboratory of Genetic Engineering
, Kasjan Szemiako
Kasjan Szemiako,,
-
, Edyta Czajkowska (FCh / DMBt / LGE)
Edyta Czajkowska ,,
- Laboratory of Genetic Engineering
, Natalia Maciejewska (FCh / DBCh / LMCh)
Natalia Maciejewska,,
- Laboratory of Medical Chemistry
, Malgorzata Skowron
Malgorzata Skowron,,
-
, Joanna Monika Łoś (FB / DMGB)
Joanna Monika Łoś,,
- Department of Molecular Genetics of Bacteria
, Marcin Łoś (FB / DMGB)
Marcin Łoś,,
- Department of Molecular Genetics of Bacteria
, Agnieszka Żylicz-Stachula (FCh / DMBt / LGE)
Agnieszka Żylicz-Stachula,,
- Laboratory of Genetic Engineering
et al.`
Journal seriesPlos One, ISSN 1932-6203, (A 35 pkt)
Issue year2018
Vol13
No4
Pages1-23
Publication size in sheets1.1
DOIDOI:10.1371/journal.pone.0195449
URL https://doi.org/ 10.1371/journal.pone.0195449
Languageen angielski
LicenseJournal (articles only); published final; Uznanie Autorstwa (CC-BY); with publication
Score (nominal)40
ScoreMinisterial score = 35.0, 26-10-2018, ArticleFromJournal
Ministerial score (2013-2016) = 40.0, 26-10-2018, ArticleFromJournal
Publication indicators WoS Impact Factor: 2016 = 2.806 (2) - 2016=3.394 (5)
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