Genome Comparison and Proteomic Characterization of Thermus thermophilus Bacteriophages P23-45 and P74-26: Siphoviruses with Triplex-forming Sequences and the Longest Known Tails

Leonid Minakhin, Manisha Goel, Zhanna Berdygulova, Erlan Ramanculov, Laurence Florens, Galina Glazko, Valeri N. Karamychev, Alexei I. Slesarev, Sergei A. Kozyavkin, Igor Khromov, Hans W. Ackermann, Michael Washburn, Arcady Mushegian, Konstantin Severinov

Research output: Contribution to journalArticle

37 Citations (Scopus)

Abstract

The genomes of two closely related lytic Thermus thermophilus siphoviruses with exceptionally long (∼800 nm) tails, bacteriophages P23-45 and P74-26, were sequenced completely. The P23-45 genome consists of 84,201 bp with 117 putative open reading frames (ORFs), and the P74-26 genome has 83,319 bp and 116 putative ORFs. The two genomes are 92% identical with 113 ORFs shared. Only 25% of phage gene product functions can be predicted from similarities to proteins and protein domains with known functions. The structural genes of P23-45, most of which have no similarity to sequences from public databases, were identified by mass spectrometric analysis of virions. An unusual feature of the P23-45 and P74-26 genomes is the presence, in their largest intergenic regions, of long polypurine-polypyrimidine (R-Y) sequences with mirror repeat symmetry. Such sequences, abundant in eukaryotic genomes but rare in prokaryotes, are known to form stable triple helices that block replication and transcription and induce genetic instability. Comparative analysis of the two phage genomes shows that the area around the triplex-forming elements is enriched in mutational variations. In vitro, phage R-Y sequences form triplexes and block DNA synthesis by Taq DNA polymerase in orientation-dependent manner, suggesting that they may play a regulatory role during P23-45 and P74-26 development.

Original languageEnglish
Pages (from-to)468-480
Number of pages13
JournalJournal of Molecular Biology
Volume378
Issue number2
DOIs
Publication statusPublished - Apr 25 2008
Externally publishedYes

Keywords

  • Thermus thermophilus
  • bioinformatics
  • thermophages
  • triplex-forming sequence
  • virion proteomics

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

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    Minakhin, L., Goel, M., Berdygulova, Z., Ramanculov, E., Florens, L., Glazko, G., Karamychev, V. N., Slesarev, A. I., Kozyavkin, S. A., Khromov, I., Ackermann, H. W., Washburn, M., Mushegian, A., & Severinov, K. (2008). Genome Comparison and Proteomic Characterization of Thermus thermophilus Bacteriophages P23-45 and P74-26: Siphoviruses with Triplex-forming Sequences and the Longest Known Tails. Journal of Molecular Biology, 378(2), 468-480. https://doi.org/10.1016/j.jmb.2008.02.018