title: Genome comparison and proteomic characterization of Thermus thermophilus bacteriophages P23-45 and P74-26: siphoviruses with triplex-forming sequences and the longest known tails.
abstract: The genomes of two closely related lytic Thermus thermophilus siphoviruses with exceptionally long (approximately 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.
authors: Waksman Institute for Microbiology, 190 Frelinghuysen Road, Piscataway, NJ 08854, USA. minakhin@waksman.rutgers.edu
authors: Leonid
authors: L
authors: Minakhin
authors: Manisha
authors: M
authors: Goel
authors: Zhanna
authors: Z
authors: Berdygulova
authors: Erlan
authors: E
authors: Ramanculov
authors: Laurence
authors: L
authors: Florens
authors: Galina
authors: G
authors: Glazko
authors: Valeri N
authors: VN
authors: Karamychev
authors: Alexei I
authors: AI
authors: Slesarev
authors: Sergei A
authors: SA
authors: Kozyavkin
authors: Igor
authors: I
authors: Khromov
authors: Hans-W
authors: HW
authors: Ackermann
authors: Michael
authors: M
authors: Washburn
authors: Arcady
authors: A
authors: Mushegian
authors: Konstantin
authors: K
authors: Severinov
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D004247:DNA / Q000737:chemistry; D004261:DNA Replication / Q000235:genetics; D018076:DNA, Complementary / Q000737:chemistry; D004279:DNA, Viral / Q000737:chemistry*; D016679:Genome, Viral; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D040901:Proteomics; D011995:Recombination, Genetic / Q000235:genetics; D017906:Siphoviridae / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D016963:Thermus thermophilus / Q000821:virology*; D014764:Viral Proteins / Q000032:analysis / Q000235:genetics / Q000378:metabolism; D014771:Virion / Q000737:chemistry / Q000235:genetics / Q000378:metabolism
chemical_list: D018076:DNA, Complementary; D004279:DNA, Viral; D014764:Viral Proteins; C051802:triplex DNA; D004247:DNA