Complete Genome Sequence of the Giant Virus OBP and Comparative Genome Analysis of the Diverse ϕKZ-Related Phages

Abstract

The 283,757-bp double-stranded DNA genome of Pseudomonas fluorescens phage OBP shares a general genomic organization with Pseudomonas aeruginosa phage EL. Comparison of this genomic organization, assembled in syntenic genomic blocks interspersed with hyperplastic regions of the KZ-related phages, supports the proposed division in the "EL-like viruses," and the "phiKZ-like viruses" within a larger subfamily. Identification of putative early transcription promoters scattered throughout the hyperplastic regions explains several features of the KZ-related genome organization (existence of genomic islands) and evolution (multi-inversion in hyperplastic regions). When hidden Markov modeling was used, typical conserved core genes could be identified, including the portal protein, the injection needle, and two polypeptides with respective similarity to the 3=-5= exonuclease domain and the polymerase domain of the T4 DNA polymerase. While the N-terminal domains of the tail fiber module and peptidoglycan-degrading proteins are conserved, the observation of C-terminal catalytic domains typical for the different genera supports the further subdivision of the KZ-related phages. P seudomonas fluorescens phage OBP (vB_PflM_OBP) (30, 47) is member of a growing group of giant phages, isolated, to date, only from Pseudomonas species and represented by the completely sequenced and well-studied Pseudomonas aeruginosa myovirus KZ (9,18,19,[31][32][33]36,42). Three other phages encoding many proteins with similarity to KZ proteins have been completely sequenced: EL (23), 2012-1 (52), and PA3 (43). Krylov et al. (33) assigned 19 unsequenced Pseudomonas phages to this group. We refer to the group as KZ-related phages. Lavigne et al. (35) have argued that EL should be classified as a genus separate from KZ and 2012-1 based on its less extensive levels of similarity. By that criterion, PA3 belongs to the "phiKZ-like viruses" and the results reported here classify OBP as the second member of the possible genus EL-like viruses.OBP shares a number of definitive properties with the other KZ-related phages. Typically, KZ-related phages have a very large icosahedral head, ϳ122 nm in diameter, and a long (ϳ190-nm) contractile tail surrounded by fibers. A KZ-related phage head contains a proteinic inner body, which has been speculated to organize the packaged DNA (18, 32). The exceptionally large genomes of the KZ-related phages (between 211 and 317 kb of nonredundant sequence) are composed of circularly permuted and terminally redundant linear double-stranded DNAs as determined for KZ and 2012-1 (42, 52). The KZ-related genomes display a pronounced difference in GϩC content (between 36.8 and 48%) and all have markedly lower GϩC content than the chromosomes of their GC-rich Pseudomonas hosts (60 to 66% GϩC).This group of phages has numerous genes involved in nucleotide metabolism (e.g., thymidylate synthase, thymidylate kinase, ribonucleoside diphosphate reductase, subunit beta [NrdB], and dihydrofolate reductase) and at least six genes enco...

Phylogenomic Network and Comparative Genomics Reveal a Diverged Member of the ϕKZ-Related Group, Marine Vibrio Phage ϕJM-2012

“…3B). This supports the recent taxonomic classification of the KZ-like phages as KZ-like and EL-like viruses (25,27), whereas the similarity values of JM-2012 suggest that it is probably an emerging member of the KZ-related group.…”

“…A mathematical model of reticulate networks based on ortholog clustering (15,20) and subsequent comparative analysis provides strong molecular support for the notion that JM-2012 diverged from a common ancestor of the KZ-related groups (23)(24)(25)(26)(27), most likely because of the imposition of distinct evolutionary forces upon its genome. Thus, given that KZ-like phages have limited genetic diversity and a narrow host range (23)(24)(25)(26)(27)(28)(29), these data provide novel insights into the diversity and pairwise similarity comparisons of each predicted protein of the JM-2012 genome (n ϭ 173) with BLAST in ACLAME; we used a Markov clustering (MCL) algorithm and the database of "viruses and prophages" (as of November 2012), within an E value threshold of 0.0001. Fifty-eight potential gene products of JM-2012 were found to be associated with protein families in ACLAME, while the remaining proteins were defined as "dummy" families, e.g., the unclassified protein families 1 to 115, and considered to assess the actual similarity between JM-2012 and those in the ACLAME database.…”

Testing hypotheses for the presence of tRNA genes in mycobacteriophage genomes

“…10,[17][18][19] However, a survey of recent studies comparing codon usage by phages and their hosts revealed a mixture of studies where the presence of tRNA genes corresponds to codons overly expressed by the phage compared to its host 10,[20][21][22][23] and studies where that is not the case. [24][25][26][27] In phage PVP-SE1, only 11 of the codons associated with its 24 tRNA genes were present at a frequency higher than in its Salmonella hosts. 28 In the 5 Acinetobacter phages studied by Jin et al, an association between the presence of tRNA genes and codon usage could only be observed for one Acinetobacter phage, ZZ1, and for only 5 out of the 8 tRNA genes.…”

Genome sequences published outside of Standards in Genomic Sciences, January-March 2012

“…Aspergillus flavus, sequence accession GSE32177 [79] Bacteriophage SPN3UB, sequence accession JQ288021 [80] Bamboo mitochondria, sequence accession JQ235166 to JQ235179 [81] Boea hygrometrica chloroplast, sequence accession JN107811 [82] Boea hygrometrica mitochondrial, sequence accession JN107812 [82] Canine Picornavirus, sequence accession JN831356 [83] Chandipura virus (CHPV) CIN0327, sequence accession GU212856.1 [84] Chandipura virus (CHPV) CIN0451, sequence accession GU212857.1 [84] Chandipura virus (CHPV) CIN0751, sequence accession GU212858.1 [84] Chandipura virus (CHPV) CIN0755, sequence accession GU190711.1 [84] Chinese Porcine Parvovirus Strain PPV2010, sequence accession JN872448 [85] Common midwife toad megavirus, sequence accession JQ231222 [86] Dengue Virus Serotype 4, sequence accession JN983813 [87] Duck Tembusu Virus, sequence accession JF270480 [88] Duck Tembusu Virus, sequence accession JQ314464 [88] Duck Tembusu Virus, sequence accession JQ314465 [88] Emiliania huxleyi Virus 202, sequence accession HQ634145 [89] Emiliania huxleyi Virus EhV-88, sequence accession JF974310 [89] Emiliania huxleyi EhV-201, sequence accession JF974311 [89] Emiliania huxleyi EhV-207, sequence accession JF974317 [89] Emiliania huxleyi EhV-208, sequence accession JF974318 [89] Glarea lozoyensis, sequence accession GUE00000000 [90] Nannochloropis gaditana, sequence accession AGNI00000000 [91] Oryza sativa cv., sequence accession DRA000499 [92] Partetravirus, sequence accession JN990269 [93] Porcine Bocavirus PBoV5, sequence accession JN831651 [94] Porcine epidemic diarrhea virus, sequence accession JQ282909 [95] Pseudomonas aeruginosa lytic bacteriophage PA1Ø, sequence accession HM624080 [96] Pseudomonas fluorescens phage OBP, sequence accesssion JN627160 [97] RNA Virus from Avocado, sequence accession JN880414 [98] Salmonella enterica Serovar Typhimuriu...…”