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Genomic Characterization of the Intron-Containing T7-Like Phage phiL7 of Xanthomonas campestris

Lee, Chia-Ni, Lin, Juey-Wen, Weng, Shu-Fen, Tseng, Yi-Hsiung
Applied and environmental microbiology 2009 v.75 no.24 pp. 7828-7837
DNA, DNA-directed DNA polymerase, DNA-directed RNA polymerase, Siphoviridae, Xanthomonas campestris pv. campestris, Xanthomonas phages, bacteriophages, gene transfer, genes, host range, mutation, nucleotide sequences, proteins, sequence analysis
The lytic phage phiL7, which morphologically belongs to the Siphoviridae family, infects Xanthomonas campestris pv. campestris. Nucleotide sequence analysis has revealed that phiL7 contains a linear double-stranded DNA genome (44,080 bp, 56% G+C) with a 3'-protruding cos site (5'-TTACCGGAC-3') and 59 possible genes. Among the deduced proteins, 32 have homologs with known functions and 18 show no database similarities; moreover, the genes encoding these 18 proteins mostly have varying G+C contents and form clusters dispersed along the genome. Only 39 genes have sequences related (27% to 78%) to those of sequenced genes of X. oryzae pv. oryzae phages, although the genome size and architecture of these Xanthomonas phages are similar. These findings suggest that phiL7 acquired genes by horizontal transfer, followed by evolution via various types of mutations. Major differences were found between phiL7 and the X. oryzae pv. oryzae phages: (i) phiL7 has a group I intron inserted in the DNA polymerase gene, the first such intron observed in Xanthomonas phages; (ii) although infection of phiL7 exerted inhibition to the host RNA polymerase, similar to the situations in X. oryzae pv. oryzae phages Xp10 and Xop411, sequence analysis did not identify a homologue of the Xp10 p7 that controls the shift from host RNA polymerase (RNAP) to viral RNAP during transcription; and (iii) phiL7 lacks the tail fiber protein gene that exhibits domain duplications thought to be important for host range determination in OP1, and sequence analysis suggested that p20 (tail protein III) instead has the potential to play this role.