Complete nucleotide sequence of a new filamentous phage, Xf109, which integrates its genome into the chromosomal DNA of Xanthomonas oryzae

Abstract

Unlike Ff-like coliphages, certain filamentous Inoviridae phages integrate their genomes into the host chromosome and enter a prophage state in their infectious cycle. This lysogenic life cycle was first reported for Xanthomonas citri Cf phage. However, except for the X. citri phages Cf and XacF1, complete genome sequence information about lysogenic Xanthomonas phages is not available to date. A proviral sequence of Xf109 phage was identified in the genome of Xanthomonas oryzae, the rice bacterial blight pathogen, and revived as infectious virions to lysogenize its host de novo. The genome of Xf109 phage is 7190 nucleotides in size and contains 12 predicted open reading frames in an organization similar to that of the Cf phage genome. Seven of the Xf109 proteins show significant sequence similarity to Cf and XacF1 phage proteins, while its ORF4 shares 92 % identity with the major coat protein of X. phage oryzae Xf. Integration of Xf109 phage DNA into the host genome is site-specific, and the attP/attB sequence contains the dif core sequence 5’-TATACATTATGCGAA-3’, which is identical to that of Cf, XacF1, and Xanthomonas campestris phage ϕLf. To my knowledge, this is the first complete genome sequence of a filamentous bacteriophage that infects X. oryzae.

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Acknowledgments

I thank Mr. Gregory Contreras for his help with data analysis and English editing.

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Correspondence to Ting Y. Yeh.

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This study was supported by Career Development and Bridge Research Fund from Auxergen.

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The author declares no conflict of interest.

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This article does not contain any study with human participants performed by the author.

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Fig. S1

Treatment of Xf109 DNA with hydrolytic enzymes followed by electrophoresis in a 1 % agarose gel in Tris-acetate-EDTA buffer and staining in ethidium bromide with bovine pancreas RNase A (1.5 μg/ml) for 15 minutes. (A) Lane 1, DNA marker; lanes 2 and 3, DNA from Xf109 phage particles (200 ng) treated with S1 nuclease and DNase I, respectively; lane 4, untreated phage DNA. (B) Lane 1, DNA marker; lane 2, Xf109 RF DNA cut with EcoRV; lane 3, uncut Xf109 RF DNA (TIFF 2188 kb)

Fig. S2

The predicted signal peptide in Xf109 ORF4 protein. The output score (C-, S-, Y-, and D-score) format is described in the SignalP 4.1 server (http://www.cbs.dtu.dk/services/SignalP /output.php). The cleavage site of the signal peptide is predicted to be between alanine 30 (gray) and serine 31 (black) based on the D-score (D=0.826). The cutoff D-score is 0.510 (pink line) (TIFF 7067 kb)

Fig. S3

Phylogenic analysis of Xf109 ORF5, phage absorption protein pIII of ϕLf (Q37972, [34]), ϕXv (AF069776), and ϕXo (AF162859), Cf1cp3 of Cf1c and ORF6 of XacF1. (A) The percent identity matrix was computed using the Clustal Omega program. (B) Phylogenic tree inferred using the neighbor-joining method and constructed using MEGA7 software [16]. The optimal tree with a sum of branch lengths of 6.71675156 is shown. The evolutionary distances were computed using the Poisson correction method. All positions containing gaps and missing data were eliminated. There were a total of 328 positions in the final dataset (TIFF 4001 kb)

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Yeh, T.Y. Complete nucleotide sequence of a new filamentous phage, Xf109, which integrates its genome into the chromosomal DNA of Xanthomonas oryzae . Arch Virol 162, 567–572 (2017). https://doi.org/10.1007/s00705-016-3105-3

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Keywords

  • Complete Genome Sequence
  • Yersinia Pestis
  • Filamentous Phage
  • attP Site
  • Replication Initiation Protein