Abstract
We sequenced and analyzed the genome of OP2 (MAFF 106404), a bacteriophage that lyses Xanthomonas oryzae pv. oryzae (Xoo). It is 464bp, and the average G + C content is 60.9%. The results suggest that the genome sequence of OP2 is circularly permuted and terminally redundant, like that of coliphages T4 or P22. Sixty-two open reading frames (ORFs) were predicted in the genome. We constructed a circular map of the restriction enzyme sites and a gene map. The genome is clearly divided into four parts according to transcription direction. The directions of 27 ORFs are leftward and those of 35 are rightward. Most leftward ORFs are commonly conserved among many other phages, and some are structure-related or expression-related genes. In contrast, most rightward ORFs contain OP2-specific genes as well as DNA polymerase, helicase, dUTPase, and HNH family endonuclease genes. Nine rightward and 25 leftward ORFs have homology with the ORFs of bacteriophage Bcep1, which lyses Burkholderia cepacia. The leftward-transcribed OP2 genes and their orthologs in Bcep1 conserve a neighboring relationship, although the putative tail fiber gene does not have homology with that of Bcep1. Several ORFs have similarity (<e−5) to phage-related genes of Xylella fastidiosa and Xanthomonas spp. Exceptionally, the dUTPase gene had 94% identity with Xoo, and no insertions or deletions were detected in it. However, its neighboring regions did not have homology with the Xoo sequence. Although OP2 is a virulent phage of Xoo, some of the genetic characters have features of temperate phages.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
SF Altschul W Gish W Miller EW Myers DJ Lipman (1990) ArticleTitleBasic local alignment search tool J Mol Biol 5 403–410
SF Altschul TL Madden AA Schäffer J Zhang Z Zhang W Miller DJ Lipman (1997) ArticleTitleGapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res 25 3389–3402 Occurrence Handle10.1093/nar/25.17.3389 Occurrence Handle1:CAS:528:DyaK2sXlvFyhu7w%3D Occurrence Handle9254694
TA Bickle DH Krüger (1993) ArticleTitleBiology of DNA restriction Microbiol Rev 57 434–450 Occurrence Handle1:CAS:528:DyaK3sXltV2ru7o%3D Occurrence Handle8336674
SH Choi CM Vera Cruz JE Leach (1998) ArticleTitleDistribution of Xanthomonas oryzae pv. oryzae DNA modification systems in Asia Appl Environ Microbiol 64 1663–1668 Occurrence Handle1:CAS:528:DyaK1cXislWmu7Y%3D Occurrence Handle9572933
ACR da Silva JA Ferro FC Reinach CS Farah LR Furlan RB Quaggio CB Monteiro-Vitorello MA Van Sluys NF Almeida LM Alves AM do Amaral MC Bertolini LEA Camargo G Camarotte F Cannavan J Cardozo F Chambergo LP Ciapina RMB Cicarelli LL Coutinho JR Cursino-Santos H El-Dorry JB Faria AJS Ferreira RCC Ferreira MIT Ferro EF Formighieri MC Franco CC Greggio A Gruber AM Katsuyama LT Kishi RP Leite EGM Lemos MVF Lemos EC Locali MA Machado AMBN Madeira NM Martinez-Rossi EC Martins J Meidanis CFM Menck CY Miyaki DH Moon LM Moreira MTM Novo VK Okura MC Oliveira VR Oliveira HA Pereira A Rossi JAD Sena C Silva RF de Souza LAF Spinola MA Takita RE Tamura EC Teixeira RID Tezza M Trindade dos Santos D Truffi SM Tsai FF White JC Setubal JP Kitajima (2002) ArticleTitleComparison of the genomes of two Xanthomonas pathogens with differing host specificities Nature 417 459–463 Occurrence Handle10.1038/417459a Occurrence Handle12024217
AL Delcher D Harmon S Kasif O White SL Salzberg (1999) ArticleTitleImproved microbial gene identification with GLIMMER Nucleic Acids Res 27 4636–4641 Occurrence Handle1:CAS:528:DyaK1MXnvVanu7o%3D Occurrence Handle10556321
A Ezuka H Kaku (2000) ArticleTitleA historical review of bacterial blight of rice Bull Natl Inst Agrobiol Resour 15 61–74
A Favello L Hillier RK Wilson (1995) ArticleTitleGenomic DNA sequencing methods Methods Cell Biol 48 551–569 Occurrence Handle1:CAS:528:DyaK2MXps1Cmu7o%3D Occurrence Handle8531742
R Hoess A Wierzbicki K Abremski (1987) ArticleTitleIsolation and characterization of intermediates in site-specific recombination Proc Natl Acad Sci USA 84 6840–6844 Occurrence Handle1:CAS:528:DyaL2sXlvFWqur0%3D Occurrence Handle2821547
PL Hsu A Landy (1984) ArticleTitleResolution of synthetic att-site Holliday structures by the integrase protein of bacteriophage lambda Nature 311 721–726 Occurrence Handle10.1038/311721a0 Occurrence Handle1:CAS:528:DyaL2MXktVOksQ%3D%3D Occurrence Handle6092961
Y Inoue T Ohara K Azegami (2004) ArticleTitleGenome sequences of Xanthomonas oryzae bacteriophage OP1 and OP2. Jpn J Phytopathol 70 292
Y Inoue T Matsuura T Ohara K Azegami (2006) ArticleTitleBacteriophage OP1, lytic for Xanthomonas oryzae pv. oryzae, changes its host range by duplication and deletion of the small domain in the deduced tail fiber gene J Gen Plant Pathol 72 111–118 Occurrence Handle10.1007/s10327-005-0240-1
BM Lee YJ Park DS Park HW Kang JG Kim ES Song IC Park UH Yoon JH Hahn BS Koo GB Lee H Kim HS Park KO Yoon JH Kim CH Jung NH Koh JS Seo SJ Go (2005) ArticleTitleThe genome sequence of Xanthomonas oryzae pathovar oryzae KACC10331, the bacterial blight pathogen of rice Nucleic Acids Res 33 577–586 Occurrence Handle10.1093/nar/gki206 Occurrence Handle1:CAS:528:DC%2BD2MXhtV2qtrs%3D Occurrence Handle15673718
JE Mueller B Kemper RP Cunningham NR Kallenbach NC Seeman (1988) ArticleTitleT4 endonuclease VII cleaves the crossover strands of Holliday junction analogs Proc Natl Acad Sci USA 85 9441–9445 Occurrence Handle1:CAS:528:DyaL1MXltFWisbc%3D Occurrence Handle3200829
H Ochiai Y Inoue M Takeya A Sasaki H Kaku (2005) ArticleTitleGenome sequence of Xanthomonas oryzae pv. oryzae suggests contribution of large numbers of effector genes and insertion sequences to its race diversity Jpn Agric Res Quart 39 275–287
N Okabe M Goto (1963) ArticleTitleBacteriophages of plant pathogens Ann Rev Phytopathol 1 397–418
AA Schäffer YI Wolf CP Ponting EV Koonin L Aravind SF Altschul (1999) ArticleTitleIMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices Bioinformatics 15 1000–1011 Occurrence Handle10745990
F Tétart F Repoila C Monod HM Krisch (1996) ArticleTitleBacteriophage T4 host range is expanded by duplications of a small domain of the tail fiber adhesin J Mol Biol 258 726–731 Occurrence Handle10.1006/jmbi.1996.0281 Occurrence Handle8637004
MA Van Sluys MC de Oliveira CB Monteiro-Vitorello CY Miyaki LR Furlan LEA Camargo ACR da Silva DH Moon MA Takita EGM Lemos MA Machado MI Ferro FR Da Silva MHS Goldman GH Goldman MVF Lemos H El-Dorry SM Tsai H Carrer DM Carraro RC De Oliveira LR Nunes WJ Siqueira LL Coutinho ET Kimura ES Ferro R Harakava EE Kuramae CL Marino E Giglioti IL Abreu LMC Alves AM Do Amaral GS Baia SR Blanco MS Brito FS Cannavan AV Celestino AF Da Cunha RC Fenille JA Ferro EF Formighieri LT Kishi SG Leoni AR Oliveira VE Rosa SuffixJr FT Sassaki JAD Sena AA De Souza D Truffi F Tsukumo GM Yanai LG Zaros EL Civerolo AJG Simpson NF Almeida SuffixJr JC Setubal JP Kitajima (2003) ArticleTitleComparative analyses of the complete genome sequences of Pierce's disease and citrus variegated chlorosis strains of Xylella fastidiosa J Bacteriol 185 1018–1026 Occurrence Handle10.1128/JB.185.3.1018-1026.2003 Occurrence Handle1:CAS:528:DC%2BD3sXosF2lsQ%3D%3D Occurrence Handle12533478
S Wakimoto (1955) ArticleTitleStudies on the multiplication of OP1 phage (Xanthomonas oryzae bacteriophage) 1. One-step growth experiment under various conditions Sci Bull Fac Agric Kyushu Univ 15 151–160
S Wakimoto (1960) ArticleTitleClassification of strains of Xanthomonas oryzae on the basis of their susceptibility against bacteriophages Ann Phytopathol Soc Jpn 25 193–198
RY Wang JG Shedlarski MB Farber D Kuebbing M Ehrlich (1980) ArticleTitleTwo sequence-specific endonucleases from Xanthomonas oryzae. Characterization and unusual properties Biochim Biophys Acta 606 371–385 Occurrence Handle1:CAS:528:DyaL3cXhsVagsrY%3D Occurrence Handle6243986
C Werts V Michel M Hofnung A Charbit (1994) ArticleTitleAdsorption of bacteriophage lambda on the LamB protein of Escherichia coli K-12: point mutations in gene J of lambda responsible for extended host range J Bacteriol 176 941–947 Occurrence Handle1:CAS:528:DyaK2cXitl2qs74%3D Occurrence Handle8106335
T Yada M Hirosawa (1996) ArticleTitleDetection of short protein coding regions within the Cyanobacterium genome: application of the hidden Markov model DNA Res 3 335–361 Occurrence Handle10.1093/dnares/3.6.355
S Yoshimura M Saito R Yoshino T Morihashi (1960) ArticleTitleProperties of a new Xanthomonas oryzae phage OP2 Proc Assoc Plant Prot Hokuriku 8 15–20
J Yuzenkova S Nechaev J Berlin D Rogulja K Kuznedelov R Inman A Mushegian K Severinov (2003) ArticleTitleGenome of Xanthomonas oryzae bacteriophage Xp10: an odd T-odd phage J Mol Biol 330 735–748 Occurrence Handle10.1016/S0022-2836(03)00634-X Occurrence Handle1:CAS:528:DC%2BD3sXlt1aqtL0%3D Occurrence Handle12850143
Author information
Authors and Affiliations
Corresponding author
Additional information
The nucleotide sequence data reported is available in the DDBJ/EMBL/GenBank databases under accession number AP008986
Rights and permissions
About this article
Cite this article
Inoue, Y., Matsuura, T., Ohara, T. et al. Sequence analysis of the genome of OP2, a lytic bacteriophage of Xanthomonas oryzae pv. oryzae. J Gen Plant Pathol 72, 104–110 (2006). https://doi.org/10.1007/s10327-005-0259-3
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/s10327-005-0259-3