Xanthomonas citri jumbo phage XacN1 exhibits a wide host range and high complement of tRNA genes

Xanthomonas citri jumbo phage XacN1 exhibits a wide host range and high complement of tRNA genes Xanthomonas virus (phage) XacN1 is a novel jumbo myovirus infecting Xanthomonas citri, the causative agent of Asian citrus canker. Its linear 384,670 bp double-stranded DNA genome encodes 592 proteins and presents the longest (66 kbp) direct terminal repeats (DTRs) among sequenced viral genomes. The DTRs harbor 56 tRNA genes, which correspond to all 20 amino acids and represent the largest number of tRNA genes reported in a viral genome. Codon usage analysis revealed a propensity for the phage encoded tRNAs to target codons that are highly used by the phage but less frequently by its host. The existence of these tRNA genes and seven additional translation-related genes as well as a chaperonin gene found in the XacN1 genome suggests a relative independence of phage replication on host molecular machinery, leading to a prediction of a wide host range for this jumbo phage. We confirmed the prediction by showing a wider host range of XacN1 than other X. citri phages in an infection test against a panel of host strains. Phylogenetic analyses revealed a clade of phages composed of XacN1 and ten other jumbo phages, indicating an evolutionary stable large genome size for this group of phages. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Scientific Reports Springer Journals

Xanthomonas citri jumbo phage XacN1 exhibits a wide host range and high complement of tRNA genes

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Publisher
Nature Publishing Group UK
Copyright
Copyright © 2018 by The Author(s)
Subject
Science, Humanities and Social Sciences, multidisciplinary; Science, Humanities and Social Sciences, multidisciplinary; Science, multidisciplinary
eISSN
2045-2322
D.O.I.
10.1038/s41598-018-22239-3
Publisher site
See Article on Publisher Site

Abstract

Xanthomonas virus (phage) XacN1 is a novel jumbo myovirus infecting Xanthomonas citri, the causative agent of Asian citrus canker. Its linear 384,670 bp double-stranded DNA genome encodes 592 proteins and presents the longest (66 kbp) direct terminal repeats (DTRs) among sequenced viral genomes. The DTRs harbor 56 tRNA genes, which correspond to all 20 amino acids and represent the largest number of tRNA genes reported in a viral genome. Codon usage analysis revealed a propensity for the phage encoded tRNAs to target codons that are highly used by the phage but less frequently by its host. The existence of these tRNA genes and seven additional translation-related genes as well as a chaperonin gene found in the XacN1 genome suggests a relative independence of phage replication on host molecular machinery, leading to a prediction of a wide host range for this jumbo phage. We confirmed the prediction by showing a wider host range of XacN1 than other X. citri phages in an infection test against a panel of host strains. Phylogenetic analyses revealed a clade of phages composed of XacN1 and ten other jumbo phages, indicating an evolutionary stable large genome size for this group of phages.

Journal

Scientific Reports – Springer Journals

Published: Mar 14, 2018

References

  • Jumbo bacteriophages
    Hendrix, RW
  • Jumbo Bacteriophages: An Overview
    Yuan, Y; Gao, M
  • Two asian jumbo phages, φRSL2 and φRSF1, infect Ralstonia solanacearum and show common features of φKZ-related phages
    Bhunchoth, A
  • Replications of Two Closely Related Groups of Jumbo Phages Show Different Level of Dependence on Host-encoded RNA Polymerase
    Matsui, T
  • Supersize me: Cronobacter sakazakii phage GAP32
    Abbasifar, R
  • Klebsiella phage vB_KleM-RaK2 - a giant singleton virus of the family Myoviridae
    Simoliūnas, E
  • Genomic analysis of bacteriophage PBECO4 infecting Escherichia coli O157:H7
    Kim, MS; Hong, SS; Park, K; Myung, H
  • Identification of capsular types in carbapenem-resistant Klebsiella pneumoniae strains by wzc sequencing and implications for capsule depolymerase treatment
    Pan, Y-J
  • Things Are Getting Hairy: Enterobacteria Bacteriophage vB_PcaM_CBB
    Buttimer, C
  • Genome Sequence of Serratia marcescens Phage BF
    Casey, E
  • Genomes of the T4-related bacteriophages as windows on microbial genome evolution
    Petrov, VM; Ratnayaka, S; Nolan, JM; Miller, ES; Karam, JD
  • Bacterial canker disease of citrus [Xanthomonas campestris]
    Civerolo, EL
  • Xanthomonas axonopodis pv. citri: factors affecting successful eradication of citrus canker
    Graham, JH; Gottwald, TR; Cubero, J; Achor, DS
  • Comparison of the genomes of two Xanthomonas pathogens with differing host specificities
    Silva, ACR
  • Expression profiling of virulence and pathogenicity genes of Xanthomonas axonopodis pv. citri
    Astua-Monge, G
  • Biofilm formation, epiphytic fitness, and canker development in Xanthomonas axonopodis pv. citri. Mol. Plant-Microbe Interact
    Rigano, LA
  • Fundamentals of citrus canker management
    Timmer, LW; Graham, JH; Chamberlain, HL
  • Phage therapy for plant disease control
    Balogh, B; Jones, JB; Iriarte, FB; Momol, MT
  • Bacteriophages for plant disease control
    Jones, JB
  • Biocontrol of Ralstonia solanacearum by treatment with lytic bacteriophages
    Fujiwara, A
  • Two-dimensional motion of DNA bands during 120 degrees pulsed-field gel electrophoresis
    Neitzey, LM; Hutson, MS; Holzwarth, G
  • The conformation of DNA packaged in bacteriophage G
    Sun, M; Serwer, P
  • The terminal redundant regions of bacteriophage T7 DNA: their necessity for phage production studied by the infectivity of T7 DNA after modification by various exonucleases
    Dreiseikelmann, B; Wackernagel, W
  • The genome of Bacillus subtilis bacteriophage SPO1
    Stewart, CR
  • Genes and regulatory sites of the ‘host-takeover module’ in the terminal redundancy of Bacillus subtilis bacteriophage SPO1
    Stewart, CR
  • Mycobacteriophage endolysins: diverse and modular enzymes with multiple catalytic activities
    Payne, KM; Hatfull, GF
  • Causes for the intriguing presence of tRNAs in phages
    Bailly-Bechet, M; Vergassola, M; Rocha, E
  • Unusual in vivo turnover of transfer RNA in Vibrio cholerae
    Mukhopadhyay, P; Gangopadhyay, T; Ghosh, RK
  • tRNA biology charges to the front
    Phizicky, EM; Hopper, AK
  • Cyanophage tRNAs may have a role in cross-infectivity of oceanic Prochlorococcus and Synechococcus hosts
    Enav, H; Béjà, O; Mandel-Gutfreund, Y
  • Characterization of bacteriophages Cp1 and Cp2, the strain-typing agents for Xanthomonas axonopodis pv. citri
    Ahmad, AA; Ogawa, M; Kawasaki, T; Fujie, M; Yamada, T
  • Probing the substrate specificity of the bacterial Pnkp/Hen1 RNA repair system using synthetic RNAs
    Zhang, C; Chan, CM; Wang, P; Huang, RH
  • Chaperonin-mediated folding of viral proteins
    Hildenbrand, ZL; Bernal, RA
  • Novel chaperonins are prevalent in the virioplankton and demonstrate links to viral biology and ecology
    Marine, RL; Nasko, DJ; Wray, J; Polson, SW; Wommack, KE
  • Chlorella viruses encode most, if not all, of the machinery to glycosylate their glycoproteins independent of the endoplasmic reticulum and Golgi
    Etten, JL; Gurnon, JR; Yanai-Balser, GM; Dunigan, DD; Graves, MV
  • Glycosyltransferases encoded by viruses
    Markine-Goriaynoff, N
  • Ribonucleotide reductases reveal novel viral diversity and predict biological and ecological features of unknown marine viruses
    Sakowski, EG
  • Development of phoH as a novel signature gene for assessing marine phage diversity
    Goldsmith, DB
  • Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments
    Sullivan, MB
  • The 1.2-megabase genome sequence of Mimivirus
    Raoult, D
  • Giant viruses with an expanded complement of translation system components
    Schulz, F
  • Involvement of tonB-exbBD1D2 operon in infection of Xanthomonas campestris phage phi L7
    Hung, CH; Yang, CF; Yang, CY; Tseng, YH
  • Screening of natural waters for viruses which infect chlorella cells
    Yamada, T; Higashiyama, T; Fukuda, T
  • GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions
    Besemer, J; Lomsadze, A; Borodovsky, M
  • Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation
    O’Leary, NA
  • CDD: NCBI’s conserved domain database
    Marchler-Bauer, A
  • Basic local alignment search tool
    Altschul, SF; Gish, W; Miller, W; Myers, EW; Lipman, DJ
  • CD-Search: protein domain annotations on the fly
    Marchler-Bauer, A; Bryant, SH
  • BLAST+: architecture and applications
    Camacho, C
  • tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence
    Lowe, TM; Eddy, SR
  • KEGG as a reference resource for gene and protein annotation
    Kanehisa, M; Sato, Y; Kawashima, M; Furumichi, M; Tanabe, M
  • Expanded microbial genome coverage and improved protein family annotation in the COG database
    Galperin, MY; Makarova, KS; Wolf, YI; Koonin, EV
  • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    Altschul, SF
  • MAFFT multiple sequence alignment software version 7: improvements in performance and usability
    Katoh, K; Standley, DM
  • RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
    Stamatakis, A
  • OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy
    Emms, DM; Kelly, S

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