nach oben

Erschienen in:

08.02.2018 | Annotated Sequence Record

Genomic characteristics of vB_PpaP_PP74, a T7-like Autographivirinae bacteriophage infecting a potato pathogen of the newly proposed species Pectobacterium parmentieri

verfasst von: Anastasia Kabanova, Mikhail Shneider, Eugenia Bugaeva, Vo Thi Ngoc Ha, Kirill Miroshnikov, Aleksei Korzhenkov, Eugene Kulikov, Stepan Toschakov, Alexander Ignatov, Konstantin Miroshnikov

Erschienen in: Archives of Virology | Ausgabe 6/2018

Einloggen, um Zugang zu erhalten

Abstract

Bacteriophage vB_PpaP_PP74 (PP74) is a novel virulent phage that infects members of the species Pectobacterium parmentieri, a newly established species of soft-rot-causing bacteria in the family Pectobacteriaceae, derived from potato-specific Pectobacterium wasabiae. vB_PpaP_PP74 was identified as a member of the family Podoviridae by transmission electron microscopy. The phage has a 39,790-bp dsDNA genome containing 50 open reading frames (ORFs). Because of the absence of genes encoding toxins or lysogeny factors, PP74 may be considered a candidate phage for pathogen biocontrol applications. The genome layout is similar to genomes of T7-like phages within the subfamily Autographivirinae, and therefore, functions can be attributed to most of ORFs. However, the closest nucleotide sequence homologs of phage PP74 are unclassified Escherichia phages. Based on phylogenetic analysis, vB_PpaP_PP74 is a sensu lato T7-like phage, but it forms a distant subgenus group together with homologous enterobacterial phages.

Nur mit Berechtigung zugänglich

Pérombelon MCM (2002) Potato diseases caused by soft rot erwinias: an overview of pathogenesis. Plant Pathol 51:1–12. https://doi.org/10.1046/j.0032-0862.2001.Shorttitle.doc.x CrossRef

Toth IK, van der Wolf JM, Saddler G et al (2011) Dickeya species: an emerging problem for potato production in Europe. Plant Pathol 60:385–399. https://doi.org/10.1111/j.1365-3059.2011.02427.x CrossRef

Czajkowski R, Grabe GJ, van der Wolf JM (2009) Distribution of Dickeya spp. and Pectobacterium carotovorum subsp. carotovorum in naturally infected seed potatoes. Eur J Plant Pathol 125:263–275. https://doi.org/10.1007/s10658-009-9480-9 CrossRef

Czajkowski R, Pérombelon MMCM, Jafra S et al (2015) Detection, identification and differentiation of Pectobacterium and Dickeya species causing potato blackleg and tuber soft rot: a review. Ann Appl Biol 166:18–38. https://doi.org/10.1111/aab.12166 CrossRefPubMed

Khayi S, Cigna J, Chong TM et al (2016) Transfer of the potato plant isolates of Pectobacterium wasabiae to Pectobacterium parmentieri sp. nov. Int J Syst Evol Microbiol 66:5379–5383. https://doi.org/10.1099/ijsem.0.001524

Nykyri J, Niemi O, Koskinen P et al (2012) Revised phylogeny and novel horizontally acquired virulence determinants of the model soft rot phytopathogen Pectobacterium wasabiae SCC3193. PLoS Pathog. https://doi.org/10.1371/journal.ppat.1003013 PubMedPubMedCentralCrossRef

Smolarska A, Rabalski L, Narajczyk M, Czajkowski R (2017) Isolation and phenotypic and morphological characterization of the first Podoviridae lytic bacteriophages ϕA38 and ϕA41 infecting Pectobacterium parmentieri (former Pectobacterium wasabiae). Eur J Plant Pathol. https://doi.org/10.1007/s10658-017-1289-3 CrossRef

Van Twest R, Kropinski AM (2009) Bacteriophage enrichment from water and soil. Methods Mol Biol 501:15–21. https://doi.org/10.1007/978-1-60327-164-6_2 CrossRefPubMed

Lavigne R, Seto D, Mahadevan P et al (2008) Unifying classical and molecular taxonomic classification: analysis of the Podoviridae using BLASTP-based tools. Res Microbiol 159:406–414. https://doi.org/10.1016/j.resmic.2008.03.005 CrossRefPubMed

10.

Bankevich A, Nurk S, Antipov D et al (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. https://doi.org/10.1089/cmb.2012.0021 CrossRefPubMedPubMedCentral

11.

Besemer J, Lomsadze A, Borodovsky M (2001) GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 29:2607–2618. https://doi.org/10.1093/nar/29.12.2607

12.

Hyatt D, Chen G-L, Locascio PF et al (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform 11:119. https://doi.org/10.1186/1471-2105-11-119 CrossRef

13.

Aziz RK, Bartels D, Best AA et al (2008) The RAST server: rapid annotations using subsystems technology. BMC Genom 9:75. https://doi.org/10.1186/1471-2164-9-75 CrossRef

14.

Altschul SF, Madden TL, Schäffer AA et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402. https://doi.org/10.1093/nar/25.17.3389 CrossRefPubMedPubMedCentral

15.

Sievers F, Wilm A, Dineen D et al (2011) Fast, scalable generation of high quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7:539CrossRefPubMedPubMedCentral

16.

Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313. https://doi.org/10.1093/bioinformatics/btu033 CrossRefPubMedPubMedCentral

17.

Schattner P, Brooks AN, Lowe TM (2005) The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res. https://doi.org/10.1093/nar/gki366 PubMedPubMedCentralCrossRef

18.

Lavigne R, Sun WD, Volckaert G (2004) PHIRE, a deterministic approach to reveal regulatory elements in bacteriophage genomes. Bioinformatics 20:629–635. https://doi.org/10.1093/bioinformatics/btg456 CrossRefPubMed

19.

Klucar L, Stano M, Hajduk M (2009) PhiSITE: database of gene regulation in bacteriophages. Nucleic Acids Res. https://doi.org/10.1093/nar/gkp911 PubMedPubMedCentralCrossRef

20.

Mertens H, Hausmann R (1982) Coliphage BA14: a new relative of phage T7. J Gen Virol 62:331–341. https://doi.org/10.1099/0022-1317-62-2-331 CrossRefPubMed

21.

Chen M, Xu J, Yao H et al (2016) Isolation, genome sequencing and functional analysis of two T7-like coliphages of avian pathogenic Escherichia coli. Gene 582:47–58. https://doi.org/10.1016/j.gene.2016.01.049 CrossRefPubMed

22.

Faidiuk IV, Tovkach EI (2014) Exclusion of polyvalent T7-like phages by prophage elements. Mikrobiol Z 76:42–50. https://www.ncbi.nlm.nih.gov/pubmed/25434214 PubMed

23.

Steven AC, Trus BL, Maizel JV et al (1988) Molecular substructure of a viral receptor-recognition protein. The gp17 tail-fiber of bacteriophage T7. J Mol Biol 200:351–365. https://doi.org/10.1016/0022-2836(88)90246-X CrossRefPubMed

24.

Garcia-Doval C, van Raaij MJ (2012) Structure of the receptor-binding carboxy-terminal domain of bacteriophage T7 tail fibers. Proc Natl Acad Sci USA 109:9390–9395. https://doi.org/10.1073/pnas.1119719109 CrossRefPubMedPubMedCentral

25.

Veesler D, Spinelli S, Mahony J et al (2012) Structure of the phage TP901-1 1.8 MDa baseplate suggests an alternative host adhesion mechanism. Proc Natl Acad Sci USA 109:8954–8958. https://doi.org/10.1073/pnas.1200966109 CrossRefPubMedPubMedCentral

Titel: Genomic characteristics of vB_PpaP_PP74, a T7-like Autographivirinae bacteriophage infecting a potato pathogen of the newly proposed species Pectobacterium parmentieri
verfasst von: Anastasia Kabanova
Mikhail Shneider
Eugenia Bugaeva
Vo Thi Ngoc Ha
Kirill Miroshnikov
Aleksei Korzhenkov
Eugene Kulikov
Stepan Toschakov
Alexander Ignatov
Konstantin Miroshnikov
Publikationsdatum: 08.02.2018
Verlag: Springer Vienna
Erschienen in: Archives of Virology / Ausgabe 6/2018
Print ISSN: 0304-8608
Elektronische ISSN: 1432-8798
DOI: https://doi.org/10.1007/s00705-018-3766-1

Leitlinien kompakt für die Innere Medizin

Mit medbee Pocketcards sicher entscheiden.

^{Seit 2022 gehört die medbee GmbH zum Springer Medizin Verlag}

Kostenlos registrieren

Neu im Fachgebiet Innere Medizin

25.04.2024 | Nierenkarzinom | Nachrichten

Update Innere Medizin

Bestellen Sie unseren Fach-Newsletter und bleiben Sie gut informiert.

Newsletter bestellen

Springer Medizin

Genomic characteristics of vB_PpaP_PP74, a T7-like Autographivirinae bacteriophage infecting a potato pathogen of the newly proposed species Pectobacterium parmentieri

Abstract

Leitlinien kompakt für die Innere Medizin

Neu im Fachgebiet Innere Medizin

Adjuvante Immuntherapie verlängert Leben bei RCC

Alectinib verbessert krankheitsfreies Überleben bei ALK-positivem NSCLC

Metformin rückt in den Hintergrund

Myokarditis nach Infekt – richtig schwierig wird es bei Profisportlern

Update Innere Medizin

Springer Medizin

Abstract

Bitte loggen Sie sich ein, um Zugang zu diesem Inhalt zu erhalten

Weitere Artikel der Ausgabe 6/2018

Detection and phylogenetic analysis of a new adenoviral polymerase gene in reptiles in Korea

Tetraspanin blockage reduces exosome-mediated HIV-1 entry

A genetic analysis of an important hydrophobic interaction at the P22 tailspike protein N-terminal domain

Two distinct begomoviruses associated with an alphasatellite coinfecting Emilia sonchifolia in Thailand

Development of a nanogold slot blot inhibition assay for the detection of antibodies against bovine herpesvirus type 1

Anti-influenza virus activity of a salcomine derivative mediated by inhibition of viral RNA synthesis

Leitlinien kompakt für die Innere Medizin

Neu im Fachgebiet Innere Medizin

Adjuvante Immuntherapie verlängert Leben bei RCC

Alectinib verbessert krankheitsfreies Überleben bei ALK-positivem NSCLC

Metformin rückt in den Hintergrund

Myokarditis nach Infekt – richtig schwierig wird es bei Profisportlern

Update Innere Medizin