Top

Published in:

01-12-2019 | Brief Report

Complete genome sequence of the novel phage vB_BthS-HD29phi infecting Bacillus thuringiensis

Authors: Yajuan Fu, Sangsang Deng, Leiqin liang, Yan Wu, Meiying Gao

Published in: Archives of Virology | Issue 12/2019

Abstract

The phage vB_BthS-HD29phi infecting Bacillus thuringiensis strain HD29 was isolated and purified. The morphology of the phage showed that it belongs to the family Siphoviridae. The phage genome was 32,181 bp in length, comprised linear double-stranded DNA with an average G + C content of 34.9%, and exhibited low similarity to known phage genomes. Genomic and phylogenetic analysis revealed that vB_BthS-HD29phi is a novel phage. In total, 50 putative ORFs were predicted in the phage genome, and only 18 ORFs encoded proteins with known functions. This article reports the genome sequence of a new tailed phage and increases the known genetic diversity of tailed phages.

Available only for authorised users

Jouzani GS, Valijanian E, Sharafi R (2017) Bacillus thuringiensis: a successful insecticide with new environmental features and tidings. Appl Microbiol Biot 101(7):2691–2711. https://doi.org/10.1007/s00253-017-8175-y CrossRef

Liao W, Sun F, Song SY, Shi W, Pang Y (2007) Biology of two lysogenic phages from Bacillus thuringiensis MZ1. Wei Sheng Wu Xue Bao 47(1):92–97PubMed

Stromsten NJ, Benson SD, Burnett RM, Bamford DH, Bamford JK (2003) The Bacillus thuringiensis linear double-stranded DNA phage Bam35, which is highly similar to the Bacillus cereus linear plasmid pBClin15, has a prophage state. J Bacteriol 185(23):6985–6989. https://doi.org/10.1128/jb.185.23.6985-6989.2003 CrossRefPubMedPubMedCentral

Verheust C, Jensen G, Mahillon J (2003) pGIL01, a linear tectiviral plasmid prophage originating from Bacillus thuringiensis serovar israelensis. Microbiology 149(Pt 8):2083–2092. https://doi.org/10.1099/mic.0.26307-0 CrossRefPubMed

Gillis A, Mahillon J (2014) Phages preying on Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis: past, present and future. Viruses 6(7):2623–2672. https://doi.org/10.3390/v6072623 CrossRefPubMedPubMedCentral

Moumen B, Nguen-The C, Sorokin A (2012) Sequence Analysis of Inducible Prophage phIS3501 Integrated into the Haemolysin II Gene of Bacillus thuringiensis var israelensis ATCC35646. Genet Res Int 2012:543286. https://doi.org/10.1155/2012/543286 CrossRefPubMedPubMedCentral

Liao W, Song S, Sun F, Jia Y, Zeng W, Pang Y (2008) Isolation, characterization and genome sequencing of phage MZTP02 from Bacillus thuringiensis MZ1. Arch Virol 153(10):1855–1865. https://doi.org/10.1007/s00705-008-0201-z CrossRefPubMed

Yuan Y, Peng Q, Yang S, Zhang S, Fu Y, Wu Y, Gao M (2018) Isolation of a novel Bacillus thuringiensis phage representing a new phage lineage and characterization of its endolysin. Viruses. https://doi.org/10.3390/v10110611 CrossRefPubMedPubMedCentral

Yuan Y, Gao M, Wu D, Liu P, Wu Y (2012) Genome characteristics of a novel phage from Bacillus thuringiensis showing high similarity with phage from Bacillus cereus. PLoS One 7(5):e37557. https://doi.org/10.1371/journal.pone.0037557 CrossRefPubMedPubMedCentral

10.

Meyer M (2010) Kircher M (2010) Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb Protoc 2010(6):pdb prot5448. https://doi.org/10.1101/pdb.prot5448 CrossRefPubMed

11.

Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19(5):455–477. https://doi.org/10.1089/cmb.2012.0021 CrossRefPubMedPubMedCentral

12.

Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genom 9:75. https://doi.org/10.1186/1471-2164-9-75 CrossRef

13.

Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M, Vonstein V, Wattam AR, Xia F, Stevens R (2014) The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res 42(Database issue):D206–D214. https://doi.org/10.1093/nar/gkt1226 CrossRefPubMed

14.

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(12):2607–2618CrossRefPubMedPubMedCentral

15.

Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer EL, Eddy SR, Bateman A, Finn RD (2012) The Pfam protein families database. Nucleic Acids Res 40(Database issue):D290–D301. https://doi.org/10.1093/nar/gkr1065 CrossRefPubMed

16.

Soding J (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics 21(7):951–960. https://doi.org/10.1093/bioinformatics/bti125 CrossRefPubMed

17.

Lowe TM, Chan PP (2016) tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res 44(W1):W54–W57. https://doi.org/10.1093/nar/gkw413 CrossRefPubMedPubMedCentral

18.

Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35(9):3100–3108. https://doi.org/10.1093/nar/gkm160 CrossRefPubMedPubMedCentral

19.

Richter M, Rossello-Mora R, Oliver Glockner F, Peplies J (2016) JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 32(6):929–931. https://doi.org/10.1093/bioinformatics/btv681 CrossRefPubMed

20.

Kumar S, Stecher G, Tamura K (2016) MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33(7):1870–1874. https://doi.org/10.1093/molbev/msw054 CrossRefPubMedPubMedCentral

21.

Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJ (2015) The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protoc 10(6):845–858. https://doi.org/10.1038/nprot.2015.053 CrossRefPubMedPubMedCentral

22.

Sullivan MJ, Petty NK, Beatson SA (2011) Easyfig: a genome comparison visualizer. Bioinformatics 27(7):1009–1010. https://doi.org/10.1093/bioinformatics/btr039 CrossRefPubMedPubMedCentral

23.

Luscombe NM, Austin SE, Berman HM, Thornton JM (2000) An overview of the structures of protein-DNA complexes. Genome Biol 1(1):REVIEWS001. https://doi.org/10.1186/gb-2000-1-1-reviews001 CrossRefPubMedPubMedCentral

24.

Gao N, Shearwin K, Mack J, Finzi L, Dunlap D (2013) Purification of bacteriophage lambda repressor. Protein Expr Purif 91(1):30–36. https://doi.org/10.1016/j.pep.2013.06.013 CrossRefPubMedPubMedCentral

25.

Ding Y, Manzo C, Fulcrand G, Leng F, Dunlap D, Finzi L (2014) DNA supercoiling: a regulatory signal for the lambda repressor. Proc Natl Acad Sci USA 111(43):15402–15407. https://doi.org/10.1073/pnas.1320644111 CrossRefPubMedPubMedCentral

26.

Susskind MM, Botstein D (1975) Mechanism of action of Salmonella phage P22 antirepressor. J Mol Biol 98(2):413–424CrossRefPubMed

27.

Bochow S, Elliman J, Owens L (2012) Bacteriophage adenine methyltransferase: a life cycle regulator? Modelled using Vibrio harveyi myovirus like. J Appl Microbiol 113(5):1001–1013. https://doi.org/10.1111/j.1365-2672.2012.05358.x CrossRefPubMed

28.

Lemire S, Figueroa-Bossi N, Bossi L (2011) Bacteriophage crosstalk: coordination of prophage induction by trans-acting antirepressors. PLoS Genet 7(6):e1002149. https://doi.org/10.1371/journal.pgen.1002149 CrossRefPubMedPubMedCentral

29.

Sandegren L, Sjoberg BM (2007) Self-splicing of the bacteriophage T4 group I introns requires efficient translation of the pre-mRNA in vivo and correlates with the growth state of the infected bacterium. J Bacteriol 189(3):980–990. https://doi.org/10.1128/JB.01287-06 CrossRefPubMed

Title: Complete genome sequence of the novel phage vB_BthS-HD29phi infecting Bacillus thuringiensis
Authors: Yajuan Fu
Sangsang Deng
Leiqin liang
Yan Wu
Meiying Gao
Publication date: 01-12-2019
Publisher: Springer Vienna
Published in: Archives of Virology / Issue 12/2019
Print ISSN: 0304-8608
Electronic ISSN: 1432-8798
DOI: https://doi.org/10.1007/s00705-019-04416-5

ACC 2024 Congress Coverage

Heart Failure Video

Keynote webinar | Spotlight on sleep in brain health

Springer Medicine

Complete genome sequence of the novel phage vB_BthS-HD29phi infecting Bacillus thuringiensis

Abstract

ACC 2024 Congress Coverage

Year in Review: Heart failure and cardiomyopathies

Semaglutide benefits people with type 2 diabetes and obesity-related heart failure

Incentivised to exercise

New intervention for STEMI-related cardiogenic shock

» View more highlights on the ACC 2024 congress hub page

Keynote webinar | Spotlight on sleep in brain health

Springer Medicine

Abstract

Please log in to get access to this content

Other articles of this Issue 12/2019

In vitro effect of branched polyethyleneimine (bPEI) on cells infected with human immunodeficiency virus: enhancement of viral replication

R18C is a new viable P2-like bacteriophage of rabbit origin infecting Citrobacter rodentium and Shigella sonnei strains

Molecular characterization of a novel potyvirus infecting noni

Circulation of multiple subtypes (A, G and CRFs 02_AG) of human immunodeficiency virus type 1 (HIV-1) in selected districts of Punjab province, Pakistan

The range of sampling times affects Zika virus evolutionary rates and divergence times

Identification and genomic characterization of grapevine Kizil Sapak virus, a novel grapevine-infecting member of the family Betaflexiviridae

ACC 2024 Congress Coverage

Year in Review: Heart failure and cardiomyopathies

Semaglutide benefits people with type 2 diabetes and obesity-related heart failure

Incentivised to exercise

New intervention for STEMI-related cardiogenic shock

» View more highlights on the ACC 2024 congress hub page