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Viruses

Complete Genome Sequence of the Streptomyces Phage Nanodon

Ivan Erill, Steven M. Caruso
Ivan Erill
Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, Maryland, USA
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Steven M. Caruso
Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, Maryland, USA
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DOI: 10.1128/genomeA.01019-16
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ABSTRACT

Streptomyces phage Nanodon is a temperate double-stranded DNA Siphoviridae belonging to cluster BD1. It was isolated from soil collected in Kilauea, HI, using Streptomyces griseus subsp. griseus as a host.

GENOME ANNOUNCEMENT

Streptomyces spp. are Gram-positive, filamentous, and spore-forming members of the Actinomycetaceae family, from which two-thirds of antibiotics have been derived (1). Here, we present the genome of the double-stranded DNA bacteriophage Nanodon, a Siphoviridae isolated from volcanic soil collected in Kilauea, HI (22°10′28.6″N 159°26′08.3″W), which was then harvested and investigated using Streptomyces griseus subsp. griseus (ATCC 10137) (S. griseus) as a host by University of Maryland, Baltimore County (UMBC) undergraduate researchers, as described previously (2).

Nanodon produced variably sized clear plaques when incubated for 48 h on lawns of S. griseus grown on supplemented nutrient agar at 30°C (3). Nanodon has an icosahedral capsid (d = 46 nm) with a flexible noncontractile tail (l = 151 nm). Shotgun sequencing was carried out by the Pittsburgh Bacteriophage Institute to approximately 1,201-fold coverage by Illumina sequencing. Nanodon has a linear 50,082-bp genome with an 11-bp 3′ sticky overhang and a 65.7% G+C content. Genomic analysis of Nanodon determined that the phage contains 75 protein-coding genes, of which 25 have been assigned predicted functions. Among these were both a serine integrase and an immunity repressor, suggesting that Nanodon is a temperate phage (4, 5).

Genomic comparison of Nanodon with the 69 Streptomyces phages sequenced to date by SEA-PHAGES participants (2) identified Nanodon as a member of cluster BD, one of nine established Streptomyces phage clusters (http://phagesdb.org/) and, specifically, as a member of subcluster BD1. Nanodon shares 84.4% ± 0.02% average ± standard deviation (SD) nucleotide identity (ANI) with other members of subcluster BD1 available in GenBank, and 71.5% ± 0.02% ANI with phages in the other four current BD subclusters (6). A comparison of Nanodon by whole-genome alignment (7) and phylogenetic analysis using the terminase gene also demonstrated that Nanodon clusters with other members of the BD1 subcluster.

Codon usage bias (CUB) analysis using the scnRCA program (8) and reference sets derived from several Firmicutes and Actinobacteria genomes revealed that protein-coding sequences in the Nanodon genome are adapted for translational optimization on Streptomyces hosts, with capsid and tail assembly proteins showing the highest level of codon optimization. However, CUB patterns revealed no specific optimization for S. griseus compared to other Streptomyces species, suggesting that Nanodon might have broad-range specificity within the Streptomyces, as seen previously for other temperate Streptomyces phages (9, 10).

Accession number(s).The complete genome sequence of the Streptomyces phage Nanodon is available in GenBank with the accession no. KX344445.

ACKNOWLEDGMENTS

This work was supported by the UMBC Department of Biological Sciences and the Howard Hughes Medical Institute SEA-PHAGES program.

The members of the 2015 UMBC Phage Hunters class are listed at http://phages.umbc.edu/home/class-lists/2015-16/.

We thank Lee E. Hughes, Graham F. Hatfull, Deborah Jacobs-Sera, Welkin H. Pope, Daniel A. Russell, Steven G. Cresawn, Chere Petty, and Ralph Murphy.

FOOTNOTES

    • Received 28 July 2016.
    • Accepted 11 August 2016.
    • Published 6 October 2016.
  • Copyright © 2016 Erill et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

REFERENCES

  1. 1.↵
    1. Barka EA,
    2. Vatsa P,
    3. Sanchez L,
    4. Gaveau-Vaillant N,
    5. Jacquard C,
    6. Klenk H-P,
    7. Clément C,
    8. Ouhdouch Y,
    9. van Wezel GP
    . 2016. Taxonomy, physiology, and natural products of Actinobacteria. Microbiol Mol Biol Rev 80:1–43. doi:10.1128/MMBR.00019-15.
    OpenUrlCrossRefPubMed
  2. 2.↵
    1. Jordan TC,
    2. Burnett SH,
    3. Carson S,
    4. Jordan TC,
    5. Burnett SH,
    6. Carson S,
    7. Caruso SM,
    8. Clase K,
    9. DeJong RJ,
    10. Dennehy JJ,
    11. Denver DR,
    12. Dunbar D,
    13. Elgin SCR,
    14. Findley AM,
    15. Gissendanner CR,
    16. Golebiewska UP,
    17. Guild N,
    18. Hartzog GA,
    19. Grillo WH,
    20. Hollowell GP,
    21. Hughes LE,
    22. Johnson A,
    23. King RA,
    24. Lewis LO,
    25. Li W,
    26. Rosenzweig F,
    27. Rubin MR,
    28. Saha MS,
    29. Sandoz J,
    30. Shaffer CD,
    31. Taylor B,
    32. Temple L,
    33. Vazquez E,
    34. Ware VC,
    35. Barker LP,
    36. Bradley KW,
    37. Jacobs-Sera D,
    38. Pope WH,
    39. Russell DA,
    40. Cresawn SG,
    41. Lopatto D,
    42. Bailey CP,
    43. Hatfull GF
    . 2014. A broadly implementable research course in phage discovery and genomics for first-year undergraduate students. mBio 5:e01051-13. doi:10.1128/mBio.01051-13.
    OpenUrlAbstract/FREE Full Text
  3. 3.↵
    1. Smith MC,
    2. Hendrix RW,
    3. Dedrick R,
    4. Mitchell K,
    5. Ko C-C,
    6. Russell D,
    7. Bell E,
    8. Gregory M,
    9. Bibb MJ,
    10. Pethick F,
    11. Jacobs-Sera D,
    12. Herron P,
    13. Buttner MJ,
    14. Hatfull GF
    . 2013. Evolutionary relationships among actinophages and a putative adaptation for growth in Streptomyces spp. J Bacteriol 195:4924–4935. doi:10.1128/JB.00618-13.
    OpenUrlAbstract/FREE Full Text
  4. 4.↵
    1. Smith MC
    . 2015. Phage-encoded serine integrases and other large serine recombinases. Microbiol Spectr 3:1–19. doi:10.1128/microbiolspec.MDNA3-0059-2014.
    OpenUrlCrossRef
  5. 5.↵
    1. Petrova ZO,
    2. Broussard GW,
    3. Hatfull GF
    . 2015. Mycobacteriophage-repressor-mediated immunity as a selectable genetic marker: Adephagia and BPs repressor selection. Microbiology 161:1539–1551. doi:10.1099/mic.0.000120.
    OpenUrlCrossRefPubMed
  6. 6.↵
    1. Hatfull GF,
    2. Jacobs-Sera D,
    3. Lawrence JG,
    4. Pope WH,
    5. Russell DA,
    6. Ko CC,
    7. Weber RJ,
    8. Patel MC,
    9. Germane KL,
    10. Edgar RH,
    11. Hoyte NN,
    12. Bowman CA,
    13. Tantoco AT,
    14. Paladin EC,
    15. Myers MS,
    16. Smith AL,
    17. Grace MS,
    18. Pham TT,
    19. O'Brien MB,
    20. Vogelsberger AM,
    21. Hryckowian AJ,
    22. Wynalek JL,
    23. Donis-Keller H,
    24. Bogel MW,
    25. Peebles CL,
    26. Cresawn SG,
    27. Hendrix RW
    . 2010. Comparative genomic analysis of 60 mycobacteriophage genomes: genome clustering, gene acquisition, and gene size. J Mol Biol 397:119–143. doi:10.1016/j.jmb.2010.01.011.
    OpenUrlCrossRefPubMedWeb of Science
  7. 7.↵
    1. Cresawn SG,
    2. Bogel M,
    3. Day N,
    4. Jacobs-Sera D,
    5. Hendrix RW,
    6. Hatfull GF
    . 2011. Phamerator: a bioinformatic tool for comparative bacteriophage genomics. BMC Bioinformatics 12:395. doi:10.1186/1471-2105-12-395.
    OpenUrlCrossRefPubMed
  8. 8.↵
    1. O'Neill PK,
    2. Or M,
    3. Erill I
    . 2013. scnRCA: a novel method to detect consistent patterns of translational selection in mutationally-biased genomes. PLoS One 8:e76177. doi:10.1371/journal.pone.0076177.
    OpenUrlCrossRefPubMed
  9. 9.↵
    1. Chater K,
    2. Carter A
    . 1979. A new, wide host-range, temperate bacteriophage (R4) of Streptomyces and its interaction with some restriction-modification systems. Microbiology 115:431–442. doi:10.1099/00221287-115-2-431.
    OpenUrlCrossRef
  10. 10.↵
    1. Zhou X,
    2. Deng Z,
    3. Hopwood DA,
    4. Kieser T
    . 1994. Characterization of phi HAU3, a broad-host-range temperate streptomyces phage, and development of phasmids. J Bacteriol 176:2096–2099.
    OpenUrlAbstract/FREE Full Text
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Complete Genome Sequence of the Streptomyces Phage Nanodon
Ivan Erill, Steven M. Caruso on behalf of the 2015 UMBC Phage Hunters
Genome Announcements Oct 2016, 4 (5) e01019-16; DOI: 10.1128/genomeA.01019-16

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Complete Genome Sequence of the Streptomyces Phage Nanodon
Ivan Erill, Steven M. Caruso on behalf of the 2015 UMBC Phage Hunters
Genome Announcements Oct 2016, 4 (5) e01019-16; DOI: 10.1128/genomeA.01019-16
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