Advertisement

Extremophiles

, Volume 23, Issue 5, pp 599–612 | Cite as

A novel thermophilic Aeribacillus bacteriophage AP45 isolated from the Valley of Geysers, Kamchatka: genome analysis suggests the existence of a new genus within the Siphoviridae family

  • V. MorozovaEmail author
  • O. Bokovaya
  • Yu. Kozlova
  • A. Kurilshikov
  • I. Babkin
  • A. Tupikin
  • A. Bondar
  • E. Ryabchikova
  • A. Brayanskaya
  • S. Peltek
  • N. TikunovaEmail author
Original Paper
  • 32 Downloads

Abstract

A novel thermophilic bacteriophage AP45 and its host strain Aeribacillus sp. CEMTC656 were isolated from the Valley of Geysers, Kamchatka Peninsula, Russia. Bacteriophage AP45 was identified as a member of the Siphoviridae family by electron microscopy. It showed high thermostability and had a slow cycle of reproduction. The AP45 genome had 51,606 base pairs (bp) and contained 71 open reading frames (ORFs), 40 of them encoding proteins of predicted function. Genes encoding DNA and RNA polymerases were not identified, indicating that AP45 used host polymerases. Based on the ORF65 encoding putative endolysin, the recombinant protein rAP45Lys was developed and its peptidoglycan-hydrolyzing activity was demonstrated. The AP45 genome exhibited limited identity to other phage sequences; the highest identity, 36%, was with the genome of the thermophilic Geobacillus myovirus D6E. The majority of putative proteins encoded by the AP45 genome had higher similarity to proteins from bacteria belonging to the Bacillaceae family, than to bacteriophages. In addition, more than half of the putative ORFs in the AP45 genome were highly similar to prophage sequences of A. pallidus strain 8m3, which was isolated in north–east China. The AP45 phage and revealed prophages might be members of a new genus belonging to the Siphoviridae family.

Keywords

Thermophilic bacteriophage Kamchatka peninsula Valley of geysers Aeribacillus sp. Prophage Siphoviridae Endolysin 

Notes

Acknowledgements

This study was supported by FSI SB RAS Project 0309-2018-0016. Collection of EMTC ICBFM SB RAS was supported by Russian State funded budget project of ICBFM SB RAS # AAAA-A17-117020210027-9.

Compliance with ethical standards

Conflict of interest

There is no conflict of interest.

Ethical approval

The article does not involve studies with human participants or animals.

Supplementary material

792_2019_1119_MOESM1_ESM.pdf (139 kb)
Supplementary file1 (PDF 138 kb)
792_2019_1119_MOESM2_ESM.pdf (301 kb)
Supplementary file2 (PDF 301 kb)
792_2019_1119_MOESM3_ESM.pdf (112 kb)
Supplementary file3 (PDF 112 kb)
792_2019_1119_MOESM4_ESM.pdf (163 kb)
Supplementary file4 (PDF 162 kb)
792_2019_1119_MOESM5_ESM.pdf (233 kb)
Supplementary file5 (PDF 232 kb)

References

  1. Bryanskaya AV, Rozanov AS, Slynko NM, Shekhovtsov SV, Peltek SE (2015) Geobacillus icigianus sp. nov., a thermophilic bacterium isolated from a hot spring. Int J Syst Evol Microbiol. 65:864–869CrossRefGoogle Scholar
  2. Burgess EA, Unrine JM, Mills GL, Romanek CS, Wiegel J (2012) Comparative geochemical and microbiological characterization of two thermal pools in the Uzon Caldera, Kamchatka, Russia. Microb Ecol 63:471–489CrossRefGoogle Scholar
  3. Cheepudom J, Lee CC, Cai B, Meng M (2015) Isolation, characterization, and complete genome analysis of P1312, a thermostable bacteriophage that infects Thermobifida fusca. Front Microbiol.  https://doi.org/10.3389/fmicb.2015.00959 Google Scholar
  4. Dobretsov NL, Lazareva EV, Zhmodik SM, Bryanskaya AV, Morozova VV, Tikunova NV, Peltek SE, Karpov GA, Taran OP, Ogorodnikova OL, Kirichenko IS, Rozanov AS, Babkin IV, Shuvaeva OV, Chebykin EP (2015) Geological, hydrogeochemical, and microbial characteristics of the “Oil site” of the Uzon caldera (Kamchatka). Russian Geol Geophys 56:39–63CrossRefGoogle Scholar
  5. Filippidou S, Jaussi M, Junier T, Wunderlin T, Jeanneret N, Regenspurg S, Li PE, Lo CC, Johnson S, McMurry K, Gleasner CD, Vuyisich M, Chain PS, Junier P (2015) Genome sequence of Aeribacillus pallidus strain GS3372, an endospore-forming bacterium isolated in a deep geothermal reservoir. Genome Announc.  https://doi.org/10.1128/genomeA.00981-15 Google Scholar
  6. Fukushima T, Sekiguchi J (2016) Zymographic techniques for the analysis of bacterial cell wall in Bacillus. Methods Mol Biol 1440:87–98CrossRefGoogle Scholar
  7. Gumerov VM, Mardanov AV, Beletskiĭ AV, Bonch-Osmolovskaia EA, Ravin NV (2011) Molecular analysis of microbial diversity in the Zavarzin Spring, the Uzon caldera. Mikrobiologiia 80:258–265 (In Russian) Google Scholar
  8. Hjorleifsdottir S, Aevarsson A, Hreggvidsson GO, Fridjonsson OH, Kristjansson JK (2014) Isolation, growth and genome of the Rhodothermus RM378 thermophilic bacteriophage. Extremophiles 18:261–270CrossRefGoogle Scholar
  9. Jalasvuori M, Pawlowski A, Bamford JKH (2010) A unique group of virus-related, genome-integrating elements found solely in the bacterial family Thermaceae and the archaeal family Halobacteriaceae. J Bacteriol 192:3231–3234CrossRefGoogle Scholar
  10. Jones P, Binns D, Chang H-Y, Fraser M, Li W, McAnulla C, McWilliam H et al (2014) InterProScan 5: genome-scale protein function classification. Bioinformatics.  https://doi.org/10.1093/bioinformatics/btu031 Google Scholar
  11. Katoh K, Kuma K, Miyata T, Toh H (2005) Improvement in the accuracy of multiple sequence alignment program MAFFT. Genome Inform 16:22–33Google Scholar
  12. Kompanichenko VN, Poturay VA, Shlufman KV (2015) Hydrothermal systems of Kamchatka are models of the prebiotic environment. Orig Life Evol Biosph 45:93–103CrossRefGoogle Scholar
  13. Kropinski AM (2009) Measurement of the rate of attachment of bacteriophage to cells. Methods Mol Biol 501:151–155CrossRefGoogle Scholar
  14. Kropinski AM, Mazzocco A, Waddell TE, Lingohr E, Johnson RP (2009) Enumeration of bacteriophages by double agar overlay plaque assay. Methods Mol Biol 501:69–76CrossRefGoogle Scholar
  15. Kublanov IV, Perevalova AA, Slobodkina GB, Lebedinsky AV, Bidzhieva SK, Kolganova TV (2009) Biodiversity of thermophilic prokaryotes with hydrolytic activities in hot springs of Uzon Caldera, Kamchatka (Russia). Appl Environ Microbiol 75:286–291CrossRefGoogle Scholar
  16. Kutter E (2009) Phage host range and efficiency of plating. Methods Mol Biol 501:141–149CrossRefGoogle Scholar
  17. Levine M, Truesdall S, Ramakrishan T, Bronson MJ (1975) Dual control of lysogeny by bacteriophage P22: an antirepressor locus and its controlling elements. J Mol Biol 91:421–43841CrossRefGoogle Scholar
  18. Lin L, Han J, Ji X, Hong W, Huang L, Wei Y (2011) Isolation and characterization of a new bacteriophage MMP17 from Meiothermus. Extremophiles 15:253–258CrossRefGoogle Scholar
  19. Liu B, Wu S, Song Q, Zhang X, Xie L (2006) Two novel bacteriophages of thermophilic bacteria isolated from deep-sea hydrothermal fields. Curr Microbiol 53:163–166CrossRefGoogle Scholar
  20. Liu B, Zhang X (2008) Deep-sea thermophilic Geobacillus bacteriophage GVE2 transcriptional profile and proteomic characterization of virions. Appl Microbiol Biotechnol 80:697–707CrossRefGoogle Scholar
  21. Liu B, Zhou F, Wu S, Xu Y, Zhang X (2009) Genomic and proteomic characterization of a thermophilic Geobacillus bacteriophage GBSV1. Res Microbiol 160:166–170CrossRefGoogle Scholar
  22. Lu G, Moriyama EN (2004) Vector NTI, a balanced all-in-one sequence analysis suite. Brief Bioinform 5:378–388CrossRefGoogle Scholar
  23. Mardanov AV, Gumerov VM, Beletsky AV, Ravin NV (2018) Microbial diversity in acidic thermal pools in the Uzon Caldera, Kamchatka. Antonie Van Leeuwenhoek 111:35–43CrossRefGoogle Scholar
  24. Marks TJ, Hamilton PT (2014) Characterization of a thermophilic bacteriophage of Geobacillus kaustophilus. Arch Virol 159:2771–2775CrossRefGoogle Scholar
  25. Minakhin L, Goel M, Berdygulova Z et al (2008) Genome comparison and proteomic characterization of Thermus thermophilus bacteriophages P23–45 and P74–26: siphoviruses with triplex-forming sequences and the longest known tails. J Mol Biol 378:468–480CrossRefGoogle Scholar
  26. Nielsen H (2017) Predicting secretory proteins with SignalP. Methods Mol Biol 1611:59–73CrossRefGoogle Scholar
  27. O’Flaherty S, Coffey A, Edwards R, Meaney W, Fitzgerald GF, Ross RP (2004) Genome of staphylococcal phage K: a new lineage of Myoviridae infecting gram-positive bacteria with a low GC content. J Bacteriol 186:2862–2871CrossRefGoogle Scholar
  28. Pajunen M, Kiljunen S, Skurnik M (2000) Bacteriophage phiYeO3-12, specific for Yersinia enterocolitica serotype O:3, is related to coliphages T3 and T7. J Bacteriol 182(18):5114–5120CrossRefGoogle Scholar
  29. Pawlowski A, Rissanen I, Bamford JKH, Krupovic M, Jalasvuori M (2014) Gammasphaerolipovirus, a newly proposed bacteriophage genus, unifies viruses of halophilic archaea and thermophilic bacteria within the novel family Sphaerolipoviridae. Arch Virol 159:1541–1554CrossRefGoogle Scholar
  30. Poltaraus AB, Sokolova DS, Grouzdev DS, Ivanov TM, Malakho SG, Korshunova AV, Rozanov AS, Tourova TP, Nazina TN (2016) Draft genome sequence of Aeribacillus pallidus strain 8m3, a thermophilic hydrocarbon-oxidizing bacterium isolated from the Dagang Oil Field (China). Genome Announc.  https://doi.org/10.1128/genomeA.00500-16 Google Scholar
  31. Remmert M, Biegert A, Hauser A, Söding J (2011) HHblits: lightning-fast iterative protein sequence searching by HMMHMM alignment. Nat Methods 9(2):173–175CrossRefGoogle Scholar
  32. Rozanov AS, Bryanskaya AV, Malup TK, Meshcheryakova IA, Lazareva EV, Taran OP, Ivanisenko TV, Ivanisenko VA, Zhmodik SM, Kolchanov NA, Peltek SE (2014) Molecular analysis of the benthos microbial community in Zavarzin thermal spring (Uzon Caldera, Kamchatka, Russia). BMC Genom 15(Suppl 12):S12CrossRefGoogle Scholar
  33. Skowron PM, Kropinski AM, Zebrowska J, Janus L, Szemiako K, Czajkowska E, Maciejewska N, Skowron M, Łoś J, Łoś M, Zylicz-Stachula A (2018) Sequence, genome organization, annotation and proteomics of the thermophilic, 47.7-kb Geobacillus stearothermophilus bacteriophage TP-84 and its classification in the new Tp84virus genus. PLoS ONE.  https://doi.org/10.1371/journal.pone.0195449 Google Scholar
  34. Slepova TV, Sokolova TG, Lysenko AM, Tourova TP, Kolganova TV, Kamzolkina OV et al (2006) Carboxydocella sporoproducens sp. nov., a novel anaerobic CO-utilizing/H2-producing thermophilic bacterium from a Kamchatka hot spring. Int J Syst Evol Microbiol 56:797–800CrossRefGoogle Scholar
  35. Tamakoshi M, Murakami A, Sugisawa M, Tsuneizumi K, Takeda S, Saheki T et al (2011) Genomic and proteomic characterization of the large Myoviridae bacteriophage ϕTMA of the extreme thermophile Thermus thermophilus. Bacteriophage 1:152–164CrossRefGoogle Scholar
  36. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729CrossRefGoogle Scholar
  37. Tippmann HF (2004) Analysis for free: comparing programs for sequence analysis. Brief Bioinform 5:82–87CrossRefGoogle Scholar
  38. Van Zyl LJ, Sunda F, Taylor MP, Cowan DA, Trindade MI (2015) Identification and characterization of a novel Geobacillus thermoglucosidasius bacteriophage, GVE3. Arch Virol 160:2269–2282CrossRefGoogle Scholar
  39. Wang Y, Zhang X (2010) Genome analysis of deep-sea thermophilic phage D6E. Appl Environ Microbiol 76:7861–7866CrossRefGoogle Scholar
  40. Yu MX, Slater MR, Ackermann HW (2006) Isolation and characterization of Thermus bacteriophages. Arch Virol 151:663–679CrossRefGoogle Scholar
  41. Zablocki O, van Zyl L, Trindade M (2018) Biogeography and taxonomic overview of terrestrial hot spring thermophilic phages. Extremophiles 22:827–837CrossRefGoogle Scholar
  42. Zhou Y, Liang Y, Lynch K, Dennis JJ, Wishart DS (2011) PHAST: a fast phage search tool. Nucl Acids Res.  https://doi.org/10.1093/nar/gkr485 Google Scholar

Copyright information

© Springer Japan KK, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Institute of Chemical Biology and Fundamental Medicine SB RASNovosibirskRussia
  2. 2.Institute of Cytology and GeneticsNovosibirskRussia
  3. 3.Novosibirsk State UniversityNovosibirskRussia

Personalised recommendations