Restriction-modification systems and DNA methylation profile of Pectobacterium carotovorum 2A

Authors

  • Yulia V. Diubo Belarusian State University, 4 Niezaliežnasci Avenue, Minsk 220030, Belarus
  • Artur E. Akhremchuk Institute of Microbiology, National Academy of Sciences of Belarus, 2 Academician V. F. Kupreviča Street, Minsk 220141, Belarus
  • Leonid N. Valentovich Belarusian State University, 4 Niezaliežnasci Avenue, Minsk 220030, Belarus; Institute of Microbiology, National Academy of Sciences of Belarus, 2 Academician V. F. Kupreviča Street, Minsk 220141, Belarus
  • Yevgeny A. Nikolaichik Belarusian State University, 4 Niezaliežnasci Avenue, Minsk 220030, Belarus

Keywords:

Oxford Nanopore sequencing, methylation, restriction-modification system, N6-methyladenosine, 5-methylcytosine

Abstract

The methylation profile of Pectobacterium carotovorum 2A genome was studied using the Oxford Nanopore sequencing technology. The specificity of the methylase subunits of the three restriction-modification systems of this strain was determined. Analysis of homologous systems showed the uniqueness of the type I restriction-modification system and the type IV restriction system specific to methylated DNA of this strain. The work confirms the applicability of Oxford Nanopore technology to the analysis of bacterial DNA modifications and is also the first example of such an analysis for Pectobacterium spp.

Author Biographies

  • Yulia V. Diubo, Belarusian State University, 4 Niezaliežnasci Avenue, Minsk 220030, Belarus

    assistant at the department of molecular biology, faculty of biology

  • Artur E. Akhremchuk, Institute of Microbiology, National Academy of Sciences of Belarus, 2 Academician V. F. Kupreviča Street, Minsk 220141, Belarus

    researcher at the laboratory «Center of analytical and genetic engineering research»

  • Leonid N. Valentovich, Belarusian State University, 4 Niezaliežnasci Avenue, Minsk 220030, Belarus; Institute of Microbiology, National Academy of Sciences of Belarus, 2 Academician V. F. Kupreviča Street, Minsk 220141, Belarus

    PhD (biology); associate professor at the department of molecular biology, faculty of biology, Belarusian State University, and head of the laboratory «Center of analytical and genetic engineering research» Institute of Microbiology, National Academy of Sciences of Belarus

  • Yevgeny A. Nikolaichik, Belarusian State University, 4 Niezaliežnasci Avenue, Minsk 220030, Belarus

    PhD (biology); associate professor at the department of molecular biology, faculty of biology

References

  1. Kennaway CK, Taylor JE, Chun Feng Song, Potrzebowski W, Nicholson W, White JH, et al. Structure and operation of the DNA-translocating type I DNA restriction enzymes. Genes & Development. 2012;26(1):92–104. DOI: 10.1101/gad.179085.111.
  2. Pingoud A, Wilson GG, Wende W. Type II restriction endonucleases – a historical perspective and more. Nucleic Acids Research. 2014;42(12):7489–7527. DOI: 10.1093/nar/gku447.
  3. Loenen WAM, Dryden DTF, Raleigh EA, Wilson GG, Murray NE. Highlights of the DNA cutters: a short history of the restriction enzymes. Nucleic Acids Research. 2014;42(1):3–19. DOI: 10.1093/nar/gkt990.
  4. Loenen WAM, Raleigh EA. The other face of restriction: modification-dependent enzymes. Nucleic Acids Research. 2014; 42(1):56–69. DOI: 10.1093/nar/gkt747.
  5. Ishikawa K, Fukuda E, Kobayashi I. Conflicts targeting epigenetic systems and their resolution by cell death: novel concepts for methyl-specific and other restriction systems. DNA Research. 2010;17(6):325–342. DOI: 10.1093/dnares/dsq027.
  6. Lepikhov K, Tchernov A, Zheleznaja L, Matvienko N, Walter J, Trautner TA. Characterization of the type IV restriction modification system BspLU11III from Bacillus sp. LU11. Nucleic Acids Research. 2001;29(22):4691–4698. DOI: 10.1093/nar/29.22.4691.
  7. Gouil Q, Keniry A. Latest techniques to study DNA methylation. Essays in Biochemistry. 2019;63(6):639–648. DOI: 10.1042/EBC20190027.
  8. Sikolenko M, Valentovich L. Barapost: binning of nucleotide sequences according to taxonomic annotation. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2020:1–1. DOI: 10.1109/TCBB.2020.3009780.
  9. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology. 2012;19(5):455–477. DOI: 10.1089/cmb.2012.0021.
  10. Kolmogorov M, Yuan J, Yu Lin, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nature Biotechnology. 2019;37(5):540–546. DOI: 10.1038/s41587-019-0072-8.
  11. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S. Pilon: an integrated tool for comprehensive microbial va­riant detection and genome assembly improvement. PLoS One. 2014;9(11):e112963. DOI: 10.1371/journal.pone.0112963.
  12. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Research. 2016;44(14):6614–6624. DOI: 10.1093/nar/gkw569.
  13. Roberts RJ, Vincze T, Posfai J, Macelis D. REBASE – a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Research. 2015;43(D1):D298 – D299. DOI: 10.1093/nar/gku1046.
  14. Boratyn G, Camacho C, Federhen S, Merezhuk Yu, Madden T, Schoch C, et al. MOLE-BLAST a new tool to search and classify multiple sequences [Internet; cited 2021 June 15]. Available from: http://mirror.ufs.ac.za/blast/documents/moleblast_poster2014.pdf.
  15. Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, et al. GenBank. Nucleic Acids Research. 2013; 41(D1):D36 – D42. DOI: 10.1093/nar/gks1195.
  16. Stoiber M, Quick J, Egan R, Ji Eun Lee, Celniker S, Neely RK, et al. De novo identification of DNA modifications enabled by genome-guided nanopore signal processing. BioRxiv 094672 [Preprint]. 2016 [cited 2021 June 15]. Available from: https://doi.org/10.1101/094672.
  17. Bailey TL, Johnson J, Grant CE, Noble WS. The MEME suite. Nucleic Acids Research. 2015;43(Web Server issue):W39 – W49. DOI: 10.1093/nar/gkv416.
  18. Nikolaichik Ye, Gorshkov V, Gogolev Yu, Valentovich L, Evtushenkov A. Genome sequence of Pectobacterium atrosepticum strain 21A. Genome Announcements. 2014;2(5):e00935-14. DOI: 10.1128/genomeA.00935-14.

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Published

2021-11-04

Issue

No. 3 (2021): Journal of the Belarusian State University. Biology

Section

Genetics and Molecular Biology

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How to Cite

Diubo, Y. V. ., Akhremchuk, A. E., Valentovich, L. N., & Nikolaichik, Y. A. (2021). Restriction-modification systems and DNA methylation profile of Pectobacterium carotovorum 2A. Experimental Biology and Biotechnology, 3, 71-77. https://doi.org/10.33581/2521-1722-2021-3-71-77