Dynamics of Escherichia coli type I-E CRISPR spacers over 42 000 years

Ekaterina Savitskaya, Anna Lopatina, Sofia Medvedeva, Mikhail Kapustin, Sergey Shmakov, Alexey Tikhonov, Irena I. Artamonova, Maria Logacheva, Konstantin Severinov

    Research output: Contribution to journalArticlepeer-review

    18 Citations (Scopus)


    CRISPR-Cas are nucleic acid-based prokaryotic immune systems. CRISPR arrays accumulate spacers from foreign DNA and provide resistance to mobile genetic elements containing identical or similar sequences. Thus, the set of spacers present in a given bacterium can be regarded as a record of encounters of its ancestors with genetic invaders. Such records should be specific for different lineages and change with time, as earlier acquired spacers get obsolete and are lost. Here, we studied type I-E CRISPR spacers of Escherichia coli from extinct pachyderm. We find that many spacers recovered from intestines of a 42 000-year-old mammoth match spacers of present-day E. coli. Present-day CRISPR arrays can be reconstructed from palaeo sequences, indicating that the order of spacers has also been preserved. The results suggest that E. coli CRISPR arrays were not subject to intensive change through adaptive acquisition during this time.

    Original languageEnglish
    Pages (from-to)2019-2026
    Number of pages8
    JournalMolecular Ecology
    Issue number7
    Publication statusPublished - Apr 2017


    • CRISPR arrays
    • CRISPR spacers
    • Escherichia coli
    • palaeo DNA


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