title: Dynamics of Escherichia coli type I-E CRISPR spacers over 42 000 years.
abstract: 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.
authors.affiliation: Skolkovo Institute of Science and Technology, Skolkovo, Russia.|Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia.
authors.forename: Ekaterina
authors.initials: E
authors.lastname: Savitskaya
authors.affiliation: Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia.|Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.
authors.forename: Anna
authors.initials: A
authors.lastname: Lopatina
authors.affiliation: Skolkovo Institute of Science and Technology, Skolkovo, Russia.|Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.
authors.forename: Sofia
authors.initials: S
authors.lastname: Medvedeva
authors.affiliation: Skolkovo Institute of Science and Technology, Skolkovo, Russia.
authors.forename: Mikhail
authors.initials: M
authors.lastname: Kapustin
authors.affiliation: Skolkovo Institute of Science and Technology, Skolkovo, Russia.
authors.forename: Sergey
authors.initials: S
authors.lastname: Shmakov
authors.affiliation: Zoological Institute, Russian Academy of Sciences, St. Petersburg, Russia.|Institute of Applied Ecology of the North, North-Eastern Federal University, Yakutsk, Russia.
authors.forename: Alexey
authors.initials: A
authors.lastname: Tikhonov
authors.affiliation: N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.|A.A. Kharkevich Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.
authors.forename: Irena I
authors.initials: II
authors.lastname: Artamonova
authors.affiliation: M.V. Lomonosov Moscow State University, Moscow, Russia.
authors.forename: Maria
authors.initials: M
authors.lastname: Logacheva
authors.affiliation: Skolkovo Institute of Science and Technology, Skolkovo, Russia.|Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia.|Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.|Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ, USA.
authors.forename: Konstantin
authors.initials: K
authors.lastname: Severinov
mesh_terms: D000818:Animals; D005075:Biological Evolution; D064112:Clustered Regularly Interspaced Short Palindromic Repeats; D000072441:DNA, Ancient; D004269:DNA, Bacterial / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics*; D007422:Intestines / Q000382:microbiology; D056665:Mammoths / Q000382:microbiology; D017422:Sequence Analysis, DNA
chemical_list: D000072441:DNA, Ancient; D004269:DNA, Bacterial
keywords: 
  Escherichia coli
  ; CRISPR arrays; CRISPR spacers; palaeo DNA