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

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.

[1]  Sergey A. Shmakov,et al.  Metagenomic Analysis of Bacterial Communities of Antarctic Surface Snow , 2016, Front. Microbiol..

[2]  Sita J. Saunders,et al.  An updated evolutionary classification of CRISPR–Cas systems , 2015, Nature Reviews Microbiology.

[3]  Christine L. Sun,et al.  Metagenomic reconstructions of bacterial CRISPR loci constrain population histories , 2015, The ISME Journal.

[4]  Giddy Landan,et al.  The Contribution of Genetic Recombination to CRISPR Array Evolution , 2015, Genome biology and evolution.

[5]  H. Stratton,et al.  CRISPR Diversity in E. coli Isolates from Australian Animals, Humans and Environmental Waters , 2015, PloS one.

[6]  Michael Gale,et al.  Genetic Diversity in the Collaborative Cross Model Recapitulates Human West Nile Virus Disease Outcomes , 2015, mBio.

[7]  Brian C. Thomas,et al.  CRISPR Immunity Drives Rapid Phage Genome Evolution in Streptococcus thermophilus , 2015, mBio.

[8]  Arne Ludwig,et al.  The future of ancient DNA: Technical advances and conceptual shifts , 2015, BioEssays : news and reviews in molecular, cellular and developmental biology.

[9]  Sergey A. Shmakov,et al.  Pervasive generation of oppositely oriented spacers during CRISPR adaptation , 2014, Nucleic acids research.

[10]  Jesse Dabney,et al.  Ancient DNA damage. , 2013, Cold Spring Harbor perspectives in biology.

[11]  Christine L. Sun,et al.  Strong bias in the bacterial CRISPR elements that confer immunity to phage , 2013, Nature Communications.

[12]  P. Glaser,et al.  The highly dynamic CRISPR1 system of Streptococcus agalactiae controls the diversity of its mobilome , 2012, Molecular microbiology.

[13]  R. Garrett,et al.  Selective and hyperactive uptake of foreign DNA by adaptive immune systems of an archaeon via two distinct mechanisms , 2012, Molecular microbiology.

[14]  Stan J. J. Brouns,et al.  CRISPR Interference Directs Strand Specific Spacer Acquisition , 2012, PloS one.

[15]  U. Qimron,et al.  Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli , 2012, Nucleic acids research.

[16]  Konstantin Severinov,et al.  Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system , 2012, Nature Communications.

[17]  M. Touchon,et al.  CRISPR Distribution within the Escherichia coli Species Is Not Suggestive of Immunity-Associated Diversifying Selection , 2011, Journal of bacteriology.

[18]  Marko Djordjevic,et al.  Transcription, processing and function of CRISPR cassettes in Escherichia coli , 2010, Molecular microbiology.

[19]  M. Touchon,et al.  The Small, Slow and Specialized CRISPR and Anti-CRISPR of Escherichia and Salmonella , 2010, PloS one.

[20]  J. García-Martínez,et al.  Diversity of CRISPR loci in Escherichia coli. , 2010, Microbiology.

[21]  Rolf Wagner,et al.  Identification and characterization of E. coli CRISPR‐cas promoters and their silencing by H‐NS , 2010, Molecular microbiology.

[22]  Stan J. J. Brouns,et al.  CRISPR-based adaptive and heritable immunity in prokaryotes. , 2009, Trends in biochemical sciences.

[23]  L. Marraffini,et al.  CRISPR Interference Limits Horizontal Gene Transfer in Staphylococci by Targeting DNA , 2008, Science.

[24]  Stan J. J. Brouns,et al.  Small CRISPR RNAs Guide Antiviral Defense in Prokaryotes , 2008, Science.

[25]  Anders F. Andersson,et al.  Virus Population Dynamics and Acquired Virus Resistance in Natural Microbial Communities , 2008, Science.

[26]  U. Stenzel,et al.  PatMaN: rapid alignment of short sequences to large databases , 2008, Bioinform..

[27]  Philippe Horvath,et al.  Phage Response to CRISPR-Encoded Resistance in Streptococcus thermophilus , 2007, Journal of bacteriology.

[28]  Philippe Horvath,et al.  Diversity, Activity, and Evolution of CRISPR Loci in Streptococcus thermophilus , 2007, Journal of bacteriology.

[29]  R. Barrangou,et al.  CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes , 2007, Science.

[30]  G. Vergnaud,et al.  CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. , 2005, Microbiology.

[31]  J. García-Martínez,et al.  Intervening Sequences of Regularly Spaced Prokaryotic Repeats Derive from Foreign Genetic Elements , 2005, Journal of Molecular Evolution.

[32]  G. Crooks,et al.  WebLogo: a sequence logo generator. , 2004, Genome research.

[33]  S. Pääbo,et al.  Molecular coproscopy: dung and diet of the extinct ground sloth Nothrotheriops shastensis. , 1998, Science.

[34]  I. Good THE POPULATION FREQUENCIES OF SPECIES AND THE ESTIMATION OF POPULATION PARAMETERS , 1953 .

[35]  Adam N. Rountrey,et al.  LIFE HISTORY OF A REMARKABLY PRESERVED WOOLLY MAMMOTH CALF FROM THE YAMAL PENINSULA, NORTHWESTERN SIBERIA , 2009 .

[36]  S. Ehrlich,et al.  Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. , 2005, Microbiology.