---
_id: '2042'
abstract:
- lang: eng
  text: 'Background: CRISPR is a microbial immune system likely to be involved in
    host-parasite coevolution. It functions using target sequences encoded by the
    bacterial genome, which interfere with invading nucleic acids using a homology-dependent
    system. The system also requires protospacer associated motifs (PAMs), short motifs
    close to the target sequence that are required for interference in CRISPR types
    I and II. Here, we investigate whether PAMs are depleted in phage genomes due
    to selection pressure to escape recognition.Results: To this end, we analyzed
    two data sets. Phages infecting all bacterial hosts were analyzed first, followed
    by a detailed analysis of phages infecting the genus Streptococcus, where PAMs
    are best understood. We use two different measures of motif underrepresentation
    that control for codon bias and the frequency of submotifs. We compare phages
    infecting species with a particular CRISPR type to those infecting species without
    that type. Since only known PAMs were investigated, the analysis is restricted
    to CRISPR types I-C and I-E and in Streptococcus to types I-C and II. We found
    evidence for PAM depletion in Streptococcus phages infecting hosts with CRISPR
    type I-C, in Vibrio phages infecting hosts with CRISPR type I-E and in Streptococcus
    thermopilus phages infecting hosts with type II-A, known as CRISPR3.Conclusions:
    The observed motif depletion in phages with hosts having CRISPR can be attributed
    to selection rather than to mutational bias, as mutational bias should affect
    the phages of all hosts. This observation implies that the CRISPR system has been
    efficient in the groups discussed here.'
article_number: '663'
article_processing_charge: No
author:
- first_name: Anne
  full_name: Kupczok, Anne
  id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87
  last_name: Kupczok
- first_name: Jonathan P
  full_name: Bollback, Jonathan P
  id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
  last_name: Bollback
  orcid: 0000-0002-4624-4612
citation:
  ama: Kupczok A, Bollback JP. Motif depletion in bacteriophages infecting hosts with
    CRISPR systems. <i>BMC Genomics</i>. 2014;15(1). doi:<a href="https://doi.org/10.1186/1471-2164-15-663">10.1186/1471-2164-15-663</a>
  apa: Kupczok, A., &#38; Bollback, J. P. (2014). Motif depletion in bacteriophages
    infecting hosts with CRISPR systems. <i>BMC Genomics</i>. BioMed Central. <a href="https://doi.org/10.1186/1471-2164-15-663">https://doi.org/10.1186/1471-2164-15-663</a>
  chicago: Kupczok, Anne, and Jonathan P Bollback. “Motif Depletion in Bacteriophages
    Infecting Hosts with CRISPR Systems.” <i>BMC Genomics</i>. BioMed Central, 2014.
    <a href="https://doi.org/10.1186/1471-2164-15-663">https://doi.org/10.1186/1471-2164-15-663</a>.
  ieee: A. Kupczok and J. P. Bollback, “Motif depletion in bacteriophages infecting
    hosts with CRISPR systems,” <i>BMC Genomics</i>, vol. 15, no. 1. BioMed Central,
    2014.
  ista: Kupczok A, Bollback JP. 2014. Motif depletion in bacteriophages infecting
    hosts with CRISPR systems. BMC Genomics. 15(1), 663.
  mla: Kupczok, Anne, and Jonathan P. Bollback. “Motif Depletion in Bacteriophages
    Infecting Hosts with CRISPR Systems.” <i>BMC Genomics</i>, vol. 15, no. 1, 663,
    BioMed Central, 2014, doi:<a href="https://doi.org/10.1186/1471-2164-15-663">10.1186/1471-2164-15-663</a>.
  short: A. Kupczok, J.P. Bollback, BMC Genomics 15 (2014).
corr_author: '1'
date_created: 2018-12-11T11:55:23Z
date_published: 2014-08-08T00:00:00Z
date_updated: 2025-09-29T11:52:17Z
day: '08'
ddc:
- '570'
department:
- _id: JoBo
doi: 10.1186/1471-2164-15-663
external_id:
  isi:
  - '000341528300001'
file:
- access_level: open_access
  checksum: 3f6d2776b90a842a28359cc957d3d04b
  content_type: application/pdf
  creator: system
  date_created: 2018-12-12T10:11:24Z
  date_updated: 2020-07-14T12:45:26Z
  file_id: '4878'
  file_name: IST-2015-396-v1+1_1471-2164-15-663.pdf
  file_size: 1489769
  relation: main_file
file_date_updated: 2020-07-14T12:45:26Z
has_accepted_license: '1'
intvolume: '        15'
isi: 1
issue: '1'
language:
- iso: eng
license: https://creativecommons.org/publicdomain/zero/1.0/
month: '08'
oa: 1
oa_version: Published Version
publication: BMC Genomics
publication_status: published
publisher: BioMed Central
publist_id: '5009'
pubrep_id: '396'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Motif depletion in bacteriophages infecting hosts with CRISPR systems
tmp:
  image: /images/cc_0.png
  legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
  name: Creative Commons Public Domain Dedication (CC0 1.0)
  short: CC0 (1.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 15
year: '2014'
...