Genome Property Definition Page

NameCRISPR system, I-E/Ecoli subtype
DescriptionCRISPR repeats are by definition Clustered Regularly Interspaced Short Palindromic Repeats, described by Jansen [1]. Certain proteins, including Cas1 to Cas4, are found only in genomes with CRISPR repeats, and are near these repeats. Jansen, et al. describe CRISPR loci as having direct repeats, varying in size from 21 to 37 bp, interspaced by similarly sized non-repetitive sequences. Variants of CRISP/Cas loci (subtypes) have been described (Haft, Selengut, et al., submitted) in which certain groups of subtype-specific genes are found in addition to characteristic sets of the more widely distributed cas genes. The Ecoli subtype, so named because this subtype is the only one found in the genome of Escherichia coli, consists of cas1-3, a subtype-specific variant of cas5 and the subtype specific genes cse1-4. The repeats associated with this subtype tend to have a periodicity of 61 nucleotides and a repeat size of 29 mucleotides. This subtype is found in a wide variety of bacteria and has also been reported to be present in an archaeon [2].
JCVI RoleOther
Parent PropertyGenProp0021: CRISPR region
Literature References
[ 1 ]Jansen R, Embden JD, Gaastra W, Schouls LM  Identification of genes that are associated with DNA repeats in prokaryotes.  Mol Microbiol 2002 Mar;43(6):1565-75.  PMID 11952905
[ 2 ]Saunders NF, Goodchild A, Raftery M, Guilhaus M, Curmi PM, Cavicchioli R  Predicted roles for hypothetical proteins in the low-temperature expressed proteome of the Antarctic archaeon Methanococcoides burtonii.  J Proteome Res 2005 Mar-Apr;4(2):464-72.  PMID 15822923
[ 3 ]Haft DH, Selengut J, Mo ngodin EF, Nelson KE  A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes.  PLoS Comput Biol. 2005 Nov;1(6):e60.  PMID 16292354

Step NameStep NumRequiredEvidence (Method)Evidence Go Terms
Cas1, Ecoli regionCas1YESTIGR00287 (HMM-CLUST): CRISPR-associated endonuclease Cas1
Cas2, Ecoli specific variantCas2YESTIGR01873 (HMM): CRISPR-associated endoribonuclease Cas2, subtype I-E/ECOLI
Cas3, Ecoli regionCas3YESTIGR01587 (HMM-CLUST): CRISPR-associated helicase Cas3
Cas5, Ecoli specific variantCas5eYESTIGR01868 (HMM): CRISPR-associated protein Cas5/CasD, subtype I-E/ECOLI
Cse1Cse1YESTIGR02547 (HMM): CRISPR type I-E/ECOLI-associated protein CasA/Cse1
Cse2Cse2YESTIGR02548 (HMM): CRISPR type I-E/ECOLI-associated protein CasB/Cse2
Cse3Cse3YESTIGR01907 (HMM): CRISPR-associated protein Cas6/Cse3/CasE, subtype I-E/ECOLI
Cse4Cse4YESTIGR01869 (HMM): CRISPR-associated protein Cas7/Cse4/CasC, subtype I-E/ECOLI

Parent Properties
GenProp0021CRISPR region

Sibling Properties
GenProp0310CRISPR system, I-F/Ypest subtype
GenProp0313CRISPR system, I-C/Dvulg subtype
GenProp0314CRISPR system, II/Nmeni subtype
GenProp0316CRISPR system, III-B/RAMP module subtype
GenProp0317CRISPR system, I-B subtype, Tneap branch
GenProp0318CRISPR system, III-A/Mtube subtype
GenProp0319CRISPR system, I-A/Apern subtype
GenProp0320CRISPR system, I-B subtype, Hmari branch
GenProp0469CRISPR system, Dpsyc subtype
GenProp0670CRISPR system, Aferr subtype
GenProp0685CRISPR system, I-D/Cyano subtype
GenProp0768CRISPR system, Pging subtype
GenProp0922CRISPR system, Myxan subtype
GenProp1061CRISPR system, PreFran subtype