Genome Property Definition Page

NameCRISPR system, I-F/Ypest 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 Ypest subtype, so named because this subtype is the only one found in the genome of Yersinia pestis, consists of cas1, cas3 and the subtype specific genes csy1-4. The cas3 gene of this subtype is sufficiently diverged from the cas3 gene of other CRISPR subtypes that the construction of a separate HMM was warranted. The spacers of these CRISPRs have been analyzed and some have been shown to have been captured from extrachromosomal sources [2]. The repeats associated with this subtype tend to have a periodicity of 60 nucleotides. This subtype is found only in the Proteobacteria.
JCVI RoleOther
Parent PropertyGenProp0021: CRISPR region
Literature References
[ 1 ]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
[ 2 ]Pourcel C, Salvignol G, Vergnaud G  CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies.  Microbiology 2005 Mar;151(Pt 3):653-63.  PMID 15758212
[ 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, Ypest regionCas1YESTIGR03637 (HMM): CRISPR-associated endonuclease Cas1, subtype I-F/YPEST
Cas3, Ypest subtype variantCas3YESTIGR02562 (HMM): CRISPR-associated helicase Cas3, subtype I-F/YPEST
Csy1Csy1YESTIGR02564 (HMM): CRISPR type I-F/YPEST-associated protein Csy1
Csy2Csy2YESTIGR02565 (HMM): CRISPR type I-F/YPEST-associated protein Csy2
Csy3Csy3YESTIGR02566 (HMM): CRISPR type I-F/YPEST-associated protein Csy3
CRISPR-derived RNA endonuclease Csy4Csy4YESTIGR02563 (HMM): CRISPR-associated endoribonuclease Cas6/Csy4, subtype I-F/YPEST

Parent Properties
GenProp0021CRISPR region

Sibling Properties
GenProp0313CRISPR system, I-C/Dvulg subtype
GenProp0314CRISPR system, II/Nmeni subtype
GenProp0315CRISPR system, I-E/Ecoli 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