CRISPRone

CRISPRone Demonstration Page

List of ExamplesCRISPR Help Page

CRISPR-Cas system in Escherichia coli K12 substr DH10B (type I-E)

  • Escherichia coli is a model microorganism for the study of microbiomes. E. coli K-12 strains were found to carry subtype I-E CRISPR-Cas system, which is composed of 2 CRISPR arrays and a set of eight cas-E genes: cas_CT1978 (belonging to cas2 E. coli subfamily), cas1, cse3, cas5e, cse4, cse2, cse1, and cas3. The proteins encoded by cse1-cse4 and cas5e make a Cascade complex and this complex contains one copy of mature crRNA, which will target foreign DNA. More information could be found in this paper: CRISPR-Cas functional module exchange in Escherichia coli. MBio.2014,28;5(1):e00767-13. [Paper Link]
  • The two CRISPR arrays are shown in locus 3 & 4 in the CRISPRone report page; CRISPRone also found a few more genes that might be involved in the immunity system (locus 1-2).

CRISPR-Cas system in Escherichia coli APEC 01 (type I-F)

  • Escherichia coli isolates are believed to carry two different CRISPR-Cas systems: either subtype I-E or subtype I-F. E. coli APEC 01 strain is an example that contains subtype I-F CRISPR-Cas system. More information could be found in this paper: CRISPR-Cas functional module exchange in Escherichia coli. MBio.2014,28;5(1):e00767-13. [Paper Link]
  • Go to the CRISPRone report page

CRISPR-Cas system in Streptococcus thermophilus LMD-9 (type II and III)

  • LMD-9 contains multiple CRISPR-Cas systems. The PAM patterns of the protospacers were confirmed experimentally in the paper: Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-Cas systems. Nucleic Acids Research, 2013, 1–14 [Paper Link]
  • Go to the CRISPRone report page

CRISPR-Cas system in Thermus thermophilus HB8

  • Thermus thermophilus HB8 is a convenient model organism to study CRISPR-Cas systems, since it has 4 different CRISPR-Cas systems: type I-E, type III-A, typeIII-B and an unclassified type I system. More information can be found in this paper: RNA Targeting by the Type III-A CRISPR-Cas Csm Complex of Thermus thermophilus. Mol Cell, 2014,56(4),518–530 [Paper Link]
  • Go to the CRISPRone report page

CRISPR-Cas system in Acidithiobacillus ferrooxidans ATCC 23270 (type I and IV)

  • A. ferrooxidans has two types of CRISPR–Cas sytems: type I and type IV.
  • The type I system is shown as locus 2 and the type IV is shown as locus 1 in the CRISPRone report page

Francisella tularensis subsp. novicida U112 (type II and V)

  • F. tularensis is a pathogenic species of gram-negative bacteria, which causes tularemia in human. It was found containing subtype II-B CRISPR-Cas system locus, which consists of four cas genes (i.e., cas9, cas1, cas2, and cas4) and a downstream CRISPR array. The predicted tracrRNA, by using our pipeline, is consistent with the ones reported in the previous published paper: The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems. RNA Biology. 2013,10(5):726–737. [Paper Link]
  • This species was also found to contain a type V, a more recently defined CRISPR–Cas system type. [Paper Link]
  • Both type II and type V are reported by CRISPRone: Go to the CRISPRone report page
  • Francisella tularensis subsp. novicida strain DPG 3A-IS