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2  structures 627  species 0  interactions 642  sequences 4  architectures

Family: CRISPR_Cse2 (PF09485)

Summary: CRISPR-associated protein Cse2 (CRISPR_cse2)

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This is the Wikipedia entry entitled "CRISPR". More...

CRISPR Edit Wikipedia article

Diagram of the possible mechanism for CRISPR.[1]

CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats) is an acronym for DNA loci that contain multiple, short, direct repetitions of base sequences. Each repetition contains a series of bases followed by the same series in reverse and then by 30 or so base pairs known as "spacer DNA". The spacers are short segments of DNA from a virus and serve as a 'memory' of past exposures.[2]

They are found in the genomes of approximately 40% of sequenced bacteria and 90% of sequenced archaea.[3][4]

CRISPR functions as a prokaryotic immune system, in that it confers resistance to exogenous genetic elements such as plasmids and phages.[5][6] The CRISPR system provides a form of acquired immunity. CRISPR spacers recognize and silence exogenous genetic elements in a manner analogous to RNAi in eukaryotic organisms.[2]

History[edit]

Bacteria have been known to incorporate foreign DNA in other circumstances and even to scavenge damaged DNA from their environment.[7][8]

Repeats were first described in 1987 for the bacterium Escherichia coli.[9] In 2000, similar clustered repeats were identified in additional bacteria and archaea and were termed Short Regularly Spaced Repeats (SRSR).[10] SRSR were renamed CRISPR in 2002.[11] A set of genes, some encoding putative nuclease or helicase proteins, were found to be associated with CRISPR repeats (the cas, or CRISPR-associated genes).[11] Further in 2005, three independent researchers showed that CRISPR spacers showed homology to several phage DNA and extrachromosomal DNA such as plasmids. This was an indication that the CRSIPR/cas system could have a role in adaptive immunity in bacteria.[12] CRISPR was first shown to work in human cells by George M. Church at Harvard University.[13]

Simplified diagram of a CRISPR locus. The three major components of a CRISPR locus are shown: cas genes, a leader sequence, and a repeat-spacer array. Repeats are shown as grey boxes and spacers are colored bars. While most CRISPR loci contain each of the three components, the arrangement is not always as shown.[1][2]

In 2005, three groups reported that spacers often matched phage DNA sequences, indicating a possible role in microbial immunity. Koonin and colleagues proposed that spacers serve as a template for RNA molecules, analogously to eukaryotic cells that use a system called RNA interference.[14]

In 2007 Barrangou, Horvath and others showed that they could alter the resistance of Streptococcus thermophilus to phage attack with spacer DNA.[14]

Doudna and Charpentier had independently been exploring CRISPR-associated proteins to learn how bacteria deploy spacers in their immune defenses. They jointly studied a simpler CRISPR system that relies on a protein called Cas9. They found that bacteria respond to an invading phage by transcribing spacers and palindromic DNA into a long RNA molecule that the cell then uses tracrRNA and Cas9 to cut it into pieces called crRNAs.[14]

Cas9 is a nuclease, an enzyme specialized for cutting DNA, with two active cutting sites, one for each strand of the double helix. The team demonstrated that they could disable one or both sites while preserving Cas9's ability to home located its target DNA. Jinek combined tracrRNA and spacer RNA into a "single-guide RNA" molecule that, mixed with Cas9, could find and cut the correct DNA targets.[14]

Libraries of tens of thousands of guide RNAs are now available.[14]

Locus structure[edit]

Repeats and spacers[edit]

CRISPR repeats range in size from 24 to 48 base pairs.[15] They usually show some dyad symmetry, implying the formation of a secondary structure such as a hairpin, but are not truly palindromic.[16] Repeats are separated by spacers of similar length.[15] Some CRISPR spacer sequences exactly match sequences from plasmids and phages,[17][18][19] although some spacers have identity to the prokaryote's own genome (self-targeting spacers).[20] New spacers can be added rapidly in response to phage infection.[21]

Cas genes and CRISPR subtypes[edit]

The CRISPR-associated (cas) genes are often associated with CRISPR repeat-spacer arrays. As of 2013, more than forty different Cas protein families had been described.[15] Of these protein families, Cas1 appears to be ubiquitous among different CRISPR/Cas systems. Particular combinations of cas genes and repeat structures have been used to define 8 CRISPR subtypes (Ecoli, Ypest, Nmeni, Dvulg, Tneap, Hmari, Apern, and Mtube), some of which are associated with an additional gene module encoding repeat-associated mysterious proteins (RAMPs).[15] More than one CRISPR subtype may occur in a single genome. The sporadic distribution of the CRISPR/Cas subtypes suggests that the system is subject to horizontal gene transfer during microbial evolution.

CRISPR associated protein
PDB 1wj9 EBI.jpg
crystal structure of a crispr-associated protein from thermus thermophilus
Identifiers
Symbol CRISPR_assoc
Pfam PF08798
Pfam clan CL0362
InterPro IPR010179
CDD cd09727
CRISPR associated protein Cas2
PDB 1zpw EBI.jpg
crystal structure of a hypothetical protein tt1823 from thermus thermophilus
Identifiers
Symbol CRISPR_Cas2
Pfam PF09827
InterPro IPR019199
CDD cd09638
CRISPR-associated protein Cse1
Identifiers
Symbol CRISPR_Cse1
Pfam PF09481
InterPro IPR013381
CDD cd09729
CRISPR-associated protein Cse2
Identifiers
Symbol CRISPR_Cse2
Pfam PF09485
InterPro IPR013382
CDD cd09670

Mechanism[edit]

Exogenous DNA is apparently processed by proteins encoded by some of the Cas genes into small elements (~30 base pairs in length), which are then somehow inserted into the CRISPR locus near the leader sequence. RNAs from the CRISPR loci are constitutively expressed and are processed by Cas proteins to small RNAs composed of individual exogenously derived sequence elements with a flanking repeat sequence. The RNAs guide other Cas proteins to silence exogenous genetic elements at the RNA or DNA level.[1][22] Evidence suggests functional diversity among CRISPR subtypes. The Cse (Cas subtype Ecoli) proteins (called CasA-E in E. coli) form a functional complex, Cascade, that processes CRISPR RNA transcripts into spacer-repeat units that Cascade retains.[23] In other prokaryotes, Cas6 processes the CRISPR transcripts. Interestingly, CRISPR-based phage inactivation in E. coli requires Cascade and Cas3, but not Cas1 and Cas2. The Cmr (Cas RAMP module) proteins found in Pyrococcus furiosus and other prokaryotes form a functional complex with small CRISPR RNAs that recognizes and cleaves complementary target RNAs. RNA-guided CRISPR enzymes are classified as type V restriction enzymes.

Evolutionary significance[edit]

A bioinformatic study showed that CRISPRs are evolutionarily conserved and cluster into related types. Many show signs of a conserved secondary structure.[16]

Through the CRISPR-Cas mechanism bacteria can acquire immunity to certain phages and thus halt further transmission of targeted phages. For this reason, some researchers have proposed that the CRISPR-Cas system is a Lamarckian inheritance mechanism.[24] Others investigated the coevolution of host and viral genomes by analysis of CRISPR sequences.[25]

Applications[edit]

The proof-of-principle demonstration of selective engineered redirection of the CRISPR-Cas system in 2012[26] provided a first step toward realization of some of the several proposals for CRISPR-derived biotechnology:[27]

  • Artificial immunization against phage by introduction of engineered CRISPR loci in industrially important bacteria, including those used in food production and large-scale fermentation
  • Genome engineering at cellular or organismic level by reprogramming of a CRISPR-Cas system to achieve RNA-guided genome engineering. Proof of concept studies demonstrated examples on this front both in vitro and in vivo[28][29][30][31][32]
  • Discrimination of different bacterial strains by comparison of CRISPR spacer sequences

Mouse models[edit]

CRISPR simplifies creation of mouse models and reduces the time required to a matter of weeks from months or longer. Knockdown of endogenous genes has been achieved by transfection with a plasmid that contains a CRISPR area with a spacer, which inhibits a target gene. Injecting mouse zygotes with Cas9 and two guide RNAs was able to disable two genes with 80% efficiency. So-called homology-directed repair involves using Cas9 to "nick" DNA, to introduce new gene parts to the zygote.

Food production[edit]

DuPont used CRISPRs to create improved bacterial strains for food production.[14]

CRISPRs have been used to knockdown genes in rice and wheat.[14]

CRISPR/Cas system in phage[edit]

Another way that bacteria can defend against phage infection is by having chromosomal islands. A subtype of chromosomal islands called phage-inducible chromosomal island (PICI) is excised from bacterial chromosome upon phage infection and can inhibit phage replication.[33] The mechanisms that induce PICI excision and how PICI inhibits phage replication are not well understood. One study showed that lytic ICP1 phage that specifically targets Vibrio cholerae serogroup O1 has acquired a CRISPR/Cas system that targets a V. cholera PICI-like element. The system has 2 CRISPR loci and 9 Cas genes. It seems to be homologous to the 1-F system found in Yersinia pestis. Moreover, like the bacterial CRISPR/Cas system, ICP1 CRISPR/Cas system can also acquire new sequences, which allows the phage to co-evolve with its host.[34]

Multi-gene targeting[edit]

CRISPRs have been used to cut as many as five genes at once.[14]

Reversible knockdown[edit]

"CRISPRi" like RNAi, turns off genes in a reversible fashion by targeting a site but not cutting. In bacteria, the presence of Cas9 alone is enough to block transcription, but for mammalian applications, a section of protein is added. Its guide RNA targets regulatory DNA, called promoters that immediately precede the gene target.[14]

Gene activation[edit]

Cas9 has been used to carry synthetic transcription factors (protein fragments that turn on genes.) This enabled the activation of specific human genes. The technique achieved a strong effect by targeting multiple CRISPR constructs to slightly different spots on the gene's promoter.[14]

The genes included some tied to human diseases, including those involved in muscle differentiation, cancer, inflammation and producing fetal hemoglobin.[14]

Infrastructure[edit]

Free software is available to design guide RNA to target any desired gene. The Addgene repository offers academics the DNA to make their own CRISPR system for $65. Since the beginning of the year, In 2013 alone Addgene distributed more than 10,000 CRISPR constructs. The facility has received CRISPR-enabling DNA sequences from 11 independent research teams.[14]

Editas Medicine, a $43 million startup, aims to develop treatments that employ CRISPR/Cas to make edits to single base pairs and larger stretches of DNA. Inherited diseases such as cystic fibrosis, sickle-cell anemia and Huntington's disease are caused by single base pair mutations; CRISPR/Cas technology has the potential correct these errors. The "corrected" gene remains in its normal location on its chromosome, which preserves the way the cell normally activate inhibits its expression. Before it can be used clinically, the company must be able to guarantee that only the targeted region will be affected and determine how to deliver the therapy to a patient’s cells.[35]

Safety[edit]

Before work proceeds much further on human genomes, improved targeting is required. Guide RNAs have been observed guides targeting sequences that differ by multiple base pairs from the intended sequence.[14]

Alternatives[edit]

In the early 2000s, researchers developed zinc finger nucleases, synthetic proteins whose DNA-binding domains enable them to cut DNA at specific spots. Later, synthetic nucleases called TALENs provided an easier way to target specific DNA and were predicted to surpass zinc fingers. They both depend on custom-making new proteins for each DNA target, a more cumbersome procedure than guide RNAs. CRISPRs are more efficient[citation needed] and can target more genes than these earlier techniques[citation needed].

References[edit]

  1. ^ a b c Horvath, P.; Barrangou, R. (2010). "CRISPR/Cas, the Immune System of Bacteria and Archaea". Science 327 (5962): 167–170. doi:10.1126/science.1179555. PMID 20056882.  edit
  2. ^ a b c Marraffini, L. A.; Sontheimer, E. J. (2010). "CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea". Nature Reviews Genetics 11 (3): 181–190. doi:10.1038/nrg2749. PMC 2928866. PMID 20125085.  edit
  3. ^ 71/79 Archaea, 463/1008 Bacteria CRISPRdb, Date: 19.6.2010
  4. ^ Grissa, I.; Vergnaud, G.; Pourcel, C. (2007). "The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats". BMC Bioinformatics 8: 172. doi:10.1186/1471-2105-8-172. PMC 1892036. PMID 17521438.  edit
  5. ^ Barrangou, R.; Fremaux, C.; Deveau, H.; Richards, M.; Boyaval, P.; Moineau, S.; Romero, D. A.; Horvath, P. (2007). "CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes". Science 315 (5819): 1709–1712. doi:10.1126/science.1138140. PMID 17379808.  edit
  6. ^ Marraffini, L. A.; Sontheimer, E. J. (2008). "CRISPR Interference Limits Horizontal Gene Transfer in Staphylococci by Targeting DNA". Science 322 (5909): 1843–1845. doi:10.1126/science.1165771. PMC 2695655. PMID 19095942.  edit
  7. ^ Overballe-Petersen, S.; Harms, K.; Orlando, L. A. A.; Mayar, J. V. M.; Rasmussen, S.; Dahl, T. W.; Rosing, M. T.; Poole, A. M.; Sicheritz-Ponten, T.; Brunak, S.; Inselmann, S.; De Vries, J.; Wackernagel, W.; Pybus, O. G.; Nielsen, R.; Johnsen, P. J.; Nielsen, K. M.; Willerslev, E. (2013). "Bacterial natural transformation by highly fragmented and damaged DNA". Proceedings of the National Academy of Sciences. doi:10.1073/pnas.1315278110.  edit
  8. ^ "Bacteria incorporate pieces of old DNA in their own genome, scientists discover". KurzweilAI. doi:10.1073/pnas.1315278110. Retrieved 2013-11-26. 
  9. ^ Ishino, Y.; Shinagawa, H.; Makino, K.; Amemura, M.; Nakata, A. (1987). "Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product". Journal of bacteriology 169 (12): 5429–5433. PMC 213968. PMID 3316184.  edit
  10. ^ Mojica, F. J.; Díez-Villaseñor, C.; Soria, E.; Juez, G. (2000). "Biological significance of a family of regularly spaced repeats in the genomes of Archaea, Bacteria and mitochondria". Molecular microbiology 36 (1): 244–246. doi:10.1046/j.1365-2958.2000.01838.x. PMID 10760181.  edit
  11. ^ a b Jansen, R.; Embden, J. D.; Gaastra, W.; Schouls, L. M. (2002). "Identification of genes that are associated with DNA repeats in prokaryotes". Molecular microbiology 43 (6): 1565–1575. doi:10.1046/j.1365-2958.2002.02839.x. PMID 11952905.  edit
  12. ^ Horvath, P.; Barrangou, R. (2010). "CRISPR/Cas, the Immune System of Bacteria and Archaea". Science 327 (5962): 167–170. doi:10.1126/science.1179555. PMID 20056882.  edit
  13. ^ "CRISPR gene therapy: Scientists call for more public debate around breakthrough technique - Science - News". The Independent. 2013-11-07. Retrieved 2013-11-25. 
  14. ^ a b c d e f g h i j k l m Pennisi, E. (2013). "The CRISPR Craze". Science 341 (6148): 833–836. doi:10.1126/science.341.6148.833. PMID 23970676.  edit
  15. ^ a b c d Haft, D. H.; Selengut, J.; Mongodin, E. F.; Nelson, K. E. (2005). "A Guild of 45 CRISPR-Associated (Cas) Protein Families and Multiple CRISPR/Cas Subtypes Exist in Prokaryotic Genomes". PLoS Computational Biology 1 (6): e60. doi:10.1371/journal.pcbi.0010060. PMC 1282333. PMID 16292354.  edit
  16. ^ a b Kunin, V.; Sorek, R.; Hugenholtz, P. (2007). "Evolutionary conservation of sequence and secondary structures in CRISPR repeats". Genome Biology 8 (4): R61. doi:10.1186/gb-2007-8-4-r61. PMC 1896005. PMID 17442114.  edit
  17. ^ Mojica, F. J. M.; Díez-Villaseñor, C. S.; García-Martínez, J. S.; Soria, E. (2005). "Intervening Sequences of Regularly Spaced Prokaryotic Repeats Derive from Foreign Genetic Elements". Journal of Molecular Evolution 60 (2): 174–182. doi:10.1007/s00239-004-0046-3. PMID 15791728.  edit
  18. ^ Bolotin, A.; Quinquis, B.; Sorokin, A.; Ehrlich, S. D. (2005). "Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin". Microbiology 151 (8): 2551–2561. doi:10.1099/mic.0.28048-0. PMID 16079334.  edit
  19. ^ Pourcel, C.; Salvignol, G.; Vergnaud, G. (2005). "CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies". Microbiology 151 (3): 653–663. doi:10.1099/mic.0.27437-0. PMID 15758212.  edit
  20. ^ Stern, A.; Keren, L.; Wurtzel, O.; Amitai, G.; Sorek, R. (2010). "Self-targeting by CRISPR: Gene regulation or autoimmunity?". Trends in Genetics 26 (8): 335–340. doi:10.1016/j.tig.2010.05.008. PMC 2910793. PMID 20598393.  edit
  21. ^ Tyson, G. W.; Banfield, J. F. (2007). "Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses". Environmental Microbiology 10 (1): 200–207. doi:10.1111/j.1462-2920.2007.01444.x. PMID 17894817.  edit
  22. ^ Makarova, K. S.; Grishin, N. V.; Shabalina, S. A.; Wolf, Y. I.; Koonin, E. V. (2006). "A putative RNA-interference-based immune system in prokaryotes: Computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action". Biology Direct 1: 7. doi:10.1186/1745-6150-1-7. PMC 1462988. PMID 16545108.  edit
  23. ^ Brouns, S. J. J.; Jore, M. M.; Lundgren, M.; Westra, E. R.; Slijkhuis, R. J. H.; Snijders, A. P. L.; Dickman, M. J.; Makarova, K. S.; Koonin, E. V.; Van Der Oost, J. (2008). "Small CRISPR RNAs Guide Antiviral Defense in Prokaryotes". Science 321 (5891): 960–964. doi:10.1126/science.1159689. PMID 18703739.  edit
  24. ^ Koonin, E. V.; Wolf, Y. I. (2009). "Is evolution Darwinian or/and Lamarckian?". Biology Direct 4: 42. doi:10.1186/1745-6150-4-42. PMC 2781790. PMID 19906303.  edit
  25. ^ Heidelberg, J. F.; Nelson, W. C.; Schoenfeld, T.; Bhaya, D. (2009). "Germ Warfare in a Microbial Mat Community: CRISPRs Provide Insights into the Co-Evolution of Host and Viral Genomes". In Ahmed, Niyaz. PLoS ONE 4 (1): e4169. doi:10.1371/journal.pone.0004169. PMC 2612747. PMID 19132092.  edit
  26. ^ Hale, C. R.; Majumdar, S.; Elmore, J.; Pfister, N.; Compton, M.; Olson, S.; Resch, A. M.; Glover Cv, C. V. C.; Graveley, B. R.; Terns, R. M.; Terns, M. P. (2012). "Essential Features and Rational Design of CRISPR RNAs that Function with the Cas RAMP Module Complex to Cleave RNAs". Molecular Cell 45 (3): 292–302. doi:10.1016/j.molcel.2011.10.023. PMC 3278580. PMID 22227116.  edit
  27. ^ Sorek, R.; Kunin, V.; Hugenholtz, P. (2008). "CRISPR — a widespread system that provides acquired resistance against phages in bacteria and archaea". Nature Reviews Microbiology 6 (3): 181–186. doi:10.1038/nrmicro1793. PMID 18157154.  edit
  28. ^ Jinek, M.; Chylinski, K.; Fonfara, I.; Hauer, M.; Doudna, J. A.; Charpentier, E. (2012). "A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity". Science 337 (6096): 816–821. doi:10.1126/science.1225829. PMID 22745249.  edit
  29. ^ Cong, L.; Ran, F. A.; Cox, D.; Lin, S.; Barretto, R.; Habib, N.; Hsu, P. D.; Wu, X.; Jiang, W.; Marraffini, L. A.; Zhang, F. (2013). "Multiplex Genome Engineering Using CRISPR/Cas Systems". Science 339 (6121): 819–823. doi:10.1126/science.1231143. PMC 3795411. PMID 23287718.  edit
  30. ^ Mali, P.; Yang, L.; Esvelt, K. M.; Aach, J.; Guell, M.; Dicarlo, J. E.; Norville, J. E.; Church, G. M. (2013). "RNA-Guided Human Genome Engineering via Cas9". Science 339 (6121): 823–826. doi:10.1126/science.1232033. PMC 3712628. PMID 23287722.  edit
  31. ^ Wang, H.; Yang, H.; Shivalila, C. S.; Dawlaty, M. M.; Cheng, A. W.; Zhang, F.; Jaenisch, R. (2013). "One-Step Generation of Mice Carrying Mutations in Multiple Genes by CRISPR/Cas-Mediated Genome Engineering". Cell 153 (4): 910–918. doi:10.1016/j.cell.2013.04.025. PMID 23643243.  edit
  32. ^ Hou, Z.; Zhang, Y.; Propson, N. E.; Howden, S. E.; Chu, L. -F.; Sontheimer, E. J.; Thomson, J. A. (2013). "Efficient genome engineering in human pluripotent stem cells using Cas9 from Neisseria meningitidis". Proceedings of the National Academy of Sciences 110 (39): 15644. doi:10.1073/pnas.1313587110.  edit
  33. ^ Novick, R. P.; Christie, G. E.; Penadés, J. R. (2010). "The phage-related chromosomal islands of Gram-positive bacteria". Nature Reviews Microbiology 8 (8): 541–551. doi:10.1038/nrmicro2393. PMC 3522866. PMID 20634809.  edit
  34. ^ Seed, K. D.; Lazinski, D. W.; Calderwood, S. B.; Camilli, A. (2013). "A bacteriophage encodes its own CRISPR/Cas adaptive response to evade host innate immunity". Nature 494 (7438): 489–491. doi:10.1038/nature11927. PMC 3587790. PMID 23446421.  edit
  35. ^ Young, Susan. "Biotech Startup Editas Medicine Wants to Cure Grievous Genetic Diseases with New Genome Editing Technology | MIT Technology Review". Technologyreview.com. Retrieved 2013-11-30. 

Further reading[edit]

  • Horvath, P.; Romero, D. A.; Coûté-Monvoisin, A. -C.; Richards, M.; Deveau, H.; Moineau, S.; Boyaval, P.; Fremaux, C.; Barrangou, R. (2007). "Diversity, Activity, and Evolution of CRISPR Loci in Streptococcus thermophilus". Journal of Bacteriology 190 (4): 1401–1412. doi:10.1128/JB.01415-07. PMC 2238196. PMID 18065539.  edit
  • Deveau, H.; Barrangou, R.; Garneau, J. E.; Labonté, J.; Fremaux, C.; Boyaval, P.; Romero, D. A.; Horvath, P.; Moineau, S. (2007). "Phage Response to CRISPR-Encoded Resistance in Streptococcus thermophilus". Journal of Bacteriology 190 (4): 1390–1400. doi:10.1128/JB.01412-07. PMC 2238228. PMID 18065545.  edit
  • Andersson, A. F.; Banfield, J. F. (2008). "Virus Population Dynamics and Acquired Virus Resistance in Natural Microbial Communities". Science 320 (5879): 1047–1050. doi:10.1126/science.1157358. PMID 18497291.  edit
  • Hale, C.; Kleppe, K.; Terns, R. M.; Terns, M. P. (2008). "Prokaryotic silencing (psi)RNAs in Pyrococcus furiosus". RNA 14 (12): 2572–2579. doi:10.1261/rna.1246808. PMC 2590957. PMID 18971321.  edit
  • Carte, J.; Wang, R.; Li, H.; Terns, R. M.; Terns, M. P. (2008). "Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes". Genes & Development 22 (24): 3489–3496. doi:10.1101/gad.1742908. PMC 2607076. PMID 19141480.  edit
  • Shah, S. A.; Hansen, N. R.; Garrett, R. A. (2009). "Distribution of CRISPR spacer matches in viruses and plasmids of crenarchaeal acidothermophiles and implications for their inhibitory mechanism". Biochemical Society Transactions 37 (Pt 1): 23–28. doi:10.1042/BST0370023. PMID 19143596.  edit
  • Lillestøl, R. K.; Shah, S. A.; Brügger, K.; Redder, P.; Phan, H.; Christiansen, J.; Garrett, R. A. (2009). "CRISPR families of the crenarchaeal genus Sulfolobus: Bidirectional transcription and dynamic properties". Molecular Microbiology 72 (1): 259–272. doi:10.1111/j.1365-2958.2009.06641.x. PMID 19239620.  edit
  • Mojica, F. J. M.; Diez-Villasenor, C.; Garcia-Martinez, J.; Almendros, C. (2009). "Short motif sequences determine the targets of the prokaryotic CRISPR defence system". Microbiology 155 (3): 733–740. doi:10.1099/mic.0.023960-0. PMID 19246744.  edit
  • Van Der Ploeg, J. R. (2009). "Analysis of CRISPR in Streptococcus mutans suggests frequent occurrence of acquired immunity against infection by M102-like bacteriophages". Microbiology 155 (6): 1966–1976. doi:10.1099/mic.0.027508-0. PMID 19383692.  edit
  • Hale, C. R.; Zhao, P.; Olson, S.; Duff, M. O.; Graveley, B. R.; Wells, L.; Terns, R. M.; Terns, M. P. (2009). "RNA-Guided RNA Cleavage by a CRISPR RNA-Cas Protein Complex". Cell 139 (5): 945–956. doi:10.1016/j.cell.2009.07.040. PMC 2951265. PMID 19945378.  edit
  • Van Der Oost, J.; Brouns, S. J. J. (2009). "RNAi: Prokaryotes Get in on the Act". Cell 139 (5): 863–865. doi:10.1016/j.cell.2009.11.018. PMID 19945373.  edit
  • Marraffini, L. A.; Sontheimer, E. J. (2010). "Self versus non-self discrimination during CRISPR RNA-directed immunity". Nature 463 (7280): 568–571. doi:10.1038/nature08703. PMC 2813891. PMID 20072129.  edit
  • Karginov, F. V.; Hannon, G. J. (2010). "The CRISPR System: Small RNA-Guided Defense in Bacteria and Archaea". Molecular Cell 37 (1): 7–19. doi:10.1016/j.molcel.2009.12.033. PMC 2819186. PMID 20129051.  edit
  • Pul, Ü.; Wurm, R.; Arslan, Z.; Geissen, R.; Hofmann, N.; Wagner, R. (2010). "Identification and characterization ofE. ColiCRISPR-caspromoters and their silencing by H-NS". Molecular Microbiology 75 (6): 1495–1512. doi:10.1111/j.1365-2958.2010.07073.x. PMID 20132443.  edit
  • Diez-Villasenor, C.; Almendros, C.; Garcia-Martinez, J.; Mojica, F. J. M. (2010). "Diversity of CRISPR loci in Escherichia coli". Microbiology 156 (5): 1351–1361. doi:10.1099/mic.0.036046-0. PMID 20133361.  edit
  • Deveau, H. L. N.; Garneau, J. E.; Moineau, S. (2010). "CRISPR/Cas System and Its Role in Phage-Bacteria Interactions". Annual Review of Microbiology 64: 475–493. doi:10.1146/annurev.micro.112408.134123. PMID 20528693.  edit
  • Koonin, E. V.; Makarova, K. S. (2009). "CRISPR-Cas: An adaptive immunity system in prokaryotes". F1000 Biology Reports 1: 95. doi:10.3410/B1-95. PMC 2884157. PMID 20556198.  edit
  • Touchon, M.; Rocha, E. P. C. (2010). "The Small, Slow and Specialized CRISPR and Anti-CRISPR of Escherichia and Salmonella". In Randau, Lennart. PLoS ONE 5 (6): e11126. doi:10.1371/journal.pone.0011126. PMC 2886076. PMID 20559554.  edit

External links[edit]

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CRISPR-associated protein Cse2 (CRISPR_cse2) Provide feedback

Clusters of short DNA repeats with non-homologous spacers, which are found at regular intervals in the genomes of phylogenetically distinct prokaryotic species, comprise a family with recognisable features. This family is known as CRISPR (short for Clustered, Regularly Interspaced Short Palindromic Repeats). A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This family of proteins, represented by CT1973 from Chlorobaculum tepidum, is encoded by genes found in the CRISPR/Cas subtype Ecoli regions of many bacteria (most of which are mesophiles), and not in Archaea. It is designated Cse2.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013382

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes [PUBMED:17442114]. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [PUBMED:17379808, PUBMED:16545108]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity.

In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci [PUBMED:16292354]. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny.

This entry represents the Cse2 family of Cas proteins, which includes CT1973 from Chlorobium tepidum. These proteins are found in the CRISPR/Cas subtype Ecoli regions of many bacteria (most of which are mesophiles), and not in Archaea [PUBMED:16292354].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(58)
Full
(642)
Representative proteomes NCBI
(399)
Meta
(12)
RP15
(34)
RP35
(87)
RP55
(105)
RP75
(120)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(58)
Full
(642)
Representative proteomes NCBI
(399)
Meta
(12)
RP15
(34)
RP35
(87)
RP55
(105)
RP75
(120)
Alignment:
Format:
Order:
Sequence:
Gaps:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(58)
Full
(642)
Representative proteomes NCBI
(399)
Meta
(12)
RP15
(34)
RP35
(87)
RP55
(105)
RP75
(120)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: TIGRFAMs
Previous IDs: CRISPR_cse2;
Type: Family
Author: TIGRFAMs, Coggill P
Number in seed: 58
Number in full: 642
Average length of the domain: 146.00 aa
Average identity of full alignment: 32 %
Average coverage of the sequence by the domain: 78.32 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.1 22.1
Trusted cut-off 23.4 22.8
Noise cut-off 20.4 20.2
Model length: 146
Family (HMM) version: 5
Download: download the raw HMM for this family

Species distribution

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the CRISPR_Cse2 domain has been found. There are 2 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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