Escherichia coli K-12 substr. MG1655 Polypeptide: crRNA endonuclease

Gene: casE Accession Numbers: G7426 (EcoCyc), b2756, ECK2751

Synonyms: ygcH, cse3, Cas6e

Regulation Summary Diagram: ?

Regulation summary diagram for casE

Component of: CRISPR-associated complex for antiviral defense (extended summary available)

CasE is the only Cascade subunit that is necessary and sufficient for cleavage of pre-CRISPR RNA (crRNA). The cleavage reaction is highly specific for the endogenous pre-crRNA [Brouns08].

CasE binds the 3' end of pre-crRNA. CasE connects to the Cascade complex through contacts with CasC (Cas7.1) and CasB (Cas2.1). CasE contains tandem RNA recognition motifs (RRMs) connected by an 8 residue linker. The RRMs form a cleft on one face of the protein that binds a short helix from the first CasC subunit. The opposite face of the protein contacts the pre-crRNA and positions it for cleavage. After cleavage, the mature crRNA remains associated with CasE [Jackson14].

A mutation in the conserved H20 residue of CasE leads to loss of pre-crRNA cleavage [Brouns08].

CasE: "CRISPR-associated" [Brouns08]

Gene Citations: [Pul10]

Map Position: [2,877,810 <- 2,878,409] (62.03 centisomes, 223°)
Length: 600 bp / 199 aa

Molecular Weight of Polypeptide: 22.293 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0009042 , DIP:DIP-12124N , EchoBASE:EB2916 , EcoGene:EG13115 , EcoliWiki:b2756 , OU-Microarray:b2756 , PortEco:casE , Pride:Q46897 , Protein Model Portal:Q46897 , RefSeq:NP_417236 , RegulonDB:G7426 , SMR:Q46897 , String:511145.b2756 , UniProt:Q46897

Relationship Links: InterPro:IN-FAMILY:IPR010179 , PDB:Structure:1VY8 , PDB:Structure:1VY9 , PDB:Structure:4DZD , PDB:Structure:4QYZ , PDB:Structure:4U7U , Pfam:IN-FAMILY:PF08798 , Smart:IN-FAMILY:SM01101

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for casE

GO Terms:

Biological Process: GO:0006396 - RNA processing Inferred from experiment [Brouns08]
GO:0051607 - defense response to virus Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Brouns08]
GO:0090305 - nucleic acid phosphodiester bond hydrolysis Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0003723 - RNA binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Jackson14]
GO:0005515 - protein binding Inferred from experiment [Jackson14, Babu11]
GO:0016787 - hydrolase activity Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Brouns08]
GO:0004518 - nuclease activity Inferred by computational analysis [UniProtGOA11a]
GO:0004519 - endonuclease activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0043234 - protein complex Inferred from experiment [Jackson14, Babu11]

MultiFun Terms: cell processes defense/survival

Essentiality data for casE knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Curated 10-Sep-2008 by Keseler I , SRI International
Last-Curated ? 10-Sep-2014 by Mackie A , Macquarie University

Subunit of: CRISPR-associated complex for antiviral defense

Synonyms: Cascade

Subunit composition of CRISPR-associated complex for antiviral defense = [CasA][CasB]2[CasC]6[CasD][CasE]
         Cascade subunit A = CasA (summary available)
         Cascade subunit B = CasB (summary available)
         Cascade subunit C = CasC (extended summary available)
         Cascade subunit D = CasD (summary available)
         crRNA endonuclease = CasE (summary available)

CRISPR (clusters of regularly interspersed short palindromic repeats) loci are associated with defense against foreign DNA and occur widely in bacteria and archaea [Young08a]. The CRISPR locus of E. coli K-12 is transcribed into a large pre-crRNA. CasE alone or within the Cascade complex is required for processing of pre-crRNA into the mature crRNA. Processed crRNAs of approximately 57 nt copurify with Cascade. In the presence of Cas3, this complex gives rise to resistance against phages whose genomes have regions of complementarity to elements in the CRISPR repeat [Brouns08].

Cryo-EM structures of the Cascade complex before and after binding to a target sequence have been solved, showing that the bound crRNA is protected from degradation while still being available for base pairing with the target [Wiedenheft11]. Target nucleotide binding results in a concerted conformational change that may result in recruitment of the Cas3 nuclease [Jore11, Wiedenheft11].

The 11 Cas proteins assemble with the crRNA into a 'sea-horse'-shaped structure. CasE forms the head of the complex and binds the 3' end of the pre-crRNA and positions it for cleavage; CasE, CasA and one subunit of CasC form the tail which contacts the 5' end of crRNA. The 6 CasC subuits form a helical backbone which along with the 2 CasB subunits connects the head and tail. The crRNA is interwoven into the Cascade complex in a manner that presents segments for target DNA binding [Jackson14]. The crRNA-target DNA hybrid adopts a ribbon conformation rather than a helix; this conformation is facilitated by the structural disruption of base pairing at every 6th nucleotide in the hybrid molecule. Protein-nucleic acid interactions between the DNA-RNA hybrid and the Cascade complex (in particular the helical backbone) stabilise the ribbon conformation [Mulepati14].

Cas3 as well as a mixture of CasC, CasD and CasE proteins catalyses ATP-independent annealing of RNA with DNA to form hybrid molecules of RNA base-paired into duplex DNA, also known as R-loops [Howard11]. The specificity of the CRISPR system is provided by the formation of R-loops [Jore11]. Strict complementarity between the target and the crRNA is only required in a seven-nucleotide seed region within the protospacer region of crRNAs [Semenova11].

Review: [Horvath10]

Molecular Weight: 405.0 kD (experimental) [Jore11]

Relationship Links: PDB:Structure:1VY8 , PDB:Structure:1VY9 , PDB:Structure:4QYZ

GO Terms:

Biological Process: GO:0051607 - defense response to virus Inferred from experiment [Brouns08]
Molecular Function: GO:0003677 - DNA binding Inferred from experiment [Jore11]
GO:0003723 - RNA binding Inferred from experiment [Jackson14, Brouns08]
GO:0008270 - zinc ion binding Inferred from experiment [Jackson14]
GO:0071667 - DNA/RNA hybrid binding Inferred from experiment [Mulepati14]
Cellular Component: GO:0043234 - protein complex Inferred from experiment [Jackson14]

Created 10-Sep-2008 by Keseler I , SRI International
Last-Curated ? 10-Sep-2014 by Mackie A , Macquarie University

Enzymatic reaction of: CRISPR RNA processing (CRISPR-associated complex for antiviral defense)

pre-crRNA <=> crRNA

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

Sequence Features

Protein sequence of crRNA endonuclease with features indicated

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
Chain 2 -> 199
UniProt: CRISPR system Cascade subunit CasE.
Mutagenesis-Variant 20
[Brouns08, PerezRodriguez11, UniProt12a]
UniProt: Loss of pre-crRNA cleavage.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Babu11: Babu M, Beloglazova N, Flick R, Graham C, Skarina T, Nocek B, Gagarinova A, Pogoutse O, Brown G, Binkowski A, Phanse S, Joachimiak A, Koonin EV, Savchenko A, Emili A, Greenblatt J, Edwards AM, Yakunin AF (2011). "A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair." Mol Microbiol 79(2);484-502. PMID: 21219465

Brouns08: Brouns SJ, Jore MM, Lundgren M, Westra ER, Slijkhuis RJ, Snijders AP, Dickman MJ, Makarova KS, Koonin EV, van der Oost J (2008). "Small CRISPR RNAs guide antiviral defense in prokaryotes." Science 321(5891);960-4. PMID: 18703739

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

Horvath10: Horvath P, Barrangou R (2010). "CRISPR/Cas, the immune system of bacteria and archaea." Science 327(5962);167-70. PMID: 20056882

Howard11: Howard JA, Delmas S, Ivancic-Bace I, Bolt EL (2011). "Helicase dissociation and annealing of RNA-DNA hybrids by Escherichia coli Cas3 protein." Biochem J 439(1);85-95. PMID: 21699496

Jackson14: Jackson RN, Golden SM, van Erp PB, Carter J, Westra ER, Brouns SJ, van der Oost J, Terwilliger TC, Read RJ, Wiedenheft B (2014). "Crystal structure of the CRISPR RNA-guided surveillance complex from Escherichia coli." Science. PMID: 25103409

Jore11: Jore MM, Lundgren M, van Duijn E, Bultema JB, Westra ER, Waghmare SP, Wiedenheft B, Pul U, Wurm R, Wagner R, Beijer MR, Barendregt A, Zhou K, Snijders AP, Dickman MJ, Doudna JA, Boekema EJ, Heck AJ, van der Oost J, Brouns SJ (2011). "Structural basis for CRISPR RNA-guided DNA recognition by Cascade." Nat Struct Mol Biol 18(5);529-36. PMID: 21460843

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Mulepati14: Mulepati S, Heroux A, Bailey S (2014). "Crystal structure of a CRISPR RNA-guided surveillance complex bound to a ssDNA target." Science. PMID: 25123481

PerezRodriguez11: Perez-Rodriguez R, Haitjema C, Huang Q, Nam KH, Bernardis S, Ke A, DeLisa MP (2011). "Envelope stress is a trigger of CRISPR RNA-mediated DNA silencing in Escherichia coli." Mol Microbiol 79(3);584-99. PMID: 21255106

Pul10: Pul U, Wurm R, Arslan Z, Geissen R, Hofmann N, Wagner R (2010). "Identification and characterization of E. coli CRISPR-cas promoters and their silencing by H-NS." Mol Microbiol 75(6):1495-512. PMID: 20132443

Semenova11: Semenova E, Jore MM, Datsenko KA, Semenova A, Westra ER, Wanner B, van der Oost J, Brouns SJ, Severinov K (2011). "Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence." Proc Natl Acad Sci U S A 108(25);10098-103. PMID: 21646539

UniProt12a: UniProt Consortium (2012). "UniProt version 2012-09 released on 2012-09-12 00:00:00." Database.

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Wiedenheft11: Wiedenheft B, Lander GC, Zhou K, Jore MM, Brouns SJ, van der Oost J, Doudna JA, Nogales E (2011). "Structures of the RNA-guided surveillance complex from a bacterial immune system." Nature 477(7365);486-9. PMID: 21938068

Young08a: Young RF (2008). "Molecular biology. Secret weapon." Science 321(5891);922-3. PMID: 18703730

Other References Related to Gene Regulation

Arslan13: Arslan Z, Stratmann T, Wurm R, Wagner R, Schnetz K, Pul U (2013). "RcsB-BglJ-mediated activation of Cascade operon does not induce the maturation of CRISPR RNAs in E. coli K12." RNA Biol 10(5). PMID: 23392250

Dyszel10: Dyszel JL, Soares JA, Swearingen MC, Lindsay A, Smith JN, Ahmer BM (2010). "E. coli K-12 and EHEC genes regulated by SdiA." PLoS One 5(1);e8946. PMID: 20126629

Wade06: Wade JT, Roa DC, Grainger DC, Hurd D, Busby SJ, Struhl K, Nudler E (2006). "Extensive functional overlap between sigma factors in Escherichia coli." Nat Struct Mol Biol 13(9);806-14. PMID: 16892065

Westra10: Westra ER, Pul U, Heidrich N, Jore MM, Lundgren M, Stratmann T, Wurm R, Raine A, Mescher M, Van Heereveld L, Mastop M, Wagner EG, Schnetz K, Van Der Oost J, Wagner R, Brouns SJ (2010). "H-NS-mediated repression of CRISPR-based immunity in Escherichia coli K12 can be relieved by the transcription activator LeuO." Mol Microbiol 77(6);1380-93. PMID: 20659289

Yang14: Yang CD, Chen YH, Huang HY, Huang HD, Tseng CP (2014). "CRP represses the CRISPR/Cas system in Escherichia coli: evidence that endogenous CRISPR spacers impede phage P1 replication." Mol Microbiol 92(5);1072-91. PMID: 24720807

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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