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Escherichia coli K-12 substr. MG1655 Protein: multifunctional nuclease



Gene: cas1 Accession Numbers: G7425 (EcoCyc), b2755, ECK2750

Synonyms: ygbT

Regulation Summary Diagram: ?

Subunit composition of multifunctional nuclease = [Cas1]2
         multifunctional nuclease = Cas1

Summary:
YgbT/Cas1 is a nuclease with activity against single-stranded DNA as well as branched DNAs such as Holliday junctions, replication forks and 5'-flaps. Cas1 is specifically recruited to DNA double strand breaks. It physically and functionally interacts with the DNA repair system and may function in the RuvABC DNA repair pathway [Babu11a]. Cas1 and Cas2 together are required for efficient adaptation of the CRISPR array [Yosef12].

Activity of Cas1 is dependent on a divalent metal cation [Babu11a].

Crystal structures of the Cas1 C-terminal domain and the full-length protein have been solved at 1.4 and 1.95 Å resolution, respectively. Possible active site residues were identified, and site-directed mutagenesis of these residues confirmed their importance [Babu11a].

A cas1 deletion mutant shows increased sensitivity to DNA damage and impaired chromosome segregation following DNA damage [Babu11a]. Induced expression of Cas1 and Cas2 leads to acquisition of new spacer elements in the CRISPR repeat [Yosef12].

Cas1: "CRISPR-associated" [Brouns08]

Reviews: [Horvath10, Karginov10, Bhaya11, Wiedenheft12]

Gene Citations: [Pul10]

Locations: cytosol

Map Position: [2,876,877 <- 2,877,794] (62.01 centisomes)
Length: 918 bp / 305 aa

Molecular Weight of Polypeptide: 33.194 kD (from nucleotide sequence)

Molecular Weight of Multimer: 70.0 kD (experimental) [Babu11a]

Unification Links: ASAP:ABE-0009038 , DIP:DIP-12118N , EchoBASE:EB2915 , EcoGene:EG13114 , EcoliWiki:b2755 , OU-Microarray:b2755 , PortEco:cas1 , Protein Model Portal:Q46896 , RefSeq:NP_417235 , RegulonDB:G7425 , SMR:Q46896 , String:511145.b2755 , UniProt:Q46896

Relationship Links: InterPro:IN-FAMILY:IPR002729 , InterPro:IN-FAMILY:IPR019851 , PDB:Structure:3NKD , PDB:Structure:3NKE , Pfam:IN-FAMILY:PF01867

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0000737 - DNA catabolic process, endonucleolytic Inferred from experiment [Babu11a]
GO:0006974 - cellular response to DNA damage stimulus Inferred from experiment Inferred by computational analysis [UniProtGOA11, Babu11a]
GO:0043571 - maintenance of CRISPR repeat elements Inferred from experiment Inferred by computational analysis [GOA06, Yosef12]
GO:0006281 - DNA repair Inferred by computational analysis [UniProtGOA11]
GO:0051607 - defense response to virus Inferred by computational analysis [UniProtGOA11, GOA06]
GO:0090305 - nucleic acid phosphodiester bond hydrolysis Inferred by computational analysis [UniProtGOA11, GOA06]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Babu11a]
GO:0008821 - crossover junction endodeoxyribonuclease activity Inferred from experiment [Babu11a]
GO:0017108 - 5'-flap endonuclease activity Inferred from experiment [Babu11a]
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11]
GO:0004518 - nuclease activity Inferred by computational analysis [UniProtGOA11]
GO:0004519 - endonuclease activity Inferred by computational analysis [UniProtGOA11, GOA06]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11, GOA06]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11]

MultiFun Terms: cell processes defense/survival
information transfer DNA related DNA repair

Essentiality data for cas1 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]

Credits:
Created 19-Jan-2011 by Keseler I , SRI International
Last-Curated ? 22-Mar-2012 by Keseler I , SRI International


Sequence Features

Feature Class Location Citations Comment
Protein-Segment 96 -> 278
[UniProt12b]
UniProt: Sufficient for cleavage of ssRNA, ssDNA and Holliday junction DNA; Sequence Annotation Type: region of interest.
Mutagenesis-Variant 141
[Babu11a, UniProt12b]
Alternate sequence: E → A; UniProt: No cleavage of any substrates, no restoration of UV or mitomycin C (MMC) resistance.
Metal-Binding-Site 141
[UniProt12b]
UniProt: Magnesium; Non-Experimental Qualifier: by similarity.
Active-Site 141
[UniProt12b]
UniProt: Non-Experimental Qualifier: potential.
Mutagenesis-Variant 141
[Babu11a]
E141A abolished nuclease activity [Babu11a].
Mutagenesis-Variant 184
[Babu11a, UniProt12b]
Alternate sequence: T → A; UniProt: No cleavage of any substrates.
Mutagenesis-Variant 188
[Babu11a, UniProt12b]
Alternate sequence: Y → A; UniProt: Partial inhibition of cleavage.
Mutagenesis-Variant 208
[Babu11a, UniProt12b]
Alternate sequence: H → A; UniProt: No cleavage of any substrates, no restoration of UV or MMC resistance.
Metal-Binding-Site 208
[UniProt12b]
UniProt: Magnesium; Non-Experimental Qualifier: by similarity.
Active-Site 208
[UniProt12b]
UniProt: Non-Experimental Qualifier: potential.
Mutagenesis-Variant 208
[Babu11a]
H208A abolished nuclease activity [Babu11a].
Mutagenesis-Variant 211
[Babu11a, UniProt12b]
Alternate sequence: K → A; UniProt: No cleavage of any substrates.
Mutagenesis-Variant 218
[Babu11a, UniProt12b]
Alternate sequence: D → A; UniProt: No cleavage of any substrates, no restoration of UV or MMC resistance.
Active-Site 218
[UniProt12b]
UniProt: Non-Experimental Qualifier: potential.
Mutagenesis-Variant 218
[Babu11a]
D218A abolished nuclease activity [Babu11a].
Mutagenesis-Variant 221
[Babu11a, UniProt12b]
Alternate sequence: D → A; UniProt: No cleavage of any substrates.
Metal-Binding-Site 221
[UniProt12b]
UniProt: Magnesium; Non-Experimental Qualifier: by similarity.
Active-Site 221
[UniProt12b]
UniProt: Non-Experimental Qualifier: potential.
Mutagenesis-Variant 221
[Babu11a]
D221A abolished nuclease activity [Babu11a].
Mutagenesis-Variant 224
[Babu11a, UniProt12b]
Alternate sequence: K → A; UniProt: No cleavage of any substrates.


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
Peter D. Karp on Thu Jan 16, 2003:
Predicted gene function revised as a result of E. coli genome reannotation by Serres et al. [Serres01 ].
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


References

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

Babu11a: 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

Bhaya11: Bhaya D, Davison M, Barrangou R (2011). "CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulation." Annu Rev Genet 45;273-97. PMID: 22060043

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

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

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

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

Karginov10: Karginov FV, Hannon GJ (2010). "The CRISPR system: small RNA-guided defense in bacteria and archaea." Mol Cell 37(1);7-19. PMID: 20129051

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

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

Serres01: Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M (2001). "A functional update of the Escherichia coli K-12 genome." Genome Biol 2(9);RESEARCH0035. PMID: 11574054

UniProt12b: UniProt Consortium (2012). "UniProt version 2012-09 released on 2012-09-12 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

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

Wiedenheft12: Wiedenheft B, Sternberg SH, Doudna JA (2012). "RNA-guided genetic silencing systems in bacteria and archaea." Nature 482(7385);331-8. PMID: 22337052

Yosef12: Yosef I, Goren MG, Qimron U (2012). "Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli." Nucleic Acids Res 40(12);5569-76. PMID: 22402487

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


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Sun Dec 21, 2014, biocyc14.