List of homing endonuclease cutting sites

From Wikipedia the free encyclopedia

Legend of nucleobases
Code Nucleotide represented
A Adenine (A)
C Cytosine (C)
G Guanine (G)
T Thymine (T)
N A, C, G or T
M A or C
R A or G
W A or T
Y C or T
S C or G
K G or T
H A, C or T
B C, G or T
V A, C or G
D A, G or T

The homing endonucleases are a special type of restriction enzymes encoded by introns or inteins. They act on the cellular DNA of the cell that synthesizes them; to be precise, in the opposite allele of the gene that encode them.[1]

Homing endonucleases

[edit]

The list includes some of the most studied examples. The following concepts have been detailed:

Enzyme SF PDB code Source D SCL Recognition sequence Cut
I-AniI[2] H1 1P8K​ Aspergillus nidulans E mito 5' TTGAGGAGGTTTCTCTGTAAATAA
3' AACTCCTCCAAAGAGACATTTATT 		5' ---TTGAGGAGGTTTC   TCTGTAAATAA--- 3'
3' ---AACTCCTCC   AAAGAGACATTTATT--- 5'
I-CeuI[3][4][5][6] H1 2EX5​ Chlamydomonas eugametos E chloro 5' TAACTATAACGGTCCTAAGGTAGCGA
3' ATTGATATTGCCAGGATTCCATCGCT 		5' ---TAACTATAACGGTCCTAA   GGTAGCGA--- 3'
3' ---ATTGATATTGCCAG   GATTCCATCGCT--- 5'
I-ChuI[7][8] H1 Q32001 Chlamydomonas humicola E chloro 5' GAAGGTTTGGCACCTCGATGTCGGCTCATC
3' CTTCCAAACCGTGGAGCTACAGCCGAGTAG 		5' ---GAAGGTTTGGCACCTCG   ATGTCGGCTCATC--- 3'
3' ---CTTCCAAACCGTG   GAGCTACAGCCGAGTAG--- 5'
I-CpaI[8][9] H1 Q39562 Chlamydomonas pallidostigmata E chloro 5' CGATCCTAAGGTAGCGAAATTCA
3' GCTAGGATTCCATCGCTTTAAGT 		5' ---CGATCCTAAGGTAGCGAA   ATTCA--- 3'
3' ---GCTAGGATTCCATC   GCTTTAAGT--- 5'
I-CpaII[10] H1 Q39559 Chlamydomonas pallidostigmata E chloro 5' CCCGGCTAACTCTGTGCCAG
3' GGGCCGATTGAGACACGGTC 		5' ---CCCGGCTAACTC   TGTGCCAG--- 3'
5' ---GGGCCGAT   TGAGACACGGTC--- 3'
I-CreI[11] H1 1BP7​ Chlamydomonas reinhardtii E chloro 5' CTGGGTTCAAAACGTCGTGAGACAGTTTGG
3' GACCCAAGTTTTGCAGCACTCTGTCAAACC 		5' ---CTGGGTTCAAAACGTCGTGA   GACAGTTTGG--- 3'
3' ---GACCCAAGTTTTGCAG   CACTCTGTCAAACC--- 5'
I-DmoI H1 1B24​ Desulfurococcus mobilis A chrm 5' ATGCCTTGCCGGGTAAGTTCCGGCGCGCAT
3' TACGGAACGGCCCATTCAAGGCCGCGCGTA 		5' ---ATGCCTTGCCGGGTAA   GTTCCGGCGCGCAT--- 3'
3' ---TACGGAACGGCC   CATTCAAGGCCGCGCGTA--- 5'
H-DreI[12] H1 1MOW​ Hybrid: I-DmoI and I-CreI AE 5' CAAAACGTCGTAAGTTCCGGCGCG
3' GTTTTGCAGCATTCAAGGCCGCGC 		5' ---CAAAACGTCGTAA   GTTCCGGCGCG--- 3'
3' ---GTTTTGCAG   CATTCAAGGCCGCGC--- 5'
I-HmuI[13][14] H3 1U3E​ Bacillus subtilis phage SP01 B phage 5' AGTAATGAGCCTAACGCTCAGCAA
3' TCATTACTCGGATTGCGAGTCGTT 		  Nicking endonuclease: *
  3' ---TCATTACTCGGATTGC   GAGTCGTT--- 5'
I-HmuII[14][15] H3 Q38137 Bacillus subtilis phage SP82 B phage 5' AGTAATGAGCCTAACGCTCAACAA
3' TCATTACTCGGATTGCGAGTTGTT 		  Nicking endonuclease: *
  3' ---TCATTACTCGGATTGCGAGTTGTTN35   NNNN--- 5'
I-LlaI[16][17] H3 P0A3U1 Lactococcus lactis B chrm 5' CACATCCATAACCATATCATTTTT
3' GTGTAGGTATTGGTATAGTAAAAA 		5' ---CACATCCATAA   CCATATCATTTTT--- 3'
3' ---GTGTAGGTATTGGTATAGTAA   AAA--- 5'
I-MsoI H1 1M5X​ Monomastix sp. E 5' CTGGGTTCAAAACGTCGTGAGACAGTTTGG
3' GACCCAAGTTTTGCAGCACTCTGTCAAACC 		5' ---CTGGGTTCAAAACGTCGTGA   GACAGTTTGG--- 3'
3' ---GACCCAAGTTTTGCAG   CACTCTGTCAAACC--- 5'
PI-PfuI H1 1DQ3​ Pyrococcus furiosus Vc1 A 5' GAAGATGGGAGGAGGGACCGGACTCAACTT
3' CTTCTACCCTCCTCCCTGGCCTGAGTTGAA 		5' ---GAAGATGGGAGGAGGG   ACCGGACTCAACTT--- 3'
3' ---CTTCTACCCTCC   TCCCTGGCCTGAGTTGAA--- 5'
PI-PkoII H1 2CW7​ Pyrococcus kodakarensis BAA-918 A 5' CAGTACTACGGTTAC
3' GTCATGATGCCAATG 		5' ---CAGTACTACG  GTTAC--- 3'
3' ---GTCATG  ATGCCAATG--- 5'
I-PorI[18][19] H3 Pyrobaculum organotrophum A chrm 5' GCGAGCCCGTAAGGGTGTGTACGGG
3' CGCTCGGGCATTCCCACACATGCCC 		5' ---GCGAGCCCGTAAGGGT   GTGTACGGG--- 3'
3' ---CGCTCGGGCATT   CCCACACATGCCC--- 5'
I-PpoI H4 1EVX​ Physarum polycephalum E plasmid 5' TAACTATGACTCTCTTAAGGTAGCCAAAT
3' ATTGATACTGAGAGAATTCCATCGGTTTA 		5' ---TAACTATGACTCTCTTAA   GGTAGCCAAAT--- 3'
3' ---ATTGATACTGAGAG   AATTCCATCGGTTTA--- 5'
PI-PspI H1 Q51334 Pyrococcus sp. A chrm 5' TGGCAAACAGCTATTATGGGTATTATGGGT
3' ACCGTTTGTCGATAATACCCATAATACCCA 		5' ---TGGCAAACAGCTATTAT   GGGTATTATGGGT--- 3'
3' ---ACCGTTTGTCGAT   AATACCCATAATACCCA--- 5'
I-ScaI[20][21] H1 P03873 Saccharomyces capensis E mito 5' TGTCACATTGAGGTGCACTAGTTATTAC
3' ACAGTGTAACTCCACGTGATCAATAATG 		5' ---TGTCACATTGAGGTGCACT   AGTTATTAC--- 3'
3' ---ACAGTGTAACTCCAC   GTGATCAATAATG--- 5'
I-SceI[4][5] H1 1R7M​ Saccharomyces cerevisiae E mito 5' AGTTACGCTAGGGATAACAGGGTAATATAG
3' TCAATGCGATCCCTATTGTCCCATTATATC 		5' ---AGTTACGCTAGGGATAA   CAGGGTAATATAG--- 3'
3' ---TCAATGCGATCCC   TATTGTCCCATTATATC--- 5'
PI-SceI[22][23] H1 1VDE​ Saccharomyces cerevisiae E 5' ATCTATGTCGGGTGCGGAGAAAGAGGTAATGAAATGGCA
3' TAGATACAGCCCACGCCTCTTTCTCCATTACTTTACCGT 		5' ---ATCTATGTCGGGTGC   GGAGAAAGAGGTAATGAAATGGCA--- 3'
3' ---TAGATACAGCC   CACGCCTCTTTCTCCATTACTTTACCGT--- 5'
I-SceII[24][25][26] H1 Saccharomyces cerevisiae E mito 5' TTTTGATTCTTTGGTCACCCTGAAGTATA
3' AAAACTAAGAAACCAGTGGGACTTCATAT 		5' ---TTTTGATTCTTTGGTCACCC   TGAAGTATA--- 3'
3' ---AAAACTAAGAAACCAG   TGGGACTTCATAT--- 5'
I-SecIII[24][27][28] H1 Saccharomyces cerevisiae E mito 5' ATTGGAGGTTTTGGTAACTATTTATTACC
3' TAACCTCCAAAACCATTGATAAATAATGG 		5' ---ATTGGAGGTTTTGGTAAC   TATTTATTACC--- 3'
3' ---TAACCTCCAAAACC   ATTGATAAATAATGG--- 5'
I-SceIV[24][29][30] H1 Saccharomyces cerevisiae E mito 5' TCTTTTCTCTTGATTAGCCCTAATCTACG
3' AGAAAAGAGAACTAATCGGGATTAGATGC 		5' ---TCTTTTCTCTTGATTA   GCCCTAATCTACG--- 3'
3' ---AGAAAAGAGAAC   TAATCGGGATTAGATGC--- 5'
I-SceV[24][31] H3 Saccharomyces cerevisiae E mito 5' AATAATTTTCTTCTTAGTAATGCC
3' TTATTAAAAGAAGAATCATTACGG 		5' ---AATAATTTTCT   TCTTAGTAATGCC--- 3'
3' ---TTATTAAAAGAAGAATCATTA   CGG--- 5'
I-SceVI[24][32] H3 Saccharomyces cerevisiae E mito 5' GTTATTTAATGTTTTAGTAGTTGG
3' CAATAAATTACAAAATCATCAACC 		5' ---GTTATTTAATG   TTTTAGTAGTTGG--- 3'
3' ---CAATAAATTACAAAATCATCA   ACC--- 5'
I-SceVII[20] H1 Saccharomyces cerevisiae E mito 5' TGTCACATTGAGGTGCACTAGTTATTAC
3' ACAGTGTAACTCCACGTGATCAATAATG 		  Unknown **
I-Ssp6803I H5 2OST​ Synechocystis sp. PCC 6803 B 5' GTCGGGCTCATAACCCGAA
3' CAGCCCGAGTATTGGGCTT 		5' ---GTCGGGCT   CATAACCCGAA--- 3'
3' ---CAGCCCGAGTA   TTGGGCTT--- 5'
I-TevI[33][34][35] H2 1I3J​ Escherichia coli phage T4 B phage 5' AGTGGTATCAACGCTCAGTAGATG
3' TCACCATAGT TGCGAGTCATCTAC 		5' ---AGTGGTATCAAC   GCTCAGTAGATG--- 3'
3' ---TCACCATAGT   TGCGAGTCATCTAC--- 5'
I-TevII[33][36] H2 Escherichia coli phage T4 B phage 5' GCTTATGAGTATGAAGTGAACACGTTATTC
3' CGAATACTCATACTTCACTTGTGCAATAAG 		5' ---GCTTATGAGTATGAAGTGAACACGT   TATTC--- 3'
3' ---CGAATACTCATACTTCACTTGTG   CAATAAG--- 5'
I-TevIII[37] H3 Escherichia coli phage RB3 B phage 5' TATGTATCTTTTGCGTGTACCTTTAACTTC
3' ATACATAGAAAACGCACATGGAAATTGAAG 		5' ---T   ATGTATCTTTTGCGTGTACCTTTAACTTC--- 3'
3' ---AT   ACATAGAAAACGCACATGGAAATTGAAG--- 5'
PI-TliI[38][39] H1 Thermococcus litoralis A chrm 5' TAYGCNGAYACNGACGGYTTYT
3' ATRCGNCTRTGNCTGCCTAARA 		5' ---TAYGCNGAYACNGACGG   YTTYT--- 3'
3' ---ATRCGNCTRTGNC   TGCCTAARA--- 5'
PI-TliII[22][39][40] H1 Thermococcus litoralis A chrm 5' AAATTGCTTGCAAACAGCTATTACGGCTAT
3' TTTAACGAACGTTTGTCGATAATGCCGATA 		  Unknown **
I-Tsp061I H1 2DCH​ Thermoproteus sp. IC-061 A 5' CTTCAGTATGCCCCGAAAC
3' GAAGTCATACGGGGCTTTG 		5' ---CTTCAGTAT   GCCCCGAAAC--- 3'
3' ---GAAGT   CATACGGGGCTTTG--- 5'
I-Vdi141I H1 3E54​ Vulcanisaeta distributa IC-141 A 5' CCTGACTCTCTTAAGGTAGCCAAA
3' GGACTGAGAGAATTCCATCGGTTT 		5' ---CCTGACTCTCTTAA   GGTAGCCAAA--- 3'
3' ---GGACTGAG   AGAATTCCATCGGTTT--- 5'

*: Nicking endonuclease: These enzymes cut only one DNA strand, leaving the other strand untouched.
**: Unknown cutting site: Researchers have not been able to determine the exact cutting site of these enzymes yet.

See also

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Information sources

[edit]

Databases and lists of restriction enzymes:

  • Very comprehensive database of restriction enzymes supported by New England Biolabs. It includes all kind of biological, structural, kinetical and commercial information about thousands of enzymes. Also includes related literature for every molecule: Roberts RJ, Vincze T, Posfai J, Macelis D. "REBASE". Retrieved 2010-01-07. Restriction Enzyme Database.
  • Database of inteins, hosted by New England Biolabs. Perler FB. "InBase". Archived from the original on 2010-08-02. Retrieved 2010-02-05. The Intein Database and Registry.[41]
  • Detailed information for biochemical experiments: "Enzyme finder". Archived from the original on 2010-01-08. Retrieved 2010-01-07. New England Biolabs enzyme finder.
  • Alphabetical list of enzymes and their restriction sites: "GenScript Restriction Enzyme webpage". Archived from the original on 2009-07-04. Retrieved 2010-01-07.
  • General information about restriction sites and biochemical conditions for restriction reactions: "Restriction Enzymes Resource". Archived from the original on 2002-02-03. Retrieved 2010-01-07. Promega restriction enzymes webpage.

Databases of proteins:

  • Database of protein structures, solved at atomic resolution: "PDB". Research Collaboratory for Structural Bioinformatics (RCSB). Archived from the original on 2015-04-07. Retrieved 2010-01-25. RCSB Protein Data Bank.
  • Databases of proteins: Swiss Institute of Bioinformatics (SIB); European Bioinformatics Institute (EBI). "UniProtKB/Swiss-Prot & TrEMBL". Retrieved 2010-01-25. Swiss-Prot is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases. TrEMBL is a computer-annotated supplement of Swiss-Prot that contains all the translations of EMBL nucleotide sequence entries not yet integrated in Swiss-Prot.

Notes and references

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  2. ^ Naito T, Kusano K, Kobayashi I (February 1995). "Selfish behavior of restriction-modification systems". Science. 267 (5199): 897–99. Bibcode:1995Sci...267..897N. doi:10.1126/science.7846533. PMID 7846533. S2CID 31128438.
  3. ^ Jacquier A, Dujon B (June 1985). "An intron-encoded protein is active in a gene conversion process that spreads an intron into a mitochondrial gene". Cell. 41 (2): 383–94. doi:10.1016/S0092-8674(85)80011-8. PMID 3886163. S2CID 20519242.
  4. ^ a b Gauthier A, Turmel M, Lemieux C (January 1991). "A group I intron in the chloroplast large subunit rRNA gene of Chlamydomonas eugametos encodes a double-strand endonuclease that cleaves the homing site of this intron". Curr Genet. 19 (1): 43–47. doi:10.1007/BF00362086. PMID 2036685. S2CID 19785524.
  5. ^ a b Marshall P, Lemieux C (August 1991). "Cleavage pattern of the homing endonuclease encoded by the fifth intron in the chloroplast large subunit rRNA-encoding gene of Chlamydomonas eugametos". Gene. 104 (2): 241–5. doi:10.1016/0378-1119(91)90256-B. PMID 1916294.
  6. ^ Turmel M, Boulanger J, Schnare MN, Gray MW, Lemieux C (March 1991). "Six group I introns and three internal transcribed spacers in the chloroplast large subunit ribosomal RNA gene of the green alga Chlamydomonas eugametos". J Mol Biol. 218 (2): 293–311. doi:10.1016/0022-2836(91)90713-G. PMID 1849178.
  7. ^ Côté V, Mercier JP, Lemieux C, Turmel M (July 1993). "The single group-I intron in the chloroplast rrnL gene of Chlamydomonas humicola encodes a site-specific DNA endonuclease (I-ChuI)". Gene. 129 (1): 69–76. doi:10.1016/0378-1119(93)90697-2. PMID 8335261.
  8. ^ a b Turmel M, Gutell RR, Mercier JP, Otis C, Lemieux C (July 1993). "Analysis of the chloroplast large subunit ribosomal RNA gene from 17 Chlamydomonas taxa. Three internal transcribed spacers and 12 group I intron insertion sites". J Mol Biol. 232 (2): 446–67. doi:10.1006/jmbi.1993.1402. PMID 8393936.
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  18. ^ Lykke-Andersen J, Thi-Ngoc HP, Garrett RA (November 1994). "DNA substrate specificity and cleavage kinetics of an archaeal homing-type endonuclease from Pyrobaculum organotrophum". Nucleic Acids Res. 22 (22): 4583–90. doi:10.1093/nar/22.22.4583. PMC 308504. PMID 7984405.
  19. ^ Dalgaard JZ, Garrett RA (November 1992). "Protein-coding introns from the 23S rRNA-encoding gene form stable circles in the hyperthermophilic archaeon Pyrobaculum organotrophum". Gene. 121 (1): 103–10. doi:10.1016/0378-1119(92)90167-N. PMID 1427083.
  20. ^ a b Szczepanek T, Lazowska J (July 1996). "Replacement of two non-adjacent amino acids in the S.cerevisiae bi2 intron-encoded RNA maturase is sufficient to gain a homing-endonuclease activity". EMBO J. 15 (14): 3758–67. doi:10.1002/j.1460-2075.1996.tb00746.x. PMC 452048. PMID 8670880.
  21. ^ Lazowska J, Szczepanek T, Macadre C, Dokova M (1992). "Two homologous mitochondrial introns from closely related Saccharomyces species differ by only a few amino acid replacements in their Open Reading Frames: one is mobile, the other is not". C. R. Acad. Sci. Paris. 315 (2): 37–41. PMID 1330224.
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  23. ^ Gimble FS, Thorner J (May 1992). "Homing of a DNA endonuclease gene by meiotic gene conversion in Saccharomyces cerevisiae". Nature. 357 (6376): 301–6. Bibcode:1992Natur.357..301G. doi:10.1038/357301a0. PMID 1534148. S2CID 4363512.
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  27. ^ Sargueil B, Delahodde A, Hatat D, Tian GL, Lazowska J, Jacq C (February 1991). "A new specific DNA endonuclease activity in yeast mitochondria". Mol Gen Genet. 225 (2): 340–1. doi:10.1007/BF00269867. PMID 1848651. S2CID 8873378.
  28. ^ Perea J, Desdouets C, Schapria M, Jacq C (January 1993). "I-Sce III: a novel group I intron-encoded endonuclease from the yeast mitochondria". Nucleic Acids Res. 21 (2): 358. doi:10.1093/nar/21.2.358. PMC 309119. PMID 8441645.
  29. ^ Moran JV, Wernette CM, Mecklenburg KL, Butow RA, Perlman PS (August 1992). "Intron 5 alpha of the COXI gene of yeast mitochondrial DNA is a mobile group I intron". Nucleic Acids Res. 20 (15): 4069–76. doi:10.1093/nar/20.15.4069. PMC 334089. PMID 1324475.
  30. ^ Seraphin B, Faye G, Hatat D, Jacq C (April 1992). "The yeast mitochondrial intron aI5 alpha: associated endonuclease activity and in vivo mobility". Gene. 113 (1): 1–8. doi:10.1016/0378-1119(92)90663-A. PMID 1314207.
  31. ^ Liang F, Romanienko PJ, Weaver DT, Jeggo PA, Jasin M (August 1996). "Chromosomal double-strand break repair in Ku80-deficient cells". PNAS. 93 (17): 8929–33. Bibcode:1996PNAS...93.8929L. doi:10.1073/pnas.93.17.8929. PMC 38571. PMID 8799130.
  32. ^ Yang J, Zimmerly S, Perlman PS, Lambowitz AM (May 1996). "Efficient integration of an intron RNA into double-stranded DNA by reverse splicing". Nature. 381 (6580): 332–5. Bibcode:1996Natur.381..332Y. doi:10.1038/381332a0. PMID 8692273. S2CID 4337808.
  33. ^ a b Bell-Pedersen D, Quirk S, Clyman J, Belfort M (July 1990). "Intron mobility in phage T4 is dependent upon a distinctive class of endonucleases and independent of DNA sequences encoding the intron core: mechanistic and evolutionary implications". Nucleic Acids Res. 18 (13): 3763–70. doi:10.1093/nar/18.13.3763. PMC 331075. PMID 2165250.
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  41. ^ Perler FB (January 2002). "InBase: the Intein Database". Nucleic Acids Res. 30 (1): 383–4. doi:10.1093/nar/30.1.383. PMC 99080. PMID 11752343.
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