Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (330K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (244)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Belfort, M.
Right arrow Articles by Roberts, R. J.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Belfort, M.
Right arrow Articles by Roberts, R. J.
Social Bookmarking
 Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, Vol 25, Issue 17 3379-3388, Copyright © 1997 by Oxford University Press


REVIEWS

Homing endonucleases: keeping the house in order

M Belfort and RJ Roberts
Molecular Genetics Program, Wadsworth Center, New York State Department of Health, and School of Public Health, State University of New York at Albany, PO Box 22002, Albany, New York 12201-2002, USA. marlene.belfort@wadsworth.org

Homing endonucleases are rare-cutting enzymes encoded by introns and inteins. They have striking structural and functional properties that distinguish them from restriction enzymes. Nomenclature conventions analogous to those for restriction enzymes have been developed for the homing endonucleases. Recent progress in understanding the structure and function of the four families of homing enzymes is reviewed. Of particular interest are the first reported structures of homing endonucleases of the LAGLIDADG family. The exploitation of the homing enzymes in genome analysis and recombination research is also summarized. Finally, the evolution of homing endonucleases is considered, both at the structure-function level and in terms of their persistence in widely divergent biological systems.
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
Proc. Natl. Acad. Sci. USAHome page
G. Gao, C. McMahon, J. Chen, and Y. S. Rong
A powerful method combining homologous recombination and site-specific recombination for targeted mutagenesis in Drosophila
PNAS, September 16, 2008; 105(37): 13999 - 14004.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
V. S. Brok-Volchanskaya, F. A. Kadyrov, D. E. Sivogrivov, P. M. Kolosov, A. S. Sokolov, M. G. Shlyapnikov, V. M. Kryukov, and I. E. Granovsky
Phage T4 SegB protein is a homing endonuclease required for the preferred inheritance of T4 tRNA gene region occurring in co-infection with a related phage
Nucleic Acids Res., April 1, 2008; 36(6): 2094 - 2105.
[Abstract] [Full Text] [PDF]


Home page
J. Biol. Chem.Home page
J. Prieto, J.-C. Epinat, P. Redondo, E. Ramos, D. Padro, F. Cedrone, G. Montoya, F. Paques, and F. J. Blanco
Generation and Analysis of Mesophilic Variants of the Thermostable Archaeal I-DmoI Homing Endonuclease
J. Biol. Chem., February 15, 2008; 283(7): 4364 - 4374.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
D. Nord and B.-M. Sjoberg
Unconventional GIY-YIG homing endonuclease encoded in group I introns in closely related strains of the Bacillus cereus group
Nucleic Acids Res., January 17, 2008; 36(1): 300 - 310.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
J. L. Eklund, U. Y. Ulge, J. Eastberg, and R. J. Monnat Jr
Altered target site specificity variants of the I-PpoI His-Cys box homing endonuclease
Nucleic Acids Res., September 27, 2007; 35(17): 5839 - 5850.
[Abstract] [Full Text] [PDF]


Home page
J. Bacteriol.Home page
D. Nord, E. Torrents, and B.-M. Sjoberg
A Functional Homing Endonuclease in the Bacillus anthracis nrdE Group I Intron
J. Bacteriol., July 15, 2007; 189(14): 5293 - 5301.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
J. B. Robbins, M. Stapleton, M. J. Stanger, D. Smith, J. T. Dansereau, V. Derbyshire, and M. Belfort
Homing endonuclease I-TevIII: dimerization as a means to a double-strand break
Nucleic Acids Res., March 12, 2007; 35(5): 1589 - 1600.
[Abstract] [Full Text] [PDF]


Home page
J. Bacteriol.Home page
A. Daniel, P. E. Bonnen, and V. A. Fischetti
First Complete Genome Sequence of Two Staphylococcus epidermidis Bacteriophages
J. Bacteriol., March 1, 2007; 189(5): 2086 - 2100.
[Abstract] [Full Text] [PDF]


Home page
J. Bacteriol.Home page
Q. Meng, Y. Zhang, and X.-Q. Liu
Rare Group I Intron with Insertion Sequence Element in a Bacterial Ribonucleotide Reductase Gene
J. Bacteriol., March 1, 2007; 189(5): 2150 - 2154.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
L. E. Rosen, H. A. Morrison, S. Masri, M. J. Brown, B. Springstubb, D. Sussman, B. L. Stoddard, and L. M. Seligman
Homing endonuclease I-CreI derivatives with novel DNA target specificities
Nucleic Acids Res., October 18, 2006; 34(17): 4791 - 4800.
[Abstract] [Full Text] [PDF]


Home page
Mol. Cell. Biol.Home page
F. Storici, J. R. Snipe, G. K. Chan, D. A. Gordenin, and M. A. Resnick
Conservative Repair of a Chromosomal Double-Strand Break by Single-Strand DNA through Two Steps of Annealing
Mol. Cell. Biol., October 15, 2006; 26(20): 7645 - 7657.
[Abstract] [Full Text] [PDF]


Home page
Eukaryot CellHome page
T. Fukuda, K. Ohta, and Y. Ohya
Investigation of the Mechanism of Meiotic DNA Cleavage by VMA1-Derived Endonuclease Uncovers a Meiotic Alteration in Chromatin Structure around the Target Site
Eukaryot. Cell, June 1, 2006; 5(6): 981 - 990.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
P. Chames, J.-C. Epinat, S. Guillier, A. Patin, E. Lacroix, and F. Paques
In vivo selection of engineered homing endonucleases using double-strand break induced homologous recombination
Nucleic Acids Res., November 23, 2005; 33(20): e178 - e178.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
L. Sandegren, D. Nord, and B.-M. Sjoberg
SegH and Hef: two novel homing endonucleases whose genes replace the mobC and mobE genes in several T4-related phages
Nucleic Acids Res., October 27, 2005; 33(19): 6203 - 6213.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
Z. Chen and H. Zhao
A highly sensitive selection method for directed evolution of homing endonucleases
Nucleic Acids Res., October 6, 2005; 33(18): e154 - e154.
[Abstract] [Full Text] [PDF]


Home page
J. Biol. Chem.Home page
M. Ghosh, G. Meiss, A. Pingoud, R. E. London, and L. C. Pedersen
Structural Insights into the Mechanism of Nuclease A, a {beta}{beta}{alpha} Metal Nuclease from Anabaena
J. Biol. Chem., July 29, 2005; 280(30): 27990 - 27997.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
N. Nomura, Y. Morinaga, N. Shirai, and Y. Sako
I-ApeI: a novel intron-encoded LAGLIDADG homing endonuclease from the archaeon, Aeropyrum pernix K1
Nucleic Acids Res., July 26, 2005; 33(13): e116 - e116.
[Abstract] [Full Text] [PDF]


Home page
Appl. Environ. Microbiol.Home page
K. Nagasaki, Y. Shirai, Y. Tomaru, K. Nishida, and S. Pietrokovski
Algal Viruses with Distinct Intraspecies Host Specificities Include Identical Intein Elements
Appl. Envir. Microbiol., July 1, 2005; 71(7): 3599 - 3607.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
A. B. Birgisdottir and S. Johansen
Site-specific reverse splicing of a HEG-containing group I intron in ribosomal RNA
Nucleic Acids Res., April 7, 2005; 33(6): 2042 - 2051.
[Abstract] [Full Text] [PDF]


Home page
Proc. Natl. Acad. Sci. USAHome page
K. I. Pyatkov, I. R. Arkhipova, N. V. Malkova, D. J. Finnegan, and M. B. Evgen'ev
Reverse transcriptase and endonuclease activities encoded by Penelope-like retroelements
PNAS, October 12, 2004; 101(41): 14719 - 14724.
[Abstract] [Full Text] [PDF]


Home page
J. Bacteriol.Home page
X.-Q. Liu and J. Yang
Bacterial Thymidylate Synthase with Intein, Group II Intron, and Distinctive ThyX Motifs
J. Bacteriol., September 15, 2004; 186(18): 6316 - 6319.
[Abstract] [Full Text] [PDF]


Home page
J. Biol. Chem.Home page
B. Dassa, H. Haviv, G. Amitai, and S. Pietrokovski
Protein Splicing and Auto-cleavage of Bacterial Intein-like Domains Lacking a C'-flanking Nucleophilic Residue
J. Biol. Chem., July 30, 2004; 279(31): 32001 - 32007.
[Abstract] [Full Text] [PDF]


Home page
J. Bacteriol.Home page
M. Landthaler, N. C. Lau, and David. A. Shub
Group I Intron Homing in Bacillus Phages SPO1 and SP82: a Gene Conversion Event Initiated by a Nicking Homing Endonuclease
J. Bacteriol., July 1, 2004; 186(13): 4307 - 4314.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
G. H. Silva and M. Belfort
Analysis of the LAGLIDADG interface of the monomeric homing endonuclease I-DmoI
Nucleic Acids Res., June 9, 2004; 32(10): 3156 - 3168.
[Abstract] [Full Text] [PDF]


Home page
Eukaryot CellHome page
J. D. Wuitschick, P. R. Lindstrom, A. E. Meyer, and K. M. Karrer
Homing Endonucleases Encoded by Germ Line-Limited Genes in Tetrahymena thermophila Have APETELA2 DNA Binding Domains
Eukaryot. Cell, June 1, 2004; 3(3): 685 - 694.
[Abstract] [Full Text] [PDF]


Home page
J. Biol. Chem.Home page
L. Sandegren and B.-M. Sjoberg
Distribution, Sequence Homology, and Homing of Group I Introns among T-even-like Bacteriophages: EVIDENCE FOR RECENT TRANSFER OF OLD INTRONS
J. Biol. Chem., May 21, 2004; 279(21): 22218 - 22227.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
P. Haugen and D. Bhattacharya
The spread of LAGLIDADG homing endonuclease genes in rDNA
Nucleic Acids Res., April 6, 2004; 32(6): 2049 - 2057.
[Abstract] [Full Text] [PDF]


Home page
J. Biol. Chem.Home page
A.-J. Noel, W. Wende, and A. Pingoud
DNA Recognition by the Homing Endonuclease PI-SceI Involves a Divalent Metal Ion Cofactor-induced Conformational Change
J. Biol. Chem., February 20, 2004; 279(8): 6794 - 6804.
[Abstract] [Full Text] [PDF]


Home page
GeneticsHome page
A. Bakhrat, M. S. Jurica, B. L. Stoddard, and D. Raveh
Homology Modeling and Mutational Analysis of Ho Endonuclease of Yeast
Genetics, February 1, 2004; 166(2): 721 - 728.
[Abstract] [Full Text] [PDF]


Home page
Mol Biol EvolHome page
P. Haugen, V. Reeb, F. Lutzoni, and D. Bhattacharya
The Evolution of Homing Endonuclease Genes and Group I Introns in Nuclear rDNA
Mol. Biol. Evol., January 1, 2004; 21(1): 129 - 140.
[Abstract] [Full Text] [PDF]


Home page
Proc. Natl. Acad. Sci. USAHome page
F. Storici, C. L. Durham, D. A. Gordenin, and M. A. Resnick
Chromosomal site-specific double-strand breaks are efficiently targeted for repair by oligonucleotides in yeast
PNAS, December 9, 2003; 100(25): 14994 - 14999.
[Abstract] [Full Text] [PDF]


Home page
J. Biol. Chem.Home page
L. Kaplun, Y. Ivantsiv, A. Bakhrat, and D. Raveh
DNA Damage Response-mediated Degradation of Ho Endonuclease via the Ubiquitin System Involves Its Nuclear Export
J. Biol. Chem., December 5, 2003; 278(49): 48727 - 48734.
[Abstract] [Full Text] [PDF]


Home page
Genes Dev.Home page
M. Belfort
Two for the price of one: a bifunctional intron-encoded DNA endonuclease-RNA maturase
Genes & Dev., December 1, 2003; 17(23): 2860 - 2863.
[Full Text] [PDF]


Home page
Genes Dev.Home page
J. M. Bolduc, P. C. Spiegel, P. Chatterjee, K. L. Brady, M. E. Downing, M. G. Caprara, R. B. Waring, and B. L. Stoddard
Structural and biochemical analyses of DNA and RNA binding by a bifunctional homing endonuclease and group I intron splicing factor
Genes & Dev., December 1, 2003; 17(23): 2875 - 2888.
[Abstract] [Full Text] [PDF]


Home page
J. Biol. Chem.Home page
X.-Q. Liu, J. Yang, and Q. Meng
Four Inteins and Three Group II Introns Encoded in a Bacterial Ribonucleotide Reductase Gene
J. Biol. Chem., November 21, 2003; 278(47): 46826 - 46831.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
N. Guhan and K. Muniyappa
Mycobacterium tuberculosis RecA intein, a LAGLIDADG homing endonuclease, displays Mn2+ and DNA-dependent ATPase activity
Nucleic Acids Res., July 15, 2003; 31(14): 4184 - 4191.
[Abstract] [Full Text] [PDF]


Home page
J. Biol. Chem.Home page
X.-Q. Liu and J. Yang
Split dnaE Genes Encoding Multiple Novel Inteins in Trichodesmium erythraeum
J. Biol. Chem., July 11, 2003; 278(29): 26315 - 26318.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
M. Landthaler and D. A. Shub
The nicking homing endonuclease I-BasI is encoded by a group I intron in the DNA polymerase gene of the Bacillus thuringiensis phage Bastille
Nucleic Acids Res., June 15, 2003; 31(12): 3071 - 3077.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
R. B. Langkjaer, S. Casaregola, D. W. Ussery, C. Gaillardin, and J. Piskur
Sequence analysis of three mitochondrial DNA molecules reveals interesting differences among Saccharomyces yeasts
Nucleic Acids Res., June 15, 2003; 31(12): 3081 - 3091.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
J.-C. Epinat, S. Arnould, P. Chames, P. Rochaix, D. Desfontaines, C. Puzin, A. Patin, A. Zanghellini, F. Paques, and E. Lacroix
A novel engineered meganuclease induces homologous recombination in yeast and mammalian cells
Nucleic Acids Res., June 1, 2003; 31(11): 2952 - 2962.
[Abstract] [Full Text] [PDF]


Home page
Proc. Natl. Acad. Sci. USAHome page
L. Lin, Y.-G. Liu, X. Xu, and B. Li
Efficient linking and transfer of multiple genes by a multigene assembly and transformation vector system
PNAS, May 13, 2003; 100(10): 5962 - 5967.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
G. Burger, B. F. Lang, H.-P. Braun, and S. Marx
The enigmatic mitochondrial ORF ymf39 codes for ATP synthase chain b
Nucleic Acids Res., May 1, 2003; 31(9): 2353 - 2360.
[Abstract] [Full Text] [PDF]


Home page
Proc. Natl. Acad. Sci. USAHome page
R. Seshadri, I. T. Paulsen, J. A. Eisen, T. D. Read, K. E. Nelson, W. C. Nelson, N. L. Ward, H. Tettelin, T. M. Davidsen, M. J. Beanan, et al.
Complete genome sequence of the Q-fever pathogen Coxiellaburnetii
PNAS, April 29, 2003; 100(9): 5455 - 5460.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
R. J. Roberts, M. Belfort, T. Bestor, A. S. Bhagwat, T. A. Bickle, J. Bitinaite, R. M. Blumenthal, S. Kh. Degtyarev, D. T. F. Dryden, K. Dybvig, et al.
A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes
Nucleic Acids Res., April 1, 2003; 31(7): 1805 - 1812.
[Abstract] [Full Text] [PDF]


Home page
Microbiol. Mol. Biol. Rev.Home page
E. S. Miller, E. Kutter, G. Mosig, F. Arisaka, T. Kunisawa, and W. Ruger
Bacteriophage T4 Genome
Microbiol. Mol. Biol. Rev., March 1, 2003; 67(1): 86 - 156.
[Abstract] [Full Text] [PDF]


Home page
J. Biol. Chem.Home page
N. Guhan and K. Muniyappa
The RecA Intein of Mycobacterium tuberculosis Promotes Cleavage of Ectopic DNA Sites. IMPLICATIONS FOR THE DISPERSAL OF INTEINS IN NATURAL POPULATIONS
J. Biol. Chem., October 18, 2002; 277(43): 40352 - 40361.
[Abstract] [Full Text] [PDF]


Home page
GeneticsHome page
V. Shcherbakov, I. Granovsky, L. Plugina, T. Shcherbakova, S. Sizova, K. Pyatkov, M. Shlyapnikov, and O. Shubina
Focused Genetic Recombination of Bacteriophage T4 Initiated by Double-Strand Breaks
Genetics, October 1, 2002; 162(2): 543 - 556.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
E. Werner, W. Wende, A. Pingoud, and U. Heinemann
High resolution crystal structure of domain I of the Saccharomyces cerevisiae homing endonuclease PI-SceI
Nucleic Acids Res., September 15, 2002; 30(18): 3962 - 3971.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
L. M. Seligman, K. M. Chisholm, B. S. Chevalier, M. S. Chadsey, S. T. Edwards, J. H. Savage, and A. L. Veillet
Mutations altering the cleavage specificity of a homing endonuclease
Nucleic Acids Res., September 1, 2002; 30(17): 3870 - 3879.
[Abstract] [Full Text] [PDF]


Home page
Proc. Natl. Acad. Sci. USAHome page
A. B. Dean, M. J. Stanger, J. T. Dansereau, P. Van Roey, V. Derbyshire, and M. Belfort
Inaugural Article: Zinc finger as distance determinant in the flexible linker of intron endonuclease I-TevI
PNAS, June 25, 2002; 99(13): 8554 - 8561.
[Abstract] [Full Text] [PDF]


Home page
J. Biol. Chem.Home page
N. Guhan and K. Muniyappa
Mycobacterium tuberculosis RecA Intein Possesses a Novel ATP-dependent Site-specific Double-stranded DNA Endonuclease Activity
J. Biol. Chem., May 3, 2002; 277(18): 16257 - 16264.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
M. Landthaler, U. Begley, N. C. Lau, and D. A. Shub
Two self-splicing group I introns in the ribonucleotide reductase large subunit gene of Staphylococcus aureus phage Twort
Nucleic Acids Res., May 1, 2002; 30(9): 1935 - 1943.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
M. Gruen, K. Chang, I. Serbanescu, and D. R. Liu
An in vivo selection system for homing endonuclease activity
Nucleic Acids Res., April 1, 2002; 30(7): e29 - e29.
[Abstract] [Full Text] [PDF]


Home page
Mol Biol EvolHome page
V. Koufopanou, M. R. Goddard, and A. Burt
Adaptation for Horizontal Transfer in a Homing Endonuclease
Mol. Biol. Evol., March 1, 2002; 19(3): 239 - 246.
[Abstract] [Full Text] [PDF]


Home page
Genes Dev.Home page
A. Belle, M. Landthaler, and D. A. Shub
Intronless homing: site-specific endonuclease SegF of bacteriophage T4 mediates localized marker exclusion analogous to homing endonucleases of group I introns
Genes & Dev., February 1, 2002; 16(3): 351 - 362.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
F. B. Perler
InBase: the Intein Database
Nucleic Acids Res., January 1, 2002; 30(1): 383 - 384.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
F. Li and D. L. Herrin
FUGOID: functional genomics of organellar introns database
Nucleic Acids Res., January 1, 2002; 30(1): 385 - 386.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
F. S. Gimble
Degeneration of a homing endonuclease and its target sequence in a wild yeast strain
Nucleic Acids Res., October 15, 2001; 29(20): 4215 - 4223.
[Abstract] [Full Text] [PDF]


Home page
Protein Eng Des SelHome page
J. M. Bujnicki, P. Rotkiewicz, A. Kolinski, and L. Rychlewski
Three-dimensional modeling of the I-TevI homing endonuclease catalytic domain, a GIY-YIG superfamily member, using NMR restraints and Monte Carlo dynamics
Protein Eng. Des. Sel., October 1, 2001; 14(10): 717 - 721.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
B. S. Chevalier and B. L. Stoddard
Homing endonucleases: structural and functional insight into the catalysts of intron/intein mobility
Nucleic Acids Res., September 15, 2001; 29(18): 3757 - 3774.
[Abstract]