Homing endonucleases: structure, function and evolution

[1]  M. Belfort,et al.  Crystal structure of the thermostable archaeal intron-encoded endonuclease I-DmoI. , 1999, Journal of molecular biology.

[2]  A. Pingoud,et al.  A similar active site for non–specific and specific endonucleases , 1999, Nature Structural Biology.

[3]  A. Pingoud,et al.  Cleavage experiments with deoxythymidine 3′,5′‐bis‐(p‐nitrophenyl phosphate) suggest that the homing endonuclease I‐PpoI follows the same mechanism of phosphodiester bond hydrolysis as the non‐specific Serratia nuclease 1 , 1999, FEBS letters.

[4]  A. Lambowitz,et al.  18 Group I and Group II Ribozymes as RNPs: Clues to the Past and Guides to the Future , 1999 .

[5]  S. Pietrokovski,et al.  Configuration of the catalytic GIY-YIG domain of intron endonuclease I-TevI: coincidence of computational and molecular findings. , 1999, Nucleic acids research.

[6]  B. Stoddard,et al.  DNA recognition and cleavage by the LAGLIDADG homing endonuclease I-CreI. , 1998, Molecular cell.

[7]  G. Mohr,et al.  Group II intron mobility in yeast mitochondria: target DNA-primed reverse transcription activity of aI1 and reverse splicing into DNA transposition sites in vitro. , 1998, Journal of molecular biology.

[8]  M. Belfort,et al.  Retrohoming of a Bacterial Group II Intron Mobility via Complete Reverse Splicing, Independent of Homologous DNA Recombination , 1998, Cell.

[9]  J. Beintema,et al.  The ribonuclease A superfamily: general discussion , 1998, Cellular and Molecular Life Sciences CMLS.

[10]  M. Emond,et al.  I-PpoI and I-CreI homing site sequence degeneracy determined by random mutagenesis and sequential in vitro enrichment. , 1998, Journal of molecular biology.

[11]  Barry L. Stoddard,et al.  DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI , 1998, Nature.

[12]  A. Gorbalenya,et al.  Non-canonical inteins. , 1998, Nucleic acids research.

[13]  F. Quiocho,et al.  Amino Acid Residues in Both the Protein Splicing and Endonuclease Domains of the PI-SceI Intein Mediate DNA Binding* , 1998, The Journal of Biological Chemistry.

[14]  A. Aggarwal,et al.  Novel site-specific DNA endonucleases. , 1998, Current opinion in structural biology.

[15]  H. Paulus,et al.  Molecular dissection of the Mycobacterium tuberculosis RecA intein: design of a minimal intein and of a trans-splicing system involving two intein fragments. , 1998, Gene.

[16]  R. Raines,et al.  Degenerate DNA recognition by I-PpoI endonuclease. , 1998, Gene.

[17]  S. Pietrokovski,et al.  Modular organization of inteins and C‐terminal autocatalytic domains , 1998, Protein science : a publication of the Protein Society.

[18]  R. Monnat,et al.  Genetic analysis of the Chlamydomonas reinhardtii I-CreI mobile intron homing system in Escherichia coli. , 1997, Genetics.

[19]  B. Stoddard,et al.  Crystallization and preliminary X‐ray studies of I‐PpoI: A nuclear, intron‐encoded homing endonuclease from Physarum polycephalum , 1997, Protein science : a publication of the Protein Society.

[20]  M. Belfort,et al.  A bacterial group II intron encoding reverse transcriptase, maturase, and DNA endonuclease activities: biochemical demonstration of maturase activity and insertion of new genetic information within the intron. , 1997, Genes & development.

[21]  I S Mian,et al.  Statistical modeling and analysis of the LAGLIDADG family of site-specific endonucleases and identification of an intein that encodes a site-specific endonuclease of the HNH family. , 1997, Nucleic acids research.

[22]  M. Belfort,et al.  Genetic definition of a protein-splicing domain: functional mini-inteins support structure predictions and a model for intein evolution. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[23]  J. Wang,et al.  Purification, biochemical characterization and protein-DNA interactions of the I-CreI endonuclease produced in Escherichia coli. , 1997, Nucleic acids research.

[24]  R J Roberts,et al.  Homing endonucleases: keeping the house in order. , 1997, Nucleic acids research.

[25]  R. Waring,et al.  A protein encoded by a group I intron in Aspergillus nidulans directly assists RNA splicing and is a DNA endonuclease. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[26]  Z. Hu,et al.  A DnaB intein in Rhodothermus marinus: indication of recent intein homing across remotely related organisms. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[27]  Monique Turmel,et al.  Evolutionarily conserved and functionally important residues in the I- CeuI homing endonuclease , 1997, Nucleic Acids Res..

[28]  B. Stoddard,et al.  The structure of I-Crel, a Group I intron-encoded homing endonuclease , 1997, Nature Structural Biology.

[29]  F. Quiocho,et al.  Crystal Structure of PI-SceI, a Homing Endonuclease with Protein Splicing Activity , 1997, Cell.

[30]  A. Jeltsch,et al.  Recognition and cleavage of DNA by type-II restriction endonucleases. , 1997, European journal of biochemistry.

[31]  R. Garrett,et al.  Profile of the DNA recognition site of the archaeal homing endonuclease I-DmoI. , 1997, Nucleic acids research.

[32]  D. Norris,et al.  Ho Endonuclease Cleaves MAT DNA in Vitro by an Inefficient Stoichiometric Reaction Mechanism* , 1997, The Journal of Biological Chemistry.

[33]  S. Kent,et al.  Protein splicing: occurrence, mechanisms and related phenomena. , 1997, Chemistry & biology.

[34]  M. Belfort,et al.  Two-domain structure of the td intron-encoded endonuclease I-TevI correlates with the two-domain configuration of the homing site. , 1997, Journal of molecular biology.

[35]  J. Wang,et al.  Substrate recognition and induced DNA distortion by the PI-SceI endonuclease, an enzyme generated by protein splicing. , 1996, Journal of molecular biology.

[36]  T. Szczepanek,et al.  Replacement of two non‐adjacent amino acids in the S.cerevisiae bi2 intron‐encoded RNA maturase is sufficient to gain a homing‐endonuclease activity. , 1996, The EMBO journal.

[37]  C. Shearman,et al.  Splicing of a group II intron in a functional transfer gene of Lactococcus lactis , 1996, Molecular microbiology.

[38]  A. Pingoud,et al.  Analysis of the mechanism of the Serratia nuclease using site-directed mutagenesis. , 1996, Nucleic acids research.

[39]  D. Mills,et al.  Splicing of a group II intron involved in the conjugative transfer of pRS01 in lactococci , 1996, Journal of bacteriology.

[40]  Alan M. Lambowitz,et al.  Efficient integration of an intron RNA into double-stranded DNA by reverse splicing , 1996, Nature.

[41]  J. E. Mueller,et al.  Intron mobility in phage T4 occurs in the context of recombination-dependent DNA replication by way of multiple pathways. , 1996, Genes & development.

[42]  H. Goodrich-Blair,et al.  Beyond Homing: Competition between Intron Endonucleases Confers a Selective Advantage on Flanking Genetic Markers , 1996, Cell.

[43]  R. Raines,et al.  Substrate binding and turnover by the highly specific I-PpoI endonuclease. , 1996, Biochemistry.

[44]  K. Weeks,et al.  Assembly of a Ribonucleoprotein Catalyst by Tertiary Structure Capture , 1996, Science.

[45]  M. Belfort,et al.  Retrohoming: cDNA-Mediated Mobility of Group II Introns Requires a Catalytic RNA , 1996, Cell.

[46]  M. Belfort,et al.  Mechanisms of Intron Mobility (*) , 1995, The Journal of Biological Chemistry.

[47]  A. Lambowitz,et al.  A group II intron RNA is a catalytic component of a DNA endonuclease involved in intron mobility , 1995, Cell.

[48]  J. E. Mueller,et al.  Intron‐encoded endonuclease I‐TevI binds as a monomer to effect sequential cleavage via conformational changes in the td homing site. , 1995, The EMBO journal.

[49]  A. Lewin,et al.  Protein-induced Folding of a Group I Intron in Cytochrome b Pre-mRNA (*) , 1995, The Journal of Biological Chemistry.

[50]  T. Stevens,et al.  Protein splicing: self-splicing of genetically mobile elements at the protein level. , 1995, Trends in biochemical sciences.

[51]  P. Perlman,et al.  Group II intron mobility occurs by target DNA-primed reverse transcription , 1995, Cell.

[52]  M. Belfort,et al.  Prokaryotic introns and inteins: a panoply of form and function , 1995, Journal of bacteriology.

[53]  J. V. Moran,et al.  Mobile group II introns of yeast mitochondrial DNA are novel site-specific retroelements , 1995, Molecular and cellular biology.

[54]  J. E. Mueller,et al.  Selection of a remote cleavage site by I-tevI, the td intron-encoded endonuclease. , 1995, Journal of molecular biology.

[55]  Frederick S. Gimble,et al.  Substitutions in Conserved Dodecapeptide Motifs That Uncouple the DNA Binding and DNA Cleavage Activities of PI-SceI Endonuclease (*) , 1995, The Journal of Biological Chemistry.

[56]  A. Aggarwal,et al.  Structure and function of restriction endonucleases. , 1995, Current opinion in structural biology.

[57]  F. Michel,et al.  Structure and activities of group II introns. , 1995, Annual review of biochemistry.

[58]  S. Pietrokovski,et al.  Conserved sequence features of inteins (protein introns) and their use in identifying new inteins and related proteins , 1994, Protein science : a publication of the Protein Society.

[59]  R. Garrett,et al.  Purification and characterization of two forms of I-DmoI, a thermophilic site-specific endonuclease encoded by an archaeal intron. , 1994, The Journal of biological chemistry.

[60]  R. Garrett,et al.  DNA substrate specificity and cleavage kinetics of an archaeal homing-type endonuclease from Pyrobaculum organotrophum. , 1994, Nucleic acids research.

[61]  S. Eddy,et al.  Amino acid sequence motif of group I intron endonucleases is conserved in open reading frames of group II introns. , 1994, Trends in biochemical sciences.

[62]  B. Meunier,et al.  Homing of a group II intron in yeast mitochondrial DNA is accompanied by unidirectional co‐conversion of upstream‐located markers. , 1994, The EMBO journal.

[63]  A. Gorbalenya.  Self‐splicing group I and group II introns encode homologous (putative) DNA endonucleases of a new family , 1994, Protein science : a publication of the Protein Society.

[64]  Mitchell D. Miller,et al.  2.1 Å structure of Serratia endonuclease suggests a mechanism for binding to double-stranded DNA , 1994, Nature Structural Biology.

[65]  V. Vogt,et al.  Interaction of the intron-encoded mobility endonuclease I-PpoI with its target site , 1993, Molecular and cellular biology.

[66]  S. Johansen,et al.  A family of nuclear homing endonucleases. , 1993, Nucleic acids research.

[67]  B. Dujon,et al.  Asymmetrical recognition and activity of the I‐SceI endonuclease on its site and on intron‐exon junctions. , 1993, The EMBO journal.

[68]  R. Garrett,et al.  A site-specific endonuclease encoded by a typical archaeal intron. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[69]  The td intron endonuclease I‐TevI makes extensive sequence‐tolerant contacts across the minor groove of its DNA target. , 1993, The EMBO journal.

[70]  J. V. Moran,et al.  Reverse transcriptase activity associated with maturase-encoding group II introns in yeast mitochondria , 1993, Cell.

[71]  M. Belfort,et al.  4 Homing Endonucleases , 1993 .

[72]  M. Belfort,et al.  Introns as mobile genetic elements. , 1993, Annual review of biochemistry.

[73]  W. Kudlicki,et al.  Cleavage and recognition pattern of a double-strand-specific endonuclease (I-creI) encoded by the chloroplast 23S rRNA intron of Chlamydomonas reinhardtii. , 1992, Gene.

[74]  A. Lambowitz,et al.  A tyrosyl-tRNA synthetase binds specifically to the group I intron catalytic core. , 1992, Genes & development.

[75]  M. Belfort,et al.  Trans and cis requirements for intron mobility in a prokaryotic system. , 1992, Genes & development.

[76]  J. Rochaix,et al.  Chloroplast ribosomal intron of Chlamydomonas reinhardtii: in vitro self‐splicing, DNA endonuclease activity and in vivo mobility. , 1991, The EMBO journal.

[77]  I-TevI, the endonuclease encoded by the mobile td intron, recognizes binding and cleavage domains on its DNA target. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[78]  L. Gold,et al.  The phage T4 nrdB intron: a deletion mutant of a version found in the wild. , 1991, Genes & development.

[79]  C. M. Joyce,et al.  The 3′‐5′ exonuclease of DNA polymerase I of Escherichia coli: contribution of each amino acid at the active site to the reaction. , 1991, The EMBO journal.

[80]  G. Schmidt,et al.  RNA splicing in Chlamydomonas chloroplasts. Self-splicing of 23 S preRNA. , 1990, The Journal of biological chemistry.

[81]  P. Kane,et al.  Protein splicing converts the yeast TFP1 gene product to the 69-kD subunit of the vacuolar H(+)-adenosine triphosphatase. , 1990, Science.

[82]  A. Lambowitz,et al.  Involvement of aminoacyl-tRNA synthetases and other proteins in group I and group II intron splicing. , 1990, Trends in biochemical sciences.

[83]  V. Vogt,et al.  Characterization of I-Ppo, an intron-encoded endonuclease that mediates homing of a group I intron in the ribosomal DNA of Physarum polycephalum , 1990, Molecular and cellular biology.

[84]  J. Nickoloff,et al.  In vivo analysis of the Saccharomyces cerevisiae HO nuclease recognition site by site-directed mutagenesis , 1990, Molecular and cellular biology.

[85]  B. Dujon,et al.  Group I introns as mobile genetic elements: facts and mechanistic speculations--a review. , 1989, Gene.

[86]  M. Belfort,et al.  A site-specific endonuclease and co-conversion of flanking exons associated with the mobile td intron of phage T4. , 1989, Gene.

[87]  R. Saldanha,et al.  A latent intron-encoded maturase is also an endonuclease needed for intron mobility , 1989, Cell.

[88]  V. Vogt,et al.  A mobile group I intron in the nuclear rDNA of physarum polycephalum , 1989, Cell.

[89]  M. Belfort,et al.  Intron mobility in the T-even phages: High frequency inheritance of group I introns promoted by intron open reading frames , 1989, Cell.

[90]  M. Belfort,et al.  The inconsistent distribution of introns in the T-even phages indicates recent genetic exchanges. , 1989, Nucleic acids research.

[91]  B. Dujon,et al.  Recognition and cleavage site of the intron-encoded omega transposase. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[92]  B. Dujon,et al.  Universal code equivalent of a yeast mitochondrial intron reading frame is expressed into E. coli as a specific double strand endonuclease , 1986, Cell.

[93]  A. Zinn,et al.  Transposition of an intron in yeast mitochondria requires a protein encoded by that intron , 1985, Cell.

[94]  Bernard Dujon,et al.  An intron-encoded protein is active in a gene conversion process that spreads an intron into a mitochondrial gene , 1985, Cell.

[95]  K. Shinozaki,et al.  Tobacco chloroplast tRNA(UUU) gene contains a 2.5-kilobase-pair intron: An open reading frame and a conserved boundary sequence in the intron. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[96]  A. Zinn,et al.  Nonreciprocal exchange between alleles of the yeast mitochondrial 21S rRNA gene: Kinetics and the involvement of a double-strand break , 1985, Cell.

[97]  M. Rahire,et al.  The chloroplast ribosomal intron of Chlamydomonas reinhardii codes for a polypeptide related to mitochondrial maturases. , 1985, Nucleic acids research.

[98]  C. Jacq,et al.  Single base substitution in an intron of oxidase gene compensates splicing defects of the cytochrome b gene , 1982, Nature.

[99]  G. Coruzzi,et al.  Assembly of the mitochondrial membrane system. Structure and nucleotide sequence of the gene coding for subunit 1 of yeast cytochrme oxidase. , 1980, The Journal of biological chemistry.

[100]  C. Jacq,et al.  Sequence of introns and flanking exons in wild-type and box3 mutants of cytochrome b reveals an interlaced splicing protein coded by an intron , 1980, Cell.

[101]  B. Dujon.  Sequence of the intron and flanking exons of the mitochondrial 21S rRNA gene of yeast strains having different alleles at the ω and rib-1 loci , 1980, Cell.

[102]  L. Grivell,et al.  Mutations affecting RNA splicing and the interaction of gene expression of the yeast mitochondrial loci cob and oxi-3 , 1980, Cell.

[103]  C. Heyting,et al.  An insert in the single gene for the large ribosomal RNA in yeast mitochondrial DNA , 1978, Nature.

[104]  P. Slonimski,et al.  Mitochondrial genetics. I. Methodology and phenomenology. , 1970, Symposia of the Society for Experimental Biology.