Mobile Introns: Pathways and Proteins

Marlene Belfort; Victoria Derbyshire; Monica M. Parker; Benoit Cousineau; Alan M. Lambowitz

doi:10.1128/9781555817954.ch31

Chapter 31 : Mobile Introns: Pathways and Proteins

Authors: Marlene Belfort¹, Victoria Derbyshire¹, Monica M. Parker¹, Benoit Cousineau², Alan M. Lambowitz³

VIEW AFFILIATIONS HIDE AFFILIATIONS

Affiliations: 1: Molecular Genetics Program, Wadsworth Center, New York State Department of Health and School of Public Health, State University of New York at Albany, Albany, NY 12201-2002; 2: Department of Microbiology and Immunology, McGill University, Montreal, Québec H3A 2B4, Canada; 3: Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry, Section of Molecular Genetics and Microbiology, School of Biological Sciences, University of Texas at Austin, Austin, TX 78712

Content Type: Monograph

Publication Year: 2002

Category: Microbial Genetics and Molecular Biology

Book DOI: 10.1128/9781555817954

Chapter DOI: 10.1128/9781555817954.ch31

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:

Mobile Introns: Pathways and Proteins, Page 1 of 2

< Previous page | Next page > /docserver/preview/fulltext/10.1128/9781555817954/9781555812096_Chap31-1.gif /docserver/preview/fulltext/10.1128/9781555817954/9781555812096_Chap31-2.gif

Abstract:

While the role of group I and group II intron-encoded proteins in homing has been well defined, the function of these proteins in intron dissemination to new sites remains the subject of intense study. These mobile introns, their intron-encoded proteins, and the mechanisms by which mobility occurs are the subject of this chapter. Although transition metals are not required for colicin DNase activity, it is likely that they play a stabilizing role related to the membrane translocation that must occur for colicin’s biological function. These data lend credence to the idea that the HNH domain, like the GIY-YIG domain, is an endonu clease cassette that can become associated with other protein domains to form multifunctional proteins. The open reading frames (ORFs) specifying group II intron-encoded proteins, when present, are located in the loop region of the structural domain IV, with most of the coding sequence outside the intron catalytic core. Of the three activities of the group II intron-encoded proteins, the maturase domain is present in all known cases. Endonuclease activity of an intron-encoded protein was first shown for the yeast mtDNA introns aI1 and aI2. Group I and group II introns are self-splicing elements with wide genomic distribution, reflecting their dispersal through active mobility mechanisms. These two types of introns represent different ways in which selfish elements exploit functions that promote their invasiveness. Basic research into the structure and function of intron-encoded proteins and of the dynamics of mobility pathways is yielding a refined view of their modus operandi.

Citation: Belfort M, Derbyshire V, Parker M, Cousineau B, Lambowitz A. 2002. Mobile Introns: Pathways and Proteins, p 761-783. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch31

Highlighted Text: Show | Hide

Full text loading...

Figures

Mobile Introns: Pathways and Proteins

[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555817954.chap31-1,webId=/content/author/10.1128/9781555817954.chap31-1,properties={foaf_givenname=Marlene, foaf_name=Marlene Belfort, foaf_surname=Belfort, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555817954.chap31-aff1]]}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555817954.chap31-2,webId=/content/author/10.1128/9781555817954.chap31-2,properties={foaf_givenname=Victoria, foaf_name=Victoria Derbyshire, foaf_surname=Derbyshire, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555817954.chap31-aff1]]}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555817954.chap31-3,webId=/content/author/10.1128/9781555817954.chap31-3,properties={foaf_givenname=Monica M., foaf_name=Monica M. Parker, foaf_surname=Parker, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555817954.chap31-aff1]]}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555817954.chap31-4,webId=/content/author/10.1128/9781555817954.chap31-4,properties={foaf_givenname=Benoit, foaf_name=Benoit Cousineau, foaf_surname=Cousineau, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555817954.chap31-aff2]]}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555817954.chap31-5,webId=/content/author/10.1128/9781555817954.chap31-5,properties={foaf_givenname=Alan M., foaf_name=Alan M. Lambowitz, foaf_surname=Lambowitz, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555817954.chap31-aff3]]}]]

/content/10.1128/9781555817954.chap31.fig31-1

Figure 1

Intron splicing pathways and structures. Introns are grouped according to splicing pathway. The intron structures shown correspond to the intron type that appears on a grey background.

10.1128/9781555817954/fig31-1_thmb.gif

10.1128/9781555817954/fig31-1.gif

Figure 1

Intron splicing pathways and structures. Introns are grouped according to splicing pathway. The intron structures shown correspond to the intron type that appears on a grey background.

/content/10.1128/9781555817954.chap31.fig31-3

Figure 3

Group II intron RNP. (A) Domains of intron-encoded proteins. Abbreviations: M, maturase; E, endonuclease; Z, conserved domain adjacent to RT. (B) The RNPbound to DNA. Abbreviations, IS, intron insertion site; CS, protein cleavage site. The intron and exon binding site interactions (IBS-EBS and δ-δ′) are defined in the text. (C) Critical target residues. The intron insertion site is marked by a downward-directed arrow, and the protein cleavage site is marked by an upward-directed arrow. Critical residues for protein recognition are shown as white letters on a black background, and important but noncritical residues are boxed.

10.1128/9781555817954/fig31-3_thmb.gif

10.1128/9781555817954/fig31-3.gif

Figure 3

/content/10.1128/9781555817954.chap31.fig31-2

Figure 2

Group I intron homing pathways. After cleavage of the recipient and exonucleolytic degradation (step 1), 3′ends of the cleaved recipient invade the intron donor allele (step 2). Thereafter, either the DSBRor synthesis-dependent strand annealing (SDSA) pathways can be followed (steps 3 to 6) as shown and described in the text. The dumbbell represents intron endonuclease, I-TevI. The intron is shown in black; grey horizontal arrows indicate exonucleolytic degradation.

10.1128/9781555817954/fig31-2_thmb.gif

10.1128/9781555817954/fig31-2.gif

Figure 2

References

/content/book/10.1128/9781555817954.chap31

1. Abelson, J.,, C. R. Trotta,, and H. Li. 1998. tRNA splicing. J. Biol. Chem. 273: 12685– 12688.

2. Anglana, M.,, and S. Bacchetti. 1999. Construction of a recombinant adenovirus for efficient delivery of the I- SceI yeast endonuclease to human cells and its application in the in vivo cleavage of chromosomes to expose new potential telomeres. Nucleic Acids Res. 27: 4276– 4281.

3. Asselbergs, F. A. M.,, and S. Rival. 1996. Creation of a novel, versatile multiple cloning site cut by four rare-cutting homing endonucleases. BioTechniques 20: 558– 562.

4. Belfort, M. 1990. Phage T4 introns: self-splicing and mobility. Annu. Rev. Genet. 24: 363– 385.

5. Belfort, M.,, and P. S. Perlman. 1995. Mechanisms of intron mobility. J. Biol. Chem. 270: 30237– 30240.

6. Belfort, M.,, and R. J. Roberts. 1997. Homing endonucleases: keeping the house in order. Nucleic Acids Res. 25: 3379– 3388.

7. Belle, A. 2000. Marker exclusion by bacteriophage T4 is mediated by site-specific non-intron encoded homing endonucleases. Dissertation. State University of New York at Albany, Albany.

8. Bell-Pedersen, D.,, S. M. Quirk,, M. Aubrey,, and M. Belfort. 1989. A site-specific endonuclease and co-conversion of flanking exons associated with the mobile td intron of phage T4. Gene 82: 119– 126.

9. Bell-Pedersen, D.,, S. M. Quirk,, M. Bryk,, and M. Belfort. 1991. I- TevI, the endonuclease encoded by the mobile td intron, recognizes binding and cleavage domains on its DNA target. Proc. Natl. Acad. Sci. USA 88: 7719– 7723.

10. Boeke, J. D.,, and J. P. Stoye,. 1997. Retrotransposons, endogenous retroviruses, and the evolution of retroelements, p. 343– 435. In J. M. Coffin,, S. H. Coffin,, S. H. Hughes,, and H. E. Varmus (ed.), Retroviruses. Cold Spring Harbor Laboratory Press, Plainview, N.Y.

10.a. Bonocora, R. P.,, and D. A. Shub. 2001. A novel group I intron-encoded endonuclease specific for the anticodon region of tRNAfMet genes. Mol. Microbiol. 39: 1299– 1306.

11. Bryk, M.,, M. Belisle,, J. E. Mueller,, and M. Belfort. 1995. Selection of a remote cleavage site by I- TevI, the td intronencoded endonuclease. J. Mol. Biol. 247: 197– 210.

12. Bryk, M.,, S. M. Quirk,, J. E. Mueller,, N. Loizos,, C. Lawrence,, and M. Belfort. 1993. The td intron endonuclease makes extensive sequence tolerant contacts across the minor groove of its DNA target. EMBO J. 12: 2141– 2149.

13. Caprara, M. G.,, V. Lehnert,, A. M. Lambowitz,, and E. Westhof. 1996. A tyrosyl-tRNA synthetase recognizes a conserved tRNA-like structural motif in the group I intron catalytic core. Cell 87: 1135– 1145.

14. Carignani, G.,, O. Groudinsky,, D. Frezza,, E. Schiavon,, E. Bergantino,, and P. P. Slonimski. 1983. An mRNA maturase is encoded by the first intron of the mitochondrial gene for the subunit I of cytochrome oxidase in S. cerevisiae. Cell 35: 733– 742.

15. Cavalier-Smith, T. 1991. Intron phylogeny: a new hypothesis. Trends Genet. 7: 145– 148.

16. Cech, T. R. 1988. Conserved sequences and structures of group I introns: building an active site for RNA catalysis—a review. Gene 73: 259– 271.

17. Cech, T. R. 1990. Self-splicing of group I introns. Annu. Rev. Biochem. 59: 543– 568.

18. Cech, T. R. 1985. Self-splicing RNA: implications for evolution. Int. Rev. Cytol. 93: 3– 22.

19. Chong, S.,, and M.-Q. Xu. 1997. Protein splicing of the Saccharomyces cerevisiae VMA intein without the endonuclease motifs. J. Biol. Chem. 272: 15587– 15590.

20. Choulika, A.,, A. Perrin,, B. Dujon,, and J. F. Nicolas. 1995. Induction of homologous recombination in mammalian chromosomes by using the I- SceI system of Saccharomyces cerevisiae. Mol. Cell. Biol. 15: 1968– 1973.

21. Christ, F.,, S. Schoettler,, W. Wende,, S. Steuer,, A. Pingoud,, and V. Pingoud. 1999. The monomeric homing endonuclease PI- SceI has two catalytic centres for cleavage of the two strands of its DNA substrate. EMBO J. 18: 6908– 6916.

22. Christ, F.,, S. Steuer,, H. Thole,, W. Wende,, A. Pingoud,, and V. Pingoud. 2000. A model for the PI-Sce I-DNA complex based on multiple base and phosphate backbone-specific photocross- links. J. Mol. Biol. 300: 841– 849.

23. Clodi, E.,, K. Semrad,, and R. Schroeder. 1999. Assaying RNA chaperone activity in vivo using a novel RNA folding trap. EMBO J. 18: 3776– 3782.

24. Clyman, J.,, and M. Belfort. 1992. Trans and cis requirements for intron mobility in a prokaryotic system. Genes Dev. 6: 1269– 1279.

25. Coen, D.,, J. Deutch,, P. Netter,, E. Petrochilo,, and P. P. Slonimski. 1970. Mitochondrial genetics. I. Methodology and phenomenology. Symp. Soc. Exp. Biol. 23: 449– 496.

26. Cohen-Tannoudji, M.,, S. Robine,, A. Choulika,, D. Pinto,, F. El Marjou,, C. Babinet,, D. Louvard,, and F. Jaisser. 1998. I SceI- induced gene replacement at a natural locus in embryonic stem cells. Mol. Cell. Biol. 18: 1444– 1448.

27. Colleaux, L.,, L. D’Auriol,, M. Betermier,, G. Cottarel,, A. Jacquier,, F. Galibert,, and B. Dujon. 1986. Universal code equivalent of a yeast mitochondrial intron reading frame is expressed into E. coli as a specific double strand endonuclease. Cell 44: 521– 533.

28. Colleaux, L.,, C. Rougeulle,, P. Avner,, and B. Dujon. 1993. Rapid physical mapping of YAC inserts by random integration of I- SceI sites. Hum. Mol. Genet. 2: 265– 271.

29. Copenhaver, G. P.,, and C. S. Pikaard. 1996. RFLP and physical mapping with an rDNA-specific endonuclease reveals that nucleolus organizer regions of Arabidopsis thaliana adjoin the telomeres on chromosomes 2 and 4a. Plant J. 9: 259– 272.

30. Copertino, D. W.,, and R. B. Hallick. 1993. Group II and group III introns of twintrons: potential relationships to nuclear pre-mRNA introns. Trends Biochem. Sci. 18: 467– 471.

31. Cousineau, B.,, S. Lawrence,, D. Smith,, and M. Belfort. 2000. Retrotransposition of a bacterial group II intron. Nature 404: 1018– 1021.

32. Cousineau, B.,, D. Smith,, S. Lawrence-Cavanagh,, J. E. Mueller,, J. Yang,, D. Mills,, D. Manias,, G. Dunny,, A. M. Lambowitz,, and M. Belfort. 1998. Retrohoming of a bacterial group II intron: mobility via complete reverse splicing, independent of homologous DNA recombination. Cell 94: 451– 462.

33. Critchlow, S. E.,, and S. P. Jackson. 1998. DNA end-joining: from yeast to man. Trends Biochem. Sci. 23: 394– 398.

34. Curcio, M. J.,, and M. Belfort. 1996. Retrohoming: cDNAmediated mobility of group II introns requires a catalytic RNA. Cell 84: 9– 12.

35. Dalgaard, J. Z.,, R. A. Garrett,, and M. Belfort. 1994. Purification and characterization of two forms of I- DmoI, a thermophilic site-specific endonuclease encoded by an archaeal intron. J. Biol. Chem. 269: 28885– 28892.

36. Dalgaard, J. Z.,, R. A. Garrett,, and M. Belfort. 1993. A sitespecific endonuclease encoded by a typical archaeal intron. Proc. Natl. Acad. Sci. USA 90: 5414– 5417.

37. Dalgaard, J. Z.,, A. Klar,, M. J. Moser,, W. R. Holley,, A. Chatterjee,, and I. S. Mian. 1997. 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 H-N-H family. Nucleic Acids Res. 25: 4626– 4638.

38. Dalgaard, J. Z.,, M. J. Moser,, R. Hughey,, and I. S. Mian. 1997. Statistical modeling, phylogenetic analysis and structure prediction of a protein splicing domain common to inteins and hedgehog proteins. J. Comput. Biol. 4: 193– 214.

39. Delahodde, A.,, V. Goguel,, A. M. Becam,, F. Creusot,, J. Perea,, J. Banroques,, and C. Jacq. 1989. Site-specific DNA endonuclease and RNA maturase activities of two homologous in tron-encoded proteins from yeast mitochondria. Cell 56: 431– 441.

40. Derbyshire, V.,, J. C. Kowalski,, J. T. Dansereau,, C. R. Hauer,, and M. Belfort. 1997. Two-domain structure of the td intronencoded endonuclease I- TevI correlates with the two-domain configuration of the homing site. J. Mol. Biol. 265: 494– 506.

41. Derbyshire, V.,, D. W. Wood,, W. Wu,, J. T. Dansereau,, J. Z. Dalgaard,, and M. Belfort. 1997. Genetic definition of a protein-splicing domain: functional mini-inteins support structure predictions and a model for intein evolution. Proc. Natl. Acad. Sci. USA 94: 11466– 11471.

42. Dickson, L.,, H.-R. Huang,, L. Liu,, M. Matsuura,, A. M. Lambowitz,, and P. S. Perlman. 2001. Retrotransposition of a yeast group II intron occurs by reverse splicing directly into ectopic DNA sites. Proc. Natl. Acad. Sci. USA 98: 13207– 13212.

43. Donoho, G.,, M. Jasin,, and P. Berg. 1998. Analysis of gene targeting and intrachromosomal homologous recombination stimulated by genomic double-strand breaks in mouse embryonic stem cells. Mol. Cell. Biol. 18: 4070– 4078.

44. Duan, X.,, F. S. Gimble,, and F. A. Quiocho. 1997. Crystal structure of PI-SceI, a homing endonuclease with protein splicing activity. Cell 89: 555– 564.

45. Dujardin, G.,, C. Jacq,, and P. P. Slonimski. 1982. Single base substitution in an intron of oxidase gene compensates splicing defects of cytochrome b gene. Nature 298: 628– 632.

46. Dujon, B. 1980. Sequence of the intron and flanking exons of the mitochondrial 21S rRNA gene of yeast strains having different alleles at the omega and ribI loci. Cell 20: 185– 197.

47. Dujon, B.,, M. Belfort,, R. A. Butow,, C. Jacq,, C. Lemieux,, P. S. Perlman,, and V. M. Vogt. 1989. Mobile introns: definition of terms and recommended nomenclature. Gene 82: 115– 118.

48. Dujon, B.,, and F. Michel. 1976. Genetics and physical characterization of a segment of the mitochondrial DNA involved in the control of genetic recombination, p. 175– 184. In C. Saccone and A. M. Kroon (ed.), The Genetic Function of Mitochondrial DNA. North-Holland Biomedical Press, Elsevier, Amsterdam, The Netherlands.

49. Eddy, S. R.,, and L. Gold. 1992. Artificial mobile DNA element constructed from the EcoRI endonuclease gene. Proc. Natl. Acad. Sci. USA 89: 1544– 1547.

50. Eddy, S. R.,, and L. Gold. 1991. The phage T4 nrdB intron: a deletion mutant of a version found in the wild. Genes Dev. 5: 1032– 1041.

51. Edgell, D. R.,, M. Belfort,, and D. A. Shub. 2000. Barriers to intron promiscuity in bacteria. J. Bacteriol. 182: 5281– 5289.

52. Edgell, D. R.,, N. M. Fast,, and W. F. Doolittle. 1996. Selfish DNA: the best defense is a good offense. Curr. Biol. 6: 385– 388.

53. Eickbush, T. H. 2000. Introns gain ground. Nature 404: 940– 943.

54. Eskes, R.,, L. Liu,, H. Ma,, M. Chao,, L. Dickson,, A. M. Lambowitz,, and P. S. Perlman. 2000. Multiple homing pathways used by yeast mitochondrial group II introns. Mol. Cell. Biol. 20: 8432– 8446.

55. Eskes, R.,, J. Yang,, A. M. Lambowitz,, and P. S. Perlman. 1997. Mobility of yeast mitochondrial group II introns: engineering a new site specificity and retrohoming via full reverse splicing. Cell 88: 865– 874.

56. Feng, Q.,, J. V. Moran,, H. H. Kazazian, Jr.,, and J. D. Boeke. 1996. Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell 87: 905– 916.

57. Flick, K. E.,, M. S. Jurica,, R. J. Monnat, Jr.,, and B. L. Stoddard. 1998. DNA binding and cleavage by the nuclear intronencoded homing endonuclease I- PpoI. Nature 394: 96– 101.

58. Fonzi, W. A.,, and M. Y. Irwin. 1993. Isogenic strain construction and gene mapping in Candida albicans. Genetics 134: 717– 728.

59. Friedhoff, P.,, I. Franke,, G. Meiss,, W. Wende,, K. L. Krause,, and A. Pingoud. 1999. A similar active site for non-specific and specific endonucleases. Nat. Struct. Biol. 6: 112– 113.

60. Galburt, E. A.,, M. S. Chadsey,, M. S. Jurica,, B. S. Chevalier,, D. Erho,, W. Tang,, R. J. Monnat, Jr.,, and B. L. Stoddard. 2000. Conformational changes and cleavage by the homing endonuclease I-PpoI: a critical role for a leucine residue in the active site. J. Mol. Biol. 300: 877– 887.

61. Galburt, E. A.,, B. Chevalier,, W. Tang,, M. S. Jurica,, K. E. Flick,, R. J. Monnat, Jr., and B. L. Stoddard. 1999. A novel endonuclease mechanism directly visualized for I- PpoI. Nat. Struct. Biol. 6: 1096– 1099.

62. George, J. W.,, and K. N. Kreuzer. 1996. Repair of doublestrand breaks in bacteriophage T4 by a mechanism that involves extensive DNA replication. Genetics 143: 1507– 1520.

63. Gimble, F. S. 2000. Invasion of a multitude of genetic niches by mobile endonuclease genes. FEMS Microbiol. Lett. 185: 99– 107.

64. Gimble, F. S.,, and B. W. Stephens. 1995. Substitutions in conserved dodecapeptide motifs that uncouple the DNA binding and DNA cleavage activities of PI- SceI endonuclease. J. Biol. Chem. 270: 5849– 5856.

65. Gimble, F. S.,, and J. Wang. 1996. Substrate recognition and induced DNA distortion by the PI- SceI endonuclease, an enzyme generated by protein splicing. J. Mol. Biol. 263: 163– 180.

66. Goldschmidt-Clermont, M.,, Y. Choquet,, J. Girard-Bascou,, F. Michel,, M. Schirmer-Rahire,, and J.-D. Rochaix. 1991. A small chloroplast RNA may be required for trans-splicing in Chlamydomonas reinhardtii. Cell 65: 135– 143.

67. Goldschmidt-Clermont, M.,, J. Girard-Bascou,, Y. Choquet,, and J.-D. Rochaix. 1990. Trans-splicing mutants of Chlamydomonas reinhardtii. Mol. Gen. Genet. 223: 417– 425.

68. Goodrich-Blair, H.,, V. Scarlato,, J. M. Gott,, M.-Q. Xu,, and D. A. Shub. 1990. A self-splicing group I intron in the DNA polymerase gene of Bacillus subtilis bacteriophage SPO1. Cell 63: 417– 424.

69. Goodrich-Blair, H.,, and D. A. Shub. 1996. Beyond homing: competition between intron endonucleases confers a selective advantage on flanking genetic markers. Cell 84: 211– 221.

70. Goodrich-Blair, H.,, and D. A. Shub. 1994. The DNA polymerase genes of several HMU-bacteriophages have similar group I introns with highly divergent open reading frames. Nucleic Acids Res. 22: 3715– 3721.

71. Gorbalenya, A. E. 1994. Self-splicing group I and group II introns encode homologous (putative) DNA endonucleases of a new family. Protein Sci. 3: 1117– 1120.

72. Gorbunova, V.,, and A. A. Levy. 1997. Non-homologous DNA end joining in plant cells is associated with deletions and filler DNA insertions. Nucleic Acids Res. 25: 4650– 4657.

73. Grindl, W.,, W. Wende,, V. Pingoud,, and A. Pingoud. 1998. The protein splicing domain of the homing endonuclease PI SceI is responsible for specific DNA binding. Nucleic Acids Res. 26: 1857– 1862.

74. Guo, H.,, M. Karberg,, M. Long,, J. P. Jones III,, B. Sullenger,, and A. M. Lambowitz. 2000. Group II introns designated to insert into therapeutically-relevantDNAtarget sites in human cells. Science 289: 452– 457.

75. Guo, H.,, S. Zimmerly,, P. S. Perlman,, and A. M. Lambowitz. 1997. Group II intron endonucleases use both RNA and protein subunits for recognition of specific sequences in doublestranded DNA. EMBO J. 16: 6835– 6848.

76. Heath, P. J.,, K. M. Stephens,, R. J. Monnat, Jr.,, and B. L. Stoddard. 1997. The structure of I- CreI, a group I intronencoded homing endonuclease. Nat. Struct. Biol. 4: 468– 476.

77. Hiller, R.,, M. Hetzer,, R. J. Schweyen,, and M. W. Mueller. 2000. Transposition and exon shuffling by group II intron RNA molecules in pieces. J. Mol. Biol. 297: 301– 308.

78. Hiom, K. 1999. DNA repair: Rad52—the means to an end. Curr. Biol. 9: R446– R448.

79. Hirata, R.,, and Y. Anraku. 1992. Mutations at the putative junction sites of the yeastVMA1protein, the catalytic subunit of the vacuolar membrane H+-ATPase inhibit its processing by protein splicing. Biochem. Biophys. Res. Commun. 188: 40– 47.

80. Hirata, R.,, Y. Ohsumi,, A. Nakano,, H. Kawasaki,, K. Suzuki,, and Y. Anraku. 1990. Molecular structure of a gene, VMA1, encoding the catalytic subunit of H+-translocating adenosine triphosphatase from vacuolar membranes of Saccharomyces cerevisiae. J. Biol. Chem. 265: 6726– 6733.

81. Holmes, A.,, and J. E. Haber. 1999. Physical monitoring of HO-induced homologous recombination. Methods Mol. Biol. 113: 403– 415.

82. Honeycutt, R. J.,, M. McClelland,, and B. W. S. Sobral. 1993. Physical map of the genome of Rhizobium meliloti 1021. J. Bacteriol. 175: 6945– 6952.

83. Hu, D.,, M. Crist,, X. Duan,, F. A. Quiocho,, and F. S. Gimble. 2000. Probing the structure of the PI- SceI-DNA complex by affinity cleavage and affinity photocross-linking. J. Biol. Chem. 275: 2705– 2712.

84. Huang, Y.-J.,, M. M. Parker,, and M. Belfort. 1999. Role of exonucleolytic degradation in group I intron homing in phage T4. Genetics 153: 1501– 1512.

85. Ichiyanagi, K.,, Y. Ishino,, M. Ariyoshi,, K. Komori,, and M. Kosuke. 2000. Crystal structure of an archaeal intein-encoded homing endonuclease PI- PfuI. J. Mol. Biol. 300: 889– 901.

86. Jacquier, A.,, and B. Dujon. 1985. An intron-encoded protein is active in a gene conversion process that spreads an intron into a mitochondrial gene. Cell 41: 383– 394.

87. Jurica, M. S.,, R. J. Monnat, Jr.,, and B. L. Stoddard. 1998. DNA recognition and cleavage by the LAGLIDADG homing endonuclease I- CreI. Mol. Cell. 2: 469– 476.

88. Kadyrov, F. A.,, V. M. Kriukov,, M. G. Shliapnikov,, and A. A. Baev. 1994. SegE—a new site-specific endodeoxyribonuclease from bacteriophage T4. Doklady Biochem. 339: 404– 406.

89. Kane, P. M.,, C. T. Yamashiro,, D. F. Wolczyk,, N. Neff,, M. Goebl,, and T. H. Stevens. 1990. Protein splicing converts the yeast TFP1 gene product to the 69-kD subunit of the vacuolar H+-adenosine triphosphatase. Science 250: 651– 657.

89.a. Karberg, M.,, H. Guo,, J. Zhong,, R. Coon,, J. Perutka,, and A. M. Lambowitz. 2001. Group II introns as controllable gene targeting vectors for genetic manipulation of bacteria. Nat. Biotechnol. 19: 1162– 1167.

90. Kennell, J. C.,, J. V. Moran,, P. S. Perlman,, R. A. Butow,, and A. M. Lambowitz. 1993. Reverse transcriptase activity associated with maturase-encoding group II introns in yeast mitochondria. Cell 73: 133– 146.

91. Kleanthous, C.,, U. C. Kuhlmann,, A. J. Pommer,, N. Ferguson,, S. E. Radford,, G. R. Moore,, R. James,, and A. M. Hemmings. 1999. Structural and mechanistic basis of immunity toward endonuclease colicins. Nat. Struct. Biol. 6: 243– 252.

92. Ko, T.-P.,, C.-C. Liao,, W.-Y. Ku,, K.-F. Chak,, and H. S. Yuan. 1999. The crystal structure of the DNase domain of colicin E7 in complex with its inhibitor 1m7 protein. Structure 7: 91– 102.

93. Kolodner, R.,, S. D. Hall,, and C. Luisi-DeLuca. 1994. Homologous pairing proteins encoded by the Escherichia coli recE and recT genes. Mol. Microbiol. 11: 23– 30.

94. Komori, K.,, N. Fujita,, K. Ichiyanagi,, H. Shinagawa,, K. Morikawa,, and Y. Ishino. 1999. PI- PfuI and PI- PfuII, intein-coded homing endonucleases from Pyrococcus furiosus. I. Purification and identification of the homing-type endonuclease activities. Nucleic Acids Res. 27: 4167– 4174.

95. Komori, K.,, K. Ichiyanagi,, K. Morikawa,, and Y. Ishino. 1999. PI- PfuI and PI- PfuII, intein-coded homing endonucleases from Pyrococcus furiosus. II. Characterization of the binding and cleavage abilities by site-directed mutagenesis. Nucleic Acids Res. 27: 4175– 4182.

96. Kowalski, J. C.,, M. Belfort,, M. A. Stapleton,, M. Holpert,, J. T. Dansereau,, S. Pietrokovski,, S. M. Baxter,, and V. Derbyshire. 1999. Configuration of the catalytic domain of intron endonuclease I- TevI: coincidence of computational and molecular findings. Nucleic Acids Res. 27: 2115– 2125.

97. Kreuzer, K. N. 2000. Recombination-dependent DNA replication in phage T4. Trends Biochem. Sci. 25: 165– 173.

98. Kuhlmann, U. C.,, G. R. Moore,, R. James,, C. Kleanthous,, and A. M. Hemmings. 1999. Structural parsimony in endonuclease active sites: should the number of homing endonuclease families be redefined? FEBS Lett. 463: 1– 2.

99. Kuhsel, M. G.,, R. Strickland,, and J. D. Palmer. 1990. An ancient group I intron shared by eubacteria and chloroplasts. Science 250: 1570– 1573.

100. Kusano, K.,, K. Sakagami,, T. Yokochi,, T. Naito,, Y. Tokinaga,, E. Ueda,, and I. Kobayashi. 1997. A new type of illegitimate recombination is dependent on restriction and homologous interaction. J. Bacteriol. 179: 5380– 5390.

101. Lambowitz, A. M. 1989. Infectious introns. Cell 56: 323– 326.

102. Lambowitz, A. M.,, and M. Belfort. 1993. Introns as mobile genetic elements. Annu. Rev. Biochem. 62: 587– 622.

103. Lambowitz, A. M.,, M. G. Caprara,, S. Zimmerly,, and P. S. Perlman,. 1999. Group I and group II ribozymes as RNPs: clues to the past and guides to the future, p. 451– 485. In R. F. Gesteland,, T. R. Cech,, and J. F. Atkins (ed.), The RNA World, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y..

104. Lambowitz, A. M.,, and P. S. Perlman. 1990. Involvement of aminoacyl-tRNA synthetases and other proteins in group I and group II intron splicing. Trends Biochem. Sci. 15: 440– 444.

105. Lazowska, J.,, B. Meunier,, and C. Macadre. 1994. Homing of a group II intron in yeast mitochondrial DNA is accompanied by unidirectional co-conversion of upstream-located markers. EMBO J. 13: 4963– 4972.

106. Lewin, A. S.,, J. Thomas, Jr.,, and H. K. Tirupati. 1995. Cotranscriptional splicing of a group I intron is facilitated by the Cbp2 protein. Mol. Cell. Biol. 15: 6971– 6978.

107. Liu, S. L.,, A. Hessel,, and K. E. Sanderson. 1993. Genomic mapping with I- CeuI, an intron-encoded endonuclease specific for genes for ribosomal RNA, in Salmonella spp., Escherichia coli, and other bacteria. Proc. Natl. Acad. Sci. USA 90: 6874– 6878.

108. Liu, S. L.,, and K. E. Sanderson. 1995. I- CeuI reveals conservation of the genome of independent strains of Salmonella typhimurium. J. Bacteriol. 177: 3355– 3357.

109. Loizos, N.,, E. R. M. Tillier,, and M. Belfort. 1994. Evolution of mobile group I introns: recognition of intron sequences by an intron-encoded endonuclease. Proc. Natl. Acad. Sci. USA 91: 11983-– 11987.

110. Luan, D. D.,, M. H. Korman,, J. L. Jakubczak,, and T. H. Eickbush. 1993. Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTRretrotransposition. Cell 72: 595– 605.

111. Lukacsovich, T.,, D. Yang,, and A. S. Waldman. 1994. Repair of a specific double-strand break generated within a mammalian chromosome by yeast endonuclease I- SceI. Nucleic Acids Res. 22: 5649– 5657.

112. Lykke-Andersen, J.,, C. Aagaard,, M. Semionenkov,, and R. A. Garrett. 1997. Archaeal introns: splicing, intercellular mobility and evolution. Trends Biochem. Sci. 22: 326– 331.

113. Lykke-Andersen, J.,, R. A. Garrett,, and J. Kjems. 1997. Mapping metal ions at the catalytic centres of two intron-encoded endonucleases. EMBO J. 16: 3272– 3281.

114. Lykke-Andersen, J.,, R. A. Garrett,, and J. Kjems. 1996. Protein footprinting approach to mapping DNA binding sites of two archaeal homing enzymes: evidence for a two-domain protein structure. Nucleic Acids Res. 24: 3982– 3989.

115. Lykke-Andersen, J.,, H. P. Thi-Ngoc,, and R. A. Garrett. 1994. DNAsubstrate specificity and cleavage kinetics of an archaeal homing-type endonuclease from Pyrobaculum organotrophum. Nucleic Acids Res. 22: 4583– 4590.

116. Macreadie, I. G.,, R. M. Scott,, A. R. Zinn,, and R. A. Butow. 1985. Transposition of an intron in yeast mitochondria requires a protein encoded by that intron. Cell 41: 395– 402.

117. Martinez-Abarca, F.,, F. M. Garcia-Rodriguez,, and N. Toro. 2000. Homing of a bacterial group II intron with an intronencoded protein lacking a recognizable endonuclease domain. Mol. Microbiol. 35: 1405– 1412.

118. Martinez-Abarca, F.,, and N. Toro. 2000. RecA-independent ectopic transposition in vivo of a bacterial group II intron. Nucleic Acids Res. 28: 4397– 4402.

119. Matsuura, M.,, R. Saldanha,, H. Ma,, H. Wank,, J. Yang,, G. Mohr,, S. Cavanagh,, G. M. Dunny,, M. Belfort,, and A. M. Lambowitz. 1997. 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. Genes Dev. 11: 2910– 2924.

120. McClure, M. A. 1991. Evolution of retroposons by acquisition or deletion of retrovirus-like genes. Mol. Biol. Evol. 8: 835– 856.

121. Meunier, B.,, G.-L. Tian,, C. Macadre,, P. P. Slonimski,, and J. Lazowska,. 1990. Group II introns transpose in yeast mitochondria, p. 169– 174. In E. Quagliariello,, S. Papa,, F. Palmieir,, and C. Saccone (ed.), Structure,Function and Biogenesis of Energy Transfer Systems. Elsevier, Amsterdam, The Netherlands.

122. Michel, F.,, and D. J. Cummings. 1985. Analysis of class I introns in a mitochondrial plasmid associated with senescence of Podospora anserina reveals extraordinary resemblance to the Tetrahymena ribosomal intron. Curr. Genet. 10: 69– 79.

123. Michel, F.,, and B. Dujon. 1986. Genetic exchanges between bacteriophage T4 and filamentous fungi? Cell 46: 323.

124. Michel, F.,, and J.-L. Ferat. 1995. Structure and activities of group II introns. Annu. Rev. Biochem. 64: 435– 461.

125. Michel, F.,, K. Umesono,, and H. Ozeki. 1989. Comparative and functional anatomy of group II catalytic introns—a review. Gene 82: 5– 30.

126. Michel, F.,, and E. Westhof. 1990. Modelling of the threedimensional architecture of group I catalytic introns based on comparative sequence analysis. J. Mol. Biol. 216: 585– 610.

127. Mills, D. A.,, D. A. Manias,, L. L. McKay,, and G. M. Dunny. 1997. Homing of a group II intron from Lactococcus lactis subsp. lactis ML3. J. Bacteriol. 179: 6107– 6111.

128. Mills, D. A.,, L. L. McKay,, and G. M. Dunny. 1996. Splicing of a group II intron involved in the conjugative transfer of pRS01 in lactococci. J. Bacteriol. 178: 3531– 3538.

129. Mohr, G.,, P. S. Perlman,, and A. M. Lambowitz. 1993. Evolutionary relationships among group II intron-encoded proteins and identification of a conserved domain that may be related to maturase function. Nucleic Acids Res. 21: 4991– 4997.

130. Mohr, G.,, D. Smith,, M. Belfort,, and A. M. Lambowitz. 2000. Rules for DNA target site recognition by a lactococcal group II intron enable retargeting of the intron to specific DNA sequences. Genes Dev. 14: 559– 573.

131. Moran, J. V.,, K. L. Mecklenburg,, P. Sass,, S. M. Belcher,, D. Mahnke,, A. Lewin,, and P. Perlman. 1994. Splicing defective mutants of the COX1 gene of yeast mitochondrial DNA: initial definition of the maturase domain of the group II intron aI2. Nucleic Acids Res. 22: 2057– 2064.

132. Moran, J. V.,, S. Zimmerly,, R. Eskes,, J. C. Kennell,, A. M. Lambowitz,, R. A. Butow,, and P. S. Perlman. 1995. Mobile group II introns of yeast mtDNA are novel site-specific retroelements. Mol. Cell. Biol. 15: 2828– 2838.

133. Mota, E. M.,, and R. A. Collins. 1988. Independent evolution of structural and coding regions in a Neurospora mitochondrial intron. Nature 332: 654– 656.

134. Mueller, J. E.,, M. Bryk,, N. Loizos,, and M. Belfort,. 1993. Homing endonucleases, p. 111– 143. In S. M. Linn,, R. S. Lloyd,, and R. J. Roberts (ed.), Nucleases, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y..

135. Mueller, J. E.,, J. Clyman,, Y.-J. Huang,, M. M. Parker,, and M. Belfort. 1996. Intron mobility in phage T4 occurs in the context of recombination-dependentDNAreplication by way of multiple pathways. Genes Dev. 10: 351– 364.

136. Mueller, J. E.,, D. Smith,, and M. Belfort. 1996. Exon coconversion biases accompanying intron homing: battle of the nucleases. Genes Dev. 10: 2158– 2166.

137. Mueller, J. E.,, D. Smith,, M. Bryk,, and M. Belfort. 1995. Intron-encoded endonuclease I-TevI binds as a monomer to effect sequential cleavage via conformational changes in the td homing site. EMBO J. 14: 5724– 5735.

138. Mueller, M. W.,, M. Allmaier,, R. Eskes,, and R. J. Schweyen. 1993. Transposition of group II intron aI1 in yeast and invasion of mitochondrial genes at new locations. Nature 366: 174– 176.

139. Muscarella, D. E.,, and V. M. Vogt. 1989. A mobile group I intron in the nuclear rDNA of Physarum polycephalum. Cell 56: 443– 454.

140. Palmer, J. D.,, and J. M. Logsdon, Jr. 1991. The recent origins of introns. Curr. Opin. Genet. Devel. 1: 470– 477.

141. Paques, F.,, and J. E. Haber. 1999. Multiple pathways of recombination induced by double-strand breaks in Saccharomyces cerevisiae. Microbiol. Mol. Biol. Rev. 63: 349– 404.

142. Parker, M. M.,, M. Belisle,, and M. Belfort. 1999. Intron homing with limited exon homology: illegitimate double-strandbreak repair in intron acquisition by phage T4. Genetics 153: 1513– 1523.

143. Parker, M. M.,, D. A. Court,, K. Preiter,, and M. Belfort. 1996. Homology requirements for double-strand break-mediated recombination in a phage lambda- td intron model system. Genetics 143: 1057– 1068.

144. Perlman, P. S.,, and R. A. Butow. 1989. Mobile introns and intron-encoded proteins. Science 246: 1106– 1109.

145. Perron, K.,, M. Goldschmidt-Clermont,, and J.-D. Rochaix. 1999. A factor related to pseudouridine synthase is required for chloroplast group II intron trans-splicing in Chlamydomonas reinhardtii. EMBO J. 18: 6481– 6490.

146. Pietrokovski, S. 1998. Modular organization of inteins and C-terminal autocatalytic domains. Protein Sci. 7: 64– 71.

147. Pingoud, V.,, H. Thole,, F. Christ,, W. Grindl,, W. Wende,, and A. Pingoud. 1999. Photocross-linking of the homing endonu clease PI-SecI to its recognition sequence. J. Biol. Chem. 274: 10235– 10243.

148. Pommer, A. J.,, U. C. Kuhlmann,, A. Cooper,, A. M. Hemmings,, G. R. Moore,, R. James,, and C. Kleanthous. 1999. Homing in on the role of transition metals in the HNH motif of colicin endonucleases. J. Biol. Chem. 274: 27153– 27160.

149. Pyle, A. M. 2000. New tricks from an itinerant intron. Nat. Struct. Biol. 7: 352– 354.

150. Quirk, S. M.,, D. Bell-Pedersen,, and M. Belfort. 1989. Intron mobility in the T-even phages: high frequency inheritance of group I introns promoted by intron open reading frames. Cell 56: 455– 465.

151. Remacle, C.,, and R. F. Matagne. 1993. Transmission, recombination and conversion of mitochondrial markers in relation to the mobility of a group I intron in Chlamydomonas. Curr. Genet. 23: 518– 525.

152. Rochaix, J. D.,, M. Rahire,, and F. Michel. 1985. The chloroplast ribosomal intron of Chlamydomonas reinhardtii codes for a polypeptide related to mitochondrial maturases. Nucleic Acids Res. 13: 975– 984.

153. Roman, J.,, and S. A. Woodson. 1997. Integration of the Tetrahymena group I intron into bacterial rRNA by reverse splicing in vivo. Proc. Natl. Acad. Sci. USA 95: 2134– 2139.

154. Rong, Y. S.,, and K. G. Golic. 2000. Gene targeting by homologous recombination in Drosophila. Science 288: 2013– 2018.

155. Rouet, P.,, F. Smih,, and M. Jasin. 1994. Expression of a sitespecific endonuclease stimulates homologous recombination in mammalian cells. Proc. Natl. Acad. Sci. USA 91: 6064– 6068.

156. Rouet, P.,, F. Smih,, and M. Jasin. 1994. Introduction of double- strand breaks into the genome of mouse cells by expression of a rare-cutting endonuclease. Mol. Cell. Biol. 14: 8096– 8106.

157. Ruby, S. W.,, and J. Abelson. 1991. Pre-mRNA splicing in yeast. Trends Genet. 7: 79– 85.

158. Rudi, K.,, and K. S. Jakobsen. 1999. Complex evolutionary patterns of tRNA Leu(UAA) group I introns in cyanobacterial radiation. J. Bacteriol. 181: 3445– 3451.

159. Russell, D. W.,, R. Jensen,, M. J. Zoller,, J. Burke,, B. Errede,, M. Smith,, and I. Herskowitz. 1986. Structure of the Saccharomyces cerevisiae HOgene and analysis of its upstream regulatory region. Mol. Cell. Biol. 6: 4281– 4294.

160. Russell, R. L.,, and R. J. Huskey. 1974. Partial exclusion between T-even bacteriophages: an incipient genetic isolation mechanism. Genetics 78: 989– 1014.

161. Saldanha, R.,, R. Chen,, H. Wank,, M. Matsuura,, J. Edwards,, and A. M. Lambowitz. 1999. RNA and protein catalysis in group II intron splicing and mobility reactions using purified components. Biochemistry 38: 9069– 9083.

162. Saldanha, R.,, G. Mohr,, M. Belfort,, and A. M. Lambowitz. 1993. Group I and group II introns. FASEB J. 7: 15– 24.

163. Segal, D. J.,, and D. Carroll. 1995. Endonuclease-induced, targeted homologous extrachromosomal recombination in Xenopus oocytes. Proc. Natl. Acad. Sci. USA 92: 806– 810.

164. Sellem, C. H.,, G. Lecellier,, and L. Belcour. 1993. Transposition of a group II intron. Nature 366: 176– 178.

165. Sharma, M.,, R. L. Ellis,, and D. M. Hinton. 1992. Identification of a family of bacteriophage T4 genes encoding proteins similar to those present in group I introns of fungi and phage. Proc. Natl. Acad. Sci. USA 89: 6658– 6662.

166. Sharma, M.,, and D. M. Hinton. 1994. Purification and characterization of the SegA protein of bacteriophage T4, an endonuclease related to proteins encoded by group I introns. J. Bacteriol. 176: 6439– 6448.

167. Sharp, P. A. 1985. On the origin of RNA splicing and introns. Cell 42: 397– 400.

168. Sharp, P. A. 1987. Splicing of messenger RNA precursors. Science 235: 766– 771.

169. Shearman, C.,, J.-J. Godon,, and M. Gasson. 1996. Splicing of a group II intron in a functional transfer gene of Lactococcus lactis. Mol. Microbiol. 21: 45– 53.

170. Shingledecker, K.,, S.-Q. Jiang,, and H. Paulus. 1998. Molecular dissection of the Mycobacterium tuberculosis RecA intein: design of a minimal intein and of a trans-splicing system involving two intein fragments. Gene 207: 187– 195.

171. Shlyapnikov, S. V.,, V. V. Lunin,, M. Perbandt,, K. M. Polyaaakov,, V. Y. Lunin,, V. M. Levdikov,, C. Betzel,, and A. M. Mikhailov. 2000. Atomic structure of the Serratia marcescens endonuclease at 1.1 Å resolution and the enzyme reaction mechanism. Acta Crystallogr. Sect D 56: 567– 572.

172. Shub, D. A.,, H. Goodrich-Blair,, and S. R. Eddy. 1994. Amino acid sequence motif of group I intron endonucleases is conserved in open reading frames of group II introns. Trends- Biochem. Sci. 19: 402– 404.

173. Silva, G.,, J. Z. Dalgaard,, M. Belfort,, and P. Van Roey. 1999. Crystal structure of the thermostable archaeal intron-encoded endonuclease I- DmoI. J. Mol. Biol. 286: 1123– 1136.

174. Simpson, G. G.,, and W. Filipowicz. 1996. Splicing of precursors to mRNA in higher plants: mechanism, regulation and sub-nuclear organisation of the spliceosomal machinery. Plant Mol. Biol. 32: 1– 41.

175. Singh, N. N.,, and A. M. Lambowitz. 2001. Interaction of a group II intron ribonucleoprotein endonuclease with its DNA target site investigated byDNAfootprinting and modification interference. J. Mol. Biol. 309: 361– 386.

176. Skelly, P. J.,, C. M. Hardy,, and G. D. Clark-Walker. 1991. A mobile group II intron of a naturally occuring rearranged mitochondrial genome in Kluyveromyces lactis. Curr. Genet. 20: 115– 120.

177. Smih, F.,, P. Rouet,, P. J. Romanienko,, and M. Jasin. 1995. Double-strand breaks at the target locus stimulate gene targeting in embryonic stem cells. Nucleic Acids Res. 23: 5012– 5019.

178. Souza, D. W.,, and D. Armentano. 1999. Novel cloning method for recombinant adenovirus construction in Escherichia coli. BioTechniques 26: 502– 508.

179. Szostak, J. W.,, T. L. Orr-Weaver,, R. J. Rothstein,, and F. W. Stahl. 1983. The double-strand-break repair model for recombination. Cell 33: 25– 35.

180. Taghian, D. G.,, and J. A. Nickoloff. 1997. Chromosomal double-strand breaks induce gene conversion at high frequency in mammalian cells. Mol. Cell. Biol. 17: 6386– 6393.

181. Thierry, A.,, L. Gaillon,, F. Galibert,, and B. Dujon. 1995. Construction of a complete genomic library of Saccharomyces cerevisiae and physical mapping of chromosome XI at 3.7 kb resolution. Yeast 11: 121– 135.

182. Tirupati, H. K.,, L. C. Shaw,, and A. S. Lewin. 1999. An RNA binding motif in the Cbp2 protein required for protein-stimulated RNA catalysis. J. Biol. Chem. 274: 30393– 30401.

183. Toda, T.,, and M. Itaya. 1995. I- CeuI recognition sites in the rrn operons of the Bacillus subtilis 168 chromosome: inherent landmarks for genome analysis. Microbiology 141: 1937– 1945.

184. Van Roey, P.,, C. A. Waddling,, K. M. Fox,, M. Belfort,, and V. Derbyshire. 2001. Intertwined structure of the DNA-binding domain of intron endonuclease I- TevI with its substrate. EMBO J. 20: 3631– 3637.

185. Verhoeven, E. E. A.,, M. Van Kesteren,, G. F. Moolenaar,, R. Visse,, and N. Goosen. 2000. Catalytic sites for 3′and 5′ incision of Escherichia coli nucleotide excision repair are both located in UvrC. J. Biol. Chem. 275: 5120– 5123.

186. Wank, H.,, J. SanFilippo,, R. N. Singh,, M. Matsuura,, and A. M. Lambowitz. 1999. A reverse-transcriptase/maturase promotes splicing by binding at its own coding segment in a group II intron RNA. Mol. Cell 4: 239– 250.

187. Weeks, K. M.,, and T. R. Cech. 1996. Assembly of a ribonucleoprotein catalyst by tertiary structure capture. Science 271: 345– 348.

188. Wenzlau, J. M.,, R. J. Saldanha,, R. A. Butow,, and P. S. Perlman. 1989. A latent intron-encoded maturase is also an endonuclease needed for intron mobility. Cell 56: 421– 430.

189. Xiong, Y.,, and T. H. Eickbush. 1990. Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J. 9: 3353– 3362.

190. Xu, M.-Q.,, S. D. Kathe,, H. Goodrich-Blair,, S. A. Nierzwicki- Bauer,, and D. A. Shub. 1990. Bacterial origin of a chloroplast intron: conserved self-splicing group I introns in Cyanobacteria. Science 250: 1566– 1570.

191. Yang, J.,, H. S. Malik,, and T. H. Eickbush. 1999. Identification of the endonuclease domain encoded by R2 and other site-specific non-long terminal repeat retrotransposable elements. Proc. Natl. Acad. Sci. USA 96: 7847– 7852.

192. Yang, J.,, G. Mohr,, P. S. Perlman,, and A. M. Lambowitz. 1998. Group II intron mobility in yeast mitochondria: target DNA-primed reverse transcription activity in aI1 and reverse splicing into DNA transposition sites in vitro. J. Mol. Biol. 282: 505– 523.

193. Yang, J.,, S. Zimmerly,, P. S. Perlman,, and A. M. Lambowitz. 1996. Efficient integration of an intron RNA into doublestranded DNA by reverse splicing. Nature 381: 332– 335.

194. Yeo, C. C.,, J. M. Tham,, M. W.-C. Yap,, and C. L. Poh. 1997. Group II intron from Pseudomonas alcaligenes NCIB 9867 (P25X): entrapment in plasmid RP4 and sequence analysis. Microbiology 143: 2833– 2840.

195. Zhang, A.,, V. Derbyshire,, J. L. Salvo,, and M. Belfort. 1995. Escherichia coli protein StpA stimulates self-splicing by promoting RNA assembly in vitro. RNA 1: 783– 793.

196. Zimmerly, S.,, H. Guo,, R. Eskes,, J. Yang,, P. S. Perlman,, and A. M. Lambowitz. 1995. A group II intron RNA is a catalytic component of a DNA endonuclease involved in intron mobility. Cell 83: 529– 538.

197. Zimmerly, S.,, H. Guo,, P. S. Perlman,, and A. M. Lambowitz. 1995. Group II intron mobility occurs by target DNA-primed reverse transcription. Cell 82: 545– 554.

198. Zimmerly, S.,, J. V. Moran,, P. S. Perlman,, and A. M. Lambowitz. 1999. Group II intron reverse transcription in yeast mitochondria. Stabilization and regulation of reverse transcriptase activity by the intron RNA. J. Mol. Biol. 289: 473– 490.

199. Zinn, A. R.,, and R. A. Butow. 1985. Nonreciprocal exchange between alleles of the yeast mitochondrial 21S rRNA gene: kinetics and involvement of a double- strand break. Cell 40: 887– 895.

Tables

Mobile Introns: Pathways and Proteins

/content/10.1128/9781555817954.chap31.tab31-1

Table 1

Intron distribution a

10.1128/9781555817954/tab31-1_thmb.gif

10.1128/9781555817954/tab31-1.gif

Table 1

Intron distribution a

/content/10.1128/9781555817954.chap31.tab31-2

Table 2

Characteristics of homing endonucleases

10.1128/9781555817954/tab31-2_thmb.gif

10.1128/9781555817954/tab31-2.gif

Table 2

Characteristics of homing endonucleases