A Likely Pathway for Formation of Mobile Group I Introns

Current Biology

Volumn 19, Issue 3, 2009, Pages 223-228

  Bonocora, Richard P ^a   Shub, David A ^a  

^a STATE UNIVERSITY OF NEW YORK   (United States)

Author keywords

DNA; EVO_ECOL; RNA

Indexed keywords

DEOXYRIBONUCLEASE I; DNA DIRECTED DNA POLYMERASE;

ARTICLE; ENZYME SPECIFICITY; GENE CONVERSION; GENETICS; INTERSPERSED REPEAT; INTRON; MOLECULAR EVOLUTION; SINGLE STRANDED DNA BREAK; VIRUS GENE;

DEOXYRIBONUCLEASE I; DNA BREAKS, SINGLE-STRANDED; DNA-DIRECTED DNA POLYMERASE; EVOLUTION, MOLECULAR; GENE CONVERSION; GENES, VIRAL; INTERSPERSED REPETITIVE SEQUENCES; INTRONS; SUBSTRATE SPECIFICITY;

ANIMALIA;

EID: 59349116229     PISSN: 09609822     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cub.2009.01.033     Document Type: Article

References (42)

1. Belfort M., Derbyshire V., Parker M.M., Cousineau B., and Lambowitz A.M. Mobile introns: pathways and proteins. In: Craig N. (Ed). DNA Mobile II (2002), ASM Press, Washington, DC 761-783
2. Biniszkiewicz D., Cesnaviciene E., and Shub D.A. Self-splicing group I intron in cyanobacterial initiator methionine tRNA: evidence for lateral transfer of introns in bacteria. EMBO J. 13 (1994) 4629-4635
3. Bonocora R.P., and Shub D.A. A novel group I intron-encoded endonuclease specific for the anticodon region of tRNA(fMet) genes. Mol. Microbiol. 39 (2001) 1299-1306
4. Orlowski J., Boniecki M., and Bujnicki J.M. I-Ssp6803I: the first homing endonuclease from the PD-(D/E)XK superfamily exhibits an unusual mode of DNA recognition. Bioinformatics 23 (2007) 527-530
5. Zhao L., Bonocora R.P., Shub D.A., and Stoddard B.L. The restriction fold turns to the dark side: a bacterial homing endonuclease with a PD-(D/E)-XK motif. EMBO J. 26 (2007) 2432-2442
6. Pajunen M.I., Kiljunen S.J., Soderholm M.E., and Skurnik M. Complete genomic sequence of the lytic bacteriophage phiYeO3-12 of Yersinia enterocolitica serotype O:3. J. Bacteriol. 183 (2001) 1928-1937
7. Kwan T., Liu J., Dubow M., Gros P., and Pelletier J. Comparative genomic analysis of 18 Pseudomonas aeruginosa bacteriophages. J. Bacteriol. 188 (2006) 1184-1187
8. Shub D.A., Goodrich-Blair H., and Eddy S.R. Amino acid sequence motif of group I intron endonucleases is conserved in open reading frames of group II introns. Trends Biochem. Sci. 19 (1994) 402-404
9. Gorbalenya A.E. Self-splicing group I and group II introns encode homologous (putative) DNA endonucleases of a new family. Protein Sci. 3 (1994) 1117-1120
10. Bonocora R.P., and Shub D.A. A self-splicing group I intron in DNA polymerase genes of T7-like bacteriophages. J. Bacteriol. 186 (2004) 8153-8155
11. Scholl D., and Merril C. The genome of bacteriophage K1F, a T7-like phage that has acquired the ability to replicate on K1 strains of Escherichia coli. J. Bacteriol. 187 (2005) 8499-8503
12. Garcia E., Elliott J.M., Ramanculov E., Chain P.S., Chu M.C., and Molineux I.J. The genome sequence of Yersinia pestis bacteriophage phiA1122 reveals an intimate history with the coliphage T3 and T7 genomes. J. Bacteriol. 185 (2003) 5248-5262
13. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 (1997) 3389-3402
14. Lambowitz A.M., and Belfort M. Introns as mobile genetic elements. Annu. Rev. Biochem. 62 (1993) 587-622
15. Miller E.S., Kutter E., Mosig G., Arisaka F., Kunisawa T., and Ruger W. Bacteriophage T4 genome. Microbiol. Mol. Biol. Rev. 67 (2003) 86-156
16. Belle A., Landthaler M., and Shub D.A. Intronless homing: site-specific endonuclease SegF of bacteriophage T4 mediates localized marker exclusion analogous to homing endonucleases of group I introns. Genes Dev. 16 (2002) 351-362
17. Kadyrov F.A., Shlyapnikov M.G., and Kryukov V.M. A phage T4 site-specific endonuclease, SegE, is responsible for a non-reciprocal genetic exchange between T-even-related phages. FEBS Lett. 415 (1997) 75-80
18. Liu Q., Belle A., Shub D.A., Belfort M., and Edgell D.R. SegG endonuclease promotes marker exclusion and mediates co-conversion from a distant cleavage site. J. Mol. Biol. 334 (2003) 13-23
19. Sharma M., Ellis R.L., and Hinton D.M. 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 (1992) 6658-6662
20. Shcherbakov V., Granovsky I., Plugina L., Shcherbakova T., Sizova S., Pyatkov K., Shlyapnikov M., and Shubina O. Focused genetic recombination of bacteriophage t4 initiated by double-strand breaks. Genetics 162 (2002) 543-556
21. Brok-Volchanskaya V.S., Kadyrov F.A., Sivogrivov D.E., Kolosov P.M., Sokolov A.S., Shlyapnikov M.G., Kryukov V.M., and Granovsky I.E. 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. 36 (2008) 2094-2105
22. Sandegren L., Nord D., and Sjoberg B.M. SegH and Hef: two novel homing endonucleases whose genes replace the mobC and mobE genes in several T4-related phages. Nucleic Acids Res. 33 (2005) 6203-6213
23. Roberts R.J., Belfort M., Bestor T., Bhagwat A.S., Bickle T.A., Bitinaite J., Blumenthal R.M., Degtyarev S., Dryden D.T., Dybvig K., et al. A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. Nucleic Acids Res. 31 (2003) 1805-1812
24. Hausmann R. The T7 group. In: Calendar R. (Ed). The Bacteriophages (1988), Plenum Press, New York
25. Belfort M., Reaban M.E., Coetzee T., and Dalgaard J.Z. Prokaryotic introns and inteins: a panoply of form and function. J. Bacteriol. 177 (1995) 3897-3903
26. Lambowitz A.M. Infectious introns. Cell 56 (1989) 323-326
27. Belfort M. Bacteriophage introns: parasites within parasites?. Trends Genet. 5 (1989) 209-213
28. Mota E.M., and Collins R.A. Independent evolution of structural and coding regions in a Neurospora mitochondrial intron. Nature 332 (1988) 654-656
29. Goddard M.R., and Burt A. Recurrent invasion and extinction of a selfish gene. Proc. Natl. Acad. Sci. USA 96 (1999) 13880-13885
30. Loizos N., Tillier E.R., and Belfort M. Evolution of mobile group I introns: recognition of intron sequences by an intron-encoded endonuclease. Proc. Natl. Acad. Sci. USA 91 (1994) 11983-11987
31. Edgell D.R., and Shub D.A. Related homing endonucleases I-BmoI and I-TevI use different strategies to cleave homologous recognition sites. Proc. Natl. Acad. Sci. USA 98 (2001) 7898-7903
32. Landthaler M., Begley U., Lau N.C., and Shub D.A. Two self-splicing group I introns in the ribonucleotide reductase large subunit gene of Staphylococcus aureus phage Twort. Nucleic Acids Res. 30 (2002) 1935-1943
33. Edgell D.R., Belfort M., and Shub D.A. Barriers to intron promiscuity in bacteria. J. Bacteriol. 182 (2000) 5281-5289
34. Derbyshire V., and Belfort M. Lightning strikes twice: intron-intein coincidence. Proc. Natl. Acad. Sci. USA 95 (1998) 1356-1357
35. Pietrokovski S. Intein spread and extinction in evolution. Trends Genet. 17 (2001) 465-472
36. Gogarten J.P., Senejani A.G., Zhaxybayeva O., Olendzenski L., and Hilario E. Inteins: structure, function, and evolution. Annu. Rev. Microbiol. 56 (2002) 263-287
37. Goodwin T.J., Butler M.I., and Poulter R.T. Multiple, non-allelic, intein-coding sequences in eukaryotic RNA polymerase genes. BMC Biol. 4 (2006) 38
38. Roman J., and Woodson S.A. Reverse splicing of the Tetrahymena IVS: evidence for multiple reaction sites in the 23S rRNA. RNA 1 (1995) 478-490
39. Roman J., and Woodson S.A. Integration of the Tetrahymena group I intron into bacterial rRNA by reverse splicing in vivo. Proc. Natl. Acad. Sci. USA 95 (1998) 2134-2139
40. Studier F.W. The genetics and physiology of bacteriophage T7. Virology 39 (1969) 562-574
41. Zeng Q., Bonocora R.P., and Shub D.A. A free-standing homing endonuclease targets an intron insertion site in the psbA gene of cyanophages. Curr. Biol. 19 (2009) 218-222 this issue
42. Petrov V.M., Nolan J.M., Bertrand C., Levy D., Desplats C., Krisch H.M., and Karam J.D. Plasticity of the gene functions for DNA replication in the T4-like phages. J. Mol. Biol. 361 (2006) 46-68