Use of Computer-designed Group II Introns to Disrupt Escherichia coli DExH/D-box Protein and DNA Helicase Genes

Journal of Molecular Biology

Volumn 336, Issue 2, 2004, Pages 421-439

  Perutka, Jiri ^a   Wang, Wenjun ^a   Goerlitz, David ^a   Lambowitz, Alan M ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

Functional genomics; Gene targeting; Reverse transcriptase; Ribozyme; RNA helicase

Indexed keywords

DNA; HELICASE; MARKER; NUCLEOTIDE; PROTEIN; PROTEIN D BOX; PROTEIN DEXH; PROTEIN SECA; UNCLASSIFIED DRUG;

ALGORITHM; ARTICLE; BACTERIAL GENE; BACTERIUM COLONY; CALCULATION; CHEMICAL MODIFICATION; COMPUTER; CONTROLLED STUDY; DATA BASE; ESCHERICHIA COLI; GENE DISRUPTION; GENE FREQUENCY; GENE INSERTION; GENETIC ANALYSIS; GENETIC CODE; INTRON; LACTOCOCCUS LACTIS; MOLECULAR RECOGNITION; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PREDICTION; PRIORITY JOURNAL; SCREENING; YEAST;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; INSERTION SEQUENCES; LACTOCOCCUS; LACTOCOCCUS LACTIS;

EID: 0742289608     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2003.12.009     Document Type: Article

References (40)

1. Lambowitz A.M., Caprara M.G., Zimmerly S., Perlman P.S. Group I and group II ribozymes as RNPs: clues to the past and guides to the future. Gesteland R.F., Cech T.R., Atkins J.F. The RNA World. 2nd edit. 1999;451-485 Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
2. Belfort M., Derbyshire V., Parker M.M., Cousineau B., Lambowitz A.M. Mobile introns: pathways and proteins. Craig N.L., Craigie R., Gellert M., Lambowitz A.M. Mobile DNA II. 2002;761-783 ASM Press, Washington, DC.
3. Singh N.N., Lambowitz A.M. Interaction of a group II intron ribonucleoprotein endonuclease with its DNA target site investigated by DNA footprinting and modification interference. J. Mol. Biol. 309:2001;361-386.
4. Aizawa Y., Xiang Q., Lambowitz A.M., Pyle A.M. The pathway for DNA recognition and RNA integration by a group II intron retrotransposon. Mol. Cell. 11:2003;795-805.
5. Zhong J., Lambowitz A.M. Group II intron mobility using nascent strands at DNA replication forks to prime reverse transcription. EMBO J. 22:2003;4555-4565.
6. Guo H., Zimmerly S., Perlman P.S., Lambowitz A.M. Group II intron endonucleases use both RNA and protein subunits for recognition of specific sequences in double-stranded DNA. EMBO J. 16:1997;6835-6848.
7. Yang J., Mohr G., Perlman P.S., Lambowitz A.M. Group II intron mobility in yeast mitochondria: target DNA-primed reverse transcription activity of al1 and reverse splicing into DNA transposition sites in vitro. J. Mol. Biol. 282:1998;505-523.
8. Jiménez-Zurdo J.I., García-Rodriguez F.M., Barrientos-Durán A., Toro N. DNA target site requirements for homing in vivo of a bacterial group II intron encoding a protein lacking the DNA endonuclease domain. J. Mol. Biol. 326:2003;413-423.
9. Karberg M., Guo H., Zhong J., Coon R., Perutka J., Lambowitz A.M. Group II introns as controllable gene targeting vectors for genetic manipulation of bacteria. Nature Biotechnol. 19:2001;1162-1167.
10. Frazier C.L., San Filippo J., Lambowitz A.M., Mills D.A. Genetic manipulation of Lactococcus lactis by using targeted group II introns: generation of stable insertions without selection. Appl. Environ. Microbiol. 69:2003;1121-1128.
11. Zhong J., Karberg M., Lambowitz A.M. Targeted and random bacterial gene disruption using a group II intron (targetron) vector containing a retrotransposition-activated selectable marker. Nucl. Acids Res. 31:2003;1656-1664.
12. Matsuura M., Saldanha R., Ma H., Wank H., Yang J., Mohr G., 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. Genes Dev. 11:1997;2910-2924.
13. Cousineau B., Smith D., Lawrence-Cavanagh S., Mueller J.E., Yang J., Mills D., et al. Retrohoming of a bacterial group II intron: mobility via complete reverse splicing, independent of homologous DNA recombination. Cell. 94:1998;451-462.
14. Guo H., Karberg M., Long M., Jones J.P. III, Sullenger B., Lambowitz A.M. Group II introns designed to insert into therapeutically relevant DNA target sites in human cells. Science. 289:2000;452-457.
15. Mohr G., Smith D., Belfort M., Lambowitz A.M. Rules for DNA target site recognition by a lactococcal group II intron enable retargeting of the intron to specific DNA sequences. Genes Dev. 14:2000;559-573.
16. Breslauer K.J., Frank R., Blocker H., Marky L.A. Predicting DNA duplex stability from the base sequence. Proc. Natl Acad. Sci. USA. 83:1986;3746-3750.
17. Stormo G.D., Schneider T.D., Gold L., Ehrenfeucht A. Use of the "Perceptron" algorithm to distinguish translational initiation sites in E. coli. Nucl. Acids Res. 10:1982;2997-3011.
18. Durbin R., Eddy S., Krogh A., Mitchison G. Biological Sequence Analysis. Probabilistic Models of Proteins and Nucleic Acids. 1998;Cambridge University Press, Cambridge, UK.
19. Burge C.B. Modeling dependencies in pre-mRNA splicing signals. Salzberg S.L., Searls D.B., Kasif S. Computational Methods in Molecular Biology. 1998;129-164 Elsevier, New York.
20. Zupan J., Gasteiger J. Neural Networks in Chemistry and Drug Design: An Introduction. 2nd edit. 1999;Wiley, New York.
21. Tanner N.K., Linder P. DExD/H box RNA helicases: from generic motors to specific dissociation functions. Mol. Cell. 8:2001;251-262.
22. de la Cruz J., Kressler D. Unwinding RNA in Saccharomyces cerevisiae: DEAD-box proteins and related families. Trends Biochem. Sci. 24:1999;192-198.
23. Mohr G., Zhang A.X., Gianelos J.A., Belfort M., Lambowitz A.M. The Neurospora CYT-18 protein suppresses defects in the phage T4 td intron by stabilizing the catalytically active structure of the intron core. Cell. 69:1992;483-494.
24. Mohr S., Stryker J.M., Lambowitz A.M. A DEAD-box protein functions as an ATP-dependent RNA chaperone in group I intron splicing. Cell. 109:2002;769-779.
25. Schultz J., Milpetz F., Bork P., Ponting C.P. SMART, a simple modular architecture research tool: identification of signaling domains. Proc. Natl Acad. Sci. USA. 95:1998;5857-5864.
26. Letunic I., Goodstadt L., Dickens N.J., Doerks T., Schultz J., Mott R., et al. Recent improvements to the SMART domain-based sequence annotation resource. Nucl. Acids Res. 30:2002;242-244.
27. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl. Acids Res. 25:1997;3389-3402.
28. Fuller-Pace F.V., Nicol S.M., Reid A.D., Lane D.P. DbpA: a DEAD box protein specifically activated by 23 S rRNA. EMBO J. 12:1993;3619-3626.
29. Diges C.M., Uhlenbeck O.C. Escherichia coli DbpA is an RNA helicase that requires hairpin 92 of 23 S rRNA. EMBO J. 20:2001;5503-5512.
30. Nilsson G., Belasco J.G., Cohen S.N., von Gabain A. Effect on premature termination of translation on mRNA stability depends on the site of ribosome release. Proc. Natl Acad. Sci. USA. 84:1987;4890-4894.
31. Lill R., Cunningham K., Brundage L., Ito K., Oliver D., Wickner W. The SecA protein hydrolyzes ATP and is an essential component of the protein translocation ATPase of Escherichia coli. EMBO J. 8:1989;961-966.
32. Charollais J., Pflieger D., Vinh J., Dreyfus M., Iost I. The DEAD-box RNA helicase SrmB is involved in the assembly of 50 S ribosomal subunits in Escherichia coli. Mol. Microbiol. 48:2003;1253-1265.
33. Murphy K.C. Use of bacteriophage lambda recombination functions to promote gene replacement in Escherichia coli. J. Bacteriol. 180:1998;2063-2071.
34. Zhang Y.M., Buchholz F., Muyrers J.P.P., Stewart A.F. A new logic for DNA engineering using recombination in Escherichia coli. Nature Genet. 20:1998;123-128.
35. Datsenko K.A., Wanner B.L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl Acad. Sci. USA. 97:2000;6640-6645.
36. Yu D., Ellis H.M., Lee E.C., Jenkins N.A., Copeland N.G., Court D.L. An efficient recombination system for chromosome engineering in Escherichia coli. Proc. Natl Acad. Sci. USA. 97:2000;5978-5983.
37. Ellis H.M., Yu D.G., DiTizio T., Court D.L. High efficiency mutagenesis, repair, and engineering of chromosomal DNA using single-stranded oligonucleotides. Proc. Natl Acad. Sci. USA. 98:2001;6742-6746.
38. Linder P. Yeast RNA helicases of the DEAD-box family involved in translation initiation. Biol. Cell. 95:2003;157-167.
39. Gorbalenya A.E., Koonin E.V. Helicases: amino acid sequence comparisons and structure-function relationships. Curr. Opin. Struct. Biol. 3:1993;419-429.
40. Tanner N.K., Cordin O., Banroques J., Doere M., Linder P. The Q motif: a newly identified motif in DEAD box helicases may regulate ATP binding and hydrolysis. Mol. Cell. 11:2003;127-138.