A group II intron-type open reading frame from the thermophile Bacillus (Geobacillus) stearothermophilus encodes a heat-stable reverse transcriptase

Applied and Environmental Microbiology

Volumn 70, Issue 12, 2004, Pages 7140-7147

  Vellore, Jaishree ^a,b   Moretz, Samuel E ^a   Lampson, Bert C ^a  

^a EAST TENNESSEE STATE UNIVERSITY   (United States)

^b NONE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOSYNTHESIS; CLONING; ENZYMES; ESCHERICHIA COLI; GENES; HIGH TEMPERATURE EFFECTS; MICROBIOLOGY; RNA;

GENE CODING; GENE LIBRARIES; GENE TRANSCRIPTION; REVERSE TRANSCRIPTION;

DNA;

BACTERIAL PROTEIN; PROTEIN TRT; RNA DIRECTED DNA POLYMERASE; UNCLASSIFIED DRUG;

GENE EXPRESSION; MICROBIOLOGY;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL STRAIN; CONTROLLED STUDY; DNA SEQUENCE; ENZYME ACTIVITY; GENE OVEREXPRESSION; GEOBACILLUS STEAROTHERMOPHILUS; INTRON; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PROTEIN PURIFICATION; THERMOSTABILITY;

AMINO ACID SEQUENCE; BACILLUS STEAROTHERMOPHILUS; BASE SEQUENCE; CLONING, MOLECULAR; ENZYME STABILITY; ESCHERICHIA COLI; GENE EXPRESSION REGULATION, BACTERIAL; HEAT; INTRONS; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; RNA-DIRECTED DNA POLYMERASE; SEQUENCE ANALYSIS, DNA;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; GEOBACILLUS STEAROTHERMOPHILUS; POSIBACTERIA; PROKARYOTA;

EID: 10444251152     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.70.12.7140-7147.2004     Document Type: Article

References (39)

1. Adamidi, C., O. Fedorova, and A. M. Pyle. 2003. A group II intron inserted into a bacterial heat-shock operon shows autocatalytic activity and unusual thermostability. Biochemistry 42:3409-3418.
2. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic logical alignment search tool. J. Mol. Biol. 215:403-410.
3. Cousineau, B., S. Lawrence, D. Smith, and M. Belfort. 2000. Retrotransposition of a bacterial group II intron. Nature 404:1018-1021.
4. Cousineau, B., D. Smith, S. Lawrence-Cavanagh, J. E. Mueller, J. Yang, D. Mills, D. A. Nanias, G. M. 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.
5. Dai, L., and S. Zimmerly. 2002. Compilation and analysis of group II intron insertions in bacterial genomes: evidence for retroelement behavior. Nucleic Acids Res. 30:1091-1102.
6. Eickbush, T. H. 1994. Origin and evolutionary relationships of retroelements, p. 127-157. In S. S. Morse (ed.), The evolutionary biology of viruses. Raven Press, New York, N.Y.
7. Fu, G. K., and L. L. Stuve. 2003. Improved method for the construction of full-length enriched cDNA libraries. BioTechniques 34:954-957.
8. Fuchs, B., K. Zhang, M. G. Rock, M. E. Bolander, and G. Sarkar. 1999. High temperature cDNA synthesis by AMV reverse transcriptase improves the specificity of PCR. Mol. Biotechnol. 12:237-240.
9. Hamilton, S. C., J. W. Farchaus, and M. C. Davis. 2001. DNA polymerases as engines for biotechnology. BioTechniques 31:370-383.
10. Hawkins, P. R., P. Jin, and G. K. Fu. 2003. Full-length cDNA synthesis for long-distance RT-PCR of large mRNA transcripts. BioTechniques 34:768-773.
11. Kim, B., J. C. Ayran, S. G. Sangar, E. T. Adman, S. M. Fuller, N. H. Tran, and J. Harrigan. 1999. New human immunodeficiency virus, type 1 reverse transcriptase (HIV-1) mutants with increased fidelity of DNA synthesis. J. Biol. Chem. 274:27666-27673.
12. Lambowitz, A. M., and M. Belfort. 1993, Introns as mobile genetic elements. Annu. Rev. Biochem. 62:587-622.
13. Lampson, B. C., M. Inouye, and S. Inouye. 2001. The msDNAs of bacteria. Prog. Nucleic Acid Res. Mol. Biol. 67:65-91.
14. Malboeuf, C. M., S. J. Isaacs, N. H. Tran, and B. Kim. 2001. Thermal effects on reverse transcription: improvement of accuracy and processivity in cDNA synthesis. BioTechniques 30:1074-1084.
15. Martinez-Abarca, F., and N. Toro. 2000. Group II introns in the bacterial world. Mol. Microbiol. 38:917-926.
16. Michel, F., K. Umesono, and H. Ozeki. 1989. Comparative and functional anatomy of group II catalytic introns - a review. Gene 82:5-30.
17. Moran, J. V., S. Zimmerly, R. Eskes, J. C. Kennell, A. M. Lambowitz, R. A. Butwo, and P. S. Perlman. 1995. Mobile group II introns of yeast mitrochondrial DNA are novel site-specific retroelements. Mol. Cell. Biol. 15:2828-2838.
18. Nakasone, K., N. Masui, Y. Takaki, R. Sasaki, G. Maeno, T. Sakiyama, C. Hirama, F. Fuji, and H. Takami. 2000. Characterization and comparative study of the rrn operons of alkaliphilic Bacillus halodurans C-125. Extremophiles 4:209-214.
19. Nazina, T. N., T. P. Tourova, A. B. Poltaraus, E. V. Novikova, A. A. Grigoryan, A. E. Ivanova, A. M. Lysenko, V. V. Petrunyaka, G. A. Osipov, S. S. Belyaev, and M. V. Ivanov. 2001. Taxonomic study of aerobic thermophilic bacilli and descriptions of Geobacillus subterraneus gen. nov., sp. nov. and Geobacillus uzenensis sp. nov. from petroleum reservoirs and transfer of Bacillus stearothermophilus, Bacillus thermocatenulatus, Bacillus thermoleovorans, Bacillus kaustophilus, Bacillus thermoglucosidasius and Bacillus thermodenitrificans to Geobacillus as the new combinations G. stearothermophilus, G. thermocatenulatus, G. thermoleovorans, G. kaustophilus, G. thermoglucosidasius and G. thermodenitrificans. Int. J. Syst. Evol. Microbiol. 51:433-466.
20. Nolling, J., G. Breton, M. V. Omelchenko, K. S. Markarva, Q. Zeng, R. Gibson, H. M. Lee, J. Dubois, D. Qiu, J. Hitti, Y. I. Wolf, R. L. Tatusova, F. Sabathe, L. Doucette-Stamm, P. Soncaille, M. J. Daly, G. N. Bennett, E. V. Koonin, and D. R. Smith. 2001. Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum. J. Bacteriol. 183:4823-4838.
21. Pyra, H., J. Boni, and J. Schupbach. 1994. Ultrasensitive retrovirus detection by a reverse transcriptase assay based on product enhancement. Proc. Natl. Acad. Sci. USA 91:1544-1548.
22. Qin, P. Z., and A. M. Pyle. 1998. The architectural organization and mechanistic function of group II intron structural elements. Curr. Opin. Struct. Biol. 8:301-308.
23. Saldanha, R., B. 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.
24. Silver, J., T. Naudru, K. Fujita, and R. Repaske. 1993. An RT-PCR assay for the enzyme activity of reverse transcriptase capable of detecting single virions. Nucleic Acids Res. 21:3593-3594.
25. Steitz, T. A. 1999. DNA polymerases: structural diversity and common mechanisms. J. Biol. Chem. 274:17395-17398.
26. Stenesh, J., and B. A. Roe. 1972. DNA polymerase from mesophilic and thermophilic bacteria I - purification and properties of the enzyme. Biochem. Biophys. Acta 272:156-166.
27. Studier, F. W., A. H. Rosenberg, J. J. Dunn, and J. W. Dubendorff. 1990. Use of T7 RNA polymerase to direct expression of cloned genes. Methods Enzymol. 185:60-89.
28. Takami, H., C.-G. Han, Y. Takaki, and E. Ohtsubo. 2001. Identification and distribution of new insertion sequences in the genome of alkaliphilic Bacillus halodurans C-125. J. Bacteriol. 183:4345-4356.
29. Taube, R., S. Loya, O. Avidan, M. Perach, and A. Hizi. 1998. Reverse transcriptase of mouse mammary tumor virus: expression in bacteria, purification, and biochemical characterization. Biochem. J. 329:579-587.
30. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties, and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
31. Toor, N., G. Hausner, and S. Zimmerly. 2001. Coevolution of group II intron RNA structures with their intron-encoded reverse transcriptases. RNA 7:1142-1152.
32. Vielle, C., and G. J. Zeikus. 2001. Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability. Microbiol. Mol. Biol. Rev. 65:1-43.
33. Voisset, C., R. R. Tonjes, P. Breyton, B. Mandrand, and G. Paranhos-Baccala. 2001. Specific detection of RT activity in culture supernatants of retrovirus-producing cells, using synthetic DNA as competitor in polymerase enhanced reverse transcriptase assay. J. Virol. Methods 94:187-193.
34. Wilhelm, M., M. Boutabout, and F.-X. Wilhelm. 2000. Expression of an active form of recombinant Ty1 reverse transcriptase in Escherichia coli: a fusion protein containing the C-terminal region of the Ty1 integrase linked to the reverse transcriptase-RNase H domain exhibits polymerase and RNase H activities. Biochem. J. 38:337-342.
35. Xiong, Y., and T. H. Eickbush. 1990. Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J. 9:3353-3362.
36. Yanisch-Perron, C., J. Vieira, and J. Messing. 1985. Improved M13 phage cloning vectors and host strains: nucleotide sequence of M13amp18 and pUC19 vectors. Gene 33:103-119.
37. 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.
38. Zimmerly, S., G. Hausner, and X.-C. Wu. 2001. Phylogenetic relationships among group II intron ORFs. Nucleic Acids Res. 29:1238-1250.
39. Zimmerly, S., J. V. Moran, P. S. Perlman, and A. M. Lambowitz. 1999. Group II intron reverse transcriptase in yeast mitochondria: stabilization and regulation of reverse transcriptase activity by intron RNA. J. Mol. Biol. 289:473-490.