Design of antisense RNA constructs for downregulation of the acetone formation pathway of Clostridium acetobutylicum

Journal of Bacteriology

Volumn 185, Issue 6, 2003, Pages 1923-1934

  Tummala, Seshu B ^a   Welker, Neil E ^b   Papoutsakis, Eleftherios T ^a  

^a Northwestern University   (United States)

^b NORTHWESTERN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACETOACETATE DECARBOXYLASE; ACETOACETIC ACID; ACETONE; BUTANOL; COENZYME A TRANSFERASE; COMPLEMENTARY RNA; DNA FRAGMENT; NUCLEOTIDE; UNCLASSIFIED DRUG;

ALGORITHM; ARTICLE; BACTERIAL STRAIN; BATCH FERMENTATION; BIOREACTOR; CLOSTRIDIUM ACETOBUTYLICUM; CORRELATION ANALYSIS; DOWN REGULATION; GENETIC TRANSCRIPTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHASE TRANSITION; PLASMID; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEIN EXPRESSION; RNA STRUCTURE; STRUCTURE ANALYSIS; WESTERN BLOTTING;

ACETONE; BIOREACTORS; CARBOXY-LYASES; CLOSTRIDIUM; COENZYME A-TRANSFERASES; CULTURE MEDIA; DOWN-REGULATION; NUCLEIC ACID CONFORMATION; RNA, ANTISENSE;

BACTERIA (MICROORGANISMS); CLOSTRIDIUM; CLOSTRIDIUM ACETOBUTYLICUM; CLOSTRIDIUM ACETOBUTYLICUM ATCC 824; POSIBACTERIA;

EID: 0037337740     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.185.6.1923-1934.2003     Document Type: Article

References (32)

1. Berghammer, H., and B. Auer. 1993. "Easypreps": fast and easy plasmid minipreparation for analysis of recombinant clones in E. coli. BioTechniques 14:524-528.
2. Buday, Z., J. C. Linden, and M. N. Karim. 1990. Improved acetone-butanol fermentation analysis using subambient HPLC column temperature. Enzyme Microb. Technol. 12:24-27.
3. Cary, J. W., D. J. Petersen, E. T. Papoutsakis, and G. N. Bennett. 1990. Cloning and expression of Clostridium acetobutylicum ATCC 824 aceto-acetyl-coenzyme A:acetate/butyrate:coenzyme A-transferase in Escherichia coli. Appl. Environ. Microbiol. 56:1576-1583.
4. Cornillot, E., R. V. Nair, E. T. Papoutsakis, and P. Soucaille. 1997. The genes for butanol and acetone formation in Clostridium acetobutylicum ATCC 824 reside on a large plasmid whose loss leads to degeneration of the strain. J. Bacteriol. 179:5442-5447.
5. Desai, R. P., and E. T. Papoutsakis. 1999. Antisense RNA strategies for the metabolic engineering of Clostridium acetobutylicum. Appl. Environ. Microbiol. 65:936-945.
6. Engdahl, H. M., T. A. Hjalt, and E. G. Wagner. 1997. A two unit antisense RNA cassette test system for silencing of target genes. Nucleic Acids Res. 25:3218-3227.
7. Fierro-Monti, I. P., S. J. Reid, and D. R. Woods. 1992. Differential expression of a Clostridium acetobutylicum antisense RNA: implications for regulation of glutamine synthetase. J. Bacteriol. 174:7642-7647.
8. Fischer, R. J., J. Helms, and P. Durre. 1993. Cloning, sequencing, and molecular analysis of the sol operon of Clostridium acetobutylicum, a chromosomal locus involved in solventogenesis. J. Bacteriol. 175:6959-6969.
9. Fridovich, I. 1972. Acetoacetate decarboxylase, p. 255-270. In P. D. Boyer (ed.), Carboxylation and decarboxylation (nonoxidative) isomerization, vol. 6. Academic Press, Inc., New York, N.Y.
10. Gerischer, U., and P. Durre. 1992. mRNA analysis of the adc gene region of Clostridium acetobutylicum during the shift to solventogenesis. J. Bacteriol. 174:426-433.
11. Harris, L. M., R. P. Desai, N. E. Welker, and E. T. Papoutsakis. 2000. Characterization of recombinant strains of the Clostridium acetobutylicum butyrate kinase inactivation mutant: need for new phenomenological models for solventogenesis and butanol inhibition? Biotechnol. Bioeng. 67:1-11.
12. Harris, L. M., N. E. Welker, and E. T. Papoutsakis. 2002. Northern, morphological, and fermentation analysis of spo0A inactivation and overexpression in Clostridium acetobutylicum ATCC 824. J. Bacteriol. 184:3586-3597.
13. Hjalt, T., and E. G. Wagner. 1992. The effect of loop size in antisense and target RNAs on the efficiency of antisensc RNA control. Nucleic Acids Res. 20:6723-6732.
14. Hjalt, T. A., and E. G. Wagner. 1995. Bulged-out nucleotides in an antisense RNA are required for rapid target RNA binding in vitro and inhibition in vivo. Nucleic Acids Res. 23:580-587.
15. Hughes, J. B., C. Y. Wang, R. Bhadra, A. Richardson, G. N. Bennett, and F. B. Rudolph. 1998. Reduction of 2,4,6-trinitrotoluene by Clostridium acetobutylicum through hydroxylamino-nitrotoluene intermediates. Environ. Toxicol. Chem. 17:343-348.
16. Lee, S. Y., and S. Rasheed. 1990. A simple procedure for maximum yield of high-quality plasmid DNA. BioTechniques 9:676-679.
17. Mermelstein, L. D., and E. T. Papoutsakis. 1993. In vivo methylation in Escherichia coli by the Bacillus subtilis phage φ3T I methyltransferase to protect plasmids from restriction upon transformation of Clostridium acetobutylicum ATCC 824. Appl. Environ. Microbiol. 59:1077-1081.
18. Mermelstein, L. D., E. T. Papoutsakis, D. J. Petersen, and G. N. Bennett. 1993. Metabolic engineering of Clostridium acetobutylicum ATCC 824 for increased solvent production by the enhancement of acetone formation enzyme activities using a synthetic acetone operon. Biotechnol. Bioeng. 42:1053-1060.
19. Nair, R. V., G. N. Bennett, and E. T. Papoutsakis. 1994. Molecular characterization of an aldehyde/alcohol dehydrogenase gene from Clostridium acetobutylicum ATCC 824. J. Bacteriol. 176:871-885.
20. Nolling, J., G. Breton, M. V. Omelchenko, K. S. Makarova, Q. Zeng, R. Gibson, H. M. Lee, J. Dubois, D. Qiu, J. Hitti, Y. I. Wolf, R. L. Tatusov, F. Sabathe, L. Doucette-Stamm, P. Soucaille, 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. Patzel, V., and G. Sczakiel. 2000. In vitro selection supports the view of a kinetic control of antisense RNA-mediated inhibition of gene expression in mammalian cells. Nucleic Acids Res. 28:2462-2466.
22. Patzel, V., and G. Sczakiel. 1998. Theoretical design of antisense RNA structures substantially improves annealing kinetics and efficacy in human cells. Nat. Biotechnol. 16:64-68.
23. Persson, C., E. G. Wagner, and K. Nordstrom. 1988. Control of replication of plasmid R1: kinetics of in vitro interaction between the antisense RNA, CopA, and its target, CopT. EMBO J. 7:3279-3288.
24. Petersen, D. J., and G. N. Bennett. 1990. Purification of acetoacetate decarboxylase from Clostridium acetobutylicum ATCC 824 and cloning of the acetoacetate decarboxylase gene in Escherichia coli. Appl. Environ. Microbiol. 56:3491-3498.
25. Petersen, D. J., J. W. Cary, J. Vanderleyden, and G. N. Bennett. 1993. Sequence and arrangement of genes encoding enzymes of the acetone-production pathway of Clostridium acetobutylicum ATCC 824. Gene 123:93-97.
26. Rittner, K., C. Burmester, and G. Sczakiel. 1993. In vitro selection of fast-hybridizing and effective antisense RNAs directed against the human immunodeficiency virus type 1. Nucleic Acids Res. 21:1381-1387.
27. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
28. Theys, J., W. Landuyt, S. Nuyts, L. Van Mellaert, E. Bosmans, A. Rijnders, W. Van Den Bogaert, A. van Oosterom, J. Anne, and P. Lambin. 2001. Improvement of Clostridium tumour targeting vectors evaluated in rat rhabdomyosarcomas. FEMS Immunol. Med. Microbiol. 30:37-41.
29. Tummala, S. B., C. Tomas, L. M. Harris, N. E. Welker, F. B. Rudolph, G. N. Bennett, and E. T. Papoutsakis. 2001. Genetic tools for solventogenic Clostridia, p. 105-123. In H. Bahl and P. Duerre (ed.), Clostridia: Biotechnology and medical applications. John Wiley & Sons, Inc., New York, N.Y.
30. Tummala, S. B., N. E. Welker, and E. T. Papoutsakis. 1999. Development and characterization of a gene expression reporter system for Clostridium acetobutylicum ATCC 824. Appl. Environ. Microbiol. 65:3793-3799.
31. Westheimer, F. H. 1969. Acetoacetate decarboxylase from Clostridium acetobutylicum, p. 231-241. In J. M. Lowenstein (ed.), Lipids, vol. 14. Academic Press, Inc., New York, N.Y.
32. Wiesenborn, D. P., F. B. Rudolph, and E. T. Papoutsakis. 1989. Coenzyme A transferase from Clostridium acetobutylicum ATCC 824 and its role in the uptake of acids. Appl. Environ. Microbiol. 55:323-329.