Paired termini stabilize antisense RNAs and enhance conditional gene silencing in Escherichia coli

Nucleic Acids Research

Volumn 34, Issue 20, 2006, Pages

  Nakashima, Nobutaka ^a,b   Tamura, Tomohiro ^b,c   Good, Liam ^a  

^a KAROLINSKA INSTITUTE   (Sweden)

^b NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^c HOKKAIDO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ACETATE KINASE; ACETIC ACID; BACTERIAL PROTEIN; CARBON; COMPLEMENTARY RNA; MESSENGER RNA; PHOSPHATE ACETYLTRANSFERASE; PROTEIN ACKA; PROTEIN FABL; ACETIC ACID DERIVATIVE; BETA GALACTOSIDASE; ENOYL ACYL CARRIER PROTEIN REDUCTASE (NADH); ESCHERICHIA COLI PROTEIN; FABI PROTEIN, E COLI; RECOMBINANT PROTEIN; TRICLOSAN;

ARTICLE; BACTERIAL CELL; BACTERIAL GENE; CONTROLLED STUDY; DNA FLANKING REGION; ENZYME ACTIVITY; ESCHERICHIA COLI; FUNCTIONAL GENOMICS; GENE EXPRESSION; GENE SILENCING; NONHUMAN; NORTHERN BLOTTING; OPERON; PRIORITY JOURNAL; REPORTER GENE; RNA ANALYSIS; STOICHIOMETRY; CHEMISTRY; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; RNA STABILITY;

ESCHERICHIA COLI;

ACETATE KINASE; ACETATES; BETA-GALACTOSIDASE; ENOYL-(ACYL-CARRIER-PROTEIN) REDUCTASE (NADH); ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE SILENCING; OPERON; RECOMBINANT PROTEINS; RNA STABILITY; RNA, ANTISENSE; TRICLOSAN;

EID: 33845667323     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl697     Document Type: Article

References (49)

1. Yin,D. and Ji,Y. (2002) Genomic analysis using conditional phenotypes generated by antisense RNA. Curr. Opin. Microbiol., 5, 330-333.
2. Engdahl,H.M., Hjalt,T.A. and Wagner,E.G. (1997) A two unit antisense RNA cassette test system for silencing of target genes. Nucleic Acids Res., 25, 3218-3227.
3. Kim,J.Y. and Cha,H.J. (2003) Down-regulation of acetate pathway through antisense strategy in Escherichia coli: Improved foreign protein production. Biotechnol. Bioeng., 83, 841-853.
4. Chen,H., Ferbeyre,G. and Cedergren,R. (1997) Efficient hammerhead ribozyme and antisense RNA targeting in a slow ribosome Escherichia coli mutant. Nat. Biotechnol., 15, 432-435.
5. Ji,Y., Yin,D., Fox,B., Holmes,D.J., Payne,D. and Rosenberg,M. (2004) Validation of antibacterial mechanism of action using regulated antisense RNA expression in Staphylococcus aureus. FEMS Microbiol. Lett., 231, 177-184.
6. Engdahl,H.M., Lindell,M. and Wagner,E.G. (2001) Introduction of an RNA stability element at the 5′ end of an antisense RNA cassette increases the inhibition of target RNA translation. Antisense Nucleic Acid Drug Dev., 11, 29-40.
7. Desai,R.P. and Papoutsakis,E.T. (1999) Antisense RNA strategies for metabolic engineering of Clostridium acetobutylicum. Appl. Environ. Microbiol., 65, 936-945.
8. Tchurikov,N.A., Chistyakova,L.G., Zavilgelsky,G.B., Manukhov,I.V., Chernov,B.K. and Golova,Y.B. (2000) Gene-specific silencing by expression of parallel complementary RNA in Escherichia coli. J. Biol. Chem., 275, 26523-26529.
9. Ji,Y., Zhang,B., Van Horn,S.F., Warren,P., Woodnutt,G., Burnham,M.K. and Rosenberg,M. (2001) Identification of critical staphylococcal genes using conditional phenotypes generated by antisense RNA. Science, 293, 2266-2269.
10. Forsyth,R.A., Haselbeck,R.J., Ohlsen,K.L., Yamamoto,R.T., Xu,H., Trawick,J.D., Wall,D., Wang,L., Brown-Driver,V., Froelich,J.M. et al. (2002) A genome-wide strategy for the identification of essential genes in Staphylococcus aureus. Mol. Microbiol., 43, 1387-1400.
11. Young,K., Jayasuriya,H., Ondeyka,J.G., Herath,K., Zhang,C., Kodali,S., Galgoci,A., Painter,R., Brown-Driver,V., Yamamoto,R. et al. (2006) Discovery of FabH/FabF inhibitors from natural products. Antimicrob. Agents Chemother., 50, 519-526.
12. Tummala,S.B., Welker,N.E. and Papoutsakis,E.T. (2003) Design of antisense RNA constructs for downregulatiion of the acetone formation pathway of Clostridium acetobutylicum. J. Bacteriol., 185, 1923-1934.
13. Wagner,E.G. and Flärdh,K. (2002) Antisense RNAs everywhere? Trends Genet., 18, 223-226.
14. Wagner,E.G., Altuvia,S. and Romby,P. (2002) Antisense RNAs in bacteria and their genetic elements. Adv. Genet., 46, 361-398.
15. Tilley,L.D., Hine,O.S., Kellogg,J.A., Hassinger,J.N., Weller,D.D., Iversen,P.L. and Geller,B.L. (2006) Gene-specific effects of antisense phosphorodiamidate morpholino oligomer-peptide conjugates on Escherichia coli and Salmonella enterica serovar typhimurium in pure culture and in tissue culture. Antimicrob. Agents Chemother., 50, 2789-2796.
16. Good,L., Awasthi,S.K., Dryselius,R., Larsson,O. and Nielsen,P.E. (2001) Bactericidal antisense effects of peptide-PNA conjugates. Nat. Biotechnol., 19, 360-364.
17. Rose,I.A., Grunberg-Manago,M., Korey,S.R. and Ochoa,S. (1954) Enzymatic phosphorylation of acetate. J. Biol. Chem., 211, 737-756.
18. Brown,T.D.K., Jose-Mortimer,M.C. and Kornberg,H.L. (1977) The enzymatic interconversion of acetate and acetyl-coenzyme A in Escherichia coli. J. Gen. Microbiol., 102, 327-336.
19. Aiba,H., Adhya,S. and de Crombrugghe,B. (1981) Evidence for two functional gal promoters in intact Escherichia coli cells. J. Biol. Chem., 256, 11905-11910.
20. Thanbichler,M. and Böck,A. (2002) The function of SECIS RNA in translational control of gene expression in Escherichia coli. EMBO J., 21, 6925-6934.
21. Yang,Y.T., Aristidou,A.A., San,K.Y. and Bennett,G.N. (1999) Metabolic flux analysis of Escherichia coli deficient in the acetate production pathway and expressing the Bacillus subtilis acetolactate synthase. Metab. Eng., 1, 26-34.
22. Cho,S., Shin,D., Ji,G.E., Heu,S. and Ryu,S. (2005) High-level recombinant protein production by overexpression of Mlc in Escherichia coli. J. Biotechnol., 119, 197-203.
23. Moll,I., Afonyushkin,T., Vytvytska,O., Kaberdin,V.R. and Bläsi,U. (2003) Coincident Hfq binding and RNase E cleavage sites on mRNA and small regulatory RNAs. RNA, 9, 1308-1314.
24. Rasmussen,A.A., Eriksen,M., Gilany,K., Udesen,C., Franch,T., Petersen,C. and Valentin-Hansen,P. (2005) Regulation of ompA mRNA stability: The role of a small regulatory RNA in growth phase-dependent control. Mol. Microbiol., 58, 1421-1429.
25. Arnold,T.E., Yu,J. and Belasco,J.G. (1998) mRNA stabilization by the ompA 5′-untranslated region: Two protective elements hinder distinct pathways for mRNA degradation. RNA, 4, 319-330.
26. Lamontagne,B. and Elela,S.A. (2004) Evaluation of the RNA determinants for bacterial and yeast RNase III binding and cleavage. J. Biol. Chem., 279, 2231-2241.
27. Baneyx,F. (1999) Recombinant protein expression in Escherichia coli. Curr. Opin. Biotechnol., 10, 411-421.
28. trc promoters by natural and synthetic inducers. Biotechnol. Prog., 18, 672-674.
29. Bevis,B.J. and Glick,B.S. (2002) Rapidly maturing variants of the Discosoma red fluorescent protein (DsRed). Nat. Biotechnol., 20, 83-87.
30. Pestka,S., Daugherty,B.L., Jung,V., Hotta,K. and Pestka,R.K. (1984) Anti-mRNA: Specific inhibition of translation of single mRNA molecules. Proc. Natl Acad. Sci. USA, 81, 7525-7528.
31. Deshler,J.O., Li,H., Rossi,J.J. and Castanotto,D. (1995) Ribozymes expressed within the loop of a natural antisense RNA form functional transcription terminators. Gene, 155, 35-43.
32. Bauer,K.A., Ben-Bassat,A., Dawson,M., de la Puente,V.T. and Neway,J.O. (1990) Improved expression of human interleukin-2 in high-cell-density fermentor cultures of Escherichia coli K-12 by a phosphotransacetylase mutant. Appl. Environ. Microbiol., 56, 1296-1302.
33. Phue,J.N., Noronha,S.B., Hattacharyya,R., Wolfe,A.J. and Shiloach,J. (2005) Glucose metabolism at high density growth of E.coli B and E.coli K: Differences in metabolic pathways are responsible for efficient glucose utilization in E.coli B as determined by microarrays and northern blot analyses. Biotechnol. Bioeng., 90, 805-820.
34. Wolfe,A.J. (2005) The acetate switch. Microbiol. Mol. Biol. Rev., 69, 12-50.
35. LeVine,S.M., Ardeshir,F. and Ames,G.F. (1980) Isolation and characterization of acetate kinase and phosphotransacetylase mutants of Escherichia coli and Salmonella typhimurium. J. Bacteriol., 143, 1081-1085.
36. Bergler,H., Fuchsbichler,S., Högenauer,G. and Turnowsky,F. (1996) The enoyl-[acyl-carrier-protein] reductase (FabI) of Escherichia coli, which catalyzes a key regulatory step in fatty acid biosynthesis, accepts NADH and NADPH as cofactors and is inhibited by palmitoyl-CoA. Eur. J. Biochem., 242, 689-694.
37. Dryselius,R., Aswasti,S.K., Rajarao,G.K., Nielsen,P.E. and Good,L. (2003) The translation start codon region is sensitive to antisense PNA inhibition in Escherichia coli. Oligonucleotides, 13, 427-433.
38. DeVito,J.A., Mills,J.A., Liu,V.G., Agarwal,A., Sizemore,C.F., Yao,Z., Stoughton,D.M., Cappiello,M.G., Barbosa,M.D., Foster,L.A. et al. (2002) An array of target-specific screening strains for antibacterial discovery. Nat. Biotechnol., 20, 478-483.
39. Massé,E., Escorcia,F.E. and Gottesman,S. (2003) Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli. Genes Dev., 17, 2374-2383.
40. Dryselius,R., Nekhotiaeva,N. and Good,L. (2005) Antimicrobial synergy between mRNA- and protein-level inhibitors. J. Antimicrob. Chemother., 56, 97-103.
41. Good,L. (2003) Translation repression by antisense sequences. Cell. Mol. Life Sci., 60, 854-861.
42. Ding,Y., Chan,C.Y. and Lawrence,C.E. (2004) Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Res., 32, W135-W141.
43. Shafferman,A., Flashner,Y., Hertman,I., Olami,Y. and Cohen,S. (1987) Molecular aspects of genetic instability of an artificial 68 by perfect palindrome in Escherichia coli. Mol. Gen. Genet., 208, 294-300.
44. Arthur,D.C., Ghetu,A.F., Gubbins,M.J., Edwards,R.A., Frost,L.S. and Glover,J.N. (2003) FinO is an RNA chaperone that facilitates sense-antisense RNA interactions. EMBO J., 22, 6346-6355.
45. Franch,T., Gultyaev,A.P. and Gerdes,K. (1997) Programmed cell death by hok/sok of plasmid R1: Processing at the hok mRNA 3′ end triggers structural rearrangements that allow translation and antisense RNA binding. J. Mol. Biol., 273, 38-51.
46. Moffat,J. and Sabatini,D.M. (2006) Building mammalian signalling pathways with RNAi screens. Nature Rev. Mol. Cell Biol., 7, 177-187.
47. Wang,J., Soisson,S.M., Young,K., Shoop,W., Kodali,S., Galgoci,A., Painter,R., Parthasarathy,G., Tang,Y.S., Cummings,R. et al. (2006) Platensimycin is a selective FabF inhibitor with potent antibiotic properties. Nature, 441, 358-361.
48. Brantl,S. and Wagner,E.G. (2002) An antisense RNA-mediated transcriptional attenuation mechanism functions in Escherichia coli. J. Bacteriol., 184, 2740-2747.
49. Condon,C. (2003) RNA processing and degradation in Bacillus subtilis. Microbiol. Mol. Biol. Rev., 67, 157-174.