RNA processing enables predictable programming of gene expression

Nature Biotechnology

Volumn 30, Issue 10, 2012, Pages 1002-1006

  Qi, Lei ^a,e,f   Haurwitz, Rachel E ^b,e   Shao, Wenjun ^b   Doudna, Jennifer A ^b,c   Arkin, Adam P ^a,c,d  

^a University of California at Berkeley   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e UNIVERSITY OF CALIFORNIA   (United States)

^f Caribou Biosciences Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEA; CIS-REGULATORY ELEMENTS; COMPLEX BIOLOGICAL SYSTEMS; COMPLEX INTERACTION; CONTEXT-FREE; GENERAL APPROACH; GENETIC ELEMENTS; PALINDROMIC; PHYSICAL SEPARATION; PLUG-AND-PLAY; PREDICTABLE FUNCTIONS; RIBOSOME BINDING SITES; RNA CLEAVAGE; RNA PROCESSING;

BACTERIA; GENE EXPRESSION;

RNA;

BACTERIAL RNA; MESSENGER RNA;

ARCHAEON; ARTICLE; BACTERIUM; EUKARYOTE; GENE EXPRESSION; MULTIGENE FAMILY; NONHUMAN; OPERON; PRIORITY JOURNAL; PROMOTER REGION; RNA ANALYSIS; RNA CLEAVAGE; RNA PROCESSING;

ESCHERICHIA COLI; GENE EXPRESSION; GENETIC ENGINEERING; INVERTED REPEAT SEQUENCES; OPERON; RNA PROCESSING, POST-TRANSCRIPTIONAL; UNTRANSLATED REGIONS;

EID: 84867389802     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt.2355     Document Type: Article

References (34)

1. Ellis, T., Wang, X. & Collins, J.J. Diversity-based, model-guided construction of synthetic gene networks with predicted functions. Nat. Biotechnol. 27, 465-471 (2009).
2. Endy, D. Foundations for engineering biology. Nature 438, 449-453 (2005). (Pubitemid 41742010)
3. Haurwitz, R.E., Jinek, M., Wiedenheft, B., Zhou, K. & Doudna, J.A. Sequence- and structure-specifc RNA processing by a CRISPR endonuclease. Science 329, 1355-1358 (2010).
4. Wiedenheft, B., Sternberg, S.H. & Doudna, J.A. RNA-guided genetic silencing systems in bacteria and archaea. Nature 482, 331-338 (2012).
5. Culler, S.J., Hoff, K.G. & Smolke, C.D. Reprogramming cellular behavior with RNA controllers responsive to endogenous proteins. Science 330, 1251-1255 (2010).
6. Barrangou, R. et al. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315, 1709-1712 (2007). (Pubitemid 46515624)
7. Al-Attar, S., Westra, E.R., van der Oost, J. & Brouns, S.J.J. Clustered regularly interspaced short palindromic repeats (CRISPRs): the hallmark of an ingenious antiviral defense mechanism in prokaryotes. Biol. Chem. 392, 277-289 (2011).
8. Karginov, F.V. & Hannon, G.J. The CRISPR system: small RNA-guided defense in bacteria and archaea. Mol. Cell 37, 7-19 (2010).
9. Gesner, E.M., Schellenberg, M.J., Garside, E.L., George, M.M. & Macmillan, A.M. Recognition and maturation of effector RNAs in a CRISPR interference pathway. Nat Struct. Mol. Biol. 18, 688-692 (2011).
10. Sashital, D.G., Jinek, M. & Doudna, J.A. An RNA-induced conformational change required for CRISPR RNA cleavage by the endoribonuclease Cse3. Nat Struct. Mol. Biol. 18, 680-687 (2011).
11. Lintner, N.G. et al. Structural and functional characterization of an archaeal clustered regularly interspaced short palindromic repeat (CRISPR)-associated complex for antiviral defense (CASCADE). J. Biol. Chem. 286, 21643-21656 (2011).
12. Carte, J., Pfster, N.T., Compton, M.M., Terns, R.M. & Terns, M.P. Binding and cleavage of CRISPR RNA by Cas6. RNA 16, 2181-2188 (2010).
13. Brouns, S.J.J. et al. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 321, 960-964 (2008).
14. Deana, A., Celesnik, H. & Belasco, J.G. The bacterial enzyme RppH triggers messenger RNA degradation by 5' pyrophosphate removal. Nature 451, 355-358 (2008).
15. Cases, I. & de Lorenzo, V. Promoters in the environment: transcriptional regulation in its natural context. Nat Rev. Microbiol. 3, 105-118 (2005). (Pubitemid 40207592)
16. Rocha, E.P.C. The organization of the bacterial genome. Annu. Rev. Genet. 42, 211-233 (2008).
17. Zaslaver, A., Baugh, L.R. & Sternberg, P.W. Metazoan operons accelerate recovery from growth-arrested states. Cell 145, 981-992 (2011).
18. Pfeger, B.F., Pitera, D.J., Smolke, C.D. & Keasling, J.D. Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes. Nat Biotechnol. 24, 1027-1032 (2006). (Pubitemid 44215398)
19. Martin, V., Pitera, D., Withers, S. & Newman, J. Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nat Biotechnol. 21, 796-802 (2003). (Pubitemid 36791399)
20. Wek, R.C., Sameshima, J.H. & Hatfeld, G.W. Rho-dependent transcriptional polarity in the ilvGMEDA operon of wild-type Escherichia coli K12. J. Biol. Chem. 262, 15256-15261 (1987).
21. Mutalik, V.K., Qi, L., Guimaraes, J.C., Lucks, J.B. & Arkin, A.P. Rationally designed families of orthogonal RNA regulators of translation. Nat Chem. Biol. 8, 447-454 (2012).
22. Lucks, J.B., Qi, L., Mutalik, V.K., Wang, D. & Arkin, A.P. Versatile RNA-sensing transcriptional regulators for engineering genetic networks. Proc. Natl. Acad. Sci. USA 108, 8617-8622 (2011).
23. Hampel, A. & Tritz, R. RNA catalytic properties of the minimum (-)sTRSV sequence. Biochemistry 28, 4929-4933 (1989). (Pubitemid 19162737)
24. Daròs, J.A., Marcos, J.F., Hernández, C. & Flores, R. Replication of avocado sunblotch viroid: evidence for a symmetric pathway with two rolling circles and hammerhead ribozyme processing. Proc. Natl. Acad. Sci. USA 91, 12813-12817 (1994).
25. Dunn, J.J. & Studier, F.W. T7 early RNAs and Escherichia coli ribosomal RNAs are cut from large precursor RNAs in vivo by ribonuclease 3. Proc. Natl. Acad. Sci. USA 70, 3296-3300 (1973).
26. Espéli, O., Moulin, L. & Boccard, F. Transcription attenuation associated with bacterial repetitive extragenic BIME elements1. J. Mol. Biol. 314, 375-386 (2001). (Pubitemid 33131842)
27. Guet, C.C., Elowitz, M.B., Hsing, W. & Leibler, S. Combinatorial synthesis of genetic networks. Science 296, 1466-1470 (2002). (Pubitemid 34553091)
28. Salis, H.M., Mirsky, E.A. & Voigt, C.A. Automated design of synthetic ribosome binding sites to control protein expression. Nat Biotechnol. 27, 946-950 (2009).
29. Wang, H.H. et al. Programming cells by multiplex genome engineering and accelerated evolution. Nature 460, 894-898 (2009).
30. Lutz, R. & Bujard, H. Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements. Nucleic Acids Res. 25, 1203-1210 (1997). (Pubitemid 27303212)
31. Nagai, T. et al. A variant of yellow fuorescent protein with fast and effcient maturation for cell-biological applications. Nat. Biotechnol. 20, 87-90 (2002). (Pubitemid 34044921)
32. Leveau, J.H. & Lindow, S.E. Predictive and interpretive simulation of green fuorescent protein expression in reporter bacteria. J. Bacteriol. 183, 6752-6762 (2001). (Pubitemid 33064187)
33. Pédelacq, J.-D., Cabantous, S., Tran, T., Terwilliger, T.C. & Waldo, G.S. Engineering and characterization of a superfolder green fuorescent protein. Nat Biotechnol. 24, 79-88 (2006). (Pubitemid 43083170)
34. Campbell, R.E. et al. A monomeric red fuorescent protein. Proc. Natl. Acad. Sci. USA 99, 7877-7882 (2002).