Accurate, Model-Based Tuning of Synthetic Gene Expression Using Introns in
Synthetic biology is gradually expanding our capability to engineer biology through rational genetic engineering of synthetic gene expression systems. These developments are already paving the way for the accelerated study of biology and applying engineered biological systems to major environmental and health problems. However, our capacity to intelligently modify and control gene expression depends on our ability to apply a broad range of genetic regulators in the engineering process. Here we show that Introns, pivotal regulators of Eukaryotic gene expression, can be rationally engineered to control a synthetic gene expression system of a Eukaryote. We developed a unique reporter-based system to evaluate the effects of engineering splicing in synthetic biology and show that the entire intron repertoire of S. cerevisiae can be accurately used to rationally engineer gene expression. Our results provide both a proof-of-concept for the integration of splicing into synthetic biology designs and a model that can be used by the scientific community for integrating splicing into their own designs. Following the extensive use of transcriptional (promoter) and translational (UTR) elements in synthetic constructs, our results introduce a new major regulatory system, splicing, that can be used to rationally engineer genetic systems.
Vyšlo v časopise:
Accurate, Model-Based Tuning of Synthetic Gene Expression Using Introns in. PLoS Genet 10(6): e32767. doi:10.1371/journal.pgen.1004407
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1004407
Souhrn
Synthetic biology is gradually expanding our capability to engineer biology through rational genetic engineering of synthetic gene expression systems. These developments are already paving the way for the accelerated study of biology and applying engineered biological systems to major environmental and health problems. However, our capacity to intelligently modify and control gene expression depends on our ability to apply a broad range of genetic regulators in the engineering process. Here we show that Introns, pivotal regulators of Eukaryotic gene expression, can be rationally engineered to control a synthetic gene expression system of a Eukaryote. We developed a unique reporter-based system to evaluate the effects of engineering splicing in synthetic biology and show that the entire intron repertoire of S. cerevisiae can be accurately used to rationally engineer gene expression. Our results provide both a proof-of-concept for the integration of splicing into synthetic biology designs and a model that can be used by the scientific community for integrating splicing into their own designs. Following the extensive use of transcriptional (promoter) and translational (UTR) elements in synthetic constructs, our results introduce a new major regulatory system, splicing, that can be used to rationally engineer genetic systems.
Zdroje
1. EgbertRG, KlavinsE (2012) Fine-tuning gene networks using simple sequence repeats. Proc Natl Acad Sci U S A 109: 16817–16822.
2. GrateL, AresMJr (2002) Searching yeast intron data at Ares lab Web site. Methods Enzymol 350: 380–392.
3. WangY, MaM, XiaoX, WangZ (2012) Intronic splicing enhancers, cognate splicing factors and context-dependent. Nat Struct Mol Biol 19: 1044–1052.
4. SpingolaM, GrateL, HausslerD, AresMJr (1999) Genome-wide bioinformatic and molecular analysis of introns in Saccharomyces. Rna 5: 221–234.
5. KupferDM, DrabenstotSD, BuchananKL, LaiH, ZhuH, et al. (2004) Introns and splicing elements of five diverse fungi. Eukaryot Cell 3: 1088–1100.
6. NevozhayD, AdamsRM, MurphyKF, JosicK, BalázsiG (2009) Negative autoregulation linearizes the dose-response and suppresses the heterogeneity of gene expression. Proc Natl Acad Sci U S A 106: 5123–5128.
7. AndrianantoandroE, BasuS, KarigDK, WeissR (2006) Synthetic biology: new engineering rules for an emerging discipline. Mol Syst Biol 2: 2006.0028.
8. AngJ, HarrisE, HusseyBJ, KilR, McMillenDR (2013) Tuning Response Curves for Synthetic Biology. ACS Synth Biol 2: 547–567.
9. KhalilAS, CollinsJJ (2010) Synthetic biology: applications come of age. Nat Rev Genet 11: 367–379.
10. PurnickPE, WeissR (2009) The second wave of synthetic biology: from modules to systems. Nat Rev Mol Cell Biol 10: 410–422.
11. WangZ, BurgeCB (2008) Splicing regulation: from a parts list of regulatory elements to an integrated. Rna 14: 802–813.
12. MatlinAJ, ClarkF, SmithCW (2005) Understanding alternative splicing: towards a cellular code. Nat Rev Mol Cell Biol 6: 386–398.
13. LinshizG, YehezkelTB, KaplanS, GronauI, RavidS, et al. (2008) Recursive construction of perfect DNA molecules from imperfect oligonucleotides. Mol Syst Biol 4: 191.
14. ShabiU, KaplanS, LinshizG, BenyehezkelT, BuaronH, et al. (2010) Processing DNA molecules as text. Syst Synth Biol 4: 227–236.
15. BrinsterRL, AllenJM, BehringerRR, GelinasRE, PalmiterRD (1988) Introns increase transcriptional efficiency in transgenic mice. Proc Natl Acad Sci U S A 85: 836–840.
16. ChoiT, HuangM, GormanC, JaenischR (1991) A generic intron increases gene expression in transgenic mice. Mol Cell Biol 11: 3070–3074.
17. NewmanJR, GhaemmaghamiS, IhmelsJ, BreslowDK, NobleM, et al. (2006) Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature 441: 840–846.
18. BergkesselM, WhitworthGB, GuthrieC (2011) Diverse environmental stresses elicit distinct responses at the level of pre-mRNA. Rna 17: 1461–1478.
19. PleissJA (2007) Department of Biochemistry and Biophysics UoCSF, San Francisco, California, United States of America WhitworthGB (2007) Department of Biochemistry and Biophysics UoCSF, San Francisco, California, United States of America (2007) BergkesselM, et al. (2007) Transcript Specificity in Yeast Pre-mRNA Splicing Revealed by Mutations in Core Spliceosomal Components. PLOS Biology 5: e90.
20. Perez-ValleJ, VilardellJ (2012) Intronic features that determine the selection of the 3′ splice site. Wiley Interdiscip Rev RNA 3: 707–717.
21. AmitM, DonyoM, HollanderD, GorenA, KimE, et al. (2012) Differential GC content between exons and introns establishes distinct strategies. Cell Rep 1: 543–556.
22. GahuraO, HammannC, ValentováA, PůtaF, FolkP (2011) Secondary structure is required for 3′ splice site recognition in yeast. Nucl. Acids Res 39: 9759–9767.
23. RogicS, MontpetitB, HoosHH, MackworthAK, OuelletteBF, et al. (2008) Correlation between the secondary structure of pre-mRNA introns and the efficiency of splicing in Saccharomyces cerevisiae. BMC Genomics 9: 355.
24. GoguelV, RosbashM (1993) Splice site choice and splicing efficiency are positively influenced by pre-mRNA. Cell 72: 893–901.
25. WarfMB, BerglundJA (2010) Role of RNA structure in regulating pre-mRNA splicing. Trends Biochem Sci 35: 169–178.
26. BarashY, CalarcoJA, GaoW, PanQ, WangX, et al. (2010) Deciphering the splicing code. Nature 465: 53–59.
27. Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, et al.. (1998) SGD: Saccharomyces Genome Database.
28. WuchtyS, FontanaW, HofackerIL, SchusterP (1999) Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers 49: 145–165.
29. Cormen CEL T H, Rivest R L, Stein C (2012) Introduction to Algorithms, ISBN 0-262-03293-7.
30. HeinzS, BennerC, SpannN, BertolinoE, LinYC, et al. (2010) Simple combinations of lineage-determining transcription factors prime. Mol Cell 38: 576–589.
Štítky
Genetika Reprodukčná medicínaČlánok vyšiel v časopise
PLOS Genetics
2014 Číslo 6
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