Study of in vitro transcriptional binding effects and noise using constitutive promoters combined with UP element sequences in Escherichia coli

Journal of Biological Engineering

Volumn 11, Issue 1, 2017, Pages

  Yan, Qiang ^a   Fong, Stephen S ^a  

^a VIRGINIA COMMONWEALTH UNIVERSITY   (United States)

Author keywords

Binding association constant; Gene expression noise; Promoter strength; RNA polymerase; RNAP subunits; Upstream element sequence

Indexed keywords

RNA POLYMERASE;

ARTICLE; BINDING AFFINITY; BINDING SITE; CONTROLLED STUDY; DISSOCIATION CONSTANT; DNA SEQUENCE; ESCHERICHIA COLI; EXPERIMENTAL STUDY; FUNCTIONAL GENOMICS; GENE CONSTRUCT; GENE EXPRESSION; GENETIC ENGINEERING; GENETIC TRANSCRIPTION; IN VITRO STUDY; NOISE; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; TRANSCRIPTION REGULATION; UPSTREAM ELEMENT SEQUENCE;

EID: 85032267816     PISSN: None     EISSN: 17541611     Source Type: Journal    
DOI: 10.1186/s13036-017-0075-2     Document Type: Article

References (45)

1. Salis HM, Mirsky EA, Voigt CA. Automated design of synthetic ribosome binding sites to control protein expression. Nat Biotechnol. 2009;27:946-50.
2. Bonde MT, Klausen MS, Anderson MV, Wallin AI, Wang HH, Sommer MO. MODEST: a web-based design tool for oligonucleotide-mediated genome engineering and recombineering. Nucleic Acids Res. 2014;42:W408-15.
3. Alper H, Fischer C, Nevoigt E, Stephanopoulos G. Tuning genetic control through promoter engineering. Proc Natl Acad Sci U S A. 2006;103:12678-83.
4. Cox RS 3rd, Surette MG, Elowitz MB. Programming gene expression with combinatorial promoters. Mol Syst Biol. 2007;3:145.
5. Mutalik VK, Guimaraes JC, Cambray G, Mai QA, Christoffersen MJ, Martin L, Yu A, Lam C, Rodriguez C, Bennett G, et al. Quantitative estimation of activity and quality for collections of functional genetic elements. Nat Methods. 2013;10:347-53.
6. Mutalik VK, Guimaraes JC, Cambray G, Lam C, Christoffersen MJ, Mai QA, Tran AB, Paull M, Keasling JD, Arkin AP, Endy D. Precise and reliable gene expression via standard transcription and translation initiation elements. Nat Methods. 2013;10:354-60.
7. Wu G, Yan Q, Jones J, Tang Y, Fong S, Koffas MAG. Metabolic burden: cornerstones in synthetic biology and metabolic engineering applications. Trends Biotechnol. 2016;34:652-64.
8. Davis CA, Capp MW, Record MT Jr, Saecker RM. The effects of upstream DNA on open complex formation by Escherichia coli RNA polymerase. Proc Natl Acad Sci U S A. 2005;102:285-90.
9. Browning DF, Busby SJ. The regulation of bacterial transcription initiation. Nat Rev Microbiol. 2004;2:57-65.
10. Ross W, Gosink KK, Salomon J, Igarashi K, Zou C, Ishihama A, Severinov K, Gourse RL. A third recognition element in bacterial promoters: DNA binding by the subunit of RNA polymerase. Science. 1993;262:1407-13.
11. Gourse RL, Ross W, Gaal T. UPs and downs in bacterial transcription initiation: the role of the alpha subunit of RNA polymerase in promoter recognition. Mol Microbiol. 2000;37(4):687-95.
12. Estrem ST, Gaal T, Ross W, Gourse RL. Identification of an UP element consensus sequence for bacterial promoters. Proc Natl Acad Sci U S A. 1998;95:9761-6.
13. Aiyar SE, Gourse RL, Ross W. Upstream A-tracts increase bacterial promoter activity through interactions with the RNA polymerase alpha subunit. Proc Natl Acad Sci U S A. 1998;95:14652-7.
14. Meng W, Belyaeva T, Savery NJ, Busby SJ, Ross WE, GAAL T, Gourse RL, Thomas MS. UP element-dependent transcription at the Escherichia coli rrnB P1 promoter positional requirements and role of the RNA polymerase a subunit linker. Nucleic Acids Res. 2001;29:4166-78.
15. Ross W, Aiyar S, Salomon J, Gourse RL. Escherichia coli promoters with UP elements of different strengths modular structure of bacterial promoters. J Bacteriol. 1998;180:5374-83.
16. Hirvonen CA, Ross W, Wozniak CE, Marasco E, Anthony JR, Aiyar SE, Newburn VH, Gourse RL. Contributions of UP element and the transcription factor FIS to expression from the seven rrnP1 promoters in Escherichia coli. J Bacteriol. 2001;183:6305-14.
17. Estrem ST, Ross W, Gaal T, Chen ZS, Niu W, Ebright RH, Gourse RL. Bacterial promoter architecture: subsite structure of UP elements and interactions with the carboxy-terminal domain of the RNA polymerase α-subunit. Genes Dev. 1999;13:2134-47.
18. Raser JM, O'Shea EK. Noise in gene expression: origins, consequences, and control. Science. 2005;309:2010-3.
19. Ozbudak EM, Thattai M, Kurtser I, Grossman AD, van Oudenaarden A. Regulation of noise in the expression of a single gene. Nat Genet. 2002;31:69-73.
20. Kierzek AM, Zaim J, Zielenkiewicz P. The effect of transcription and translation initiation frequencies on the stochastic fluctuations in prokaryotic gene expression. J Biol Chem. 2001;276:8165-72.
21. Thattai M, van Oudenaarden A. Intrinsic noise in gene regulatory networks. Proc Natl Acad Sci U S A. 2001;98:8614-9.
22. Raser JM, O'Shea EK. Control of stochasticity in eukaryotic gene expression. Science. 2004;304:1811-4.
23. Blake WJ, Kaern M, Cantor CR, Collins J. Noise in eukaryotic gene expression. Nature. 2003;422:633-6.
24. Kellis M, Blrren BW, Lander ES. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature. 2004;428:617-24.
25. Torella JP, Boehm CR, Lienert F, Chen J-H, Way JC, Silver PA. Rapid construction of insulated genetic circuits via synthetic sequence-guided isothermmal assembly. Nucleic Acids Res. 2014;42(1):681-9.
26. Gibson DG, Young L, Chuang RY, Venter JC, Hutchison CA 3rd, Smith HO. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods. 2009;6:343-5.
27. Hellman LM, Fried MG. Electrophoretic mobility shift assay (EMSA) for detecting protein-nucleic acid interactions. Nat Protoc. 2007;2:1849-61.
28. Fried MG. Measurement of protein-DNA interaction parameters by electrophoresis mobility shift assay. Electrophoresis. 1989;10:366-76.
29. Rojo F. Repression of transcription initiation in bacteria. J Bacteriol. 1999;181:2987-91.
30. Ellinger T, Behnke D, Bujard H, Gralla JD. Stalling of Escherichia coli RNA polymerase in the +6 to +12 region in vivo is associated with tight binding to consensus promoter elements. J Mol Biol. 1994;239:455-65.
31. Ross W, Aiyar SE, Salomon J, Gourse RL. Escherichia coli promoters with UP elements of different strengths modular structure of bacterial promoters. J Bacteriol. 1998;180:5374-83.
32. Ross W, Gourse RL. Sequence-independent upstream DNA-alphaCTD interactions strongly stimulate Escherichia coli RNA polymerase-lacUV5 promoter association. Proc Natl Acad Sci U S A. 2005;102:291-6.
33. Brewster RC, Jones DL, Phillips R. Tuning promoter strength through RNA polymerase binding site design in Escherichia coli. PLoS Comput Biol. 2012;8(12):e1002811.
34. E. Proc Natl Acad Sci U S A. 2010;107(7):2854-9.
35. Schmiedel JM, Klemm SL, Zheng Y, Sahay A, Bliithgen N, Marks DS, van Oudenaarden A. MicroRNA control of protein expression noise. Science. 2015;348:128-32.
36. Walters MC, Fiering S, Eidemiller J, Magis W, Groudine M, Martin DI. Enhancers increase the probability but not the level of gene expression. Proc Natl Acad Sci U S A. 1995;92:7125-9.
37. Sharon E, van Dijk D, Kalma Y, Keren L, Manor O, Yakhini Z, Segal E. Probing the effect of promoters on noise in gene expression using thousands of designed sequences. Genome Res. 2014;24:1698-706.
38. Blake WJ, Kaern M, Cantor CR, Collins JJ. Noise in eukaryotic gene expression. Nature. 2003;422:633-7.
39. Ebert MS, Sharp PA. Roles for microRNAs in conferring robustness to biological processes. Cell. 2012;149:515-24.
40. Noorbakhsh J, Lang AH, Mehta P. Intrinsic noise of microRNA-regulated genes and the ceRNA hypothesis. PLoS One. 2013;8:e72676-93.
41. Liu J, Francois JM, Capp JP. Use of noise in gene expression as an experimental parameter to test phenotypic effects. Yeast. 2016;33:209-16.
42. Xu P, Gu Q, Wang WY, Wong L, Bower AGW, Collins CH, Koffas MAG. Modular optimization of multigene pathways for fatty acids production in E. coli. Nat Commun. 2013;4:8.
43. Zhou S, Du G, Kang Z, Li J, Chen J, Li H, Zhou J. The application of powerful promoters to enhance gene expression in industrial microorganisms. World J Microbiol Biotechnol. 2017;33:23.
44. Sheppard MJ, Kunjapur AM, Prather KLJ. Modular and selective biosynthesis of gasoline-range alkanes. Metab Eng. 2016;33:76-85.
45. Zhou S. Obtaining a panel of cascade promoter-5'-UTR complexes in Escherichia coli. ACS Synth Biol. 2017;6:1065-75.