Literature DB >> 23479654

Library of synthetic transcriptional AND gates built with split T7 RNA polymerase mutants.

David L Shis1, Matthew R Bennett.   

Abstract

The construction of synthetic gene circuits relies on our ability to engineer regulatory architectures that are orthogonal to the host's native regulatory pathways. However, as synthetic gene circuits become larger and more complicated, we are limited by the small number of parts, especially transcription factors, that work well in the context of the circuit. The current repertoire of transcription factors consists of a limited selection of activators and repressors, making the implementation of transcriptional logic a complicated and component-intensive process. To address this, we modified bacteriophage T7 RNA polymerase (T7 RNAP) to create a library of transcriptional AND gates for use in Escherichia coli by first splitting the protein and then mutating the DNA recognition domain of the C-terminal fragment to alter its promoter specificity. We first demonstrate that split T7 RNAP is active in vivo and compare it with full-length enzyme. We then create a library of mutant split T7 RNAPs that have a range of activities when used in combination with a complimentary set of altered T7-specific promoters. Finally, we assay the two-input function of both wild-type and mutant split T7 RNAPs and find that regulated expression of the N- and C-terminal fragments of the split T7 RNAPs creates AND logic in each case. This work demonstrates that mutant split T7 RNAP can be used as a transcriptional AND gate and introduces a unique library of components for use in synthetic gene circuits.

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Year:  2013        PMID: 23479654      PMCID: PMC3612686          DOI: 10.1073/pnas.1220157110

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  36 in total

1.  Model-driven engineering of RNA devices to quantitatively program gene expression.

Authors:  James M Carothers; Jonathan A Goler; Darmawi Juminaga; Jay D Keasling
Journal:  Science       Date:  2011-12-23       Impact factor: 47.728

2.  Structural basis for the transition from initiation to elongation transcription in T7 RNA polymerase.

Authors:  Y Whitney Yin; Thomas A Steitz
Journal:  Science       Date:  2002-09-19       Impact factor: 47.728

3.  An externally tunable bacterial band-pass filter.

Authors:  Takayuki Sohka; Richard A Heins; Ryan M Phelan; Jennifer M Greisler; Craig A Townsend; Marc Ostermeier
Journal:  Proc Natl Acad Sci U S A       Date:  2009-06-05       Impact factor: 11.205

4.  Engineering static and dynamic control of synthetic pathways.

Authors:  William J Holtz; Jay D Keasling
Journal:  Cell       Date:  2010-01-08       Impact factor: 41.582

5.  Gene expression from plasmids containing the araBAD promoter at subsaturating inducer concentrations represents mixed populations.

Authors:  D A Siegele; J C Hu
Journal:  Proc Natl Acad Sci U S A       Date:  1997-07-22       Impact factor: 11.205

6.  T7 RNA polymerase mutants with altered promoter specificities.

Authors:  C A Raskin; G A Diaz; W T McAllister
Journal:  Proc Natl Acad Sci U S A       Date:  1993-04-15       Impact factor: 11.205

7.  Genetic switchboard for synthetic biology applications.

Authors:  Jarred M Callura; Charles R Cantor; James J Collins
Journal:  Proc Natl Acad Sci U S A       Date:  2012-03-27       Impact factor: 11.205

8.  Interactions of a proteolytically nicked RNA polymerase of bacteriophage T7 with its promoter.

Authors:  R A Ikeda; C C Richardson
Journal:  J Biol Chem       Date:  1987-03-15       Impact factor: 5.157

9.  A combined in vitro/in vivo selection for polymerases with novel promoter specificities.

Authors:  J Chelliserrykattil; G Cai; A D Ellington
Journal:  BMC Biotechnol       Date:  2001-12-28       Impact factor: 2.563

10.  A fast, robust and tunable synthetic gene oscillator.

Authors:  Jesse Stricker; Scott Cookson; Matthew R Bennett; William H Mather; Lev S Tsimring; Jeff Hasty
Journal:  Nature       Date:  2008-10-29       Impact factor: 49.962

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  47 in total

Review 1.  Recent advances and opportunities in synthetic logic gates engineering in living cells.

Authors:  Vijai Singh
Journal:  Syst Synth Biol       Date:  2014-08-28

2.  Split T7 RNA polymerase biosensors to study multiprotein interaction dynamics.

Authors:  Jeffrey A Dewey; Bryan C Dickinson
Journal:  Methods Enzymol       Date:  2020-06-15       Impact factor: 1.600

3.  Evolution of a split RNA polymerase as a versatile biosensor platform.

Authors:  Jinyue Pu; Julia Zinkus-Boltz; Bryan C Dickinson
Journal:  Nat Chem Biol       Date:  2017-02-13       Impact factor: 15.040

4.  The Timing of Transcriptional Regulation in Synthetic Gene Circuits.

Authors:  Yu-Yu Cheng; Andrew J Hirning; Krešimir Josić; Matthew R Bennett
Journal:  ACS Synth Biol       Date:  2017-09-05       Impact factor: 5.110

5.  Engineered temperature compensation in a synthetic genetic clock.

Authors:  Faiza Hussain; Chinmaya Gupta; Andrew J Hirning; William Ott; Kathleen S Matthews; Kresimir Josic; Matthew R Bennett
Journal:  Proc Natl Acad Sci U S A       Date:  2014-01-06       Impact factor: 11.205

6.  CRISPR-based curing and analysis of metabolic burden of cryptic plasmids in Escherichia coli Nissle 1917.

Authors:  Halimatun S Zainuddin; Yanfen Bai; Thomas J Mansell
Journal:  Eng Life Sci       Date:  2019-06-03       Impact factor: 2.678

7.  Evolution of C-Terminal Modification Tolerance in Full-Length and Split T7 RNA Polymerase Biosensors.

Authors:  Jinyue Pu; Michael Disare; Bryan C Dickinson
Journal:  Chembiochem       Date:  2019-04-17       Impact factor: 3.164

Review 8.  Principles of genetic circuit design.

Authors:  Jennifer A N Brophy; Christopher A Voigt
Journal:  Nat Methods       Date:  2014-05       Impact factor: 28.547

9.  Bacteriophage-based synthetic biology for the study of infectious diseases.

Authors:  Robert J Citorik; Mark Mimee; Timothy K Lu
Journal:  Curr Opin Microbiol       Date:  2014-07-03       Impact factor: 7.934

10.  A Split Transcriptional Repressor That Links Protein Solubility to an Orthogonal Genetic Circuit.

Authors:  Yimeng Zeng; Alicia M Jones; Emily E Thomas; Barbara Nassif; Jonathan J Silberg; Laura Segatori
Journal:  ACS Synth Biol       Date:  2018-08-23       Impact factor: 5.110

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