Literature DB >> 24736794

A versatile framework for microbial engineering using synthetic non-coding RNAs.

Lei S Qi1, Adam P Arkin2.   

Abstract

Synthetic non-coding RNAs have emerged as a versatile class of molecular devices that have a diverse range of programmable functions, including signal sensing, gene regulation and the modulation of molecular interactions. Owing to their small size and the central role of Watson-Crick base pairing in determining their structure, function and interactions, several distinct types of synthetic non-coding RNA regulators that are functional at the DNA, mRNA and protein levels have been experimentally characterized and computationally modelled. These engineered devices can be incorporated into genetic circuits, enabling the more efficient creation of complex synthetic biological systems. In this Review, we summarize recent progress in engineering synthetic non-coding RNA devices and their application to genetic and cellular engineering in a broad range of microorganisms.

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Year:  2014        PMID: 24736794     DOI: 10.1038/nrmicro3244

Source DB:  PubMed          Journal:  Nat Rev Microbiol        ISSN: 1740-1526            Impact factor:   60.633


  130 in total

1.  Synthetic riboswitches that induce gene expression in diverse bacterial species.

Authors:  Shana Topp; Colleen M K Reynoso; Jessica C Seeliger; Ian S Goldlust; Shawn K Desai; Dorothée Murat; Aimee Shen; Aaron W Puri; Arash Komeili; Carolyn R Bertozzi; June R Scott; Justin P Gallivan
Journal:  Appl Environ Microbiol       Date:  2010-10-08       Impact factor: 4.792

Review 2.  Regulation of translation via mRNA structure in prokaryotes and eukaryotes.

Authors:  Marilyn Kozak
Journal:  Gene       Date:  2005-10-05       Impact factor: 3.688

3.  Targeted genome modification of crop plants using a CRISPR-Cas system.

Authors:  Qiwei Shan; Yanpeng Wang; Jun Li; Yi Zhang; Kunling Chen; Zhen Liang; Kang Zhang; Jinxing Liu; Jianzhong Jeff Xi; Jin-Long Qiu; Caixia Gao
Journal:  Nat Biotechnol       Date:  2013-08       Impact factor: 54.908

4.  Translational control of IS10 transposition.

Authors:  R W Simons; N Kleckner
Journal:  Cell       Date:  1983-09       Impact factor: 41.582

5.  Genetic control of mammalian T-cell proliferation with synthetic RNA regulatory systems.

Authors:  Yvonne Y Chen; Michael C Jensen; Christina D Smolke
Journal:  Proc Natl Acad Sci U S A       Date:  2010-04-26       Impact factor: 11.205

6.  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

Review 7.  Transcriptional regulatory circuits: predicting numbers from alphabets.

Authors:  Harold D Kim; Tal Shay; Erin K O'Shea; Aviv Regev
Journal:  Science       Date:  2009-07-24       Impact factor: 47.728

8.  Design principles for ligand-sensing, conformation-switching ribozymes.

Authors:  Xi Chen; Andrew D Ellington
Journal:  PLoS Comput Biol       Date:  2009-12-24       Impact factor: 4.475

9.  RNA-guided editing of bacterial genomes using CRISPR-Cas systems.

Authors:  Wenyan Jiang; David Bikard; David Cox; Feng Zhang; Luciano A Marraffini
Journal:  Nat Biotechnol       Date:  2013-01-29       Impact factor: 54.908

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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  29 in total

1.  Exploring the Dynamics and Mutational Landscape of Riboregulation with a Minimal Synthetic Circuit in Living Cells.

Authors:  Guillermo Rodrigo; Eszter Majer; Satya Prakash; José-Antonio Daròs; Alfonso Jaramillo; Juan F Poyatos
Journal:  Biophys J       Date:  2015-09-01       Impact factor: 4.033

2.  Creating small transcription activating RNAs.

Authors:  James Chappell; Melissa K Takahashi; Julius B Lucks
Journal:  Nat Chem Biol       Date:  2015-02-02       Impact factor: 15.040

3.  Primerize-2D: automated primer design for RNA multidimensional chemical mapping.

Authors:  Siqi Tian; Rhiju Das
Journal:  Bioinformatics       Date:  2017-05-01       Impact factor: 6.937

4.  Dynamic ensemble of HIV-1 RRE stem IIB reveals non-native conformations that disrupt the Rev-binding site.

Authors:  Chia-Chieh Chu; Raphael Plangger; Christoph Kreutz; Hashim M Al-Hashimi
Journal:  Nucleic Acids Res       Date:  2019-07-26       Impact factor: 16.971

Review 5.  Rapid prototyping of microbial cell factories via genome-scale engineering.

Authors:  Tong Si; Han Xiao; Huimin Zhao
Journal:  Biotechnol Adv       Date:  2014-11-20       Impact factor: 14.227

6.  AptaBlocks: Designing RNA complexes and accelerating RNA-based drug delivery systems.

Authors:  Yijie Wang; Jan Hoinka; Yong Liang; Tomasz Adamus; Piotr Swiderski; Teresa M Przytycka
Journal:  Nucleic Acids Res       Date:  2018-09-19       Impact factor: 16.971

Review 7.  Regulatory RNAs in Bacillus subtilis: a Gram-Positive Perspective on Bacterial RNA-Mediated Regulation of Gene Expression.

Authors:  Ruben A T Mars; Pierre Nicolas; Emma L Denham; Jan Maarten van Dijl
Journal:  Microbiol Mol Biol Rev       Date:  2016-10-26       Impact factor: 11.056

Review 8.  Bacterial CRISPR: accomplishments and prospects.

Authors:  Jason M Peters; Melanie R Silvis; Dehua Zhao; John S Hawkins; Carol A Gross; Lei S Qi
Journal:  Curr Opin Microbiol       Date:  2015-09-10       Impact factor: 7.934

Review 9.  Genomes by design.

Authors:  Adrian D Haimovich; Paul Muir; Farren J Isaacs
Journal:  Nat Rev Genet       Date:  2015-08-11       Impact factor: 53.242

Review 10.  Genetically encoded RNA nanodevices for cellular imaging and regulation.

Authors:  Qikun Yu; Kewei Ren; Mingxu You
Journal:  Nanoscale       Date:  2021-05-06       Impact factor: 7.790

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