Literature DB >> 24356572

Regulatory RNAs: charming gene management styles for synthetic biology applications.

Jorge Vazquez-Anderson1, Lydia M Contreras1.   

Abstract

RNAs have many important functional properties, including that they are independently controllable and highly tunable. As a result of these advantageous properties, their use in a myriad of sophisticated devices has been widely explored. Yet, the exploitation of RNAs for synthetic applications is highly dependent on the ability to characterize the many new molecules that continue to be discovered by large-scale sequencing and high-throughput screening techniques. In this review, we present an exhaustive survey of the most recent synthetic bacterial riboswitches and small RNAs while emphasizing their virtues in gene expression management. We also explore the use of these RNA components as building blocks in the RNA synthetic biology toolbox and discuss examples of synthetic RNA components used to rewire bacterial regulatory circuitry. We anticipate that this field will expand its catalog of smart devices by mimicking and manipulating natural RNA mechanisms and functions.

Entities:  

Keywords:  RNA regulation; RNAs and biotechnology; riboswitches; small RNAs; synthetic RNAs; transcriptional control; translational control

Mesh:

Substances:

Year:  2013        PMID: 24356572      PMCID: PMC3917981          DOI: 10.4161/rna.27102

Source DB:  PubMed          Journal:  RNA Biol        ISSN: 1547-6286            Impact factor:   4.652


  137 in total

Review 1.  Gene regulation by riboswitches.

Authors:  Maumita Mandal; Ronald R Breaker
Journal:  Nat Rev Mol Cell Biol       Date:  2004-06       Impact factor: 94.444

2.  Post-transcriptional Boolean computation by combining aptazymes controlling mRNA translation initiation and tRNA activation.

Authors:  Benedikt Klauser; Athanasios Saragliadis; Simon Ausländer; Markus Wieland; Michael R Berthold; Jörg S Hartig
Journal:  Mol Biosyst       Date:  2012-07-09

Review 3.  Expanding the metabolic engineering toolbox: more options to engineer cells.

Authors:  Keith E Tyo; Hal S Alper; Gregory N Stephanopoulos
Journal:  Trends Biotechnol       Date:  2007-01-24       Impact factor: 19.536

4.  RNA quadruplex-based modulation of gene expression.

Authors:  Markus Wieland; Jörg S Hartig
Journal:  Chem Biol       Date:  2007-07

Review 5.  Hfq structure, function and ligand binding.

Authors:  Richard G Brennan; Todd M Link
Journal:  Curr Opin Microbiol       Date:  2007-03-28       Impact factor: 7.934

6.  Improved aptazyme design and in vivo screening enable riboswitching in bacteria.

Authors:  Markus Wieland; Jörg S Hartig
Journal:  Angew Chem Int Ed Engl       Date:  2008       Impact factor: 15.336

7.  Synthetic riboswitches for the conditional control of gene expression in Streptomyces coelicolor.

Authors:  Martin M Rudolph; Michael-Paul Vockenhuber; Beatrix Suess
Journal:  Microbiology (Reading)       Date:  2013-05-15       Impact factor: 2.777

8.  Translational control of IS10 transposition.

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

9.  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

10.  Use of a riboswitch-controlled conditional hypomorphic mutation to uncover a role for the essential csrA gene in bacterial autoaggregation.

Authors:  Ye Jin; Rory M Watt; Antoine Danchin; Jian-dong Huang
Journal:  J Biol Chem       Date:  2009-08-25       Impact factor: 5.157

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  16 in total

Review 1.  Synthetic small regulatory RNAs in microbial metabolic engineering.

Authors:  Wen-Hai Xie; Hong-Kuan Deng; Jie Hou; Li-Juan Wang
Journal:  Appl Microbiol Biotechnol       Date:  2020-11-17       Impact factor: 4.813

2.  A comparative study of sequence- and structure-based features of small RNAs and other RNAs of bacteria.

Authors:  Amita Barik; Santasabuj Das
Journal:  RNA Biol       Date:  2017-11-13       Impact factor: 4.652

3.  Optimization of a novel biophysical model using large scale in vivo antisense hybridization data displays improved prediction capabilities of structurally accessible RNA regions.

Authors:  Jorge Vazquez-Anderson; Mia K Mihailovic; Kevin C Baldridge; Kristofer G Reyes; Katie Haning; Seung Hee Cho; Paul Amador; Warren B Powell; Lydia M Contreras
Journal:  Nucleic Acids Res       Date:  2017-05-19       Impact factor: 16.971

4.  Integrative FourD omics approach profiles the target network of the carbon storage regulatory system.

Authors:  Steven W Sowa; Grant Gelderman; Abigail N Leistra; Aishwarya Buvanendiran; Sarah Lipp; Areen Pitaktong; Christopher A Vakulskas; Tony Romeo; Michael Baldea; Lydia M Contreras
Journal:  Nucleic Acids Res       Date:  2017-02-28       Impact factor: 16.971

5.  Transcriptional analysis of Deinococcus radiodurans reveals novel small RNAs that are differentially expressed under ionizing radiation.

Authors:  Chen-Hsun Tsai; Rick Liao; Brendan Chou; Lydia M Contreras
Journal:  Appl Environ Microbiol       Date:  2014-12-29       Impact factor: 4.792

6.  A Genome-Wide Search for Ionizing-Radiation-Responsive Elements in Deinococcus radiodurans Reveals a Regulatory Role for the DNA Gyrase Subunit A Gene's 5' Untranslated Region in the Radiation and Desiccation Response.

Authors:  Jordan K Villa; Paul Amador; Justin Janovsky; Arijit Bhuyan; Roland Saldanha; Thomas J Lamkin; Lydia M Contreras
Journal:  Appl Environ Microbiol       Date:  2017-05-31       Impact factor: 4.792

7.  Discovery and Characterization of Native Deinococcus radiodurans Promoters for Tunable Gene Expression.

Authors:  Angela Chen; Mark W Sherman; Cynthia Chu; Natalia Gonzalez; Tulshi Patel; Lydia M Contreras
Journal:  Appl Environ Microbiol       Date:  2019-10-16       Impact factor: 4.792

Review 8.  Synthetic Biology of Small RNAs and Riboswitches.

Authors:  Jordan K Villa; Yichi Su; Lydia M Contreras; Ming C Hammond
Journal:  Microbiol Spectr       Date:  2018-05

9.  Exploiting post-transcriptional regulation to probe RNA structures in vivo via fluorescence.

Authors:  Steven W Sowa; Jorge Vazquez-Anderson; Chelsea A Clark; Ricardo De La Peña; Kaitlin Dunn; Emily K Fung; Mark J Khoury; Lydia M Contreras
Journal:  Nucleic Acids Res       Date:  2014-11-21       Impact factor: 16.971

10.  Optimizing metabolite production using periodic oscillations.

Authors:  Steven W Sowa; Michael Baldea; Lydia M Contreras
Journal:  PLoS Comput Biol       Date:  2014-06-05       Impact factor: 4.475

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