Applications and limitations of regulatoryRNAelements in synthetic biology and biotechnology

Abstract

Summary Synthetic biology requires the design and implementation of novel enzymes, genetic circuits or even entire cells, which can be controlled by the user. RNA‐based regulatory elements have many important functional properties in this regard, such as their modular nature and their ability to respond to specific external stimuli. These properties have led to the widespread exploration of their use as gene regulation devices in synthetic biology. In this review, we focus on two major types of RNA elements: riboswitches and RNA thermometers (RNATs). We describe their general structure and function, before discussing their potential uses in synthetic biology (e.g. in the production of biofuels and biodegradable plastics). We also discuss their limitations, and novel strategies to implement RNA‐based regulatory devices in biotechnological applications. We close with a description of some common model organisms used in synthetic biology, with a focus on the current applications and limitations of RNA‐based regulation.

Quantitative mapping of mRNA 3’ ends in Pseudomonas aeruginosa reveals a pervasive role for premature 3’ end formation in response to azithromycin

“…The activities of riboregulators are often mediated by interaction of the nascent transcript with small molecules, ribosomes, tRNAs, or regulatory proteins. As such, riboregulators are potential therapeutic targets, and may provide synthetic biology applications [52][53][54][55]. Since conditional premature transcription termination regulates biofilm formation, virulence, and expression of antibiotic resistance genes in other bacteria [40,51,56,57], efforts to identify and characterize genes likely to be controlled by riboregulators in P. aeruginosa would be beneficial.…”

Approaches to genetic tool development for rapid domestication of non-model microorganisms

“…Gene expression can also be regulated post-transcriptionally. Riboswitches are regulatory mRNA elements in the 5′ untranslated region that are capable of regulating gene expression through small molecule-induced structural switching [214]. They add a layer of regulation, but are less explored for the engineering of non-model microbes relative to model organisms like E. coli.…”

“…In this mechanism, mRNA forms two distinct shapes depending on the presence of a specific small molecule, which either blocks or allows translation. Examples of the use of riboswitches for engineering of non-model microbes include theophylline for inducible production of biofuels and other compounds [215], lysine to balance flux for competing pathways [214,216], and flavonoids such as naringenin for increased production of flavonoids [217]. Recently, thermophilic riboswitches have also been identified and used to regulate biofuel production [218].…”

A Novel Non-Coding RNA CsiR Regulates the Ciprofloxacin Resistance in Proteus vulgaris by Interacting with emrB mRNA

“…A large number of studies have shown that ncRNAs are widely involved in the regulation of bacterial oxidative stress resistance [ 4 , 5 ], biofilm formation [ 6 , 7 , 8 ], osmotic pressure [ 9 , 10 ], virulence factor expression [ 11 , 12 ], bacterial antibiotic resistance [ 13 , 14 , 15 ], and many other physiological processes, among which the research of ncRNAs on the regulation of antibiotic resistance has become an important issue in recent years due to global drug resistance emergence. In view of their regulatory flexibility and low metabolic burden, ncRNAs have become one of the most versatile biobricks in the field of synthetic biology and metabolic engineering [ 16 , 17 , 18 ]. According to a number of studies, bacterial ncRNAs play regulatory roles in different modes, the most widely known of which are functioning via the interaction with the target mRNA [ 5 , 19 , 20 ].…”