Using RNA as Molecular Code for Programming Cellular Function

Kushwaha, Manish; Rostain, William; Prakash, Satya; Duncan, John N.; Jaramillo, Alfonso

doi:10.1021/acssynbio.5b00297

Cited by 48 publications

(47 citation statements)

References 216 publications

(434 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Over the last years, riboswitches have increasingly gained attention in the field of synthetic biology, as they allow conditional control of gene expression by external ligands, representing a versatile tool for reprogramming of cells (54–56). The combination of in vitro generated aptamer domains specific for a whole plethora of target molecules with suited regulatory domains opens the principle possibility to generate custom-designed orthogonal devices regulating gene expression in pro- and eukaryotes (57,55,10,58,59).…”

Section: Discussionmentioning

confidence: 99%

Applicability of a computational design approach for synthetic riboswitches

et al. 2016

View full text Add to dashboard Cite

Riboswitches have gained attention as tools for synthetic biology, since they enable researchers to reprogram cells to sense and respond to exogenous molecules. In vitro evolutionary approaches produced numerous RNA aptamers that bind such small ligands, but their conversion into functional riboswitches remains difficult. We previously developed a computational approach for the design of synthetic theophylline riboswitches based on secondary structure prediction. These riboswitches have been constructed to regulate ligand-dependent transcription termination in Escherichia coli. Here, we test the usability of this design strategy by applying the approach to tetracycline and streptomycin aptamers. The resulting tetracycline riboswitches exhibit robust regulatory properties in vivo. Tandem fusions of these riboswitches with theophylline riboswitches represent logic gates responding to two different input signals. In contrast, the conversion of the streptomycin aptamer into functional riboswitches appears to be difficult. Investigations of the underlying aptamer secondary structure revealed differences between in silico prediction and structure probing. We conclude that only aptamers adopting the minimal free energy (MFE) structure are suitable targets for construction of synthetic riboswitches with design approaches based on equilibrium thermodynamics of RNA structures. Further improvements in the design strategy are required to implement aptamer structures not corresponding to the calculated MFE state.

show abstract

Section: Discussionmentioning

confidence: 99%

Applicability of a computational design approach for synthetic riboswitches

et al. 2016

View full text Add to dashboard Cite

show abstract

“…In addition to these technologies, the discovery, understanding and application of gene expression devices (e.g. riboswitches and aptamers) allow for the fine-tune regulation of gene expression in complex pathways (Kushwaha et al, 2016). Likewise, the development of biosensors has helped in screening and improving the synthesis of both bulk and fine chemicals.…”

Section: Escherichia Colimentioning

confidence: 99%

Chasing bacterial chassis for metabolic engineering: a perspective review from classical to non‐traditional microorganisms

Calero

Nikel

2018

Microbial Biotechnology

209

184

View full text Add to dashboard Cite

The last few years have witnessed an unprecedented increase in the number of novel bacterial species that hold potential to be used for metabolic engineering. Historically, however, only a handful of bacteria have attained the acceptance and widespread use that are needed to fulfil the needs of industrial bioproduction - and only for the synthesis of very few, structurally simple compounds. One of the reasons for this unfortunate circumstance has been the dearth of tools for targeted genome engineering of bacterial chassis, and, nowadays, synthetic biology is significantly helping to bridge such knowledge gap. Against this background, in this review, we discuss the state of the art in the rational design and construction of robust bacterial chassis for metabolic engineering, presenting key examples of bacterial species that have secured a place in industrial bioproduction. The emergence of novel bacterial chassis is also considered at the light of the unique properties of their physiology and metabolism, and the practical applications in which they are expected to outperform other microbial platforms. Emerging opportunities, essential strategies to enable successful development of industrial phenotypes, and major challenges in the field of bacterial chassis development are also discussed, outlining the solutions that contemporary synthetic biology-guided metabolic engineering offers to tackle these issues.

show abstract

“…RNA‐based regulatory elements have many important functional properties that have led to the widespread exploration of their potential use as regulatory tools in synthetic biology (Kushwaha et al . ). For instance, they are theoretically modular in nature (i.e.…”

Section: Introductionmentioning

confidence: 97%

“…In contrast, riboswitches are excellent candidates to modulate gene expression in a ligand-dependent manner without the involvement of organism-specific promoter sequences or factors (Tucker and Breaker 2005;Scott et al 2010;Ma et al 2014). RNA-based regulatory elements have many important functional properties that have led to the widespread exploration of their potential use as regulatory tools in synthetic biology (Kushwaha et al 2016). For instance, they are theoretically modular in nature (i.e.…”

Section: Introductionmentioning

confidence: 99%

Applications and limitations of regulatoryRNAelements in synthetic biology and biotechnology

et al. 2019

View full text Add to dashboard Cite

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.

show abstract

Using RNA as Molecular Code for Programming Cellular Function

Cited by 48 publications

References 216 publications

Applicability of a computational design approach for synthetic riboswitches

Applicability of a computational design approach for synthetic riboswitches

Chasing bacterial chassis for metabolic engineering: a perspective review from classical to non‐traditional microorganisms

Applications and limitations of regulatoryRNAelements in synthetic biology and biotechnology

Contact Info

Product

Resources

About