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Serganov, A. & Patel, D.J. Ribozymes, riboswitches and beyond: regulation of gene expression without proteins. Nat. Rev. Genet. 8, 776-790

Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA.
Nature Reviews Genetics (Impact Factor: 36.98). 11/2007; 8(10):776-90. DOI: 10.1038/nrg2172
Source: PubMed

ABSTRACT

Although various functions of RNA are carried out in conjunction with proteins, some catalytic RNAs, or ribozymes, which contribute to a range of cellular processes, require little or no assistance from proteins. Furthermore, the discovery of metabolite-sensing riboswitches and other types of RNA sensors has revealed RNA-based mechanisms that cells use to regulate gene expression in response to internal and external changes. Structural studies have shown how these RNAs can carry out a range of functions. In addition, the contribution of ribozymes and riboswitches to gene expression is being revealed as far more widespread than was previously appreciated. These findings have implications for understanding how cellular functions might have evolved from RNA-based origins.

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    • "Hence, increasingly complex regulatory mechanisms are and will be designed by assembling RNA in a modular fashion to attain nonlinearly responding circuit components. This will render the use of transcription factors for the construction of sophisticated genetic circuits superfluous (Serganov and Patel, 2007). It should however be mentioned that sRNAs and transcription factors can work seamlessly together in hybrid synthetic circuits or that the differences in sRNA and transcription factor characteristics can be exploited to obtain the desired regulatory behaviour (Hussein and Lim, 2012). "
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    ABSTRACT: Synthetic biology, in close concert with systems biology, is revolutionizing the field of metabolic engineering by providing novel tools and technologies to rationally, in a standardized way, reroute metabolism with a view to optimally converting renewable resources into a broad range of bio-products, bio-materials and bio-energy. Increasingly, these novel synthetic biology tools are exploiting the extensive programmable nature of RNA, vis-à-vis DNA- and protein-based devices, to rationally design standardized, composable, and orthogonal parts, which can be scaled and tuned promptly and at will. This review gives an extensive overview of the recently developed parts and tools for i) modulating gene expression ii) building genetic circuits iii) detecting molecules, iv) reporting cellular processes and v) building RNA nanostructures. These parts and tools are becoming necessary armamentarium for contemporary metabolic engineering. Furthermore, the design criteria, technological challenges, and recent metabolic engineering success stories of the use of RNA devices are highlighted. Finally, the future trends in transforming metabolism through RNA engineering are critically evaluated and summarized.
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    • "Among many functionally important motional modes, changes in RNA secondary structure can expose or sequester key regulatory elements, and thereby provide the basis for molecular switches that regulate and control a wide range of biochemical processes (Breaker, 2011; Dethoff, Chugh, et al., 2012; Serganov & Patel, 2007). For example, riboswitches (Grundy, Winkler, & Henkin, 2002; Winkler, Nahvi, & Breaker, 2002) are RNA-based genetic elements typically embedded in the 5 0 untranslated region (5 0 UTR) of bacterial genes that employ changes in secondary structure in order to regulate expression of metabolic genes in response to changes in cellular metabolite concentration (Schwalbe et al., 2007; Serganov & Patel, 2007). In a prototypical metabolite riboswitch (Tucker & Breaker, 2005), a ligand metabolite, such as adenine, binds the aptamer domain and induces a conformational change, which typically sequesters an RNA element into a helix (Fig. 1A). "
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    ABSTRACT: Changes in RNA secondary structure play fundamental roles in the cellular functions of a growing number of noncoding RNAs. This chapter describes NMR-based approaches for characterizing microsecond-to-millisecond changes in RNA secondary structure that are directed toward short-lived and low-populated species often referred to as "excited states." Compared to larger scale changes in RNA secondary structure, transitions toward excited states do not require assistance from chaperones, are often orders of magnitude faster, and are localized to a small number of nearby base pairs in and around noncanonical motifs. Here, we describe a procedure for characterizing RNA excited states using off-resonance R1ρ NMR relaxation dispersion utilizing low-to-high spin-lock fields (25-3000Hz). R1ρ NMR relaxation dispersion experiments are used to measure carbon and nitrogen chemical shifts in base and sugar moieties of the excited state. The chemical shift data are then interpreted with the aid of secondary structure prediction to infer potential excited states that feature alternative secondary structures. Candidate structures are then tested by using mutations, single-atom substitutions, or by changing physiochemical conditions, such as pH and temperature, to either stabilize or destabilize the candidate excited state. The resulting chemical shifts of the mutants or under different physiochemical conditions are then compared to those of the ground and excited states. Application is illustrated with a focus on the transactivation response element from the human immune deficiency virus type 1, which exists in dynamic equilibrium with at least two distinct excited states. © 2015 Elsevier Inc. All rights reserved.
    Full-text · Article · Jun 2015 · Methods in enzymology
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    • "Riboswitches represent a common type of noncoding RNA that is present in the 5 0 UTRs of certain mRNAs (Serganov & Nudler, 2013). They offer important specialized components involved in the regulation of cellular function and operate through a conformational switch upon binding to a ligand (Barrick & Breaker, 2007; Breaker, 2012; Serganov & Patel, 2007). The regulatory mechanisms involved include, for example, formation or deletion of transcription terminator (Peselis & Serganov, 2012; Proshkin, Mironov, & Nudler, 2014), sequestration of ribosome-binding sites (Winkler & Breaker, 2005), and emergence of alternative cleavage sites (Cheah, Wachter, Sudarsan, & Breaker, 2007). "
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    ABSTRACT: The modular organization of RNA structure has been exploited in various computational and theoretical approaches to identify RNA tertiary (3D) motifs and assemble RNA structures. Riboswitches exemplify this modularity in terms of both structural and functional adaptability of RNA components. Here, we extend our computational approach based on tree graph sampling to the prediction of riboswitch topologies by defining additional edges to mimick pseudoknots. Starting from a secondary (2D) structure, we construct an initial graph deduced from predicted junction topologies by our data-mining algorithm RNAJAG trained on known RNAs; we sample these graphs in 3D space guided by knowledge-based statistical potentials derived from bending and torsion measures of internal loops as well as radii of gyration for known RNAs. We present graph sampling results for 10 representative riboswitches, 6 of them with pseudoknots, and compare our predictions to solved structures based on global and local RMSD measures. Our results indicate that the helical arrangements in riboswitches can be approximated using our combination of modified 3D tree graph representations for pseudoknots, junction prediction, graph moves, and scoring functions. Future challenges in the field of riboswitch prediction and design are also discussed. © 2015 Elsevier Inc. All rights reserved.
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