Cellular logic with orthogonal ribosomes. J Am Chem Soc

Mrc Harwell, Oxford, England, United Kingdom
Journal of the American Chemical Society (Impact Factor: 11.44). 01/2006; 127(50):17584-5. DOI: 10.1021/ja055338d
Source: PubMed

ABSTRACT The creation and use of unnatural molecules to control cellular function is a long standing goal of the chemical community, but in general, these efforts have been directed at finding molecules to inhibit or activate a particular molecular target or function, or to elicit a particular phenotype. Here we show that multiple unnatural molecules (orthogonal ribosomes) can be used combinatorially, in a single cell, to program Boolean logic functions. These experiments show how attention to the molecular specificity of noncovalent interactions between unnatural macromolecules allows the synthesis of complex function from the "bottom-up" in living matter.

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Available from: Oliver Rackham, Aug 23, 2015
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    • "However, because orthogonal ribosomes (O-ribosomes) are not constrained by any requirement to translate the proteome, they can be extensively mutated to alter and explore their properties. This property has been used to perform large-scale mutagenesis of the rRNA residues that make up the interface between large and small ribosomal subunits [40] and also to build synthetic gene regulatory circuits controlled at the level of translation [41] [42] [43]. "
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    ABSTRACT: It was previously thought that the proteins produced by ribosomes were dictated only by the sequences of the mRNAs they translated, however now it is apparent that subpopulations of ribosomes can have unique properties that influence the functions of the proteins they produce. Ribosomes have been engineered to discriminate between different mRNA templates or with unique decoding properties, and many new applications of unnatural ribosomes can be foreseen. In natural systems ribosomes with alternate protein and RNA composition have been shown to selectively translate specific mRNAs. As more is learned about ribosome structure and the mechanisms of translation, new opportunities to engineer ribosomes for applications in biotechnology and synthetic biology can be developed and new examples of ribosome-mediated regulation of translation are likely to emerge in nature.
    FEBS letters 02/2013; 587(8). DOI:10.1016/j.febslet.2013.02.032 · 3.34 Impact Factor
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    • "He first developed a genetic selection through which we could select for or against the expression of a single gene fusion and then showed that he could use this to select mRNA leader sequences, containing alternative Shine Dalgarno sequences (Hui and de Boer, 1987; Rackham and Chin, 2005a), that were not recognized by the endogenous ribosome, but are specifically and efficiently read by a new orthogonal ribosome (Rackham and Chin, 2005a) (Figure 2B). Oliver Rackham began to take advantage of this new nonessential orthogonal ribosome and showed that it is possible to use different orthogonal ribosomes to produce Boolean logic in gene expression (Rackham and Chin, 2005b). More recently, Wenlin An has shown that it is possible to select genetic elements that direct orthogonal transcription by T7 RNAP and orthogonal translation by an orthogonal ribosome (An and Chin, 2009). "
    The EMBO Journal 06/2011; 30(12):2312-24. DOI:10.1038/emboj.2011.160 · 10.75 Impact Factor
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    • "Originally pioneered by de Boer and colleagues [85], anti-Shine-Dalgarno sequences can be engineered into 16S ribosomal RNA to enable a group of ribosomes (orthogonal from the host) to translate specific mRNA populations. This has shown advantages for performing logic operations [85] [86], synthesizing proteins with nonnatural amino acids, such as p-benzoyl-(L)-phenylalanine [87], and efficiently incorporating quadruplet codons [88]. Orthogonal ribosomes will provide useful tools in programming synthetic function and expanding the genetic code to make nonnatural products for biotechnology. "
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    ABSTRACT: Synthetic biology is a nascent technical discipline that seeks to enable the design and construction of novel biological systems to meet pressing societal needs. However, engineering biology still requires much trial and error because we lack effective approaches for connecting basic "parts" into higher-order networks that behave as predicted. Developing strategies for improving the performance and sophistication of our designs is informed by two overarching perspectives: "bottom-up" and "top-down" considerations. Using this framework, we describe a conceptual model for developing novel biological systems that function and interact with existing biological components in a predictable fashion. We discuss this model in the context of three topical areas: biochemical transformations, cellular devices and therapeutics, and approaches that expand the chemistry of life. Ten years after the construction of synthetic biology's first devices, the drive to look beyond what does exist to what can exist is ushering in an era of biology by design.
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