A network of orthogonal ribosome·mRNA pairs

@article{Rackham2005ANO,
  title={A network of orthogonal ribosome·mRNA pairs},
  author={Oliver Rackham and Jason W. Chin},
  journal={Nature Chemical Biology},
  year={2005},
  volume={1},
  pages={159-166}
}
Synthetic biology promises the ability to program cells with new functions. Simple oscillators, switches, logic functions, cell-cell communication and pattern-forming circuits have been created by the connection of a small set of natural transcription factors and their binding sites in different ways to produce different networks of molecular interactions. However, the controlled synthesis of more complex synthetic networks and functions will require an expanded set of functional molecules with… 
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References

SHOWING 1-10 OF 47 REFERENCES
Combinatorial Synthesis of Genetic Networks
TLDR
Combinatorial synthesis provides an alternative approach for studying biological networks, as well as an efficient method for producing diverse phenotypes in vivo, with the use of a combinatorial method in Escherichia coli.
A synthetic oscillatory network of transcriptional regulators
TLDR
This work used three transcriptional repressor systems that are not part of any natural biological clock to build an oscillating network, termed the repressilator, in Escherichia coli, which periodically induces the synthesis of green fluorescent protein as a readout of its state in individual cells.
Specialized ribosome system: preferential translation of a single mRNA species by a subpopulation of mutated ribosomes in Escherichia coli.
  • A. Hui, H. D. de Boer
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 1987
TLDR
A system in which a subpopulation of modified ribosomes are directed to a single mutated mRNA species offers an approach to the study of mutations elsewhere in the 16S-rRNA gene that otherwise would be lethal to the cell.
Mutagenesis at the mRNA decoding site in the 16S ribosomal RNA using the specialized ribosome system in Escherichia coli.
TLDR
It is concluded that some, but not all, of the nucleotides in the conserved C1400 region play a key role in translation.
Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression
TLDR
It is reported here that mRNAs encoding enzymes involved in thiamine (vitamin B1) biosynthesis in Escherichia coli can bindThiamine or its pyrophosphate derivative without the need for protein cofactors and provides an example of a 'riboswitch' whose evolutionary origin might pre-date the emergence of proteins.
Engineered riboregulators enable post-transcriptional control of gene expression
TLDR
A post-transcriptional regulation system in Escherichia coli that uses RNA to both silence and activate gene expression is presented, inserting a complementary cis sequence directly upstream of the ribosome binding site in a target gene.
Initiation of Protein Synthesis in Bacteria
TLDR
A detailed description of current knowledge about the structure, function, and interactions of the individual components involved in bacterial translation initiation is presented and the mechanisms of regulation of the translation initiation event are provided.
Gene regulatory network growth by duplication
TLDR
The role of gene duplication in network evolution is investigated and it is concluded that evolution has been incremental, rather than making entire regulatory circuits or motifs by duplication with inheritance of interactions.
Directed evolution of a genetic circuit
TLDR
It is demonstrated that a nonfunctional circuit containing improperly matched components can evolve rapidly into a functional one and generated a library of genetic devices with a range of behaviors that can be used to construct more complex circuits.
...
...