208 10 Programming Gene Expression by Engineering Transcript Stability Control and Processing in Bacteria
that, for instance, fuse multiple control mechanisms will become easier to design
and construct. Moreover, increasing knowledge of the underlying biochemical
and biophysical principles governing RNA degradation will make it easier to
anticipate how transcript stability may function contrary to genetic device
output goals. We expect that TSC engineering will create ways to align mRNA
half-life with design goals and thus will be a vital component of increasing
system predictability and avoiding confounding effects. The current state of
research portends the use of TSC to help design synthetic biological systems that
can dynamically and rapidly respond to their environment with low-burden,
orthogonal RNA components designed entirely in silico.Acknowledgments
We thank W.M. Voje, Jr. and R.C. Correa for helpful discussions and comments.
Work in the authors’ laboratory is supported by the Molecular Engineering &
Sciences Institute, the University of Washington, and the National Science
Foundation Synthetic Biology Engineering Research Center (NSF SynBERC).
J.M.C. is a fellow of the Alfred P. Sloan Foundation.Definitions
RNA synthetic biology Large-scale genetic engineering that makes use of
RNA-based components (e.g., aptamers, aptazymes, riboswitches) to con-
struct control devices and systems for programming cellular function
Transcript stability control Regulation of genetic output by engineering
mRNA degradation rate
mRNA degradation The process by which a transcript is hydrolyzed to compo-
nent monomers by the concerted efforts of the degradosome and associated
enzymes
Aptamer Functional RNA structure, typically generated through in vitro selec-
tion, that binds target ligands
Ribozyme Functional RNA structure with catalytic activity (e.g., hammerhead
ribozymes catalyze phosphodiester bond cleavage reactions)
Aptazyme Composite functional RNA structure consisting of an aptamer and a
phosphodiester bond-cleaving ribozyme such that the catalytic activity is
modulated by aptamer ligand binding
Riboswitch RNA structure that controls gene expression by employing a ligand-
binding aptamer domain that regulates access of the ribosome to the ribosome
binding site in cis
Riboregulator A riboswitch-like RNA unit that regulates access to the ribo-
some binding site in response to binding by a trans-RNA
sRNA Small RNAs, usually tens to hundreds of nucleotides long, that bind
regions of a target mRNA (typically near the 5′ UTR or start codon) to hasten
mRNA degradation and prevent translation by occluding ribosome docking