Adaptor for translational to transcriptional regulation
In metabolic engineering, hitherto for the determination of the Flux Control Coefficients(FCC)-one of the sensitivities that relates the system parameters to the system variable- regulatory promoters have been placed upstream of the genes coding for enzymes in the pathway being studied. The principle is that a regulatory promoter allows introduction of changes in the magnitude of enzyme activity while keeping all other metabolic parameters at constant value and the FCCs are determined as a slope of the tangent in a plot capturing the variation of Flux with enzyme activity. Regulatory riboswitches too provide the ability to similarly modulate the magnitude of enzyme activity with a lot more control because the entropy of single stranded RNA secondary structures is high leading to the formation of different stable(the associated Gibbs free energy change becomes more negative with increase in entropy) secondary structures even facilitating the de novo synthesis of riboswitch from thermodynamic principles-this kind of flexibility is not available for regulatory promoters. But riboswitches can’t be used, as translation initiation at the RBS is a distributive process hence a riboswitch would have to be used for every gene to be expressed unlike a regulatory promoter where all genes are expressed simultaneously. But using the above proposed adaptor this limitation is subverted leading to the expression of multiple genes using a regulatory riboswitch.
The advantage of transcription over translation is that, in translation a single gene requires a ribosome and translational regulators such as RNA thermometers to get translated into a protein molecule, but in case of transcription multiple genes can be transcribed under a single operon. Hence this adaptor can be used for the regulation of entire operons using translational riboswitches/riboregulators.
GENETIC CIRCUITRY AND BIOLOGICAL COMPUTATION
This adaptor can be used by any synthetic biology group/team which intends to convert the translational regulatory property of a riboswitch to transcriptional regulation. This adaptor is both easy to engineer and can be easily assembled into higher order function (Genetic logic gates) thereby serving as an ideal regulator for protein synthesis.
Additionally, the burgeoning field of constructing biomolecule based-computation systems, requires complex logic gate design. An ideal biological gate is one which provides an adequate output signal corresponding to a predefined input signal as a function of the logic gate (Beneson et al, 2004). The folding patterns of an RNA molecule such as ribozymes and riboswitches into secondary and tertiary structure gives rise to unique functionality that is ideal as regulatory nodes for logic gates. But sometimes their scalability becomes difficult owing to problems associated with reusing such regulatory components in cascades (Bonnet et al,2013). The use of the above mentioned translation to transcription adaptor would be a powerful tool in mitigating this limitation where it’s easier for a particular regulator will be gated to the decision of the previous regulator resembling those in complex computation systems.
Promoter Strength Predictor
Any genetic engineer who wants to characterize the promoters they intend to use in their genetic engineering experiment without spending money and in less than 10 seconds can use our platform.
The riboswitch classifier is capable of predicting the class of riboswitch upon sequence input, the current iteration of the software is capable of recognizing 4 : Purine riboswitches, Lysine riboswitches, Molybdenum co-factor riboswitches and SAMIV riboswitches.
Any team or lb which intends to have pH based translational regulation can use this part. This part initiates translation only at alkaline conditions.