Difference between revisions of "Part:BBa K4601131"

Latest revision as of 19:31, 2 October 2023

Synthetic RBS designed for LacZalpha

This part is a synthetic RBS specifically designed for the LacZ-alpha (pUC19 like) (BBa_K2448003) using the Salis Lab RBS Library Calculator v2.0 [1-3].

Usage and Biology

This RBS was used to drive the expression of LacZ-alpha (pUC19 like) (BBa_K2448003) under the control of the J23110 promoter and of the Na+ RiboSwitch v1 (BBa_K4601021) in the composite part BBa_K4601231. In this context, the predicted features of this RBS, according to Salis Lab RBS Calculator v2.1.1 [1,4-7], are:

Translation Initiation Rate (au)	:	20923.75
dG_total (kcal/mol)	:	-6.29
dG_mRNA_rRNA (kcal/mol)	:	-30.06
dG_spacing (kcal/mol)	:	0.01
dG_stacking (kcal/mol)	:	-0.30
dG_standby (kcal/mol)	:	0.02
dG_start (kcal/mol)	:	-2.76
dG_mRNA (kcal/mol)	:	-26.81
Warnings	:	none

This RBS was selected fortuitously during the cloning process from a library of 96 RBSes (ASWTTAATAATKTAKAGAGGVGGTATAK) for which the estimated Translation Initiation Rates (TIR) range from 4223.38 to 393272.53.

References

[1] Reis AC, Salis HM. An automated model test system for systematic development and improvement of gene expression models. ACS synthetic biology (2020) 9: 3145–3156.

[2] Farasat I, Kushwaha M, Collens J, Easterbrook M, Guido M, Salis HM. Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria. Molecular Systems Biology (2014) 10: 731.

[3] Ng CY, Farasat I, Maranas CD, Salis HM. Rational design of a synthetic Entner-Doudoroff pathway for improved and controllable NADPH regeneration. Metabolic Engineering (2015) 29: 86–96.

[4] Cetnar DP, Salis HM. Systematic quantification of sequence and structural determinants controlling mRNA stability in bacterial operons. ACS Synthetic Biology (2021) 10: 318–332.

[5] Espah Borujeni A, Cetnar D, Farasat I, Smith A, Lundgren N, Salis HM. Precise quantification of translation inhibition by mRNA structures that overlap with the ribosomal footprint in N-terminal coding sequences. Nucleic Acids Research (2017) 45: 5437–5448.

[6] Espah Borujeni A, Channarasappa AS, Salis HM. Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites. Nucleic Acids Research (2014) 42: 2646–2659.

[7] Salis HM, Mirsky EA, Voigt CA. Automated design of synthetic ribosome binding sites to control protein expression. Nature Biotechnology (2009) 27: 946–950.

Sequence and Features