Difference between revisions of "Collections/BIOFAB"

Latest revision as of 04:07, 12 October 2022

This collection is curated by the FSU iGEM teams

How is the BIOFAB collection useful to you?

The BIOFAB collection contains constitutive promoters, transcription terminators, and 5' untranslated regions (5' UTRs). The promoters and terminators were added to the iGEM Parts Registry by the 2018 and 2020 FSU iGEM teams. The promoters have a range of strength that spans four orders of magnitude. Promoters of different strengths can be selected from the BIOFAB collection based on the desired levels of gene expression. The original BIOFAB promoters and terminators were tested using a specific transcription unit designed by the BIOFAB team. The FSU iGEM teams are measuring the strength of the promoters in a genetic context composed of iGEM parts. Specifically, using the pSB1C3 and pSB1K3 backbones. It is recommended that users of the BIOFAB Collection select several promoters with the desired strength when working on a new design to determine experimentally which promoter provides the desired level of gene expression.

How do the BIOFAB promoters work?

The promoters on this page are listed in order of decreasing strength based on the measurements reported by the BIOFAB team. The strongest promoters are expected to produce more messenger RNA (mRNA) than the weaker promoters. The promoter strength is determined by how frequently the DNA sequence recruits RNA polymerases and encourages transcription.

How are the BIOFAB promoters being measured?

The FSU iGEM teams are measuring the strengths of the BIOFAB promoters in a measurement device composed of a BIOFAB promoter, a ribosome binding site (BBa_B0034), mRFP1 (BBa_E1010), and a terminator (BBa_B0015). The measurement devices are inserted into pSB1C3 and pSB1K3 backbones using a scarless DNA assembly method (NEB HiFi DNA Assembly). The resulting plasmid vectors are used to transform the E. coli NEBExpress chassis. The promoter strengths are measured via the amount of fluorescence detected in a flow cytometer. The levels of fluorescence are reported in molecules of equivalent PE-Texas Red (MEPTR) units.

Libraries

Modular Promoter Library

Randomized Promoter Library

Terminator Library (the graph is under construction...)

References

Mutalik, V., Guimaraes, J., Cambray, G. et al. Quantitative estimation of activity and quality for collections of functional genetic elements. Nat Methods 10, 347–353 (2013). https://doi.org/10.1038/nmeth.2403

Mutalik, V., Guimaraes, J., Cambray, G. et al. Precise and reliable gene expression via standard transcription and translation initiation elements. Nat Methods 10, 354–360 (2013). https://doi.org/10.1038/nmeth.2404

Guillaume Cambray, Joao C. Guimaraes, Vivek K. Mutalik, Colin Lam, Quynh-Anh Mai, Tim Thimmaiah, James M. Carothers, Adam P. Arkin, Drew Endy, Measurement and modeling of intrinsic transcription terminators, Nucleic Acids Research, Volume 41, Issue 9, 1 May 2013, Pages 5139–5148, https://doi.org/10.1093/nar/gkt163

The data visualization is provided by the Charts.css library.

Tables Generated by the Parts Registry

Modular Promoters Table

Randomized Promoters Table

Terminators Table