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Contents 1 Overview 2 The different sources for our RNA polymerases 3 WT polymerases 4 Chris' Engineered polymerases 5 Results 6 References

Overview

The purpose of different RNAPs used in our project is to control expression from suitable promoters inserted into phage genome. Addition of inducers to the medium will trigger transcription of polymerases needed to promote transcription of phage’s genes, thus allowing the phage to complete its lytic cycle. At first we thought to use three native polymerases to control our AND gates – T7, T3 and SP6 RNAPs. Those polymerases arise from T7, T3 and SP6 bacteriophages, respectively and belong to the same family of polymerases. They were chosen to be used in our project for 2 main reasons {1}:

1. Those polymerases have high specificity recognizing their own promoters, but not native E.coli‘s or other polymerases’ promoters, those minimizing dangers of unwanted cross-reactivity.
2. pT7, pSP6 and pT3 are very strong promoters, so their activity is very tightly regulated by inducers that can't be found in a specific E.coli we used in our project. Also, using this promoters prevents possible leakiness.

However, we had discovered that phage polymerases can exhibit toxicity to host cells, so we began to search after less toxic variants. Luckily, Ilya have found an article published by Chris Voight et al. Chris’ research focused around creating a set of orthogonal polymerases based on T7 wild type (WT) RNA polymerase (RNAP) that will be less toxic to the host cells and will recognize different promoters.

Chris had agreed to share his work with our team, so in total during our project we had worked with 7 different polymerases: T7, T3 and SP6 WT RNAPS and eT7, eK1F, eN4, eT3 mutants produced by Chris and his team (‘e’ before RNAP’s name means engineered polymerase).

The different sources for our RNA polymerases

Some of the polymerases used during our project were donated to us. We want to thank the researchers that helped us out:

• Christopher A. Voight – for donating his synthetic engineered polymerases with suitable promoters: eT7, eT3, eK1F, eN4.
• Ann K. Ganesan – for donating a plasmid with WT T7 RNA polymerase.
• Changwon Kang - for donating a plasmid with the SP6 RNAP.

WT polymerases

During our project we have worked with 3 wild type polymerases produced by phages: T7 RNAP, SP6 RNAP and T3 RNAP.

T7 RNAP is transcripted from gene 1 of T7 bacteriophage. It consists of single polypeptide chain with weight of 98 kDa. {2}

SP6 RNAP is produced by SP6 bacteriophage that grows on Salmonella typhimurium LT2. It consists of single polypeptide chain with weight of 96 kDa. {2,3}

T3 RNAP is produced by T3 bacteriophage (T7-like virus that infects E. coli). It consists of single polypeptide chain with weight of 100 kDa. {4,5}

T7, T3 and SP6 polymerases belong to same polymerase family and share some common features {2,4}:

1. They require Mg+2 as a cofactor and their activity can be stimulated by addition of BSA or spermidine.
2. The RNAPS possess very stringent promoters meaning that there is almost none cross-talking between them.
3. Unlike bacterial polymerases they are not inhibited by rifampicin antibiotic.

In molecular biology those RNAPS are used for in vitro/in vivo specific RNA synthesis.

Chris' Engineered polymerases

Results

References

1. Lodge J., Lund P., Minchin S. (2007) "Gene Cloninng: Principles and Applications", Taylor & Francis Group, New York, NY. p. 258.

2. Dr. Aehle W. (ed.) (2007) "Enzymes in Industry", WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. pp. 370, 372

3. Butler E. T., Chamberlin M. J. (1982) "Bacteriophage SP6-specific RNA Polymerase", The Journal of Biological Chemistry. Vol. 257 (10),pp. 5772-5778.