The araBAD promoter (BBa-I0500)

In our project to control sRNA chiXR expression we used the arabinose promoter (PBAD) from the araBAD operon that is regulated by the AraC protein[10]. AraC can work both as a repressor and activator of PBAD. In the absence of arabinose, AraC represses transcription from PBAD while a conformational change turns it into an activator in the presence of arabinose. In addition, the promoter is subject to catabolite rerpession and is thus further repressed in the presence of glucose.

PBAD is a very frequently used promoter because of its extreme tightness. In the presence of glucose, this promoter triggers negligible amount of transcription which allows cloning of toxic genes downstream of it however it is also relatively weak even upon full induction preventing high level expression which could be necessary for protein purification for example. Even though the response of the PBAD promoter appears graded to inducer concentration at the population level[7][10], it has been demonstrated that this is not the case at the individual cell level[6] where is displays an "all or nothing" behaviors with cells being either completely "OFF" or fully "ON" and only the fraction of OFF/ON cells varying upon arabinose concentration modification. induction of cell culture is one of them. As a result only a subset of cells becomes induced with the arabinose. This can be very problematic when trying to express poorly soluble functions or when working at the single cell level. This "all or nothing" behavior stems from the arabinose transporters being also positively regulated by arabinose. Upon entry of a little bit of inducer, a feed forward loop sets in where transporters are strongly upregulated as they bring more and more arabinose into the cell until the inducer is exhausted in teh immediate vicinity of the cell and the systems turns off. To circumvent this pitfall, researchers have devised strains which are constitutively permissive for arabinose entry thus breaking teh feed forward loop. Such approaches however necessitate the introduction of many mutations inside a strain and is therefore difficult to implement in other microbes but E. coli where the strains already exist[7] [11]. Besides, if an intermediate level of induction is required for a system to be optimal, reproducibly adding the exact precise concentration of arabinose in the culture can a significant hurdle.

We have approached the problem through another angle. If it is difficult to obtain reproducible results by changing the inducer concentration, why not try and change the promoter strength and systemaically use a saturating amount of inducer? Our approach was therefore based on last year's iGEM DTU team work on Synthetic Promoter Libraries but applied to an inducible promoter. In the process we were also hoping to obtain stronger than wild-type, but arabinose regulated promoters which could better match other induced system like the Ptet promoter PLEASE add this https://www-ncbi-nlm-nih-gov.globalproxy.cvt.dk/pubmed/21261817 reference here or the prompionate induced PprpB[8]</span>[10].

Approach

Since control of the system is essential to the applicability of our system we attempted to modify the dynamic range of the arabinose promoter ([http://partsregistry.org/Part:BBa_I0500 BBa_I0500]) by two means:

• rationally designing the -10 and -35 sequences of the promoter region since both the -35 (CTGACG) and the -10 (TACTGT) of the arabinose promoter are far from wild-type (TTGACA and TATAAT respectively).
• changing the nucleotides around and between the -10 and the -35 using synthetic promoter library (SPL), without changing the -10 and -35 from wildtype.

The arabinose promoter we were improving was fused to GFP and this construct came as a biobrick [http://partsregistry.org/Part:BBa_I746908 BBa_I746908]. To introduce the changes a set of primers was used to PCR P_BAD. Four primers, SRS56 from 1 to 4, were used to make PCR products with mutated nucleotides within -10 and -35 and SRS56SPL primer was used to make the SPL PCR products. Then a round of restriction digestions and ligations followed which allowed to exchange the wild type P_BAD with the mutated ones. In the next step they were transformed into E. coli strain DH5$\alpha$. Finally, all the rationally changed P_BAD promoters and randomly selected SPL mutants were characterized using Biolektor.

Detailed description of the experiments, including information on primers used, can be found in labnotebook.

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Results

All 4 rationally designed (in strains called 1b, 2a, 3h, 4d) and 18 SPL-changed arabinose promoters (in strains called SPL-1 up to SPL-24) fused to GFP were tested under induction of arabinose at concentration 0.2% and compared to non-induced state. Also, the original [http://partsregistry.org/Part:BBa_I746908 BBa_I746908], in strain strain 300, was characterized in the same fashion. In all the figures the GFP expression and the biomass concentration are expressed in fluorescence unit (FU) and light scattering unit (LSU) respectively.

Figure 1 presents the characterization for the rationally designed arabinose promoters. When uninduced (left part of the figure) the background GFP expression level for strains 1b and 3h is slightly above the background in original promoter (black line) which indicates that these promoters are less tight. In case of strains 2a and 4d the basal expression level is comparable to the original promoter. From the right part of the figure we can see that the induction didn't influence expression in strain 4d which implies that mutations abolished arabinose regulation in that promoter. In case of strain 2a induction is maintained, however its level is much lower than that of original promoter.

Figure 1 Characterization of rationally designed araBAD promoters fused to GFP in DH5$\alpha$ cells. Strain 300 has the unchanged BBa_I746908. Induction at 0.2% arabinose concentration. FU - fluorescence unit, LSU - light scattering unit.

Characterization of SPL changed araBAD promoters fused to GFP in DH5$\alpha$ cells. Strain 300 has the unchanged BBa_I746908. Induction at 0.2% arabinose concentration. FU - fluorescence unit, LSU - light scattering unit.

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References

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[2] Figueroa-Bossi, Nara, Martina Valentini, Laurette Malleret, and Lionello Bossi. “Caught at its own game: regulatory small RNA inactivated by an inducible transcript mimicking its target.” Genes & Development 23, no. 17 (2009): 2004 -2015.

[3] Hayashi, Koji, Naoki Morooka, Yoshihiro Yamamoto, Katsutoshi Fujita, Katsumi Isono, Sunju Choi, Eiichi Ohtsubo, et al. “Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110.” Molecular Systems Biology 2 (2006): 2006.0007. http://www.ncbi.nlm.nih.gov/pubmed/16738553.

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[5] Overgaard, Martin, Jesper Johansen, Jakob Møller‐Jensen, and Poul Valentin‐Hansen. “Switching off small RNA regulation with trap‐mRNA.” Molecular Microbiology 73, no. 5 (September 2009): 790-800.

[6] Novick, A. & Weiner, M. “Enzyme induction as an all-or-none phenomenon“ Proc. Natl. Acad. Sci. USA 43 (1957), 533–556.

[7] Khlebnikov, A., K. Datsenko, T. Skaug, B. L. Wanner, and J. D. Keasling. “Homogeneous expression of the P(BAD) promoter in Escherichia coli by constitutive expression of the low-affinity high-capacity AraE transporter.” Microbiology (Reading, England) 147, no. Pt 12 (December 2001): 3241-7. http://www.ncbi.nlm.nih.gov/pubmed/11739756.

[8] Lee, Sung Kuk, and Jay D Keasling. “A Propionate-Inducible Expression System for Enteric Bacteria.” Society 71, no. 11 (2005): 6856-6862.

[9] Lee, Sung Kuk, and Jay D Keasling. “Propionate-Regulated High-Yield Protein Production in Escherichia coli.” Biotechnology (2005).

[10] Guzman, L M, D Belin, M J Carson, and J Beckwith. “Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter.” Journal of bacteriology 177, no. 14 (July 1995): 4121-30. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=177145&tool=pmcentrez&rendertype=abstract.

[11] Morgan-Kiss, Rachael M, Caryn Wadler, and John E Cronan. “Long-term and homogeneous regulation of the Escherichia coli araBAD promoter by use of a lactose transporter of relaxed specificity.” Proceedings of the National Academy of Sciences of the United States of America 99, no. 11 (May 28, 2002): 7373-7. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=124238&tool=pmcentrez&rendertype=abstract.

[12] Rasmussen, Anders Aamann, Jesper Johansen, Jesper S Nielsen, Martin Overgaard, Birgitte Kallipolitis, and Poul Valentin‐Hansen. “A conserved small RNA promotes silencing of the outer membrane protein YbfM.” Molecular Microbiology 72, no. 3 (May 2009): 566-577.