Team:Uppsala University/Translational

Conclusion
We managed to engineer artificial small RNA (sRNA) inhibiting the translation of the antibiotic resistance gene AAC(6’)Ib-cr isolated from a multiresistant bacterial outbreak in a hospital in Sweden. In the process, we managed to demonstrate a standardized method for construction and screening for sRNA successfully against a target mRNA. In practice, sRNA induced silencing of any gene of interest.

BBa_K864444 is our template target part in which the gene of interest should be inserted.

For detailed experimental approach see the project description page.

Silencing Truncated AAC(6') by use of fluorescent reporter
Measurements were made on isolated clones expressing engineered artificial sRNA together with the antibiotic resistance gene fused with a fluorescent marker, Super Yellow Fluorescent Protein (SYFP2). This showed that the artificial sRNA downregulated the fluorescence. The loss of fluorescent indicates that the engineered sRNA inhibits the expression the target mRNA, compared to the control without the sRNA. The control for normal SYFP2 fluorescence was the native unmodified spot42 in the otherwise identical vector, transformed into a cell with the reporter.

A critical issue was to determine whether out sRNA actually matched the AAC(6’)-5’UTR, or if the downregulation of fluorescence was due to a direct inhibition interacting with the SYFP2 coding region. The isolated clones were sequenced and analyzed and determine where there sRNA binds on the mRNA.

Validation of sRNA-mRNA interactions

IntaRNA, an RNA-RNA-interaction prediction software adapted for sRNA and ncRNA interactions [1] was used to predict the sRNA-mRNA interactions of the candidate sRNAs against the target mRNA containing the fusion between AAC(6’)-5’UTR. See modelling page for details. Some of the sRNAs corresponding to the highest SYFP2 downregulation showed a significant basepair matching close to the RBS of the AAC(6’)-5’UTR. A few of the sRNAs was predicted to hybridize in the SYFP2 region of the mRNA.

Below are predicted interactions between our sRNA and the AAC(6’)-5’UTR

Antibiotic resistance downregulation The next proof of concept was to test if the isolated sRNA also showed downregulation of the actual antibiotic resistance gene. The graphs below from the Etests [] show that the antibiotic resistance gene was repressed. This supports the hypothesis that it is the actual 5’UTR that is the key to control the the expression of the gene with sRNA.

Bildtext:The Etest with a minimal F-plasmid containing the AAC(6’) in translational fusion with the sRNA clones. A down regulation from MIC>256µl/ml to MIC=53±9µl was the largest measured. Measurement of clone 17,37,55 are all triplicates

To better understand the nature of small RNA downregulation and inhibiting translation, we also made some more in detail modelling of the interactions between sRNA and mRNA. (link)