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Bacterial Resistance to Antisense Peptide-Phosphorodiamidate Morpholino Oligomers

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  • Peptide phosphorodiamidate morpholino oligomers (PPMO) are synthetic DNA mimics that bind complementary RNA and inhibit bacterial gene expression. (RFF)₃RXB- AcpP PPMO (R, arginine; F, phenylalanine; X, 6-aminohexanoic acid; B, β-alanine) is complementary to 11 bases of the essential gene acpP (encodes acyl carrier protein). The MIC of (RFF)₃RXB-AcpP was 2.5 μM (14 μg/ml) in Escherichia coli W3110. The rate of spontaneous resistance of E. coli to (RFF)₃RXB-AcpP was 4 x 10⁻⁷ mutations/cell division. A spontaneous (RFF)₃RXB-AcpP-resistant mutant (PR200.1) was isolated. The MIC of (RFF)₃RXB-AcpP was 40 μM (224 μg/ml) in PR200.1. The MICs of standard antibiotics were identical in PR200.1 and W3110. The sequence of acpP was identical in PR200.1 and W3110. PR200.1 was also resistant to other PPMOs conjugated to (RFF)₃RXB or peptides with a similar composition or pattern of cationic and non-polar residues. Genomic sequencing of PR200.1 identified a mutation in sbmA, which encodes an active transport protein. In separate experiments, a (RFF)₃RXB-AcpP-resistant isolate (RR3) was selected from a transposome library, and the insertion was mapped to sbmA. Genetic complementation of PR200.1 or RR3 with sbmA restored susceptibility to (RFF)₃RXB-AcpP. Deletion of sbmA caused resistance to (RFF)₃RXB-AcpP. We conclude that resistance to (RFF)₃RXB-AcpP was linked to the peptide and not the PMO, dependent on the composition or repeating pattern of amino acids, and caused by mutations in sbmA. The data further suggest that (RFF)₃R-XB PPMOs may be transported across the plasma membrane by SbmA.
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  • Puckett, S. E., Reese, K. A., Mitev, G. M., Mullen, V., Johnson, R. C., Pomraning, K. R., . . . Geller, B. L. (2012). Bacterial resistance to antisense peptide phosphorodiamidate morpholino oligomers. Antimicrobial Agents and Chemotherapy, 56(12), 6147.
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  • 56
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  • 12
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  • This work was supported by AVI BioPharma and the Howard Hughes Medical Institute (through undergraduate student research fellowships to Susan E. Puckett and Valerie Mullen).
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