Vitamin B12-peptide nucleic acids use the BtuB receptor to pass through the Escherichia coli outer membrane

Short modified oligonucleotides that bind in a sequence-specific way to messenger RNA essential for bacterial growth could be useful to fight bacterial infections. One such promising oligonucleotide is peptide nucleic acid (PNA), a synthetic DNA analog with a peptide-like backbone. However, the limitation precluding the use of oligonucleotides, including PNA, is that bacteria do not import them from the environment. We have shown that vitamin B-12, which most bacteria need to take up for growth, delivers PNAs to Escherichia coli cells when covalently linked with PNAs. Vitamin B-12 enters E. coli via a TonB-dependent transport system and is recognized by the outer-membrane vitamin B-12-specific BtuB receptor. We engineered the E. coli Delta btuB mutant and found that transport of the vitamin B-12-PNA conjugate requires BtuB. Thus, the conjugate follows the same route through the outer membrane as taken by free vitamin B-12. From enhanced sampling all-atom molecular dynamics simulations, we determined the mechanism of conjugate permeation through BtuB. BtuB is a beta-barrel occluded by its luminal domain. The potential of mean force shows that conjugate passage is unidirectional and its movement into the BtuB beta-barrel is energetically favorable upon luminal domain unfolding. Inside BtuB, PNA extends making its permeation mechanically feasible. BtuB extracellular loops are actively involved in transport through an induced-fit mechanism. We prove that the vitamin B-12 transport system can be hijacked to enable PNA delivery to E. coli cells.

Automated summary

By covalently linking vitamin B-12 with PNA, researchers were able to utilize the vitamin B-12 transport system to deliver PNA to E. coli cells. The conjugate follows the same route through the outer membrane as free vitamin B-12, with BtuB playing a crucial role in the transport process. Molecular dynamics simulations provided insights into the mechanism of conjugate permeation through BtuB, highlighting the potential for hijacking the vitamin B-12 system for efficient PNA delivery.