Exit tunnel modulation as resistance mechanism of S. aureus erythromycin resistant mutant

Yehuda Halfon,Jette Kjeldgaard,Zohar Eyal,Anat Bashan,Hanne Ingmer,Ella Zimmerman,Ada Yonath,Donna Matzov

doi:10.1038/s41598-019-48019-1

Yehuda Halfon, Jette Kjeldgaard + Show 6 more

Open Access

https://doi.org/10.1038/s41598-019-48019-1

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Abstract

The clinical use of the antibiotic erythromycin (ery) is hampered owing to the spread of resistance genes that are mostly mutating rRNA around the ery binding site at the entrance to the protein exit tunnel. Additional effective resistance mechanisms include deletion or insertion mutations in ribosomal protein uL22, which lead to alterations of the exit tunnel shape, located 16 Å away from the drug’s binding site. We determined the cryo-EM structures of the Staphylococcus aureus 70S ribosome, and its ery bound complex with a two amino acid deletion mutation in its ß hairpin loop, which grants the bacteria resistance to ery. The structures reveal that, although the binding of ery is stable, the movement of the flexible shorter uL22 loop towards the tunnel wall creates a wider path for nascent proteins, thus enabling bypass of the barrier formed by the drug. Moreover, upon drug binding, the tunnel widens further.

Highlights

Several ribosomal antibiotics inhibit protein biosynthesis by targeting functional sites in the ribosome, including the decoding center, the peptidyl transferase center (PTC) and the ribosomal exit tunnel (NPET) in which the nascent proteins migrate until they emerge out of the ribosome
It has been shown that for macrolides, the most common resistance mechanisms are by A2058G mutation (E. coli numbering is used throughout) at the antibiotic binding site or by the erm encoded methylase that methylates the exocyclic nitrogen of the adenine base[16,17,18,19,20]
The mutations in uL22 including insertions, deletions and single amino acid substitutions are mostly located on the ß hairpin loop of uL22, which extends from the globular domain of the protein and reaches the tunnel wall

Summary

Introduction

Several ribosomal antibiotics inhibit protein biosynthesis by targeting functional sites in the ribosome, including the decoding center, the peptidyl transferase center (PTC) and the ribosomal exit tunnel (NPET) in which the nascent proteins migrate until they emerge out of the ribosome. We present here the single particle cryo-EM high resolution structures of the apo and ery bound SAuL22m mutant ribosome, which demonstrates how deletion of R88-A89 in S. aureus ribosomal protein uL22 ß hairpin loop leads to ery resistance it does not hamper the binding of the antibiotic itself.

Results

Conclusion