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bioRxiv · 10.1101/2023.04.16.537070

The structure of a hibernating ribosome in a Lyme disease pathogen

Sharma, M. R.·Manjari, S. R.·Agrawal, E. K.·Keshavan, P.·Koripella, R. K.·Majumdar, S.·Marcinkiewicz, A. L.·Lin, Y.-P.·Agrawal, R. K.·Banavali, N. K.
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Abstract

The spirochete bacterial pathogen Borrelia (Borreliella) burgdorferi (Bbu) affects more than 10% of the world population and causes Lyme disease in about half a million people in the US annually. Therapy for Lyme disease includes antibiotics that target the Bbu ribosome. We determined the structure of the Bbu 70S ribosome by single particle cryo-electron microscopy (cryo-EM) at a resolution of 2.9 [A], revealing its distinctive features. In contrast to a previous study suggesting that the single hibernation promoting factor protein present in Bbu (bbHPF) may not bind to its ribosome, our structure reveals a clear density for bbHPF bound to the decoding center of the small ribosomal 30S subunit. The 30S subunit has a non-annotated ribosomal protein, bS22, that has been found only in mycobacteria and Bacteroidetes so far. The protein bL38, recently discovered in Bacteroidetes, is also present in the Bbu large 50S ribosomal subunit. The protein bL37, previously seen only in mycobacterial ribosomes, is replaced by an N-terminal -helical extension of uL30, suggesting that the two bacterial ribosomal proteins uL30 and bL37 may have evolved from one longer uL30 protein. The longer uL30 protein interacts with both the 23S rRNA and the 5S rRNA, is near the peptidyl transferase center (PTC), and could impart greater stability to this region. Its analogy to proteins uL30m and mL63 in mammalian mitochondrial ribosomes also suggests a plausible evolutionary pathway for expansion of protein content in mammalian mitochondrial ribosomes. Computational binding free energies are predicted for antibiotics, bound to the decoding center or PTC and are in clinical use for Lyme disease, that account for subtle distinctions in antibiotic-binding regions in the Bbu ribosome structure. Besides revealing unanticipated structural and compositional features for the Bbu ribosome, our study thus provides groundwork to enable ribosome-targeted antibiotic design for more effective treatment of Lyme disease.

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Sharma, M. R., Manjari, S. R., Agrawal, E. K., Keshavan, P., Koripella, R. K., Majumdar, S., Marcinkiewicz, A. L., Lin, Y.-P., Agrawal, R. K., Banavali, N. K.. 2023-04-17. The structure of a hibernating ribosome in a Lyme disease pathogen. https://doi.org/10.1101/2023.04.16.537070

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