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Cited by 6RNA and protein synthesis mechanismsAdvanced Electron Microscopy Techniques and ApplicationsRNA modifications and cancer

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The structure of a hibernating ribosome in a Lyme disease pathogen

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Sharma, Manjuli R., Manjari, Swati R., Agrawal, Ekansh K., Keshavan, Pooja, Koripella, Ravi K., Majumdar, Soneya, Marcinkiewicz, Ashley L., Lin, Yi-Pin, Agrawal, Rajendra K., Banavali, Nilesh K.·2023·Nature Communications
DOI 10.1038/s41467-023-42266-7PMC PMC10618245

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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. Here we present the structure of the Bbu 70S ribosome obtained by single particle cryo-electron microscopy at 2.9 Å resolution, revealing a bound hibernation promotion factor protein and two genetically non-annotated ribosomal proteins bS22 and bL38. The ribosomal protein uL30 in Bbu has an N-terminal α-helical extension, partly resembling the mycobacterial bL37 protein, suggesting evolution of bL37 and a shorter uL30 from a longer uL30 protein. 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 energy predictions for antibiotics reflect subtle distinctions in antibiotic-binding sites in the Bbu ribosome. Discovery of these features in the Bbu ribosome may enable better ribosome-targeted antibiotic design for Lyme disease treatment.

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Figures

Fig. 1 Bbu 70S hibernating ribosome structure and protein components. a Cryo-EM density map of 70S with local resolution indicated by color. b Model fit into cryo-EM density map with 30S density in khaki, 50S density in blue, 16S RNA and 5S RNA in orange, 23S RNA in red, 30S proteins in green, and 50S proteins in blue. c Notable components in the structure shown within the cryo-EM density map. These components of the hibernating 70S ribosome, shown in ribbon format with known sidechains in stick format, are d the E-site tRNA (orange), e the bS22 protein (cyan), f the bL38 protein (green), g the longer uL30 protein (dark green), and h the bbHPF protein (blue).
Fig. 1 Bbu 70S hibernating ribosome structure and protein components. a Cryo-EM density map of 70S with local resolution indicated by color. b Model fit into cryo-EM density map with 30S density in khaki, 50S density in blue, 16S RNA and 5S RNA in orange, 23S RNA in red, 30S proteins in green, and 50S proteins in blue. c Notable components in the structure shown within the cryo-EM density map. These components of the hibernating 70S ribosome, shown in ribbon format with known sidechains in stick format, are d the E-site tRNA (orange), e the bS22 protein (cyan), f the bL38 protein (green), g the longer uL30 protein (dark green), and h the bbHPF protein (blue).CC BY · PubMed Central
Fig. 2 The bbHPF binding site orientation and bacterial HPF protein structural variability. (a) Subunit interface (left), mRNA exit (middle), and mRNA entry (right) site views of bbHPF in its decoding center binding site in the Bbu ribosome with full 30S view shown above. Labels indicate location of ribosomal proteins (in blue) uS7, uS9, uS12, E-site tRNA (in yellowish orange, labeled E-tRNA), and large subunit RNA helix 69 (in dark orange, labeled H69) of the 23S ribosomal RNA. 16S ribosomal RNA shown in semitransparent light orange. Known bacterial HPF structures, with resolutions better than 3.5 Å, shown in transparent khaki, b aligned by HPF protein residues, showing internal structural variability, and c aligned by 16S ribosomal RNA residues, showing position variability in their ribosomal binding site. BbHPF is shown as opaque red in all panels. Views shown in panels b, c are analogous to those shown in panel (a). Details of structures used in panels b, c are listed in Supplementary Table 2.
Fig. 2 The bbHPF binding site orientation and bacterial HPF protein structural variability. (a) Subunit interface (left), mRNA exit (middle), and mRNA entry (right) site views of bbHPF in its decoding center binding site in the Bbu ribosome with full 30S view shown above. Labels indicate location of ribosomal proteins (in blue) uS7, uS9, uS12, E-site tRNA (in yellowish orange, labeled E-tRNA), and large subunit RNA helix 69 (in dark orange, labeled H69) of the 23S ribosomal RNA. 16S ribosomal RNA shown in semitransparent light orange. Known bacterial HPF structures, with resolutions better than 3.5 Å, shown in transparent khaki, b aligned by HPF protein residues, showing internal structural variability, and c aligned by 16S ribosomal RNA residues, showing position variability in their ribosomal binding site. BbHPF is shown as opaque red in all panels. Views shown in panels b, c are analogous to those shown in panel (a). Details of structures used in panels b, c are listed in Supplementary Table 2.CC BY · PubMed Central
Fig. 3 The bS22 protein structure in Bbu and other organisms. a Bbu bS22 (blue) in the Bbu ribosome binding pocket; b Msm bS22 (cyan) in the Msm ribosome binding pocket; c Fjo bS22 (green) in the Fjo ribosome binding pocket; d Overlay of all three bS22 proteins and their respective binding pockets showing the high structural similarity in the three binding pockets with 16S RNA shown in orange and 23S RNA shown in red; e Bbu bS22 protein; f Homo sapiens (Hsa) eL41 protein; g Hsa mitochondrial mS38 protein; h overlay of Bbu bS22, Hsa eL41, Hsa mS38 proteins; i Molecular interactions of Bbu bS22 protein with the ribosomal RNA components of the binding pocket, interacting 16S RNA helix numbers in orange, interacting 23S RNA helix numbers in red.
Fig. 3 The bS22 protein structure in Bbu and other organisms. a Bbu bS22 (blue) in the Bbu ribosome binding pocket; b Msm bS22 (cyan) in the Msm ribosome binding pocket; c Fjo bS22 (green) in the Fjo ribosome binding pocket; d Overlay of all three bS22 proteins and their respective binding pockets showing the high structural similarity in the three binding pockets with 16S RNA shown in orange and 23S RNA shown in red; e Bbu bS22 protein; f Homo sapiens (Hsa) eL41 protein; g Hsa mitochondrial mS38 protein; h overlay of Bbu bS22, Hsa eL41, Hsa mS38 proteins; i Molecular interactions of Bbu bS22 protein with the ribosomal RNA components of the binding pocket, interacting 16S RNA helix numbers in orange, interacting 23S RNA helix numbers in red.CC BY · PubMed Central
Fig. 4 The structure of the longer uL30 protein in Borreliella species and its relationship with the bL37 protein in mycobacteria, the Hsa uL30 protein, and the Hsa mL30 and mL63 proteins. a The Bbu uL30 protein (blue) in its structurally conserved 23S RNA (light orange) and 5S RNA (purple) environment, with the extracted uL30 and 5S RNA shown below for clarity. b The Msm uL30 protein (green) and the Msm bL37 protein (yellow) in its structurally conserved 23S RNA (light orange) and 5S RNA (red) environment, with the extracted uL30, bL37, and 5S RNA shown below. c Overlays of the Bbu uL30 protein and the Msm uL30 and bL37 proteins (left), and the neighboring Bbu (purple) and Msm (red) 5S RNA segments (right). d The ribosomal RNA binding pocket for the uL30 N-terminal extension (residue 2-40), blue asterisk indicates 5S RNA. e The Bbu uL30 protein. f The Hsa uL30 protein. g The Hsa uL30m protein. h Overlay of the Bbu uL30 protein (blue) and the Hsa mL63 protein (yellow). i Overlay of the Bbu uL30 protein and the Hsa uL30m and Hsa mL63 proteins.
Fig. 4 The structure of the longer uL30 protein in Borreliella species and its relationship with the bL37 protein in mycobacteria, the Hsa uL30 protein, and the Hsa mL30 and mL63 proteins. a The Bbu uL30 protein (blue) in its structurally conserved 23S RNA (light orange) and 5S RNA (purple) environment, with the extracted uL30 and 5S RNA shown below for clarity. b The Msm uL30 protein (green) and the Msm bL37 protein (yellow) in its structurally conserved 23S RNA (light orange) and 5S RNA (red) environment, with the extracted uL30, bL37, and 5S RNA shown below. c Overlays of the Bbu uL30 protein and the Msm uL30 and bL37 proteins (left), and the neighboring Bbu (purple) and Msm (red) 5S RNA segments (right). d The ribosomal RNA binding pocket for the uL30 N-terminal extension (residue 2-40), blue asterisk indicates 5S RNA. e The Bbu uL30 protein. f The Hsa uL30 protein. g The Hsa uL30m protein. h Overlay of the Bbu uL30 protein (blue) and the Hsa mL63 protein (yellow). i Overlay of the Bbu uL30 protein and the Hsa uL30m and Hsa mL63 proteins.CC BY · PubMed Central
Fig. 5 Ribosome interactions of the Bbu bL38 protein. a 50S subunit neighborhood of Bbu bL38 (green), b 50S subunit neighborhood of Fjo bL38 (yellow), c Overlay using 23S RNA of (a) and (b) showing displacement of Bbu bL38 as compared to Fjo bL38 while the neighborhood remains structurally conserved, d relative displacement of Bbu bL38 as compared to Fjo bL38 in overlay, e Internal structural differences between Bbu bL38 and Fjo bL38 when overlaid on each other, f detailed atomic interactions of Bbu bL38 with Bbu 50S subunit shown from two opposite views. The coloring is as follows: uL6 in cyan, uL14 in pink, bL19 in orange, Bbu bL38 in dark green, Fjo bL38 in yellow, 23S RNA in red. The Fjo models are shown in transparent view to facilitate comparison with Bbu in the overlay.
Fig. 5 Ribosome interactions of the Bbu bL38 protein. a 50S subunit neighborhood of Bbu bL38 (green), b 50S subunit neighborhood of Fjo bL38 (yellow), c Overlay using 23S RNA of (a) and (b) showing displacement of Bbu bL38 as compared to Fjo bL38 while the neighborhood remains structurally conserved, d relative displacement of Bbu bL38 as compared to Fjo bL38 in overlay, e Internal structural differences between Bbu bL38 and Fjo bL38 when overlaid on each other, f detailed atomic interactions of Bbu bL38 with Bbu 50S subunit shown from two opposite views. The coloring is as follows: uL6 in cyan, uL14 in pink, bL19 in orange, Bbu bL38 in dark green, Fjo bL38 in yellow, 23S RNA in red. The Fjo models are shown in transparent view to facilitate comparison with Bbu in the overlay.CC BY · PubMed Central

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Research works printed but not linked: 1

  1. Bhattacharjee, S., Frank, J. & Feng, X. Mechanism of HflX-mediated recycling of E. coli ribosome studied by time-resolved cryo-EM. Preprint at bioRxiv https://doi.org/10.1101/2023.01.25.525430 (2023). · DOI

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Metadata

Authors
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.
Affiliations
New York State Department of Health (US)
Corresponding author
  • Agrawal, Rajendra K.
  • Banavali, Nilesh K.
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2023-10-31
Volume
14
Issue
1
Pages
6961-6961
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-023-42266-7
PMC
PMC10618245
OpenAlex
W4388040938
Cited by
6
References
76
Citations by year
2026: 1 · 2025: 2 · 2024: 3
FWCI
0.53
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (GM061576, GM139277)
  • Division of Intramural Research, National Institute of Allergy and Infectious Diseases (AI132422, AI155473)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA modifications and cancer
Keywords
Borrelia burgdorferi, ribosome structure, ribosome hibernation, antibiotic binding sites, ribosome-targeted antibiotics, antibiotic design, Lyme disease
MeSH terms
Animals, Anti-Bacterial Agents, Bacterial Proteins, Humans, Lyme Disease, Mammals, Ribosomal Proteins, Ribosomes, Cryoelectron Microscopy

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