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Structure paper

TitleRare ribosomal RNA sequences from archaea stabilize the bacterial ribosome.
Journal, issue, pagesNucleic Acids Res, Vol. 51, Issue 4, Page 1880-1894, Year 2023
Publish dateFeb 28, 2023
AuthorsAmos J Nissley / Petar I Penev / Zoe L Watson / Jillian F Banfield / Jamie H D Cate /
PubMed AbstractThe ribosome serves as the universally conserved translator of the genetic code into proteins and supports life across diverse temperatures ranging from below freezing to above 120°C. Ribosomes are ...The ribosome serves as the universally conserved translator of the genetic code into proteins and supports life across diverse temperatures ranging from below freezing to above 120°C. Ribosomes are capable of functioning across this wide range of temperatures even though the catalytic site for peptide bond formation, the peptidyl transferase center, is nearly universally conserved. Here we find that Thermoproteota, a phylum of thermophilic Archaea, substitute cytidine for uridine at large subunit rRNA positions 2554 and 2555 (Escherichia coli numbering) in the A loop, immediately adjacent to the binding site for the 3'-end of A-site tRNA. We show by cryo-EM that E. coli ribosomes with uridine to cytidine mutations at these positions retain the proper fold and post-transcriptional modification of the A loop. Additionally, these mutations do not affect cellular growth, protect the large ribosomal subunit from thermal denaturation, and increase the mutational robustness of nucleotides in the peptidyl transferase center. This work identifies sequence variation across archaeal ribosomes in the peptidyl transferase center that likely confers stabilization of the ribosome at high temperatures and develops a stable mutant bacterial ribosome that can act as a scaffold for future ribosome engineering efforts.
External linksNucleic Acids Res / PubMed:36660825 / PubMed Central
MethodsEM (single particle)
Resolution2.21 - 2.39 Å
Structure data

28165

8eiu

EMDB-28165: E. coli 70S ribosome with A-loop mutations U2554C and U2555C (Composite Map)
PDB-8eiu: E. coli 70S ribosome with A-loop mutations U2554C and U2555C
Method: EM (single particle) / Resolution: 2.24 Å

EMDB-28218: E. coli 70S ribosome with A-loop mutations U2554C and U2555C (50S Focus Refinement)
Method: EM (single particle) / Resolution: 2.21 Å

EMDB-28229: E. coli 70S ribosome with A-loop mutations U2554C and U2555C (30S Focus Refinement)
Method: EM (single particle) / Resolution: 2.39 Å

EMDB-28230: E. coli 70S ribosome with A-loop mutations U2554C and U2555C: A-site tRNA class 2
Method: EM (single particle) / Resolution: 2.34 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-PAR:
PAROMOMYCIN / Antimicrobial, medication*YM / Paromomycin

ChemComp-MG:
Unknown entry

ChemComp-SPD:
SPERMIDINE / Spermidine

ChemComp-8AN:
3'-amino-3'-deoxyadenosine 5'-(dihydrogen phosphate)

ChemComp-SPM:
SPERMINE / Spermine

ChemComp-MET:
METHIONINE / Methionine

ChemComp-HOH:
WATER / Water

Source
  • escherichia coli (E. coli)
KeywordsRIBOSOME / RNA / thermophile / A loop

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