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TitleArfB can displace mRNA to rescue stalled ribosomes.
Journal, issue, pagesNat Commun, Vol. 11, Issue 1, Page 5552, Year 2020
Publish dateNov 3, 2020
AuthorsChristine E Carbone / Gabriel Demo / Rohini Madireddy / Egor Svidritskiy / Andrei A Korostelev /
PubMed AbstractRibosomes stalled during translation must be rescued to replenish the pool of translation-competent ribosomal subunits. Bacterial alternative rescue factor B (ArfB) releases nascent peptides from ...Ribosomes stalled during translation must be rescued to replenish the pool of translation-competent ribosomal subunits. Bacterial alternative rescue factor B (ArfB) releases nascent peptides from ribosomes stalled on mRNAs truncated at the A site, allowing ribosome recycling. Prior structural work revealed that ArfB recognizes such ribosomes by inserting its C-terminal α-helix into the vacant mRNA tunnel. In this work, we report that ArfB can efficiently recognize a wider range of mRNA substrates, including longer mRNAs that extend beyond the A-site codon. Single-particle cryo-EM unveils that ArfB employs two modes of function depending on the mRNA length. ArfB acts as a monomer to accommodate a shorter mRNA in the ribosomal A site. By contrast, longer mRNAs are displaced from the mRNA tunnel by more than 20 Å and are stabilized in the intersubunit space by dimeric ArfB. Uncovering distinct modes of ArfB function resolves conflicting biochemical and structural studies, and may lead to re-examination of other ribosome rescue pathways, whose functions depend on mRNA lengths.
External linksNat Commun / PubMed:33144582 / PubMed Central
MethodsEM (single particle)
Resolution3.2 - 3.8 Å
Structure data

22459

7jss

EMDB-22459, PDB-7jss:
ArfB Rescue of a 70S Ribosome stalled on truncated mRNA with a partial A-site codon (+2-II)
Method: EM (single particle) / Resolution: 3.7 Å

22461

7jsw

EMDB-22461, PDB-7jsw:
ArfB Rescue of a 70S Ribosome stalled on truncated mRNA with a partial A-site codon (+2-III)
Method: EM (single particle) / Resolution: 3.8 Å

22464

7jsz

EMDB-22464, PDB-7jsz:
ArfB Rescue of a 70S Ribosome stalled on truncated mRNA with a partial A-site codon (+2-IV)
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-22465:
70S ribosome stalled on truncated mRNA
Method: EM (single particle) / Resolution: 3.7 Å

22466

7jt1

EMDB-22466, PDB-7jt1:
70S ribosome stalled on long mRNA with ArfB-1 and ArfB-2 bound (+9-III)
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-22467:
70S rotated ribosome stalled on truncated mRNA
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-22468:
70S ribosome stalled on long mRNA with ArfB C-terminus bound in the mRNA tunnel
Method: EM (single particle) / Resolution: 3.4 Å

22469

7jt2

EMDB-22469, PDB-7jt2:
70S ribosome stalled on long mRNA with ArfB bound in the A site
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-22470:
70S ribosome stalled on long mRNA with ArfB bound in the A site (+9-VI)
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-22471:
Rotated 70S ribosome stalled on long mRNA with ArfB-1 bound in the A site (+9-V)
Method: EM (single particle) / Resolution: 3.3 Å

22472

7jt3

EMDB-22472, PDB-7jt3:
Rotated 70S ribosome stalled on long mRNA with ArfB-1 and ArfB-2 bound in the A site (+9-IV)
Method: EM (single particle) / Resolution: 3.7 Å

Source
  • escherichia coli (strain k12) (bacteria)
  • escherichia coli k-12 (bacteria)
  • escherichia coli (E. coli)
KeywordsRibosome/TRANSLATION / Ribosome / ArfB / mRNA / TRANSLATION / Ribosome-TRANSLATION complex

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