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TitleThe landscape of translational stall sites in bacteria revealed by monosome and disome profiling.
Journal, issue, pagesRNA, Vol. 28, Issue 3, Page 290-302, Year 2022
Publish dateDec 14, 2021
AuthorsTomoya Fujita / Takeshi Yokoyama / Mikako Shirouzu / Hideki Taguchi / Takuhiro Ito / Shintaro Iwasaki /
PubMed AbstractRibosome pauses are associated with various cotranslational events and determine the fate of mRNAs and proteins. Thus, the identification of precise pause sites across the transcriptome is desirable; ...Ribosome pauses are associated with various cotranslational events and determine the fate of mRNAs and proteins. Thus, the identification of precise pause sites across the transcriptome is desirable; however, the landscape of ribosome pauses in bacteria remains ambiguous. Here, we harness monosome and disome (or collided ribosome) profiling strategies to survey ribosome pause sites in Compared to eukaryotes, ribosome collisions in bacteria showed remarkable differences: a low frequency of disomes at stop codons, collisions occurring immediately after 70S assembly on start codons, and shorter queues of ribosomes trailing upstream. The pause sites corresponded with the biochemical validation by integrated nascent chain profiling (iNP) to detect polypeptidyl-tRNA, an elongation intermediate. Moreover, the subset of those sites showed puromycin resistance, presenting slow peptidyl transfer. Among the identified sites, the ribosome pause at Asn586 of was validated by biochemical reporter assay, tRNA sequencing (tRNA-seq), and cryo-electron microscopy (cryo-EM) experiments. Our results provide a useful resource for ribosome stalling sites in bacteria.
External linksRNA / PubMed:34906996 / PubMed Central
MethodsEM (single particle)
Resolution3.3 Å
Structure data

30431

7cpj

EMDB-30431, PDB-7cpj:
ycbZ-stalled 70S ribosome
Method: EM (single particle) / Resolution: 3.3 Å

Chemicals

ChemComp-ILE:
ISOLEUCINE / Isoleucine

ChemComp-PRO:
PROLINE / Proline

Source
  • escherichia coli (E. coli)
  • escherichia coli 2362-75 (bacteria)
  • escherichia coli 113303 (bacteria)
  • escherichia coli h420 (bacteria)
  • escherichia coli (strain k12) (bacteria)
  • escherichia coli 907713 (bacteria)
  • escherichia coli umea 3718-1 (bacteria)
  • escherichia coli 2.3916 (bacteria)
  • escherichia coli kte112 (bacteria)
  • escherichia coli 4.0522 (bacteria)
  • escherichia coli o7:k1 (strain iai39 / expec) (bacteria)
  • escherichia coli o26:h11 (bacteria)
  • escherichia coli kte73 (bacteria)
  • escherichia coli ms 198-1 (bacteria)
  • escherichia coli ms 117-3 (bacteria)
  • escherichia coli hvh 87 (4-5977630) (bacteria)
  • escherichia coli m863 (bacteria)
  • escherichia coli 2-427-07_s4_c3 (bacteria)
  • escherichia coli kte64 (bacteria)
  • escherichia coli o121:h19 (bacteria)
  • escherichia coli ta054 (bacteria)
  • escherichia coli dec1d (bacteria)
  • escherichia coli 3-373-03_s4_c2 (bacteria)
  • escherichia coli 99.0741 (bacteria)
  • escherichia coli kte75 (bacteria)
  • escherichia coli o177 (bacteria)
  • escherichia coli ms 84-1 (bacteria)
  • escherichia coli g3/10 (bacteria)
  • escherichia coli h461 (bacteria)
  • escherichia coli 908573 (bacteria)
KeywordsANTIBIOTIC / ribosome

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