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TitleModulation of translational decoding by mA modification of mRNA.
Journal, issue, pagesNat Commun, Vol. 14, Issue 1, Page 4784, Year 2023
Publish dateAug 8, 2023
AuthorsSakshi Jain / Lukasz Koziej / Panagiotis Poulis / Igor Kaczmarczyk / Monika Gaik / Michal Rawski / Namit Ranjan / Sebastian Glatt / Marina V Rodnina /
PubMed AbstractN-methyladenosine (mA) is an abundant, dynamic mRNA modification that regulates key steps of cellular mRNA metabolism. mA in the mRNA coding regions inhibits translation elongation. Here, we show how ...N-methyladenosine (mA) is an abundant, dynamic mRNA modification that regulates key steps of cellular mRNA metabolism. mA in the mRNA coding regions inhibits translation elongation. Here, we show how mA modulates decoding in the bacterial translation system using a combination of rapid kinetics, smFRET and single-particle cryo-EM. We show that, while the modification does not impair the initial binding of aminoacyl-tRNA to the ribosome, in the presence of mA fewer ribosomes complete the decoding process due to the lower stability of the complexes and enhanced tRNA drop-off. The mRNA codon adopts a π-stacked codon conformation that is remodeled upon aminoacyl-tRNA binding. mA does not exclude canonical codon-anticodon geometry, but favors alternative more dynamic conformations that are rejected by the ribosome. These results highlight how modifications outside the Watson-Crick edge can still interfere with codon-anticodon base pairing and complex recognition by the ribosome, thereby modulating the translational efficiency of modified mRNAs.
External linksNat Commun / PubMed:37553384 / PubMed Central
MethodsEM (single particle)
Resolution2.04 - 2.88 Å
Structure data

16015

8bf7

EMDB-16015, PDB-8bf7:
Elongating E. coli 70S ribosome containing deacylated tRNA(iMet) in the P-site and AAA mRNA codon with cognate dipeptidyl-tRNA(Lys) in the A-site
Method: EM (single particle) / Resolution: 2.33 Å

16029

8bge

EMDB-16029, PDB-8bge:
Elongating E. coli 70S ribosome containing acylated tRNA(iMet) in the P-site and AAm6A mRNA codon in the A-site after uncompleted di-peptide formation
Method: EM (single particle) / Resolution: 2.11 Å

16031

8bgh

EMDB-16031, PDB-8bgh:
Elongating E. coli 70S ribosome containing acylated tRNA(iMet) in the P-site and AAA mRNA codon in the A-site after uncompleted di-peptide formation
Method: EM (single particle) / Resolution: 2.88 Å

16047

8bh4

EMDB-16047, PDB-8bh4:
Elongating E. coli 70S ribosome containing deacylated tRNA(iMet) in the P-site and AAm6A mRNA codon with cognate dipeptidyl-tRNA(Lys) in the A-site
Method: EM (single particle) / Resolution: 2.62 Å

16057

8bhj

EMDB-16057, PDB-8bhj:
Elongating E. coli 70S ribosome containing deacylated tRNA(iMet) in the P-site and Am6AA mRNA codon with cognate dipeptidyl-tRNA(Lys) in the A-site
Method: EM (single particle) / Resolution: 2.81 Å

16059

8bhl

EMDB-16059, PDB-8bhl:
Elongating E. coli 70S ribosome containing acylated tRNA(iMet) in the P-site and Am6AA mRNA codon in the A-site after uncompleted di-peptide formation
Method: EM (single particle) / Resolution: 2.21 Å

16062

8bhn

EMDB-16062, PDB-8bhn:
Elongating E. coli 70S ribosome containing deacylated tRNA(iMet) in the P-site and m6AAA mRNA codon with cognate dipeptidyl-tRNA(Lys) in the A-site
Method: EM (single particle) / Resolution: 2.85 Å

16065

8bhp

EMDB-16065, PDB-8bhp:
Elongating E. coli 70S ribosome containing acylated tRNA(iMet) in the P-site and m6AAA mRNA codon in the A-site after uncompleted di-peptide formation
Method: EM (single particle) / Resolution: 2.37 Å

16081

8bil

EMDB-16081, PDB-8bil:
Initiation complex of the E. coli 70S ribosome with mRNA containing AAA codon in the A-site.
Method: EM (single particle) / Resolution: 2.04 Å

16082

8bim

EMDB-16082, PDB-8bim:
Initiation complex of the E. coli 70S ribosome with mRNA containing AAm6A codon in the A-site
Method: EM (single particle) / Resolution: 2.04 Å

Chemicals

ChemComp-FME:
N-FORMYLMETHIONINE / N-Formylmethionine

Source
  • escherichia coli k-12 (bacteria)
  • synthetic construct (others)
KeywordsTRANSLATION / m6A / mRNA modification / tRNA recognition

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