ArfA recognizes the lack of mRNA in the mRNA channel after RF2 binding for ribosome rescue

Daisuke Kurita, Yuhei Chadani, Akira Muto, Tatsuhiko Abo, Hyouta Himeno

Research output: Contribution to journalArticle

16 Citations (Scopus)

Abstract

Although trans-translation mediated by tmRNA-SmpB has long been known as the sole system to relieve bacterial stalled ribosomes, ArfA has recently been identified as an alternative factor for ribosome rescue in Escherichia coli. This process requires hydrolysis of nascent peptidyl-tRNA by RF2, which usually acts as a stop codon-specific peptide release factor. It poses a fascinating question of how ArfA and RF2 recognize and rescue the stalled ribosome. Here, we mapped the location of ArfA in the stalled ribosome by directed hydroxyl radical probing. It revealed an ArfA-binding site around the neck region of the 30S subunit in which the N- and C-terminal regions of ArfA are close to the decoding center and the mRNA entry channel, respectively. ArfA and RF2 sequentially enter the ribosome stalled in either the middle or 3′ end of mRNA, whereas RF2 induces a productive conformational change of ArfA only when ribosome is stalled at the 3′ end of mRNA. On the basis of these results, we propose that ArfA functions as the sensor to recognize the target ribosome after RF2 binding.

Original languageEnglish
Pages (from-to)13339-13352
Number of pages14
JournalNucleic acids research.
Volume42
Issue number21
DOIs
Publication statusPublished - Dec 1 2014

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Ribosomes
Messenger RNA
Terminator Codon
Hydroxyl Radical
Hydrolysis
Neck
Binding Sites
Escherichia coli
Peptides

ASJC Scopus subject areas

  • Genetics

Cite this

ArfA recognizes the lack of mRNA in the mRNA channel after RF2 binding for ribosome rescue. / Kurita, Daisuke; Chadani, Yuhei; Muto, Akira; Abo, Tatsuhiko; Himeno, Hyouta.

In: Nucleic acids research., Vol. 42, No. 21, 01.12.2014, p. 13339-13352.

Research output: Contribution to journalArticle

Kurita, Daisuke ; Chadani, Yuhei ; Muto, Akira ; Abo, Tatsuhiko ; Himeno, Hyouta. / ArfA recognizes the lack of mRNA in the mRNA channel after RF2 binding for ribosome rescue. In: Nucleic acids research. 2014 ; Vol. 42, No. 21. pp. 13339-13352.
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