Polysomes Bypass a 50-Nucleotide Coding Gap Less Efficiently Than Monosomes Due to Attenuation of a 5′ mRNA Stem–Loop and Enhanced Drop-off

S. O'Loughlin; M. Capece; M. Klimova; N. Wills; A. Coakley; E. Samatova; P. O'Connor; G. Loughran; J. Weissman; P. Baranov; M. Rodnina; J. Puglisi; J. Atkins

Статья

Polysomes Bypass a 50-Nucleotide Coding Gap Less Efficiently Than Monosomes Due to Attenuation of a 5′ mRNA Stem–Loop and Enhanced Drop-off

S. O'Loughlin, M. Capece, M. Klimova, N. Wills, A. Coakley, E. Samatova, P. O'Connor, G. Loughran, J. Weissman, P. Baranov, M. Rodnina, J. Puglisi, J. Atkins,

2020

https://doi.org/10.1016/j.jmb.2020.05.010

Efficient translational bypassing of a 50-nt non-coding gap in a phage T4 topoisomerase subunit gene (gp60) requires several recoding signals. Here we investigate the function of the mRNA stem-loop 5' of the take-off codon, as well as the importance of ribosome loading density on the mRNA for efficient bypassing. We show that polysomes are less efficient at mediating bypassing than monosomes, both in vitro and in vivo, due to their preventing formation of a stem-loop 5' of the take-off codon and allowing greater peptidyl-tRNA drop off. A ribosome profiling analysis of phage T4-infected Escherichia coli yielded protected mRNA fragments within the normal size range derived from ribosomes stalled at the take-off codon. However, ribosomes at this position also yielded some 53-nucleotide fragments, 16 longer. These were due to protection of the nucleotides that form the 5' stem-loop. NMR shows that the 5' stem-loop is highly dynamic. The importance of different nucleotides in the 5' stem-loop is revealed by mutagenesis studies. These data highlight the significance of the 5' stem-loop for the 50-nt bypassing and further enhance appreciation of relevance of the extent of ribosome loading for recoding.

Цитирование

Версии

1. Version of Record от 2020-05-23

Метаданные

Об авторах

S. O'Loughlin
School of Biochemistry, University College Cork, Western Gateway Building, Western Road, Cork, T12 XF62, Ireland; School of Microbiology, University College Cork, Western Gateway Building, Western Road, Cork, T12 YT57, Ireland.
M. Capece
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-4090, USA.
M. Klimova
Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
N. Wills
Department of Human Genetics, University of Utah, Salt Lake City, UT 84112-5330, USA.
A. Coakley
School of Biochemistry, University College Cork, Western Gateway Building, Western Road, Cork, T12 XF62, Ireland.
E. Samatova
Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
P. O'Connor
School of Biochemistry, University College Cork, Western Gateway Building, Western Road, Cork, T12 XF62, Ireland.
G. Loughran
School of Biochemistry, University College Cork, Western Gateway Building, Western Road, Cork, T12 XF62, Ireland.
J. Weissman
Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.
P. Baranov
School of Biochemistry, University College Cork, Western Gateway Building, Western Road, Cork, T12 XF62, Ireland; Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow 117997, Russia.
M. Rodnina
Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
J. Puglisi
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-4090, USA.
J. Atkins
School of Biochemistry, University College Cork, Western Gateway Building, Western Road, Cork, T12 XF62, Ireland; School of Microbiology, University College Cork, Western Gateway Building, Western Road, Cork, T12 YT57, Ireland; Department of Human Genetics, University of Utah, Salt Lake City, UT 84112-5330, USA. Electronic address: j.atkins@ucc.ie.

Название журнала

Journal of Molecular Biology

Том

Выпуск

Страницы

4369-4387

Издатель

Elsevier

Тип документа

journal article

Тип лицензии Creative Commons

CC BY

Правовой статус документа

Свободная лицензия

Источник

dimensions

Поиск по репозиторию

Статья

Polysomes Bypass a 50-Nucleotide Coding Gap Less Efficiently Than Monosomes Due to Attenuation of a 5′ mRNA Stem–Loop and Enhanced Drop-off

Похожие публикации

Версии

Метаданные