Attenuating ribosome load improves protein output from mRNA by limiting translation-dependent mRNA decay

Alicia A. Bicknell; David W. Reid; Marissa C. Licata; Adriana K. Jones; Yi Min Cheng; Mengying Li; Chiaowen Joyce Hsiao; Christopher S. Pepin; Mihir Metkar; Yevgen Levdansky; Brian R. Fritz; Elizaveta A. Andrianova; Ruchi Jain; Eugene Valkov; Caroline Köhrer; Melissa J. Moore

Cell Reports (Apr 2024)

Attenuating ribosome load improves protein output from mRNA by limiting translation-dependent mRNA decay

Alicia A. Bicknell,
David W. Reid,
Marissa C. Licata,
Adriana K. Jones,
Yi Min Cheng,
Mengying Li,
Chiaowen Joyce Hsiao,
Christopher S. Pepin,
Mihir Metkar,
Yevgen Levdansky,
Brian R. Fritz,
Elizaveta A. Andrianova,
Ruchi Jain,
Eugene Valkov,
Caroline Köhrer,
Melissa J. Moore

Affiliations

Alicia A. Bicknell: Moderna, Inc, 325 Binney Street, Cambridge, MA 02142, USA; Corresponding author
David W. Reid: Moderna, Inc, 325 Binney Street, Cambridge, MA 02142, USA
Marissa C. Licata: Moderna, Inc, 325 Binney Street, Cambridge, MA 02142, USA
Adriana K. Jones: Moderna, Inc, 325 Binney Street, Cambridge, MA 02142, USA
Yi Min Cheng: Moderna, Inc, 325 Binney Street, Cambridge, MA 02142, USA
Mengying Li: Moderna, Inc, 325 Binney Street, Cambridge, MA 02142, USA
Chiaowen Joyce Hsiao: Moderna, Inc, 325 Binney Street, Cambridge, MA 02142, USA
Christopher S. Pepin: Moderna, Inc, 325 Binney Street, Cambridge, MA 02142, USA
Mihir Metkar: Moderna, Inc, 325 Binney Street, Cambridge, MA 02142, USA
Yevgen Levdansky: RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
Brian R. Fritz: Moderna, Inc, 325 Binney Street, Cambridge, MA 02142, USA
Elizaveta A. Andrianova: Moderna, Inc, 325 Binney Street, Cambridge, MA 02142, USA
Ruchi Jain: Moderna, Inc, 325 Binney Street, Cambridge, MA 02142, USA
Eugene Valkov: RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
Caroline Köhrer: Moderna, Inc, 325 Binney Street, Cambridge, MA 02142, USA
Melissa J. Moore: Moderna, Inc, 325 Binney Street, Cambridge, MA 02142, USA; Corresponding author

Journal volume & issue: Vol. 43, no. 4
p. 114098

Abstract

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Summary: Developing an effective mRNA therapeutic often requires maximizing protein output per delivered mRNA molecule. We previously found that coding sequence (CDS) design can substantially affect protein output, with mRNA variants containing more optimal codons and higher secondary structure yielding the highest protein outputs due to their slow rates of mRNA decay. Here, we demonstrate that CDS-dependent differences in translation initiation and elongation rates lead to differences in translation- and deadenylation-dependent mRNA decay rates, thus explaining the effect of CDS on mRNA half-life. Surprisingly, the most stable and highest-expressing mRNAs in our test set have modest initiation/elongation rates and ribosome loads, leading to minimal translation-dependent mRNA decay. These findings are of potential interest for optimization of protein output from therapeutic mRNAs, which may be achieved by attenuating rather than maximizing ribosome load.

CP: Molecular biology

Published in Cell Reports

ISSN: 2211-1247 (Online)
Publisher: Elsevier
Country of publisher: Netherlands
LCC subjects: Science: Biology (General)
Website: http://www.cell.com/cell-reports/home

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