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

Author:

Bicknell, Alicia A

Reid, David W

Licata, Marissa C

Jones, Adriana K

Cheng, Yi Min

Li, Mengying

Hsiao, Chiaowen Joyce

Pepin, Christopher S

Metkar, Mihir

Levdansky,Yevgen

Fritz, Brian R

Andrianova, Elizaveta A

Jain, Ruchi

Valkov,Eugene

Köhrer, Caroline

Moore, Melissa J
Author Address

Moderna, Inc, 325 Binney Street, Cambridge, MA 02142, USA. Electronic address: alicia.bicknell@modernatx.com., RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA., Moderna, Inc, 325 Binney Street, Cambridge, MA 02142, USA. Electronic address: melissa.moore@modernatx.com.,

Abstract:

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. Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.

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