Attenuating ribosome load improves protein output from mRNA by limiting translation-dependent mRNA decay
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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.
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mRNAs characterized by high translation initiation rates exhibit high ribosomal loading, which increases frequency of ribosome collisions, leading to accelerated mRNA decay and reduced product yield.
“On the other hand, mRNAs characterized by high translation initiation rates exhibit high ribosomal loading, which increases the frequency of ribosome collisions, leading to accelerated mRNA decay and, consequently, reduced product yield [37].”
From Identification of novel 5’ UTR variants for enhanced mRNA translation and vaccine immunogenicity (2026) · cites this paper as [37]
The Results link faster initiation to higher ribosome load and faster mRNA decay in one tested mRNA subset; the Discussion links high load to lower protein output. The Discussion also says denser ribosome loading is associated with more collisions, but presents collisions as a possible mechanism for the faster decay, not an established cause in these mRNAs. The citing sentence states that causal link without the paper’s qualification. Page numbers are unavailable in our copy. (LLM, conf=0.90)
Experimental — accuracy not yet measuredThe rate of mRNA degradation also plays a pivotal role in reporter protein accumulation.
“The rate of mRNA degradation also plays a pivotal role in reporter protein accumulation.”
From Identification of novel 5’ UTR variants for enhanced mRNA translation and vaccine immunogenicity (2026) · cites this paper as [37]
Open reading frame (ORF) may affect the mRNA secondary structure and, consequently, impact its translation efficiency.
“The in vivo evaluation of these 5′ and 3′ UTR combinations highlighted the fact that open reading frame (ORF) may affect the mRNA secondary structure and, consequently, impact its translation efficiency.45”
From Evaluation of synthetic mRNA with selected UTR sequences and alternative poly(A) tail, in vitro and in vivo (2025) · cites this paper as [45]
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- Authors
- Bicknell, A. A., Reid, D. W., Licata, M. C., Jones, A. K., Cheng, Y. M., Li, M., Hsiao, C. J., Pepin, C. S., Metkar, M., Levdansky, Y., Fritz, B. R., Andrianova, E. A., Jain, R., Valkov, E., Köhrer, C., & Moore, M. J.
- Affiliations
- National Cancer Institute (US)
- Corresponding author
- Bicknell, Alicia A.
- Moore, Melissa J.
- ORCID
- Venue
- Cell Reports
- Publisher
- Elsevier BV
- Published
- 2024-04
- Volume
- 43
- Issue
- 4
- Pages
- 114098
- ISSN
- 2211-1247 (ISSN-L)
- OpenAlex
- W4394823561
- Cited by
- 68
- References
- 11
- Citations by year
- 2026: 20 · 2025: 40 · 2024: 8
- FWCI
- 8.80
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Cell Reports (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- National Institutes of Health
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Interference and Gene Delivery
- Keywords
- deadenylation, mRNA half-life, codon optimization, mRNA secondary structure, translation initiation rate, translation elongation rate, mRNA therapeutics, protein production
- MeSH terms
- Humans, Ribosomes, RNA, Messenger, Protein Biosynthesis, RNA Stability
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