Model-Driven Engineering of Gene Expression from RNA Replicons

Beal, Jacob; Wagner, Tyler E.; Kitada, Tasuku; Azizgolshani, Odisse; Parker, Jordan Moberg; Densmore, Douglas; Weiss, Ron

doi:10.1021/sb500173f

Cited by 38Gene Regulatory Network AnalysisRNA and protein synthesis mechanismsViral Infectious Diseases and Gene Expression in Insects

Model-Driven Engineering of Gene Expression from RNA Replicons

Beal, Jacob, Wagner, Tyler E., Kitada, Tasuku, Azizgolshani, Odisse, Parker, Jordan Moberg, Densmore, Douglas, Weiss, Ron·2015·ACS Synthetic Biology

DOI 10.1021/sb500173f

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Abstract

RNA replicons are an emerging platform for engineering synthetic biological systems. Replicons self-amplify, can provide persistent high-level expression of proteins even from a small initial dose, and, unlike DNA vectors, pose minimal risk of chromosomal integration. However, no quantitative model sufficient for engineering levels of protein expression from such replicon systems currently exists. Here, we aim to enable the engineering of multigene expression from more than one species of replicon by creating a computational model based on our experimental observations of the expression dynamics in single- and multireplicon systems. To this end, we studied fluorescent protein expression in baby hamster kidney (BHK-21) cells using a replicon derived from Sindbis virus (SINV). We characterized expression dynamics for this platform based on the dose-response of a single species of replicon over 50 h and on a titration of two cotransfected replicons expressing different fluorescent proteins. From this data, we derive a quantitative model of multireplicon expression and validate it by designing a variety of three-replicon systems, with profiles that match desired expression levels. We achieved a mean error of 1.7-fold on a 1000-fold range, thus demonstrating how our model can be applied to precisely control expression levels of each Sindbis replicon species in a system.

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One copy of saRNA produces multiple copies of RNA transcripts by the above-described mechanism to initiate self-amplification of antigen genes in the cell.
“As a result, one copy of saRNA produces multiple copies of RNA transcripts by the above-described mechanism to initiate self-amplification of antigen genes in the cell.35,195,196”
From Advances in COVID-19 mRNA vaccine development (2022) · cites this paper as [196]

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Authors: Beal, J., Wagner, T. E., Kitada, T., Azizgolshani, O., Parker, J. M., Densmore, D., & Weiss, R.
Affiliations: Raytheon (United States) (US)
Boston University (US)
Massachusetts Institute of Technology (US)
University of California, Los Angeles (US)
Corresponding author: Beal, Jacob
ORCID: Beal, Jacob
Kitada, Tasuku
Parker, Jordan Moberg
Densmore, Douglas
Weiss, Ron
Venue: ACS Synthetic Biology
Publisher: American Chemical Society (ACS)
Published: 2014-06-06
Volume: 4
Issue: 1
Pages: 48-56
ISSN: 2161-5063 (ISSN-L)
DOI: 10.1021/sb500173f
OpenAlex: W2104313404
Cited by: 38
References: 42
Citations by year: 2025: 2 · 2024: 2 · 2023: 1 · 2022: 6 · 2021: 3 · 2020: 1 · 2019: 4 · 2018: 4 · 2017: 5 · 2016: 1 · 2015: 6 · 2014: 2 · 2012: 1
FWCI: 1.91
Type: journal article
Language: en
Open access: closed
Locations: ACS Synthetic Biology (publishedVersion)
PubMed (publishedVersion)
Funders: Defense Sciences Office, DARPA (W911NF-11-054)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Viral Infectious Diseases and Gene Expression in Insects
Keywords: RNA replicon, gene expression modeling, protein abundance, fluorescent protein expression, BHK-21 cells, dose-response relationship, cotransfection, synthetic biology
MeSH terms: Animals, Cell Line, Genetic Engineering, Cricetinae, Luminescent Proteins, Models, Genetic, Replicon, RNA, Viral, Sindbis Virus, Transfection, Gene Expression, Synthetic Biology

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Model-Driven Engineering of Gene Expression from RNA Replicons

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