Modeling mRNA Translation With Ribosome Abortions

• Published in: IEEE/ACM transactions on computational biology and bioinformatics Vol. 20; no. 2; pp. 1600 - 1605
• Main Authors: Jain, Aditi, Gupta, Arvind Kumar
• Format: Journal Article
• Language: English
• Published: United States IEEE 01.03.2023; The Institute of Electrical and Electronics Engineers, Inc. (IEEE)
• Subjects: abortions; Biological system modeling; Codon - metabolism; Codons; Computational modeling; contraction theory; Elongation; Gene translation; Mathematical models; Models, Biological; mRNA; Production; Protein Biosynthesis - genetics; Proteins; ribosome collisions; ribosome flow model; Ribosomes; Ribosomes - genetics; Ribosomes - metabolism; RNA, Messenger - genetics; RNA, Messenger - metabolism; Steady-state; Translation
• ISSN: 1545-5963; 1557-9964
• DOI: 10.1109/TCBB.2022.3203171

We derive a deterministic mathematical model for the flow of ribosomes along a mRNA called the ribosome flow model with extended objects and abortions (RFMEOA). This model incorporates important cellular features such as every ribosome covers several codons and they may detach from various regions along the track due to more realistic biological situations including phenomena of ribosome-ribosome collisions. We prove that the ribosome density profile along the mRNA in the RFMEOA and in particular, the protein production rate converge to a unique steady-state. Simulations of the RFMEOA demonstrate a surprising result that an increase in the initiation rate may sometimes lead to a decrease in the production rate. We believe that this model could be helpful to provide insight into the effects of premature termination on the protein expression and be useful for understanding and re-engineering the translation process.