IDEAS home Printed from https://ideas.repec.org/a/eee/phsmap/v637y2024ics0378437124000827.html
   My bibliography  Save this article

mRNA translation from a unidirectional traffic perspective

Author

Listed:
  • T.V., Binil Shyam
  • Sharma, Rati

Abstract

mRNA translation is a crucial process that leads to protein synthesis in living cells. Therefore, it is a process that needs to work optimally for a cell to stay healthy and alive. With advancements in microscopy and novel experimental techniques, a lot of the intricate details about the translation mechanism are now known. However, the why and how of this mechanism are still ill understood, and therefore, is an active area of research. Theoretical studies of mRNA translation typically view it in terms of the Totally Asymmetric Simple Exclusion Process or TASEP. Various works have used the TASEP model in order to study a wide range of phenomena and factors affecting translation, such as ribosome traffic on an mRNA under noisy (codon-dependent or otherwise) conditions, ribosome stalling, premature termination, ribosome reinitiation and dropoff, codon-dependent elongation and competition among mRNA for ribosomes, among others. In this review, we relay the history and physics of the translation process in terms of the TASEP framework. In particular, we discuss the viability and evolution of this model and its limitations while also formulating the reasons behind its success. Finally, we also identify gaps in the existing literature and suggest possible extensions and applications that will lead to a better understanding of ribosome traffic on the mRNA.

Suggested Citation

  • T.V., Binil Shyam & Sharma, Rati, 2024. "mRNA translation from a unidirectional traffic perspective," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 637(C).
    • Handle: RePEc:eee:phsmap:v:637:y:2024:i:c:s0378437124000827
    DOI: 10.1016/j.physa.2024.129574
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0378437124000827
    Download Restriction: Full text for ScienceDirect subscribers only. Journal offers the option of making the article available online on Science direct for a fee of $3,000
    File URL: https://libkey.io/10.1016/j.physa.2024.129574?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. Evans, M.R. & Sugden, K.E.P., 2007. "An exclusion process for modelling fungal hyphal growth," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 384(1), pages 53-58.
    2. Daehyun Baek & Judit Villén & Chanseok Shin & Fernando D. Camargo & Steven P. Gygi & David P. Bartel, 2008. "The impact of microRNAs on protein output," Nature, Nature, vol. 455(7209), pages 64-71, September.
    3. Sandip Datta & Brian Seed, 2018. "Influence of multiplicative stochastic variation on translational elongation rates," PLOS ONE, Public Library of Science, vol. 13(1), pages 1-27, January.
    4. Alexey A Gritsenko & Marc Hulsman & Marcel J T Reinders & Dick de Ridder, 2015. "Unbiased Quantitative Models of Protein Translation Derived from Ribosome Profiling Data," PLOS Computational Biology, Public Library of Science, vol. 11(8), pages 1-26, August.
    5. Schadschneider, Andreas, 2000. "Statistical physics of traffic flow," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 285(1), pages 101-120.
    6. Sophia Rudorf & Reinhard Lipowsky, 2015. "Protein Synthesis in E. coli: Dependence of Codon-Specific Elongation on tRNA Concentration and Codon Usage," PLOS ONE, Public Library of Science, vol. 10(8), pages 1-22, August.
    7. Michael VanInsberghe & Jeroen Berg & Amanda Andersson-Rolf & Hans Clevers & Alexander Oudenaarden, 2021. "Single-cell Ribo-seq reveals cell cycle-dependent translational pausing," Nature, Nature, vol. 597(7877), pages 561-565, September.
    8. Luis Mier-y-Terán-Romero & Mary Silber & Vassily Hatzimanikatis, 2010. "The Origins of Time-Delay in Template Biopolymerization Processes," PLOS Computational Biology, Public Library of Science, vol. 6(4), pages 1-15, April.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Dailisan, Damian N. & Lim, May T., 2016. "Agent-based modeling of lane discipline in heterogeneous traffic," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 457(C), pages 138-147.
    2. Shang, Du & Xu, Mengjia & Shang, Pengjian, 2017. "Generalized sample entropy analysis for traffic signals based on similarity measure," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 474(C), pages 1-7.
    3. Josupeit, Mario & Krug, Joachim, 2021. "The fitness landscapes of translation," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 569(C).
    4. Ray M Marín & Jiří Vaníček, 2012. "Optimal Use of Conservation and Accessibility Filters in MicroRNA Target Prediction," PLOS ONE, Public Library of Science, vol. 7(2), pages 1-11, February.
    5. Zhang, Yali & Shang, Pengjian & Sun, Zhenghui, 2018. "Diversity analysis based on ordered patterns," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 506(C), pages 1126-1133.
    6. Yue, Hao & Hao, Herui & Chen, Xiaoming & Shao, Chunfu, 2007. "Simulation of pedestrian flow on square lattice based on cellular automata model," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 384(2), pages 567-588.
    7. Alicia Hurtado & Irene Mota-Gómez & Miguel Lao & Francisca M. Real & Johanna Jedamzick & Miguel Burgos & Darío G. Lupiáñez & Rafael Jiménez & Francisco J. Barrionuevo, 2024. "Complete male-to-female sex reversal in XY mice lacking the miR-17~92 cluster," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    8. Wenshu Zeng & Lu Yue & Kim S. W. Lam & Wenxin Zhang & Wai-Kin So & Erin H. Y. Tse & Tom H. Cheung, 2022. "CPEB1 directs muscle stem cell activation by reprogramming the translational landscape," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
    9. Dailisan, Damian N. & Lim, May T., 2019. "Vehicular traffic modeling with greedy lane-changing and inordinate waiting," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 521(C), pages 715-723.
    10. Larisa Afanasyeva & Ekaterina Bulinskaya, 2013. "Asymptotic Analysis of Traffic Lights Performance Under Heavy Traffic Assumption," Methodology and Computing in Applied Probability, Springer, vol. 15(4), pages 935-950, December.
    11. Adam A Margolin & Shao-En Ong & Monica Schenone & Robert Gould & Stuart L Schreiber & Steven A Carr & Todd R Golub, 2009. "Empirical Bayes Analysis of Quantitative Proteomics Experiments," PLOS ONE, Public Library of Science, vol. 4(10), pages 1-15, October.
    12. Chikako Ragan & Michael Zuker & Mark A Ragan, 2011. "Quantitative Prediction of miRNA-mRNA Interaction Based on Equilibrium Concentrations," PLOS Computational Biology, Public Library of Science, vol. 7(2), pages 1-11, February.
    13. Bin Shao & Jiawei Yan & Jing Zhang & Lili Liu & Ye Chen & Allen R. Buskirk, 2024. "Riboformer: a deep learning framework for predicting context-dependent translation dynamics," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    14. Zheng, Zuduo, 2014. "Recent developments and research needs in modeling lane changing," Transportation Research Part B: Methodological, Elsevier, vol. 60(C), pages 16-32.
    15. L. G. Afanasyeva, 2020. "Asymptotic Analysis of Queueing Models Based on Synchronization Method," Methodology and Computing in Applied Probability, Springer, vol. 22(4), pages 1417-1438, December.
    16. Wenliang Zhu & Xuan Kan, 2014. "Neural Network Cascade Optimizes MicroRNA Biomarker Selection for Nasopharyngeal Cancer Prognosis," PLOS ONE, Public Library of Science, vol. 9(10), pages 1-7, October.
    17. Yuheng Lu & Christina S Leslie, 2016. "Learning to Predict miRNA-mRNA Interactions from AGO CLIP Sequencing and CLASH Data," PLOS Computational Biology, Public Library of Science, vol. 12(7), pages 1-18, July.
    18. Parawee Lekprasert & Michael Mayhew & Uwe Ohler, 2011. "Assessing the Utility of Thermodynamic Features for microRNA Target Prediction under Relaxed Seed and No Conservation Requirements," PLOS ONE, Public Library of Science, vol. 6(6), pages 1-13, June.
    19. Azelle Hawdon & Niall D. Geoghegan & Monika Mohenska & Anja Elsenhans & Charles Ferguson & Jose M. Polo & Robert G. Parton & Jennifer Zenker, 2023. "Apicobasal RNA asymmetries regulate cell fate in the early mouse embryo," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    20. Jian, Li & Lizhong, Yang & Daoliang, Zhao, 2005. "Simulation of bi-direction pedestrian movement in corridor," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 354(C), pages 619-628.

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:eee:phsmap:v:637:y:2024:i:c:s0378437124000827. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Catherine Liu (email available below). General contact details of provider: http://www.journals.elsevier.com/physica-a-statistical-mechpplications/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.