Determinants of efficient modulation of ribosomal traffic jams

Computational and Structural Biotechnology Journal - Tập 19 - Trang 6064-6079 - 2021
Sophie Vinokour1, Tamir Tuller1,2
1Department of Biomedical Engineering, Engineering Faculty, Tel Aviv University, Israel
2The Sagol School of Neuroscience, Tel Aviv University, Tel-Aviv 69978, Israel

Tài liệu tham khảo

Lane, 2010, The energetics of genome complexity, Nature, 467, 929, 10.1038/nature09486 Buttgereit, 1995, A hierarchy of ATP-consuming processes in mammalian cells, Biochem. J., 312, 163, 10.1042/bj3120163 Mahalik, 2014, Genome engineering for improved recombinant protein expression in escherichia coli, Microb. Cell Fact., 13, 10.1186/s12934-014-0177-1 Gorochowski, 2016, A Minimal Model of Ribosome Allocation Dynamics Captures Trade-offs in Expression between Endogenous and Synthetic Genes, ACS Synth. Biol., 5, 710, 10.1021/acssynbio.6b00040 Gustafsson, 2012, Engineering genes for predictable protein expression, Protein Expr. Purif., 83, 37, 10.1016/j.pep.2012.02.013 Boyle, J. Molecular biology of the cell, 5th edition by B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts, and P. Walter. Biochem. Mol. Biol. Educ. 36, 317–318 (2008). Tuller, 2010, An evolutionarily conserved mechanism for controlling the efficiency of protein translation, Cell, 141, 344, 10.1016/j.cell.2010.03.031 Bahir, 2009, Viral adaptation to host: a proteome-based analysis of codon usage and amino acid preferences, Mol. Syst. Biol., 5, 311, 10.1038/msb.2009.71 Gustafsson, C., Govindarajan, S. & Minshull, J. Codon bias and heterologous protein expression. Trends in Biotechnology vol. 22 346–353 (Elsevier Current Trends, 2004). Shachrai, 2010, Cost of Unneeded Proteins in E. coli Is Reduced after Several Generations in Exponential Growth, Mol. Cell, 38, 758, 10.1016/j.molcel.2010.04.015 Warner, 1999, The economics of ribosome biosynthesis in yeast, Trends Biochem Sci, 24, 437, 10.1016/S0968-0004(99)01460-7 Raveh, 2016, A model for competition for ribosomes in the cell, J. R. Soc. Interface, 13, 20151062, 10.1098/rsif.2015.1062 Kudla, 2009, Coding-sequence determinants of gene expression in Escherichia coli, Science, 324, 255, 10.1126/science.1170160 Gyorgy, A. & Del Vecchio, D. Limitations and trade-offs in gene expression due to competition for shared cellular resources. Proc. IEEE Conf. Decis. Control 2015-February, 5431–5436 (2014). Zur, 2020, Algorithms for ribosome traffic engineering and their potential in improving host cells’ titer and growth rate, Sci. Rep., 10, 21202, 10.1038/s41598-020-78260-y Sauna, 2011, Understanding the contribution of synonymous mutations to human disease, Nat. Rev. Genet., 12, 683, 10.1038/nrg3051 Tuller, 2015, Multiple roles of the coding sequence 5’ end in gene expression regulation, Nucleic Acids Res., 43, 13, 10.1093/nar/gku1313 Ingolia, 2009, Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling, Science (80-.), 324, 218, 10.1126/science.1168978 Bennetzen, J. L. & Hall, B. D. Codon selection in yeast. J. Biol. Chem. (1982). Sharp, 1987, The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications, Nucleic Acids Res., 15, 1281, 10.1093/nar/15.3.1281 Tuller, 2010, Translation efficiency is determined by both codon bias and folding energy, Proc. Natl. Acad. Sci. U. S. A., 107, 3645, 10.1073/pnas.0909910107 Kudla, 2009, Coding-sequence determinants of expression in escherichia coli, Science (80-.), 324, 255, 10.1126/science.1170160 dos Reis, 2004, Solving the riddle of codon usage preferences: a test for translational selection, Nucleic Acids Res., 32, 5036, 10.1093/nar/gkh834 Bahiri-Elitzur, 2021, Codon-based indices for modeling gene expression and transcript evolution, Comput Struct Biotechnol J, 19, 2646, 10.1016/j.csbj.2021.04.042 Bazzini, 2016, Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition, EMBO J., 35, 2087, 10.15252/embj.201694699 Presnyak, 2015, Codon Optimality Is a Major Determinant of mRNA Stability, Cell, 160, 1111, 10.1016/j.cell.2015.02.029 Edri, 2014, Quantifying the Effect of Ribosomal Density on mRNA Stability, PLoS ONE, 9, e102308, 10.1371/journal.pone.0102308 McManus, 2014, Ribosome profiling reveals post-transcriptional buffering of divergent gene expression in yeast, Genome Res., 24, 422, 10.1101/gr.164996.113 Kinsella, R. J. et al. Ensembl BioMarts: A hub for data retrieval across taxonomic space. Database 2011, (2011). Zenklusen, 2008, Single-RNA counting reveals alternative modes of gene expression in yeast, Nat. Struct. Mol. Biol., 15, 1263, 10.1038/nsmb.1514 Reuveni, 2011, Genome-scale analysis of translation elongation with a ribosome flow model, PLoS Comput. Biol., 7, 1002127, 10.1371/journal.pcbi.1002127 Zia, 2011, Modeling Translation in Protein Synthesis with TASEP: A Tutorial and Recent Developments, J. Stat. Phys., 144, 405, 10.1007/s10955-011-0183-1 Lb, 2003, Totally asymmetric exclusion process with extended objects: a model for protein synthesis, Phys. Rev. E. Stat. Nonlin. Soft Matter Phys., 68, 17 Schadschneider, 2011, Stochastic Transport in Complex Systems, Stochastic Transport in Complex Systems (Elsevier Poker, 2014, Maximizing protein translation rate in the non-homogeneous ribosome flow model: a convex optimization approach, J. R. Soc. Interface, 11, 20140713, 10.1098/rsif.2014.0713 Chu, 2014, Translation elongation can control translation initiation on eukaryotic mRNAs, EMBO J., 33, 21, 10.1002/embj.201385651 Wolin, 1988, Ribosome pausing and stacking during translation of a eukaryotic mRNA, EMBO J., 7, 3559, 10.1002/j.1460-2075.1988.tb03233.x Levin, 2018, Genome-Scale Analysis of Perturbations in Translation Elongation Based on a Computational Model, Sci. Rep., 8, 10.1038/s41598-018-34496-3 Poker, 2015, Sensitivity of mRNA translation, Sci. Rep., 5, 10.1038/srep12795