Determinants of efficient modulation of ribosomal traffic jams
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