Codon Bias as a Means to Fine-Tune Gene Expression
Tài liệu tham khảo
Agris, 2007, tRNA’s wobble decoding of the genome: 40 years of modification, J. Mol. Biol., 366, 1, 10.1016/j.jmb.2006.11.046
Andersson, 1990, Codon preferences in free-living microorganisms, Microbiol. Rev., 54, 198, 10.1128/MMBR.54.2.198-210.1990
Angov, 2008, Heterologous protein expression is enhanced by harmonizing the codon usage frequencies of the target gene with those of the expression host, PLoS ONE, 3, e2189, 10.1371/journal.pone.0002189
Begley, 2007, Trm9-catalyzed tRNA modifications link translation to the DNA damage response, Mol. Cell, 28, 860, 10.1016/j.molcel.2007.09.021
Bentele, 2013, Efficient translation initiation dictates codon usage at gene start, Mol. Syst. Biol., 9, 675, 10.1038/msb.2013.32
Berg, 1997, Growth rate-optimised tRNA abundance and codon usage, J. Mol. Biol., 270, 544, 10.1006/jmbi.1997.1142
Buchan, 2006, tRNA properties help shape codon pair preferences in open reading frames, Nucleic Acids Res., 34, 1015, 10.1093/nar/gkj488
Cannarozzi, 2010, A role for codon order in translation dynamics, Cell, 141, 355, 10.1016/j.cell.2010.02.036
Chan, 2012, Reprogramming of tRNA modifications controls the oxidative stress response by codon-biased translation of proteins, Nat. Commun., 3, 937, 10.1038/ncomms1938
Charneski, 2013, Positively charged residues are the major determinants of ribosomal velocity, PLoS Biol., 11, e1001508, 10.1371/journal.pbio.1001508
Charneski, 2014, Positive charge loading at protein termini is due to membrane protein topology, not a translational ramp, Mol. Biol. Evol., 31, 70, 10.1093/molbev/mst169
Chen, 2004, Codon usage between genomes is constrained by genome-wide mutational processes, Proc. Natl. Acad. Sci. U S A, 101, 3480, 10.1073/pnas.0307827100
Chu, 2014, Translation elongation can control translation initiation on eukaryotic mRNAs, EMBO J., 33, 21, 10.1002/embj.201385651
Coleman, 2008, Virus attenuation by genome-scale changes in codon pair bias, Science, 320, 1784, 10.1126/science.1155761
Crick, 1966, Codon–anticodon pairing: the wobble hypothesis, J. Mol. Biol., 19, 548, 10.1016/S0022-2836(66)80022-0
Dana, 2014, The effect of tRNA levels on decoding times of mRNA codons, Nucleic Acids Res., 42, 9171, 10.1093/nar/gku646
Dittmar, 2005, Selective charging of tRNA isoacceptors induced by amino-acid starvation, EMBO Rep., 6, 151, 10.1038/sj.embor.7400341
Dittmar, 2006, Tissue-specific differences in human transfer RNA expression, PLoS Genet., 2, e221, 10.1371/journal.pgen.0020221
dos Reis, 2004, Solving the riddle of codon usage preferences: a test for translational selection, Nucleic Acids Res., 32, 5036, 10.1093/nar/gkh834
Drummond, 2008, Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution, Cell, 134, 341, 10.1016/j.cell.2008.05.042
Elf, 2005, What makes ribosome-mediated transcriptional attenuation sensitive to amino acid limitation?, PLoS Comput. Biol., 1, e2, 10.1371/journal.pcbi.0010002
Elf, 2003, Selective charging of tRNA isoacceptors explains patterns of codon usage, Science, 300, 1718, 10.1126/science.1083811
Fluman, 2014, mRNA-programmed translation pauses in the targeting of E. coli membrane proteins, eLife, 3, e03440, 10.7554/eLife.03440
Frenkel-Morgenstern, 2012, Genes adopt non-optimal codon usage to generate cell cycle-dependent oscillations in protein levels, Mol. Syst. Biol., 8, 572, 10.1038/msb.2012.3
Gardin, 2014, Measurement of average decoding rates of the 61 sense codons in vivo, eLife, 3, 1, 10.7554/eLife.03735
Gibson, 2014, Programming biological operating systems: genome design, assembly and activation, Nat. Methods, 11, 521, 10.1038/nmeth.2894
Gingold, 2014, A dual program for translation regulation in cellular proliferation and differentiation, Cell, 158, 1281, 10.1016/j.cell.2014.08.011
Godinic-Mikulcic, 2014, Archaeal aminoacyl-tRNA synthetases interact with the ribosome to recycle tRNAs, Nucleic Acids Res., 42, 5191, 10.1093/nar/gku164
Goodman, 2013, Causes and effects of N-terminal codon bias in bacterial genes, Science, 342, 475, 10.1126/science.1241934
Gould, 2014, Computational tools and algorithms for designing customized synthetic genes, Front. Bioeng. Biotechnol., 2, 41, 10.3389/fbioe.2014.00041
Gouy, 1982, Codon usage in bacteria: correlation with gene expressivity, Nucleic Acids Res., 10, 7055, 10.1093/nar/10.22.7055
Grantham, 1980, Codon catalog usage and the genome hypothesis, Nucleic Acids Res., 8, r49, 10.1093/nar/8.1.197-c
Gromadski, 2006, A uniform response to mismatches in codon-anticodon complexes ensures ribosomal fidelity, Mol. Cell, 21, 369, 10.1016/j.molcel.2005.12.018
Grosjean, 2010, Deciphering synonymous codons in the three domains of life: co-evolution with specific tRNA modification enzymes, FEBS Lett., 584, 252, 10.1016/j.febslet.2009.11.052
Gustafsson, 2004, Codon bias and heterologous protein expression, Trends Biotechnol., 22, 346, 10.1016/j.tibtech.2004.04.006
Gustafsson, 2012, Engineering genes for predictable protein expression, Protein Expr. Purif., 83, 37, 10.1016/j.pep.2012.02.013
Gutman, 1989, Nonrandom utilization of codon pairs in Escherichia coli, Proc. Natl. Acad. Sci. U S A, 86, 3699, 10.1073/pnas.86.10.3699
Hershberg, 2008, Selection on codon bias, Annu. Rev. Genet., 42, 287, 10.1146/annurev.genet.42.110807.091442
Ikemura, 1985, Codon usage and tRNA content in unicellular and multicellular organisms, Mol. Biol. Evol., 2, 13
Ingolia, 2014, Ribosome profiling: new views of translation, from single codons to genome scale, Nat. Rev. Genet., 15, 205, 10.1038/nrg3645
Ingolia, 2009, Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling, Science, 324, 218, 10.1126/science.1168978
Ingolia, 2011, Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes, Cell, 147, 789, 10.1016/j.cell.2011.10.002
Kanaya, 1999, Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAs: gene expression level and species-specific diversity of codon usage based on multivariate analysis, Gene, 238, 143, 10.1016/S0378-1119(99)00225-5
Khade, 2011, Messenger RNA interactions in the decoding center control the rate of translocation, Nat. Struct. Mol. Biol., 18, 1300, 10.1038/nsmb.2140
Kimchi-Sarfaty, 2007, A “silent” polymorphism in the MDR1 gene changes substrate specificity, Science, 315, 525, 10.1126/science.1135308
Knight, 2001, A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes, Genome Biol., 2
Komar, 2009, A pause for thought along the co-translational folding pathway, Trends Biochem. Sci., 34, 16, 10.1016/j.tibs.2008.10.002
Kudla, 2009, Coding-sequence determinants of gene expression in Escherichia coli, Science, 324, 255, 10.1126/science.1170160
Lajoie, 2013, Probing the limits of genetic recoding in essential genes, Science, 342, 361, 10.1126/science.1241460
Li, 2012, The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria, Nature, 484, 538, 10.1038/nature10965
Li, 2014, Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources, Cell, 157, 624, 10.1016/j.cell.2014.02.033
Maertens, 2010, Gene optimization mechanisms: a multi-gene study reveals a high success rate of full-length human proteins expressed in Escherichia coli, Protein Sci., 19, 1312, 10.1002/pro.408
Malyshev, 2014, A semi-synthetic organism with an expanded genetic alphabet, Nature, 509, 385, 10.1038/nature13314
Mukai, 2015, Highly reproductive Escherichia coli cells with no specific assignment to the UAG codon, Sci. Rep., 5, 9699, 10.1038/srep09699
Mutalik, 2013, Precise and reliable gene expression via standard transcription and translation initiation elements, Nat. Methods, 10, 354, 10.1038/nmeth.2404
Novoa, 2012, A role for tRNA modifications in genome structure and codon usage, Cell, 149, 202, 10.1016/j.cell.2012.01.050
Pechmann, 2013, Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding, Nat. Struct. Mol. Biol., 20, 237, 10.1038/nsmb.2466
Pechmann, 2014, Local slowdown of translation by nonoptimal codons promotes nascent-chain recognition by SRP in vivo, Nat. Struct. Mol. Biol., 21, 1100, 10.1038/nsmb.2919
Pop, 2014, Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation, Mol. Syst. Biol., 10, 770, 10.15252/msb.20145524
Purvis, 1987, The efficiency of folding of some proteins is increased by controlled rates of translation in vivo. A hypothesis, J. Mol. Biol., 193, 413, 10.1016/0022-2836(87)90230-0
Qian, 2012, Balanced codon usage optimizes eukaryotic translational efficiency, PLoS Genet., 8, e1002603, 10.1371/journal.pgen.1002603
Quax, 2013, Differential translation tunes uneven production of operon-encoded proteins, Cell Rep., 4, 938, 10.1016/j.celrep.2013.07.049
Ran, 2012, Contributions of speed and accuracy to translational selection in bacteria, PLoS ONE, 7, e51652, 10.1371/journal.pone.0051652
Rovner, 2015, Recoded organisms engineered to depend on synthetic amino acids, Nature, 518, 89, 10.1038/nature14095
Saunders, 2010, Synonymous codon usage influences the local protein structure observed, Nucleic Acids Res., 38, 6719, 10.1093/nar/gkq495
Shah, 2013, Rate-limiting steps in yeast protein translation, Cell, 153, 1589, 10.1016/j.cell.2013.05.049
Shao, 2012, Synonymous codon ordering: a subtle but prevalent strategy of bacteria to improve translational efficiency, PLoS ONE, 7, e33547, 10.1371/journal.pone.0033547
Sharp, 1986, An evolutionary perspective on synonymous codon usage in unicellular organisms, J. Mol. Evol., 24, 28, 10.1007/BF02099948
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
Söll, 1966, Specificity of sRNA for recognition of codons as studied by the ribosomal binding technique, J. Mol. Biol., 19, 556, 10.1016/S0022-2836(66)80023-2
Spencer, 2012, Silent substitutions predictably alter translation elongation rates and protein folding efficiencies, J. Mol. Biol., 422, 328, 10.1016/j.jmb.2012.06.010
Stadler, 2011, Wobble base-pairing slows in vivo translation elongation in metazoans, RNA, 17, 2063, 10.1261/rna.02890211
Stoletzki, 2007, Synonymous codon usage in Escherichia coli: selection for translational accuracy, Mol. Biol. Evol., 24, 374, 10.1093/molbev/msl166
Supek, 2010, On relevance of codon usage to expression of synthetic and natural genes in Escherichia coli, Genetics, 185, 1129, 10.1534/genetics.110.115477
Tats, 2008, Preferred and avoided codon pairs in three domains of life, BMC Genomics, 9, 463, 10.1186/1471-2164-9-463
Tuller, 2015, Multiple roles of the coding sequence 5′ end in gene expression regulation, Nucleic Acids Res., 43, 13, 10.1093/nar/gku1313
Tuller, 2010, An evolutionarily conserved mechanism for controlling the efficiency of protein translation, Cell, 141, 344, 10.1016/j.cell.2010.03.031
Tulloch, 2014, RNA virus attenuation by codon pair deoptimisation is an artefact of increases in CpG/UpA dinucleotide frequencies, eLife, 3, e04531, 10.7554/eLife.04531
Welch, 2009, You’re one in a googol: optimizing genes for protein expression, J. R. Soc. Interface, 6, S467, 10.1098/rsif.2008.0520.focus
Welch, 2009, Design parameters to control synthetic gene expression in Escherichia coli, PLoS ONE, 4, e7002, 10.1371/journal.pone.0007002
Wiedenheft, 2011, Structures of the RNA-guided surveillance complex from a bacterial immune system, Nature, 477, 486, 10.1038/nature10402
Woolstenhulme, 2013, Nascent peptides that block protein synthesis in bacteria, Proc. Natl. Acad. Sci. U S A, 110, E878, 10.1073/pnas.1219536110
Xu, 2013, Non-optimal codon usage is a mechanism to achieve circadian clock conditionality, Nature, 495, 116, 10.1038/nature11942
Zhang, 2009, Transient ribosomal attenuation coordinates protein synthesis and co-translational folding, Nat. Struct. Mol. Biol., 16, 274, 10.1038/nsmb.1554
Zhang, 2013, Non-random arrangement of synonymous codons in archaea coding sequences, Genomics, 101, 362, 10.1016/j.ygeno.2013.04.008
Zhou, 2009, Translationally optimal codons associate with structurally sensitive sites in proteins, Mol. Biol. Evol., 26, 1571, 10.1093/molbev/msp070
Zhou, 2013, Non-optimal codon usage affects expression, structure and function of clock protein FRQ, Nature, 495, 111, 10.1038/nature11833