Adaptation of mRNA structure to control protein folding

References

• Shah P, Ding Y, Niemczyk M, Kudla G, Plotkin JB. Rate-limiting steps in yeast protein translation. Cell 2013; 153:1589-601; PMID:23791185; https://doi.org/10.1016/j.cell.2013.05.049
   PubMed Web of Science ®Google Scholar
• Kortmann J, Narberhaus F. Bacterial RNA thermometers: Molecular zippers and switches. Nat Rev Microbiol 2012; 10:255-65; PMID:22421878; https://doi.org/10.1038/nrmicro2730
   PubMed Web of Science ®Google Scholar
• Subramaniam AR, Zid BM, O'Shea EK. An integrated approach reveals regulatory controls on bacterial translation elongation. Cell 2014; 159:1200-11; PMID:25416955; https://doi.org/10.1016/j.cell.2014.10.043
   PubMed Web of Science ®Google Scholar
• Klumpp S, Scott M, Pedersen S, Hwa T. Molecular crowding limits translation and cell growth. Proc Natl Acad Sci U S A 2013; 110:16754-59; PMID:24082144; https://doi.org/10.1073/pnas.1310377110
   PubMed Web of Science ®Google Scholar
• Dana A, Tuller T. The effect of tRNA levels on decoding times of mRNA codons. Nucleic Acids Res 2014; 42:9171-81; PMID:25056313; https://doi.org/10.1093/nar/gku646
   PubMed Web of Science ®Google Scholar
• Gorochowski TE, Ignatova Z, Bovenberg RA, Roubos JA. Trade-offs between tRNA abundance and mRNA secondary structure support smoothing of translation elongation rate. Nucleic Acids Res 2015; 43:3022-32; PMID:25765653; https://doi.org/10.1093/nar/gkv199
   PubMed Web of Science ®Google Scholar
• Fredrick K, Ibba M. How the sequence of a gene can tune its translation. Cell 2010; 141:227-9; PMID:20403320; https://doi.org/10.1016/j.cell.2010.03.033
   PubMed Web of Science ®Google Scholar
• Novoa EM, Ribas de Pouplana L. Speeding with control: Codon usage, tRNAs, and ribosomes. Trends Genet 2012; 28:574-81; PMID:22921354; https://doi.org/10.1016/j.tig.2012.07.006
   PubMed Web of Science ®Google Scholar
• Meyer IM, Miklos I. Statistical evidence for conserved, local secondary structure in the coding regions of eukaryotic mRNAs and pre-mRNAs. Nucleic Acids Res 2005; 33:6338-48; PMID:16275783; https://doi.org/10.1093/nar/gki923
   PubMed Web of Science ®Google Scholar
• Somogyi P, Jenner AJ, Brierley I, Inglis SC. Ribosomal pausing during translation of an RNA pseudoknot. Mol Cell Biol 1993; 13:6931-40; PMID:8413285; https://doi.org/10.1128/MCB.13.11.6931
   PubMed Web of Science ®Google Scholar
• Dana A, Tuller T. Determinants of translation elongation speed and ribosomal profiling biases in mouse embryonic stem cells. PLoS Comput Biol 2012; 8:e1002755; PMID:23133360; https://doi.org/10.1371/journal.pcbi.1002755
   PubMed Web of Science ®Google Scholar
• Charneski CA, Hurst LD. Positively charged residues are the major determinants of ribosomal velocity. PLoS Biol 2013; 11:e1001508; PMID:23554576; https://doi.org/10.1371/journal.pbio.1001508
   PubMed Web of Science ®Google Scholar
• Artieri CG, Fraser HB. Accounting for biases in riboprofiling data indicates a major role for proline in stalling translation. Genome Res 2014; 24:2011-21; PMID:25294246; https://doi.org/10.1101/gr.175893.114
   PubMed Web of Science ®Google Scholar
• Wilson DN, Arenz S, Beckmann R. Translation regulation via nascent polypeptide-mediated ribosome stalling. Curr Opin Struct Biol 2016; 37:123-33; PMID:26859868; https://doi.org/10.1016/j.sbi.2016.01.008
   PubMed Web of Science ®Google Scholar
• Ito K, Chiba S. Arrest peptides: Cis-acting modulators of translation. Annu Rev Biochem 2013; 82:171-202; PMID:23746254; https://doi.org/10.1146/annurev-biochem-080211-105026
   PubMed Web of Science ®Google Scholar
• Shabalina SA, Ogurtsov AY, Spiridonov NA. A periodic pattern of mRNA secondary structure created by the genetic code. Nucleic Acids Res 2006; 34:2428-37; PMID:16682450; https://doi.org/10.1093/nar/gkl287
   PubMed Web of Science ®Google Scholar
• Gu W, Zhou T, Wilke CO. A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes. PLoS Comput Biol 2010; 6:e1000664; PMID:20140241; https://doi.org/10.1371/journal.pcbi.1000664
   PubMed Web of Science ®Google Scholar
• Tuller T, Zur H. Multiple roles of the coding sequence 5′ end in gene expression regulation. Nucleic Acids Res 2015; 43:13-28; PMID:25505165; https://doi.org/10.1093/nar/gku1313
   PubMed Web of Science ®Google Scholar
• Wolin SL, Walter P. Ribosome pausing and stacking during translation of a eukaryotic mRNA. EMBO J 1988; 7:3559-69; PMID:2850168
   PubMed Web of Science ®Google Scholar
• Ignatova Z, Narberhaus F. Systematic probing of the bacterial RNA structurome to reveal new functions. Curr Opin Microbiol 2017; 36:14-19; PMID:28160611; https://doi.org/10.1016/j.mib.2017.01.003
   PubMed Web of Science ®Google Scholar
• Nackley AG, Shabalina SA, Tchivileva IE, Satterfield K, Korchynskyi O, Makarov SS, Maixner W, Diatchenko L. Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure. Science 2006; 314:1930-3; PMID:17185601; https://doi.org/10.1126/science.1131262
   PubMed Web of Science ®Google Scholar
• Zhang F, Saha S, Shabalina SA, Kashina A. Differential arginylation of actin isoforms is regulated by coding sequence-dependent degradation. Science 2010; 329:1534-37; PMID:20847274; https://doi.org/10.1126/science.1191701
   PubMed Web of Science ®Google Scholar
• Lopinski JD, Dinman JD, Bruenn JA. Kinetics of ribosomal pausing during programmed -1 translational frameshifting. Mol Cell Biol 2000; 20:1095-103; PMID:10648594; https://doi.org/10.1128/MCB.20.4.1095-1103.2000
   PubMed Web of Science ®Google Scholar
• Kimchi-Sarfaty C, Oh JM, Kim IW, Sauna ZE, Calcagno AM, Ambudkar SV, Gottesman MM. A “silent” polymorphism in the MDR1 gene changes substrate specificity. Science 2007; 315:525-8; PMID:17185560; https://doi.org/10.1126/science.1135308
   PubMed Web of Science ®Google Scholar
• Czech A, Fedyunin I, Zhang G, Ignatova Z. Silent mutations in sight: Co-variations in tRNA abundance as a key to unravel consequences of silent mutations. Mol Biosyst 2010; 6:1767-72; PMID:20617253; https://doi.org/10.1039/c004796c
   PubMed Web of Science ®Google Scholar
• Agashe D, Martinez-Gomez NC, Drummond DA, Marx CJ. Good codons, bad transcript: Large reductions in gene expression and fitness arising from synonymous mutations in a key enzyme. Mol Biol Evol 2013; 30:549-60; PMID:23223712; https://doi.org/10.1093/molbev/mss273
   PubMed Web of Science ®Google Scholar
• Shabalina SA, Spiridonov NA, Kashina A. Sounds of silence: Synonymous nucleotides as a key to biological regulation and complexity. Nucleic Acids Res 2013; 41:2073-94; PMID:23293005; https://doi.org/10.1093/nar/gks1205
   PubMed Web of Science ®Google Scholar
• Shabalina SA, Ogurtsov AY, Spiridonov NA, Koonin EV. Evolution at protein ends: Major contribution of alternative transcription initiation and termination to the transcriptome and proteome diversity in mammals. Nucleic Acids Res 2014; 42:7132-44; PMID:24792168; https://doi.org/10.1093/nar/gku342
   PubMed Web of Science ®Google Scholar
• Faure G, Ogurtsov AY, Shabalina SA, Koonin EV. Role of mRNA structure in the control of protein folding. Nucleic Acids Res 2016; 44:10898-911; PMID:27466388; https://doi.org/10.1093/nar/gkw671
   PubMed Web of Science ®Google Scholar
• Faure G, Callebaut I. Comprehensive repertoire of foldable regions within whole genomes. PLoS Comput Biol 2013; 9:e1003280; PMID:24204229; https://doi.org/10.1371/journal.pcbi.1003280
   PubMed Web of Science ®Google Scholar
• Thommen M, Holtkamp W, Rodnina MV. Co-translational protein folding: Progress and methods. Curr Opin Struct Biol 2017; 42:83-89; PMID:27940242; https://doi.org/10.1016/j.sbi.2016.11.020
   PubMed Web of Science ®Google Scholar
• O'Brien EP, Vendruscolo M, Dobson CM. Kinetic modelling indicates that fast-translating codons can coordinate cotranslational protein folding by avoiding misfolded intermediates. Nat Commun 2014; 5:2988; PMID:24394622; https://doi.org/10.1038/ncomms3988
   PubMed Web of Science ®Google Scholar
• Bonneau R, Ruczinski I, Tsai J, Baker D. Contact order and ab initio protein structure prediction. Protein Sci 2002; 11:1937-44; PMID:12142448; https://doi.org/10.1110/ps.3790102
   PubMed Web of Science ®Google Scholar
• Watts JM, Dang KK, Gorelick RJ, Leonard CW, Bess JW Jr., Swanstrom R, Burch CL, Weeks KM. Architecture and secondary structure of an entire HIV-1 RNA genome. Nature 2009; 460:711-6; PMID:19661910; https://doi.org/10.1038/nature08237
   PubMed Web of Science ®Google Scholar
• Dyson HJ, Wright PE. Coupling of folding and binding for unstructured proteins. Curr Opin Struct Biol 2002; 12:54-60; PMID:11839490; https://doi.org/10.1016/S0959-440X(02)00289-0
   PubMed Web of Science ®Google Scholar
• Natan E, Wells JN, Teichmann SA, Marsh JA. Regulation, evolution and consequences of cotranslational protein complex assembly. Curr Opin Struct Biol 2017; 42:90-7; PMID:27969102; https://doi.org/10.1016/j.sbi.2016.11.023
   PubMed Web of Science ®Google Scholar
• Sanjuan R, Borderia AV. Interplay between RNA structure and protein evolution in HIV-1. Mol Biol Evol 2011; 28:1333-38; PMID:21135148; https://doi.org/10.1093/molbev/msq329
   PubMed Web of Science ®Google Scholar
• Goz E, Tuller T. Evidence of a direct evolutionary selection for strong folding and mutational robustness within HIV coding regions. J Comput Biol 2016; 23:641-50; PMID:27347769; https://doi.org/10.1089/cmb.2016.0052
   PubMed Web of Science ®Google Scholar
• Sharp PM, Averof M, Lloyd AT, Matassi G, Peden JF. DNA sequence evolution: The sounds of silence. Philos Trans R Soc Lond B Biol Sci 1995; 349:241-7; PMID:8577834; https://doi.org/10.1098/rstb.1995.0108
   PubMed Web of Science ®Google Scholar
• Resch AM, Carmel L, Marino-Ramirez L, Ogurtsov AY, Shabalina SA, Rogozin IB, Koonin EV. Widespread positive selection in synonymous sites of mammalian genes. Mol Biol Evol 2007; 24:1821-31; PMID:17522087; https://doi.org/10.1093/molbev/msm100
   PubMed Web of Science ®Google Scholar
• Chursov A, Walter MC, Schmidt T, Mironov A, Shneider A, Frishman D. Sequence-structure relationships in yeast mRNAs. Nucleic Acids Res 2012; 40:956-62; PMID:21954438; https://doi.org/10.1093/nar/gkr790
   PubMed Web of Science ®Google Scholar
• Roderer DJ, Scharer MA, Rubini M, Glockshuber R. Acceleration of protein folding by four orders of magnitude through a single amino acid substitution. Sci Rep 2015; 5:11840; PMID:26121966; https://doi.org/10.1038/srep11840
   PubMed Web of Science ®Google Scholar
• Taketomi H, Kano F, Go N. The effect of amino acid substitution on protein-folding and -unfolding transition studied by computer simulation. Biopolymers 1988; 27:527-59; PMID:3370293; https://doi.org/10.1002/bip.360270402
   PubMed Web of Science ®Google Scholar
• Lynch M, Conery JS. The origins of genome complexity. Science 2003; 302:1401-4; PMID:14631042; https://doi.org/10.1126/science.1089370
   PubMed Web of Science ®Google Scholar
• Ottolenghi C. Some traces of hidden codes. Riv Biol 1998; 91:515-42; PMID:10212571
   PubMed Web of Science ®Google Scholar
• Trifonov E, Volkovich Z, Frenkel ZM. Multiple levels of meaning in DNA sequences, and one more. Ann N Y Acad Sci 2012; 1267:35-8; PMID:22954214; https://doi.org/10.1111/j.1749-6632.2012.06589.x
   PubMed Web of Science ®Google Scholar
• Yang Z. PAML 4: Phylogenetic analysis by maximum likelihood. Mol Biol Evol 2007; 24:1586-91; PMID:17483113; https://doi.org/10.1093/molbev/msm088
   PubMed Web of Science ®Google Scholar