Genetic code flexibility in microorganisms: novel mechanisms and impact on physiology
Open accessAbstract
The genetic code, initially thought to be universal and immutable, is now known to contain many variations, including biased codon usage, codon reassignment, ambiguous decoding and recoding. As a result of recent advances in the areas of genome sequencing, biochemistry, bioinformatics and structural biology, our understanding of genetic code flexibility has advanced substantially in the past decade. In this Review, we highlight the prevalence, evolution and mechanistic basis of genetic code variations in microorganisms, and we discuss how this flexibility of the genetic code affects microbial physiology.
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Many deviations from the universal code exist, particularly in organelles and prokaryotes with small genomes.
“Although many deviations from the universal code exist, particularly in organelles and prokaryotes with small genomes”
From Origin and Evolution of the Universal Genetic Code (2017) · cites this paper as [47]
The introductory passage in the Abstract section describes many deviations from the standard code, including yeast mitochondria and bacteria and archaea. It does not establish that deviations are particularly common in prokaryotes with small genomes; searches for “small genomes” and “reduced genome” found no passage making that connection. Page numbers were not available in our copy. (LLM, conf=0.84)
Experimental — accuracy not yet measuredLimited deviations from the standard genetic code have been detected in many groups, particularly organelles and parasitic or endosymbiotic bacteria with highly reduced genomes.
“The genetic code is nearly universal in all extant life forms although limited deviations from the SGC have been detected in many groups of organisms, particularly in organelles and parasitic or endosymbiotic bacteria with highly reduced genomes [11,16,17].”
From Frozen Accident Pushing 50: Stereochemistry, Expansion, and Chance in the Evolution of the Genetic Code (2017) · cites this paper as [17]
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Cites
Multiplex Genome Engineering Using CRISPR/Cas Systems
Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P. D., Wu, X., Jiang, W., Marraffini, L. A., et al. (2013) · Science · doi:10.1126/science.1231143 · Cited by 15,339 · see citing works
Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome
Gibson, D. G., Glass, J. I., Lartigue, C., Noskov, V. N., Chuang, R.-Y., Algire, M. A., Benders, G. A., Montague, M. G., Ma, L., Moodie, M. M., et al. (2010) · Science · doi:10.1126/science.1190719 · Cited by 2,638 · see citing works
The thioredoxin antioxidant system
Lu, J., & Holmgren, A. (2014) · Free Radical Biology and Medicine · doi:10.1016/j.freeradbiomed.2013.07.036 · Cited by 2,055 · see citing works
RNA-guided genetic silencing systems in bacteria and archaea
Wiedenheft, B., Sternberg, S. H., & Doudna, J. A. (2012) · Nature · doi:10.1038/nature10886 · Cited by 1,851 · see citing works
Adding New Chemistries to the Genetic Code
Liu, C. C., & Schultz, P. G. (2010) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.052308.105824 · Cited by 1,725 · see citing works
Synonymous but not the same: the causes and consequences of codon bias
Plotkin, J. B., & Kudla, G. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2899 · Cited by 1,677 · see citing works
Programming cells by multiplex genome engineering and accelerated evolution
Wang, H. H., Isaacs, F. J., Carr, P. A., Sun, Z. Z., Xu, G., Forest, C. R., & Church, G. M. (2009) · Nature · doi:10.1038/nature08187 · Cited by 1,529 · see citing works
The selection-mutation-drift theory of synonymous codon usage.
Bulmer, M. G. (1991) · Genetics · doi:10.1093/genetics/129.3.897 · Cited by 1,024 · see citing works
Genomically Recoded Organisms Expand Biological Functions
Lajoie, M. J., Rovner, A. J., Goodman, D. B., Aerni, H. R., Haimovich, A. D., Kuznetsov, G., Mercer, J. A. M., Wang, H. H., Carr, P. A., Mosberg, J. A., et al. (2013) · Science · doi:10.1126/science.1241459 · Cited by 859 · see citing works
Stadtman, T. C. (1996) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.65.070196.000503 · Cited by 827 · see citing works
Codon catalog usage and the genome hypothesis
Grantham, R. L., Gautier, C., Gouy, M., Mercier, R., & Pavé, A. (1980) · Nucleic Acids Research · doi:10.1093/nar/8.1.197-c · Cited by 801 · see citing works
Codon Bias as a Means to Fine-Tune Gene Expression
Quax, T. E. F., Claassens, N. J., Söll, D. G., & John van der, O. O. S. T. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.05.035 · Cited by 779 · see citing works
Self-citationThe anti-Shine–Dalgarno sequence drives translational pausing and codon choice in bacteria
Li, G., Oh, E., & Weissman, J. S. (2012) · Nature · doi:10.1038/nature10965 · Cited by 640 · see citing works
Pyrrolysine Encoded by UAG in Archaea: Charging of a UAG-Decoding Specialized tRNA
Srinivasan, G., James, C. M., & Krzycki, J. A. (2002) · Science · doi:10.1126/science.1069588 · Cited by 629 · see citing works
Wollaston, W. H. (1810) · Philosophical Transactions of the Royal Society of London · doi:10.1098/rstl.1810.0002 · Cited by 624 · see citing works
Genetically encoding Nε-acetyllysine in recombinant proteins
Neumann, H., Peak‐Chew, S., & Chin, J. W. (2008) · Nature Chemical Biology · doi:10.1038/nchembio.73 · Cited by 593 · see citing works
Causes and effects of N-terminal codon bias in bacterial genes
Goodman, D. B., Church, G. M., & Kosuri, S. (2013) · Science · doi:10.1126/science.1241934 · Cited by 573 · see citing works
Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement
Isaacs, F. J., Carr, P. A., Wang, H. H., Lajoie, M. J., Sterling, B., Kraal, L., Tolonen, A. C., Gianoulis, T. A., Goodman, D. B., Reppas, N. B., et al. (2011) · Science · doi:10.1126/science.1205822 · Cited by 550 · see citing works
Total Synthesis of a Functional Designer Eukaryotic Chromosome
Annaluru, N., Muller, H., MITCHELL, L. A., Ramalingam, S., Stracquadanio, G., Richardson, S. M., Dymond, J. S., Kuang, Z., Scheifele, L. Z., Cooper, E. M., et al. (2014) · Science · doi:10.1126/science.1249252 · Cited by 547 · see citing works
Self-citationExpanding and Reprogramming the Genetic Code of Cells and Animals
Chin, J. W. (2014) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-060713-035737 · Cited by 476 · see citing works
Biocontainment of genetically modified organisms by synthetic protein design
Mandell, D. J., Lajoie, M. J., Mee, M. T., Takeuchi, R., Kuznetsov, G., Norville, J. E., Gregg, C. J., Stoddard, B. L., & Church, G. M. (2015) · Nature · doi:10.1038/nature14121 · Cited by 474 · see citing works
A New UAG-Encoded Residue in the Structure of a Methanogen Methyltransferase
Hao, B., Gong, W., Ferguson, T. K., James, C. M., Krzycki, J. A., & Chan, M. K. (2002) · Science · doi:10.1126/science.1069556 · Cited by 420 · see citing works
Non-optimal codon usage affects expression, structure and function of clock protein FRQ
Zhou, M., Guo, J., Cha, J., Chae, M., Chen, S., Barral, J. M., Sachs, M. S., & Liu, Y. (2013) · Nature · doi:10.1038/nature11833 · Cited by 418 · see citing works
A novel RNA binding protein, SBP2, is required for the translation of mammalian selenoprotein mRNAs
Copeland, P. R., Fletcher, J. E., Carlson, B. A., Hatfield, D. L., & Driscoll, D. M. (2000) · The EMBO Journal · doi:10.1093/emboj/19.2.306 · Cited by 398 · see citing works
Fidelity at the Molecular Level: Lessons from Protein Synthesis
Zaher, H. S., & Green, R. (2009) · Cell · doi:10.1016/j.cell.2009.01.036 · Cited by 381 · see citing works
Aminoacyl-tRNA Synthesis and Translational Quality Control
Ling, J., Reynolds, N. M., & Ibba, M. (2009) · Annual Review of Microbiology · doi:10.1146/annurev.micro.091208.073210 · Cited by 368 · see citing works
Self-citationRecoded organisms engineered to depend on synthetic amino acids
Rovner, A. J., Haimovich, A. D., Katz, S. R., Li, Z., Grome, M. W., Gassaway, B. M., Amiram, M., Patel, J. R., Gallagher, R. R., Rinehart, J., et al. (2015) · Nature · doi:10.1038/nature14095 · Cited by 366 · see citing works
Natural expansion of the genetic code
Ambrogelly, A., Palioura, S., & Söll, D. (2007) · Nature Chemical Biology · doi:10.1038/nchembio847 · Cited by 361 · see citing works
Self-citationInnate immune and chemically triggered oxidative stress modifies translational fidelity
Netzer, N., Goodenbour, J. M., David, A., Dittmar, K. A., Jones, R. B., Schneider, J. R., Boone, D. L., Eves, E. M., Rosner, M. R., Gibbs, J. S., et al. (2009) · Nature · doi:10.1038/nature08576 · Cited by 349 · see citing works
RNA codewords and protein synthesis, VII. On the general nature of the RNA code.
Nirenberg, M., Leder, P., Bernfield, M. R., Brimacombe, R. L. C., Trupin, J. S., ROTTMAN, F. M., & O'Neal, C. (1965) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.53.5.1161 · Cited by 334 · see citing works
Selenoproteins—What unique properties can arise with selenocysteine in place of cysteine?
Arnér, E. S. J. (2010) · Experimental Cell Research · doi:10.1016/j.yexcr.2010.02.032 · Cited by 325 · see citing works
Johnson, J. A., Lu, Y. Y., Deventer, J. A. V., & Tirrell, D. A. (2010) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2010.09.013 · Cited by 320 · see citing works
UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota
Campbell, J. H., O’Donoghue, P., Campbell, A. G., Schwientek, P., Sczyrba, A., Woyke, T., Söll, D. G., & Podar, M. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1303090110 · Cited by 296 · see citing works
Self-citationBorrel, G., Parisot, N., Harris, H. M. B., Peyretaillade, É., Gaci, N., Tottey, W., Bardot, O., Raymann, K., Gribaldo, S., Peyret, P., et al. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-679 · Cited by 294 · see citing works
Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity
Shabalina, S. A., Spiridonov, N. A., & Kashina, A. S. (2013) · Nucleic Acids Research · doi:10.1093/nar/gks1205 · Cited by 287 · see citing works
Direct charging of tRNACUA with pyrrolysine in vitro and in vivo
Blight, S. K., Larue, R. C., Mahapatra, A., Longstaff, D. G., Chang, E. S., Zhao, G., Kang, P. T., Green‐Church, K. B., Chan, M. K., & Krzycki, J. A. (2004) · Nature · doi:10.1038/nature02895 · Cited by 265 · see citing works
Axley, M. J., Böck, A., & Stadtman, T. C. (1991) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.88.19.8450 · Cited by 231 · see citing works
The prokaryotic selenoproteome
Kryukov, G. V., & Gladyshev, V. N. (2004) · EMBO Reports · doi:10.1038/sj.embor.7400126 · Cited by 229 · see citing works
Structure of pyrrolysyl-tRNA synthetase, an archaeal enzyme for genetic code innovation
Kavran, J. M., Gundllapalli, S. B., O’Donoghue, P., Englert, M., Söll, D. G., & Steitz, T. A. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0704769104 · Cited by 212 · see citing works
Self-citationWan, W., Huang, Y. R., Wang, Z., Russell, W. K., Pai, P., Russell, D. H., & Liu, W. R. (2010) · Angewandte Chemie International Edition · doi:10.1002/anie.201000465 · Cited by 211 · see citing works
Lobanov, A. V., Fomenko, D. E., Zhang, Y., Sengupta, A., Hatfield, D. L., & Gladyshev, V. N. (2007) · Genome biology · doi:10.1186/gb-2007-8-9-r198 · Cited by 204 · see citing works
Highly reproductive Escherichia coli cells with no specific assignment to the UAG codon
Mukai, T., Hoshi, H., Ohtake, K., Takahashi, M., Yamaguchi, A., Hayashi, A., Yokoyama, S., & Sakamoto, K. (2015) · Scientific Reports · doi:10.1038/srep09699 · Cited by 203 · see citing works
Codon reassignment in the Escherichia coli genetic code
Mukai, T., Hayashi, A., Iraha, F., Sato, A., Ohtake, K., Yokoyama, S., & Sakamoto, K. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq707 · Cited by 200 · see citing works
An aminoacyl-tRNA synthetase that specifically activates pyrrolysine
Polycarpo, C. R., Ambrogelly, A., Bérubé, A., Winbush, S. M., McCloskey, J. A., Crain, P. F., Wood, J. L., & Söll, D. G. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0405362101 · Cited by 195 · see citing works
Self-citationThe selenium to selenoprotein pathway in eukaryotes: More molecular partners than anticipated
Allmang, C., Wurth, L., & Krol, A. (2009) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2009.03.003 · Cited by 189 · see citing works
Mycobacterial mistranslation is necessary and sufficient for rifampicin phenotypic resistance
Javid, B., Sorrentino, F., Toosky, M., Zheng, W., Pinkham, J. T., Jain, N. K., Pan, M., Deighan, P., & Rubin, E. J. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1317580111 · Cited by 188 · see citing works
Pyrrolysyl-tRNA synthetase–tRNAPyl structure reveals the molecular basis of orthogonality
Nozawa, K., O’Donoghue, P., Gundllapalli, S. B., Araiso, Y., Ishitani, R., Umehara, T., Söll, D. G., & Nureki, O. (2008) · Nature · doi:10.1038/nature07611 · Cited by 185 · see citing works
Self-citationMuramatsu, T., Yokoyama, S., Horie, N., Matsuda, A., Ueda, T., Yamaizumi, Z., Kuchino, Y., Nishimura, S., & Miyazawa, T. (1988) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)76533-8 · Cited by 182 · see citing works
Kim, H., & Gladyshev, V. N. (2005) · PLoS Biology · doi:10.1371/journal.pbio.0030375 · Cited by 182 · see citing works
Identification and characterization of phosphoseryl-tRNA [Ser]Sec kinase
Carlson, B. A., Xu, X.-M., Kryukov, G. V., Rao, M., Berry, M. J., Gladyshev, V. N., & Hatfield, D. L. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0402636101 · Cited by 182 · see citing works
Li, M., & Tzagoloff, A. (1979) · Cell · doi:10.1016/0092-8674(79)90352-0 · Cited by 174 · see citing works
Non-optimal codon usage is a mechanism to achieve circadian clock conditionality
Xu, Y. Q., Ma, P., Shah, P., Rokas, A., Liu, Y., & Johnson, C. H. (2013) · Nature · doi:10.1038/nature11942 · Cited by 174 · see citing works
The Human SepSecS-tRNA Sec Complex Reveals the Mechanism of Selenocysteine Formation
Palioura, S., Sherrer, R. L., Steitz, T. A., Söll, D. G., & Simonović, M. (2009) · Science · doi:10.1126/science.1173755 · Cited by 169 · see citing works
Self-citationZhang, Y., Romero, H., Salinas, G., & Gladyshev, V. N. (2006) · Genome biology · doi:10.1186/gb-2006-7-10-r94 · Cited by 169 · see citing works
Transfer RNA Mutation and the Malleability of the Genetic Code
Schultz, D. W., & Yarus, M. (1994) · Journal of Molecular Biology · doi:10.1006/jmbi.1994.1094 · Cited by 168 · see citing works
Borrel, G., Harris, H. M. B., Tottey, W., Mihajlovski, A., Parisot, N., Peyretaillade, E., Peyret, P., Gribaldo, S., O'Toole, P. W., & Brugère, J.-F. (2012) · Journal of Bacteriology · doi:10.1128/jb.01867-12 · Cited by 166 · see citing works
Transfer ribonucleic acid-mediated suppression of termination codons in Escherichia coli
Eggertsson, G., & Söll, D. G. (1988) · Microbiological Reviews · doi:10.1128/mr.52.3.354-374.1988 · Cited by 162 · see citing works
Self-citationThe accuracy of codon recognition by polypeptide release factors
Freistroffer, D. V., Kwiatkowski, M., Buckingham, R. H., & Ehrenberg, M. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.030541097 · Cited by 157 · see citing works
Upgrading protein synthesis for synthetic biology
O’Donoghue, P., Ling, J., Wang, Y., & Söll, D. G. (2013) · Nature Chemical Biology · doi:10.1038/nchembio.1339 · Cited by 155 · see citing works
Self-citationPyrrolysine analogues as substrates for pyrrolysyl‐tRNA synthetase
Polycarpo, C. R., Herring, S. C., Bérubé, A., Wood, J. L., Söll, D. G., & Ambrogelly, A. (2006) · FEBS Letters · doi:10.1016/j.febslet.2006.11.028 · Cited by 154 · see citing works
Self-citationNormal tRNAs promote ribosomal frameshifting
Atkins, J. F., Gesteland, R. F., Reid, B. R., & Anderson, C. W. (1979) · Cell · doi:10.1016/0092-8674(79)90225-3 · Cited by 153 · see citing works
Söll, D. G., Ohtsuka, E., Jones, D. S., Lohrmann, R., Hayatsu, H., Nishimura, S., & Khorana, H. G. (1965) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.54.5.1378 · Cited by 152 · see citing works
Self-citationStop codon reassignments in the wild
Ivanova, N., Schwientek, P., Tripp, H. J., Rinke, C., Pati, A., Huntemann, M., Visel, A., Woyke, T., Kyrpides, N. C., & Rubin, E. M. (2014) · Science · doi:10.1126/science.1250691 · Cited by 152 · see citing works
Alfonzo, J. D., Blanc, V., Estévez, A. M., Rubio, M. A. T., & Simpson, L. (1999) · The EMBO Journal · doi:10.1093/emboj/18.24.7056 · Cited by 150 · see citing works
Use of the UGA terminator as a tryptophan codon in yeast mitochondria.
Macino, G., Coruzzi, G. M., Nóbrega, F. G., Li, M., & Tzagoloff, A. (1979) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.76.8.3784 · Cited by 148 · see citing works
Agmatine-conjugated cytidine in a tRNA anticodon is essential for AUA decoding in archaea
Ikeuchi, Y., 木村聡, Numata, T., Nakamura, D., Yokogawa, T., Ogata, T., Wada, T., Suzuki, T., & Suzuki, T. (2010) · Nature Chemical Biology · doi:10.1038/nchembio.323 · Cited by 141 · see citing works
The complete biosynthesis of the genetically encoded amino acid pyrrolysine from lysine
Gaston, M. A., Zhang, L., Green‐Church, K. B., & Krzycki, J. A. (2011) · Nature · doi:10.1038/nature09918 · Cited by 140 · see citing works
Genetic Code Supports Targeted Insertion of Two Amino Acids by One Codon
Turanov, A. A., Lobanov, A. V., Fomenko, D. E., Morrison, H. G., Sogin, M. L., Klobutcher, L. A., Hatfield, D. L., & Gladyshev, V. N. (2009) · Science · doi:10.1126/science.1164748 · Cited by 139 · see citing works
Ribosome fidelity: tRNA discrimination, proofreading and induced fit
Rodnina, M. V., & Wintermeyer, W. (2001) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(00)01737-0 · Cited by 136 · see citing works
Budiman, M. E., Bubenik, J. L., Miniard, A. C., Middleton, L. M., Gerber, C. A., Cash, A., & Driscoll, D. M. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.06.026 · Cited by 130 · see citing works
Mandal, D., Köhrer, C., Su, D., Russell, S. P., Krivos, K. L., Castleberry, C. M., Blum, P., Limbach, P. A., Söll, D. G., & RajBhandary, U. L. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0914869107 · Cited by 130 · see citing works
Self-citationPyrrolysine is not hardwired for cotranslational insertion at UAG codons
Ambrogelly, A., Gundllapalli, S. B., Herring, S., Polycarpo, C. R., Frauer, C., & Söll, D. G. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0611634104 · Cited by 126 · see citing works
Self-citationFormate dehydrogenase – a versatile enzyme in changing environments
Jormakka, M., Byrne, B., & Iwata, S. (2003) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(03)00098-8 · Cited by 123 · see citing works
The mechanisms of codon reassignments in mitochondrial genetic codes
Sengupta, S., Yang, X., & Higgs, P. G. (2007) · Journal of Molecular Evolution · doi:10.1007/s00239-006-0284-7 · Cited by 121 · see citing works
Selenocysteine, Pyrrolysine, and the Unique Energy Metabolism of Methanogenic Archaea
Rother, M., & Krzycki, J. A. (2010) · Archaea · doi:10.1155/2010/453642 · Cited by 118 · see citing works
Polyspecific pyrrolysyl-tRNA synthetases from directed evolution
Guo, L.-T., Wang, Y., Nakamura, A., Eiler, D. R., Kavran, J. M., Wong, M. L., Kiessling, L. L., Steitz, T. A., O’Donoghue, P., & Söll, D. G. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1419737111 · Cited by 115 · see citing works
Self-citationRelease Factor One Is Nonessential in Escherichia coli
Johnson, D. B., Wang, C., Xu, J., Schultz, M. D., Schmitz, R. J., Ecker, J. R., & Wang, L. (2012) · ACS Chemical Biology · doi:10.1021/cb300229q · Cited by 113 · see citing works
Li, L., Boniecki, M. T., Jaffe, J. D., Imai, B. S., Yau, P. M., Luthey-Schulten, Z. A., & Martinis, S. A. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1016460108 · Cited by 110 · see citing works
Adaptive Translation as a Mechanism of Stress Response and Adaptation
Pan, T. (2013) · Annual Review of Genetics · doi:10.1146/annurev-genet-111212-133522 · Cited by 110 · see citing works
The many levels of control on bacterial selenoprotein synthesis
Yoshizawa, S., & Böck, A. (2009) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2009.03.010 · Cited by 109 · see citing works
Snider, G. W., Ruggles, E. L., Khan, N. I., & Hondal, R. J. (2013) · Biochemistry · doi:10.1021/bi400462j · Cited by 108 · see citing works
Heinemann, I. U., Rovner, A. J., Aerni, H. R., Rogulina, S., Cheng, L., Olds, W. H., Fischer, J. T., Söll, D. G., Isaacs, F. J., & Rinehart, J. (2012) · FEBS Letters · doi:10.1016/j.febslet.2012.08.031 · Cited by 108 · see citing works
Self-citationFunction of genetically encoded pyrrolysine in corrinoid-dependent methylamine methyltransferases
Krzycki, J. A. (2004) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2004.08.012 · Cited by 101 · see citing works
Protein mistranslation protects bacteria against oxidative stress
Fan, Y., Wu, J., Ung, M. H., Lay, N. R. D., Cheng, C., & Ling, J. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1404 · Cited by 100 · see citing works
Self-citationLoss of Editing Activity during the Evolution of Mitochondrial Phenylalanyl-tRNA Synthetase
Roy, H., Ling, J., Alfonzo, J. D., & Ibba, M. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m508281200 · Cited by 99 · see citing works
Self-citationNatural and synthetic selenoproteins
Metanis, N., & Hilvert, D. (2014) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2014.09.010 · Cited by 98 · see citing works
Umehara, T., Kim, J., Lee, S., Guo, L., Söll, D. G., & Park, H.-S. (2012) · FEBS Letters · doi:10.1016/j.febslet.2012.01.029 · Cited by 97 · see citing works
Self-citationMarniemi, J., & Parkki, M. G. (1975) · Biochemical Pharmacology · doi:10.1016/0006-2952(75)90080-5 · Cited by 96 · see citing works
Candida albicans CUG Mistranslation Is a Mechanism To Create Cell Surface Variation
Miranda, I., Silva-Dias, A., Rocha, R., Teixeira-Santos, R., Coelho, C., Gonçalves, T., Santos, M. A. S., Pina-Vaz, C., Solis, N., Filler, S., et al. (2013) · mBio · doi:10.1128/mbio.00285-13 · Cited by 96 · see citing works
Selenoproteins in Archaea and Gram-positive bacteria
Stock, T., & Rother, M. (2009) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2009.03.022 · Cited by 95 · see citing works
Zhang, Y., & Gladyshev, V. N. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000095 · Cited by 92 · see citing works
Bezerra, A. R., Simões, J., Lee, W., Rung, J., Weil, T., Gut, I. G., Gut, M., Bayés, M., Rizzetto, L., Cavalieri, D., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1302094110 · Cited by 92 · see citing works
Subramaniam, A. R., Pan, T., & Cluzel, P. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1211077110 · Cited by 89 · see citing works
Ticak, T., Kountz, D. J., Girosky, K. E., Krzycki, J. A., & Ferguson, D. J. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1409642111 · Cited by 88 · see citing works
Bilokapić, S., Maier, T., Ahel, D., Gruic‐Sovulj, I., Söll, D. G., Weygand-Đurašević, I., & Ban, N. (2006) · The EMBO Journal · doi:10.1038/sj.emboj.7601129 · Cited by 85 · see citing works
Self-citationTransfer ribonucleic acid-mediated suppression of termination codons in Escherichia coli.
Eggertsson, G., & Söll, D. G. (1988) · Microbiological Reviews · doi:10.1128/mmbr.52.3.354-374.1988 · Cited by 84 · see citing works
Self-citationReassignment of a rare sense codon to a non-canonical amino acid inEscherichia coli
Mukai, T., Yamaguchi, A., Ohtake, K., Takahashi, M., Hayashi, A., Iraha, F., Kira, S., Yanagisawa, T., Yokoyama, S., Hoshi, H., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv787 · Cited by 83 · see citing works
Structural basis for mRNA recognition by elongation factor SelB
Yoshizawa, S., Rasubala, L., Ose, T., Kohda, D., Fourmy, D., & Maenaka, K. (2005) · Nature Structural & Molecular Biology · doi:10.1038/nsmb890 · Cited by 81 · see citing works
Expanded use of sense codons is regulated by modified cytidines in tRNA
Cantara, W. A., Murphy, F. V., DeMi̇rci̇, H., & Agris, P. F. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1222641110 · Cited by 79 · see citing works
Recoding the Genetic Code with Selenocysteine
Bröcker, M. J., Ho, J. M. L., Church, G. M., Söll, D. G., & O’Donoghue, P. (2013) · Angewandte Chemie International Edition · doi:10.1002/anie.201308584 · Cited by 79 · see citing works
Self-citationYuan, J., O'Donoghue, P., Ambrogelly, A., Gundllapalli, S., Sherrer, R. L., Palioura, S., Simonović, M., & Söll, D. (2010) · FEBS Letters · doi:10.1016/j.febslet.2009.11.005 · Cited by 76 · see citing works
Self-citationRevealing the amino acid composition of proteins within an expanded genetic code
Aerni, H. R., Shifman, M. A., Rogulina, S., O’Donoghue, P., & Rinehart, J. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1087 · Cited by 76 · see citing works
Self-citationA serine sensor for multicellularity in a bacterium
Subramaniam, A. R., DeLoughery, A., Bradshaw, N., Chen, Y., O’Shea, E. K., Losick, R. M., & Chai, Y. (2013) · eLife · doi:10.7554/elife.01501 · Cited by 74 · see citing works
Rewiring Translation for Elongation Factor Tu‐Dependent Selenocysteine Incorporation
Aldag, C., Bröcker, M. J., Hohn, M. J., Prat, L., Hammond, G., Plummer, A., & Söll, D. G. (2012) · Angewandte Chemie International Edition · doi:10.1002/anie.201207567 · Cited by 71 · see citing works
Self-citationEvolving tRNASec for Efficient Canonical Incorporation of Selenocysteine
Thyer, R. T., Robotham, S. A., Brodbelt, J. S., & Ellington, A. D. (2014) · Journal of the American Chemical Society · doi:10.1021/ja510695g · Cited by 69 · see citing works
Decameric SelA•tRNA Sec Ring Structure Reveals Mechanism of Bacterial Selenocysteine Formation
Itoh, Y., Bröcker, M. J., Sekine, S., Hammond, G., Suetsugu, S., Söll, D. G., & Yokoyama, S. (2013) · Science · doi:10.1126/science.1229521 · Cited by 66 · see citing works
Self-citationEmergence of the universal genetic code imprinted in an RNA record
Hohn, M. J., Park, H.-S., O’Donoghue, P., Schnitzbauer, M., & Söll, D. G. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0608762103 · Cited by 63 · see citing works
Self-citationYokoyama, S., Muramatsu, T., Horie, N., Nishikawa, K., Matsuda, A., Ueda, T., Yamaizumi, Z., Kuchino, Y., Nishimura, S., & Miyazawa, T. (1989) · Pure and Applied Chemistry · doi:10.1351/pac198961030573 · Cited by 63 · see citing works
Characterization of a Methanosarcina acetivorans mutant unable to translate UAG as pyrrolysine
Mahapatra, A., Patel, A. V., Soares, J. A., Larue, R. C., Zhang, J. K., Metcalf, W. W., & Krzycki, J. A. (2005) · Molecular Microbiology · doi:10.1111/j.1365-2958.2005.04927.x · Cited by 62 · see citing works
Engineering the elongation factor Tu for efficient selenoprotein synthesis
Haruna, K., Alkazemi, M. H., Liu, Y., Söll, D. G., & Englert, M. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku691 · Cited by 61 · see citing works
Self-citationIn vivo role of three fused corrinoid/methyl transfer proteins in Methanosarcina acetivorans
Oelgeschläger, E., & Rother, M. (2009) · Molecular Microbiology · doi:10.1111/j.1365-2958.2009.06723.x · Cited by 60 · see citing works
Jiang, R., & Krzycki, J. A. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.396754 · Cited by 60 · see citing works
Reprogramming the Genetic Code
Chin, J. W. (2012) · Science · doi:10.1126/science.1221761 · Cited by 58 · see citing works
In vivo contextual requirements for UAG translation as pyrrolysine
Longstaff, D. G., Blight, S. K., Zhang, L., Green‐Church, K. B., & Krzycki, J. A. (2006) · Molecular Microbiology · doi:10.1111/j.1365-2958.2006.05500.x · Cited by 57 · see citing works
The appearance of pyrrolysine in tRNA His guanylyltransferase by neutral evolution
Heinemann, I. U., O’Donoghue, P., Madinger, C. L., Benner, J. S., Randau, L., Noren, C. J., & Söll, D. G. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0912072106 · Cited by 56 · see citing works
Self-citationCarbon source-dependent expansion of the genetic code in bacteria
Prat, L., Heinemann, I. U., Aerni, H. R., Rinehart, J., O’Donoghue, P., & Söll, D. G. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1218613110 · Cited by 56 · see citing works
Self-citationA synthetic tRNA for EF‐Tu mediated selenocysteine incorporation in vivo and in vitro
Miller, C. A., Bröcker, M. J., Prat, L., Ip, K. L., Chirathivat, N., Feiock, A., Veszprémi, M., & Söll, D. G. (2015) · FEBS Letters · doi:10.1016/j.febslet.2015.06.039 · Cited by 56 · see citing works
Self-citationRother, M., Mathes, I., Lottspeich, F., & Böck, A. (2002) · Journal of Bacteriology · doi:10.1128/jb.185.1.107-114.2003 · Cited by 55 · see citing works
Tomita, K., Ueda, T., Ishiwa, S., Crain, P. F., McCloskey, J. A., & Watanabe, K. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.21.4291 · Cited by 54 · see citing works
Crystal Structure of Methylornithine Synthase (PylB): Insights into the Pyrrolysine Biosynthesis
Quitterer, F., List, A., Eisenreich, W., Bacher, A., & Groll, M. (2011) · Angewandte Chemie International Edition · doi:10.1002/anie.201106765 · Cited by 53 · see citing works
Mechanism of oxidant-induced mistranslation by threonyl-tRNA synthetase
Wu, J., Fan, Y., & Ling, J. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku271 · Cited by 48 · see citing works
Self-citationStadtman, T. C., Jn, D., Zehelein, E., & Böck, A. (1989) · PubMed · Cited by 47 · see citing works
In vivorequirement of selenophosphate for selenoprotein synthesis in archaea
Stock, T., Selzer, M., & Rother, M. (2009) · Molecular Microbiology · doi:10.1111/j.1365-2958.2009.06970.x · Cited by 45 · see citing works
Bacteriophages use an expanded genetic code on evolutionary paths to higher fitness
Hammerling, M. J., Ellefson, J. W., Boutz, D. R., Marcotte, E. M., Ellington, A. D., & Barrick, J. E. (2014) · Nature Chemical Biology · doi:10.1038/nchembio.1450 · Cited by 44 · see citing works
Yadavalli, S. S., & Ibba, M. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1240 · Cited by 44 · see citing works
Mansell, J. B., Guévremont, D., Poole, E. S., & Tate, W. P. (2001) · The EMBO Journal · doi:10.1093/emboj/20.24.7284 · Cited by 42 · see citing works
An unusual tRNAThr derived from tRNAHis reassigns in yeast mitochondria the CUN codons to threonine
Su, D., Lieberman, A. E., Lang, B. F., Simonović, M., Söll, D. G., & Ling, J. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr073 · Cited by 42 · see citing works
Self-citationSherrer, R. L., O’Donoghue, P., & Söll, D. G. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkm1134 · Cited by 41 · see citing works
Self-citationThe Croonian Lecture, 1966 - The genetic code
Crick, F. H. C. (1967) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.1967.0031 · Cited by 40 · see citing works
The path of lysine to pyrrolysine
Krzycki, J. A. (2013) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2013.06.023 · Cited by 38 · see citing works
Mitochondrial tRNA Structure, Identity, and Evolution of the Genetic Code
Lang, B. F., Lavrov, D. V., Beck, N., & Steinberg, S. V. (2011) · Springer eBooks · doi:10.1007/978-3-642-22380-8_17 · Cited by 35 · see citing works
Expanded Genetic Code Technologies for Incorporating Modified Lysine at Multiple Sites
Yanagisawa, T., Umehara, T., Sakamoto, K., & Yokoyama, S. (2014) · ChemBioChem · doi:10.1002/cbic.201402266 · Cited by 34 · see citing works
Translation termination in pyrrolysine‐utilizing archaea
Alkalaeva, E. Z., Eliseev, B., Ambrogelly, A., Vlasov, P. K., Kondrashov, F. A., Gundllapalli, S., Frolova, L. I., Söll, D. G., & Kisselev, L. L. (2009) · FEBS Letters · doi:10.1016/j.febslet.2009.09.044 · Cited by 31 · see citing works
Self-citationTranslational recoding in archaea
Cobucci‐Ponzano, B., Rossi, M., & Moracci, M. (2012) · Extremophiles · doi:10.1007/s00792-012-0482-8 · Cited by 30 · see citing works
Ling, J., Peterson, K. M., Simonović, I., Cho, C., Söll, D. G., & Simonović, M. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1200109109 · Cited by 29 · see citing works
Self-citationReprogramming the genetic code
Chin, J. W. (2011) · The EMBO Journal · doi:10.1038/emboj.2011.160 · Cited by 29 · see citing works
Wobble decoding by the Escherichia coli selenocysteine insertion machinery
Xu, J., Croitoru, V., Rutishauser, D., Cheng, Q., & Arnér, E. S. J. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt764 · Cited by 25 · see citing works
Natural reassignment of CUU and CUA sense codons to alanine in Ashbya mitochondria
Ling, J., Daoud, R., Lajoie, M. J., Church, G. M., Söll, D. G., & Lang, B. F. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt842 · Cited by 23 · see citing works
Self-citationHow an obscure archaeal gene inspired the discovery of selenocysteine biosynthesis in humans
Su, D., Hohn, M. J., Palioura, S., Sherrer, R. L., Yuan, J., Söll, D. G., & O’Donoghue, P. (2008) · IUBMB Life · doi:10.1002/iub.136 · Cited by 23 · see citing works
Self-citationThe Distinction Between Recoding and Codon Reassignment
Atkins, J. F., & Baranov, P. V. (2010) · Genetics · doi:10.1534/genetics.110.119016 · Cited by 23 · see citing works
Reducing the genetic code induces massive rearrangement of the proteome
O’Donoghue, P., Prat, L., Kucklick, M., Schäfer, J. G., Riedel, K., Rinehart, J., Söll, D. G., & Heinemann, I. U. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1420193111 · Cited by 22 · see citing works
Self-citationGenetic analysis of selenocysteine biosynthesis in the archaeon Methanococcus maripaludis
Hohn, M. J., Palioura, S., Su, D., Yuan, J., & Söll, D. G. (2011) · Molecular Microbiology · doi:10.1111/j.1365-2958.2011.07690.x · Cited by 21 · see citing works
Self-citationTetteh, A. Y., Sun, K. H., Hung, C., Kittur, F. S., Ibeanu, G. C., Williams, D., & Xie, J. (2014) · International Journal of Microbiology · doi:10.1155/2014/394835 · Cited by 18 · see citing works
Bifano, A. L., Atassi, T., Ferrara, T. M., & Driscoll, D. M. (2013) · BMC Molecular Biology · doi:10.1186/1471-2199-14-12 · Cited by 18 · see citing works
Hurley, J., & Dunlap, J. (2013) · Nature · doi:10.1038/nature11952 · Cited by 16 · see citing works
Pyrrolysine Analogs as Substrates for Bacterial Pyrrolysyl-tRNA Synthetasein Vitroandin Vivo
Katayama, H., Nozawa, K., Nureki, O., Nakahara, Y., & Hojo, H. (2012) · Bioscience Biotechnology and Biochemistry · doi:10.1271/bbb.110653 · Cited by 13 · see citing works
Gröbe, T., Reuter, M., Gursinsky, T., Söhling, B., & Andreesen, J. R. (2006) · Archives of Microbiology · doi:10.1007/s00203-006-0169-6 · Cited by 5 · see citing works
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- [20]Lang BF Lavrov D Beck N Steinberg SV Bullerwell CE Organelle Genetics 2012 431 474 Springer
- [46]Mascarenhas AP An S Rosen AE Martinis SA Musier-Forsyth K RajBhandary UL Köhrer C Protein Engineering 2008 153 200 Springer
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Sorted by citations
Fitness Costs of Plasmids: a Limit to Plasmid Transmission
Millán, Á. S., & MacLean, R. C. (2017) · Microbiology Spectrum · doi:10.1128/microbiolspec.mtbp-0016-2017 · Cited by 560 · see citing works
An integrated, structure- and energy-based view of the genetic code
Grosjean, H., & Westhof, E. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw608 · Cited by 278 · see citing works
“Outside the circle, are indicated the reassignment of stop codon UGA and UAG into Sec (21st proteogenic amino acid) and Pyl (22nd amino acid), respectively (2).”
BackgroundDesign, synthesis, and testing toward a 57-codon genome
Ostrov, N., Landon, M., Güell, M., Kuznetsov, G., Teramoto, J., Cervantes, N., Zhou, M. H., Singh, K., Napolitano, M. G., Moosburner, M., et al. (2016) · Science · doi:10.1126/science.aaf3639 · Cited by 289 · see citing works
Translation Elongation and Recoding in EukaryotesPreprint
Dever, T. E., Dinman, J. D., & Green, R. (2018) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a032649 · Cited by 250 · see citing works
“Recoding Definition It is generally assumed that (1) all codons encode identical information in all organisms (with few exceptions [Ling et al. 2015]), and (2) the reading frame is invariant.”
BackgroundBiocatalysis with Unnatural Amino Acids: Enzymology Meets Xenobiology
Agostini, F., Völler, J., Koksch, B., Acevedo‐Rocha, C. G., Kubyshkin, V., & Budiša, N. (2017) · Angewandte Chemie International Edition · doi:10.1002/anie.201610129 · Cited by 232 · see citing works
Origin and Evolution of the Universal Genetic Code
Koonin, E. V., & Novozhilov, A. S. (2017) · Annual Review of Genetics · doi:10.1146/annurev-genet-120116-024713 · Cited by 200 · see citing works
Mukai, T., Lajoie, M. J., Englert, M., & Söll, D. G. (2017) · Annual Review of Microbiology · doi:10.1146/annurev-micro-090816-093247 · Cited by 159 · see citing works
“The genetic code of mitochondria deviates significantly from the standard genetic code (61, 76) (Supplemental Figure 1), probably because there are only a few genes (encoding membrane proteins) in mitochondrial genomes.”
BackgroundSelf-citationTransfer RNAs: diversity in form and function
Berg, M. D., & Brandl, C. J. (2020) · RNA Biology · doi:10.1080/15476286.2020.1809197 · Cited by 131 · see citing works
Záhonová, K., Kostygov, A. Y., Ševčíková, T., Yurchenko, V., & Eliáš, M. (2016) · Current Biology · doi:10.1016/j.cub.2016.06.064 · Cited by 113 · see citing works
“The second, more common category includes codes changing a standard termination codon to a sense one [1, 3, 4].”
BackgroundBarbieri, M. (2017) · Biosystems · doi:10.1016/j.biosystems.2017.10.005 · Cited by 117 · see citing works
Engineering the Genetic Code in Cells and Animals: Biological Considerations and Impacts
Wang, L. (2017) · Accounts of Chemical Research · doi:10.1021/acs.accounts.7b00376 · Cited by 107 · see citing works
Synthetic biology approaches to biological containment: pre-emptively tackling potential risks
Torres, L. L., Krüger, A., Csibra, E., Gianni, E., & Pinheiro, V. B. (2016) · Essays in Biochemistry · doi:10.1042/ebc20160013 · Cited by 103 · see citing works
Evolutionary instability of CUG-Leu in the genetic code of budding yeasts
Krassowski, T., Coughlan, A. Y., Shen, X., Zhou, X., Kominek, J., Opulente, D. A., Riley, R. W., Grigoriev, I. V., Maheshwari, N., Shields, D. C., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-04374-7 · Cited by 102 · see citing works
Nielsen, C. F., Lange, L., & Meyer, A. S. (2019) · Biotechnology Advances · doi:10.1016/j.biotechadv.2019.06.007 · Cited by 98 · see citing works
Su, H.-W., Zhu, J., Li, H., Cai, R.-J., Ealand, C. S., Wang, X., Chen, Y., Kayani, M. U. R., Zhu, T. F., Moradigaravand, D., et al. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.147 · Cited by 87 · see citing works
Mechanisms of protein evolution
Jayaraman, V., Toledo‐Patiño, S., Noda‐García, L., & Laurino, P. (2022) · Protein Science · doi:10.1002/pro.4362 · Cited by 85 · see citing works
“Similarly, ambiguous decoding (translation of a given codon to two different amino acids) was genetically accommodated in certain organisms via divergence of a dedicated tRNA.(117) More recently, it was also shown that phenotypic mutation can reduce the mutational load in a population by efficiently purging deleteriou…”
BackgroundKoonin, E. (2017) · Life · doi:10.3390/life7020022 · Cited by 85 · see citing works
“The genetic code is nearly universal in all extant life forms although limited deviations from the SGC have been detected in many groups of organisms, particularly in organelles and parasitic or endosymbiotic bacteria with highly reduced genomes [11,16,17].”
BackgroundMultiple mechanisms drive phage infection efficiency in nearly identical hosts
Howard‐Varona, C., Hargreaves, K. R., Solonenko, N., Markillie, L. M., White, R. A., III, Brewer, H. M., Ansong, C. K., Orr, G., Adkins, J., & Sullivan, M. B. (2018) · The ISME Journal · doi:10.1038/s41396-018-0099-8 · Cited by 76 · see citing works
“Such genes might help a generalist phage utilize host translation and replicate phage DNA, respectively, across diverse hosts [67] given that phage genomes are known to code for genes that reprogram host metabolism [68, 69] and that they are not identified in a specialist phage (phi18:3).”
BackgroundPathways to disease from natural variations in human cytoplasmic tRNAs
Lant, J. T., Berg, M. D., Heinemann, I. U., Brandl, C. J., & O’Donoghue, P. (2019) · Journal of Biological Chemistry · doi:10.1074/jbc.rev118.002982 · Cited by 73 · see citing works
“Indeed, although the genetic code is nearly universal in the living world, several exceptions to the standard code occur in diverse organisms (10).”
BackgroundSelf-citationGenetically encoding new bioreactivity
Wang, L. (2016) · New Biotechnology · doi:10.1016/j.nbt.2016.10.003 · Cited by 69 · see citing works
The complex evolutionary history of aminoacyl-tRNA synthetases
Chaliotis, A., Vlastaridis, P., Mossialos, D., Ibba, M., Becker, H. D., Stathopoulos, C., & Amoutzias, G. D. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1182 · Cited by 69 · see citing works
“Genetic code decoding is a much more variable step than originally thought and needs to be quantified (9).”
BackgroundXenomicrobiology: a roadmap for genetic code engineering
Acevedo‐Rocha, C. G., & Budiša, N. (2016) · Microbial Biotechnology · doi:10.1111/1751-7915.12398 · Cited by 67 · see citing works
“10, Berlin 10623, Germany.”
BackgroundFan, Y., Evans, C. R., Barber, K. W., Banerjee, K., Weiss, K., Margolin, W., Igoshin, O. A., Rinehart, J., & Ling, J. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.07.010 · Cited by 63 · see citing works
“Recent evidence suggests that increased translational errors paradoxically provides benefits to microorganisms under certain stress conditions (Bezerra et al., 2013; Ling et al., 2015; Pan, 2013; Ribas de Pouplana et al., 2014).”
Self-citationFacile Recoding of Selenocysteine in Nature
Mukai, T., Englert, M., Tripp, H. J., Miller, C., Ivanova, N. N., Rubin, E. M., Kyrpides, N. C., & Söll, D. (2016) · Angewandte Chemie International Edition · doi:10.1002/anie.201511657 · Cited by 61 · see citing works
Self-citationNaturally Occurring tRNAs With Non-canonical Structures
Krahn, N., Fischer, J. T., & Söll, D. G. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.596914 · Cited by 57 · see citing works
“Recognition of A1:U72 is possible due to mutations in the CP1 domain (Figure 4C) (Liu et al., 2012).”
BackgroundSelf-citationtRNAPyl: Structure, function, and applications
Tharp, J. M., Ehnbom, A., & Liu, W. R. (2017) · RNA Biology · doi:10.1080/15476286.2017.1356561 · Cited by 53 · see citing works
“organism is biased with some codons occurring more frequently than others.(63) To minimize the adverse effects of sense codon reassignment using the PylRS/tRNA pair, early efforts”
Selenoprotein synthesis and regulation in Archaea
Rother, M., & Quitzke, V. (2018) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2018.04.008 · Cited by 48 · see citing works
Evans, C. R., Fan, Y., Weiss, K., & Ling, J. (2018) · mBio · doi:10.1128/mbio.01018-18 · Cited by 46 · see citing works
“It is worth pointing out that under certain circumstances, recoding resulting from translational readthrough or frameshifting depends on the context of mRNA sequences and can lead to production of alternative functional proteins and provide a selective advantage during evolution (20, 23).”
BackgroundSelf-citationGenetic selection for mistranslation rescues a defective co-chaperone in yeast
Hoffman, K. S., Berg, M. D., Shilton, B. H., Brandl, C. J., & O’Donoghue, P. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1021 · Cited by 42 · see citing works
“Alterations to the standard genetic code are also found in yeast mitochondrial organelles, bacteria, archaea and viruses (62,63).”
BackgroundSelf-citationVisualizing tRNA-dependent mistranslation in human cells
Lant, J. T., Berg, M. D., Sze, D. H. W., Hoffman, K. S., Akinpelu, I. C., Turk, M., Heinemann, I. U., Duennwald, M. L., Brandl, C. J., & O’Donoghue, P. (2017) · RNA Biology · doi:10.1080/15476286.2017.1379645 · Cited by 44 · see citing works
“ural genetic code expansion in species representing the complete diversity of life.(5)”
BackgroundSelf-citationTransfer RNAs with novel cloverleaf structures
Mukai, T., Vargas‐Rodriguez, O., Englert, M., Tripp, H. J., Ivanova, N., Rubin, E. M., Kyrpides, N. C., & Söll, D. G. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw898 · Cited by 40 · see citing works
“While recent research has focused on the non-translational functions of tRNAs (3–6), the rapidly increasing expanse of genomic and metagenomic sequence information has revived the interests in the canonical function of tRNAs (7).”
BackgroundSelf-citationUnorthodox features in two venerid bivalves with doubly uniparental inheritance of mitochondria
Capt, C., Bouvet, K., Guerra, D., Robicheau, B. M., Stewart, D. T., Pante, E., & Breton, S. (2020) · Scientific Reports · doi:10.1038/s41598-020-57975-y · Cited by 39 · see citing works
Mammalian proteome expansion by stop codon readthrough
Manjunath, L. E., Singh, A., Som, S., & Eswarappa, S. M. (2022) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1739 · Cited by 35 · see citing works
“Further, the genetic code is expanded in certain organisms to accommodate selenocysteine and pyrrolysine, considered the 21 st and the 22 nd amino acids, respectively (Ling et al., 2015).”
BackgroundNuclear genetic codes with a different meaning of the UAG and the UAA codon
Pánek, T., Žihala, D., Sokol, M., Derelle, R., Klimeš, V., Hradilova, M., Zadrobílková, E., Susko, E., Roger, A., Čepička, I., et al. (2017) · BMC Biology · doi:10.1186/s12915-017-0353-y · Cited by 38 · see citing works
“Indeed, exclusive reassignment of UAG as a sense codon has been documented in some mitochondria [21, 22], and certain prokaryotes employ UAG, but not UAA, to encode pyrrolysine [2].”
BackgroundError-prone protein synthesis in parasites with the smallest eukaryotic genome
Melnikov, S. V., Rivera, K. D., Ostapenko, D., Makarenko, A., Sanscrainte, N. D., Becnel, J. J., Solomon, M. J., Texier, C., Pappin, D., & Söll, D. G. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1803208115 · Cited by 35 · see citing works
“One the other hand, some organisms use inaccurate protein synthesis as a meaningful adaptive strategy (79 82).”
BackgroundSelf-citationBiokatalyse mit nicht‐natürlichen Aminosäuren: Enzymologie trifft Xenobiologie
Agostini, F., Völler, J., Koksch, B., Acevedo‐Rocha, C. G., Kubyshkin, V., & Budiša, N. (2017) · Angewandte Chemie · doi:10.1002/ange.201610129 · Cited by 34 · see citing works
On universal coding events in protein biogenesis
Kubyshkin, V., Acevedo‐Rocha, C. G., & Budiša, N. (2017) · Biosystems · doi:10.1016/j.biosystems.2017.10.004 · Cited by 32 · see citing works
Eukaryotic tRNA sequences present conserved and amino acid-specific structural signatures
Westhof, É., Thornlow, B. P., Chan, P. P., & Lowe, T. M. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac222 · Cited by 31 · see citing works
Effect of mRNA/tRNA mutations on translation speed: Implications for human diseases
Davyt, M., Bharti, N., & Ignatova, Z. (2023) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2023.105089 · Cited by 31 · see citing works
“In some organisms or organelles, two of the stop codons (UGA and UAG) are reassigned into sense codons (54, 55).”
BackgroundLoss of protein synthesis quality control in host-restricted organisms
Melnikov, S. V., van den Elzen, A. M. G., Stevens, D. L., Thoreen, C. C., & Söll, D. G. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1815992115 · Cited by 30 · see citing works
“In fact, beneficial use of mistranslation has been reported for several pathogens, including the parasitic fungi albicans (25, 39, 40).”
BackgroundSelf-citationMutational and Selective Processes Involved in Evolution during Bacterial Range Expansions
Bosshard, L., Peischl, S., Ackermann, M., & Excoffier, L. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz148 · Cited by 29 · see citing works
Impact of Genome Reduction in Microsporidia
Jespersen, N. E., Monrroy, L., & Barandun, J. (2022) · Experientia supplementum · doi:10.1007/978-3-030-93306-7_1 · Cited by 27 · see citing works
Berg, M. D., Hoffman, K. S., Genereaux, J. L., Mian, S., Trussler, R. S., Haniford, D. B., O’Donoghue, P., & Brandl, C. J. (2017) · Genetics · doi:10.1534/genetics.117.203232 · Cited by 26 · see citing works
Self-citationFitness Costs of Plasmids: A Limit to Plasmid Transmission
Millán, Á. S., & MacLean, R. C. (2019) · ASM Press eBooks · doi:10.1128/9781555819743.ch4 · Cited by 24 · see citing works
Perseverance of protein homeostasis despite mistranslation of glycine codons with alanine
Hasan, F., Lant, J. T., & O’Donoghue, P. (2023) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2022.0029 · Cited by 27 · see citing works
Self-citationFunctional characterization of prokaryotic dark matter: the road so far and what lies ahead
Escudeiro, P., Henry, C. S., & Dias, R. P. M. (2022) · Current Research in Microbial Sciences · doi:10.1016/j.crmicr.2022.100159 · Cited by 24 · see citing works
Clinically Relevant Mutations of Mycobacterial GatCAB Inform Regulation of Translational Fidelity
Li, Y.-Y., Cai, R.-J., Yang, J., Hendrickson, T. L., Xiang, Y., & Javid, B. (2021) · mBio · doi:10.1128/mbio.01100-21 · Cited by 20 · see citing works
“a trade-off between speed and accuracy of protein synthesis, but also because translational errors, mistranslation, may allow adaptation to hostile environments, particularly in contexts of environmental stress (3-5).”
BackgroundCode Biology, Peircean Biosemiotics, and Rosen’s Relational Biology
Barbieri, M. (2018) · Biological Theory · doi:10.1007/s13752-018-0312-z · Cited by 19 · see citing works
The central role of transfer RNAs in mistranslation
Schuntermann, D. B., Jaskółowski, M., Reynolds, N. M., & Vargas‐Rodriguez, O. (2024) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2024.107679 · Cited by 17 · see citing works
Synthetic genome recoding: new genetic codes for new features
Kuo, J., Stirling, F., Lau, Y. H., Shulgina, Y., Way, J. C., & Silver, P. A. (2017) · Current Genetics · doi:10.1007/s00294-017-0754-z · Cited by 18 · see citing works
“Recoding, or changing a codon’s use in a genome, has been observed naturally in dozens of organisms, but often for stop codons (Ivanova et al. 2014; Ling et al. 2015).”
Update of the Pyrrolysyl-tRNA Synthetase/tRNA Pyl Pair and Derivatives for Genetic Code Expansion
Gong, X., Zhang, H., Shen, Y., & Fu, X. (2023) · Journal of Bacteriology · doi:10.1128/jb.00385-22 · Cited by 18 · see citing works
“It is now known that variations to the standard genetic code table are present in nature, including, but not limited to, codon reassignment and ambiguous decoding (1).”
BackgroundBacterial translation machinery for deliberate mistranslation of the genetic code
Vargas‐Rodriguez, O., Badran, A. H., Hoffman, K. S., Chen, M., Crnković, A., Ding, Y., Krieger, J. R., Westhof, É., Söll, D. G., & Melnikov, S. V. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2110797118 · Cited by 18 · see citing works
Self-citationBurger, G., Moreira, S., & Valach, M. (2016) · Trends in Genetics · doi:10.1016/j.tig.2016.06.005 · Cited by 17 · see citing works
Somatic mutation driven codon transition bias in human cancer
Son, H., Kang, H., Kim, H. S., & Kim, S. (2017) · Scientific Reports · doi:10.1038/s41598-017-14543-1 · Cited by 16 · see citing works
“∑ ∑ = = ∈ = m N ctr C C C N C P m ({ ( , ): }) ( ), (4) i n”
Yan, Q., Philmus, B. J., Hesse, C. N., Kohen, M., Chang, J. H., & Loper, J. E. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00497 · Cited by 16 · see citing works
Chemically Engineered Affinity Protein Drugs for Covalent Targeted Cancer Therapy
Xia, X., Gao, W., Yang, X., Huang, W., Xia, X., & Yan, D. (2025) · Journal of the American Chemical Society · doi:10.1021/jacs.5c02212 · Cited by 15 · see citing works
CoreTracker: accurate codon reassignment prediction, applied to mitochondrial genomes
Noutahi, E., Calderon, V., Blanchette, M., Lang, B. F., & El-Mabrouk, N. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx421 · Cited by 15 · see citing works
Characterization of redundant tRNAIles with CAU and UAU anticodons in Lactobacillus plantarum
Tomikawa, C., Auxilien, S., Guérineau, V., Yoshioka, Y., Miyoshi, K., Hori, H., Fourmy, D., Takai, K., & Yoshizawa, S. (2017) · The Journal of Biochemistry · doi:10.1093/jb/mvx075 · Cited by 15 · see citing works
“Likewise tRNA(UAU) might be involved in mechanisms that leads to genetic code flexibility (32) that confers L.”
BackgroundLiu, Y., An, L., Wang, X., Dai, Y., Zhang, C., Wen, Q., & Zhang, X. (2024) · Journal of Hematology & Oncology · doi:10.1186/s13045-024-01648-0 · Cited by 14 · see citing works
The Boggarts of biology: how non-genetic changes influence the genotype
Samhita, L. (2020) · Current Genetics · doi:10.1007/s00294-020-01108-5 · Cited by 4 · see citing works
“Overall, non-genetic changes can influence phenotype via multiple routes 105 (reviewed in Ackermann 2015; Ling et al. 2015; Stajic and Bank 2020).”
BackgroundThe Biology of tRNA t6A Modification and Hypermodifications—Biogenesis and Disease Relevance
Zhang, W., & Westhof, É. (2025) · Journal of Molecular Biology · doi:10.1016/j.jmb.2025.169091 · Cited by 13 · see citing works
Mistranslation of the genetic code by a new family of bacterial transfer RNAs
Schuntermann, D. B., Fischer, J. T., Bile, J. M., Gaier, S. A., Shelley, B. A., Awawdeh, A., Jahn, M., Hoffman, K. S., Westhof, É., Söll, D. G., et al. (2023) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2023.104852 · Cited by 13 · see citing works
Self-citationKleikamp, H. B. C., Palacios, P. A., Kofoed, M. V. W., Papacharalampos, G., Bentien, A., & Nielsen, J. L. (2024) · Environmental Science & Technology · doi:10.1021/acs.est.3c07725 · Cited by 13 · see citing works
Macher, J., Coots, N. L., Poh, Y.-P., Girard, E. B., Langerak, A., Muñoz-Gómez, S. A., Sinha, S. D., Jírsová, D., Vos, R. A., Wissels, R., et al. (2023) · mBio · doi:10.1128/mbio.00302-23 · Cited by 14 · see citing works
Mistranslation: from adaptations to applications
Hoffman, K. S., O’Donoghue, P., & Brandl, C. J. (2017) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2017.01.031 · Cited by 12 · see citing works
Self-citationTrapping Transient Protein Species by Genetic Code Expansion
Tinzl, M., & Hilvert, D. (2020) · ChemBioChem · doi:10.1002/cbic.202000523 · Cited by 11 · see citing works
Structure and Phylogeny of the Curly Birch Chloroplast Genome
Shestibratov, K. A., Baranov, О. Y., Mescherova, E. N., Kiryanov, P. S., Panteleev, S. V., Mozharovskaya, L. V., Krutovsky, K. V., & Евгеньевич, П. В. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.625764 · Cited by 11 · see citing works
Determining the fidelity of tRNA aminoacylation via microarrays
Schwartz, M. H., & Pan, T. (2016) · Methods · doi:10.1016/j.ymeth.2016.09.004 · Cited by 11 · see citing works
“While mistranslation can be engendered in any of the processes that mediate the conversion of DNA to protein, the most prominent mistranslational processes have so far been shown to occur during mRNA translation via ribosomal miscoding or tRNA mischarging [4-6].”
BackgroundSystems to study codon effect on post-transcriptional regulation of gene expression
Wu, Q., & Bazzini, A. (2017) · Methods · doi:10.1016/j.ymeth.2017.11.006 · Cited by 11 · see citing works
Molecular Mechanisms of Drug Tolerance in Mycobacterium tuberculosis
Антонова, А. В., Gryadunov, D. A., & Zimenkov, D. V. (2018) · Molecular Biology · doi:10.1134/s0026893318030020 · Cited by 11 · see citing works
“A contribution to heterogeneity is additionally made by mistranslation, or ambiguous decoding, which is a mechanism of genetic code f lexibility and results in that newly synthesized polypeptide chains have amino acid substitutions due to mistakes made by the ribosome or aminoacyl-tRNA synthetases [45].”
BackgroundAnalysis of Stop Codons within Prokaryotic Protein-Coding Genes Suggests Frequent Readthrough Events
Belinky, F., Ganguly, I., Poliakov, E., Yurchenko, V., & Rogozin, I. B. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22041876 · Cited by 11 · see citing works
Natural and artificial variations of the standard genetic code
Lukeš, J., Eliáš, M., Kachale, A., van der Gulik, P. T. S., & Speijer, D. (2025) · Current Biology · doi:10.1016/j.cub.2025.09.071 · Cited by 10 · see citing works
“It is beyond the scope of this review to discuss in detail all known codon reassignments and the underlying molecular mechanisms, so the reader may wish to consult other reviews 42,49,64,65 and original reports listed in Tables S1 and S2.”
Transfer RNA and small molecule therapeutics for aminoacyl‐ tRNA synthetase diseases
Samuels, T. N., Wu, F., Mahmood, M., Abuzaid, W. A., Sun, N., Moresco, A., Siu, V. M., O’Donoghue, P., & Heinemann, I. U. (2024) · FEBS Journal · doi:10.1111/febs.17361 · Cited by 10 · see citing works
Self-citationPu, F., Wang, R., Yang, X., Hu, X., Wang, J., Zhang, L., Zhao, Y., Zhang, D., Liu, Z., & Liu, J. (2023) · Journal of Basic Microbiology · doi:10.1002/jobm.202200624 · Cited by 10 · see citing works
“This biased synonymous codon usage is not neutral but involved in nucleotide usage bias [25, 26], mRNA stability [27, 28], translation accuracy, efficiency [29, 30], and protein folding formation [31].”
BackgroundWang, C., Yan, Y., Chen, X., Alfarraj, S. A., El‐Serehy, H. A., & Gao, F. (2019) · Zoologica Scripta · doi:10.1111/zsc.12380 · Cited by 10 · see citing works
Genome recoding strategies to improve cellular properties: mechanisms and advances
Singh, T., Yadav, S. K., Vainstein, A., & Kumar, V. S. (2020) · aBIOTECH · doi:10.1007/s42994-020-00030-1 · Cited by 9 · see citing works
Wang, H. H., Wang, M., Feng, X., Li, Y., Zhang, D., Cheng, Y., Liu, J., Wang, X., Zhang, L., La, H., et al. (2022) · Frontiers in Veterinary Science · doi:10.3389/fvets.2022.984962 · Cited by 9 · see citing works
The role of non-standard translation in Candida albicans pathogenesis
Bezerra, A. R., Oliveíra, C., Correia, I., Guimarães, A. R., Sousa, G., Carvalho, M. J., Moura, G., & Santos, M. A. S. (2021) · FEMS Yeast Research · doi:10.1093/femsyr/foab032 · Cited by 9 · see citing works
Genome-wide screening reveals metabolic regulation of stop-codon readthrough by cyclic AMP
Lyu, Z., Villanueva, P., O’Malley, L., Murphy, P., Augenstreich, J., Briken, V., Singh, A., & Ling, J. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad725 · Cited by 9 · see citing works
“Mutations in aaRSs and tRNAs may lead to the production of misacylated tRN As, w hich are used by the ribosome to make err oneous pr oteins ( 4 , 7 , 20– 23 ).”
MethodSelf-citationBernhardt, H. S. (2016) · Life · doi:10.3390/life6010010 · Cited by 9 · see citing works
“A related dynamism is of course also seen in the variant genetic codes found in mitochondria and certain eukaryotic species [36].”
BackgroundHow Did the Eukaryotes Evolve?
Barbieri, M. (2016) · Biological Theory · doi:10.1007/s13752-016-0253-3 · Cited by 9 · see citing works
Coordination between aminoacylation and editing to protect against proteotoxicity
Zhang, H., Murphy, P., Yu, J., Lee, S., Tsai, F., van Hoof, A., & Ling, J. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad778 · Cited by 8 · see citing works
“Except for selenocysteine, each of the 22 natural proteinogenic amino acids is recognized by a specialized aminoacyl-tRNA synthetase (aaRS) and ligated to the corresponding tRNAs through an aminoacylation reaction ( 5 , 6 ).”
BackgroundSelf-citationRewiring protein synthesis: From natural to synthetic amino acids
Fan, Y., Evans, C. R., & Ling, J. (2017) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2017.01.014 · Cited by 9 · see citing works
“The standard genetic code features 20 natural amino acids encoding 61 triplet sense codons, with the remaining three codons (TAA, TAG, and TGA) signaling translation termination [1].”
BackgroundSelf-citationHan, S., Hu, W. P., Kan, W., Ge, Z., Song, X., Li, L., Shang, Y., Zeng, Q., & Zhou, J. (2020) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2020.104293 · Cited by 8 · see citing works
Essential Logic and Facts Behind the Expansion of the Genetic Code: A Critical Assessment
Luu, H. T. L., Karbalaei‐Heidari, H. R., & Budiša, N. (2025) · ChemCatChem · doi:10.1002/cctc.202500809 · Cited by 8 · see citing works
Machine learning classification of archaea and bacteria identifies novel predictive genomic features
Bobbo, T., Biscarini, F., Yaddehige, S. K., Alberghini, L., Rigoni, D., Bianchi, N., & Taccioli, C. (2024) · BMC Genomics · doi:10.1186/s12864-024-10832-y · Cited by 7 · see citing works
“This need for diverse tRNA sets could lead to higher entropy in their tRNA genes [48]; • Horizontal Gene Transfer (HGT): the potential for HGT in bacteria to introduce new genetic material, such as tRNA genes from diverse organisms, can significantly enhance the diversity of the bacterial tRNA gene…”
The nucleotide usages significantly impact synonymous codon usage inMycoplasma hyorhinis
Wu, Y., Jin, L. H., Li, Y., Zhang, D., Zhao, Y., Chu, Y., Ma, Z., Ma, X., & Shang, Y. (2021) · Journal of Basic Microbiology · doi:10.1002/jobm.202000592 · Cited by 7 · see citing works
Evolutionary dynamics of codon usages for peste des petits ruminants virus
Wang, X., Sun, J., Lü, L., Pu, F., Zhang, D., & Xie, F. (2022) · Frontiers in Veterinary Science · doi:10.3389/fvets.2022.968034 · Cited by 7 · see citing works
Surface Modification of Bacteria to Optimize Immunomodulation for Advanced Immunotherapy
Xue, K., Wang, L., & Liu, J. (2022) · ChemMedChem · doi:10.1002/cmdc.202200574 · Cited by 6 · see citing works
Programmed Deviations of Ribosomes From Standard Decoding in Archaea
Lise, F. D., Strazzulli, A., Iacono, R., Curci, N., Fenza, M. D., Maurelli, L., Moracci, M., & Cobucci‐Ponzano, B. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.688061 · Cited by 6 · see citing works
The “periodic table” of the genetic code: A new way to look at the code and the decoding process
Komar, A. A. (2016) · Translation · doi:10.1080/21690731.2016.1234431 · Cited by 6 · see citing works
“The genetic code is nearly universal, meaning that in almost all living organisms, the identity of the amino acid encoded by a given triplet codon is the same.(4,5) With 4 bases (A, G, U, and C), there are 64 possible triplet codons; 61 sense (encoding amino acids) and 3 nonsense (UAA, UAG, and UGA, socalled stop codo…”
BackgroundFacts and Anomalies to Keep in Perspective When Designing an Artificial IntelligencePreprint
Ipe, N. K. (2020) · doi:10.36227/techrxiv.12299945.v1 · Cited by 6 · see citing works
Giulio, M. D. (2026) · Biosystems · doi:10.1016/j.biosystems.2026.105787 · Cited by 5 · see citing works
Nonsense Mutations in Eukaryotes
Potapova, N. A. (2022) · Biochemistry (Moscow) · doi:10.1134/s0006297922050029 · Cited by 5 · see citing works
Methanogenic archaea encoding Pyrrolysine maintain ambiguous amber codon usage
Shalvarjian, K. E., Chadwick, G. L., Pérez, P. I., Woods, P. H., Orphan, V. J., & Nayak, D. D. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2517473122 · Cited by 4 · see citing works
“Natural genetic code expansion is a distinct case of codon reassignment, wherein a stop codon is recoded to an amino acid beyond the standard 20 amino acids ( 10 ).”
Feng, X., Liu, Z., Mo, Y. J., Zhang, S., & Ma, X. (2025) · Archives of Virology · doi:10.1007/s00705-025-06250-4 · Cited by 4 · see citing works
“Codon usage bias occurs due to the preferential and non-random use of synonymous codons, which can be influenced by nucleotide pair bias [ 8, 9 ] and differences in mRNA stability [ 10 , 11 ], translation accuracy and effi - ciency [12, 13 ], and protein folding kinetics [ 14].”
Genetic Code Expansion System for Tight Control of Gene Expression in Bombyx mori Cell Lines
Lü, W., Wang, R., Wang, P., Ma, S., & Xia, Q. (2021) · Insects · doi:10.3390/insects12121081 · Cited by 4 · see citing works
Kim, J. M., Lee, H. Y., & Jung, J. (2022) · Applied Biological Chemistry · doi:10.1186/s13765-022-00748-0 · Cited by 4 · see citing works
Gołębiewska, K., Gregorová, P., Sarin, L. P., & Gawroński, P. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.06.14.598963 · Cited by 4 · see citing works
- Authors
- Ling, J., O'Donoghue, P., & Söll, D.
- Affiliations
- The University of Texas Health Science Center at Houston (US)
- Yale University (US)
- Corresponding author
- Söll, Dieter
- Venue
- Nature Reviews Microbiology
- Published
- 2015-09-22
- Volume
- 13
- Issue
- 11
- Pages
- 707-721
- ISSN
- 1740-1526 (ISSN-L)
- 1740-1534
- PMC
- PMC4712924
- OpenAlex
- W2298792983
- Cited by
- 135
- References
- 146
- Citations by year
- 2026: 5 · 2025: 10 · 2024: 12 · 2023: 10 · 2022: 14 · 2021: 12 · 2020: 11 · 2019: 8 · 2018: 12 · 2017: 22 · 2016: 19
- FWCI
- 1.71
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Reviews Microbiology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- University of Texas Health Science Center at Houston
- Canada Research Chairs
- Canadian Institutes of Health Research (950‑229917)
- Natural Sciences and Engineering Research Council of Canada
- National Institute of General Medical Sciences (GM 022854, GM115431, R01GM115431, R01GM022854, R37GM022854)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- codon usage bias, codon reassignment, microbial physiology, microorganisms, genetic code evolution
- MeSH terms
- Archaea, Bacteria, Codon, Genetic Code, Evolution, Molecular
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