Published Jan 15, 2023



PLUMX
Almetrics
 
Dimensions
 

Google Scholar
 
Search GoogleScholar


Adhityo Wicaksono

Viol Dhea Kharisma

Arli Aditya Parikesit

##plugins.themes.bootstrap3.article.details##

Abstract

Since the 1950s, reverse translation has been an enigmatic part of Crick’s central dogma of molecular biology. It might be described as the possibility to back-translate information from proteins to nucleic acids (or codons). A few studies have attempted to theorize and/or conduct in vitro experiments to test the likelihood of reverse translation, with ideas often involving the creation of peptide recognition sites that bridge the peptide and the codon. However, due to many constraints including an asymmetrical informational transfer, the stability of protein-peptide bonds, the structural non-uniformity of protein R-groups, and the informational loss in post-translational protein modifications, this concept requires follow-up studies. On the other hand, current bioinformatic tools that rely on computational programs and biological databases represent a growing branch of biology. Bioinformatics-based reverse translation
can utilize codon usage tables to predict codons from their peptide counterparts. In addition, the development of machine learning tools may allow for the exploration of biological reverse translation in vitro. Thus, while in vivo reverse translation appears to be nearly impossible (due to biological complexity), related biological and bioinformatics studies might be useful to understand better the
central dogma’s informational transfer and to develop more complex biological machinery.

Keywords

amino acids, central dogma, genetic transfer, polypeptide, RNA

References
[1] Crick F. On Protein Synthesis. Symposia of the Society for Experimental Biology, 12: 139–163, 1958.

[2] Crick F. Central dogma of molecular biology. Nature, 227(5258): 561–563, 1970.
doi: 10.1038/227561a0

[3] Baltimore D. RNA-dependent DNA polymerase in virions of RNA tumour viruses. Nature, 226(5252): 1209–1211, 1970.
doi: 10.1038/2261209a0

[4] Temin HM, Mizutani S. RNA-dependent DNA polymerase in virions of Rous sarcoma virus. Nature, 226(5252): 1211–1213, 1970.
doi: 10.1038/2261211a0

[5] Baltimore D, Eggers HJ, Franklin RM, Tamm I. Poliovirus-induced RNA polymerase and the effects of virus-specific inhibitors on its production. Proceedings of National Academy of Science USA, 49(6): 843–849, 1963.
doi: 10.1073/pnas.49.6.843

[6] Koonin EV. Does the central dogma still stand? Biology Direct, 7(1): 27, 2012.
doi: 10.1186/1745-6150-7-27

[7] Koonin EV. Why the Central Dogma: on the nature of the great exclusion principle. Biology Direct, 10(1): 52, 2015.
doi: 10.1186/s13062-015-0084-3

[8] Rich A. On the problems of evolution and biochemical information transfer. In: Kasha M., Pullman B. (eds.). Horizons in Biochemistry. Academic Press; New York, NY, USA: 1962. pp. 103–126

[9] Lehman N. The RNA World: 4,000,000,050 years old. Life, 5(4): 1583–1586, 2015.
doi: 10.3390/life5041583

[10] Gilbert W. Origin of life: The RNA world. Nature, 319(6055): 618, 1986.
doi: 10.1038/319618a0

[11] Bernhardt HS. The RNA world hypothesis: the worst theory of the early evolution of life (except for all the others). Biology Direct, 7(1): 23, 2012.
doi: 10.1186/1745-6150-7-23

[12] Forterre P. The two ages of the RNA world, and the transition to the DNA world: a story of viruses and cells. Biochimie, 87(9-10): 793–803, 2005.
doi: 10.1016/j.biochi.2005.03.015

[13] Nashimoto M. The RNA/protein symmetry hypothesis: experimental support for reverse translation of primitive proteins. Journal of Theoretical Biology, 209(2): 181–187, 2001.
doi: 10.1006/jtbi.2000.2253

[14] Lee DH, Granja JR, Martinez JA, Severin K, Ghadiri MR. A self-replicating peptide. Nature, 382(6591): 525–528, 1996.
doi: 10.1038/382525a0

[15] Beekes M, McBride PA. The spread of prions through the body in naturally acquired transmissible spongiform encephalopathies. The FEBS Journal, 274(3): 588–605, 2007.
doi: 10.1111/j.1742-4658.2007.05631.x

[16] Chiti F, Dobson CM. Protein misfolding, functional amyloid, and human disease. Annual Review of Biochemistry, 75: 333–366, 2006.
doi: 10.1146/annurev.biochem.75.101304.123901

[17] Ridley RM. What Would Thomas Henry Huxley Have Made of Prion Diseases? In: Baker HF (ed.). Molecular Pathology of the Prions; Humana Press Inc., NY, 2001; Vol. 59, pp.1-16.

[18] Serio TR, Cashikar AG, Kowal AS, Sawicki GJ, Lindquist SL. Self-perpetuating changes in Sup35 protein conformation as a mechanism of heredity in yeast. Biochemical Society Symposia, 68: 35–43, 2001.
doi: 10.1042/bss0680035

[19] Serio TR, Lindquist SL. [PSI+]: an epigenetic modulator of translation termination efficiency. Annual Review of Cell and Development Biology, 15: 661–703, 1999.
doi: 10.1146/annurev.cellbio.15.1.661

[20] Mekler LB. Mechanism of biological memory. Nature, 215(5100): 481–484, 1967.
doi: 10.1038/215481a0

[21] Cook ND. The case for reverse translation. Journal of Theoretical Biology, 64: 113–135, 1977.
doi: 10.1016/0022-5193(77)90116-3

[22] Tawfik DS, Gruic‐Sovulj I. How evolution shapes enzyme selectivity–lessons from aminoacyl‐ tRNA synthetases and other amino acid utilizing enzymes. The FEBS Journal, 287(7): 1284–1305, 2020.
doi: 10.1111/febs.15199

[23] Symons RH. Small catalytic RNAs. Annual Review of Biochemistry, 61: 641–671, 1992.
doi: 10.1146/annurev.bi.61.070192.003233

[24] Connell GJ, Illangesekare M, Yarus M. Three small ribooligonucleotides with specific arginine sites. Biochemistry, 32(21): 5497–5502, 1993.
doi: 10.1021/bi00072a002

[25] Ellington AD, Szostak JW. In vitro selection of RNA molecules that bind specific ligands. Nature, 346(6287): 818–822, 1990.
doi: 10.1038/346818a0

[26] Tuerk C, Gold L. Systematic Evolution of Ligands by Exponential Enrichment: RNA Ligands to Bacteriophage T4 DNA Polymerase. Science, 249(4968): 505–510, 1990.
doi: 10.1126/science/2200121

[27] Krokhotin A, Houlihan K, Dokholyan NV. iFoldRNA v2: folding RNA with constraints. Bioinformatics, 31(17): 2891–2893, 2015.
doi: 10.1093/bioinformatics/btv221

[28] Bowser MT. SELEX: Just another separation? Analyst, 130(2): 128–130, 2005.
doi: 10.1039/B412492H

[29] Famulok M, Szostak JW. Stereospecific recognition of tryptophan agarose by in vitro selected RNA. Journal of American Chemical Society, 114(10): 3990–3991, 1992.
doi: 10.1021/ja00036a065

[30] Gilbert SD, Rambo SP, Van Tyne D, Batey RT. Structure of the SAM-II riboswitch bound to S-adenosylmethionine. Nature Structural & Molecular Biology, 15(2): 177–182, 2008.
doi: 10.1038/nsmb.1371

[31] Lu C, Smith, A.M., Fuchs, R.T., Ding, F., Rajashankar, K., Henkin, T.M., Ke, A. Crystal structures of the SAM-III/S(MK) riboswitch reveal the SAM-dependent translation inhibition mechanism. Nature Structural & Molecular Biology, 15(10): 1076–1083, 2008.
doi: 10.1038/nsmb.1494

[32] Montange RK, Batey RT. Structure of the S-adenomethionine riboswitch regulatory mRNA element. Nature, 441(7097): 1172–1175, 2006.
doi: 10.1038/nature04819

[33] Garst AD, Heroux A, Rambo RP, Batey RT. Crystal structure of the lysine riboswitch regulatory mRNA element. Journal of Biological Chemistry, 283(33): 22347–22351, 2008.
doi: 10.1074/jbc.C800120200

[34] Serganov A, Huang L, Patel DJ. Structural insight into amino acid binding and gene control by a lysine riboswitch. Nature, 455(7217): 1263–1267, 2008.
doi: 10.1038/nature07326

[35] Yang Y, Kochoyan M, Burgstaller P, Westhof E, Famulok F. Structural basis of ligand discrimination by two related RNA aptamers resolved by NMR spectroscopy. Science, 272(5266): 1343–1346, 1996.
doi: 10.1126/science.272.5266.1343

[36] Stefaniak F, Bujnicki JM. AnnapuRNA: A scoring function for predicting RNA-small molecule binding poses. PloS Computational Biology, 17(2): p.e1008309, 2021.
doi: 10.1371/journal.pcbi.1008309

[37] Trott O, Olson AJ. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2): 455–461, 2010.
doi: 10.1002/jcc.21334

[38] Martin MT. Methods and compositions for reverse translation. United State Patent, no: US 7,169,894 B2 (Jan 30, 2007).

[39] Zhang G, Hubalewska M, Ignatova Z. Transient ribosomal attenuation coordinates protein synthesis and co-translational folding. Nature Structural & Molecular Biology, 16(3): 274–280, 2009.
doi: 10.1038/nsmb.1554

[40] Cottrell TL. The strengths of chemical bonds (2nd ed). Butterworths, London 1958.

[41] Dickson KS., Burns CM, Richardson JP. Determination of the free-energy change for repair of a DNA phosphodiester bond. Journal of Biological Chemistry, 275(21): 15828–15831, 2000.
doi: 10.1074/jbc.M910044199

[42] Martin RB. Free energies and equilibria of peptide bond hydrolysis and formation. Biopolymers, 45(5): 351–353, 1998.
doi: 10.1002

[43] Tu X., Das K, Han Q, Bauman JD, Clark Jr, AD, Hou, X, Frenkel YV, Gaffney BL, Jones RA, Boyer PL, Hughes SH. Structural basis of HIV-1 resistance to AZT by excision. Nature Structural & Molecular Biology, 17(10): 1202–1209, 2010.
doi: 10.1038/nsmb.1908

[44] Alhazmi HA. Mobility shift-affinity capillary electrophoresis for investigation of proteinmetal ion interactions: aspects of method development, validation and high throughput screening. Doctorate Thesis, Faculty of Life Sciences, Technische Universität Braunschweig, Germany. p.2.

[45] Bakış Y, Otu HH, Sezerman OU. Inferring Phylogenies from Physico Chemical Properties of DNA. American Journal of Bioinformatics Research, 2(1): 1–6, 2012.
doi: 10.5923/j.bioinformatics.20120201.01

[46] Andréola ML, Parissi V, Litvak S. 2013. DNA Polymerases: Reverse Transcriptase Integrase, and Retrovirus Replication. In: Lennarz WJ, Lane MD (eds.). Encyclopedia of Biological Chemistry (2nd edition). Academic Press, Massachusetts, USA. pp.101–107, 2013.
doi: 10.1016/B978-0-12-378630-2.00258-9

[47] Ahlquist P. RNA-dependent RNA polymerases, viruses, and RNA silencing. Science, 296(5571): 1270–1273, 2002.
doi: 10.1126/science.1069132

[48] Kumar S, Nussinov R. Close‐range electrostatic interactions in proteins. ChemBioChem, 3(7): 604–617, 2002.
doi: 10.1002/1439-7633(20020703)

[49] McClain WH. Rules that Govern tRNA Identity in Protein Synthesis. Journal of Molecular Biology, 234(2): 257–280.
doi: 10.1006/jmbi.1993.1582

[50] Swanson R, Hoben P, Sumner-Smith M, Uemura H, Watson L, Söll D. Accuracy of in Vivo Aminoacylation Requires Proper Balance of tRNA and Aminoacyl-tRNA Synthetase. Science, 242(4885): 1548–1551.
doi: 10.1126/science.3144042

[51] Shen C-H. Diagnostic Molecular Biology, Academic Press, Massachusetts, USA. pp.87–116, 2019.
doi: 10.1016/B978-0-12-802823-0.00004-3

[52] Rose GD, Fleming PJ, Banavar JR, Maritan A. A backbone-based theory of protein folding. Proceedings of the National Academy of Sciences of the United States of America 103(45): 16623–16633.
doi: 10.1073/pnas.0606843103

[53] Anfinsen CB. Principles that Govern the Folding of Protein Chains. Science, 181(4096): 223–229.
doi: 10.1126/science.181.4096.223

[54] Yuan TZ, Ormonde CF, Kudlacek ST, Kunche S, Smith JN, Brown WA, Pugliese KM, Olsen TJ, Iftikhar M, Raston CL, Weiss GA. Shear‐Stress‐Mediated Refolding of Proteins from Aggregates and Inclusion Bodies. ChemBioChem, 16(3): 393–396, 2015.
doi: 10.1002/cbic.201402427

[55] Rogers LD, Overall CM. Proteolytic Post-translational Modification of Proteins: Proteomic Tools and Methodology. Molecular & Cellular Proteomics, 12(12): 3532–3542.
doi: 10.1074/mcp.M113.031310

[56] Edman P, Begg G. A protein sequenator. European Journal of Biochemistry, 1: 80–91, 1967.
doi: 10.1007/978-3-662-25813-2_14

[57] Medzihradszky KF, Chalkley RJ. Lessons in de novo peptide sequencing by tandem mass spectrometry. Mass Spectrometry Reviews, 34(1): 43–63, 2015.
doi: 10.1002/mas.21406

[58] Poinar HN, Schwarz C, Qi J, Shapiro B, MacPhee RD, Buigues B, Tikhonov A, Huson DH, Tomsho LP, Auch A, Rampp M. Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA. Science, 311(5759): 392–394, 2006.
doi: 10.1126/science.1123360

[59] Lee YC, Chiang CC, Huang PY, Chung CY, Huang TD, Wang CC, Chen CI, Chang RS, Liao CH, Reisz RR 2017. Evidence of preserved collagen in an Early Jurassic sauropodomorph dinosaur revealed by synchrotron FTIR microspectroscopy. Nature Communications, 8:
14220.
doi: 10.1038/ncomms14220

[60] Arnold C., Clewley JP. From ABI Sequence Data to LASERGENE’s EDITSEQ. In: Swindell SR. (eds) Sequence Data Analysis Guidebook. Methods In Molecular Medicine™, Springer, Totowa, 70: 65–74, 1997.
doi: 10.1385/0-89603-358-9:65

[61] Nakamura Y, Gojobori T, Ikemura T. Codon usage tabulated from the international DNA sequence databases. Nucleic Acids Research, 28(1): 334–334, 1998.
doi: 10.1093/nar/26.1.334

[62] Bhattacharya M, Sharma AR, Ghosh P, Patra P, Patra BC, Lee SS, Chakraborty C. Bioengineering of novel non-replicating mRNA (NRM) and self-amplifying mRNA (SAM) vaccine candidates against SARS-CoV-2 using immunoinformatics approach. Molecular
Biotechnology, 64(5): 510–525, 2022.
doi: 10.1007/s12033-021-00432-6

[63] Hosseini NG, Tebianian M, Farhadi A, Khani, AH, Rahimi A, Mortazavi M, Hosseini SY, Taghizadeh M, Rezaei M, Mahdavi M. In silico analysis of L1/L2 sequences of human papillomaviruses: implication for universal vaccine design. Viral Immunology, 30(3): 210–223,
2017.
doi: 10.1089/vim.2016.0142

[64] Yazdani Z, Rafiei A, Yazdani M, Valadan R. 2020. Design an efficient multi-epitope peptide vaccine candidate against SARS-CoV-2: an in silico analysis. Infection and Drug Resistance, 13: 3007–3022, 2020.
doi: 10.2147/IDR.S264573

[65] Li R, Li L, Xu Y, Yang J. 2022. Machine learning meets omics: applications and perspectives. Briefings in Bioinformatics, 23(1): bbab460, 2022.
doi: 10.1093/bib/bbab460

[66] Verma R, Schwaneberg U, Roccatano D. Computer-aided protein directed evolution: a review of web servers, databases and other computational tools for protein engineering. Computational and Structural Biotechnology Journal, 2(3): e201209008, 2012.
doi: 10.5936/csbj.201209008

[67] Lheureux S, Braunstein M, Oza AM. Epithelial ovarian cancer: evolution of management in the era of precision medicine. CA: A Cancer Journal for Clinicians, 69(4): 280–304, 2019.
doi: 10.3322/caac.21559

[68] Kinghorn AB, Fraser LA, Liang S, Shiu SCC, Tanner JA. 2017. Aptamer bioinformatics. International Journal of Molecular Sciences, 18(12): 2516.
doi: 10.3390/ijms18122516
How to Cite
Wicaksono , A., Kharisma, V. D., & Parikesit, A. A. (2023). New Perspectives on Reverse Translation: Brief History and Updates. Universitas Scientiarum, 28(1), 1–20. https://doi.org/10.11144/Javeriana.SC281.npor
Section
Biología molecular / Molecular biology / Biologia molecular