Orígenes físicos del citoplasma y la emergencia del código genético
##plugins.themes.bootstrap3.article.main##
El origen de la vida está ligado al origen del código genético, ningún organismo podría considerarse vivo si no posee la capacidad de transmitir y ejecutar instrucciones químicas replicables, mutables, variables y heredables a futuras generaciones. En esta revisión se aborda el problema de qué condiciones son necesarias para iniciar el origen de los bloques del código genético.
Además se discute el origen ancestral del citoplasma como una matriz bioquímica que soporta la replicación, síntesis y preservación del código genético. La discusión se centra sobre el origen de la vida con pruebas experimentales sobre la síntesis de ADN/ARN ex vivo, sino también con las descripciones fundamentales de los principios biológicos esenciales para el origen de los seres vivos.
##plugins.themes.bootstrap3.article.details##
Aran, M., Ferrer-Sueta, G., & Radi, R. (2011). ATP and Mg2+ promote the reversible oligomerization and aggregation of chloroplast 2-Cys periredoxin. The Journal of Biological Chemistry, 286(26), 23441-23451. doi: 10.1074/jbc.M111.224964
Abbas, M., & Kakkar, V. (2021). Peptide-based coacervates as biomimetic protocells. Chemical Society Reviews, 50(7), 3690-3705. doi: 10.1039/d0cs00307g
Arsene, S., Delcea, M., & Kelemen, L. (2018). Coupled catabolism and anabolism in autocatalytic RNA sets. Nucleic Acids Research, 46(18), 9384-9393. https://doi.org/10.1093/nar/gky699
Arai, Y., Nomura, T., Sakuma, S., Nagai, T., & Urano, Y. (2018). RGB-color intensiometric indicators visualize spatiotemporal dynamics of ATP in single cells. Angewandte Chemie International Edition in English, 57(34), 10873-10878. https://doi.org/10.1002/anie.201804304
Baev, A. Y., Cheryasov, G. V., & Skulachev, V. P. (2020). Inorganic polyphosphate is produced and hydrolyzed in F0F1-ATP synthase of mammalian mitochondria. Biochemical Journal, 477(8), 1515-1524. doi: 10.1042/BCJ20200141
Brangwynne, C. P., Eckmann, C. R., Courson, D. S., Rybarska, A., Hoege, C., Gharakhani, J., … Hyman, A. A. (2011). Active liquid-like behavior of nucleoli determines their size and shape in Xenopus laevis oocytes. Proceedings of the National Academy of Sciences of the United States of America, 108(11), 4334-4339. https://doi.org/10.1073/pnas.1017150108
Bose, T., Lee, K. H., Lu, S., Xu, J., & Zhang, Y. (2022). Liquid-to-solid phase transition of oskar ribonucleoprotein granules is essential for their function in Drosophila embryonic development. Cell, 185(8), 1308-1324. https://doi.org/10.1016/j.cell.2022.02.022
Chandrasekhar, R., Melin, J., & Lindgren, A. (2019). A molecular sensor reveals differences in macromolecular crowding between the cytoplasms and nucleoplasm. ACS Sensors, 4(8), 1835-1843. https://doi.org/10.1021/acssensors.9b00569
Chen, H., Zheng, X., Zheng, Y., & Anderson, D. H. (2019). Nucleoplasmin is a Limiting Component in the Scaling of Nuclear Size with Cytoplasmic Volume. Journal of Cell Biology, 218(12), 4063-4078. https://doi.org/10.1083/jcb.201908059
Diaz-Delgadillo, A. F. (2016). Temperature drives P granule formation in C. elegans. Editorial: Sächsiches Library TUDresden.
Diaz-Delgadillo, A. F. (2021). Local thermodynamics govern formation and dissolution of Caenorhabditis elegans P granule condensates. Proceedings of the National Academy of Sciences of the United States of America, 118(37), e2102772118. https://doi.org/10.1073/pnas.2102772118
Duan, X., Li, Y., & Pang, X. (2019). Protocell: A new strategy for drug delivery. Current Pharmaceutical Design, 25(29), 3099–3106.
Eigen, M., McCaskill, J., & Schuster, P. (1988). Molecular quasi-species. The Journal of Physical Chemistry, 92(24), 6881-6891. https://doi.org/10.1021/j100335a010
Flory, P. J. (1985). Thermodynamics of high polymer solutions. The Journal of Chemical Physics, 83(3), 1564-1570. doi: 10.1063/1.449343
Fraccia, T. P., Iacovella, C. R., & Abbott, N. L. (2020). Liquid crystal coacervates composed of short double-stranded DNA and cationic peptides. ACS Nano, 14(11), 15071-15082. doi: 10.1021/acsnano.0c06746
Ferris, J. P., Hill, A. R., Jr., & Liu, R. (1996). Synthesis of long prebiotic oligomers on mineral surfaces. Nature, 381(6577), 59-61. doi: 10.1038/381059a0
Fu, K., Wu, H., & Su, Z. (2021). Self-assembling peptide-based hydrogels: Fabrication, properties, and applications. Biotechnology Advances, 49, 107752. https://doi.org/10.1016/j.biotechadv.2021.107752
Gaspers, L. D., Bakowski, D., & Nadolski, M. J. (2017). Spatial Ca2+ Profiling: Decrypting the Universal Cytosolic Ca2+ Oscillation. Journal of Physiology, 595(10), 3053-3062. https://doi.org/10.1113/jp273212
Gray, M. J., Wholey, W. Y., & Jakob, U. (2014). Polyphosphate is a primordial chaperone. Molecular Cell, 53(5), 689-699. doi: 10.1016/j.molcel.2014.01.025
Gil, R. R., & Bruchez, M. P. (2015). Stability of energy metabolites - An often overlooked issue in metabolomics studies: A review. Electrophoresis, 36(17), 2156-2169. doi: 10.1002/elps.201400585
Geiger, F. C., Kjær, J., & Andersen, K. R. (2021). Liquid-liquid phase separation underpins the formation of replication factories in rotaviruses. The EMBO Journal, 40(18), e107711. https://doi.org/10.15252/embj.2020107711
Green, N. J., & Maréchal, A. (2021). Illuminating life's origins: UV photochemistry in abiotic synthesis of biomolecules. Journal of the American Chemical Society, 143(18), 7219-7236. doi: 10.1021/jacs.0c13200
Hudson, J. L., Field, R. J., & Noyes, R. M. (1981). Chaos in Belousov-Zhabotinsky reaction. The Journal of Chemical Physics, 74, 6171. doi: 10.1063/1.441007
Hyman, A. A., Weber, C. A., & Jülicher, F. (2011). Beyond stereospecificity: Liquids and mesoscale organization of cytoplasm. Developmental Cell, 21(1), 14-16. https://doi.org/10.1016/j.devcel.2011.06.013
Hyman, A. A., Weber, C. A., & Jülicher, F. (2014). Liquid-liquid phase separation in biology. Annual Review of Cell and Developmental Biology, 30, 39-58. https://doi.org/10.1146/annurev-cellbio-100913-013325
Ianeselli, L., Dose, B., & Maurel, M. C. (2019). Periodic melting of oligonucleotides by oscillating salt concentrations triggered by microscale water cycles inside heated rock pores. Angewandte Chemie International Edition, 58(38), 13289-13294. https://doi.org/10.1002/anie.201905005
Kostic, D. A., Lynch, K. M., & Schubert, C. J. (2020). The second law and entropy misconceptions demystified. Entropy, 22, 648. doi: 10.3390/e22060648
Kim, J. T., & Terman, G. (2006). Multi-scale computational model of fuel homeostasis during exercise: Effect of hormonal control. Annals of Biomedical Engineering, 35(1), 1-11. doi: 10.1007/s10439-006-9219-1
Keil, P., Spasic, I., Utz, M., & Winterhalter, M. (2017). Proton gradients and pH oscillations emerge from heat flow at the microscale. Nature Communications, 8, 1-11. https://doi.org/10.1038/s41467-017-02065-3
Keil, P., Spasic, I., Utz, M., & Winterhalter, M. (2016). Probing of molecular replication and accumulation in shallow heat gradients through numerical simulations. Physical Chemistry Chemical Physics, 18(30), 20153-20166. https://doi.org/10.1039/c6cp00577b
Lukacs, G. L., Haggie, P., Seksek, O., Lechardeur, D., Freedman, N., & Verkman, A. S. (2000). Size-dependent DNA Mobility in Cytoplasm and Nucleus. Journal of Biological Chemistry, 275(3), 1625-1629. https://doi.org/10.1074/jbc.275.3.1625
Martin, W. F., Garg, S., & Zimorski, V. (2010). Evolutionary Origins of Metabolic Compartmentalization in Eukaryotes. Philosophical Transactions of the Royal Society B: Biological Sciences, 365(1541), 847-855. https://doi.org/10.1098/rstb.2009.0252
Mariani, A., Munn, A. S., & Swain, P. M. (2018). pH-driven RNA strand separation under prebiotically plausible conditions. ACS Biochemistry, 57(43), 1308-1315. https://doi.org/10.1021/acs.biochem.8b01080
Martynov, V. G., & Vorob'eva, O. V. (2014). Dry polymerization of 3',5'-cyclic GMP to long strands of RNA. ChemBioChem, 15(6), 879-889. doi: 10.1002/cbic.201300773
Mansy, S. S., Schrum, J. P., & Krishnamurthy, M. (2015). Heat flux across an open pore enables the continuous replication and selection of oligonucleotides towards increasing length. Nature Chemistry, 7(4), 315-321. doi: 10.1038/nchem.2202
Ma, G. (2014). Microencapsulation of protein drugs for drug delivery: Strategy, preparation, and applications. Journal of Controlled Release, 193, 324–340. https://doi.org/10.1016/j.jconrel.2014.09.003
Needleman, D., Dogic, Z., & Fraden, S. (2017). Active Matter at the Interface Between Materials Science and Cell Biology. Advanced Materials Interfaces, 4(17), 170048. https://doi.org/10.1002/admi.201700048
Odermatt, P. D., Shrestha, R. L., & Rüdiger, M. (2021). Variations of Intracellular Density During the Cell Cycle Arise from Tip-growth Regulation in Fission Yeast. eLife, 10, e64901. https://doi.org/10.7554/eLife.6490
Oró, J. (1960). Synthesis of adenine from ammonium cyanide. Biochemical and Biophysical Research Communications, 2(6), 407-412. doi: 10.1016/0006-291X(60)90270-4
Oparin, A. I. (1924). The origin of life. In E. D. Fröhlich (Ed.), The origin of life on earth (pp. 71-88). New York: Macmillan.
Patel, A. J., Varner, J. D., & Flagel, L. E. (2017). ATP as a biological hydrotrope. Science, 356(6334), 753-756. doi: 10.1126/science.aaf6846
Perazzo, A., Preziosi, V., & Guido, S. (2015). Phase inversion emulsification: Current understanding and applications. Advances in Colloid and Interface Science, 222, 581–599. https://doi.org/10.1016/j.cis.2015.01.001
Pardi, N., Hogan, M. J., Porter, F. W., & Weissman, D. (2018). mRNA vaccines — a new era in vaccinology. Nature Reviews Drug Discovery, 17(4), 261–279. https://doi.org/10.1038/nrd.2017.243
Reinke, A., Chen, J. C., Aronova, S., Powers, T., & Cui, Y. (2006). Genomewide Oscillation of Transcription in Yeast. Trends in Biochemical Sciences, 31(4), 166-173. https://doi.org/10.1016/j.tibs.2006.01.006
Rasmus, F. W. (2000). Darwin on variation and heredity. Journal of the History of Biology, 33(3), 425-455. doi: 10.1023/A:1004760716015
Ritson, D. J., Sutherland, J. D., & Sutherland, J. D. (2013). Prebiotic synthesis of simple sugars by photoredox systems chemistry. Nature Chemistry, 4(11), 895-899. doi: 10.1038/nchem.1476
Rai, R., Alwani, S., & Badea, I. (2019). Polymeric nanoparticles in gene therapy: New avenues of design and optimization for delivery applications. Polymers, 11(4), 745. https://doi.org/10.3390/polym11040745
Saric, A., Sitte, E., & Krause, E. (2021). Solutes as controllers of endomembrane dynamics. Nature Reviews, 22, April 2021. doi: 10.1038/s41579-020-00519-3
Scharf, C., Virgo, N., Cleaves II, H. J., Aono, M., Aubert-Kato, N., Aydinoglu, A., … Yarus, M. (2016). Quantifying the origins of life on a planetary scale. Proceedings of the National Academy of Sciences of the United States of America, 113(29), 8127-8132. https://doi.org/10.1073/pnas.1523233113
Schulman, R., Winfree, E., & Seeman, N. C. (2012). Robust self-replication of combinatorial information via crystal growth and scission. Proceedings of the National Academy of Sciences, 109(17), 6405-6410. doi: 10.1073/pnas.1119770109
Seal, M., Weil-Ktorza, O., Despotović, D., Tawfik, D. S., Levy, Y., Metanis, N., Longo, L. M., & Goldfarb, D. (2022). Peptide-RNA coacervates as a cradle for the evolution of folded domains. Journal of the American Chemical Society, 144(31), 14150-14160. doi: 10.1021/jacs.2c03819
Srimungkala, S., Noguchi, K., & Yoshida, Z. (1999). Bromination reactions important in the mechanism of the Belousov-Zhabotinsky system. The Journal of Physical Chemistry A, 103(7), 1038-1043. https://doi.org/10.1021/jp984201o
Schuster, P. (1984). Polynucleotide evolution, hypercycles, and the origin of the genetic code. Advances in Space Research, 4(12), 143-151.
Szathmáry, E. (2013). On the propagation of a conceptual error concerning hypercycles and cooperation. Journal of Systems Chemistry, 4(1), 1-6. https://doi.org/10.1186/1759-2208-4-1
Tsien, R. Y., Pozzan, T., & Rink, T. J. (1982). Calcium Homeostasis in Intact Lymphocytes: Cytoplasmic Free Calcium Monitored With a New, Intracellularly Trapped Fluorescent Indicator. The Journal of Cell Biology, 94(2), 325-334.
Uchida, S., & Kataoka, K. (2019). Design concepts of polyplex micelles for in vivo therapeutic delivery of plasmid DNA and messenger RNA. Journal of Biomedical Materials Research Part A, 107(5), 978-990. https://doi.org/10.1002/jbm.a.36614
Wikstrom, M., Hummer, G., & Kaila, V. R. I. (2020). Thermodynamic efficiency, reversibility, and degree of coupling in energy conservation by the mitochondrial respiratory chain. Communications Biology, 3(1), 1-12. doi: 10.1038/s42003-020-01260-7
Walter, H., Brooks III, D. E., & Fisher, E. F. (1995). Phase separation in cytoplasm due to macromolecular crowding, is the basis for microcompartmentalization. FEBS Letters, 361(2-3), 135-139. https://doi.org/10.1016/0014-5793(95)00173-3
Wang, X., Yang, L., Chen, Z., & Wang, Z. (2019). Sol–gel immobilized biomolecules: advantages, recent developments, applications and future perspectives. Journal of Materials Chemistry B, 7(45), 7021-7031. doi: 10.1039/C9TB01772B
Yang, L., Wang, X., & Li, Y. (2006). Crystal shape control manipulating supersaturation cooling crystalization. Crystal Growth & Design, 6(12), 2907-2915. doi: 10.1021/cg060363c
Zhang, S., Holmes, T., Lockshin, C., & Rich, A. (2005). Supramolecular assembly of extracellular matrix glycoproteins for synthetic biomaterials. Biomaterials, 26(30), 7586-7594. DOI: 10.1016/j.biomaterials.2005.05.049.
Zellmer, G. F., Schmidt, M. W., & Arculus, R. J. (2015). Volatiles in subduction zone magmatism. Evolution and Eruption of Arc Magmas. Geological Society of London. Special Publications, 410, 1-17. doi: 10.1144/SP410.7