• Repositorio Institucional Universidad de Pamplona
  • Tesis de maestría y doctorado
  • Facultad de Ciencias Básicas
  • Maestría en Química
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    dc.contributor.authorRojas Diego, Ándres.-
    dc.date.accessioned2025-05-15T16:15:58Z-
    dc.date.available2022-
    dc.date.available2025-05-15T16:15:58Z-
    dc.date.issued2022-
    dc.identifier.citationRojas Diego, A. (2022). Minería de datos del residuo Terminal-N y análisis del tiempo de vida de las Enzimas presentes en Proteomas de referencia (Escherichia coli, Nicotiana tabacum, Oryctolagus cuniculus, Saccharomyces cerevisiae y Virus inmunodeficiencia humana (VIH-1)) [Trabajo de Grado Maestría, Universidad de Pamplona]. Repositorio Hulago Universidad de Pamplona. http://repositoriodspace.unipamplona.edu.co/jspui/handle/20.500.12744/9505es_CO
    dc.identifier.urihttp://repositoriodspace.unipamplona.edu.co/jspui/handle/20.500.12744/9505-
    dc.descriptionLa regla del Terminal-N indica que el tiempo de vida de las proteínas está determinado por su residuo aminoacídico Terminal-N. Estudiar esta regla experimentalmente, in vivo, ha sido una tarea muy compleja y, por ende, el número de proteínas en las que se ha estudiado es muy pequeño en comparación con el índice de proteínas que pueden ser expresadas por un genoma, el proteoma. En esta tesis de maestría se analizó el efecto estabilizador o desestabilizador del terminal-N en el tiempo de vida de las enzimas pertenecientes a los proteomas de los organismos Oryctolagus cuniculus, Nicotiana tabacum, Saccharomyces cerevisiae, Escherichia coli y del virus de inmunodeficiencia humana (VIH-1). Además, se identificaron las relaciones entre el terminal-N de las enzimas, las rutas metabólicas a las que pertenecen y la superfamilia de plegamiento proteico. Este estudio se enfocó en las enzimas con estatus de revisada pertenecientes a los proteomas de estudio y reportadas en la base de datos Uniprot. Las tendencias se identificaron utilizando las herramientas computacionales Power BI, Power Query y la hoja de cálculo de Excel y las relaciones se determinaron por medio del análisis de agrupamientos con el programa Cytoscape. Los resultados permitieron concluir que las oxidorreductasas (EC:1), transferasa (EC:2) e hidrolasas (EC:3) son las clases de enzimas con mayor número de proteínas con tiempos de vida estables, con mayor asignación de superfamilia y las que participan en un mayor número de rutas metabólicas. Además, al cruzar la información obtenida de cada uno de los proteomas, se encontró que la mayoría de las enzimas de los proteomas de Escherichia coli, Saccharomyces cerevisiae y Nicotiana tabacum pertenecen a la superfamilia proteica SSF52540 (Hidrolasas de trifosfato de nucleósido que contienen bucles P), mientras que la mayoría de las enzimas de del proteoma Oryctolagus cuniculus tienden a pertenecer a la superfamilia proteica SSF56112 (similar a la proteína quinasa (PK-like)).es_CO
    dc.description.abstractEl autor no proporciona la información sobre este ítem.es_CO
    dc.format.extent137es_CO
    dc.format.mimetypeapplication/pdfes_CO
    dc.language.isoeses_CO
    dc.publisherUniversidad de Pamplona – Facultad de Ciencias Básicas.es_CO
    dc.subjectEl autor no proporciona la información sobre este ítem.es_CO
    dc.titleMinería de datos del residuo Terminal-N y análisis del tiempo de vida de las Enzimas presentes en Proteomas de referencia (Escherichia coli, Nicotiana tabacum, Oryctolagus cuniculus, Saccharomyces cerevisiae y Virus inmunodeficiencia humana (VIH-1)).es_CO
    dc.typehttp://purl.org/coar/resource_type/c_bdcces_CO
    dc.date.accepted2022-
    dc.relation.referencesAlvarez-Castelao, B., & Schuman, E. M. (2015). The regulation of synaptic protein turnover. Journal of Biological Chemistry, 290(48), 28623–28630. https://doi.org/10.1074/jbc.R115.657130.es_CO
    dc.relation.referencesBachmair, A., Finley, D., & Varshavsky, A. (1986). In Vivo Half-Life of a Protein Is a Function of Its Amino-Terminal Residue, 523(1985). https://doi.org/10.1126/science.3018930.es_CO
    dc.relation.referencesBairoch, A. (2000). The ENZYME database in 2000. Nucleic Acids Research, 28(1), 304– 305. https://doi.org/10.1093/nar/28.1.304.es_CO
    dc.relation.referencesBalaji, S. (2021). The transferred translocases: An old wine in a new bottle. Biotechnology and Applied Biochemistry. https://doi.org/10.1002/BAB.2230.es_CO
    dc.relation.referencesBasisty, N., Holtz, A., & Schilling, B. (2019). Accumulation of “Old Proteins” and the Critical Need for MS‐based Protein Turnover Measurements in Aging and Longevity. Proteomics, 1800403, 1800403. https://doi.org/10.1002/pmic.201800403.es_CO
    dc.relation.referencesBalaji, S. (2021). The transferred translocases: An old wine in a new bottle. Biotechnology and Applied Biochemistry. https://doi.org/10.1002/BAB.2230.es_CO
    dc.relation.referencesBateman, A., Martin, M. J., Orchard, S., Magrane, M., Agivetova, R., Ahmad, S., Alpi, E., Bowler-Barnett, E. H., Britto, R., Bursteinas, B., Bye-A-Jee, H., Coetzee, R., Cukura, A., da Silva, A., Denny, P., Dogan, T., Ebenezer, T. G., Fan, J., Castro, L. G., … Teodoro, D. (2021). UniProt: the universal protein knowledgebase in 2021. Nucleic Acids Research, 49(D1), D480–D489. https://doi.org/10.1093/NAR/GKAA1100.es_CO
    dc.relation.referencesBozaykut, P., Ozer, N. K., & Karademir, B. (2014). Regulation of protein turnover by heat shock proteins. Free Radical Biology and Medicine, 77, 195–209. https://doi.org/10.1016/j.freeradbiomed.2014.08.012.es_CO
    dc.relation.referencesCheignon, C., Tomas, M., Bonnefont-Rousselot, D., Faller, P., Hureau, C., & Collin, F. (2018). Oxidative stress and the amyloid beta peptide in Alzheimer’s disease. Redox Biology, 14(October 2017), 450–464. https://doi.org/10.1016/j.redox.2017.10.014.es_CO
    dc.relation.referencesChen, S.-J., Wu, X., Wadas, B., Oh, J.-H., & Varshavsky, A. (2017). An N-end rule pathway that recognizes proline and destroys gluconeogenic enzymes. Science, 355(6323), eaal3655. https://doi.org/10.1126/science.aal3655.es_CO
    dc.relation.referencesCiechanover, A. (2005). Proteolysis: from the lysosome to ubiquitin and the proteasome. Nature Reviews Molecular Cell Biology, 6(1), 79–87. https://doi.org/10.1038/nrm1552.es_CO
    dc.relation.referencesCollins, G. A., & Goldberg, A. L. (2017). The Logic of the 26S Proteasome. Cell, 169(5), 792–806. https://doi.org/10.101 6/j.cell.2017.04.023.es_CO
    dc.relation.referencesDe Groot, R. J., Rumenapf, T., Kuhn, R. J., Strauss, E. G., & Strauss, J. H. (1991). Sindbis virus RNA polymerase is degraded by the N-end rule pathway. Proceedings of the National Academy of Sciences of the United States of America, 88(20), 8967–8971. https://doi.org/10.1073/pnas.88.20.8967.es_CO
    dc.relation.referencesDissmeyer, N. (2019). Conditional Protein Function via N-Degron Pathway–Mediated Proteostasis in Stress Physiology. Annual Review of Plant Biology, 70(1), 83–117. https://doi.org/10.1146/annurev-arplant-050718-095937.es_CO
    dc.relation.referencesDissmeyer, N., Rivas, S., & Graciet, E. (2018). Life and death of proteins after protease cleavage: protein degradation by the N-end rule pathway. New Phytologist, 218(3), 929– 935. https://doi.org/10.1111/nph.14619.es_CO
    dc.relation.referencesDohmen, J. (2015). Starting with a degron: N-terminal formyl-methionine of nascent bacterial proteins contributes to their proteolytic control. Microbial Cell, 2(10), 356– 359. https://doi.org/10.15698/mic2015.10.235.es_CO
    dc.relation.referencesDong, C., Zhang, H., Li, L., Tempel, W., Loppnau, P., & Min, J. (2018). Molecular basis of GID4-mediated recognition of degrons for the Pro/N-end rule pathway. Nature Chemical Biology, 14(5), 466–473. https://doi.org/10.1038/s41589-018-0036-1.es_CO
    dc.relation.referencesDonida, B., Jacques, C. E. D., Mescka, C. P., Rodrigues, D. G. B., Marchetti, D. P., Ribas, G., … Vargas, C. R. (2017). Oxidative damage and redox in Lysosomal Storage Disorders: Biochemical markers. Clinica Chimica Acta, 466, 46–53. https://doi.org/10.1016/j.cca.2017.01.007.es_CO
    dc.relation.referencesDougan, D. A., Micevski, D., & Truscott, K. N. (2012). The N-end rule pathway: From recognition by N-recognins, to destruction by AAA+proteases. Biochimica et Biophysica Acta - Molecular Cell Research, 1823(1), 83–91. https://doi.org/10.1016/j.bbamcr.2011.07.002.es_CO
    dc.relation.referencesDougan, D. A., Truscott, K. N., & Zeth, K. (2010). The bacterial N-end rule pathway: Expect the unexpected. Molecular Microbiology. Blackwell Publishing Ltd. https://doi.org/10.1111/j.1365-2958.2010.07120.x.es_CO
    dc.relation.referencesDougan, David A., & Varshavsky, A. (2018). Understanding the Pro/N-end rule pathway. Nature Chemical Biology, 14(5), 415–416. https://doi.org/10.1038/s41589-018-0045-0.es_CO
    dc.relation.referencesDownload Microsoft Power Query para Excel from Official Microsoft Download Center. (n.d.). Retrieved June 26, 2022, from https://www.microsoft.com/esco/download/details.aspx?id=39379.es_CO
    dc.relation.referencesEldeeb, M., & Fahlman, R. (2016). The-N-End Rule: The Beginning Determines the End. Protein & Peptide Letters, 23(4), 343–348. https://doi.org/10.2174/0929866523666160108115809.es_CO
    dc.relation.referencesGibbs, D. J., Lee, S. C., Md Isa, N., Gramuglia, S., Fukao, T., Bassel, G. W., … Holdsworth, M. J. (2011). Homeostatic response to hypoxia is regulated by the N-end rule pathway in plants. Nature, 479(7373), 415–418. https://doi.org/10.1038/nature10534.es_CO
    dc.relation.referencesGonda, D. K., Bachmair, A., Wunning, I., Tobias, J. W., Lane, W. S., & Varshavsky, A. (1989). Universality and stucture of the N-end rule. Journal of Biological Chemistry, 264(28), 16700–16712.es_CO
    dc.relation.referencesGough J., Karplus K., Hughey R., Chorhia C. Genome sequences using a library of hidden Markov models that represent all proteins of known structure. (2001). Journal of Molecular Biology, 903-919, 313(4). https://doi.org/10.1006/jmbi.2001.5080.es_CO
    dc.relation.referencesGraciet, E., Mesiti, F., & Wellmer, F. (2010). Structure and evolutionary conservation of the plant N-end rule pathway. The Plant Journal, 61(5), 741 –751. https://doi.org/10.1111/j.1365-313X.2009.04099.x.es_CO
    dc.relation.referencesGreer, J. B., Early, B. P., Durbin, K. R., Patrie, S. M., Thomas, P. M., Kelleher, N. L., LeDuc, R. D., & Fellers, R. T. (2022). ProSight Annotator: Complete control and customization of protein entries in UniProt XML files. PROTEOMICS, 22(11–12), 2100209. https://doi.org/10.1002/PMIC.202100209.es_CO
    dc.relation.referencesHanson, A. D., Henry, C. S., Fiehn, O., & de Crécy-Lagard, V. (2016). Metabolite Damage and Metabolite Damage Control in Plants. Annual Review of Plant Biology, 67(1), 131– 152. https://doi.org/10.1146/annurev-arplant-043015-111648.es_CO
    dc.relation.referencesHetzer, M. W., & Toyama, B. H. (2013). Protein homeostasis: live long, won’t prosper. Nature Reviews Molecular Cell Biology, 14(1), 55–61. https://doi.org/10.1016/j.biotechadv.2011.08.021.Secreted.es_CO
    dc.relation.referencesHu, R.-G., Sheng, J., Qi, X., Xu, Z., Takahashi, T. T., & Varshavsky, A. (2005). The N-end rule pathway as a nitric oxide sensor controlling the levels of multiple regulators. Nature, 437(7061), 981–986. https://doi.org/10.1038/nature04027.es_CO
    dc.relation.referencesIzard, J. W., & Kendall, D. A. (1994). Signal peptides: exquisitely designed transport promoters. Molecular Microbiology, 13(5), 765–773. https://doi.org/10.1111/j.1365- 2958.1994.tb00469.x.es_CO
    dc.relation.referencesKim, H.-K., Kim, R.-R., Oh, J.-H., Cho, H., Varshavsky, A., & Hwang, C.-S. (2014). The NTerminal Methionine of Cellular Proteins as a Degradation Signal. Cell, 156(1–2), 158– 169. https://doi.org/10.1016/j.cell.2013.11.031.es_CO
    dc.relation.referencesKim, J. M., & Hwang, C. S. (2014). Crosstalk between the Arg/N-end and Ac/N-end rule. Cell Cycle, 13(9), 1366–1367. https://doi.org/10.4161/cc.28751.es_CO
    dc.relation.referencesKim, J. M., Seok, O. H., Ju, S., Heo, J. E., Yeom, J., Kim, D. S., … Hwang, C. S. (2018). Formyl-methionine as an N-degron of a eukaryotic N-end rule pathway. Science, 362(6418), 6418 (1-28). https://doi.org/10.1126/science.aat0174.es_CO
    dc.relation.referencesKlionsky, D. J. (2005). The molecular machinery of autophagy: unanswered questions. Journal of Cell Science, 118(1), 7–18. https://doi.org/10.1242/jcs.01620.es_CO
    dc.relation.referencesKwon, Y. T., & Ciechanover, A. (2017). The Ubiquitin Code in the Ubiquitin-Proteasome System and Autophagy. Trends in Biochemical Sciences, 42(11), 873–886. https://doi.org/10.1016/j.tibs.2017.09.002.es_CO
    dc.relation.referencesLange, P. F., Huesgen, P. F., Nguyen, K., & Overall, C. M. (2014). Annotating N termini for the human proteome project: N termini and Nα-acetylation status differentiate stable cleaved protein species from degradation remnants in the human erythrocyte proteome. Journal of Proteome Research, 13(4), 2028–2044. https://doi.org/10.1021/pr401191w.es_CO
    dc.relation.referencesLi, L., Yan, G., & Zhang, X. (2019). A rapid and efficient method for N-termini analysis in short-lived proteins. Talanta, 204, 367–371. https://doi.org/10.1016/j.talanta.2019.06.025.es_CO
    dc.relation.referencesMartinez, A., Traverso, J. A., Valot, B., Ferro, M., Espagne, C., Ephritikhine, G., … Meinnel, T. (2008). Extent of N-terminal modifications in cytosolic proteins from eukaryotes. Proteomics, 8(14), 2809–2831. https://doi.org/10.1002/pmic.200701191.es_CO
    dc.relation.referencesMartoglio, B., & Dobberstein, B. (1998). Signal sequences: More than just greasy peptides. Trends in Cell Biology, 8(10), 410–415. https://doi.org/10.1016/S0962-8924(98)01360- 9 Mccaffrey, K., & Braakman, I. (2016). Protein quality control at the endoplasmic reticulum Protein folding at the endoplasmic reticulum Targeting and translocation. Essays in Biochemistry, 227–235. https://doi.org/10.1042/EBC20160003.es_CO
    dc.relation.referencesMészáros, B., Kumar, M., Gibson, T. J., Uyar, B., & Dosztányi, Z. (2017). Degrons in cancer. Science Signaling, 10(470), eaak9982. https://doi.org/10.1126/scisignal.aak9982.es_CO
    dc.relation.referencesMulder, L. C. F., & Muesing, M. A. (2000). Degradation of HIV-1 integrase by the N-end rule pathway. Journal of Biological Chemistry, 275(38), 29749–29753. https://doi.org/10.1074/jbc.M004670200.es_CO
    dc.relation.referencesNguyen, K. T., Mun, S. H., Lee, C. S., & Hwang, C. S. (2018). Control of protein degradation by N-terminal acetylation and the N-end rule pathway. Experimental and Molecular Medicine, 50(7), 1–8. https://doi.org/10.1038/s12276-018-0097-y.es_CO
    dc.relation.referencesOtasek, D., Morris, J. H., Bouças, J., Pico, A. R., & Demchak, B. (2019). Cytoscape Automation: Empowering workflow-based network analysis. Genome Biology, 20(1). https://doi.org/10.1186/S13059-019-1758-4.es_CO
    dc.relation.referencesOwji, H., Nezafat, N., Negahdaripour, M., Hajiebrahimi, A., & Ghasemi, Y. (2018). A comprehensive review of signal peptides: Structure, roles, and applications. European Journal of Cell Biology, 97(6), 422–441. https://doi.org/10.1016/j.ejcb.2018.06.003.es_CO
    dc.relation.referencesPiatkov, K., Vu, T., Hwang, C.-S., & Varshavsky, A. (2015). Formyl-methionine as a degradation signal at the N-termini of bacterial proteins. Microbial Cell, 2(10), 376– 393. https://doi.org/10.15698/mic2015.10.231.es_CO
    dc.relation.referencesPorto de Souza Vandenberghe, L., Karp, S. G., Binder Pagnoncelli, M. G., von Linsingen Tavares, M., Libardi Junior, N., Valladares Diestra, K., Viesser, J. A., & Soccol, C. R. (2020). Classification of enzymes and catalytic properties. Biomass, Biofuels, Biochemicals, 11–30. https://doi.org/10.1016/B978-0-12-819820-9.00002-8.es_CO
    dc.relation.referencesPower BI Desktop: informes interactivos | Microsoft Power BI. (n.d.). Retrieved June 26, 2022, from https://powerbi.microsoft.com/es-es/desktop/.es_CO
    dc.relation.referencesSaez, I., & Vilchez, D. (2014). The Mechanistic Links Between Proteasome Activity, Aging and Agerelated Diseases. Current Genomics, 15(1), 38–51. https://doi.org/10.2174/138920291501140306113344.es_CO
    dc.relation.referencesSchmidt, R., Zahn, R., Bukau, B., & Mogk, A. (2009). ClpS is the recognition component for Escherichia coli substrates of the N-end rule degradation pathway. Molecular Microbiology, 72(2), 506–517. https://doi.org/10.1111/j.1365-2958.2009.06666.x.es_CO
    dc.relation.referencesShannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., … Ideker, T. (2003). Cytoscape: A Software Environment for Integrated Model of Biomolecular Interaction Networks. Genome Research, 13(22), 2498–2504. https://doi.org/10.1101/gr.1239303.es_CO
    dc.relation.referencesSharpless, N. E., & Sherr, C. J. (2015). Forging a signature of in vivo senescence. Nature Reviews Cancer, 15(7), 397–408. https://doi.org/10.1038/nrc3960.es_CO
    dc.relation.referencesStriebel, F., Imkamp, F., Özcelik, D., & Weber-Ban, E. (2014). Pupylation as a signal for proteasomal degradation in bacteria. Biochimica et Biophysica Acta - Molecular Cell Research, 1843(1), 103–113. https://doi.org/10.1016/j.bbamcr.2013.03.022.es_CO
    dc.relation.referencesTamás, M. J., Fauvet, B., Christen, P., & Goloubinoff, P. (2018). Misfolding and aggregation of nascent proteins: a novel mode of toxic cadmium action in vivo. Current Genetics, 64(1), 177–181. https://doi.org/10.1007/s00294-017-0748-x.es_CO
    dc.relation.referencesTao, Z., Dong, B., Teng, Z., & Zhao, Y. (2020). The Classification of Enzymes by Deep Learning. IEEE Access, 8, 89802–89811. https://doi.org/10.1109/ACCESS.2020.2992468.es_CO
    dc.relation.referencesTasaki, T., Sriram, S. M., Park, K. S., & Kwon, Y. T. (2012). The N-End Rule Pathway. Annual Review of Biochemistry, 81(1), 261–289. https://doi.org/10.1146/annurevbiochem-051710-093308.es_CO
    dc.relation.referencesTasaki, T., Zakrzewska, A., Dudgeon, D. D., Jiang, Y., Lazo, J. S., & Kwon, Y. T. (2009). The substrate recognition domains of the N-end rule pathway. Journal of Biological Chemistry, 284(3), 1884–1895. https://doi.org/10.1074/jbc.M803641200.es_CO
    dc.relation.referencesTobias, J., Shrader, T., Rocap, G., & Varshavsky, A. (1991). The N-end rule in bacteria. Science, 254(5036), 1374–1377. https://doi.org/10.1126/science.1962196.es_CO
    dc.relation.referencesUbíeta, R., & Santiago, N. (1993). Degradacion de proteinas en Escherichia coli: papel de la estructura proteica. Biotecnologia Aplicada, 1(3).es_CO
    dc.relation.referencesVarshavsky, A. (1992). The N-end rule. Cell, 69(5), 725–735. https://doi.org/10.1016/0092- 8674(92)90285-K.es_CO
    dc.relation.referencesVarshavsky, A. (1997). The N-end rule pathway of protein degradation. Genes to Cells, 2(1), 13–28. https://doi.org/10.1046/j.1365-2443.1997.1020301.x.es_CO
    dc.relation.referencesVarshavsky, A. (2008). Discovery of Cellular Regulation by Protein Degradation, 283(50), 34469–34489. https://doi.org/10.1074/jbc.X800009200.es_CO
    dc.relation.referencesVarshavsky, A. (2011). The N-end rule pathway and regulation by proteolysis. Protein Science, 20(8), 1298–1345. https://doi.org/10.1002/pro.666.es_CO
    dc.relation.referencesVarshavsky, A. (2019). N-degron and C-degron pathways of protein degradation. Proceedings of the National Academy of Sciences, 116(2), 358–366. https://doi.org/10.1073/pnas.1816596116.es_CO
    dc.relation.referencesVittal, V., Stewart, M. D., Brzovic, P. S., & Klevit, R. E. (2015). Regulating the regulators: Recent revelations in the control of E3 ubiquitin ligases. Journal of Biological Chemistry, 290(35), 21244–21251. https://doi.org/10.1074/jbc.R115.675165.es_CO
    dc.relation.referencesWouters, E. F. M., & Baarends, E. M. (2006). ENERGY METABOLISM. Encyclopedia of Respiratory Medicine, Four-Volume Set, 86–90. https://doi.org/10.1016/B0-12- 370879-6/00126-5.es_CO
    dc.relation.referencesZeiler, E., List, A., Alte, F., Gersch, M., Wachtel, R., Poreba, M., … Sieber, S. A. (2013). Structural and functional insights into caseinolytic proteases reveal an unprecedented regulation principle of their catalytic triad. Proceedings of the National Academy of Sciences of the United States of America, 110(28), 11302–11307. https://doi.org/10.1073/pnas.1219125110.es_CO
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