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Proteomics, Holm Oak (Quercus ilex L.) and Other Recalcitrant and Orphan Forest Tree Species: How do They See Each Other?
Int J Mol Sci. 2019 Feb 06; 20(3)IJ

Abstract

Proteomics has had a big impact on plant biology, considered as a valuable tool for several forest species, such as Quercus, Pines, Poplars, and Eucalyptus. This review assesses the potential and limitations of the proteomics approaches and is focused on Quercus ilex as a model species and other forest tree species. Proteomics has been used with Q. ilex since 2003 with the main aim of examining natural variability, developmental processes, and responses to biotic and abiotic stresses as in other species of the genus Quercus or Pinus. As with the progress in techniques in proteomics in other plant species, the research in Q. ilex moved from 2-DE based strategy to the latest gel-free shotgun workflows. Experimental design, protein extraction, mass spectrometric analysis, confidence levels of qualitative and quantitative proteomics data, and their interpretation are a true challenge with relation to forest tree species due to their extreme orphan and recalcitrant (non-orthodox) nature. Implementing a systems biology approach, it is time to validate proteomics data using complementary techniques and integrate it with the -omics and classical approaches. The full potential of the protein field in plant research is quite far from being entirely exploited. However, despite the methodological limitations present in proteomics, there is no doubt that this discipline has contributed to deeper knowledge of plant biology and, currently, is increasingly employed for translational purposes.

Authors+Show Affiliations

Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain. b52resam@uco.es.Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain. bb2casam@uco.es.Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain. g82salur@uco.es.Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain. b12gusav@uco.es.Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain. n12lohic@uco.es.Departamento de Fitoquímica, Dirección de Investigación de la Facultad de Ciencias Químicas de la Universidad Nacional de Asunción, Asunción 1001-1925, Paraguay. mromero@rec.una.py.Department of Chemical and Biological Science, Biomedicine Science Institute, Autonomous University of Ciudad Juárez, Anillo Envolvente del Pronaf y Estocolmo s/n, Ciudad Juarez 32310, Mexico. jose.valero@uacj.mx.Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain. sghaierbesma@yahoo.fr.Plant Molecular Biology Department, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl 21, 1113 Sofia, Bulgaria. lsimova@mail.bg.Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain. sira@biognosys.com.Department of Vascular Biology and Inflammation (BVI), Spanish National Centre for Cardiovascular Research, Melchor Fernández Almagro 3, 28029 Madrid, Spain. inmaculada.jorge@cnic.es.Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain. isa.m.goga@gmail.com.Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain. mepv33@gmail.com.Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain. carvalho.kmll@gmail.com.Laboratorio de Biología, Instituto Tecnológico de Santo Domingo, República Dominicana. luisrod95@gmail.com.Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain. bb2maala@uco.es.Department of Organisms and Systems Biology and University Institute of Biotechnology (IUBA), University of Oviedo, Santiago Gascón Building, 2nd Floor (Office 2.9), 33006 Oviedo, Spain. valledorluis@uniovi.es.Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain. bf1jonoj@uco.es.

Pub Type(s)

Journal Article
Review

Language

eng

PubMed ID

30736277

Citation

Rey, María-Dolores, et al. "Proteomics, Holm Oak (Quercus Ilex L.) and Other Recalcitrant and Orphan Forest Tree Species: How Do They See Each Other?" International Journal of Molecular Sciences, vol. 20, no. 3, 2019.
Rey MD, Castillejo MÁ, Sánchez-Lucas R, et al. Proteomics, Holm Oak (Quercus ilex L.) and Other Recalcitrant and Orphan Forest Tree Species: How do They See Each Other? Int J Mol Sci. 2019;20(3).
Rey, M. D., Castillejo, M. Á., Sánchez-Lucas, R., Guerrero-Sanchez, V. M., López-Hidalgo, C., Romero-Rodríguez, C., Valero-Galván, J., Sghaier-Hammami, B., Simova-Stoilova, L., Echevarría-Zomeño, S., Jorge, I., Gómez-Gálvez, I., Papa, M. E., Carvalho, K., Rodríguez de Francisco, L. E., Maldonado-Alconada, A. M., Valledor, L., & Jorrín-Novo, J. V. (2019). Proteomics, Holm Oak (Quercus ilex L.) and Other Recalcitrant and Orphan Forest Tree Species: How do They See Each Other? International Journal of Molecular Sciences, 20(3). https://doi.org/10.3390/ijms20030692
Rey MD, et al. Proteomics, Holm Oak (Quercus Ilex L.) and Other Recalcitrant and Orphan Forest Tree Species: How Do They See Each Other. Int J Mol Sci. 2019 Feb 6;20(3) PubMed PMID: 30736277.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Proteomics, Holm Oak (Quercus ilex L.) and Other Recalcitrant and Orphan Forest Tree Species: How do They See Each Other? AU - Rey,María-Dolores, AU - Castillejo,María Ángeles, AU - Sánchez-Lucas,Rosa, AU - Guerrero-Sanchez,Victor M, AU - López-Hidalgo,Cristina, AU - Romero-Rodríguez,Cristina, AU - Valero-Galván,José, AU - Sghaier-Hammami,Besma, AU - Simova-Stoilova,Lyudmila, AU - Echevarría-Zomeño,Sira, AU - Jorge,Inmaculada, AU - Gómez-Gálvez,Isabel, AU - Papa,María Eugenia, AU - Carvalho,Kamilla, AU - Rodríguez de Francisco,Luis E, AU - Maldonado-Alconada,Ana María, AU - Valledor,Luis, AU - Jorrín-Novo,Jesús V, Y1 - 2019/02/06/ PY - 2019/01/10/received PY - 2019/01/28/revised PY - 2019/01/30/accepted PY - 2019/2/10/entrez PY - 2019/2/10/pubmed PY - 2019/5/30/medline KW - 2-DE proteomics KW - Quercus ilex KW - holm oak KW - non-orthodox seed KW - population variability KW - shotgun proteomics KW - stresses responses JF - International journal of molecular sciences JO - Int J Mol Sci VL - 20 IS - 3 N2 - Proteomics has had a big impact on plant biology, considered as a valuable tool for several forest species, such as Quercus, Pines, Poplars, and Eucalyptus. This review assesses the potential and limitations of the proteomics approaches and is focused on Quercus ilex as a model species and other forest tree species. Proteomics has been used with Q. ilex since 2003 with the main aim of examining natural variability, developmental processes, and responses to biotic and abiotic stresses as in other species of the genus Quercus or Pinus. As with the progress in techniques in proteomics in other plant species, the research in Q. ilex moved from 2-DE based strategy to the latest gel-free shotgun workflows. Experimental design, protein extraction, mass spectrometric analysis, confidence levels of qualitative and quantitative proteomics data, and their interpretation are a true challenge with relation to forest tree species due to their extreme orphan and recalcitrant (non-orthodox) nature. Implementing a systems biology approach, it is time to validate proteomics data using complementary techniques and integrate it with the -omics and classical approaches. The full potential of the protein field in plant research is quite far from being entirely exploited. However, despite the methodological limitations present in proteomics, there is no doubt that this discipline has contributed to deeper knowledge of plant biology and, currently, is increasingly employed for translational purposes. SN - 1422-0067 UR - https://www.unboundmedicine.com/medline/citation/30736277/Proteomics_Holm_Oak__Quercus_ilex_L___and_Other_Recalcitrant_and_Orphan_Forest_Tree_Species:_How_do_They_See_Each_Other L2 - http://www.mdpi.com/resolver?pii=ijms20030692 DB - PRIME DP - Unbound Medicine ER -