Proteomics, Holm Oak (<i>Quercus ilex L.</i>) and Other Recalcitrant and Orphan Forest Tree Species: How do They See Each Other?
Proteomics has had a big impact on plant biology, considered as a valuable tool for several forest species, such as <i>Quercus</i>, <i>Pines</i>, <i>Poplars</i>, and <i>Eucalyptus</i>. This review assesses the potential and limitations of the proteomic...
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| Format: | Article |
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MDPI AG
2019-02-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/20/3/692 |
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| author | María-Dolores Rey María Ángeles Castillejo Rosa Sánchez-Lucas Victor M. Guerrero-Sanchez Cristina López-Hidalgo Cristina Romero-Rodríguez José Valero-Galván Besma Sghaier-Hammami Lyudmila Simova-Stoilova Sira Echevarría-Zomeño Inmaculada Jorge Isabel Gómez-Gálvez María Eugenia Papa Kamilla Carvalho Luis E. Rodríguez de Francisco Ana María Maldonado-Alconada Luis Valledor Jesús V. Jorrín-Novo |
| author_facet | María-Dolores Rey María Ángeles Castillejo Rosa Sánchez-Lucas Victor M. Guerrero-Sanchez Cristina López-Hidalgo Cristina Romero-Rodríguez José Valero-Galván Besma Sghaier-Hammami Lyudmila Simova-Stoilova Sira Echevarría-Zomeño Inmaculada Jorge Isabel Gómez-Gálvez María Eugenia Papa Kamilla Carvalho Luis E. Rodríguez de Francisco Ana María Maldonado-Alconada Luis Valledor Jesús V. Jorrín-Novo |
| author_sort | María-Dolores Rey |
| collection | DOAJ |
| description | Proteomics has had a big impact on plant biology, considered as a valuable tool for several forest species, such as <i>Quercus</i>, <i>Pines</i>, <i>Poplars</i>, and <i>Eucalyptus</i>. This review assesses the potential and limitations of the proteomics approaches and is focused on <i>Quercus ilex</i> as a model species and other forest tree species. Proteomics has been used with <i>Q. ilex</i> 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 <i>Quercus</i> or <i>Pinus</i>. As with the progress in techniques in proteomics in other plant species, the research in <i>Q. ilex</i> 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. |
| first_indexed | 2024-04-13T06:02:24Z |
| format | Article |
| id | doaj.art-71968c84ae7544998cd69f7da94558b6 |
| institution | Directory Open Access Journal |
| issn | 1422-0067 |
| language | English |
| last_indexed | 2024-04-13T06:02:24Z |
| publishDate | 2019-02-01 |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-71968c84ae7544998cd69f7da94558b62022-12-22T02:59:24ZengMDPI AGInternational Journal of Molecular Sciences1422-00672019-02-0120369210.3390/ijms20030692ijms20030692Proteomics, Holm Oak (<i>Quercus ilex L.</i>) and Other Recalcitrant and Orphan Forest Tree Species: How do They See Each Other?María-Dolores Rey0María Ángeles Castillejo1Rosa Sánchez-Lucas2Victor M. Guerrero-Sanchez3Cristina López-Hidalgo4Cristina Romero-Rodríguez5José Valero-Galván6Besma Sghaier-Hammami7Lyudmila Simova-Stoilova8Sira Echevarría-Zomeño9Inmaculada Jorge10Isabel Gómez-Gálvez11María Eugenia Papa12Kamilla Carvalho13Luis E. Rodríguez de Francisco14Ana María Maldonado-Alconada15Luis Valledor16Jesús V. Jorrín-Novo17Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, SpainDepartment of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, SpainDepartment of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, SpainDepartment of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, SpainDepartment of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, SpainDepartamento de Fitoquímica, Dirección de Investigación de la Facultad de Ciencias Químicas de la Universidad Nacional de Asunción, Asunción 1001-1925, ParaguayDepartment of Chemical and Biological Science, Biomedicine Science Institute, Autonomous University of Ciudad Juárez, Anillo Envolvente del Pronaf y Estocolmo s/n, Ciudad Juarez 32310, MexicoDepartment of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, SpainPlant Molecular Biology Department, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl 21, 1113 Sofia, BulgariaDepartment of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, SpainDepartment of Vascular Biology and Inflammation (BVI), Spanish National Centre for Cardiovascular Research, Melchor Fernández Almagro 3, 28029 Madrid, SpainDepartment of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, SpainDepartment of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, SpainDepartment of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, SpainLaboratorio de Biología, Instituto Tecnológico de Santo Domingo, República DominicanaDepartment of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, SpainDepartment of Organisms and Systems Biology and University Institute of Biotechnology (IUBA), University of Oviedo, Santiago Gascón Building, 2nd Floor (Office 2.9), 33006 Oviedo, SpainDepartment of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, SpainProteomics has had a big impact on plant biology, considered as a valuable tool for several forest species, such as <i>Quercus</i>, <i>Pines</i>, <i>Poplars</i>, and <i>Eucalyptus</i>. This review assesses the potential and limitations of the proteomics approaches and is focused on <i>Quercus ilex</i> as a model species and other forest tree species. Proteomics has been used with <i>Q. ilex</i> 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 <i>Quercus</i> or <i>Pinus</i>. As with the progress in techniques in proteomics in other plant species, the research in <i>Q. ilex</i> 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.https://www.mdpi.com/1422-0067/20/3/692holm oak<i>Quercus ilex</i>2-DE proteomicsshotgun proteomicsnon-orthodox seedpopulation variabilitystresses responses |
| spellingShingle | María-Dolores Rey María Ángeles Castillejo Rosa Sánchez-Lucas Victor M. Guerrero-Sanchez Cristina López-Hidalgo Cristina Romero-Rodríguez José Valero-Galván Besma Sghaier-Hammami Lyudmila Simova-Stoilova Sira Echevarría-Zomeño Inmaculada Jorge Isabel Gómez-Gálvez María Eugenia Papa Kamilla Carvalho Luis E. Rodríguez de Francisco Ana María Maldonado-Alconada Luis Valledor Jesús V. Jorrín-Novo Proteomics, Holm Oak (<i>Quercus ilex L.</i>) and Other Recalcitrant and Orphan Forest Tree Species: How do They See Each Other? International Journal of Molecular Sciences holm oak <i>Quercus ilex</i> 2-DE proteomics shotgun proteomics non-orthodox seed population variability stresses responses |
| title | Proteomics, Holm Oak (<i>Quercus ilex L.</i>) and Other Recalcitrant and Orphan Forest Tree Species: How do They See Each Other? |
| title_full | Proteomics, Holm Oak (<i>Quercus ilex L.</i>) and Other Recalcitrant and Orphan Forest Tree Species: How do They See Each Other? |
| title_fullStr | Proteomics, Holm Oak (<i>Quercus ilex L.</i>) and Other Recalcitrant and Orphan Forest Tree Species: How do They See Each Other? |
| title_full_unstemmed | Proteomics, Holm Oak (<i>Quercus ilex L.</i>) and Other Recalcitrant and Orphan Forest Tree Species: How do They See Each Other? |
| title_short | Proteomics, Holm Oak (<i>Quercus ilex L.</i>) and Other Recalcitrant and Orphan Forest Tree Species: How do They See Each Other? |
| title_sort | proteomics holm oak i quercus ilex l i and other recalcitrant and orphan forest tree species how do they see each other |
| topic | holm oak <i>Quercus ilex</i> 2-DE proteomics shotgun proteomics non-orthodox seed population variability stresses responses |
| url | https://www.mdpi.com/1422-0067/20/3/692 |
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