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Rey MD, Castillejo MÁ, Sánchez-Lucas R, Guerrero-Sanchez VM, López-Hidalgo C, Romero-Rodríguez C, Valero-Galván J, Sghaier-Hammami B, Simova-Stoilova L, Echevarría-Zomeño S, Jorge I, Gómez-Gálvez I, Papa ME, Carvalho K, Rodríguez de Francisco LE, Maldonado-Alconada AM, Valledor L, Jorrín-Novo JV. 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:ijms20030692. [PMID: 30736277 PMCID: PMC6386906 DOI: 10.3390/ijms20030692] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 01/28/2019] [Accepted: 01/30/2019] [Indexed: 02/07/2023] Open
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.
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Affiliation(s)
- María-Dolores Rey
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
| | - María Ángeles Castillejo
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
| | - Rosa Sánchez-Lucas
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
| | - Victor M Guerrero-Sanchez
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
| | - Cristina López-Hidalgo
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
| | - Cristina Romero-Rodríguez
- Departamento de Fitoquímica, Dirección de Investigación de la Facultad de Ciencias Químicas de la Universidad Nacional de Asunción, Asunción 1001-1925, Paraguay.
| | - José Valero-Galván
- 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.
| | - Besma Sghaier-Hammami
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
| | - Lyudmila Simova-Stoilova
- Plant Molecular Biology Department, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl 21, 1113 Sofia, Bulgaria.
| | - Sira Echevarría-Zomeño
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
| | - Inmaculada Jorge
- Department of Vascular Biology and Inflammation (BVI), Spanish National Centre for Cardiovascular Research, Melchor Fernández Almagro 3, 28029 Madrid, Spain.
| | - Isabel Gómez-Gálvez
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
| | - María Eugenia Papa
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
| | - Kamilla Carvalho
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
| | | | - Ana María Maldonado-Alconada
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
| | - Luis Valledor
- 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.
| | - Jesús V Jorrín-Novo
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
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Echevarría-Zomeño S, Fernández-Calvino L, Castro-Sanz AB, López JA, Vázquez J, Castellano MM. Dissecting the proteome dynamics of the early heat stress response leading to plant survival or death in Arabidopsis. Plant Cell Environ 2016; 39:1264-78. [PMID: 26580143 DOI: 10.1111/pce.12664] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/14/2015] [Accepted: 10/16/2015] [Indexed: 05/18/2023]
Abstract
In many plant species, an exposure to a sublethal temperature triggers an adaptative response called acclimation. This response involves an extensive molecular reprogramming that allows the plant to further survive to an otherwise lethal increase of temperature. A related response is also launched under an abrupt and lethal heat stress that, in this case, is unable to successfully promote thermotolerance and therefore ends up in plant death. Although these molecular programmes are expected to have common players, the overlapping degree and the specific regulators of each process are currently unknown. We have carried out a high-throughput comparative proteomics analysis during acclimation and during the early stages of the plant response to a severe heat stress that lead Arabidopsis seedlings either to survival or death. This analysis dissects these responses, unravels the common players and identifies the specific proteins associated with these different fates. Thermotolerance assays of mutants in genes with an uncharacterized role in heat stress demonstrate the relevance of this study to uncover both positive and negative heat regulators and pinpoint a pivotal role of JR1 and BAG6 in heat tolerance.
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Affiliation(s)
- Sira Echevarría-Zomeño
- Centro de Biotecnología y Genómica de Plantas, INIA-UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | | | - Ana B Castro-Sanz
- Centro de Biotecnología y Genómica de Plantas, INIA-UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Juan Antonio López
- Centro Nacional de Investigaciones Cardiovasculares, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Jesús Vázquez
- Centro Nacional de Investigaciones Cardiovasculares, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - M Mar Castellano
- Centro de Biotecnología y Genómica de Plantas, INIA-UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
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Echevarría-Zomeño S, Yángüez E, Fernández-Bautista N, Castro-Sanz AB, Ferrando A, Castellano MM. Regulation of Translation Initiation under Biotic and Abiotic Stresses. Int J Mol Sci 2013; 14:4670-83. [PMID: 23443165 PMCID: PMC3634475 DOI: 10.3390/ijms14034670] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 02/20/2013] [Accepted: 02/20/2013] [Indexed: 01/12/2023] Open
Abstract
Plants have developed versatile strategies to deal with the great variety of challenging conditions they are exposed to. Among them, the regulation of translation is a common target to finely modulate gene expression both under biotic and abiotic stress situations. Upon environmental challenges, translation is regulated to reduce the consumption of energy and to selectively synthesize proteins involved in the proper establishment of the tolerance response. In the case of viral infections, the situation is more complex, as viruses have evolved unconventional mechanisms to regulate translation in order to ensure the production of the viral encoded proteins using the plant machinery. Although the final purpose is different, in some cases, both plants and viruses share common mechanisms to modulate translation. In others, the mechanisms leading to the control of translation are viral- or stress-specific. In this paper, we review the different mechanisms involved in the regulation of translation initiation under virus infection and under environmental stress in plants. In addition, we describe the main features within the viral RNAs and the cellular mRNAs that promote their selective translation in plants undergoing biotic and abiotic stress situations.
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Affiliation(s)
- Sira Echevarría-Zomeño
- Centro de Biotecnología y Genómica de Plantas, INIA-UPM, Campus de Montegancedo, 28223 Madrid, Spain; E-Mails: (S.E.-Z.); (E.Y.); (N.F.-B.); (A.C.-S.)
| | - Emilio Yángüez
- Centro de Biotecnología y Genómica de Plantas, INIA-UPM, Campus de Montegancedo, 28223 Madrid, Spain; E-Mails: (S.E.-Z.); (E.Y.); (N.F.-B.); (A.C.-S.)
| | - Nuria Fernández-Bautista
- Centro de Biotecnología y Genómica de Plantas, INIA-UPM, Campus de Montegancedo, 28223 Madrid, Spain; E-Mails: (S.E.-Z.); (E.Y.); (N.F.-B.); (A.C.-S.)
| | - Ana B. Castro-Sanz
- Centro de Biotecnología y Genómica de Plantas, INIA-UPM, Campus de Montegancedo, 28223 Madrid, Spain; E-Mails: (S.E.-Z.); (E.Y.); (N.F.-B.); (A.C.-S.)
| | - Alejandro Ferrando
- Instituto de Biología Molecular y Celular de Plantas CSIC-Universidad Politécnica de Valencia, Valencia, Spain; E-Mail:
| | - M. Mar Castellano
- Centro de Biotecnología y Genómica de Plantas, INIA-UPM, Campus de Montegancedo, 28223 Madrid, Spain; E-Mails: (S.E.-Z.); (E.Y.); (N.F.-B.); (A.C.-S.)
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Jorrín-Novo JV, Maldonado AM, Echevarría-Zomeño S, Valledor L, Castillejo MA, Curto M, Valero J, Sghaier B, Donoso G, Redondo I. Plant proteomics update (2007–2008): Second-generation proteomic techniques, an appropriate experimental design, and data analysis to fulfill MIAPE standards, increase plant proteome coverage and expand biological knowledge. J Proteomics 2009; 72:285-314. [DOI: 10.1016/j.jprot.2009.01.026] [Citation(s) in RCA: 174] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Echevarría-Zomeño S, Ariza D, Jorge I, Lenz C, Del Campo A, Jorrín JV, Navarro RM. Changes in the protein profile of Quercus ilex leaves in response to drought stress and recovery. J Plant Physiol 2009; 166:233-45. [PMID: 18778874 DOI: 10.1016/j.jplph.2008.05.008] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2008] [Revised: 05/23/2008] [Accepted: 05/26/2008] [Indexed: 05/22/2023]
Abstract
To characterize the molecular response of holm oak to drought stress and its capacity to recover 9-month-old Quercus ilex seedlings were subjected to three treatments for a 14-d period: (i) continuous watering to field capacity (control plants, W), (ii) no irrigation (drought treatment, D), and (iii) no irrigation for 7d followed by a watering period of 7d (recovery treatment, R). In drought plants, leaf water potential decreased from -0.72 (day 0) to -0.99MPa (day 7), and -1.50MPa (day 14). Shoot relative water content decreased from 49.3% (day 0) to 47.7% (day 7) and 40.8% (day 14). Photosystem II quantum yield decreased from 0.80 (day 0) to 0.72 (day 7) and 0.73 (day 14). Plants subjected to water withholding for 7d reached, after a 7-d rewatering period, values similar to those of continuously irrigated control plants. Changes in the leaf protein pattern in response to drought and recovery treatments were analyzed by using a proteomic approach. Twenty-three different spots were observed when comparing the two-dimensional electrophoresis profile of control to both drought and recovered plants. From these, 14 proteins were identified from tryptic peptides tandem mass spectra by using the new Paragon algorithm present in the ProteinPilot software. The proteins identified belong to the photosynthesis, carbohydrate and nitrogen metabolism, and stress-related protein functional categories.
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Affiliation(s)
- Sira Echevarría-Zomeño
- Plant and Agricultural Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba, Córdoba, Spain
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Echevarría-Zomeño S, Pérez-de-Luque A, Jorrín J, Maldonado AM. Pre-haustorial resistance to broomrape (Orobanche cumana) in sunflower (Helianthus annuus): cytochemical studies. J Exp Bot 2006; 57:4189-200. [PMID: 17095573 DOI: 10.1093/jxb/erl195] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Sunflower broomrape (Orobanche cumana Wallr.) is a root holoparasitic angiosperm considered as one of the major constraints for sunflower production in Mediterranean areas. Breeding for resistance is regarded as the most effective, feasible, and environmentally friendly solution to control this parasite. However, the existing sources of genetic resistance are defeated by the continuous emergence of new more virulent races of the parasite. In this work, the interaction between sunflower and O. cumana has been analysed in order to gain insights into the mechanisms involved in resistance. Two sunflower genotypes were selected showing different behaviour against the new race F of O. cumana, HE-39998 (susceptible) and HE-39999 (resistant), and both compatible and incompatible interactions were compared. Pot and Petri dish bioassays revealed that only HE-39998 plants were severely affected, supporting a high number of successfully established broomrapes to mature flowering, whereas in HE-39999 root tubercles were never observed, resistance being associated with browning symptoms of both parasite and host tissues. Histological aspects of the resistance were further investigated. Suberization and protein cross-linking at the cell wall were seen in the resistant sunflower cells in contact with the parasite, preventing parasite penetration and connection to the host vascular system. In addition, fluorescence and confocal laser microscopy (CLM) observations revealed accumulation of phenolic compounds during the incompatible reaction, which is in agreement with these metabolites playing a defensive role during H. annuus-O. cumana interaction.
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Affiliation(s)
- Sira Echevarría-Zomeño
- Agricultural and Plant Biochemistry Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba, Campus de Rabanales, Edificio Severo Ochoa, E-14071 Córdoba, Spain
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