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Article

Proteomics Data Analysis for the Identification of Proteins and Derived Proteotypic Peptides of Potential Use as Putative Drought Tolerance Markers for Quercus ilex

1
Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, Spain
2
Agricultural Microbiology, Faculty of Agricultural Science, National University of Cordoba, CONICET, 5001 Cordoba, Argentina
3
Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Althanstrasse 14, A-1090 Vienna, Austria
*
Author to whom correspondence should be addressed.
Academic Editor: Frank M. You
Int. J. Mol. Sci. 2021, 22(6), 3191; https://doi.org/10.3390/ijms22063191
Received: 13 February 2021 / Revised: 12 March 2021 / Accepted: 18 March 2021 / Published: 21 March 2021
(This article belongs to the Special Issue Plant Proteomic Research 4.0)
Drought is one of the main causes of mortality in holm oak (Quercus ilex) seedlings used in reforestation programs. Although this species shows high adaptability to the extreme climate conditions prevailing in Southern Spain, its intrinsic genetic variability may play a role in the differential response of some populations and individuals. The aim of this work was to identify proteins and derived proteotypic peptides potentially useful as putative markers for drought tolerance in holm oak by using a targeted post-acquisition proteomics approach. For this purpose, we used a set of proteins identified by shotgun (LC-MSMS) analysis in a drought experiment on Q. ilex seedlings from four different provenances (viz. the Andalusian provinces Granada, Huelva, Cadiz and Seville). A double strategy involving the quantification of proteins and target peptides by shotgun analysis and post-acquisition data analysis based on proteotypic peptides was used. To this end, an initial list of proteotypic peptides from proteins highly represented under drought conditions was compiled that was used in combination with the raw files from the shotgun experiment to quantify the relative abundance of the fragment’s ion peaks with the software Skyline. The most abundant peptides under drought conditions in at least two populations were selected as putative markers of drought tolerance. A total of 30 proteins and 46 derived peptides belonging to the redox, stress-related, synthesis,-folding and degradation, and primary and secondary metabolism functional groups were thus identified. Two proteins (viz., subtilisin and chaperone GrpE protein) were found at increased levels in three populations, which make them especially interesting for validation drought tolerance markers in subsequent experiments. View Full-Text
Keywords: peptide markers; Quercus ilex; drought tolerance; targeted post-acquisition proteomics peptide markers; Quercus ilex; drought tolerance; targeted post-acquisition proteomics
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MDPI and ACS Style

San-Eufrasio, B.; Bigatton, E.D.; Guerrero-Sánchez, V.M.; Chaturvedi, P.; Jorrín-Novo, J.V.; Rey, M.-D.; Castillejo, M.Á. Proteomics Data Analysis for the Identification of Proteins and Derived Proteotypic Peptides of Potential Use as Putative Drought Tolerance Markers for Quercus ilex. Int. J. Mol. Sci. 2021, 22, 3191. https://doi.org/10.3390/ijms22063191

AMA Style

San-Eufrasio B, Bigatton ED, Guerrero-Sánchez VM, Chaturvedi P, Jorrín-Novo JV, Rey M-D, Castillejo MÁ. Proteomics Data Analysis for the Identification of Proteins and Derived Proteotypic Peptides of Potential Use as Putative Drought Tolerance Markers for Quercus ilex. International Journal of Molecular Sciences. 2021; 22(6):3191. https://doi.org/10.3390/ijms22063191

Chicago/Turabian Style

San-Eufrasio, Bonoso, Ezequiel D. Bigatton, Victor M. Guerrero-Sánchez, Palak Chaturvedi, Jesús V. Jorrín-Novo, María-Dolores Rey, and María Á. Castillejo 2021. "Proteomics Data Analysis for the Identification of Proteins and Derived Proteotypic Peptides of Potential Use as Putative Drought Tolerance Markers for Quercus ilex" International Journal of Molecular Sciences 22, no. 6: 3191. https://doi.org/10.3390/ijms22063191

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