Proteomics Data Analysis for the Identification of Proteins and Derived Proteotypic Peptides of Potential Use as Putative Drought Tolerance Markers for <i>Quercus ilex</i>
Drought is one of the main causes of mortality in holm oak (<i>Quercus ilex</i>) 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 th...
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MDPI AG
2021-03-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/22/6/3191 |
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| author | Bonoso San-Eufrasio Ezequiel Darío Bigatton Victor M. Guerrero-Sánchez Palak Chaturvedi Jesús V. Jorrín-Novo María-Dolores Rey María Ángeles Castillejo |
| author_facet | Bonoso San-Eufrasio Ezequiel Darío Bigatton Victor M. Guerrero-Sánchez Palak Chaturvedi Jesús V. Jorrín-Novo María-Dolores Rey María Ángeles Castillejo |
| author_sort | Bonoso San-Eufrasio |
| collection | DOAJ |
| description | Drought is one of the main causes of mortality in holm oak (<i>Quercus ilex</i>) 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 <i>Q. ilex</i> 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. |
| first_indexed | 2024-03-10T13:02:59Z |
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| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T13:02:59Z |
| publishDate | 2021-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-7ebeb1fd23e14a5d8d903ba84e1703472023-11-21T11:21:45ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672021-03-01226319110.3390/ijms22063191Proteomics Data Analysis for the Identification of Proteins and Derived Proteotypic Peptides of Potential Use as Putative Drought Tolerance Markers for <i>Quercus ilex</i>Bonoso San-Eufrasio0Ezequiel Darío Bigatton1Victor M. Guerrero-Sánchez2Palak Chaturvedi3Jesús V. Jorrín-Novo4María-Dolores Rey5María Ángeles Castillejo6Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, SpainAgroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, SpainAgroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, SpainMolecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Althanstrasse 14, A-1090 Vienna, AustriaAgroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, SpainAgroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, SpainAgroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, SpainDrought is one of the main causes of mortality in holm oak (<i>Quercus ilex</i>) 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 <i>Q. ilex</i> 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.https://www.mdpi.com/1422-0067/22/6/3191peptide markers<i>Quercus ilex</i>drought tolerancetargeted post-acquisition proteomics |
| spellingShingle | Bonoso San-Eufrasio Ezequiel Darío Bigatton Victor M. Guerrero-Sánchez Palak Chaturvedi Jesús V. Jorrín-Novo María-Dolores Rey María Ángeles Castillejo Proteomics Data Analysis for the Identification of Proteins and Derived Proteotypic Peptides of Potential Use as Putative Drought Tolerance Markers for <i>Quercus ilex</i> International Journal of Molecular Sciences peptide markers <i>Quercus ilex</i> drought tolerance targeted post-acquisition proteomics |
| title | Proteomics Data Analysis for the Identification of Proteins and Derived Proteotypic Peptides of Potential Use as Putative Drought Tolerance Markers for <i>Quercus ilex</i> |
| title_full | Proteomics Data Analysis for the Identification of Proteins and Derived Proteotypic Peptides of Potential Use as Putative Drought Tolerance Markers for <i>Quercus ilex</i> |
| title_fullStr | Proteomics Data Analysis for the Identification of Proteins and Derived Proteotypic Peptides of Potential Use as Putative Drought Tolerance Markers for <i>Quercus ilex</i> |
| title_full_unstemmed | Proteomics Data Analysis for the Identification of Proteins and Derived Proteotypic Peptides of Potential Use as Putative Drought Tolerance Markers for <i>Quercus ilex</i> |
| title_short | Proteomics Data Analysis for the Identification of Proteins and Derived Proteotypic Peptides of Potential Use as Putative Drought Tolerance Markers for <i>Quercus ilex</i> |
| title_sort | proteomics data analysis for the identification of proteins and derived proteotypic peptides of potential use as putative drought tolerance markers for i quercus ilex i |
| topic | peptide markers <i>Quercus ilex</i> drought tolerance targeted post-acquisition proteomics |
| url | https://www.mdpi.com/1422-0067/22/6/3191 |
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