Seed protein profile of Pinus greggii and Pinus patula through functional genomics analysis

SUMMARY: The present work was carried out with the aim of analyzing and describing the seed proteome of Pinus patula and Pinus greggii. The analysis was performed using the "shotgun" ("gel-free") strategy. Proteins were extracted using the TCA/Phenol/Acetone protocol, subsequentl...

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Autores principales:	Alfonso,Orlis B, Ariza Mateos,David, Palacios Rodríguez,Guillermo, Ginhas,Manuel Alexandre, Ruiz Gómez,Francisco J
Lenguaje:	English
Publicado:	Universidad Austral de Chile, Facultad de Ciencias Forestales 2020
Materias:	coniferous genetic variability molecular markers tandem mass spectrometry
Acceso en línea:	http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-92002020000300333
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spelling	oai:scielo:S0717-920020200003003332020-12-21Seed protein profile of Pinus greggii and Pinus patula through functional genomics analysisAlfonso,Orlis BAriza Mateos,DavidPalacios Rodríguez,GuillermoGinhas,Manuel AlexandreRuiz Gómez,Francisco J coniferous genetic variability molecular markers tandem mass spectrometry SUMMARY: The present work was carried out with the aim of analyzing and describing the seed proteome of Pinus patula and Pinus greggii. The analysis was performed using the "shotgun" ("gel-free") strategy. Proteins were extracted using the TCA/Phenol/Acetone protocol, subsequently separated by liquid chromatography and analyzed by mass spectrometry (nLC LTQ Orbitrap). Protein identification was performed by consulting the specific database for Pinus spp and functional classification taking into account the three functional terms (biological processes, cellular components and molecular functions) of Gene Ontology. To extract relevant Gene Ontology terms, a singular enrichment analysis (SEA) was performed, the terms were considered relevant for a minimum threshold of significance FDR < 0.05. After analyzing protein profiles, a total of 1091 proteins were identified, 362 proteins common in both species, 100 exclusives to P. greggii and 267 exclusive proteins to P. patula. The comparative analysis of the distribution of proteins as a function of the three functional terms reveals similarity between the two species. The most abundant proteins were associated with oxidation-reduction processes, in terms of cellular components; in both species integral membrane proteins predominate. Regarding molecular function, the predominant expression of proteins in both species was related to ATP synthesis. The metabolic pathway with the highest participation of proteins (17 in P. greggii and 19 in P. patula) was the glycolysis/gluconeogenesis pathway. These results demonstrate that there is little genetic variability between the two species, with proteins associated with metabolic processes prior to germination prevailing.info:eu-repo/semantics/openAccessUniversidad Austral de Chile, Facultad de Ciencias ForestalesBosque (Valdivia) v.41 n.3 20202020-12-01text/htmlhttp://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-92002020000300333en10.4067/S0717-92002020000300333
institution	Scielo Chile
collection	Scielo Chile
language	English
topic	coniferous genetic variability molecular markers tandem mass spectrometry
spellingShingle	coniferous genetic variability molecular markers tandem mass spectrometry Alfonso,Orlis B Ariza Mateos,David Palacios Rodríguez,Guillermo Ginhas,Manuel Alexandre Ruiz Gómez,Francisco J Seed protein profile of Pinus greggii and Pinus patula through functional genomics analysis
description	SUMMARY: The present work was carried out with the aim of analyzing and describing the seed proteome of Pinus patula and Pinus greggii. The analysis was performed using the "shotgun" ("gel-free") strategy. Proteins were extracted using the TCA/Phenol/Acetone protocol, subsequently separated by liquid chromatography and analyzed by mass spectrometry (nLC LTQ Orbitrap). Protein identification was performed by consulting the specific database for Pinus spp and functional classification taking into account the three functional terms (biological processes, cellular components and molecular functions) of Gene Ontology. To extract relevant Gene Ontology terms, a singular enrichment analysis (SEA) was performed, the terms were considered relevant for a minimum threshold of significance FDR < 0.05. After analyzing protein profiles, a total of 1091 proteins were identified, 362 proteins common in both species, 100 exclusives to P. greggii and 267 exclusive proteins to P. patula. The comparative analysis of the distribution of proteins as a function of the three functional terms reveals similarity between the two species. The most abundant proteins were associated with oxidation-reduction processes, in terms of cellular components; in both species integral membrane proteins predominate. Regarding molecular function, the predominant expression of proteins in both species was related to ATP synthesis. The metabolic pathway with the highest participation of proteins (17 in P. greggii and 19 in P. patula) was the glycolysis/gluconeogenesis pathway. These results demonstrate that there is little genetic variability between the two species, with proteins associated with metabolic processes prior to germination prevailing.
author	Alfonso,Orlis B Ariza Mateos,David Palacios Rodríguez,Guillermo Ginhas,Manuel Alexandre Ruiz Gómez,Francisco J
author_facet	Alfonso,Orlis B Ariza Mateos,David Palacios Rodríguez,Guillermo Ginhas,Manuel Alexandre Ruiz Gómez,Francisco J
author_sort	Alfonso,Orlis B
title	Seed protein profile of Pinus greggii and Pinus patula through functional genomics analysis
title_short	Seed protein profile of Pinus greggii and Pinus patula through functional genomics analysis
title_full	Seed protein profile of Pinus greggii and Pinus patula through functional genomics analysis
title_fullStr	Seed protein profile of Pinus greggii and Pinus patula through functional genomics analysis
title_full_unstemmed	Seed protein profile of Pinus greggii and Pinus patula through functional genomics analysis
title_sort	seed protein profile of pinus greggii and pinus patula through functional genomics analysis
publisher	Universidad Austral de Chile, Facultad de Ciencias Forestales
publishDate	2020
url	http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-92002020000300333
work_keys_str_mv	AT alfonsoorlisb seedproteinprofileofpinusgreggiiandpinuspatulathroughfunctionalgenomicsanalysis AT arizamateosdavid seedproteinprofileofpinusgreggiiandpinuspatulathroughfunctionalgenomicsanalysis AT palaciosrodriguezguillermo seedproteinprofileofpinusgreggiiandpinuspatulathroughfunctionalgenomicsanalysis AT ginhasmanuelalexandre seedproteinprofileofpinusgreggiiandpinuspatulathroughfunctionalgenomicsanalysis AT ruizgomezfranciscoj seedproteinprofileofpinusgreggiiandpinuspatulathroughfunctionalgenomicsanalysis
_version_	1718444257912553472

Seed protein profile of Pinus greggii and Pinus patula through functional genomics analysis

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