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

Abstract

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 oxidationreduction 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.

Comprehensive Organ-Specific Profiling of Douglas Fir (Pseudotsuga menziesii) Proteome

“…Nevertheless, this discrepancy clearly illustrates the difficulty of extracting all proteins from an organ, as explained in a recent publication on this subject [ 48 ]. This technical difficulty is not limited to our study; however, we observe organ-specific protein counts quite similar to those obtained for other species: 3082 in the wood of Populus tremula [ 49 ], 1533 in the seeds of Pinus radiata [ 33 ] but only 629 in Pinus patula seeds [ 32 ]; 503, 1250 or 3000 for different stages somatic embryogenesis of Larix principis-rupprechtii [ 33 ], of Picea glauca [ 50 ] or of Quercus suber [ 51 ], respectively.…”

“…The abundance of this protein is likely attributable to its importance in post-germination nucleic syntheses. Similarly, Alfonso et al (2020) [32] demonstrated the importance of proteins involved in oxidation-reduction reactions to seed preparation for germination. Finally, we observed much higher abundances of BP terms in the immature somatic embryo proteome than in the other organs (Table S5), likely due to the totipotent nature of this type of tissue and its involvement in organogenesis.…”

“…The experimental observation of proteins in a large set of organs makes it possible to validate the presence of proteins initially predicted using genome bioinformatics approaches. However, a few studies present shotgun proteomic data from different plant organs: seeds (in Pinus greggii and Pinus patula [ 32 ]), leaves ( Pinus radiata and Quercus ilex [ 33 ]), shoot apical meristem ( Cunninghamia lanceolata [ 34 ]), different stages of somatic embryos ( Larix principis-rupprechtii [ 35 ]); as well as a cells fraction with this study of nuclear proteome of seedling ( Pinus radiata [ 36 ]) and or of cell wall proteins of Arabidopsis mature stems [ 37 ]. Additional proteomic studies have been conducted for some Quercus species that also include analysis of many organs [ 38 ].…”