Characterization of the orthodox Pinus occidentalis seed and pollen proteomes by using complementary gel-based and gel-free approaches

Francisco, Luis; Romero-Rodríguez, M. Cristina; Navarro-Cerrillo, Rafael M.; Miniño, Virgilio; Perdomo, Omar Paíno; Jorrín‐Novo, Jesús V.

doi:10.1016/j.jprot.2016.03.041

Cited by 10 publications

(8 citation statements)

References 44 publications

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“…These methods have been proposed as valid tools for evaluating the productivity, growth and response to biotic and abiotic stresses in different forest species and are applicable to any type of vegetative material; therefore, permitting the correct identification of the species with a reasonably low effort (Rodríguez de Francisco et al 2016).…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2020

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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.

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Section: Introductionmentioning

confidence: 99%

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

et al. 2020

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“…ballota [Desf.] Samp., and, to a lesser extent, on various Pinus spp., including P. radiata [10], P. occidentalis [11], P. halepensis [12], and P. pinea [13]. All these forest tree species can be classified and catalogued as orphan due to the absence of molecular studies and, depending on their seed characteristics, properties, and maturation, as highly recalcitrant (non-orthodox) plant systems [8], because unlike orthodox seeds, non-orthodox seeds are damaged by loss of water and are unstorable for practical purposes.…”

Section: Introductionmentioning

confidence: 99%

Proteomics, Holm Oak (Quercus ilex L.) and Other Recalcitrant and Orphan Forest Tree Species: How do They See Each Other?

Rey

Castillejo

Sánchez-Lucas

et al. 2019

IJMS

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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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“…Both these works thus demonstrate that database specificity rather than exhaustivity is a key factor to consider for proteomics analyses; we also report this on C. sativa . When studying non-model plant species for which no genomic sequencing data is available, searching the viridiplantae database and its sub-taxonomies has proven invaluable to explore their proteomes, as was evidenced in pomegranate [ 71 ], quinoa [ 72 ], Pinus occidentalis [ 73 ] and cumin [ 74 ].…”

Section: Resultsmentioning

confidence: 99%

The Power of Three in Cannabis Shotgun Proteomics: Proteases, Databases and Search Engines

et al. 2020

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Cannabis research has taken off since the relaxation of legislation, yet proteomics is still lagging. In 2019, we published three proteomics methods aimed at optimizing protein extraction, protein digestion for bottom-up and middle-down proteomics, as well as the analysis of intact proteins for top-down proteomics. The database of Cannabis sativa proteins used in these studies was retrieved from UniProt, the reference repositories for proteins, which is incomplete and therefore underrepresents the genetic diversity of this non-model species. In this fourth study, we remedy this shortcoming by searching larger databases from various sources. We also compare two search engines, the oldest, SEQUEST, and the most popular, Mascot. This shotgun proteomics experiment also utilizes the power of parallel digestions with orthogonal proteases of increasing selectivity, namely chymotrypsin, trypsin/Lys-C and Asp-N. Our results show that the larger the database the greater the list of accessions identified but the longer the duration of the search. Using orthogonal proteases and different search algorithms increases the total number of proteins identified, most of them common despite differing proteases and algorithms, but many of them unique as well.

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Characterization of the orthodox Pinus occidentalis seed and pollen proteomes by using complementary gel-based and gel-free approaches

Cited by 10 publications

References 44 publications

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

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

Proteomics, Holm Oak (Quercus ilex L.) and Other Recalcitrant and Orphan Forest Tree Species: How do They See Each Other?

The Power of Three in Cannabis Shotgun Proteomics: Proteases, Databases and Search Engines

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