Comparative Proteomical Analysis of Zygotic Embryo and Endosperm from Coffea arabica Seeds

Koshino, Livia L.; Gomes, Clarissa P.C.; Silva, Luciano; Eira, M. T. S.; Bloch, Carlos; Franco, Octávio L.; Mehta, Ângela

doi:10.1021/jf801734m

Cited by 9 publications

(9 citation statements)

References 38 publications

(43 reference statements)

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“…Concerning C. canephora , we observed an expression prevalence of PR-10 genes in late stages of fruit development (SE3 e SE4; Additional File 8). A proteomic analysis indicated that a C. arabica PR-10 was expressed only in the endosperm but not in zygotic embryos [64]. This result is similar to that found by Botton et al [65], who reported the accumulation of a peach PR-10 during the fruit ripening stage.…”

Section: Resultssupporting

confidence: 80%

An EST-based analysis identifies new genes and reveals distinctive gene expression features of Coffea arabica and Coffea canephora

et al. 2011

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BackgroundCoffee is one of the world's most important crops; it is consumed worldwide and plays a significant role in the economy of producing countries. Coffea arabica and C. canephora are responsible for 70 and 30% of commercial production, respectively. C. arabica is an allotetraploid from a recent hybridization of the diploid species, C. canephora and C. eugenioides. C. arabica has lower genetic diversity and results in a higher quality beverage than C. canephora. Research initiatives have been launched to produce genomic and transcriptomic data about Coffea spp. as a strategy to improve breeding efficiency.ResultsAssembling the expressed sequence tags (ESTs) of C. arabica and C. canephora produced by the Brazilian Coffee Genome Project and the Nestlé-Cornell Consortium revealed 32,007 clusters of C. arabica and 16,665 clusters of C. canephora. We detected different GC3 profiles between these species that are related to their genome structure and mating system. BLAST analysis revealed similarities between coffee and grape (Vitis vinifera) genes. Using KA/KS analysis, we identified coffee genes under purifying and positive selection. Protein domain and gene ontology analyses suggested differences between Coffea spp. data, mainly in relation to complex sugar synthases and nucleotide binding proteins. OrthoMCL was used to identify specific and prevalent coffee protein families when compared to five other plant species. Among the interesting families annotated are new cystatins, glycine-rich proteins and RALF-like peptides. Hierarchical clustering was used to independently group C. arabica and C. canephora expression clusters according to expression data extracted from EST libraries, resulting in the identification of differentially expressed genes. Based on these results, we emphasize gene annotation and discuss plant defenses, abiotic stress and cup quality-related functional categories.ConclusionWe present the first comprehensive genome-wide transcript profile study of C. arabica and C. canephora, which can be freely assessed by the scientific community at http://www.lge.ibi.unicamp.br/coffea. Our data reveal the presence of species-specific/prevalent genes in coffee that may help to explain particular characteristics of these two crops. The identification of differentially expressed transcripts offers a starting point for the correlation between gene expression profiles and Coffea spp. developmental traits, providing valuable insights for coffee breeding and biotechnology, especially concerning sugar metabolism and stress tolerance.

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Section: Resultssupporting

confidence: 80%

An EST-based analysis identifies new genes and reveals distinctive gene expression features of Coffea arabica and Coffea canephora

et al. 2011

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“…Seeds utilize globulins, such as 11S, as nitrogen source for germination. 25 The presence of the 11S proteins was initially observed during the exponential growth phase of the endosperm 25 as well as in mature fruits, seeds, coffee embryos 11,14 and even in initial stages of somatic embryogenesis. 13 Transcriptional studies with fruits at the initial stages of development reported 11S transcripts at the early stages of fruit development, when the main fruit tissue is the perisperm.…”

Section: ■ Results and Discussionmentioning

confidence: 99%

“…Spot 21 (6) was 1.57 times more abundant in IPR59-GDO 90 DAF than in IPR59. This class of proteins was abundant in coffee tissues under significant cellular division activity such as during the induction of somatic embryogenesis 34 and developing endosperm, 11 suggesting also involvement in plant growth, cell division, and developmental processes. 6 Interestingly, in our observations spots 2 (1) and 21 (6) genotypes at 60 and 90 DAF, but faced a drastic reduction in % vol at 180 DAF (Figure S2).…”

Section: ■ Results and Discussionmentioning

confidence: 99%

Differentially Accumulated Proteins in Coffea arabica Seeds during Perisperm Tissue Development and Their Relationship to Coffee Grain Size

Alves

Magalhães

Labate

et al. 2016

J. Agric. Food Chem.

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Coffee is one of the most important crops for developing countries. Coffee classification for trading is related to several factors, including grain size. Larger grains have higher market value then smaller ones. Coffee grain size is determined by the development of the perisperm, a transient tissue with a highly active metabolism, which is replaced by the endosperm during seed development. In this study, a proteomics approach was used to identify differentially accumulated proteins during perisperm development in two genotypes with regular (IPR59) and large grain sizes (IPR59-Graudo) in three developmental stages. Twenty-four spots were identified by MALDI-TOF/TOF-MS, corresponding to 15 proteins. We grouped them into categories as follows: storage (11S), methionine metabolism, cell division and elongation, metabolic processes (mainly redox), and energy. Our data enabled us to show that perisperm metabolism in IPR59 occurs at a higher rate than in IPR59-Graudo, which is supported by the accumulation of energy and detoxification-related proteins. We hypothesized that grain and fruit size divergences between the two coffee genotypes may be due to the comparatively earlier triggering of seed development processes in IPR59. We also demonstrated for the first time that the 11S protein is accumulated in the coffee perisperm.

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“…While specific functional roles remain enigmatic, the synthesis and accumulation of cupins and cupin-related proteins is a normal component of seed development (Dunwell et al, 2004 ; Koshino et al, 2008 ; Laudencia-Chingcuanco and Vensel, 2008 ). Almost half of the peptides identified in this study were fragments of cupins.…”

Section: Discussionmentioning

confidence: 99%

Do Cupins Have a Function Beyond Being Seed Storage Proteins?

et al. 2016

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Plants continue to flourish around the site of the Chernobyl Nuclear Power Plant disaster. The ability of plants to transcend the radio-contaminated environment was not anticipated and is not well understood. The aim of this study was to evaluate the proteome of flax (Linum usitatissimum L.) during seed filling by plants grown for a third generation near Chernobyl. For this purpose, seeds were harvested at 2, 4, and 6 weeks after flowering and at maturity, from plants grown in either non-radioactive or radio-contaminated experimental fields. Total proteins were extracted and the two-dimensional gel electrophoresis (2-DE) patterns analyzed. This approach established paired abundance profiles for 130 2-DE spots, e.g., profiles for the same spot across seed filling in non-radioactive and radio-contaminated experimental fields. Based on Analysis of Variance (ANOVA) followed by sequential Bonferroni correction, eight of the paired abundance profiles were discordant. Results from tandem mass spectrometry show that four 2-DE spots are discordant because they contain fragments of the cupin superfamily-proteins. Most of the fragments were derived from the N-terminal half of native cupins. Revisiting previously published data, it was found that cupin-fragments were also involved with discordance in paired abundance profiles of second generation flax seeds. Based on these observations we present an updated working model for the growth and reproductive success of flax in a radio-contaminated Chernobyl environment. This model suggests that the increased abundance of cupin fragments or isoforms and monomers contributes to the successful growth and reproduction of flax in a radio-contaminated environment.

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Comparative Proteomical Analysis of Zygotic Embryo and Endosperm from Coffea arabica Seeds

Cited by 9 publications

References 38 publications

An EST-based analysis identifies new genes and reveals distinctive gene expression features of Coffea arabica and Coffea canephora

An EST-based analysis identifies new genes and reveals distinctive gene expression features of Coffea arabica and Coffea canephora

Differentially Accumulated Proteins in Coffea arabica Seeds during Perisperm Tissue Development and Their Relationship to Coffee Grain Size

Do Cupins Have a Function Beyond Being Seed Storage Proteins?

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