Comparative proteomics analysis of the effect of combined red and blue lights on sugarcane somatic embryogenesis

Heringer, Angelo Schuabb; Reis, Robert L.; Passamani, Lucas Zanchetta; Filho, Gonçalo A. de Souza; Santa–Catarina, Claudete; Silveira, Vanildo

doi:10.1007/s11738-017-2349-1

Cited by 37 publications

(26 citation statements)

References 58 publications

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“…Glycolysis, a key and ubiquitous metabolic pathway by which the plant cell converts carbohydrates to the energetic coin ATP, is a central pathway to generate energy and metabolic intermediaries that sustain the biosynthesis of intra- and extra-cellular molecules required by the cell. Proteins of the glycolysis pathway such as phosphofructokinase, fructose-1,6-biphosphate aldolase, glyceraldehyde-3-phosphate dehydrogenase, triosephosphate isomerase, phosphoglycerate mutase, 2,3-bisphosphoglycerate-independent phosphoglycerate mutase, phosphoglycerate kinase, enolase, and pyruvate decarboxylase were reported to be more abundant in the EC stage of African oil palm ( Silva et al, 2014 ), G. hirsutum ( Ge et al, 2017 ), maize ( Sun et al, 2013 ; Varhaníková et al, 2014 ; Ge et al, 2017 ), saffron ( Sharifi et al, 2012 ), Cyphomandra betacea ( Correia et al, 2012b ), Musa ( Kumaravel et al, 2017 ), Vitis vinifera ( Zhang et al, 2009 ), Larix principis-rupprechtii ( Beversdorf, 1987 ; Zhao et al, 2015a ), A. angustifolia ( dos Santos et al, 2016 ), P. nigra ( Klubicová et al, 2017 ), Theobroma cacao ( Niemenak et al, 2015 ), and sugarcane ( Heringer et al, 2017 ).…”

Section: Glycolysis-supplied Energy Leads Embryo Formationmentioning

confidence: 99%

“…Lipid transfer proteins, a collection of extracellular proteins with a secretory peptide, are thought to participate in the movement of surface lipids required for the formation of wax and cutin ( Wirtz, 1991 ; Li-Beisson et al, 2013 ). A lipid transfer protein was upregulated in CSE from G. hirsutum ( Ge et al, 2014 ) and phospholipid transfer protein 1 was upregulated during somatic embryo maturation of sugarcane embryos in a light quality-dependent fashion (meaning embryo maturation under white light plus medium blue, red, and far-red) ( Heringer et al, 2017 ), suggesting that surface lipids are an essential factor in embryo maturation.…”

Section: Fatty Acidsmentioning

confidence: 99%

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Advanced Proteomic Approaches to Elucidate Somatic Embryogenesis

Aguilar-Hernández

Loyola‐Vargas

2018

Front. Plant Sci.

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Somatic embryogenesis (SE) is a cell differentiation process by which a somatic cell changes its genetic program and develops into an embryonic cell. Investigating this process with various explant sources in vitro has allowed us to trace somatic embryo development from germination to plantlets and has led to the generation of new technologies, including genetic transformation, endangered species conservation, and synthetic seed production. A transcriptome data comparison from different stages of the developing somatic embryo has revealed a complex network controlling the somatic cell’s fate, suggesting that an interconnected network acts at the protein level. Here, we discuss the current progress on SE using proteomic-based data, focusing on changing patterns of proteins during the establishment of the somatic embryo. Despite the advanced proteomic approaches available so far, deciphering how the somatic embryo is induced is still in its infancy. The new proteomics techniques that lead to the quantification of proteins with different abundances during the induction of SE are opening this area of study for the first time. These quantitative differences can elucidate the different pathways involved in SE induction. We envisage that the application of these proteomic technologies can be pivotal to identifying proteins critical to the process of SE, demonstrating the cellular localization, posttranslational modifications, and turnover protein events required to switch from a somatic cell to a somatic embryo cell and providing new insights into the molecular mechanisms underlying SE. This work will help to develop biotechnological strategies for mass production of quality crop material.

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Section: Glycolysis-supplied Energy Leads Embryo Formationmentioning

confidence: 99%

Section: Fatty Acidsmentioning

confidence: 99%

Advanced Proteomic Approaches to Elucidate Somatic Embryogenesis

Aguilar-Hernández

Loyola‐Vargas

2018

Front. Plant Sci.

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“…The ideal protein extraction method should capture as many contents and proteins as possible while minimizing degradation and contamination (including phenolic compounds, starches, oils, and cell wall polysaccharides) . Therefore, the urea/thiourea protocol, which involves grinding a sample in liquid nitrogen, resuspending the sample in urea/thiourea extraction buffer (consisting of 7 m urea, 2 m thiourea, 1% dithiothreitol (DTT), 2% Triton X‐100, and protease inhibitors), and collecting the supernatant following centrifugation (Figure ), is preferred for surveying embryogenic callus or somatic embryo proteomes . In samples with a high contaminant load, the previously used trichloroacetic acid (TCA)/acetone precipitation (10% TCA in acetone) method, followed by resuspension in urea/thiourea buffer (Figure ), can be used.…”

Section: Evolution Of the Plant Proteomic Platformmentioning

confidence: 99%

“…Additional and complementary approaches in proteomics, such as phosphoproteomics, subcellular proteomics, and mass spectrometry immunohistochemistry (MSIHC), have great potential as complementary methods to help elucidate particular aspects of cellular metabolism. Recent publications have suggested that the gel‐free workflow will be the initial step to achieve a thorough overview of cellular proteins related to somatic embryogenesis competence and development . In addition to generating a catalog of proteins, proteomics can provide real biological knowledge; however, this achievement first requires the use of plant model systems.…”

Section: Further Perspectivesmentioning

confidence: 99%

Insights from Proteomic Studies into Plant Somatic Embryogenesis

2018

Self Cite

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Somatic embryogenesis is a biotechnological approach mainly used for the clonal propagation of different plants worldwide. In somatic embryogenesis, embryos arise from somatic cells under appropriate culture conditions. This plasticity in plants is a demonstration of true cellular totipotency and is the best approach among the genetic transformation protocols used for plant regeneration. Despite the importance of somatic embryogenesis, knowledge regarding the control of the somatic embryogenesis process is limited. Therefore, the elucidation of both the biochemical and molecular processes is important for understanding the mechanisms by which a single somatic cell becomes a whole plant. Modern proteomic techniques rely on an alternative method for the identification and quantification of proteins with different abundances in embryogenic cell cultures or somatic embryos and enable the identification of specific proteins related to somatic embryogenesis development. This review focuses on somatic embryogenesis studies that use gel-free shotgun proteomic analyses to categorize proteins that could enhance our understanding of particular aspects of the somatic embryogenesis process and identify possible targets for future studies.

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“…Over the last few years, the expression profiles of SE related genes and other differentially expressed genes during SE had been extensively excavated by RNA-seq sequencing in various species, including Gossypium hirsutum [9][10][11][12] [ [22], Rice [23], Lilium pumilum [24], Mangosteen [25], Papaya [26], and Triticum aestivum [27]. Meanwhile, the comparative proteome analysis during SE also characterized numerous proteins that associated with SE in many plant species, such as Maize [28], Papaya [29], Cacao [30], Sugarcane [31], Musa. spp [32], and Gossypium hirsutum [33].…”

Section: Introductionmentioning

confidence: 99%

Global scale transcriptome analysis reveals differentially expressed genes involve in early somatic embryogenesis in Dimocarpus longan Lour.

Chen

Liu

et al. 2019

Preprint

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Background: Somatic embryogenesis (SE) is a process of somatic cells that dedifferentiate to totipotent embryonic stem cells and generate embryos in vitro. Longan SE has been established and wildly used as model system for studying embryogenesis in woody plants, SE-related genes had been characterized. In spite of that, a comprehensive overview of SE at a molecular level is still absent. To understand the molecular mechanisms during longan SE, we examined the transcriptome changes by using Illumina HiSeq from the four distinct developmental stages, including NEC, EC, ICpEC, GE. Results: RNA-seq of the four samples generated a total of 243.78 million high quality reads, approximately 81.5% of the data were mapped to longan genome. The cDNA libraries of NEC, EC, ICpEC and GE, generated 22743, 19745, 21144, 21102 expressed transcripts, 1935, 1710, 1816, 1732 novel transcripts, 2645, 366, 505, 588 unique genes, respectively. Comparative transcriptome analysis showed that a total of 10,642, 4,180, 5,846 and 1,785 genes were differentially expressed in the pairwise comparisons of NEC_vs_EC, EC_vs_ICpEC, EC_vs_GE, ICpEC_vs_GE, respectively. Among them, plant hormones signalling related genes were significantly enriched, especially the auxin and cytokinin signalling components. The transcripts of flavonoid biosynthesis related genes were mainly expressed in NEC, while fatty acid biosynthesis related genes mainly accumulated in early SE. In addition, the extracelluar protein encoding genes LTP, CHI, GLP, AGP, EP1 were related to longan SE. Combined with the FPKM of longan nine tissues transcription, 27 SE specific or preferential genes (LEC1, LEC1-like, PDF1.3, GH3.6, AGL80, PIN1, BBM, WOX9, WOX2, et al.) and 28 NEC preferential genes (LEA5, CNOT3, DC2.15, PR1-1, NsLTP2, DIR1, PIP1, PIP2.1 and POD5 et al.) were characterized as molecular markers for longan early SE. qRT-PCR validation of SE-related genes showed a high correlation between RNA-seq and qRT-PCR data. Conclusion: This study provides new insights into the role of the transcriptome during early SE in longan. Differentially expressed genes reveal that plant hormones signalling, flavonoid and fatty acid biosynthesis, and extracelluar protein related genes were involved in longan early SE. It could serve as a valuable platform resource for further functional studies addressing embryogenesis in woody plants.

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Comparative proteomics analysis of the effect of combined red and blue lights on sugarcane somatic embryogenesis

Cited by 37 publications

References 58 publications

Advanced Proteomic Approaches to Elucidate Somatic Embryogenesis

Advanced Proteomic Approaches to Elucidate Somatic Embryogenesis

Insights from Proteomic Studies into Plant Somatic Embryogenesis

Global scale transcriptome analysis reveals differentially expressed genes involve in early somatic embryogenesis in Dimocarpus longan Lour.

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