Computational study of FaEXPA1, a strawberry alpha expansin protein, through molecular modeling and molecular dynamics simulation studies

Valenzuela-Riffo, Felipe; Ramos, Patricio; Morales-Quintana, Luis

doi:10.1016/j.compbiolchem.2018.05.018

Cited by 15 publications

(14 citation statements)

References 45 publications

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“…The increase in the mRNA levels of FaEG1 supports this hypothesis. In strawberries, the textural changes were related to the loosening of the xyloglucan-cellulose network [2,6,7] and were related to the depolymerization and solubilization of hemicelluloses and pectins within the cell wall, respectively [1,2]. Recently, the integrity, structural organization and stability of the polymers that conform to the cell wall in the fruit during the ripening process were evaluated with TGA curves [4].…”

Section: Resultsmentioning

confidence: 99%

“…Molecular docking studies were performed using Autodock Vina program v1.1.2 [44] to predict the putative binding interaction modes of the FaEG1 with three different octasaccharides (cellulose molecule according to [45] and two different xyloglucans (XG) (XXXGXXXG and XXFGXXFG polymers). The methodology was realized according to [6,46]. After the molecular docking, each ligand was evaluated inside to the active site of FaEG1 structural model by molecular dynamics (MD) simulation.…”

Section: Methodsmentioning

confidence: 99%

“…These differences in the TGA curve could result from plant cell wall metabolism. Different authors have described that the disassembly is the main process that leads to fruit softening during ripening and postharvest [1,2,5,6,7]. For this reason, several enzymes and proteins have been widely studied [6,7,8,9,10].…”

Section: Introductionmentioning

confidence: 99%

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Molecular Insights into FaEG1, a Strawberry Endoglucanase Enzyme Expressed during Strawberry Fruit Ripening

Jara

Castro

Ramos

et al. 2019

Plants

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The endo-β-1,4-glucanases (EGs) that belong to the glycosyl hydrolase family 9 (GH9) have roles in cell wall synthesis, remodeling and degradation. Previous studies have suggested that EGs may play a key role in the ripening of different fruits including strawberries. In this study, we used reverse-transcription quantitative polymerase chain reaction (RT-qPCR) assays to determine the transcript accumulation of an endo-β-1,4-glucanase (FaEG1) during fruit development in two different strawberry ‘Camarosa’ and ‘Monterey’ with contrasting softening ratios. Phylogenetic analyses suggest that FaEG1 belongs to the α group of the GH9 family with other proteins previously described with roles in elongation, abscission and ripening. Comparative modeling was used to obtain the FaEG1 structure. The model displays a α-barrel–type structure that is typical of the GH9 enzyme family, and comprises 12 α-helices, 2 310 helices and 6 β-sheets. The catalytic residues were oriented to the solvent in the middle of an open groove. Protein–ligand interactions were explored with cellulose and two xyloglucans as ligands; the results suggest that the FaEG1-cellulose and FaEG1-XXXGXXXG (the most abundant xyloglucan in strawberries) complexes were more stable complexes than XXFGXXFG. The cell wall degradation was observed by scanning electron microscopy (SEM). The data are congruent with the probable role of the FaEG1 protein in the dissembly of the cellulose-hemicellulose fraction during the ripening of strawberry fruit.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Molecular Insights into FaEG1, a Strawberry Endoglucanase Enzyme Expressed during Strawberry Fruit Ripening

Jara

Castro

Ramos

et al. 2019

Plants

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“…The role of expansin proteins in cell wall loosening has been well characterised in Arabidopsis [80], tomato [81,82], strawberry [83][84][85], peach [86] and kiwi fruits [87] where its activity is upregulated during the softening of ripening fruits [88]. Expansins initiate cell wall loosening and extension through the breakage of hydrogen bonds between cellulose and hemicellulose molecules, in particular xyloglucans [89,90], and their expression is regulated by crosstalk between many plant growth regulators including abscisic acid, indol-3-acetic acid, auxins, brassinosteroids, cytokines, ethylene [88].…”

Section: Cell Wall Metabolism Under Post-harvest Storagementioning

confidence: 99%

De novo sequencing and analysis of the transcriptome of two highbush blueberry (Vaccinium corymbosum L.) cultivars ‘Bluecrop’ and ‘Legacy’ at harvest and following post-harvest storage

et al. 2021

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Fruit firmness and in particular the individual components of texture and moisture loss, are considered the key quality traits when describing blueberry fruit quality, and whilst these traits are genetically regulated, the mechanisms governing their control are not clearly understood. In this investigation, RNAseq was performed on fruits of two blueberry cultivars with very different storage properties, ‘Bluecrop’ and ‘Legacy’, at harvest, three weeks storage in a non-modified environment at 4 °C and after three weeks storage at 4 °C followed by three days at 21 °C, with the aim of understanding the transcriptional changes that occur during storage in cultivars with very different post-harvest fruit quality. De novo assemblies of the transcriptomes of the two cultivars were performed separately and a total of 39,335 and 41,896 unigenes for ‘Bluecrop’ and ‘Legacy’ respectively were resolved. Differential gene expression analyses were grouped into four cluster profiles based on changes in transcript abundance between harvest and 24 days post-harvest. A total of 290 unigenes were up-regulated in ‘Legacy’ only, 685 were up-regulated in ‘Bluecrop’, 252 were up-regulated in both cultivars and 948 were down-regulated in both cultivars between harvest and 24 days post-harvest. Unigenes showing significant differential expression between harvest and following post-harvest cold-storage were grouped into classes of biological processes including stress responses, cell wall metabolism, wax metabolism, calcium metabolism, cellular components, and biological processes. In total 21 differentially expressed unigenes with a putative role in regulating the response to post-harvest cold-storage in the two cultivars were identified from the de novo transcriptome assemblies performed. The results presented provide a stable foundation from which to perform further analyses with which to functionally validate the candidate genes identified, and to begin to understand the genetic mechanisms controlling changes in firmness in blueberry fruits post-harvest.

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“…The role of expansin proteins in cell wall loosening has been well characterised in Arabidopsis [59], tomato [60,61], strawberry [62][63][64], peach [65] and kiwi fruits [66] where its activity is upregulated during the softening of ripening fruits [67]. Expansins initiate cell wall loosening and extension through the breakage of hydrogen bonds between cellulose and hemicellulose molecules, in particular xyloglucans [68,69], and their expression is regulated by cross-talk between many plant growth regulators including abscisic acid, indol-3-acetic acid, auxins, brassinosteroids, cytokines, ethylene [67].…”

Section: Cell Wall Metabolism Under Post-harvest Storagementioning

confidence: 99%

De novo sequencing and analysis of the transcriptome of two highbush blueberry (V. corymbosum L.) cultivars ‘Bluecrop’ and ‘Legacy’ at harvest and following post-harvest storage

Concepcion

Šurbanovski²,

Colgan

et al. 2021

Preprint

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Background: Fruit firmness and in particular the individual components of texture and moisture loss, are considered the key quality traits when describing blueberry fruit quality, and whilst these traits are genetically regulated, the mechanisms governing their control are not clearly understood. In this investigation, RNAseq was performed on fruits of two blueberry cultivars with very different storage properties, ‘Bluecrop’ and ‘Legacy’, at harvest, three weeks storage in a non-modified environment at 4 oC and after three weeks storage at 4 oC followed by three days at 21 oC, with the aim of understanding the transcriptional changes that occur during storage in cultivars with very different post-harvest fruit quality.Results: De novo assemblies of the transcriptomes of the two cultivars were performed separately and a total of 39,335 and 41,896 unigenes for ‘Bluecrop’ and ‘Legacy’ respectively were resolved. Differential gene expression analyses were grouped into four cluster profiles based on changes in transcript abundance between harvest and 24 days post-harvest. A total of 264 unigenes were up-regulated in ‘Legacy’ and down-regulated in ‘Bluecrop’, 103 were down-regulated in ‘Legacy’ and up-regulated in ‘Bluecrop’, 43 were up-regulated in both cultivars and 355 were down-regulated in both cultivars between harvest and 24 days post-harvest. Unigenes showing significant differential expression between harvest and following post-harvest cold-storage were grouped into classes of biological processes including stress responses, cell wall metabolism, wax metabolism, calcium metabolism, cellular components, and biological processes.Conclusions: In total 21 differentially expressed unigenes with a putative role in regulating the response to post-harvest cold-storage in the two cultivars were identified from the de novo transcriptome assemblies performed. The results presented provide a stable foundation from which to perform further analyses with which to functionally validate the candidate genes identified, and to begin to understand the genetic mechanisms controlling changes in firmness in blueberry fruits post-harvest.

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Computational study of FaEXPA1, a strawberry alpha expansin protein, through molecular modeling and molecular dynamics simulation studies

Cited by 15 publications

References 45 publications

Molecular Insights into FaEG1, a Strawberry Endoglucanase Enzyme Expressed during Strawberry Fruit Ripening

Molecular Insights into FaEG1, a Strawberry Endoglucanase Enzyme Expressed during Strawberry Fruit Ripening

De novo sequencing and analysis of the transcriptome of two highbush blueberry (Vaccinium corymbosum L.) cultivars ‘Bluecrop’ and ‘Legacy’ at harvest and following post-harvest storage

De novo sequencing and analysis of the transcriptome of two highbush blueberry (V. corymbosum L.) cultivars ‘Bluecrop’ and ‘Legacy’ at harvest and following post-harvest storage

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