Changes in the transcript and protein profiles of Quercus ilex seedlings in response to drought stress

Guerrero‐Sanchez, Víctor M.; Castillejo, María Ángeles; López-Hidalgo, Cristina; Alconada, Ana M. Maldonado; Jorrín‐Novo, Jesús V.; Rey, María‐Dolores

doi:10.1016/j.jprot.2021.104263

Cited by 19 publications

(36 citation statements)

References 53 publications

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“…et Guerrero-Sánchez et al, 2021). The organ specific profile of proteases was reported by Hüynck et al (2019).…”

Section: Discussionmentioning

confidence: 76%

“…Proteases and PIs in the species-specific Q. ilex transcriptome database ( Guerrero-Sánchez et al, 2017 , 2019 , 2021 ) were subjected to in silico analysis ( Supplementary Table S1 ). This database contains 45,815 transcripts 2,240 and 97 of which are annotated as proteases and protease inhibitors, respectively.…”

Section: Resultsmentioning

confidence: 99%

“…Proteases and PIs in the species-specific Q. ilex database ( Guerrero-Sánchez et al, 2017 , 2019 , 2021 ) were validated and classified against the Merops (see Footnote 2), Gene Ontology 3 and Panther 4 databases. The transcriptome Q. ilex DB is deposited at NCBI GEO (Gene Expression Omnibus) repository with the accession GSE145009.…”

Section: Methodsmentioning

confidence: 99%

“…The only resulting band was excised and digested with trypsin and the peptides thus obtained were dissolved in 50 μl of a 4% acetonitrile/0.25% formic acid mixture for loading into an Ultimate 3,000 nano-LC-MS-UHPLC- Orbitrap Fusion instrument from Thermo Fisher Scientific (Waltham, MA, United States; Gómez-Gálvez et al, 2020 ). MS/MS data were processed with the software Proteome Discoverer v. 2.3, also from Thermo Fischer Scientific, and identified by using the SEQUEST algorithm against the species-specific database of Q. ilex developed from the transcriptome ( Guerrero-Sánchez et al, 2017 , 2019 , 2021 ), using the setting reported by San-Eufrasio et al (2021) . Proteins were quantified in relative form from the peak areas for the precursor ions, using the three strongest peptide ion signals for each protein ( Al Shweiki et al, 2017 ).…”

Section: Methodsmentioning

confidence: 99%

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Identification of Proteases and Protease Inhibitors in Seeds of the Recalcitrant Forest Tree Species Quercus ilex

et al. 2022

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Proteases and protease inhibitors have been identified in the recalcitrant species Quercus ilex using in silico and wet methods, with focus on those present in seeds during germination. In silico analyses showed that the Q. ilex transcriptome database contained 2,240 and 97 transcripts annotated as proteases and protease inhibitors, respectively. They belonged to the different families according to MEROPS,1 being the serine and metallo ones the most represented. The data were compared with those previously reported for other Quercus species, including Q. suber, Q. lobata, and Q. robur. Changes in proteases and protease inhibitors alongside seed germination in cotyledon and embryo axis tissues were assessed using proteomics and in vitro and in gel activity assays. Shotgun (LC–MSMS) analysis of embryo axes and cotyledons in nonviable (NV), mature (T1) and germinated (T3) seeds allowed the identification of 177 proteases and 12 protease inhibitors, mostly represented by serine and metallo types. Total protease activity, as determined by in vitro assays using azocasein as substrate, was higher in cotyledons than in embryo axes. There were not differences in activity among cotyledon samples, while embryo axis peaked at germinated T4 stage. Gel assays revealed the presence of protease activities in at least 10 resolved bands, in the Mr range of 60–260 kDa, being some of them common to cotyledons and embryo axes in either nonviable, mature, and germinated seeds. Bands showing quantitative or qualitative changes upon germination were observed in embryo axes but not in cotyledons at Mr values of 60–140 kDa. Proteomics shotgun analysis of the 10 bands with protease activity supported the results obtained in the overall proteome analysis, with 227 proteases and 3 protease inhibitors identified mostly represented by the serine, cysteine, and metallo families. The combined use of shotgun proteomics and protease activity measurements allowed the identification of tissue-specific (e.g., cysteine protease inhibitors in embryo axes of mature acorns) and stage-specific proteins (e.g., those associated with mobilization of storage proteins accumulated in T3 stage). Those proteins showing differences between nonviable and viable seeds could be related to viability, and those variables between mature and germinated could be associated with the germination process. These differences are observed mostly in embryo axes but not in cotyledons. Among them, those implicated in mobilization of reserve proteins, such as the cathepsin H cysteine protease and Clp proteases, and also the large number of subunits of the CNS and 26S proteasome complex differentially identified in embryos of the several stages suggests that protein degradation via CNS/26S plays a major role early in germination. Conversely, aspartic proteases such as nepenthesins were exclusively identified in NV seeds, so their presence could be used as indicator of nonviability.

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“…et Guerrero-Sánchez et al, 2021). The organ specific profile of proteases was reported by Hüynck et al (2019).…”

Section: Discussionmentioning

confidence: 76%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Identification of Proteases and Protease Inhibitors in Seeds of the Recalcitrant Forest Tree Species Quercus ilex

et al. 2022

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“…Environmental stress affects these AS regulators and further regulates the expression of AS and other stress-related genes in plants, thus ensuring that plants can respond and adapt rapidly to environmental changes ( Achard et al, 2006 ; Baena-González et al, 2007 ; Barta et al, 2010 ; Jia et al, 2012 ; Scharf et al, 2012 ). Recent transcriptomic and proteomic analyses of 6-month-old Quercus ilex seedlings under severe drought conditions revealed a decrease in the accumulation of metabolism-related transcripts and proteins, but an increase in the accumulation of stress-related transcripts and proteins (e.g., HSP22) ( Guerrero-Sánchez et al, 2021 ). The overexpression of the A. thaliana WRKY30 (AtWRKY30) transcription factor in wheat under drought and high-temperature stress conditions revealed that the expression levels of antioxidant enzyme genes and the stress-responsive WRKY19 gene are significantly higher in transgenic wheat plants than in wild-type plants, enabling the transgenic plants to limit the damages caused by drought and high temperatures ( El-Esawi et al, 2019 ).…”

Section: Discussionmentioning

confidence: 99%

Analysis of Whole-Transcriptome RNA-Seq Data Reveals the Involvement of Alternative Splicing in the Drought Response of Glycyrrhiza uralensis

Huang

et al. 2022

Front. Genet.

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Alternative splicing (AS) is a post-transcriptional regulatory mechanism that increases protein diversity. There is growing evidence that AS plays an important role in regulating plant stress responses. However, the mechanism by which AS coordinates with transcriptional regulation to regulate the drought response in Glycyrrhiza uralensis remains unclear. In this study, we performed a genome-wide analysis of AS events in G. uralensis at different time points under drought stress using a high-throughput RNA sequencing approach. We detected 2,479 and 2,764 AS events in the aerial parts (AP) and underground parts (UP), respectively, of drought-stressed G. uralensis. Of these, last exon AS and exon skipping were the main types of AS. Overall, 2,653 genes undergoing significant AS regulation were identified from the AP and UP of G. uralensis exposed to drought for 2, 6, 12, and 24 h. Gene Ontology analyses indicated that AS plays an important role in the regulation of nitrogen and protein metabolism in the drought response of G. uralensis. Notably, the spliceosomal pathway and basal transcription factor pathway were significantly enriched with differentially spliced genes under drought stress. Genes related to splicing regulators in the AP and UP of G. uralensis responded to drought stress and underwent AS under drought conditions. In summary, our data suggest that drought-responsive AS directly and indirectly regulates the drought response of G. uralensis. Further in-depth studies on the functions and mechanisms of AS during abiotic stresses will provide new strategies for improving plant stress resistance.

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Integrative leaf anatomy structure, physiology, and metabolome analyses revealed the response to drought stress in sainfoin at the seedling stage

Yao,

Nan,

Wang

et al. 2024

Phytochemical Analysis

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IntroductionSainfoin (Onobrychis viciaefolia) is a vital legume forage, and drought is the primary element impeding sainfoin growth.ObjectiveThe anatomical structure, physiological indexes, and metabolites of the leaves of sainfoin seedlings with a drought‐resistant line of P1 (DRL) and a drought‐sensitive material of 2049 (DSM) were analyzed under drought (−1.0 MPa) with polyethylene glycol‐6000 (PEG‐6000).MethodsThe leaf anatomy was studied by the paraffin section method. The related physiological indexes were measured by the hydroxylamine oxidation method, titanium sulfate colorimetric method, thiobarbituric acid method, acidic ninhydrin colorimetric method, and Coomassie brilliant blue method. The metabolomics analysis was composed of liquid chromatography tandem high‐resolution mass spectrometry (LC‐MS/MS).ResultsThe results revealed that the thickness of the epidermis, palisade tissue, and sponge tissue of DRL were significantly greater than those of DSM. The leaves of DRL exhibited lower levels of superoxide anion (O2•−) production rate, hydrogen peroxide (H2O2) content, and malondialdehyde (MDA) content compared with DSM, while proline (Pro) content and soluble protein (SP) content were significantly higher than those of DSM. A total of 391 differential metabolites were identified in two samples. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment showed that the primary differential metabolites were concentrated into the tyrosine metabolism; isoquinoline alkaloid biosynthesis; ubiquinone and other terpenoid quinone biosynthesis; neomycin, kanamycin, and gentamicin biosynthesis; and anthocyanin biosynthesis metabolic pathways.ConclusionCompared with DSM, DRL had more complete anatomical structure, lower active oxygen content, and higher antioxidant level. The results improved our insights into the drought‐resistant mechanisms in sainfoin.

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Changes in the transcript and protein profiles of Quercus ilex seedlings in response to drought stress

Cited by 19 publications

References 53 publications

Identification of Proteases and Protease Inhibitors in Seeds of the Recalcitrant Forest Tree Species Quercus ilex

Identification of Proteases and Protease Inhibitors in Seeds of the Recalcitrant Forest Tree Species Quercus ilex

Analysis of Whole-Transcriptome RNA-Seq Data Reveals the Involvement of Alternative Splicing in the Drought Response of Glycyrrhiza uralensis

Integrative leaf anatomy structure, physiology, and metabolome analyses revealed the response to drought stress in sainfoin at the seedling stage

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