Root proteomic and metabolic analyses reveal specific responses to drought stress in differently tolerant grapevine rootstocks

Prinsi, Bhakti; Negri, Attilio; Failla, O.; Scienza, A.; Espen, Luca

doi:10.1186/s12870-018-1343-0

Cited by 50 publications

(56 citation statements)

References 101 publications

(126 reference statements)

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“…In this study; however, there were three times as many DEGs in WD shoot than in WD root in strong contrast to a previous WD study in grapevine rootstocks [18]. The difference between the present study and the rootstock study [18] may be due to differences in genotype, WD sensitivity or differences in the length of the water deficit treatment [50].…”

Section: Discussioncontrasting

confidence: 96%

Transcriptomic response is more sensitive to water deficit in shoots than roots of Vitis riparia (Michx.)

et al. 2019

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Background Drought is an important constraint on grapevine sustainability. Vitis riparia, widely used in rootstock and scion breeding, has been studied in isolated leaf drying response studies; however, it is essential to identify key root and shoot water deficit signaling traits in intact plants. This information will aid improved scion and rootstock selection and management practices in grapevine. RNAseq data were generated from V. riparia roots and shoots under water deficit and well-watered conditions to determine root signaling and shoot responses to water deficit. Results Shoot elongation, photosynthetic rate, and stomatal conductance were significantly reduced in water deficit (WD) treated than in well-watered grapevines. RNAseq analysis indicated greater transcriptional differences in shoots than in roots under WD, with 6925 and 1395 genes differentially expressed, respectively (q-value < 0.05). There were 50 and 25 VitisNet pathways significantly enriched in WD relative to well-watered treatments in grapevine shoots and roots, respectively. The ABA biosynthesis genes beta-carotene hydroxylase, zeaxanthin epoxidase, and 9-cis-epoxycarotenoid dioxygenases were up-regulated in WD root and WD shoot. A positive enrichment of ABA biosynthesis genes and signaling pathways in WD grapevine roots indicated enhanced root signaling to the shoot. An increased frequency of differentially expressed reactive oxygen species scavenging (ROS) genes were found in the WD shoot. Analyses of hormone signaling genes indicated a strong ABA, auxin, and ethylene network and an ABA, cytokinin, and circadian rhythm network in both WD shoot and WD root. Conclusions This work supports previous findings in detached leaf studies suggesting ABA-responsive binding factor 2 ( ABF2 ) is a central regulator in ABA signaling in the WD shoot. Likewise, ABF2 may have a key role in V. riparia WD shoot and WD root. A role for ABF3 was indicated only in WD root. WD shoot and WD root hormone expression analysis identified strong ABA, auxin, ethylene, cytokinin, and circadian rhythm signaling networks. These results present the first ABA, cytokinin, and circadian rhythm signaling network in roots under water deficit. These networks point to organ specific regulators that should be explored to further define the communication network from soil to shoot. Electronic supplementary material The online version of this article (10.1186/s12870-019-1664-7) contains supplementary material, which is available to authorized users.

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Section: Discussioncontrasting

confidence: 96%

Transcriptomic response is more sensitive to water deficit in shoots than roots of Vitis riparia (Michx.)

et al. 2019

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“…In both genotypes, a chitinase class I basic (#51 and #54 in 101.14 and M4, respectively) was up-accumulated under salt stress conditions (Tables 2 and 3). A similar result was previously found in roots of the 101.14 and M4 genotypes in response to drought stress [25], thus reinforcing the idea that enhanced synthesis of this enzyme could be a response useful to counteracting the risk of infection in stress-weakened plants [60,61]. In 101.14, two germin-like proteins (#201, #214) showed an evident increase in abundance, while another one slightly diminished (#128).…”

Section: Proteomic Changes Involved In Secondary Metabolism Stress Asupporting

confidence: 84%

“…The proteomic study was performed using the GeLC-MS/MS (gel liquid chromatography-tandem mass spectrometry) approach [24]. In detail, we combined the protein extraction method previously optimized for the root proteomes of grapevine plants grown in the soil [25] with an analytical streamlined procedure recently proposed [26], based on partial 1D SDS-PAGE purification and in gel-digestion procedure. The technical parameters related to protein identification and quantitation were very similar for the two genotypes and highlighted the good reliability of the adopted protocol ( Table 1).…”

Section: Proteomic Analysesmentioning

confidence: 99%

“…The total protein fraction was extracted from three biological replicates for each experimental condition as previously described [25,73] and dissolved in SDS-buffer (150 mM Tris-HCl, pH 6.8, 10% (w/w) glycerol, 2% (w/w) sodium dodecyl sulphate (SDS), 2% (v/v) 2-mercaptoethanol). After 5 min at 95 • C, samples were centrifuged at 10,000× g for 10 min and the supernatant was collected and stored at −80 • C. The protein concentration was determined by the 2-D Quant Kit (GE Healthcare Europe GmbH, Freiburg, Germany).…”

Section: Protein Extractionmentioning

confidence: 99%

“…The identified proteins were classified into metabolic functional classes according to the MapMan BIN ontology. The schematic metabolic pathways were obtained by MapMan software as previously described [25].…”

Section: Gel Electrophoresis In-gel Digestion and Mass Spectrometry mentioning

confidence: 99%

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Root Proteomic Analysis of Two Grapevine Rootstock Genotypes Showing Different Susceptibility to Salt Stress

Prinsi¹,

Failla²,

Scienza³

et al. 2020

IJMS

Self Cite

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Salinity represents a very limiting factor that affects the fertility of agricultural soils. Although grapevine is moderately susceptible to salinity, both natural causes and agricultural practices could worsen the impact of this abiotic stress. A promising possibility to reduce this problem in vineyards is the use of appropriate graft combinations. The responses of grapevine rootstocks to this abiotic stress at the root level still remain poorly investigated. In order to obtain further information on the multifaceted responses induced by salt stress at the biochemical level, in the present work we analyzed the changes that occurred under control and salt conditions in the root proteomes of two grapevine rootstock genotypes, M4 and 101.14. Moreover, we compared the results considering that M4 and 101.14 were previously described to have lower and higher susceptibility to salt stress, respectively. This study highlighted the greater capability of M4 to maintain and adapt energy metabolism (i.e., synthesis of ATP and NAD(P)H) and to sustain the activation of salt-protective mechanisms (i.e., Na sequestration into the vacuole and synthesis of osmoprotectant compounds). Comparitively, in 101.14 the energy metabolism was deeply affected and there was an evident induction of the enzymatic antioxidant system that occurred, pointing to a metabolic scenario typical of a suffering tissue. Overall, this study describes for the first time in grapevine roots some of the more crucial events that characterize positive (M4) or negative (101.14) responses evoked by salt stress conditions.

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Long noncoding RNA transcriptome analysis reveals novel lncRNAs in Morus alba ‘Yu‐711’ response to drought stress

et al. 2022

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Drought stress has been a key environmental factor affecting plant growth and development. The plant genome is capable of producing long noncoding RNAs (lncRNAs). To better understand white mulberry (Morus alba L.) drought response mechanism, we conducted a comparative transcriptome study comparing two treatments: drought‐stressed (EG) and well‐watered (CK) plants. A total of 674 differentially expressed lncRNAs (DElncRNAs) were identified. In addition, 782 differentially expressed messenger RNAs (DEmRNAs) were identified. We conducted Gene Ontology (GO) and KEGG enrichment analyses focusing on the differential lncRNAs cis‐target genes. The target genes of the DElncRNAs were most significantly involved in the biosynthesis of secondary metabolites. Gene regulatory networks of the target genes involving DElncRNAs–mRNAs–DEmRNAs and DElncRNA–miRNA–DEmRNA were constructed. In the DElncRNAs–DEmRNAs network, 30 DEmRNAs involved in the biosynthesis of secondary metabolites are collocated with 46 DElncRNAs. The interaction between DElncRNAs and candidate genes was identified using LncTar. In summary, quantitative real‐time polymerase chain reaction (qRT‐PCR) validated nine candidate genes and seven target lncRNAs including those identified by LncTar. We predicted that the DElncRNAs–DEmRNAs might recruit microRNAs (miRNAs) to interact with gene regulatory networks under the drought stress response in mulberry. The findings will contribute to our understanding of the regulatory functions of lncRNAs under drought stress and will shed new light on the mulberry–drought stress interactions.

show abstract

Root proteomic and metabolic analyses reveal specific responses to drought stress in differently tolerant grapevine rootstocks

Cited by 50 publications

References 101 publications

Transcriptomic response is more sensitive to water deficit in shoots than roots of Vitis riparia (Michx.)

Transcriptomic response is more sensitive to water deficit in shoots than roots of Vitis riparia (Michx.)

Root Proteomic Analysis of Two Grapevine Rootstock Genotypes Showing Different Susceptibility to Salt Stress

Long noncoding RNA transcriptome analysis reveals novel lncRNAs in Morus alba ‘Yu‐711’ response to drought stress

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