Genome-wide analysis of SnRK gene family in Brachypodium distachyon and functional characterization of BdSnRK2.9

Wang, Lianzhe; Hu, Wei; Sun, Jiutong; Liang, Xiaoyu; Yang, Xiaoyue; Wei, Shuya; Wang, Xiatian; Zhou, Yi; Xiao, Qiang; Yang, Guangxiao; He, Guoqing

doi:10.1016/j.plantsci.2015.05.008

Cited by 56 publications

(51 citation statements)

References 71 publications

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“…The number of exons or introns varied in different subfamilies and genes. The FvSnRK1.1 had 10 exons, which was the same as that reported for EgrSnRK1s and BdSnRK1s [25,26]. Most of FvSnRK2s had nine exons or eight introns, except FvSnRK2.4, FvSnRK2.8 and FvSnRK2.9, which are consistent with that of most Arabidopsis, rice, maize, sorghum, tea and grape SnRK2 genes [27][28][29][30], suggesting that most SnRK2s in plants have a conserved structure with nine exons or eight introns.…”

Section: Discussionsupporting

confidence: 82%

“…As the plant has evolved, the subfamilies SnRK2 and SnRK3 have emerged, which are larger and relatively more diverse compared with SnRK1 [8]. Bioinformatic analysis of SnRK family has isolated a total of 39 AtSnRKs including three AtSnRK1s, 10 AtSnRK2s and 26 AtSnRK3s in Arabidopsis [21][22][23][24], 44 BdSnRKs including three BdSnRK1s, 10 BdSnRK2s and 31 BdSnRK3s in Brachypodium distachyon [25], 34 EgrSnRK including two EgrSnRK1s, eight EgrSnRK2s and 24 EgrSnRK3s in Eucalyptus grandis [26]. Here, we identified 26 FvSnRKs composed of one FvSnRK1, nine FvSnRK2s, 16 FvSnRK3s in the wild strawberry (Fragaria vesca).…”

Section: Discussionmentioning

confidence: 99%

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Genome-Wide Characterization of Snf1-Related Protein Kinases (SnRKs) and Expression Analysis of SnRK1.1 in Strawberry

Zhang

Jiang

et al. 2020

Genes

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The plant sucrose nonfermenting 1 (SNF1)-related protein kinases (SnRKs) are key regulators in the interconnection of various signaling pathways. However, little is known about the SnRK family in strawberries. In this study, a total of 26 FvSnRKs including one FvSnRK1, nine FvSnRK2s and 16 FvSnRK3s were identified from the strawberry genome database. They were respectively designated as FvSnRK1.1, FvSnRK2.1 to FvSnRK2.9 and FvSnRK3.1 to FvSnRK3.16, according to the conserved domain of each subfamily and multiple sequence alignment with Arabidopsis. FvSnRK family members were unevenly distributed in seven chromosomes. The number of exons or introns varied among FvSnRK1s, FvSnRK2s and FvSnRK3s, but highly conserved in the same subfamily. The FvSnRK1.1 had 10 exons. Most of FvSnRK2s had nine exons or eight introns, except FvSnRK2.4, FvSnRK2.8 and FvSnRK2.9. FvSnRK3 genes were divided into intron-free and intron-harboring members, and the number of introns in intron-harboring group ranged from 11 to 15. Moreover, the phylogenetic analysis showed SnRK1, SnRK2 and SnRK3 subfamilies respectively clustered together in spite of the different species of strawberry and Arabidopsis, indicating the genes were established prior to the divergence of the corresponding taxonomic lineages. Meanwhile, conserved motif analysis showed that FvSnRK sequences that belonged to the same subgroup contained their own specific motifs. Cis-element in promoter and expression pattern analyses of FvSnRK1.1 suggested that FvSnRK1.1 was involved in cold responsiveness, light responsiveness and fruit ripening. Taken together, this comprehensive analysis will facilitate further studies of the FvSnRK family and provide a basis for the understanding of their function in strawberry.

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Section: Discussionsupporting

confidence: 82%

Section: Discussionmentioning

confidence: 99%

Genome-Wide Characterization of Snf1-Related Protein Kinases (SnRKs) and Expression Analysis of SnRK1.1 in Strawberry

Zhang

Jiang

et al. 2020

Genes

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“…Therefore, the characterization of B. distachyon genes could provide reference for studies of other species in Pooideae subfamily. Our previous study identified 32 CIPK ( SnRK3 ) genes in the Brachypodium genome (Wang et al, 2015). However, none of these BdCIPKs has been functionally characterized.…”

Section: Introductionmentioning

confidence: 99%

BdCIPK31, a Calcineurin B-Like Protein-Interacting Protein Kinase, Regulates Plant Response to Drought and Salt Stress

et al. 2017

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Calcineurin B-like protein interacting protein kinases (CIPKs) are vital elements in plant abiotic stress signaling pathways. However, the functional mechanism of CIPKs has not been understood clearly, especially in Brachypodium distachyon, a new monocot model plant. In this study, BdCIPK31, a CIPK gene from B. distachyon was characterized. BdCIPK31 was downregulated by polyethylene glycol, NaCl, H2O2, and abscisic acid (ABA) treatments. Transgenic tobacco plants overexpressing BdCIPK31 presented improved drought and salt tolerance, and displayed hypersensitive response to exogenous ABA. Further investigations revealed that BdCIPK31 functioned positively in ABA-mediated stomatal closure, and transgenic tobacco exhibited reduced water loss under dehydration conditions compared with the controls. BdCIPK31 also affected Na+/K+ homeostasis and root K+ loss, which contributed to maintain intracellular ion homeostasis under salt conditions. Moreover, the reactive oxygen species scavenging system and osmolyte accumulation were enhanced by BdCIPK31 overexpression, which were conducive for alleviating oxidative and osmotic damages. Additionally, overexpression of BdCIPK31 could elevate several stress-associated gene expressions under stress conditions. In conclusion, BdCIPK31 functions positively to drought and salt stress through ABA signaling pathway. Overexpressing BdCIPK31 functions in stomatal closure, ion homeostasis, ROS scavenging, osmolyte biosynthesis, and transcriptional regulation of stress-related genes.

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“…Approaches including sequence and domain/motif analysis have been widely used along tree-based sequence clustering for the identification and description of many plant gene families, including the SnRK family. These strategies combined sequence-based methods with the evaluation of the identified sequences expression patterns in order to link them to particular stresses [28,38,39]. Other works [28,40] complemented this approach with the prediction of the proteins associated to the newly identified ones through databases such as STRING containing known relations between the orthologs to these elements.…”

Section: Discussionmentioning

confidence: 99%

The Analysis of Pinus pinaster SnRKs Reveals Clues of the Evolution of This Family and a New Set of Abiotic Stress Resistance Biomarkers

et al. 2020

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Climate change is increasing the intensity and incidence of environmental stressors, reducing the biomass yields of forestry species as Pinus pinaster. Selection of new stress-tolerant varieties is thus required. Many genes related to plant stress signaling pathways have proven useful for this purpose with sucrose non-fermenting related kinases (SnRK), conserved across plant evolution and connected to different phosphorylation cascades within ABA- and Ca2+-mediated signaling pathways, as a good example. The modulation of SnRKs and/or the selection of specific SnRK alleles have proven successful strategies to increase plant stress resistance. Despite this, SnRKs have been barely studied in gymnosperms. In this work P. pinaster SnRK sequences (PpiSnRK) were identified through a homology- and domain-based sequence analysis using Arabidopsis SnRK sequences as query. Moreover, PpiSnRKs links to the gymnosperm stress response were modeled out of the known interactions of PpiSnRKs orthologs from other species with different signaling complexity. This approach successfully identified the pine SnRK family and predicted their central role into the gymnosperm stress response, linking them to ABA, Ca2+, sugar/energy and possibly ethylene signaling. These links made the gymnosperm kinases promising candidates into the search for new stress resistance-related biomarkers, which would be useful into future breeding strategies.

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Genome-wide analysis of SnRK gene family in Brachypodium distachyon and functional characterization of BdSnRK2.9

Cited by 56 publications

References 71 publications

Genome-Wide Characterization of Snf1-Related Protein Kinases (SnRKs) and Expression Analysis of SnRK1.1 in Strawberry

Genome-Wide Characterization of Snf1-Related Protein Kinases (SnRKs) and Expression Analysis of SnRK1.1 in Strawberry

BdCIPK31, a Calcineurin B-Like Protein-Interacting Protein Kinase, Regulates Plant Response to Drought and Salt Stress

The Analysis of Pinus pinaster SnRKs Reveals Clues of the Evolution of This Family and a New Set of Abiotic Stress Resistance Biomarkers

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