Genome-wide analysis and evolutionary study of sucrose non-fermenting 1-related protein kinase 2 (SnRK2) gene family members in Arabidopsis and Oryza

Saha, Jayita; Chatterjee, C.; Sengupta, Atreyee; Gupta, Kamala

doi:10.1016/j.compbiolchem.2013.09.005

Cited by 47 publications

(56 citation statements)

References 73 publications

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“…The transcript length of GmSnRK2s ranged from 1.3 to 2.2 kb, but the length of GmSnRK2 proteins ranged from 309 to 364 aa (amino acid). Generally, the SnRK2 gene family has two conserved signatures: An adenosine triphosphate (ATP)-binding region signature, and a Serine/Threonine protein kinase active-site signature [ 13 ]. In our results, all the SnRK2s of soybean contained ATP binding sites (IPR017441) and Serine/threonine-protein kinase active sites (IPR008271) at the N-terminal ( Table 1 ).…”

Section: Resultsmentioning

confidence: 99%

“…SnRK2s belong to the family of sucrose non-fermenting-1 (SNF1)-related protein kinases (SnRKs), which is a class of serine/threonine (Ser/Thr) protein kinases [ 10 , 11 , 12 ]. The members of SnRK2s family have been found in various plant species including Arabidopsis thaliana ( AtSnRK2.1–2.10 ), Oryza sativa ( SAPK1–10 ) [ 11 , 13 ], Malus prunifolia ( MpSnRK2.1–2.12 ) [ 14 ], maize ( ZmSnRK2.1–2.11 ) [ 15 ], wheat ( TaSnRK2.3 , 2.4 , 2.7 , and 2.8 ) [ 16 , 17 , 18 , 19 ], Brassica napus ( BnSnRK2.1–2.14 ) [ 20 ], Vitis vinifera ( VvSnRK2.1–2.6 ) [ 21 ], Pak-choi ( BcSnRK2.1–2.13 ) [ 22 ], and cotton ( GhSnRK2.1–2.20 ) [ 23 ]. Each SnRK2 protein contains three functional domains, including an adenosine triphosphate (ATP) binding domain, a conserved Ser/Thr kinase domain, and a diverse regulatory C-terminal.…”

Section: Introductionmentioning

confidence: 99%

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Genome-Wide Identification and Characterization of the GmSnRK2 Family in Soybean

Zhao

Cheng

Zhang

et al. 2017

IJMS

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Sucrose non-fermenting-1 (SNF1)-related protein kinase 2s (SnRK2s) that were reported to be involved in the transduction of abscisic acid (ABA) signaling, play important roles in response to biotic and abiotic stresses in plants. Compared to the systemic investigation of SnRK2s in Arabidopsis thaliana and Oryza sativa, little is known regarding SnRK2s in soybean, which is one of the most important oil and protein crops. In the present study, we performed genome-wide identification and characterization of GmSnRK2s in soybean. In summary, 22 GmSnRK2s were identified and clustered into four groups. Phylogenetic analysis indicated the expansion of SnRK2 gene family during the evolution of soybean. Various cis-acting elements such as ABA Response Elements (ABREs) were identified and analyzed in the promoter regions of GmSnRK2s. The results of RNA sequencing (RNA-Seq) data for different soybean tissues showed that GmSnRK2s exhibited spatio-temporally specific expression patterns during soybean growth and development. Certain GmSnRK2s could respond to the treatments including salinity, ABA and strigolactones. Our results provide a foundation for the further elucidation of the function of GmSnRK2 genes in soybean.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification and Characterization of the GmSnRK2 Family in Soybean

Zhao

Cheng

Zhang

et al. 2017

IJMS

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“…They probably derive from the gene duplication of SnRK1s and then diverge rapidly during plant evolution to fulfil new roles that enable plants to develop networks that link stress and abscisic acid (ABA) signaling with metabolic signaling [5,8]. Members of the SnRK2 subfamily have kinase domain, ATP binding domain, serine/threonine active site and four N-fourteen sites [9,10]. The first SnRK2 cDNA clone (PKABA1) was identified from an ABA-treated wheat embryo cDNA library, which was induced by salinity, cold, dehydration and osmotic stresses [11,12].…”

Section: Introductionmentioning

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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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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“…Intron loss in GDSL-lipase genes was prevalent in grasses, especially in sorghum. By contrast, in the widely distributed regulatory SnRK2 kinase family, monocots and eudicots are distinct regarding their patterns of intron retention, with the rice genes retaining more introns than those in Arabidopsis [67]. Most CACTA transposases without introns were found in sorghum, although this may merely represent sampling error.…”

Section: Discussionmentioning

confidence: 99%

Analysis of CACTA transposases reveals intron loss as major factor influencing their exon/intron structure in monocotyledonous and eudicotyledonous hosts

et al. 2014

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BackgroundCACTA elements are DNA transposons and are found in numerous organisms. Despite their low activity, several thousand copies can be identified in many genomes. CACTA elements transpose using a ‘cut-and-paste’ mechanism, which is facilitated by a DDE transposase. DDE transposases from CACTA elements contain, despite their conserved function, different exon numbers among various CACTA families. While earlier studies analyzed the ancestral history of the DDE transposases, no studies have examined exon loss and gain with a view of mechanisms that could drive the changes.ResultsWe analyzed 64 transposases from different CACTA families among monocotyledonous and eudicotyledonous host species. The annotation of the exon/intron boundaries showed a range from one to six exons. A robust multiple sequence alignment of the 64 transposases based on their protein sequences was created and used for phylogenetic analysis, which revealed eight different clades. We observed that the exon numbers in CACTA transposases are not specific for a host genome. We found that ancient CACTA lineages diverged before the divergence of monocotyledons and eudicotyledons. Most exon/intron boundaries were found in three distinct regions among all the transposases, grouping 63 conserved intron/exon boundaries.ConclusionsWe propose a model for the ancestral CACTA transposase gene, which consists of four exons, that predates the divergence of the monocotyledons and eudicotyledons. Based on this model, we propose pathways of intron loss or gain to explain the observed variation in exon numbers. While intron loss appears to have prevailed, a putative case of intron gain was nevertheless observed.

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Genome-wide analysis and evolutionary study of sucrose non-fermenting 1-related protein kinase 2 (SnRK2) gene family members in Arabidopsis and Oryza

Cited by 47 publications

References 73 publications

Genome-Wide Identification and Characterization of the GmSnRK2 Family in Soybean

Genome-Wide Identification and Characterization of the GmSnRK2 Family in Soybean

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

Analysis of CACTA transposases reveals intron loss as major factor influencing their exon/intron structure in monocotyledonous and eudicotyledonous hosts

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