Skip to main content
SpringerLink
Log in

Computational study of sucrose non-fermenting 1-related kinase 2 (SnRK2): An in-silico approach for homology modelling and structural characterization of drought related SAPK9 gene in rice (Oryza sativa L.)

  • Research Article
  • Published:
Genetic Resources and Crop Evolution Aims and scope Submit manuscript

Abstract

Sucrose non-fermenting-1-related protein kinase 2 (SnRK2) are plant-specific serine/threonine (Ser/Thr) protein kinases that form the central region of abscisic acid (ABA) signaling pathways and are major contributors in imparting abiotic stress tolerance in plants by activating protein phosphorylation pathways. SAPK9 (member of the SnRK2 family) plays a role in providing drought tolerance in rice but scanty literature is available related to its structural and physico-chemical characterization. Hence, the present study aimed at in-silico characterization and structural modelling of SAPK9 from Oryza sativa japonica (OsjSAPK9). The results revealed that OsjSAPK9 is highly conserved at the amino acid sequence level. A single Ser/Thr kinase domain along with ATP binding domain was found in OsjSAPK9. It is 361 amino acid residues long having 40 kDa molecular weight and 4.81 pI. All SnRK2 proteins are stable in nature (instability index > 40). 11 motifs were identified where motif 1 represents the SnRK2 domain. All SnRK2s were found to be localized in the nucleus. The larger number of phosphorylation sites for serine and threonine as compared to tyrosine and 10 antigenic determinant sites were observed. The structure showed 7-β-strands, 15-α-helices, 39-β-turns, 18-γ-turns, and 4-beta hairpins. ATP was found to be a preferred ligand for OsjSAPK9. SAPK9 was found to interact with BZIP46 and BZIP23 transcription factors which behave as positive modulators of drought stress resistance. As SAPK9 protein plays a crucial role in ABA and stress signaling pathways, a deeper knowledge of its structural and functional attributes will open up new avenues for future research to strengthen rice's ability to withstand drought stress.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7

Similar content being viewed by others

Abbreviations

ABA:

Abscisic acid

Ai:

Aliphatic index

EC:

Extinction coefficient

GFP:

Green fluorescent protein

GRAVY:

Grand average of hydropathy

MEGA:

Molecular evolutionary genetic analysis

MSA:

Multiple sequence alignment

PP2C:

Protein phosphatase 2C

PrDOS:

Protein disorder prediction server

SMART:

Simple molecular architecture research

SnRK2:

Sucrose non-fermenting 1-related kinase 2

References

  • Boudsocq M, Barbier-Brygoo H, Lauriere C (2004) Identification of nine sucrose nonfermenting 1-related protein kinases 2 activated by hyperosmotic and saline stresses in Arabidopsis thaliana. J Biol Chem 279:41758–41766

    Article  PubMed  CAS  Google Scholar 

  • Chae MJ, Lee JS, Nam MH, Cho K, Hong JY, Yi SA, Suh SC, Yoon IS (2007) A rice dehydration-inducible SNF1-related protein kinase 2 phosphorylates an abscisic acid responsive element-binding factor and associates with ABA signaling. Plant Mol Biol 63:151–169

    Article  PubMed  CAS  Google Scholar 

  • Dey A, Samanta MK, Gayen S, Maiti MK (2016) The sucrose non-fermenting 1-related kinase 2 gene SAPK9 improves drought tolerance and grain yield in rice by modulating cellular osmotic potential, stomatal closure and stress-responsive gene expression. BMC Plant Biol 16:1–20

    Article  Google Scholar 

  • Dong W, Wang M, Xu F, Quan T, Peng K, Xiao L et al (2013) Wheat oxophytodienoate reductase gene TaOPR1 confers salinity tolerance via enhancement of abscisic acid signaling and reactive oxygen species scavenging. Plant Physiol 161:1217–1228

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Estruch F, Treitel MA, Yang X, Carlson M (1992) N-terminal mutations modulate yeast SNF1 kinase function. Genetics 132:639–650

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Feng J, Wang L, Wu Y, Luo Q, Zhang Y, Qiu D, He G (2019) TaSnRK2.9, sucrose non-fermenting 1-related protein kinase gene, positively regulates plant response to drought and salt stress in transgenic tobacco. Front Plant Sci. https://doi.org/10.3389/fpls.2018.02003

    Article  PubMed  PubMed Central  Google Scholar 

  • Fujita Y, Yoshida T, Yamaguchi-Shinozaki K (2013) Pivotal role of the AREB/ABF-SnRK2 pathway in ABRE mediated transcription in response to osmotic stress in plants. Physiol Plant 147:15–27

    Article  PubMed  CAS  Google Scholar 

  • Gancedo JM (1998) Yeast carbon catabolic repression. Microbiol Mol Biol Rev 62:341–361

    Article  Google Scholar 

  • Hardie DG, Carling D, Carlson M (1998) The AMP-activated/SNF1 protein kinase subfamily: metabolic sensors of the eukaryotic cell? Ann Rev Biochem 67:821–855

    Article  PubMed  CAS  Google Scholar 

  • Hauser F, Waadt R, Schroeder JI (2011) Evolution of abscisic acid synthesis and signaling mechanisms. Curr Biol 21(9):346–355

    Article  Google Scholar 

  • Hrabak EM, Chan CW, Gribskov M, Harper JF, Choi JH, Halford N et al (2003) The Arabidopsis CDPK-SnRK superfamily of protein kinases. Plant Physiol 132(2):666–680

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Huai J, Wang M, He J, Zheng J, Dong Z, Lv H et al (2008) Cloning and characterization of the SnRK2 gene family from Zea mays. Plant Cell Rep 27:1861–1868

    Article  PubMed  CAS  Google Scholar 

  • Johnson GL, Lapadat R (2002) Mitogen activated protein kinase pathway mediated by ERK, JNK, and p38 protein kinases. Sci 298:1911–1912

    Article  CAS  Google Scholar 

  • Kagaya Y, Hobo T, Murata M, Ban A, Hattori T (2002) Abscisic acid-induced transcription is mediated by phosphorylation of an abscisic acid response element binding factor, TRAB1. Plant Cell 14:3177–3189

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kaiser WM, Huber SC (2001) Post-translational regulation of nitrate reductase: mechanism, physiological relevance and environmental triggers. J Exp Bot 52:1981–1989

    Article  PubMed  CAS  Google Scholar 

  • Kim N, Moon SJ, Min MK, Choi EH, Kim JA, Koh EY et al (2015) Functional characterization and reconstitution of ABA signaling components using transient gene expression in rice protoplasts. Front Plant Sci 6:614

    Article  PubMed  PubMed Central  Google Scholar 

  • Kobayashi Y, Yamamoto S, Minami H, Kagaya Y, Hattori T (2004) Differential activation of the rice sucrose nonfermenting1-related protein kinase2 family by hyperosmotic stress and abscisic acid. Plant Cell 16:1163–1177

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kulik A, Wawer I, Krzywińska E, Bucholc M, Dobrowolska G (2011) SnRK2 protein kinases-key regulators of plant response to abiotic stresses. Omics J Integ Biol 15:859–872

    Article  CAS  Google Scholar 

  • Li X, Yu B, Wu Q, Min Q, Zeng R, Xie Z, Huang J (2021) OsMADS23 phosphorylated by SAPK9 confers drought and salt tolerance by regulating ABA biosynthesis in rice. PLoS Genet 17:e1009699

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Liu Z, Ge X, Yang Z, Zhang C, Zhao G, Chen E et al (2017) Genome-wide identification and characterization of SnRK2 gene family in cotton (Gossypium hirsutum L.). BMC Genet 18:1–14

    Article  Google Scholar 

  • Mittler R, Blumwald E (2015) The roles of ROS and ABA in systemic acquired acclimation. Plant Cell 27:64–70

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Mustilli AC, Merlot S, Vavasseur A, Fenzi F, Giraudat J (2002) Arabidopsis OST1 protein kinase mediates the regulation of stomatal aperture by abscisic acid and acts upstream of reactive oxygen species production. Plant Cell 14:3089–3099

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Narayanan P, Sanyal SK, Pandey GK (2020) Role of CBL-interacting protein kinases in regulating plant stress responses. Protein Kinases Stress Signal Plants Funct Genom Persp. https://doi.org/10.1002/9781119541578.ch12

    Article  Google Scholar 

  • Ng LM, Soon FF, Zhou XE, West GM, Kovach A, Suino-Powell KM et al (2011) Structural basis for basal activity and autoactivation of abscisic acid (ABA) signaling SnRK2 kinases. Proc Natl Acad Sci 108:21259–21264

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Raghavendra AS, Gonugunta VK, Christmann A, Grill E (2010) ABA perception and signalling. Trends Plant Sci 15:395–401

    Article  PubMed  CAS  Google Scholar 

  • Sultana MS, Ojha RK, Islam MM, Ashfaq MA, Khan KF, Sutradhar P (2013) Computational study of SnRK2 in Arabidopsis thaliana: An in silico approach for homology modeling and functional characterization of SRK2G/SnRK2. Int J Comput Bioinform Silico Model 2:249–256

    Google Scholar 

  • Tang N, Zhang H, Li X, Xiao J, Xiong L (2012) Constitutive activation of transcription factor OsbZIP46 improves drought tolerance in rice. Plant Physiol 158:1755–1768

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Tang N, Ma S, Zong W, Yang N, Lv Y, Yan C, Guo Z, Li J, Li X, Xiang Y, Song H (2016) MODD mediates deactivation and degradation of OsbZIP46 to negatively regulate ABA signaling and drought resistance in rice. Plant Cell 28:2161–2177

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Tian S, Mao X, Zhang H, Chen S, Zhai C, Yang S, Jing R (2013) Cloning and characterization of TaSnRK2.3, a novel SnRK2 gene in common wheat. J Exp Bot 64(7):2063–2080

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Umezawa T, Yoshida R, Maruyama K, Yamaguchi-Shinozaki K, Shinozaki K (2004) SRK2C, a SNF1-related protein kinase 2, improves drought tolerance by controlling stress-responsive gene expression in Arabidopsis thaliana. Proc Natl Acad Sci USA 101:17306–17311

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Wang X, Guo C, Peng J, Li C, Wan F, Zhang S et al (2018) ABRE-binding factors play a role in the feedback regulation of ABA signaling by mediating rapid ABA induction of ABA co-receptor genes. New Phytol 22:341–255

    Google Scholar 

  • Wang Y, Hou Y, Qiu J, Wang H, Wang S, Tang L et al (2020) Abscisic acid promotes jasmonic acid biosynthesis via a ’SAPK10-bZIP72-AOC’ pathway to synergistically inhibit seed germination in rice (Oryza sativa). New Phytol 228:1336–1353

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Xiang Y, Tang N, Du H, Ye H, Xiong L (2008) Characterization of OsbZIP23 as a key player of the basic leucine zipper transcription factor family for conferring abscisic acid sensitivity and salinity and drought tolerance in rice. Plant Physiol 148:1938–1952

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Yang S, Xu K, Chen S, Li T, Xia H, Chen L, Liu H, Luo L (2019) A stress-responsive bZIP transcription factor OsbZIP62 improves drought and oxidative tolerance in rice. BMC Plant Biol 19:1–5

    Article  Google Scholar 

  • Yoshida R, Umezawa T, Mizoguchi T, Takahashi S, Takahashi F, Shinozaki K (2006) The regulatory domain of SRK2E/OST1/SnRK2.6 interacts with ABI1 and integrates abscisic acid (ABA) and osmotic stress signals controlling stomatal closure in Arabidopsis. J Biol Chem 281:5310–5318

    Article  PubMed  CAS  Google Scholar 

  • Zhang H, Mao X, Wang C, Jing R (2010) Overexpression of a common wheat gene TaSnRK2.8 enhances tolerance to drought, salt and low temperature in Arabidopsis. PLoS ONE 5:e16041

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zhang H, Jia H, Liu G, Yang S, Zhang S, Yang Y, Cui H (2014) Cloning and characterization of NtSnRK2. 7 and NtSnRK2. 8 genes involved in abiotic stress responses from Nicotiana tabacum. Acta Physiol Plant 36:1673–1682

    Article  CAS  Google Scholar 

  • Zhou XE, Soon FF, Ng LM, Kovach A, Suino-Powell KM, Li J et al (2012) Catalytic mechanism and kinase interactions of ABA-signaling PP2C phosphatases. Plant Signal Behav 7:581–588

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zong W, Tang N, Yang J, Peng L, Ma S, Xu Y, Li G, Xiong L (2016) Feedback regulation of ABA signaling and biosynthesis by a bZIP transcription factor targets drought-resistance-related genes. Plant Physiol 171:2810–2825

    Article  PubMed  PubMed Central  CAS  Google Scholar 

Download references

Funding

The authors have not disclosed any funding.

Author information

Authors and Affiliations

  1. Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India

    Nand Lal Meena, Chirag Maheshwari & Aruna Tyagi

  2. Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India

    Nand Lal Meena

Authors
  1. Nand Lal Meena
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Chirag Maheshwari
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Aruna Tyagi
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Aruna Tyagi.

Ethics declarations

Conflict of interest

The authors declare no conflict of interest.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Meena, N.L., Maheshwari, C. & Tyagi, A. Computational study of sucrose non-fermenting 1-related kinase 2 (SnRK2): An in-silico approach for homology modelling and structural characterization of drought related SAPK9 gene in rice (Oryza sativa L.). Genet Resour Crop Evol 71, 497–510 (2024). https://doi.org/10.1007/s10722-023-01642-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10722-023-01642-4

Keywords

Search

Navigation