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RNA-seq analysis reveals the role of a small GTP-binding protein, Rab7, in regulating clathrin-mediated endocytosis and salinity-stress resistance in peanut

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Abstract

Small GTP-binding proteins, Rab7, are known to be responsive to abiotic stresses in plants, but the molecular mechanism is poorly understood. To investigate how AhRab7 increases resistance to salinity stress in peanut, this study compared a transgenic genotype (S5) that overexpressed the AhRab7 gene and that had high salinity resistance with a non-transgenic genotype (S7) that had low salinity resistance. Digital gene expression (DGE) sequencing was performed with leaves of S5 and S7 before and after salinity-stress treatment. In total, 2697 differentially expressed genes (DEGs) were identified between S5 and S7, and KEGG enrichment analyses showed that the DEGs are involved pathways including endocytosis, lysosome, hormone signaling, phosphatidylinositol signaling, calcium, and others. Among them, 164 were differentially regulated after salinity-stress treatment. Of 164 DEGs, 110 were responsive to salinity stress in S5 and/or S7. The 110 DEGs included genes that encode the following kinds of transcription factors and proteins known to be involved in resistance to salinity stress: WRKY, NAC, MYM-type zinc finger, late embryogenesis abundant proteins, lipid transfer protein, 1-cys peroxiredoxin, aquaporin, oleosin, and others. AhRab7 gene might mediate signaling pathways including phosphatidylinositol, calcium, abscisic acid, etc., and then regulate the expression of transcription factors and downstream genes for ROS scavenging in peanut. The results of this study will be useful for further investigations of the mechanism underlying the role of the AhRab7 gene in resistance to salinity stress in peanut.

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Abbreviations

ABA:

Abscisic acid

ROS:

Reactive oxygen species

DGE:

Digital gene expression

DEG:

Differentially expressed gene

NADPH:

Hydroxymethylglutaryl-CoA reductase

PM:

Plasma membrane

ARF:

ADP ribosylation factor

ARFGEF:

ARF-guanine nucleotide exchange factor

AP:

Adaptor protein

PIP2:

Phosphatidylinositol (4, 5)-bisphosphate

PIP3:

Phosphatidylinositol (3, 4, 5)-bisphosphate

PIP:

Phosphatidylinositol

PI5K:

Phosphatidylinositol-3-phosphate 5-kinase

PLC:

Phosphatidylinositol phospholipase C

CALM:

Calmodulin

SNARE:

Soluble NSF attachment protein receptor

VAMP:

Vesicle-associated membrane protein

ECSRT:

Endosomal complexes required for transport

IP3:

1, 4, 5-trisphosphate

DAG:

1, 2-diacyl-glycerol

TF:

Transcription factor

References

  • Agarwal PK, Agarwal P, Jain P, Jha B, Reddy MK, Sopory SK (2008) Constitutive overexpression of a stress-inducible small GTP-binding protein PgRab7 from Pennisetum glaucum enhances abiotic stress tolerance in transgenic tobacco. Plant Cell Rep 27:105–115

    Article  CAS  PubMed  Google Scholar 

  • Bolte S, Schiene K, Dietz KJ (2000) Characterization of a small GTP-binding protein of the rab5 family in Mesembryanthemum crystallinum with increased level of expression during early salt stress. Plant Mol Biol 42:923–936

    Article  CAS  PubMed  Google Scholar 

  • Boucrot E, Saffarian S, Zhang RY, Kirchhausen (2010) Roles of AP-2 in clathrin-mediated endocytosis. PLoS One 5:e10597

    Article  PubMed  PubMed Central  Google Scholar 

  • Brighouse A, Dacks JB, Field MC (2010) Rab protein evolution and the history of the eukaryotic endomembrane system. Cell Mol Life Sci 67:3449–3465

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Croizet-Berger K, Daumerie C, Couvreur M, Courtoy PJ, van den Hove MF (2002) The endocytic catalysts, Rab5a and Rab7, are tandem regulators of thyroid hormone production. Proc Natl Acad Sci USA 99:8277–8282

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ford MGJ, Mills IG, Peter BJ, Vallis Y, Praefcke GJK, Evans PR, McMahon HT (2002) Curvature of clathrin-coated pits driven by epsin. Nature 419:361–366

    Article  CAS  PubMed  Google Scholar 

  • Kang JG, Yun J, Kim DH, Chung KS, Fujioka S, Kim JI, Dae HW, Yoshida S, Takatsuto S, Song PS, Park CM (2001) Light and brassinosteroid signals are integrated via a dark-induced small G protein in etiolated seedling growth. Cell 105:625–636

    Article  CAS  PubMed  Google Scholar 

  • Mazel A, Lehem Y, Tiwari BS, Levine A (2004) Induction of salt and osmotic stress tolerance by overexpression of an intracellular vesicle trafficking protein AtRab7 (AtRabG3e). Plant Physiol 134:118–128

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • McMahon HT, Boucrot E (2011) Molecular mechanism and physiological functions of clathrin-mediated endocytosis. Nat Rev Mol Cell Biol 12:517–533

    Article  CAS  PubMed  Google Scholar 

  • Nahm MY, Kim SW, Yun D, Lee SY, Cho MJ, Bahk JD (2003) Molecular and biochemical analyses of OsRab7, a rice Rab7 homolog. Plant Cell Physiol 44:1341–1349

    Article  CAS  PubMed  Google Scholar 

  • Naramoto S, Keine-Vehn J, Robert S, Fujimoto M, Dainobu T, Paciorek T, Ueda T, Nakano A, Van Montagu MC, Fukuda H, Friml J (2010) ADP-ribosylation factor machinery mediates endocytosis in plant cells. Proc Natl Acad Sci USA 107:21890–21895

  • Nicola´s C, Nicola´s G, Rodrı´guez D (1998) Transcripts of a gene, encoding a small GTP-binding protein from Fagus sylvatica, are induced by ABA and accumulated in the embryonic axis of dormant seeds. Plant Mol Biol 36:487–491

    Article  Google Scholar 

  • O’Mahony PJ, Oliver MJ (1999) Characterization of a desiccation responsive small GTP binding protein (Rab2) from the desiccation-tolerant grass Sporobolus stapfianus. Plant Mol Biol 39:809–821

    Article  PubMed  Google Scholar 

  • Ohya T, Miaczynska M, Coskun U, Lommer B, Runge A, Drechsel D, Kalaidzidis Y, Zerial M (2009) Reconstitution of Rab- and SNARE-dependent membrane fusion by synthetic endosomes. Nature 459:1091–1097

    Article  CAS  PubMed  Google Scholar 

  • Pereira-Leal JB, Seabra MC (2001) Evolution of the Rab family of small GTP binding proteins. J Mol Biol 313:889–901

    Article  CAS  PubMed  Google Scholar 

  • Rajan N, Agarwal P, Patel K, Sanadhya P, Khedia J, Agarwal1 PK (2015) Molecular characterization and identification of target protein of an important vesicle trafficking gene AlRab7 from a salt excreting halophyte Aeluropus lagopoides. DNA Cell Biol 34:83–91

  • Schimmoller F, Reizman H (1993) Involvement of Ypt7p, a small GTPase, in traffic from late endosome to the vacuole in yeast. J Cell Sc 106:823–830

    Google Scholar 

  • Short B, Preisinger C, Schaletzky J, Kopajtich R, Barr FA (2002) The Rab6 GTPase regulates recruitment of the dynactin complex to Golgi membranes. Curr Biol 12:1792–1795

    Article  CAS  PubMed  Google Scholar 

  • Sui JM, Li R, Fan QC, Song L, Zheng CH, Wang JS, Qiao LX, Yu SL (2013) Isolation and characterization of a stress responsive small GTP-binding protein AhRabG3b in peanut (Arachis hypogaea L.). Euphytica 189:161–172

    Article  CAS  Google Scholar 

  • Traub LM, Bonifacino JS (2013) Cargo recognition in clathrin-mediated endocytosis. Cold Spring Harb Perspect Biol 5:a016790

    Article  PubMed  PubMed Central  Google Scholar 

  • Vinocur B, Altman A (2005) Recent advances in engineering plant tolerance to abiotic stress: achievements and limitations. Curr Opin Biotech 16:123–132

    Article  CAS  PubMed  Google Scholar 

  • Wichmann H, Hengst L, Gallwitz D (1992) Endocytosis in yeast: evidence for the involvement of a small GTP binding protein (Ypt7p). Cell 71:1131–1142

    Article  CAS  PubMed  Google Scholar 

  • Xing Y, Böcking T, Wolf M, Grigorieff N, Kirchhausen T, Harrison SC (2010) Structure of clathrin coat with bound Hsc70 and auxilin: mechanism of Hsc70-facilitated disassembly. EMBO J 29:655–665

    Article  CAS  PubMed  Google Scholar 

  • Yang Z (2002) Small GTPases: versatile signaling switches in plants. Plant Cell 14:S375–S388

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang M, Chen L, Wang S, Wang T (2009) Rab7: roles in membrane trafficking and disease. Biosci Rep 29:193–209

    Article  PubMed  Google Scholar 

Download references

Acknowledgements

We thank Prof. Bruce Jaffee for critical reading of the manuscript. The research was supported by the National Natural Science Foundation of China (Grant No. 31301356, No. 31571705 and No. 31471542), and the Shandong Province Science and Technology Development Plan Project (Grant No. 2014GNC110002).

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    Authors and Affiliations

    1. Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Key Lab of Plant Biotechnology in Universities of Shandong, College of Life Science, Qingdao Agricultural University, Qingdao, 266109, China

      Jiongming Sui, Guan Li, Guanxu Chen, Chunmei Zhao, Xiangyuan Kong, Xiaomin Hou, Lixian Qiao & Jingshan Wang

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    1. Jiongming Sui
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    Corresponding author

    Correspondence to Jingshan Wang.

    Additional information

    Jiongming Sui and Guan Li contributed equally to this study.

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    Table S1. The summary of DGE profiles sequencing and analysis (DOC 55 KB)

    Table S2. DEGs at five time points between S5 and S7 genotypes (XLS 1420 KB)

    Table S3. Primers for RT-qPCR analysis (XLS 18 KB)

    Table S4. Result comparison of expression level of 10 DEGs between RNA-seq and real-time PCR (XLS 16 KB)

    Table S5. Selected differentially expressed genes involved in endocytosis (XLS 17 KB)

    Table S6. Selected differentially expressed kinesins and dyneins (XLS 71 KB)

    Table S7. Selected DEGs responsive to salinity stress based on comparison of S5 vs. S7 (XLS 102 KB)

    Fig. S1. The expression validation of DEGs by real-time PCR (TIF 234 KB)

    11816_2017_428_MOESM9_ESM.tif

    Fig. S2. DEGs of downregulation and upregulation in the “Endocytosis” pathway after overexpression of AhRab7. The figure was quoted from Kanehisa laboratories and then was marked with different color boxes. The upregulated DEGs were marked with red boxes, the downregulated DEGs were marked with green boxes. If the different member from the same gene family showed both upregulation and downregulation, they will be marked with yellow boxes (TIF 245 KB)

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    Sui, J., Li, G., Chen, G. et al. RNA-seq analysis reveals the role of a small GTP-binding protein, Rab7, in regulating clathrin-mediated endocytosis and salinity-stress resistance in peanut. Plant Biotechnol Rep 11, 43–52 (2017). https://doi.org/10.1007/s11816-017-0428-9

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    • DOI: https://doi.org/10.1007/s11816-017-0428-9

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