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Genome-wide analysis of autophagy-related genes (ARGs) in grapevine and plant tolerance to copper stress

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Abstract

Main conclusion

Grapevine autophagy-related genes (ARGs) include 35 members that have unique evolutionary backgrounds and expression patterns, with some of them responding to abiotic stresses, including copper stress.

Autophagy is one of the most crucial self-regulating phenomena in livings organisms, including animals, plants, yeasts, etc. In the genomes of plants, like Arabidopsis, rice, tobacco, and barley, more than 30 autophagy-related genes (ARGs) have been found. These ARGs are involved in plant development, programed cell death, and the stress response process. In plants, and particularly in grapevine, high copper stress results from the application of the Bordeaux mixture, a widely used fungicide. However, the function of autophagy in plant tolerance to copper stress is unknown. Accordingly, in this study, a genome-wide analysis was performed to identify Vitis vinifera ARGs (VvARGs), and 35 VvARGs were detected. A gene family analysis revealed that the tandem and segmental duplication events played significant roles in the VvARG gene family expansion. Moreover, there was more intense signature of purifying selection for the comparison between grape and rice than between grape and Arabidopsis. In response to copper treatment, both the autophagosome number and malondialdehyde concentration increased during the initial 4 h post-treatment, and reached maximal values at 24 h. An expression analysis indicated that most VvARGs responded to copper stress at 4 h post-treatment, and some VvARGs (e.g., VvATG6, VvATG8i, and VvATG18h) exhibited responses to most abiotic stresses. These results provide a detailed overview of the ARGs in grapevine and indicate multiple functions of autophagy in fruit development and abiotic stresses in grapevine. The key ARG (e.g., ATG8i) should be investigated in more detail in grapevine and other plant species.

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Abbreviations

ARGs:

Autophagy-related genes

ATG:

Autophagy

MV:

Methyl viologen

ROS:

Oxidative species

SOD:

Superoxide dismutase

POD:

Peroxidase

CAT:

Catalase

JTT:

Jones–Taylor–Thornton

K a :

Non-synonymous substitutions per non-synonymous site

Ks:

Synonymous substitutions per synonymous site

RPKM:

Reads per kilobase per million mapped reads

MDC:

Monodansyl-cadaverine

MDA:

Malondialdehyde

References

  • Adams KL, Wendel JF (2005) Polyploidy and genome evolution in plants. Curr Opin Plant Biol 8(2):135–141

    Article  CAS  PubMed  Google Scholar 

  • Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25(17):3389–3402

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Avila-Ospina L, Marmagne A, Soulay F, Masclaux-Daubresse C (2016) Identification of barley (Hordeum vulgare L.) autophagy genes and their expression levels during leaf senescence, chronic nitrogen limitation and in response to dark exposure. Agronomy 6(1):15

    Article  Google Scholar 

  • Ban Q, Liu G, Wang Y (2011) A DREB gene from Limonium bicolor mediates molecular and physiological responses to copper stress in transgenic tobacco. J Plant Physiol 168(5):449–458

    Article  CAS  PubMed  Google Scholar 

  • Blanc G, Wolfe KH (2004) Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell Online 16(7):1667–1678

    Article  CAS  Google Scholar 

  • Brun L, Maillet J, Hinsinger P, Pepin M (2001) Evaluation of copper availability to plants in copper-contaminated vineyard soils. Environ Pollut 111(2):293–302

    Article  CAS  PubMed  Google Scholar 

  • Cadwell K, Liu JY, Brown SL, Miyoshi H, Loh J, Lennerz JK, Kishi C, Kc W, Carrero JA, Hunt S (2008) A key role for autophagy and the autophagy gene Atg16l1 in mouse and human intestinal Paneth cells. Nature 456(7219):259–263

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Crane PR, Friis EM, Pedersen KR (1995) The origin and early diversification of angiosperms. Nature 374(6517):27–33

    Article  CAS  Google Scholar 

  • Frankel LB, Wen J, Lees M, Høyer-Hansen M, Farkas T, Krogh A, Jäättelä M, Lund AH (2011) microRNA-101 is a potent inhibitor of autophagy. EMBO J 30(22):4628–4641

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gaut BS, Morton BR, McCaig BC, Clegg MT (1996) Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. Proc Natl Acad Sci 93(19):10274–10279

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gill T, Dogra V, Kumar S, Ahuja PS, Sreenivasulu Y (2012) Protein dynamics during seed germination under copper stress in Arabidopsis over-expressing Potentilla superoxide dismutase. J Plant Res 125(1):165–172

    Article  CAS  PubMed  Google Scholar 

  • Gwak H-S, Kim TH, Jo GH, Kim Y-J, Kwak H-J, Kim JH, Yin J, Yoo H, Lee SH, Park JB (2012) Silencing of microRNA-21 confers radio-sensitivity through inhibition of the PI3K/AKT pathway and enhancing autophagy in malignant glioma cell lines. PLoS One 7(10):e47449

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hu B, Jin J, Guo A-Y, Zhang H, Luo J, Gao G (2014) GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics 31(8):1296–1297

    Article  PubMed  PubMed Central  Google Scholar 

  • Ihaka R, Gentleman R (1996) R: a language for data analysis and graphics. J Comput Graph Stat 5(3):299–314

    Google Scholar 

  • Jaillon O, Aury J-M, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449(7161):463–467

    Article  CAS  PubMed  Google Scholar 

  • Juretic N, Hoen DR, Huynh ML, Harrison PM, Bureau TE (2005) The evolutionary fate of MULE-mediated duplications of host gene fragments in rice. Genome Res 15(9):1292–1297

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kellogg EA (2001) Evolutionary history of the grasses. Plant Physiol 125(3):1198–1205

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL (2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14(4):R36

    Article  PubMed  PubMed Central  Google Scholar 

  • Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA (2009) Circos: an information aesthetic for comparative genomics. Genome Res 19(9):1639–1645

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 3:msw054

    Google Scholar 

  • Kuzuoglu-Ozturk D, Yalcinkaya OC, Akpinar BA, Mitou G, Korkmaz G, Gozuacik D, Budak H (2012) Autophagy-related gene, TdAtg8, in wild emmer wheat plays a role in drought and osmotic stress response. Planta 236(4):1081–1092

    Article  CAS  PubMed  Google Scholar 

  • Kwon SI, Park OK (2008) Autophagy in plants. J Plant Biol 51(5):313–320

    Article  CAS  Google Scholar 

  • Lai Z, Wang F, Zheng Z, Fan B, Chen Z (2011) A critical role of autophagy in plant resistance to necrotrophic fungal pathogens. Plant J 66(6):953–968

    Article  CAS  PubMed  Google Scholar 

  • Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9(4):357–359

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Leng X, Jia H, Sun X, Shangguan L, Mu Q, Wang B, Fang J (2015a) Comparative transcriptome analysis of grapevine in response to copper stress. Nat Publ Group Sci Rep 5:17749

    CAS  Google Scholar 

  • Leng X, Mu Q, Wang X, Li X, Zhu X, Shangguan L, Fang J (2015b) Transporters, chaperones, and P-type ATPases controlling grapevine copper homeostasis. Funct Integr Genom 15(6):673–684

    Article  CAS  Google Scholar 

  • Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25(16):2078–2079

    Article  PubMed  PubMed Central  Google Scholar 

  • Li F, Chung T, Vierstra RD (2014) AUTOPHAGY-RELATED11 plays a critical role in general autophagy-and senescence-induced mitophagy in Arabidopsis. Plant Cell 26(2):788–807

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li F, Chung T, Pennington JG, Federico ML, Kaeppler HF, Kaeppler SM, Otegui MS, Vierstra RD (2015) Autophagic recycling plays a central role in maize nitrogen remobilization. Plant Cell 27(5):1389–1408

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li W, Chen M, Wang E, Hu L, Hawkesford MJ, Zhong L, Chen Z, Xu Z, Li L, Zhou Y (2016) Genome-wide analysis of autophagy-associated genes in foxtail millet (Setaria italica L.) and characterization of the function of SiATG8a in conferring tolerance to nitrogen starvation in rice. BMC Genom 17(1):797

    Article  Google Scholar 

  • Liu Y, Schiff M, Czymmek K, Tallóczy Z, Levine B, Dinesh-Kumar S (2005) Autophagy regulates programmed cell death during the plant innate immune response. Cell 121(4):567–577

    Article  CAS  PubMed  Google Scholar 

  • Liu Y, Xiong Y, Bassham DC (2009) Autophagy is required for tolerance of drought and salt stress in plants. Autophagy 5(7):954–963

    Article  CAS  PubMed  Google Scholar 

  • Marchler-Bauer A, Derbyshire MK, Gonzales NR, Lu S, Chitsaz F, Geer LY, Geer RC, He J, Gwadz M, Hurwitz DI (2014) CDD: NCBI’s conserved domain database. Nucleic Acids Res 43:gku1221

    Google Scholar 

  • Nakatogawa H, Ichimura Y, Ohsumi Y (2007) Atg8, a ubiquitin-like protein required for autophagosome formation, mediates membrane tethering and hemifusion. Cell 130(1):165–178

    Article  CAS  PubMed  Google Scholar 

  • Ohsumi Y (2001) Molecular dissection of autophagy: two ubiquitin-like systems. Nat Rev Mol Cell Biol 2(3):211–216

    Article  CAS  PubMed  Google Scholar 

  • Pei D, Zhang W, Sun H, Wei X, Yue J, Wang H (2014) Identification of autophagy-related genes ATG4 and ATG8 from wheat (Triticum aestivum L.) and profiling of their expression patterns responding to biotic and abiotic stresses. Plant Cell Rep 33(10):1697–1710

    Article  CAS  PubMed  Google Scholar 

  • Qin G, Ma Z, Zhang L, Xing S, Hou X, Deng J, Liu J, Chen Z, Qu L-J, Gu H (2007) Arabidopsis AtBECLIN 1/AtAtg6/AtVps30 is essential for pollen germination and plant development. Cell Res 17(3):249–263

    Article  CAS  PubMed  Google Scholar 

  • Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26(1):139–140

    Article  CAS  PubMed  Google Scholar 

  • Rose TL, Bonneau L, Der C, Marty-Mazars D, Marty F (2006) Starvation-induced expression of autophagy-related genes in Arabidopsis. Biol Cell 98(1):53–67

    Article  CAS  PubMed  Google Scholar 

  • Shangguan L, Mu Q, Fang X, Zhang K, Jia H, Li X, Bao Y, Fang J (2017) RNA-sequencing reveals biological networks during table grapevine (‘Fujiminori’) fruit development. PLoS One 12(1):e0170571

    Article  PubMed  PubMed Central  Google Scholar 

  • Shin J-H, Yoshimoto K, Ohsumi Y, J-s Jeon, An G (2009) OsATG10b, an autophagosome component, is needed for cell survival against oxidative stresses in rice. Mol Cells 27(1):67–74

    Article  CAS  PubMed  Google Scholar 

  • Slavikova S, Ufaz S, Avin-Wittenberg T, Levanony H, Galili G (2008) An autophagy-associated Atg8 protein is involved in the responses of Arabidopsis seedlings to hormonal controls and abiotic stresses. J Exp Bot 59(14):4029–4043

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Song Y, Cui J, Zhang H, Wang G, Zhao F-J, Shen Z (2013) Proteomic analysis of copper stress responses in the roots of two rice (Oryza sativa L.) varieties differing in Cu tolerance. Plant Soil 366(1–2):647–658

    Article  CAS  Google Scholar 

  • Surpin M, Zheng H, Morita MT, Saito C, Avila E, Blakeslee JJ, Bandyopadhyay A, Kovaleva V, Carter D, Murphy A (2003) The VTI family of SNARE proteins is necessary for plant viability and mediates different protein transport pathways. Plant Cell 15(12):2885–2899

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Suttangkakul A, Li F, Chung T, Vierstra RD (2011) The ATG1/ATG13 protein kinase complex is both a regulator and a target of autophagic recycling in Arabidopsis. Plant Cell 23(10):3761–3779

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Thompson AR, Vierstra RD (2005) Autophagic recycling: lessons from yeast help define the process in plants. Curr Opin Plant Biol 8(2):165–173

    Article  CAS  PubMed  Google Scholar 

  • Thounaojam TC, Panda P, Mazumdar P, Kumar D, Sharma G, Sahoo L, Sanjib P (2012) Excess copper induced oxidative stress and response of antioxidants in rice. Plant Physiol Biochem 53:33–39

    Article  CAS  PubMed  Google Scholar 

  • Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7(3):562

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Velasco R, Zharkikh A, Troggio M, Cartwright DA, Cestaro A, Pruss D, Pindo M, FitzGerald LM, Vezzulli S, Reid J (2007) A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLoS One 2(12):e1326

    Article  PubMed  PubMed Central  Google Scholar 

  • Wang Y, Tang H, DeBarry JD, Tan X, Li J, Wang X, T-h Lee, Jin H, Marler B, Guo H (2012) MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res 40(7):e49–e49

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang P, Sun X, Jia X, Wang N, Gong X, Ma F (2016) Characterization of an autophagy-related gene MdATG8i from apple. Front Plant Sci 7:720

    PubMed  PubMed Central  Google Scholar 

  • Wang P, Sun X, Wang N, Jia X, Ma F (2017) Ectopic expression of an autophagy-associated MdATG7b gene from apple alters growth and tolerance to nutrient stress in Arabidopsis thaliana. Plant Cell Tissue Organ Cult (PCTOC) 128(1):9–23

    Article  CAS  Google Scholar 

  • Wickham H (2009) ggplot2: Elegant graphics for data analysis. Springer-Verlag, New York

    Book  Google Scholar 

  • Wolfe KH, Gouy M, Yang Y-W, Sharp PM, Li W-H (1989) Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data. Proc Natl Acad Sci 86(16):6201–6205

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xia K, Liu T, Ouyang J, Wang R, Fan T, Zhang M (2011) Genome-wide identification, classification, and expression analysis of autophagy-associated gene homologues in rice (Oryza sativa L.). DNA Res 18:dsr024

    Google Scholar 

  • Xiong Y, Contento AL, Nguyen PQ, Bassham DC (2007) Degradation of oxidized proteins by autophagy during oxidative stress in Arabidopsis. Plant Physiol 143(1):291–299

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yoshimoto K, Takano Y, Sakai Y (2010) Autophagy in plants and phytopathogens. FEBS Lett 584(7):1350–1358

    Article  CAS  PubMed  Google Scholar 

  • Yu J, Wang J, Lin W, Li S, Li H, Zhou J, Ni P, Dong W, Hu S, Zeng C (2005) The genomes of Oryza sativa: a history of duplications. PLoS Biol 3(2):e38

    Article  PubMed  PubMed Central  Google Scholar 

  • Yu Y, Cao L, Yang L, Kang R, Lotze M, Tang D (2012) microRNA 30A promotes autophagy in response to cancer therapy. Autophagy 8(5):853–855

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang Z, Li J, Zhao X-Q, Wang J, Wong GK-S, Yu J (2006) KaKs_Calculator: calculating K a and K s through model selection and model averaging. Genom Proteom Bioinform 4(4):259–263

    Article  CAS  Google Scholar 

  • Zhang Y, Wang C, Yu H, Cai B, Fang J (2010) Screening of RNA extraction methods for various grapevine organs and tissues. Acta Agric Boreali-Occident Sinica 19(11):135–140

    Google Scholar 

  • Zhang Z, Xiao J, Wu J, Zhang H, Liu G, Wang X, Dai L (2012) ParaAT: a parallel tool for constructing multiple protein-coding DNA alignments. Biochem Biophys Res Commun 419(4):779–781

    Article  CAS  PubMed  Google Scholar 

  • Zhou J, Wang J, Cheng Y, Chi Y-J, Fan B, Yu J-Q, Chen Z (2013) NBR1-mediated selective autophagy targets insoluble ubiquitinated protein aggregates in plant stress responses. PLoS Genet 9(1):e1003196

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhou J, Wang J, Yu J-Q, Chen Z (2014) Role and regulation of autophagy in heat stress responses of tomato plants. Front Plant Sci 5:174

    PubMed  PubMed Central  Google Scholar 

  • Zhou X, Zhao P, Wang W, Zou J, Cheng T, Peng X, Sun M (2015) A comprehensive, genome-wide analysis of autophagy-related genes identified in tobacco suggests a central role of autophagy in plant response to various environmental cues. DNA Res 22(4):245–257

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhuang X, Cui Y, Gao C, Jiang L (2015) Endocytic and autophagic pathways crosstalk in plants. Curr Opin Plant Biol 28:39–47

    Article  CAS  PubMed  Google Scholar 

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Funding

This work was supported by the National Natural Science Foundation of China (31772283 and 31401846).

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Authors and Affiliations

  1. Horticultural Department, Nanjing Agricultural University, Nanjing, 210095, China

    Lingfei Shangguan, Xiang Fang, Lide Chen, Liwen Cui & Jinggui Fang

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  1. Lingfei Shangguan
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  2. Xiang Fang
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  3. Lide Chen
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  4. Liwen Cui
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Correspondence to Jinggui Fang.

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425_2018_2864_MOESM1_ESM.xlsx

Supplementary material 1 Table S1 Summary of target genes used in this study. Table S2 Detailed information for grapevine autophagy-related genes. Table S3 Detailed information for rice autophagy-related genes. Table S4 Detailed information for Arabidopsis autophagy-related genes. Table S5 Detailed information for tobacco autophagy-related genes. Table S6 Ka/Ks analysis of duplicated VvARG and AtARG homologues. Table S7 Ka/Ks analysis of duplicated VvARG and OsARG homologues (XLSX 63 kb)

425_2018_2864_MOESM2_ESM.docx

Supplementary material 2 Figure 1. Protein alignment of the autophagy-related genes families. (a). Protein alignment of the ATG1 family; (b). Protein alignment of the ATG13 family; (c). Protein alignment of the ATG18 family; (d). Protein alignment of the VTI12 family. Figure 2 Phylogenetic trees of ATG1 (a), ATG13 (b), VTI12 (c), and ATG18 (d). Different species belonging to the dicot and monocot lineages are marked with different symbols (empty symbol represents monocots and solid symbol represents dicots. M, monocotyledon; D, dicotyledon) (DOCX 6657 kb)

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Shangguan, L., Fang, X., Chen, L. et al. Genome-wide analysis of autophagy-related genes (ARGs) in grapevine and plant tolerance to copper stress. Planta 247, 1449–1463 (2018). https://doi.org/10.1007/s00425-018-2864-3

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