Transcriptome wide characterization of water deficit responsive grape mTERF transcription

  • Behcet İnalEmail author
  • Emre İlhan
  • İlker Büyük
  • Serdar Altıntaş
Original Article


Plant mitochondrial transcription termination factor (mTERF) is a large and important family with valuable roles in organizing of organelle gene expression under the various stresses. In this study, genome wide analysis of mTERF regulatory genes was achieved and twenty-five potential mTERF genes response water deficit in grape (Vitis vinifera L.) were determined. Most of them were targeted to organelles genome especially mitochondria. It was found that Grape mTERFs were clustered into six main groups based on phylogenetic analysis. As a result of comprehensive expression analysis of these genes, using RNA-seq data in this study revealed that these genes have various expression profiles. With this study, various important roles of mTERF genes of grape under the water deficit stress were reported at first in grape. All results were found will be useful for elucidating the roles of mTERF genes in the growth, development and stress response of grape and fundamental for functional genomic studies.


Grape mTERF Mitochondria RNA-seq Water stress 



Biological processes


Cellular component


Molecular functions


Mitochondrial transcription termination factor




Compliance with ethical standards

Conflict of interest

The authors report no potential conflicts of interest


  1. Babiychuk E, Vandepoele K, Wissing J, Garcia-Diaz M, De Rycke R, Akbari H, Joubès J, Beeckman T, Jänsch L, Frentzen M (2011) Plastid gene expression and plant development require a plastidic protein of the mitochondrial transcription termination factor family. Proc Natl Acad Sci 108(16):6674–6679CrossRefGoogle Scholar
  2. Bailey TL, Williams N, Misleh C, Li WW (2006) MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res 34(Web Server issue):W369–W373. CrossRefGoogle Scholar
  3. Baloglu MC, Eldem V, Hajyzadeh M, Unver T (2014) Genome-wide analysis of the bZIP transcription factors in cucumber. PLoS ONE 9(4):e96014CrossRefGoogle Scholar
  4. Caraux G, Pinloche S (2005) PermutMatrix: a graphical environment to arrange gene expression profiles in optimal linear order. Bioinformatics 21(7):1280–1281. CrossRefGoogle Scholar
  5. Chaves M, Zarrouk O, Francisco R, Costa J, Santos T, Regalado A, Rodrigues M, Lopes C (2010) Grapevine under deficit irrigation: hints from physiological and molecular data. Ann Bot 105(5):661–676CrossRefGoogle Scholar
  6. Emanuelsson O, Brunak S, von Heijne G, Nielsen H (2007) Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc 2(4):953–971CrossRefGoogle Scholar
  7. FAO (2014) FAOSTAT. Food and Agriculture Organization of the United Nations, Rome, ItalyGoogle Scholar
  8. Fernandez-Silva P, Martinez-Azorin F, Micol V, Attardi G (1997) The human mitochondrial transcription termination factor (mTERF) is a multizipper protein but binds to DNA as a monomer, with evidence pointing to intramolecular leucine zipper interactions. EMBO J 16(5):1066–1079CrossRefGoogle Scholar
  9. Ghan R, Van Sluyter SC, Hochberg U, Degu A, Hopper DW, Tillet RL, Schlauch KA, Haynes PA, Fait A, Cramer GR (2015) Five omic technologies are concordant in differentiating the biochemical characteristics of the berries of five grapevine (Vitis vinifera L.) cultivars. BMC Genom 16(1):946CrossRefGoogle Scholar
  10. Goodstein DM, Shu SQ, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N, Rokhsar DS (2012) Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res 40(D1):D1178–D1186CrossRefGoogle Scholar
  11. Guo AY, Zhu QH, Chen X, Luo JC (2007) GSDS: a gene structure display server. Yi chuan = Hereditas/Zhongguo yi chuan xue hui bian ji 29(8):1023–1026CrossRefGoogle Scholar
  12. Horton P, Park KJ, Obayashi T, Fujita N, Harada H, Adams-Collier CJ, Nakai K (2007) WoLF PSORT: protein localization predictor. Nucleic Acids Res 35(Web Server issue):W585–W587. CrossRefGoogle Scholar
  13. Jefferys BR, Kelley LA, Sternberg MJ (2010) Protein folding requires crowd control in a simulated cell. J Mol Biol 397(5):1329–1338CrossRefGoogle Scholar
  14. Kim M, Lee U, Small I, des Francs-Small CC, Vierling E (2012) Mutations in an Arabidopsis mitochondrial transcription termination factor-related protein enhance thermotolerance in the absence of the major molecular chaperone HSP101. Plant Cell 24(8):3349–3365CrossRefGoogle Scholar
  15. Kleine T (2012) Arabidopsis thaliana mTERF proteins: evolution and functional classification. Front Plant Sci 3:233CrossRefGoogle Scholar
  16. Kushwaha H, Gupta S, Singh VK, Rastogi S, Yadav D (2011) Genome wide identification of Dof transcription factor gene family in sorghum and its comparative phylogenetic analysis with rice and Arabidopsis. Mol Biol Rep 38(8):5037–5053. CrossRefGoogle Scholar
  17. Letunic I, Bork P (2011) Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res 39:W475–W478CrossRefGoogle Scholar
  18. Lijavetzky D, Carbonero P, Vicente-Carbajosa J (2003) Genome-wide comparative phylogenetic analysis of the rice and Arabidopsis Dof gene families. BMC Evol Biol 3:17. CrossRefGoogle Scholar
  19. Luo M, Gao Z, Li H, Li Q, Zhang C, Xu W, Song S, Ma C, Wang S (2018) Selection of reference genes for miRNA qRT-PCR under abiotic stress in grapevine. Sci Rep 8(1):4444CrossRefGoogle Scholar
  20. Lynch M, Conery JS (2003) The evolutionary demography of duplicate genes. J Struct Funct Genom 3(1–4):35–44CrossRefGoogle Scholar
  21. Meskauskiene R, Würsch M, Laloi C, Vidi PA, Coll NS, Kessler F, Baruah A, Kim C, Apel K (2009) A mutation in the Arabidopsis mTERF-related plastid protein SOLDAT10 activates retrograde signaling and suppresses 1O2-induced cell death. Plant J 60(3):399–410CrossRefGoogle Scholar
  22. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5(7):621–628. CrossRefGoogle Scholar
  23. Pagliarani C, Vitali M, Ferrero M, Vitulo N, Incarbone M, Lovisolo C, Valle G, Schubert A (2017) Accumulation of microRNAs differentially modulated by drought is affected by grafting in grapevine. Plant Physiol 173:2180–2195CrossRefGoogle Scholar
  24. Quesada V, Sarmiento-Mañús R, González-Bayón R, Hricová A, Pérez-Marcos R, Graciá-Martínez E, Medina-Ruiz L, Leyva-Díaz E, Ponce MR, Micol JL (2011) Arabidopsis RUGOSA2 encodes an mTERF family member required for mitochondrion, chloroplast and leaf development. Plant J 68(4):738–753CrossRefGoogle Scholar
  25. Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R (2005) InterProScan: protein domains identifier. Nucleic Acids Res 33(Web Server issue):W116–W120. CrossRefGoogle Scholar
  26. Roberti M, Bruni F, Polosa PL, Manzari C, Gadaleta MN, Cantatore P (2006) MTERF3, the most conserved member of the mTERF-family, is a modular factor involved in mitochondrial protein synthesis. Biochim Biophys Acta (BBA) Bioenerg 1757(9):1199–1206CrossRefGoogle Scholar
  27. Roberti M, Polosa PL, Bruni F, Manzari C, Deceglie S, Gadaleta MN, Cantatore P (2009) The MTERF family proteins: mitochondrial transcription regulators and beyond. Biochim Biophys Acta (BBA) Bioenerg 1787(5):303–311CrossRefGoogle Scholar
  28. Robles P, Micol JL, Quesada V (2012) Unveiling plant mTERF functions. Mol Plant 5(2):294–296CrossRefGoogle Scholar
  29. Sazegari S, Niazi A, Ahmadi FS (2015) A study on the regulatory network with promoter analysis for Arabidopsis DREB-genes. Bioinformation 11(2):101CrossRefGoogle Scholar
  30. Schönfeld C, Wobbe L, Borgstädt R, Kienast A, Nixon PJ, Kruse O (2004) The nucleus-encoded protein MOC1 is essential for mitochondrial light acclimation in Chlamydomonas reinhardtii. J Biol Chem 279(48):50366–50374CrossRefGoogle Scholar
  31. Snyman MC, Solofoharivelo M-C, Souza-Richards R, Stephan D, Murray S, Burger JT (2017) The use of high-throughput small RNA sequencing reveals differentially expressed microRNAs in response to aster yellows phytoplasma-infection in Vitis vinifera cv.‘Chardonnay’. PloS ONE 12(8):e0182629CrossRefGoogle Scholar
  32. Suyama M, Torrents D, Bork P (2006) PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res 34:W609–W612CrossRefGoogle Scholar
  33. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25(24):4876–4882CrossRefGoogle Scholar
  34. Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93(1):77–78CrossRefGoogle Scholar
  35. Yang Z, Nielsen R (2000) Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol 17(1):32–43CrossRefGoogle Scholar
  36. Yang Z, Gu S, Wang X, Li W, Tang Z, Xu C (2008) Molecular evolution of the CPP-like gene family in plants: insights from comparative genomics of Arabidopsis and rice. J Mol Evol 67(3):266–277. CrossRefGoogle Scholar
  37. Zhang Y (2005) miRU: an automated plant miRNA target prediction server. Nucleic Acids Res 33(Web Server issue):W701–W704. CrossRefGoogle Scholar
  38. Zhao Y, Cai M, Zhang X, Li Y, Zhang J, Zhao H, Kong F, Zheng Y, Qiu F (2014) Genome-wide identification, evolution and expression analysis of mTERF gene family in maize. PLoS ONE 9(4):e94126CrossRefGoogle Scholar

Copyright information

© Society for Plant Biochemistry and Biotechnology 2019

Authors and Affiliations

  1. 1.Department of Agricultural Biotechnology, Faculty of AgricultureSiirt UniversitySiirtTurkey
  2. 2.Department of Molecular Biology and Genetics, Faculty of ScienceErzurum Technical UniversityErzurumTurkey
  3. 3.Department of Biology, Faculty of ScienceAnkara UniversityAnkaraTurkey

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