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Genome-Wide Identification and Characterization of DIR Genes in Medicago truncatula

  • Min SongEmail author
  • Xiangyong Peng
Original Article
First Online:

Abstract

Dirigent proteins (DIRs) are critically involved in the formation of lignans, a diverse and widely distributed class of secondary plant metabolites exhibiting interesting pharmacological activities and implicated in natural plant defense. However, no detailed information is available about DIR gene family in Medicago truncatula. In this study, a total of 45 DIR genes were identified in M. truncatula. DIR proteins have variability in sequence. Most MtDIR genes have no intron. All MtDIR proteins contain single dirigent domain. A large number of MtDIR genes were expanded via gene duplication, and 37 MtDIR genes were duplicated in tandem. Digital expression data showed that 40% MtDIR genes had a higher expression level in the root. Analysis of RNA-seq and microarray data indicated that more than 30% MtDIR genes were responsive to biotic and/or abiotic treatments. This study will facilitate further studies on DIR family and provide useful clues for functional validation of DIR genes in higher plants.

Keywords

Medicago truncatula Dirigent domain Gene family Expression pattern 
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Notes

Author Contributions

MS designed the experiments and wrote the paper. XYP analyzed the data. All authors read and approved the final manuscript.

Funding

This work was supported by the Science and Technology project of Shandong Education Department to Min Song (Grant No. J15LE02), and China Postdoctoral Science Foundation funded project to Min Song (Grant No. 2018M632646).

Compliance with Ethical Standards

Conflict of interest

Min Song declares that she does not have conflict of interest. Xiangyong Peng declares that he does not have conflict of interest.

Ethical Approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Informed Consent

This article does not contain any studies with human participants.

Supplementary material

10528_2019_9903_MOESM1_ESM.docx (28 kb)
Supplementary file1 (DOCX 28 kb) Text S1. Sequences of MtDIR CDSs and proteins.
10528_2019_9903_MOESM2_ESM.docx (305 kb)
Supplementary file2 (DOCX 305 kb) Figure S1. Phylogenetic tree (Left) and gene structure (Right) of MtDIRs. Orange boxes represent exons, blue lines represent UTRs, and black lines show introns. The lengths of the exons, introns and UTRs were drawn to scale. Figure S2. Hierarchial clustering display of DIR genes of M. truncatula seedlings exposed to salinity. Two week-old seedlings were grown in hydroponics media with 180mM NaCl for 0, 6, 24 and 48h (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc¬GSE13921). The logFC values were shown in heatmap drown by ClustVis tool. Rows were centered, no scaling was applied to rows. Rows were clustered using Euclidean distance and average linkage.
10528_2019_9903_MOESM3_ESM.docx (16 kb)
Supplementary file3 (DOCX 16 kb) Table S1. Subcellular localization, N-Glyc (Asn) position andsignal peptide of DIR genes in M. truncatula.
10528_2019_9903_MOESM4_ESM.docx (16 kb)
Supplementary file4 (DOCX 16 kb) Table S2. Motif sequences identified by the MEME Suite.
10528_2019_9903_MOESM5_ESM.xlsx (21 kb)
Supplementary file5 (XLSX 21 kb) Table S3. Cis-elements in the promoter region of 45 MtDIR genes.
10528_2019_9903_MOESM6_ESM.docx (21 kb)
Supplementary file6 (DOCX 20 kb) Table S4. Expression levels of MtDIR genes measured by transcriptome analysis.

References

  1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410Google Scholar
  2. Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L (2009) Meme suite: tools for motif discovery and searching. Nucl Acids Res 37:W202–W208Google Scholar
  3. Boudet AM (2000) Lignins and lignification: selected issues. Plant Physiol Biochem 38:81–96Google Scholar
  4. Burlat V, Kwon M, Davin LB, Lewis NG (2001) Dirigent proteins and dirigent sites in lignifying tissues. Phytochemistry 57:883–897Google Scholar
  5. Cannon SB, Mitra A, Baumgarten A, Young ND, May G (2004) The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana. BMC Plant Biol 4(1):10Google Scholar
  6. Chen CJ, Xia R, Chen H, He YH (2018) TBtools, a Toolkit for Biologists integrating various HTS-data handling tools with a user-friendly interface. bioRxiv. doi: 10.1101/289660Google Scholar
  7. Cheng X, Su X, Muhammad A, Li M, Zhang J, Sun Y et al (2018) Molecular characterization, evolution, and expression profiling of the dirigent (DIR) family genes in Chinese White Pear (Pyrus bretschneideri). Front Genet 9:136Google Scholar
  8. Damaj MB, Kumpatla SP, Emani C, Beremand PD, Avutu S, Reddy AS et al (2010) Sugarcane DIRIGENT and O-METHYLTRANSFERASE promoters confer stem-regulated gene expression in diverse monocots. Planta 231:1439–1458Google Scholar
  9. Daniels CH, Fristensky B, Wagoner W, Hadwiger LA (1987) Pea genes associated with non-host disease resistance to Fusarium are also active in race-specific disease resistance to Pseudomonas. Plant Mol Biol 8:309–316Google Scholar
  10. Darzentas N (2010) Circoletto: visualizing sequence similarity with circos. Bioinformatics 26(20):2620Google Scholar
  11. Davin LB, Lewis NG (2000) Dirigent proteins and dirigent sites explain the mystery of specificity of radical precursor coupling in lignan and lignin biosynthesis. Plant Physiol 123:453–461Google Scholar
  12. Davin LB, Wang HB, Crowell AL, Bedgar DL, Martin DM, Sarkanen S, Lewis NG (1997) Stereoselective bimolecular phenoxy radical coupling by anauxiliary (dirigent) protein without an active center. Science 275:362–366Google Scholar
  13. Funatsuki H, Suzuki M, Hirose A, Inaba H, Yamada T, Hajika M et al (2014) Molecular basis of a shattering resistance boosting global dissemination of soybean. Proc Natl Acad Sci USA 111(50):17797Google Scholar
  14. Gao CQ, Liu GF, Wang YC, Jiang J, Yang CP (2010) Cloning and analysis of dirigent-like protein in gene from Tamarix androssowii. Bull Bot Res 30(1):81–86Google Scholar
  15. Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR., Appel RD, Bairoch A (2005) Protein identification and analysis tools on the ExPASy Server. In: Walker JM (eds) The proteomics protocols handbook. Humana Press 571-607Google Scholar
  16. Guo AY, Zhu QH, Chen X, Luo JC (2007) GSDS: a gene structure display server. Yi Chuan 29:1023–1026Google Scholar
  17. Guo JL, Xu LP, Su YC, Fu HY, Que YX, Xu JS (2012) A novel dirigent protein gene with highly stem-specific expression from sugarcane, response to drought, salt and oxidative stresses. Plant Cell Rep 31(10):1801–1812Google Scholar
  18. Gupta, R., Jung, E. Brunak, S (2004) Prediction of N-glycosylation sites in human proteins. In preparationGoogle Scholar
  19. Hadwiger LA, Chiang CC, Horovitz D (1992) Expression of disease resistance response genes in near-isogenic pea cultivars following challenge by Fusarium oxysporum race 1. Physiol Mol Plant P 40: 259-269Google Scholar
  20. Horton P, Park KJ, Obayashi T, Fujita N, Harada H, Adams-Collier CJ, Nakai K (2007) WoLF PSORT: protein localization predictor. Nucl Acids Res 35:585–587Google Scholar
  21. Hosmani PS, Kamiya T, Danku J, Naseer S, Geldner N, Guerinot ML (2013) Dirigent domain-containing protein is part of the machinery required for formation of the lignin-based Casparian strip in the root. Proc Natl Acad Sci USA 110:14498–14503Google Scholar
  22. Hruz T, Laule O, Szabo G, Wessendorp F, Bleuler S, Oertle L, et al. (2008) Genevestigator V3: a reference expression database for the meta-analysis of transcriptomes. Adv Bioinformatics 2008:420747Google Scholar
  23. Khan A, Li RJ, Sun JT, Ma F, Zhang HX,Jin JH, et al. (2018) Genome-wide analysis of dirigent gene family in pepper (Capsicum annuum L.) and characterization of CaDIR7 in biotic and abiotic stresses. Sci Rep 8:5500Google Scholar
  24. Kim MK, Jeon JH, Davin LB, Lewis NG (2002a) Monolignol radical-radical coupling networks in western red cedar and Arabidopsis and their evolutionary implications. Phytochemistry 61(3):311–322Google Scholar
  25. Kim MK, Jeon J-H, Fujita M, Davin LB, Lewis NG (2002b) The western red cedar (Thuja plicata) 8–8′ DIRIGENT family displays diverse expression patterns and conserved monolignol coupling specificity. Plant Mol Biol 49:199–214Google Scholar
  26. Kim KW, Moinuddin SGA, Atwell KM, Costa MA, Davin LB, Lewis NG (2012) Opposite stereoselectivities of dirigent proteins in Arabidopsis and Schizandra species. J Biol Chem 287:33957–33972Google Scholar
  27. Lamesch P, Berardini TZ, Li D, Swarbreck D, Wilks C, Sasidharan R et al (2012) The Arabidopsis information resource (tair): improved gene annotation and new tools. Nucl Acids Res 40:1202–1210Google Scholar
  28. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H et al (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948Google Scholar
  29. Lee TH, Tang H, Wang X, Paterson AH (2013) PGDD: a database of gene and genome duplication in plants. Nucleic Acids Res 41:1152–1158Google Scholar
  30. Lewis NG, Davin LB (1999) Lignans: biosynthesis and function. In: Barton DHR, Nakanishi K, Meth-Cohn O (eds) Comprehensive natural products chemistry. Elsevier, London, pp 639–712Google Scholar
  31. Li Q, Chen J, Xiao Y, Di P, Zhang L, Chen W (2014) The dirigent multigene family in Isatis indigotica: gene discovery and differential transcript abundance. BMC Genom 15:388Google Scholar
  32. Li N, Zhao M, Liu T, Dong L, Cheng Q, Wu J et al (2017) A novel soybean dirigent gene GmDIR22 contributes to promotion of lignan biosynthesis and enhances resistance to Phytophthora sojae. Front Plant Sci 8:1185Google Scholar
  33. Liao Y, Liu S, Jiang Y, Hu C, Zhang X, Cao X et al (2017) Genome-wide analysis and environmental response profiling of dirigent family genes in rice ( Oryza sativa ). Genes Genom 39(1):47–62Google Scholar
  34. Liu J, Stipanovic RD, Bell AA, Puckhaber LS, Magill CW (2008) Stereoselective coupling of hemigossypol to form (+)-gossypol in moco cotton is mediated by a dirigent protein. Phytochemistry 69(18):3038–3042Google Scholar
  35. Liu W, Xiang L, Zheng T, Jin J, Zhang G (2018) TranslatomeDB: a comprehensive database and cloud-based analysis platform for translatome sequencing data. Nucl Acids Res 46:D206–D212Google Scholar
  36. Ma QH, Liu YC (2015) Tadir13, a dirigent protein from wheat, promotes lignan biosynthesis and enhances pathogen resistance. Plant Mol Biol Rep 33(1):143–152Google Scholar
  37. Metsalu T, Vilo J (2015) ClustVis: a web tool for visualizing clustering of multivariate data using principal component analysis and heatmap. Nucl Acids Res 43:W566–W570Google Scholar
  38. Pickel B, Constantin MA, Pfannstiel J, Beifuss U, Schaller DA (2010) An enantiocomplementary dirigent protein for the enantioselective laccase-catalyzed oxidative coupling of phenols. Angew Chem Int Ed Engl 49(1):202–204Google Scholar
  39. Pickel B, Pfannstiel J, Steudle A, Lehmann A, Gerken U, Pleiss J, Schaller A (2012) A model of dirigent proteins derived from structural and functional similarities with allene oxide cyclase and lipocalins. FEBS J 279:1980–1993Google Scholar
  40. Ralph SG, Park JY, Bohlmann J, Mansfield SD (2006) Dirigent proteins in conifer defense: gene discovery, phylogeny, and differential wound- and insect-induced expression of a family of DIR and DIR-like genes in spruce (Picea spp.). Plant Mol Biol 60:21–40Google Scholar
  41. Ralph SG, Jancsik S, Bohlmann J (2007) Dirigent proteins in conifer defense II: extended gene discovery, phylogeny, and constitutive and stress-induced gene expression in spruce (Picea spp.). Phytochemistry 68:1975–2199Google Scholar
  42. Shi H, Liu Z, Zhu L, Zhang C, Chen Y, Zhou Y, Li F, Li X (2012) Overexpression of cotton (Gossypium hirsutum) dirigent1 gene enhances lignification that blocks the spread of Verticillium dahliae. Acta Biochem Biophys Sin 44:555–564Google Scholar
  43. Shu Y, Liu Y, Zhang J, Song L, Guo C (2016) Genome-wide analysis of the AP2/ERF superfamily genes and their responses to abiotic stress in Medicago truncatula. Front Plant Sci 6(676):1247Google Scholar
  44. Song M, Xu W, Xiang Y, Jia H, Zhang L, Ma Z (2013) Association of jacalin-related lectins with wheat responses to stresses revealed by transcriptional profiling. Plant Mol Biol 84:95–110Google Scholar
  45. Subramanyam S, Sardesai N, Puthoff DP, Meyer JM, Nemacheck JA, Gonzalo M, Williams CE (2006) Expression of two wheat defense-response genes, Hfr-1 and Wci-1, under biotic and abiotic stresses. Plant Sci 170:90–103Google Scholar
  46. Subramanyam S, Smith DF, Clemens JC, Webb MA, Sardesai N, Williams CE (2008) Functional characterization of HFR1, a high-mannose N-glycan-specific wheat lectin induced by Hessian fly larvae. Plant Physiol 147(3):1412–1426Google Scholar
  47. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28(10):2731Google Scholar
  48. Tang Y, Zhao PX, Murray JD, Wang M, Benedito VA, Ji H et al (2009) The Medicago truncatula gene expression atlas web server. BMC Bioinform 10(1):441Google Scholar
  49. Tang H, Krishnakumar V, Bidwell S, Rosen B, Chan A, Zhou S, et al. (2014) An improved genome release (version mt4.0) for the model legume Medicago truncatula. BMC Genom 15 (1):312–312Google Scholar
  50. Thamil Arasan SK, Park JI, Ahmed NU, Jung HJ, Hur Y, Kang KK et al (2013) Characterization and expression analysis of dirigent family genes related to stresses in brassica. Plant Physiol Biochem 67(3):144–153Google Scholar
  51. Voorrips RE (2002) Mapchart: software for the graphical presentation of linkage maps and QTLs. J Hered 93(1):77–78Google Scholar
  52. Winter D, Vinegar B, Nahal H, Ammar R, Wilson GV, Provart NJ (2007) An “Electronic Fluorescent Pictograph” browser for exploring and analyzing large-scale biological data sets. PLoS One 2(8):e718Google Scholar
  53. Wu R, Wang L, Wang Z, Shang H, Liu X, Zhu Y, Qi D, Deng X (2009) Cloning and expression analysis of a dirigent protein gene from the resurrection plant Boea hygrometrica. Prog Nat Sci 19:347–352Google Scholar
  54. Xia ZQ, Costa MA, Proctor J, Davin LB, Lewis NG (2000) Dirigent-mediated podophyllotoxin biosynthesis in Linum flavum and Podophyllum peltatum. Phytochemistry 55:537–549Google Scholar
  55. Zhou J, Lee C, Zhong R, Ye ZH (2009) MYB58 and MYB63 are transcriptional activators of the lignin biosynthetic pathway during secondary cell wall formation in Arabidopsis. Plant Cell 21:48–266Google Scholar

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© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.College of Life ScienceQufu Normal UniversityQufuPeople’s Republic of China

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