Genome-wide identification of pear HD-Zip gene family and expression patterns under stress induced by drought, salinity, and pathogen

• Autorzy: Wang H. , Lin J. , Li X.G. , Chang Y.
• Języki publikacji: EN

Abstrakty

EN

Homeodomain-leucine zipper (HD-Zip) transcription factor genes are unique in the plant kingdom. Studies have shown that HD-Zip transcription factor has four subfamilies (subfamilies I–IV), and each subfamily exerts similar or diverse functions in the growth and development as well as environmental stress responses of plants. Although a genome-wide analysis of this transcription factor has been performed in some species, systematic identification of sequences and expression patterns under biotic and abiotic stress have not been carried out in pear. In this study, we identified 52 putative HD-Zip genes within the pear genome. Based on the phylogenetic analysis, HD-Zip transcription factors were classified into four subfamilies: 18, 13, 5, and 16 members were identified separately in subfamilies I, II, III, and IV, respectively. Genes in the same subfamily shared the constituent structure and conserved motifs, thereby implying that the HDZip genes that shared similar structures may exert similar functions. Moreover, abundant stress-related and pathogenrelated cis-elements were observed in the promoter region of the pear HD-Zip I and II genes. Transcript abundance level of 20 selected HD-Zip I and II genes were analyzed by quantitative real-time RT-PCR (qRT-PCR) during the infection of Alternaria alternata, and abiotic stress conditions such as drought and salinity treatment. The results confirmed that some genes display stress-inducible and pathogen-inducible expression patterns.

• Wydawca: -
• Czasopismo: Acta Physiologiae Plantarum
• Rocznik: 2015
• Tom: 37
• Numer: 09
• Opis fizyczny: Article: 189 [19 p.], fig.,ref.

Twórcy

autor

Wang H.

• Institute of Horticulture, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China

autor

Lin J.

• Institute of Horticulture, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China

autor

Li X.G.

• Institute of Horticulture, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China

autor

Chang Y.

• Institute of Horticulture, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China

Bibliografia

• Abe H, Yamaguchi-Shinozaki K, Urao T, Iwasaki T, Hosokawa D, Shinozaki K (1997) Role of Arabidopsis MYC and MYB homologs in drought- and abscisic acid-regulated gene expression. Plant Cell 9:1859–1868
• Agalou A et al (2008) A genome-wide survey of HD-Zip genes in rice and analysis of drought-responsive family members. Plant Mol Biol 66:87–103
• Ariel F, Diet A, Verdenaud M, Gruber V, Frugier F, Chan R, Crespi M (2010) Environmental regulation of lateral root emergence in Medicago truncatula requires the HD-Zip I transcription factor HB1. Plant Cell 22:2171–2183
• Bailey TL, Elkan C (1995) The value of prior knowledge in discovering motifs with MEME. Proc Int Conf Intell Syst Mol Biol 3:21–29
• Chen X, Chen Z, Zhao H, Zhao Y, Cheng B, Xiang Y (2014) Genome-wide analysis of soybean HD-Zip gene family and expression profiling under salinity and drought treatments. PLoS One 9:e87156
• Deng X et al (2006) A homeodomain leucine zipper gene from Craterostigma plantagineum regulates abscisic acid responsive gene expression and physiological responses. Plant Mol Biol 61:469–489
• Dezar CA, Gago GM, Gonzalez DH, Chan RL (2005) Hahb-4, a sunflower homeobox-leucine zipper gene, is a developmental regulator and confers drought tolerance to Arabidopsis thaliana plants. Transgenic Res 14:429–440
• Dezar CA et al (2011) HAHB10, a sunflower HD-Zip II transcription factor, participates in the induction of flowering and in the control of phytohormone-mediated responses to biotic stress. J Exp Bot 62:1061–1076
• Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797
• Finn RD et al (2006) Pfam: clans, web tools and services. Nucleic Acids Res 34:D247–D251
• Frank W, Phillips J, Salamini F, Bartels D (1998) Two dehydrationinducible transcripts from the resurrection plant Craterostigma plantagineum encode interacting homeodomain-leucine zipper proteins. Plant J 15:413–421
• Guo AY, Zhu QH, Chen X, Luo JC (2007) GSDS: a gene structure display server. Hereditas 29:1023–1026
• Guo Y et al (2014) Comparative genomic analysis of Klebsiella pneumonia (LCT-KP214) and a mutant strain (LCT-KP289) obtained after spaceflight. BMC Genom 15:589
• Harris JC, Hrmova M, Lopato S, Langridge P (2011) Modulation of plant growth by HD-Zip class I and II transcription factors in response to environmental stimuli. New Phytol 190:823–837
• Henriksson E, Olsson A, Johannesson H, Johansson H, Hanson J, Engstrom P, Soderman E (2005) Homeodomain leucine zipper class I genes in Arabidopsis. Expression patterns and phylogenetic relationships. Plant Physiol 139:509–518
• Higo K, Ugawa Y, Iwamoto M, Korenaga T (1999) Plant cis-acting regulatory DNA elements (PLACE) database. Nucl Acids Res 27:297–300
• Hu R, Chi X, Chai G et al (2012) Genome-wide identification, evolutionary expansion, and expression profile of homeodomainleucine zipper gene family in poplar (Populus trichocarpa). PLoS One 7:e31149. doi:10.1371/journal.pone.0031149
• Johannesson H, Wang Y, Engstrom P (2001) DNA-binding and dimerization preferences of Arabidopsis homeodomain-leucine zipper transcription factors in vitro. Plant Mol Biol 45:63–73
• Johannesson H, Wang Y, Hanson J, Engstrom P (2003) The Arabidopsis thaliana homeobox gene ATHB5 is a potential regulator of abscisic acid responsiveness in developing seedlings. Plant Mol Biol 51:719–729
• Leblay C, Chevreau E, Raboin LM (1991) Adventitious shoot regeneration from in vitro leaves of several pear cultivars (Pyrus communis L.). Plant Cell Rep 25:99–105
• Letunic I, Doerks T, Bork P (2009) SMART 6: recent updates and new developments. Nucleic Acids Res 37:D229–D232
• Liu W, Fu R, Li Q, Li J, Wang L, Ren Z (2013) Genome-wide identification and expression profile of homeodomain-leucine zipper Class I gene family in Cucumis sativus. Gene 531:279–287
• Liu J et al (2014) Genome-wide analysis and expression profile of the bZIP transcription factor gene family in grapevine (Vitis vinifera). BMC Genom 15:281
• Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods 25:402–408
• Manavella PA, Dezar CA, Bonaventure G, Baldwin IT, Chan RL (2008) HAHB4, a sunflower HD-Zip protein, integrates signals from the jasmonic acid and ethylene pathways during wounding and biotic stress responses. Plant J 56:376–388
• Moens CB, Selleri L (2006) Hox cofactors in vertebrate development. Dev Biol 291:193–206
• Murashige T, Skoog F (1962) A revised medium for rapid growth and bioassays with tobacco tissue culture. Physiol Plant 15:473–497
• Nakashima K, Ito Y, Yamaguchi-Shinozaki K (2009) Transcriptional regulatory networks in response to abiotic stresses in Arabidopsis and grasses. Plant Physiol 149:88–95
• Nicholas K, Nicholas H, Deerfield D (1997) GeneDoc: analysis and visualization of genetic variation. EMBNEW.NEWS 4:14
• Olsson AS, Engstrom P, Soderman E (2004) The homeobox genes ATHB12 and ATHB7 encode potential regulators of growth in response to water deficit in Arabidopsis. Plant Mol Biol 55:663–677
• Righetti L et al (2014) Elimination of the nptII marker gene in transgenic apple and pear with a chemically inducible R/Rs recombinase. Plant Cell Tissue Org 117:335–348
• Schena M, Davis RW (1992) HD-Zip proteins: members of an Arabidopsis homeodomain protein superfamily. Proc Natl Acad Sci USA 89:3894–3898
• Sessa G, Morelli G, Ruberti I (1993) The Athb-1 and -2 HD-Zip domains homodimerize forming complexes of different DNA binding specificities. EMBO J 12:3507–3517
• Shao Y, Qin Y, Zou Y, Ma F (2014) Genome-wide identification and expression profiling of the SnRK2 gene family in Malus prunifolia. Gene 552:87–97
• Skinner D, Gasser C (2009) Expression-based discovery of candidate ovule development regulators through transcriptional profiling of ovule mutants. BMC Plant Biol 9:29
• Soderman E, Hjellstrom M, Fahleson J, Engstrom P (1999) The HDZip gene ATHB6 in Arabidopsis is expressed in developing leaves, roots and carpels and up-regulated by water deficit conditions. Plant Mol Biol 40:1073–1083
• Son O et al (2010) ATHB12, an ABA-inducible Homeodomain-Leucine Zipper (HD-Zip) protein of Arabidopsis, negativelyregulates the growth of the inflorescence stem by decreasing the expression of a gibberellin 20-oxidase gene. Plant Cell Physiol 51:1537–1547
• Sultan SE (2010) Plant developmental responses to the environment: eco-devo insights. Curr Opin Plant Biol 13:96–101
• Suzuki T, Shinogi T, Narusaka Y, Park P (2003) Infection behavior of Alternaria alternata Japanese pear pathotype and localization of 1,3-b-d-glucan in compatible and incompatible interactions between the pathogen and host plants. J Gen Plant Pathol 69:91–100
• 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 28:2731–2739
• Tron AE, Bertoncini CW, Chan RL, Gonzalez DH (2002) Redox regulation of plant homeodomain transcription factors. J Biol Chem 277:34800–34807
• Urao T, Yamaguchi-Shinozaki K, Urao S, Shinozaki K (1993) An Arabidopsis myb homolog is induced by dehydration stress and its gene product binds to the conserved MYB recognition sequence. Plant Cell 5:1529–1539
• Wang H, Chang YH, Chen ZY (2006) Study on biological characteristics of Alternaria alternate caused occurrence of pear black spot. J Fruit Sci 23:247–251
• Wang H, Liu G, Li C, Powell AL, Reid MS, Zhang Z, Jiang CZ (2013a) Defence responses regulated by jasmonate and delayed senescence caused by ethylene receptor mutation contribute to the tolerance of petunia to Botrytis cinerea. Mol Plant Pathol 14:453–469
• Wang H, Stier G, Lin J, Liu G, Zhang Z, Chang YH, Reid MS, Jiang CZ (2013b) Transcriptome changes associated with delayed flower senescence on transgenic petunia by inducing expression of etr1-1, a mutant ethylene receptor. PLoS One 8:e65800
• Wang H, Li GB, Zhang DY, Lin J, Sheng BL, Han JL, Chang YH (2013c) Biological functions of HD-Zip transcription factors. Yi Chuan 35(10):1179–1188
• Yoshida T, Fujita Y, Sayama H, Kidokoro S, Maruyama K, Mizoi J, Shinozaki K, Yamaguchi-Shinozaki K (2010) AREB1, AREB2, and ABF3 are master transcription factors that cooperatively regulate ABRE-dependent ABA signaling involved in drought stress tolerance and require ABA for full activation. Plant J 61:672–685
• Zhang S, Haider I, Kohlen W, Jiang L, Bouwmeester H, Meijer AH, Schluepmann H, Liu CM, Ouwerkerk PB (2012) Function of the HD-Zip I gene Oshox22 in ABA-mediated drought and salt tolerances in rice. Plant Mol Biol 80:571–585
• Zhang CH, Ma RJ, Shen ZJ, Sun X, Korir NK, Yu ML (2014) Genome-wide analysis of the Homeodomain-Leucine Zipper (HD-ZIP) gene family in peach (Prunus persica). Genet Mol Res 13:2654–2668
• Zhao Y, Zhou Y, Jiang H, Li X, Gan D, Peng X, Zhu S, Cheng B (2011) Systematic analysis of sequences and expression patterns of drought-responsive members of the HD-Zip gene family in maize. PLoS One 6:e28488