Identification of TIFY Family Genes and Analysis of Their Expression Profiles in Response to Phytohormone Treatments and Infection in Poplar

Overview

Journal Front Plant Sci

Date 2017 Apr 21

PMID 28424731

Citations 26

Authors

Wenxiu Xia

Hongyan Yu

Pei Cao

Jie Luo

Nian Wang

Affiliations

Soon will be listed here.

Abstract

The TIFY domain contains approximately 36 conserved amino acids that form the core motif TIF[F/Y]XG, and they were reported to play important roles in plant growth, tissue development and defense regulation. Moreover, more and more evidence has shown that some members of the TIFY gene family perform their functions by modulating plant hormone signaling pathways. Poplar trees are found worldwide, and they comprise approximately 30 species. Benefit from the importance of poplar and its advanced platform, this tree is considered to be the model perennial plant. Here, we conducted a genome-wide identification of TIFY genes in poplar, and 24 TIFY genes were found. These 24 TIFY genes were assigned to different subfamilies according to the presence or absence of domains and motifs that they harbored. Careful analyses of their locations, structures, evolution and duplication patterns revealed an overview of this gene family in poplar. The expression profiles of these 24 TIFY genes were then analyzed in different tissues using publicly available expression data; their expression profiles following different JA/SA treatments and infection with leaf rust pathogen were also carefully examined by qRT-PCR assays. Based on their expression profiles, the functions of a number of TIFY genes could be predicted. By performing this study, we have provided valuable information for further functional characterisation of TIFY genes in poplar and candidate genes for the improvement of poplar disease resistance.

Citing Articles

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References

Nishii A, Takemura M, Fujita H, Shikata M, Yokota A, Kohchi T . Characterization of a novel gene encoding a putative single zinc-finger protein, ZIM, expressed during the reproductive phase in Arabidopsis thaliana. Biosci Biotechnol Biochem. 2000; 64(7):1402-9. DOI: 10.1271/bbb.64.1402. View

Livak K, Schmittgen T . Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods. 2002; 25(4):402-8. DOI: 10.1006/meth.2001.1262. View

de Hoon M, Imoto S, Nolan J, Miyano S . Open source clustering software. Bioinformatics. 2004; 20(9):1453-4. DOI: 10.1093/bioinformatics/bth078. View

White D . PEAPOD regulates lamina size and curvature in Arabidopsis. Proc Natl Acad Sci U S A. 2006; 103(35):13238-43. PMC: 1550771. DOI: 10.1073/pnas.0604349103. View

Tuskan G, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U . The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science. 2006; 313(5793):1596-604. DOI: 10.1126/science.1128691. View

Rinaldi C, Kohler A, Frey P, Duchaussoy F, Ningre N, Couloux A . Transcript profiling of poplar leaves upon infection with compatible and incompatible strains of the foliar rust Melampsora larici-populina. Plant Physiol. 2007; 144(1):347-66. PMC: 1913798. DOI: 10.1104/pp.106.094987. View

Vanholme B, Grunewald W, Bateman A, Kohchi T, Gheysen G . The tify family previously known as ZIM. Trends Plant Sci. 2007; 12(6):239-44. DOI: 10.1016/j.tplants.2007.04.004. View

Miranda M, Ralph S, Mellway R, White R, Heath M, Bohlmann J . The transcriptional response of hybrid poplar (Populus trichocarpa x P. deltoides) to infection by Melampsora medusae leaf rust involves induction of flavonoid pathway genes leading to the accumulation of proanthocyanidins. Mol Plant Microbe Interact. 2007; 20(7):816-31. DOI: 10.1094/MPMI-20-7-0816. View

Staswick P . JAZing up jasmonate signaling. Trends Plant Sci. 2008; 13(2):66-71. DOI: 10.1016/j.tplants.2007.11.011. View

10.

Azaiez A, Boyle B, Levee V, Seguin A . Transcriptome profiling in hybrid poplar following interactions with Melampsora rust fungi. Mol Plant Microbe Interact. 2009; 22(2):190-200. DOI: 10.1094/MPMI-22-2-0190. View

11.

Chung H, Howe G . A critical role for the TIFY motif in repression of jasmonate signaling by a stabilized splice variant of the JASMONATE ZIM-domain protein JAZ10 in Arabidopsis. Plant Cell. 2009; 21(1):131-45. PMC: 2648087. DOI: 10.1105/tpc.108.064097. View

12.

Flagel L, Wendel J . Gene duplication and evolutionary novelty in plants. New Phytol. 2009; 183(3):557-564. DOI: 10.1111/j.1469-8137.2009.02923.x. View

13.

Ye H, Du H, Tang N, Li X, Xiong L . Identification and expression profiling analysis of TIFY family genes involved in stress and phytohormone responses in rice. Plant Mol Biol. 2009; 71(3):291-305. DOI: 10.1007/s11103-009-9524-8. View

14.

Wilkins O, Waldron L, Nahal H, Provart N, Campbell M . Genotype and time of day shape the Populus drought response. Plant J. 2009; 60(4):703-15. DOI: 10.1111/j.1365-313X.2009.03993.x. View

15.

Niu Y, Figueroa P, Browse J . Characterization of JAZ-interacting bHLH transcription factors that regulate jasmonate responses in Arabidopsis. J Exp Bot. 2011; 62(6):2143-54. PMC: 3060693. DOI: 10.1093/jxb/erq408. View

16.

Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S . MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 2011; 28(10):2731-9. PMC: 3203626. DOI: 10.1093/molbev/msr121. View

17.

Bai Y, Meng Y, Huang D, Qi Y, Chen M . Origin and evolutionary analysis of the plant-specific TIFY transcription factor family. Genomics. 2011; 98(2):128-36. DOI: 10.1016/j.ygeno.2011.05.002. View

18.

Zhu D, Bai X, Chen C, Chen Q, Cai H, Li Y . GsTIFY10, a novel positive regulator of plant tolerance to bicarbonate stress and a repressor of jasmonate signaling. Plant Mol Biol. 2011; 77(3):285-97. DOI: 10.1007/s11103-011-9810-0. View

19.

Pauwels L, Goossens A . The JAZ proteins: a crucial interface in the jasmonate signaling cascade. Plant Cell. 2011; 23(9):3089-100. PMC: 3203442. DOI: 10.1105/tpc.111.089300. View

20.

Wang Y, Wang X, Tang H, Tan X, Ficklin S, Feltus F . Modes of gene duplication contribute differently to genetic novelty and redundancy, but show parallels across divergent angiosperms. PLoS One. 2011; 6(12):e28150. PMC: 3229532. DOI: 10.1371/journal.pone.0028150. View