Genome-wide identification and expression analysis of the PHD-finger gene family in Solanum tuberosum
Autoři:
Mingyue Qin aff001; Wenbin Luo aff004; Yan Zheng aff001; Huazhong Guan aff002; Xiaofang Xie aff001
Působiště autorů:
College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, China
aff001; Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture & Forestry University, Fuzhou, China
aff002; Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture & Forestry University, Fuzhou, China
aff003; The Crop Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
aff004
Vyšlo v časopise:
PLoS ONE 14(12)
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pone.0226964
Souhrn
Plant homeodomain (PHD) proteins are prevalent in eukaryotes and play important roles in plant growth, development and abiotic stress response. In this study, the comprehensive study of the PHD family (StPHD) was performed in potato (Solanum tuberosum L.). Seventy-two PHD genes (named StPHD1-72) were identified and grouped into 10 subfamilies based on phylogenetic analysis. Similar structure organizations were found within each subfamily according to the exon/intron structures and protein motif analysis. These genes were unequally scattered on the chromosomes of potato, with 9 pairs of segmental duplicated genes and 6 pairs of tandem duplicated genes showing that both segmental duplicated and tandem duplicated events contributed to the expansion of the potato PHD family. The gene ontology (GO) analysis suggests that StPHD mainly functioned at the intracellular level and was involved in various binding, metabolic and regulation processes. The analysis of expression patterns of StPHD genes showed that these genes were differentially expressed in 10 different tissues and responded specifically to heat, salt and drought stress based on the FPKM (Fragments per kilobase of transcript per million mapped reads) values of the RNA-seq data. Furthermore, the real-time quantitative PCR for 12 selected StPHD genes revealed the various levels of gene expression corresponding to abiotic stress. Our results provide useful information for a better understanding of PHD genes and provide the foundation for additional functional exploration of the potato PHD gene family.
Klíčová slova:
Gene expression – Maize – Sequence alignment – Phylogenetic analysis – Sequence motif analysis – Potato – Arabidopsis thaliana – Duplicated genes
Zdroje
1. Takatsuji H. Zinc-finger transcription factors in plants. Cell Mol Life Sci. 1998; 54(6):582–596. doi: 10.1007/s000180050186 9676577
2. Aasland R, Gibson TJ, Stewart AF. The PHD finger: Implications for chromatin-mediated transcriptional regulation. Trends Biochem Sci. 1995; 20(2):56–59. doi: 10.1016/s0968-0004(00)88957-4 7701562
3. Kaadige MR, Ayer DE. The polybasic region that follows the plant homeodomain zinc finger 1 of Pf1 is necessary and sufficient for specific phosphoinositide binding. J Biol Chem. 2006; 281(39):28831–28836. doi: 10.1074/jbc.M605624200 16893883
4. Bienz M. The PHD finger, a nuclear protein-interaction domain. Trends Biochem Sci. 2006; 31(1):35–40. doi: 10.1016/j.tibs.2005.11.001 16297627
5. Nakamura Y, Umehara T, Hamana H, Hayashizaki Y, Inoue M, Kigawa T, et al. Crystal Structure Analysis of the PHD Domain of the Transcription Co-activator Pygopus. J Mol Biol. 2007; 370(1):80–92. doi: 10.1016/j.jmb.2007.04.037 17499269
6. Schindler U, Beckmann H, Cashmore AR. HAT3.1, a novel Arabidopsis homeodomain protein containing a conserved cysteine-rich region. Plant J. 1993; 4(1):137–150. doi: 10.1046/j.1365-313x.1993.04010137.x 8106082
7. Wei W, Huang J, Hao YJ, Zou HF, Wang HW, Zhao JY, et al. Soybean GmPHD-Type Transcription Regulators Improve Stress Tolerance in Transgenic Arabidopsis Plants. PLoS ONE. 2009; 4(9):e7209. doi: 10.1371/journal.pone.0007209 19789627
8. Reddy TV, Kaur J, Agashe B, Sundaresan V, Siddiqi I. The DUET gene is necessary for chromosome organization andprogression during male meiosis in Arabidopsis and encodes a PHD finger protein. Development. 2003; 130(24):5975. doi: 10.1242/dev.00827 14573517
9. Woo HR, Pontes O, Pikaard CS, Richards EJ. VIM1, a methylcytosine-binding protein required for centromeric heterochromatinization. Genes Dev. 2007; 21(3):267–277. doi: 10.1101/gad.1512007 17242155
10. Thangasamy S, Guo CL, Chuang MH, Lai MH, Chen JC, and Jauh GY. Rice SIZ1, a SUMO E3 ligase, controls spikelet fertility through regulation of anther dehiscence. New Phytol. 2011; 189(3):869–882. doi: 10.1111/j.1469-8137.2010.03538.x 21083564
11. Wang HD, Makeen K, Yan Y, Cao Y, Sun SB, and X GH. OsSIZ1 Regulates the Vegetative Growth and Reproductive Development in Rice. Plant Mol Biol Rep. 2011; 29(2):411–417.
12. Matsubara K, Yamanouchi U, Nonoue Y, Sugimoto K, Wang ZX, and Minobe Y. Ehd3, encoding a plant homeodomain finger-containing protein, is a critical promoter of rice flowering. Plant J. 2011; 66(4):603–612. doi: 10.1111/j.1365-313X.2011.04517.x 21284756
13. Barlow JH, Faryabi RB, Callen E, Wong N, Malhowski A, Chen HT, et al. Identification of early replicating fragile sites that contribute to genome instability. Cell. 2013; 152(3):620–632. doi: 10.1016/j.cell.2013.01.006 23352430
14. Liang C, Zhang XL, Song SS, Tian CY, Yin YX, Xing GC, et al. Identification of UHRF1/2 as new N-methylpurine DNA glycosylase-interacting proteins. Biochem Biophy Res Co. 2013; 433(4):415–419.
15. Saleh A, Alvarez-Venegas R, Yilmaz M, Le O, Hou GC, Sadder M, et al. The highly similar Arabidopsis homologs of trithorax ATX1 and ATX2 encode proteins with divergent biochemical functions. Plant Cell. 2008; 20(3):568–579. doi: 10.1105/tpc.107.056614 18375658
16. Wang Y, Wang QQ, Zhao Y, Han GM, Zhu SW. Systematic analysis of maize class III peroxidase gene family reveals a conserved subfamily involved in abiotic stress response. Gene. 2015; 566(1):95–108. doi: 10.1016/j.gene.2015.04.041 25895479
17. Wang QQ, Liu JY, Wang Y, Zhao Y, Jiang HY, Cheng BJ. Systematic Analysis of the Maize PHD-Finger Gene Family Reveals a Subfamily Involved in Abiotic Stress Response. Int. J. Mol. Sci. 2015; 16(10):23517. doi: 10.3390/ijms161023517 26437398
18. Wu SN, Wu M, Dong Q, Jiang HY, Cai RH, Xiang Y. Genome-wide identification, classification and expression analysis of the PHD-finger protein family in Populus trichocarpa. Gene. 2015; 575(1):75. doi: 10.1016/j.gene.2015.08.042 26314912
19. Cao YP, Han YH, Meng DD, Abdullah M, Li DH, Jin Q, et al. Systematic analysis and comparison of the PHD-Finger gene family in Chinese pear (Pyrus bretschneideri) and its role in fruit development. Funct Integr Genomics. 2018; 18(5):1–13.
20. Gao YM, Liu HL, Wang YJ, Li F, Xiang Y. Genome-wide identification of PHD-finger genes and expression pattern analysis under various treatments in moso bamboo (Phyllostachys edulis). Plant Physiol Bioch. 2017; 123:378.
21. Potato Genome Sequencing Consortium. Genome sequence and analysis of the tuber crop potato. Nature. 2011.
22. Hirsch CD, Hamilton JP, Childs KL, Cepela J, Crisovan E, Vaillancourtb B, et al. Spud DB: A Resource for Mining Sequences, Genotypes, and Phenotypes to Accelerate Potato Breeding. Plant Genome. 2014; 7(1):93–113.
23. Marchler-Bauer A, Bo Y, Han L, He J, Lanczycki CJ, Lu SN, et al. CDD/SPARCLE: functional classification of proteins via subfamily domain architectures. Nucleic Acids Res. 2017; 45(D1):D200–D203. doi: 10.1093/nar/gkw1129 27899674
24. Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, Bairoch A. ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res. 2003; 31:3784–3788. doi: 10.1093/nar/gkg563 12824418
25. Guo AY, Zhu QH, Chen X. GSDS: a gene structure display server. Hereditas. 2007; 29(8):1023–1026. 17681935
26. Bailey TL, Bodén M, Buske FA, Frith A, Grant CE, Clementi L, et al. MEME SUITE: tools for motif discovery and searching, Nucleic Acids Research, 2009; 37:202–208.
27. Gu Z, Cavalcanti A, Chen FC, Bouman P, Li WH. Extent of Gene Duplication in the Genomes of Drosophila, Nematode, and Yeast. Mol Biol Evol. 2002; 19(3):256–262. doi: 10.1093/oxfordjournals.molbev.a004079 11861885
28. Yang S, Zhang X, Yue JX, Tian D, Chen JQ. Recent duplications dominate NBS-encoding gene expansion in two woody species. Mol Genet Genomics. 2008; 280(3):187–198. doi: 10.1007/s00438-008-0355-0 18563445
29. Wang LQ, Guo K, Li Y, Tu YY, Hu HZ, Wang BR, et al. Expression profiling and integrative analysis of the CESA/CSL superfamily in rice. BMC Plant Biol. 2010; 10(1):282.
30. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997.
31. Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015; 32 (1):268–274. doi: 10.1093/molbev/msu300 25371430
32. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997; 25(17):3389–3402. doi: 10.1093/nar/25.17.3389 9254694
33. Warnes G, Bolker B, Bonebakker L, Gentleman R, Huber W, Liaw A, et al. Various R programming tools for plotting data. 2015; https://cran.r-project.org/.
34. Hammer PA, Tibbitts TW, Langhans RW, Mcfarlane JC. Baseline growth studies of ‘Grand Rapids’ lettuce in controlled environments. Journal-American Society for Horticultural Science (USA). 1978.
35. Livak K, Schmittgen T. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods. 2001; 25(4):402–408. doi: 10.1006/meth.2001.1262 11846609
36. Zhang F, Yang ZN, Zhang S. Genome-wide analysis of PHD-finger protein family in Arabidopsis thalinana. Acta Bot. 2009; 45(3):227–238.
37. Capili AD, Schultz DC, Rauscher FJ, Borden KL. Solution structure of the PHD domain from the KAP-1 corepressor: Structural determinants for PHD, RING and LIM zinc-binding domains. EMBO J. 2001; 20: 165–177. doi: 10.1093/emboj/20.1.165 11226167
38. Winicov II, Bastola DR. Transgenic overexpression of the transcription factor alfin1 enhances expression of the endogenous MsPRP2 gene in alfalfa and improves salinity tolerance of the plants. Plant physiol. 1999; 120(2):473–480. doi: 10.1104/pp.120.2.473 10364398
39. Pauwels L, Barbero GF, Geerinck J, Tilleman S, Grunewald W, Pérez AC, et al. NINJA connects the co-repressor TOPLESS to jasmonate signalling. Nature. 2010; 464(7289):788–791. doi: 10.1038/nature08854 20360743
40. Callebaut I, Courvalin JC, Mornon JP. The BAH (bromo-adjacent homology) domain: A link between DNA methylation, replication and transcriptional regulation. FEBS Lett. 1999; 446:189–193. doi: 10.1016/s0014-5793(99)00132-5 10100640
41. Saiga S, Furumizu C, Yokoyama R, Kurata T, Sato S, Kato T, et al. The Arabidopsis OBERON1 and OBERON2 genes encode plant homeodomain finger proteins and are required for apical meristem maintenance. Development. 2008; 135(10):1751–1759. doi: 10.1242/dev.014993 18403411
42. Cannon SB, Mitra A, Baumgarten A, Young ND, May G. The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana. BMC Plant Biology. 2004; 4(1):10.
43. Li H, Yuan Z, Vizcay-Barrena G, Yang CY, Liang WQ, Zong J, et al. PERSISTENT TAPETAL CELL1 encodes a PHD-finger protein that is required for tapetal cell death and pollen development in rice. Plant physiol. 2011; 156(2):615–630. doi: 10.1104/pp.111.175760 21515697
44. Sanchez R, Zhou MM. The PHD finger: a versatile epigenome reader. Trends Biochem Sci. 2011; 36(7):364–372. doi: 10.1016/j.tibs.2011.03.005 21514168
45. Ying F, Liu QP, Xue QZ. Comparative Phylogenetic Analysis of the Rice and Arabidopsis PHD-finger Proteins. Acta Genetica Sinica. 2004; 31(11):1284–1293. 15651682
46. Barker MS, Vogel H, Schranz ME. Paleopolyploidy in the Brassicales: Analyses of the Cleome Transcriptome Elucidate the History of Genome Duplications in Arabidopsis and Other Brassicales. Genome Biol Evol. 2009; 1(1):391–399.
47. Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, et al. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science. 2006.
48. Peng ZH, Lu Y, Li LB, Zhao Q, Feng Q, Gao ZM, et al. The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla). Nature Genetics. 2013; 45(4):456–461. doi: 10.1038/ng.2569 23435089
49. Guillaume B, Wolfe KH. Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell. 2004; 16(7):1679–1691. doi: 10.1105/tpc.021410 15208398
50. Zhao P, Wang DD, Wang RQ, Kong NN, Zhang C, Yang CH, et al. Genome-wide analysis of the potato Hsp20 gene family: identification, genomic organization and expression profiles in response to heat stress. BMC Genomics. 2018; 19(1):61. doi: 10.1186/s12864-018-4443-1 29347912
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