Genome-Wide Identification and Expression Profile Analysis of DUF760 Gene Family in Rice

doi:10.7668/hbnxb.20193226

Abstract

Abstract:

To investigate the potential functions of DUF760s in rice growth and development,the genome-wide identification,classification,promoter sequence and expression profile analysis of the DUF760 gene family were performed.This research identified 6 and 8 members of DUF760 gene family in rice and Arabidopsis respectively by bioinformatics analysis.Phylogenetic tree analysis divided these members into two subfamilies,there were also some characteristic differences between the two subfamilies in protein conserved motif and gene structure.Multiple cis-acting elements responding to stresses and phytohormones existed in the promoter regions of rice DUF760 family genes.ABRE(abscisic acid response)element was present in the promoter sequence of all DUF760 family members,the promoter region of OsDUF760-1 possessed 9 abscisic acid(ABA)related response elements.The transcriptional expression level of OsDUF760-1 in rice was significantly down-regulated after ABA treatment,while OsDUF760-3 was significantly up-regulated.The expression change patterns of these two genes in rice after drought stress treatment were consistent with that after ABA treatment,which indicated that these two genes may participate in rice drought stress response through ABA signaling pathway,and play different roles.In addition to strong responses to ABA and drought stress treatments,members of rice DUF760 family also showed relatively strong expression changes in response to JA(Jasmonic acid),low temperature and M.oryzae treatments.

Key words: Rice, DUF760 gene family, Stress, Phytohormone, Expression profile analysis

DU Qiang, HAN Lingling, XIAO Xiuwen, LI Jincheng, SHEN Mengyu, WANG Zhilong, CHEN Qiuhong. Genome-Wide Identification and Expression Profile Analysis of DUF760 Gene Family in Rice[J]. Acta Agriculturae Boreali-Sinica, 2023, 38(1): 1-8. doi: 10.7668/hbnxb.20193226.

/ / Recommend / Download Citations

URL: http://www.hbnxb.net/EN/10.7668/hbnxb.20193226

http://www.hbnxb.net/EN/Y2023/V38/I1/1

Figures/Tables 9

References 23

[1]	Galperin M Y, Koonin E V. From complete genome sequence to 'complete' understanding?[J]. Trends in Biotechnology, 2010, 28(8):398-406.doi:10.1016/j.tibtech.2010.05.006. doi: 10.1016/j.tibtech.2010.05.006 pmid: 20647113
[2]	Galperin M Y. Conserved 'hypothetical' proteins:new hints and new puzzles[J]. Comparative and Functional Genomics, 2001, 2(1):14-18.doi:10.1002/cfg.66. doi: 10.1002/cfg.66 pmid: 18628897
[3]	Galperin M Y, Koonin E V. 'Conserved hypothetical' proteins:prioritization of targets for experimental study[J]. Nucleic Acids Research, 2004, 32(18):5452-5463.doi:10.1093/nar/gkh885. doi: 10.1093/nar/gkh885 pmid: 15479782
[4]	Finn R D, Bateman A, Clements J, Coggill P, Eberhardt R Y, Eddy S R, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer E L L, Tate J, Punta M. Pfam:the protein families database[J]. Nucleic Acids Research, 2014, 42(D1):D222-D230.doi:10.1093/nar/gkt1223. doi: 10.1093/nar/gkt1223 URL
[5]	Bateman A, Coggill P, Finn R D. DUFS:families in search of function[J]. Acta Crystallographica Section F, 2010, 66(10):1148-1152.doi:10.1017/S1744309110001685. doi: 10.1017/S1744309110001685
[6]	Punta M, Coggill P C, Eberhardt R Y, Mistry J, Tate J, Boursnell C, Pang N Z, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer E L L, Eddy S R, Bateman A, Finn R D. The Pfam protein families database[J]. Nucleic Acids Research, 2012, 40(Database issue):D290-D301.doi:10.1093/nar/gkr1065. doi: 10.1093/nar/gkr1065
[7]	Schultz J, Milpetz F, Bork P, Ponting C P. SMART,a simple modular architecture research tool:Identification of signaling domains[J]. PNAS, 1998, 95(11):5857-5864.doi:10.1073/pnas.95.11.5857. doi: 10.1073/pnas.95.11.5857 pmid: 9600884
[8]	Wang L, Shen R X, Chen L T, Liu Y G. Characterization of a novel DUF1618 gene family in rice[J]. Journal of Integrative Plant Biology, 2014, 56(2):151-158.doi:10.1111/jipb.12130. doi: 10.1111/jipb.12130
[9]	Zhong H, Zhang H Y, Guo R, Wang Q, Huang X P, Liao J L, Li Y S, Huang Y J, Wang Z H. Characterization and functional divergence of a novel DUF668 gene family in rice based on comprehensive expression patterns[J]. Genes, 2019, 10(12):980.doi:10.3390/genes10120980. doi: 10.3390/genes10120980 URL
[10]	Mudgal R, Sandhya S, Chandra N, Srinivasan N. De-DUFing the DUFs:deciphering distant evolutionary relationships of domains of unknown function using sensitive homology detection methods[J]. Biology Direct, 2015, 10(1):38.doi:10.1186/s13062-015-0069-2. doi: 10.1186/s13062-015-0069-2 URL
[11]	Xin Z G, Mandaokar A, Chen J P, Last R L, Browse J. Arabidopsis ESK1 encodes a novel regulator of freezing tolerance[J]. The Plant Journal, 2007, 49(5):786-799.doi:10.1111/j.1365-313X.2006.02994.x. doi: 10.1111/j.1365-313X.2006.02994.x URL
[12]	Nietzsche M, Schieβl I, Börnke F. The complex becomes more complex:Protein-protein interactions of SnRK1 with DUF581 family proteins provide a framework for cell-and stimulus type-specific SnRK1 signaling in plants[J]. Frontiers in Plant Science, 2014, 5:54.doi:10.3389/fpls.2014.00054. doi: 10.3389/fpls.2014.00054 pmid: 24600465
[13]	Cao X, Yang K Z, Xia C, Zhang X Q, Chen L Q, Ye D. Characterization of DUF724 gene family in Arabidopsis thaliana[J]. Plant Molecular Biology, 2009, 72(1/2):61-73.doi:10.1007/s11103-009-9551-5. doi: 10.1007/s11103-009-9551-5 URL
[14]	Kim S J, Ryu M Y, Kim W T. Suppression of Arabidopsis RING-DUF1117 E3 ubiquitin ligases,AtRDUF1 and AtRDUF2,reduces tolerance to ABA-mediated drought stress[J]. Biochemical and Biophysical Research Communications, 2012, 420(1):141-147.doi:10.1016/j.bbrc.2012.02.131. doi: 10.1016/j.bbrc.2012.02.131 URL
[15]	Wang M L, Lu X D, Xu G Y, Yin X M, Cui Y C, Huang L F, Rocha P S C F, Xia X J. OsSGL,a novel pleiotropic stress-related gene enhances grain length and yield in rice[J]. Scientific Reports, 2016, 6:38157.doi:10.1038/srep38157. doi: 10.1038/srep38157
[16]	Liu J F, Chen J, Zheng X M, Wu F Q, Lin Q B, Heng Y Q, Tian P, Cheng Z J, Yu X W, Zhou K N, Zhang X, Guo X P, Wang J L, Wang H Y, Wan J M. GW5 acts in the brassinosteroid signalling pathway to regulate grain width and weight in rice[J]. Nature Plants, 2017, 3:17043.doi:10.1038/nplants.2017.43. doi: 10.1038/nplants.2017.43 pmid: 28394310
[17]	Guo C M, Luo C K, Guo L J, Li M, Guo X L, Zhang Y X, Wang L J, Chen L. OsSIDP366,a DUF1644 gene,positively regulates responses to drought and salt stresses in rice[J]. Journal of Integrative Plant Biology, 2016, 58(5):492-502.doi:10.1111/jipb.12376. doi: 10.1111/jipb.12376 URL
[18]	Luo C K, Guo C M, Wang W J, Wang L J, Chen L. Overexpression of a new stress-repressive gene OsDSR2 encoding a protein with a DUF966 domain increases salt and simulated drought stress sensitivities and reduces ABA sensitivity in rice[J]. Plant Cell Reports, 2014, 33(2):323-336.doi:10.1007/s00299-013-1532-0. doi: 10.1007/s00299-013-1532-0 URL
[19]	He X L, Hou X N, Shen Y Z, Huang Z J. TaSRG,a wheat transcription factor,significantly affects salt tolerance in transgenic rice and Arabidopsis[J]. FEBS Letters, 2011, 585(8):1231-1237.doi:10.1016/j.febslet.2011.03.055. doi: 10.1016/j.febslet.2011.03.055 URL
[20]	Soltani B M, Ehlting J, Hamberger B, Douglas C J. Multiple Cis-regulatory elements regulate distinct and complex patterns of developmental and wound-induced expression of Arabidopsis thaliana 4CL gene family members[J]. Planta, 2006, 224(5):1226-1238.doi:10.1007/s00425-006-0296-y. doi: 10.1007/s00425-006-0296-y pmid: 16738863
[21]	Walther D, Brunnemann R, Selbig J. The regulatory code for transcriptional response diversity and its relation to genome structural properties in A.thaliana[J]. PLoS Genetics, 2007, 3(2):e11.doi:10.1371/journal.pgen.0030011. doi: 10.1371/journal.pgen.0030011 pmid: 17291162
[22]	Abdullah M, Cheng X, Cao Y P, Su X P, Manzoor M A, Gao J S, Cai Y P, Lin Y. Zinc finger-homeodomain transcriptional factors(ZHDs)in upland cotton(Gossypium hirsutum):Genome-wide identification and expression analysis in fiber development[J]. Frontiers in Genetics, 2018, 9:357.doi:10.3389/fgene.2018.00357. doi: 10.3389/fgene.2018.00357 URL
[23]	黎家, 李传友. 新中国成立70年来植物激素研究进展[J]. 中国科学(生命科学), 2019, 49(10):1227-1281.doi:10.1360/SSV-2019-0197. doi: 10.1360/SSV-2019-0197
	Li J, Li C Y. Seventy-year major research progress in plant hormones by Chinese scholars[J]. Science in China (Series C), 2019, 49(10):1227-1281.

基因名称 Gene name	引物序列(5'—3') Primer sequence (5'—3')
OsDUF760-1	F: CCGGCCAAGATAACTGTATTTG
	R: CCAACAATAGTCAGGTTGCAAA
OsDUF760-2	F: CTACATCCGAGGTCTTGAGTAC
	R: TCTTTCTGAGGAGAAATGCAGT
OsDUF760-3	F: AAACGAATTTCTCCTGGCTCTA
	R: GAACTAACAGCTGCACATTAGG
OsDUF760-4	F: GCATGTATTGTTAGTCGCACAA
	R: AAATGCATCCTCCACTAGAACA
OsDUF760-5	F: CTGATTCTTGCTCAGTCACAAG
	R: GGATCAAAGCCCATCATGTAAC
OsDUF760-6	F: CAGCCCCTGATATCTATTCCTC
	R: GGAGATCATGAATGTGCATCAC
Ubiquitin	F: AACCAGCTGAGGCCCAAGA
	R: ACGATTGATTTAACCAGTCCATGA

基因名称 Gene name	引物序列(5'—3') Primer sequence (5'—3')
OsDUF760-1	F: CCGGCCAAGATAACTGTATTTG
	R: CCAACAATAGTCAGGTTGCAAA
OsDUF760-2	F: CTACATCCGAGGTCTTGAGTAC
	R: TCTTTCTGAGGAGAAATGCAGT
OsDUF760-3	F: AAACGAATTTCTCCTGGCTCTA
	R: GAACTAACAGCTGCACATTAGG
OsDUF760-4	F: GCATGTATTGTTAGTCGCACAA
	R: AAATGCATCCTCCACTAGAACA
OsDUF760-5	F: CTGATTCTTGCTCAGTCACAAG
	R: GGATCAAAGCCCATCATGTAAC
OsDUF760-6	F: CAGCCCCTGATATCTATTCCTC
	R: GGAGATCATGAATGTGCATCAC
Ubiquitin	F: AACCAGCTGAGGCCCAAGA
	R: ACGATTGATTTAACCAGTCCATGA

基因名称 Gene name	基因序列号 Gene locus ID	编码序列长度/bp CDS length	氨基酸长度/aa Amino acid length	等电点 pI	分子量/ku MW
OsDUF760-1	Os02g0833400	1 011	336	6.58	36.931
OsDUF760-2	Os03g0607500	1 218	405	4.94	44.787
OsDUF760-3	Os03g0717900	1 368	455	9.24	49.956
OsDUF760-4	Os04g0596300	1 218	405	5.51	45.306
OsDUF760-5	Os11g0456100	1 167	388	8.28	44.084
OsDUF760-6	Os12g0581700	1 182	393	5.10	43.185
AtDUF760-1	At1g32160	1 221	406	5.54	45.868
AtDUF760-2	At1g48450	1 272	423	5.86	47.189
AtDUF760-3	At1g63610	1 023	340	6.26	37.955
AtDUF760-4	At2g14910	1 161	386	5.04	43.396
AtDUF760-5	At3g07310	1 107	368	8.46	41.368
AtDUF760-6	At3g17800	1 266	421	9.20	46.067
AtDUF760-7	At5g14970	1 068	355	5.57	39.570
AtDUF760-8	At5g48590	1 035	344	7.67	38.959

基因名称 Gene name	基因序列号 Gene locus ID	编码序列长度/bp CDS length	氨基酸长度/aa Amino acid length	等电点 pI	分子量/ku MW
OsDUF760-1	Os02g0833400	1 011	336	6.58	36.931
OsDUF760-2	Os03g0607500	1 218	405	4.94	44.787
OsDUF760-3	Os03g0717900	1 368	455	9.24	49.956
OsDUF760-4	Os04g0596300	1 218	405	5.51	45.306
OsDUF760-5	Os11g0456100	1 167	388	8.28	44.084
OsDUF760-6	Os12g0581700	1 182	393	5.10	43.185
AtDUF760-1	At1g32160	1 221	406	5.54	45.868
AtDUF760-2	At1g48450	1 272	423	5.86	47.189
AtDUF760-3	At1g63610	1 023	340	6.26	37.955
AtDUF760-4	At2g14910	1 161	386	5.04	43.396
AtDUF760-5	At3g07310	1 107	368	8.46	41.368
AtDUF760-6	At3g17800	1 266	421	9.20	46.067
AtDUF760-7	At5g14970	1 068	355	5.57	39.570
AtDUF760-8	At5g48590	1 035	344	7.67	38.959

Please choose a citation manager

Content to export