二穗短柄草RING Finger基因家族的鉴定及表达分析

doi:10.3969/j.issn.1674-7968.2024.06.008

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Abstract RING finger proteins, which usually have E3 ubiquitin ligase activity, are important in regulating plant growth and development and in response to biotic and abiotic stresses. However, studies on the RING finger gene family of Brachypodium distachyon are limited. In this study, the RING finger gene family of B. distachyon was systematically analyzed using bioinformatics methods, and its expression under drought, salt, and abscisic acid (ABA) stress treatments was preliminarily analyzed by qPCR. The results showed that a total of 666 RING finger genes were identified in the B. distachyon genome, which were unevenly distributed on 5 chromosomes, and 39 intergenic duplications occurred. The phylogenetic analysis divided the RING finger gene family into 9 subclusters, and the members of each subcluster were highly homologous and contained similar conserved structural domains and motifs. The covariance analysis among species showed that the RING finger gene family originated from genome duplication, and that gene fragment duplications and tandem duplications played a key role in its expansion and evolution. There were 303 RING finger collinearity gene pairs in rice (Oryza sativa) and B. distachyon, whereas there were only 48 pairs in Arabidopsis thaliana and B. distachyon, and a total of 39 RING finger gene pairs in B. distachyon genomes. Tissue expression profiles showed that 547 RING finger genes were expressed in different tissues of B. distachyon, and 39.8% of the genes were highly expressed in male flowers of B. distachyon. Differential expression analysis showed that 29 RING finger genes might be involved in the response to drought, salt and abscisic acid (ABA) stress. qPCR results showed that 26 RING finger genes were significantly up-regulated in drought stress (P<0.05), 3 RING finger genes were down-regulated, 27 RING finger genes were up-regulated and 2 were down-regulated in salt stress; 15 RING finger genes were up-regulated, 9 RING finger genes were down-regulated, and 5 RING finger genes were at the same level as the control in ABA stress. The present study provides a theoretical basis for revealing the function and evolution of the RING finger gene family and its role in the regulation of drought stress.

Key words： Brachypodium distachyon RING Finger Gene family Genetic evolution Stress response

Received: 06 June 2023

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Corresponding Authors: *qiuyizeng@aqnu.edu.cn

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	Articles by authors
	ZENG De-Er
	ZHANG Li-Ping
	NI Xin-Yue
	XU Li
	HU Jing
	ZHAO Yang -Zi-Jun
	WEI He-Ping

Cite this article:

ZENG De-Er,ZHANG Li-Ping,NI Xin-Yue, et al. Identification and Expression Analysis of the RING Finger Gene Family in Brachypodium distachyon[J]. 农业生物技术学报, 2024, 32(6): 1316-1328.

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https://journal05.magtech.org.cn/Jwk_ny/EN/10.3969/j.issn.1674-7968.2024.06.008 OR https://journal05.magtech.org.cn/Jwk_ny/EN/Y2024/V32/I6/1316

[1] Alam I, Yang Y Q, Wang Y, et al.2017. Genome-wide identification, evolution and expression analysis of RING finger protein genes in Brassica rapa[J]. Scientific Reports, 7: 40690.
[2] Brugière N, Zhang W, Xu Q, et al.2017. Overexpression of RING domain E3 ligase ZmXerico1 confers drought tolerance through regulation of ABA homeostasis[J]. Plant Physiology, 175(3): 1350-1369.
[3] Chen C, Chen H, Zhang Y, et al.2020. TBtools: An integrative toolkit developed for interactive analyses of big biological data[J]. Molecular Plant, 13(8): 1194-1202.
[4] Cho S K, Ryu M Y, Kim J H, et al.2017. RING E3 ligases: Key regulatory elements are involved in abiotic stress responses in plants[J]. Biochemistry and Molecular Biology Reports, 50(8): 393-400.
[5] Fang F, Zhou W, Liu Y, et al.2023. Characterization of RING-type ubiquitin SINA E3 ligases and their responsive expression to salt and osmotic stresses in Brassica napus[J]. Plant Cell Reports, 42(5): 859-877.
[6] Finn R D, Coggill P, Eberhardt R Y, et al.2016. The Pfam protein family database: Towards a more sustainable future[J]. Nucleic Acids Research, 44(D1): D279-285.
[7] Gao T, Wu Y, Zhang Y, et al.2011. OsSDIR1 overexpression greatly improves drought tolerance in transgenic rice[J]. Plant Molelular Biology, 76(1-2): 145-156.
[8] Han G, Qiao Z, Li Y, et al.2022. RING zinc finger proteins in plant abiotic stress tolerance[J]. Frontiers in Plant Science, 13: 877011.
[9] Jiménez-López D.,et al.F. Muñóz-Belman, J. M. González-Prieto, 2018. Repertoire of plant RING E3 ubiquitin ligases revisited: New groups counting gene families and single genes[J]. PLOS ONE 13: e0203442.
[10] Jung Y J, Lee I H, Nou I S, et al.2013. BrRZFP1 a Brassica rapa C3HC4-type RING zinc finger protein involved in cold, salt and dehydration stress[J]. Plant Biology, 15(2): 274-283.
[11] Ko J H, Yang S H, Han K H.2006. Upregulation of an Arabidopsis RING-H2 gene, XERICO, confers drought tolerance through increased abscisic acid biosynthesis[J]. Plant Journal, 47(3): 343-355.
[12] Kosarev P, Mayer K F, Hardtke C S.2002. Evaluation and classification of RING-finger domains encoded by the Arabidopsis genome[J]. Genome Biology, 3(4): RESEARCH0016.
[13] Letunic I, Bork P.2018. 20 years of the SMART protein domain annotation resource[J]. Nucleic Acids Research, 46(1): 493-496.
[14] Letunic I, Bork P.2021. Interactive tree of life (iTOL) v5: An online tool for phylogenetic tree display and annotation[J]. Nucleic Acids Research, 49(W1): W293-W296.
[15] Li Y, Wu B, Yu Y, et al.2011. Genome-wide analysis of the RING finger gene family in apple[J]. Molecular Genetics and Genomics, 286(1): 81-94.
[16] Lim S D, Yim W C, Moon J C, et al.2010. A gene family encoding RING finger proteins in rice: Their expansion, expression diversity, and co-expressed genes[J]. Plant Molecular Biology, 72(4-5): 369-380.
[17] Livak K J, Schmittgen T D.2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2 (-Delta Delta C(T)) method[J]. Methods, 25(4): 402-408.
[18] Marchler-Bauer A, Derbyshire M K, Gonzales N R, et al.2015. CDD: NCBI's conserved domain database[J]. Nucleic Acids Research, 43(Database issue): D222-226.
[19] Moreno P, Fexova S, George N, et al.2022. Expression atlas update: Gene and protein expression in multiple species[J]. Nucleic Acids Research, 50(D1): D129-D140.
[20] Park J, Nguyen K T, Park E, et al.2013. DELLA proteins and their interacting RING Finger proteins repress gibberellin responses by binding to the promoters of a subset of gibberellin-responsive genes in Arabidopsis[J]. Plant Cell, 25(3): 927-43.
[21] Park Y C, Chapagain S, Jang C S.2018. A negative regulator in response to salinity in rice: Oryza sativa salt-, ABA- and drought-induced RING Finger protein 1 (OsSADR1)[J]. Plant Cell Physiology, 59(3): 575-589.
[22] Prasad M E, Stone S L.2010. Further analysis of XBAT32, an Arabidopsis RING E3 ligase, involved in ethylene biosynthesis[J]. Plant Signaling & Behavior, 5(11): 1425-1429.
[23] Qin F, Sakuma Y, Tran L S, et al.2008. Arabidopsis DREB2A-interacting proteins function as RING E3 ligases and negatively regulate plant drought stress-responsive gene expression[J]. Plant Cell, 20(6): 1693-1707.
[24] Stone S L, Hauksdóttir H, Troy A, et al.2005. Functional analysis of the RING-type ubiquitin ligase family of Arabidopsis[J]. Plant Physiology, 137(1): 13-30.
[25] Wang X, Chen E, Ge X, et al.2018. Overexpressed BRH1, a RING finger gene, alters rosette leaf shape in Arabidopsis thaliana[J]. Science China Life Sciences, 61(1): 79-87.
[26] Wang Y, Tang H, Debarry J D, et al.2012. MCScanX: A toolkit for detection and evolutionary analysis of gene synteny and collinearity[J]. Nucleic Acids Research, 40(7): e49.
[27] Wu W, Cheng Z, Liu M, et al.2014. C3HC4-type RING finger protein NbZFP1 is involved in growth and fruit development in Nicotiana benthamiana[J]. PLOS ONE, 9(6): e99352.
[28] Xie Q, Guo H S, Dallman G, et al.2002. SINAT5 promotes ubiquitin-related degradation of NAC1 to attenuate auxin signals[J]. Nature, 419(6903): 167-170.
[29] Yang L, Miao M, Lyu H, et al.2019. Genome-Wide identification, evolution, and expression analysis of RING Finger gene family in Solanum lycopersicum[J]. International Journal of Molecular Sciences, 20(19): 4864.