Weighted Gene Co-expression Network Analysis (WGCNA) Reveals the Hub Role of Protein Ubiquitination in the Acquisition of Desiccation Tolerance in Boea hygrometrica

doi:10.1093/pcp/pcz160

	Weighted Gene Co-expression Network Analysis (WGCNA) Reveals the Hub Role of Protein Ubiquitination in the Acquisition of Desiccation Tolerance in Boea hygrometrica
	Lin, Chih-Ta ; Xu, Tao ; Xing, Shi-Lai ; Zhao, Li ; Sun, Run-Ze ; Liu, Yang 1; Moore, John Paul 2; Deng, Xin1
	2019
发表期刊	PLANT AND CELL PHYSIOLOGY
ISSN	0032-0781
卷号	60 期号:12 页码:2707-2719
摘要	Boea hygrometrica can survive extreme drought conditions and has been used as a model to study desiccation tolerance. A genome-wide transcriptome analysis of B. hygrometrica showed that the plant can survive rapid air-drying after experiencing a slow soil-drying acclimation phase. In addition, a weighted gene co-expression network analysis was used to study the transcriptomic datasets. A network comprising 22 modules was constructed, and seven modules were found to be significantly related to desiccation response using an enrichment analysis. Protein ubiquitination was observed to be a common process linked to hub genes in all the seven modules. Ubiquitin-modified proteins with diversified functions were identified using immunoprecipitation coupled with mass spectrometry. The lowest level of ubiquitination was noted at the full soil drying priming stage, which coincided the accumulation of dehydration-responsive gene BhLEA2. The highly conserved RY motif (CAT GCA) was identified from the promoters of ubiquitin-related genes that were downregulated in the desiccated samples. An in silico gene expression analysis showed that the negative regulation of ubiquitin-related genes is potentially mediated via a B3 domain-containing transcription repressor VAL1. This study suggests that priming may involve the transcriptional regulation of several major processes, and the transcriptional regulation of genes in protein ubiquitination may play a hub role to deliver acclimation signals to posttranslational level in the acquisition of desiccation tolerance in B. hygrometrica.
关键词	Boea hygrometrica Protein ubiquitination Resurrection plant Transcription repressor VAL1 WGCNA
学科领域	Plant Sciences ; Cell Biology
DOI	10.1093/pcp/pcz160
收录类别	SCI
语种	英语
WOS关键词	PLANT-CELL-WALLS ; RESURRECTION PLANT ; TORTULA-RURALIS ; TRANSCRIPTIONAL REPRESSOR ; STRESS ; DEHYDRATION ; EXPRESSION ; LIGASE ; ACCUMULATION ; INVOLVEMENT
WOS研究方向	Plant Sciences ; Cell Biology
WOS记录号	WOS:000504924100011
出版者	OXFORD UNIV PRESS
Special Issue	SI
文献子类	Article
出版地	OXFORD
EISSN	1471-9053
资助机构	National Natural Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [31270312, 31770293, 31470361] ; Chinese Academy of Sciences Taiwan Young Talent Programme [2016TW2SA0001] ; South Africa-China Bilateral Grant ; National Research Foundation (South Africa)National Research Foundation - South Africa [88484] ; Ministry of Science and Technology (China)Ministry of Science and Technology, China [2003-256-9]
作者邮箱	deng@ibcas.ac.cn
引用统计	被引频次：18[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.ibcas.ac.cn/handle/2S10CLM1/19713
专题	中科院北方资源植物重点实验室
作者单位	1.Chinese Acad Sci, Inst Bot, Key Lab Plant Resources, Beijing 100093, Peoples R China 2.Chinese Acad Sci, Inst Bot, Beijing Bot Garden, Beijing 100093, Peoples R China 3.Stellenbosch Univ, Inst Wine Biotechnol, Dept Viticulture & Oenol, ZA-7602 Matieland, South Africa
推荐引用方式 GB/T 7714	Lin, Chih-Ta,Xu, Tao,Xing, Shi-Lai,et al. Weighted Gene Co-expression Network Analysis (WGCNA) Reveals the Hub Role of Protein Ubiquitination in the Acquisition of Desiccation Tolerance in Boea hygrometrica[J]. PLANT AND CELL PHYSIOLOGY,2019,60(12):2707-2719.
APA	Lin, Chih-Ta.,Xu, Tao.,Xing, Shi-Lai.,Zhao, Li.,Sun, Run-Ze.,...&Deng, Xin.(2019).Weighted Gene Co-expression Network Analysis (WGCNA) Reveals the Hub Role of Protein Ubiquitination in the Acquisition of Desiccation Tolerance in Boea hygrometrica.PLANT AND CELL PHYSIOLOGY,60(12),2707-2719.
MLA	Lin, Chih-Ta,et al."Weighted Gene Co-expression Network Analysis (WGCNA) Reveals the Hub Role of Protein Ubiquitination in the Acquisition of Desiccation Tolerance in Boea hygrometrica".PLANT AND CELL PHYSIOLOGY 60.12(2019):2707-2719.

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