Tomato nuclear proteome reveals the involvement of specific E2 ubiquitin-conjugating enzymes in fruit ripening

doi:10.1186/s13059-014-0548-2

	Tomato nuclear proteome reveals the involvement of specific E2 ubiquitin-conjugating enzymes in fruit ripening
	Wang, Yuying ; Wang, Weihao 1; Cai, Jianghua 1; Zhang, Yanrui 1; Qin, Guozheng; Tian, Shiping1
	2014
发表期刊	GENOME BIOLOGY
ISSN	1474-760X
卷号	15 期号:12
摘要	Background: Fruits are unique to flowering plants and play a central role in seed maturation and dispersal. Molecular dissection of fruit ripening has received considerable interest because of the biological and dietary significance of fruit. To better understand the regulatory mechanisms underlying fruit ripening, we report here the first comprehensive analysis of the nuclear proteome in tomato fruits. Results: Nuclear proteins were isolated from tomatoes in different stages of ripening, and subjected to iTRAQ (isobaric tags for relative and absolute quantification) analysis. We show that the proteins whose abundances change during ripening stages are involved in various cellular processes. We additionally evaluate changes in the nuclear proteome in the ripening-deficient mutant, ripening-inhibitor (rin), carrying a mutation in the transcription factor RIN. A set of proteins were identified and particular attention was paid to SlUBC32 and PSMD2, the components of ubiquitin-proteasome pathway. Through chromatin immunoprecipitation and gel mobility shift assays, we provide evidence that RIN directly binds to the promoters of SlUBC32 and PSMD2. Moreover, loss of RIN function affects protein ubiquitination in nuclei. SlUBC32 encodes an E2 ubiquitin-conjugating enzyme and a genome-wide survey of the E2 gene family in tomatoes identified five more E2s as direct targets of RIN. Virus-induced gene silencing assays show that two E2s are involved in the regulation of fruit ripening. Conclusions: Our results uncover a novel function of protein ubiquitination, identifying specific E2s as regulators of fruit ripening. These findings contribute to the unraveling of the gene regulatory networks that control fruit ripening.
学科领域	Biotechnology & Applied Microbiology ; Genetics & Heredity
DOI	10.1186/s13059-014-0548-2
收录类别	SCI
语种	英语
WOS关键词	26S PROTEASOME ; GENE ; EXPRESSION ; ARABIDOPSIS ; REGULATOR ; PROTEINS ; NETWORK ; RIN ; TRANSCRIPTOME ; PATHWAY
WOS研究方向	Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS记录号	WOS:000346609500020
出版者	BMC
文献子类	Article
出版地	LONDON
资助机构	National Basic Research Program of China (973 Program) [2011CB100604] ; National Natural Science Foundation of China (NSFC) [31030051, 31172004] ; Ministry of Science and Technology of China [2012BAD38B05]
作者邮箱	gzqin@ibcas.ac.cn ; tsp@ibcas.ac.cn
作品OA属性	Green Published, gold
引用统计	被引频次：78[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/2S10CLM1/27370
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, Grad Univ, Beijing 100049, Peoples R China
推荐引用方式 GB/T 7714	Wang, Yuying,Wang, Weihao,Cai, Jianghua,et al. Tomato nuclear proteome reveals the involvement of specific E2 ubiquitin-conjugating enzymes in fruit ripening[J]. GENOME BIOLOGY,2014,15(12).
APA	Wang, Yuying,Wang, Weihao,Cai, Jianghua,Zhang, Yanrui,Qin, Guozheng,&Tian, Shiping.(2014).Tomato nuclear proteome reveals the involvement of specific E2 ubiquitin-conjugating enzymes in fruit ripening.GENOME BIOLOGY,15(12).
MLA	Wang, Yuying,et al."Tomato nuclear proteome reveals the involvement of specific E2 ubiquitin-conjugating enzymes in fruit ripening".GENOME BIOLOGY 15.12(2014).

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