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

Wang, Yuying; Wang, Weihao; Cai, Jianghua; Zhang, Yanrui; Qin, Guozheng; Tian, Shiping

doi:10.1186/s13059-014-0548-2

Cited by 100 publications

(84 citation statements)

References 76 publications

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“…The sonicated chromatin complexes were incubated with affinity purified polyclonal anti-SlVPE3/anti-RIN antibodies or pre-immune serum IgG (negative control) as previously described [28]. The cross-linking was then reversed, and the amount of each precipitated DNA fragment was determined by real-time PCR using specific primers (Additional file 8: Table S7).…”

Section: Methodsmentioning

confidence: 99%

Post-transcriptional regulation of fruit ripening and disease resistance in tomato by the vacuolar protease SlVPE3

et al. 2017

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BackgroundProteases represent one of the most abundant classes of enzymes in eukaryotes and are known to play key roles in many biological processes in plants. However, little is known about their functions in fruit ripening and disease resistance, which are unique to flowering plants and required for seed maturation and dispersal. Elucidating the genetic mechanisms of fruit ripening and disease resistance is an important goal given the biological and dietary significance of fruit.ResultsThrough expression profile analyses of genes encoding tomato (Solanum lycopersicum) cysteine proteases, we identify a number of genes whose expression increases during fruit ripening. RNA interference (RNAi)-mediated repression of SlVPE3, a vacuolar protease gene, results in alterations in fruit pigmentation, lycopene biosynthesis, and ethylene production, suggesting that SlVPE3 is necessary for normal fruit ripening. Surprisingly, the SlVPE3 RNAi fruit are more susceptible to the necrotrophic pathogen Botrytis cinerea. Quantitative proteomic analysis identified 314 proteins that differentially accumulate upon SlVPE3 silencing, including proteins associated with fruit ripening and disease resistance. To identify the direct SlVPE3 targets and mechanisms contributing to fungal pathogen resistance, we perform a screening of SlVPE3-interacting proteins using co-immunoprecipitation coupled with mass spectrometry. We show that SlVPE3 is required for the cleavage of the serine protease inhibitor KTI4, which contributes to resistance against the fungal pathogen B. cinerea.ConclusionsOur findings contribute to elucidating gene regulatory networks and mechanisms that control fruit ripening and disease resistance responses.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-017-1178-2) contains supplementary material, which is available to authorized users.

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Section: Methodsmentioning

confidence: 99%

Post-transcriptional regulation of fruit ripening and disease resistance in tomato by the vacuolar protease SlVPE3

et al. 2017

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“…One of the SNPs causing missense mutations was located at a putative ubiquitin-likespecific cysteine proteinase. Recent studies have shown the role of proteolysis in the regulation of fruit ripening in tomato (Wang et al, 2014(Wang et al, , 2017. Particularly, a vacuolar cysteine proteinase (SlVPE3) was shown to affect the accumulation of numerous ripening-related proteins, acting as a posttranscriptional regulator (Wang et al, 2017).…”

Section: Biological Insights Into the Genetic Basis Of Fruit-related mentioning

confidence: 99%

Insights Into the Genetic Basis of Blueberry Fruit-Related Traits Using Diploid and Polyploid Models in a GWAS Context

et al. 2018

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Polyploidization is an ancient and recurrent process in plant evolution, impacting the diversification of natural populations and plant breeding strategies. Polyploidization occurs in many important crops; however, its effects on inheritance of many agronomic traits are still poorly understood compared with diploid species. Higher levels of allelic dosage or more complex interactions between alleles could affect the phenotype expression. Hence, the present study aimed to dissect the genetic basis of fruit-related traits in autotetraploid blueberries and identify candidate genes affecting phenotypic variation. We performed a genome-wide association study (GWAS) assuming diploid and tetraploid inheritance, encompassing distinct models of gene action (additive, general, different orders of allelic interaction, and the corresponding diploidized models). A total of 1,575 southern highbush blueberry individuals from a breeding population of 117 full-sib families were genotyped using sequence capture and next-generation sequencing, and evaluated for eight fruit-related traits. For the diploid allele calling, 77,496 SNPs were detected; while 80,591 SNPs were obtained in tetraploid, with a high degree of overlap (95%) between them. A linear mixed model that accounted for population and family structure was used for the GWAS analyses. By modeling tetraploid genotypes, we detected 15 SNPs significantly associated with five fruit-related traits. Alternatively, seven significant SNPs were detected for only two traits using diploid genotypes, with two SNPs overlapping with the tetraploid scenario. Our results showed that the importance of tetraploid models varied by trait and that the use of diploid models has hindered the detection of SNP-trait associations and, consequently, the genetic architecture of some commercially important traits in autotetraploid species. Furthermore, 14 SNPs co-localized with candidate genes, five of which lead to non-synonymous amino acid changes. The potential functional significance of these SNPs is discussed.

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“…The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium [95] via the PRIDE partner repository [96] with the dataset identifier PXD001414 [97].…”

Section: Data Accessmentioning

confidence: 99%