Towards defining the nuclear proteome

Fink, J. Lynn; Karunaratne, Seetha; Mittal, Amit; Gardiner, Donald M.; Hamilton, Nicholas A.; Mahony, Timothy J.; Cui, Kai; Suzuki, Harukazu; Hayashizaki, Y.; Teasdale, Rohan D.

doi:10.1186/gb-2008-9-1-r15

Cited by 35 publications

(29 citation statements)

References 40 publications

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“…We present here for the first time a comprehensive characterization of the nuclear sub-proteome of tomato fruits to seek the proteins involved in the regulation of fruit ripening. Sub-proteomic analysis enables the study of protein expression localized to a particular organelle, thereby providing additional insight into the protein function in a given condition [28][29][30]. The proteins associated with various cellular functions, for example, signaling, gene regulation, structure, proteolysis, detoxification, and translation were identified, implying the complexity of protein expression in the nucleus during fruit ripening.…”

Section: Discussionmentioning

confidence: 99%

“…In recent years, high-throughput nuclear proteome analysis has been performed in various plants, including Arabidopsis [24], rice [25], chickpea [26], and Medicago [27], to analyze the function of specific nuclear proteins. Organelle proteomics is a promising strategy that reduces the complexity of the total cellular proteome, focusing on a specific group of proteins that are central to the biological process under investigation [28][29][30]. At present, however, knowledge regarding the global expression profile of nuclear proteins during fruit ripening is still lacking.…”

Section: Introductionmentioning

confidence: 99%

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

Wang

Cai

et al. 2014

Genome Biol

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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.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Wang

Cai

et al. 2014

Genome Biol

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“…These proteins are then intersected with the full Nucprot mouse nuclear proteome data set [39]. Nucprot identifies 2568 proteins with clear experimental evidence of nuclear localization and 2854 mouse proteins predicted to be nuclear by a number of computational methods.…”

Section: Methodsmentioning

confidence: 99%

The proteins of intra-nuclear bodies: a data-driven analysis of sequence, interaction and expression

Mohamad

Bodén

2010

BMC Syst Biol

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BackgroundCajal bodies, nucleoli, PML nuclear bodies, and nuclear speckles are morpohologically distinct intra-nuclear structures that dynamically respond to cellular cues. Such nuclear bodies are hypothesized to play important regulatory roles, e.g. by sequestering and releasing transcription factors in a timely manner. While the nucleolus and nuclear speckles have received more attention experimentally, the PML nuclear body and the Cajal body are still incompletely characterized in terms of their roles and protein complement.ResultsBy collating recent experimentally verified data, we find that almost 1000 proteins in the mouse nuclear proteome are known to associate with one or more of the nuclear bodies. Their gene ontology terms highlight their regulatory roles: splicing is confirmed to be a core activity of speckles and PML nuclear bodies house a range of proteins involved in DNA repair. We train support-vector machines to show that nuclear proteins contain discriminative sequence features that can be used to identify their intra-nuclear body associations. Prediction accuracy is highest for nucleoli and nuclear speckles. The trained models are also used to estimate the full protein complement of each nuclear body. Protein interactions are found primarily to link proteins in the nuclear speckles with proteins from other compartments. Cell cycle expression data provide support for increased activity in nucleoli, nuclear speckles and PML nuclear bodies especially during S and G2 phases.ConclusionsThe large-scale analysis of the mouse nuclear proteome sheds light on the functional organization of physically embodied intra-nuclear compartments. We observe partial support for the hypothesis that the physical organization of the nucleus mirrors functional modularity. However, we are unable to unambiguously identify proteins' intra-nuclear destination, suggesting that critical drivers behind of intra-nuclear translocation are yet to be identified.

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“…Proteomic characterization of individual plant subcellular components provides focussed characterization of protein location in relation to function as it reduces protein complexity and increases technical resolution (Dreger 2003;Jiang et al 2005;Jung et al 2000;Pandey et al 2008). The nucleus is one of the most important organelles in the cell as it regulates various biological activities, including gene expression, transports regulatory factors and also functions in many signalling responses in response to stress (Fink et al 2008;Komatsu and Tanaka 2005;Moriguchi et al 2005;Repetto et al 2008). Proteomic analysis of the nuclei of three model plants, A. thaliana (Bae et al 2003), rice (Khan and Komatsu 2004) and Medicago truncatula (Repetto et al 2008), and the non model legume, chickpea (Pandey et al 2006) have been published recently.…”

Section: Introductionmentioning

confidence: 99%

Proteomic analysis of nuclear proteins during dehydration of the resurrection plant Xerophyta viscosa

2010

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Xerophyta viscosa (family Velloziaceae) is a monocotyledonous poikilochlorophyllous desiccation tolerant plant capable of surviving drying its leaf tissue to 5% relative water content (RWC) for prolonged periods and resuming full physiological activity upon rehydration. X. viscosa and other resurrection plants are excellent model systems for the study of desiccation tolerance mechanisms. In this work, the X. viscosa nuclear protein profile was investigated in response to dehydration stress using 2D gel electrophoresis, protein map analysis and mass spectrometry identification. From an average of 438 protein spots detected on the gels, 18 spots were significantly shown to increase in abundance upon dehydration at 35% RWC. Analysis of the 18 dehydration-induced nuclear protein spots resulted in the identification of proteins associated with gene transcription and regulation, cell signalling, molecular chaperone and proteolysis type activities, protein translation, energy metabolism, and novel proteins. This study revealed that X. viscosa nucleus responded to dehydration stress and that desiccation tolerance was controlled by multiple genes within the plant nucleus. This study indicated that adjusting gene regulation and expression of appropriate stress response proteins in the nucleus was sufficient to protect the cellular structures during dehydration and in the dried state.

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Towards defining the nuclear proteome

Abstract: Background: The nucleus is a complex cellular organelle and accurately defining its protein content is essential before any systematic characterization can be considered.

Cited by 35 publications

References 40 publications

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

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

The proteins of intra-nuclear bodies: a data-driven analysis of sequence, interaction and expression

Proteomic analysis of nuclear proteins during dehydration of the resurrection plant Xerophyta viscosa

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