Specialized compartments of cardiac nuclei exhibit distinct proteomic anatomy

Department of Anesthesiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.
Molecular & Cellular Proteomics (Impact Factor: 6.56). 01/2011; 10(1):M110.000703. DOI: 10.1074/mcp.M110.000703
Source: PubMed


As host to the genome, the nucleus plays a critical role as modulator of cellular phenotype. To understand the totality of proteins that regulate this organelle, we used proteomics to characterize the components of the cardiac nucleus. Following purification, cardiac nuclei were fractionated into biologically relevant fractions including acid-soluble proteins, chromatin-bound molecules and nucleoplasmic proteins. These distinct subproteomes were characterized by liquid chromatography-tandem MS. We report a cardiac nuclear proteome of 1048 proteins--only 146 of which are shared between the distinct subcompartments of this organelle. Analysis of genomic loci encoding these molecules gives insights into local hotspots for nuclear protein regulation. High mass accuracy and complementary analytical techniques allowed the discrimination of distinct protein isoforms, including 54 total histone variants, 17 of which were distinguished by unique peptide sequences and four of which have never been detected at the protein level. These studies are the first unbiased analysis of cardiac nuclear subcompartments and provide a foundation for exploration of this organelle's proteomes during disease.

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    • "Also, the nucleus serves a multi-functional role, as a regulator and modulator during cell division, and controller and integrator for fertilization and inheritance. Thus, nucleus plays a critical role as a modulator of cellular phenotype (Franklin et al., 2011). The nucleus must therefore be dynamic as cells divide, modulating its composition and architecture during its formation and after it has been disintegrated. "
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    ABSTRACT: Organeller proteomics is an emerging technology that is critical in determining the cellular signal transduction pathways. Nucleus, the regulatory hub of the eukaryotic cell is a dynamic system and a repository of various macromolecules that serve as modulators of such signaling that dictate cell fate decisions. Nuclear proteins (NPs) are predicted to comprise about 10-20% of the total cellular proteins, suggesting the involvement of the nucleus in a number of diverse functions. Indeed, NPs constitute a highly organized but complex network that plays diverse roles during development and physiological processes. In plants, relatively little is known about the nature of the molecular components and mechanisms involved in coordinating NP synthesis, their action and function. Proteomic study hold promise to understand the molecular basis of nuclear function using an unbiased comparative and differential approach. We identified a few hundred proteins that include classical and non-canonical nuclear components presumably associated with variety of cellular functions impinging on the complexity of nuclear proteome. Here, we review the nuclear proteome based on our own findings, available literature, and databases focusing on detailed comparative analysis of NPs and their functions in order to understand how plant nucleus works. The review also shed light on the current status of plant nuclear proteome and discusses the future prospect.
    Full-text · Article · Apr 2013 · Frontiers in Plant Science
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    • "Removing the 2DE gel also removes one further major caveat with 2DE which is that membrane proteins are usually underrepresented because of their poor solubility in the isoelectric-focusing sample buffer. With this in mind, Franklin et al. used subcellular gradient fractionation to isolate murine cardiac nuclei followed by further fractionation into acid soluble proteins, chromatin bound molecules, and nucleoplasmic proteins and identified a nuclear proteome of 1048 proteins many of which isolated uniquely to one sub-fraction in the nucleus [16]. They identified 142 integral membrane proteins, the majority of which were exclusive to the nucleoplasmic fraction. "
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