Yun Wah Lam

Directed Proteomic Analysis of the Human Nucleolus

BACKGROUND The nucleolus is a subnuclear organelle containing the ribosomal RNA gene clusters and ribosome biogenesis factors. Recent studies suggest it may also have roles in RNA transport, RNA modification, and cell cycle regulation. Despite over 150 years of research into nucleoli, many aspects of their structure and function remain uncharacterized. RESULTS We report a proteomic analysis of human nucleoli. Using a combination of mass spectrometry (MS) and sequence database searches, including online analysis of the draft human genome sequence, 271 proteins were identified. Over 30% of the nucleolar proteins were encoded by novel or uncharacterized genes, while the known proteins included several unexpected factors with no previously known nucleolar functions. MS analysis of nucleoli isolated from HeLa cells in which transcription had been inhibited showed that a subset of proteins was enriched. These data highlight the dynamic nature of the nucleolar proteome and show that proteins can either associate with nucleoli transiently or accumulate only under specific metabolic conditions. CONCLUSIONS This extensive proteomic analysis shows that nucleoli have a surprisingly large protein complexity. The many novel factors and separate classes of proteins identified support the view that the nucleolus may perform additional functions beyond its known role in ribosome subunit biogenesis. The data also show that the protein composition of nucleoli is not static and can alter significantly in response to the metabolic state of the cell.

Identifying specific protein interaction partners using quantitative mass spectrometry and bead proteomes

The identification of interaction partners in protein complexes is a major goal in cell biology. Here we present a reliable affinity purification strategy to identify specific interactors that combines quantitative SILAC-based mass spectrometry with characterization of common contaminants binding to affinity matrices (bead proteomes). This strategy can be applied to affinity purification of either tagged fusion protein complexes or endogenous protein complexes, illustrated here using the well-characterized SMN complex as a model. GFP is used as the tag of choice because it shows minimal nonspecific binding to mammalian cell proteins, can be quantitatively depleted from cell extracts, and allows the integration of biochemical protein interaction data with in vivo measurements using fluorescence microscopy. Proteins binding nonspecifically to the most commonly used affinity matrices were determined using quantitative mass spectrometry, revealing important differences that affect experimental design. These data provide a specificity filter to distinguish specific protein binding partners in both quantitative and nonquantitative pull-down and immunoprecipitation experiments.

Paraspeckles : a novel nuclear domain

BACKGROUND The cell nucleus contains distinct classes of subnuclear bodies, including nucleoli, splicing speckles, Cajal bodies, gems, and PML bodies. Many nuclear proteins are known to interact dynamically with one or other of these bodies, and disruption of the specific organization of nuclear proteins can result in defects in cell functions and may cause molecular disease. RESULTS A proteomic study of purified human nucleoli has identified novel proteins, including Paraspeckle Protein 1 (PSP1) (see accompanying article, this issue of Current Biology). Here we show that PSP1 accumulates in a new nucleoplasmic compartment, termed paraspeckles, that also contains at least two other protein components: PSP2 and p54/nrb. A similar pattern of typically 10 to 20 paraspeckles was detected in all human cell types analyzed, including primary and transformed cells. Paraspeckles correspond to discrete bodies in the interchromatin nucleoplasmic space that are often located adjacent to splicing speckles. A stable cell line expressing YFP-PSP1 has been established and used to demonstrate that PSP1 interacts dynamically with nucleoli and paraspeckles in living cells. The three paraspeckle proteins relocalize quantitatively to unique cap structures at the nucleolar periphery when transcription is inhibited. CONCLUSIONS We have identified a novel nuclear compartment, termed paraspeckles, found in both primary and transformed human cells. Paraspeckles contain at least three RNA binding proteins that all interact dynamically with the nucleolus in a transcription-dependent fashion.

Analysis of nucleolar protein dynamics reveals the nuclear degradation of ribosomal proteins.

Summary Background The nucleolus is a subnuclear organelle in which rRNAs are transcribed, processed, and assembled with ribosomal proteins into ribosome subunits. Mass spectrometry combined with pulsed incorporation of stable isotopes of arginine and lysine was used to perform a quantitative and unbiased global analysis of the rates at which newly synthesized, endogenous proteins appear within mammalian nucleoli. Results Newly synthesized ribosomal proteins accumulated in nucleoli more quickly than other nucleolar components. Studies involving time-lapse fluorescence microscopy of stable HeLa cell lines expressing fluorescent-protein-tagged nucleolar factors also showed that ribosomal proteins accumulate more quickly than other components. Photobleaching and mass-spectrometry experiments suggest that only a subset of newly synthesized ribosomal proteins are assembled into ribosomes and exported to the cytoplasm. Inhibition of the proteasome caused an accumulation of ribosomal proteins in the nucleus but not in the cytoplasm. Inhibition of rRNA transcription prior to proteasomal inhibition further increased the accumulation of ribosomal proteins in the nucleoplasm. Conclusions Ribosomal proteins are expressed at high levels beyond that required for the typical rate of ribosome-subunit production and accumulate in the nucleolus more quickly than all other nucleolar components. This is balanced by continual degradation of unassembled ribosomal proteins in the nucleoplasm, thereby providing a mechanism for mammalian cells to ensure that ribosomal protein levels are never rate limiting for the efficient assembly of ribosome subunits. The dual time-lapse strategy used in this study, combining proteomics and imaging, provides a powerful approach for the quantitative analysis of the flux of newly synthesized proteins through a cell organelle.

Repo-Man recruits PP1γ to chromatin and is essential for cell viability

Protein phosphatase 1 (PP1) is a ubiquitous serine/threonine phosphatase regulating many cellular processes. PP1α and -γ are closely related isoforms with distinct localization patterns, shown here by time-lapse microscopy of stably expressed fluorescent protein fusions. A pool of PP1γ is selectively loaded onto chromatin at anaphase. Using stable isotope labeling and proteomics, we identified a novel PP1 binding protein, Repo-Man, which selectively recruits PP1γ onto mitotic chromatin at anaphase and into the following interphase. This approach revealed both novel and known PP1 binding proteins, quantitating their relative distribution between PP1α and -γ in vivo. When overexpressed, Repo-Man can also recruit PP1α to chromatin. Mutating Repo-Mans PP1 binding domain does not disrupt chromatin binding but abolishes recruitment of PP1 onto chromatin. RNA interference–induced knockdown of Repo-Man caused large-scale cell death by apoptosis, as did overexpression of this dominant-negative mutant. The data indicate that Repo-Man forms an essential complex with PP1γ and is required for the recruitment of PP1 to chromatin.

A Quantitative Proteomics Analysis of Subcellular Proteome Localization and Changes Induced by DNA Damage

A major challenge in cell biology is to identify the subcellular distribution of proteins within cells and to characterize how protein localization changes under different cell growth conditions and in response to stress and other external signals. Protein localization is usually determined either by microscopy or by using cell fractionation combined with protein blotting techniques. Both these approaches are intrinsically low throughput and limited to the analysis of known components. Here we use mass spectrometry-based proteomics to provide an unbiased, quantitative, and high throughput approach for measuring the subcellular distribution of the proteome, termed “spatial proteomics.” The spatial proteomics method analyzes a whole cell extract created by recombining differentially labeled subcellular fractions derived from cells in which proteins have been mass-labeled with heavy isotopes. This was used here to measure the relative distribution between cytoplasm, nucleus, and nucleolus of over 2,000 proteins in HCT116 cells. The data show that, at steady state, the proteome is predominantly partitioned into specific subcellular locations with only a minor subset of proteins equally distributed between two or more compartments. Spatial proteomics also facilitates a proteome-wide comparison of changes in protein localization in response to a wide range of physiological and experimental perturbations, shown here by characterizing dynamic changes in protein localization elicited during the cellular response to DNA damage following treatment of HCT116 cells with etoposide. DNA damage was found to cause dissociation of the proteasome from inhibitory proteins and assembly chaperones in the cytoplasm and relocation to associate with proteasome activators in the nucleus.

Nuclear penetration of surface functionalized gold nanoparticles.

Free gold nanoparticles easily aggregate when the environment conditions change. Here, gold nanoparticles (AuNPs) with average diameter of 3.7 nm were prepared and then modified with poly(ethylene glycol) (PEG) to improve stability. The gold nanoparticles were first surface-modified with 3-mercaptopropionic acid (MPA) to form a self-assembled monolayer and subsequently conjugated with NH(2)-PEG-NH(2) through amidation between the amine end groups on PEG and the carboxylic acid groups on the particles. The biocompatibility and intracellular fate of PEG-modified gold nanoparticles (AuNP@MPA-PEG) were then studied in human cervical cancer (HeLa) cells. Cell viability test showed that AuNP@MPA-PEG did not induce obvious cytotoxicity. Both confocal laser scanning microscopy and transmission electron microscopy demonstrated that AuNP@MPA-PEG entered into mammalian cells and the cellular uptake of AuNP@MPA-PEG was time-dependent. Inductively coupled plasma mass spectrometry and confocal microscopy imaging further demonstrated that AuNP@MPA-PEG penetrated into the nucleus of mammalian cells upon exposure for 24 h. These results suggest that surface modification can enhance the stability and improve the biocompatibility. This study also indicates that AuNP@MPA-PEG can be used as potential nuclear targeted drug delivery carrier.

Quantitative kinetic analysis of nucleolar breakdown and reassembly during mitosis in live human cells

One of the great mysteries of the nucleolus surrounds its disappearance during mitosis and subsequent reassembly at late mitosis. Here, the relative dynamics of nucleolar disassembly and reformation were dissected using quantitative 4D microscopy with fluorescent protein-tagged proteins in human stable cell lines. The data provide a novel insight into the fates of the three distinct nucleolar subcompartments and their associated protein machineries in a single dividing cell. Before the onset of nuclear envelope (NE) breakdown, nucleolar disassembly started with the loss of RNA polymerase I subunits from the fibrillar centers. Dissociation of proteins from the other subcompartments occurred with faster kinetics but commenced later, coincident with the process of NE breakdown. The reformation pathway also follows a reproducible and defined temporal sequence but the order of reassembly is shown not to be dictated by the order in which individual nucleolar components reaccumulate within the nucleus after mitosis.

3C-SiC nanocrystals as fluorescent biological labels.

Quantum dots are superior to dye molecules in many aspects from size-tunable fluorescence and resistance to photobleaching and they have thus been widely used in biology as fluorescent probes. However, the cytotoxicity of some quantum dots limits their use in biological systems, and exploiting green nanoparticles with low cytotoxicity has become one major concern in this field. Silicon carbide, one well-known power electronic semiconductor material, is considered one of the best biocompatible materials, especially to blood. In addition, it has superior properties such as low density, high hardness, high strength, and chemical inertness. In recent years, much effort has been made to synthesize nanocrystalline SiC and study its photoluminescence (PL) properties. Some synthesized SiC nanostructures showed emission in the blue-to-UV range with their properties depending sensitively on the fabrication method and even on specific experiments. Although some variations have been reported, in general the observed emissions can be ascribed to some surface or defect states in the SiC nanostructures. However, owing to their relatively large size, low emission intensity, lack of controlled synthesis, and variable optical properties, these interconnected SiC nanostructures can hardly be used as fluorescent biological labels. Kassiba and co-workers synthesized SiC nanoparticles with diameters of tens of nanometers

Reversible Accumulation of PEGylated Single-Walled Carbon Nanotubes in the Mammalian Nucleus

Carbon nanotubes (CNTs) have been shown to cross cell membranes and can mediate the internalization of macromolecules. These characteristics have constituted CNTs as an exciting new tool for drug delivery and biological sensing. While CNTs exhibit great potential in biomedical and pharmaceutical applications, neither the cell penetration mechanism of CNTs nor the intracellular fate of the internalized CNTs are fully understood. In this study, time-lapse fluorescence microscopy was used to investigate the intracellular distribution of FITC labeled PEGylated single-walled CNTs (FITC-PEG-SWCNTs) in living cells and shown that PEGylated SWCNTs entered the nucleus of several mammalian cell lines in an energy-dependent process. The presence of FITC-PEG-SWCNTs in the cell nucleus did not cause discernible changes in the nuclear organization and had no effect on the growth kinetics and cell cycle distribution for up to 5 days. Remarkably, upon removal of the FITC-PEG-SWCNTs from the culture medium, the internalized FITC-PEG-SWCNTs rapidly moved out of the nucleus and were released from the cells. Thus, the intracellular PEGylated SWCNTs were highly dynamic and the cell penetration of PEGylated SWCNTs appeared as bidirectional. These observations suggest SWCNTs may be used as an ideal nanovector in biomedical and pharmaceutical applications.