Subcellular Fractionation Methods Research Articles

Subcellular Proteomic Mapping of Lysine Lactylation.

Protein lactylation is a novel post-translational modification (PTM) involved in many important physiological processes such as macrophage polarization, immune regulation, and tumor cell growth. However, traditional methodologies for studying lactylation have predominantly relied on peptide enrichment from whole-cell lysates, which tend to favor the detection of high-abundance peptides, thus limiting the identification of low-abundance lactylated peptides. To address this limitation, here, we employed subcellular fractionation to separate proteins and map lactylated peptides from each isolated subcellular fraction using a model cell line. In brief, we identified 1,217 lysine lactylation (Kla) sites on 553 proteins across four subcellular fractions. Subsequent pathway enrichment analysis revealed that Kla proteins participate in distinct pathways depending on the subcellular contexts. In addition, this subcellular fractionation method enabled the discovery of 36 previously unreported Kla proteins and 223 novel Kla sites, many of which are present in low abundance. Notably, several proteins contain multiple newly identified Kla sites, exemplified by the transcriptional regulator ATRX. Furthermore, our results indicate the possibility of PTM crosstalk between Kla and other PTMs such as ubiquitination and sumoylation. In conclusion, subcellular fractionation facilitates the identification of Kla proteins that have been previously uncovered and could be overlooked by affinity enrichment of whole-cell lysates.

Cytoplasmic Shotgun Proteomic Points to Key Proteins and Pathways in Temozolomide-Resistant Glioblastoma Multiforme.

Temozolomide (TMZ) is the first line of chemotherapy to treat primary brain tumors of the type glioblastoma multiforme (GBM). TMZ resistance (TMZR) is one of the main barriers to successful treatment and is a principal factor in relapse, resulting in a poor median survival of 15 months. The present paper focuses on proteomic analyses of cytosolic fractions from TMZ-resistant (TMZR) LN-18 cells. The experimental workflow includes an easy, cost-effective, and reproducible method to isolate subcellular fraction of cytosolic (CYTO) proteins, mitochondria, and plasma membrane proteins for proteomic studies. For this study, enriched cytoplasmic fractions were analyzed in replicates by nanoflow liquid chromatography tandem high-resolution mass spectrometry (nLC-MS/MS), and proteins identified were quantified using a label-free approach (LFQ). Statistical analysis of control (CTRL) and temozolomide-resistant (TMZR) proteomes revealed proteins that appear to be differentially controlled in the cytoplasm. The functions of these proteins are discussed as well as their roles in other cancers and TMZ resistance in GBM. Key proteins are also described through biological processes related to gene ontology (GO), molecular functions, and cellular components. For protein-protein interactions (PPI), network and pathway involvement analyses have been performed, highlighting the roles of key proteins in the TMZ resistance phenotypes. This study provides a detailed insight into methods of subcellular fractionation for proteomic analysis of TMZ-resistant GBM cells and the potential to apply this approach to future large-scale studies. Several key proteins, protein-protein interactions (PPI), and pathways have been identified, underlying the TMZ resistance phenotype and highlighting the proteins' biological functions.

Subcellular Accumulation and Depuration of Zinc in Periphytic Algae during Episodic and Continuous Exposures

As the severity of extreme precipitation events increases with global climate change, so will episodic pulses of contamination into lotic systems. Periphytic algae represents bioindicator species in most freshwater systems due to their rapid accumulation of toxicants; therefore, it is vital to understand how accumulation in this group differs across temporally variable exposure regimes. The ability to rapidly accrue contaminants has additional implications for the trophic transfer of metals to primary consumers. While dietary toxicity has been studied in algivorous consumers, techniques used to prepare contaminated periphytic algae for consumption have not been compared. This study used a modified subcellular fractionation method to compare the partitioning of zinc (Zn) in periphyton cultures exposed for various durations (cultured in the presence of Zn and 15 min, 24 h, and 48 h exposures). Three exposure groups were additionally depurated over a period of 24 h in order to compare retention of Zn, an important aspect of preparing diets used in dietary toxicity studies. The results not only provide evidence for increased retention by periphytic algae cultured in the presence of Zn but reveal relationships among treatments and subcellular partitioning that suggest time-dependent accumulation and detoxification. These relationships suggest that episodic exposure of periphytic algae to contaminants may pose a greater risk than that of chronic regimes. Based on these results, we additionally advocate for culturing periphytic algae in the presence of contamination to produce a more reliable diet for dietary exposure testing in algivorous organisms.

Hsa_circ_0008344 Promotes Glioma Tumor Progression and Angiogenesis Presumably by Regulating miR-638/SZRD1 Pathway.

Hsa_circRNA_0008344 (circ_0008344) is a new glioma-related circular RNA. Our study aims to explore its functions in glioma tumor progression. Real-time quantitative PCR and western blotting were used to detect RNA and protein abundances. RNase R assay, actinomycin D assay, and subcellular fractionation method were performed to identify the features of circ_0008344. Cell-counting kit-8, 5-ethynyl-2'-deoxyuridine assays, transwell assays, tube formation assay, flow cytometry, and nude mice xenograft tumor model were performed. Target relationship was predicted by bioinformatics algorithms and confirmed by dual-luciferase reporter assay. Abundances of circ_0008344 and SUZ RNA binding domain containing 1 (SZRD1) were highly elevated, while miR-638 was downregulated in glioma tumors and cells. Circ_0008344 was identified as a stable circRNA with a circular structure. Silencing circ_0008344 could restrain glioma proliferation, migration, invasion, and angiogenesis. Circ_0008344 functioned as a sponge for miR-638. The negative regulation of circ_0008344 knockdown on glioma progression and angiogenesis could be reversed by miR-638 inhibitor. SZRD1 was a target of miR-318, and its overexpression overturned the inhibition effect of miR-638 mimic on glioma progression and angiogenesis. Meanwhile, we confirmed that circ_0008344 knockdown inhibited SZRD1 expression, and its effect was reversed by miR-638 inhibitor. Also, circ_00008344 knockdown suppressed glioma tumor growth. Circ_0008344 might contribute to glioma progression through miR-638/SZRD1 axis, which might be a novel pathology and treatment target in glioma.

P38 MAPK-mediated loss of nuclear RNase III enzyme Drosha underlies amyloid beta-induced neuronal stress in Alzheimer's disease.

MicroRNAs (miRNAs) are small noncoding RNAs ubiquitously expressed in the brain and regulate gene expression at the post‐transcriptional level. The nuclear RNase III enzyme Drosha initiates the maturation process of miRNAs in the nucleus. Strong evidence suggests that dysregulation of miRNAs is involved in many neurological disorders including Alzheimer's disease (AD). Dysfunction of miRNA biogenesis components may be involved in the processes of those diseases. However, the role of Drosha in AD remains unknown. By using immunohistochemistry, biochemistry, and subcellular fractionation methods, we show here that the level of Drosha protein was significantly lower in the postmortem brain of human AD patients as well as in the transgenic rat model of AD. Interestingly, Drosha level was specifically reduced in neurons of the cortex and hippocampus but not in the cerebellum in the AD brain samples. In primary cortical neurons, amyloid‐beta (Aβ) oligomers caused a p38 MAPK‐dependent phosphorylation of Drosha, leading to its redistribution from the nucleus to the cytoplasm and a decrease in its level. This loss of Drosha function preceded Aβ‐induced neuronal death. Importantly, inhibition of p38 MAPK activity or overexpression of Drosha protected neurons from Aβ oligomers‐induced apoptosis. Taken together, these results establish a role for p38 MAPK‐Drosha pathway in modulating neuronal viability under Aβ oligomers stress condition and implicate loss of Drosha as a key molecular change in the pathogenesis of AD.

Identifying Cytoplasmic and Nuclear C‐Terminal to LisH (CTLH) Complex Interactors Using High‐Throughput Proteomics

The C-terminal to LisH (CTLH) complex is a tumour-suppressive E3 Really Interesting New Gene (RING) ubiquitin ligase that regulates intracellular signaling pathways and maintains cellular homeostasis. It is comprised of 8 individual proteins that have been shown to mediate a variety of intracellular protein-protein interactions; of these proteins, Required for Meiotic Division 5 Homolog A (RMND5A) and Macrophage Erythroblast Attacher (MAEA) contain the RING domains required for the CTLH complex to mediate ubiquitin transfer to specific protein substrates. Although its E3 ligase activity has been recently characterized, the endogenous subcellular localization of the complex and compartment-specific protein interaction network – which encompasses many unidentified E3 ligase substrates – has not been identified. In this study, we hypothesized that the CTLH complex is present in the cytoplasm and nucleus, and that the CTLH complex mediates compartment-specific protein-protein interactions with cytoplasmic and nuclear proteins. To test this hypothesis, we used a chemical-based subcellular fractionation method combined with low- and high-throughput proteomics. We first optimized the chemical fractionation method and used Western blot to detect each endogenous CTLH complex member in HeLa cell cytoplasmic and nuclear protein extracts. We then identified compartment-specific CTLH complex interactors using Affinity Purification Coupled to Mass Spectrometry (AP-MS) using the main CTLH complex scaffold protein – Ran Binding Protein M (RanBPM) – as bait in cytoplasmic and nuclear HeLa protein extracts. Following Liquid Chromatography Electrospray Ionizing Tandem Mass Spectrometry (LC-ESI-MS/MS) and subsequent in silico filtering using the MiST algorithm, we identified 27 cytoplasmic, 155 nuclear, and 31 nucleocytoplasmic high-confidence (MiST Score ≥ 0.75) RanBPM interactors. STRING enrichment analysis of the high-confidence interactors revealed that RanBPM and its associated CTLH complex may be involved in a variety of conserved Gene Ontology (GO) processes including Epigenetic Regulation of Gene Expression and Chromatin Assembly. As such, we validated a number of newly-identified compartment-specific RanBPM interactors associated with the enriched GO terms by co-immunoprecipitation – using RanBPM as bait – and resulting Western blot. Furthermore, we focussed on an interesting novel putative interactor that is present in the two aforementioned GO processes – histone variant MacroH2A1 – and further validated its interaction with the CTLH complex in vivo using Proximity Ligation Assay (PLA), suggesting that this interaction may be physiologically relevant. Overall, by using this workflow, we identified and validated a number of novel compartment-specific potential CTLH complex interactors in vitro, further validated a promising novel interaction between the CTLH complex and MacroH2A1 in vivo, and successfully implicated the CTLH complex in a number of previously unexplored cellular mechanisms.

GTSE1 promotes SNAIL1 degradation by facilitating its nuclear export in hepatocellular carcinoma cells.

Snail family transcriptional repressor 1 (SNAIL1) is a master inducer of the epithelial-to-mesenchymal transition (EMT) process, contributing to tumor metastasis and recurrence. Our previous study reported that G2 and S phase-expressed-1 (GTSE1) served a role in regulating SNAIL1 expression in hepatocellular carcinoma (HCC). However, the underlying mechanism remains unknown. Therefore, the present study aimed to reveal the regulatory mechanism of GTSE1 on SNAIL1 expression using in vitro assays performed in HCC cell models. It was demonstrated that endogenous SNAIL1 expression was downregulated and upregulated by GTSE1 overexpression or small interfering RNA-mediated knockdown, respectively. Via cycloheximide chase experiments, it was identified that GTSE1 overexpression increased the protein turnover of SNAIL1, while knockdown of GTSE1 reduced its degradation rate. Furthermore, it was demonstrated that GTSE1 overexpression induced the cytoplasmic expression of SNAIL1 using immunofluorescence and subcellular fractionation methods. The nuclear export inhibitor leptomycin B was able to decrease the cytoplasmic retention of SNAIL1 caused by GTSE1 overexpression. In addition, TGF-βI treatment increased both the mRNA and protein expression levels of GTSE1, and decreased the protein expression level of SNAIL1 without affecting its mRNA transcription in Huh7 cells. It was also found that TGF-β signaling could upregulate the transcription of GTSE1 expression by transactivating the Smad binding elements in the GTSE1 promoter. Moreover, the TGF-βI-induced decrease in SNAIL1 protein expression was GTSE1-dependent in Huh7 cells. In conclusion, the current study provides a novel mechanism via which GTSE1 affects the stability of SNAIL1 by regulating its subcellular localization in HCC cells.

A Membrane-Bound Diacylglycerol Species Induces PKCϵ-Mediated Hepatic Insulin Resistance

Nonalcoholic fatty liver disease is strongly associated with hepatic insulin resistance (HIR); however, the key lipid species and molecular mechanisms linking these conditions are widely debated. We developed a subcellular fractionation method to quantify diacylglycerol (DAG) stereoisomers and ceramides in the endoplasmic reticulum (ER), mitochondria, plasma membrane (PM), lipid droplets, and cytosol. Acute knockdown (KD) of diacylglycerol acyltransferase-2 in liver induced HIR in rats. This was due to PM sn-1,2-DAG accumulation, which promoted PKCϵ activation and insulin receptor kinase (IRK)-T1160 phosphorylation, resulting in decreased IRK-Y1162 phosphorylation. Liver PM sn-1,2-DAG content and IRK-T1160 phosphorylation were also higher in humans with HIR. In rats, liver-specific PKCϵ KD ameliorated high-fat diet-induced HIR by lowering IRK-T1160 phosphorylation, while liver-specific overexpression of constitutively active PKCϵ-induced HIR by promoting IRK-T1160 phosphorylation. These data identify PM sn-1,2-DAGs as the key pool of lipids that activate PKCϵ and that hepatic PKCϵ is both necessary and sufficient in mediating HIR.

Neuronal Transcriptome from C9orf72 Repeat Expanded Human Tissue is Associated with Loss of C9orf72 Function.

A hexanucleotide G4C2 repeat expansion in C9orf72 is the most common genetic cause of familial and sporadic cases of amyotrophic lateral sclerosis (ALS) and frontotemporal degeneration (FTD). The mutation is associated with a reduction of C9orf72 protein and accumulation of toxic RNA and dipeptide repeat aggregates. The accumulation of toxic RNA has been proposed to sequester RNA binding proteins thereby altering RNA processing, consistent with previous transcriptome studies that have shown that the C9orf72 repeat expansion is linked to abundant splicing alterations and transcriptome changes. Here, we used a subcellular fractionation method and FACS to enrich for neuronal nuclei from C9orf72 repeat expanded post-mortem human ALS/FTD brains, and to remove neuronal nuclei with TDP-43 pathology which are observed in nearly all symptomatic C9orf72 repeat expanded cases. We show that the C9orf72 expansion is associated with relatively mild gene expression changes. Dysregulated genes were enriched for vesicle transport pathways, which is consistent with the known functions of C9orf72 protein. Further analysis suggests that the C9orf72 transcriptome is not driven by toxic RNA but is rather shaped by the depletion of pathologic TDP-43 nuclei and the loss of C9orf72 expression. These findings argue against RNA binding protein sequestration in neurons as a major contributor to C9orf72 mediated toxicity.

Optimization of a subcellular metal fractionation method for fish liver: Homogenization, subcellular separation, and trial isolation of nuclear materials

AbstractThe subcellular compartmentalization of metals within aquatic organisms reflects their internal behavior after metal uptake and can provide important information about their potential toxicity. Commonly, the fractionation protocol used to determine subcellular metal partitioning in aquatic organisms consists of mechanically homogenizing the tissue, separating subcellular components into fractions by differential centrifugation and heat‐denaturation steps, and determining the amount of metals associated with each fraction. However, the accurate separation of subcellular cell components is challenging and the nature and purity of the operationally defined subcellular fractions are rarely assessed. In the absence of this type of validation, however, the interpretation of subcellular metal fractionation results could be compromised. The aim of the present study was to adjust a subcellular fractionation protocol for the liver of field‐collected fish and to test the adjusted protocol using fraction‐specific enzyme markers. Overall, our results illustrate the need to optimize fractionation procedures when studying a new species or organ. In the course of this study, the categorization of some fractions was revised in accordance with the enzymatic results obtained, in order to yield a more credible subcellular fraction distribution scheme. In addition, trial assays aimed at isolating nuclear materials from the cellular debris were conducted, using DNA as a marker for nuclear material. Tested protocols failed to isolate the nuclei and results suggested that nuclei were probably trapped by disrupted cellular membranes. Recommendations on how to improve future subcellular fractionation studies on freshwater fish are discussed.

205-OR: Hepatic Protein Kinase C-e Is Necessary and Sufficient in Mediating Lipid-Induced Hepatic Insulin Resistance

Nonalcoholic fatty liver disease (NAFLD) is strongly associated with hepatic insulin resistance (HIR), however the key lipid species and molecular mechanisms linking these conditions are widely debated. In order to address these questions, we examined the metabolic impact of a liver-specific antisense oligonucleotide against PKCε and found that liver-specific PKCε knockdown ameliorated high-fat diet-induced HIR in rats, reflected by ∼2x increase in insulin-stimulated hepatic glycogen synthesis rate and improved insulin-mediated suppression of endogenous glucose production during a hyperinsulinemic-hyperglycemic (HH) clamp. This was associated with increased IRK Y1162 and Akt S473 phosphorylation and could be attributed to decreased PKCε-mediated IRK T1160 phosphorylation. Overexpressing a constitutively active PKCε (A159E) in the liver induced HIR in regular chow-fed rats, reflected by reduced insulin-stimulated glycogen synthesis rate during an HH clamp. This was associated with impaired IRK Y1162 and Akt S473 phosphorylation and could be attributed to increased PKCε-mediated IRK T1160 phosphorylation. We also developed a subcellular fractionation method to quantify diacylglycerol (DAG) stereoisomers and ceramides in the endoplasmic reticulum, mitochondria, plasma membrane (PM), lipid droplet and cytosol and applied this method to a cohort of obese human subjects with and without NAFLD and HIR. Liver PM sn-1,2 DAG content was ∼5x higher in HIR individuals with NAFLD compared to insulin-sensitive individuals without NAFLD, associated with ∼3x higher IRK T1160 phosphorylation, supporting the importance of PM sn-1,2 DAG-PKCε-IRK pT1160 pathway to mediate HIR in humans with NAFLD. In contrast there were no significant differences in ceramide content in any of the subcellular compartments. Conclusion: These data identify PM sn-1,2 DAGs as the key lipids that activate PKCε, and that hepatic PKCε is both necessary and sufficient in mediating HIR. Disclosure K. Lyu: None. D. Zhang: None. M. Kahn: None. M.R.S. Rodrigues: None. S. Hirabara: None. P. Luukkonen: None. S. Lee: None. S. Bhanot: None. J. Rinehart: None. N. Blume: Employee; Self; Novo Nordisk A/S. Stock/Shareholder; Self; Novo Nordisk A/S. M. Rasch: Employee; Self; Novo Nordisk A/S. Stock/Shareholder; Self; Novo Nordisk A/S. M.J. Serlie: None. J. Bogan: None. G. Cline: None. V. Samuel: None. G.I. Shulman: Advisory Panel; Self; AstraZeneca, Janssen Research & Development, LLC, Merck & Co., Inc. Advisory Panel; Spouse/Partner; Merck & Co., Inc. Consultant; Self; Novo Nordisk A/S. Consultant; Spouse/Partner; Novo Nordisk A/S. Other Relationship; Self; Gilead Sciences, Inc., iMetabolic Biopharma Corporation. Other Relationship; Spouse/Partner; iMetabolic Biopharma Corporation. Other Relationship; Self; Maze Therapeutics. Funding U.S. Public Health Service (R01DK116774, R01DK119968, R01DK113984, P30DK045735, R01 DK092661); U.S. Department of Veternas Affairs (I01BX000901)

Profiling Cysteine Reactivity and Oxidation in the Endoplasmic Reticulum.

The endoplasmic reticulum (ER) is the initial site of biogenesis of secretory pathway proteins, including proteins localized to the ER, Golgi, lysosomes, intracellular vesicles, plasma membrane, and extracellular compartments. Proteins within the secretory pathway contain a high abundance of disulfide bonds to protect against the oxidative extracellular environment. These disulfide bonds are typically formed within the ER by a variety of oxidoreductases, including members of the protein disulfide isomerase (PDI) family. Here, we establish chemoproteomic platforms to identify oxidized and reduced cysteine residues within the ER. Subcellular fractionation methods were utilized to enrich for the ER and significantly enhance the coverage of ER-localized cysteine residues. Reactive-cysteine profiling ranked ∼900 secretory pathway cysteines by reactivity with an iodoacetamide-alkyne probe, revealing functional cysteines annotated to participate in disulfide bonds, or S-palmitoylation sites within proteins. Through application of a variation of the OxICAT protocol for quantifying cysteine oxidation, the percentages of oxidation for each of ∼700 ER-localized cysteines were calculated. Lastly, perturbation of ER function, through chemical induction of ER stress, was used to investigate the effect of initiation of the unfolded protein response (UPR) on ER-localized cysteine oxidation. Together, these studies establish a platform for identifying reactive and functional cysteine residues on proteins within the secretory pathway as well as for interrogating the effects of diverse cellular stresses on ER-localized cysteine oxidation.

Distinct Kinetics in Electrophoretic Extraction of Cytoplasmic RNA from Single Cells.

The physical fractionation of cytoplasmic versus nuclear components of cells is a key step for studying the subcellular localization of molecules. The application of an electric field is an emerging method for subcellular fractionation of proteins and nucleic acids from single cells. However, the multibiophysical process that involves electrical lysis of cytoplasmic membranes, electrophoresis, and diffusion of charged molecules remains unclear. Here we study RNA dynamics in single cells during the electrophoretic extraction via a microfluidic system that enables stringent fractionation of the subcellular components leveraging a focused electric field. We identified two distinct kinetics in the extraction of RNA molecules, which were respectively associated with soluble RNA and mitochondrial RNA. We show that the extraction kinetics of soluble RNA is dominated by electrophoresis over diffusion and has a time constant of 0.15 s. Interestingly, the extraction of mitochondrial RNA showed unexpected heterogeneity in the extraction with slower kinetics (3.8 s), whilereproducibly resulting in the extraction of 98.9% ± 2% after 40 s. Together, we uncover that the microfluidic system uniquely offers length bias-free fractionation of RNA molecules for quantitative analysis of correlations among subcellular compartments by exploiting the homogeneous electrophoretic properties of RNA.

Cavin-1/PTRF mediates insulin-dependent focal adhesion remodeling and ameliorates high-fat diet–induced inflammatory responses in mice

Cavin-1/polymerase I and transcript release factor (PTRF) is a requisite component of caveolae, small plasma membrane invaginations that are highly abundant in adipocytes. Cavin-1 is a dynamic molecule whose dissociation from caveolae plays an important role in mechanoprotection and rRNA synthesis. In the former situation, the acute dissociation of cavin-1 from caveolae allows cell membrane expansion that occurs upon insulin-aided lipid uptake into the fat cells. Cavin-1 dissociation from caveolae and membrane flattening alters the cytoskeleton and the interaction of plasma membrane proteins with the extracellular matrix through interactions with focal adhesion structures. Here, using cavin-1 knockout mice, subcellular fractionation, and immunoblotting methods, we addressed the relationship of cavin-1 with focal adhesion complexes following nutritional stimulation. We found that cavin-1 is acutely translocated to focal complex compartments upon insulin stimulation, where it regulates focal complex formation through an interaction with paxillin. We found that loss of cavin-1 impairs focal complex remodeling and focal adhesion formation and causes a mechanical stress response, concomitant with activation of proinflammatory and senescence/apoptosis pathways. We conclude that cavin-1 plays key roles in dynamic remodeling of focal complexes upon metabolic stimulation. This mechanism also underlies the crucial role of caveolae in the long-term healthy expansion of the adipocyte.

Anticancer auranofin engages 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGCR) as a target.

Auranofin (AuRF) has been reported to display anticancer activity and has entered several clinical trials; however, its mechanism of action remains largely unknown. In this work, the anticancer mechanism of auranofin was investigated using a proteomics strategy entailing subcellular fractionation prior to mass spectrometric analysis. Bioinformatics analysis of the nuclear sub-proteomes revealed that tumor suppressor p14ARF is a key regulator of transcription. Through independent analysis, we validated that up-regulation of p14ARF is associated with E2F-dependent transcription and increased p53 expression. Our analyses further reveal that 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGCR), which is the rate-determining enzyme of the mevalonate pathway, is a novel target of auranofin with half maximal inhibitory concentration at micromolar levels. The auranofin-induced cancer cell death could be partially reverted by the addition of downstream products of the mevalonate pathway (mevalonolactone or geranyleranyl pyrophosphate (GGPP)), implying that auranofin may target the mevalonate pathway to exert its anticancer effect.

Fractionation of Subcellular Compartments from Human Brain Tissue.

Subcellular fractionation methods permit the isolation, purification, and/or enrichment of specific cellular compartments from complex tissue samples. Enrichment of multiple subcellular compartments from the same tissue sample permits comparisons of the spatial distribution of target proteins between specific intracellular compartments and, in some cases, can provide information about spatiotemporal processing of key cellular components. Here we describe a method to generate subcellular fractions enriched for heavy membranes and nuclei, rough and smooth endoplasmic reticulum membranes, light membranes and cytosol, synapses, and other intermediate cellular membranes from postmortem human brain tissue. These subcellular fractions can be used in a variety of downstream applications to assess the localization, relative abundance, and stoichiometry of glutamate receptor subunits along the forward trafficking pathway.

Methodologies to monitor protein turnover at the inner nuclear membrane.

Lamin B receptor (LBR) is an inner nuclear membrane protein that associates with the nuclear lamina and harbors sterol reductase activity essential for cholesterol biosynthesis. Several LBR mutations implicated in human congenital disorders give rise to C-terminal truncations which render LBR metabolically unstable, resulting in their rapid turnover in the nucleus. These LBR variants serve as model substrates for investigating the poorly understood protein quality control pathways in the mammalian nuclear envelope (NE). Here we describe a split-GFP-based method for tagging these model substrates to enable live cell imaging and flow cytometry for the identification and characterization of NE-resident protein turnover machinery. Furthermore, we describe a facile subcellular fractionation method to isolate a soluble LBR degradation intermediate, allowing the deconvolution of the membrane extraction and proteasomal turnover steps. The combination of imaging-based and biochemical approaches described here facilitates detailed mechanistic studies to dissect protein turnover in the nuclear compartment.

Activity-dependent bulk endocytosis proteome reveals a key presynaptic role for the monomeric GTPase Rab11

Activity-dependent bulk endocytosis (ADBE) is the dominant mode of synaptic vesicle endocytosis during high-frequency stimulation, suggesting it should play key roles in neurotransmission during periods of intense neuronal activity. However, efforts in elucidating the physiological role of ADBE have been hampered by the lack of identified molecules which are unique to this endocytosis mode. To address this, we performed proteomic analysis on purified bulk endosomes, which are a key organelle in ADBE. Bulk endosomes were enriched via two independent approaches, a classical subcellular fractionation method and isolation via magnetic nanoparticles. There was a 77% overlap in proteins identified via the two protocols, and these molecules formed the ADBE core proteome. Bioinformatic analysis revealed a strong enrichment in cell adhesion and cytoskeletal and signaling molecules, in addition to expected synaptic and trafficking proteins. Network analysis identified Rab GTPases as a central hub within the ADBE proteome. Subsequent investigation of a subset of these Rabs revealed that Rab11 both facilitated ADBE and accelerated clathrin-mediated endocytosis. These findings suggest that the ADBE proteome will provide a rich resource for the future study of presynaptic function, and identify Rab11 as a regulator of presynaptic function.

Brain Metabolic DNA in Rat Cytoplasm.

Brain metabolic DNA (BMD) is not involved in cell division or DNA repair but is modulated by memory acquisition, sleep processing, and circadian oscillations. Using routine methods of subcellular fractionation, newly synthesized BMD from male rats is shown to be localized in crude nuclear, mitochondrial, and microsomal fractions and in two fractions of purified nuclei. Sub-fractionation of the mitochondrial fraction indicates the prevalent localization of BMD in free mitochondria and to a lesser degree in synaptosomes and myelin. Cesium density profiles of homogenate, subcellular fractions, and purified nuclei obtained after incorporation periods from 30min to 4h indicate that BMD synthesis takes place by reverse transcription in cytoplasmic organelles. Following the acquisition of the double-stranded structure, BMD is transferred to nuclei. Kinetic analyses lasting several weeks highlight the massive BMD turnover in subcellular fractions and purified nuclei and its dependence on age. Data are in agreement with the role of BMD as a temporary information store of cell responses of potential use in comparable forthcoming experiences.

Soluble uric acid increases PDZK1 and ABCG2 expression in human intestinal cell lines via the TLR4-NLRP3 inflammasome and PI3K/Akt signaling pathway

BackgroundIn addition to the kidney, the intestine is one of the most important organs involved in uric acid excretion. However, the mechanism of urate excretion in the intestine remains unclear. Therefore, the relationship between soluble uric acid and the gut excretion in human intestinal cells was explored. The relevant signaling molecules were then also examined.MethodsHT-29 and Caco-2 cell lines were stimulated with soluble uric acid. Western blotting and qRT-PCR were used to measure protein and mRNA levels. Subcellular fractionation methods and immunofluorescence were used to quantify the proteins in different subcellular compartments. Flow cytometry experiments examined the function of ATP-binding cassette transporter, subfamily G, member 2 (ABCG2). Small interfering RNA transfection was used to assess the interaction between ABCG2 and PDZ domain-containing 1 (PDZK1).ResultsSoluble uric acid increased the expression of PDZK1 and ABCG2. The stimulation of soluble uric acid also facilitated the translocation of ABCG2 from the intracellular compartment to the plasma membrane and increased its transport activity. Moreover, the upregulation of PDZK1 and ABCG2 by soluble uric acid was partially decreased by either TLR4-NLRP3 inflammasome inhibitors or PI3K/Akt signaling inhibitors. Furthermore, PDZK1 knockdown significantly inhibited the expression and transport activity of ABCG2 regardless of the activation by soluble uric acid, demonstrating a pivotal role for PDZK1 in the regulation of ABCG2.ConclusionsThese findings suggest that urate upregulates the expression of PDZK1 and ABCG2 for excretion in intestinal cells via activating the TLR4-NLRP3 inflammasome and PI3K/Akt signaling pathway.