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1.
Cell ; 152(3): 599-611, 2013 Jan 31.
Article in English | MEDLINE | ID: mdl-23374352

ABSTRACT

Tumor cells have high-energetic and anabolic needs and are known to adapt their metabolism to be able to survive and keep proliferating under conditions of nutrient stress. We show that PKCζ deficiency promotes the plasticity necessary for cancer cells to reprogram their metabolism to utilize glutamine through the serine biosynthetic pathway in the absence of glucose. PKCζ represses the expression of two key enzymes of the pathway, PHGDH and PSAT1, and phosphorylates PHGDH at key residues to inhibit its enzymatic activity. Interestingly, the loss of PKCζ in mice results in enhanced intestinal tumorigenesis and increased levels of these two metabolic enzymes, whereas patients with low levels of PKCζ have a poor prognosis. Furthermore, PKCζ and caspase-3 activities are correlated with PHGDH levels in human intestinal tumors. Taken together, this demonstrates that PKCζ is a critical metabolic tumor suppressor in mouse and human cancer.


Subject(s)
Adenocarcinoma/metabolism , Adenoma/metabolism , Colonic Neoplasms/metabolism , Protein Kinase C/metabolism , Adenomatous Polyposis Coli Protein/genetics , Adenomatous Polyposis Coli Protein/metabolism , Animals , Biosynthetic Pathways , Cell Transformation, Neoplastic , Glucose/metabolism , Humans , Mice , Serine/biosynthesis , Specific Pathogen-Free Organisms , Stress, Physiological
2.
Proc Natl Acad Sci U S A ; 114(22): E4462-E4471, 2017 05 30.
Article in English | MEDLINE | ID: mdl-28500272

ABSTRACT

The molecular pathogenesis of bipolar disorder (BPD) is poorly understood. Using human-induced pluripotent stem cells (hiPSCs) to unravel such mechanisms in polygenic diseases is generally challenging. However, hiPSCs from BPD patients responsive to lithium offered unique opportunities to discern lithium's target and hence gain molecular insight into BPD. By profiling the proteomics of BDP-hiPSC-derived neurons, we found that lithium alters the phosphorylation state of collapsin response mediator protein-2 (CRMP2). Active nonphosphorylated CRMP2, which binds cytoskeleton, is present throughout the neuron; inactive phosphorylated CRMP2, which dissociates from cytoskeleton, exits dendritic spines. CRMP2 elimination yields aberrant dendritogenesis with diminished spine density and lost lithium responsiveness (LiR). The "set-point" for the ratio of pCRMP2:CRMP2 is elevated uniquely in hiPSC-derived neurons from LiR BPD patients, but not with other psychiatric (including lithium-nonresponsive BPD) and neurological disorders. Lithium (and other pathway modulators) lowers pCRMP2, increasing spine area and density. Human BPD brains show similarly elevated ratios and diminished spine densities; lithium therapy normalizes the ratios and spines. Consistent with such "spine-opathies," human LiR BPD neurons with abnormal ratios evince abnormally steep slopes for calcium flux; lithium normalizes both. Behaviorally, transgenic mice that reproduce lithium's postulated site-of-action in dephosphorylating CRMP2 emulate LiR in BPD. These data suggest that the "lithium response pathway" in BPD governs CRMP2's phosphorylation, which regulates cytoskeletal organization, particularly in spines, modulating neural networks. Aberrations in the posttranslational regulation of this developmentally critical molecule may underlie LiR BPD pathogenesis. Instructively, examining the proteomic profile in hiPSCs of a functional agent-even one whose mechanism-of-action is unknown-might reveal otherwise inscrutable intracellular pathogenic pathways.


Subject(s)
Bipolar Disorder , Induced Pluripotent Stem Cells/drug effects , Lithium/pharmacology , Models, Biological , Protein Processing, Post-Translational/drug effects , Animals , Bipolar Disorder/genetics , Bipolar Disorder/metabolism , Bipolar Disorder/physiopathology , Brain Chemistry , Calcium/metabolism , Cells, Cultured , Humans , Induced Pluripotent Stem Cells/physiology , Intercellular Signaling Peptides and Proteins/chemistry , Intercellular Signaling Peptides and Proteins/metabolism , Mice , Nerve Tissue Proteins/chemistry , Nerve Tissue Proteins/metabolism , Proteomics
3.
Neurobiol Dis ; 127: 390-397, 2019 07.
Article in English | MEDLINE | ID: mdl-30928642

ABSTRACT

Tuberous sclerosis (TSC) is an autosomal dominant disorder caused by heterozygous mutations in the TSC1 or TSC2 gene. TSC is often associated with neurological, cognitive, and behavioral deficits. TSC patients also express co-morbidity with anxiety and mood disorders. The mechanism of pathogenesis in TSC is not entirely clear, but TSC-related neurological symptoms are accompanied by excessive glutamatergic activity and altered synaptic spine structures. To address whether extrasynaptic (e)NMDA-type glutamate receptor (NMDAR) antagonists, as opposed to antagonists that block physiological phasic synaptic activity, can ameliorate the synaptic and behavioral features of this disease, we utilized the Tsc2+/- mouse model of TSC to measure biochemical, electrophysiological, histological, and behavioral parameters in the mice. We found that antagonists that preferentially block tonic activity as found at eNMDARs, particularly the newer drug NitroSynapsin, provide biological and statistically significant improvement in Tsc2+/- phenotypes. Accompanying this improvement was correction of activity in the p38 MAPK-TSC-Rheb-mTORC1-S6K1 pathway. Deficits in hippocampal long-term potentiation (LTP), histological loss of synapses, and behavioral fear conditioning in Tsc2+/- mice were all improved after treatment with NitroSynapsin. Taken together, these results suggest that amelioration of excessive excitation, by limiting aberrant eNMDAR activity, may represent a novel treatment approach for TSC.


Subject(s)
Excitatory Amino Acid Antagonists/therapeutic use , Hippocampus/drug effects , Receptors, N-Methyl-D-Aspartate/antagonists & inhibitors , Tuberous Sclerosis/drug therapy , Animals , Disease Models, Animal , Excitatory Amino Acid Antagonists/pharmacology , Hippocampus/metabolism , Mice , Mice, Knockout , Tuberous Sclerosis/genetics , Tuberous Sclerosis/metabolism , Tuberous Sclerosis Complex 2 Protein/genetics , Tuberous Sclerosis Complex 2 Protein/metabolism
4.
Circ Res ; 117(2): 142-56, 2015 Jul 03.
Article in English | MEDLINE | ID: mdl-26034040

ABSTRACT

RATIONALE: Wnt signaling regulates key aspects of diabetic vascular disease. OBJECTIVE: We generated SM22-Cre;LRP6(fl/fl);LDLR(-/-) mice to determine contributions of Wnt coreceptor low-density lipoprotein receptor-related protein 6 (LRP6) in the vascular smooth muscle lineage of male low-density lipoprotein receptor-null mice, a background susceptible to diet (high-fat diet)-induced diabetic arteriosclerosis. METHODS AND RESULTS: As compared with LRP6(fl/fl);LDLR(-/-) controls, SM22-Cre;LRP6(fl/fl);LDLR(-/-) (LRP6-VKO) siblings exhibited increased aortic calcification on high-fat diet without changes in fasting glucose, lipids, or body composition. Pulse wave velocity (index of arterial stiffness) was also increased. Vascular calcification paralleled enhanced aortic osteochondrogenic programs and circulating osteopontin (OPN), a matricellular regulator of arteriosclerosis. Survey of ligands and Frizzled (Fzd) receptor profiles in LRP6-VKO revealed upregulation of canonical and noncanonical Wnts alongside Fzd10. Fzd10 stimulated noncanonical signaling and OPN promoter activity via an upstream stimulatory factor (USF)-activated cognate inhibited by LRP6. RNA interference revealed that USF1 but not USF2 supports OPN expression in LRP6-VKO vascular smooth muscle lineage, and immunoprecipitation confirmed increased USF1 association with OPN chromatin. ML141, an antagonist of cdc42/Rac1 noncanonical signaling, inhibited USF1 activation, osteochondrogenic programs, alkaline phosphatase, and vascular smooth muscle lineage calcification. Mass spectrometry identified LRP6 binding to protein arginine methyltransferase (PRMT)-1, and nuclear asymmetrical dimethylarginine modification was increased with LRP6-VKO. RNA interference demonstrated that PRMT1 inhibits OPN and TNAP, whereas PRMT4 supports expression. USF1 complexes containing the histone H3 asymmetrically dimethylated on Arg-17 signature of PRMT4 are increased with LRP6-VKO. Jmjd6, a demethylase downregulated with LRP6 deficiency, inhibits OPN and TNAP expression, USF1: histone H3 asymmetrically dimethylated on Arg-17 complex formation, and transactivation. CONCLUSIONS: LRP6 restrains vascular smooth muscle lineage noncanonical signals that promote osteochondrogenic differentiation, mediated in part via USF1- and arginine methylation-dependent relays.


Subject(s)
Arteriosclerosis/prevention & control , Calcinosis/prevention & control , Diabetes Mellitus, Experimental/complications , Low Density Lipoprotein Receptor-Related Protein-6/physiology , Muscle, Smooth, Vascular/physiopathology , Myocytes, Smooth Muscle/metabolism , Receptors, LDL/deficiency , Wnt Signaling Pathway , Animals , Arginine/analogs & derivatives , Arginine/metabolism , Arteriosclerosis/etiology , Arteriosclerosis/metabolism , Calcinosis/etiology , Calcinosis/metabolism , Diabetes Mellitus, Experimental/pathology , Dietary Fats/adverse effects , Frizzled Receptors/physiology , Gene Expression Regulation/physiology , Histones/metabolism , Low Density Lipoprotein Receptor-Related Protein-6/deficiency , Low Density Lipoprotein Receptor-Related Protein-6/genetics , Male , Mice , Mice, Knockout , Myocytes, Smooth Muscle/pathology , Osteopontin/biosynthesis , Osteopontin/genetics , Paracrine Communication , Protein Interaction Mapping , Protein-Arginine N-Methyltransferases/metabolism , Receptors, Cell Surface , Receptors, LDL/genetics , Upstream Stimulatory Factors/physiology , Vascular Stiffness/physiology
5.
Mol Cell ; 36(1): 141-52, 2009 Oct 09.
Article in English | MEDLINE | ID: mdl-19818717

ABSTRACT

eIF3 promotes translation initiation, but relatively little is known about its full range of activities in the cell. Here, we employed affinity purification and highly sensitive LC-MS/MS to decipher the fission yeast eIF3 interactome, which was found to contain 230 proteins. eIF3 assembles into a large supercomplex, the translasome, which contains elongation factors, tRNA synthetases, 40S and 60S ribosomal proteins, chaperones, and the proteasome. eIF3 also associates with ribosome biogenesis factors and the importins-beta Kap123p and Sal3p. Our genetic data indicated that the binding to both importins-beta is essential for cell growth, and photobleaching experiments revealed a critical role for Sal3p in the nuclear import of one of the translasome constituents, the proteasome. Our data reveal the breadth of the eIF3 interactome and suggest that factors involved in translation initiation, ribosome biogenesis, translation elongation, quality control, and transport are physically linked to facilitate efficient protein synthesis.


Subject(s)
Eukaryotic Initiation Factor-3/metabolism , Multiprotein Complexes/physiology , Proteasome Endopeptidase Complex/physiology , Protein Biosynthesis/physiology , Schizosaccharomyces pombe Proteins/metabolism , Schizosaccharomyces/metabolism , Actin Cytoskeleton/metabolism , Active Transport, Cell Nucleus/physiology , Enzymes/metabolism , Models, Molecular , Protein Interaction Mapping/methods , Ribosome Subunits/metabolism , Schizosaccharomyces pombe Proteins/analysis , Tandem Mass Spectrometry , beta Karyopherins/metabolism
6.
PLoS Genet ; 10(5): e1004348, 2014 May.
Article in English | MEDLINE | ID: mdl-24809345

ABSTRACT

The endoplasmic reticulum (ER) responds to changes in intracellular homeostasis through activation of the unfolded protein response (UPR). Yet, it is not known how UPR-signaling coordinates adaptation versus cell death. Previous studies suggested that signaling through PERK/ATF4 is required for cell death. We show that high levels of ER stress (i.e., ischemia-like conditions) induce transcription of the ubiquitin ligases Siah1/2 through the UPR transducers PERK/ATF4 and IRE1/sXBP1. In turn, Siah1/2 attenuates proline hydroxylation of ATF4, resulting in its stabilization, thereby augmenting ER stress output. Conversely, ATF4 activation is reduced upon Siah1/2 KD in cultured cells, which attenuates ER stress-induced cell death. Notably, Siah1a(+/-)::Siah2(-/-) mice subjected to neuronal ischemia exhibited smaller infarct volume and were protected from ischemia-induced death, compared with the wild type (WT) mice. In all, Siah1/2 constitutes an obligatory fine-tuning mechanism that predisposes cells to death under severe ER stress conditions.


Subject(s)
Isoenzymes/metabolism , Ubiquitin-Protein Ligases/metabolism , Unfolded Protein Response , Animals , CHO Cells , Cells, Cultured , Cricetinae , Cricetulus , Endoplasmic Reticulum/metabolism , Enzyme Activation , Humans , Mice , RNA, Messenger/genetics , Real-Time Polymerase Chain Reaction , Stress, Physiological , Transcription, Genetic , Ubiquitin-Protein Ligases/genetics
7.
Proc Natl Acad Sci U S A ; 110(16): 6418-23, 2013 Apr 16.
Article in English | MEDLINE | ID: mdl-23550155

ABSTRACT

Studies showing reduced PKCζ expression or enzymatic activity in different types of human cancers support the clinical relevance of PKCζ as a tumor suppressor. However, the in vivo role of PKCζ and its mechanisms of action in prostate cancer remain unclear. Here we demonstrate that the genetic inactivation of PKCζ in mice results in invasive prostate carcinoma in vivo in the context of phosphatase and tensin homolog deficiency. Bioinformatic analysis of human prostate cancer gene-expression sets revealed increased c-Myc transcriptional activity in PKCζ-inactive cells, which correlated with increased cell growth, invasion, and metastasis. Interestingly, PKCζ knockdown or the overexpression of a kinase-inactive mutant resulted in enhanced cell proliferation and invasion in vitro through increased c-Myc mRNA and protein levels and decreased Ser-373 phosphorylation of c-Myc. Analysis of prostate cancer samples demonstrated increased expression and decreased phosphorylation of c-Myc at Ser-373 in PKCζ knockout tumors. In vivo xenograft studies revealed that c-Myc phosphorylation by PKCζ is a critical event in the control of metastasis. Collectively, these results establish PKCζ as an important tumor suppressor and regulator of c-Myc function in prostate cancer.


Subject(s)
Cell Transformation, Neoplastic/metabolism , Gene Expression Regulation, Neoplastic/physiology , Neoplasm Metastasis/physiopathology , Prostatic Neoplasms/metabolism , Protein Kinase C/metabolism , Proto-Oncogene Proteins c-myc/metabolism , Animals , Blotting, Western , Computational Biology , Luciferases , Male , Mice , Microarray Analysis , PTEN Phosphohydrolase/metabolism , Phosphorylation , Real-Time Polymerase Chain Reaction
8.
J Neurosci ; 34(13): 4640-53, 2014 Mar 26.
Article in English | MEDLINE | ID: mdl-24672010

ABSTRACT

Mutations in the ataxia telangiectasia mutated (ATM) gene, which encodes a kinase critical for the normal DNA damage response, cause the neurodegenerative disorder ataxia-telangiectasia (AT). The substrates of ATM in the brain are poorly understood. Here we demonstrate that ATM phosphorylates and activates the transcription factor myocyte enhancer factor 2D (MEF2D), which plays a critical role in promoting survival of cerebellar granule cells. ATM associates with MEF2D after DNA damage and phosphorylates the transcription factor at four ATM consensus sites. Knockdown of endogenous MEF2D with a short-hairpin RNA (shRNA) increases sensitivity to etoposide-induced DNA damage and neuronal cell death. Interestingly, substitution of endogenous MEF2D with an shRNA-resistant phosphomimetic MEF2D mutant protects cerebellar granule cells from cell death after DNA damage, whereas an shRNA-resistant nonphosphorylatable MEF2D mutant does not. In vivo, cerebella in Mef2d knock-out mice manifest increased susceptibility to DNA damage. Together, our results show that MEF2D is a substrate for phosphorylation by ATM, thus promoting survival in response to DNA damage. Moreover, dysregulation of the ATM-MEF2D pathway may contribute to neurodegeneration in AT.


Subject(s)
DNA Damage/physiology , Neurons/physiology , Animals , Ataxia Telangiectasia Mutated Proteins/antagonists & inhibitors , Ataxia Telangiectasia Mutated Proteins/deficiency , Ataxia Telangiectasia Mutated Proteins/physiology , Cell Survival/physiology , Cells, Cultured , Cerebellum/cytology , Cerebellum/metabolism , Enzyme Inhibitors/pharmacology , Female , HEK293 Cells , Humans , In Vitro Techniques , MEF2 Transcription Factors/genetics , MEF2 Transcription Factors/metabolism , Male , Mice , Mice, Knockout , Neurons/cytology , Neurons/metabolism , Phosphorylation , Promoter Regions, Genetic/genetics , RNA Interference/physiology , Superoxides/metabolism
9.
Methods ; 48(3): 311-9, 2009 Jul.
Article in English | MEDLINE | ID: mdl-19272449

ABSTRACT

We describe a detailed and widely applicable method for comprehensive proteomic profiling of the fission yeast Schizosaccharomyces pombe by 2-dimensional high performance liquid chromatography-electrospray ionization-tandem mass spectrometry that demonstrates high sensitivity and robust operation. Steps ranging from the preparation of total proteins, digestion of proteins to peptides, and separation of peptides by two-dimensional (1. strong cation exchange and 2. reversed-phase) high performance liquid chromatography followed by tandem mass spectrometry and data processing have been optimized for our instrumentation platform. Using this technology, we identify ca. 3400 proteins per sample and have identified an estimated 4600 proteins in vegetative cells (equal to ca. 90% of the predicted S. pombe proteome) at a false discovery rate of 0.02. Considering the fact that approximately 500 genes are strongly induced during sexual differentiation, and sexual differentiation was not included in our experiments, the proteomic profiling technique affords what should be virtually complete coverage of the vegetative S. pombe proteome. In addition, these methods are widely applicable, having been used for proteomic profiling of several other organisms.


Subject(s)
Chromatography, High Pressure Liquid/methods , Proteome/analysis , Schizosaccharomyces pombe Proteins/analysis , Schizosaccharomyces/chemistry , Tandem Mass Spectrometry/methods , Chromatography, High Pressure Liquid/instrumentation , Spectrometry, Mass, Electrospray Ionization/instrumentation , Spectrometry, Mass, Electrospray Ionization/methods , Tandem Mass Spectrometry/instrumentation
10.
Mol Genet Genomics ; 282(1): 1-15, 2009 Jul.
Article in English | MEDLINE | ID: mdl-19488786

ABSTRACT

Lectins are a diverse group of carbohydrate-binding proteins that are found within and associated with organisms from all kingdoms of life. Several different classes of plant lectins serve a diverse array of functions. The most prominent of these include participation in plant defense against predators and pathogens and involvement in symbiotic interactions between host plants and symbiotic microbes, including mycorrhizal fungi and nitrogen-fixing rhizobia. Extensive biological, biochemical, and molecular studies have shed light on the functions of plant lectins, and a plethora of uncharacterized lectin genes are being revealed at the genomic scale, suggesting unexplored and novel diversity in plant lectin structure and function. Integration of the results from these different types of research is beginning to yield a more detailed understanding of the function of lectins in symbiosis, defense, and plant biology in general.


Subject(s)
Plant Lectins/genetics , Plant Lectins/physiology , Plant Physiological Phenomena , Symbiosis/physiology , Genes, Plant , Models, Biological , Models, Molecular , Mycorrhizae/physiology , Plant Lectins/chemistry , Plant Root Nodulation/genetics , Plant Root Nodulation/physiology , Plants/genetics , Protein Structure, Tertiary , Symbiosis/genetics
11.
Biochemistry ; 45(51): 15529-40, 2006 Dec 26.
Article in English | MEDLINE | ID: mdl-17176074

ABSTRACT

Overexpression of the ErbB2 receptor tyrosine kinase is common in human cancers and is associated with an increased level of metastasis. To better understand the cellular signaling networks activated by ErbB2, a phosphoproteomic analysis of tyrosine-phosphorylated proteins was carried out in ErbB2-overexpressing breast and ovarian cancer cell lines. A total of 153 phosphorylation sites were assigned on 78 proteins. Treatment of cells with Herceptin, a monoclonal antibody that inhibits ErbB2 activity, significantly reduced the number of detectable protein phosphorylation sites, suggesting that many of these proteins participate in ErbB2-driven cell signaling. Of the 71 proteins that were differentially phosphorylated, only 13 were previously reported to directly associate with ErbB2. The differentially phosphorylated proteins included kinases, adaptor/docking proteins, proteins involved in cell proliferation and migration, and several uncharacterized RNA binding proteins. Selective depletion of some of these proteins, including RNA binding proteins SRRM2, SFRS1, SFRS9, and SFRS10, by siRNAs reduced the rate of migration of ErbB2-overexpressing ovarian cancer cells.


Subject(s)
Phosphoproteins/analysis , Proteomics , Receptor, ErbB-2/chemistry , Receptor, ErbB-2/physiology , Signal Transduction/physiology , Amino Acid Sequence , Cell Adhesion/physiology , Cell Line, Tumor , Cell Movement/physiology , Chromatography, Liquid , Humans , Molecular Sequence Data , Phosphopeptides/analysis , Phosphorylation , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
12.
Mol Biol Cell ; 27(17): 2757-70, 2016 09 01.
Article in English | MEDLINE | ID: mdl-27385333

ABSTRACT

The EphA2 receptor tyrosine kinase plays key roles in tissue homeostasis and disease processes such as cancer, pathological angiogenesis, and inflammation through two distinct signaling mechanisms. EphA2 "canonical" signaling involves ephrin-A ligand binding, tyrosine autophosphorylation, and kinase activity; EphA2 "noncanonical" signaling involves phosphorylation of serine 897 (S897) by AKT and RSK kinases. To identify small molecules counteracting EphA2 canonical signaling, we developed a high-content screening platform measuring inhibition of ephrin-A1-induced PC3 prostate cancer cell retraction. Surprisingly, most hits from a screened collection of pharmacologically active compounds are agents that elevate intracellular cAMP by activating G protein-coupled receptors such as the ß2-adrenoceptor. We found that cAMP promotes phosphorylation of S897 by protein kinase A (PKA) as well as increases the phosphorylation of several nearby serine/threonine residues, which constitute a phosphorylation hotspot. Whereas EphA2 canonical and noncanonical signaling have been viewed as mutually exclusive, we show that S897 phosphorylation by PKA can coexist with EphA2 tyrosine phosphorylation and block cell retraction induced by EphA2 kinase activity. Our findings reveal a novel paradigm in EphA2 function involving the interplay of canonical and noncanonical signaling and highlight the ability of the ß2-adrenoceptor/cAMP/PKA axis to rewire EphA2 signaling in a subset of cancer cells.


Subject(s)
Cyclic AMP-Dependent Protein Kinases/metabolism , Receptor, EphA2/metabolism , Cell Line, Tumor , Cell Movement/physiology , Cyclic AMP/metabolism , Ephrin-A1/metabolism , Humans , Phosphorylation , Protein-Tyrosine Kinases , Proto-Oncogene Proteins c-akt/metabolism , Receptors, Adrenergic/metabolism , Serine/metabolism , Signal Transduction , Small Molecule Libraries
13.
Cell Rep ; 14(9): 2059-2067, 2016 Mar 08.
Article in English | MEDLINE | ID: mdl-26923601

ABSTRACT

Deficiency of S6 kinase (S6K) extends the lifespan of multiple species, but the underlying mechanisms are unclear. To discover potential effectors of S6K-mediated longevity, we performed a proteomics analysis of long-lived rsks-1/S6K C. elegans mutants compared to wild-type animals. We identified the arginine kinase ARGK-1 as the most significantly enriched protein in rsks-1/S6K mutants. ARGK-1 is an ortholog of mammalian creatine kinase, which maintains cellular ATP levels. We found that argk-1 is possibly a selective effector of rsks-1/S6K-mediated longevity and that overexpression of ARGK-1 extends C. elegans lifespan, in part by activating the energy sensor AAK-2/AMPK. argk-1 is also required for the reduced body size and increased stress resistance observed in rsks-1/S6K mutants. Finally, creatine kinase levels are increased in the brains of S6K1 knockout mice. Our study identifies ARGK-1 as a longevity effector in C. elegans with reduced RSKS-1/S6K levels.


Subject(s)
Arginine Kinase/physiology , Caenorhabditis elegans Proteins/physiology , Caenorhabditis elegans/physiology , Creatine Kinase/physiology , Longevity , Ribosomal Protein S6 Kinases, 70-kDa/physiology , AMP-Activated Protein Kinases/metabolism , Animals , Caenorhabditis elegans Proteins/metabolism , Enzyme Activation , Female , Male , Mice, Knockout , Neuroglia/enzymology , Protein Serine-Threonine Kinases/metabolism
14.
Stem Cell Reports ; 7(3): 527-542, 2016 09 13.
Article in English | MEDLINE | ID: mdl-27569059

ABSTRACT

Controlled differentiation of human embryonic stem cells (hESCs) can be utilized for precise analysis of cell type identities during early development. We established a highly efficient neural induction strategy and an improved analytical platform, and determined proteomic and phosphoproteomic profiles of hESCs and their specified multipotent neural stem cell derivatives (hNSCs). This quantitative dataset (nearly 13,000 proteins and 60,000 phosphorylation sites) provides unique molecular insights into pluripotency and neural lineage entry. Systems-level comparative analysis of proteins (e.g., transcription factors, epigenetic regulators, kinase families), phosphorylation sites, and numerous biological pathways allowed the identification of distinct signatures in pluripotent and multipotent cells. Furthermore, as predicted by the dataset, we functionally validated an autocrine/paracrine mechanism by demonstrating that the secreted protein midkine is a regulator of neural specification. This resource is freely available to the scientific community, including a searchable website, PluriProt.


Subject(s)
Cell Differentiation , Neurons/metabolism , Phosphoproteins/metabolism , Pluripotent Stem Cells/cytology , Pluripotent Stem Cells/metabolism , Proteome , Proteomics , Animals , Cell Differentiation/genetics , Cell Lineage/genetics , Cells, Cultured , Computational Biology/methods , Gene Expression Profiling , Gene Knockdown Techniques , Humans , Neurons/cytology , Proteomics/methods , Signal Transduction , Transcriptome
15.
Cancer Cell ; 27(3): 354-69, 2015 Mar 09.
Article in English | MEDLINE | ID: mdl-25759021

ABSTRACT

Many tumor cells are fueled by altered metabolism and increased glutamine (Gln) dependence. We identify regulation of the L-glutamine carrier proteins SLC1A5 and SLC38A2 (SLC1A5/38A2) by the ubiquitin ligase RNF5. Paclitaxel-induced ER stress to breast cancer (BCa) cells promotes RNF5 association, ubiquitination, and degradation of SLC1A5/38A2. This decreases Gln uptake, levels of TCA cycle components, mTOR signaling, and proliferation while increasing autophagy and cell death. Rnf5-deficient MMTV-PyMT mammary tumors were less differentiated and showed elevated SLC1A5 expression. Whereas RNF5 depletion in MDA-MB-231 cells promoted tumorigenesis and abolished paclitaxel responsiveness, SLC1A5/38A2 knockdown elicited opposing effects. Inverse RNF5(hi)/SLC1A5/38A2(lo) expression was associated with positive prognosis in BCa. Thus, RNF5 control of Gln uptake underlies BCa response to chemotherapies.


Subject(s)
Amino Acid Transport System ASC/metabolism , Amino Acid Transport System A/metabolism , Antineoplastic Agents/pharmacology , Breast Neoplasms/metabolism , DNA-Binding Proteins/physiology , Endoplasmic Reticulum Stress/drug effects , Paclitaxel/pharmacology , Ubiquitin-Protein Ligases/physiology , Amino Acid Transport System A/genetics , Amino Acid Transport System ASC/genetics , Animals , Antineoplastic Agents/therapeutic use , Apoptosis/drug effects , Autophagy/drug effects , Breast Neoplasms/drug therapy , Breast Neoplasms/genetics , Citric Acid Cycle/drug effects , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Endoplasmic Reticulum/drug effects , Endoplasmic Reticulum Stress/genetics , Female , Humans , Mice, Inbred BALB C , Mice, Inbred C57BL , Mice, Nude , Minor Histocompatibility Antigens , Paclitaxel/therapeutic use , Proteolysis/drug effects , Signal Transduction/drug effects , TOR Serine-Threonine Kinases/metabolism , Ubiquitin-Protein Ligases/genetics , Ubiquitin-Protein Ligases/metabolism , Ubiquitination
16.
Mol Plant Microbe Interact ; 17(1): 16-26, 2004 Jan.
Article in English | MEDLINE | ID: mdl-14714864

ABSTRACT

Legume lectins have been proposed to have important symbiotic roles during Rhizobium-legume symbioses. To test this hypothesis, the symbiotic responses of transgenic alfalfa plants that express a portion of the putative alfalfa lectin gene MsLEC1 or MsLEC2 in either the antisense or sense orientation were analyzed following inoculation with wild-type Sinorhizobium meliloti 1021. MsLEC1-antisense (LEC1AS) plants were stunted, exhibited hypernodulation, and developed not only abnormally large nodules but also numerous small nodules, both of which senesced prematurely. MsLEC2-antisense plants were intermediate in growth and nodule number compared with LEC1AS and vector control plants. The symbiotic abnormalities of MsLEC1-sense transgene plants were similar to but milder than the responses shown by the LEC1AS plants, whereas MsLEC2-sense transgene plants exhibited symbiotic responses that were identical to those of vector and nontransgenic control plants. MsLEC1 mRNA accumulation was not detected in nodule RNA by Northern blot analysis but was localized to alfalfa nodule meristems and the adjacent cells of the invasion zone by in situ hybridization; transcripts were also detected in root meristems. A similar spatial pattern of MsLEC2 expression was found by using a whole-mount in situ hybridization procedure. Moreover, mRNAs for an orthologous lectin gene (MaLEC) were detected in white sweetclover (Melilotus alba) nodules and root tips.


Subject(s)
Medicago sativa/genetics , Plant Lectins/genetics , Symbiosis/genetics , Transgenes/genetics , Gene Expression Regulation, Plant , Medicago sativa/growth & development , Medicago sativa/microbiology , Molecular Sequence Data , Phenotype , Plant Lectins/metabolism , Plant Proteins/genetics , Plant Proteins/metabolism , Plant Roots/genetics , Plant Roots/growth & development , Plant Roots/microbiology , Plants, Genetically Modified , RNA, Messenger/genetics , RNA, Messenger/metabolism , Sinorhizobium meliloti/growth & development
17.
F1000Res ; 3: 115, 2014.
Article in English | MEDLINE | ID: mdl-25177484

ABSTRACT

NKX3.1 is a homeobox transcription factor whose function as a prostate tumor suppressor remains insufficiently understood because neither the transcriptional program governed by NKX3.1, nor its interacting proteins have been fully revealed. Using affinity purification and mass spectrometry, we have established an extensive NKX3.1 interactome which contains the DNA repair proteins Ku70, Ku80, and PARP, thus providing a molecular underpinning to previous reports implicating NKX3.1 in DNA repair. Transcriptomic profiling of NKX3.1-negative prostate epithelial cells acutely expressing NKX3.1 revealed a rapid and complex response that is a near mirror image of the gene expression signature of human prostatic intraepithelial neoplasia (PIN). Pathway and network analyses suggested that NKX3.1 actuates a cellular reprogramming toward luminal cell differentiation characterized by suppression of pro-oncogenic c-MYC and interferon-STAT signaling and activation of tumor suppressor pathways. Consistently, ectopic expression of NKX3.1 conferred a growth arrest depending on TNFα and JNK signaling. We propose that the tumor suppressor function of NKX3.1 entails a transcriptional program that maintains the differentiation state of secretory luminal cells and that disruption of NKX3.1 contributes to prostate tumorigenesis by permitting luminal cell de-differentiation potentially augmented by defects in DNA repair.

18.
PLoS One ; 8(12): e84497, 2013.
Article in English | MEDLINE | ID: mdl-24386391

ABSTRACT

Signaling regulated by NFκB and related transcription factors is centrally important to many inflammatory and autoimmune diseases, cancer, and stress responses. The kinase that directly regulates the canonical NFκB transcriptional pathway, Inhibitor of κB kinase ß (IKKß), undergoes activation by Ser phosphorylation mediated by NIK or TAK1 in response to inflammatory signals. Using titanium dioxide-based phosphopeptide enrichment (TiO2)-liquid chromatography (LC)-high mass accuracy tandem mass spectrometry (MS/MS), we analyzed IKKß phosphorylation in human HEK293 cells expressing IKKß and FGFR2, a Receptor tyrosine kinase (RTK) essential for embryonic differentiation and dysregulated in several cancers. We attained unusually high coverage of IKKß, identifying an abundant site of Tyr phosphorylation at Tyr169 within the Activation Loop. The phosphomimic at this site confers a level of kinase activation and NFκB nuclear localization exceeding the iconic mutant S177E/S181E, demonstrating that RTK-mediated Tyr phosphorylation of IKKß has the potential to directly regulate NFκB transcriptional activation.


Subject(s)
I-kappa B Kinase/metabolism , Signal Transduction/physiology , Amino Acid Substitution , Enzyme Activation/physiology , HEK293 Cells , Humans , I-kappa B Kinase/genetics , Mutation, Missense , NF-kappa B/genetics , NF-kappa B/metabolism , Phosphorylation/physiology , Protein Structure, Secondary , Receptor, Fibroblast Growth Factor, Type 2/genetics , Receptor, Fibroblast Growth Factor, Type 2/metabolism , Transcriptional Activation/physiology , Tyrosine/genetics , Tyrosine/metabolism
19.
Methods Mol Biol ; 1029: 163-89, 2013.
Article in English | MEDLINE | ID: mdl-23756949

ABSTRACT

Despite advances in understanding pluripotency through traditional cell biology and gene expression profiling, the signaling networks responsible for maintenance of pluripotency and lineage-specific differentiation are poorly defined. To aid in an improved understanding of these networks at the systems level, we present procedures for the combined analysis of the total proteome and total phosphoproteome (termed (phospho)proteome) from human embryonic stem cells (hESCs), human induced pluripotent stem cells (hiPSCs), and their differentiated derivatives. Because there has been considerable heterogeneity in the literature on the culture of pluripotent cells, we first briefly describe our feeder-free cell culture protocol. The focus, however, is on procedures necessary to generate large-scale (phospho)proteomic data from the cells. Human cells are described here, but the (phospho)proteomic procedures are broadly applicable. Detailed procedures are given for lysis of the cells, protein sample preparation and digestion, multidimensional liquid chromatography, analysis by tandem mass spectrometry, and database searches for peptide/protein identification (ID). We summarize additional data analysis procedures, the subject of ongoing efforts.


Subject(s)
Phosphoproteins/metabolism , Pluripotent Stem Cells/metabolism , Proteomics/methods , Alkylation , Ammonium Sulfate , Animals , Cell Fractionation , Cells, Cultured , Chemical Precipitation , Chromatography, Gel , Chromatography, High Pressure Liquid , Chromatography, Ion Exchange , Chromatography, Reverse-Phase , Databases, Protein , Humans , Mass Spectrometry , Mice , Phosphopeptides/isolation & purification , Statistics as Topic , Titanium
20.
Mol Cell Biol ; 33(13): 2510-26, 2013 Jul.
Article in English | MEDLINE | ID: mdl-23608534

ABSTRACT

Folding of newly synthesized polypeptides (NSPs) into functional proteins is a highly regulated process. Rigorous quality control ensures that NSPs attain their native fold during or shortly after completion of translation. Nonetheless, signaling pathways that govern the degradation of NSPs in mammals remain elusive. We demonstrate that the stress-induced c-Jun N-terminal kinase (JNK) is recruited to ribosomes by the receptor for activated protein C kinase 1 (RACK1). RACK1 is an integral component of the 40S ribosome and an adaptor for protein kinases. Ribosome-associated JNK phosphorylates the eukaryotic translation elongation factor 1A isoform 2 (eEF1A2) on serines 205 and 358 to promote degradation of NSPs by the proteasome. These findings establish a role for a RACK1/JNK/eEF1A2 complex in the quality control of NSPs in response to stress.


Subject(s)
GTP-Binding Proteins/metabolism , JNK Mitogen-Activated Protein Kinases/metabolism , Neoplasm Proteins/metabolism , Peptide Elongation Factor 1/metabolism , Peptides/metabolism , Receptors, Cell Surface/metabolism , Animals , Base Sequence , Cell Line , GTP-Binding Proteins/genetics , Humans , JNK Mitogen-Activated Protein Kinases/genetics , MAP Kinase Kinase 7/genetics , MAP Kinase Kinase 7/metabolism , Molecular Sequence Data , Neoplasm Proteins/genetics , Peptide Elongation Factor 1/genetics , Phosphorylation , Polyribosomes/metabolism , Proteasome Endopeptidase Complex/metabolism , Protein Stability , Receptors for Activated C Kinase , Receptors, Cell Surface/genetics , Ribosomes/metabolism , Serine/metabolism , Signal Transduction
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