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OUP accepted manuscript. Brain 2022; 145:2250-2275. [DOI: 10.1093/brain/awac096] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 01/21/2022] [Accepted: 01/23/2022] [Indexed: 11/13/2022] Open
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Do Carmo S, Kannel B, Cuello AC. The Nerve Growth Factor Metabolic Pathway Dysregulation as Cause of Alzheimer's Cholinergic Atrophy. Cells 2021; 11:16. [PMID: 35011577 PMCID: PMC8750266 DOI: 10.3390/cells11010016] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/17/2021] [Accepted: 12/20/2021] [Indexed: 12/12/2022] Open
Abstract
The cause of the loss of basal forebrain cholinergic neurons (BFCNs) and their terminal synapses in the cerebral cortex and hippocampus in Alzheimer's disease (AD) has provoked a decades-long controversy. The cholinergic phenotype of this neuronal system, involved in numerous cognitive mechanisms, is tightly dependent on the target-derived nerve growth factor (NGF). Consequently, the loss of BFCNs cholinergic phenotype in AD was initially suspected to be due to an NGF trophic failure. However, in AD there is a normal NGF synthesis and abundance of the NGF precursor (proNGF), therefore the NGF trophic failure hypothesis for the atrophy of BCNs was abandoned. In this review, we discuss the history of NGF-dependency of BFCNs and the atrophy of these neurons in Alzheimer's disease (AD). Further to it, we propose that trophic factor failure explains the BFCNs atrophy in AD. We discuss evidence of the occurrence of a brain NGF metabolic pathway, the dysregulation of which, in AD explains the severe deficiency of NGF trophic support for the maintenance of BFCNs cholinergic phenotype. Finally, we revise recent evidence that the NGF metabolic dysregulation in AD pathology starts at preclinical stages. We also propose that the alteration of NGF metabolism-related markers in body fluids might assist in the AD preclinical diagnosis.
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Affiliation(s)
- Sonia Do Carmo
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC H3G 1Y6, Canada;
| | - Benjamin Kannel
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC H3A 2B4, Canada;
| | - A. Claudio Cuello
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC H3G 1Y6, Canada;
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC H3A 2B4, Canada;
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC H3A 0C7, Canada
- Department of Pharmacology, Oxford University, Oxford OX1 3QT, UK
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Shared distal regulatory regions may contribute to the coordinated expression of human ribosomal protein genes. Genomics 2020; 112:2886-2893. [PMID: 32240723 DOI: 10.1016/j.ygeno.2020.03.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/12/2020] [Accepted: 03/29/2020] [Indexed: 11/21/2022]
Abstract
To identify the potential distal regulatory regions of human ribosomal protein genes (RPGs) and to understand their characteristics, we studied the chromatin interactions in seven cell lines and four primary cell types. We identified 22,797 putative regulatory regions that directly or indirectly interact with human RPG promoters. A large proportion of these regions are only present in one cell line or one cell type, implying that RPGs may be differentially regulated across experimental conditions. We also noticed that groups of RPGs, which are the same groups across cell lines and cell types, share common regulatory regions. These shared regulatory regions by RPGs may contribute to their coordinated regulation. By studying the overrepresented motifs in the identified regulatory regions, we showed that there are about two dozen motifs in these regions shared across cell lines and cell types. Our study shed new light on the coordinated transcriptional regulation of human RPGs.
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Savada RP, Bonham-Smith PC. Differential transcript accumulation and subcellular localization of Arabidopsis ribosomal proteins. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 223:134-45. [PMID: 24767123 DOI: 10.1016/j.plantsci.2014.03.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Revised: 03/12/2014] [Accepted: 03/14/2014] [Indexed: 05/26/2023]
Abstract
Arabidopsis cytoplasmic ribosomes are an assembly of four rRNAs and 81 ribosomal proteins (RPs). With only a single molecule of each RP incorporated into any given ribosome, an adequate level of each RP in the nucleolus is a prerequisite for efficient ribosome biogenesis. Using Genevestigator (microarray data analysis tool), we have studied transcript levels of 192 of the 254 Arabidopsis RP genes, as well as the sub-cellular localization of each of five two-member RP families, to identify the extent to which these two processes contribute to the nucleolar pool of RPs available for ribosome biogenesis. While transcript levels from different RP genes show up to a 300-fold difference across the RP population, this difference is drastically reduced to ∼8-fold when considering RP gene families. Under various stimuli, while the transcript level for most RP genes remains unchanged some show a significantly increased or decreased level. Subcellular localization studies in tobacco not only showed differential targeting of RPs to the cytoplasm, nucleus and nucleolus, but also differential nucleolar import rates. This degree of variation in gene regulation and subcellular localization of RPs hints at the possibility of extra-ribosomal functions for some RP isoforms.
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Affiliation(s)
- Raghavendra P Savada
- Department of Biology, University of Saskatchewan, Saskatoon, SK S7N 5E2, Canada
| | - Peta C Bonham-Smith
- Department of Biology, University of Saskatchewan, Saskatoon, SK S7N 5E2, Canada.
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Arisi I, D'Onofrio M, Brandi R, Malerba F, Paoletti F, Storti AE, Florenzano F, Fasulo L, Cattaneo A. proNGF/NGF mixtures induce gene expression changes in PC12 cells that neither singly produces. BMC Neurosci 2014; 15:48. [PMID: 24713110 PMCID: PMC4098786 DOI: 10.1186/1471-2202-15-48] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 03/27/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Growing evidence shows that, in vivo, the precursor of Nerve Growth Factor (NGF), proNGF, displays biological activities different from those of its mature NGF counterpart, mediated by distinct, and somewhat complementary, receptor binding properties. NGF and proNGF induce distinct transcriptional signatures in target cells, highlighting their different bioactivities. In vivo, proNGF and mature NGF coexist. It was proposed that the relative proNGF/NGF ratio is important for their biological outcomes, especially in pathological conditions, since proNGF, the principal form of NGF in Central Nervous System (CNS), is increased in Alzheimer's disease brains. These observations raise a relevant question: does proNGF, in the presence of NGF, influence the NGF transcriptional response and viceversa? In order to understand the specific proNGF effect on NGF activity, depending on the relative proNGF/NGF concentration, we investigated whether proNGF affects the pattern of well-known NGF-regulated mRNAs. RESULTS To test any influence of proNGF on pure NGF expression fingerprinting, the expression level of a set of candidate genes was analysed by qReal-Time PCR in rat adrenal pheochromocytoma cell line PC12, treated with a mixture of NGF and proNGF recombinant proteins, in different stoichiometric ratios. These candidates were selected amongst a set of genes well-known as being rapidly induced by NGF treatment. We found that, when PC12 cells are treated with proNGF/NGF mixtures, a unique pattern of gene expression, which does not overlap with that deriving from treatment with either proNGF or NGF alone, is induced. The specific effect is also dependent on the stoichiometric composition of the mixture. The proNGF/NGF equimolar mixture seems to partially neutralize the specific effects of the proNGF or NGF individual treatments, showing a weaker overall response, compared to the individual contributions of NGF and proNGF alone. CONCLUSIONS Using gene expression as a functional read-out, our data demonstrate that the relative availability of NGF and proNGF in vivo might modulate the biological outcome of these ligands.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Antonino Cattaneo
- Neurotrophic Factors and Neurodegenerative Diseases Laboratory, European Brain Research Institute (EBRI) "Rita Levi-Montalcini", Via del Fosso di Fiorano, 64, 00143 Roma, Italy.
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Ettinger K, Lecht S, Arien-Zakay H, Cohen G, Aga-Mizrachi S, Yanay N, Saragovi HU, Nedev H, Marcinkiewicz C, Nevo Y, Lazarovici P. Nerve growth factor stimulation of ERK1/2 phosphorylation requires both p75NTR and α9β1 integrin and confers myoprotection towards ischemia in C2C12 skeletal muscle cell model. Cell Signal 2012; 24:2378-88. [PMID: 22960610 DOI: 10.1016/j.cellsig.2012.08.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 08/06/2012] [Accepted: 08/23/2012] [Indexed: 01/11/2023]
Abstract
The functions of nerve growth factor (NGF) in skeletal muscles physiology and pathology are not clear and call for an updated investigation. To achieve this goal we sought to investigate NGF-induced ERK1/2 phosphorylation and its role in the C2C12 skeletal muscle myoblasts and myotubes. RT-PCR and western blotting experiments demonstrated expression of p75(NTR), α9β1 integrin, and its regulator ADAM12, but not trkA in the cells, as also found in gastrocnemius and quadriceps mice muscles. Both proNGF and βNGF induced ERK1/2 phosphorylation, a process blocked by (a) the specific MEK inhibitor, PD98059; (b) VLO5, a MLD-disintegrin with relative selectivity towards α9β1 integrin; and (c) p75(NTR) antagonists Thx-B and LM-24, but not the inactive control molecule backbone Thx. Upon treatment for 4 days with either anti-NGF antibody or VLO5 or Thx-B, the proliferation of myoblasts was decreased by 60-70%, 85-90% and 60-80% respectively, indicative of trophic effect of NGF which was autocrinically released by the cells. Exposure of myotubes to ischemic insult in the presence of βNGF, added either 1h before oxygen-glucose-deprivation or concomitant with reoxygenation insults, resulted with about 20% and 33% myoprotection, an effect antagonized by VLO5 and Thx-B, further supporting the trophic role of NGF in C2C12 cells. Cumulatively, the present findings propose that proNGF and βNGF-induced ERK1/2 phosphorylation in C2C12 cells by functional cooperation between p75(NTR) and α9β1 integrin, which are involved in myoprotective effects of autocrine released NGF. Furthermore, the present study establishes an important trophic role of α9β1 in NGF-induced signaling in skeletal muscle model, resembling the role of trkA in neurons. Future molecular characterization of the interactions between NGF receptors in the skeletal muscle will contribute to the understanding of NGF mechanism of action and may provide novel therapeutic targets.
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Affiliation(s)
- Keren Ettinger
- Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
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Nitration of tryptophan in ribosomal proteins is a novel post-translational modification of differentiated and naïve PC12 cells. Nitric Oxide 2011; 25:176-82. [PMID: 21642007 DOI: 10.1016/j.niox.2011.05.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2010] [Revised: 05/19/2011] [Accepted: 05/21/2011] [Indexed: 12/30/2022]
Abstract
Neuron growth factor (NGF) signaling in PC12 cell, which is derived from pheochromocytoma of rat adrenal medulla, induces expression of neuronal nitric oxide synthase (nNOS) and nitric oxide (NO) production. Subsequently, NO causes differentiation of PC12 cell to neuronal cell with morphological changes, such as neurite extension. In this study, we showed that 6-nitrotryptophan-containing proteins were produced in PC12 cell (naïve PC12 cell) and/or NGF-induced PC12 cell (differentiated PC12 cell). Western blot analysis of the protein extract of naïve PC12 cell and differentiated PC12 cell using anti 6-nitrotryptophan antibody showed several immunoreactive bands, which were subsequently subjected to trypsin digestion and LC-ESI-MS-MS analysis. The peptides from five ribosomal proteins, namely, 60S ribosomal protein L7 (Trp154), 60S acidic ribosomal protein P1 (Trp43), 40S ribosomal protein S2 (Trp60), 40S ribosomal protein S6 (Trp45), and 40S ribosomal protein S19 (Trp52), were identified as nitrotryptophan residue-containing proteins with significant ion score levels (p<0.05). Among these, tryptophan nitration was observed only in differentiated PC12 cell for S19 protein, and only in naïve PC12 cell for L7 protein. Tryptophan nitration of the other ribosomal proteins P1, S2, and S6 was observed in both naive and differentiated PC12 cells. The positive signal of nitrotryptophan-containing proteins in the Western blotting around 16 kDa (Band 1), which includes 40S ribosomal protein S19, was suppressed by treatment with NOS inhibitor, L-NAME. The tryptophan nitration of 40S ribosomal protein was not observed by LC-ESI-MS-MS analysis of this sample. This is the first study to identify several specific sites of nitrated tryptophan on proteins not only in viable culture cells but also in a physiological process: cell differentiation.
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Vacca M, Albania L, Della Ragione F, Carpi A, Rossi V, Strazzullo M, De Franceschi N, Rossetto O, Filippini F, D'Esposito M. Alternative splicing of the human gene SYBL1 modulates protein domain architecture of Longin VAMP7/TI-VAMP, showing both non-SNARE and synaptobrevin-like isoforms. BMC Mol Biol 2011; 12:26. [PMID: 21609427 PMCID: PMC3123573 DOI: 10.1186/1471-2199-12-26] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Accepted: 05/24/2011] [Indexed: 11/15/2022] Open
Abstract
Background The control of intracellular vesicle trafficking is an ideal target to weigh the role of alternative splicing in shaping genomes to make cells. Alternative splicing has been reported for several Soluble N-ethylmaleimide-sensitive factor Attachment protein REceptors of the vesicle (v-SNAREs) or of the target membrane (t-SNARES), which are crucial to intracellular membrane fusion and protein and lipid traffic in Eukaryotes. However, splicing has not yet been investigated in Longins, i.e. the most widespread v-SNAREs. Longins are essential in Eukaryotes and prototyped by VAMP7, Sec22b and Ykt6, sharing a conserved N-terminal Longin domain which regulates membrane fusion and subcellular targeting. Human VAMP7/TI-VAMP, encoded by gene SYBL1, is involved in multiple cell pathways, including control of neurite outgrowth. Results Alternative splicing of SYBL1 by exon skipping events results in the production of a number of VAMP7 isoforms. In-frame or frameshift coding sequence modifications modulate domain architecture of VAMP7 isoforms, which can lack whole domains or domain fragments and show variant or extra domains. Intriguingly, two main types of VAMP7 isoforms either share the inhibitory Longin domain and lack the fusion-promoting SNARE motif, or vice versa. Expression analysis in different tissues and cell lines, quantitative real time RT-PCR and confocal microscopy analysis of fluorescent protein-tagged isoforms demonstrate that VAMP7 variants have different tissue specificities and subcellular localizations. Moreover, design and use of isoform-specific antibodies provided preliminary evidence for the existence of splice variants at the protein level. Conclusions Previous evidence on VAMP7 suggests inhibitory functions for the Longin domain and fusion/growth promoting activity for the Δ-longin molecule. Thus, non-SNARE isoforms with Longin domain and non-longin SNARE isoforms might have somehow opposite regulatory functions. When considering splice variants as "natural mutants", evidence on modulation of subcellular localization by variation in domain combination can shed further light on targeting determinants. Although further work will be needed to characterize identified variants, our data might open the route to unravel novel molecular partners and mechanisms, accounting for the multiplicity of functions carried out by the different members of the Longin proteins family.
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Affiliation(s)
- Marcella Vacca
- Institute of Genetics and Biophysics A.Buzzati Traverso Consiglio Nazionale delle Ricerche, via P. Castellino 111, 80131 Naples, Italy
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Dijkmans TF, van Hooijdonk LWA, Schouten TG, Kamphorst JT, Vellinga ACA, Meerman JHN, Fitzsimons CP, de Kloet ER, Vreugdenhil E. Temporal and functional dynamics of the transcriptome during nerve growth factor-induced differentiation. J Neurochem 2010; 105:2388-403. [PMID: 18346208 DOI: 10.1111/j.1471-4159.2008.05338.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The rat pheochromocytoma cell line (PC12) is an extensively used model to study neuronal differentiation. The initial signaling cascades triggered by nerve growth factor (NGF) stimulation have been subject to thorough investigation and are well characterized. However, knowledge of temporal transcriptomal regulation during NGF-induced differentiation of PC12 cells remains far from complete. We performed a microarray study that characterized temporal and functional changes of the transcriptome during 4 subsequent days of differentiation of Neuroscreen-1 PC12 cells. By analyzing the transcription profiles of 1595 NGF-regulated genes, we show a large diversity of transcriptional regulation in time. Also, we quantitatively identified 26 out of 243 predefined biological process and 30 out of 255 predefined molecular function classes that are specifically regulated by NGF. Combining the temporal and functional transcriptomal data revealed that NGF selectively exerts a temporally coordinated regulation of genes implicated in protein biosynthesis, intracellular signaling, cell structure, chromatin packaging and remodeling, intracellular protein traffic, mRNA transcription, and cell cycle. We will discuss how NGF-induced changes may modulate the transcriptional response to NGF itself during differentiation.
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Affiliation(s)
- Thomas F Dijkmans
- Division of Medical Pharmacology, Leiden/Amsterdam Center for Drug Research and Leiden University Medical Center, Leiden, The Netherlands.
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Uittenbogaard M, Baxter KK, Chiaramello A. NeuroD6 genomic signature bridging neuronal differentiation to survival via the molecular chaperone network. J Neurosci Res 2010; 88:33-54. [PMID: 19610105 DOI: 10.1002/jnr.22182] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
During neurogenesis, expression of the basic helix-loop-helix NeuroD6/Nex1/MATH-2 transcription factor parallels neuronal differentiation and is maintained in differentiated neurons in the adult brain. To dissect NeuroD6 differentiation properties further, we previously generated a NeuroD6-overexpressing stable PC12 cell line, PC12-ND6, which displays a neuronal phenotype characterized by spontaneous neuritogenesis, accelerated NGF-induced differentiation, and increased regenerative capacity. Furthermore, we reported that NeuroD6 promotes long-term neuronal survival upon serum deprivation. In this study, we identified the NeuroD6-mediated transcriptional regulatory pathways linking neuronal differentiation to survival, by conducting a genome-wide microarray analysis using PC12-ND6 cells and serum deprivation as a stress paradigm. Through a series of filtering steps and a gene-ontology analysis, we found that NeuroD6 promotes distinct but overlapping gene networks, consistent with the differentiation, regeneration, and survival properties of PC12-ND6 cells. By using a gene-set-enrichment analysis, we provide the first evidence of a compelling link between NeuroD6 and a set of heat shock proteins in the absence of stress, which may be instrumental in conferring stress tolerance on PC12-ND6 cells. Immunocytochemistry results showed that HSP27 and HSP70 interact with cytoskeletal elements, consistent with their roles in neuritogenesis and preserving cellular integrity. HSP70 also colocalizes with mitochondria located in the soma, growing neurites, and growth cones of PC12-ND6 cells prior to and upon stress stimulus, consistent with its neuroprotective functions. Collectively, our findings support the notion that NeuroD6 links neuronal differentiation to survival via the network of molecular chaperones and endows the cells with increased stress tolerance.
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Affiliation(s)
- Martine Uittenbogaard
- Department of Anatomy and Regenerative Biology, George Washington University Medical Center, Washington, DC, USA
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Landry DM, Hertz MI, Thompson SR. RPS25 is essential for translation initiation by the Dicistroviridae and hepatitis C viral IRESs. Genes Dev 2009; 23:2753-64. [PMID: 19952110 PMCID: PMC2788332 DOI: 10.1101/gad.1832209] [Citation(s) in RCA: 166] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Accepted: 10/06/2009] [Indexed: 02/05/2023]
Abstract
Most eukaryotic mRNAs are translated using a cap-dependent mechanism of translation. However, approximately 10% of mammalian mRNAs initiate translation using a cap-independent mechanism that is not well understood. These mRNAs contain an internal ribosome entry site (IRES) located in the 5' untranslated region. The cricket paralysis virus (CrPV) intergenic region IRES (IGR IRES) functions in yeast, mammals, and plants, and does not require any translation initiation factors. We used yeast genetics to understand how ribosomes are recruited directly to the mRNA by an IRES. We found that Rps25p has an essential role in CrPV IGR IRES activity in yeast and mammalian cells but not in cap-dependent translation. Purified 40S ribosomal subunits lacking Rps25 are unable to bind to the IGR IRES in vitro. The hepatitis C virus (HCV) IRES also requires Rps25, demonstrating the function of Rps25 is conserved across IRES types. Yeast strains lacking Rps25 exhibit only slight defects in global translation, readthrough, ribosome biogenesis, and programmed ribosomal frameshifting. This work is the first demonstration of a ribosomal protein that is specifically required for IRES-mediated translation initiation. Our findings provide us with the beginnings of a model for the molecular interactions of an IRES with the ribosome.
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Affiliation(s)
- Dori M. Landry
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Marla I. Hertz
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Sunnie R. Thompson
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
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The neurogenic basic helix-loop-helix transcription factor NeuroD6 concomitantly increases mitochondrial mass and regulates cytoskeletal organization in the early stages of neuronal differentiation. ASN Neuro 2009; 1:AN20090036. [PMID: 19743964 PMCID: PMC2785511 DOI: 10.1042/an20090036] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Mitochondria play a central role during neurogenesis by providing energy in the form of ATP for cytoskeletal remodelling, outgrowth of neuronal processes, growth cone activity and synaptic activity. However, the fundamental question of how differentiating neurons control mitochondrial biogenesis remains vastly unexplored. Since our previous studies have shown that the neurogenic bHLH (basic helix–loop–helix) transcription factor NeuroD6 is sufficient to induce differentiation of the neuronal progenitor-like PC12 cells and that it triggers expression of mitochondrial-related genes, we investigated whether NeuroD6 could modulate the mitochondrial biomass using our PC12-ND6 cellular paradigm. Using a combination of flow cytometry, confocal microscopy and mitochondrial fractionation, we demonstrate that NeuroD6 stimulates maximal mitochondrial mass at the lamellipodia stage, thus preceding axonal growth. NeuroD6 triggers remodelling of the actin and microtubule networks in conjunction with increased expression of the motor protein KIF5B, thus promoting mitochondrial movement in developing neurites with accumulation in growth cones. Maintenance of the NeuroD6-induced mitochondrial mass requires an intact cytoskeletal network, as its disruption severely reduces mitochondrial mass. The present study provides the first evidence that NeuroD6 plays an integrative role in co-ordinating increase in mitochondrial mass with cytoskeletal remodelling, suggestive of a role of this transcription factor as a co-regulator of neuronal differentiation and energy metabolism.
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Key Words
- COX, cytochrome c oxidase
- E, embryonic day
- ESC, embryonic stem cell
- F-actin, filamentous actin
- GAPDH, glyceraldehyde-3-phosphate dehydrogenase
- MAP, microtubule-associated protein
- MMP, mitochondrial membrane potential
- MTG, MitoTracker® Green
- MTR, MitoTracker® Red
- NGF, nerve growth factor
- NRF, nuclear respiratory factor
- NeuroD family
- PDL, poly-d-lysine
- PGC-1, peroxisome-proliferator-activated receptor-γ co-activator-1
- SOD2, superoxide dismutase 2
- WGA, wheat germ agglutinin
- bHLH, basic helix–loop–helix
- basic helix–loop–helix transcription factor
- cytoskeletal remodelling
- mitochondrial biogenesis
- mtDNA, mitochondrial DNA
- neuronal differentiation
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Draghetti C, Salvat C, Zanoguera F, Curchod ML, Vignaud C, Peixoto H, Di Cara A, Fischer D, Dhanabal M, Andreas G, Abderrahim H, Rommel C, Camps M. Functional whole-genome analysis identifies Polo-like kinase 2 and poliovirus receptor as essential for neuronal differentiation upstream of the negative regulator alphaB-crystallin. J Biol Chem 2009; 284:32053-65. [PMID: 19700763 DOI: 10.1074/jbc.m109.009324] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
This study aimed at identifying transcriptional changes associated to neuronal differentiation induced by six distinct stimuli using whole-genome microarray hybridization analysis. Bioinformatics analyses revealed the clustering of these six stimuli into two categories, suggesting separate gene/pathway dependence. Treatment with specific inhibitors demonstrated the requirement of both Janus kinase and microtubule-associated protein kinase activation to trigger differentiation with nerve growth factor (NGF) and dibutyryl cAMP. Conversely, activation of protein kinase A, phosphatidylinositol-3-kinase alpha, and mammalian target of rapamycin, although required for dibutyryl cAMP-induced differentiation, exerted a negative feedback on NGF-induced differentiation. We identified Polo-like kinase 2 (Plk2) and poliovirus receptor (PVR) as indispensable for NGF-driven neuronal differentiation and alphaB-crystallin (Cryab) as an inhibitor of this process. Silencing of Plk2 or PVR blocked NGF-triggered differentiation and Cryab down-regulation, while silencing of Cryab enhanced NGF-induced differentiation. Our results position both Plk2 and PVR upstream of the negative regulator Cryab in the pathway(s) leading to neuronal differentiation triggered by NGF.
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Affiliation(s)
- Cristina Draghetti
- Departments of Target Research, Merck Serono International S.A. 9, Chemin de Mines, 1202 Geneva, Switzerland
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Caldarola S, De Stefano MC, Amaldi F, Loreni F. Synthesis and function of ribosomal proteins--fading models and new perspectives. FEBS J 2009; 276:3199-210. [PMID: 19438715 DOI: 10.1111/j.1742-4658.2009.07036.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The synthesis of ribosomal proteins (RPs) has long been known to be a process strongly linked to the growth status of the cell. In vertebrates, this coordination is dependent on RP mRNA translational efficiency, which changes according to physiological circumstances. Despite many years of investigation, the trans-acting factors and the signaling pathways involved in this regulation are still elusive. At the same time, however, new techniques and classic approaches have opened up new perspectives as regards RP regulation and function. In fact, the proteasome seems to play a crucial and unpredicted role in regulating the availability of RPs for subunit assembly. In addition, the study of human ribosomal pathologies and animal models for these diseases has revealed that perturbation in the synthesis and/or function of an RP activates a p53-dependent stress response. Surprisingly, the effect of the ribosomal stress is more dramatic in specific physiological processes: hemopoiesis in humans, and pigmentation in mice. Moreover, alteration of each RP impacts differently on the development of an organism.
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Affiliation(s)
- Sara Caldarola
- Department of Biology, University 'Tor Vergata', Roma, Italy
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Dijkmans T, van Hooijdonk L, Schouten T, Kamphorst J, Fitzsimons C, Vreugdenhil E. Identification of new Nerve Growth Factor-responsive immediate-early genes. Brain Res 2009; 1249:19-33. [DOI: 10.1016/j.brainres.2008.10.050] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2008] [Revised: 09/16/2008] [Accepted: 10/11/2008] [Indexed: 12/16/2022]
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Mihm M, Baker PJ, Fleming LM, Monteiro AM, O'Shaughnessy PJ. Differentiation of the bovine dominant follicle from the cohort upregulates mRNA expression for new tissue development genes. Reproduction 2008; 135:253-65. [DOI: 10.1530/rep-06-0193] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
This study was designed to identify genes that regulate the transition from FSH- to LH-dependent development in the bovine dominant follicle (DF). Serial analysis of gene expression (SAGE) was used to compare the transcriptome of granulosa cells isolated from the most oestrogenic growing cohort follicle (COH), the newly selected DF and its largest subordinate follicle (SF) which is destined for atresia. Follicle diameter, follicular fluid oestradiol (E) and E:progesterone ratio confirmed follicle identity. Results show that there are 93 transcript species differentially expressed in DF granulosa cells, but only 8 of these encode proteins known to be involved in DF development. Most characterised transcripts upregulated in the DF are from tissue development genes that regulate cell differentiation, proliferation, apoptosis, signalling and tissue remodelling. Semiquantitative real-time PCR analysis confirmed seven genes with upregulated (P≤0.05) mRNA expression in DF compared with both COH and SF granulosa cells. Thus, the new genes identified by SAGE and real-time PCR, which show enhanced mRNA expression in the DF, may regulate proliferation (cyclin D2;CCND2), prevention of apoptosis or DNA damage (growth arrest and DNA damage-inducible, β;GADD45B), RNA synthesis (splicing factor, arginine/serine rich 9;SFRS9) and unknown processes associated with enhanced steroidogenesis (ovary-specific acidic protein; DQ004742) in granulosa cells of DF at the onset of LH-dependent development. Further studies are required to show whether the expression of identified genes is dysregulated when abnormalities occur during DF selection or subsequent development.
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Perry RP. Balanced production of ribosomal proteins. Gene 2007; 401:1-3. [PMID: 17689889 PMCID: PMC5370545 DOI: 10.1016/j.gene.2007.07.007] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2007] [Revised: 07/02/2007] [Accepted: 07/03/2007] [Indexed: 11/26/2022]
Abstract
Eukaryotic ribosomes contain one molecule each of 79 different proteins. The genes encoding these proteins are usually at widely scattered loci and have distinctive promoters with certain common features. This minireview discusses the means by which cells manage to balance the production of ribosomal proteins so as to end up with equimolar quantities in the ribosome. Regulation at all levels of gene expression, from transcription to protein turnover, is considered.
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Abstract
The ribosome filter hypothesis postulates that ribosomes are not simply translation machines but also function as regulatory elements that differentially affect or filter the translation of particular mRNAs. On the basis of new information, we take the opportunity here to review the ribosome filter hypothesis, suggest specific mechanisms of action, and discuss recent examples from the literature that support it.
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19
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Tan W, Sun L, Zhang D, Sun J, Qian J, Hu X, Wang W, Sun Y, Ma L, Zhu C. Cloning and overexpression of ribosomal protein L39 gene from deltamethrin-resistant Culex pipiens pallens. Exp Parasitol 2007; 115:369-78. [PMID: 17092499 DOI: 10.1016/j.exppara.2006.09.020] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2006] [Revised: 09/26/2006] [Accepted: 09/29/2006] [Indexed: 11/25/2022]
Abstract
The complete sequence of ribosomal protein L39 has been cloned from deltamethrin-resistant strain of Culex pipiens pallens (DR1 strain). Quantitative RT-PCR analysis indicated that the RPL39 transcription level was 23.4 times higher in DR1 strain than in susceptible strain at 4th instar larvae. The RPL39 expression was also found to be consistently higher throughout the life cycle of DR1 strain. A protein of predicted size 17 kDa has been detected by Western blotting in RPL39-transfected mosquito C6/36 cells. These RPL39-transfected cells also showed enhanced deltamethrin resistance compared to plasmid vector-transfected cells as determined by methyl tritiated thymidine ((3)H-TdR) incorporation. These results indicate that RPL39 is expressed at higher levels in DR1 strain, and may confer some insecticide resistance in Cx. pipiens pallens.
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Affiliation(s)
- Wenbin Tan
- Department of Pathogenic Biology, Nanjing Medical University, Nanjing, Jiangsu Province, PR China
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20
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Hecht J, Kuhl H, Haas SA, Bauer S, Poustka AJ, Lienau J, Schell H, Stiege AC, Seitz V, Reinhardt R, Duda GN, Mundlos S, Robinson PN. Gene identification and analysis of transcripts differentially regulated in fracture healing by EST sequencing in the domestic sheep. BMC Genomics 2006; 7:172. [PMID: 16822315 PMCID: PMC1578570 DOI: 10.1186/1471-2164-7-172] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2006] [Accepted: 07/05/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The sheep is an important model animal for testing novel fracture treatments and other medical applications. Despite these medical uses and the well known economic and cultural importance of the sheep, relatively little research has been performed into sheep genetics, and DNA sequences are available for only a small number of sheep genes. RESULTS In this work we have sequenced over 47 thousand expressed sequence tags (ESTs) from libraries developed from healing bone in a sheep model of fracture healing. These ESTs were clustered with the previously available 10 thousand sheep ESTs to a total of 19087 contigs with an average length of 603 nucleotides. We used the newly identified sequences to develop RT-PCR assays for 78 sheep genes and measured differential expression during the course of fracture healing between days 7 and 42 postfracture. All genes showed significant shifts at one or more time points. 23 of the genes were differentially expressed between postfracture days 7 and 10, which could reflect an important role for these genes for the initiation of osteogenesis. CONCLUSION The sequences we have identified in this work are a valuable resource for future studies on musculoskeletal healing and regeneration using sheep and represent an important head-start for genomic sequencing projects for Ovis aries, with partial or complete sequences being made available for over 5,800 previously unsequenced sheep genes.
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Affiliation(s)
- Jochen Hecht
- Max Planck Institute for Molecular Genetics, Berlin, Germany.
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21
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Neill JD, Ridpath JF, Liebler-Tenorio E. Global gene expression profiling of Bovine immature B cells using serial analysis of gene expression. Anim Biotechnol 2006; 17:21-31. [PMID: 16621757 DOI: 10.1080/10495390500460957] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The Peyer's patches of the small intestine are important sites of antigen processing. The follicles of the Peyer's patches receive the antigen transported by the M cells at the mucosal surface and then play a major role in development of both protective humoral and mucosal immune responses. Serial analysis of gene expression (SAGE) was employed to derive the global gene expression profile of B lymphocytes isolated from the IPPF. Analysis of the SAGE data revealed the identity of genes and the level to which they are expressed by IPPF B lymphocytes. This analysis indicated that they were metabolically active and that the transcripts encoding proteins necessary for a response to antigen presentation were expressed. These transcripts included the B cell receptor components CD76a and b (Ig-alpha and Ig-beta) and accessory c-Src family kinases Lyn and Blk. Furthermore, many of the positive and negative regulators, and accessory proteins that are necessary for B cell antigen receptor signaling were identified. Also present were transcripts encoding interleukins and their cognate receptors. Overall, this SAGE analysis yielded a global picture of gene expression in IPPF B lymphocytes and provides a starting point for the comparison of gene expression in further functional studies.
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Affiliation(s)
- John D Neill
- Virus and Prion Diseases of Livestock Research Unit, USDA, ARS, National Animal Disease Center, Ames, Iowa 50010, USA.
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22
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Larraya LM, Boyce KJ, So A, Steen BR, Jones S, Marra M, Kronstad JW. Serial analysis of gene expression reveals conserved links between protein kinase A, ribosome biogenesis, and phosphate metabolism in Ustilago maydis. EUKARYOTIC CELL 2006; 4:2029-43. [PMID: 16339721 PMCID: PMC1317500 DOI: 10.1128/ec.4.12.2029-2043.2005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The switch from budding to filamentous growth is a key aspect of invasive growth and virulence for the fungal phytopathogen Ustilago maydis. The cyclic AMP (cAMP) signaling pathway regulates dimorphism in U. maydis, as demonstrated by the phenotypes of mutants with defects in protein kinase A (PKA). Specifically, a mutant lacking the regulatory subunit of PKA encoded by the ubc1 gene displays a multiple-budded phenotype and fails to incite disease symptoms, although proliferation does occur in the plant host. A mutant with a defect in a catalytic subunit of PKA, encoded by adr1, has a constitutively filamentous phenotype and is nonpathogenic. We employed serial analysis of gene expression to examine the transcriptomes of a wild-type strain and the ubc1 and adr1 mutants to further define the role of PKA in U. maydis. The mutants displayed changes in the transcript levels for genes encoding ribosomal proteins, genes regulated by the b mating-type proteins, and genes for metabolic functions. Importantly, the ubc1 mutant displayed elevated transcript levels for genes involved in phosphate acquisition and storage, thus revealing a connection between cAMP and phosphate metabolism. Further experimentation indicated a phosphate storage defect and elevated acid phosphatase activity for the ubc1 mutant. Elevated phosphate levels in culture media also enhanced the filamentous growth of wild-type cells in response to lipids, a finding consistent with PKA regulation of morphogenesis in U. maydis. Overall, these findings extend our understanding of cAMP signaling in U. maydis and reveal a link between phosphate metabolism and morphogenesis.
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Affiliation(s)
- Luis M Larraya
- Michael Smith Laboratories, 2185 East Mall, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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23
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Ellis SR, Massey AT. Diamond Blackfan anemia: A paradigm for a ribosome-based disease. Med Hypotheses 2006; 66:643-8. [PMID: 16239073 DOI: 10.1016/j.mehy.2005.09.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2005] [Accepted: 09/05/2005] [Indexed: 01/12/2023]
Abstract
Diamond Blackfan anemia is characterized by a severe hypoplastic anemia and a heterogeneous collection of other clinical features. Approximately 25% of Diamond Blackfan anemia cases are associated with mutations in the gene encoding ribosomal protein S19. The hypothesis presented here ties together molecular and clinical features of the disease, and establishes a conceptual framework for understanding many of the unusual characteristics of a growing number of diseases linked to factors involved in ribosome synthesis. The hypothesis states that ribosomal proteins are expressed in amounts that differ relative to one another in a tissue-specific manner, and that haploinsufficiency for a particular protein may make that protein limiting for ribosome assembly in some tissues, while other tissues remain unaffected. Further, polymorphisms in factors controlling the expression of a particular ribosomal protein gene may alter its expression and expand or contract the number of tissues affected from individual to individual. Support for the hypothesis comes from the observation that promoters in ribosomal protein genes exhibit little conservation and transcription profiling indicates that the absolute amounts of mRNAs for individual ribosomal proteins can vary dramatically relative to one another. Balanced expression of ribosomal proteins is achieved post-translationally, where excess proteins not assembled into ribosomal subunits are often rapidly degraded. The number of ribosomes per cell is therefore determined by the factors that limit assembly. In principle, any essential ribosomal protein could become limiting for assembly if its level of expression falls below a critical threshold. Whether an inactivating mutation in ribosomal protein gene would affect protein synthetic capacity of a tissue would depend on the ratio of the ribosomal protein relative to other ribosomal proteins in that tissue. If the ratio were high, the tissue may not be affected as the level of functional protein may not fall to a point where it becomes limiting for subunit assembly. In contrast, if the ratio were low, an inactivating mutation could make the protein limiting for subunit assembly resulting in a clinical phenotype. Polymorphisms in the myriad of cis- and trans-acting factors, which govern the expression of ribosomal proteins in response to developmental and physiological signals, could act to increase or decrease ribosomal protein expression and thereby impact the profile and severity of clinical phenotypes. Therefore, these factors represent targets for the development of new therapies to treat Diamond Blackfan anemia and other ribosome based diseases.
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Affiliation(s)
- Steven R Ellis
- Department of Biochemistry and Molecular Biology, University of Louisville, 319 Abraham Flexner Way, Louisville, KY 40292, USA.
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24
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Chatr-Aryamontri A, Angelini M, Garelli E, Tchernia G, Ramenghi U, Dianzani I, Loreni F. Nonsense-mediated and nonstop decay of ribosomal protein S19 mRNA in Diamond-Blackfan anemia. Hum Mutat 2005; 24:526-33. [PMID: 15523650 DOI: 10.1002/humu.20117] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Mutations in the ribosomal protein (RP)S19 gene have been found in about 25% of the cases of Diamond-Blackfan anemia (DBA), a rare congenital hypoplastic anemia that includes variable physical malformations. Various mutations have been identified in the RPS19 gene, but no investigations regarding the effect of these alterations on RPS19 mRNA levels have been performed. It is well established that mutated mRNA containing a premature stop codon (PTC) or lacking a stop codon can be rapidly degraded by specific mechanisms called nonsense mediated decay (NMD) and nonstop decay. To study the involvement of such mechanisms in DBA, we analyzed immortalized lymphoblastoid cells and primary fibroblasts from patients presenting different kinds of mutations in the RPS19 gene, generating allelic deletion, missense, nonsense, and nonstop messengers. We found that RPS19 mRNA levels are decreased in the cells with allelic deletion and, to a variable extent, also in all the cell lines with PTC or nonstop mutations. Further analysis showed that translation inhibition causes a stabilization of the mutated RPS19 mRNA. Our findings indicate that NMD and nonstop decay affect the expression of mutated RPS19 genes; this may help to clarify genotype-phenotype correlations in DBA.
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25
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Ivanov AV, Malygin AA, Karpova GG. Human ribosomal protein S26 suppresses the splicing of its pre-mRNA. ACTA ACUST UNITED AC 2005; 1727:134-40. [PMID: 15716004 DOI: 10.1016/j.bbaexp.2004.12.011] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2004] [Revised: 10/21/2004] [Accepted: 12/28/2004] [Indexed: 11/18/2022]
Abstract
Human recombinant ribosomal protein S26 (rpS26) was shown to interact with its pre-mRNA intron I and mRNA fragment. Endogenous rpS26 in HeLa nuclear extract was also found to bind to the intron I, and with a lower extent to the mRNA fragment. The addition of recombinant rpS26 to the nuclear extract increased the binding largely. The in vitro splicing of an RNA that contained exon I, intron I and part of exon II of the rpS26 pre-mRNA yielded conventional and alternative mRNAs. Recombinant rpS26 was found to suppress the formation of both mRNAs. Sites of the pre-mRNA involved in the binding to rpS26 were detected by toe-printing. Nucleotides that caused a stop (pause) of the reverse transcription formed two clusters on the RNA secondary structure. One cluster including A69, A287 and A303 arranged the conventional 3' site of splicing, another one including A131, A136, G156, A166 and A264 arranged the alternative 3' site of splicing.
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Affiliation(s)
- Anton V Ivanov
- Laboratory of Structure and Function of Ribosomes, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, pr. Lavrentieva, 8, Novosibirsk, 630090, Russia
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26
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Schimmelpfeng J, Weibezahn KF, Dertinger H. Quantification of NGF-dependent neuronal differentiation of PC-12 cells by means of neurofilament-L mRNA expression and neuronal outgrowth. J Neurosci Methods 2004; 139:299-306. [PMID: 15488244 DOI: 10.1016/j.jneumeth.2004.05.010] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2003] [Revised: 04/29/2004] [Accepted: 05/17/2004] [Indexed: 11/27/2022]
Abstract
We demonstrate that the degree of neuronal development of PC-12 cell differentiation can be quantified by the expression of neurofilament-L (NF-L) mRNA, when an optimal concentration of NGF (50 ng/ml) is used. During the first 7 days of NGF treatment, the relative amount of NF-L mRNA was found to increase continuously and to correlate with the outgrowth of neurites in a statistically significant way. Thus, mRNA expression is, under these conditions, a suitable means for reliably monitoring the differentiation of PC-12 cells as early as after 3 days of NGF treatment. The results obtained with 5 ng/ml NGF differ from those with 50 ng/ml: during the first 3 days of NGF treatment, neuronal outgrowth was less than with 50 ng/ml, although the NF-L mRNA levels did not depend significantly on NGF concentration. Beyond day 3, NF-L mRNA levels did not increase further at 5 ng/ml as opposed to 50 ng/ml NGF. These differences point to different signal transduction processes involved in neuronal differentiation at high and low NGF concentration. Expression of NF-L protein in response to NGF treatment was also demonstrated. In summary, our results stress that stable and sustained differentiation of PC-12 cells can only be achieved with 50 ng/ml NGF.
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Affiliation(s)
- J Schimmelpfeng
- Forschungszentrum Karlsruhe, Institute for Medical Engineering and Biophysics, P.O. Box 3640, D-76021 Karlsruhe, Germany.
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27
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Konu O, Xu X, Ma JZ, Kane J, Wang J, Shi SJ, Li MD. Application of a customized pathway-focused microarray for gene expression profiling of cellular homeostasis upon exposure to nicotine in PC12 cells. ACTA ACUST UNITED AC 2004; 121:102-13. [PMID: 14969741 DOI: 10.1016/j.molbrainres.2003.11.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2003] [Indexed: 11/19/2022]
Abstract
Maintenance of cellular homeostasis is integral to appropriate regulation of cellular signaling and cell growth and division. In this study, we report the development and quality assessment of a pathway-focused microarray comprising genes involved in cellular homeostasis. Since nicotine is known to have highly modulatory effects on the intracellular calcium homeostasis, we therefore tested the applicability of the homeostatic pathway-focused microarray on the gene expression in PC-12 cells treated with 1 mM nicotine for 48 h relative to the untreated control cells. We first provided a detailed description of the focused array with respect to its gene and pathway content and then assessed the array quality using a robust regression procedure that allows for the exclusion of unreliable measurements while decreasing the number of false positives. As a result, the mean correlation coefficient between duplicate measurements of the arrays used in this study (control vs. nicotine treatment, three samples each) has increased from 0.974+/-0.017 to 0.995+/-0.002. Furthermore, we found that nicotine affected various structural and signaling components of the AKT/PKB signaling pathway and protein synthesis and degradation processes in PC-12 cells. Since modulation of intracellular calcium concentrations ([Ca(2+)](i)) and phosphatidylinositol signaling are important in various biological processes such as neurotransmitter release and tissue pathogenesis including tumor formation, we expect that the homeostatic pathway-focused microarray potentially can be used for the identification of unique gene expression profiles in comparative studies of drugs of abuse and diverse environmental stimuli, such as starvation and oxidative stress.
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Affiliation(s)
- Ozlen Konu
- Program in Genomics and Bioinformatics on Drug Addiction, Department of Psychiatry, The University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, Mail Code 7792, San Antonio, TX 78229-3900, USA
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28
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Araki T, Hayashi M, Saruta T. Cloning and characterization of a novel gene promoting ureteric bud branching in the metanephros. Kidney Int 2003; 64:1968-77. [PMID: 14633119 DOI: 10.1046/j.1523-1755.2003.00304.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND The ureteric buds and metanephric mesenchymal cells reciprocally induce each other's maturation during kidney development, and implicated transcription factors, secreted growth factors, and cell surface signaling peptides are critical regulators of renal branching morphogenesis. Protein kinase C (PKC) is a key enzyme in the signal transduction mechanisms in various biologic processes, including development, because it regulates growth and differentiation. Inhibition of PKC by the sphingolipid product ceramide interferes with nephron formation in the developing kidney, but the molecule that controls ureteric bud branching downstream of PKC is still unknown. METHODS Differential display polymerase chain reaction (PCR) of metanephroi cultured with a PKC activator and inhibitor was performed. We also examined the role of a novel gene in kidney development with organ culture system. RESULTS A novel gene encoding a 759 bp mRNA was identified, and we named it metanephros-derived tubulogenic factor (MTF)/L47. Inhibition of MTF with antisense oligonucleotide impaired ureteric bud branching by cultured metanephroi, and addition of recombinant MTF protein promoted ureteric bud branching in cultured metanephroi and increased cell proliferation. CONCLUSION We identified a novel molecule in developing kidney that is capable of modulating ureteric bud branching and kidney differentiation.
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Affiliation(s)
- Takashi Araki
- Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
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29
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Becquet C, Blachon S, Jeudy B, Boulicaut JF, Gandrillon O. Strong-association-rule mining for large-scale gene-expression data analysis: a case study on human SAGE data. Genome Biol 2003; 3:RESEARCH0067. [PMID: 12537556 PMCID: PMC151169 DOI: 10.1186/gb-2002-3-12-research0067] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2001] [Revised: 07/02/2002] [Accepted: 09/25/2002] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND The association-rules discovery (ARD) technique has yet to be applied to gene-expression data analysis. Even in the absence of previous biological knowledge, it should identify sets of genes whose expression is correlated. The first association-rule miners appeared six years ago and proved efficient at dealing with sparse and weakly correlated data. A huge international research effort has led to new algorithms for tackling difficult contexts and these are particularly suited to analysis of large gene-expression matrices. To validate the ARD technique we have applied it to freely available human serial analysis of gene expression (SAGE) data. RESULTS The approach described here enables us to designate sets of strong association rules. We normalized the SAGE data before applying our association rule miner. Depending on the discretization algorithm used, different properties of the data were highlighted. Both common and specific interpretations could be made from the extracted rules. In each and every case the extracted collections of rules indicated that a very strong co-regulation of mRNA encoding ribosomal proteins occurs in the dataset. Several rules associating proteins involved in signal transduction were obtained and analyzed, some pointing to yet-unexplored directions. Furthermore, by examining a subset of these rules, we were able both to reassign a wrongly labeled tag, and to propose a function for an expressed sequence tag encoding a protein of unknown function. CONCLUSIONS We show that ARD is a promising technique that turns out to be complementary to existing gene-expression clustering techniques.
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Affiliation(s)
- Céline Becquet
- Equipe Signalisations et identités cellulaires, Centre de Génétique Moléculaire et Cellulaire CNRS UMR 5534, Université Claude Bernard Lyon 1, 16 rue Dubois, F-69622 Villeurbanne cedex, France
| | - Sylvain Blachon
- Equipe Signalisations et identités cellulaires, Centre de Génétique Moléculaire et Cellulaire CNRS UMR 5534, Université Claude Bernard Lyon 1, 16 rue Dubois, F-69622 Villeurbanne cedex, France
| | - Baptiste Jeudy
- Laboratoire d'Ingénierie des Systèmes d'Information, Institut National des Sciences Appliquées de Lyon, Bâtiment Blaise Pascal, F-69621 Villeurbanne cedex, France
| | - Jean-Francois Boulicaut
- Laboratoire d'Ingénierie des Systèmes d'Information, Institut National des Sciences Appliquées de Lyon, Bâtiment Blaise Pascal, F-69621 Villeurbanne cedex, France
| | - Olivier Gandrillon
- Equipe Signalisations et identités cellulaires, Centre de Génétique Moléculaire et Cellulaire CNRS UMR 5534, Université Claude Bernard Lyon 1, 16 rue Dubois, F-69622 Villeurbanne cedex, France
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