Nuclear PI3K Signaling in Cell Growth and Tumorigenesis
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P110α and P110β Isoforms of PI3K Are Involved in Protection Against H 2O2 Induced Oxidative Stress in Cancer Cells
Breast Cancer (2019) 26:378–385 https://doi.org/10.1007/s12282-018-0933-x ORIGINAL ARTICLE p110α and p110β isoforms of PI3K are involved in protection against H2O2 induced oxidative stress in cancer cells Paramjeet Singh1,2 · Nasima Bano1,2 · Md Mehedi Hossain1,2 · Rafia Basit1,2 · Mohd Jamal Dar1,2 Received: 17 July 2018 / Accepted: 15 November 2018 / Published online: 29 November 2018 © The Japanese Breast Cancer Society 2018 Abstract Purpose Phosphatidylinositol-3 kinases (PI3Ks) are involved in regulating cell growth, proliferation, differentiation, apop- tosis and survival. p110α and p110β, two ubiquitously expressed isoforms of PI3K signalling, are involved in growth factor mediated signaling and survival by generating second messengers. Earlier, we have generated GFP-fusion proteins of p110α and p110β and expressed them in normal and cancer cell-lines to investigate their subcellular localization and their role in various activities. Here, we sought to examine the role of p110α and p110β isoforms in protecting MCF-7 breast cancer cells against oxidative stress. Material methods We performed cytotoxicity assays, DNA transfection, Plasmid DNA preparation, western blotting, flour- scence microscopy and statistical analysis. Results To know whether p110α and p110β are involved in protecting MCF-7 breast cancer cells against oxidative stress, we subjected MCF-7 cells to H2O2 treatment and observed a dose dependent decrease in cell viability and a marked increase in the levels of pro-apoptotic markers which include PARP, Bcl-2, Bax and procaspase-9. We then over-expressed recombinant GFP-fusion p110α and p110β proteins in MCF-7 cells and observed a significant decrease in apoptosis and a concomitant increase in pAkt levels. -
Evidence for a Unique DNA-Dependent RNA Polymerase in Cereal Crops
bioRxiv preprint doi: https://doi.org/10.1101/272708; this version posted February 28, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Evidence for a unique DNA-dependent RNA polymerase in cereal crops 2 Joshua T. Trujillo1, Arun S. Seetharam2, Matthew B. Hufford3, Mark A. Beilstein1,4, and 3 Rebecca A. Mosher1,4,* 4 5 1 Department of Molecular & Cellular Biology, The University of Arizona, Tucson, AZ 6 85721, USA 7 2 Genome Informatics Facility, Iowa State University, Ames, IA 50011, USA 8 3 Department of Ecology, Evolution, and Organismal Biology, Iowa State University, 9 Ames, IA 50011, USA 10 4 The School of Plant Sciences, The University of Arizona, Tucson, AZ 85721, USA 11 12 * Corresponding author: Dr. Rebecca Mosher, 520-626-4185, 13 [email protected] 14 15 ORCiDs: 0000-0001-9817-4161 (JTT), 0000-0002-6789-9298 (ASS), 0000-0001-6379- 16 1899 (MBH), 0000-0002-3392-1389 (MAB), 0000-0003-2195-0825 (RAM) 17 18 Keywords: DNA-dependent RNA polymerase V, RNA-directed DNA methylation, gene 19 duplication, Poaceae 1 bioRxiv preprint doi: https://doi.org/10.1101/272708; this version posted February 28, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. -
Yeast Genome Gazetteer P35-65
gazetteer Metabolism 35 tRNA modification mitochondrial transport amino-acid metabolism other tRNA-transcription activities vesicular transport (Golgi network, etc.) nitrogen and sulphur metabolism mRNA synthesis peroxisomal transport nucleotide metabolism mRNA processing (splicing) vacuolar transport phosphate metabolism mRNA processing (5’-end, 3’-end processing extracellular transport carbohydrate metabolism and mRNA degradation) cellular import lipid, fatty-acid and sterol metabolism other mRNA-transcription activities other intracellular-transport activities biosynthesis of vitamins, cofactors and RNA transport prosthetic groups other transcription activities Cellular organization and biogenesis 54 ionic homeostasis organization and biogenesis of cell wall and Protein synthesis 48 plasma membrane Energy 40 ribosomal proteins organization and biogenesis of glycolysis translation (initiation,elongation and cytoskeleton gluconeogenesis termination) organization and biogenesis of endoplasmic pentose-phosphate pathway translational control reticulum and Golgi tricarboxylic-acid pathway tRNA synthetases organization and biogenesis of chromosome respiration other protein-synthesis activities structure fermentation mitochondrial organization and biogenesis metabolism of energy reserves (glycogen Protein destination 49 peroxisomal organization and biogenesis and trehalose) protein folding and stabilization endosomal organization and biogenesis other energy-generation activities protein targeting, sorting and translocation vacuolar and lysosomal -
The Mammalian and Yeast A49 and A34 Heterodimers: Homologous but Not the Same
G C A T T A C G G C A T genes Review The Mammalian and Yeast A49 and A34 Heterodimers: Homologous but Not the Same Rachel McNamar , Katrina Rothblum and Lawrence I. Rothblum * Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; [email protected] (R.M.); [email protected] (K.R.) * Correspondence: [email protected] Abstract: Ribosomal RNA synthesis is the rate-limiting step in ribosome biogenesis. In eukaryotes, RNA polymerase I (Pol I) is responsible for transcribing the ribosomal DNA genes that reside in the nucleolus. Aberrations in Pol I activity have been linked to the development of multiple cancers and other genetic diseases. Therefore, it is key that we understand the mechanisms of Pol I transcription. Recent studies have demonstrated that there are many differences between Pol I transcription in yeast and mammals. Our goal is to highlight the similarities and differences between the polymerase- associated factors (PAFs) in yeast and mammalian cells. We focus on the PAF heterodimer A49/34 in yeast and PAF53/49 in mammals. Recent studies have demonstrated that while the structures between the yeast and mammalian orthologs are very similar, they may function differently during Pol I transcription, and their patterns of regulation are different. Keywords: rRNA transcription; ribosome biogenesis; RNA polymerase I Citation: McNamar, R.; Rothblum, 1. Introduction K.; Rothblum, L.I. The Mammalian Ribosome biogenesis is the process that produces the machinery responsible for syn- and Yeast A49 and A34 Heterodimers: thesizing all the proteins in a cell. This process is extraordinarily complex. -
Extensive Purification of a Putative RNA Polymerase I Holoenzyme
Proc. Natl. Acad. Sci. USA Vol. 94, pp. 11869–11874, October 1997 Biochemistry Extensive purification of a putative RNA polymerase I holoenzyme from plants that accurately initiates rRNA gene transcription in vitro (nucleolusyrDNAygene expression) JULIO SAEZ-VASQUEZ AND CRAIG S. PIKAARD* Biology Department, Washington University, Campus Box 1137, One Brookings Drive, St. Louis, MO 63130 Edited by Masayasu Nomura, University of California, Irvine, CA, and approved August 25, 1997 (received for review May 19, 1997) ABSTRACT RNA polymerase I (pol I) is a nuclear enzyme Encouraged by brief reports that cell-free rRNA gene whose function is to transcribe the duplicated genes encoding transcription could be achieved in plant extracts (22, 23), we set the precursor of the three largest ribosomal RNAs. We report out to develop a cell-free system from broccoli (Brassica a cell-free system from broccoli (Brassica oleracea) inflores- oleracea) to further our studies of rRNA gene regulation in cence that supports promoter-dependent RNA pol I transcrip- Brassica and Arabidopsis (24–28). We show that a pol I- tion in vitro. The transcription system was purified extensively containing activity sufficient for promoter-dependent tran- by DEAE-Sepharose, Biorex 70, Sephacryl S300, and Mono Q scription can be purified extensively, with biochemical prop- chromatography. Activities required for pre-rRNA transcrip- erties suggesting a single complex. Approximately 30 polypep- tion copurified with the polymerase on all four columns, tides are present in fractions purified to near-homogeneity, suggesting their association as a complex. Purified fractions consistent with the estimated mass of the putative holoenzyme programmed transcription initiation from the in vivo start site complex and the expected complexity of the pol I transcription and utilized the same core promoter sequences required in system. -
Which Distinguish Between RNA Polymerases I and III* (Chromatography on DEAE-Ion-Exchangers/Salt-Activation Profiles/RNA Nucleotidyltransferase) LOREN D
Proc. Nat. Acad. Sci. USA Vol. 73, No. 4, pp. 1029-10&3, April 1976 Biochemistry Transcription in yeast: a-Amanitin sensitivity and other properties which distinguish between RNA polymerases I and III* (chromatography on DEAE-ion-exchangers/salt-activation profiles/RNA nucleotidyltransferase) LOREN D. SCHULTZt AND BENJAMIN D. HALL* t Department of Biochemistry and t'Department of Genetics, University of Washington, Seattle, Wash. 98195 Communicated by Herschel L. Roman, December 29, 1975 ABSTRACT Three peaks of DNA-dependent RNA poly- umns can be interpreted either as a failure of DEAE-cellu- merase (RNA nucleotidyltransferase) activity are resolved by lose to resolve two different enzymes or, alternatively, as the chromatography of a sonicated yeast cell extract on DEAE- Sephadex. The enzymes, which are named RNA polymerases tendency of a single enzyme, polymerase A, to chromato- I, II, and III in order of elution, show similar catalytic prop- graph as two peaks on DEAE-Sephadex as a result of some erties to the vertebrate class I, class II, and class III RNA po- trivial alteration that occurs during the chromatography. lymerases, respectively. Yeast RNA polymerase III is readily For vertebrate RNA polymerases, the first of these interpre- distinguished from yeast polymerase I by its biphasic ammo- tations is the correct one. Sklar, Schwartz, and Roeder (10) nium sulfate activation profile with native DNA templates, have shown, for mouse plasmacytoma RNA polymerases, greater enzymatic activity with poly[d(I-C) than with native that each of the three classes of RNA salmon sperm DNA, and distinctive chromatographic elution polymerase eluted positions from DEAE-cellulose (0.12 M ammonium sulfate) from DEAE-Sephadex has a distinctive pattern of protein compared with DEAE-Sephadex (0.32 M ammonium sulfate). -
Non-Coding Rnas As Regulators of Transcription and Genome Organization Katalin Fejes Toth and Greg Hannon
| 311 13 Non-Coding RNAs as Regulators of Transcription and Genome Organization Katalin Fejes Toth and Greg Hannon 13.1 Introduction “Junk DNA” was used as the provisional label for the portions of a genome for which no discernible function had been identified [1]. In a 1980 review in Nature Leslie Orgel and Francis Crick described junk DNA as having “little specificity and conveying little or no selective advantage to the organism” [2]. For decades, sci- entist considered the non-protein-coding portions of the genome as dispensable. Protein-coding genes comprise an astonishingly small part of eukaryotic genomes (less than 2% in humans, corresponding to roughly 20 000 genes; Chapter 1). However, as less complex eukaryotes, such as Caenorhabditis elegans, have a very similar number of protein-coding genes, it is clear that the developmental and physiological complexity of humans cannot be explained solely by the number of protein-coding genes. Alternative splicing and post-translational modification of proteins increase the diversity and functionality of the proteome likely explaining at least part of its increased complexity. However, it seems evident that much of the regulatory complexity that may contribute to the development of more complex organisms can be established by non-coding RNAs (ncRNAs), as discussed in further detail in Chapter 14. In accord with the notion that much of the genome represents an evolutionary junk heap, many non-coding transcripts have been proposed to result from leaky or pervasive non-specific transcription. Recent high throughput studies indicate that the transcription of our genomes extends far beyond the limited sequences comprising protein-coding genes, with almost the every base in the genome appearing in non-coding RNAs or ncRNAs. -
Sensing the Epigenome
Review Special Issue: Noncoding and small RNAs Sensing the epigenome Jay B. Hollick Department of Plant and Microbial Biology, 111 Koshland Hall, University of California, Berkeley, CA 94720-3102, USA Recent studies of plant development and environmental DRD1 : Arabidopsis gene DEFECTIVE IN RNA-DIRECTED DNA METHYLATION1, stress responses have converged on the roles of RNA encoding a Rad54-type ATPase necessary for RNA-directed DNA methylation. and its metabolism as primary regulators of gene action. En/Spm : a well-characterized autonomous TIR CACTA-type DNA transposon, Enhancer/Suppressor-mutator, described in maize. This RNA-based system appears to represent a versatile FCA : Arabidopsis gene FLOWERING TIME CONTROL PROTEIN, encoding a platform both for maintaining epigenetic memory and RNA-binding protein regulating flower development. FLC : Arabidopsis gene FLOWERING LOCUS C, encoding a MADS-type protein for reprogramming gene control in response to external that acts as a repressor of flowering. signals. The fast-paced research reviewed here high- FLD : Arabidopsis gene FLOWERING LOCUS D, encoding a histone deacetylase lights exciting new trends in plant research relating to that acts to promote flower development. FPA : Arabidopsis gene (At2g43410), encoding a RNA-binding protein regulat- mechanisms and roles of the RNA-dependent epigen- ing flower development. ome in both development and evolution. Imprinted module : a set of neighboring genes showing differential action depending on parent-of-origin transmission. Emerging regulatory roles of RNA lbl1 : maize locus leafbladeless1, expressing a SGS3-type protein required for tasiRNA production. Barbara McClintock was the first to surmise that the LINE : eukaryotic retrotransposon of the long-interspersed nuclear element activation of previously silenced transposons was related class. -
Subunits Shared by Eukaryotic Nuclear RNA Polymerases
Downloaded from genesdev.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press Subunits shared by eukaryotic nuclear RNA polymerases Nancy A. Woychik, Sha-Mei Liao, Peter A. Kolodziej, and Richard A. Young Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142 USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 USA RNA polymerases I, II, and III share three subunits that are immunologically and biochemically indistinguishable. The Saccharomyces cerevisiae genes that encode these subunits (RPBS, RPB6, and RPBS) were isolated and sequenced, and their transcriptional start sites were deduced. RPB5 encodes a 25-kD protein, RPB6, an 18-kD protein, and RPB8, a 16-kD protein. These genes are single copy, reside on different chromosomes, and are essential for viability. The fact that the genes are single copy, corroborates previous evidence suggesting that each of the common subunits is identical in RNA polymerases I, II, and III. Furthermore, immunoprecipitation of RPB6 coprecipitates proteins whose sizes are consistent with RNA polymerase I, II, and III subunits. Sequence similarity between the yeast RPB5 protein and a previously characterized human RNA polymerase subunit demonstrates that the common subunits of the nuclear RNA polymerases are well conserved among eukaryotes. The presence of these conserved and essential subunits in all three nuclear RNA polymerases and the absence of recognizable sequence motifs for DNA and nucleoside triphosphate-binding indicate that the common subunits do not have a catalytic role but are important for a function shared by the RNA polymerases such as transcriptional efficiency, nuclear localization, enzyme stability, or coordinate regulation of rRNA, mRNA, and tRNA synthesis. -
Structural Disorder in Plant Proteins : Where Plasticity Meets Sessility
This is a repository copy of Structural disorder in plant proteins : where plasticity meets sessility. White Rose Research Online URL for this paper: http://eprints.whiterose.ac.uk/152165/ Version: Accepted Version Article: Covarrubias, A.A., Cuevas-Velazquez, C.L., Romero-Pérez, P.S. et al. (2 more authors) (2017) Structural disorder in plant proteins : where plasticity meets sessility. Cellular and Molecular Life Sciences, 74 (17). pp. 3119-3147. ISSN 1420-682X https://doi.org/10.1007/s00018-017-2557-2 This is a post-peer-review, pre-copyedit version of an article published in Cellular and Molecular Life Sciences. The final authenticated version is available online at: http://dx.doi.org/10.1007/s00018-017-2557-2 Reuse Items deposited in White Rose Research Online are protected by copyright, with all rights reserved unless indicated otherwise. They may be downloaded and/or printed for private study, or other acts as permitted by national copyright laws. The publisher or other rights holders may allow further reproduction and re-use of the full text version. This is indicated by the licence information on the White Rose Research Online record for the item. Takedown If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing [email protected] including the URL of the record and the reason for the withdrawal request. [email protected] https://eprints.whiterose.ac.uk/ 1 2 3 4 5 STRUCTURAL DISORDER IN PLANT PROTEINS: 6 WHERE PLASTICITY MEETS SESSILITY 7 8 Alejandra A. Covarrubias*, Cesar L. -
Polivb Influences RNA-Directed DNA Methylation Independently of Its Role in Sirna Biogenesis
PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis Rebecca A. Mosher*, Frank Schwach†, David Studholme, and David C. Baulcombe*‡ Sainsbury Laboratory, Norwich NR4 7UH, United Kingdom Edited by James C. Carrington, Center for Genome Research and Biocomputing, Corvallis, OR, and accepted by the Editorial Board December 31, 2007 (received for review October 10, 2007) DNA-dependent RNA polymerase (Pol)IV in Arabidopsis exists in There are two genes in Arabidopsis encoding the putative two isoforms (PolIVa and PolIVb), with NRPD1a and NRPD1b as largest subunit of PolIV (NRPD1A and NRPD1B), and it is likely their respective largest subunits. Both isoforms are implicated in that they share the second largest subunit (NRPD2A) to gen- production and activity of siRNAs and in RNA-directed DNA meth- erate two PolIV isoforms. Mutations in either of the two NRPD1 ylation (RdDM). Deep sequence analysis of siRNAs in WT Arabi- subunits affect siRNA accumulation, although nrpd1b affects dopsis flowers and in nrpd1a and nrpd1b mutants identified siRNA accumulation at only a subset of the loci affected by >4,200 loci producing siRNAs in a PolIV-dependent manner, with nrpd1a (3, 5, 20, 21). This differential effect prompted the PolIVb reinforcing siRNA production by PolIVa. Transposable ele- proposal that PolIVb acts downstream of PolIVa at repeated ment identity and pericentromeric localization are both features sequence loci to amplify siRNA production and methylate DNA, that predispose a locus for siRNA production via PolIV proteins and whereas, at less repetitive loci, PolIVa functions without PolIVb determine the extent to which siRNA production relies on PolIVb. -
Targeting the RNA Polymerase I Transcription for Cancer Therapy Comes of Age
Targeting the RNA Polymerase I Transcription for Cancer Therapy Comes of Age Ferreira, R., Schneekloth, J. S., Panov, K. I., Hannan, K. M., & Hannan, R. D. (2020). Targeting the RNA Polymerase I Transcription for Cancer Therapy Comes of Age. Cells, 9(2). https://doi.org/10.3390/cells9020266 Published in: Cells Document Version: Publisher's PDF, also known as Version of record Queen's University Belfast - Research Portal: Link to publication record in Queen's University Belfast Research Portal Publisher rights © 2020 The Authors. This is an open access article published under a Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium, provided the author and source are cited. General rights Copyright for the publications made accessible via the Queen's University Belfast Research Portal is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The Research Portal is Queen's institutional repository that provides access to Queen's research output. Every effort has been made to ensure that content in the Research Portal does not infringe any person's rights, or applicable UK laws. If you discover content in the Research Portal that you believe breaches copyright or violates any law, please contact [email protected]. Download date:26. Sep. 2021 cells Review Targeting the RNA Polymerase I Transcription for Cancer Therapy Comes of Age Rita Ferreira 1,* , John S.