Endogenous Overexpression of an Active Phosphorylated Form of DNA Polymerase Β Under Oxidative Stress in Trypanosoma Cruzi
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DNA Polymerase Exchange and Lesion Bypass in Escherichia Coli
DNA Polymerase Exchange and Lesion Bypass in Escherichia Coli The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Kath, James Evon. 2016. DNA Polymerase Exchange and Lesion Bypass in Escherichia Coli. Doctoral dissertation, Harvard University, Graduate School of Arts & Sciences. Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:26718716 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA ! ! ! ! ! ! ! DNA!polymerase!exchange!and!lesion!bypass!in!Escherichia)coli! ! A!dissertation!presented! by! James!Evon!Kath! to! The!Committee!on!Higher!Degrees!in!Biophysics! ! in!partial!fulfillment!of!the!requirements! for!the!degree!of! Doctor!of!Philosophy! in!the!subject!of! Biophysics! ! Harvard!University! Cambridge,!Massachusetts! October!2015! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ©!2015!L!James!E.!Kath.!Some!Rights!Reserved.! ! This!work!is!licensed!under!the!Creative!Commons!Attribution!3.0!United!States!License.!To! view!a!copy!of!this!license,!visit:!http://creativecommons.org/licenses/By/3.0/us! ! ! Dissertation!Advisor:!Professor!Joseph!J.!Loparo! ! ! !!!!!!!!James!Evon!Kath! ! DNA$polymerase$exchange$and$lesion$bypass$in$Escherichia)coli$ $ Abstract$ ! Translesion! synthesis! (TLS)! alleviates! -
Yeast DNA Polymerase Zeta ()Is Essential for Error-Free Replication Past Thymine Glycol
Downloaded from genesdev.cshlp.org on September 24, 2021 - Published by Cold Spring Harbor Laboratory Press Yeast DNA polymerase zeta ()is essential for error-free replication past thymine glycol Robert E. Johnson, Sung-Lim Yu, Satya Prakash, and Louise Prakash1 Sealy Center for Molecular Science, University of Texas Medical Branch at Galveston, Galveston, Texas 77555-1061, USA DNA polymerase zeta (Pol) promotes the mutagenic bypass of DNA lesions in eukaryotes. Genetic studies in Saccharomyces cerevisiae have indicated that relative to the contribution of other pathways, Pol makes only a modest contribution to lesion bypass. Intriguingly, however, disruption of the REV3 gene, which encodes the catalytic subunit of Pol, causes early embryonic lethality in mice. Here, we present genetic and biochemical evidence for the requirement of yeast Pol for predominantly error-free replication past thymine glycol (Tg), a DNA lesion formed frequently by free radical attack. These results raise the possibility that, as in yeast, in higher eukaryotes also, Pol makes a major contribution to the replicative bypass of Tgs as well as other lesions that block synthesis by replicative DNA polymerases. Such a preeminent role of Pol in lesion bypass would ensure that rapid cell divisions continue unabated during early embryonic development, thereby minimizing the generation of DNA strand breaks, chromosome aberrations, and the ensuing apoptotic response. [Keywords: DNApolymerase ; thymine glycol; translesion DNAsynthesis; Pol as an extender; error-free translesion DNAsynthesis by Pol ; yeast] Received October 4, 2002; revised version accepted October 31, 2002. Genetic studies in the yeast Saccharomyces cerevisiae et al. 2000b; Washington et al. 2000). Genetic studies in have indicated the requirement of Rad6–Rad18-depen- yeast have additionally indicated a role for Pol in the dent processes in promoting replication of damaged error-free bypass of cyclobutane pyrimidine dimers DNA. -
DNA Polymerase V Activity Is Autoregulated by a Novel Intrinsic DNA-Dependent
1 2 DNA polymerase V activity is autoregulated by a novel intrinsic DNA-dependent 3 ATPase 4 Aysen L. Erdem1, Malgorzata Jaszczur1, Jeffrey G. Bertram1, Roger Woodgate2, Michael M. Cox3 & 5 Myron F. Goodman1 6 1Departments of Biological Sciences and Chemistry, University of Southern California, University 7 Park, Los Angeles, California 90089-2910, USA. 2Laboratory of Genomic Integrity, National 8 Institute of Child Health and Human Development, National Institutes of Health, Bethesda, 9 Maryland 20892-3371, USA. 3Department of Biochemistry, University of Wisconsin-Madison, 10 Madison, Wisconsin 53706, USA. 11 12 Escherichia coli DNA polymerase V (pol V), a heterotrimeric complex composed of UmuD′2C, 13 is marginally active. ATP and RecA play essential roles in the activation of pol V for DNA 14 synthesis including translesion synthesis (TLS). We have established three features of the roles 15 of ATP and RecA. 1) RecA-activated DNA polymerase V (pol V Mut), is a DNA-dependent 16 ATPase; 2) bound ATP is required for DNA synthesis; 3) pol V Mut function is regulated by 17 ATP, with ATP required to bind primer/template (p/t) DNA and ATP hydrolysis triggering 18 dissociation from the DNA. Pol V Mut formed with an ATPase-deficient RecA E38K/K72R 19 mutant hydrolyzes ATP rapidly, establishing the DNA-dependent ATPase as an intrinsic 20 property of pol V Mut distinct from the ATP hydrolytic activity of RecA when bound to 21 single-stranded (ss)DNA as a nucleoprotein filament (RecA*). No similar ATPase activity or 22 autoregulatory mechanism has previously been found for a DNA polymerase. -
Table SI. Genes Upregulated ≥ 2-Fold by MIH 2.4Bl Treatment Affymetrix ID
Table SI. Genes upregulated 2-fold by MIH 2.4Bl treatment Fold UniGene ID Description Affymetrix ID Entrez Gene Change 1558048_x_at 28.84 Hs.551290 231597_x_at 17.02 Hs.720692 238825_at 10.19 93953 Hs.135167 acidic repeat containing (ACRC) 203821_at 9.82 1839 Hs.799 heparin binding EGF like growth factor (HBEGF) 1559509_at 9.41 Hs.656636 202957_at 9.06 3059 Hs.14601 hematopoietic cell-specific Lyn substrate 1 (HCLS1) 202388_at 8.11 5997 Hs.78944 regulator of G-protein signaling 2 (RGS2) 213649_at 7.9 6432 Hs.309090 serine and arginine rich splicing factor 7 (SRSF7) 228262_at 7.83 256714 Hs.127951 MAP7 domain containing 2 (MAP7D2) 38037_at 7.75 1839 Hs.799 heparin binding EGF like growth factor (HBEGF) 224549_x_at 7.6 202672_s_at 7.53 467 Hs.460 activating transcription factor 3 (ATF3) 243581_at 6.94 Hs.659284 239203_at 6.9 286006 Hs.396189 leucine rich single-pass membrane protein 1 (LSMEM1) 210800_at 6.7 1678 translocase of inner mitochondrial membrane 8 homolog A (yeast) (TIMM8A) 238956_at 6.48 1943 Hs.741510 ephrin A2 (EFNA2) 242918_at 6.22 4678 Hs.319334 nuclear autoantigenic sperm protein (NASP) 224254_x_at 6.06 243509_at 6 236832_at 5.89 221442 Hs.374076 adenylate cyclase 10, soluble pseudogene 1 (ADCY10P1) 234562_x_at 5.89 Hs.675414 214093_s_at 5.88 8880 Hs.567380; far upstream element binding protein 1 (FUBP1) Hs.707742 223774_at 5.59 677825 Hs.632377 small nucleolar RNA, H/ACA box 44 (SNORA44) 234723_x_at 5.48 Hs.677287 226419_s_at 5.41 6426 Hs.710026; serine and arginine rich splicing factor 1 (SRSF1) Hs.744140 228967_at 5.37 -
Reca Acts As a Switch to Regulate Polymerase Occupancy in a Moving Replication Fork
RecA acts as a switch to regulate polymerase occupancy in a moving replication fork Chiara Indiania,1, Meghna Patelb, Myron F. Goodmanb, and Mike E. O’Donnellc,1 aManhattan College, Riverdale, NY 10471; bDepartment of Biological Sciences, University of Southern California, Los Angeles, CA 90089; and cHoward Hughes Medical Institute, Rockefeller University, New York, NY 10065 Contributed by Mike O’Donnell, February 19, 2013 (sent for review February 6, 2013) This report discovers a role of Escherichia coli RecA, the cellular regulates DNA polymerase access to the replication fork. Sur- recombinase, in directing the action of several DNA polymerases prisingly, RecA strongly inhibits fork progression by Pol III repli- at the replication fork. Bulk chromosome replication is performed somes, yet RecA stimulates TLS Pol II and Pol IV replisomes. The by DNA polymerase (Pol) III. However, E. coli contains translesion mechanism that underlies the opposite effects of RecA on Pol III synthesis (TLS) Pols II, IV, and V that also function with the helicase, and the TLS Pol replisomes involves single-strand binding protein primase, and sliding clamp in the replisome. Surprisingly, we find (SSB). Although all of the polymerases function with SSB on the that RecA specifically activates replisomes that contain TLS Pols. In template strand, SSB inhibits TLS Pol function in the context of sharp contrast, RecA severely inhibits the Pol III replisome. Given a replisome, presumably acting in trans by binding lagging-strand the opposite effects of RecA on Pol III and TLS replisomes, we pro- ssDNA. RecA relieves the SSB induced repression of TLS Pol pose that RecA acts as a switch to regulate the occupancy of poly- replisomes and stimulates their action, while inhibiting the Pol III merases within a moving replisome. -
Y-Family DNA Polymerases in Escherichia Coli
Y-family DNA polymerases in Escherichia coli The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Jarosz, Daniel F. et al. “Y-family DNA Polymerases in Escherichia Coli.” Trends in Microbiology 15.2 (2007): 70–77. Web. 13 Apr. 2012. © 2007 Elsevier Ltd. As Published http://dx.doi.org/10.1016/j.tim.2006.12.004 Publisher Elsevier Version Final published version Citable link http://hdl.handle.net/1721.1/70041 Terms of Use Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. Review TRENDS in Microbiology Vol.15 No.2 Y-family DNA polymerases in Escherichia coli Daniel F. Jarosz1, Penny J. Beuning2,3, Susan E. Cohen2 and Graham C. Walker2 1 Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA 2 Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA 3 Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA The observation that mutations in the Escherichia coli that is also lexA-independent [4]. This might have genes umuC+ and umuD+ abolish mutagenesis induced particularly important implications for bacteria living by UV light strongly supported the counterintuitive under conditions of nutrient starvation. The SOS response notion that such mutagenesis is an active rather than also seems to be oscillatory at the single-cell level, and this passive process. Genetic and biochemical studies have oscillation is dependent on the umuDC genes [5]. -
DNA Polymerase Zeta-Dependent Mutagenesis: Molecular Specificity, Extent of Error-Prone Synthesis, and the Role of Dntp Pools
University of Nebraska Medical Center DigitalCommons@UNMC Theses & Dissertations Graduate Studies Fall 12-16-2016 DNA Polymerase Zeta-Dependent Mutagenesis: Molecular Specificity, Extent of Error-Prone Synthesis, and the Role of dNTP Pools Olga V. Kochenova University of Nebraska Medical Center Follow this and additional works at: https://digitalcommons.unmc.edu/etd Part of the Biochemistry Commons, Genetics Commons, Molecular Biology Commons, and the Molecular Genetics Commons Recommended Citation Kochenova, Olga V., "DNA Polymerase Zeta-Dependent Mutagenesis: Molecular Specificity, Extent of Error- Prone Synthesis, and the Role of dNTP Pools" (2016). Theses & Dissertations. 153. https://digitalcommons.unmc.edu/etd/153 This Dissertation is brought to you for free and open access by the Graduate Studies at DigitalCommons@UNMC. It has been accepted for inclusion in Theses & Dissertations by an authorized administrator of DigitalCommons@UNMC. For more information, please contact [email protected]. DNA POLYMERASE ζ -DEPENDENT MUTAGENESIS: MOLECULAR SPECIFICITY, EXTENT OF ERROR-PRONE SYNTHESIS, AND THE ROLE OF dNTP POOLS by Olga Kochenova A DISSERTATION Presented to the Faculty of The University of Nebraska Graduate College In Partial Fulfillment of the Requirements For the Degree of Doctor of Philosophy Cancer Research Graduate Program Under the Supervision of Professor Polina V. Shcherbakova University of Nebraska Medical Center Omaha, Nebraska October, 2016 Supervisory Committee: Youri Pavlov, Ph. D. Tadayoshi Bessho, Ph. D. Michel Ouellette, Ph. D. DNA POLYMERASE ζ -DEPENDENT MUTAGENESIS: MOLECULAR SPECIFICITY, EXTENT OF ERROR-PRONE SYNTHESIS, AND THE ROLE OF dNTP POOLS Olga V. Kochenova, Ph.D. University of Nebraska, 2016 Supervisor: Polina V. Shcherbakova, Ph.D. Despite multiple DNA repair pathways, DNA lesions can escape repair and compromise normal chromosomal replication, leading to genome instability. -
Ubiquitin and Ubiquitin-Like Proteins Are Essential Regulators of DNA Damage Bypass
cancers Review Ubiquitin and Ubiquitin-Like Proteins Are Essential Regulators of DNA Damage Bypass Nicole A. Wilkinson y, Katherine S. Mnuskin y, Nicholas W. Ashton * and Roger Woodgate * Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA; [email protected] (N.A.W.); [email protected] (K.S.M.) * Correspondence: [email protected] (N.W.A.); [email protected] (R.W.); Tel.: +1-301-435-1115 (N.W.A.); +1-301-435-0740 (R.W.) Co-first authors. y Received: 29 August 2020; Accepted: 29 September 2020; Published: 2 October 2020 Simple Summary: Ubiquitin and ubiquitin-like proteins are conjugated to many other proteins within the cell, to regulate their stability, localization, and activity. These modifications are essential for normal cellular function and the disruption of these processes contributes to numerous cancer types. In this review, we discuss how ubiquitin and ubiquitin-like proteins regulate the specialized replication pathways of DNA damage bypass, as well as how the disruption of these processes can contribute to cancer development. We also discuss how cancer cell survival relies on DNA damage bypass, and how targeting the regulation of these pathways by ubiquitin and ubiquitin-like proteins might be an effective strategy in anti-cancer therapies. Abstract: Many endogenous and exogenous factors can induce genomic instability in human cells, in the form of DNA damage and mutations, that predispose them to cancer development. Normal cells rely on DNA damage bypass pathways such as translesion synthesis (TLS) and template switching (TS) to replicate past lesions that might otherwise result in prolonged replication stress and lethal double-strand breaks (DSBs). -
The Microbiota-Produced N-Formyl Peptide Fmlf Promotes Obesity-Induced Glucose
Page 1 of 230 Diabetes Title: The microbiota-produced N-formyl peptide fMLF promotes obesity-induced glucose intolerance Joshua Wollam1, Matthew Riopel1, Yong-Jiang Xu1,2, Andrew M. F. Johnson1, Jachelle M. Ofrecio1, Wei Ying1, Dalila El Ouarrat1, Luisa S. Chan3, Andrew W. Han3, Nadir A. Mahmood3, Caitlin N. Ryan3, Yun Sok Lee1, Jeramie D. Watrous1,2, Mahendra D. Chordia4, Dongfeng Pan4, Mohit Jain1,2, Jerrold M. Olefsky1 * Affiliations: 1 Division of Endocrinology & Metabolism, Department of Medicine, University of California, San Diego, La Jolla, California, USA. 2 Department of Pharmacology, University of California, San Diego, La Jolla, California, USA. 3 Second Genome, Inc., South San Francisco, California, USA. 4 Department of Radiology and Medical Imaging, University of Virginia, Charlottesville, VA, USA. * Correspondence to: 858-534-2230, [email protected] Word Count: 4749 Figures: 6 Supplemental Figures: 11 Supplemental Tables: 5 1 Diabetes Publish Ahead of Print, published online April 22, 2019 Diabetes Page 2 of 230 ABSTRACT The composition of the gastrointestinal (GI) microbiota and associated metabolites changes dramatically with diet and the development of obesity. Although many correlations have been described, specific mechanistic links between these changes and glucose homeostasis remain to be defined. Here we show that blood and intestinal levels of the microbiota-produced N-formyl peptide, formyl-methionyl-leucyl-phenylalanine (fMLF), are elevated in high fat diet (HFD)- induced obese mice. Genetic or pharmacological inhibition of the N-formyl peptide receptor Fpr1 leads to increased insulin levels and improved glucose tolerance, dependent upon glucagon- like peptide-1 (GLP-1). Obese Fpr1-knockout (Fpr1-KO) mice also display an altered microbiome, exemplifying the dynamic relationship between host metabolism and microbiota. -
Mcf7specificall
Glycoprotein hormones alpha chain Hormone ligand-binding receptors Glycoprotein hormones Mineralocorticoid biosynthesis TFAP2 (AP-2) family regulates transcriptionAndrogenThyroid of biosynthesis growth stimulating factors hormone and their receptor receptors Reactions specificThyroxine to the complex biosynthesis N-glycan synthesis pathway Multidrug resistance-associated proteinGlucagon-like 5 peptide 1 receptor 78 kDa glucose-regulated protein Hyaluronan biosynthesis and export Glucagon-type ligand receptors Platelet degranulation G alpha (s)ABC-family signalling proteinsevents mediated transport PERKATF6 regulates(ATF6-alpha) gene activates expression chaperones Guanine nucleotide-binding protein G(s), subunit alpha Regulation of HSF1-mediated heat shock response Glucagon-like Peptide-1 (GLP1) regulates insulin secretion ATF6 (ATF6-alpha)IRE1alpha activates activates chaperone chaperones genes Parathyroid hormone receptor Serotonin (5-HT)Prostacyclin receptorG alpha signalling (z) signalling through events prostacyclin receptor Ras-related protein Rab-9A G alpha (q) signalling events GlucagonHedgehog signaling 'off' in metabolic state regulation PKA activation in glucagon signalling RAB geranylgeranylation Ubiquitin carboxyl-terminal hydrolase 1 Vasopressin regulates renal water homeostasis via Aquaporins Rap guanine nucleotide exchange factor 3 Class B/2 (Secretin Neuropeptidefamily receptors) S receptor Rap guanine nucleotide exchange factor 4 RetrogradeRAB transportGEFs exchange at the Trans-Golgi-Network GTP for GDP on RABs Serotonin -
Roles of DNA Polymerases V and II in SOS-Induced Error-Prone and Error-Free Repair in Escherichia Coli
Colloquium Roles of DNA polymerases V and II in SOS-induced error-prone and error-free repair in Escherichia coli Phuong Pham*, Savithri Rangarajan*, Roger Woodgate†, and Myron F. Goodman*‡ *Departments of Biological Sciences and Chemistry, Hedco Molecular Biology Laboratories, University of Southern California, Los Angeles, CA 90089-1340; and †Section on DNA Replication, Repair and Mutagenesis, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-2725 DNA polymerase V, composed of a heterotrimer of the DNA regulated at the transcriptional level by the LexA protein (14). damage-inducible UmuC and UmuD2 proteins, working in conjunc- Many of these genes encode proteins required to repair DNA tion with RecA, single-stranded DNA (ssDNA)-binding protein damage (15). The overriding importance of DNA repair is (SSB),  sliding clamp, and ␥ clamp loading complex, are respon- apparent from the observation that a single pyrimidine dimer is sible for most SOS lesion-targeted mutations in Escherichia coli,by lethal in E. coli strains defective for excision and recombinational catalyzing translesion synthesis (TLS). DNA polymerase II, the repair (16). These experiments were among the first to demon- product of the damage-inducible polB (dinA ) gene plays a pivotal strate the essential contribution of DNA repair to cell survival. role in replication-restart, a process that bypasses DNA damage in Excision and recombination repair pathways are referred to as an error-free manner. Replication-restart takes place almost im- ‘‘error-free’’ because they do not result in an increase in muta- mediately after the DNA is damaged (Ϸ2 min post-UV irradiation), tion rate above spontaneous background levels (1). -
Supplementary Information
Supplementary information (a) (b) Figure S1. Resistant (a) and sensitive (b) gene scores plotted against subsystems involved in cell regulation. The small circles represent the individual hits and the large circles represent the mean of each subsystem. Each individual score signifies the mean of 12 trials – three biological and four technical. The p-value was calculated as a two-tailed t-test and significance was determined using the Benjamini-Hochberg procedure; false discovery rate was selected to be 0.1. Plots constructed using Pathway Tools, Omics Dashboard. Figure S2. Connectivity map displaying the predicted functional associations between the silver-resistant gene hits; disconnected gene hits not shown. The thicknesses of the lines indicate the degree of confidence prediction for the given interaction, based on fusion, co-occurrence, experimental and co-expression data. Figure produced using STRING (version 10.5) and a medium confidence score (approximate probability) of 0.4. Figure S3. Connectivity map displaying the predicted functional associations between the silver-sensitive gene hits; disconnected gene hits not shown. The thicknesses of the lines indicate the degree of confidence prediction for the given interaction, based on fusion, co-occurrence, experimental and co-expression data. Figure produced using STRING (version 10.5) and a medium confidence score (approximate probability) of 0.4. Figure S4. Metabolic overview of the pathways in Escherichia coli. The pathways involved in silver-resistance are coloured according to respective normalized score. Each individual score represents the mean of 12 trials – three biological and four technical. Amino acid – upward pointing triangle, carbohydrate – square, proteins – diamond, purines – vertical ellipse, cofactor – downward pointing triangle, tRNA – tee, and other – circle.