Research Progress in the Molecular Functions of Plant Mterf Proteins
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
Rho Dependent Termination of Transcription in Prokaryotes
Rho Dependent Termination Of Transcription In Prokaryotes Organoleptic Tymon scrimshaws no athenaeums yean fleetly after Teodorico whiled tunably, quite scrawliest. Amalgamative and honeyed Ximenes syllables her bullheads picket stork's-bill and debouch visually. Colory Jeffery concentred her avidity so injudiciously that Sergio briquet very injunctively. Dna in prokaryotic polymerase in termination may vary. Dna sequence by enzymes and fall off of transcripts, and marylène bertrand for the conformation of rho in the stalled rna helicases, rho dependent termination of in transcription. The other physiological functions are the basis for rna polymerase and longer as elongation complex forming a series of one of rho termination in transcription factors recognizing promoters in four steps. Eukaryotes require cookies from prokaryotes, depending on a fifth subunit involved. Thus, when translation termination occurs within same gene it the cause transcriptional termination, preventing expression of downstream genes. Atp synthase alpha and therefore be specialized rnas make a bsr, in termination of rho transcription prokaryotes. Dna must accept cookies and also found later in part because of rho termination occurs by the initiation site that bind to understand how they cannot be logged in replicating dna. Concerned about the Coronavirus? It is made rna polymerase causes rna in termination of rho transcription termination mechanisms to specific genes. Depending upon request your changes indicating that prokaryotic rnap with and prokaryotes. The DNA strand within this an is transcribed by the RNA polymerase. The basic promoter region in prokaryotic transcription is referred to two the Pribnow box. Formation of which prokaryotic and on the hfq is shown as the transcript of action of rho dependent termination transcription in prokaryotes have far more about ten base that elongation complex cell components and cell. -
Resistance to Rifampicin: a Review
The Journal of Antibiotics (2014) 67, 625–630 & 2014 Japan Antibiotics Research Association All rights reserved 0021-8820/14 www.nature.com/ja REVIEW ARTICLE Resistance to rifampicin: a review Beth P Goldstein Resistance to rifampicin (RIF) is a broad subject covering not just the mechanism of clinical resistance, nearly always due to a genetic change in the b subunit of bacterial RNA polymerase (RNAP), but also how studies of resistant polymerases have helped us understand the structure of the enzyme, the intricacies of the transcription process and its role in complex physiological pathways. This review can only scratch the surface of these phenomena. The identification, in strains of Escherichia coli, of the positions within b of the mutations determining resistance is discussed in some detail, as are mutations in organisms that are therapeutic targets of RIF, in particular Mycobacterium tuberculosis. Interestingly, changes in the same three codons of the consensus sequence occur repeatedly in unrelated RIF-resistant (RIFr) clinical isolates of several different bacterial species, and a single mutation predominates in mycobacteria. The utilization of our knowledge of these mutations to develop rapid screening tests for detecting resistance is briefly discussed. Cross-resistance among rifamycins has been a topic of controversy; current thinking is that there is no difference in the susceptibility of RNAP mutants to RIF, rifapentine and rifabutin. Also summarized are intrinsic RIF resistance and other resistance mechanisms. The Journal of Antibiotics (2014) 67, 625–630; doi:10.1038/ja.2014.107; published online 13 August 2014 INTRODUCTION laboratory studies and emerging in patients who received mono- In celebrating the life of Professor Piero Sensi and his discovery of therapy with RIF. -
A Divergent Pumilio Repeat Protein Family for Pre-Rrna Processing and Mrna Localization
A divergent Pumilio repeat protein family for pre-rRNA processing and mRNA localization Chen Qiua, Kathleen L. McCannb, Robert N. Winea, Susan J. Basergab,c,d,1, and Traci M. Tanaka Halla,1 aEpigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709; and Departments of bGenetics, cMolecular Biophysics and Biochemistry, and dTherapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520 Edited by David Baker, University of Washington, Seattle, WA, and approved November 19, 2014 (received for review April 25, 2014) Pumilio/feminization of XX and XO animals (fem)-3 mRNA-binding cell (15). In addition to these functional differences, it is unclear factor (PUF) proteins bind sequence specifically to mRNA targets how these new PUM repeat proteins would interact with target using a single-stranded RNA-binding domain comprising eight RNA. For example, only six PUM repeats are predicted in Puf-A Pumilio (PUM) repeats. PUM repeats have now been identified in and Puf6, and their RNA base-interacting residues are poorly proteins that function in pre-rRNA processing, including human conserved. Puf-A and yeast Puf6. This is a role not previously ascribed to PUF Vertebrate Puf-A functions appear to be important for diseases proteins. Here we present crystal structures of human Puf-A that and embryonic development, but more knowledge is needed to reveal a class of nucleic acid-binding proteins with 11 PUM repeats connect vertebrate morbidities with molecular mechanisms. Human arranged in an “L”-like shape. In contrast to classical PUF proteins, Puf-A changes localization from predominantly nucleolar to nu- Puf-A forms sequence-independent interactions with DNA or RNA, clear when cells are treated with transcriptional or topoisomerase mediated by conserved basic residues. -
Bicyclomycin Sensitivity and Resistance Affect Rho Factor-Mediated Transcription Termination in the Tna Operon of Escherichia Coli
JOURNAL OF BACTERIOLOGY, Aug. 1995, p. 4451–4456 Vol. 177, No. 15 0021-9193/95/$04.0010 Copyright 1995, American Society for Microbiology Bicyclomycin Sensitivity and Resistance Affect Rho Factor-Mediated Transcription Termination in the tna Operon of Escherichia coli CHARLES YANOFSKY* AND VIRGINIA HORN Department of Biological Sciences, Stanford University, Stanford, California 94305-5020 Received 13 March 1995/Accepted 27 May 1995 The growth-inhibiting drug bicyclomycin, known to be an inhibitor of Rho factor activity in Escherichia coli, was shown to increase basal level expression of the tryptophanase (tna) operon and to allow growth of a tryptophan auxotroph on indole. The drug also relieved polarity in the trp operon and permitted growth of a trp double nonsense mutant on indole. Nine bicyclomycin-resistant mutants were isolated and partially characterized. Recombination data and genetic and biochemical complementation analyses suggest that five have mutations that affect rho, three have mutations that affect rpoB, and one has a mutation that affects a third locus, near rpoB. Individual mutants showed decreased, normal, or increased basal-level expression of the tna operon. All but one of the resistant mutants displayed greatly increased tna operon expression when grown in the presence of bicyclomycin. The tna operon of the wild-type drug-sensitive parent was also shown to be highly expressed during growth with noninhibitory concentrations of bicyclomycin. These findings demonstrate that resistance to this drug may be acquired by mutations at any one of three loci, two of which appear to be rho and rpoB. Zwiefka et al. (24) found that the antibiotic bicyclomycin segment and interacts with the transcribing RNA polymerase (bicozamycin), an inhibitor of the growth of several gram- molecule, causing it to terminate transcription (7, 9). -
Mitochondrial Genetics
Mitochondrial genetics Patrick Francis Chinnery and Gavin Hudson* Institute of Genetic Medicine, International Centre for Life, Newcastle University, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK Introduction: In the last 10 years the field of mitochondrial genetics has widened, shifting the focus from rare sporadic, metabolic disease to the effects of mitochondrial DNA (mtDNA) variation in a growing spectrum of human disease. The aim of this review is to guide the reader through some key concepts regarding mitochondria before introducing both classic and emerging mitochondrial disorders. Sources of data: In this article, a review of the current mitochondrial genetics literature was conducted using PubMed (http://www.ncbi.nlm.nih.gov/pubmed/). In addition, this review makes use of a growing number of publically available databases including MITOMAP, a human mitochondrial genome database (www.mitomap.org), the Human DNA polymerase Gamma Mutation Database (http://tools.niehs.nih.gov/polg/) and PhyloTree.org (www.phylotree.org), a repository of global mtDNA variation. Areas of agreement: The disruption in cellular energy, resulting from defects in mtDNA or defects in the nuclear-encoded genes responsible for mitochondrial maintenance, manifests in a growing number of human diseases. Areas of controversy: The exact mechanisms which govern the inheritance of mtDNA are hotly debated. Growing points: Although still in the early stages, the development of in vitro genetic manipulation could see an end to the inheritance of the most severe mtDNA disease. Keywords: mitochondria/genetics/mitochondrial DNA/mitochondrial disease/ mtDNA Accepted: April 16, 2013 Mitochondria *Correspondence address. The mitochondrion is a highly specialized organelle, present in almost all Institute of Genetic Medicine, International eukaryotic cells and principally charged with the production of cellular Centre for Life, Newcastle energy through oxidative phosphorylation (OXPHOS). -
Pathological Ribonuclease H1 Causes R-Loop Depletion and Aberrant DNA Segregation in Mitochondria
Pathological ribonuclease H1 causes R-loop depletion PNAS PLUS and aberrant DNA segregation in mitochondria Gokhan Akmana,1, Radha Desaia,1, Laura J. Baileyb, Takehiro Yasukawab,2, Ilaria Dalla Rosaa, Romina Durigona, J. Bradley Holmesb,c, Chloe F. Mossa, Mara Mennunia, Henry Houldend, Robert J. Crouchc, Michael G. Hannad, Robert D. S. Pitceathlyd,e, Antonella Spinazzolaa,3, and Ian J. Holta,3 aMedical Research Council, Mill Hill Laboratory, London NW7 1AA, United Kingdom; bMedical Research Council Mitochondrial Biology Unit, Cambridge CB1 9SY, United Kingdom; cDivision of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892; dMedical Research Council Centre for Neuromuscular Diseases, University College London Institute of Neurology and National Hospital for Neurology and Neurosurgery, London WC1N 3BG, United Kingdom; and eDepartment of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, United Kingdom Edited by Douglas Koshland, University of California, Berkeley, CA, and approved June 7, 2016 (received for review January 18, 2016) The genetic information in mammalian mitochondrial DNA is densely Results packed; there are no introns and only one sizeable noncoding, or Analysis of RNA hybridized to mtDNA must contend with the control, region containing key cis-elements for its replication and ready degradation of the RNA during extraction (16). Previous expression. Many molecules of mitochondrial DNA bear a third analysis of fragments of mtDNA encompassing the CR dem- strand of DNA, known as “7S DNA,” which forms a displacement onstrated that they included molecules with 7S DNA, as (D-) loop in the control region. -
Termination of RNA Polymerase II Transcription by the 5’-3’ Exonuclease Xrn2
TERMINATION OF RNA POLYMERASE II TRANSCRIPTION BY THE 5’-3’ EXONUCLEASE XRN2 by MICHAEL ANDRES CORTAZAR OSORIO B.S., Universidad del Valle – Colombia, 2011 A thesis submitted to the Faculty of the Graduate School of the University of Colorado in partial fulfillment of the requirements for the degree of Doctor of Philosophy Molecular Biology Program 2018 This thesis for the Doctor of Philosophy degree by Michael Andrés Cortázar Osorio has been approved for the Molecular Biology Program by Mair Churchill, Chair Richard Davis Jay Hesselberth Thomas Blumenthal James Goodrich David Bentley, Advisor Date: Aug 17, 2018 ii Cortázar Osorio, Michael Andrés (Ph.D., Molecular Biology) Termination of RNA polymerase II transcription by the 5’-3’ exonuclease Xrn2 Thesis directed by Professor David L. Bentley ABSTRACT Termination of transcription occurs when RNA polymerase (pol) II dissociates from the DNA template and releases a newly-made mRNA molecule. Interestingly, an active debate fueled by conflicting reports over the last three decades is still open on which of the two main models of termination of RNA polymerase II transcription does in fact operate at 3’ ends of genes. The torpedo model indicates that the 5’-3’ exonuclease Xrn2 targets the nascent transcript for degradation after cleavage at the polyA site and chases pol II for termination. In contrast, the allosteric model asserts that transcription through the polyA signal induces a conformational change of the elongation complex and converts it into a termination-competent complex. In this thesis, I propose a unified allosteric-torpedo mechanism. Consistent with a polyA site-dependent conformational change of the elongation complex, I found that pol II transitions at the polyA site into a mode of slow transcription elongation that is accompanied by loss of Spt5 phosphorylation in the elongation complex. -
3-End Formation of Baculovirus Late Rnas
JOURNAL OF VIROLOGY, Oct. 2000, p. 8930–8937 Vol. 74, No. 19 0022-538X/00/$04.00ϩ0 Copyright © 2000, American Society for Microbiology. All Rights Reserved. 3Ј-End Formation of Baculovirus Late RNAs 1 1,2 JIANPING JIN AND LINDA A. GUARINO * Departments of Biochemistry and Biophysics1 and Entomology,2 Texas A&M University, College Station, Texas 77843-2128 Received 13 March 2000/Accepted 30 June 2000 Baculovirus late RNAs are transcribed by a four-subunit RNA polymerase that is virus encoded. The late viral mRNAs are capped and polyadenylated, and we have previously shown that capping is mediated by the LEF-4 subunit of baculovirus RNA polymerase. Here we report studies undertaken to determine the mecha- Downloaded from nism of 3-end formation. A globin cleavage/polyadenylation signal, which was previously shown to direct 3-end formation of viral RNAs in vivo, was cloned into a baculovirus transcription template. In vitro assays with purified baculovirus RNA polymerase revealed that 3 ends were formed not by a cleavage mechanism but rather by termination after transcription of a T-rich region of the globin sequence. Terminated RNAs were released from ternary complexes and were subsequently polyadenylated. Mutational analyses indicated that the T-rich sequence was essential for termination and polyadenylation, but the poly(A) signal and the GT-rich region of the globin polyadenylation/cleavage signal were not required. Termination was not dependent on ATP hydrolysis, indicating a slippage mechanism. http://jvi.asm.org/ mRNA 3Ј-end formation is a complicated process that re- promoters used for overexpression in baculovirus vectors be- quires protein-nucleic acid and protein-protein interactions. -
Regulatory Interplay Between Small Rnas and Transcription Termination Factor Rho Lionello Bossi, Nara Figueroa-Bossi, Philippe Bouloc, Marc Boudvillain
Regulatory interplay between small RNAs and transcription termination factor Rho Lionello Bossi, Nara Figueroa-Bossi, Philippe Bouloc, Marc Boudvillain To cite this version: Lionello Bossi, Nara Figueroa-Bossi, Philippe Bouloc, Marc Boudvillain. Regulatory interplay be- tween small RNAs and transcription termination factor Rho. Biochimica et Biophysica Acta - Gene Regulatory Mechanisms , Elsevier, 2020, pp.194546. 10.1016/j.bbagrm.2020.194546. hal-02533337 HAL Id: hal-02533337 https://hal.archives-ouvertes.fr/hal-02533337 Submitted on 6 Nov 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Regulatory interplay between small RNAs and transcription termination factor Rho Lionello Bossia*, Nara Figueroa-Bossia, Philippe Bouloca and Marc Boudvillainb a Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France b Centre de Biophysique Moléculaire, CNRS UPR4301, rue Charles Sadron, 45071 Orléans cedex 2, France * Corresponding author: [email protected] Highlights Repression -
Characterizing Genomic Duplication in Autism Spectrum Disorder by Edward James Higginbotham a Thesis Submitted in Conformity
Characterizing Genomic Duplication in Autism Spectrum Disorder by Edward James Higginbotham A thesis submitted in conformity with the requirements for the degree of Master of Science Graduate Department of Molecular Genetics University of Toronto © Copyright by Edward James Higginbotham 2020 i Abstract Characterizing Genomic Duplication in Autism Spectrum Disorder Edward James Higginbotham Master of Science Graduate Department of Molecular Genetics University of Toronto 2020 Duplication, the gain of additional copies of genomic material relative to its ancestral diploid state is yet to achieve full appreciation for its role in human traits and disease. Challenges include accurately genotyping, annotating, and characterizing the properties of duplications, and resolving duplication mechanisms. Whole genome sequencing, in principle, should enable accurate detection of duplications in a single experiment. This thesis makes use of the technology to catalogue disease relevant duplications in the genomes of 2,739 individuals with Autism Spectrum Disorder (ASD) who enrolled in the Autism Speaks MSSNG Project. Fine-mapping the breakpoint junctions of 259 ASD-relevant duplications identified 34 (13.1%) variants with complex genomic structures as well as tandem (193/259, 74.5%) and NAHR- mediated (6/259, 2.3%) duplications. As whole genome sequencing-based studies expand in scale and reach, a continued focus on generating high-quality, standardized duplication data will be prerequisite to addressing their associated biological mechanisms. ii Acknowledgements I thank Dr. Stephen Scherer for his leadership par excellence, his generosity, and for giving me a chance. I am grateful for his investment and the opportunities afforded me, from which I have learned and benefited. I would next thank Drs. -
Structure of the Essential MTERF4:NSUN4 Protein Complex Reveals How an MTERF Protein Collaborates to Facilitate Rrna Modification
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Structure Article Structure of the Essential MTERF4:NSUN4 Protein Complex Reveals How an MTERF Protein Collaborates to Facilitate rRNA Modification Elena Yakubovskaya,1,2 Kip E. Guja,1,2 Edison Mejia,1,2 Steven Castano,1 Elena Hambardjieva,1 Woo Suk Choi,1 and Miguel Garcia-Diaz1,* 1Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA 2These authors contributed equally to this work *Correspondence: [email protected] http://dx.doi.org/10.1016/j.str.2012.08.027 SUMMARY nizes a sequence in the mitochondrial tRNA-Leu(UUR) gene, which is downstream and adjacent to the 16S rRNA gene MTERF4 is the first MTERF family member shown to and promotes bidirectional transcriptional termination (Asin- bind RNA and plays an essential role as a regulator of Cayuela et al., 2005; Yakubovskaya et al., 2010). MTERF2 and ribosomal biogenesis in mammalian mitochondria. It MTERF3 have been proposed to associate with mitochondrial forms a complex with the rRNA methyltransferase DNA in a nonsequence-specific manner and regulate mtDNA NSUN4 and recruits it to the large ribosomal subunit. transcription (Park et al., 2007; Roberti et al., 2009; Wenz In this article, we characterize the interaction et al., 2009). Recently, crystal structures of MTERF1 (Jime´ nez-Mene´ ndez between both proteins, demonstrate that MTERF4 et al., 2010; Yakubovskaya et al., 2010) and MTERF3 (Spa˚ hr strongly stimulates the specificity of NSUN4 during et al., 2010) have revealed that these proteins share a unique in vitro methylation experiments, and present the superhelical fold.