Untranslated Regions Regulate the RNA Stability of the Deep-Sea
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Mayr, Annu Rev Genet 2017
GE51CH09-Mayr ARI 12 October 2017 10:21 Annual Review of Genetics Regulation by 3-Untranslated Regions Christine Mayr Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; email: [email protected] Annu. Rev. Genet. 2017. 51:171–94 Keywords First published as a Review in Advance on August noncoding RNA, regulatory RNA, alternative 3-UTRs, alternative 30, 2017 polyadenylation, cotranslational protein complex formation, cellular The Annual Review of Genetics is online at organization, mRNA localization, RNA-binding proteins, cooperativity, genet.annualreviews.org accessibility of regulatory elements https://doi.org/10.1146/annurev-genet-120116- 024704 Abstract Copyright c 2017 by Annual Reviews. 3 -untranslated regions (3 -UTRs) are the noncoding parts of mRNAs. Com- All rights reserved pared to yeast, in humans, median 3-UTR length has expanded approx- imately tenfold alongside an increased generation of alternative 3-UTR isoforms. In contrast, the number of coding genes, as well as coding region length, has remained similar. This suggests an important role for 3-UTRs in the biology of higher organisms. 3-UTRs are best known to regulate ANNUAL REVIEWS Further diverse fates of mRNAs, including degradation, translation, and localiza- Click here to view this article's tion, but they can also function like long noncoding or small RNAs, as has Annu. Rev. Genet. 2017.51:171-194. Downloaded from www.annualreviews.org online features: • Download figures as PPT slides been shown for whole 3 -UTRs as well as for cleaved fragments. Further- • Navigate linked references • Download citations more, 3 -UTRs determine the fate of proteins through the regulation of Access provided by Memorial Sloan-Kettering Cancer Center on 11/30/17. -
Entry of the Membrane-Containing Bacteriophages Into Their Hosts
Entry of the membrane-containing bacteriophages into their hosts - Institute of Biotechnology and Department of Biosciences Division of General Microbiology Faculty of Biosciences and Viikki Graduate School in Molecular Biosciences University of Helsinki ACADEMIC DISSERTATION To be presented for public examination with the permission of the Faculty of Biosciences, University of Helsinki, in the auditorium 3 of Info center Korona, Viikinkaari 11, Helsinki, on June 18th, at 8 a.m. HELSINKI 2010 Supervisor Professor Dennis H. Bamford Department of Biosciences University of Helsinki, Finland Reviewers Professor Martin Romantschuk Department of Ecological and Environmental Sciences University of Helsinki, Finland Professor Mikael Skurnik Department of Bacteriology and Immunology University of Helsinki, Finland Opponent Dr. Alasdair C. Steven Laboratory of Structural Biology Research National Institute of Arthritis and Musculoskeletal and Skin Diseases National Institutes of Health, USA ISBN 978-952-10-6280-3 (paperback) ISBN 978-952-10-6281-0 (PDF) ISSN 1795-7079 Yliopistopaino, Helsinki University Printing House Helsinki 2010 ORIGINAL PUBLICATIONS This thesis is based on the following publications, which are referred to in the text by their roman numerals: I. 6 - Verkhovskaya R, Bamford DH. 2005. Penetration of enveloped double- stranded RNA bacteriophages phi13 and phi6 into Pseudomonas syringae cells. J Virol. 79(8):5017-26. II. Gaidelyt A*, Cvirkait-Krupovi V*, Daugelaviius R, Bamford JK, Bamford DH. 2006. The entry mechanism of membrane-containing phage Bam35 infecting Bacillus thuringiensis. J Bacteriol. 188(16):5925-34. III. Cvirkait-Krupovi V, Krupovi M, Daugelaviius R, Bamford DH. 2010. Calcium ion-dependent entry of the membrane-containing bacteriophage PM2 into Pseudoalteromonas host. -
Interactions of Bacteriophages with Animal and Human Organisms—Safety Issues in the Light of Phage Therapy
International Journal of Molecular Sciences Review Interactions of Bacteriophages with Animal and Human Organisms—Safety Issues in the Light of Phage Therapy Magdalena Podlacha 1 , Łukasz Grabowski 2 , Katarzyna Kosznik-Kaw´snicka 2 , Karolina Zdrojewska 1 , Małgorzata Stasiłoj´c 1 , Grzegorz W˛egrzyn 1 and Alicja W˛egrzyn 2,* 1 Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; [email protected] (M.P.); [email protected] (K.Z.); [email protected] (M.S.); [email protected] (G.W.) 2 Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822 Gdansk, Poland; [email protected] (Ł.G.); [email protected] (K.K.-K.) * Correspondence: [email protected]; Tel.: +48-58-523-6024 Abstract: Bacteriophages are viruses infecting bacterial cells. Since there is a lack of specific receptors for bacteriophages on eukaryotic cells, these viruses were for a long time considered to be neutral to animals and humans. However, studies of recent years provided clear evidence that bacteriophages can interact with eukaryotic cells, significantly influencing the functions of tissues, organs, and systems of mammals, including humans. In this review article, we summarize and discuss recent discoveries in the field of interactions of phages with animal and human organisms. Possibilities of penetration of bacteriophages into eukaryotic cells, tissues, and organs are discussed, and evidence of the effects of phages on functions of the immune system, respiratory system, central nervous system, gastrointestinal system, urinary tract, and reproductive system are presented and discussed. -
Regulation of Translation by the 3' Untranslated Region of Barley Yellow Dwarf Virus-PAV RNA Shanping Wang Iowa State University
Iowa State University Capstones, Theses and Retrospective Theses and Dissertations Dissertations 1996 Regulation of translation by the 3' untranslated region of barley yellow dwarf virus-PAV RNA Shanping Wang Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/rtd Part of the Molecular Biology Commons, and the Plant Pathology Commons Recommended Citation Wang, Shanping, "Regulation of translation by the 3' untranslated region of barley yellow dwarf virus-PAV RNA " (1996). Retrospective Theses and Dissertations. 11426. https://lib.dr.iastate.edu/rtd/11426 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Retrospective Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. INFORMATION TO USERS This manuscript has been reproduced from the microfilm master. UMI films the text directly from the original or copy submitted. Thus, some thesis and dissertation copies are in typewriter face, while others may be from any type of computer printer. The quality of this reproduction is dependent upon the quality of the copy submitted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleedthrough, substandard margins, and improper alignment can adversely afTect reproduction. In the unlikely event that the author did not send UMI a complete manuscript and there are missing pages, these will be noted. Also, if unauthorized copyright material had to be removed, a note will indicate the deletion. Oversize materials (e.g., maps, drawings, charts) are reproduced by sectioning the original, beginning at the upper left-hand comer and continuing from left to right in equal sections with small overlaps. -
Evaluation of the Genomic Diversity of Viruses Infecting Bacteria, Archaea and Eukaryotes Using a Common Bioinformatic Platform: Steps Towards a Unified Taxonomy
RESEARCH ARTICLE Aiewsakun et al., Journal of General Virology 2018;99:1331–1343 DOI 10.1099/jgv.0.001110 Evaluation of the genomic diversity of viruses infecting bacteria, archaea and eukaryotes using a common bioinformatic platform: steps towards a unified taxonomy Pakorn Aiewsakun,1,2 Evelien M. Adriaenssens,3 Rob Lavigne,4 Andrew M. Kropinski5 and Peter Simmonds1,* Abstract Genome Relationship Applied to Virus Taxonomy (GRAViTy) is a genetics-based tool that computes sequence relatedness between viruses. Composite generalized Jaccard (CGJ) distances combine measures of homology between encoded viral genes and similarities in genome organizational features (gene orders and orientations). This scoring framework effectively recapitulates the current, largely morphology and phenotypic-based, family-level classification of eukaryotic viruses. Eukaryotic virus families typically formed monophyletic groups with consistent CGJ distance cut-off dividing between and within family divergence ranges. In the current study, a parallel analysis of prokaryotic virus families revealed quite different sequence relationships, particularly those of tailed phage families (Siphoviridae, Myoviridae and Podoviridae), where members of the same family were generally far more divergent and often not detectably homologous to each other. Analysis of the 20 currently classified prokaryotic virus families indeed split them into 70 separate clusters of tailed phages genetically equivalent to family-level assignments of eukaryotic viruses. It further divided several bacterial (Sphaerolipoviridae, Tectiviridae) and archaeal (Lipothrixviridae) families. We also found that the subfamily-level groupings of tailed phages were generally more consistent with the family assignments of eukaryotic viruses, and this supports ongoing reclassifications, including Spounavirinae and Vi1virus taxa as new virus families. The current study applied a common benchmark with which to compare taxonomies of eukaryotic and prokaryotic viruses. -
ICTV Code Assigned: 2011.001Ag Officers)
This form should be used for all taxonomic proposals. Please complete all those modules that are applicable (and then delete the unwanted sections). For guidance, see the notes written in blue and the separate document “Help with completing a taxonomic proposal” Please try to keep related proposals within a single document; you can copy the modules to create more than one genus within a new family, for example. MODULE 1: TITLE, AUTHORS, etc (to be completed by ICTV Code assigned: 2011.001aG officers) Short title: Change existing virus species names to non-Latinized binomials (e.g. 6 new species in the genus Zetavirus) Modules attached 1 2 3 4 5 (modules 1 and 9 are required) 6 7 8 9 Author(s) with e-mail address(es) of the proposer: Van Regenmortel Marc, [email protected] Burke Donald, [email protected] Calisher Charles, [email protected] Dietzgen Ralf, [email protected] Fauquet Claude, [email protected] Ghabrial Said, [email protected] Jahrling Peter, [email protected] Johnson Karl, [email protected] Holbrook Michael, [email protected] Horzinek Marian, [email protected] Keil Guenther, [email protected] Kuhn Jens, [email protected] Mahy Brian, [email protected] Martelli Giovanni, [email protected] Pringle Craig, [email protected] Rybicki Ed, [email protected] Skern Tim, [email protected] Tesh Robert, [email protected] Wahl-Jensen Victoria, [email protected] Walker Peter, [email protected] Weaver Scott, [email protected] List the ICTV study group(s) that have seen this proposal: A list of study groups and contacts is provided at http://www.ictvonline.org/subcommittees.asp . -
Mechanisms of Mrna Polyadenylation
Turkish Journal of Biology Turk J Biol (2016) 40: 529-538 http://journals.tubitak.gov.tr/biology/ © TÜBİTAK Review Article doi:10.3906/biy-1505-94 Mechanisms of mRNA polyadenylation Hızlan Hıncal AĞUŞ, Ayşe Elif ERSON BENSAN* Department of Biology, Arts and Sciences, Middle East Technical University, Ankara, Turkey Received: 26.05.2015 Accepted/Published Online: 21.08.2015 Final Version: 18.05.2016 Abstract: mRNA 3’-end processing involves the addition of a poly(A) tail based on the recognition of the poly(A) signal and subsequent cleavage of the mRNA at the poly(A) site. Alternative polyadenylation (APA) is emerging as a novel mechanism of gene expression regulation in normal and in disease states. APA results from the recognition of less canonical proximal or distal poly(A) signals leading to changes in the 3’ untranslated region (UTR) lengths and even in some cases changes in the coding sequence of the distal part of the transcript. Consequently, RNA-binding proteins and/or microRNAs may differentially bind to shorter or longer isoforms. These changes may eventually alter the stability, localization, and/or translational efficiency of the mRNAs. Overall, the 3’ UTRs are gaining more attention as they possess a significant posttranscriptional regulation potential guided by APA, microRNAs, and RNA-binding proteins. Here we provide an overview of the recent developments in the APA field in connection with cancer as a potential oncogene activator and/or tumor suppressor silencing mechanism. A better understanding of the extent and significance of APA deregulation will pave the way to possible new developments to utilize the APA machinery and its downstream effects in cancer cells for diagnostic and therapeutic applications. -
MED25670735 Am.Pdf
1 “Big Things in Small Packages: The genetics of filamentous phage and effects on fitness of 2 their host” 3 4 Anne Mai-Prochnow1,#, Janice Gee Kay Hui1, Staffan Kjelleberg1,2, Jasna Rakonjac3, Diane 5 McDougald1,2 and Scott A. Rice1,2* 6 7 1 The Centre for Marine Bio-Innovation and the School of Biotechnology and Biomolecular 8 Sciences, The University of New South Wales Australia 9 2 The Singapore Centre on Environmental Life Sciences Engineering and The School of Biological 10 Sciences, Nanyang Technological University Singapore 11 3 Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand 12 # Present address: CSIRO Materials Science and Engineering, PO Box 218, Lindfield NSW 2070, 13 Australia 14 15 Running head: Filamentous phage and effects on fitness of their host 16 17 Key words: Inoviridae, Inovirus, filamentous phage, M13, Ff, CTX phage, bacteriophage, E. coli, 18 Pseudomonas, Vibrio cholerae, Biotechnology 19 20 One sentence summary: It is becoming increasingly apparent that the genus Inovirus, or 21 filamentous phage, significantly influence bacterial behaviours including virulence, stress 22 adaptation and biofilm formation, demonstrating that these phage exert a significant influence on 23 their bacterial host despite their relatively simple genomes. 24 1 25 Abstract 26 This review synthesises recent and past observations on filamentous phage and describes how these 27 phage contribute to host phentoypes. For example, the CTXφ phage of Vibrio cholerae, encodes 28 the cholera toxin genes, responsible for causing the epidemic disease, cholera. The CTXφ phage 29 can transduce non-toxigenic strains, converting them into toxigenic strains, contributing to the 30 emergence of new pathogenic strains. -
Translation from the 5′ Untranslated Region Shapes the Integrated Stress Response Shelley R
RESEARCH ◥ duce tracer peptides. These translation prod- RESEARCH ARTICLE SUMMARY ucts are processed and loaded onto major histocompatibility complex class I (MHC I) molecules in the ER and transit to the cell STRESS RESPONSE surface, where they can be detected by specific T cell hybridomas that are activated and quan- ′ tified using a colorimetric reagent. 3T provides Translation from the 5 untranslated an approach to interrogate the thousands of predicted uORFs in mammalian genomes, char- region shapes the integrated acterize the importance of uORF biology for regulation, and generate fundamental insights stress response into uORF mutation-based diseases. Shelley R. Starck,* Jordan C. Tsai, Keling Chen, Michael Shodiya, Lei Wang, RESULTS: 3T proved to be a sensitive and Kinnosuke Yahiro, Manuela Martins-Green, Nilabh Shastri,* Peter Walter* robust indicator of uORF expression. We mea- sured uORF expression in the 5′ UTR of INTRODUCTION: Protein synthesis is con- mRNAs, such as ATF4 and CHOP, that harbor mRNAs at multiple distinct regions, while trolled by a plethora of developmental and small upstream open reading frames (uORFs) ◥ simultaneously detecting environmental conditions. One intracellular in their 5′ untranslated regions (5′ UTRs). Still ON OUR WEB SITE expression of the CDS. We signaling network, the integrated stress re- other mRNAs sustain translation despite ISR Read the full article directly measured uORF sponse (ISR), activates one of four kinases in activation. We developed tracing translation at http://dx.doi. peptide expression from response to a variety of distinct stress stimuli: by T cells (3T) as an exquisitely sensitive tech- org/10.1126/ ATF4 mRNA and showed the endoplasmic reticulum (ER)–resident kinase nique to probe the translational dynamics of science.aad3867 that its translation per- ................................................. -
(12) United States Patent (10) Patent No.: US 6,852,907 B1 Padidam Et Al
USOO6852907B1 (12) United States Patent (10) Patent No.: US 6,852,907 B1 Padidam et al. (45) Date of Patent: Feb. 8, 2005 (54) RESISTANCE IN PLANTS TO INFECTION (56) References Cited BY SSDNAVIRUS USING INOVRIDAE PUBLICATIONS VIRUS SSDNA-BINDING PROTEIN, COMPOSITIONS AND METHODS OF USE (Plant Virology, Matthews, R.E.F. 3rd Ed., 1991, Academic Press, San Diego, Calif, p. 424).* (75) Inventors: Malla Padidam, Lansdale, PA (US); Padidam, et al., A phage single-stranded DNA (ssDNA) Roger N. Beachy, St. Louis, MO (US); binding protein complements SSDNA accumulation of a Claude M. Fauquet, Del Mar, CA (US) geminivirus and interferes with viral movement, 1999, J. Virol.., 73(2):1609–1616. 73) AssigSCC Thee Scripps RResearch h Institute,Insti LLa Padidam, et al., Tomato leaf curl geminivirus from India has Jolla, CA (US) a bipartite genome and coat protein is not essential for c: NotiOtice: Subjubject to anyy disclaimer,disclai theh term off thisthi infectivity, 1995, J. Gen. Virol, 76:25-35. patent is extended or adjusted under 35 Horsch, et al., A Simple and general method for transferring genes into plants, 1985, Science, 227: 1229-1231. U.S.C. 154(b) by 0 days. Sanford, et al., Optimizing the biolistic process for different (21) Appl. No.: 09/622,500 biological applications, 1993, Meth. Enzymol., 217:483-509. (22) PCT Filed: Mar. 3, 1999 Bates, Electroporation of plant protoplasts and tissues, 1995, (86) PCT No.: PCT/US99/04716 Meth. Cell Biol., 50:363-373. Timmermans, et al., Geminiviruses and their uses as extra S371 (c)(1), chromosomal replicons, 1994, Annu. -
Gene Expression Regulation by Upstream Open Reading Frames In
Silva J, Fernandes R, Romão L. J Rare Dis Res Treat. (2017) 2(4): 33-38 Journal of www.rarediseasesjournal.com Rare Diseases Research & Treatment Mini review Open Access Gene expression regulation by upstream open reading frames in rare diseases Joana Silva1,2, Rafael Fernandes1,2, and Luísa Romão1,2* 1Department of Human Genetics, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisboa, Portugal 2Gene Expression and Regulation Group, Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal Article Info ABSTRACT Article Notes Upstream open reading frames (uORFs) constitute a class of cis-acting Received: June 19, 2017 elements that regulate translation initiation. Mutations or polymorphisms that Accepted: July 21, 2017 alter, create or disrupt a uORF have been widely associated with several human *Correspondence: disorders, including rare diseases. In this mini-review, we intend to highlight the Dr. Luísa Romão, Department of Human Genetics, Instituto mechanisms associated with the uORF-mediated translational regulation and Nacional de Saúde Doutor Ricardo Jorge, Av. Padre Cruz, describe recent examples of their deregulation in the etiology of human rare 1649-016, Lisboa, Portugal; Tel: (+351) 21 750 8155; Fax: diseases. Additionally, we discuss new insights arising from ribosome profiling (+351) 21 752 6410; studies and reporter assays regarding uORF features and their intrinsic role E-mail: [email protected]. in translational regulation. This type of knowledge is of most importance to © 2017 Romão L. This article is distributed under the terms of design and implement new or improved diagnostic and/or treatment strategies the Creative Commons Attribution 4.0 International License. -
Reviews/0004.1
http://genomebiology.com/2002/3/3/reviews/0004.1 Review Untranslated regions of mRNAs comment Flavio Mignone*, Carmela Gissi*, Sabino Liuni† and Graziano Pesole* Addresses: *Dipartimento di Fisiologia e Biochimica Generali, Università di Milano, Via Celoria, 26, 20133 Milano, Italy. †Centro di Studio sui Mitocondri e Metabolismo Energetico, Via Amendola 166/5, 70126 Bari, Italy. Correspondence: Graziano Pesole. E-mail: [email protected] reviews Published: 28 February 2002 Genome Biology 2002, 3(3):reviews0004.1–0004.10 The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2002/3/3/reviews/0004 © BioMed Central Ltd (Print ISSN 1465-6906; Online ISSN 1465-6914) Abstract reports Gene expression is finely regulated at the post-transcriptional level. Features of the untranslated regions of mRNAs that control their translation, degradation and localization include stem-loop structures, upstream initiation codons and open reading frames, internal ribosome entry sites and various cis-acting elements that are bound by RNA-binding proteins. deposited research The recent analysis of the human genome [1,2] and the data 5? untranslated region (5? UTR), a coding region made up of available about other higher eukaryotic genomes have triplet codons that each encode an amino acid and a 3? revealed that only a small fraction of the genetic material - untranslated region (3? UTR). Figure 1 shows these and about 1.5 % - codes for protein. Indeed, most genomic DNA other features of mRNAs. is