Identification and Characterization of a New Transcriptional Termination

Total Page:16

File Type:pdf, Size:1020Kb

Identification and Characterization of a New Transcriptional Termination Proc. Nati. Acad. Sci. USA Vol. 81, pp. 7373-7377, December 1984 Biochemistry Identification and characterization of a new transcriptional termination factor from Escherichia coli (tau factor/T7 phage terminator/RNA polymerase) JEAN-FRANCOIS BRIAT AND MICHAEL J. CHAMBERLIN Department of Biochemistry, University of California, Berkeley, CA 94720 Communicated by H. A. Barker, August 9, 1984 ABSTRACT We have identified and partially purified an stem with a four-base loop (ref. 7; see below). Termination at activity from Escherichia coli that enhances transcription ter- this site is not affected by rho mutations (9) and is not com- mination at the bacteriophage T7 early terminator when pletely efficient in vivo (9) or in vitro (10). It has been found cloned on the plasmid pAR1707. The factor also causes the that about 50% of T7 RNA chains terminate in vitro at T7 transcript to be terminated at a site several nucleotides earlier nucleotide 7588 ending in a 3' OH cytidine, while the remain- than in its absence. The resulting 3' OH ends of the transcripts der terminate at the adjacent guanosine residue (11), al- are identical to those found in vivo by S1 nuclease mapping. though other sequences have been reported (12). We show From this we conclude that the factor we have identified is here that the efficiency of in vitro termination at Te is en- probably responsible for determination of the 3' OH ends of hanced by an E. coli protein factor that shifts the 3' OH ter- T7 RNA transcripts in vivo. This factor does not act by pro- minus four bases, to a site coincident with that found for cessing a preformed RNA transcript, nor is it replaced by rho termination in vivo. protein or nusA or nusB proteins. Therefore, it appears to be a new transcription termination factor, and we have designated it "tau factor." Elucidation of its role in transcription in E. MATERIALS AND METHODS coli will depend on its purification to homogeneity and further studies of its properties. Materials. Nucleoside triphosphates were purchased from P-L Biochemicals. [a-32P]CTP was prepared as described by Control of cell growth and gene expression in bacterial cells Symons (13). DEAE-cellulose (DE-52) was from Whatman. is achieved mainly at the level of transcription. While regula- Heparin-agarose was prepared as described by Davison et tion can take place at any step in the transcription process, al. (14). E. coli RNA polymerase holoenzyme was purified much attention has focused recently on the steps of elonga- as described by Burgess and Jendrisak (15) as modified by tion and termination (1-4). Regulation of these processes by Gonzales et al. (16). The plasmid pAR1707 (Fig. 1) was gen- attenuation and antitermination plays a major role in bacteri- erously provided by W. F. Studier (Brookhaven National al systems, yet many of the components and mechanisms are Laboratory). not yet well understood. pAR1707 DNA was prepared by using the boiling proce- Termination of bacterial transcription is believed to in- dure described by Holmes and Quigley (17) and purified by volve a specific signal that stops elongation by RNA poly- two successive CsCl gradient centrifugations. pAR1707 merase and then allows release of the nascent RNA chain. DNA was used as in vitro template after digestion with Sal I, The bacterial transcription termination signals that have heat inactivation of restriction endonuclease for 10 min at been studied thus far generally include a potential stem-loop 70'C, and precipitation with ethanol. Restriction enzyme-di- structure in the RNA just upstream of the 3' OH terminus of gested DNA was resuspended in 10 mM Tris HCl, pH 8.0/1 the completed RNA chain. They commonly have been clas- mM EDTA to a concentration of 1 mg/ml. sified as "rho independent" or "rho dependent," depending The probe for S1 nuclease mapping was prepared from a on whether efficient termination occurs in vitro with purified 448-bp BamHI-Sal I DNA fragment (see Fig. 1) purified by Escherichia coli RNA polymerase alone or only in the pres- polyacrylamide gel electrophoresis and eluted as described ence of the termination factor rho (1). This classification is by Maxam and Gilbert (18). The 3' end of the BamHI site not sharply drawn; some rho-independent termination sites was labeled by using [a-32P]dGTP (3000 Ci/mmol, ICN; 1 Ci are enhanced when rho protein is added in vitro (5) and ter- = 37 GBq) and the large Klenow fragment (New England mination in vivo is reduced by rho mutations at some sites Biolabs) following the procedure of Smith et al. (19). Strand that do not respond to rho protein in vitro (6). In addition, it separation and sequencing of the probe were carried out as appears that termination at some sites requires the nusA pro- described by Maxam and Gilbert (18). tein (7), which may play a role in both elongation and termi- RNA Preparation and Assay of tau Factor Activity. In vitro nation (8). Finally, there is at least one site-the T3 phage RNA synthesis was carried out in a reaction mixture (50 Al) early terminator-that is highly efficient in vivo, but not in containing 40 mM Tris-HCl (pH 8.0); 10 mM 2-mercapto- vitro, and that is unaffected by rho mutations (9) or by nusA ethanol; 10 mM MgCI2; bovine serum albumin at 0.1 mg/ml; protein (unpublished observations), which has led to the sug- 0.4 mM each of GTP, UTP, ATP, and [a-32P]CTP (500-1000 gestion that other termination factors may exist. cpm/pmol); E. coli RNA polymerase holoenzyme at 40 One of the most studied rho-independent terminators is gg/ml; and Sal I-digested pAR1707 DNA at 20 ,ug/ml. When the early terminator (Te) of phage T7. This site maps at about appropriate, extract was added at a final concentration of 1.8 19% on the phage genome and consists of an 8-base-pair (bp) mg/ml to replace the purified RNA polymerase. The assay for termination factor activity during its partial purification The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" Abbreviations: bp, base pair(s); nt, nucleotide(s); PA, and Te, early in accordance with 18 U.S.C. §1734 solely to indicate this fact. promoter Al and early terminator of phage T7. 7373 Downloaded by guest on September 27, 2021 7374 Biochemistry: Briat and Chamberlin Proc. NatL Acad ScL USA 81 (1984) was carried out by adding 4 pl of each fraction to a 25-jil orl reaction mixture containing purified E. coli RNA polymer- ase as described above. After 10 min at 370C, heparin was added (final concentration, 100 pug/ml) to block reinitiation of RNA chains, and incubation was continued for 10 min at 370C to allow full runoff of elongating transcripts. Then RNA transcripts were extracted with phenol as described by Kingston and Chamberlin (20) except that stop mix was add- ed prior to phenol extraction. Analysis of RNAs was per- formed on 5% polyacrylamide/7 M urea gels or on high-reso- lution 8% polyacrylamide/7 M urea gels as described by Kingston and Chamberlin (20). Gels were dried and autora- diographed with Kodak XAR5 films. In vivo RNAs were prepared as described by Gilman and Chamberlin (21). The assay we have used for tau factor is only semiquanti- tative. As increasing amounts of partially purified factor are added to the reaction, there is first a reduction in the size of the 160-nucleotide (nt) terminated transcript, followed at higher concentrations by a progressive reduction in the yield Sall HI of read-through transcript. We have used the latter effect to measure activity, since it is difficult to measure the amount of each of the shorter transcripts. A "unit" of tau activity is that amount needed to reduce the yield of 502-nt read- through transcript by about 50%. In some cases we simply estimate tau activity by the percentage yield of read-through transcript, which varies from 35% (no tau) to 0% (excess FIG. 1. Transcription map of pAR1707. pAR1707 was construct- tau). ed by ligation of a 286-bp HindII fragment and of a 142-bp Fnu IV Protein concentrations were determined by using the Hi fragment from T7 DNA containing, respectively, the Al promot- Bradford method (22) with bovine serum albumin as stan- er PA, and the early terminator Te in the BamHI (HI) site of pBR322 dard. by using a BamHI linker (24). Black segments of map are T7 se- S1 Nuclease Mapping. S1 nuclease mapping experiments quences; white and shaded segments are pBR322 and linker se- were performed as described by Gilman and Chamberlin quences. Sizes (160 and 502) are shown in nt. (21). Preparation of Cell Extracts. E. coli fraction 1 extracts (su- Transcription of DNA from this plasmid in vitro by purified pernatants at 200,000 x g) were prepared from the following E. coli RNA polymerase holoenzyme gave predominantly a E. coli strains: DG156 (RNaseI-), BL107 (RNaseI-, RN- mixture of 160- and 161-nt transcripts, read from PA1 to Te, aseIII-), W3110 psu+ (lacZ4118, trpR, trpE4829, trpA4761), together with some read-through (Fig. 2, track H). This read- W3110 psu4; a procedure similar to that described by Fuller through could be visualized as a 502-nt transcript when the et al. (23) as modified by Reynolds and Chamberlin (unpub- DNA was cleaved with restriction endopuclease Sal I before lished data) was used. transcription (Fig. 2). About 35% read-through was found in Fractionation of tau Factor.
Recommended publications
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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).
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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
    [Show full text]
  • Sral Srna Interaction Regulates the Terminator by Preventing Premature Transcription Termination of Rho Mrna
    SraL sRNA interaction regulates the terminator by preventing premature transcription termination of rho mRNA Inês Jesus Silvaa,1, Susana Barahonaa,2, Alex Eyraudb,2, David Lalaounab, Nara Figueroa-Bossic, Eric Masséb, and Cecília Maria Arraianoa,1 aInstituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal; bRNA Group, Department of Biochemistry, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada; and cInstitute for Integrative Biology of the Cell (I2BC), Commissariat à l’énergie atomique, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France Edited by Tina M. Henkin, The Ohio State University, Columbus, OH, and approved December 28, 2018 (received for review July 5, 2018) Transcription termination is a critical step in the control of gene sequence, leading to changes in translation and/or mRNA degra- expression. One of the major termination mechanisms is mediated dation (9–11). However, distinct mechanisms of action have been by Rho factor that dissociates the complex mRNA-DNA-RNA poly- increasingly reported in the literature (11). For instance, the Sal- merase upon binding with RNA polymerase. Rho promotes termina- monella sRNA ChiX was shown to induce premature transcription tion at the end of operons, but it can also terminate transcription termination within the coding sequence of chiP as a result of its within leader regions, performing regulatory functions and avoiding interaction with 5′-UTR of the operon chiPQ, thus affecting the pervasive transcription. Transcription of rho is autoregulated through expression of both genes of the operon (12). Conversely, it was a Rho-dependent attenuation in the leader region of the transcript.
    [Show full text]
  • Transcription Termination by Nuclear RNA Polymerases
    Downloaded from genesdev.cshlp.org on September 23, 2021 - Published by Cold Spring Harbor Laboratory Press REVIEW Transcription termination by nuclear RNA polymerases Patricia Richard and James L. Manley1 Department of Biological Sciences, Columbia University, New York, New York 10027, USA Gene transcription in the cell nucleus is a complex and few base pairs to several kilobases downstream from the highly regulated process. Transcription in eukaryotes 39-end of the mature RNA (Proudfoot 1989). RNAPII requires three distinct RNA polymerases, each of which transcription termination is coupled to 39-end processing employs its own mechanisms for initiation, elongation, of the pre-mRNA (Birse et al. 1998; Hirose and Manley and termination. Termination mechanisms vary consid- 2000; Yonaha and Proudfoot 2000; Proudfoot 2004; erably, ranging from relatively simple to exceptionally Buratowski 2005), and an intact polyadenylation signal complex. In this review, we describe the present state of has long been known to be necessary for transcription knowledge on how each of the three RNA polymerases termination of protein-coding genes in human and yeast terminates and how mechanisms are conserved, or vary, cells (Whitelaw and Proudfoot 1986; Logan et al. 1987; from yeast to human. Connelly and Manley 1988). RNAPIII and RNAPI termination appear simpler than Transcription in eukaryotes is performed by three RNA RNAPII termination. RNAPIII terminates transcription polymerases, which are functionally and structurally at T-rich sequences located a short distance from the related (Cramer et al. 2008). RNA polymerase II (RNAPII) mature RNA 39-end and seems to involve at most a is responsible for transcription of protein-coding genes limited number of auxiliary factors (Cozzarelli et al.
    [Show full text]
  • Different Phosphoisoforms of RNA Polymerase II Engage the Rtt103 Termination Factor in a Structurally Analogous Manner
    Different phosphoisoforms of RNA polymerase II PNAS PLUS engage the Rtt103 termination factor in a structurally analogous manner Corey M. Nemeca, Fan Yangb, Joshua M. Gilmorec, Corinna Hintermaird, Yi-Hsuan Hoe,1, Sandra C. Tsenga, Martin Heidemannd, Ying Zhangc, Laurence Florensc, Audrey P. Gasche,f, Dirk Eickd, Michael P. Washburnc,g, Gabriele Varanib, and Aseem Z. Ansaria,f,2 aDepartment of Biochemistry, University of Wisconsin–Madison, Madison, WI 53706; bDepartment of Chemistry, University of Washington, Seattle, WA 98195; cStowers Institute for Medical Research, Kansas City, MO 64110; dDepartment of Molecular Epigenetics, Helmholtz Center Munich, Center for Integrated Protein Science, 81377 Munich, Germany; eLaboratory of Genetics, University of Wisconsin–Madison, Madison, WI 53706; fGenome Center of Wisconsin, University of Wisconsin–Madison, Madison, WI 53706; and gDepartment of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66150 Edited by Alan G. Hinnebusch, National Institutes of Health, Bethesda, MD, and approved April 10, 2017 (received for review January 3, 2017) The carboxyl-terminal domain (CTD) of the largest subunit of RNA Previous studies suggest that pThr4 has roles in transcriptional polymerase II (Pol II) orchestrates dynamic recruitment of specific elongation, 3ʹ-end processing, and termination (12–14,18).Our cellular machines during different stages of transcription. Signature data, as well as other recent studies, suggest that CTD bearing phosphorylation patterns of Y1S2P3T4S5P6S7 heptapeptide repeats of pThr4 is bound by Rtt103 (16, 18), a well-known component of the the CTD engage specific “readers.” Whereas phospho-Ser5 and phos- Rat1 exosome that is thought to play a role in transcription ter- pho-Ser2 marks are ubiquitous, phospho-Thr4 is reported to only mination of protein-coding genes.
    [Show full text]
  • Unravelling the Means to an End: RNA Polymerase II Transcription Termination
    REVIEWS Unravelling the means to an end: RNA polymerase II transcription termination Jason N. Kuehner, Erika L. Pearson and Claire Moore Abstract | The pervasiveness of RNA synthesis in eukaryotes is largely the result of RNA polymerase II (Pol II)‑mediated transcription, and termination of its activity is necessary to partition the genome and maintain the proper expression of neighbouring genes. Despite its ever-increasing biological significance, transcription termination remains one of the least understood processes in gene expression. However, recent mechanistic studies have revealed a striking convergence among several overlapping models of termination, including the poly(A)- and Sen1‑dependent pathways, as well as new insights into the specificity of Pol II termination among its diverse gene targets. Broader knowledge of the role of Pol II carboxy‑terminal domain phosphorylation in promoting alternative mechanisms of termination has also been gained. Cryptic unstable transcripts Regulation of gene expression, which is essential for Transcription termination serves many vital func- Non-coding RNAs norma­l cellular development and homeostasis, often tions in the cell. For example, it prevents Pol II from (~200–600 nucleotides long) occurs at the level of transcription. In eukaryotes, nuclear interfering with downstream DNA elements, such as discovered in yeast that are RNA polymerase II (Pol II) is responsible for synthe- promoters, and promotes polymerase recycling4–6. typically transcribed from intergenic regions of the sizing all protein-coding RNAs and most non-coding Contrary to being limited to a constitutive process at genome (such as promoters) RNAs, including small nuclear RNAs (snRNAs), small the end of a gene, transcription termination is dynamic and are rapidly degraded nucleolar RNAs (snoRNAs), microRNAs (mi­RNAs), and can occur upstream, downstream and within open by the exosome.
    [Show full text]
  • Research Progress in the Molecular Functions of Plant Mterf Proteins
    cells Review Research Progress in the Molecular Functions of Plant mTERF Proteins Pedro Robles and Víctor Quesada * Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain; [email protected] * Correspondence: [email protected]; Tel.: +34-(96)-6658812; Fax: +34-96-665-85-11 Abstract: Present-day chloroplast and mitochondrial genomes contain only a few dozen genes in- volved in ATP synthesis, photosynthesis, and gene expression. The proteins encoded by these genes are only a small fraction of the many hundreds of proteins that act in chloroplasts and mitochondria. Hence, the vast majority, including components of organellar gene expression (OGE) machineries, are encoded by nuclear genes, translated into the cytosol and imported to these organelles. Consequently, the expression of nuclear and organellar genomes has to be very precisely coordinated. Furthermore, OGE regulation is crucial to chloroplast and mitochondria biogenesis, and hence, to plant growth and development. Notwithstanding, the molecular mechanisms governing OGE are still poorly under- stood. Recent results have revealed the increasing importance of nuclear-encoded modular proteins capable of binding nucleic acids and regulating OGE. Mitochondrial transcription termination factor (mTERF) proteins are a good example of this category of OGE regulators. Plant mTERFs are located in chloroplasts and/or mitochondria, and have been characterized mainly from the isolation and analyses of Arabidopsis and maize mutants. These studies have revealed their fundamental roles in different plant development aspects and responses to abiotic stress. Fourteen mTERFs have been hitherto characterized in land plants, albeit to a different extent. These numbers are limited if we consider that 31 and 35 mTERFs have been, respectively, identified in maize and Arabidopsis.
    [Show full text]
  • The Functions of the RNA Polymerase II CTD in Transcription and RNA Processing
    The functions of the RNA polymerase II CTD in transcription and RNA processing Jing-Ping Hsin Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2013 © 2013 Jing-Ping Hsin All rights reserved Abstract The functions of the RNA polymerase II CTD in transcription and RNA processing Jing-Ping Hsin RNA polymerase II (RNAP II), transcribing messenger RNAs (mRNAs), small nuclear RNAs (snRNAs), and non-coding RNAs (ncRNAs), is composed of 12 subunits. Rpb1, the largest subunit with catalytic polymerase activity, possesses a unique c-terminal domain (CTD) that consists of tandem heptad repeats with the consensus sequence of Tyr-Ser-Pro-Thr-Ser-Pro-Ser (Y1S2P3T4S5P6S7). Somewhat reflecting the complexity of the organism, the number of repeats varies, from 26 in yeast to 52 in vertebrates. The CTD, intensively phosphorylated during transcription, serves a means to coordinate transcription and RNA processing- capping, splicing, and 3’ end formation. For example, Ser 5, phosphorylated in the start of transcription, promotes the recruitment of capping enzyme, and Ser 2 phosphorylation facilitates RNA 3’ end formation and transcription termination by acting as a landing pad for Pcf11. Detailed introduction is described in Chapter 1. Because of the importance of the CTD in these events, I created an Rpb1 conditional knock-out DT40 cell line (DT40-Rpb1) to further study the CTD with an initial focus on Thr 4, the function of which was unclear. Using DT40-Rpb1 system, we found that Thr 4 was phosphorylated in yeast, fly, chicken, and human cells, and cyclin-dependent kinase (CDK9) was likely the kinase to carry out this phosphorylation.
    [Show full text]