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Annu. Rev Birchem.1991. 60:689-715Copyright©2991by AnnualReviews nc. All rights reserved

RNA POLYMERASE I

Richard A. Young

Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge,Massachusetts 02142andDepartment of Biology, Massachusetts Institute of Technology, Cambridge,Massachuse.tts 02139KEYWORDS:ranscription, mRNAynthesis.

CONTENTS

PERSPECTIVESND UMMARY.............................................................690DEFININGHE NZYME........................................................................691

RNA olymeraseurification .................................................................

691

General roperties..............................................................................

692

TheSubunitProblem............................................................................

692

Molecular rchitectureof RNAPolymerase

.............................................693YEASTNA OLYMERASEI ..................................................................693

ElevenUnique ubunitGenes.................................................................

693

SubunitFeatures ndFunctions..............................................................

695

SubunitStoichiometry ndPhosphorylation................................................

701

Subunit Interactions and RNA olymerase tructure ......................................

702HIGHERUKARYOTICNAPOLYMERASEI ............................................703

Conserved eaturesof SubunitArchitecture ...............................................

703

HighlyConservedubunitSequences........................................................

703THE LARGE UBUNITCARBOXYERMINALOMAIN.............................. 704

Conservedtructure

.............................................................................704

EssentialFunction...............................................................................

706

Evidenceor a Role n Initiation ..............................................................

707

GeneralModelsor CTD unction...........................................................7! 1

ACTIVATIONF RNA OLYMERASEI ....................................................711CONCLUDINGEMARKS.......................................................................7126890066-4154/91/0701-0689502.00

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A n n u . R e v . B i o c h e m . 1 9 9 1 . 6 0 : 6 8 9 - 7 1 5 . D o w n l o a d e d f r o m a r j o u r n a l s . a n n u a l r e v i e w s . o r g b y P o n t i f i c i a U n i v e r s i d a d C a t o l i c a d e C h i l e o n 0 3 / 0 4 / 0 9 . F o r p e r s o n a l u s e o n l y .

690 YOUNGPERSPECTIVES AND SUMMARYThe control of transcription in eukaryotes requires a greater repertoire ofproteins than it does in prokaryotes. In prokaryotes, a single core RNApolymerase enzyme composed of three subunits is responsible for alltranscription. Selective promotor ecognition and other regulatory controls areconferred by the association of one or moreadditional polypeptides with thecore polymerase(1-8). By contrast, eukaryotic cells contain three nuclearDNA-dependentRNA olymerases that transcribe different sets of genes.RNA olymerase I (or A) synthesizes rRNA recursors, RNA olymerase(or B) transcribes pre-mRNA,nd RNA olymerase III (or C) transcribesrRNAand tRNAgenes. The three eukaryotic nuclear RNA olymerases areeach composed f 8-14 polypeptides. Each of these enzymes equires the aidof a variety of additional factors for selective promoter recognition andregulated transcription initiation (9-16). The relative number nd complexityof the eukaryotic RNA olymerases and their transcription factors probablyreflects the need for moreelaborate controls on transcription in eukaryotes.Dramaticprogress has been madeduring the past decade in our understand-ing of the components f the mRNAranscription apparatus that are importantfor regulated transcription initiation. The picture that has developed, inoutline, is one in which RNA olymerase 11 associates with a set of TATA-associated general transcription factors at the promoter; gene-specifictranscription factors bind to upstream elements (enhancers and UpstreamActivating Sequences) and influence the rate of transcription initiation byinteracting with components of the TATA-associated transcription com-plex. The TATA-associated ranscription complex has at least five com-ponents, TFIIA, TFIIB, TFIID, RNA olymerase II, and TFIIE (17, 18,reviewed n 19), and is competent o initiate transcription accurately in vitroin the absence of regulatory factors. Upstream promoter elements and thetranscription factors that bind them are largely responsible for the regula-tion of transcription initiation (10-15). How ignals to begin RNAynthe-sis are transmitted to RNAolymerase I is not yet clear, despite some ecentclues (20-27).Interest in the dialogue between ransciption factors and RNA olymeraseII has stimulated renewed nterest in the polymerase tself. Several excellentreviews address the subject of eukaryotic nuclear RNA olymerases (19,28-32). However, considerable new information has come from recentmolecular genetic analysis of RNA olymeraseII subunit genes isolated froma variety of eukaryotic organisms.This is especially true for yeast, where heisolation of genes encoding all 11 RNA olymerase II subunits is nowcomplete. In addition, new information has recently emergedon the functionof the unusual carboxy terminal repeat domain CTD)of the large subunit.

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A n n u . R e v . B i o c h e m . 1 9 9 1 . 6 0 : 6 8 9 - 7 1 5 . D o w n l o a d e d f r o m a r j o u r n a l s . a n n u a l r e v i e w s . o r g b y P o n t i f i c i a U n i v e r s i d a d C a t o l i c a d e C h i l e o n 0 3 / 0 4 / 0 9 . F o r p e r s o n a l u s e o n l y .

RNAPOLYMERASEI 691The conservation of many features of eukaryotic RNA olymerase IIsubunit structure and function makes the yeast enzymea good model foreukaryotic RNA olymerase II. The picture of RNA olymerase II that hasemerged fl’om molecular genetic analysis of the 11

S. cerevisiae

RNApolymerase I subunits is reviewedherein. Structural and functional studies ofyeast RNAolymerase I genes and their products have revealed that the threelargest subunits are related to the prokaryotic core RNAolymerase ubunitsand are largely responsible for RNA atalysis. Three smaller subunits areessential components hared by all three nuclear RNA olymerases. Twoofthe remaining small subunits form a dissociable subcomplex hat influencesthe efficiency of transcription initiation in vitro. The structure and function ofthe RNA olymerase II large subunit CTD s also reviewed here. Recentevidence ndicates that the CTDs involved n the regulation of transcriptioninitiation.DEFINING THE ENZYME

RNA Polymerase Purification

Three types of DNA-dependent NA olymerases are found in the nucleus ofall eukaryotic cells, each responsible for the synthesis of different classes ofRNA.Roeder & Rutter (33-35) first separated the three mammalian nzymesby DEAE-i~,ephadexhromatography,and named hem I, II, and III accordingto their order of elution by increasing concentrations of ammoniumulfate.RNA olymerase 1 is responsible for transcription of rDNA,RNA olymeraseII transcribes protein-coding genes, and RNA olymerase II transcribes thegenes for small stable RNAs uch as tRNAand 5S rRNA. RNA olymerasesI, II, and III are sometimes also called RNA olymerases A, B, and C,respectively (28, 29).RNA olymerase II has been studied somewhatmore extensively than theother two nuclear RNA olymerases. Columnchromatography has been usedto purify I~’LNA olymerase11 from a large numberof eukaryotes, including

Saccharomyces

(32),

Neurospora

(36),

Acanthamoeba

37),

Dictyostelium

(38),

Physarum

39),

Caenorhabditis

(40),

Drosophila

(41),

Xenopus

(42),mouse 4311, calf thymus 44), human 45), and a variety of plants (46-50).Descriptions of the standard purification methodscan be found in Sentenac(32), and modifications that effectively minimizeproteolysis have been re-ported (44,, 51). Immunologicalmethods have been developed recently thatpermit rapid purification of enzyme hat is highly active in transcriptionassays in vitro (52-54).Multiple chromatographicand electrophoretic forms of RNA olymeraseIIare detected in purified preparations of the enzyme. These various formsgenerally differ in the integrity of the CTDnd in the extent to which he CTD

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A n n u . R e v . B i o c h e m . 1 9 9 1 . 6 0 : 6 8 9 - 7 1 5 . D o w n l o a d e d f r o m a r j o u r n a l s . a n n u a l r e v i e w s . o r g b y P o n t i f i c i a U n i v e r s i d a d C a t o l i c a d e C h i l e o n 0 3 / 0 4 / 0 9 . F o r p e r s o n a l u s e o n l y .

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