MOLECULAR BIOLOGY (BMB-414)

SEMINAR ON :EUKARYOTIC TRANSCRIPTIONSEMINAR BY :SASWAT KUMAR MOHANTYMSc BMB 2ND SEM. REG.NO. : 14368037

DIFFERENT TYPES OF RNA POLYMERASE

3 TYPES OF RNA POLYMERASE

1. RNA POLYMERASE -I

2. RNA POLYMERASE -II

3. RNA POLYMERASE –III

ALL ARE DISTINCT COMPLEXS BUT HAVE CERTAIN SUBUNIT IN COMMON

EACH POLYMERASE HAS SPECIFIC FUNCTION

RNA POLYERASE- IRESIDES IN THE NUCLEOLUS

SYNTHESIZED- 28srRNA , 18srRNA & 5.8srRNA

CONTAIN 14 SUBUNITS

RNA POLYMERASE : IIFOUND IN NUCLEOPLASM

SYNTHESIZES PRECURSORS TO MESSENGER RNA

ALSO SYNTHESIZES SMALL NUCLEOLAR RNA

CONTAINS 12 SUBUNITS

RNA POLYMERASE: IIIFOUND IN NUCLEOPLASM

SYNTHESIZES TRANSFER RNA, 5SrRNA

CONTAIN 17 SUBUNITS

TRANSCRIPTIONPROTEIN

NO. OF SUBUNITS

FUNCTION

POL : II 12 CATALYZES RNA SYNTHESIS

TBP 1 SPECIFICALLY RECOGNIZES THE TATA BOX

TFIIA 3 STABILIZES BINDING OF TFIIB AND TBPNTO THE PROMOTER

TFIIB 1 BINDS TO TBP, RECRUITS POLII-TFIIF COMPLEX

TFIIE 2 RECRUITS TFIIH, HAS ATPase AND HELICASE ACTIVITIES

TFIIF 2 BINDS TIGHTLY TO POL II, BINDS TO TFIIB & PREVENTS BINDING OF POL II TO NONSPECIFIC DNA SEQUENCE

TFIIH 12 UNWIND DNA AT PROMOTORPHOSPHORYLASE POLII WITHIN CTD

ELLPTEFBTFIIS

PHOSPHORYLATES POLII WITHIN CTD

THREE CLASSES OF PROMOTERS ARE FOUND IN EUKARYOTIC NUCLEAR GENES, ONE FOR EACH TYPE OF RNA POLYMERASEPRMOTER FOR RNA POL. I

PRODUCE PRECURSOR FOR 3 LARGEST RIBOSOMAL RNA

THREE CLASSES OF PROMOTERS ARE FOUND IN EUKARYOTIC NUCLEAR GENES, ONE FOR EACH TYPE OF RNA POLYMERASEPRMOTER FOR RNA POL. II

TATA DRIVEN PROMOTERDPE DRIVEN PROMOTER

THREE CLASSES OF PROMOTERS ARE FOUND IN EUKARYOTIC NUCLEAR GENES, ONE FOR EACH TYPE OF RNA POLYMERASERNA POLYMERASE III

RNA POLYMERASE II FORMS A PRE-INITIATION COMPLEX WITH GENERAL TRANSCRIPTION AT THE PROMOTER

RNA POLYMERASE II FORMS A PRE-INITIATION COMPLEX WITH GENERAL TRANSCRIPTION AT THE PROMOTER

RNA POLYMERASE II FORMS A PRE-INITIATION COMPLEX WITH GENERAL TRANSCRIPTION AT THE PROMOTER

RNA POLYMERASE II FORMS A PRE-INITIATION COMPLEX WITH GENERAL TRANSCRIPTION AT THE PROMOTER

ABORTIVE INITIATION1.FORMATION OF RNA POL. – PROMOTER COMPLEX

2.RNA POL. UNWINDS 1 TURN OF DNA SRROUNDING THE TRANSCRIPTION STATRT SITE TO YIELD AN RNA POL- PROMOTER OPENCOMPLEX

3.RNA POL ENTERS IN TO ABORTIVE CYCLE---- RELEASE SHORT RNA PRODUCT ( 10 NUCLEOTIDE)

4.RNA POL ESCAPE THE PROMOTER & ENTERS IN TO ELONGATION STEP OF TRANSCRIPTION

DNA SCRUNCHING

PROMOTER CLEARANCE TRANSCRIPT ATTAINS THE THRESHOLD LENGTH OF 10 NUCLEOTIDE, IT ENTERS THE

RNA EXIT CHANNEL

RNA POL BREAKS IT INTERACTIONS WITH THE PROMOTER ELEMENTS AND ANY REGULATORY PROTEINS ASSOCIATED WITH THE INITIATION COMLEX THAT IT NO LONGER NEEDS.

CTD OF POL II CONTAINS SERIES OF REPEAT OF THE HEPTADE SEQUENCE --- Tyr-Ser-Pro-Thr-Ser-Pro-Ser.

EACH SITE CONTAINS SITES FOR PHOSPHORYLATION BY SPECIFIC KINASES INCLUDING 1 i.e A SUBUNIT OF TFIIH

CDK9, WHICH IS A PART OF THE COMPLEX pTEFb (POSITIVE TRANSCRIPTION ELONGATION FACTOR b ) PHOSPHORYLATES CTD, PRIMARILY ON THE Ser RESIDUE OF THE CTD REPEAT SEQUENCE.

ELONGATIONRNA POL MOVES ALONG THE DNA AND MAKES A RNA COPY OF

DNA TEMPLET STRAND .

FOR EVERY DNA BASE PAIR SEPARATED BY THE ADVANCING POLYMERASE , ONE HYBRID RNA:DNA BASE PAIR IS IMMEDIATELY FORMED

DNA STRANDS AND NASCENT RNA CHAIN EXIT FROM SEPARATE CHANNELS.

2 DNA STRANDS REUNIT AT THE TRAILING END OF THE TANSCRIPTION BUBBLE WHILE SINGLE STRAND RNA EMERGES ALONE

ELONGATION CONTINUE..ELONGATION FACTORPTEFb – PHOSPHORYLATES 2ND RESIDEUE Ser OF CTD REPEATS OF

BOUND POL II

PTEFb ALSO PHOSPHORYLATES AND ACTIVATES SPT5 AND TAT-SF1.

SPT5- UNIVERSAL TRANSCRIPTION FACTOR HELPS RECRUIT 5’-CAPPING ENZYME TO POL II & CTD PHOSPHORYLATES AT Ser-5

TAT-SF1 RECRUITS COMPONENTS OF THE RNA SPLICING MACHINARY TO THE Ser-2 PHOSPORYLATED CTD.

PAUSING, POISING & BACKTRACKING

PAUSING IS MEDIATED BY A COMPLEX CALLED

NELF(NEGATIVE ELONGATION FACTOR) IN

COLLABORATION WITH DSIF ( DRB SENSITIVE INDUCING FACTOR CONTAINING SPT4/SPT5)

BLOCKAGE IS RELEASED ONCE POLYMERASE RECEIVE ACTIVATION SIGNAL SUCH AS PHOSPHORYLATION OF Ser-2 OF CTD TAIL BY PTEFb.

NOT A SMOOTH RIDE ON A DNA RAILWAY

TERMINATIONLAST STAGE OF TRANSCRIPTION

LEADS TO DISSOCIATION OF COMPLETE TRANSCRIPT & RELEASE OF RNA POLYMERASE FROM THE TEMPLETE DNA

TERMINATION CONTINUE…FACTOR DEPENDENT TERMINATION FOR RNA POL I ----- EUKARYORIC CELL CONTAIN

HUNDREDS OF RIBOSOMAL DNA REPEATS.

TERMINATION OCCURS IN RIBOSOMAL INTERGENIC SPECER REGION THAT CONTIN SEVERAL TRANSCRIPTION TERMINATION SITE UPSTREAM OF POL I PAUSING SITE.

3’ END CLEAVED GENERATING A LARGE PRIMARY RIBOSOMA RNA i.e. FURTHER PROSSED IN TO THE MATURE 18S,5.8S,&28S RIBOSOMAL RNA

TERMINATION CONTINUE…FACTOR DEPENDENT TERMINATION

TERMINATION CONTINUE…FACTOR DEPENDENT TERMINATION AS POL II RECHES THE END OF A GENE, 2 PROTEIN

COMPLEX CARRIED BY CTD - CPSF ( CLEAVAGE &

POLYADENYLATION SPECIFICITY FACTOR)& CSTF ( CLEAVAGE STIMULATION FACTOR ), RECOGNISE THE POLY-A SIGNAL IN THE TRANSCRIBED RNA.

POLY –A BOUND CPSF AND CSTF RECRUIT OTHER PROTEINS TO CARRY OUT RNA CLEAVAGE AND POLYADENYLATION

TERMINATION CONTINUE…FACTOR DEPENDENT TERMINATION

TWO MODEL

1. ALLOSTERIC MODEL

2. TORPEDO MODEL

FACTOR – INDEPENDENT TERMINATIONPOL III TERMINATION SIGNAL CONSISTS OF A STRETCH OF

THYAMINS LOCATED WITHIN 40BP DOWNSTREAM FROM THE 3’ END OF MATURE RNAs.

THIS POLY T TERMINATION SIGNAL PAUSES PO II AND CAUSES IT TO BACK TRACK TO THE NEAREST RNA HAIR PIN TO BECOME A DEAD-END COMPLEX.

HAIR IN ALLOSTERICALLY OPENS POL III

REFFERENCELEHNINGER PRINCIPLES OF BIOCHEMISTRY, FIFTH EDITION –

DAVID

THE WORLD OF THE CELL, 6TH EDITION, BY BECKER,KLEINSMITH & HARDIN

www.ncbi.nm.nih.gov/books/NBK9935

MOLECULAR BIOLOGY OF THE GENE, 5TH EDITION- WATSON

en.wikipedia.org/wiki/Abortive_initiation