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BiochemistrySixth Edition
Chapter 29RNA Synthesis and Processing
Part I: RNA synthesis
Copyright © 2007 by W. H. Freeman and Company
Berg • Tymoczko • Stryer
RNA synthesis is a key step in the expression of genetic information
Christmas tree:Active transcription
RNA synthesis, or transcription, is catalyzed by RNA polymerase
Structural conservation
(more complex regulation)
Mg2+ ion
RNA synthesis (or biological polymerization):initiation, elongation, and termination
RNA polymerase’s functions:1. Search “promoters” (initiation sites;
or cis-acting elements)2. Unwind short stretch of dsDNA3. Formation of phophodiester bonds
(using rNTP) processivity4. Detect termination signals5. Interact with activator and repressor
(transcription factors or trans-acting factors) regulation of txn rate
RNA synthesis for mRNA, tRNA, and rRNA:
Common in chemistry and steps
Different: RNA polymerase, regulation, and post-transcriptional processing
Transcription in E coli
(holoenzyme)
Core enzyme (contains catalytic site)
: finds promoter, initiates txn, then dissociates
RNA polymerase active sites:Similar to DNA pol. but overall structure is dif.
Transcription initiation:Identification of promoter sites
footprinting technique
Two common motifs are present on the 5’ (upstream) side of the transcription start site
-35 sequence and -10 sequence
Core promoter
(consensus seq.)
Two common motifs are present on the 5’ (upstream) side of the transcription start site
-35 sequence and -10 sequence
Core promoter
(consensus seq.)
Start site = +1 (+2…, -1, -2, etc.)Template strand vs. coding strand
antisense (-) sense (+)
Transcription initiation:promoter activity (or efficiency)
1. strong promoter vs. weak promoter (in relation to consensus seq.)
2. Distance between two conserved seq.
Other factors:* Promoter-binding proteins, or polymerase-binding proteins* UP element (upstream): -40~-60 of highly expressed genes (for subunit)
Transcription initiation:recognition of promoter sites subunit
Help RNA pol. bindcore promoter
Transcription initiation:Search for promoter sites
* Holoenzyme slides along dsDNA* Promoter is encountered by a random
walk in one dimension* subunit dissociates when nascent RNA
chain = 9-10 nt* subunit next assists another initiation
There are multiple types of subunit
70
32: recognize heat-shock genes54: responds to nitrogen starvation
determines where txn starts
Transcription initiation:Template unwinding
Closed promoter complex open promoter complex:Important step in txn initiation
Negative supercoiling facilitates unwinding
Exception: promoter of Topoisomerase II gene negative supercoils decreases txn
(negative feedback)
Supercoils: change structual relation of the –10 and –35 regions
RNA synthesis can start de novo
First base at 5’end: pppG or pppA
RNA synthesis grow in the 5’-3’ direction
Transcription elongation:Txn bubble on DNA template
Elongation: 1. formation of first bond 2. dissociation of strong binding of core 3. 50 nt/sec
txn bubble
8bp
Surface model of a bubble
“melted” DNA
RNA-DNA hybrid separation by RNA pol.
Fixed structure of the txn bubble
Fidelity of the RNA pol.
Contains proofreading nuclease activity 104 – 105
(DNA polymerase: 107)
Higher error rate can be tolerated:*Mistakes are not transmitted*Many RNA transcripts for most genes
Transcription elongation:
Transcription termination:
• Formation of phosphodiester bond stops• RNA-DNA hybrid dissociates• Melted DNA rewinds• RNA pol. releases DNA
Transcribed region of DNA contains top signal
In DNA:Palindromic GC-rich regionfollowed by AT-rich
Stable hairpin because of GC-rich
Txn stop
How does this structure terminate transcription?
1. RNA pol. pauses after such structure2. rU-dA: highly unstable3. Weakly bound nascent RNA dissociates
Transcription termination:Additional factor, rho ()
How does termination of RNA synthesis?
Hexameric rho is ATPase in the presence of ssRNA Activated by C-rich & G-poor RNA region Hydrolysis RNA-DNA helicase: breaking hybrid helix
72 nt
Transcription termination:Additional factor, nusA protein
binds specific termination signals in E. coli:“Attenuators”
Important feature of the termination mechanism: signals lie in RNA (not DNA)
Antibiotics: inhibitors of transcription
Example no. 1
Rifampicin blocks txn initiation
Binds a pocket occupied by newly formed DNA-RNA hybrid Competitor
Conserved in prok. not in euk. antibiotic
Example no. 2: actinomycin D* Binds specifically and tightly to dsDNA* Intercalation: between neighboring base-pair* at low concentrations, inhibit txn but not DNA replication (both prok. and euk.)
Eukaryotic transcription: more complex regulation
Differential txn regulation cell types
Three keys in euk.:1. Nuclear membrane2. Txn regulation:
more promoters,enhancer
3. RNA processing:ex. splicing
Three different types of euk. RNA polymerases
* Large proteins* 8-14 subunits
Similarity:
RNA pol. II: 220-kd (largest) subunit has a carboxyl-terminal domain (CTD) YSPTSPS repeats serine phosphorylation
Binds to pol. II tightly and inhibits elongation(action is conserved in euk.)
Euk. transcriptional initiation: promoters
1. Conserved sequences for pol. binding2. Different in sequence and position3. RNA polymerase-dependent
RNA polymerase I: rDNA gene
X hundreds
TATA-like seq.:Ribosomal initiator element
Promoter binding proteins
RNA pol. I
RNA polymerase II
a set of conserved elements: combination
Enhancer: unique to euk., more than 1 kb from promoter
RNA polymerase III: intergenic (within transcribed region)
RNA polymerase II promoter: 3 common elements
Mutagenesis exp’ts, footprinting, and sequence comparisons
1 2
3
Initiator element (-3 ~ +5)
Downstream core promoter element (+28 ~ +32)
-30 ~ -100(similar to prok. –10)
-40 ~ -150 (similar to prok. –35)On template (antisense) strand
Constitutively expressed genes
Euk. promoter elements: recognized by txn factors
Txn initiation:TFII’s
TFIID to TATA box (seq. specific)
Basal txn apparatus
Binds “mediator”
TBP and TATA-box DNA
* Unwinding (minor groove)* Hydrophobic interaction* Phenylalanine intercalation* Asymmetry
(by TFIIH)
initation elongation
* Stabilize txn elongation* Recruit RNA-processing enzymes
* Basal txn apparatus: minimal transcription (low)
* Additional txn factors: bind other sites for high txn rate
* Upstream stimulatory sites: variable (sequence & location)
Multiple transcription factors bind euk. promoters
There are many transcription factors
Ex. heat-shock transcription factor (HSTF) bind directly to consensus seq. in response to high temperature
Another level of promoter activity: enhancers
* Have no promoter activity* Act from several thousand bp away* Can be downstream, upstream, or intragenic* Cell type-specific
In yeast: upstream activator sequences (UASs)
txn factors and cis-acting elements: key to txn regulationtranscription: key to gene expression