Transcript Chapter 13

Chapter 13
Regulatory RNA
13.1 Introduction
 RNA functions as a regulator by forming a region of
secondary structure (either inter- or intramolecular)
that changes the properties of a target sequence.
Figure 13.1: Regulator RNA binds RNA
target.
13.2 Attenuation: Alternative RNA Secondary
Structure Control
• Termination of transcription can be attenuated
by controlling formation of the necessary hairpin
structure in RNA.
• The most direct mechanisms for attenuation
involve proteins that either stabilize or
destabilize the hairpin.
13.2 Attenuation: Alternative RNA Secondary
Structure Control
Figure 13.2: Termination occurs when hairpin forms.
13.3 Termination of Bacillus subtilis trp Genes
Is Controlled by Tryptophan and by tRNATrp
• A terminator protein called
TRAP is activated by
tryptophan to prevent
transcription of trp genes.
Figure 13.3: TRAP controls the B. subtilis trp
operon.
13.3 Termination of Bacillus
subtilis trp Genes Is
Controlled by Tryptophan and
by tRNATrp
• Activity of TRAP is (indirectly)
inhibited by uncharged
tRNATrp.
Figure 13.4: Anti-TRAP is controlled by tRNATrp.
13.4 The Escherichia coli Tryptophan Operon Is
Controlled by Attenuation
• An attenuator (intrinsic terminator) is located
between the promoter and the first gene of the
trp cluster.
• The absence of Trp-tRNA suppresses
termination and results in a 10x increase in
transcription.
13.4 The Escherichia coli Tryptophan Operon Is
Controlled by Attenuation
Figure 13.5: Termination can be
controlled via changes in RNA
secondary structure that are determined
by ribosome movement.
13.4 The Escherichia coli
Tryptophan Operon Is
Controlled by Attenuation
Figure 13.6: Transcription is controlled by
translation.
13.5 Attenuation Can Be Controlled by
Translation
• The leader region of the trp operon has a
fourteen-codon open reading frame that includes
two codons for tryptophan.
• The structure of RNA at the attenuator depends
on whether this reading frame is translated.
13.5 Attenuation Can Be Controlled by
Translation
Figure 13.7: The control region of the trp operon codes
for a leader peptide.
13.5 Attenuation Can Be Controlled by
Translation
• In the presence of Trp-tRNA:
– the leader is translated
– the attenuator is able to form the hairpin that causes
termination
• In the absence of Trp-tRNA:
– the ribosome stalls at the tryptophan codons
– an alternative secondary structure prevents formation
of the hairpin, so that transcription continues
13.5 Attenuation Can Be Controlled by Translation
Figure 13.8: Alternative secondary structures control termination.
13.5 Attenuation Can Be Controlled by Translation
Figure 13.9: Tryptophan controls ribosome
position.
13.5 Attenuation Can Be Controlled by
Translation
Figure 13.10: Trp-tRNA controls the E. coli trp operon directly.
13.6 A Riboswitch in the 5 UTR Region Can
Control Translation of the mRNA
• A riboswitch is an RNA whose activity is controlled
by a small ligand.
• A riboswitch may be a ribozyme.
13.6 A Riboswitch in the 5 UTR Region Can
Control Translation of the mRNA
Figure 13.11: GlcN6P activates a ribozyme that cleaves the mRNA.
13.7 Bacteria Contain Regulator sRNAs
• Bacterial regulator RNAs are called sRNAs.
• Several of the sRNAs are bound by the RNA
binding protein Hfq, which increases their
effectiveness.
• The oxyS sRNA activates or represses
expression of >10 loci at the posttranscriptional
level.
13.7 Bacteria Contain Regulator sRNAs
Figure 13.13: A 3' terminal loop in oxyS RNA pairs with the initiation site of
flhA nRNA.
13.8 Eukaryotes Contain Regulator RNAs
• Eukaryote genomes produce antisense RNAs.
• Antisense RNAs regulate gene expression at the
level of transcription and translation.
• Eukaryote genomes code for many short (~22
base) RNA molecules called microRNAs.
13.8 Eukaryotes Contain Regulator RNAs
• MicroRNAs regulate gene expression by base
pairing with complementary sequences in target
mRNAs.
• RNA interference triggers degradation or
translation inhibition of mRNAs complementary
to miRNA or siRNA.
• dsRNA may cause silencing of host genes.
13.8 Eukaryotes Contain Regulator RNAs
Figure 13.14: PHO84 antisense RNA stabilization is paralleled by
histone deacetylase recruitment, histone deacetylation and PHO84
transcription. Under normal conditions, the RNA is rapidly degraded.
In aging cells, antisense transcripts are stabilized and recruit the
histone deactylase to repress transcription.
13.8 Eukaryotes Contain Regulator RNAs
Figure 13.15: lin4 RNA regulates expression of
lin14 by binding to the 3’ nontranslated region.
13.8 Eukaryotes Contain Regulator RNAs
Figure 13.16:
Long dsRNA inhibits protein synthesis and
triggers degradation of all mRNA in
mammalian cells, as well as having
sequence-specific effects. Short dsRNA
(<26nt) leads to degradation of only
complementary mRNAs.