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.