4-4_-_Post-transcriptional_regulation

Lecture Overview

• Overview of post-transcriptional regulation in bacteria.

• Focus on RNA-based regulatory mechanisms: sRNAs and riboswitches.

• Discussion on post-translational regulation.

• Relevant Textbook Sections: 7.12, 7.13, 7.15, 7.16

Page 2: Regulation at the Level of RNA

• Significant regulation occurs after transcription starts but before protein synthesis.

• Transcriptional Attenuation:

  • Process of terminating mRNA synthesis prior to complete transcription of genes.

• mRNA Stability Control:

  • Influences the degradation rate of mRNA; longer mRNA lifetime leads to more protein production.

• Translation Efficiency:

  • Regulated by accessibility of the ribosome binding site (RBS); RBS structure is crucial.

• Many regulation mechanisms involve RNA regulatory elements.

Page 3: mRNA Lifetime Effects on Protein Levels

• Degradation of mRNA:

  • Multiple ribonucleases (RNases) in cells manage mRNA degradation.

  • Varying half-lives for different mRNAs.

  • Complexity in targeting specific mRNAs by RNases.

  • Regulatory proteins/RNAs influence mRNA half-life.

  • Average mRNA lifetime in bacteria ranges from seconds to about an hour—affects protein production volume.

Page 4: RNA Structures & Gene Expression

• Transcriptional Termination:

  • rho-independent (intrinsic) terminators can halt transcription early.

• For effective translation initiation, RBS must be unbound and free from base-pairing.

• Stem-Loop Structures:

  • Can inhibit gene expression by either sequestering the RBS or forming a transcriptional terminator upstream.

Page 5: Small RNAs (sRNAs)

• All cells contain regulatory noncoding RNAs that modulate gene expression.

• Bacterial sRNAs:

  • Typically 50-300 nucleotides in length; often operate through base-pairing with mRNA.

  • Base-pairing influences RBS availability and RNase targeting, regulating protein synthesis.

  • One sRNA can regulate multiple distinct target mRNAs.

Page 6: sRNAs and Hfq Protein

• sRNAs may only partially complement target mRNAs (5-11 nucleotides).

• Hfq:

  • RNA chaperone that stabilizes sRNA-mRNA interactions.

  • May recruit RNases for targeted degradation of mRNA.

Page 7: Riboswitches

• Definition: Riboswitches are RNA elements that bind small ligands, changing their structure to regulate gene expression.

• Located in the 5’ untranslated region (UTR) of specific bacterial mRNAs, they regulate downstream gene expression.

• Ligand binding alters RNA structure, influencing expression.

• Found primarily in bacteria, with some evidence in all life domains.

Page 8: Riboswitch Mechanisms

• Riboswitch aptamer domains specifically bind ligands, affecting 5' UTR base-pairing.

  • Changes can either block translation (via stem-loop formation sequestering RBS) or prevent transcription.

• Functional binding events can induce or repress gene expression; this is variable.

Page 9: Riboswitch Evolutionary Perspective

• Riboswitches are considered relics from the RNA world; they bind diverse metabolites.

• Aptamer domains are structurally conserved across lineages, indicating an ancient origin.

• Binding of metabolites in the RNA world would have been essential for environmental sensing.

Page 10: Post-Translational Regulation

• Post-translational regulation adjusts protein levels and activities:

  • Feedback Inhibition: End products of pathways inhibit their own biosynthetic enzymes.

  • Protein-Protein Interactions: One protein can regulate another’s activity.

  • Post-Translational Modifications: Chemical groups (e.g., phosphate) added to proteins can modify functionality.

Page 11: Protein Degradation and Turnover

• Proteins can be degraded and recycled via proteases.

• Proteases play a role in:

  • Clearing misfolded proteins.

  • Specific regulatory degradation of proteins in the cell.

  • Some proteins require degradation activation (e.g., cleaving peptide linkages).

Page 12: Overview of Regulatory Mechanisms

• The essence of regulation is viable only with sensing capabilities.

• Reflects the importance of regulatory mechanisms in bacterial life.