Gene Expression and its control- BIOS5010 Lecture 10: mRNA stability

Gene Expression Basics

  • Process: Transition from DNA to RNA to protein involves several steps:

    • DNA Replication

    • Transcription (DNA to RNA)

    • Reverse Transcription (rare)

    • Translation (RNA to protein)

mRNA Characteristics

  • Structure: mRNA is single-stranded and highly processed.

  • Processing Requirements: mRNA produced by RNA Pol II complex must undergo:

    • Splicing

    • Capping

    • Transport to the ER for Translation

  • Stability: mRNA is inherently unstable and requires stabilization. Additional RNA and proteins can enhance or reduce stability.

Pre-mRNA vs. Mature mRNA

  • Pre-mRNA: Located solely in the nucleus until fully processed.

  • Mature mRNA: Contains joined exons, a 5' cap, and a 3' poly-A tail. Used for translation in the cytoplasm.

RNA Processing in Eukaryotes

  • Stages of Processing:

    • 5' Capping: Addition of a protective cap at the 5' end.

    • RNA Splicing: Removal of introns and connecting exons.

    • 3' Polyadenylation: Addition of a poly-A tail at the 3' end.

Untranslated Regions (UTRs)

  • 5' and 3' UTRs:

    • Help in maintaining mRNA stability.

    • Influence degradation, translation, and localization processes.

mRNA Structural Features

  • Prokaryotic mRNA:

    • Not modified after transcription.

    • 3' terminus often forms a hairpin loop for stability.

  • Eukaryotic mRNA:

    • Modified with a cap and poly-A tail.

    • Contains various base-paired structures.

mRNA Instability and Degradation

  • Ribonucleases: Cause mRNA instability.

    • Endoribonucleases: Cleave RNA at internal sites.

    • Exoribonucleases: Remove ribonucleotides from RNA ends.

Prokaryotic mRNA Degradation

  • Occurs during translation in prokaryotes.

  • Mechanism:

    • E. coli mRNA degradation involves endonucleases and 3' to 5' exonucleases.

    • RNase E initiates degradation post removal of pyrophosphate from the 5' end.

    • Cleavage yields a downstream fragment that is then further degraded.

mRNA Lifetime and Variability

  • mRNA half-lives vary significantly across organisms:

    • E. coli: ~3 min

    • Yeast: 3-100 min

    • Metazoans: Varies from minutes to days.

Capping and Poly-A Tails

  • 5' Cap: Aids mRNA stability and translation initiation.

    • Formed during transcription by adding G to the first base of the transcript.

    • Involves modifications by methyltransferases.

  • 3' Poly-A Tail: Protection from degradation and is crucial for translation efficiency.

Eukaryotic mRNA Degradation Pathways

  • Deadenylation-Dependent Pathways: Two major pathways include:

    1. 5' to 3' Decay: Triggered by deadenylation and subsequent decapping.

    2. 3' to 5' Decay: Involves exonuclease digestion by the exosome complex.

Surveillance Mechanisms

  • TRAMP complex: Recognizes improperly processed RNAs and aids in their degradation with the help of the exosome.

  • Cytoplasmic Surveillance Systems: Detects translation-related defects (NMD, NSD, NGD).

Nonsense Mediated Decay (NMD)

  • Targets mRNAs with premature termination codons (PTC).

  • Processes include:

    • Recognition by an exon junction complex (EJC).

    • Involvement of Upf proteins in marking for degradation.

    • Link to disease pathology via PTCs and truncated proteins.

mRNA Localization

  • mRNA localization regulates where proteins are synthesized within the cell leading to localized translation essential for cell functions and development.

    • Important for cell division, migration, and differentiation.

Conclusions

  • Key Points:

    • mRNA stabilization relies on 5' capping and 3' poly-A tails.

    • Destabilization is often initiated by de-adenylation and decapping.

    • The TRAMP complex monitors mRNA integrity in the nucleus.

    • Localized translation impacts developmental processes.