Molecular Biology: Translation and mRNA Regulation

Initiation Factors

• Eukaryotic translation initiation is a complex process involving multiple initiation factors (eIFs)
• These factors bind to the small subunit of the ribosome, mRNA, and other factors to facilitate translation initiation
• Key initiation factors:
  • eIF1: binds to the small subunit of the ribosome and prevents premature binding of mRNA
  • eIF1A: helps to recruit the small subunit to the mRNA
  • eIF2: binds to the initiator methionyl-tRNA and GTP, and directs the ribosome to the start codon
  • eIF3: binds to the small subunit and mRNA, and helps to recruit the 60S ribosomal subunit
  • eIF4: binds to the mRNA cap and helps to recruit the small subunit
  • eIF5: helps to join the small and large subunits of the ribosome

Ribosome Profiling

• Ribosome profiling is a technique used to study translation in vivo
• It involves the sequencing of ribosome-protected mRNA fragments to determine the position of ribosomes on mRNAs
• Provides information on:
  • Translation initiation and elongation rates
  • Ribosome occupancy and density
  • Translation efficiency and accuracy
  • Identification of novel open reading frames (ORFs)

Nonsense-mediated Decay

• Nonsense-mediated decay (NMD) is a surveillance pathway that degrades mRNAs containing premature stop codons
• Helps to prevent the production of truncated proteins that could be toxic to the cell
• Key components of the NMD pathway:
  • UPF1: a helicase that binds to the ribosome and scans the mRNA for premature stop codons
  • UPF2: a protein that binds to UPF1 and helps to recruit the degradation machinery
  • UPF3: a protein that binds to the exon junction complex and helps to recruit the degradation machinery
  • SMG1: a protein kinase that phosphorylates UPF1 and triggers the degradation pathway

MicroRNA Regulation

• MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression by binding to target mRNAs
• miRNAs inhibit translation by:
  • Blocking the initiation of translation
  • Inducing the degradation of target mRNAs
  • Inhibiting the translation elongation step
• Key components of the miRNA pathway:
  • Dicer: an enzyme that cleaves precursor miRNAs to generate mature miRNAs
  • Argonaute: a protein that binds to miRNAs and targets mRNAs for degradation or translation inhibition

mRNA Localization

• mRNA localization is the process of targeting specific mRNAs to specific regions of the cell
• Helps to regulate protein synthesis and activity in response to local cues
• Key mechanisms of mRNA localization:
  • mRNA zipcodes: specific sequences in the mRNA that are recognized by RNA-binding proteins
  • RNA-binding proteins: proteins that bind to mRNA zipcodes and direct the mRNA to specific locations
  • Microtubules and motor proteins: help to transport mRNAs to specific locations
  • Localization elements: specific sequences in the mRNA that are recognized by the localization machinery