Ch3 gene expression

avatar
Created by
BreakableGavial2499

Cards (41)

  • G0G74A Advanced Biochemistry and Biotechnology (ABB) Lecture 3 Coding sequence determinants of gene expression involves tRNA GAU Asp and tRNA GAC Asp.
  • Gene copy number determines the number of tRNA isoaccepting sites.
  • mRNA 5’ 3’ C D DD D DD translates into protein.
  • Translation decoding and wobbling are processes in protein synthesis.
  • The aa - tRNA pool is the collection of all tRNAs that can be used in protein synthesis.
  • Protein Synonymous codon usage is adapted to the aa - tRNA pool.
  • Biased codon usage may affect translation rates … or maybe not?
  • GC content at position 3 affects Codon adaptation index.
  • Kudla et al. 2009 Science 324, 255 - 8 found that codon adaptation index is influenced by the GC content at position 3.
  • Kudla et al. 2009 Science 324, 255 - 8 found that expression level did not correlate with codon adaptation.
  • Kudla et al. 2009 Science 324, 255 - 8 found that expression level correlates with 5’ mRNA folding energy (position -4 to +37 relative to translation start).
  • Li & Biggin 2015, Science 347: 1066 - 1067
  • Coupled transcription initiation and 5’ capping
  • Transcription initiation, Promoters and enhancers, new model!
  • Prokaryotes versus Eukaryotes: Promoter, exon, ATG, TAA, Intron, REs, 5’ cap, AUG, UAA, AAAAA, Transcription, Translation, Splicing, Pre-mRNA, mRNA, AUG, UAA, AAAAA, Export, Poly(A) Addition signal, gDNA, cap, mRNA, 5’, 3’, ATG, TAA, AUG, UAA, AUG, 5’PPP, ATG, TAA, ATG, TAA, RBS, 12.
  • Coupled transcription elongation and mRNA splicing
  • Translation initiation is rate-limiting, rather than elongation.
  • Importance of Dynamics for the Relationship between mRNA and Proteins
  • EJC, Exon junction complex; eIF4A-III, eukaryotic initiation factor 4A-III; RNA clamp, RNA-binding protein.
  • Linder et al. 2011, Nature Rev Mol Cell Biol
  • Coupling and coordination in eukaryotic gene expression processes
  • Expression model (Maniatis and Reed, 2002) “Molecular machines”: PIC, pre-initiation complex; TF, transcription factor; CAP, capping factor; SF, splicing factor; pA, polyadenylation factor.
  • Promoter, RBS, ORF/Operon, ATG, TAA, AUG, UAA, Terminator, Transcription, Translation, gDNA, mRNA, RNA pol, 5’ PPP, 3’.
  • Ligand binding: Nuclear (steroid) receptor can regulate transcription factor activity.
  • Transcription (co)repression can occur through competition, inhibition, TATA, direct repression, chromatin modification, and indirect repression.
  • Combinatorial control, NFAT + AP1, mating type factors can regulate transcription factor activity.
  • Combinatorial control: AP1 + NFAT can regulate transcription factor activity.
  • Localization: SREBP can regulate transcription factor activity.
  • Mechanisms of the functional cycle of mammalian heat shock transcription factor 1 (Hsf1) can regulate transcription factor activity.
  • Ligand binding, nuclear receptors can regulate transcription factor activity.
  • Transcription repressors, a 2 mating type factor, Mig1/Tup1 can regulate transcription factor activity.
  • Case: Heat shock factor, HSF1 has a trimerization domain, activation domain, and DNA-binding domain.
  • PTM + Co - activator recruitment: CREB P Basal complex cAMP PKA activation Co - activators CBP/ p300 RNA Pol II RNA Pol II CREB DB AD CREB phosphorylation Mediator complex CRE: cAMP response element CREB: CRE - binding protein CBP: CREB - binding protein
  • Co-repressor recruitment can occur through unmasking of activation domain, coactivator recruitment, posttranslational modification, and proteolytic processing.
  • Targeted localization, SERBP, LEF-1, HSF1 can regulate transcription factor activity.
  • Activator acetylation by (p300) HAT can lead to stimulation or inactivation, depending on the target.
  • Activator SUMOylation can lead to sequestration by targeting to nuclear bodies.
  • Activator ubiquitinylation can occur through mono-ubiquitinylation or poly-ubiquitinylation, leading to stimulation or inactivation respectively.
  • Van der Feltz, 2012, Biochemistry 51, 3321 - 3333, describes coupled cleavage and polyadenylation.
  • The expression model includes elements such as EJC, EJC21, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC, EJC,