The transition from the closed to the open complex involves structural changes in the enzyme and the opening of the DNA double helix to reveal the template and nontemplate strands. This “melting” occurs between positions –11 and +2, with respect to the transcription start site.

#Id: 6760

#Unit 3. Fundamental Processes

RNase E and PNPase, along with a helicase and another accessory enzyme, form a multiprotein complex called the degradosome.

#Id: 6761

#Unit 3. Fundamental Processes

Cytoplasmic mRNAs are degraded by one of the three pathways. For most mRNAs, the deadenylation-dependent pathway is followed These dense regions of cytoplasm contain the decapping enzyme (DCP1/DCP2), activators of decapping (DHH, PAT1, LSM1-7), and the major 5′→3′ exoribonuclease XRN1, as well as densely associated mRNAs

#Id: 6762

#Unit 3. Fundamental Processes

The exposed cap is then removed by a decapping enzyme (DCP1/DCP2), unprotected mRNA susceptible to degradation by XRN1, a 5′→3′ exoribonuclease. Removal of the poly(A) tail also makes mRNAs susceptible to degradation by cytoplasmic exosomes containing 3′→5′ exonucleases.

#Id: 6763

#Unit 3. Fundamental Processes

#Id: 6764

#Unit 3. Fundamental Processes

#Id: 6765

#Unit 3. Fundamental Processes

P bodies are dense cytoplasmic domains many times the size of a ribosome. They are sites of translational repression that contain no ribosomes or translation factors. They are also major sites of mRNA degradation in the cytoplasm. Exon-junction complexes upf complex functions in nonsense-mediated decay and induces degradation of the mRNA by P body–associated 5′→3′ exoribonuclease XRN1