Building on the Ccr4-Not architecture

Abstract

In a recent issue of Nature Communications Ukleja and co-workers reported a cryo-EM 3D reconstruction of the Ccr4-Not complex from Schizosaccharomyces pombe with an immunolocalization of the different subunits. The newly gained architectural knowledge provides cues to apprehend the functional diversity of this major eukaryotic regulator. Indeed, in the cytoplasm alone, Ccr4-Not regulates translational repression, decapping and deadenylation, and the Not module additionally plays a positive role in translation. The spatial distribution of the subunits within the structure is compatible with a model proposing that the Ccr4-Not complex interacts with the 5' and 3' ends of target mRNAs, allowing different functional modules of the complex to act at different stages of the translation process, possibly within a circular constellation of the mRNA. This work opens new avenues, and reveals important gaps in our understanding regarding structure and mode of function of the Ccr4-Not complex that need to be addressed in the future.

Keywords: Ccr4-Not complex; architecture; deadenylation; mRNA circularization; mRNA decay; protein folding; subunit localization.

Figure 1

Ccr4‐Not complex of S. pombe with and without a projection of docking sites for various eukaryotic interaction partners. This figure was adapted from 29. It shows two orthogonal views of the Ccr4‐Not complex with (left) or without its interaction partners (right). Left, binding sites of the known eukaryotic Ccr4‐Not‐interacting partners: Tob/BTG (that binds to Caf1) and Nanos, TTP and DDX6 (that bind to different parts of Not1), the GW182 is also shown as it is an essential component of miRNA‐targeted recruitment of the Ccr4‐Not complex to mRNA.

Figure 2

Interaction of Ccr4‐Not with the decapping and mRNA decay machinery. This figure was adapted from 50. The mRNA decapping and decay machinery including the Ccr4‐Not complex are organized in a circular constellation.

Figure 3

Model for the interaction between mRNA and the Ccr4‐Not complex during the translation process. The Ccr4‐Not complex structure was adapted from 29. Not4 via its RNA Recognition Motif (RRM) could tether the mRNA with a translating ribosome in close proximity to the Ccr4‐Not complex, in particular to Not5, such that it can help chaperone or interacting partner association with the nascent polypeptide chain and more generally allow the Not proteins to participate in co‐translational events. As translation elongation proceeds, the 5′ end of the mRNA can become accessible to the site where DDX6 docks onto the Ccr4‐Not complex. The 3′ end of the mRNA instead is accessible to the other side of the Ccr4‐Not complex, where it can be tethered by RNA binding proteins (not depicted), such that the poly(A) sequences are accessible to the Ccr4 and Caf1 nucleases. Size proportion of the shapes representing macromolecules are similar to the real size proportion of the represented macromolecules. The mRNA depicted is 160 nucleotides in length. Scale bar ≈ 100 Å.