Dcp2 C-terminal <i>Cis</i>-Binding Elements Control Selective Targeting of the Decapping Enzyme by Forming Distinct Decapping Complexes

He, Fei; Wu, Chen; Jacobson, Allan

doi:10.1101/2021.10.01.462794

Cited by 4 publications

(12 citation statements)

References 66 publications

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“…In vitro pull-down assays demonstrated that each of these HLMs, except for HLMs 1 and 9, can directly interact with the decapping activator PatL1 (Pat1) ( Charenton et al, 2017 ). In vivo deletions further suggested that HLMs 2–6 (equivalent to HLMs 1-5 in the He et al study) contributed the bulk of PatL1 (Pat1) binding ( He et al, 2021 ). Intriguingly, a strain bearing the deletion of HLMs 2–9 (equivalent to all HLMs in the He et al study) still decays endogenous decapping targets as efficiently as wild-type ( He et al, 2021 ).…”

Section: The Dcp1/2 Complex Is the Main Decapping Holo-enzyme In Euka...mentioning

confidence: 93%

Eukaryotic mRNA Decapping Activation

Vidya

2022

Front. Genet.

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The 5′-terminal cap is a fundamental determinant of eukaryotic gene expression which facilitates cap-dependent translation and protects mRNAs from exonucleolytic degradation. Enzyme-directed hydrolysis of the cap (decapping) decisively affects mRNA expression and turnover, and is a heavily regulated event. Following the identification of the decapping holoenzyme (Dcp1/2) over two decades ago, numerous studies revealed the complexity of decapping regulation across species and cell types. A conserved set of Dcp1/2-associated proteins, implicated in decapping activation and molecular scaffolding, were identified through genetic and molecular interaction studies, and yet their exact mechanisms of action are only emerging. In this review, we discuss the prevailing models on the roles and assembly of decapping co-factors, with considerations of conservation across species and comparison across physiological contexts. We next discuss the functional convergences of decapping machineries with other RNA-protein complexes in cytoplasmic P bodies and compare current views on their impact on mRNA stability and translation. Lastly, we review the current models of decapping activation and highlight important gaps in our current understanding.

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Section: The Dcp1/2 Complex Is the Main Decapping Holo-enzyme In Euka...mentioning

confidence: 93%

Eukaryotic mRNA Decapping Activation

Vidya

2022

Front. Genet.

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“…Strains containing complete gene deletions of UPF1, UPF2, and UPF3 (HFY871, HFY115, HFY861, HFY467) were described previously 25,45 . HFY2996 and HFY3039 were described previously 28 . YRG5205 was generated from HFY3039 with a complete gene deletion of UPF1 as in HFY871.…”

Section: Methodsmentioning

confidence: 99%

“…Dcp2, the catalytic component of the decapping enzyme, is also found on translating ribosomes 26 , and the co-translational recruitment of Dcp2 to NMD substrates is likely to occur via two highly similar Upf1-binding sites on Dcp2 27 . To address whether ribosome-associated Upf1 plays a role in recruitment of Dcp2, centromeric UPF1-FLAG was expressed in strains containing genomic HA-tagged DCP2 or the HA-dcp2-U1D-U2D allele in which the two Upf1 binding sites have been deleted 28 . Sucrose gradient fractionation and western blotting demonstrated that deletion of the Upf1-binding sites on Dcp2 slightly shifted Dcp2 to lighter fractions (Figure 2b).…”

Section: Distinct States Of Polysome Association By Upf1 and Its Binding Partnersmentioning

confidence: 99%

“…NMD in yeast initiates with mRNA decapping 43 while mRNAs are polysome-associated 44 and this process is dependent on Dcp2, the catalytic component of the decapping enzyme. We have shown recently that Dcp2 contains two nearly identical binding sites for Upf1 27,28 and that Upf1:Dcp2 association controls the selective targeting of the decapping enzyme to NMD substrates. 28 The ability of Upf1 to dimerize 24 , and the presence of two Upf1 binding sites on Dcp2, suggests that Dcp2 may be recruited to polyribosomes by dimerization of ribosome-associated Upf1 with Dcp2-associated Upf1.…”

Section: Preferential Association Of Nmd Substrates With Ribosomes Harboring Bound Upf Factors: Implications For the Nmd Pathwaymentioning

confidence: 99%

“…We have shown recently that Dcp2 contains two nearly identical binding sites for Upf1 27,28 and that Upf1:Dcp2 association controls the selective targeting of the decapping enzyme to NMD substrates. 28 The ability of Upf1 to dimerize 24 , and the presence of two Upf1 binding sites on Dcp2, suggests that Dcp2 may be recruited to polyribosomes by dimerization of ribosome-associated Upf1 with Dcp2-associated Upf1. The effect size measures the degree of difference between median log 2 fold change of NMD substrates and that of non-substrates.…”

Section: Preferential Association Of Nmd Substrates With Ribosomes Harboring Bound Upf Factors: Implications For the Nmd Pathwaymentioning

confidence: 99%

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Progressive polysomal association of Upf1, Upf2, and Upf3 as ribosomes traverse mRNA coding regions

Ganesan

Mangkalaphiban

Baker

et al. 2021

Preprint

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SUMMARYUpf1, Upf2, and Upf3 are the central regulators of nonsense-mediated mRNA decay (NMD), the eukaryotic mRNA quality control pathway generally triggered when a premature termination codon is recognized by the ribosome. The NMD-related functions of the Upf proteins likely commence while these factors are ribosome-associated, but little is known of the timing of their ribosome binding, their specificity for ribosomes translating NMD substrates, or the nature and role of any ribosome:Upf complexes. Here, we have elucidated details of the ribosome-associated steps of NMD. By combining yeast genetics with selective ribosome profiling and co-sedimentation analyses of polysomes with wild-type and mutant Upf proteins, our approaches have identified distinct states of ribosome:Upf association. All three Upf factors manifest progressive polysome association as mRNA translation proceeds, but these events appear to be preceded by formation of a Upf1:80S complex as mRNAs initiate translation. This complex is likely executing an early mRNA surveillance function.

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Ribosome-bound Upf1 forms distinct 80S complexes and conducts mRNA surveillance

Ganesan

Mangkalaphiban

Baker

et al. 2022

RNA

Self Cite

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Upf1, Upf2, and Upf3, the central regulators of nonsense-mediated mRNA decay (NMD), appear to exercise their NMD functions while bound to elongating ribosomes, and evidence for this conclusion is particularly compelling for Upf1. Hence, we employed selective profiling of yeast Upf1:ribosome association to define that step in greater detail, understand whether the nature of the mRNA being translated influences Upf1:80S interaction, and elucidate the functions of ribosome-associated Upf1. Our approach has allowed us to clarify the timing and specificity of Upf1 association with translating ribosomes, obtain evidence for a Upf1 mRNA surveillance function that precedes the activation of NMD, identify a unique ribosome state that generates 37-43 nt ribosome footprints whose accumulation is dependent on Upf1’s ATPase activity, and demonstrate that a mutated form of Upf1 can interfere with normal translation termination and ribosome release. In addition, our results strongly support the existence of at least two distinct functional Upf1 complexes in the NMD pathway.

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Dcp2 C-terminal Cis-Binding Elements Control Selective Targeting of the Decapping Enzyme by Forming Distinct Decapping Complexes

Cited by 4 publications

References 66 publications

Eukaryotic mRNA Decapping Activation

Eukaryotic mRNA Decapping Activation

Progressive polysomal association of Upf1, Upf2, and Upf3 as ribosomes traverse mRNA coding regions

Ribosome-bound Upf1 forms distinct 80S complexes and conducts mRNA surveillance

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