| Functional aspect | Key finding | Evidence type | Experimental/analysis approach | Quantitative data | Source (paper; year; publication date if available; URL) | Citation ID |
|---|---|---|---|---|---|---|
| Complex role | Pop2/Caf1 is a core subunit of the major cytoplasmic Ccr4-Not deadenylase, and both Ccr4p and Caf1p are required for normal deadenylation in vivo. | Primary | Reporter mRNA transcriptional pulse-chase; biochemical copurification | MFA2pG deadenylation in WT ~13 nt/min vs ~2–3 nt/min in ccr4Δ and caf1Δ; MFA2pG stabilized ~2–3-fold in mutants | Tucker et al., *Cell*, 2001, Feb; https://doi.org/10.1016/S0092-8674(01)00225-2 | (pqac-00000011, pqac-00000023) |
| Complex architecture | Not1 acts as scaffold; its central MIF4G-like domain binds Caf1, and Caf1 binds the Ccr4 LRR domain to tether the Ccr4 nuclease into the nuclease module. | Primary | Structural biology of yeast nuclease module | Multiprotein complex mass ~1 MDa noted; no catalytic rate reported | Basquin et al., *Molecular Cell*, 2012, Oct 26; https://doi.org/10.1016/j.molcel.2012.08.014 | (pqac-00000005, pqac-00000021) |
| Enzymatic activity | The Pop2 RNase D domain has intrinsic in vitro RNase activity, supporting its annotation as a poly(A) ribonuclease/deadenylase subunit. | Primary | X-ray crystallography plus in vitro RNase assays with purified domain | Structure solved at 2.3 Å; catalytic loss in S44A/E46A mutant | Thore et al., *EMBO Reports*, 2003, Dec; https://doi.org/10.1038/sj.embor.7400020 | (pqac-00000003, pqac-00000020) |
| Substrate specificity | Pop2 degrades poly(A) and also poly(U)/poly(C) in vitro, but not oligo(G), indicating preference for poly(A) with broader RNA reactivity than a strict poly(A)-only enzyme. | Primary | In vitro RNase substrate panel and competition assays | Active on poly(A), poly(U), poly(C); inactive on oligo(G); distributive cleavage pattern | Thore et al., *EMBO Reports*, 2003, Dec; https://doi.org/10.1038/sj.embor.7400020 | (pqac-00000000, pqac-00000020) |
| Catalytic residues/domain | Pop2 belongs to the RNase D/DEDD family; mutating S44 and E46 in the active-site motif abolishes detectable RNase activity. | Primary | Structure-guided mutagenesis and enzymatic assay | S44A/E46A abolishes activity | Thore et al., *EMBO Reports*, 2003, Dec; https://doi.org/10.1038/sj.embor.7400020 | (pqac-00000000, pqac-00000009, pqac-00000020) |
| In vivo functional interpretation | Although Pop2 has intrinsic nuclease activity in vitro, genetic work in budding yeast suggests Ccr4 is the primary catalytic deadenylase in vivo and Pop2 also contributes through noncatalytic functions. | Primary | Mutagenesis, in vivo deadenylation assays, genetic interaction analysis | caf1Δ causes deadenylation defect but less severe than ccr4Δ; catalytic-site inactivation of CAF1 did not abolish in vivo function | Ohn et al., *Nucleic Acids Research*, 2007, Apr; https://doi.org/10.1093/nar/gkm196 | (pqac-00000001, pqac-00000006, pqac-00000008) |
| Localization | Ccr4p and Caf1p localize primarily to the cytoplasm, consistent with a direct role in cytoplasmic mRNA turnover. | Primary | Subcellular localization in yeast coupled to mRNA decay assays | No specific fraction percentage reported | Tucker et al., *Cell*, 2001, Feb; https://doi.org/10.1016/S0092-8674(01)00225-2 | (pqac-00000011, pqac-00000023) |
| Stress localization | Under stress, Ccr4-Not subunits including Pop2/Caf1 can relocalize to P-bodies, whereas in unstressed cells Pop2/Ccr4 are not prominent P-body residents during ongoing decay. | Review | Synthesis of microscopy/localization literature | Deletion of CCR4 or POP2 causes only minor reduction in P-body formation | Miller & Reese, *Crit Rev Biochem Mol Biol*, 2012, Jun; https://doi.org/10.3109/10409238.2012.667214 | (pqac-00000015, pqac-00000026) |
| Deadenylation mechanism | Expert synthesis indicates Caf1 acts mainly on exposed/naked poly(A), is blocked by Pab1, and cannot efficiently proceed past non-A residues, whereas Ccr4 trims Pab1-protected poly(A). | Review | Comparative biochemical/structural review | Pan2/Pan3 acts on tails >150 nt; combined Ccr4/Caf1 action yields ~27-nt periodic decrements | Hagkarim & Grand, *Cells*, 2020, Oct; https://doi.org/10.3390/cells9112379 | (pqac-00000014, pqac-00000022) |
| Mutant phenotype: transcription elongation | caf1/pop2 mutants show 6-azauracil sensitivity and mycophenolic-acid sensitivity, supporting a genetic connection between CCR4-NOT and transcription elongation control. | Primary | Drug-sensitivity genetics | Qualitative 6AU and MPA sensitivity; rescue by excess guanine reported for CCR4-NOT defects | Denis et al., *Genetics*, 2001, Jun; https://doi.org/10.1093/genetics/158.2.627 | (pqac-00000016, pqac-00000017, pqac-00000025) |
| Mutant phenotype: rDNA stability | pop2Δ causes severe rDNA instability, accumulation of extrachromosomal rDNA circles, elevated E-pro noncoding RNA, and reduced rRNA, linking Pop2/Caf1 to rDNA maintenance. | Primary | PFGE, Southern/ERC assay, mutant reconstruction | ERCs ~50-fold above WT and ~4-fold above sir2; rRNA reduced to about half of WT | Hosoyamada et al., *Molecular and Cellular Biology*, 2020, Jan; https://doi.org/10.1128/MCB.00320-19 | (pqac-00000002, pqac-00000024) |
| Mediating/tethering role in rDNA pathway | In rDNA maintenance, Pop2 presence rather than Pop2 catalytic activity is needed because Pop2 tethers Ccr4 to the complex; pop2 deletion removes both Pop2 and Ccr4-associated deadenylase activity. | Primary | Catalytic-dead allele complementation with chromosomal phenotype readout | pop2 S44A,E46A complements rDNA instability, whereas ccr4 E556A does not | Hosoyamada et al., *Molecular and Cellular Biology*, 2020, Jan; https://doi.org/10.1128/MCB.00320-19 | (pqac-00000002, pqac-00000024) |
| Pathway role: autophagy | The yeast Ccr4-Not complex, containing Pop2/Caf1, directly deadenylates specific ATG mRNAs under nutrient-rich conditions to restrain basal autophagy and switches roles after nitrogen starvation to support induction. | Primary | Auxin-inducible depletion, ATG mRNA measurements, autophagy assays | Approx. 50% increase in ATG1, ATG7, ATG9, and ATG19 mRNAs upon Ccr4 depletion in the cited experiment | Yin et al., *Autophagy*, 2023, Feb; https://doi.org/10.1080/15548627.2022.2036476 | (pqac-00000018, pqac-00000027) |
| Recent quantitative estimate | Transcriptome-wide direct RNA sequencing/modeling in yeast estimated a global cytoplasmic deadenylation rate of about 10 A/min, providing a current systems-level benchmark for Ccr4-Not/Pan2/3-driven deadenylation. | Primary | Nanopore direct RNA sequencing and mathematical modeling | Transcriptomic deadenylation rate estimated at 10 A/min; RPG mRNAs constitute ~40% of transcriptome | Czarnocka-Cieciura et al., *The EMBO Journal*, 2024, published online Oct 11; https://doi.org/10.1038/s44318-024-00258-3 | (pqac-00000028) |
| Recent systems-level reinterpretation | Rapid depletion experiments indicate that for many yeast mRNAs, poly(A)-tail perturbation does not correlate strongly with stability, implying Pop2/Caf1-mediated deadenylation is critical for selected regulatory programs rather than universally rate-limiting decay. | Primary | Rapid depletion of deadenylases/decapping enzymes; transcriptome-wide poly(A) and stability measurements | Oligoadenylated states can vary by up to ~1000-fold in degradation speed across mRNAs (reviewed in introduction/context) | Audebert et al., *The EMBO Journal*, 2024, published online Sep 25; https://doi.org/10.1038/s44318-024-00250-x | (pqac-00000019) |


*Table: This table compiles key functional annotation evidence for the Saccharomyces cerevisiae Pop2/Caf1 protein (UniProt P39008), covering its CCR4-NOT complex role, catalytic properties, localization, mutant phenotypes, pathway functions, and recent quantitative systems-level estimates. It is useful as a concise evidence map linking specific claims to experimental approaches and citable sources.*