dcr1 (Dicer) — S. pombe — Curation Notes

UniProt: Q09884 (DCR1_SCHPO). PomBase: SPCC188.13c. 1374 aa. NCBITaxon:284812.

Summary

Dcr1 is the sole Dicer (ribonuclease III enzyme) of fission yeast. It is the
endoribonuclease that initiates RNAi by processing double-stranded RNA into ~22-23 nt
siRNA duplexes that are loaded onto Argonaute (Ago1). It is essential for
RNAi-directed heterochromatin formation at centromeres (and the mating-type locus,
telomeres), and hence for accurate chromosome segregation. It has additional reported
roles in co-transcriptional gene silencing (CTGS) at euchromatic loci, RNA Pol II/I/III
release / transcription termination at sites of replication stress (genome stability),
and in cell cycle / quiescence (G0).

Domain architecture

N-terminal DExD/H-box ATP-dependent RNA helicase (ATP-binding 32-MRTGAGKT-39; DECH box
145-DECH-148), Platform/PAZ-like region, tandem RNase III domains (RIIIa/RIIIb), and a
C-terminal extended dsRNA-binding fold with a novel zinc-binding (CHCC) motif important
for nuclear retention. Catalytic-dead allele D937A/D1127A abolishes siRNA generation.

Key evidence (verbatim)

RNase III / dsRNA processing into ~23 nt siRNA (MF core)

PMID:12482946
PMID:12482946
RNase III activity IDA from PMID:12482946.

Helicase / ATP-binding (domain-based, MF)

PMID:12482946
Note: helicase activity and ATP binding are domain/keyword-based; no direct demonstration of helicase catalysis in pombe Dcr1 found. Treat ATP binding as supported (structural motif), helicase activity as plausible but uncertain for catalysis.

dsRNA binding / dsDNA binding / zinc binding (MF)

PMID:21847092
PMID:21847092
PMID:21847092
Important caveat: PMID:21847092 — the C-terminal dsRBD dsRNA/dsDNA binding is dispensable for RNAi; the zinc motif's role is nuclear retention. So dsDNA binding is a real biochemical property but not the core functional contribution.

siRNA-mediated pericentric heterochromatin formation / H3K9me (BP core)

PMID:12193640
PMID:21847092
[PMID:15615848 amplification loop — Rdp1/Dicer self-enforcing loop coupling siRNA production to heterochromatin]
PMID:22895252

Chromosome segregation (BP, core/keep)

PMID:12482946

Co-transcriptional gene silencing (CTGS) at euchromatin (BP)

PMID:21151114
PMID:22431512

Subcellular location

PMID:21847092 (nucleus is functionally important)
PMID:22431512 euchromatin / cytosol / nuclear periphery IDA
PMID:21151114 chromatin / pericentric heterochromatin IDA
PMID:16823372 HDA cytoplasm/cytosol (global localization screen)

Transcription termination / Pol II,I,III release at replication stress (BP)

PMID:25417108
PMID:25417108
Caveat: this is Dcr1-specific and independent of canonical RNAi/Ago1; the GO terms "termination of RNA polymerase I/II/III transcription" capture this. Catalytic-dead and ago1Δ do NOT phenocopy at these loci.

Cell cycle / G0 quiescence (BP)

PMID:27738016
UniProt FUNCTION: "Required for G1 arrest and mating in response to nitrogen starvation."

Post-transcriptional regulation (BP, peripheral)

PMID:17981703

Stress robustness / Hsp104 feedback (BP, peripheral)

PMID:25543137

Mating-type silencing

PMID:16246721 (RNAi-directed nucleation at mat locus)

Curation decisions

• Core MF: ribonuclease III activity (IDA, ACCEPT), and the more specific GO:0016891
  RNA endonuclease activity producing 5'-phosphomonoesters (ACCEPT - mechanistically correct for RNase III).
• dsRNA binding: ACCEPT (IDA). dsDNA binding: KEEP_AS_NON_CORE (real but dispensable). zinc binding: ACCEPT.
• ATP binding: ACCEPT (domain motif). helicase activity not in GOA explicitly (only IEA keyword in uniprot DR); RNA binding IBA generalize/accept.
• DNA binding IEA (GO:0003677) is generic InterPro from helicase domain — MARK as over-general/MODIFY. Actually dsDNA binding is experimentally shown; generic DNA binding IEA is weak. MARK_AS_OVER_ANNOTATED.
• RNA processing IEA / gene expression IEA / hydrolase IEA: over-general, KEEP_AS_NON_CORE or accept as generic parents.
• BP core: siRNA-mediated pericentric heterochromatin formation; siRNA processing; CTGS; regulatory ncRNA-mediated gene silencing; chromosome segregation (keyword), silent mating-type cassette heterochromatin formation.
• Transcription termination Pol I/II/III: ACCEPT (well-supported, Dcr1-specific, PMID:25417108).
• G0 to G1 / quiescence: KEEP_AS_NON_CORE.
• negative regulation of gene expression (CACAO, PMID:17981703): KEEP_AS_NON_CORE (PTGS, peripheral).