RRP4

RRP4 (PF3D7_0410400) is a non-catalytic structural subunit of the RNA exosome core complex in Plasmodium falciparum (PMID:32487761). Recombinant PfRrp4 exhibits no exoribonuclease activity against either single- or double-stranded RNA in vitro, marking it as a scaffolding rather than a catalytic component of the exosome (PMID:29664138). In asexual-stage parasites the protein localizes to the cytoplasm by immunofluorescence (PMID:29664138), and in dual-tagged transgenic lines it co-localizes with the catalytic subunit PfRrp6 at the nuclear periphery, establishing its physical incorporation into the exosome core in vivo (PMID:32487761). Used as a marker for the core complex, PfRrp4 associates with RUF6 non-coding RNA loci by RIP-seq, placing the exosome at these loci, though the functional consequence at these sites was attributed to PfRrp6 rather than to RRP4 itself (PMID:32487761). Beyond its membership in the exosome core and this genomic occupancy, no independent regulatory or enzymatic function of RRP4 has been characterized in the available corpus.

1. 2018 Medium

   Whether PfRrp4 itself carries RNA-degrading activity was unknown; establishing that it does not clarified that the subunit is structural rather than catalytic within the exosome.

   Evidence In vitro exoribonuclease assay on recombinant protein against ssRNA and dsRNA substrates

   PMID:29664138

   Open questions at the time

   • A negative in vitro result does not exclude activity requiring cofactors or assembly into the full complex
   • Does not define which structural role RRP4 plays in the core
2. 2018 Medium

   The subcellular distribution of RRP4 was undefined; immunofluorescence localized it to the parasite cytoplasm during asexual stages, providing the first spatial context.

   Evidence Indirect immunofluorescence with anti-recombinant-protein antibody across asexual time points

   PMID:29664138

   Open questions at the time

   • Single-antibody, single-lab localization not reconciled with later nuclear-periphery signal
   • Does not address localization in sexual or other stages
3. 2020 Medium

   Whether RRP4 assembles with the catalytic exosome subunit in vivo was unresolved; reciprocal epitope tagging showed co-localization with PfRrp6 at the nuclear periphery, establishing RRP4 as a bona fide component of the exosome core complex.

   Evidence Co-immunofluorescence in a dual-tagged CRISPR-Cas9 line (PfRrp6-Ty1::HA-PfRrp4) with Western blot validation

   PMID:32487761

   Open questions at the time

   • Co-IFA shows co-localization but not direct physical interaction (no reciprocal Co-IP shown)
   • Nuclear-periphery signal contrasts with the earlier cytoplasmic localization
   • Stoichiometry and full subunit composition of the complex not defined
4. 2020 Medium

   The genomic targets of the exosome core were unknown; using tagged PfRrp4 as a marker, RIP-seq placed the complex at RUF6 ncRNA loci, linking the exosome to non-coding RNA regulation.

   Evidence RNA immunoprecipitation sequencing with Ty1-HA-tagged PfRrp4

   PMID:32487761

   Open questions at the time

   • Functional consequence at these loci was attributed to PfRrp6, not directly to RRP4
   • Does not establish whether RRP4 contributes to target selection or is merely a passive scaffold

• It remains unknown whether RRP4 has any function beyond passive incorporation into the exosome core, including its precise structural role, full interactome, and contribution to RNA processing.
• No genetic knockdown/knockout phenotype for RRP4 reported
• No structural model of the P. falciparum exosome core
• Direct physical interaction and stoichiometry with other subunits unresolved