qkr58E-1 (CG3613) encodes a nuclear KH-domain RNA-binding protein of the STAR (signal transduction and activation of RNA) family. Despite its quaking-related name, it belongs to an insect-specific expansion of the KHDRBS (Sam68/SLM) clade of STAR proteins rather than to the QKI/How subfamily. The protein has a single central type-I KH domain flanked by long disordered, basic and low-complexity regions. In cultured Drosophila cells it associates with many mRNAs, with targets enriched for genes that produce many transcript isoforms and for 5' UTR binding. It co-purifies with spliceosomal B and C complexes and with U2 snRNP proteins, and it co-immunoprecipitates with the nuclear m6A reader YT521-B. Knockdown alters fl(2)d alternative splicing, which supports a role as a regulator of selected alternative-splicing events. Its RNA recognition sequence, direct targets in vivo and organismal function have not been defined. The UniProt entry Q9W255 is the 396-residue PA product, the longest of three annotated polypeptides.
Existing Annotations Review
GO Term
Evidence
Action
Reason
GO:0000381 regulation of alternative mRNA splicing, via spliceosome
IBA GO_REF:0000033
ACCEPT
Summary: Inherited from the KHDRBS (Sam68/SLM) clade node PTN000879731, which contains qkr58E-1 and the other SF140 fly paralogs; corroborated by direct fly knockdown data.
Reason: PTN000879731 is the KHDRBS clade node (descendants include human KHDRBS1/2/3, rodent Khdrbs genes, qkr54B and every fly SF140 member, including qkr58E-1), and its donors include KHDRBS1/Sam68 (Q07666), a well-characterised regulator of alternative splicing. qkr58E-1 sits inside that clade, so the inheritance is phylogenetically sound. Independent target-specific support comes from PMID:27919077 Extended Data Fig. 10b, where Qkr58E-1 knockdown altered fl(2)d splicing, and from RIP-seq showing that its RNA targets are strongly enriched for ultracomplex (isoform-rich) genes. This supports regulation of selected events, not a general requirement for splicing.
Supporting Evidence:
file:DROME/qkr58E-1/qkr58E-1-nature20568.txt
Three proteins, Hrb27C, Qkr58E-1 and Nito, in addition to m 6 A components, control fl(2)d splicing in the same direction.
IC PMID:18981222 Conservation of the protein composition and electron microsc...
KEEP AS NON CORE
Summary: Curator inference from the protein's recovery in affinity-purified Drosophila spliceosomal B and C complexes. True in the sense of acting within spliceosomes, but peripheral to its regulatory role.
Reason: FlyBase inferred participation in splicing from the HDA spliceosome-complex assignments. The primary table lists QKR58E-1 among the fly proteins recovered, and PMID:26294687 adds protein interactions with the U2 snRNP proteins CG2807 (SF3B1) and CG16941 (SF3A1). Its relatives in the KHDRBS clade are splicing regulators, not core spliceosome components, and no evidence shows that qkr58E-1 is required for constitutive splicing. The curator's inference is retained but kept as non-core; regulation of alternative splicing (GO:0000381) is the core process.
Summary: Correct but very general; KH-domain mapping. RIP-seq evidence and the IBA support the more specific mRNA binding.
Reason: The KH domain (IPR004087) is an RNA-binding module, and QKR58E-1 associates with many mRNAs in RIP-seq, including 5' UTR-enriched targets. mRNA binding (GO:0003729), which the gene already carries by IBA, is the specific supported descendant.
Summary: Correct but general; the experimentally observed targets are mRNAs, so mRNA binding is the better term.
Reason: The type-I KH superfamily match (IPR036612) supports RNA binding, and the PTHR11208 family review treats RNA binding as the family-wide activity. For this protein, RIP-seq targets are mRNAs, so the existing IBA term mRNA binding (GO:0003729) is the specific supported descendant.
Summary: mRNA binding is inherited from a deep STAR-family node (PTN000129548), and target-specific RIP-seq data support it.
Reason: The donors (QKI, How, GLD-1, Arabidopsis STAR proteins) span the STAR radiation, and qkr58E-1 has an intact type-I KH domain, so inheriting mRNA binding is well founded. In S2R+ cells, tagged QKR58E-1 recovers specific mRNAs, with enrichment in 5' UTRs and in RNAs with 3' UTR extensions. Because RIP is done without crosslinking, the assay does not prove direct contact with every target, and no consensus motif is established for this protein.
HDA PMID:25294944 Subcellular localisations of the CPTI collection of YFP-tagg...
ACCEPT
Summary: The YFP protein-trap survey in embryos found the protein in the nucleus, consistent with its spliceosomal and splicing-regulatory associations.
Reason: Experimental high-throughput localization of the endogenous protein-trap fusion, scored without knowledge of which gene was tagged. This matches the nuclear spliceosome association and the interaction with the nuclear m6A reader YT521-B.
Summary: Nuclear activity is inherited across the STAR/SF1 family node and agrees with the fly HDA localization.
Reason: Nuclear localization is supported by experimental donors throughout the family (SF1, the KHDRBS proteins, QKI) and is corroborated for qkr58E-1 itself by the CPTI protein-trap HDA row. Its splicing-related associations place its activity in the nucleus.
HDA PMID:18981222 Conservation of the protein composition and electron microsc...
KEEP AS NON CORE
Summary: Recovered by mass spectrometry in affinity-purified fly spliceosomal B complexes; an experimental curator assignment, retained as non-core.
Reason: The primary study's protein table lists QKR58E-1 (CG3613) among proteins in the purified fly B/C complexes (checked through the indexed PMC table; the local cache is abstract-only, so the curator's assignment is trusted). Splicing-regulatory RBPs commonly co-purify with spliceosomes at sub-stoichiometric levels, and nothing indicates that qkr58E-1 is a stable structural component. The assignment is kept as non-core, not as a defining complex membership.
HDA PMID:18981222 Conservation of the protein composition and electron microsc...
KEEP AS NON CORE
Summary: Recovered in affinity-purified fly spliceosomal C complexes; retained as non-core for the same reasons as the B-complex assignment.
Reason: This is a high-throughput proteomic assignment by the FlyBase curator from a study that purified both B and C complexes. It is consistent with the U2 snRNP interactions reported in PMID:26294687, but it does not show that qkr58E-1 is a stoichiometric C-complex component or acts in the second catalytic step.
Here we affinity purified Drosophila melanogaster spliceosomal B and C complexes formed in Kc cell nuclear extract.
Core Functions
Nuclear KH-domain mRNA-binding protein of the KHDRBS (Sam68/SLM) STAR clade that associates with spliceosomal complexes and the m6A reader YT521-B and regulates selected alternative-splicing events, such as fl(2)d splicing.
Q: Does qkr58E-1 retain the QUA1 dimerization and QUA2 RNA-contact elements of KHDRBS/Sam68 proteins, and what RNA sequence does its KH-QUA2 unit recognise?
Q: Are the seven fly SF140 paralogs (qkr58E-1, -2, -3, nsr, CG10384, CG4021, CG3927) functionally redundant splicing regulators, or have they subfunctionalised by tissue?
Q: Which of the fly KHDRBS-clade proteins correspond to mammalian KHDRBS1/2/3 in splice-site selection, given that the fly genes are lineage-specific duplicates under PTN000879731?
Suggested Experiments
Experiment: CLIP-seq or iCLIP of endogenous qkr58E-1 in S2R+ cells or adult heads to map direct binding sites and test overlap with m6A sites and with fl(2)d and other YT521-B-dependent splice events.
Type: CLIP-seq
Experiment: In vitro binding (EMSA or SELEX) with purified KH-QUA2 protein to define its recognition motif.
Type: biochemical binding assay
External Prediction Reviews
These computational predictions are reviewed separately from the GOA annotation set used for this review. The assessments below are from this project and do not constitute official GO annotations or endorsement by GO/UniProt. They are not included in the existing annotation review above.
qkr58E-1 is a nuclear KH-domain RNA-binding protein associated with spliceosomes. The broad RNA-binding and gene-expression predictions are supported but less precise than existing functional assignments.
Review rationale: Spliceosomal processing and regulation of alternative mRNA splicing support a role in gene expression; existing GOA contains the more precise splicing assignments.
Supporting Evidence:
PMID:18981222: "Here we affinity purified Drosophila melanogaster spliceosomal B and C complexes formed in Kc cell nuclear extract."