Affinage

PFN3

Profilin-3 · UniProt P60673

Length
137 aa
Mass
14.6 kDa
Annotated
2026-04-28
23 papers in source corpus 6 papers cited in narrative 6 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

PFN3 (Profilin 3) is a testis-specific, intronless actin-binding protein essential for spermiogenesis, where it localizes to the Golgi complex, proacrosomal vesicles, and the acroplaxome-manchette complex and forms a stabilizing complex with ARPM1 (ACTRT3) in the perinuclear theca (PMID:34869336, PMID:41668650). Pfn3-knockout male mice exhibit type II globozoospermia with failed acrosome biogenesis, abnormal manchette and flagellum development, and subfertility, accompanied by mTOR activation, AMPK suppression, and impaired autophagy that disrupts proacrosomal vesicle fusion (PMID:34869336). The PFN3 locus also produces a natural antisense transcript overlapping SLC34A1, and co-expression of sense and antisense transcripts generates endo-siRNAs with tissue-specific strand selectivity (PMID:19237395, PMID:11867228).

Mechanistic history

Synthesis pass · year-by-year structured walk · 5 steps
  1. 2002 Medium

    Establishing that PFN3 is a distinct, intronless gene expressed exclusively in testis—not a kidney transcript—resolved confusion arising from its genomic overlap with SLC34A1 and localized its mRNA to late spermatogenic cells.

    Evidence Northern hybridization, in situ hybridization, and genomic sequencing in mouse tissues

    PMID:11867228

    Open questions at the time
    • Protein-level expression and subcellular localization in spermatids not yet demonstrated
    • No functional assays to determine requirement in spermatogenesis
  2. 2009 Medium

    Demonstrating that the PFN3 antisense transcript and SLC34A1 sense transcript are processed into endo-siRNAs revealed a non-coding regulatory function of the PFN3 locus beyond its protein-coding role.

    Evidence Sense/antisense co-expression in Xenopus oocytes with truncation mutagenesis and Northern blotting for endo-siRNAs

    PMID:19237395

    Open questions at the time
    • Physiological relevance of endo-siRNAs in regulating SLC34A1 or PFN3 protein levels in vivo not established
    • Mechanism of tissue-specific strand selectivity unknown
  3. 2021 High

    Genetic ablation of Pfn3 established it as essential for acrosome biogenesis and spermiogenesis, linking its function to AMPK/mTOR-regulated autophagy and proacrosomal vesicle trafficking, and identifying its subcellular localization and binding partners (ARPM1, TRIM27).

    Evidence CRISPR/Cas9 Pfn3 knockout mouse with immunofluorescence, co-IP, RNA-seq, Western blotting, and sperm functional assays

    PMID:34869336

    Open questions at the time
    • Direct biochemical mechanism by which PFN3 regulates AMPK/mTOR signaling not defined
    • Functional significance of the PFN3-TRIM27 interaction not characterized beyond co-IP
    • Whether PFN3 binds actin monomers in the canonical profilin manner during spermiogenesis is untested
  4. 2022 Medium

    Showing that sense (SLC34A1) and antisense (PFN3) transcription are concordantly regulated in cis via epigenetic changes clarified how the shared locus coordinates expression of both genes.

    Evidence CRISPR knock-in in renal cell lines, dexamethasone treatment, bisulfite sequencing, and ChIP for histone marks

    PMID:35202092

    Open questions at the time
    • Whether this cis-regulatory mechanism operates in testicular cells is unknown
    • Functional consequence of altered PFN3 antisense levels for SLC34A1 protein expression not measured in vivo
  5. 2026 Medium

    Reciprocal knockout studies confirmed that ARPM1 (ACTRT3) and PFN3 are mutually stabilizing subunits of a perinuclear theca complex required for acrosome biogenesis, with ARPM1 tethering PFN3 to the perinuclear theca.

    Evidence Actrt3 knockout mouse with co-IP, Western blotting, and immunofluorescence; reciprocal data from Pfn3-KO

    PMID:41668650

    Open questions at the time
    • Stoichiometry and structural basis of the PFN3-ARPM1 complex not determined
    • Whether additional actin-related proteins (ACTRT1, ACTRT2, ACTL7A) directly contact PFN3 is untested
    • Mechanism by which the complex promotes proacrosomal vesicle fusion remains undefined

Open questions

Synthesis pass · forward-looking unresolved questions
  • The direct biochemical activity of PFN3—whether it functions as a canonical profilin sequestering actin monomers or has acquired a distinct mechanism in the perinuclear theca—and how it mechanistically controls AMPK/mTOR signaling and autophagy during spermiogenesis remain open questions.
  • No in vitro actin-binding or polymerization assays reported for PFN3
  • No structural model of PFN3 or the PFN3-ARPM1 complex
  • Human genetic evidence linking PFN3 mutations to male infertility is lacking

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0008092 cytoskeletal protein binding 2
Localization
GO:0005634 nucleus 2 GO:0005794 Golgi apparatus 1 GO:0031410 cytoplasmic vesicle 1
Pathway
R-HSA-1266738 Developmental Biology 2 R-HSA-1474165 Reproduction 2 R-HSA-9612973 Autophagy 1
Partners
ACTRT3TRIM27
Complex memberships
PFN3-ARPM1 perinuclear theca complex

Evidence

Reading pass · 6 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2002 Human and mouse PFN3 (Profilin-III) genes are single-exon (intronless) genes located in close genomic vicinity to the renal sodium-phosphate transport gene SLC34A1 (NPT2). The ~4.5 kb 'PFN3 mRNA' detected in kidney by Northern hybridization is actually an SLC34A1 transcript that includes the antisense PFN3 open reading frame in its 3'-UTR, while genuine PFN3 mRNA (~1 kb) is expressed exclusively in testis. In situ hybridization localized PFN3 mRNA to cells in late-stage spermatogenesis. Northern hybridization, in situ hybridization, genomic sequencing Gene Medium 11867228
2009 An alternatively spliced PFN3 transcript serves as a natural antisense transcript (NAT) to SLC34A1 in mouse testis and kidney. Co-expression of sense (SLC34A1) and antisense (PFN3) transcripts in Xenopus oocytes leads to processing of the overlapping region into endo-siRNAs, requiring a minimum overlap of 29 base pairs. In mouse kidney the endo-siRNAs are complementary to the NAT, while in testis both orientations are found, indicating tissue-specific strand selectivity. In vitro sense/antisense co-expression in Xenopus oocytes, Northern blotting for endo-siRNAs, truncation experiments Nucleic acids research Medium 19237395
2021 PFN3 is essential for spermiogenesis: Pfn3-knockout male mice (generated by CRISPR/Cas9) are subfertile with type II globozoospermia, impaired acrosome biogenesis starting from the Golgi phase, abnormal manchette development, amorphous sperm head shape, and reduced sperm motility from flagellum deformities. Loss of PFN3 activates mTOR and suppresses AMPK, inhibiting autophagy (marked by LC3B accumulation and increased SQSTM1), which disrupts proacrosomal vesicle fusion needed for acrosome formation. PFN3 localizes to the Golgi complex, proacrosomal vesicles, and the acroplaxome-manchette complex during spermiogenesis. TRIM27 co-immunoprecipitates with PFN3 from testis extracts. ARPM1 is absent from the nuclear fraction of Pfn3-null testes and sperm, indicating PFN3 is required for stability of the PFN3-ARPM1 complex. Loss of PFN3 also leads to upregulation of cofilin-1, cofilin-2, and ADF. CRISPR/Cas9 knockout mouse, immunofluorescence/localization, co-immunoprecipitation, RNA-seq, Western blotting, sperm functional assays Frontiers in cell and developmental biology High 34869336
2022 Induction of SLC34A1/PFN3 locus transcription in renal cell lines by dexamethasone reduces sense promoter methylation and increases activating histone marks. Constitutive expression of a 5'-truncated SLC34A1 transcript stimulates antisense (PFN3) expression and vice versa, and this concordant expression acts in cis (since transient transfection fails to stimulate the opposite transcript), implicating local epigenetic changes in regulating PFN3 antisense transcription. CRISPR-Cas9 knock-in, dexamethasone treatment, bisulfite sequencing, ChIP for histone marks, transient transfection experiments Non-coding RNA Medium 35202092
2026 ACTRT3 (ARPM1) co-immunoprecipitates with PFN3 in murine spermatids, and ACTRT3-deficiency significantly reduces PFN3 protein levels, indicating ACTRT3 and PFN3 are part of the same complex in the perinuclear theca. Loss of ACTRT3 phenocopies aspects of Pfn3 deficiency including impaired acrosome biogenesis. Co-immunoprecipitation, Actrt3 knockout mouse model, Western blotting, immunofluorescence Development (Cambridge, England) Medium 41668650
2025 ARPM1 (ACTRT3) forms a complex with PFN3 in the perinuclear theca of spermatids; this interaction was demonstrated by co-immunoprecipitation. In Pfn3-deficient sperm, the ARPM1-PFN3 complex is lost. ARPM1 tethers PFN3 to the perinuclear theca to regulate Golgi-related acrosome development, and ARPM1 additionally interacts with ACTRT1, ACTRT2, ACTL7A, and ZPBP. Co-immunoprecipitation, Arpm1 knockout mouse, Western blotting, immunofluorescence bioRxivpreprint Medium bio_10.1101_2025.03.27.645694

Source papers

Stage 0 corpus · 23 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2011 Potential forensic application of DNA methylation profiling to body fluid identification. International journal of legal medicine 88 21626087
1996 Arabidopsis profilins are functionally similar to yeast profilins: identification of a vascular bundle-specific profilin and a pollen-specific profilin. The Plant journal : for cell and molecular biology 77 8771785
2013 Body fluid identification by integrated analysis of DNA methylation and body fluid-specific microbial DNA. International journal of legal medicine 67 24052059
2007 Genome sequence of Fusobacterium nucleatum subspecies polymorphum - a genetically tractable fusobacterium. PloS one 61 17668047
2012 DNA methylation-specific multiplex assays for body fluid identification. International journal of legal medicine 59 22653424
2021 MXD3 as an onco-immunological biomarker encompassing the tumor microenvironment, disease staging, prognoses, and therapeutic responses in multiple cancer types. Computational and structural biotechnology journal 39 34584637
2002 Genomic organization of profilin-III and evidence for a transcript expressed exclusively in testis. Gene 34 11867228
2009 Strand selective generation of endo-siRNAs from the Na/phosphate transporter gene Slc34a1 in murine tissues. Nucleic acids research 33 19237395
2011 Bending amplitude - a new quantitative assay of C. elegans locomotion: identification of phenotypes for mutants in genes encoding muscle focal adhesion components. Methods (San Diego, Calif.) 32 22126736
2006 Caenorhabditis elegans expresses three functional profilins in a tissue-specific manner. Cell motility and the cytoskeleton 30 16317718
2019 Pluronic gel-based burrowing assay for rapid assessment of neuromuscular health in C. elegans. Scientific reports 23 31645584
2013 A replication study for three nephrolithiasis loci at 5q35.3, 7p14.3 and 13q14.1 in the Japanese population. Journal of human genetics 22 23719187
2021 Loss of Profilin3 Impairs Spermiogenesis by Affecting Acrosome Biogenesis, Autophagy, Manchette Development and Mitochondrial Organization. Frontiers in cell and developmental biology 21 34869336
2001 Heterologous expression of the Bacillus pumilus endo-beta-xylanase (xynA) gene in the yeast Saccharomyces cerevisiae. Applied microbiology and biotechnology 14 11549015
2016 Natural antisense transcription from a comparative perspective. Genomics 12 27241791
2016 Distribution analysis of profilin isoforms at transcript resolution with mRNA-seq and secondary structure in various organs of Rattus norvegicus. Gene 11 27185630
2024 FHOD-1 and profilin protect sarcomeres against contraction-induced deformation> in C. elegans. Molecular biology of the cell 7 39259762
2022 Interdependent Transcription of a Natural Sense/Antisense Transcripts Pair (SLC34A1/PFN3). Non-coding RNA 4 35202092
2021 Profilin 3 genetic architecture in glioma formalin fixed paraffin embedded (FFPE) archive. Gene 3 33775850
2022 [Biocompatibility evaluation of electrospun PLCL/fibrinogen nanofibers in anterior cruciate ligament reconstruction]. Sheng wu yi xue gong cheng xue za zhi = Journal of biomedical engineering = Shengwu yixue gongchengxue zazhi 2 35788524
2026 "Zip-to-Cytosol": Glutathione-Cleavable Fluorinated Polyplexes Deliver siRNA at Single-Digit Nanomolar Dose with >90% Gene Silencing. Bioconjugate chemistry 0 41518301
2026 Actin-related protein T3 is required for acrosome biogenesis and sperm function in mice. Development (Cambridge, England) 0 41668650
2024 FHOD-1/profilin-mediated actin assembly protects sarcomeres against contraction-induced deformation in C. elegans. bioRxiv : the preprint server for biology 0 38559004