# Microsporidian Encephalitozoon hellem inhibits host mitophagy by inducing ERAD to degrade BNIP3L

**Authors:** Ziyun Zou, Yibo Hu, Zhongxia Guan, Jiajing Chen, Qingyao Zhang, Yinze Han, Junyu Zhu, Chunxia Wang, Bing Han, Tian Li, Zeyang Zhou

PMC · DOI: 10.1371/journal.ppat.1014078 · PLOS Pathogens · 2026-03-23

## TL;DR

A microsporidian parasite inhibits host cell mitophagy by using a secreted protein to manipulate ERAD and histone acetylation, impairing mitochondrial cleanup.

## Contribution

Discovery of a novel parasite strategy to suppress mitophagy via ERAD activation and epigenetic regulation of BNIP3L degradation.

## Key findings

- EhPTP4, a secreted protein from Encephalitozoon hellem, induces ERAD components to degrade BNIP3L, a mitophagy regulator.
- EhPTP4 interacts with RCOR1 and histone H3 to modulate H3K14ac acetylation, influencing ERAD gene expression.
- This dual mechanism of ER stress and epigenetic control suppresses host mitophagy, aiding parasite survival.

## Abstract

Microsporidia are known intracellular pathogens that infect nearly all animals and deeply manipulate host mitochondrial homeostasis for survival. Here, we report a novel mechanism by which the human-pathogenic Encephalitozoon hellem modulates the mitophagy machinery of its host. We identified the secreted protein EhPTP4 as a key effector in disrupting selective degradation processes in the infected cells. EhPTP4 is found to localize within the nucleus of infected cells, where it induces increased expression of endoplasmic reticulum-associated degradation (ERAD) pathway components, including HSPA5, HERPUD1, and PDIA4. This induction enhances protein ubiquitination in host cells and leads to the degradation of BNIP3L, a critical regulator of mitophagy. Investigation into the molecular interaction network revealed that EhPTP4 interacts with host corepressor RCOR1 and histone H3. This interaction modulates histone acetylation, specifically at H3K14ac sites, thereby further influencing the expression of a key ERAD gene, HERPUD1. This study uncovers a sophisticated strategy by which microsporidia manipulates both ER stress response and the histone acetylation to suppress mitophagy. These findings provide new insights into the mechanisms of microsporidian pathogenesis.

Microsporidian parasites, known for their intricate manipulation of host cellular processes, have been found to employ novel mechanisms in disrupting mitochondrial homeostasis. This study investigates Encephalitozoon hellem, a human-pathogenic microsporidian, and its strategy to inhibit mitophagy, the cellular process responsible for degrading damaged mitochondria. The research reveals that E. hellem secretes a key effector protein, EhPTP4, which localizes within the nucleus of host cells. This protein enhances the expression of components related to the Endoplasmic Reticulum-Associated Degradation (ERAD) pathway, leading to increased degradation of BNIP3L, a crucial regulator of mitophagy. Without BNIP3L, the host’s ability to perform mitophagy is significantly impaired, potentially aiding the parasite’s survival. Furthermore, EhPTP4 interacts with RCOR1 and histone H3, influencing histone acetylation at specific sites (H3K14ac), which in turn affects the expression of ERAD-related genes. This dual regulation, via both ER stress pathways and epigenetic modifications, highlights a sophisticated strategy by E. hellem to suppress mitophagy. This study enhances our understanding of microsporidian pathogenesis and identifies potential therapeutic targets, offering insights into host-parasite interactions that could inform future treatments.

## Linked entities

- **Genes:** BNIP3L (BCL2 interacting protein 3 like) [NCBI Gene 665], HSPA5 (heat shock protein family A (Hsp70) member 5) [NCBI Gene 3309], HERPUD1 (homocysteine inducible ER protein with ubiquitin like domain 1) [NCBI Gene 9709], PDIA4 (protein disulfide isomerase family A member 4) [NCBI Gene 9601], RCOR1 (REST corepressor 1) [NCBI Gene 23186]
- **Proteins:** RLN3 (relaxin 3), RCOR1 (REST corepressor 1)
- **Species:** Encephalitozoon hellem (taxon 27973)

## Full-text entities

- **Genes:** PRL (prolactin) [NCBI Gene 5617] {aka GHA1, pPRL}, CACNA1E (calcium voltage-gated channel subunit alpha1 E) [NCBI Gene 777] {aka BII, CACH6, CACNL1A6, Cav2.3, DEE69, EIEE69}, DNM1L (dynamin 1 like) [NCBI Gene 10059] {aka DLP1, DRP1, DVLP, DYMPLE, EMPF, EMPF1}, HSPA5 (heat shock protein family A (Hsp70) member 5) [NCBI Gene 3309] {aka BIP, GRP78, HEL-S-89n}, CNTNAP1 (contactin associated protein 1) [NCBI Gene 8506] {aka CASPR, CHN3, CNTNAP, NRXN4, P190}, CXCR4 (C-X-C motif chemokine receptor 4) [NCBI Gene 7852] {aka CD184, D2S201E, FB22, HM89, HSY3RR, LCR1}, CASP3 (caspase 3) [NCBI Gene 836] {aka CPP32, CPP32B, SCA-1}, RCOR1 (REST corepressor 1) [NCBI Gene 23186] {aka COREST, RCOR}, SLC1A4 (solute carrier family 1 member 4) [NCBI Gene 6509] {aka ASCT1, SATT, SPATCCM}, NCCRP1 (NCCRP1, F-box associated domain containing) [NCBI Gene 342897] {aka FBXO50, NCCRP-1}, BNIP3L (BCL2 interacting protein 3 like) [NCBI Gene 665] {aka BNIP3a, NIP3L, NIX}, NUP62 (nucleoporin 62) [NCBI Gene 23636] {aka IBSN, SNDI, p62}, NLRX1 (NLR family member X1) [NCBI Gene 79671] {aka CLR11.3, DLNB26, NOD26, NOD5, NOD9}, KDM1A (lysine demethylase 1A) [NCBI Gene 23028] {aka AIMAH3, AOF2, BHC110, CPRF, KDM1, LSD1}, TOMM20 (translocase of outer mitochondrial membrane 20) [NCBI Gene 9804] {aka MAS20, MOM19, TOM20}, MAP1LC3B (microtubule associated protein 1 light chain 3 beta) [NCBI Gene 81631] {aka ATG8F, LC3B, MAP1A/1BLC3, MAP1LC3B-a}, SCAMP4 (secretory carrier membrane protein 4) [NCBI Gene 113178] {aka SCAMP-4}, TBCE (tubulin folding cofactor E) [NCBI Gene 6905] {aka HRD, KCS, KCS1, PEAMO, pac2}, HMGA1 (high mobility group AT-hook 1) [NCBI Gene 3159] {aka HMG-R, HMGA1A, HMGIY}, GM2A (ganglioside GM2 activator) [NCBI Gene 2760] {aka GM2-AP, GM2AP, SAP-3}, TP53 (tumor protein p53) [NCBI Gene 7157] {aka BCC7, BMFS5, LFS1, P53, TRP53}, HERPUD1 (homocysteine inducible ER protein with ubiquitin like domain 1) [NCBI Gene 9709] {aka HERP, HERPUD1-IT1, Mif1, SUP}, SLC5A3 (solute carrier family 5 member 3) [NCBI Gene 6526] {aka BCW2, SMIT, SMIT1, SMIT2}, SLC4A7 (solute carrier family 4 member 7) [NCBI Gene 9497] {aka NBC2, NBC3, NBCN1, SBC2, SLC4A6}, PDIA4 (protein disulfide isomerase family A member 4) [NCBI Gene 9601] {aka ERP70, ERP72, ERp-72}, APEX2 (apurinic/apyrimidinic endodeoxyribonuclease 2) [NCBI Gene 27301] {aka APE2, APEXL2, XTH2, ZGRF2}, DERL3 (derlin 3) [NCBI Gene 91319] {aka C22orf14, IZP6, LLN2, derlin-3}, PRKN (parkin RBR E3 ubiquitin protein ligase) [NCBI Gene 5071] {aka AR-JP, LPRS2, PARK2, PDJ}, PODXL2 (podocalyxin like 2) [NCBI Gene 50512] {aka EG, PODLX2}
- **Diseases:** Microsporidia (MESH:D016881), infection (MESH:D007239), ERAD (MESH:D055959), mitochondrial (MESH:D028361)
- **Chemicals:** PVDF (MESH:C024865), sodium azide (MESH:D019810), CCCP (MESH:D002258), Dulbecco's modified Eagle Medium (-), fatty acid (MESH:D005227), tricarboxylic acid (MESH:D014233), TritonX-100 (MESH:D017830), H2O2 (MESH:D006861), amino acid (MESH:D000596), Na2CO3 (MESH:C005686), Leu (MESH:D007930), KCl (MESH:D011189), phenol (MESH:D019800), 4',6-diamidino-2-phenylindole (MESH:C007293), SDS (MESH:D012967), paraformaldehyde (MESH:C003043), inositol (MESH:D007294), Trolox (MESH:C010643), sulfur (MESH:D013455), Tween 20 (MESH:D011136), DPBS (MESH:C012939), CO2 (MESH:D002245), His (MESH:D006639), sodium ascorbate (MESH:D001205), MG132 (MESH:C072553), Alexa Fluor 488 (MESH:C000711379), biotin (MESH:D001710), nitrogen (MESH:D009584), NaCl (MESH:D012965), lipid (MESH:D008055), Trp (MESH:D014364), Alexa Fluor 647 (MESH:C569686)
- **Species:** Encephalitozoon cuniculi (species) [taxon 6035], Mus musculus (house mouse, species) [taxon 10090], Oryctolagus cuniculus (domestic rabbit, species) [taxon 9986], Microsporidia (microsporidians, phylum) [taxon 6029], Homo sapiens (human, species) [taxon 9606], Encephalitozoon hellem (species) [taxon 27973], Hepatitis C Virus [taxon 11103], Listeria monocytogenes (species) [taxon 1639], Vittaforma corneae (species) [taxon 42399], Saccharomyces cerevisiae (baker's yeast, species) [taxon 4932], Hepatitis B virus (no rank) [taxon 10407], Ovis aries (domestic sheep, species) [taxon 9940]
- **Mutations:** C for 2-3, C for 3-5, R045A
- **Cell lines:** CCL-37 — Mus musculus (Mouse), Undefined cell line type (CVCL_M023), pGL3::luciferase — Mus musculus (Mouse), Mouse glioblastoma, Cancer cell line (CVCL_ZJ60), CRL-1573 — Sigmodon hispidus (Hispid cotton rat), Spontaneously immortalized cell line (CVCL_YD58), CRL-2522 — Homo sapiens (Human), Bloom syndrome, Transformed cell line (CVCL_7488), RK13 — Oryctolagus cuniculus (Rabbit), Spontaneously immortalized cell line (CVCL_3155), HEK293 — Homo sapiens (Human), Transformed cell line (CVCL_0045), HFF — Homo sapiens (Human), Finite cell line (CVCL_3285)

## Full text

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## Figures

9 figures with captions in the complete paper: https://tomesphere.com/paper/PMC13029686/full.md

## References

45 references — full list in the complete paper: https://tomesphere.com/paper/PMC13029686/full.md

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Source: https://tomesphere.com/paper/PMC13029686