# Ubc9‐Mediated SUMOylation of RPL3, an Unappreciated Mechanism against Hepatocyte Senescence by Repressing the DHX9‐p16 Axis

**Authors:** Hao Xie, Zhichao Gao, Xin Liu, Shiyi Zhang, Yuhan Wang, Jia Gao, Ping Qi, Lu Zhang, Jiawei Zhao, Tian Xiong, Teng Huang, Jia Song, Qilin Yu, Shu Zhang, Yanjun Liu, Ping Yang, Maryam S. Al‐Motawa, Quan Gong, Junfeng Dong, Hao Yin, Fei Sun, Shiwei Liu, Cong‐Yi Wang

PMC · DOI: 10.1002/advs.202510240 · Advanced Science · 2025-10-20

## TL;DR

The paper shows that Ubc9-mediated SUMOylation of RPL3 prevents liver aging by blocking p16 expression, offering a new therapeutic target for liver diseases.

## Contribution

The study identifies a novel mechanism involving Ubc9-mediated SUMOylation of RPL3 to repress hepatocyte senescence via the DHX9-p16 axis.

## Key findings

- Reduced Ubc9 expression in aging livers correlates with increased hepatocyte senescence and MASLD susceptibility.
- Ubc9-mediated SUMOylation of RPL3 prevents its nuclear translocation and represses p16 expression.
- Targeting Ubc9 could be a promising therapeutic strategy for liver aging and related diseases.

## Abstract

Although Ubc9‐mediated SUMOylation are recognized to regulate the multiple aspects of hepatic biological processes, its impact on hepatic senescence and metabolic dysfunction‐associated steatotic liver disease (MASLD), however, is yet to be fully addressed. Herein noted an age‐dependent decrease of hepatic Ubc9 expression is first noted along with an escalated decrease of protein SUMOylation, which is coupled with enhanced senescent marker expressions both in humans and mice. Interestingly, Ubc9 is dispensable for liver development at the embryonic stage. However, Ubc9 deficiency in hepatocytes rendered mice with an exacerbated hepatic aging phenotype and more susceptible to fatty liver disease and steatohepatitis following the challenge of a methionine‐ and choline‐deficient (MCD)‐diet. Ii is further demonstrated that nuclear ribosomal protein L3 (RPL3) interacts with DExD/H‐box (DDX/DHX) helicases (DHX9), which then recruits RNA polymerase II to the p16 promoter to transcribe its expression, thereby exacerbating the hepatocyte aging process. However, Ubc9‐mediated SUMOylation prevents RPL3 nuclear translocation, by which it represses the expression of senescent markers such as p16 to attenuate the hepatic aging process. Together, the study highlights that Ubc9‐mediated SUMOylation of RPL3 could be an unappreciated mechanism against hepatic aging in clinical settings.

Liver aging is characterized by a decline in the expression of the SUMO‐conjugating enzyme Ubc9, resulting in reduced SUMOylation levels in hepatocytes, particularly in the case of ribosomal protein RPL3. Disruption of RPL3 SUMOylation increases its nuclear translocation. Interestingly, ribosome‐free RPL3 facilitates the recruitment of helicase DHX9 to the promoter region of p16 within the nuclear, subsequently engaging RNA Pol II and enhancing the expression of the aging trigger factor p16. Consequently, targeting Ubc9 holds promise as a therapeutic strategy for treating liver aging in clinical settings.

## Linked entities

- **Genes:** UBE2I (ubiquitin conjugating enzyme E2 I) [NCBI Gene 7329], RPL3 (ribosomal protein L3) [NCBI Gene 6122], DHX9 (DExH-box helicase 9) [NCBI Gene 1660], CDKN2A (cyclin dependent kinase inhibitor 2A) [NCBI Gene 1029]
- **Proteins:** UBE2I (ubiquitin conjugating enzyme E2 I), RPL3 (ribosomal protein L3), DHX9 (DExH-box helicase 9), RNA polymerase II (DNA-directed RNA polymerase II subunit RPB7)
- **Diseases:** metabolic dysfunction-associated steatotic liver disease (MONDO:0013209)

## Full-text entities

- **Genes:** Rpl3 (ribosomal protein L3) [NCBI Gene 27367] {aka F2, J1}, Cdkn2a (cyclin dependent kinase inhibitor 2A) [NCBI Gene 12578] {aka ARF-INK4a, Arf, INK4a-ARF, Ink4a/Arf, MTS1, Pctr1}, Ube2i (ubiquitin-conjugating enzyme E2I) [NCBI Gene 22196] {aka 5830467E05Rik, UBC9, Ubce2i, Ubce9}, Dhx9 (DExH-box helicase 9) [NCBI Gene 13211] {aka Ddx9, HEL-5, NDHII, RHA, mHEL-5}
- **Diseases:** fatty liver disease (MESH:D005234), metabolic dysfunction (MESH:D008659), MASLD (MESH:D008107)
- **Chemicals:** methionine (MESH:D008715), choline (MESH:D002794)
- **Species:** Homo sapiens (human, species) [taxon 9606], Mus musculus (house mouse, species) [taxon 10090]

## Full text

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## Figures

7 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12767081/full.md

## References

59 references — full list in the complete paper: https://tomesphere.com/paper/PMC12767081/full.md

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Source: https://tomesphere.com/paper/PMC12767081