DDRGK1, a crucial player of ufmylation system, is indispensable for autophagic degradation by regulating lysosomal function

Yan Cao,Yafei Cai,Shuo Liu,Yan Zou,Qiang Jiang,Honglin Li,Honglin Liu,Rongyang Li,Ming Shen,Chengyu Li,Chunwan Lu

doi:10.1038/s41419-021-03694-9

Yan Cao, Yafei Cai + Show 9 more

Open Access

https://doi.org/10.1038/s41419-021-03694-9

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Abstract

DDRGK domain-containing protein 1 (DDRGK1) is an important component of the newly discovered ufmylation system and its absence has been reported to induce extensive endoplasmic reticulum (ER) stress. Recently, emerging evidence indicates that the ufmylation system is correlated with autophagy, although the exact mechanism remains largely unknown. To explore the regulation mechanism of DDRGK1 on autophagy, in this study, we established an immortalized mouse embryonic fibroblast (MEF) cell lines harvested from the DDRGK1F/F:ROSA26-CreERT2 mice, in which DDRGK1 depletion can be induced by 4-hydroxytamoxifen (4-OHT) treatment. Here, we show that DDRGK1 deficiency in MEFs has a dual effect on autophagy, which leads to a significant accumulation of autophagosomes. On one hand, it promotes autophagy induction by impairing mTOR signaling; on the other hand, it blocks autophagy degradation by inhibiting autophagosome–lysosome fusion. This dual effect of DDRGK1 depletion on autophagy ultimately aggravates apoptosis in MEFs. Further studies reveal that DDRGK1 loss is correlated with suppressed lysosomal function, including impaired Cathepsin D (CTSD) expression, aberrant lysosomal pH, and v-ATPase accumulation, which might be a potential trigger for impairment in autophagy process. Hence, this study confirms a crucial role of DDRGK1 as an autophagy regulator by controlling lysosomal function. It may provide a theoretical basis for the treatment strategies of various physiological diseases caused by DDRGK1 deficiency.

Highlights

The ubiquitin-fold modifier 1 (Ufm1) conjugation system is a novel ubiquitin-like modification system that consists of a set of ubiquitin-like proteins (UBLs), including Ufm[1], Ufm1-activating E1 enzyme (Uba5), Ufm1-conjugating E2 enzyme (Ufc1), and Ufm1-specific E3 ligase (Ufl[1], known as RACD, NLBP and Maxer)[1,2,3]
We found that DDRGK domain-containing protein 1 (DDRGK1) deficiency led to cell apoptosis, for a subset of proapoptotic genes, including Noxa, Bim, and Bax were significantly upregulated and Bcl-2, an antiapoptotic gene were remarkably downregulated in mouse embryonic fibroblast (MEF) (Fig. 1d)
In the present study, we show that DDRGK1 deficiency in MEFs leads to an aberrant accumulation of autophagosomes due to the enhanced autophagy induction and impaired autophagic degradation, which aggravates apoptosis in MEFs

Summary

Introduction

The ubiquitin-fold modifier 1 (Ufm1) conjugation system is a novel ubiquitin-like modification system that consists of a set of ubiquitin-like proteins (UBLs), including Ufm[1], Ufm1-activating E1 enzyme (Uba5), Ufm1-conjugating E2 enzyme (Ufc1), and Ufm1-specific E3 ligase (Ufl[1], known as RACD, NLBP and Maxer)[1,2,3]. Recent studies have shown that DDRGK1 deficiency can cause a variety of physiological and pathological diseases, including hematopoietic dysfunction[8], impaired intestinal homeostasis[9], and compromised plasma cell development[10]. Macrophagy (hereafter referred to as autophagy), an evolutionary conserved biological process in eukaryotes, is considered to maintain cell homeostasis by engulfing the cytoplasmic proteins or damaged organelles in doublemembrane-bound structures, known as autophagosomes, and deliver them to the lysosome for degradation[11,12]. Autophagosome–lysosome fusion is another essential step in autophagy process It drives autophagic degradation, which is generally achieved by soluble N-ethylmaleimide-sensitive factor attachment protein receptor proteins (SNAREs). The STX17 (syntaxin 17)–SNAP29 (synaptosome associated protein 29)–VAMP8 (vesicle-associated membrane protein 8) complex is widely considered to mediate autophagosome–lysosome fusion[23,24]

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