Structural study of UFL1-UFC1 interaction uncovers the role of UFL1 N-terminal helix in ufmylation

Ufmylation plays a crucial role in various cellular processes including DNA damage response, protein translation, and ER homeostasis. To date, little is known about how the enzymes responsible for ufmylation coordinate their action. Here, we study the details of UFL1 (E3) activity, its binding to UFC1 (E2), and its relation to UBA5 (E1), using a combination of structural modeling, X-ray crystallography, NMR, and biochemical assays. Guided by Alphafold2 models, we generate an active UFL1 fusion construct that includes its partner DDRGK1 and solve the crystal structure of this critical interaction. This fusion construct also unveiled the importance of the UFL1 N-terminal helix for binding to UFC1. The binding site suggested by our UFL1-UFC1 model reveals a conserved interface, and competition between UFL1 and UBA5 for binding to UFC1. This competition changes in the favor of UFL1 following UFM1 charging of UFC1. Altogether, our study reveals a novel, terminal helix-mediated regulatory mechanism, which coordinates the cascade of E1-E2-E3-mediated transfer of UFM1 to its substrate and provides new leads to target this modification.

Loss of DDRGK1 impairs IRE1α UFMylation in spondyloepiphyseal dysplasia

Spondyloepiphyseal dysplasia (SEMD) is a rare disease in which cartilage growth is disrupted, and the DDRGK1 mutation is one of the causative genes. In our study, we established Ddrgk1fl/fl, Col2a1-ERT Cre mice, which showed a thickened hypertrophic zone (HZ) in the growth plate, simulating the previous reported SEMD pathology in vivo. Instead of the classical modulation mechanism towards SOX9, our further mechanism study found that DDRGK1 stabilizes the stress sensor endoplasmic reticulum-to-nucleus signaling 1 (IRE1α) to maintain endoplasmic reticulum (ER) homoeostasis. The loss of DDRGK1 decreased the UFMylation and subsequently led to increased ubiquitylation-mediated IRE1α degradation, causing ER dysfunction and activating the PERK/CHOP/Caspase3 apoptosis pathway. Further DDRGK1 K268R-mutant mice revealed the importance of K268 UFMylation site in IRE1α degradation and subsequent ER dysfunction. In conclusion, DDRGK1 stabilizes IRE1α to ameliorate ER stress and following apoptosis in chondrocytes, which finally promote the normal chondrogenesis.

A missense mutation in DDRGK1 gene associated to Shohat-type spondyloepimetaphyseal dysplasia: Two case reports and a review of literature

Spondylo-epi-metaphyseal dysplasia Shohat type (SEMDSH, OMIM # 602557) is a rare skeletal dysplasia. Until recently, only eight patients of five families have been reported. The disorder is characterized by severely disproportionate short stature with a short neck, small trunk with abdominal distension, and short lower limbs. Joint laxity and bowed legs are seen. The same homozygous splicing pathogenic variant in the DDRGK1 gene was found in four Iraqi families. Here we report a homozygous missense pathogenic variant in DDRGK1 in two children from unrelated two Moroccan families. The clinical and radiological phenotypes of the affected children were similar to those previously described.

Salubrinal, a novel inhibitor of eIF-2α dephosphorylation, promotes erythropoiesis at early stage targeted by ufmylation pathway

Ufmylation was proved to play a crucial role in hematopoietic stem cell (HSC) survival and erythroid differentiation, ufmylation deficiency induces acute anemia and lethality of embryos and adults in mouse models. To screen some compounds to rescue phenotypes induced by gene deletion, in this study, we used DDRGK1^F/F ; CreERT2 conditional knockout mice, DDRGK1^F/F ; CreERT2 bone marrow (BM) and fetal liver cells (FL), Uba5, and DDRGK1 knockdown human CD34 cell in vivo and in vitro, we found salubrinal, a novel inhibitor of eIF-2α dephosphorylation, promoted erythropoiesis at early stage, and partly rescued the acute anemia induce by DDRGK1 deficiency through upregulation of ufmylation and erythroid transcription factors. In phenylhydrazine (PHZ)-induced hemolytic anemia mice, interestingly, salubrinal could significantly improve hemocrit and red blood cell (RBC) indices of the mice treated with PHZ via upregulation of ufmylation. Its novel function was verified to attenuate unfolded protein response (UPR) and cell death programs, and to keep endoplasmic reticulum (ER) homeostasis in HSCs. Taken together results, it suggested that salubrinal may be a promising antianemic agent targeted by ufmylation.

Low expression of CDK5RAP3 and DDRGK1 indicates a poor prognosis in patients with gastric cancer

AIM

To investigate the effects of different levels of expression of CDK5RAP3 and DDRGK1 on long-term survival of patients undergoing radical gastrectomy.

METHODS

The expression of CDK5RAP3 and DDRGK1 was detected by immunohistochemistry in 135 patients who received standard gastrectomy were enrolled in the study. Western Blot was used to detect the expression of CDK5RAP3 and DDRGK1 in gastric cancer and its adjacent tissues and cell lines. The correlations between the expression of CDK5RAP3 and DDRGK1 and clinicopathological factors were analyzed, and the value of each parameter to the prognosis of the patients was compared. Receiver operating characteristic analysis was used to compare the accuracy of the prediction of clinical outcome by the parameters.

RESULTS

CDK5RAP3 and DDRGK1 expression was down-regulated in the gastric cancer compared to its respective adjacent non-tumor tissues. The expression of CDK5RAP3 was closely related to the age of the patients (P = 0.035) and the T stage of the tumor (P = 0.017). The expression of DDRGK1 was correlated with the sex of the patients (P = 0.080), the degree of tumor differentiation (P = 0.036), the histological type (P = 0.036) and the N stage of the tumor (P = 0.014). Low expression CDK5RAP3 or DDRGK1 is a poor prognostic factor for gastric cancer patients. Prognostic analysis showed that the co-expression of CDK5RAP3 and DDRGK1 was an independent prognostic factor correlating with the overall survival of gastric cancer patients. Combined expression analysis of CDK5RAP3 and DDRGK1 may provide a more accurate prognostic value for overall survival.

CONCLUSION

The co-expression of CDK5RAP3 and DDRGK1 is an independent prognostic factor for gastric cancer, which can provide a more accurate model for the long-term prognosis.

Association analyses of variants of SIPA1L2, MIR4697, GCH1, VPS13C, and DDRGK1 with Parkinson's disease in East Asians

A recent large-scale European-originated genome-wide association data meta-analysis followed by a replication study identified 6 new risk loci for Parkinson's disease (PD), which include rs10797576/SIPA1L2, rs117896735/INPP5F, rs329648/MIR4697, rs11158026/GCH1, rs2414739/VPS13C, and rs8118008/DDRGK1. However, whether these new loci are associated with PD in Asian populations remain elusive. The INPP5F is nonpolymorphic in Asians. The present study aimed to understand the effects of the other 5 new loci in a Han Chinese population comprising 579 sporadic PD patients and 642 controls. Significant associations with PD were observed in the variants of SIPA1L2 (p = 0.001) and VPS13C (p = 0.007), where the T (odd ratio [OR] = 1.484, 95% confidence interval [CI] 1.186-1.858) and A (OR = 1.362, 95% CI 1.087-1.707) alleles serve as the risk alleles, respectively. The genotype distributions in the SIPA1L2 and VPS13C variants were also different between the patients and controls (p = 0.002 and p = 0.023, respectively). In contrast, no significant association with PD was found in the variants of MIR4697, GCH1, and DDRGK1 either in allele or genotype frequencies. Noteworthy, a followed meta-analysis of East Asian studies suggested an association of the GCH1 variant with PD (p = 0.04, OR 1.08, 95% CI 1.00-1.16), while the other results are in line with those of our cohort. In conclusion, our study together with meta-analyses demonstrates that the variants of SIPA1L2 and VPS13C, potentially GCH1, but not of MIR4697 and DDRGK1, are associated with PD susceptibility in East Asians.

RCAD/BiP pathway is necessary for the proper synthesis of digestive enzymes and secretory function of the exocrine pancreas

Alcoholism causes an imbalance of endoplasmic reticulum (ER) homeostasis in pancreatic acini. In those cells, the ER is involved in the synthesis and folding of pancreatic enzymes. Ubiquitin-fold modifier 1 (Ufm1) is part of a novel ubiquitin-like modification system involved in maintaining ER homeostasis. Among the components of the Ufm1 system, Regulator of C53 and DDRGK1 (RCAD) has recently been identified as a Ufm1-specific E3 ligase that promotes ufmylation of DDRGK1, an RCAD-interacting protein. We determined the importance of RCAD in the proper synthesis and secretion of pancreatic enzymes using mice with genetically deleted RCAD. The pancreas of RCAD-deficient mice was of normal size and histology. Using quantitative PCR and Western blotting, we found that amylase was upregulated in pancreas organs from RCAD-knockout (KO) mice. Constitutive amylase secretion was much higher in isolated pancreatic acini from RCAD KO mice, whereas CCK-stimulated amylase secretion was disturbed. RCAD deficiency caused a downregulation in expression of ER chaperone BiP, which affected ER homeostasis and activated both apoptosis and trypsin. We also found that both RCAD and DDRGK1 transcript levels were upregulated in pancreatic acini from alcohol-preferring rats. Elevated expression of RCAD and DDRGK1 was associated with increased ER stress and UPR activation. Because of the lack of BiP expression, caspase 3 and trypsin activation we enhanced in RCAD-deficient pancreatic acini upon treatment with ethanol and CCK. In conclusion, the RCAD/BiP pathway is required for proper synthesis and secretion of pancreatic enzymes. In alcoholism, increased levels of components of the Ufm1 system could prevent the deleterious effects of alcohol in the pancreas by regulating BiP levels.NEW & NOTEWORTHY RCAD/BiP pathway is required for the proper synthesis and secretion of amylase from pancreatic acini, as well as for the maintenance of the ER homeostasis. In alcoholism, the exocrine pancreas could increase the levels of components of the Ufm1 system to protect itself from alcohol's deleterious effects by regulating the expression of ER chaperone BiP.

DDRGK1 in urine indicative of tubular cell injury in intensive care patients with serious infections

BACKGROUND

Acute kidney injury (AKI) is a life threatening condition. Despite intensive care treatment the occurrence cannot be predicted as very little indicators exist for direct measurement when tubular epithelial cell injury takes place. We therefore searched for novel peptide indicators expressed at intracellular level at the proximal kidney tubule for its appearance in urine samples.

OBJECTIVES

Establishing a test for urinary C20orf116 protein measurement.

PATIENTS AND METHODS

Generation of immunoreagents against C20orf116 also named DDRGK1. These were used to measure its presence in urine collected at 8-24 hours interval in a prospective study from 99 ICU patients at 4-6 time points. These patients received therapy because of serious infection and were categorized into 4 groups.

RESULTS

1) Ten tested highly for C20orf116 undergoing AKI graded Failure or Loss (3210 ± 4268 ng/mL) according to RIFLE criteria, all requiring renal replacement therapy (RRT) out of them 9 died. 2) Six patients with pre-existing kidney disease developed AKI and required RRT but had much lower C20orf116 levels of (33 ± 19), two of them died. 3) In contrast, out of 11 patients undergoing AKI grade Risk or Injury, four tested positive for C20orf116 but to much lower extent (66 ± 43) who recovered fully. 4) Out of 72 patients 25 tested positive (18 ± 12 ng/mL) not fulfilling criteria of AKI but with serum creatinine (sCr) rises of 1.2-1.4 (n = 52). Healthy donors (n = 48) showed no detectable C20orf116 at any time point.

CONCLUSIONS

C20orf116 excretion was detectable more than 24 hours before sCr rise could be measured; high level seemed to indicate severity of organ failure.