Ribosomal biogenesis regulator DIMT1 controls β-cell protein synthesis, mitochondrial function, and insulin secretion

Gaurav Verma,Alexander Bowen,Sevda Gheibi,Alexander Hamilton,Sowndarya Muthukumar,Luis Rodrigo Cataldo,Olof Asplund,Jonathan Esguerra,Alexandros Karagiannopoulos,Claire Lyons,Elaine Cowan,Cristian Bellodi,Rashmi Prasad,Malin Fex,Hindrik Mulder

doi:10.1016/j.jbc.2022.101692

Abstract

We previously reported that loss of mitochondrial transcription factor B1 (TFB1M) leads to mitochondrial dysfunction and is involved in the pathogenesis of type 2 diabetes (T2D). Whether defects in ribosomal processing impact mitochondrial function and could play a pathogenetic role in β-cells and T2D is not known. To this end, we explored expression and the functional role of dimethyladenosine transferase 1 homolog (DIMT1), a homolog of TFB1M and a ribosomal RNA (rRNA) methyltransferase implicated in the control of rRNA. Expression of DIMT1 was increased in human islets from T2D donors and correlated positively with expression of insulin mRNA, but negatively with insulin secretion. We show that silencing of DIMT1 in insulin-secreting cells impacted mitochondrial function, leading to lower expression of mitochondrial OXPHOS proteins, reduced oxygen consumption rate, dissipated mitochondrial membrane potential, and a slower rate of ATP production. In addition, the rate of protein synthesis was retarded upon DIMT1 deficiency. Consequently, we found that DIMT1 deficiency led to perturbed insulin secretion in rodent cell lines and islets, as well as in a human β-cell line. We observed defects in rRNA processing and reduced interactions between NIN1 (RPN12) binding protein 1 homolog (NOB-1) and pescadillo ribosomal biogenesis factor 1 (PES-1), critical ribosomal subunit RNA proteins, the dysfunction of which may play a part in disturbing protein synthesis in β-cells. In conclusion, DIMT1 deficiency perturbs protein synthesis, resulting in mitochondrial dysfunction and disrupted insulin secretion, both potential pathogenetic processes in T2D.

Highlights

Type 2 diabetes (T2D) is the result of dual defects of insulin secretion and action [1, 2]
Our studies showed that transcription factor B1 mitochondrial (TFB1M) deficiency leads to mitochondrial dysfunction and impaired insulin secretion resulting in diabetes [18]
Given that dimethyladenosine transferase 1 homolog (DIMT1) is a homolog of TFB1M, a methyltransferase implicated in mitochondrial function and T2D, we mined our human islet RNA sequencing database [20]

Summary

Results

DIMT1 expression in human islets, regulation in T2D, and correlations with glycemic traits. In cells treated with the mitochondrial uncoupler FCCP, the increase in TMRM fluorescence intensity from baseline was significantly more pronounced in scrambled siRNA-treated control cells than in DIMT1-silenced cells (Fig. 5, C and D) These observations indicate that DIMT1 deficiency dissipated the ΔΨm in EndoC-βH1 cells. We found that two of the upregulated genes, NBR1 (neighbor of BRCA1 gene 1) and DNAJC19 (DnaJ (Hsp40) homolog, subfamily C, member 19), are listed in the human Mitocarta inventory of genes (Human Mitocarta 2.0, Broad Institute), further suggesting a role of DIMT1 in mitochondrial function In view of these results, we reasoned that upregulation of NBR1 and DNAJC19 could be, at least partially, responsible for the impact of DIMT1 deficiency on insulin content and protein synthesis. Downregulation of INS1 transcripts could be an additional target of DIMT1 further impacting insulin secretion

Discussion

Experimental procedures

List of the differentially expressed genes after DIMT1 knockdown