Vps13D Encodes a Ubiquitin-Binding Protein that Is Required for the Regulation of Mitochondrial Size and Clearance

Abstract

The clearance of mitochondria by autophagy, mitophagy, is important for cell and organism health [1], and known to be regulated by ubiquitin. During Drosophila intestine development, cells undergo a dramatic reduction in cell size and clearance of mitochondria that depends on autophagy, the E1 ubiquitin-activating enzyme Uba1, and ubiquitin [2]. Here we screen a collection of putative ubiquitin-binding domain-encoding genes for cell size reduction and autophagy phenotypes. We identify the endosomal sorting complex required for transport (ESCRT) components TSG101 and Vps36, as well as the novel gene Vps13D. Vps13D is an essential gene that is necessary for autophagy, mitochondrial size, and mitochondrial clearance in Drosophila. Interestingly, a similar mitochondrial phenotype is observed in VPS13D mutant human cells. The ubiquitin-associated (UBA) domain of Vps13D binds K63 ubiquitin chains, and mutants lacking the UBA domain have defects in mitochondrial size and clearance and exhibit semi-lethality, highlighting the importance of Vps13D ubiquitin binding in both mitochondrial health and development. VPS13D mutant cells possess phosphorylated DRP1 and mitochondrial fission factor (MFF) as well as DRP1 association with mitochondria, suggesting that VPS13D functions downstream of these known regulators of mitochondrial fission. In addition, the large Vps13D mitochondrial and cell size phenotypes are suppressed by decreased mitochondrial fusion gene function. Thus, these results provide a previously unknown link between ubiquitin, mitochondrial size regulation, and autophagy.

Mutations in VPS13D lead to a new recessive ataxia with spasticity and mitochondrial defects

“…While this article was under review, Anding et al published findings showing VPS13D to be a ubiquitin‐binding protein affecting mitochondrial fission and fusion, consistent with our findings, and also implemented VPS13D in autophagy, a process that we have recently reported to be involved in ataxia …”

Recessive mutations in VPS13D cause childhood onset movement disorders

“…Yeast Vps13p (homologue of human VPS13A) has a role in mitochondrial stability and possibly impedes mitochondrial autophagy . Recently, Vps13D was shown to play a role in mitochondrial fission, clearance, and autophagy (mitophagy) in Drosophila , and its knockout in human HeLa cells led to enlarged mitochondria . Based on pairwise comparisons between VPS13 gene family members and yeast Vps13p, Velayos‐Baeza et al have identified the UBA domain (amino acid 2637–2673), which confers target specificity to multiple enzymes of the ubiquitination system .…”

“…Based on pairwise comparisons between VPS13 gene family members and yeast Vps13p, Velayos‐Baeza et al have identified the UBA domain (amino acid 2637–2673), which confers target specificity to multiple enzymes of the ubiquitination system . This domain is absent from other VPS13 proteins, and Anding et al have shown that this domain is in part responsible for the ability of VPS13D to regulate mitochondrial size . We did find some indications of mitochondrial alterations in muscle biopsy but found normal enzymatic activities in fibroblast cell lines.…”

“…VPS13D is part of the VPS13 family of ubiquitously expressed genes encoding 4 proteins highly conserved in eukaryotic cells (VPS13A–D) . Recently Vps13D has been shown to play an important role in mitochondrial size, autophagy, and clearance . Genetic defects in VPS13A lead to the neurodegenerative disorder choreoacanthocytosis (Online Mendelian Inheritance in Man database [OMIM] 200150), whereas mutations of VPS13B and VPS13C cause Cohen syndrome (OMIM 216550) and autosomal recessive early onset Parkinson disease (OMIM 616840), respectively .…”

Collaborative science unites researchers and a novel spastic ataxia gene

“…The gene is highly intolerant to missense variation and even more so to loss of function variants . VPS13D has recently been shown to be essential for mitochondrial metabolism in Drosophila , including viability, autophagy, and clearance . The gene is also essential in human cell lines, and its deletion leads to abnormal mitochondrial morphology .…”