Phylogenetic and Molecular Evolutionary Analysis of Mitophagy Receptors under Hypoxic Conditions

Abstract

As animals evolved to use oxygen as the main strategy to produce ATP through the process of mitochondrial oxidative phosphorylation, the ability to adapt to fluctuating oxygen concentrations is a crucial component of evolutionary pressure. Three mitophagy receptors, FUNDC1, BNIP3 and NIX, induce the removal of dysfunctional mitochondria (mitophagy) under prolonged hypoxic conditions in mammalian cells, to maintain oxygen homeostasis and prevent cell death. However, the evolutionary origins and structure-function relationships of these receptors remain poorly understood. Here, we found that FUN14 domain-containing proteins are present in archaeal, bacterial and eukaryotic genomes, while the family of BNIP3 domain-containing proteins evolved from early animals. We investigated conservation patterns of the critical amino acid residues of the human mitophagy receptors. These residues are involved in receptor regulation, mainly through phosphorylation, and in interaction with LC3 on the phagophore. Whereas FUNDC1 may be able to bind to LC3 under the control of post-translational regulations during the early evolution of vertebrates, BINP3 and NIX had already gained the ability for LC3 binding in early invertebrates. Moreover, FUNDC1 and BNIP3 each lack a layer of phosphorylation regulation in fishes that is conserved in land vertebrates. Molecular evolutionary analysis revealed that BNIP3 and NIX, as the targets of oxygen sensing HIF-1α, showed higher rates of substitution in fishes than in mammals. Conversely, FUNDC1 and its regulator MARCH5 showed higher rates of substitution in mammals. Thus, we postulate that the structural traces of mitophagy receptors in land vertebrates and fishes may reflect the process of vertebrate transition from water onto land, during which the changes in atmospheric oxygen concentrations acted as a selection force in vertebrate evolution. In conclusion, our study, combined with previous experimental results, shows that hypoxia-induced mitophagy regulated by FUDNC1/MARCH5 might use a different mechanism from the HIF-1α-dependent mitophagy regulated by BNIP3/NIX.

The Oxymonad Genome Displays Canonical Eukaryotic Complexity in the Absence of a Mitochondrion

“…As might be expected, we could not find any orthologs of the proteins specifically involved in mitophagy (i.e., SLT2, UTH1, PTC6, FUNDC1, BNIP3, and BNIP3L) or pexophagy (i.e., PINK1, PARK2, PEX3, and PEX14) encoded in the M. exilis genome. Although a comprehensive analysis of the mitophagy-specific machinery, with deep sampling of eukaryotic genomes, has not been performed, analyses have shown that at least some of the machinery is conserved across the breadth of eukaryotes (Wu et al. 2017).…”

Endoplasmic Reticulum–Mitochondrial Contactology: Structure and Signaling Functions

“…Besides the Grp75/VDAC1 complex, IRBIT (AHCYL1), an IP3Rs binding protein released with IP3 has also been shown to promote ER-to-mitochondrial Ca 2+ signal propagation and ER-mito contact formation dependent on its phosphorylation [115]. Very recently, FUNDC1, a small integral OMM protein earlier known as a MAM-associated mitophagy receptor (reviewed in [116]) has been put forward as a binding partner with IP3R (IP3R2), MAM promoter and IP3R–to-mitochondria Ca 2+ signaling promoter in cardiac muscle [117]. However, the significance of this potential interaction in local Ca 2+ communication will need further elucidation since FUNDC1 deletion seemed to be associated with diminished levels of IP3R2 and the MAM regulator PACS2, and caused diminished IP3R-mediated cytosolic [Ca 2+ ] signals [117].…”

Mitophagy in Cancer: A Tale of Adaptation

“…FUN14 Domain Containing 1 (FUNDC1) is another OMM protein capable to bind directly LC3 and trigger mitophagy (Figure 1) [62,63]. Alike BNIP3 and NIX, also FUNDC1 can trigger hypoxia-induced mitophagy [62]—even though it is not a HIF1α target [64]—and its phosphorylation in the LIR domain (serine 17) can increase its affinity for LC3 [65]. Interestingly, FUNDC1 can interact with both Opa1 and DRP1 and this interaction is modulated by FUNDC1 phosphorylation on serine 13.…”