The mystery of mitochondrial plasticity: TMBIM5 integrates metabolic state and proteostasis

How cellular cues alter the mitochondrial proteome and impact the composition of mitochondrial proteins remains poorly understood. In this issue of The EMBO Journal, Patron et al (2022) identify TMBIM5 as an important link between calcium homeostasis, proton motive force, and mitochondrial proteolysis, by which the organelle can modify its protein composition. The results may be crucial for our understanding of the plasticity of mitochondria.

Recent work identifies TMBIM5 as inner mitochondrial membrane Ca²⁺/H⁺ exchanger, linking hyperpolarisation regulation to proteome control and energy metabolism.

Mitochondria contain about 1,100 proteins (Morgenstern et al, 2021), yet their makeup varies between cell types, developmental stages, and physiologic conditions. Mitochondria may adapt their protein composition either by altering the steps of biogenesis, such as transcription, translation, and import, or by the selective degradation of proteins catalyzed by mitochondrial proteases. First, these proteases were thought to attack only damaged and unfolded peptides in order to prevent the accumulation of aberrant proteins. However, lately it has been appreciated that proteases also modify the mitochondrial proteome, and as a result mitochondrial function, by selectively degrading intact proteins (Deshwal et al, 2020). Of particular importance in that regard are two ATP‐dependent metallopeptidases of the inner mitochondrial membrane, known as i‐AAA and m‐AAA, respectively (Levytskyy et al, 2017).

While the significance of AAA proteases for mitochondrial homeostasis has been firmly established, it has remained unknown how their activities are regulated. In particular, it is not clear how AAA proteases sense the physiologic state of the cell and how this is transformed into the discriminatory removal of proteins. In this issue of The EMBO Journal, a novel mechanism is described that ascertains a link between the mitochondrial membrane potential and the activity of m‐AAA, which has profound implications for the composition of the mitochondrial proteome (Patron et al, 2022).

Patron et al (2022) discovered that m‐AAA interacts with TMBIM5 (MICS1), an inner membrane protein without hitherto established function. They demonstrate that TMBIM5 is a Ca²⁺/H⁺ exchanger that expels Ca²⁺ from mitochondria at the expense of the proton gradient. At the same time, TMBIM5 inhibits m‐AAA activity, which limits proteolysis. Thus, TMBIM5 stimulates respiration, stabilizes respiratory enzymes, and prevents the excessive accumulation of Ca²⁺ in the matrix. In other words, it promotes the well‐being of actively respiring mitochondria (Fig 1A). However, when mitochondria become hyperpolarized, TMBIM5 loses its inhibitory activity toward m‐AAA by a yet to be defined mechanism. The now active m‐AAA turns first on TMBIM5 and, if hyperpolarization persists, on other proteins of the mitochondria, leading to a broad remodeling of the proteome (Fig 1B). These data suggest that TMBIM5 is a critical element that coordinates mitochondrial protein turnover with the energetic status of the mitochondria.

Figure 1. Critical function of TMBIM5 in coordinating mitochondrial protein turnover with the energetic status.

(A) TMBIM5 is a Ca²⁺/H⁺ exchanger that has an inhibitory effect on m‐AAA. (B) TMBIM5 loses the inhibitory effect on m‐AAA in hyperpolarized mitochondria. Abbreviations: MCU, mitochondrial calcium uniporter complex; RC, respiratory chain complexes.

In terms of feedback control, it makes intuitively sense to believe that the mitochondrial membrane potential may have an effect on the m‐AAA activity because m‐AAA remodels proteins of the inner membrane, the site where the potential is created. More remarkable though is the link between m‐AAA activity and the mitochondrial Ca²⁺ cycle as demonstrated by Patron et al (2022). It is well established that mitochondria take up Ca²⁺ from the cytosol and release it back into the cytosol by independent influx and efflux pathways (Nicholls, 2005; Garbincius & Elrod, 2022). The Ca²⁺ cycle is significant for at least four reasons. First, it promotes oxidative phosphorylation because mitochondrial Ca²⁺ stimulates key respiratory and TCA cycle enzymes. Second, it allows cells to buffer transient spikes in the cytosolic Ca²⁺ concentration. Third, it ties mitochondria to transcriptional control mechanisms via retrograde signaling. And fourth, it may trigger apoptosis when excessive accumulation of Ca²⁺ in the mitochondrial matrix activates the permeability transition pore, collapsing the proton gradient and releasing mitochondrial contents (Garbincius & Elrod, 2022). In short, the mitochondrial Ca²⁺ cycle integrates the state of the organelle into the global state of the cell, which makes it an ideal regulator of the mitochondrial protein composition. The new findings by Patron et al (2022) are significant because they provide first mechanistic insight into how Ca²⁺ cycling, together with the membrane potential, is connected to mitochondrial plasticity. Beyond that, the paper is important because it identifies a specific protein of the Ca²⁺ efflux apparatus, the part of the Ca²⁺ cycle that is least understood.

This brings us to the question of what actually changes in the mitochondrial proteome in response to TMBIM5‐mediated m‐AAA activation. Patron et al (2022) used enzyme activity measurements and label‐free relative quantitative proteomics to find an answer. They showed, perhaps not unexpectedly, that a multitude of proteins are affected, defying a simple narrative. However, one m‐AAA substrate that clearly emerged from the data is respiratory complex I. The turnover of complex I is interesting because its many subunits cover a wide range of half‐lives (Morgenstern et al, 2021). Specifically, the peripheral arm of complex I, the one that was implicated in the current study, has a relatively short half‐life whereas the membrane arm of complex I belongs to the longest‐lived proteins of the cell (Bomba‐Warczak et al, 2021; Krishna et al, 2021). One may speculate that complex I plays a dual role in the regulation of the mitochondrial proteome where the membranous subunits form a stable platform that remains assembled throughout extended periods of time whereas the peripheral subunits undergo continuous degradation and re‐synthesis in order to tune the respiratory apparatus to the metabolic needs.

In summary, Patron et al (2022) identified a novel mechanism of proteome remodeling in mitochondria, one that is intertwined with the proton gradient and with Ca²⁺ cycling and, therefore, with the bioenergetics status of mitochondria. Of note, the Ca²⁺/H⁺ antiporter function of TMBIM5 was confirmed by a recent preprint (Austin et al, 2021) but was partially contradicted in a current study by Zhang et al (2022). Disagreements on the channel activity aside, the latter publication carries intriguing phenotypic data of a mouse TMBIM5 mutant that shows skeletal myopathy and increased perinatal mortality. Finally, some interesting questions arise from the work on TMBIM5. How does the novel Ca²⁺ channel sense the potential across the inner membrane, how is the ion transport activity of the channel related to its effect on the m‐AAA, and how does the m‐AAA achieve selective degradation of specific mitochondrial proteins?

Disclosure and competing interests statement

The authors declare that they have no conflict of interest.