Determinism and contingencies shaped the evolution of mitochondrial protein import

Mitochondrial protein import requires outer membrane receptors that evolved independently in different lineages. Here we used quantitative proteomics and in vitro binding assays to investigate the substrate preferences of ATOM46 and ATOM69, the two mitochondrial import receptors of Trypanosoma brucei. The results show that ATOM46 prefers presequence-containing, hydrophilic proteins that lack transmembrane domains (TMDs), whereas ATOM69 prefers presequence-lacking, hydrophobic substrates that have TMDs. Thus, the ATOM46/yeast Tom20 and the ATOM69/yeast Tom70 pairs have similar substrate preferences. However, ATOM46 mainly uses electrostatic, and Tom20 hydrophobic, interactions for substrate binding. In vivo replacement of T. brucei ATOM46 by yeast Tom20 did not restore import. However, replacement of ATOM69 by the recently discovered Tom36 receptor of Trichomonas hydrogenosomes, while not allowing for growth, restored import of a large subset of trypanosomal proteins that lack TMDs. Thus, even though ATOM69 and Tom36 share the same domain structure and topology, they have different substrate preferences. The study establishes complementation experiments, combined with quantitative proteomics, as a highly versatile and sensitive method to compare in vivo preferences of protein import receptors. Moreover, it illustrates the role determinism and contingencies played in the evolution of mitochondrial protein import receptors.

Intracellular endosymbionts lack protein import systems, whereas such systems are a defining feature of mitochondria and plastids, both of which evolved from bacterial endosymbionts (1–3). Today, more than 95% of all mitochondrial proteins are imported from the cytosol, which makes mitochondrial protein import a key process required for mitochondrial biogenesis (4–6). The question of how mitochondrial protein import evolved is therefore central to understand how the endosymbiotic bacterial ancestor of mitochondria converted into an organelle that is genetically integrated into the host cell (7–9).Proteins are targeted to mitochondria by internal or external import signals, the most frequent one of which is the N-terminal presequence found in 60 to 70% of all imported proteins (10, 11). Interestingly, the various mitochondrial import signals are conserved even between highly diverged eukaryotes (6). The import signals are decoded by receptors, which are integral mitochondrial outer membrane (OM) proteins that are associated with the heterooligomeric protein translocase of the OM (TOM complex) (6, 12). Contrary to the core components of the TOM complex (Tom40, Tom22, and Tom7), which are highly conserved in essentially all eukaryotes, these receptors evolved independently in different eukaryotic lineages, even though they recognize the same conserved import signals (6).The best studied prototypical import receptors are Tom20 and Tom70 of yeast, orthologs of which are found in all members of the eukaryotic supergroup of the opisthokonts (13). Tom20 is an N-terminally anchored OM membrane protein, and its cytosolic domain contains a single tetratricopeptide repeat (TPR). Tom20 preferentially recognizes precursor proteins that have N-terminal presequences. It binds to the hydrophobic surface of the presequence and transfers the precursors to the highly conserved Tom22 that functions as a secondary receptor (14–17). Tom70 is the primary receptor for proteins that have multiple membrane spanning domains, such as mitochondrial carrier proteins, but also binds to hydrophobic precursor proteins that have presequences (18–20). Moreover, it has been shown that binding of Tom70 to the mitochondrial presequence-like stretches that are present in the mature part of many precursor proteins increases the import efficiency (21). Tom70 is N-terminally anchored in the membrane. Its large cytosolic domain consists of 11 TPR motifs. The three TPR motifs proximal to the membrane interact with cytosolic Hsp70 or Hsp90, from which Tom70 can receive precursor proteins (22, 23). The remaining eight TPR motifs directly recognize substrate proteins (24, 25). In yeast, Tom20 and Tom70 have partially redundant functions. Tom70 is not essential for growth and respiration. Loss of Tom20 causes a stronger phenotype; it abolishes respiration but is not lethal. Finally, even the deletion of Tom70 and Tom20 does not kill the cells, provided that the secondary receptor Tom22 is still present (15, 26–29).A single import receptor, termed Tom20, is associated with the TOM complex of plant mitochondria. Yeast and plant Tom20 (30) are superficially similar: both have a single transmembrane domain (TMD) and a soluble domain containing one (in yeast) and two TPR motifs (in plants). Furthermore, both proteins have the same domain organization provided that they are aligned in an antiparallel way. Thus, whereas yeast Tom20 is N-terminally anchored, plant Tom20 is a C-terminally anchored protein. This strongly suggests that yeast and plant Tom20, while both being import receptors, have different evolutionary origins (31, 32). Moreover, plants have another TPR domain-containing OM protein, termed OM64, that is not associated with the TOM complex, but implicated in protein import (31, 33).ATOM46 and ATOM69 are the two receptor subunits of the atypical translocase of the OM (ATOM) of trypanosomatids (34). ATOM69 is superficially similar to yeast Tom70. Both have the same molecular mass and multiple TPR-like motifs. ATOM69, in addition, has an N-terminal CS/Hsp20-like domain, which potentially can bind to cytosolic chaperones. Analogous to plant Tom20, ATOM69 is C-terminally membrane-anchored, whereas yeast Tom70 has an N-terminal TMD. ATOM46 also has an N-terminal membrane anchor and a cytosolic armadillo (ARM) repeat domain, a protein–protein interaction module specific for eukaryotes. The cytosolic domains of ATOM69 and ATOM46 were shown to bind a number of different precursor proteins and are essential for normal growth (34). ATOM69 and ATOM46 have been found in all kinetoplastids as well as in euglenoids (35). Except for the TPR domain in ATOM69, the two import receptors of trypanosomes do not resemble the TOM subunits of other species, indicating that they evolved independently from both the yeast and the plant receptors.Recently, an analysis of the TOM complex in Trichomonas vaginalis hydrogenosomes, which are mitochondria-derived hydrogen-producing organelles that lack their own genome (36), identified Tom36 and Tom46 (37). The two proteins are paralogues and consist of an N-terminal CS/Hsp20-like domain, three TPR-like sequences, and a C-terminal membrane anchor, which is reminiscent of trypanosomal ATOM69, although the mass of both hydrogenosomal proteins is much lower than that of ATOM69. Moreover, HHpred analysis, using Tom36 as a query, retrieved ATOM69 as the first hit (37). The cytosolic domains of Tom36 and Tom46 were able to bind hydrogenosomal precursor proteins, suggesting they may function as protein import receptors. However, despite the similarities between ATOM69 and Trichomonas Tom36/Tom46, phylogenetic analysis suggests that they evolved independently of each other, and therefore reflect yet another example of convergent evolution, although a diversification of a common ancestor cannot be ruled out (37).Here, we have investigated the substrate specificity of the trypanosomal import receptors ATOM46 and ATOM69 using inducible RNA interference (RNAi) cell lines and biochemical methods. We could correlate the observed receptor preference with specific features of the recognized substrate proteins, such as the presence of a predicted presequence, average hydrophobicity, and presence of TMDs. Moreover, we devised a method that allows for identification of which trypanosomal precursor proteins can be recognized by heterologous import receptors. Using this method, the mitochondrial proteomes are quantitatively compared between Trypanosoma brucei cell lines lacking either ATOM46 or ATOM69 and with T. brucei cell lines in which ATOM46 or ATOM69 were replaced by either Tom20 from yeast or Tom36 from Trichomonas.