Convergent Evolution: Shaping the import system of mitochondria

Evidence is accumulating that unrelated species have independently evolved the same way of importing proteins in their mitochondria.
  1. Kostas Tokatlidis  Is a corresponding author
  1. University of Glasgow, United Kingdom

Mitochondria are organelles that fulfil a variety of critical functions in eukaryotic cells, and the event that resulted in their creation two billion years ago – when a bacterium fused with an ancient cell – was a defining moment in the evolution of life (Gray et al., 1999). However, the mitochondrial genome encodes a mere 13 different polypeptides, so the vast majority of the roughly 1500 mitochondrial proteins are made in the cytosol, and then imported into the organelle. These proteins are recognized and processed by various complexes which are embedded in the two membranes (the inner and outer mitochondrial membrane) that enclose a mitochondrion (Schmidt et al., 2010; Dolezal et al., 2006).

The import proteins present in the mitochondrial membranes can fold to form one of two structures: an α-helix or a β-barrel. How β-barrel proteins are taken into the mitochondrial outer membrane in the first place has been studied in much detail, and this process requires the translocase complex of the outer membrane, or TOM, to work with a structure called SAM (sorting and assembly machinery). The TOM complex is thought to be the main entrance for all mitochondrial proteins, irrespective of their final location within the organelle.

By contrast, it is less clear how α-helix proteins are brought to the outer membrane of mitochondria. However, several studies have suggested that, in fungi, a third ‘MIM’ (for mitochondrial import machinery) complex is involved (Figure 1; Becker et al., 2008). So far, it is known that Mim1 and Mim2 – the two proteins that form the MIM complex – are present in fungi but not in other eukaryotes.

Protein import complexes in mitochondria.

The outer mitochondrial membrane (OM) contains embedded protein complexes – such as the SAM, TOM and MIM complexes – that import proteins from the cytosol into the mitochondria. The SAM and TOM complexes interact to import β-barrel proteins (left). Certain subunits in the complexes (Tom22, Tom40 and Sam50) are highly conserved in all eukaryotes. However, the MIM complex, which imports α-helix proteins (right), is only present in fungi. Vitali et al. now show that pATOM36, an import protein found in the trypanosome T. brucei, and the MIM complex are functionally equivalent, despite their sequences being very different. This presents an exciting case of convergent evolution in a core protein import machinery of mitochondria. TOM: translocase complex of the outer membrane; SAM: sorting and assembly machinery; MIM: mitochondrial import machinery.

IMAGE CREDIT: Dr Afroditi Chatzi.

Biochemical and genome analyses of the TOM and SAM complexes across different organisms show that only a few subunits (Tom22, Tom40 and Sam50) are conserved in all eukaryotes. It is likely that the protein import system in the bacteria that became the modern mitochondria was made from these subunits. Other subunits are not conserved: for example, sequence analyses of two subunits of the TOM complex, Tom20 and Tom70, indicated that they evolved separately in fungi and plants. However, structural experiments showed that these subunits have adopted common structures that allow them to recognize and import mitochondrial proteins (Perry et al., 2006).

This was the first time a process known as convergent evolution – when species that are not related independently evolve similar structures to perform identical roles – had been observed in the mitochondrial import system. Further studies revealed that the trypanosome T. brucei also has receptors that have evolved separately from those in fungi and animals, but then converged to perform the same role (Mani et al., 2015). Now, in eLife, Doron Rapaport of the University of Tübingen, André Schneider of the University of Bern, and colleagues – Daniela Vitali, Sandro Käser and Antonia Kolb (as joint first authors), and Kai Dimmer – report another exciting example of convergent evolution, this time not for accessory receptor subunits but for a core import complex (Vitali et al., 2018).

In T. brucei, a protein called pATOM36 is found in the outer membrane of the mitochondria, where it helps to import other proteins. It is not related to the Mim1 receptor found in fungi, and their sequences are very dissimilar, but Vitali et al. have found that fungi in which the MIM complex has been replaced with pATOM36 can still import proteins. However, pATOM36 is not as effective as Mim1, possibly because it has evolved to prefer substrates that are only found in trypanosomes.

Likewise, Vitali et al. show that the MIM complex can take the place of pATOM36 in trypanosomes, providing that Mim1 and Mim2 are expressed at approximately the same levels. These largely unexpected results suggest that the MIM complex and pATOM36 perform their roles alone; indeed, it is unlikely that they could have found molecular partners to work with when placed in an unfamiliar environment.

How can MIM and pATOM36 replace each other when they are so distantly related? Both are embedded in the outer mitochondrial membrane, and are formed of several subunits, but the exact topology of pATOM36 is unknown. Structural analyses may provide important clues because a similarity in their structure could explain the overlap in their function. This would not be unprecedented; for example, proteins found in yeast mitochondria and bacteria fold into similar structures that allow them to bind to the same types of molecules (Alcock et al., 2008).

Another possibility is that MIM and pATOM36 have distinct structures that work in different ways but reach the same outcome – and attach to the same proteins. Again this would not be unprecedented; enzymes present in yeast and bacteria can use distinct mechanisms to create identical chemical links known as disulfide bonds in proteins (Riemer et al., 2009).

The work of Vitali et al. provides an intriguing hint that convergent evolution may have added components to the ancestral core import machinery in a modular way. In the future, biochemical, structural and genomics analyses of distant species could be combined to provide interesting clues, and maybe some surprises, about the evolution of the protein import systems of mitochondria. These answers may help us understand how an ancestral bacterium morphed into the organelle that powers most eukaryotic species today.

References

Article and author information

Author details

  1. Kostas Tokatlidis

    Kostas Tokatlidis is in the Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow, United Kingdom

    For correspondence
    Kostas.Tokatlidis@glasgow.ac.uk
    Competing interests
    No competing interests declared
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6295-8183

Publication history

  1. Version of Record published: June 20, 2018 (version 1)

Copyright

© 2018, Tokatlidis

This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 1,790
    Page views
  • 228
    Downloads
  • 1
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Kostas Tokatlidis
(2018)
Convergent Evolution: Shaping the import system of mitochondria
eLife 7:e38209.
https://doi.org/10.7554/eLife.38209

Further reading

    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics
    Karolina Honzejkova, Dalibor Kosek ... Tomas Obsil
    Research Article

    Apoptosis signal-regulating kinase 1 (ASK1) is a crucial stress sensor, directing cells toward apoptosis, differentiation, and senescence via the p38 and JNK signaling pathways. ASK1 dysregulation has been associated with cancer and inflammatory, cardiovascular, and neurodegenerative diseases, among others. However, our limited knowledge of the underlying structural mechanism of ASK1 regulation hampers our ability to target this member of the MAP3K protein family towards developing therapeutic interventions for these disorders. Nevertheless, as a multidomain Ser/Thr protein kinase, ASK1 is regulated by a complex mechanism involving dimerization and interactions with several other proteins, including thioredoxin 1 (TRX1). Thus, the present study aims at structurally characterizing ASK1 and its complex with TRX1 using several biophysical techniques. As shown by cryo-EM analysis, in a state close to its active form, ASK1 is a compact and asymmetric dimer, which enables extensive interdomain and interchain interactions. These interactions stabilize the active conformation of the ASK1 kinase domain. In turn, TRX1 functions as a negative allosteric effector of ASK1, modifying the structure of the TRX1-binding domain and changing its interaction with the tetratricopeptide repeats domain. Consequently, TRX1 reduces access to the activation segment of the kinase domain. Overall, our findings not only clarify the role of ASK1 dimerization and inter-domain contacts but also provide key mechanistic insights into its regulation, thereby highlighting the potential of ASK1 protein-protein interactions as targets for anti-inflammatory therapy.

    1. Biochemistry and Chemical Biology
    Jake W Anderson, David Vaisar ... Natalie G Ahn
    Research Article

    Activation of the extracellular signal-regulated kinase-2 (ERK2) by phosphorylation has been shown to involve changes in protein dynamics, as determined by hydrogen-deuterium exchange mass spectrometry (HDX-MS) and NMR relaxation dispersion measurements. These can be described by a global exchange between two conformational states of the active kinase, named ‘L’ and ‘R,’ where R is associated with a catalytically productive ATP-binding mode. An ATP-competitive ERK1/2 inhibitor, Vertex-11e, has properties of conformation selection for the R-state, revealing movements of the activation loop that are allosterically coupled to the kinase active site. However, the features of inhibitors important for R-state selection are unknown. Here, we survey a panel of ATP-competitive ERK inhibitors using HDX-MS and NMR and identify 14 new molecules with properties of R-state selection. They reveal effects propagated to distal regions in the P+1 and helix αF segments surrounding the activation loop, as well as helix αL16. Crystal structures of inhibitor complexes with ERK2 reveal systematic shifts in the Gly loop and helix αC, mediated by a Tyr-Tyr ring stacking interaction and the conserved Lys-Glu salt bridge. The findings suggest a model for the R-state involving small movements in the N-lobe that promote compactness within the kinase active site and alter mobility surrounding the activation loop. Such properties of conformation selection might be exploited to modulate the protein docking interface used by ERK substrates and effectors.