Evolution of macromolecular import pathways in mitochondria, hydrogenosomes and mitosomes

Abstract

All eukaryotes require mitochondria for survival and growth. The origin of mitochondria can be traced down to a single endosymbiotic event between two probably prokaryotic organisms. Subsequent evolution has left mitochondria a collection of heterogeneous organelle variants. Most of these variants have retained their own genome and translation system. In hydrogenosomes and mitosomes, however, the entire genome was lost. All types of mitochondria import most of their proteome from the cytosol, irrespective of whether they have a genome or not. Moreover, in most eukaryotes, a variable number of tRNAs that are required for mitochondrial translation are also imported. Thus, import of macromolecules, both proteins and tRNA, is essential for mitochondrial biogenesis. Here, we review what is known about the evolutionary history of the two processes using a recently revised eukaryotic phylogeny as a framework. We discuss how the processes of protein import and tRNA import relate to each other in an evolutionary context.

Figure 1.

Occurrence of mitochondria, hydrogenosomes and mitosomes within the six eukaryotic supergroups. Branching order reflects the phylogenetic relationship of taxons but branch length is not to scale. All mitochondria-like organelles derive from the same endosymbiotic event. Hydrogenosomes and mitosomes evolved at least three and four times independently. The mitochondrial-like organelle in Blastocystis shows feature of mitochondria and hydrogenosomes and therefore blurs the distinction between these two organelles. Acronyms for species: Sc, Sacharomyces cerevisiae; Ec, Encephalitozoon cuniculi; Eh, Entamoeba histolytica; Dd, Dictyostelium discoideum; Tv, Trichomonas vaginalis; Gi, Giardia intestinalis; Eg, Euglena gracilis; Ra, Reclinomonas americana; Tp, Tetrahymena pyriformis; Pf, Plasmodium falciparum; Cp, Cryptosporidium parvum.

Figure 2.

The range in complexity of mitochondrial protein transport machines. The protein import machinery from yeast (Saccharomyces cerevisiae) is depicted. Protein substrates (black) translated on cytoplasmic ribosomes contain N-terminal, helical targeting segments that enable their binding to the TOM complex on the mitochondrial surface. There are seven components of the TOM complex, with the Tom40, Tom7 and Tom22 subunits (dark grey) being found generally in eukaryotes, while the other subunits (light grey) are found only in opisthokont. Similarly, the Sam50 subunit of the SAM complex has a common occurrence in eukaryotes, while the other subunits of this complex are more restricted. Four subunits of the TIM23 complex (dark grey) are common to the eukaryotic kingdoms, while the subunits shown in light grey are restricted in their occurrence and probably evolved later. The TIM22 complex might be considered a later addition to the protein import pathway (Schneider et al. 2008). Protein substrates pass from the TOM complex to either the SAM, TIM22 or TIM23 complexes for their transport to the outer membrane, inner membrane or matrix, respectively.

Figure 3.

Protein transport machines in ‘classic’ mitochondria and mitosomes: a tale from two kingdoms. The opisthokont kingdom includes fungi and microsporidia. Protein sequence similarity between species of fungi and microsporidia is high, enabling confident predictions of mitochondrial protein import components in microsporidia (Burri et al. 2006; Waller et al. 2009), and leading to the suggestion that microsporidia have managed a secondary loss of numerous modules from the protein import machinery. At least in the context of the small proteome likely for the mitosomes, small TIM chaperones and the TIM22 complex can be dispensed with and the TOM, SAM and TIM23 complexes can be highly simplified. In the case of Amoebozoa, we might anticipate that further components of the protein import machinery, specific to this lineage, might be found. In Dictyostelium discoideum, the common ‘core’ components in the TOM, TIM23 and TIM22 complexes and the small TIM chaperones are recognizable (Dolezal et al. 2006). However, much of this machinery appears to have been dispensed with secondarily in the amoeba E. histolytica.

Figure 4.

Occurrence of mitochondrial tRNA import. Unrooted phylogenetic tree of the six eukaryotic supergroups (indicated in capitals). Branching order reflects the phylogenetic relationship of taxons but branch length is not to scale. Bioinformatic analysis of complete mitochondrial genome sequences allows to predict whether the encoded tRNAs are sufficient to read all codons that are used by the corresponding mitochondrial translation systems. Based on this analysis, eukaryotes were divided into two groups: the ones having a complete set of mitochondrial tRNA genes (shown in dark grey) and the ones that lack a variable number of apparently essential mitochondrial tRNA genes (shown in light grey). Taxons shown were chosen to represent organisms having the most complete as well as the most reduced mitochondrial tRNA gene contents, respectively. The numbers of tRNA genes encoded in the different mitochondrial genomes are indicated. ‘All’ indicates that the mitochondrial-encoded tRNA gene set is complete and ‘0’ indicates complete absence of mitochondrial tRNA genes. If organisms retain a single mitochondrial tRNA gene only it is always the tRNA^Met. The minimal number of tRNAs required for mitochondrial translation is, depending on the wobble rules and the genetic code variations, between 20–22. Thus, all organisms having 20 or less mitochondrial tRNA genes must import at least some tRNAs from the cytosol. However, even in organisms having more than 22 mitochondrial tRNA genes, the set of mitochondrial-encoded tRNA is often not complete and import of cytosolic tRNAs is required. In most of these cases, it is the tRNA^Thr that is imported. In a few systems, import of a cytosolic tRNA that has the same decoding capacity as a still existing mitochondrial-encoded tRNA gene has been shown experimentally (shown underlined). Import of these tRNAs is expected to be redundant. Acronyms for species: Hs, Homo sapiens; Ve, Vanhornia eucnemidarum; Na, Neomaskellia andropogonis; My, Mizuhopecten yessoensis; Eb, Epiperipatus biolleyi; Hl, Hypospongia lachne; In, Igornella notabilis; Sp, Spizellomyces punctatus; Sc, Saccharomyces cerevisiae; Ng, Naegleria gruberi; Ra, Reclinomonas americana; Tp, Tetrahymena pyriformis; Pa, Paramecium aurelia; Pc, Polytomella capuana; Cr, Chlamydomonas reinhardtii; Sc, Scenedesmus obliquus; Pa, Pseudendoclonium akinetum; No, Nephroselmis olivacea; Mp, Marchantia polymorpha; Ec, Entamoeba castelanii; Pp, Physarum polycephalum; Dc, Dictyostelium citrinum.

Figure 5.

Current state of knowledge of mitochondrial tRNA import machineries. Components required for targeting and/or membrane translocation of tRNAs have been identified in yeast (S. cerevisiae), potato (Solanum tuberosum) and the Trypanosomatidae (L. tropica and T. brucei). Outer (OM) and inner mitochondrial membranes (IM) are indicated. Factors whose involvement in tRNA import has directly been shown are shaded in grey. Saccharomyces cerevisiae: the tRNA^Lys is targeted to mitochondria by enolase. Subsequently, the tRNA is co-imported with the precursor of mitochondrial lysyl-tRNA synthetase (pre-MSK). Pre-sequence of pre-MSK is shown as a box. Import of the tRNA^Lys is coupled to import of pre-MSK indicating that the entire protein import machinery is required for tRNA import. Saccharomyces tuberosum: the three outer membrane proteins VDAC, Tom40 and Tom20 are required to translocate tRNAs across the outer membrane. Unlike in yeast, tRNAs are not co-imported with proteins. Tom20 and Tom40 appear to function as receptors, whereas the VDAC may build the actual import channel. Trypanosomatidae: mitochondrial tRNA import has been analysed in detail in L. tropica. Inner membrane translocation of tRNAs appears to require a large protein complex termed RIC complex, consisting of six essential proteins (FeS-protein and subunit 6b of complex III, cytochrome oxidase subunit 6 of complex IV, F1a subunit of complex V and two unknown trypanosomatid specific proteins) and five non-essential proteins. In T. brucei, it was shown that eukaryotic elongation factor 1a (eEF1a) is essential for in vivo targeting of tRNAs to the mitochondria.