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A Single Tim Translocase in the Mitosomes of Giardia Intestinalis Illustrates Convergence of Protein Import Machines in Anaerobic Eukaryotes

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A Single Tim Translocase in the Mitosomes of Giardia Intestinalis Illustrates Convergence of Protein Import Machines in Anaerobic Eukaryotes GBE A Single Tim Translocase in the Mitosomes of Giardia intestinalis Illustrates Convergence of Protein Import Machines in Anaerobic Eukaryotes Eva Pyrihova1,Alzbeta Motyckova1,Lubos Voleman1, Natalia Wandyszewska1, Radovan Fiser2, Gabriela Seydlova2,AndrewRoger3, Martin Kolısko3,4,*, and Pavel Dolezal1,* 1Department of Parasitology, Faculty of Science, Charles University, Vestec, Czech Republic 2Department of Genetics and Microbiology, Charles University, Praha 2, Czech Republic 3Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada 4Biology Centre CAS, Cesk eBud ejovice, Czech Republic *Corresponding authors: E-mails: [email protected]; [email protected]. Accepted: September 27, 2018 Data deposition: This project has been deposited at DATADryad repository under the accession DOI: https://doi.org/10.5061/dryad.1p67145. Abstract Mitochondria have evolved diverse forms across eukaryotic diversity in adaptation to anoxia. Mitosomes are the simplest and the least well-studied type of anaerobic mitochondria. Transport of proteins via TIM complexes, composed of three proteins of the Tim17 protein family (Tim17/22/23), is one of the key unifying aspects of mitochondria and mitochondria- derived organelles. However, multiple experimental and bioinformatic attempts have so far failed to identify the nature of TIM in mitosomes of the anaerobic metamonad protist, Giardia intestinalis, one of the few experimental models for mitosome biology. Here, we present the identification of a single G. intestinalis Tim17 protein (GiTim17), made possible only by the implementation of a metamonad-specific hidden Markov model. While very divergent in primary sequence and in predicted membrane topology, experimental data suggest that GiTim17 is an inner membrane mitosomal protein, forming a disulphide-linked dimer. We suggest that the peculiar GiTim17 sequence reflects adaptation to the unusual, detergent resistant, inner mitosomal membrane. Specific pull-down experiments indicate interaction of GiTim17 with mitosomal Tim44, the tethering component of the import motor complex. Analysis of TIM complexes across eukaryote diversity suggests that a “single Tim” translocase is a convergent adaptation of mitosomes in anaerobic protists, with Tim22 and Tim17 (but not Tim23), providing the protein backbone. Key words: mitochondrial evolution, protein transport, TIM translocase, Tim17, mitosomes, Giardia, anaerobic protists. Introduction protein translocases, comprising >35 different protein The endosymbiotic acquisition of mitochondria (Roger components (Dudek et al. 2013). et al. 2017) was a key event in the evolution of eukar- The unicellular anaerobic parasite, G. intestinalis, possesses yotes. The establishment of an effective system for protein highly reduced mitochondria, tiny organelles called mito- import from the cytosol into mitochondria involved both, somes. Currently, their only known function is iron–sulfur the adaptation of the original endosymbiont translocases cluster synthesis through the ISC pathway (Tovaretal. and the creation of eukaryote-specific protein transport 2003). Mitosomes have lost most other canonical mitochon- complexes (Dolezal et al. 2006; Fukasawa et al. 2017; drial functions (Jedelsky et al. 2011).Theylackagenomeand Vitali et al. 2018). In canonical mitochondria, the protein are devoid of cristae; yet, they are still surrounded by two import machinery is a complex network of specialized membranes (Tovaretal.2003). ß The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Genome Biol. Evol. 10(10):2813–2822. doi:10.1093/gbe/evy215 Advance Access publication September 28, 2018 2813 Pyrihova et al. GBE Canonical mitochondria employ several independent types bioinformatics approaches often fail to identify clear homol- of protein transport systems, including the TOM and SAM ogy to known mitochondrial components, even when they complexes in the outer membrane, the MIA pathway in the are present (Collins et al. 2003), as was the case for mitosomal intermembrane space, and the TIM23 and TIM22 complexes Tom40 (Dagley et al. 2009)andTim44(Martincovaetal. transporting proteins across or into the inner membrane, re- 2015). The mechanism of protein translocation across the in- spectively (Dudek et al. 2013). Proteins from the Tim17/22/23 ner mitosomal membrane thus remains one of the “last great protein family form the core of both TIM complexes. The mysteries” of these organelles. protein-conducting channel of the TIM23 complex is formed Here, we present evidence for the latter hypothesis. By a by two Tim17/22/23 family proteins, Tim23 and Tim17 tailored HMM-based bioinformatic analysis we identified the (Mokranjac and Neupert 2010). Transport through the long sought-after Tim17 orthologue in Giardia.Ourexperi- TIM23 complex is initially energized by membrane potential, ments suggest that this extremely divergent Tim17 functions whereas translocation is driven by the mtHsp70 chaperone in the inner mitosomal membrane, where it interacts with (Chacinska et al. 2009). Mitochondrial Hsp70 is part of the other mitosomal protein import components. PAM motor complex, which is tethered to the TIM23 complex via the Tim44 protein (Schneider et al. 1994). The channel of the TIM22 complex is formed by a single Tim17 family protein, Results and Discussion Tim22, and the TIM22 translocase requires only energy from We performed several rounds of hmmsearch against a the membrane potential to insert proteins into the inner mi- Metamonada protein database enriched with recently pub- tochondrial membrane (Kovermann et al. 2002). lished transcriptomes of Carpediemonas-like organisms The presence of similar protein targeting signals and ho- (CLOs) (Leger et al. 2017) and the predicted proteome of mologous SAM, TOM, and TIM machineries have been con- Giardia (Aurrecoechea et al. 2017). The initial HMM model sidered crucial supporting evidence for a common origin of was built from a Pfam seed alignment for the Tim17 family mitochondria, mitosomes, and hydrogen-producing hydroge- (PF02466) and enriched for newly identified sequences after nosomes (Dolezal et al. 2005; Lithgow and Schneider 2010; each of the iterations. After the third round, there were no Shiflett and Johnson 2010; Garg et al. 2015). However, of the new sequences recovered. This search returned a single three molecular machines, only a minimal TOM complex is Giardia Tim17 candidate sequence, GL50803_10452, encod- known from Giardia (Dagley et al. 2009), even though its ing a protein of 180 amino acids and a predicted molecular genome has been fully sequenced (Morrison et al. 2007) mass of 19.4 kDa. Hereafter this protein is referred to as and proteomic data from mitosomes are available (Jedelsky GiTim17. The primary sequence of GiTim17 is extremely di- et al. 2011; Martincova et al. 2015; Rout et al. 2016). Only vergent relative to homologs, to the extent that even one of four components of the import motor complex, PAM, are the most sensitive protein homology detection tools, HHpred known. A hidden Markov model (HMM) search identified (Alva et al. 2016), failed to recognize this protein as a member mitosomal Pam18 (Dolezal et al. 2005), while proteomics of of the Tim17/22/23 protein family, whereas all other meta- density gradient-derived cell fractions resulted in the identifi- monad sequences were clearly identified as Tim17/22/23 pro- cation of Pam16 (Jedelsky et al. 2011). These J- and J-like teins (fig. 1A). Enriching the HMM profile with proteins, respectively, modulate the activity of the actual mo- phylogenetically related orthologues was crucial for identifi- tor molecule mtHsp70 (Dolezal et al. 2005). cation of the GiTim17 candidate (Likic et al. 2010). Recently, another core component of the mitosomal pro- Attempts to recover a well-resolved phylogenetic tree of tein transport, Tim44, was identified using high-affinity copre- polytopic membranes such as Tim17/22/23 family proteins are cipitation of in vivo biotin-tagged mitosomal bait proteins hindered by the extreme divergence of the proteins across (Martincova et al. 2015). species (Sojo et al. 2016). In case of Tim17/22/23, the rela- Despite all of these efforts, the essential channel-forming tivelyshortlengthoftheaminoacidsequencealsoplaysa Tim17 family protein remained elusive in mitosomes. Two role. However, our phylogenetic analysis has clearly demon- alternate hypotheses explaining the absence of a Tim17 family strated, with high statistical support, that GiTim17 is closely protein in Giardia have been drawn: 1) import into mitosomes related to Tim17 proteins from Giardia’s closest relatives, the is facilitated through a lineage-specific protein channel or CLOs (BP support 91, fig. 1B, supplementary fig. 1, some other molecular mechanism—this would be in line Supplementary Material online). Moreover, GiTim17 also with the presence of many unique Giardia-specific proteins shares a short deletion between TMD1 and 2 with its closest with no clear orthologues in other eukaryotes (Martincova free-living relative Dysnectes brevis (Leger et al. 2017) et al. 2015; Rout et al. 2016); or 2) the primary
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