Vestiges of the Bacterial Signal Recognition Particle-Based Protein Targeting in Mitochondria
The main bacterial pathway for inserting proteins into the plasma membrane relies on the signal recognition particle (SRP), composed of the Ffh protein and an associated RNA component, and the SRP-docking protein FtsY. Eukaryotes use an equivalent system of archaeal origin to deliver proteins into the endoplasmic reticulum, whereas a bacteria-derived SRP and FtsY function in the plastid. Here we report on the presence of homologs of the bacterial Ffh and FtsY proteins in various unrelated plastid-lacking unicellular eukaryotes, namely Heterolobosea, Alveida, Goniomonas, and Hemimastigophora. The monophyly of novel eukaryotic Ffh and FtsY groups, predicted mitochondrial localization experimentally confirmed for Naegleria gruberi, and a strong alphaproteobacterial affinity of the Ffh group, collectively suggest that they constitute parts of an ancestral mitochondrial signal peptide-based protein-targeting system inherited from the last eukaryotic common ancestor, but lost from the majority of extant eukaryotes. The ability of putative signal peptides, predicted in a subset of mitochondrial-encoded N. gruberi proteins, to target a reporter fluorescent protein into the endoplasmic reticulum of Trypanosoma brucei, likely through their interaction with the cytosolic SRP, provided further support for this notion. We also illustrate that known mitochondrial ribosome-interacting proteins implicated in membrane protein targeting in opisthokonts (Mba1, Mdm38, and Mrx15) are broadly conserved in eukaryotes and nonredundant with the mitochondrial SRP system. Finally, we identified a novel mitochondrial protein (MAP67) present in diverse eukaryotes and related to the signal peptide-binding domain of Ffh, which may well be a hitherto unrecognized component of the mitochondrial membrane protein-targeting machinery.
Keywords: Ffh; FtsY; LECA; evolution; mitochondrion; protein targeting; protists; signal recognition particle.
Introduction
The mitochondrion evolved from an endosymbiont belonging to alphaproteobacteria (Roger et al. 2017; Martijn et al. 2018) and as a cellular component has transitioned into particularly varied forms in different branches of the eukaryotic tree. The key factors underpinning mitochondrial diversity in the extant eukaryotes are lineage-specific innovations and acquisitions, paralleled to a varying degree by losses of ancestral traits. Although mitochondria of conventional model organisms are rather canonical organelles, extremes are found among lesser-known unicellular eukaryotes (Smith and Keeling 2015; Leger et al. 2019; Gray et al. 2020). An example of an especially pronounced lineage-specific elaboration is provided by the kinetoplastid and diplonemid flagellates with baroquely complex structure and functions of their mitochondrial genomes and transcriptomes (Lukeš et al. 2018; Aphasizheva et al. 2020; Kaur et al. 2020). On the other hand, simplifications have dominated the mitochondrial adaptations of obligate anaerobes, which resulted in organelles without a genome and sometimes even without a function in energy metabolism (Leger et al. 2017; Santos et al. 2018). One such lineage, represented by the oxymonad Monocercomonoides exilis, has lost the mitochondrion completely (Karnkowska et al. 2016, 2019).
Pyrih J., Pánek T., Durante I.M., Rašková V., Cimrhanzlová K., Kriegová E., Tsaousis A.D., Eliáš M., Lukeš J. 2021: Vestiges of the bacterial signal recognition particle-based protein targeting in mitochondria. Molecular Biology and evolution 38: 3170–3187. doi: 10.1093/molbev/msab090
