Introduction: Workshop on the Contribution of Airborne Pollutants to Respiratory Cancer

For production of proteins that are encoded by the mitochondrial genome, mitochondria rely on their own mitochondrial translation system, with the mitoribosome as its central component. Using extensive homology searches, we have reconstructed the evolutionary history of the mitoribosomal proteome that is encoded by a diverse subset of eukaryotic genomes, revealing an ancestral ribosome of alpha-proteobacterial descent that more than doubled its protein content in most eukaryotic lineages. We observe large variations in the protein content of mitoribosomes between different eukaryotes, with mammalian mitoribosomes sharing only 74 and 43% of its proteins with yeast and Leishmania mitoribosomes, respectively. We detected many previously unidentified mitochondrial ribosomal proteins (MRPs) and found that several have increased in size compared to their bacterial ancestral counterparts by addition of functional domains. Several new MRPs have originated via duplication of existing MRPs as well as by recruitment from outside of the mitoribosomal proteome. Using sensitive profile–profile homology searches, we found hitherto undetected homology between bacterial and eukaryotic ribosomal proteins, as well as between fungal and mammalian ribosomal proteins, detecting two novel human MRPs. These newly detected MRPs constitute, along with evolutionary conserved MRPs, excellent new screening targets for human patients with unresolved mitochondrial oxidative phosphorylation disorders. INTRODUCTION Mitochondria are primary ATP-producing organelles which originated from an ancestral alpha-proteobacterial endosymbiont (1,2). The oxidative phosphorylation (OXPHOS) pathway, consisting of the mitochondrial respiratory chain and the ATP synthase complex, is the final biochemical pathway in energy conversion (3). However, mitochondria have been found to perform pivotal roles in many other metabolic, regulatory and developmental processes. During the evolution of the mitochondria, most genes of the ancestral endosymbiont have been transferred from the mitochondrial to the nuclear genome. The genes that reside on the mitochondrial DNA (mtDNA), e.g. 13 OXPHOS-related genes in human, are translated into their respective protein products by the mitochondrial translation machinery, which resembles the prokaryotic translation system (4), comprising a mitochondrial ribosome (mitoribosome) and several translation factors. In mammals, all proteins that constitute the mitochondrial translation machinery are encoded by the nuclear genome. Also the mitochondrial genomes of fungi generally encode only very few mitochondrial ribosomal proteins (MRPs). In contrast, the mitochondrial genome of many protozoa and plants encode numerous MRPs. Most notably, the ‘primitive’ mitochondrial genome of the freshwater protist Reclinomonas americana was found to contain as many as 27 MRP-encoding genes (5). Mitoribosomes have undergone major remodeling during their evolution. For instance, it has been found that, despite the fact that their rRNA content is only half the content of bacterial ribosomes (6), mitoribosomes generally exceed the bacterial ribosomes both in molecular mass as well as in physical dimensions (6–8). Mass spectrometry studies of the bovine and yeast Present address: Thijs J. G. Ettema, Department of Molecular Evolution, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden. *To whom correspondence should be addressed. Email: thijs.ettema@ebc.uu.se