On the bacterial ancestry of mitochondria: new insights with triangulated approaches

Abstract

We breathe at the molecular level when mitochondria in our cells consume oxygen to extract energy from nutrients. Mitochondria are characteristic cellular organelles that derive from aerobic bacteria similar to some of those thriving in the oceans nowadays. These organelles carry out most metabolic pathways in eukaryotic cells. The precise bacterial origin of mitochondria and, consequently, the metabolic ancestry of our cells remains controversial - despite the vast genomic information that is now available. Here we triangulate across multiple phylogenomic and molecular approaches to pinpoint the most likely living relatives of the ancestral bacteria from which mitochondria originated.

Multiple approaches of cellular metabolism define the bacterial ancestry of mitochondria

“…(11)]. Moreover, the MPP proteins of eukaryotes have been recently reported to be closely related to the M16B proteins of alphaproteobacteria (65), confirming our previous results (59). The selection of the genomes for our analyses was based on extensive efforts to thoroughly deal with the issue of taxonomic sampling, most critical for evaluating the bacterial origin of mitochondria (1-8, 32, 54).…”

“…(58)]. This fusion left a large insert between the second and third TM of the 7TM COX3 of various bacteria (59), which is common among the proteins of gammaproteobacteria such as Nitrococcus. However, this insert was lost in the COX3 proteins of basal alphaproteobacteria such as Caenispirillum and other members of the Rhodospirillaceae family (56), which have a simple variant of the COX operon without CtaB and SURF1 [Fig.…”

“…Using all 23 traits produced a more flattened distribution of values than in our previous analysis of 18 traits (fig. S2A), reported in the BioRxiv precursor version of this paper (59). We then selected the intermediate set of 20 traits listed in Table 1 to represent the quantitative distribution of aerobic metabolism (Fig.…”

“…We have also re-evaluated the raw metagenomic data from (61) to expand the genome completeness of alpha J134, as described below. Conversely, we merged the order of Rhodothalassiales with Kordiimonadales, as well as that of Zavarziniales with Emcibacterales, by considering common features such as the number of INDELs in respiratory proteins (59). Representatives of all major families were included to encompass the genomic diversity of Rhizobiales (2,56).…”

Eukaryotes inherited inositol lipids from bacteria: implications for the models of eukaryogenesis

“…Notably, such taxa generally contain genes for the biosynthesis of ceramide, the precursor of sphingolipids and PI-glycolipids that are present in these bacteria [25,26,60]. For example, the genome of Nitrospirillum amazonense CBAmc has the three-gene cluster containing BEPIS [25] separated by only two genes from the specialized acyl carrier protein and the aminotransferase required for ceramide biosynthesis in alphaproteobacteria [54,60]. In contrast, archaea do not have the same proteins, consistent with the notion that archaea use inositol 3-phosphate to produce ArcIns [18,43,56].…”