ATP requirements for growth reveal the bioenergetic impact of mitochondrial symbiosis

This is the crux of Lane and Martin’s [4] energetic proposal: Mitochondria do not simply supply more ATP to make cells become bigger [18,30], they enable the cell to do more of its most expensive and creative evolutionary task: express protein, hence invent novel proteins and functions specific to the (complexity of) the eukaryotic lineage [4]. Such evolutionary invention is vetted and filtered by selection and thus comes at a trial-and-error energetic cost, which gradualist theories miss [19–33]. In order to explore protein sequence space, the cell requires ATP in amounts that allow exploratory protein synthesis at no penalty [6]. That is, the host compartment can experiment with overexpressing structural proteins such as prokaryotic actins or tubulins, the latter for chromosome division [15], in addition to expressing proteins that generate shape and modulate membrane flux [11,13]. That differs from simply making more of the same proteins leading to larger cell size [19,30]. Grown on NH4+, the energetic benefit of mitochondrial symbiosis [4,6] incurred from amino acid metabolism, 24 mmol ATP per g, is sufficient to synthesize cell’s worth of exploratory proteins while generating the required copy of the original cell’s protein content (19 mmol ATP per g) (Table 4).

If the host was N2-fixing (Table 4), the amount of ATP liberated by importing amino acids as opposed to synthesizing them from H2, CO2 and N2 increases further to 74.4 mmol ATP per gram of cells (93.5–19.1), enough to synthesize roughly 4 cell’s worth of peptide bonds on (archaeal) cytosolic ribosomes. That is a very substantial amount of liberated, uncommitted ATP that could fuel the exploration of protein structural space and forge protein-based novelties that were present in the eukaryote common ancestor and that are specific to the eukaryotic clade. For those still in search of an energetic benefit for mitochondria [19–33], heterotrophy is yet one more.

The present example of amino acid synthesis underscores energetic advantages of mitochondrial symbiosis that only become manifest if the host is an autotroph and if costs are calculated in accordance with physiology [34–36]. If a postulated transition from chemolithoautotrophy to heterotrophy at eukaryote origin was evolutionarily advantageous, did other lineages of methanogens undertake a similar physiological transition? Possibly. Archaeal halophiles are transformed methanogens that acquired a large donation of genes from a bacterial donor to convert them from strictly anaerobic, H2 dependent autotrophs into O2 dependent heterotrophs, yet without formation of a bacterial organelle [88]. The origin of archaeal halophiles, which thrive on very salty peptone-rich media, mirrors that of eukaryotes in a physiological and energetic context, yet without the fixation of a mitochondrion equivalent and without the product of the symbiosis having attained eukaryote complexity. Halophiles did not evolve along a trajectory that led to cellular complexity. What did they do with their ATP surplus during their transition to heterotrophy? Archaeal halophiles are conspicuously polyploid, with some species harboring in excess of 20 copies of the genome per cell [89]. While DNA synthesis in E. coli grown on NH4+ is not expensive, if multiplied by 20 per cell, the ATP cost of DNA in halophile increases to the level required to make a cell’s worth of peptide bonds (Table 4). That is an energetic cost that a methanogen-turned heterotroph could readily afford, either for synthesizing new proteins or, alternatively, to bask in the luxury of 20 genomes, when one would suffice. Pronounced polyploidy in archaeal halophiles could be a relic of the energetic advantage conferred by the origin of heterotrophy [88] in their lineage.

The issue here is whether mitochondrial energetically contributed to eukaryote origin, or not. The answer is that (i) it depends on whether the ATP costs of growth are calculated in such a way that the energy budget, cell mass and growth add up, which Stouthamer [34] did, Lane and Martin [4] did, but Lynch and Marinov [19] did not, and (ii) it depends on what kind of a symbiosis one models at eukaryote origin. As outlined above, a heterotrophic host has no need for a heterotrophic mitochondrial symbiont [3,60], because both cells will compete for the same heterotrophic resources. There is currently much excitement about archaeal clades inferred from metagenomic data that possess some interesting genes related to eukaryotic cell biological functions, and that are being considered as models for the host of mitochondria at eukaryote origin [90–92]. However, only two such archaea have been cultured so far. They are, like the famous spaghetti-shaped Korachaeon cryptofilum isolated by Stetter [93], amino acid fermenters [94,95], but with an interesting appendage-producing morphology that (i) probably serves to increase surface area for substrate acquisition and that (ii) was previously observed in other archaeal fermenters [96,97]. In this context it is notable that recent phylogenetic investigations of the new archaeal lineages have uncovered evidence in favor of a H2-dependent, autotrophic ancestry of the host lineage that acquired the mitochondrion [92], as the hydrogen hypothesis predicted.

Since Margulis’s day [2], all models for the origin of eukaryotes assume that the host for the origin of mitochondria was heterotroph, with one exception [3,65]. For a heterotroph, in particular an amino acid fermenting archaeon, there is indeed little energetic benefit to be construed from acquiring a mitochondrion. By contrast, a methanogen that drifts away from a geological source of H2 [3] unconditionally needs its H2-producing symbiont to survive. The new clades of archaea that branch near eukaryotes in phylogenetic trees all seem to be derived from methanogens, in a phylogenetic sense, and it is possible if not likely that all archaea are derived from methanogens to begin with [68,69,98–104]. It is thus well within the realm of microbial reason, and within the resolution of phylogenetic reconstructions, that the host cell at eukaryote origin was a H2-dependent autotrophic archaeon [92]. Methanogens present favorable symbiotic partners for the origin of mitochondria [3], as the latter can substantially improve the energetics of the former [4] through endosymbiosis.

Supplementary data to this article can be found online at https://doi.org/10.1016/j.bbabio.2025.149564.