nucleation

CLAIM-508: Gene ancestries alone cannot tell a symbiotic partner from a source of transferred genes: a partner whose genes were mostly lost, replaced or spread thin would leave the diffuse trace that Tobiasson and colleagues read as piecemeal transfer, and Bernabeu and colleagues concede that their donor signals say nothing of the kind of interaction

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Properties9
StatusActive
Version2
Rolethesis
Warrantinterpretive
Tagsendosymbiosis, natural-sciences
Linedistributed-agency
Bears onQUESTION-277 — When formerly autonomous partners come to depend on one another, which of mutual dependence, reproductive cohesion, the distribution of essential functions across genomes, the host's regulatory control and the alignment of selection does each route to dependence bring about, and which of them, alone or together, make the partnership a new evolutionary individual?
GroundsTHEORY-1104 — In Tobiasson, Luo, Wolf and Koonin's constrained-tree survey of widespread eukaryotic protein families, Asgard archaea are the largest single prokaryotic source, with about half the likelihood weight in the best-resolved families and the lead in nearly every functional system, while Alphaproteobacteria contribute a small, coherent set centred on the mitochondrion and other bacteria about a third of families, scattered across functions with no pathway led by one donor except a narrow Myxococcota signal in nucleotide-sugar and nicotinate metabolism; the authors read this as one Asgard host lineage, one endosymbiont and piecemeal gene transfer rather than further symbioses, THEORY-1105 — In Bernabeu, Manzano-Morales, Marcet-Houben and Gabaldón's reconstruction of the last eukaryotic common ancestor's proteome, two bacterial phyla besides the mitochondrial ancestor, Myxococcota and Planctomycetota, each account for a share of the proteome comparable to that of Alphaproteobacteria and Asgard archaea under thresholds calibrated on those accepted partners, and stem-length distributions order the acquisitions as waves, Asgard first, then Planctomycetota, then the mitochondrial ancestor and Myxococcota together; the authors read this as serial associations with several partners, while conceding that their data cannot say whether any donor was a symbiont
Corroborated byTHEORY-1100 — On Sørensen and colleagues' review, a bacterial endosymbiont becomes genetically integrated, the authors' mark of an organelle, when nuclear genes whose products are imported into it functionally replace essential genes it has lost, and this does not require gene transfer from the endosymbiont: in the Paulinella chromatophore and the nitroplast, the two systems with hundreds of imported proteins, many of which fill gaps left by lost genes, the imported proteins come mostly from the host's own genes or from other bacteria, and in the nitroplast no gene transfer from the endosymbiont has been found

Graph View

The claim

Tobiasson and colleagues (THEORY-1104) read the absence of functional coherence among non-alphaproteobacterial genes as the mark of isolated transfers rather than further endosymbioses. But coherence is what a partner leaves only if its genes survive together. A partner whose genes were mostly lost, replaced by host or other genes, or retained thinly across pathways would leave the same diffuse trace. Bernabeu and colleagues (THEORY-1105) find major donors and say themselves that their data “do not provide information on potential types of interaction”. On either reading, whether a donor was a partner is a question gene ancestries do not settle.

Known partnerships bear the premise out. In the nitroplast no gene transfer from the endosymbiont has been found, though more than 350 nucleus-encoded proteins are imported into it; in the pea aphid no functional transfer from Buchnera occurred, and the one host protein shown inside it is encoded by a gene from another bacterium; in Paulinella about 60 nuclear genes come from the chromatophore and about 170 from other bacteria (Sørensen and colleagues, read in NOTE-1241; THEORY-1100). A partner’s trace can be small or absent, and genes from bacteria that were not partners can outnumber it.

What it does not say

Not that there were further partners. Tobiasson and colleagues’ reading may be right; the claim is only that the ancestries cannot show it, and that the same holds for Bernabeu and colleagues’ donors.

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