The author questioned the results of a Nature publication that concluded mitochondria were acquired late during eukaryogenesis by showing phylogenetically that the eukaryotic proteins that were concluded to have non-alphabacterial origins in the Nature publication actually can be traced back to proteobacteria (ancestor of mitochondria).

The researchers from the Nature publication made incorrect inferences in their phylogeny concerning the origin of more than 50% of mitochondrial protein families analyzed. They had showed non-alphaproteobacterial origins for more than 50% of those protein families. However, the author states that mitochondrial genes have ancestral roots to aerobic proteobacteria, and the author provides evidence with a gene phylogeny. The gene phylogeny clearly shows mitochondrial genes in the same clade as α-proteobacteria genes. This clade is sister to another clade that includes β- and γ-proteobacterial genes. After reconstructing the mitochondrial and proteobacterial gene phylogeny the author shows that a large majority of the genes in the Nature publication had been erroneously assigned non-alphaproteobacterial instead of proteobacterial origins.

Authors

Esposti, M.D.

Abstract

This article provides a timely critique of a recent Nature paper by Pittis and Gabaldón that has suggested a late origin of mitochondria in eukaryote evolution. It shows that the inferred ancestry of many mitochondrial proteins has been incorrectly assigned by Pittis and Gabaldón to bacteria other than the aerobic proteobacteria from which the ancestor of mitochondria originates, thereby questioning the validity of their suggestion that mitochondrial acquisition may be a late event in eukaryote evolution. The analysis and approach presented here may guide future studies to resolve the true ancestry of mitochondria.

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The author examined the Archezoan hypothesis and showed that its premises are false after research showed “archezoan’s” with genes that were acquired after an endosymbiotic event with mitochondria.

The author walks through the history of eukaryogenesis theory and explains the faultiness of the Archezoan hypothesis through the examination of new research evidence. The Archezoan hypothesis relies on extant eukaryotes not containing or ever have contained mitochondria or a peroxisome. The theory is that these amitochondriate eukaryotes diverged prior to the endosymbiotic event occurring in another lineage of eukaryotes. Sequencing evidence has shown that the Archezoans contain genes linked to mitochondria or hydrogenosomes. This dispels the theory that there is a separate branch of eukaryotes that never acquired a mitochondria or hydrogenosome.

Authors

Keeling, P.J.

Abstract

The taxon Archezoa was proposed to unite a group of very odd eukaryotes thatlack many of the characteristics classically associated with nucleated cells, inparticular the mitochondrion. The hypothesis was that these cells diverged fromother eukaryotes before these characters ever evolved, and therefore they repre-sent ancient and primitive eukaryotic lineages. The kingdom comprised fourgroups: Metamonada, Microsporidia, Parabasalia, and Archamoebae. Until re-cently, molecular work supported their primitive status, as they consistentlybranched deeply in eukaryotic phylogenetic trees. However, evidence has nowemerged that many Archezoa contain genes derived from the mitochondrialsymbiont, revealing that they actually evolved after the mitochondrial symbiosis. Inaddition, some Archezoa have now been shown to have evolved more recentlythan previously believed, especially the Microsporidia for which considerableevidence now indicates a relationship with fungi. In summary, the mitochondrialsymbiosis now appears to predate all Archezoa and perhaps all presently knowneukaryotes.

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The authors proposed a hypothesis where the host cell from an endosymbiotic event became dependent upon the H2 aproduced by the symbiont as an energy source as a way of adapting to a disruption of natural H2 from the environment.

The authors propose a scenario that begins with a soon-to-be host and a H2- and CO2 producing soon-to-be symbiont living in an anoxic environment with a sufficient supply of H2. An unknown event occurs to the geologic source of H2 causing the host to become dependent upon the H2- and CO2- producer for nutrients. This leads to the host increasing its surface area around the producer limiting the latter’s ability to excrete the materials sought after by the host. A transfer of symbiont genes to the host could occur which would allow for the expression of membrane proteins in the host that could import organic material to the symbiont so that it could continue to produce material that the host cell utilizes for ATP production. This is an example of a “mito-early” argument because this theory suggests that the endosymbiotic event that eventually led to the mitochondria was the initial step in eukaryogenesis.

Authors

Martin, M., Müller, M.

Abstract

A new hypothesis for the origin of eukaryotic cells is proposed, based on the comparative biochemistry of energy metabolism. Eukaryotes are suggested to have arisen through symbiotic association of an anaerobic, strictly hydrogen-dependent, strictly autotrophic archaebacterium (the host) with a eubacterium (the symbiont) that was able to respire, but generated molecular hydrogen as a waste product of anaerobic heterotrophic metabolism. The host's dependence upon molecular hydrogen produced by the symbiont is put forward as the selective principle that forged the common ancestor of eukaryotic cells.

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The endosymbiotic event of an alpha-proteobacteria coming to reside in the cytosol of a host cell eventually led to the formation of a proto-nucleus in order for the splicing of introns to occur separately from the translation of mRNA.

The authors use a prokaryote (no nucleus) as their host of choice and an alphaproteobacteria (ancestor of mitochondria) as their symbiont, and state that lysis of one of the two organisms would naturally occur at some point. If the symbiont undergoes lysis its DNA would be freely floating in the host’s cytosol and could recombine with the host’s genome (origin of introns in eukaryotes). If this occurs the host has at least two issues that it needs to solve. First, it needs to remove the introns so that it does not produce nonsense proteins during translation. The second issue is compartmentalizing the cytosol so that splicing occurs separately from translation because splicing is a slower process when compared to the translation of mRNA. The authors hypothesize that a proto-nucleus with pores would have had to evolve in order to solve this issue. This supports a “mito-early” hypothesis because the endosymbiotic event is directly responsible for the formation of a proto-nucleus (i.e. a key eukaryotic feature).

Authors

Martin, M., Koonin, E.V.

Abstract

The origin of the eukaryotic nucleus marked a seminal evolutionary transition. We propose that the nuclear envelope's incipient function was to allow mRNA splicing, which is slow, to go to completion so that translation, which is fast, would occur only on mRNA with intact reading frames. The rapid, fortuitous spread of introns following the origin of mitochondria is adduced as the selective pressure that forged nucleus–cytosol compartmentalization.

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An endosymbiotic event of a prokaryote engulfing an ancestor of mitochondria led to a fitness landscape change where eukaryotes had an increased “energy budget” allowing them to express exponentially more genes than a prokaryotic cell.

The authors state that prokaryotic cells are hindered by an inability to produce enough energy that would allow for genome expansion which would ultimately lead to greater cellular complexity. Prior to the symbiont of the host cell turning into a mitochondrion the host would have had similar energy constraints. However, once the eukaryotic cell has mitochondria it is able to exceed energy barriers by utilizing the oxidative phosphorylation process of mitochondria to generate enough ATP. This ultimately allows the eukaryotic cell to express more genes and expand its genome size.

Authors

Lane, N., Martin, W.

Abstract

All complex life is composed of eukaryotic (nucleated) cells. The eukaryotic cell arose from prokaryotes just once in four billion years, and otherwise prokaryotes show no tendency to evolve greater complexity. Why not? Prokaryotic genome size is constrained by bioenergetics. The endosymbiosis that gave rise to mitochondria restructured the distribution of DNA in relation to bioenergetic membranes, permitting a remarkable 200,000-fold expansion in the number of genes expressed. This vast leap in genomic capacity was strictly dependent on mitochondrial power, and prerequisite to eukaryote complexity: the key innovation en route to multicellular life.

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