Evidence for a Gram-positive, Eubacterial Root of the Tree of Life

Abstract

Directed indels, insertions, and deletions within paralogous genes, have the potential to root the tree of life. Here we apply a newly developed rooting algorithm, top-down rooting, to indels found in informational and operational gene sets, introduce new computational tools for indel analyses, and present evidence (P < .01) that the root of the tree of life is not present in its traditional location, between the Eubacteria and the Archaebacteria. Using indels contained in the dihydroorotate dehydrogenase/uroporphyrinogen decarboxylase gene pair and in the ribosomal protein S12/beta prime subunit of the RNA polymerase gene pair, we exclude the root from within the clade consisting of the Firmicutes plus the Archaebacteria and their most recent common ancestor. These results, plus previous directed indel studies excluding the root from the eukaryotes, restrict the root to just four possible sites. One potential root is on the branch leading to the double-membrane prokaryotes, another is on the branch leading to the Actinobacteria, another is within the Actinobacteria, and the fourth is on the branch leading to the Firmicutes-Archaea clade. These results imply (1) that the cenancestral population was not hyperthermophilic, but moderate thermophily cannot be excluded for the root on the branch leading to the Firmicutes-Archaea clade, (2) that the cenancestral population was surrounded by ester lipids and a peptidoglycan layer, and (3) that parts of the mevalonate synthesis pathway were present in the population ancestral to the Bacilli and the Archaebacteria, including geranylgeranylglyceryl phosphate synthase, an enzyme thought to be partially responsible for the unique sn-1 stereochemistry of the archaeal glycerol phosphate backbone.

An archaeal origin of eukaryotes supports only two primary domains of life

“…These results imply that the mitochondrion was acquired before the radiation of known eukaryotes; therefore, the observation that the mitochondrion descends from an endosymbiotic member of the alphaproteobacteria 64,88 provides strong evidence that the origin of eukaryotes postdates the origin of that bacterial group 2,89 . A relatively late origin of eukaryotes compared to Bacteria is consistent with the best evidence from the geological record and with either the three-domains or eocyte tree rooted on the bacterial stem or within the Bacteria [5][6][7][8][9][10][11] . Moreover, if all eukaryotes have both mitochondria and a nucleus, then we can no longer be sure which structure arose first during evolution: in other words, the host cell that acquired the mitochondrion need not have already possessed a nucleus.…”

“…However, this record is very incomplete and subject to deep and sometimes heated controversy. The first fossil that is indisputably eukaryotic is of a bangiophyte red alga dated to between 1.2 billion and 720 million years ago 75 , but earlier microfossils with a possible eukaryotic origin are found in rocks dated to approximately 1.8 billion depicting the relationships between Archaea and the eukaryotic nuclear lineage, consistent with recent analyses of core genes using new methods [47][48][49] and rooted using the Bacteria as the outgroup [5][6][7][8][9][10][11] . The phylogenetic position of Korarchaeum was not consistently resolved in these different analyses and hence is depicted as part of a polytomy.…”

“…Evolutionary biologists now have access to more data and better phylogenetic methods than ever before, although there is still much room for improvement and many uncertainties remain. These caveats apply equally to all attempts to infer ancient relationships, affecting not only the debate over whether the three-domains or eocyte tree best depicts the history of core eukaryotic genes, but also the placement of the universal root 5,[9][10][11][12]21 and the relationships among major eukaryotic phyla 26,102,103 . The pioneering analyses of molecular sequence data led by Carl Woese and his coworkers culminated in the three-domains tree recognizing the Archaea, Bacteria and Eukaryota as the three primary domains of cellular life.…”

“…Although similar to Bacteria in terms of cell structure, molecular phylogenies for ribosomal RNA and a small core of genes, that mainly have essential roles in protein translation 3 , suggested that the Archaea were more closely related to the eukaryotic nuclear lineage; that is, to the host cell that acquired the mitochondrion 4 . The idea that Archaea and eukaryotes are more closely related to each other than either is to Bacteria depends on analyses suggesting that the root of the tree should be placed on the bacterial stem, or within the Bacteria [5][6][7][8][9][10][11][12] , implying that the prokaryotes-cells that lack a nucleus-are a paraphyletic group 13 . The main question now debated is whether core components of the eukaryotic nuclear lineage descend from a common ancestor shared with Archaea, as in the three-domains tree 14 (Fig.…”

Structural Analysis of Polarizing Indels Argues the Root of the Tree of Life is Near the Chloroflexi

“…The small indel in PyrD has been polarized using several different outgroups to reach contradictory conclusions that are not mutually compatible [2,5]. The best outgroup is probably HisA, which implies the Gram-negatives and Actinobacteria are derived.…”