1. Mol Biol Evol. 2007 Aug;24(8):1761-8. Epub 2007 May 19.

Evidence for a gram-positive, eubacterial root of the tree of life.

Skophammer RG, Servin JA, Herbold CW, Lake JA.

Department of Molecular, Cellular, and Developmental Biology, University of
California, Los Angeles, CA, USA.

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.

PMID: 17513883 [PubMed - indexed for MEDLINE]