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MBE Advance Access published online on May 19, 2007
Molecular Biology and Evolution, doi:10.1093/molbev/msm096
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© The Author 2007. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Article

Evidence for a Gram Positive, Eubacterial Root of the Tree of Life

Ryan G. Skophammer1,4, Jacqueline A. Servin2,4, Craig W. Herbold2,4 and James A. Lake1,2,3,4

1 Department of Molecular, Cellular, and Developmental Biology
2 Molecular Biology Institute
3 Department of Human Genetics
4 UCLA Astrobiology Institute, University of California, Los Angeles, CA 90095, USA

Corresponding Author: Jim Lake, 232 Boyer Hall, 611 South Young Drive, UCLA, Los Angeles, CA 90095, USA, Tele: (310) 825-2546, Fax: (310) 206-7286, Email: Lake{at}mbi.ucla.edu

Received for publication March 2, 2007. Revision received May 2, 2007. Accepted for publication May 9, 2007.

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 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 Firmicute/Archaeal 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 Firmicute/Archaeal 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.

Key Words: Tree of life • Root • Indels • Cenancestor • Firmicutes • Archaebacteria • Double-Membrane Prokaryotes


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