The genetic core of the universal ancestor - PubMed (original) (raw)

The genetic core of the universal ancestor

J Kirk Harris et al. Genome Res. 2003 Mar.

Abstract

Molecular analysis of conserved sequences in the ribosomal RNAs of modern organisms reveals a three-domain phylogeny that converges in a universal ancestor for all life. We used the Clusters of Orthologous Groups database and information from published genomes to search for other universally conserved genes that have the same phylogenetic pattern as ribosomal RNA, and therefore constitute the ancestral genetic core of cells. Our analyses identified a small set of genes that can be traced back to the universal ancestor and have coevolved since that time. As indicated by earlier studies, almost all of these genes are involved with the transfer of genetic information, and most of them directly interact with the ribosome. Other universal genes have either undergone lateral transfer in the past, or have diverged so much in sequence that their distant past could not be resolved. The nature of the conserved genes suggests innovations that may have been essential to the divergence of the three domains of life. The analysis also identified several genes of unknown function with phylogenies that track with the ribosomal RNA genes. The products of these genes are likely to play fundamental roles in cellular processes.

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Figures

Figure 1.

Figure 1.

Examples of three-domain and non-three-domain phylogenetic trees from analyses of the COG database protein alignments. The trees are the single shortest trees found by a maximum parsimony (MP) analysis of the amino acid alignments (neighbor-joining [NJ] analysis gave the same topology). Names of organisms belonging to the Bacteria are in italics; names of Archaea are in bold italics, and names of Eucarya are in all capital letters. (A) The phylogeny of COG0231 (efp in E. coli) recapitulates the basic three-domain topology given by ribosomal RNA, and the numbers indicate bootstrap support for the monophyly of the archaeal, bacterial, and eucaryal sequences in this COG. Results from MP bootstrap analysis are given above the branches, and results from NJ bootstrap analysis are given below. (B) The phylogeny of COG0018 (argS in E. coli) violates the three-domain paradigm, as none of the three domains are monophyletic. Indications of horizontal gene transfer events are presented in enlarged font along with corresponding bootstrap support for the nodes demarking lateral transfer.

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