Ribosomal protein-sequence block structure suggests complex prokaryotic evolution with implications for the origin of eukaryotes Prashanth Vishwanath a , Paola Favaretto a , Hyman Hartman b , Scott C. Mohr c , Temple F. Smith a, * a BioMolecular Engineering Research Center, Boston University, 36 Cummington St., Boston, MA 02215, USA b Center for Biomedical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA c Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA 02215, USA Received 15 March 2004; revised 29 June 2004 Available online 12 September 2004 Abstract Amino acid sequence alignments of orthologous ribosomal proteins found in Bacteria, Archaea, and Eukaryota display, relative to one another, an unusual segment or block structure, with major evolutionary implications. Within each of the prokaryotic phylo- domains the sequences exhibit substantial similarity, but cross-domain alignments break up into (a) universal blocks (conserved in both phylodomains), (b) bacterial blocks (unalignable with any archaeal counterparts), and (c) archaeal blocks (unalignable with any bacterial counterparts). Sequences of those eukaryotic cytoplasmic riboproteins that have orthologs in both Bacteria and Archaea, exclusively match the archaeal block structure. The distinct blocks do not correlate consistently with any identifiable func- tional or structural feature including RNA and protein contacts. This phylodomain-specific block pattern also exists in a number of other proteins associated with protein synthesis, but not among enzymes of intermediary metabolism. While the universal blocks imply that modern Bacteria and Archaea (as defined by their translational machinery) clearly have had a common ancestor, the phylodomain-specific blocks imply that these two groups derive from single, phylodomain-specific types that came into existence at some point long after that common ancestor. The simplest explanation for this pattern would be a major evolutionary bottleneck, or other scenario that drastically limited the progenitors of modern prokaryotic diversity at a time considerably after the evolution of a fully functional translation apparatus. The vast range of habitats and metabolisms that prokaryotes occupy today would thus reflect divergent evolution after such a restricting event. Interestingly, phylogenetic analysis places the origin of eukaryotes at about the same time and shows a closer relationship of the eukaryotic ribosome-associated proteins to crenarchaeal rather than euryar- chaeal counterparts. Ó 2004 Elsevier Inc. All rights reserved. Keywords: Ribosomal proteins; Ribosome phylogeny; Molecular evolution; Amino acid sequence-alignment blocks; Prokaryotic phylogeny; Eukaryote origin(s) 1. Introduction The ribosome, with its conserved central role in pro- tein synthesis, has long constituted a prime subject for phylogenetic analysis. The study of small-subunit (SSU) ribosomal RNA sequences led Woese to his sem- inal recognition of two extant prokaryotic phylodo- mains, Bacteria and Archaea (Woese et al., 1990). Recent rapid growth of genomic and structural informa- tion on ribosomes (Ramakrishnan and Moore, 2001) has opened the way to broad comparisons, particularly of the ribosomal proteins (Caetano-Anolles, 2002; Le- compte et al., 2002; Mears et al., 2002; Tung et al., 2002; Wuyts et al., 2001). Here we report an unusual multisequence alignment block structure for these 1055-7903/$ - see front matter Ó 2004 Elsevier Inc. All rights reserved. doi:10.1016/j.ympev.2004.07.003 * Corresponding author. Fax: +617 353 7020. E-mail address: tsmith@darwin.bu.edu (T.F. Smith). Molecular Phylogenetics and Evolution 33 (2004) 615–625 MOLECULAR PHYLOGENETICS AND EVOLUTION www.elsevier.com/locate/ympev