Albany 2013: Book of Abstracts
June 11-15 2013
©Adenine Press (2012)
Ribosomal Evidence Suggests That Archaea Evolved After Fungi
We are exploring the potential to trace species evolution with the ribosomal proteins (RibPs) present in bacterial, eukaryotic, and archaeal ribosomes and to compare the independent trees for consistency. The complete genomes of over 8400 bacteria, eukaryota, and archaea are presently in the SwissPro/TrEMBL (SPT) database. A search of SPT using a vector designed with ScanProsite formats (V1) finds and aligns 8405 sequences (5312 bacterial, 2905 eukaryotic, and 169 archaeal) that are homologous with bone fide bacterial S19 ribosomal proteins(S19s). When the 8405 are perfectly aligned 15 residues are conserved at 90% identity and 40 are conserved at 70% identity. We are not aware of any previous publication reporting sequence alignment of 8400 members of any single family including all bacteria, eukaryota and archaea for which complete genomes have been published.
A Pro and a Gly separated by 11 residues are 100% conserved in the 8405 S19s. In the position immediately before the fully conserved Gly, two residues (Asp and Asn) are present in 98.3% of the 8405 sequences. The Asp residue is found almost exclusively in 2190 Gram-positive bacteria. The Asn residue is found in 3065 Gram-negative bacteria, 123 Archaea, 1939 eukaryotes and 64 specific species of Gram-positive bacteria. There is biochemical evidence for the existence of distinct mitochondrial, chloroplast, and cytosolic ribosomes and reports that plants have all three forms and mammals only two. Reliable data concerning how individual ribosomal proteins differ in different types of ribosomes is meager. Examination of the eukaryotic S19s reveals the existence of three distinct types. Two of the distinctly different types are found in most fungi, three of the types are found in some viridiplante, and only one type is found in metazoa and archaea. We demonstrate the sequence homology between the mitochondrial form found in fungi and plants and the S19 proteins of alpha proteobacteria, between the chloroplast S19s and the S19s of cyanobacteria, and among the cytosolic S19s found only in fungi, metazoa, archaea, and some viridiplantae. Our findings suggest that most archaeal species appeared after a gene duplication event in fungi that correlates with the origin of the cytosolic ribosome.
William L. Duax
Hauptman Woodward Medical Research Institute