Origin of eukaryotic cell nuclei by symbiosis of Archaea in Bacteria is revealed by homology-hit analysis

The origin of eukaryotic cell nuclei by symbiosis of Archaea in Bacteria wa s proposed on the basis of the phylogenetic topologies of genes(1-3). Howev er, it was not possible to conclude whether or not the genes involved were authentic representative genes'. Furthermore, using the BLAST(5) and FASTA( 6) programs, the similarity of open reading frame (ORF) groups between thre e domains (Eukarya, Archaea and Bacteria) was estimated at one threshold(7, 8). Therefore, their similarities at other thresholds could not be clarifie d. Here we use our newly developed 'homology-hit analysis' method, which us es multiple thresholds, to determine the origin of the nucleus. We removed mitochondria related ORFs from yeast ORFs, and determined the number of yea st orthologous ORFs in each functional category to the ORFs in six Archaea and nine Bacteria at several thresholds (E-values) using the BLAST. Our res ults indicate that yeast ORFs related to the nucleus may share their origin s with archaeal ORFs, whereas ORFs that are related to the cytoplasm may sh are their origins with bacterial ORFs. Our results thus strongly support th e idea of nucleus symbiosis.