Kazuo Hamada

The Origin of Eukaryotes Is Suggested as the Symbiosis of Pyrococcus into γ-Proteobacteria by Phylogenetic Tree Based on Gene Content

Attempts were made to define the relationship among the three domains (eukaryotes, archaea, and eubacteria) using phylogenetic tree analyses of 16S rRNA sequences as well as of other protein sequences. Since the results are inconsistent, it is implied that the eukaryotic genome has a chimeric structure. In our previous studies, the origin of eukaryotes to be the symbiosis of archaea into eubacteria using the whole open reading frames (ORF) of many genomes was suggested. In these studies, the species participating in the symbiosis were not clarified, and the effect of gene duplication after speciation (in-paralog) was not addressed. To avoid the influence of the in-paralog, we developed a new method to calculate orthologous ORFs. Furthermore, we separated eukaryotic in-paralogs into three groups by sequence similarity to archaea, eubacteria (other than α-proteobacteria), and α-proteobacteria and treated them as individual organisms. The relationship between the three ORF groups and the functional classification was clarified by this analysis. The introduction of this new method into the phylogenetic tree analysis of 66 organisms (4 eukaryotes, 13 archaea, and 49 eubacteria) based on gene content suggests the symbiosis of pyrococcus into γ-proteobacteria as the origin of eukaryotes.

Phylogenetic construction of 17 bacterial phyla by new method and carefully selected orthologs

Here, we constructed a phylogenetic tree of 17 bacterial phyla covering eubacteria and archaea by using a new method and 102 carefully selected orthologs from their genomes. One of the serious disturbing factors in phylogeny construction is the existence of out-paralogs that cannot easily be found out and discarded. In our method, out-paralogs are detected and removed by constructing a phylogenetic tree of the genes in question and examining the clustered genes in the tree. We also developed a method for comparing two tree topologies or shapes, ComTree. Applying ComTree to the constructed tree we computed the relative number of orthologs that support a node of the tree. This number is called the Positive Ortholog Ratio (POR), which is conceptually and methodologically different from the frequently used bootstrap value. Our study concretely shows drawbacks of the bootstrap test. Our result of bacterial phylogeny analysis is consistent with previous ones showing that hyperthermophilic bacteria such as Thermotogae and Aquificae diverged earlier than the others in the eubacterial phylogeny studied. It is noted that our results are consistent whether thermophilic archaea or mesophilic archaea is employed for determining the root of the tree. The earliest divergence of hyperthermophilic eubacteria is supported by genes involved in fundamental metabolic processes such as glycolysis, nucleotide and amino acid syntheses.

Does endo-symbiosis explain the origin of the nucleus? - Reply

To the editor — Horiike et al. give an excellent bioinformatic analysis showing relationships between yeast genes that function in the nucleus and archaeal genes, and between yeast genes that function in the cytoplasm and bacterial genes. However, their conclusion that the nucleus originated as an archaeal endosymbiont fails to explain the following features of the nucleus: the structure of the nuclear envelope; the nuclear pore complex; linear chromosomes; absence of phagocytic bacteria; the preservation of RNA-world relics in eukaryotes, and reduction of these in prokaryotes. Furthermore, their explanation contradicts the general trend of gene loss reported in parasitic, endosymbiotic and organellar genomes. Clear parallels exist between bacterial, mitochondrial, hydrogenosomal and chloroplast membranes. No such parallel exists for the nuclear envelope where the inner and outer membranes are continuous. Likewise, the nuclear pore complex bears no resemblance to prokaryotic transmembrane pores. Hence, unlike for other organelles, ultrastructure does not favour endosymbiotic origins. The nucleus contains linear chromosomes with telomeres, which have not been found in archaea and arguably predate circular chromosomes. Forterre’s thermoreduction hypothesis, that prokaryotes arose through reductive evolution at high temperature, argues for circularization being derived; circular DNA is more thermostable than linear. Maintenance of telomeres by telomerase probably originated in the RNA world, before modern cells; telomerase has an RNA core and is highly conserved among eukaryotes. Using RNA relics to root the tree of life argues that some eukaryote nuclear traits are ancestral, having been lost through reductive evolution in prokaryotes; thermoreduction explains this pattern because RNA is thermolabile. If some eukaryote nuclear traits predate archaeal traits, these cannot be explained by an archaeal endosymbiont. The conclusion of Horiike and colleagues requires that the endosymbiont gained genes from its host, which is counter to known examples of endosymbiosis (including eukaryotic organelles) and intracellular parasitism, where the unifying feature is gene loss. Intracellular existence makes primary synthetic pathways redundant. Furthermore, the yeast cytoplasmic–bacterial gene relationship described can be explained by Muller’s ratchet — the irreversible accumulation of mutations in small asexual populations. Relocation of organellar genes to the nucleus results in escape of the effects of the ratchet but extensive transfer from host to endosymbiont would place genes under greater mutational pressure. Neither reductive evolution nor endosymbiosis explains nuclear origins. The former, however, explains RNA-world relics and linear chromosomes in eukaryotes, is consistent with Horiike and colleagues’ results and argues against an archaeal origin for the nucleus.