Archaea horizontal gene transfer

Horizontal gene transfer (HGT) could also explain some unsolved riddles, such as the fact that genes which normally occur in bacteria are present in some archaea. HGT has been recognised for some time, but no one realised that the phenomenon was an important principle of the development of living systems, even at the dawn of life. 

II. Domain Families in Archaea, Bacteria, and Eukarya A. Horizontal Gene Transfer... 

Enzymes that are structurally related to the eukaryotic V-ATPase are also found in certain eubacteria (Speelmans etal., 1994 Takase etal., 1994 Yokoyama etal., 1990). Based on nucleotide sequence analysis, it is believed that these bacterial V-like ATPases have been introduced into the eubacteria via horizontal gene transfer from Archaea (Hilario and Gogarten, 1993, 1998). The subunit composition of the bacterial V-like ATPase is indeed more similar to the archaeal A-ATPase than to the eukaryotic V-ATPase, and we will therefore treat the bacterial V-ATPase—like enzyme together with the archaeal A-ATPase (see below). In the following, we will use the name V-ATPase only for the eukaryotic enzyme, and we will call the bacterial enzyme the A/V-type ATPase as suggested by Hilario and Gogarten (1998). 

Based on sequence comparison, the eubacterial V-type ATPase is a product of horizontal gene transfer from the Archaea. Much of the information about the subunit arrangement in the eubacterial A/V-type—like ATPase comes from studies with the enzymes from C. fervidus and T. thermophilus (Boekema et al, 1997, 1999 Ubbink-Kok et al, 2000 Yokoyama et al, 2003a). A recent 3D reconstruction of the A/V- ATPase from T. thermophilus (Bernal and Stock, 2004) revealed the structural similarity to both the eukaryotic V-ATPase (Domgall et al., 2002 Wilkens et al., 2004, 2005) and the archaeal A-ATPase (Coskun et al., 2004a,b). The x-ray crystal structure for the C-subunit of the bacterial A/V-like ATPase has been reported recently (Iwata et al, 2004). The C-subunit of the bacterial V-like ATPase shows limited but significant sequence homology to the cZ-subunit of the eukaryotic V-ATPase. 

Dimethyl-8-ribityllumazine synthase and the pentameric, archaeal riboflavin synthase appear to have diverged from a common ancestor at an early time point in the evolution of Archaea. Genes that may specify riboflavin synthases of the eubacterial type in a few Archaea may have been acquired relatively recently by horizontal gene transfer. 

Widely practiced horizontal gene transfers failed to uproot the Tree of Life (Figures 21 and 22). If a first pre-cellular domain of life existed in the form of viruses extending from viroids synthesized in pre-cellular ribozyme-armed ribosomes, and fused into very large, but inert viruses, that melted into the now existing three domains prokaryota, archaea, and eukaryota, as their dependent parasite. It has been accepted that mitochondria and chloroplasts derived from endosymbiotic bacteria (Figure 23). The exact sequence of these events remains a speculative matter. 

Figure 21 Network of Horizontally Transferred Genes In Prokaiyota and Archaea. With kind permission Barth F. Smets, Ph.D. All Rights reserved. 2015. Reference Appendix 2, Explanations to the Figures...

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