Is Carl Woese losing a Kingdom?

Maria Gogarten Maria at carrot.mcb.uconn.edu
Sun Sep 29 17:37:25 EST 1996

	It seems to me that Gupta (and others) are throwing out the child with 
the bath-water.  The finding that all archaebacteria studied so far contain many 
genes that are similar to their eukaryotic counterparts and that these 
archaebacterial genes are very dissimilar to their homologues found in other 
prokaryotes certainly sets the archaebacteria as a group clearly and distinctly 
apart from all of the eubacteria.  One should keep an open mind as to whether 
the currently known archaebacteria are mono- or paraphyletic, the above 
mentioned genes strongly argue that a major component of the archaebacteria is 
not polyphyletic with respect to the eubacteria.  Given that deeper branching 
archaebacteria are being discovered, it seems only a question of time that sooner 
or later a group of archaebacteria will be discovered that is closer to the 
eukaryotes than other archaebacteria (and many will argue that the eocytes 
already fit this description).  Yes, there are major distinction between pro- and 
eukaryotes; however, this should not lead one to overlook the major differences 
between archae- and eubacteria.  

That some genes (e.g. HSP70s and glutamine synthetases) do not reflect a 
"fundamental distinction" between archae- and eubacteria cannot and should not 
be ignored; however, one can hardly take these genes and ignore all the 
characters that define the archaebacteria as a distinct group and claim the 
archaebacteria should be considered a part of the gram positives.  [Following this 
discussion it might be news to some that not all genes that encode enzymes 
involved in biosynthetic pathways and bioenergetics group the archaebacterial 
homologues among their eubacterial counterparts.  Examples that group the 
archaebacterial homologues as a distinct group include ATPsynthases, 
cytochrome C oxidases, and argininosuccinate synthase.]  

The genes that group the archaebacteria among the eubacteria can be put into 
two categories (often it is not clear which one of these, because the rooting of the 
respective phylogenies is controversial):   
Category 1: genes that were contributed to the eukaryotic cell either via the 
mitochondrial endosymbiont (R. Hensel and F. Doolittle think that many 
glycolytic enzymes belong into this category) or via an earlier eubacterial 
contributor to the eukaryotic cell (in my opinion the latter alternative is still mainly 
based on wishful thinking).  For this category the alpha purple bacterial genes 
appear as the sister group to the eukaryotic homologues. The deeper branches, 
which also contain the archaebacteria, often are not well resolved.  
Category 2:  well resolved phylogenies that group the archaebacterial genes 
among the eubacteria.  The longest internal branch connects all the prokaryotes 
to all of the eukaryotes (e.g. HSP70).  Midpoint rooting would place the root in 
this longest internal branch.  I think that the best explanation for these 
phylogenies is horizontal transfer of genes from a eubacterium to the 
archaebacteria.  (Gupta et al.'s explanation needs to assume major variations in 
substitution rate to fit the data, without solving the puzzle of the close 
association between archaebacteria and gram positives).

	Assuming horizontal gene transfer, or the fusion of formerly 
independent lines of descent, certainly complicates the interpretation of 
molecular phylogenies.  However, given that some examples exist that 
demonstrate cross-domin horizontal transfer, and that horizontal transfers and 
symbioses between extant organisms occur frequently, it seems strange to 
assume that these events did not play an important role also in the early 
evolution.  If one looks at the data from a less "eukaryocentric" perspective one 
recognizes that these processes also played an important role in the evolution of 
the other cellular lineages.  Just because it complicates things, or because the 
remnants of these events have not left distinct cell organelles (like in the case of 
mitochondria and chloroplasts), does not mean it has not happened.  Given the 
limited resolution of molecular phylogenies it is at present difficult to pinpoint 
these events on an organismal tree of life, or even to decide how many 
independent events occurred or of which magnitude (i.e. how many genes were 
simultaneously transferred) these events were.  At one extreme one can envision 
the formation of a chimera at the root of the archaebacterial domain, at the other 
extreme is a scenario with many single gene transfers involving eubacteria 
(mostly gram positives, but also a variety of gram negatives) and different 
archaebacteria.  The finding of extensive horizontal gene transfer between eu- and 
archaebacteria should not distract from the major horizontal transfer (fusion) 
events associated with the emergence of the eukaryotes.  However, the 
accumulated molecular data indicate that these events were not restricted to the 
origins of eukaryotes.  
			Peter Gogarten 

PS.: A more detailed discussion off the roles of  horizontal transfer and 
paralogous genes is/will be published by  J. Peter Gogarten, Elena Hilario, and 
Lorraine Olendzenski (1996)  "Gene Duplications and Horizontal Gene Transfer 
during Early Evolution." In: "Evolution of Microbial Life", Society for General 
Microbiology Volume 54

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