From: lip@s1.gov (Loren I. Petrich)
Newsgroups: sci.bio,bionet.molbio.evolution,talk.origins
Subject: Woese's Work on Bacterial Evolution -- How Seriously is it Taken?
Date: 17 Aug 92 12:34:39 GMT
Organization: LLNL


	In the late 1970's and early 1980's, microbiologist Carl Woese
and others compared some ribosomal RNA sequences from various bacteria
and other organisms and arrived at the conception of "three
urkingdoms" --

	Eubacteria, the "true" bacteria

	Archaebacteria, an group of unusual bacteria

	Eucaryotae, everything with a distinct cell nucleus.

	How well as this work stood up? I ask this question because
some researchers, such as Lake, would divide the Archaebacteria into
two groups, the "photocytes" (extreme halophiles) and the "eocytes"
(the rest); he posits that the photocytes are the closest to the
eubacteria and that the eocytes to the eukaryotes.

	Here are details, for anyone interested; I briefly describe
the hypothesized universal ancestor at the end of this post.

	The first of these groups has several subgroups; the three
biggest ones are:

	The Purple Bacteria: bacteria with one-step photosynthesis
that depend on organic compounds or sulfur. Mixed in among them are
many of the better-known Gram-negative non-photosynthetic bacteria,
like _Escherichia coli_. A subgrouping of them has a tendency to form
symbioses with eukaryotic organisms; plant root-nodule bacteria are
among them. From this group apparently came the ancestor(s) of the
eukaryotic mitochondria.

	The Gram-Positive Bacteria: These are named after their
response to a certain stain; they have a distinctive cell-wall
composition. It contains one photosynthesizer, _Heliobacterium_, the
actinomycetes, and a grouping that includes the clostridia, the
mycoplasmas (bacteria without cell walls, only cell membranes), and
the spore-formers.

	The Cyanobacteria: These include the blue-green "algae" and
the prokaryotic green "algae"; eukaryote chloroplasts are also
members, probably having been acquired by their hosts several times.
This is the only group that practices two-step, oxygen-releasing
photosynthesis.

	There are several smaller ones like the spirochetes, the green
sulfur bacteria, and green nonsulfur bacteria (both one-step
photosynthetic), and so forth.

	Aerobes (those that use oxygen as an oxidant) appear mixed in
with the anaerobes, the anaerobes typically surrounding the aerobes in
the family trees. One concludes that aerobic metabolism appeared
independently in several different lineages; this would be consistent
with the hypothesis of oxygen becoming available _after_ the
eubacteria had become considerably diversified. This is consistent
with the final segments of the respiratory chains (those that turn the
oxygen into water) being very variable, while the earlier segments are
much less variable, as if they had been worked out befor oxygen
started appearing.

	Eubacterial photosynthesis is a rather complex process, one
that probably did not evolve more than once; its widespread occurrence
suggests that the ancestral eubacterium practiced it. It works by
energizing electrons from various substrates and donating them to
various organic compounds, which then become more reduced or
hydrogen-ified. The non-cyanobacterial one-step photosynthesis is
probably the original kind of photosynthesis, probably working from
hydrogen sulfide or similar reduced mineral compounds, and almost
certainly not releasing oxygen. The two-step variety may have arisen
by a duplication of the genes for the original photosystem and
specialization of one of the two resulting photosystems for harder and
harder nuts to crack, chemically speaking, until it succeeded in
working on water.

	Less plausibly, one may conclude that the original eubacterium
was autotrophic, that is, it depended on no outside sources of organic
molecules. In this perspective, the heterotrophic anaerobes, for
example the clostridia, are not primitive at all but suffer from
atrophied metabolism, so that they cannot obtain all the organic
molecules they need from inorganic sources.


	Our next group is the archaebacteria, which have three main
groups:

	The extreme halophiles: _Halobacterium_ and its relatives live
in extremely salty conditions and have a simple form of
non-eubacterial photosynthesis involving a rhodopsin-like pigment.

	The methanogens: To get energy, these take in hydrogen and
carbon dioxide and release water and methane. Though they are strictly
anaerobic and almost always autotrophic, they are essentially
ubiquitous in oxygen-poor environements, such as swamps, lake bottoms,
and digestive tracts. The extreme halophiles are probably an offshoot
of this group.

	The thermoacidophiles: These live in hot springs with high
concentrations of sulfuric acid. They live off of combining sulfur and
sulfuric acid with hydrogen. The methanogens are an offshoot of one
group of them.


	Interestingly, there are also some TA'phile eubacteria, which
are also early branchers off of the eubacterial tree. We may conclude
that both the eubacteria and the archaebacteria are descended from
TA'philes.


	Our third group, the eukaryotes, includes everything else.
Well after their origin, there appears to have been a major radiation,
giving the ancestors of such familiar varieties as the animals, the
plants and green algae, fungi such as yeast and bread mold, the
ciliates, at least some of the dinoflagellates, and so forth.
Branching off earlier were various flagellates and amoebas and slime
molds (what's the latest on eukaryote phylogeny?). Some of the
earliest to branch off are some parasites that do not have
mitochondria like _Vairimorpha_ and _Giardia_. Though not having
mitochondria is what is expected of the original eukaryote, the fact
that the survivors of the early branchings are parasites tells us
little of their original lifestyles, since there would originally have
been no hosts to parasitize. Thus, one cannot tell if the ancestral
eukaryote was a TA'phile, as seems apparent for the other two groups.

	There are other differences, such as those in membrane lipids
and polymerase segmentation, that are consistent with this
three-urkingdom picture.

	And one other thing: to date, Woese's work has involved the
16S fraction of ribosomal RNA; 5S rRNA is too short to be informative,
and 23S rRNA has been a bit long to sequence. Has there been any work
on 23S rRNA sequences, and how does it compare to results from 16S
rRNA ones? Are there any other good sequences for this kind of
long-distance work? How well have transfer RNA's worked out for this
purpose? (yes, I know, they're rather short and probably not too much
good)

	One limitation of molecular-phylogeny techniques is that if
one tries to compensate for variations in molecular-evolution rate,
one becomes unable to find the root of the family tree. This
limitation can be circumvented by employing an outside sequence, but
that is by definition impossible for the universal ancestor. A way out
of that is available if there was a gene that got duplicated in an
ancestor of the universal ancestor, a gene whose descendants can still
be found. For example, certain "elongation factors" seem to fit the
bill quite readily, and a tree constructed with them seems to indicate
that the eukaryotes are descended from certain archaebacteria.

	If this result is correct, then we have an idea of what the
youngest common ancestor was like (or at least that of all those
looked at in any detail):

	It was a TA'phile, preferring to live in sulfuric-acid hot
springs, and it was autotrophic, subsisting on inorganic compounds and
carbon dioxide. It may have had some simple form of photosynthesis.

	This is contrary to a certain received wisdom about the
original organism, as explained earlier about the eubacterial
ancestor; instead of being dependent on its environment for organic
molecules, it was self-sufficient in that regard.

	This is a rather complex organism, with full-fledged DNA ->
RNA -> protein information transfer, complete biosynthesis pathways,
and so forth, and not what one might expect of a
spotaneously-generated one.

	In another post, I will tackle the question of how _it_ may
have evolved.
Xref: sparky sci.bio:2994 sci.skeptic:14800 soc.men:15322 soc.women:15598