Which part of eucariotic DNA is similar to archaebacteria?
Robert Maas
eucariotic cells is closer to DNA in archaebacteria than it is to DNA
in eubacteria. (It used newer terminalogy; I'm translating into the
terminology in Five Kingdoms by Lynn Margulis, with which I'm more
familiar and more likely to spell correctly.)
One problem with that statement is that each eucariotic cell is the
result of a long period of co-evolution from an original symbiosis of
two different kinds of bacteria, one of which formed the mitochondria,
and one of which formed the nucleus. (In plants, add a third which
formed the chloroplasts.) I assume the article was referring to either
the nucleus or mitochondria, but which of those two? Was it sloppy of
the author to refer to the DNA in eucariotic cells without specifying
which of the two it was?
(I think the article was in the SCIENCE issue of 1996.Aug.23, p.1023 &
1043-45 & 1058-73, J. Craig Venter, because I have that citation
accompanying the notes I'm using to compose this query, but I'm not
sure.)
I searched DejaNews to see if there's anything on this topic already
posted, and found:
> Subject: Re: difference between arhaea, eucarya & bacteria
> From: Brian Foley <b...@t10.lanl.gov>
> Date: 1998/06/04
> Message-ID: <35772E...@t10.lanl.gov>
> Newsgroups: sci.bio.microbiology
<<Some of the best DNA evidence supporting the idea of 3 equal domains
(Archebacteria, Eubacteria, Eukaryote) comes from the sequences of
ribosomal proteins and other protein associated with the ribosome such
as elongation factor 2.>>
Does anybody know where the DNA for coding those ribosomal proteins in
Eukaryotes is located (in the nucleus, or in the mitochondria)? If it's
in the nucleus, does anybody know whether that DNA was originally in
the nucleus at the time of original symbiosis, or it was in the
mitochondria but later miagrated to the nucleus?
Whichever those genes came from, does anybody have a good explanation
why the 3-way split in phenotype is nearly equal, instead of Eukaryotes
being closer to whatever that half of its symbiosis came from?
Subject: Re: difference between arhaea, eucarya & bacteria
From: nla...@eden.rutgers.edu (Nicholas Landau)
Date: 1998/06/08
Message-ID: <6lhj14$2...@er6.rutgers.edu>
Newsgroups: sci.bio.microbiology
<<Older texts will refer to Archaea as "archaebacteria," a misnomer, as
they are not bacteria.>>
Howso? Isn't this simply a name game, whereby you define the terms
whatever way you like, and then anybody who defines them different you
say is wrong? Why do you feel it's inappropriate to refer to all simple
cells (not symbiosis such as eucariots) as "bacteria", and to then
sub-divide them into archaebacteria and eubacteria?
It seems to me that structurally the archaebacteria and eubacteria are
very similar, either of which is totally different from eucariots
(because the latter derives from a symbiosis of bacteria followed by
evolution of mitosis, much more complicated result). In fact it seems
that plants (with their third symbiot) are more different in structure
from most of the other eucariots than archaebacteria are from
eubacteria. Why is it wrong to keep those names which emphasize both
their similarities and differences, but instead to adopt names "archea"
or somesuch for the former making them sound totally different from
bacteria?
Chemistry/metabolism is no excuse, because the archaebacteria are so
different from each other that if you split them from eubacteria you
might as well split them from each other. Ribosomal proteins are just
ONE factor to consider, probably enough to say they are two different
kingdoms, but not in my opinion not enough to totally ignore their
similarities.
mel turner
Maas...@worldnet.att.net says...
>A while back I read an article in SCIENCE which claimed the DNA in
>eucariotic cells is closer to DNA in archaebacteria than it is to DNA
>in eubacteria. (It used newer terminalogy; I'm translating into the
>terminology in Five Kingdoms by Lynn Margulis, with which I'm more
>familiar and more likely to spell correctly.)
>
>One problem with that statement is that each eucariotic cell is the
>result of a long period of co-evolution from an original symbiosis of
>two different kinds of bacteria, one of which formed the
mitochondria,
>and one of which formed the nucleus. (In plants, add a third which
>formed the chloroplasts.) I assume the article was referring to
either
>the nucleus or mitochondria, but which of those two? Was it sloppy of
>the author to refer to the DNA in eucariotic cells without specifying
>which of the two it was?
Preusmably it's the nuclear genomes of the eukaryotes that were being
compared in the article you read, and it would be surprising if that
were not made clear somewhere in the text. Mitochondrial and plastid
genes are also often studied and compared, but that should also be
specified.
[big snip]
Here's a selection of likely-sounding refs taken from a quick
BioAbstracts search:
TI Archaeal-eubacterial mergers in the origin of Eukarya: Phylogenetic
classification of life.
AU Margulis-L
SO Proceedings of the National Academy of Sciences of the United
States of America 93(3): 1071-1076
PY 1996
AB A symbiosis-based phylogeny leads to a consistent, useful
classification system for all life. "Kingdoms" and "Domains" are
replaced by biological names for the most inclusive taxa: Prokarya
(bacteria) and Eukarya (symbiosis-derived nucleated organisms). The
earliest Eukarya, anaerobic mastigotes, hypothetically originated from
permanent whole-cell fusion between members of Archaea (e.g.,
Thermoplasma-like organisms) and of Eubacteria (e.g., Spirochaeta-like
organisms). Molecular biology, life-history, and fossil record
evidence support the reunification of bacteria as Prokarya while
subdividing Eukarya into uniquely defined subtaxa: Protoctista,
Animalia, Fungi, and Plantae.
TI The root of the universal tree and the origin of eukaryotes based
on elongation factor phylogeny.
AU Baldauf-S-L; Palmer-J-D; Doolittle-W-F
SO Proceedings of the National Academy of Sciences of the United
States of America 93(15): 7749-7754
PY 1996
AB The genes for the protein synthesis elongation factors Tu (EF-Tu)
and G (EF-G) are the products of an ancient gene duplication, which
appears to predate the divergence of all extant organismal lineages.
Thus, it should be possible to root a universal phylogeny based on
either protein using the second protein as an outgroup. This approach
was originally taken independently with two separate gene duplication
pairs, (i) the regulatory and catalytic subunits of the proton ATPases
and (ii) the protein synthesis elongation factors EF-TU and EF-G.
Questions about the orthology of the ATPase genes have obscured the
former results, and the elongation factor data have been criticized
for inadequate taxonomic representation and alignment errors. We have
expanded the latter analysis using a broad representation of taxa from
all three domains of life. All phylogenetic methods used strongly
place the root of the universal tree between two highly distinct
groups, the archaeons/eukaryotes and the eubacteria. We also find that
a combined data set of EF-Tu and EF-G sequences favors placement of
the eukaryotes within the Archaea, as the sister group to the
Crenarchaeota. This relationship is supported by bootstrap values of
60-89% with various distance and maximum likelihood methods, while
unweighted parsimony gives 58% support for archaeal monophyly.
TI Determining divergence times of the major kingdoms of living
organisms with a protein clock.
AU Doolittle-R-F; Feng-D-F; Tsang-S; Cho-G; Little-E
SO Science (Washington D C) 271(5248): 470-477
PY 1996
AB Amino acid sequence data from 57 different enzymes were used to
determine the divergence times of the major biological groupings.
Deuterostomes and protostomes split about 670 million years ago and
plants, animals, and fungi last shared a common ancestor about a
billion years ago. With regard to these protein sequences, plants are
slightly more similar to animals than are the fungi. In contrast,
phylogenetic analysis of the same sequences indicates that fungi and
animals shared a common ancestor more recently than either did with
plants, the greater difference resulting from the fungal lineage
changing faster than the animal and plant lines over the last 965
million years. The major protist lineages have been changing at a
somewhat faster rate than other eukaryotes and split off about 1230
million years ago. If the rate of change has been approximately
constant, then prokaryotes and eukaryotes last shared a common
ancestor about 2 billion years ago, archaebacterial sequences being
measurably more similar to eukaryotic ones than are eubacterial ones.
TI Molecular classification of living organisms.
AU Saccone-C; Gissi-C; Lanave-C; Pesole-G
SO Journal of Molecular Evolution 40(3): 273-279
PY 1995
AB Recent studies in molecular evolution have generated strong
conflicts in opinion as to how world living organisms should be
classified. The traditional classification of life into five kingdoms
has been challenged by the molecular analysis carried out mostly on
rRNA sequences, which supported the division of the extant living
organisms into three major groups: Archaebacteria, Eubacteria, and
Eukaryota. As to the problem of placing the root of the tree of life,
the analysis carried out on a few genes has provided discrepant
results. In order to measure the genetic distances between species, we
have carried out an evolutionary analysis of the glutamine synthetase
genes, which previously have been revealed to be good molecular
clocks, and of the small and large rRNA genes. All data demonstrate
that archaebacteria are more closely related to eubacteria than to
eukaryota, thus supporting the classical division of living organisms
into two main superkingdoms, Prokaryota and Eukaryota.
TI HSP70 Phylogeny and the relationship between archaebacteria,
eubacteria, and eukaryotes.
AU Gupta-R-S; Golding-G-B; Singh-B
SO Journal of Molecular Evolution 39(5): 537-540
PY 1994
DE LETTER; HEAT SHOCK PROTEIN 70; EVOLUTION
TI Phylogenetic analysis of carbamoylphosphate synthetase genes:
Complex evolutionary history includes an internal duplication within a
gene which can root the tree of life.
AU Lawson-F-S; Charlebois-R-L; Dillon-J-A-R
SO Molecular Biology and Evolution 13(7): 970-977
PY 1996
AB Carbamoylphosphate synthetase (CPS) catalyzes the first committed
step in pyrimidine biosynthesis, arginine biosynthesis, or the urea
cycle. Organisms may contain either one generalized or two specific
CPS enzymes, and these enzymes may be heterodimeric (encoded by linked
or unlinked genes), monomeric, or part of a multifunctional protein.
In order to help elucidate the evolution of CPS, we have performed a
comprehensive phylogenetic analysis using the 21 available complete
CPS sequences, including a sequence from Sulfolobus solfataricus P2
which we report in this paper. This is the first report of a complete
CPS gene sequence from an archaeon, and sequence analysis suggests
that it encodes an enzyme similar to heterodimeric CPSII. We confirm
that internal similarity within the synthetase domain of CPS is the
result of an ancient gene duplication that preceded the divergence of
the Bacteria, Archaea, and Eukarya, and use this internal duplication
in phylogenetic tree construction to root the tree of life. Our
analysis indicates with high confidence that this archaeal sequence is
more closely related to those of Eukarya than to those of Bacteria. In
addition to this ancient duplication which created the synthetase
domain, our phylogenetic analysis reveals a complex history of further
gene duplications, fusions, and other events which have played an
integral part in the evolution of CPS.
TI Protein phylogenies and signature sequences: Evolutionary
relationships within prokaryotes and between prokaryotes and
eukaryotes.
AU Gupta-R-S
SO Antonie van Leeuwenhoek 72(1): 49-61
PY 1997
AB The evolutionary relationships within prokaryotes and between
prokaryotes and eukaryotes is examined based on protein sequence data.
Phylogenies and common signature sequences in some of the most
conserved proteins point to a close evolutionary relationship between
Archaebacteria and Gram-positive bacteria. The monophyletic nature and
distinctness of the Archaebacterial domain is not supported by many of
the phylogenies. Within Gram-negative bacteria, cyanobacteria are
indicated as the deepest branching lineage, and a clade consisting of
Archaebacteria, Gram-positive bacteria and cyanobacteria is supported
by signature sequences in many proteins. However, the division within
the prokaryotic species, viz. Archaebacteria dblarw Gram-positive
bacteria fwdarw Cyanobacteria fwdarw other groups of Gram-negative
bacteria, is indicated to be not very rigid but, instead is an
evolutionary continuum. It is expected that certain species will be
found which represent intermediates in the above transitions. By
contrast to the evolutionary relationships within prokaryotes, the
eukaryotic species, which are structurally very different, appear to
have originated by a very different mechanism. Protein phylogenies and
signature sequences provide evidence that the eukaryotic nuclear
genome is a chimera which has received major contributions from both
an Archaebacterium and a Gram-negative bacterium. To explain these
observations, it is suggested that the ancestral eukaryotic cell arose
by a symbiotic fusion event between the above parents and that this
fusion event led to the origin of both nucleus and endoplasmic
reticulum. The monophyletic nature of all extant eukaryotic species
further suggests that a 'successful primary fusion' between the
prokaryotic species that gave rise to the ancestral eukaryotic cell
took place only once in the history of this planet.
TI The emergence of major cellular processes in evolution.
AU Ouzounis-C; Kyrpides-N
SO FEBS Letters 390(2): 119-123
PY 1996
AB The phylogenetic distribution of divergently related protein
families into the three domains of life (archaea, bacteria and
eukaryotes) can signify the presence or absence of entire cellular
processes in these domains and their ancestors. We can thus study the
emergence of the major transitions during cellular evolution, and
resolve some of the controversies surrounding the evolutionary status
of archaea and the origins of the eukaryotic cell. In view of the
ongoing projects that sequence the complete genomes of several
Archaea, this work forms a testable prediction when the genome
sequences become available. Using the presence of the protein families
as taxonomic traits, and linking them to biochemical pathways, we are
able to reason about the presence of the corresponding cellular
processes in the last universal ancestor of contemporary cells. The
analysis shows that metabolism was already a complex network of
reactions which included amino acid, nucleotide, fatty acid, sugar and
coenzyme metabolism. In addition, genetic processes such as
translation are conserved and close to the original form. However,
other processes such as DNA replication and repair or transcription
are exceptional and seem to be associated with the structural changes
that drove eukaryotes and bacteria away from their common ancestor.
There are two major hypotheses in the present work: first, that
archaea are probably closer to the last universal ancestor than any
other extant life form, and second, that the major cellular processes
were in place before the major splitting. The last universal ancestor
had metabolism and translation very similar to the contemporary ones.
while having an operonic genome organization and archaean-like
transcription. Evidently, all cells today contain remnants of the
primordial genome of the last universal ancestor.
TI Ancestral relationships of the major eukaryotic lineages.
AU Sogin-M-L; Morrison-H-G; Hinkle-G; Silberman-J-D
SO Microbiologia (Madrid) 12(1): 17-28
PY 1996
AB Molecular systematics has revolutionized our understanding of
microbial evolution. Phylogenetic frameworks relating all organisms in
this biosphere can be inferred from comparisons of slowly evolving
molecules such as the small and large subunit ribosomal RNAs. Unlike
today's text book standard, the "Five Kingdoms" (plants, animals,
fungi, protists and bacteria), molecular studies define three primary
lines of descent (Eukaryotes, Eubacteria, and Archaebacteria). Within
the Eukaryotes, the "higher" kingdoms (Fungi, Plantae, and Animalia)
are joined by at least two novel complex evolutionary assemblages, the
"Alveolates" (ciliates, dinoflagellates and apicomplexans) and the
"Stramenopiles" (diatoms, oomycetes, labyrinthulids, brown algae and
chrysophytes). The separation of these eukaryotic groups (described as
the eukaryotic "crown") occurred approximately 10-9 years ago and was
preceded by a succession of earlier diverging protist lineages, some
as ancient as the separation of the prokaryotic domains. The molecular
phylogenies suggest that multiple endosymbiotic events introduced
plastids into discrete eukaryotic lineages.
TI Determining divergence times with a protein clock: Update and
reevaluation.
AU Feng-D-F; Cho-G; Doolittle-R-F
SO Proceedings of the National Academy of Sciences of the United
States of America 94(24): 13028-13033
PY 1997
AB A recent study of the divergence times of the major groups of
organisms as gauged by amino acid sequence comparison has been
expanded and the data have been reanalyzed with a distance measure
that corrects for both constraints on amino acid interchange and
variation in substitution rate at different sites. Beyond that, the
availability of complete genome sequences for several eubacteria and
an archaebacterium has had a great impact on the interpretation of
certain aspects of the data. Thus, the majority of the archaebacterial
sequences are not consistent with currently accepted views of the Tree
of Life which cluster the archaebacteria with eukaryotes. Instead,
they are either outliers or mixed in with eubacterial orthologs. The
simplest resolution of the problem is to postulate that many of these
sequences were carried into eukaryotes by early eubacterial
endosymbionts about 2 billion years ago, only very shortly after or
even coincident with the divergence of eukaryotes and archaebacteria.
The strong resemblances of these same enzymes among the major
eubacterial groups suggest that the cyanobacteria and Gram-positive
and Gram-negative eubacteria also diverged at about this same time,
whereas the much greater differences between archaebacterial and
eubacterial sequences indicate these two groups may have diverged
between 3 and 4 billion years ago.
cheers
Robert Maas
> Author: mel turner
> Email: mtu...@snipthis.acpub.duke.edu
> Date: 1998/07/15
> Forums: sci.bio.microbiology, talk.origins
> Message-ID: <6oht9g$hrm$1...@news.duke.edu>
> References: <6ohlfk$j...@bgtnsc03.worldnet.att.net>
> Here's a selection of likely-sounding refs taken from a quick
> BioAbstracts search:
> TI Archaeal-eubacterial mergers in the origin of Eukarya: Phylogenetic
> classification of life.
> AU Margulis-L
> SO Proceedings of the National Academy of Sciences of the United
> States of America 93(3): 1071-1076
> PY 1996
I doubt I have access to that journal. Wish I did, sigh.
> AB A symbiosis-based phylogeny leads to a consistent, useful
> classification system for all life. "Kingdoms" and "Domains" are
> replaced by biological names for the most inclusive taxa: Prokarya
> (bacteria) and Eukarya (symbiosis-derived nucleated organisms). ...
I agree with that decision.
> The earliest Eukarya, anaerobic mastigotes, hypothetically originated
> from permanent whole-cell fusion between members of Archaea (e.g.,
> Thermoplasma-like organisms) and of Eubacteria (e.g., Spirochaeta-like
> organisms).
Five Kingdoms shows as "mastigotes": Euglenophyta & Zoo mastigina, both
of which are too complicated to be similar to that first Eukaryotic
cell. Is the assumption that a much simpler version of the same phylum
existed then, or something much different but which is still considered
a kind of "mastigote".
> TI The root of the universal tree and the origin of eukaryotes based on
> elongation factor phylogeny.
> AU Baldauf-S-L; Palmer-J-D; Doolittle-W-F
> ...
> All phylogenetic methods used strongly place the root of the universal
> tree between two highly distinct groups, the archaeons/eukaryotes and
> the eubacteria. We also find that
May I assume by "eukaryotes" they really mean only the nuclei of
eukaryotes?
> We also find that a combined data set of EF-Tu and EF-G sequences
> favors placement of the eukaryotes within the Archaea, as the sister
> group to the Crenarchaeota.
Ditto: only the nucleus of the eukaryotes is sister to Crenarchaeota?
What would the mitochondria be sister to?
By the way, does everyone still agree with Margulis in Five Kingdoms
that Plantae evolved from something like Chlorophyta? Did plastids (in
Chlorophyta then in Plantae) come from Cyanobacteria or
Chloroxybacteria according to expert opinion based on best data
currently available?
> TI Determining divergence times of the major kingdoms of living
> organisms with a protein clock.
> AU Doolittle-R-F; Feng-D-F; Tsang-S; Cho-G; Little-E
> SO Science (Washington D C) 271(5248): 470-477
> PY 1996
> AB Amino acid sequence data from 57 different enzymes were used to
> determine the divergence times of the major biological groupings.
I assume they used a combined measure of differences between all of
them together to increase signal/noise ratio, right? If each different
enzyme is computed separately, do the resultant noisy pre-enzyme trees
basically agree with each other, indicating all of the 57 enzymes
co-evolved for most or all of their history? Or do they show different
results way back near their roots indicating that some of them might
have evolved separately for a while then merged with the main clump of
them and all co-evolved together from then to the present?
> Deuterostomes and protostomes split about 670 million years ago and
> plants, animals, and fungi last shared a common ancestor about a
> billion years ago.
This result seemed slightly at odds with fossel evidence until
recently, but just this year I saw a new article in SCIENCE presenting
possible evidence of wormlike animals (apparently within phylum
Annelida) burrowing along one layer in bacterial mats, as revealed by
their fossilized tunnels, roughly a billion years ago (if I recall
correctly). If fully developed animals were around that long ago, it
clearly establishes that animals diverged from the rest at least that
long ago.
Update: After I wrote that paragraph but before I could finish editing
and post this followup: An article in a more recent issue of SCIENCE
disputes the date of the fossilized tunnels, claiming they are much
younger. I guess this question is currently a hot topic, a question not
yet resolved to everyone's satisfaction.
> prokaryotes and eukaryotes last shared a common ancestor about 2
> billion years ago, archaebacterial sequences being measurably more
> similar to eukaryotic ones than are eubacterial ones.
Again, may I assume by "eukaryotic sequences" they really mean
"eukaryotic nuclear sequences" only? I wish they'd make that clear in
the abstract. All they had to add was one (1) word.
> TI Molecular classification of living organisms.
> AU Saccone-C; Gissi-C; Lanave-C; Pesole-G
> PY 1995
> ...
> The traditional classification of life into five kingdoms ...
Gee, Five Kingdoms came out in 1982 (second edition, which I have,
1987, with post-dated 1988 copyright), and I understand that way of
organizing cellular life had only recently been adopted by textbook
authors. Funny that only 13 years after her first edition, the system
is called "traditional". I usually think of "traditional" as referring
to something that's been common for at least 50 years. Does somebody
know the years when the five-kingdom system changed from "new" to
"standard" and thence to "traditional"?
> the molecular analysis carried out mostly on rRNA sequences, which
> supported the division of the extant living organisms into three major
> groups: Archaebacteria, Eubacteria, and Eukaryota.
Are rRNA in Eukaryota generated from DNA in the nucleus, or in the
mitochondria? Aren't rRNA sequences indicative of the origin of the
particular DNA that generates them, not of the cell as a whole, since
the cell as a whole comes from a symbiosis/merger of cells with two
different origins (and 3 for plants etc. with plastids)?
I'd like to see geneologies computed for each different gene in both
nuclei and mitochondria of several (many) different Eukaryotes, then
those geneologies compared to see which genes from nuclei were
originally there at the time of the merger vs. which came from the
mitochondria originally. Then we'll know, assuming rRNA is generated by
present nuclear DNA, whether that DNA originally came from mitochondria
or not, hence whether rRNA sequences are indicative of the origin of
the nuclei or of the mitochondria.
> TI Phylogenetic analysis of carbamoylphosphate synthetase genes:
> Complex evolutionary history includes an internal duplication within a
> gene which can root the tree of life.
> AU Lawson-F-S; Charlebois-R-L; Dillon-J-A-R
> ...
(regarding one specific gene that was duplicated prior to divergence
between Archaea and Eubacteria etc.)
> this archaeal sequence is more closely related to those of Eukarya than
> to those of Bacteria.
In this case they are dealing with a single gene, so they are analyzing
the variants of that single gene as found in the two bacterial kingdoms
and in eukaryotes, so their language is clear. They are saying this one
gene in eukaryotes is closer to that gene in Archaea, not saying the
whole cell of an eukaryote is sister to some Archaea cell.
> point to a close evolutionary relationship between Archaebacteria and
> Gram-positive bacteria. The monophyletic nature and distinctness of the
> Archaebacterial domain is not supported by many of the phylogenies.
I hadn't heard of this development at all. Thanks much for this
abstract!! If this opinion is valid, that kills the separation of
Archaebacteria as a separate kingdom or even sub-kingdom. More
generally: It shows how VERY little we yet really know about the
genetics and evolution of Prokaryota. The good news is their genomes
are so small it'll be relatively easy to sequence a whole slew of them
in the next few years so as to calculate a correct evolutionary tree
for each of their genes.
> The monophyletic nature of all extant eukaryotic species further
> suggests that a 'successful primary fusion' between the prokaryotic
> species that gave rise to the ancestral eukaryotic cell took place only
> once in the history of this planet.
I don't think we've mapped enough genomes to be sure of that
conclusion, but if true it solidly establishes Eukaryota as a single
super-kingdom based on evolutionary history rather than merely an ad
hoc grouping based only on cell structure and lifestyle (such as
mitosis).
Note: It's possible that other primary fusions occurred, but all the
other such lines, except that which led to today's Eukaryota, went
extinct long ago.
Side question that came to mind: Are there any specific genes that we
know moved from mitochondria to nuclei because some eukaryotes still
have them in mitochondria while others have them in their nuclei?
> TI Ancestral relationships of the major eukaryotic lineages.
> AU Sogin-M-L; Morrison-H-G; Hinkle-G; Silberman-J-D
> ...
> The molecular phylogenies suggest that multiple endosymbiotic events
> introduced plastids into discrete eukaryotic lineages.
Given how easily some protoctists can lose their plastids and then
re-gain them by brand-new encapsulation of a freeliving photosynthetic
bacterium, I rather expected this conclusion, and am glad to learn that
it's tentatively confirmed. When we compare the genetic tree of
plastids themselves with nuclear&mitochondrial DNA, we will learn how
long each line of plastid+theRest have been co-evolving. Also we'll
learn whether closely-related plastids occur in not-closely-related
theRest (nucl+mito) lines, indicating that some species of plastids
became expert at joining with different eukaryotic lines, or whether
closely-related theRest (nucl+mito) lines have not-closely-related
plastids, indicating that some species of eukaryotes became expert at
collecting various kinds of plastids as needed.
> TI Determining divergence times with a protein clock: Update and
> reevaluation.
> AU Feng-D-F; Cho-G; Doolittle-R-F
> ...
(Eukaryotic DNA seems to contain genes from several different kinds of
Archaebacteria and Eubacteria all thrown together.)
> The simplest resolution of the problem is to postulate that many of
> these sequences were carried into eukaryotes by early eubacterial
> endosymbionts about 2 billion years ago, ...
All the more reason to create family trees for each particular gene
separately and THEN see which of them have co-evolved for various
periods of time after previously having evolved independently, and
thereby discover the timing of various major mixings that occurred and
any single-segment-of-genes transfer (via plasmid or virus or bacterial
'sexual' reproduction) that may have occurred.
P.S. I'm very lonely. I don't have any friends. If anybody who lives
near Mountain View, CA, likes my ideas that I post to the net, and
wants to consider becoming my friend, please let me know. Otherwise
I'll have to assume that nobody around here likes me enough to care
whether I live or die.
MoE
That is probably not a good idea.. (Although it is likely that the
primitive eukaryotes hadn't acquired their plastids and mitochondria
yet.)
> > We also find that a combined data set of EF-Tu and EF-G sequences
> > favors placement of the eukaryotes within the Archaea, as the sister
> > group to the Crenarchaeota.
>
> Ditto: only the nucleus of the eukaryotes is sister to Crenarchaeota?
Yes.
> What would the mitochondria be sister to?
The closest relatives to mitochondria are the members of the alpha
subgroup of Gram-negative purple bacteria, which includes goodies
like Rhodobacter sphaeroides.
> By the way, does everyone still agree with Margulis in Five Kingdoms
> that Plantae evolved from something like Chlorophyta?
> Did plastids (in
> Chlorophyta then in Plantae) come from Cyanobacteria or
> Chloroxybacteria according to expert opinion based on best data
> currently available?
The photosynthetic machinery found in chloroplasts and cyanobacteria
strongly resemble each other. In particular, the subunit cytochrome
f (my favorite) which is found throughout cyanobacteria and
chloroplasts has a sequence identity of about 60% between
cyanobacterial and plant species. That's about as low as it goes.
Personally, I think of chloroplasts as funny-looking cyanobacteria
that got hijacked.
[snip the rest - others can answer better]
Chris
John Harshman
> Robert Maas wrote:
> > > Here's a selection of likely-sounding refs taken from a quick
> > > BioAbstracts search:
> >
> > > TI Archaeal-eubacterial mergers in the origin of Eukarya: Phylogenetic
> > > classification of life.
> > > AU Margulis-L
> > > SO Proceedings of the National Academy of Sciences of the United
> > > States of America 93(3): 1071-1076
> > > PY 1996
> >
> > I doubt I have access to that journal. Wish I did, sigh.
> > > All phylogenetic methods used strongly place the root of the universal
> > > tree between two highly distinct groups, the archaeons/eukaryotes and
> > > the eubacteria. We also find that
> >
> > May I assume by "eukaryotes" they really mean only the nuclei of
> > eukaryotes?
Yes. Other genomes within eukaryotes are of course related to other organisms.
> That is probably not a good idea.. (Although it is likely that the
> primitive eukaryotes hadn't acquired their plastids and mitochondria
> yet.)
Obviously not their plastids. We probably have no evidence about the
mitochondria; so far it's generally construed that all eukaryotes lacking
mitochondria have lost them secondarily. But this also depends on how you
define "eukaryote". If you mean the crown group (including the last common
ancestor of all extant eukaryotes), then probably they had mitochondria.
If you mean a group defined by presence of some character, like a nuclear
membrane, maybe not. But remember that the various characters by which we
identify eukaryotes today probably evolved over a long period, and
probably one at a time.
> > By the way, does everyone still agree with Margulis in Five Kingdoms
> > that Plantae evolved from something like Chlorophyta?
Yes. But in modern terminology this means plants *are* Chlorophyta;
Plantae is a subgroup of Chlorophyta.
--
*Note the obvious spam-defeating modification
to my address if you reply by email.
John Harshman
Maas) wrote:
> > Re: Which part of eucariotic DNA is similar to archaebacteria?
> > Author: mel turner
> > Email: mtu...@snipthis.acpub.duke.edu
> > Date: 1998/07/15
> > Forums: sci.bio.microbiology, talk.origins
> > Message-ID: <6oht9g$hrm$1...@news.duke.edu>
> > References: <6ohlfk$j...@bgtnsc03.worldnet.att.net>
>
> > Here's a selection of likely-sounding refs taken from a quick
> > BioAbstracts search:
>
> > TI Archaeal-eubacterial mergers in the origin of Eukarya: Phylogenetic
> > classification of life.
> > AU Margulis-L
> > SO Proceedings of the National Academy of Sciences of the United
> > States of America 93(3): 1071-1076
> > PY 1996
>
> I doubt I have access to that journal. Wish I did, sigh.
Sure you do. Any university library will have it. Stanford, for example.
If you couldn't find PNAS, I can't imagine what other journal you *could*
find, except maybe Science.
Stanley Friesen
>Robert Maas wrote:
>> May I assume by "eukaryotes" they really mean only the nuclei of
>> eukaryotes?
>
>That is probably not a good idea.. (Although it is likely that the
>primitive eukaryotes hadn't acquired their plastids and mitochondria
>yet.)
I would certainly agree here.
>
>> Ditto: only the nucleus of the eukaryotes is sister to Crenarchaeota?
>
>Yes.
I am not so sure here, though. I suspect that the nucleus and the
extranuclear cytoplasm have the same origin. That is, I am skeptical
that the nucleus originated via endosymbiosis.
>
>> What would the mitochondria be sister to?
>
>The closest relatives to mitochondria are the members of the alpha
>subgroup of Gram-negative purple bacteria, which includes goodies
>like Rhodobacter sphaeroides.
>
Not to mention that famous lab stand-by: _E. coli_.
[Also, note, there are at least *two* origins of chloroplasts, from
different bacterial groups, plus a number of cases of meta-chloroplasts
- chloroplasts that were themselves originally eukaryotes].
The peace of God be with you.
Stanley Friesen
J.R. Pelmont
> ...........
>
> The closest relatives to mitochondria are the members of the alpha
> subgroup of Gram-negative purple bacteria, which includes goodies
> like Rhodobacter sphaeroides.
> ..............
See the genome sequence of Rickettsia prowazekii described by S.G.
Andersson .... C.G. Kurland in Sweden (Nature 396, November 1998,
133-140). They conclude that R.prowazekii is more closely related to
mitochondria than is any other microbe studied so far.
--
jean.p...@ujf-grenoble.fr
Fax (33)0 476 51 4336
Robert Maas
> Author: Stanley Friesen
> Email: sar...@ix.netcom.com
> Date: 1998/11/24
> Forums: sci.bio.microbiology, talk.origins
> Message-ID: <36638b9a....@nntp.ix.netcom.com>
I (Robert) previously said <<May I assume by "eukaryotes" they really
mean only the nuclei of eukaryotes?>>
and somebody else said <<That is probably not a good idea.. (Although
it is likely that the primitive eukaryotes hadn't acquired their
plastids and mitochondria yet.)>>
I don't quite understand what is not a good idea, what they published,
or what I asked they really meant?
then the just-previous poster (Stanley) said: <<I would certainly agree
here.>>
Agree with original abstract, or agree with my question, or agree with
the inscrutable remark of the poster before Stanley?
I (Robert) previously said <<Ditto: only the nucleus of the eukaryotes
is sister to Crenarchaeota?>>
Middle poster said: <<Yes.>>
Just-previous poster (Stanley) said: <<I am not so sure here, though.
I suspect that the nucleus and the extranuclear cytoplasm have the same
origin. That is, I am skeptical that the nucleus originated via
endosymbiosis.>>
I was speaking only of "immortal coils" (DNA), which are simply
replicated from their exact opposite (with occasional mistakes), not of
cytoplasm and other parts of the cell which are manufactured directly
or indirectly from triples of RNA which are copied from DNA. When I
referred to "only the nucleus", I meant "only the DNA in the nucleus".
I agree that probably the cytoplasm of the eukaryotic cell derives from
the cytoplasm of the original Crenarchaeota cell that started to
incorporate other strains of bacteria to make the mitochondria etc.,
although any chemicals currently in the cytoplasm of any eukaryotic
cell would almost surely be manufactured from more recent DNA rather
than still there after hundreds of millions of years since the original
cytoplasm of the first eukaryotic cell. This is unlike the DNA which
was not manufactured from other chemicals and patterns but really has
come from the original eukaryotic cell via a direct pattern-line of
alternating stands of DNA. So my original statement should have been
that only nuclear DNA in eukaryotic cells is sister to DNA in
Crenarchaeota (and eukaryotic cytoplasm manufactured mostly using
instructions in that nuclear DNA just as Crenarchaeota cytoplasm was
manfactured using instructions in its DNA, so cytoplasm in the two are
sort of like cousins whose creators were sisters).
For the nitpickers: The DNA are sister only insofar as DNA hasn't
miagrated from mitochondria to nucleus. When we completely finish
seqencing some of these genomes, as well as mitochondrial DNA, and
matching up everything that is similar, we'll probalby learn which
parts of nuclear DNA really are sister to Crenarchaeota, which are
derived from mitochondria hence are sister to purple-sulphur bacteria
instead, and which arrived via other means such as plasmids&viruses.
Likewise there are chemicals in the cytoplasm that traverse to or from
mitochondria, so some of those chemicals are really cousin to
purple-sulphur badteria instead of Crenarchaeota, and some chemicals
are cousin to nothing because they couldn't possibly be chemically
produced without the chemical engines of BOTH the nucleus and the
mitochondria.
As for endosymbiosis, I agree the Crenarchaeota was probably the host
into which smaller purple-sulphur bacteria and cyanobacteria became
endosymbiots. By the way, in Lynn Martulis's book "Symbiosis in Cell
Evolution" she speculates that the spindle and all other 9+2 or 9+0
flagella etc. in eukaryotic cells came from yet another endosymbiot
whose genome has completely miagrated into the nucleus so there's no
trace of that genome as a separate entity remaining. (But when we do
sequence matching we may discover a group of genes that code for those
structures and do NOT derive from Crenarchaeota nor purple-sulphur
bacteria nor cyanobacteria, but DO all seem to come from one other
specific phylum of bacteria, which would then prove her conjecture.)
What's the current status of that conjecture?
<<Also, note, there are at least *two* origins of chloroplasts, from
different bacterial groups, plus a number of cases of meta-chloroplasts
- chloroplasts that were themselves originally eukaryotes.>>
Ah, yes, I was thinking specifically of chloroplasts in plants, which I
believe all come from the same phylum, which somebody said is almost
definitely cyanobacteria. But indeed some protoctists have completely
different chloroplasts and the like that derive from other phyla of
photosynthetic bacteria. So there were several photosynthetic
endosymbiosis events in eukaryots, but only one of those happened to be
in a clade that later evolved to form organized multi-cellular tissues
and creatures i.e. plants. (It would be an interesting experiment to
take some of those other phyla of photosynthetic protoctists completely
away from competition with plants and let them evolve a few hundred
million years and see whether any of them ever evolve to a different
way of making plant-like creatures, convergent evolution.)
Side question: Why are there exactly three kingdoms of truly
multi-cellular life? Is it because there are exactly three major
natural niches: primary food production from sunlight, actively
stealing that kind of biomass to use as food, and semi-passively
growing into dead or nearly-dead biomass as if it were a nutrient
broth. But fermenting bacteria are in direct competition with fungi for
decomposing dead or near-dead biomass, so why can both totally
different kinds of life survive so long in that same mega-niche? Might
one or the other eventually out-compete the other for that mega-niche
so well that the other goes extinct?
mel turner
>[big snip]
><<Also, note, there are at least *two* origins of chloroplasts, from
>different bacterial groups, plus a number of cases of meta-chloroplasts
>- chloroplasts that were themselves originally eukaryotes.>>
>
>Ah, yes, I was thinking specifically of chloroplasts in plants, which I
>believe all come from the same phylum, which somebody said is almost
>definitely cyanobacteria. But indeed some protoctists have completely
>different chloroplasts and the like that derive from other phyla of
>photosynthetic bacteria.
And as I recall, some seem to have secondarily derived chloroplasts by
endosymbiosis with eukaryotic cells already with plastids.
So there were several photosynthetic
>endosymbiosis events in eukaryots, but only one of those happened to be
>in a clade that later evolved to form organized multi-cellular tissues
>and creatures i.e. plants.
No, there are also multicellular "plants" in the form of seaweeds [e,g.,
Phaeophyta, Rhodophyta] that have also apparently separately acquired
chloroplasts from those of green land plants and the green algae. Separate
origins of cloroplasts, separate origins of multicellularity.
(It would be an interesting experiment to
>take some of those other phyla of photosynthetic protoctists completely
>away from competition with plants and let them evolve a few hundred
>million years and see whether any of them ever evolve to a different
>way of making plant-like creatures, convergent evolution.)
In the sea that's already happened. Kelp are pretty big plant-like creatures of
independent origin from land plants.
>Side question: Why are there exactly three kingdoms of truly
>multi-cellular life?
Well, that's largely an artifact of classification. The commonly recognized
"kingdoms" aren't necessarily all monophyletic groups. There are indeed more
than three origins of multicellularity in eukaryotes. 1] in metazoan animals;
2] within red algae 3] in brown algae 4] more than one independent origin of
multicellularity in "green algae", one line of which includes the green land
plants; 5] more than one origin of different types of multicellularity among
fungus-like organisms, slimemolds and such...
>Is it because there are exactly three major
>natural niches: primary food production from sunlight, actively
>stealing that kind of biomass to use as food, and semi-passively
>growing into dead or nearly-dead biomass as if it were a nutrient
>broth. But fermenting bacteria are in direct competition with fungi for
>decomposing dead or near-dead biomass, so why can both totally
>different kinds of life survive so long in that same mega-niche?
There are some fungus-like bacterial types with branching filamentous cells.
>Might
>one or the other eventually out-compete the other for that mega-niche
>so well that the other goes extinct?
They've had a thousand million years or so to do it, and it hasn't happened so
far. Anyway, each species in each of the groups is essentially on its own to
survive or go extinct; it's not competition between "bacteria" as a group and
"fungi" as a group.
cheers