Re: Article: Is the Term 'Prokaryote' Obsolete?
- From: John Wilkins <john@xxxxxxxxxxxxx>
- Date: Thu, 1 Jun 2006 01:10:40 -0400 (EDT)
Robert Karl Stonjek wrote:
Is the Term 'Prokaryote' Obsolete?From what I can gather, historically, "prokaryote" simply meant non-eukaryote
The following points are made by Norman R. Pace (Nature 2006 441:289):
1) The explosive accumulation of gene sequences over the past few decades
has brought a new perspective on life and its history. Some of the results
indicate that we need to reassess our understanding of the course of
evolution at the most fundamental level. The current textbook paradigm for
biological diversity and evolution is based on the prokaryote/eukaryote
model. This posits that there are two kinds of cells: prokaryotic, those
without nuclei (specifically, without nuclear membranes) and eukaryotic,
those with a classical membrane-bounded nucleus. The model further posits
that the former gave rise to the latter. The historical antecedents of this
model are complex and rooted in the nineteenth century; for example, German
biologist Ernst Haeckel positioned "monera" (masses of protoplasm without a
nucleus, later termed "prokaryotes") at the base of his four-kingdoms
phylogenetic tree.
2) The recognition that the main eukaryotic organelles, mitochondria and
chloroplasts, were derived from bacteria by symbiosis between the bacteria
and an ancestral eukaryotic cell prompted speculation on a similar origin
for the eukaryotic nucleus. And the discovery of archaea -- microbes that in
many molecular ways resemble eukaryotes more than bacteria -- resulted in
proposals for archaeal origins for nuclear and cytoplasmic components of
eukaryotic cells. Such proposals have sustained the concept that prokaryotes
evolved into eukaryotes -- an evolutionary model invoked by the terms
themselves.
3) Molecular-sequence comparisons, first of ribosomal RNA genes in the late
1970s and of many other genes since, replaced analyses based on
morphological subjectivities (such as the presence or absence of a nuclear
membrane) with credible maps of evolutionary relationships between genes.
These sequence comparisons have rendered the prokaryote/eukaryote model
obsolete. Ribosomal RNA, because of its ubiquity and slow rate of evolution,
provides the most reliable view of the earliest evolutionary events.
Comparisons of ribosomal RNA sequences show a three-domain tree of life.
Although some details of ribosomal RNA-based trees remain controversial, the
basic three-domains structure and the relationships between the domains are
generally accepted and are supported by observed biochemical variation.
Phylogenetic trees based on all genes encoding the information-processing
machinery needed to express genetic sequences are congruent with the
three-domains tree. So the tree represents the evolutionary course of the
genetic machinery, the functional core of genomes.
4) The lessons of the three-domains tree are profound. Instead of two kinds
of organism, prokaryotes and eukaryotes, there are three: bacteria, eukarya
(eukaryotes) and archaea. The root, or origin, of this universal tree,
cannot be determined from ribosomal RNA sequences, but other phylogenetic
results and biochemical correlates show that the genetic lines of eukarya
and archaea have a common ancestral branch that is independent of that
giving rise to the bacteria. That is, eukaryotes and archaea are more
closely related to one another than either is to bacteria. [1-3]
References:
1. Woese, C. R. Microbiol. Rev. 58, 1-9 (1994)
2. Woese, C. R. Microbiol. Mol. Biol. Rev. 68, 173-186 (2004)
3. Sapp, J. Microbiol. Mol. Biol. Rev. 69, 292-305 (2005)
Full Text at ScienceWeek
http://scienceweek.com/2006/sw060602-1.htm
Posted by
Robert Karl Stonjek
organisms (and more particularly, those without nuclear membranes). So it
always was an artificial category.
On the present distinctions, the paper by Rivera and Lake in Science,
Rivera, Maria C., and James A. Lake (2004), "The ring of life provides
evidence for a genome fusion origin of eukaryotes", Nature 431 (7005):152-155.
is interesting. In it, they propose a "ring" of life at the base - where
lateral transfer forms a ring rather than a tree or Woese's progenotic
organisms, from which bacilli, cyanobacteria, proteobacteria evolve on one
side, and euryarchaea, eocyta from the other, and in a hybrid event, eukaryota
formed. See also
Simonson, Anne B., Jacqueline A. Servin, Ryan G. Skophammer, Craig W. Herbold,
Maria C. Rivera, and James A. Lake (2005), "Decoding the genomic tree of
life", PNAS 102 (Suppl. 1):6608-6613.
--
John S. Wilkins, Postdoctoral Research Fellow, Biohumanities Project
University of Queensland - Blog: evolvethought.blogspot.com
"He used... sarcasm. He knew all the tricks, dramatic irony, metaphor, bathos,
puns, parody, litotes and... satire. He was vicious."
.
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