I had posted an email here from Carl Woese to Mitch Sogin (with Mitch’s permission). However, in retrospect I feel uncomfortable posting private emails of Carl Woese’s here as he is not around to give permission. So I have removed them. Apologies to all who may have felt uncomfortable about the posting and to those who wish it would remain public. But I just do not feel comfortable with this anymore.
Tag: Mitch Sogin
Most important paper ever in microbiology? Woese & Fox, 1977, discovery of archaea
Well, today in my “Microbial phylogenomics” class at UC Davis we are discussing what I think might be the most important paper (well, actually, series of papers) in the history of microbiology. The papers are the ones where Carl Woese, George Fox and colleagues outline the evidence for the existence of a “hidden” third major branch in the tree of life – what is now known as the archaea. The evidence for this third branch was first laid out in a series of papers in 1977 including:
- An ancient divergence among the bacteria. Balch WE, Magrum LJ, Fox GE, Wolfe RS, Woese CR.J Mol Evol. 1977 Aug 5;9(4):305-11.
- Classification of methanogenic bacteria by 16S ribosomal RNA characterization. Fox GE, Magrum LJ, Balch WE, Wolfe RS, Woese CR. Proc Natl Acad Sci U S A. 1977 Oct;74(10):4537-4541.
Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Woese CR, Fox GE. Proc Natl Acad Sci U S A. 1977 Nov;74(11):5088-90.
ABSTRACT A phylogenetic analysis based upon ribosomal RNA sequence characterization reveals that living sys.tems represent one of three aboriginal lines of descent: (i) the eubacteria, comprising all typical bacteria; (ii) the archaebacteria, containing methanogenic bacteria; and (iii) the urkaryotes, now represented in the cytoplasmic component of eukaryotic cells.
A comparative analysis of these data, summarized in Table 1, shows that the organisms clearly cluster into several primary kingdoms. The first of these contains all of the typical bacteria so far characterized …. (lots of names here) … It is appropriate to call this urkingdom the eubacteria.
A second group is defined by the 18S rRNAs of the eukaryotic cytoplasm-animal, plant, fungal, and slime mold (unpublished data). … (They call this lineage the urkaryotes).
Eubacteria and urkaryotes correspond approximately to the conventional categories “prokaryote” and “eukaryote” when they are used in a phylogenetic sense. However, they do not constitute a dichotomy; they do not collectively exhaust the class of living systems. There exists a third kingdom which, to date, is represented solely by the methanogenic bacteria, a relatively unknown class of anaerobes that possess a unique metabolism based on the reduction of carbon dioxide to methane (19-21). These “bacteria” appear to be no more related to typical bacteria than they are to eukaryotic cytoplasms. Although the two divisions of this kingdom appear as remote from one another as blue-green algae are from other eubacteria, they nevertheless correspond to the same biochemical phenotype. The apparent antiquity of the methanogenic phenotype plus the fact that it seems well suited to the type of environment presumed to exist on earth 3-4 billion years ago lead us tentatively to name this urkingdom the archaebacteria. Whether or not other biochemically distinct phenotypes exist in this kingdom is clearly an important question upon which may turn our concept of the nature and ancestry of the first prokaryotes.
With the identification and characterization of the urkingdoms we are for the first time beginning to see the overall phylogenetic structure of the living world. It is not structured in a bipartite way along the lines of the organizationally dissimilar prokaryote and eukaryote. Rather, it is (at least) tripartite, comprising (i) the typical bacteria, (ii) the line of descent manifested in eukaryotic cytoplasms, and (iii) a little explored grouping, represented so far only by methanogenic bacteria.
Woese CR, & Fox GE (1977). Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proceedings of the National Academy of Sciences of the United States of America, 74 (11), 5088-90 PMID: 270744
Fox GE, Magrum LJ, Balch WE, Wolfe RS, & Woese CR (1977). Classification of methanogenic bacteria by 16S ribosomal RNA characterization. Proceedings of the National Academy of Sciences of the United States of America, 74 (10), 4537-4541 PMID: 16592452
Balch WE, Magrum LJ, Fox GE, Wolfe RS, & Woese CR (1977). An ancient divergence among the bacteria. Journal of molecular evolution, 9 (4), 305-11 PMID: 408502
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