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How Carl Woese discovered the Deepest Branchings of our Biota's Family Tree

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How Carl Woese discovered the Deepest Branchings of our Biota's Family Tree

Post by lpetrich » Wed Nov 22, 2017 4:45 am

I had already posted on his work in RIP, Carl Woese - Secular Café, and in another forum, I'd posted on how he made the discovery of his three domains. So I'm bringing it here.

Here is what he did.

In the early 1970's, protein sequencing had been well-developed but gene sequencing less so. Biologists had to content themselves with snipping up a gene into snippets about 5 to 10 bases long and then sequencing those snippets. We still have to work with snippets, it must be said, but nowadays, they can be 500 or so bases long.

Carl Woese considered what might be a good molecule to sequence. It had to be ubiquitous in cellular organisms, have the same function in all of them, and be slow-evolving. He decided on the small-subunit ribosomal RNA (SSU rRNA). Ribosomes are RNA-protein structures for assembling proteins, and they are composed of a large and a small subunit. The SSU rRNA is also called the 16S rRNA in prokaryotes and the 18S rRNA in eukaryotes, after the "Svedberg number", a sort of "size" factor found from using an ultracentrifuge.

One can follow how CW's work developed by following the papers in PubMed.

Procaryote phylogeny. I. Concerning the relatedness of Aerobacter aerogenes to Escherichia coli. 1974 -- no further details. Checking on Wikipedia, the first organism is now Enterobacter aerogenes, and it's a fairly close relative of E. coli.

Sequence studies on 16S ribosomal RNA from a blue-green alga. 1975
The 16S ribosomal RNA of the blue green alga Anacystis nidulans has been characterized in terms of the oligomers generated by digestion with T1 ribonuclease. A. nidulans by this criterion is definitely a procaryote; being no more distant from Bacilli or Enterics than the latter two are from one another. A. nidulans appears to be somewhat more closely related to the Bacilli than to the Enterics.
BGA = cyanobacterium, Enterics are in Gamma Proteobacteria, Bacilli are in Firmicutes

The phylogenetic status of Pasteurella pestis. 1975
Yersinia pestis has been characterized in terms of fingerprints of digests (pancreatic and/or T1 ribonuclease) of its 16S and 5S ribosomal RNAs. These show clearly that Y. pestis is a member of the Enterobacteriaceae and suggest that within the Family it is most closely related to Serratia and/or Proteus.
More enterics.

Phylogenetic origin of the chloroplast and prokaryotic nature of its ribosomal RNA. 1975
The 16S ribosomal RNA of the Euglena gracilis chloroplast has been characterized in terms of its two-dimensional electrophoretic "fingerprint" (T1 ribonuclease). Results show it to be a typically prokaryotic 16 S rRNA. By the present criterion, different chloroplasts are shown to be related to one another and at least distantly to blue-green algae and perhaps to Bacillaceae. These results argue in favor of an endosymbiont origin of the chloroplast.
Chloroplasts: descendants of some cyanobacterium that was "eaten" long ago but that escaped digestion and made itself useful.

Procaryote phylogeny IV: concerning the phylogenetic status of a photosynthetic bacterium. 1975
The 16S ribosomal RNA (30S subunit) of Rhodopseudomonas spheroides has been characterized in terms of T1 ribonuclease digestion products. This "fingerprint" ultimately permits the placement of R. spheroides into a detailed procaryotic phylogenetic tree. Given the number of major procaryotic lines that have been characterized in these terms to date, one can tentatively place the Athiorhodaceae closer to the Vibrio-Enteric group than to the Bacillaceae or Cyanophyta.
That's a purple photosynthetic bacterium, one with simpler photosynthesis that doesn't split water to make oxygen.

An ancient divergence among the bacteria. 1977
The 16S ribosomal RNAs from two species of methanogenic bacteria, the mesophile Methanobacterium ruminantium and the thermophile Methanobacterium thermoautotrophicum, have been characterized in terms of the oligonucleotides produced by digestion with T1 ribonuclease. These two organisms are found to be sufficiently related that they can be considered members of the same genus or family. However, they bear only slight resemblance to "typical" Procaryotic genera; such as Escherichia, Bacillus and Anacystis. The divergence of the methanogenic bacteria from other bacteria may be the most ancient phylogenetic event yet detected--antedating considerably the divergence of the blue green algal line for example, from the main bacterial line.
OMG, a deep split.

Classification of methanogenic bacteria by 16S ribosomal RNA characterization. 1977
The 16S ribosomal RNAs from 10 species of methanogenic bacteria have been characterized in terms of the oligonucleotides produced by T(1) RNase digestion. Comparative analysis of these data reveals the methanogens to constitute a distinct phylogenetic group containing two major divisions. These organisms appear to be only distantly related to typical bacteria.
Phylogenetic structure of the prokaryotic domain: the primary kingdoms. 1977
A phylogenetic analysis based upon ribosomal RNA sequence characterization reveals that living systems 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.
The first statement of his three-domain split.

Are extreme halophiles actually "bacteria"? 1978
Comparative cataloging of the 16SrRNA of Halobacterium halobium indicates that the organism did not arise, as a halophilic adaptation, from some typical bacterium. Rather, H. halobium is a member of the Archaebacteria, an ancient group of organisms that are no more related to typical bacteria than they are to eucaryotes.
Archaebacteria. 1978
Experimental work published elsewhere has shown that the Archaebacteria encompass several distinct subgroups including methanogens, extreme halophiles, and various thermoacidophiles. The common characteristics of Archaebacteria known to date are these: (1) the presence of characteristic tRNAs and ribosomal RNAs; (2) the absence of peptidoglycan cell walls, with in many cases, replacement by a largely proteinaceous coat; (3) the occurrence of ether linked lipids built from phytanyl chains and (4) in all cases known so far, their occurrence only in unusual habitats. These organisms contain a number of 'eucaryotic features' in addition to their many bacterial attributes. This is interpreted as a strong indication that the Archaebacteria, while not actually eucaryotic, do indeed represents a third separate, line of descent as originally proposed.
Lots of phenotypic differences.

Methanogens: reevaluation of a unique biological group. 1979

Phylogenetic analysis of the mycoplasmas. 1980
The phylogenetic relationships between the mycoplasmas and bacteria have been established from a comparative analysis of their 16S rRNA oligonucleotide catalogs. The genera Mycoplasma, Spiroplasma, and Acholeplasma arose by degenerative evolution, as a deep branch of the subline of clostridial ancestry that led to Bacillus and Lactobacillus. Thermoplasma has no specific relationship to the other mycoplasmas; it belongs with the archaebacteria.
The phylogeny of prokaryotes. 1980
First page of article at Science magazine
A detailed look. The revolution is complete.


Since then, an alternate hypothesis about the origin of eukaryotes has emerged: that it is a hybrid between an archaeon and a eubacterium, likely an archaeon that "ate" an alpha-proteobacterium, making the first mitochondrion.

Also interesting is the Carl Woese did not set out to discover the deep split between Eubacteria and Archaea. But he was willing to recognize it when he came across it, and he and I'm sure some other biologists looked for phenotypic features that might be correlated with that deep split. They found several.

Phenotype = features of an organism outside its genetic information, often mentioned as a contrast to genetic features.

In the early days of Carl Woese's three-domain proposal, some biologists were skeptical because Eubacteria and Archaea both share the overall prokaryote phenotype, something very different from the overall eukaryote phenotype. In less technical language, they look much alike, despite that deep split in their family tree.

I thought it appropriate to illustrate how to use that jargon word.

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