How does the discovery of "extremophiles" change our understanding of the tree of life?
Extremophiles have been known about for many years, since the 1950s; at this point in time they were not well understood - scientists have now recognised that places once assumed to be sterile abound with microbial life1. The first classification system was put forward by Carolus Linnaeus (1707-1178); other 'designs' were introduced over the years, until 1937 when the French marine biologist Edouard Chatton suggested the term 'procaryotique' and 'eucaryotique' to distinguish animal and plants cells from those of the bacteria2. From this the 'Five Kingdom' theory was proposed, and it 'worked' for many years - for the most part, all organisms discovered could be categorised within the 'Five Kingdoms'.
It was Carl Woese who led the research regarding extremophiles, some 20 years ago, using the technique oligonucleotide cataloging. This technique consisted of breaking a rRNA molecule into fragments (or oligonucleotides) at every G residue. These were then broken into subfragments with enzymes that sliced at different residues; from these Woese reconstructed the sequence of original rRNA fragment. Once they were reconstructed Woese could compare them to other oligonucleotides from other microbes, and thus determine how closely they were related3. This process was labour intensive - 20 years had passed by the time 60 bacteria had been rRNA sequenced.
The results from this research did not vary greatly from the general design of the 'Five Kingdoms'; it was when he sequenced the rRNA from a bacterium that produced methane as a side product (a methanogen), that the five kingdoms tree of life did not work. Even morphologically these bacteria were diverse, and could not be classified satisfactorily. Carl Woese found that the oligonucleotide sequences characteristic of bacteria were not present in this species, and thus came to the conclusion that "these things aren't even bacteria"4. But for the curiosity of Ralph Wolfe (a friend of Woese), the discovery of the 'Archaea' would have been delayed many more years - it took 20 years for Woese to be taken seriously26 even when he had all the scientific evidence to hand!
Woese's tree of life consists of three 'domains' rather than kingdoms (Eukarya, Archaea, and Bacteria), and each of the domains contain kingdoms28 - for example: the eukarya contains plants, animals, fungi, slime moulds (to name a few). It was only in 1996 that all the nucleotides in every gene of Methanococcus jannaschii were deciphered by a number of scientists5, and Woese's claims confirmed. The most conclusive evidence gained from this research was that 56 per cent of M. jannaschii's 1738 genes do not resemble any known DNA sequence6 - a clear distinction for the third domain. Most research has been focused on the gene for an RNA component of ribosomes - the 16S rRNA gene; part of the gene is characteristic of a particular class of organisms. To differentiate between the 'Bacteria', and 'Archaea & Eucarya', a hairpin loop on the rRNA can be looked at (at positions 500 and 545) - the loop consists of 6 nucleotides in bacteria, whereas in the other domains there are seven27. This rRNA gene evolves very slowly, and it is because of this feature that the sequence of nucleotides is identical in every member of a species7. The method used is that of the polymerase chain reaction (PCR)8, which makes millions of copies of the rRNA gene from the bacterium, and therefore easier to compare to other bacteria.
Extremophiles have been known about for many years, since the 1950s; at this point in time they were not well understood - scientists have now recognised that places once assumed to be sterile abound with microbial life1. The first classification system was put forward by Carolus Linnaeus (1707-1178); other 'designs' were introduced over the years, until 1937 when the French marine biologist Edouard Chatton suggested the term 'procaryotique' and 'eucaryotique' to distinguish animal and plants cells from those of the bacteria2. From this the 'Five Kingdom' theory was proposed, and it 'worked' for many years - for the most part, all organisms discovered could be categorised within the 'Five Kingdoms'.
It was Carl Woese who led the research regarding extremophiles, some 20 years ago, using the technique oligonucleotide cataloging. This technique consisted of breaking a rRNA molecule into fragments (or oligonucleotides) at every G residue. These were then broken into subfragments with enzymes that sliced at different residues; from these Woese reconstructed the sequence of original rRNA fragment. Once they were reconstructed Woese could compare them to other oligonucleotides from other microbes, and thus determine how closely they were related3. This process was labour intensive - 20 years had passed by the time 60 bacteria had been rRNA sequenced.
The results from this research did not vary greatly from the general design of the 'Five Kingdoms'; it was when he sequenced the rRNA from a bacterium that produced methane as a side product (a methanogen), that the five kingdoms tree of life did not work. Even morphologically these bacteria were diverse, and could not be classified satisfactorily. Carl Woese found that the oligonucleotide sequences characteristic of bacteria were not present in this species, and thus came to the conclusion that "these things aren't even bacteria"4. But for the curiosity of Ralph Wolfe (a friend of Woese), the discovery of the 'Archaea' would have been delayed many more years - it took 20 years for Woese to be taken seriously26 even when he had all the scientific evidence to hand!
Woese's tree of life consists of three 'domains' rather than kingdoms (Eukarya, Archaea, and Bacteria), and each of the domains contain kingdoms28 - for example: the eukarya contains plants, animals, fungi, slime moulds (to name a few). It was only in 1996 that all the nucleotides in every gene of Methanococcus jannaschii were deciphered by a number of scientists5, and Woese's claims confirmed. The most conclusive evidence gained from this research was that 56 per cent of M. jannaschii's 1738 genes do not resemble any known DNA sequence6 - a clear distinction for the third domain. Most research has been focused on the gene for an RNA component of ribosomes - the 16S rRNA gene; part of the gene is characteristic of a particular class of organisms. To differentiate between the 'Bacteria', and 'Archaea & Eucarya', a hairpin loop on the rRNA can be looked at (at positions 500 and 545) - the loop consists of 6 nucleotides in bacteria, whereas in the other domains there are seven27. This rRNA gene evolves very slowly, and it is because of this feature that the sequence of nucleotides is identical in every member of a species7. The method used is that of the polymerase chain reaction (PCR)8, which makes millions of copies of the rRNA gene from the bacterium, and therefore easier to compare to other bacteria.
