How does the discovery of “extremophiles” change our understanding of the tree of life - Assignment Example

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.

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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. annaschii’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. The new tree of life has led to a better understanding of how ‘life’ has evolved from the common ancestor.

One of the main reason’s Woese could redesign the tree of life is due to his biophysical point of view; he did not have the usual bias associated with biologists9 (and the ‘five kingdom’ theory). New interest then developed in the search of organisms displaying similar characteristics; scientists have found many more species of Archaea as they looked in the appropriate environments (hot springs, hydrothermal vents, deep sea, etc); these were added to the new tree of life (as can be seen below)10. Woese’s ‘tree of life’11.

Since ‘extremophiles’, ie the methanogens, have been known about for many years, but not properly classified12, Carl Woese has essentially triggered the search for more of the Archaea – by giving them a grouping, there must be more organisms of a similar design (there are in all other phyla). As a result of this many extremophiles are now known. There are hyperthermophiles, psychrophiles, acidophiles, alkaliphiles, and halophiles (to name a few). There are important characteristics of these organisms that enable them to survive in these extreme conditions.

For example: hyperthermophiles contain large amounts of the glycolytic derivative, cyclic 2,3-diphosphoglycerate, dissolved in the cytoplasm; this is thought to act as a thermostabilising agent, to prevent denaturation of the enzymes and DNA in the cell13. Acidophiles survive by keeping the acid outside the cell, and halophiles survive in salty solutions by retaining solute from outside the cell (thus becoming isotonic)14. Another reason why Woese’s tree of life makes so much sense is that there have been a lot of questions concerning early life.

The environment on the earth 4 billion years ago was almost certainly hotter than it is now15, and also 4 billion years ago the earth was being constantly bombarded by meteorites16 (these will also have increased the temperature of environment). The reason the climate was warmer is to do with the high levels of CO2 in the atmosphere (and little ozone as a consequence), thus leading to much UV hitting the earth17 – therefore, extremophiles of the hyperthermophile nature, are likely to have survived. Many hyperthermophiles have an optimum temperature of 80?

C18, thus giving the impression that this may have been the ambient temperature 4 billion years ago. (Some archaebacteria (eg Pyrolobus fumarii) stop growing at temperatures below 90? C25 – this is too cold! ) It is the Methanopyrus (a gram-positive rod-shaped methanogen19) which is the earliest life form discovered to date; its temperature optimum is 100? C20, thus suggesting early earth was of this temperature; it was only when the temperature decreased, that more life forms could develop (the high temperature limited the possible diversity).

It is thought that their tolerance to high temperatures is also the reason why they have evolved so slowly21, and hence the Archaea of today are similar to those 4 billion years ago. Due to the discovery of so many extremophiles, and their incredible characteristics, there are many uses for them in industry. Features of archaebacteria are the ‘extremozymes’ that some of them produce: for example, in the laundry detergent22 industry the highly alkaline environment denatures enzymes (proteases and lipases); the potential use of alkaliphiles is clear.

For this to be a viable method it must be easy and cheap to produce the extremozymes (it would be inefficient and expensive to culture the archaebacteria at 100? C) – recombinant DNA technology can be used23. The genes responsible for these extremozymes can then be inserted into ‘ordinary’ microbes, which can then produce pure supplies of the enzymes. Woese’s tree of life has now been accepted by scientists, and will become part of the school curriculum in a few years, but not every scientist agrees with it.

Radhey Gupta believes that a relationship lies between the archaebacteria and the gram-positive bacteria, with the gram-negative being phylogenetically different (he has looked at the sequence features and phylogenies). Both the Archaea and the gram-positive bacteria are prokaryotes surrounded by a single cell membrane, and Gupta suggests the division in prokaryotes is “between Monoderm prokaryotes and Diderm prokaryotes” – he claims that this is consistent with both the protein sequences and cell morphology.

Finally, Gupta thinks that the hypothesis that ‘archaebacteria and eukaryotes shared a common ancestor exclusive of eubacteria’ is incorrect – his research has shown that all eukaryotic cells have received significant gene contributions from both an archaebacterium and a gram-negative eubacteria24. This evidence obviously infers that there may be some flaws in Woese’s tree of life. As can be seen from this essay, Carl Woese has revolutionised taxonomy for the 1990s. The main point made by Woese is that there are three evolutionary lineages, not two, as was previously thought – the division being between the Archaea, Eucarya and Bacteria.

The other important information is that of these three domains the Archaea are closer to the eukaryotes than the bacteria – ie they are closest to the foot of the tree of life. Although classification of species was morphological up until the 1970s (when Woese first put forward his ‘tree of life’), there are problems associated with morphological classification – similarities between eubacteria and archaebacteria can be misleading, and some species can be misidentified due to their similar characteristics.

As organisms have evolved, there have been some cases of convergence, thus giving the impression that two species are very alike – molecular analysis avoids this possibility by looking at the original building blocks for life; the nucleotide sequences on the genes (specifically the 16S rRNA gene), which will hopefully give the clearest picture of evolution yet. Those people, who are voicing differing opinions from that of Carl Woese at the moment, will probably have to wait another twenty years to have their voice heard.