Extremophiles' Prove Their Worth

[Ivan Seeking]

The creatures are known as "extremophiles," and they earn the name: They live in toxic Superfund cleanup sites, boiling deep-sea rift vents, volcanic craters and polar glaciers -- some of the planet's harshest environments.

These single-celled creatures owe their hardiness to genes, and that has drawn the attention of a few biotech companies. The companies train the genes to mass-produce industrial-strength enzymes for such products as better detergents, cleaner chemicals and more-effective DNA fingerprints.

Such "bio-prospecting" efforts have huge potential for good. They just might make hazardous waste cleanup more affordable, reduce pollution and make better medicines if the microbes' genetic durability can be exploited and controlled.

But tough questions are being raised as well -- about the morality of allowing private companies to patent and profit from Mother Nature. [continued]

http://www.wired.com/news/medtech/0,1286,63993,00.html?tw=wn_tophead_7

[Monique]

Oh sure, enzymes from extremophiles are used in the lab everyday. Things as deep vent dna polymerase which is a high-fidelity thermostable dna polymerase with a 5-10 fold higher fidelity than regular taq dna polymerase :)

[Ivan Seeking]

Why is this significant? By fidelity do you mean that it yields results in a PCR 5 to 10 times more accurate than does a low fidelity polymerase?

[Monique]

Since the polymerase comes from a deep-sea-vent organism, it is supposed to work at very high temperatures where it is easy for the enzyme to incorporate the wrong bases or to simply fall off the template. The error rate of this polymerase is much less than of a polymerase from an organism that lives at more temperate temperatures.

I don't think there should be an issue with patenting this kind of thing since the application of these enzymes is very clear. Unlike patenting genes. Also, haven't we been patenting mother nature for as long as patents are available? I mean, just look at medications. If someone finds a molecule that is therapeutic, a patent is issued after which they hold monopoly on the compound's application for several years.

[iansmith]

Since the polymerase comes from a deep-sea-vent organism, it is supposed to work at very high temperatures where it is easy for the enzyme to incorporate the wrong bases or to simply fall off the template. The error rate of this polymerase is much less than of a polymerase from an organism that lives at more temperate temperatures.

They choose these enzyme because it is not denatured at high temperature required to deannealed double stranded DNA. The error rate of these enzyme is somewhat similar to the polymerase found in mesophiles bacteria.

[Monique]

Vent, Deep vent and Pfu dna polymerase have 3'->5' proofreading exonuclease activity.

[iansmith]

E. coli and other bacterial polymerase have a 3'->5' exonuclease activity. Also many polymerase used in PCR have their 3'->5' exonuclease activity knock-out.

Again, DNA polymerase found mesophile bacteria denature at 50C, polymerase of thermophilic organisms denature at above 100C and genomic DNA denature at around 95C. pfu, deep ven, vent and taq are only used because they are stable at 95C.

there researcher look at artic and antartic bacteria so they can use their enzyme in cold setting. It is a matter of stability and activity at these temperature that are important.

[Oyéah]

One of the worries of using DNA from bacteria stable at high heat, would be the creation of predator strains, that do not die at high heat, that can't be washed off the dishes. Very poor people don't experience much sanitation, and if we make super bugs, they are defenseless.

[iansmith]

This thing could happen in nature not necessary in a lab. Microorganism can exchange DNA easly. However, it is not the DNA that is stable at high temperature but rather it is their protein/enzyme. In the lab we only use the enzyme not the DNA.

If a "bug" acquire only part of the enzymes, it would still requires other genes to be able to survive these conditions. Also there already heat resistant species of bacteria and there is also spores which can resist boiling water in some case more than 15 minutes. The spore producing bacteria are more of problem and of a worry than creating superbug in lab. The probably of creating a superbug is just too low to consider this happening