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The World’s Second Best Molecule of the Year

While 2020’s science headlines were dominated by the coronavirus’ spike protein, an unrecognized molecular hero was diagnosing people with COVID-19.

The COVID-19 pandemic has made visible so many unsung heroes. Essential workers, parents who must work from home and care for their children, healthcare personnel. But there is one hero whose positive impact on the pandemic remains unsung and for good reasons. It doesn’t technically qualify as a hero because it’s not even alive. It’s a molecule but not any molecule, mind you. The prestigious journal Science dedicated its Christmas 1989 cover to throwing flowers at it, calling it “the molecule of the year.”

Since then, its commonplace nature has moved it out of the limelight. The headlines that used to be devoted to it now dazzle readers with CRISPR or unnerve them with spike proteins. It has not been molecule of the year for over three decades, and yet it is the invisible detective that can tell scientists if you have the coronavirus or not by making the imperceptible detectable.

Its name is Taq DNA polymerase and it would get some scientists in hot water, both literally and metaphorically.

Hot spring breakthrough

Life as we know it relies on genetic material, usually in the form of DNA. This long molecule of complementary double helices has stretches called genes that code for the proteins life forms need to live long and prosper. That DNA is found inside a cell, and when that cell needs to divide into two cells, the DNA must be copied. Otherwise, you can imagine that a human embryo wouldn’t get very far if that initial cell with mom and dad’s DNA kept dividing into more and more cells without making copies of the DNA itself.

There is a family of proteins that do the work of locking onto a strand of DNA and grabbing the building material floating around to create a new, matching DNA strand. They are called DNA polymerases. The suffix “-ase” refers to enzymes, a class of proteins that act as catalysts to drive chemical reactions in biological systems. The prefix “polymer” means that it builds chains using individual building blocks, much like stringing coloured paper clips together. DNA is a polymer of As (adenine), Ts (thymine), Cs (cytosine) and Gs (guanine), and DNA polymerase is the seamstress that sew the fabrics of life together.

We humans have DNA polymerases running around and copying our DNA. So do cats and dogs, and bacteria too. It may sound silly to hear of scientists going around to peculiar places on Earth, collecting bacteria, and characterizing their DNA polymerases. After all, there’s no apparent commercial application for this sort of basic research which aims to satiate our curiosity about our universe. In 1969, as the first human being was taking a giant leap on the Moon, two research scientists from the department of microbiology at Indiana University published a paper in which they described a new bacterium they had discovered: Thermus aquaticus. Thomas D. Brock and Hudson Freeze (not a joke) wrote about this bacterium they isolated not from the freezing Hudson river but from hot springs, specifically those in Yellowstone National Park in the United States. They labelled it an “extreme thermophile,” meaning it loved or thrived in very, very hot temperatures. They also found it in hot tap water in locations around Bloomington, Indiana, indicating that these heat-loving microorganisms might be growing in the hot water heaters themselves.

Seven years later, a Master’s student by the name of Alice Chien co-wrote a paper published in the same journal that had introduced Thermus aquaticus to the scientific world, detailing how she had isolated the DNA polymerase used by this extreme thermophile. It turns out that if you were to put the DNA polymerases of most life forms in a very hot water bath, they would simply lose their shape and, with it, their ability to copy DNA. But not the one Thermus aquaticus had developed randomly through evolution. Its polymerase worked optimally at a balmy 80˚C. The scientific community at the time looked at this and thought, “Good for that bacterium,” and moved on. The DNA polymerase made by Thermus aquaticus, or Taq for short, did not know it would be front-page news 13 years later.

There has to be a better way!

Finding disease-causing mutations in the early 1980s was not always easy. It’s not like you can take your baby’s DNA and manually read it to spot the error that leads to, for example, sickle cell anemia. There were methods that worked, but they were burdensome and some were at the mercy of the particular bits of genetic code surrounding the mutation. But in 1985, a team of scientists at Cetus Corporation in California published a new way of going about finding these mutations, a technique they called the polymerase chain reaction or PCR. It was a way to make copies of the stretch of DNA you were interested in looking at so that it became, in a manner of speaking, more visible. (I have described how PCR works in a previous article.) It is traditionally done in three steps: the temperature of the solution that contains the DNA of interest is brought almost to the boiling point of water to separate the two DNA strands; then it is lowered to allow tiny pieces of DNA called primers to bind to the DNA sample and frame the region of interest; then the temperature is raised to allow a DNA polymerase to make a copy of this region of interest. At the end of this cycle, the three steps are repeated over and over again, like photocopying a single page from a book many times over until it drowns out the rest of the book in a massive pile of paper.

This PCR technique was revolutionary and earned one of the authors of this groundbreaking paper, Kary B. Mullis, the 1993 Nobel Prize in Chemistry alongside Michael Smith. But there was one major annoyance with the process. Scientists were using the DNA polymerase made by the bacterium E. coli, which innocently lives in our gut (though some strains are responsible for outbreaks of food poisoning). The problem is that E. coli’s DNA polymerase, needed for each cycle of the PCR reaction, would crap out when the temperature was raised to near boiling at the beginning of each cycle. So scientists would have to manually add a new batch of polymerase each cycle. Given that a PCR reaction can go through 20 to 40 cycles on average, it meant a lot of hands-on attention. It also meant the possibility of forgetfulness.

If only there was a DNA polymerase out there that could survive at really high temperatures! In January 1988, two years before it would award Taq polymerase the title of molecule of the year, the journal Science published a new article by Mullis and his colleagues. They were now using Taq polymerase for their PCR protocol. It made the procedure simpler and allowed them to raise the temperature some more to increase the specificity of the reaction.

This would lead the Cetus Corporation to file a patent for the use of Taq polymerase for PCR, a patent they sold to the pharmaceutical giant Hoffmann-La Roche for USD 300 million but which was invalidated by a federal judge ten years later. The ruling stated Cetus had obtained the patent by deliberately misleading the U.S. Patent and Trademark Office, by claiming they had been the first to isolate DNA polymerase from Thermus aquaticus in the way they described, whereas it was ruled not to have been so. The case was sent back to a lower court but eventually, this legal quarrelling became moot: the patent expired in the mid-2000s, opening the doors to anyone who wants to isolate and sell this molecule without paying for a pricey license.

Isolating this polymerase from the hot spring bacterium itself is certainly one way to access this valuable resource, but there is another method now widely used by biotech companies. It’s called recombinant DNA and it employs the same principle used to trick bacteria into producing insulin for people with diabetes. If the bacteria have the gene that codes for insulin, they will make insulin; likewise, when scientists insert the gene that codes for Taq polymerase inside of E. coli, these bacteria start making Taq polymerase, a protein that will then be easy to purify since, unlike the rest of E. coli’s proteins, it is able to withstand a heat treatment while every other protein loses its shape and precipitates out of solution.

Today, Taq polymerase is a reliable workhorse of molecular biology laboratories, helping scientists pin down criminals, diagnose specific illnesses, and even say if the milkman is indeed a certain baby’s daddy. While the coronavirus’ spike protein may deserve the title of 2020’s molecule of the year, as it was both that year’s villain and vaccine hero, a molecular seamstress with a love of hot springs may just be worthy of a silver medal.

Take-home message:
- The laboratory test to detect the coronavirus uses a molecule called Taq polymerase
- Taq polymerase is made in the wild by a bacterium called Thermus aquaticus that lives in hot springs and can thus survive very high temperatures
- Its polymerase is used widely by laboratories for the purpose of molecular diagnostics, paternity testing, and crime scene identification and can now be produced by E. coli bacteria in which the gene that codes for this heat-resistant polymerase has been inserted


@CrackedScience

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