How Extreme Microbes Are Helping Us Test for COVID-19

How Extreme Microbes Are Helping Us Test for COVID-19

Microbes that live in extreme environments, like geysers and hydrothermal vents, are able to survive in extreme temperatures. Scientists have figured out ways to use this thermostability to supercharge DNA studies, including the study of fast-mutating viruses like COVID-19.

Hot springs and hydrothermal vents might notbe the first places you’d look to find ways to fight a pandemic. But they’ve given us some of the most important tools we have for identifying, tracking, and understanding pathogens. In fact, without them, the entire field of molecular biology would be stuck in the 1960s, and not in the fun way. See, that’s when researchers discovereda microbe in Yellowstone that allowed them to actually replicate DNA at will. This process—known as Polymerase Chain Reaction,or PCR for short—was really a game changer for genetics. And we here at SciShow do not use that phraselightly. The pathway to developing PCR began way backin the middle of the twentieth century. Scientists had just really seen DNA for thefirst time, but already, they were searching for ways to read these genetic blueprints.FST01 Problem was, sequencing DNA—and its simplercousin, RNA—required a lot of genetic material, because it relied on cutting longer stringsinto smaller ones with enzymes that sliced at certain sequences, and then back-calculatingwhat the whole string looked like from those pieces. And, simply put, it wasn’t easy to obtainthat volume of genetic material—especially for anything not microbial in nature. So they knew being able to make copies ofDNA would open the door to all kinds of research. And the potential to do that traces back to1957—just a few years after the structure of DNA was first described—when researchers identified the first DNA polymerase.

These enzymes build strands of DNA from nucleotides,the essential building blocks of nucleic acids. They take a single strand of DNA as a template,and string together a complementary strand. And all organisms have the blueprints forat least one of these enzymes written into their genetic code. That’s how they makecopies of their genome when their cells divide. Researchers soon discovered that they could isolate these enzymes from bacteria like E. coli, which meant, hypothetically, they coulduse them to replicate any DNA they wanted. Except, there was a small catch. Before the polymerase can start copying DNA,the tightly wound, paired strands of DNA found in organisms like us have to be separatedinto single strands. That way, short sequences of single-strandedDNA called primers can bind to the open strand and tell the polymerase where to start andstop copying. In nature, this unwinding requires yet anotherenzyme, plus a several other proteins—too complicated to recreate in a tube. Luckily, DNA strands can be separated anotherway. Above 90°C, the bonds holding the strandstogether break apart.

So you can heat up DNA to get single strands,then cool things down a bit to let the primers bind and so DNA polymerase can make its copies. After each heating and cooling cycle, youessentially double the amount of DNA. Today, each of these cycles takes about fiveminutes, so within a few hours, you can go from a very small number of copies to millionsof copies of a given DNA sequence. But in the ‘60s, the whole process tookmuch longer than that. See, heat also permanently inactivates theDNA polymerases from E. coli. So, in early DNA replication efforts, freshpolymerase had to be added each time a copy of DNA was made—making the process veryslow and very expensive. That’s where extreme microbes come intoplay. P05In 1966, scientists discovered a microbe living in the 70-plus degree waters of hot springsin Yellowstone National Park. They named it Thermus aquaticus, after itsability to thrive in the hot spring’s high temperatures. And in 1976, researchers isolated one of itsDNA polymerases. They called it Taq polymerase—or, just Taq,for short. And, like the microbe itself, it could withstandthe high temperatures needed for separating DNA strands.

So you could throw it in with your sample,some primers, and nucleic acids, and then let a machine heat and cool everything overand over again to produce millions of copies of DNA. And that, in a nutshell, is Polymerase ChainReaction. Ever since researchers developed these methodsin the mid eighties, PCR has allowed scientists to turn teeny amounts of DNA into much largerones in a matter of hours. For geneticists, it was like going from carbon-copypaper to a Xerox machine! It meant they could figure out whose cellsare on the end of a hair at a crime scene. Or, spot the genes of a virus hiding in someone’sblood. In short, Taq polymerase revolutionized genetics.And it’s still widely used for PCR today. But newer enzymes are coming into play, too. See, Taq sometimes makes mistakes. It grabsthe wrong nucleotide and attaches it instead. This is a problem for applications that needa high level of accuracy—like, if you’re trying to detect the small mutations thatcan happen to a virus over time. Doing that can help experts understand howthe pathogen is moving about and changing. Luckily, researchers discovered Pyrococcus abyssi—a deep sea microbe that lives ineven more extreme conditions. Its enzymes are more resilient than Taq, butmore importantly, they also proofread themselves while making copies—which is why they’reforty to fifty times more accurate.

They’re now among the several specializedpolymerases available to geneticists. And researchers keep going back to extremeenvironments because their microbes have all sorts of unique and useful molecular tricksup their sleeves. So who knows what else we’ll discover bystudying these remarkably resourceful organisms. PCR didn’t just provide new tools for studyingviral outbreaks, of course.

Suddenly, scientists could use genetic information to study allsorts of evolutionary and biological questions.

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