Enzymes are crucial for speeding up slow chemical reactions. Anyone who has worked in a genetics lab is familiar with a common enzyme called Taq polymerase, because it's a reliable workhorse that can be used to copy DNA sequences. The Taq enzyme was first identified in a microbe called Thermos aquaticus, which gave the enzyme its name. Polymerase chain reaction or PCR, which is a foundation of many techniques including DNA sequencing, relies on Taq. Reporting in Science Advances, researchers have now learned some surprising things about the Taq enzyme that could change genetic methods.
"Enzymes make life possible by catalyzing chemical transformations that otherwise would just take too long for an organism," noted co-corresponding study author Greg Weiss, a professor of chemistry at the University of California Irvine (UCI). "One of the transformations we're really interested in," the process for copying and repairing DNA, "is essential for all life on the planet," Weiss added.
In this study, the researchers determined that Taq isn't doing what scientists have long assumed it was. They revealed that the enzyme is not an efficient machine, selectively but quickly creating new copies of DNA; rather, it behaves wildly.
"Instead of carefully selecting each piece to add to the DNA chain, the enzyme grabs dozens of misfits for each piece added successfully," said Weiss. "Like a shopper checking items off a shopping list, the enzyme tests each part against the DNA sequence it's trying to replicate."
Taq will reject bases that don't belong in the sequence being copied, so it will faithfully replicate DNA. However, it seems to also reject bases that are correct, and it does so frequently. Weiss explained that's it's as if a shopper dumps six identical items into their cart, checking them all when they only need to pick a single one. Basically, the study has suggested that Taq is far less efficient than we thought, and researchers may be able to design a similar enzyme that works better. Commercially available Taq polymerases are often sold with a 'proofreading' function, but it may still be possible to dramatically accelerate the action of this type of enzyme if it works in a more efficient way such that proofreading is not as crucial.
The study authors are hopeful that this research could also show whether human genomes are sequenced accurately. In some cases, very small changes in the genome can have huge functional consequences. In other cases, those changes have no effect at all. So it's critical to identify all of those little differences correctly.
Since we don't know everything about the mechanisms of these enzymes, there are open questions. "How do you guarantee to a patient that you've accurately sequenced their DNA when it's different from the accepted human genome? Does the patient really have a rare mutation, or did the enzyme simply make a mistake," suggested co-corresponding study author Philip Collins, a professor in the UCI Department of Physics & Astronomy.
If we have a better DNA-copying enzyme, we may be able to answer those questions, and make the right calls when it comes to using DNA for any number of things, such as making decisions about healthcare or studying human history.
Now that we can readily access so much genetic data, we are gaining a new understanding of various aspects of biology, "but that genomic information is only useful if it's accurate," said Collins.