For decades, biology textbooks have enshrined a simple rule: DNA is made by copying a template. After one enzyme unzips a DNA double helix into separate strands, another called a polymerase builds a complementary sequence, base by base, for each strand. Presto: two copies of the original DNA. But new research into how bacteria defend themselves from viruses now shows this synthesis rule isn’t absolute. Today in Science, a Stanford University team describes a bacterial enzyme that synthesizes a long repetitive DNA sequence without a nucleic acid template, using its own structure as a guide.
“The research is groundbreaking,” says Philip Kranzusch, a biochemist at Harvard Medical School who studies bacterial defenses. “Pretty cool!” adds Adi Millman, a computational biologist at the Massachusetts Institute of Technology. The use of a protein as a template for DNA synthesis, she says, “is a meaningful conceptual shift from the classical central dogma,” in which information flows in one direction from nucleic acids like DNA to protein. Other biologists take issue with the idea that dogma has been challenged, arguing the mysterious DNA sequence made by the enzyme doesn't then become part of the bacterium's genome. Still, the Stanford team and other scientists hope the novel form of DNA synthesis can be adapted as a tool for basic biological research, much like the powerful genome editor CRISPR was developed from another bacterial defense system.
In canonical DNA replication, the rules of base pairing reign supreme: Polymerases assemble their complementary DNA strand by matching adenine with thymine and guanine with cytosine on the template. Replication can also proceed with RNA as the template, thanks to polymerases called reverse transcriptases that use that nucleic acid to guide the fabrication of single-stranded DNA.
The new finding centers on DRT3, a defense system that protects bacteria from viruses, known as phages, that infect them. DRT3, the researchers found, bypasses the logic of base pairing. It relies on two reverse transcriptases: a conventional one that builds single-stranded DNA from an RNA template, and a second, unusual one that assembles its complement from its own built-in template. This unusual enzyme, called Drt3b, has amino acids in its active site that mimic a template RNA strand.
“The protein itself serves as the blueprint for the DNA sequence,” says Stanford biochemist Alex Gao, senior author on the study. “That was quite a surprise,” he says. “This is a fundamentally new way that life produces DNA.” Yet Gao acknowledges that Drt3b only makes a single, specific repetitive sequence. "It does not represent a general mechanism for proteins to write genetic code," he says.
The DRT3 system appears to be widespread across bacteria, suggesting it is not a biochemical curiosity. Yet how it thwarts phages is still a mystery.
One possibility, Gao says, is that DNA helices made by this unique replication method act as molecular sponges that glom onto phage components, either directly hindering the phage or enabling other bacterial immune elements to recognize the infection. If that idea holds up, Kranzusch says, DRT3 would complement recent discoveries of polymeraselike proteins in other bacterial defense systems that produce nucleic acid polymers to detect and inhibit phage infection.
DRT3 also represents another mind-bending role for reverse transcriptases, long associated with retroviruses such as HIV, which uses one to synthesize a DNA copy of its RNA genome and slip into a cell’s chromosomes. In recent years, these enzymes have been revealed to be key players in some CRISPR bacterial defense systems and in the generation of entirely new bacterial genes. RTs are now appreciated as “highly adaptable scaffolds that have been repeatedly co-opted” for functions beyond DNA replication, Gao says.
Like CRISPR, DRT3 could have practical applications. “DRT3 represents an ‘all-in-one’ molecular machine for sequence-specific DNA synthesis, which is a rare find in nature,” Gao says. If scientists could figure out how to engineer Drt3b to produce other sequences, he adds, they might make customized DNA strands, for instance to create advanced biomaterials such as DNA hydrogels.
More broadly, the discovery underscores how much remains hidden in microbial biology. DRT3, Gao says, should be viewed as “a catalyst to re-examine the dark matter of the microbial world.” And with numerous bacterial defense systems still uncharacterized, adds Aude Bernheim, a microbiologist at the Pasteur Institute, “it’s fantastic to imagine that many of these encode exotic biochemical functions like the one uncovered here.”
No comments:
Post a Comment