Richardo Stone. Science

For decades, biology textbooks have enshrined a simple rule: DNA is created by copying a template. After one enzyme unwinds a DNA double helix into separate strands, another called polymerase builds a complementary sequence, base by base, for each strand. Prestige: two copies of the original DNA. But new research on how bacteria defend themselves against viruses now shows that this rule of synthesis isn't absolute. Today in Science, a team from Stanford University describes a bacterial enzyme that synthesizes DNA 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. "Really cool!" adds Adi Millman, a computational biologist at MIT. Using a protein as a template for DNA synthesis, she says, "is a significant conceptual shift from the classical central dogma," in which information flows in one direction from nucleic acids like DNA to protein. Scientists hope this novel form of DNA synthesis can be adapted as a tool for basic biological research, similar to how the powerful CRISPR genome editor was developed from another bacterial defense system.

In canonical DNA replication, the rules of base pairing are fundamental: polymerases assemble their complementary DNA strand by pairing adenine with thymine and guanine with cytosine in the template. Replication can also proceed with RNA as a template, thanks to polymerases called reverse transcriptases that use this nucleic acid to guide the production of single-stranded DNA.

The new finding focuses on DRT3, a defense system that protects bacteria from viruses, known as phages, that infect them. The researchers discovered that DRT3 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 a template for the DNA sequence," says Stanford biochemist Alex Gao, senior author of the study. "It's been quite a surprise," he says. "This is a fundamentally new way that life produces DNA."

DRT3 appears to be widespread among bacteria, suggesting it's not just a biochemical curiosity. However, how it thwarts phages remains a mystery.

One possibility, says Gao, is that the DNA helices produced by this unique replication method act like molecular sponges that stick to phage components, either directly hindering the phage or allowing other bacterial immune elements to recognize the infection. If that idea holds up, says Kranzusch, DRT3 would complement recent discoveries of polymerase-like proteins in other bacterial defense systems that produce nucleic acid polymers to detect and inhibit phage infection.

DRT3 also plays another mind-bending role for reverse transcriptases, long associated with retroviruses like HIV, which uses one to synthesize a DNA copy of its RNA genome and insert itself into a cell's chromosomes. In recent years, these enzymes have been shown 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, says Gao.

Like CRISPR, DRT3 could have practical applications. "DRT3 represents an 'all-in-one' molecular machine for sequence-specific DNA synthesis, something rare in nature," says Gao. Drt3b produces a specific DNA sequence. If scientists could figure out how to engineer it to produce other sequences, he says, they could create custom DNA strands, for example, to create advanced biomaterials such as DNA hydrogels.

More broadly, the discovery underscores how much remains hidden in microbial biology. DRT3, says Gao, should be seen as "a catalyst for re-examining 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 discovered here."