The central dogma of molecular biology explains the flow of genetic information from self-replicating DNA to RNA and from RNA to protein. The critical molecular machines responsible for this unidirectional flow of information, polymerases, were until now, believed to be incapable of writing RNA recipes back into DNA code.
In a new discovery, scientists provide the first evidence that RNA segments can be written back into DNA. The finding challenges the central dogma and could have wide implications, raising questions that need to be explored, especially now that RNA vaccines are centerstage in public health.
The study led by scientists at the Thomas Jefferson University, Philadelphia, is published in Science Advances, in an article titled “PolΘ reverse transcribes RNA and promotes RNA-templated DNA repair.” Scientists from University of Southern California, Los Angeles, Beckman Research Institute of the City of Hope, Duarte, and New York University School of Medicine collaborated in the study.
“This work opens the door to many other studies that will help us understand the significance of having a mechanism for converting RNA messages into DNA in our own cells,” says Richard Pomerantz, PhD, associate professor of biochemistry and molecular biology at Thomas Jefferson University, whose lab focuses on understanding genome integrity and instability in normal and cancerous cells.
“The reality that a human polymerase can do this with high efficiency, raises many questions,” says Pomerantz. Among other inferences, the finding suggests that RNA messages can be used as templates for repairing or rewriting genomic DNA.
Pomerantz’s team started by investigating an unusual polymerase, polymerase theta. Of the 14 DNA polymerases in mammalian cells, only three do the bulk of the work of replicating the genome before the cell divides. The remaining 11 polymerases largely detect errors and make repairs when the double-stranded helix nicks, breaks or incorporates a base it should not.
Polymerase theta repairs DNA, but not very well, its carelessness resulting in many errors or mutations in its repair efforts. These undesirable attributes of polymerase theta nudged the researchers to notice its similarities with viral reverse transcriptase.
Because polymerase theta is highly error-prone and promiscuous and contains an inactive proofreading domain, the authors of the study decided to test the hypothesis that it has the ability to synthesize DNA from an RNA template. Retroviral HIV reverse transcriptase, like polymerase theta acts as a DNA polymerase, but can also bind RNA and change it back into a DNA strand.
The researchers test polymerase theta against the HIV reverse transcriptase, one of the best studied of its kind, and show that polymerase theta can convert RNA messages into DNA. It does just as good a job of synthesizing DNA from RNA as the HIV reverse transcriptase, and an even better job at duplicating DNA.
Polymerase theta, the authors demonstrate, is more efficient and accurate when using an RNA template to write new DNA messages, than when duplicating DNA, suggesting that this function may be its primary cellular function.
Pomerantz’ group collaborated with Xiaojiang S. Chen, PhD, University of Southern California, Dornsife, to use the lab’s x-ray crystallography expertise. They define the crystal structure of polymerase theta on a DNA/RNA primer-template with bound deoxyribonucleotides to reveal that the enzyme undergoes a major structural transformation to accommodate the A-form DNA/RNA hybrid and forms multiple hydrogen bonds with template ribose hydroxyl groups like retroviral reverse transcriptase.
Polymerase theta is expressed in only a few tissue types, but it is highly expressed in many cancer cells. The presence of polymerase theta corresponds to a poor clinical outcome, conferring resistance to genotoxic cancer therapies and promoting the survival of abnormal cells deficient in DNA damage response pathways.
“Our research suggests that polymerase theta’s main function is to act as a reverse transcriptase,” says Pomerantz. “In healthy cells, the purpose of this molecule may be toward RNA-mediated DNA repair. In unhealthy cells, such as cancer cells, polymerase theta is highly expressed and promotes cancer cell growth and drug resistance. It will be exciting to further understand how polymerase theta’s activity on RNA contributes to DNA repair and cancer-cell proliferation.” The study indicates polymerase theta represents a promising cancer drug target.