The human genome contains an estimated 30,000 genes, the instructions that give our cells the information it needs to create everything that makes up the human body. To do this, our cells must access the DNA, convert it into a more open form (RNA) – much like you need to open a book to read it – and then use the information to create the proteins necessary for life. We have a good understanding of how DNA is converted into RNA, called transcription, except for how the cells know when to stop reading (called transcription termination).
For years, scientists believed that a protein called Rho would climb up the RNA during its production and, upon reaching specific termination sequences, pull the RNA away from the transcription machinery (RNA polymerase). But there has always been the question of how Rho can find the correct region to intervene and stop transcription.
“We started studying Rho, and realized it cannot possibly work in ways people tell us it works,” said Irina Artsimovitch, co-lead author of the study and professor of microbiology at The Ohio State University, in a statement.
Their research, published in the journal Science, suggests the textbooks may be wrong. Instead of binding to the complex at the end, Rho "hitchhikes" on the RNA polymerase during transcription.
The difficulty with investigating transcription termination is that it happens relatively quickly and the proteins involved then break apart from each other. To overcome this obstacle, the scientists used revolutionary cryo-electron microscopy to visualize the complex in impressive detail and make it stick around longer than it naturally would.
They discovered that Rho is actually associated with the RNA polymerase complex for the duration of transcription, and upon arriving at the site of termination, Rho and the complex recruit further proteins to detach the transcription machinery from the RNA strand.
While this presents a possible mechanism for how Rho works to stop transcription, it also answers the burning question of how Rho can stop producing RNA when there is no termination sequences, the exact mechanism of which has eluded scientists for years.
As it turns out, Rho also acts as a quality-assurance manager. Even when termination sequences that signal Rho to stop producing RNA are not there, Rho always manages to stop it at the correct place. Now, scientists believe that instead of simply binding to Rho-specific termination sequences, it associates with RNA polymerase before binding to RNA and works in conjunction with the transcription machinery to select wanted RNA. The scientists observed that Rho can identify RNA that is wanted and discards any unwanted pieces as it rides with the RNA polymerase.
“It answers a fundamental question – transcription is fundamental to life, but if it were not controlled, nothing would work. RNA polymerase by itself has to be completely neutral. It has to be able to make any RNA, including those that are damaged or could harm the cell. While traveling with RNA polymerase, Rho can tell if the synthesized RNA is worth making – and if not, Rho releases it,” Artsimovitch continued.
The authors believe this is a milestone in understanding how our cells produce the correct transcripts from our DNA. Whilst this study was performed in bacteria, they emphasize that cellular processes such as this are often similar in bacteria and eukaryotes.
“It appears to be common,” she said. “In general, cells use similar working mechanisms from a common ancestor. They all learned the same tricks as long as these tricks were useful.”