High fidelity keeps human DNA assembly line humming

Turns out building cars and building life have a lot in common – it all comes down to quality control.

Scientists at Michigan State University have made a major discovery on the inner workings of genetic coding, mapping out mechanisms of one of life’s most elemental functions: RNA synthesis. Their work has crucial implications for how a normal cell forms a tumor and how a virus runs amok. The work is published in the May 13 edition of the scientific journal Molecular Cell.

Behind the basic research is a story that melds exquisite nanotechnology in living systems and cutting-edge biochemistry and molecular biology with a system of checks and balances. “RNA synthesis is at the hub of human genetic control. It’s important for understanding cancers, viral infections and normal human development,” said Zachary Burton, professor of biochemistry and molecular biology. “If you want to understand and control things like viral infections and tumors this fundamental process has to be understood in every detail. This is basic science, but basic science with practical application.”

Burton and his team study how RNA is made from a DNA template. DNA is the genetic material that holds the blueprint for life. DNA dictates orders to RNA to make proteins, which give a cell its identity. Mistakes in RNA synthesis can lead to cancer or can support the life cycle of an invading virus. Researchers consider control of RNA synthesis to be a huge issue in human health. It is also the foundation of how living systems function.

In the world of molecular biology, much attention has been given to how RNA is made. Burton explains that it is similar to an industrial assembly line, with DNA being a conveyer belt to load building blocks, or bases, called nucleoside triphosphates (NTPs) to hook up with a growing strand of RNA.

Burton’s insight was to discover that the NTP bases preload to the DNA template several steps before they are added to the growing RNA chain.

This idea contradicts the prevalent view of how RNA and NTP bases hook up. Preloading of NTPs hints at a previously unknown quality control station to maintain accuracy of RNA synthesis. If an NTP doesn’t match up properly with DNA, the system stalls – and even backs up to correct the error. “We’re able to show how an error will be sensed and corrected,” Burton said. “The quality control system checks NTP loading several ways. If it doesn’t match the criteria, it gets booted out.”

In addition to better understanding how errors are prevented, Burton’s research team also learned ways errors are corrected during rapid RNA synthesis. To learn about error correction, Burton’s team stalled the DNA conveyer belt. They did this using a deadly mushroom toxin, alpha-amanitin.

Alpha-amanitin is the poison of the death cap mushroom, which can be deadly to humans. In 54 A.D., Emperor Tiberius Claudius was fed a death cap mushroom by his wife Agrippina to put her son Nero on the throne of ancient Rome. Alpha-amanitin kills people by stalling movement of the DNA conveyer belt.

Finding evidence of quality control gives some perspective to the elegance of cell creation. Burton said it does not mean mistakes never occur. The assembly line analogy holds up there. The human system has an acceptable level of error required to allow for the speed at which cells must reproduce. “RNA polymerase is one of nature’s great designs,” Burton said. RNA polymerases are found in bacteria, yeast, plants and humans. The design has endured because of this fidelity mechanism for RNA synthesis. “This is a tried and true design and our study explains why this is an enduring design.”

The paper, “Dynamic Error Correction and Regulation of Downstream Bubble Opening by Human RNA Polymerase II,” also is authored by research associates Xue Gong and Chunfen Zhang in Burton’s lab and Michael Feig, MSU assistant professor of biochemistry and chemistry.