Solving Puzzles

Research news from the Howard Hughes Medical Institute in an article entitled 'Joining Hands to Solve a DNA Replication Puzzle' provides a good description of viral dynamics in the form of interaction between viral proteins and cellular replication protein A (RPA) which has a protective function related to ssDNA (single-stranded DNA). As the author indicates RPA is involved in replication and repair pathways both of which have important implications for intelligent inferences. From the italicized article:

Every organism has an ssDNA-binding protein for DNA replication and repair pathways. In eukaryotes or organisms whose cells have a nucleus, it is called replication protein A (RPA). One of the common functions of RPA in DNA processing pathways is facilitating “hand-off,” a process that ensures that the correct proteins move into place along the ssDNA to begin DNA processing.

RPA plays an important protective role for ssDNA. “You don't want to have naked single-stranded DNA lying around in a cell,” explained Fanning. “It will get tangled, make hairpins within itself, get chewed up by nucleases. Ss binding proteins keep ssDNA straight and accessible to the right processing enzyme.”

RPA binds with at least a dozen different repair and replication proteins. The question has been how RPA gets dislodged, allowing various enzymes access to the DNA for necessary processing. Fanning and Chazin have developed a working model to answer that question.

Using SV40 as a model system, the scientists mapped atomic level interaction on the surfaces of proteins involved in DNA processing. They used biochemical and genetic tools to determine how the interactions of those proteins promote synthesis of small segments of RNA known as primers, which are required for initiation of DNA replication.

In the SV40 system, three key proteins interact. The viral protein T antigen (Tag) interacts with RPA and an enzyme known as DNA polymerase-primase (pol-prim). Tag is a helicase, or DNA unwinding enzyme. After it has unwound the DNA, it also places the pol-prim on the DNA to make primers. The researchers studied this last step: how Tag pulls RPA away sufficiently to load the pol-prim onto the DNA, allowing it to synthesize primers.

Fanning and Chazin showed that interaction between Tag and RPA requires multiple contact points. They found that, along with a domain on RPA called RPA70, a second one, RPA32C, also needs to bind to Tag before processing can begin.

The scientists suggest that Tag associates first with RPA32C and then with RPA70 as the RPA molecule sits on ssDNA. Binding at both of these points alters the conformation of RPA, scrunching it up to expose a small stretch of ssDNA. Tag brings with it pol-prim, which is deposited in the short stretch of unbound ssDNA. Once pol-prim is in place, Tag and RPA are no longer needed, so they are displaced as the third protein begins its work on the ssDNA. This is the “hand-off.”


How would viruses like SV40 come into existence? The functional value of their proteins is clear as is the need for a host. Interaction with a host entails interaction with specific proteins of that host. How would a natural selection process explain how and why the viral genome came about?