The Integrated Program in Biochemistry (IPiB) — the joint graduate program of the Department of Biochemistry and Department of Biomolecular Chemistry — is full of collaborative faculty. One partnership in particular between the labs of biochemistry professor Michael Cox and biomolecular chemistry professor James Keck goes back nearly two decades. And a new National Institutes of Health grant to study the creation and repair of DNA gaps is further pushing forward their research and opportunities for their students.
The groups — along with Cox’s longtime collaborators at the University of Wollongong in Australia and researchers at the University of Southern California — study how bacterial cells repair damaged DNA when it appears in gaps.
“Mike and I have collaborated since day one, since I came to campus,” Keck explains. “We’ve had joint group meetings for 18 plus years and have a really integrated relationship. We each have our own work and lab meetings but also come together to tackle problems from different angles. Our collaboration has led to about a dozen papers and several grants together. It’s been very fruitful.”
The researchers are now part of a new and still rare grant mechanism from the NIH called RM1. The award supports collaborative science and totals $1.2 million a year for the next five years that’s divided in different pieces among the groups.
Their work revolves around the process of DNA replication and repair. DNA polymerases, along with other proteins, create a replication fork that moves along DNA to replicate it. Researchers know that somehow this replication fork is sometimes able to bypass a spot of DNA damage and then continue, leaving a gap behind. However, that gap formation and repair has been an afterthought until now — it’s this critical repair of post-replication gaps that the scientists are particularly interested in.
“My lab and others have been looking into how the cell deals with gaps that appear behind the replication fork,” Cox says. “This has involved a major refocusing in the lab so that we are studying several new proteins involved in the metabolism of these gaps.”
In a gap, DNA is single stranded, rather than in its usual double-stranded configuration. When double stranded, the important genetic information is protected, but when it’s single stranded it’s open to potentially damaging modifications by numerous molecules and chemicals in the cell.
The goal of the cell is to limit gap formation to avoid damage and to maintain genome stability. However, repairing damaged DNA in these post-replication gaps requires several actors. So, a flurry of proteins come in to help protect the vulnerable DNA, as well as repair it.
One protein the groups study is called RarA. It is critical for repairing some kinds of these gaps. Another protein is called RecA, which is known to be involved in single-stranded DNA recognition and repair. They both are involved in early steps of the repair process but there is much the scientists must untangle, such as if they start independent processes or perhaps compete against each other. For example, they have solved the structure of RarA but are still investigating how it is engaging and specifically performing repair. These proteins are just a small sample of the larger system they are investigating.
The grant opens up new opportunities for students in the UW–Madison labs. Cox, for example, already travels to Australia to visit collaborators about once a year. He’ll now be able to go even twice a year, taking multiple students for a few weeks so they can learn about the technology being developed in the lab of Professor Antoine van Oijen.
“Our labs can become even more integrated and collaborative,” Cox says. “There’s even an opportunity now for a graduate student to spend an entire year there getting trained in different technologies. Antoine is a leader in some of the technology development that has allowed us to probe these proteins and quantify gaps so to be able to work with them in Australia is invaluable to our research.”
One of Cox’s IPiB students, Kanika Jain, works on the RarA project in this grant. For her, the collaboration is extremely valuable. The ability to collaborate in person and learn the microscopy techniques their Australian colleagues are using is more important than one would think. Using their technology, they are able to tag and visualize individual proteins as they move in the cell and interact.
“Being there in person, you’re able to engage in a way that’s impossible over email or Skype, and it betters our research,” Jain says. “I’ve had the opportunity to travel to Australia twice and now more students will be able to as well, even undergraduates. We get a different perspective on our research working with them. It’s so valuable for us.”
Keck says this work can lead to important insights into the basic mechanisms at work here but also into problems that mutations can cause, such as cancer. Issues with DNA repair allow more mutations to take place. While many mutations are either harmless or cause the single cell to just die, an error in an important process like cell division can trigger the beginnings of cancer.
“What we’ve seen over the last several decades is that studies in bacterial genome maintenance can lead to a better understanding of mutagenesis and carcinogenesis,” Keck says. “Although we are working in E. coli, we are learning fundamentals that may have direct applications in understanding how mutations are derived in human cells.”