Driven to understand the origins of their existence, human beings have sought enlightenment for centuries. How a primordial stew of molecules became life as we know it today is still shrouded in mystery. But scientists have caught glimpses of an ancient world where RNA dominated. As they lift the veil on this world and try to recreate it, it is indisputable that at some point organisms composed of DNA, RNA, and protein won out.
Sitting at that crossroads between the ancient and the modern is the ribosome—an RNA machine that translates the messages encoded in RNA into proteins. Every crossroads offers a choice, and Rachel Green has navigated those choices as she explores the ribosome and the ancient "RNA World" that gave rise to it.
"I feel like I worked in these two great fields at just the right time," says Green, who after focusing on reengineering the ancient world, currently studies the principles that govern the ribosome's ability to synthesize proteins with such high fidelity.
Green entered graduate school at Harvard University in the mid 1980s shortly after a Nobel Prize–winning discovery by Thomas R. Cech and Sidney Altman established that RNA, a sister molecule to DNA thought to serve as a mere messenger, could catalyze reactions in the absence of proteins. With an undergraduate degree in chemistry, she entered HHMI Investigator Jack Szostak's lab at a time when he was focused on replicating the elements of the RNA World.
"Jack Szostak's lab was a place where I could unite my chemistry background with biology," Green says. "The notion of being able to think about the origins of life from a chemical perspective was really appealing to me."
To populate an RNA World, RNA would need to replicate. However, such activity would require that a single piece of RNA serve both as a replication enzyme and a template. Green used in vitro selection techniques to engineer RNA molecules capable of a simple type of self-replication. She also discovered something about herself—she isn't an engineer.
It's not that she doesn't appreciate the scientific importance of reengineering the molecules that sparked life in this world. It's just that the process goes against her temperament. "When you're trying to recapitulate a world that doesn't exist anymore, your experiments are geared toward a certain outcome," Green says. "I eventually found that I preferred to do experiments where either outcome would be interesting."
It's an experience Green began to relish after she moved cross-country to work on the ribosome with Harry F. Noller at the University of California, Santa Cruz. During her tenure in Noller's lab, it became clear that the ribosome is basically an RNA machine surrounded by proteins. As the structure of the ribosome become clearer, Green discovered something else about herself.
"We were at a crossroads," Green says. "The structure of the ribosome was coming into focus at a very high level resolution—at the level of [individual hydrogen atoms]. I had to rethink how I approached my research."
Focusing on mutagenesis and "hard-core" enzymology, Green has been exploring just what makes the ribosome so good at producing the correct protein. By undergoing specific conformational changes, the ribosome makes decisions about whether to continue making a protein. Green has begun exploring how external factors "talk" to the ribosome. "The ribosome needs to be regulated. There are hints all over the literature about how this occurs," Green says. In the context of what Green and her colleagues have learned about core ribosome function and how it is controlled, they believe it is likely that microRNAs and other extraribosomal factors will communicate directly with the basic ribosome machinery to dictate the fate of specific proteins as well as causing wide ranging effects in the cell.
Equally important is the role transfer RNAs perform. The ribosome creates protein by reading the encoded instructions on the messenger RNA and matching that code with an appropriate transfer RNA (tRNA) containing an amino acid—the individual building blocks of proteins. Long seen as a static cog in the machine, tRNA proved to be something else when Green and her colleagues discovered that the tRNA itself and its dynamic properties enhanced the fidelity of protein synthesis. Such activity would be crucial for the evolution of protein synthesis in the RNA World.
"I'm happy to be pulled back from trying to recapitulate the RNA World," Green notes. "But understanding that world is part of what pulls me to the ribosome. When you open it up, its core being is a nest of RNA. I'm happy to be studying the thing that won out in evolution."