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UPFRONT: Nerve Tonic
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Same But Not Equal by Ingfei Chen
A code within the genetic code explains why identical proteins are produced at varying speeds.
A rendering of the high resolution structure of the ribosome sits on top of a copy of the original lab notes recording the deciphering of the genetic code.
Hanging on Jonathan Weissman’s office wall is a treasure from scientific history: a rare copy of the 1965 lab book notes—with corrections, asterisks, and numbers circled in red—documenting the deciphering of the genetic code. Penned by the late Nobel laureate Marshall Nirenberg and his team, the notes established that triplets of genetic “letters” map to the 20 different amino acids in proteins.
Lately, Weissman has been making some groundbreaking notes of his own. Nirenberg would no doubt find them fascinating, as the two became close before the biochemist passed away in 2010. Weissman’s work is revealing another layer of nuanced meaning within the genetic language that directs cellular protein production—a code within “The Code.”
After DNA in a gene is transcribed into messenger RNA (mRNA), molecular machines called ribosomes cruise along and read the mRNA strand. Each triplet of letters in its genetic sequence is known as a codon. By stringing together specific amino acids corresponding to those codons, the ribosomes manufacture proteins. Nirenberg had discovered that a given amino acid can be made from several different codons, like synonyms for the same word.
But why would nature devise several ways of saying the same thing? That question has largely remained a mystery in the half-century since Nirenberg’s seminal work. As biologists later sequenced genes in bacteria and other organisms, they saw that some synonymous codons were used far more commonly than others—like a person always expressing hunger by stating, “I’m famished” instead of “I’m hungry.” Some subtle, yet-undiscerned meaning must explain these striking codon preferences.
“There was an aspect of information in how genes were being encoded that we didn’t understand,” says Weissman, an HHMI investigator at the University of California, San Francisco. A big part of the answer, he found, has to do with speed.
Researchers learned in the 1980s that swapping one synonymous codon for another in an mRNA message could change how fast a cell made the same exact protein. That implied that ribosomes could slow down or speed up their protein synthesis. But the mechanism controlling that process was unclear. Now, in a study published in Nature on April 26, 2012, postdoctoral fellow Gene-Wei Li, graduate student Eugene Oh, and Weissman show that in bacteria, protein synthesis temporarily pauses at certain mRNA sequences—because the ribosome gets stuck on them.
The experiments used ribosome profiling, a technique Weissman’s group first published in 2009. “It lets us look at this process of how proteins are being made with a precision that’s completely unprecedented” in the living cell, Weissman says.
The method starts with a long-known trick: Take a cell, stop its protein production using a chemical or flash freezing, break it open, and add an enzyme that digests its mRNAs. What remains are just the short snippets that were actively being read and protected inside the ribosomes. Then, by using new, astonishingly fast sequencing technology to decode all these ribosome “footprints” across the entire cell, Weissman says, you can identify the piece of mRNA each ribosome was scanning and the amino acid it was handling. Counting those footprints in a computational analysis gives an in-depth reconstruction of which proteins were being made from exactly which mRNA messages, and in what quantities.
In this lecture, Weissman gives an overview of the methodology that allows the sequence of DNA to be determined.