A cell is "a well-run factory," according to scientists at the University of Utah. Its protein assembly machines — ribosomes — do their work reliably and efficiently most of the time. On rare occasions, though, a nascent protein stalls inside the machine. When that happens, it’s a crisis that can kill the cell or lead to serious diseases.

Fortunately, the cell has a plan to rescue itself:

Ribosomes are machines on a protein assembly line, linking together amino acids in an order specified by the genetic code. When something goes wrong, the ribosome can stall, and a quality control crew is summoned to the site. To clean up the mess, the ribosome is disassembled, the blueprint is discarded, and the partly made protein is recycled. (Emphasis added.)

A surprise surfaced when the Utah researchers, in an "extensive biochemical analysis," sought to understand the steps involved in tagging the stalled protein for destruction. Stalling causes the two parts of the ribosome, 40S and 60S, to separate. Immediately afterward, two "rare" quality-control proteins, Ltn1p and Rqc2p, bind to the stalled protein in the 60S part. Ltn1p binds near the exit tunnel and attaches the usual tag for destruction, ubiquitin. (Biochemists have a sense of humor sometimes; the "RING" domain of Ltn1p stands for "Really Interesting New Gene.")

It’s the other participant, Rqc2p, that plays an unexpected role: it continues assembling the stalled protein without the benefit of a template or transfer RNA! "In this case, we have a protein, Rqc2, playing a role similar to that of mRNA" (messenger RNA), researcher Adam Frost says. "I love this story because it blurs the lines of what we thought proteins could do." But what kind of information can a template-free protein add to a stalled protein? The story gets even more bizarre:

Yet this study reveals a surprising role for one member of the quality control team, a protein conserved from yeast to man named Rqc2. Before the incomplete protein is recycled, Rqc2 prompts the ribosomes to add just two amino acids (of 20 total) — alanine and threonine — over and over, and in any order. Think of an auto assembly line that keeps going despite having lost its instructions. It picks up what it can and slaps it on: horn-wheel-wheel-horn-wheel-wheel-wheel-wheel-horn.

Is this a factory gone berserk? No. Using design thinking, the researchers figured there must be a purpose behind the seemingly wacky process:

Like a half-made car with extra horns and wheels tacked to one end, a truncated protein with an apparently random sequence of alanines and threonines looks strange, and probably doesn’t work normally. But the nonsensical sequence likely serves specific purposes. The code could signal that the partial protein must be destroyed, or it could be part of a test to see whether the ribosome is working properly. Evidence suggests that either or both of these processes could be faulty in neurodegenerative diseases such as Alzheimer’s, Amyotrophic lateral sclerosis (ALS), or Huntington’s.

In fact, earlier experiments have shown a link between Rqc2p and the "heat shock" response of a cell under stress. This response up-regulates the manufacture of heat shock proteins. These proteins come to the aid of a cell that gets too hot, too cold, or oxygen deprived. The heat shock proteins act as chaperones and damage-control agents. They can re-fold partially folded proteins, tag misfolded proteins, or move proteins to safe-houses in the cell. In multicellular eukaryotes, they can even target proteins for the cell surface to be recognized by the immune system.

The linkage between Rqc2p and heat shock gave the researchers a clue. The alanine-threonine tags on the stalled protein (named, whimsically, "CAT tails" for "carboxy-terminal Ala and Thr extensions") might turn on the heat shock response. In their paper in Science, they put the story together:

Integrating our observations, we propose the model schematized in fig. S13. Ribosome stalling leads to dissociation of the 60S and 40S subunits, followed by recognition of the peptidyl-tRNA-60S species by Rqc2p and Ltn1p. Ltn1p ubiquitylates the stalled nascent chain, and this leads to Cdc48 recruitment for extraction and degradation of the incomplete translation product. Rqc2p, through specific binding to Ala(IGC) and Thr(IGU) tRNAs, directs the template-free and 40S-free elongation of the incomplete translation product with CAT tails. CAT tails induce a heat shock response through a mechanism that is yet to be determined.

It wouldn’t be enough, in other words, for Ltn1p to tag the bad protein with ubiquitin. All that would do is silently send the protein to the trashcan (the proteasome). No, the cell needs an alarm signal that a ribosome might have gone haywire. The CAT tails added by Rqc2p somehow inform the cell that a heat shock response team is needed to investigate.

To add the CAT tails, Rqc2p cannot rely on the failed ribosome. It also cannot rely on the messenger-RNA and transfer-RNA pathways from the genetic code in the nucleus. Without a template, it has to work autonomously, using its own active sites for alanine and threonine, and the ability to fasten them to the incomplete protein. By stitching on these extra amino acids to the stalled protein, Rqc2p sends something like an SOS message to the cell, using the actual defective protein as evidence. It’s all quite elegant and unexpected.

"There are many interesting implications of this work and none of them would have been possible if we didn’t follow our curiosity," says Brandman. "The primary driver of discovery has been exploring what you see, and that’s what we did. There will never be a substitute for that."

That statement is pregnant with design implications, however unintended. If the researchers stopped at Darwinian ideas of random, purposeless matter in motion, would they have found this new process? It was their curiosity about "what we thought proteins could do" — what purposeful roles they could play — that led them to expand our knowledge of cell quality control.

So whether or not these biochemists "believe in" intelligent design — we assume they don’t — their actions speak louder than words. By viewing the cell as "a well-run factory" with "machines on a protein assembly line," they added to a growing view that "Nature is capable of more than we realize."

Lastly, don’t miss that incidental statement about the "member of the quality control team" Rqc2p being "a protein conserved from yeast to man," implying that for hundreds of millions of years, evolution had nothing to do with it.

Image credit: "Caught in the act: Rqc2 protein adds amino acids to a new protein," Janet Iwasa, PhD, University of Utah.