As far as research subjects go, it’s not always easy to find common ground with a single-celled bacterium. Yet the more Paul Wiggins studies his model bacteria, Acinetobacter baylyi, the more he sees surprising commonalities between their behavior and our own as humans.
“It was mortifying to be stumped for so long by what appeared to be completely counterintuitive behavior only to realize that I engage in exactly the same behavior everyday,” said Wiggins, an associate professor of both physics and bioengineering at the University of Washington.
Scientists in Wiggins’ lab use experiments and modeling to understand the global principles that govern gene expression, and protein abundance in particular. In new research published March 20 in Science Advances, Wiggins’ team discovered that A. baylyi cells amass huge surpluses of essential proteins, rather than taking the seemingly more efficient approach of making just enough to survive. UW News chatted with Wiggins to learn about the remarkably relatable reason for this puzzling behavior.
The cell says, “Screw it, it’s virtually free. Let’s make extra.”
This work grew out of a mystery you and your team uncovered. Tell us about that mystery.
Paul Wiggins: Genes are the blueprints for proteins — we say they “code for proteins.” A. baylyi has a number of genes that code for proteins that we know are essential for cell growth. But we didn’t know exactly what each of these proteins do. In 2016, we were attempting to uncover these proteins’ specific functions in collaboration with the Manoil Lab. To do this we disrupted each gene so that the cells couldn’t make any more protein — they were left with a now dwindling supply of whatever they’d previously made. Then we would watch the cells under a microscope to determine when and how cellular processes would fail.
As an example, we knocked out a gene that coded for a protein that we found was responsible for cell wall synthesis — it makes the protein-sugar chainmail that prevents the cells from rupturing, or lysing. And you can watch the video we recorded to see what happened: The cells grew and divided for a while, but then all of a sudden they inflated and just popped.
In that example, something strange happened. We would expect the cell walls to start to fail almost immediately after the disruption happened because every time the cells divide, the remaining protein is divided among the offspring cells, so pretty quickly there wouldn’t be enough to sustain the new cell walls. However, growth continued, one generation after another, before the cells finally failed after four rounds of division!
Why did it take so long? Gene after gene showed the same pattern. We realized that each cell must have made a ton of extra proteins — far more than it needed. So after we knocked out that essential gene, the cell was able to run on fumes for a while — and was even able to pass stores of that protein on to its offspring. That finding was initially a huge surprise. We all expected, naively, that if a cell only needed a few copies of a protein to function, it would only make a few — anything more would be a waste of resources and energy. It’d be like taking a seven-day trip and packing 30 pairs of socks. And yet, this behavior seemed to be common for lots of essential genes.
What do you think is the cause of this protein overabundance?
PW: Baking is a good analogy. If you want to make an apple pie, you probably only buy as many apples as you need for that recipe. But you keep a large quantity of salt in your pantry. You might only need a teaspoon of salt to make any given meal, but none of us go to the store and buy salt a teaspoon at a time. Salt is so cheap and easy to store that, relative to the cost of other ingredients in your meal, it’s basically free to keep in large quantities. And critically, you don’t want to run out of salt when you’re cooking.
We demonstrated that something analogous is happening in A. baylyi cells for most of the essential genes. Only about 30% of a cell’s essential genes code for proteins that are “expensive” in that the cells need these proteins in large numbers. It would be very costly to, say, double an already large number. These are the apples in our apple pie analogy — the cell makes just enough of those proteins to get by.
The remaining 70% of essential genes, however, code for proteins that the cell does not need in large numbers. In fact, relative to that other 30%, the cell needs so few of these proteins that it’s basically free to produce a bunch of extras. Doubling the production of those proteins, say from 30 to 60 copies, is a drop in the bucket if the cell’s overall budget is three million proteins. So the cell says, “Screw it, it’s virtually free. Let’s make extra so we don’t run out.” In some cases a cell might make 10 times more protein than it will ever need.
Why is this strategy useful for the cells?
PW: This overabundance strategy is important because otherwise a cell might fail to produce enough of something critical. Protein synthesis is an imprecise process — cells sometimes make a little more or a little less of things than they’re programmed to make. Some essential proteins are made at such low numbers that any deviation from the plan could leave a cell with zero copies of that protein. This is less of a problem for essential proteins that are made in much higher numbers.
How do these findings support or challenge previous ideas about how cells function?
PW: Depending on who you talk to, this is either definitely wrong or completely obvious. On the one hand, it’s a really ingrained idea that organisms are always optimizing everything, which would naively suggest that cells should make exactly what they need — no more, no less. However, this is clearly not the case. Other studies have observed these kinds of protein surpluses in cells before, but it wasn’t appreciated quite how wide-spread this phenomenon was. Previously researchers proposed that overabundance might be a hedge against changing conditions — maybe cells are stockpiling proteins in case times get tough. We’re suggesting that it’s a hedge against the cells failing to make the right number of essential proteins.
Co-authors include H. James Choi, a UW postdoctoral researcher of physics; Teresa W. Lo and Dean Huang, former UW doctoral students of physics; Kevin J. Cutler, a UW graduate student of physics; and William Ryan Will, a UW postdoctoral researcher of laboratory medicine and pathology.
This research was funded by the National Science Foundation and the National Institutes of Health.
For more information, contact Wiggins at pwiggins@uw.edu.