by Edward Chen
figures by Corena Loeb

Within any biological system, interactions abound. Organisms, cells, and individual molecules all affect the world in their own way, whether that’s caribou grazing, immune cells patrolling, or caffeine binding to neuronal receptors These infinitely many events and processes together form the networks that shape life.

Within these networks, the effect of a process sometimes dampens down the process itself—we call this special interaction a negative feedback loop. This can be sleeping when we feel exhausted, because we wake up less tired, or sweating when we are hot, because the evaporation of sweat cools us. This can also be seen in something we humans cannot do: the biosynthesis of an essential building block of life—tryptophan.

What is tryptophan?

Tryptophan (abbreviated as Trp) is 1 of the 20 amino acids, the basic building blocks that are strung together to make proteins. Proteins have many and complex functions that allow our cells, and by extension our bodies, to survive. Our genes – through the genetic code – provide instructions to string amino acids together, building the thousands of distinct proteins that compose the human body. Not all amino acids are equal though; tryptophan is one of 9 that us humans cannot synthesize—what’s known as an “essential amino acid.”

Many organisms don’t have that luxury to cannot; tryptophan is essential for them too. We can absorb tryptophan from the food we eat and then blame it for making us sleepy. Naturally, bacteria cannot; they don’t eat cheese, chicken, or fish so they have to make tryptophan themselves (Figure 1). (Plus, Figure 1 notwithstanding, bacteria don’t sleep like we do.)

Figure 1: Oh, the Things You’ll Do! (And the things a bacterium will not). Should I ferment cheese? Farm chickens? Catch fish? As humans, there are so many options! A bacterium has but one: to be more self-sufficient.

Why is this significant?

Bacteria must make a lot of things themselves. In fact, they have to make many more things themselves than we do. Depending on the species, a bacterium has anywhere from 2.5 to 25 times more proteins in the same volume than do human cells.

But there’s a downside to making things. Just as we must spend energy (and time!) to build factories, manufacture computers, and write science articles in our familiar, macroscopic world, bacteria need to use energy to make amino acids and anything else that they need in order to survive in their smaller-scale universe. Of the 20 amino acids, tryptophan also just happens to be the most energy-intensive to produce. This synthesis is costly, and it wouldn’t be sensible to make more tryptophan than you need (Figure 2).

Figure 2: Oh, and a bacterium can’t shop at the market. When we stock up on groceries, there are several reasons we might not buy enough for a whole year; fridge space, shelf life, and cost are a few. The third reason – cost – plays an outsized role in the decision-making of a bacterium, which can be thought of as a factory that serves to make more of itself. Like human factories, bacterial ones only make what they need when they need it in the required amounts. If they don’t need something, there’s no point in keeping it on hand. Industrialists of the 20th century have applied this exact principle to “just-in-time manufacturing.” Early is on time and on time is late? Not always, it turns out.

How do bacteria make tryptophan?

To make any molecule, a cell – human, bacteria, or otherwise – will have a whole suite of dedicated enzymes, a class of proteins that help chemical reactions take place. In the case of tryptophan, cells that make it have a production line of 5 enzymes.

This is where cells are not all the same. Some cells, like our human cells, control most of their genes by using a one-to-one strategy. When these cells need more of a particular protein, they can make more of that protein and only that protein by turning on a single gene. Other cells, like bacterial cells, employ a one-to-many strategy and control genes with a related function together; these genes are physically close together and collectively form an operon. In the case of tryptophan, bacteria can easily modulate how much of the 5 enzymes they make through a single operon termed the trp operon.

How do bacterial cells regulate each operon then?

Cells know how to make proteins by following instructions stored in their DNA. When these instructions are to be used, certain proteins scan the DNA to make a similar but less stable molecule called RNA. Protein complexes called ribosomes then read the RNA to make proteins. This presents two opportunities to control how much of these 5 trp operon enzymes are made: regulate either the process of making RNA from DNA or the process of making protein from RNA. Because of their cellular organization, bacteria start making protein even while RNA is being made. Hence, the regulation tends to happen at the DNA to RNA interface.

What makes this regulation particularly interesting is that tryptophan—yes, the amino acid itself—is the one responsible for limiting production of the 5 enzymes. In other words, the end product of the trp operon, tryptophan, decreases further use of the trp operon, making this is a textbook example of a negative feedback loop.

This negative feedback loop occurs through two mechanisms (Figure 3). The first mechanism, an example of repression, is simple: tryptophan can bind to a specific protein known as a repressor protein to form a tryptophan-repressor complex. This complex binds to part of the trp operon and physically blocks RNA from being synthesized, preventing more trp operon enzymes from being made.

The second mechanism is an example of attenuation and relies on the fact that bacteria make RNA and protein simultaneously. As a ribosome scans RNA, the speed at which it moves depends on the availability of the amino acids coded in the RNA, including tryptophan. When tryptophan is readily available, the ribosome moves too quickly, tangling the RNA in the process. This particular entwined structure halts RNA synthesis prematurely, preventing trp operon proteins from being made. When tryptophan is scarce, the ribosome stalls because it takes longer for it to find a tryptophan molecule. The RNA-terminating structure no longer forms, and so tryptophan is made.

With both mechanisms, the message is the same: the presence of tryptophan decreases the production of enzymes needed to make itself, therefore decreasing the amount of tryptophan made and saving the bacterium energy. Today, we now know that attenuation also plays a role in regulating operons that ultimately make the other essential amino acids threonine, leucine, isoleucine, valine, phenylalanine, and histidine.

Is this concept seen elsewhere?

The tryptophan operon isn’t unique. The need to save energy is a powerful one and methods by which cells regulate their nutrient usage abound. Organisms are limited to operons, which have not been identified in humans and are highly uncommon in cells with a nucleus. Insulin, for example, is not made from an operon, but does exemplify a common negative feedback loop. When blood sugar is high, insulin is released to decrease and keep blood glucose levels in check. In addition to regulating blood sugar levels through insulin,  there are countless other negative feedback loops at play in our lives, from politics to pain response (Figure 4).

Figure 4: Ouch! Negative feedback loops can be found in almost all aspects of life: the weather, politics, and machine learning algorithms are only a few examples. Negative feedback loops can also arise through negative feelings. This friendly chef neuron accidentally touched a hot stove once and reflexively pulled back his arm. The result of touching the stove, a sensation of pain, has caused him to be more alert and avoid setting off the same painful process.

You probably know of other feedback loops, both biological and beyond. Just as a single cell is unremarkable only before you think about it, physical life resembles the cellular the more you look out for it.

Edward Chen is a first-year Immunology MMSc student at Harvard Medical School. Though bacteria can indeed be harmful, he finds it intriguing that they are so much more than “bad.”

Corena Loeb is a first-year Ph.D. student in the Harvard-MIT program in Speech, Hearing, Bioscience and Technology.

Cover image by Angela Rose from Pixabay.

For More Information:

  • Want to view an interactive explanation of repression? Check out this webpage from LabXchange.
  • Curious about bacteria and cheese? Turns out, the assumption that bacteria don’t make cheese is an oversimplification. Check out this short article from Current Biology or this longer article from the American Society for Microbiology.
  • Interested in the lac operon? Check out this webpage from LabXchange.

This article is part of our special edition on networks. To read more, check out our special edition homepage!

One thought on “Trps of the Trade: Underneath the efficient biology of the tryptophan operon

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