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Does a Kitchen Sponge Have a Function?

kitchen sponge.jpg

"Function" is a broad term. The Merriam-Webster Dictionary defines it as "the action for which a person or thing is specially fitted or used or for which a thing exists: PURPOSE." This definition has drawbacks, because not all functions involve action. A brick shows no action, but might function as part of a wall. Dictionary.com adds, "the purpose for which something is designed or exists; role." In both cases, purpose and design are integral to the concept of function, even if an object just "exists" without showing any action.

Does a kitchen sponge have a function? Most of the time, it just sits idly on the sink. The action is done by a person who grabs the sponge to soak up spilled milk. That qualifies as a function: the sponge is designed for that; it exists for that; it is "specially fitted or used" for that. Milk is a good thing, unless it is out of place, or there's too much of it. That's why we keep sponges around, even if they don't do anything most of the time.

Cells can get into situations where there is too much of a good thing. In many bacteria, various protein "tools" with clear functions accumulate, like too many workers running after too few jobs. A recent paper in Nature shows that there is a small, non-coding RNA, transcribed from DNA, that acts as a "protein sponge" to soak up the excess. It can then "squeeze" the extra proteins back out for work, when conditions are favorable. What's interesting is that this functional molecule is not a protein. It's a small RNA molecule from a non-coding region of the genome, named RsmZ, that is able to soak up excess proteins named RsmE. Its function, therefore, is "sequestration" of the excess RsmE: it snatches the extra proteins, essentially de-activating them temporarily without destroying them, while protecting them from wandering trash collectors (RNase E).

Here we show for Pseudomonas fluorescens that RsmE protein dimers assemble sequentially, specifically and cooperatively onto the ncRNA [non-coding RNA] RsmZ within a narrow affinity range. This assembly yields two different native ribonucleoprotein structures. Using a powerful combination of nuclear magnetic resonance and electron paramagnetic resonance spectroscopy we elucidate these 70-kilodalton solution structures, thereby revealing the molecular mechanism of the sequestration process and how RsmE binding protects the ncRNA from RNase E degradation. Overall, our findings suggest that RsmZ is well-tuned to sequester, store and release RsmE and therefore can be viewed as an ideal protein 'sponge'. (Emphasis added.)

This is no ordinary sponge. It has a "well-defined" structure that is "well-tuned" to sequester proteins. It looks like a scaffold with five locations where RsmE proteins can dock. RsmZ molecules soak up excess RsmE proteins one at a time, as conditions require. Later, when conditions change, RsmZ releases them unharmed. In this way, the quantity of RsmE proteins is well regulated. That's why they call it an "ideal" protein sponge.

Molecular "sponges" have been described before. What's new about RsmZ is the discovery that the molecule works in a "cooperative, well-defined and regulated manner," as opposed to the "random fashion" assumed for circular RNA sponges. Now, scientists will have to re-think their assumptions:

Cooperative binding of RsmE to RsmZ does not involve protein-protein interactions but rather allosteric changes in the RNA allowing subsequent protein binding, a mode of binding that is more reminiscent to bacterial ribosome assembly. As a comparison, it will be interesting to see whether the circular RNA sponges sequester microRNA in a random fashion or also bind in a cooperative, well-defined and regulated manner.

The function of this sponge is important, because the RsmE protein is a translation suppressor. When RsmZ sequesters it, translation can resume. RsmZ is therefore an important regulator of protein production.

Here we see a new-found function for a small, non-coding RNA that earlier scientists might have considered molecular junk. Not only that, the discovery may inspire a search for more "cooperative, well-defined" design in other molecular sponges.

Did this protein sponge evolve? The authors note that RsmZ is "evolutionarily conserved," meaning unchanged across many species of bacteria. Other small RNAs, by contrast, show a great deal of diversity in length, secondary structures, and binding surfaces. (Some of the bacteria mentioned in the paper are virulent disease germs. Once again, we state that ID's job is to detect design, not judge whether it is "good" or "evil" design. That question is left in the capable hands of philosophers and theologians.)

The authors were surprised to see such finely tuned design in a simple molecule whose only role is to act as a sponge. Each binding induces a conformational change, so that proteins are bound and released in sequence. They noted several advantages of this "sequential and ordered assembly" as it attaches the RsmE proteins one by one to its five binding sites:

This evolutionary [sic, evolutionarily] conserved sequential and ordered assembly has several advantages compared to a random sequestration process. It prevents the formation of long-lived misassembled intermediates or aggregates, which could either have poor sequestration capacity or be too stable for eventual degradation. Furthermore, this hierarchical assembly equips the sRNA with a well-defined and optimized binding process for RsmE that has been evolutionarily tuned to maximize its sequestration capacity and modulate the concentration range in which it efficiently sequesters RsmE. This sequential assembly also allows the storage of the protein, the RNP becoming insensitive to degradation after a 4:1 ratio of protein to RNA. Finally, coupling between the binding sites for RsmE and RNase E in the sRNA enables the release of the sequestered RsmE proteins from the RNP. The capacity for an RNA to sequester, store and release RNA is reminiscent of the recently discovered circular RNAs that act as microRNA sponges. By analogy, RsmZ can be seen in light of our findings as a protein sponge.

The authors clearly believe that unguided evolution produced this advantageous system, even though what they found looks designed. Readers can decide whether the phrase "evolutionarily tuned" makes any sense, or performs any "function" in understanding biological designs.

Photo credit: Susan Sermoneta/Flickr.