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Cells may be using protons to detect leaks, says study

Illustration : Purabi Deshpande / Research Matters

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Cells are the structural and functional unit of life – that’s middle school biology, learnt and forgotten. For many, however, cells continue to be a positively fascinating subject despite everything that is known about it. The fascination stems from the fact that cells are like factories, each with numerous machines – called organelles – working in synchrony to function as one whole unit. The coordination amongst these organelles, necessary to facilitate cellular function, is a topic of research pursued by many.

One among the many is Prof. Mukund Thattai, who is applying his knowledge of physics to cell biology. After moving to the National Centre for Biological Sciences (NCBS), he set up a synthetic biology lab to build genetic circuits in bacteria. “Around 2010, I started looking for a new problem to work on, which could bring together my physics side with a problem that always interested me – evolution. In a workshop in 2010, we called together some of the best cell biologists and evolutionary biologists to ask whether we could retrace the origins of eukaryotes. Ever since then I’ve been doing ‘evolutionary cell biology’”, he quips. It was along this course that he began following the studies of a few of his colleagues, who were studying various elements of endosome function.

What are endosomes and how do they work?

Endosomes are tiny parcels, containing anything ranging from microbes to food molecules that cells ingest. Let’s say a cell comes across a virus; it engulfs the virus by forming a pocket around it. The pocket closes, and the virus is trapped inside a bag (made of the cell’s membrane) within the cell. This bag, called the endosome, is now transported deep inside the cell for degradation.

Now, at the same time, the cell also produces tiny sacs of enzymes – proteins that can shred biomolecules into otiose bits. At some point, the endosome, with the virus, fuses with the bag of enzymes, forming what is known as a lysosome. Following the fusion, the enzymes – called hydrolases – begin to destroy the virus or whatever else the endosome may have contained, and we escape from the consequences that the virus could have induced. The endocytic system in the cell exists to break down such complex structures into simple molecules that the cell can reuse.

This recycling system, present only in eukaryotes (the more ‘evolved’ organisms), is absent in prokaryotes like bacteria, which lack cell organelles and a membrane-bound nucleus. So, eukaryotes, including humans, take stuff inside the cell for digestion and molecular break down happens within the lysosomes. But in bacterial cells, digestion occurs outside the cells. Bacteria break down complex molecules by spitting enzymes outside the cell and then consuming the digested bits. In fact, many times when food in our pantry goes bad, it is because of bacterial enzymes that have broken down the food into simple molecules, so that the bacteria can consume it.

Another interesting aspect of lysosomes is the cocktail of enzymes in them. These enzymes are called hydrolases, and lysosomes contain more than 50 different kinds of them – each to break down specific types of biomolecules like carbohydrates, proteins, fats, etc. So how is it that these enzymes, which reside within the lysosomes in our cells, do not break down the cell itself? The answer lies in a little mechanism called acidification.

Lysosomal enzymes work only in acidic conditions. Endosomes, containing matter to be digested, have pumps on their membrane that sucks protons (or positively charged hydrogen ions), from its outside to its inside. The H+ ions make the endosomes acidic. When the endosome fuses with the vesicle containing the lysosomal enzymes, the enzymes are activated, and then they get to work. In fact, the purpose of acidic pH in endosomes has always been credited to its role in activating lysosomal enzymes.

In his new study, however, Prof. Thattai has a whole new rationale for the acidic pH found in endosomes. He proposes that lysosome acidification must have evolved as a leak detection system, a theory that brings in a paradigm shift to the current understanding of lysosomal biology. This study was recently published in the journal BMC Biology.

The leak detection theory

Prof. Thattai argues that lysosomal enzymes are costly for a cell to produce. And having made it, the cell would ensure not to waste it. To do so, the cell would need to ascertain that the endosomes that formed by the fusion of the cell membrane are completely sealed. Else, the expensive enzyme would leak out into the cell during fusion. But, how can a cell detect leakage? To answer this, Prof. Thattai puts forth the leak detection dye theory.

Many real-world engineers approach the issue of leak detection with a simple solution – a dye is continuously pumped into the structure that is suspected of leaking. The dye will leak outside the structure, as long as there is no seal; once it is completely sealed the dye will accumulate – a sign that the structure is leak-proof. Prof. Thattai explains, “My line of thought was not why the endosomes are acidic, but rather, how to detect leaks, like an engineer. I knew there must be a leak-detection dye. The proton [H+] seemed like a good choice – it is inexpensive for the cell to produce, abundant, rapidly diffusing, and easily sensed. To me, acidification is a by-product.”

Prof. Thattai says that he has spoken to many cell biologists about this idea and that although they find it to be an interesting thought, nobody has so far has ever considered this leak-detection hypothesis. “The issue is that there are so many obvious things acidic pH can do, that nobody felt there was anything further that even required explanation.  I am not saying that all those processes don’t make use of pH. I’m saying that organelle acidification first arose for leak detection”, he explains of his hypothesis.

Prof. Thattai’s theory is an exciting one, especially when you consider the evolution of eukaryotes from prokaryotes. Prokaryotes do not have lysosomes, but eukaryotes do. If the theory is true, then the evolution of a ‘leak detection system’ in eukaryotic cells is a very intriguing concept. Prof. Thattai points out that we don’t have much information about how this evolutionary jump from prokaryotes to eukaryotes occurred 2.5 billion years ago. “Any hints about that process would be valuable. Finding something that functions as a leak detector adds a fresh angle to that story,” he adds.

The leak detection theory holds good for most of our cells. But, what about eukaryotic cells that grow in acidic conditions? Their endosomes would already be acidic. “This is something I have thought of,” says Prof. Thattai. “Incidentally, according to my hypothesis both acidic (H+) and alkaline (OH-) ions would work equally well – they’re equally abundant and move nearly as rapidly. So maybe somewhere on earth, there’s a cell that makes its organelles alkaline to test for leaks. That would be very cool.”

The theory, of course, is a new perspective that has not occurred to many biologists. “It is sometimes useful to ask ‘why’ questions in biology. It’s not always possible to answer them, but it does allow you to discover unexpected connections sometimes”, he signs off.