The Compartment Codes

Eukaryotic cells not only produce molecules of countless different types but manage to deliver them to different destinations with astonishing precision, and this gives us the problem of understanding how they manage to cope with such an immensely intricate traffic. The first step in the solution of this mystery came with the discovery that the Golgi apparatus is involved not only in the biochemical modification of innumerable molecules but also in the choice of their geographical destination. But the truly remarkable thing is that all this is achieved with an extremely simple mechanism. More precisely, the Golgi apparatus delivers an astonishing number of molecules to their destinations with only three types of vesicles. One type has labels for the transport of proteins outside the cell and another for their delivery to the cell interior, whereas the vesicles of the third type carry no destination label, and are programmed, by default, to reach the plasma membrane. As we can see, the solution is extraordinarily efficient. With a single mechanism and only two types of labels, the cell delivers a great amount of proteins to their destinations, and also manages to continually renew its plasma membrane.

The Golgi apparatus, however, is a transit place only for a fraction of the cell proteins. The synthesis of all eukaryotic proteins begins in the soluble part of the cytoplasm (the cytosol), together with that of a signal that specifies their geographical destination. The piece of the amino acid chain that emerges first from the ribosome (the peptide leader) can contain a sequence that the cell interprets as an export signal to the endoplasmic reticulum. If such a signal is present, the ribosome binds itself to the reticulum and delivers the protein into its lumen. If not, the synthesis continues on free ribosomes, and the proteins are shed into the cytosol. Of these, however, only a fraction remains there, because the amino acid chain can carry, in its interior, one or more signals which specify other destinations, such as the nucleus, the mitochondria, and other cell compartments. Proteins, in conclusion, carry with them the signals of their geographical destination, and even the absence of such signals has a meaning, because it implies that the protein is destined to remain in the cytosol.

The crucial point is that there is no necessary correspondence between protein signals and geographical destinations. The export-to-the-nucleus signals, for example, could have been used for other compartments, or could have been totally different. They and all the other geographical signals are purely conventional labels, like the names that we give to streets, cities, airports, and holiday resorts. The existence of eukaryotic compartments, in other words, is based on natural conventions, and to their rules of correspondence we can legitimately give the name of compartment codes (Barbieri, 2003).

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