Genes VII
8.1 Introduction |
| Key terms defined in this section |
| Leader of a protein is a short N-terminal sequence responsible for passage into or through a membrane. |
| Figure 8.1 Overview: proteins that are localized post-translationally are released into the cytosol after synthesis on free ribosomes. Some have signals for targeting to organelles such as the nucleus or mitochondria. Proteins that are localized cotranslationally associate with the ER membrane during synthesis, so their ribosomes are "membrane-bound". The proteins pass into the endoplasmic reticulum, along to the Golgi, and then through the plasma membrane, unless they have signals that cause retention at one of the steps on the pathway. They may also be directed to other organelles, such as endosomes or lysosomes. |
Proteins can be divided into two general classes with regard to localization: those that are not associated with membranes; and those that are associated with membranes. (For an introduction, see Membranes and membrane proteins). Each class can be subdivided further, depending on whether the protein associates with a particular structure in the cytosol or type of membrane. Figure 8.1 maps the cell in terms of the possible ultimate destinations for a newly synthesized protein and the systems that transport it:
- Cytosolic (or "soluble") proteins are not localized in any particular organelle. They are synthesized in the cytosol, and remain there, where they function as individual catalytic centers, acting on metabolites that are in solution in the cytosol.
- Macromolecular structures may be located at particular sites in the cytoplasm; for example, centrioles are associated with the regions that become the poles of the mitotic spindle.
- Nuclear proteins must be transported from their site of synthesis in the cytosol through the nuclear envelope.
- Cytoplasmic organelles contain proteins synthesized in the cytosol and transported specifically to (and through) the organelle membrane, for example, to the mitochondrion or (in plant cells) to the chloroplast. (Some mitochondrial and chloroplast proteins are synthesized within the organelle.)
- The cytoplasm contains a series of membranous bodies, including endoplasmic reticulum, Golgi apparatus, endosomes, and lysosomes. This is sometimes referred to as the "reticuloendothelial system." Proteins that reside within these compartments are inserted into ER membranes, and then are directed to their particular locations by the transport system of the Golgi apparatus. (For an introduction see supplement ER and Golgi).
- Proteins that are secreted from the cell are transported to the plasma membrane and then must pass through it to the exterior. They start their synthesis in the same way as proteins associated with the reticuloendothelial system, but pass entirely through the system instead of halting at some particular point within it.
Proteins that are not associated with membranes are released into the cytosol when their synthesis is completed by a ribosome. Some proteins remain free in the cytosol in quasi-soluble form; others associate with macromolecular cytosolic structures, such as filaments, microtubules, centrioles, etc. This class also includes nuclear proteins (which pass into the nucleus through large aqueous pores). The ribosomes on which these proteins are synthesized are sometimes called "free ribosomes", because they fractionate separately from membranes. The "default" for a protein released from "free" ribosomes is to remain in the cytosol; to be targeted to a specific location, it requires an appropriate signal, typically a sequence motif that causes it to be assembled into a macromolecular structure or recognized by a transport system.
| Figure 8.2 Proteins synthesized on free ribosomes in the cytosol are directed after their release to specific destinations by short signal motifs. |
Figure 8.2 summarizes some signals used by proteins released from cytosolic ribosomes. Import into the nucleus results from the presence of a variety of rather short sequences within proteins. These "nuclear localization signals" enable the proteins to pass through nuclear pores (see later). One type of signal that determines transport to the peroxisome is a very short C-terminal sequence.
The process of inserting into or passing through a membrane is called protein translocation. Proteins that associate with membranes follow one of two routes.
Mitochondrial and chloroplast proteins are synthesized on "free" ribosomes; after their release into the cytosol they associate with the organelle membranes by means of N-terminal sequences of ~25 amino acids in length that are recognized by receptors on the organelle envelope. Because this process takes place after synthesis of the protein has been completed, it is called post-translational translocation.
Proteins that reside within the reticuloendothelial system enter the endoplasmic reticulum while they are being synthesized. This process is called co-translational translocation. Because the ribosomes are associated with the ER membranes during synthesis of these proteins, and are therefore found in membrane fractions of the cell, they are sometimes described as "membrane-bound."
A common feature is found in proteins that use N-terminal sequences to be transported co-translationally to the ER or post-translationally to mitochondria or chloroplasts. The N-terminal sequence is cleaved from the protein during protein translocation. The N-terminal sequence comprises a leader that is not part of the mature protein. The protein carrying this leader is called a preprotein, and is a transient precursor to the mature protein.
Proteins that associate with membranes via N-terminal leaders use a hierarchy of signals to find their final destination. In the case of the reticuloendothelial system, the ultimate location of a protein depends on how it is directed as it transits the endoplasmic reticulum and Golgi apparatus. The leader sequence itself introduces the protein to the membrane; the intrinsic consequence of the interaction is for the protein to pass through the membrane into the compartment on the other side. For a protein to reside within the membrane, a further signal is required to stop passage through the membrane. Other types of signals are required for a protein to be sorted to a particular destination, that is, to remain within the membrane or lumen of some particular compartment. The general process of finding its ultimate destination by transport through successive membrane systems is called protein sorting or protein trafficking, and is discussed in 25 Protein trafficking.
| Figure 8.3 Membrane-bound ribosomes have proteins with N-terminal sequences that enter the ER during synthesis. The proteins may flow through to the plasma membrane or may be diverted to other destinations by specific signals. |
Some of the destinations and signals are summarized in Figure 8.3. They show that some sort of permit is required to reside in any part of the membrane system. The permit most often takes the form of a short amino acid sequence, but there are also other types of information. The "default pathway" takes a protein through the ER, into the Golgi, and on to the plasma membrane. Proteins that reside in the ER possess a C-terminal tetrapeptide (KDEL, which actually provides a signal for them to return to the ER from the Golgi). The signal that diverts a protein to the lysosome is a covalent modification: the addition of a particular sugar residue. We discuss direction to these locations in 25 Protein trafficking.