The study of subcellular compartments is the study of efficiency and divided labor within the cell. Just as our society has professions in which people do a specific job very well, the cell creates subregions, each of which allows certain cell functions to operate more effectively. As such, the subdivision of cells into discrete compartments or parts enables the cell to create specialized environments for specific functions. These compartments can be organelles, specific structures that take on sets of tasks within the cell, or they can be local regions of the cell defined by the concentration of molecules or distinct physical characteristics and proportions.
Subcellular compartments are key to the way we organize the domains of life. In fact, if there is a key characteristic that separates the eukaryotes from the prokaryotes, it is likely the presence of specialized compartments within the cell. Although the nucleus is the defining structure (eukaryote is Greek for "true kernel," referring to the highly visible nucleus), almost all eukaryotic cells also contain a variety of structures not found in prokaryotes. Many of these structures are surrounded by one or two membranes that separate the contents from the rest of the cytoplasm. These compartments allow a variety of environments to exist within a single cell, each with its own pH and ionic composition, and permit the cell to carry out specific functions more efficiently than if they were all in the same environment. For example, the lysosome has a pH of about 5.0 compared with the rest of the cytoplasm at pH 7.2. Not surprisingly, the enzymes that work within this organelle have a pH optimum at about 5, which makes them distinct from those in the main cellular cytoplasm.
One challenge for subcellular compartments is how to get materials in and out across the membranes, and each compartment has its own solution. The complexity of the structures ranges from mitochondria and plastids (with their own DNA and ribosomes), to the Golgi apparatus with its multiple cisternae, to fairly simple vacuoles and vesicles. In addition to the membrane-bound structures, eukaryotes also have a complex cytoskeleton made of three distinctly different components: microtubules, actin filaments, and intermediate filaments. Each of the three plays a role in maintaining cell shape, and microtubules and actin are also involved in internal transport as well as cell motility. Defects in any of these structures may lead to clinical disorders. For example, altered intermediate filaments in the nuclear envelope causes a cardiomyopathy, mitochondrial defects can lead to a variety of neuromuscular disorders, and mutations in cilia or flagella may lead to polycystic kidney disease or sterility.
The study of subcellular structures involves many questions. How and under what conditions does a mitchondrion divide? How do viruses take over a cell's endocytic machinery to propagate themselves? What controls the movement of mRNA from one region of cytoplasm to another? Such research involves nearly all tools available to cell biologists. Initial research was done with specific staining and light microscopy. Closer scrutiny of micrometer- and nanometer-sized subcellular structures was later enabled by the rise of electron microscopy, which illuminated the complexity of organelles and their varying positions within the cell. The current use of fluorescent antibodies coupled with three-dimensional imaging using confocal microscopy allows us to observe these organelles via time-lapse images and reveals how they function in living cells. Other key techniques are the use of differential centrifugation to purify components, autoradiography to follow processes over space and time, biochemistry to understand what each component is doing at the molecular level, and the use of inhibitors to selectively turn key events on and off and observe the outcome. Finally, genetics, in all its forms, has allowed us to dissect the structure and function of these subcellular compartments by selective disruption of individual cell components. The more all these structures are studied, the more it becomes clear how they all interact in a variety of ways (e.g., molecular motors carry vesicles along microtubules from the Golgi to the plasma membrane), and it is important to view all the cell's substructures not as isolated parts but as an integrated whole.
Future research in these areas of cell biology are likely to continue current trends. For instance, the role of primary cilia and intraflagellar transport are two rapidly growing areas, with implications for treatment of various disorders, including cancer. Research into alternative energy sources will certainly pay attention not only to the role of mitochondria and chloroplasts, but also to less known organelles such as the hydrogenosome, which makes hydrogen. As with all research, however, it may well be that the unexpected discoveries become the most important, opening new fields for our understanding of the cell‘s operations and providing new technologies for use in medicine, agriculture, and the environment.
Image: Mariana Ruiz.
