The largest of the membrane-bound organelles, the nucleus first was described in 1710 by Antoni van Leeuwenhoek using a simple microscope. In 1831 the Scottish botanist Robert Brown characterized the organelle in detail, calling it the "nucleus," from the Latin word for "little nut." The nucleus is the site of gene expression and gene regulation.
Distinctive Features
A distinguishing characteristic of eukaryotes, the nucleus contains the genetic information (genome) of the cell in the form of its chromosomes. It is within the nucleus that the DNA in the chromosomes is duplicated prior to cell division and where the RNAs are synthesized. Ribosomes are partially assembled around the newly synthesized ribosomal RNAs (rRNA) while still in the nucleus and then transported into the cytoplasm to continue their final assembly. Similarly, messenger RNAs (mRNA) are synthesized, packaged, and subsequently transported to the cytoplasmic ribosomes, where they are translated into protein.
Typically spherical in shape and taking up 10 percent of the volume of a cell, the nucleus is bounded by a double membrane called the nuclear envelope (Figures 1 and 2). Most material passes in and out of the nuclear envelope through large openings called the nuclear pores. The outside surface of the envelope is directly connected to the endoplasmic reticulum of the cytoplasm and is surrounded by a network of cytoplasmic intermediate filaments. The inside surface of the nuclear envelope is lined with the nuclear lamina. Internally, the nucleus contains several structures: the chromosomes themselves, which together constitute the chromatin; the interchromatin compartment; the large nucleolus; and a variety of different granules collectively called the subnuclear bodies, which include Cajal (coiled) bodies, gems, PML bodies, and speckles. Every time a cell divides, the nuclear envelope must break down to release the recently duplicated chromosomes. After the chromosomes have segregated to the new daughter cells, the nucleus and its components must be rebuilt.
If the DNA of each cell were stretched out linearly, it would be over six feet in length. Although the chromosomes of a nucleus appear as a diffuse network in the electron microscope, they are highly compacted into nucleosomal units. Because of nucleosomal folding, the six feet of DNA yields an organelle tightly packed with chromosomal material. Consequently, it was thought that the nucleus in nondividing cells was a fairly static structure, with its various substructures locked into place. Since the 1980s, however, technological advances have permitted investigators to "paint" chromosomes, parts of chromosomes, genes, proteins, RNAs, or subnuclear bodies with genetically defined fluorescent tags. Combined with new techniques that permit these procedures in living cells, and coupled with time-lapse photography and computer simulation, an entirely different image of the cell nucleus is emerging. The nucleus is now understood to be a dynamic organelle composed of a highly ordered architecture that permits a great deal of structural flexibility and movement of molecules and particles between its various subcompartments.
Chromosomal Territories
Each chromosome is specifically anchored through its telomeres to a discrete place on the nuclear envelope by the proteins of the nuclear lamina. Thus each occupies a geographically distinct nuclear space called a chromosomal territory (Figure 2). The homologous chromosomal pairs (matching chromosomes derived from mother and father) do not necessarily lie next to each other.
Chromosomal territories are separated by channels of open nucleoplasm called the interchromatin compartment. Within each territory, DNA can be highly condensed (heterochromatin) or less condensed (euchromatin). Heterochromatin, defined as DNA that is not currently undergoing active transcription, can contain important chromosomal elements such as centromeres. Euchromatin are those chromosomal areas more likely to be active in gene transcription. The heterochromatin of any given chromosome is found within its territory close to the nuclear envelope (Figure 1), but can often project into the interior of the nucleus as patches and/or surround the nucleolus. The euchromatin of each territory extends into the center of the nucleus. In addition, those specific areas of euchromatin undergoing active RNA transcription (gene expression) are typically found on the very periphery of the chromosomal territory, at its juncture with the interchromatin channels.
Chromosomal territories contain at least one other known functional subdomain. Those portions of the DNA that replicate late are found near the nuclear envelope, while earlier-replicating DNA is found in the interior of each territory, projecting into the center of the nucleus. Thus each chromosome not only occupies a discrete place in the nucleus, but each is additionally highly organized into different functional subcompartments. The DNA in each chromosome is highly contorted, looping back and forth within its territory. Chromosomes appear capable of shuffling segments to the correct spot within their territories to carry out gene expression or DNA replication. Indeed, painting of chromosomal segments, including specific genes, with fluorescent tags clearly indicates that chromosomes are constantly shifting around within their territories. Thus the architecture of the chromosomal territories, although highly organized, has a considerable degree of flexibility that is closely tied to both gene expression and DNA replication.
Interchromatin Compartment
The interchromatin (interchromosomal) compartment is best viewed as a series of channels in and around the individual chromosomal territories that are in direct connection with the nuclear pores of the nuclear envelope. It is filled with nucleoplasm containing subnuclear bodies, nuclear proteins, and RNAs, which move rapidly through its channels. It is thought that as RNA is transcribed from genes along the periphery of the chromosomal territory, it drops into the interchromatin compartment for processing, packaging, and transport out of the nucleus through the nuclear pores.
Hormone receptors, histones, and DNA repair enzymes are all known to move actively through these channels, seeking their nuclear targets. Trafficking of molecules is highly efficient; it takes only seconds for a newly synthesized RNA particle to exit through a nuclear pore. Thus the nucleus is a very busy place, with a rapid and continuous exchange of proteins involved in nuclear function and genomic expression occurring both between nuclear compartments and deep within individual compartments, through which access is guaranteed by transportation through the interchromatin compartment.
Nucleolus
The most prominent nuclear feature, the nucleolus is a ribosomal factory. To make the large number of ribosomes needed, eukaryotic genomes carry multiple rRNA gene copies. The human genome contains 180 rRNA genes located on the tips of five different chromosomes (chromosomes 13, 14, 15, 21, and 22). Anchored by the opposite end to the nuclear envelope, each in their own chromosomal territory, the tip of these five chromosomal pairs (ten chromosomes in a diploid cell) extend into the center of the nucleus and come together, and the rRNA genes align to form what is called the nucleolar organizer. Transcription of the rRNA genes 28S, 18S, and 5S occurs rapidly. The transcripts are immediately processed and sequentially packaged through multiple stages into ribosomal subunits. The processing is complicated, requiring many cytoplasmic proteins and enzymes that are transported through the nuclear pores, diffusing through the interchromatin compartment until they reach the nucleolus, where they bind and remain. The nucleolus itself is composed of three subdomains: the nucleolar organizer; rRNA in the process of being transcribed, which is seen as dense fibrils; and granules, which are ribosomes very early in the assembly process.
Proteomic analysis indicates that human nucleoli contain at least 271 different proteins of a diverse array of known functions, with 31 percent encoded by unknown genes. This has raised the distinct possibility that the nucleolus performs other functions besides ribosome synthesis. Corroborating data suggest that the nucleolus entraps specific cell-cycle regulatory proteins (such as CDC14), inhibiting their activity until needed. When released from the nucleolus, they regain activity. Nucleoli may also synthesize and/or transport other ribonucleoprotein particles besides the ribosome, and may play a role in the processing and transport of mRNA or tRNA. Because nucleoli are often seen associating with other subnuclear bodies such as Cajal bodies, additional functions are likely.
Subnuclear Bodies
Although the function of many of the subnuclear bodies remains elusive, they are indeed true nuclear structures. They are seen both by light and electron microscopy and can be studied in living cells through the use of fluorescent tags. They are known to contain complexes of proteins with or without RNA. Like nucleoli, they are not surrounded by a membrane. They often move through interchromatin channels and are thought to represent dynamic complexes that may form and re-form with each other and other nuclear components to process and transport nuclear components.
Cajal (Coiled) Bodies
By electron microscopy, Cajal bodies are seen as tangled balls of thread. They number one to ten per nucleus, with more seen in growing cells. They are often found in association with nucleoli or specific chromosomal territories. Although their true function remains unknown, their ability to associate regularly with nucleoli has led to speculation that they are somehow involved in processing either mRNA or rRNA.
Gems
More tightly coiled, smaller versions of Cajal bodies, gems are frequently seen interacting with Cajal bodies and are distinct structures. They are known to contain a protein called SMN (which stands for "survival of motor neurons") that, when mutated, is responsible for a severe inherited form of a human muscular wasting disease called spinal muscular atrophy. Based upon the known function of the normal SMN protein, it is speculated that gems are involved in trafficking mRNA spliceosome subunits through the nucleus and may indirectly help remove mRNA introns.
Pml Bodies
Nuclei typically have ten to twenty PML bodies (also known as PODs, Kremer bodies, or ND10) that take the shape of dense rings. They contain proteins that, when mutated, have been identified with such disease processes as retinoblastoma and Bloom's syndrome. Their normal pattern is altered in the nuclei of human acute promyelocytic leukemia. When cells are infected with herpes simplex virus type 1, adenovirus, or human cytomegalovirus, PML bodies are disrupted. Although their function remains unknown, the fact that they are altered in diseased or malignant cells suggests that they play an important role in the normal cell, including growth control and apoptosis.
Speckles (Interchromatin Granules)
Speckles are clusters of dense structures seen by electron microscopy that, when stained with fluorescent tags specific to small nuclear ribonucleoproteins (snRNP), give rise to a "speckled" nucleus. Small nuclear ribonucleoproteins are RNA-protein complexes that are subunits of the spliceosome involved in mRNA intron removal. The twenty to fifty speckles per nuclei are typically found in the interchromatin compartment, where mRNA undergoes processing prior to transport through the nuclear pore and into the cytoplasm.
Nuclear Envelope
Completely surrounding the nucleus, the nuclear envelope sequesters the genomic information of the cell, probably protecting it from the various enzymes and processes that occur within the cytoplasm. It is composed of two concentric membranes, each of which has a distinct protein composition: the outer membrane, which faces the cytoplasm; and the inner membrane, facing the nuclear interior. The inner and outer membranes are separated by the perinuclear space. Both the outer membrane and the perinuclear space are continuous with the endoplasmic reticulum and studded with ribosomes. Any proteins made on the nuclear outer membrane-bound ribosomes drop into the perinuclear space and are transported through the inner membrane into the nucleus. The major transport pathway in and out of the nucleus, however, is thought to be through nuclear pores.
The inner membrane is coated with a mesh-like network of intermediate filaments called the nuclear lamina. Various nuclear structures, including the chromosomes, attach directly to the lamina, which is essential for maintaining the overall architecture and function of the nucleus. Mutations in the lamina proteins, lamin and emerin, can cause the chromosomes to dissociate from the nuclear envelope and disrupt the organization and properties of the nuclear pores, both of which result in embryonic death. In humans, other lamin mutations cause several rare, inherited diseases, including Emery-Dreifuss muscular dystrophy, an inherited form of muscular dystrophy, or Dunnigan-type lipodystrophy, a disease that results in loss of adipose tissue and late-onset, insulin-resistant diabetes beginning at puberty. How lamina protein mutations cause these two diseases is unknown.
Nuclear Pores
Perhaps the most startling feature of the nuclear envelope are the very large, basket-like transport structures called the nuclear pores (figure 4). These structures have a molecular weight of 125 million daltons, making them thirty times larger than a ribosome. Composed of 100 to 200 different proteins collectively called nucleoporins, each nuclear pore pierces through both membranes of the nuclear envelope and probably opens into the interchromatin space of the nucleus. Some nucleoporins are structural components of the nuclear pore; others facilitate transport. Each mammalian cell nucleus contains 3,000 to 5,000 of these pores. The large number is needed to transport the tremendous quantity of proteins, enzymes, RNAs, factors, and complexes in and out of the nucleus to maintain its function and integrity. Small molecules, ions, and proteins up to 45,000 daltons passively diffuse through the pores. However, the vast majority of material transported is through a highly controlled process called "gating," which is responsible for keeping complexes such as the ribosomes in the cytoplasm from entering the nucleus.
Some proteins require multiple crossings through the nuclear pore. Ribosomal proteins are first made in the cytoplasm, transported into the nucleus, assembled into ribosome subunits by the nucleolus, and then transported back out into the cytoplasm. Viruses infect nuclei by taking advantage of the presence of nuclear pores. Some can be transported intact, while others "dock" on the cytoplasmic side of the pore and inject their DNA into the nucleus through the pore's opening. Each nuclear pore can both import and export material in one of two ways.
Any protein transported in or out of the nucleus must contain a nuclear localization signal, which is a specific sequence of four to eight amino acids that triggers either nuclear import or export. Each nuclear pore contains nucleoporins that recognize either the import or export signal, called importins or exportins, respectively. Importins, located on the cytoplasmic side of the nuclear pore, bind their import "cargo" and flip or slide it to the inside of the nucleus. They then move back into their original position, ready to "transport" their next "cargo." The opposite happens on the side of the nuclear pore facing the interior of the nucleus. Here, exportins bind proteins within the nucleus carrying the export signal and flip or slide them through the pore and into the cytoplasm. RNA molecules and complexes can also move through the pores, but only if the importins and or exportins recognize them as cargo.
Bibliography
Alberts, Bruce, et al. "The Cell Nucleus." In Molecular Biology of the Cell, 3rd ed. NewYork: Garland, 1995.
Dundr, Miroslav, and Tom Misteli. "Functional Architecture in the Cell Nucleus."Biochemical Journal 356 (2001): 297-310.
Lamond, Angus I., and William C. Earnshaw. "Structure and Function in the Nucleus." Science 280 (1998): 547-553.
Lewis, Joe D., and David Tollervey. "Like Attracts Like: Getting RNA ProcessingTogether in the Nucleus." Science 288 (2000): 1385-1389.
Olson, Mark O. J., Miroslav Dundr, and Attila Szebeni. "The Nucleolus: An Old Factory with Unexpected Capabilities." Trends in Cell Biology 10 (2000): 189-196.
Pederson, Thoru. "Protein Mobility within the Nucleus: What Are the Right Moves?"Cell 104 (2001): 635-638.
Wilson, Katherine L. "The Nuclear Envelope, Muscular Dystrophy and GeneExpression." Trends in Cell Biology 10 (2000): 125-129.
Wilson, Katherine, et al. "Lamins and Disease: Insights into Nuclear Infrastructure."Cell 104 (2001): 647-650.
Wolffe, Alan P., and Jeffrey C. Hansen. "Nuclear Visions: Functional Flexibility from Structural Instability." Cell (2001) 104: 631-634.
—Diane C. Rein
