The most prominent organelle of the eukaryotic cell is the nucleus.Within the nucleus, substructures called nucleoli are visible by light microscopy, each nucleolus as a small spot.

Generally, nucleoli are most prominent in nondividing cells, and they are not visible in dividing cells in which the nuclear membrane has disassembled.

The nucleolus is composed of genes that encode the ribonucleic acid (RNA) molecules found in ribosomes (ribosomal RNA, or rRNA), the “working” copies or transcripts of these genes (the rRNA itself), and proteins. Nucleoli are the sites of ribosome synthesis in eukaryotic cells.

The ribosome is the site of protein synthesis in the cell. All proteins made by cells are made on ribosomes, so cells need an abundant supply of ribosomes to support the synthesis of all the cellular proteins.

Mature ribosomes are found in the cytoplasm of eukaryotic cells, either attached to the membrane of the endoplasmic reticulum or “free” within the cytoplasm. Although ribosomes function outside the nucleus in the cytoplasm, they are synthesized in the nucleus at the nucleolus.

Nucleolar Structure

Nucleoli are clearly visible with light microscopy. They disassemble and reassemble with the cell cycle and exhibit different staining properties than the rest of the nucleus. They range in diameter from 1 micrometer in small yeast cells to 10 micrometers in larger cells, such as the root cells of pea plants and wheat.

When observed using electron microscopy, nucleoli appear to have roughly three distinct regions: the fibrillar center (FC), the dense fibrillar center (DFC), and the granular component (GC). In some plant cells, the nucleolus also has a centrally located clear region, sometimes called the nuclear vacuole.

Although the precise molecular structures within nucleoli have not yet been thoroughly described, the regions of the nucleolus appear to correspond roughly to content and function, rRNA transcription, processing, and assembly.

rRNA Genes

A typical cell contains around one million ribosomes. To produce this number of ribosomes, a cell needs to be able to mass-produce the ribosomal components.

To provide enough ribosomes for daughter cells produced from cell divisions, a cell must synthesize new ribosomes at the rate of several hundred per second. Additionally, these ribosomes must be exported from the nucleus into the cytoplasm, where proteins are synthesized.

In order to mass-produce the RNA components of ribosomes, the three rRNA genes that are transcribed (copied) in the nucleolus are present inmultiple copies.

The genes for the 5.8S, 18S, and 28S rRNAs (rRNAs are named for their sedimentation rate, “S,” a measure of their size) are arranged in tandem repeats on the chromosomes of the cells. Typically, each repeat contains the 18S, the 5.8S, and the 28S genes, in that order, preceded by a region called a nontranscribed spacer (NTS) and separated by internal nontranscribed spacers.

The NTS’s are typically as small as two thousand to three thousand base pairs of deoxyribonucleic acid (DNA) in yeast and plants. These spacer regions may be involved in regulating gene expression in these regions of DNA or in attaching these areas of the chromosomes to protein structures inside the nucleolus.

Among different organisms, the number of copies of rRNA genes varies greatly. In fact, the number of copies of rRNA genes can even vary within different cells of a single organism.

The human genome (haploid set) contains approximately one hundred copies of these genes, but many organisms, especially plants, have several thousand copies of the rRNA genes. By having hundreds or thousands of copies of the genes, the cells are able to mass-produce the rRNAs that these genes encode.

Nucleolar Organizing Regions

The genes that encode the rRNAs are found along metaphase chromosomes at constrictions called nucleolar organizing regions, or NORs. When the cell completes division and reenters interphase, NORs are the sites where the nucleoli will form.

In plants, experiments to stain the specific rRNA genes reveal a complex organization of the genomic DNA. Large areas of inactive or untranscribed rRNA gene repeats appear at the periphery of the plant nucleoli, and several spots containing inactive rRNA genes also appear at the center of the nucleoli.

However, many areas of active transcription of a single copy of the rRNA genes appear dispersed throughout the nucleolus. These areas of active rRNA gene transcription may correspond to the fibrillar center regions.

Ribosome Assembly and rRNA Processing

The three rRNA genes are initially copied as one large molecule of RNA, called the pre-rRNA. This large piece of RNA is processed to make the three smaller 18S, 5.8S, and 28s rRNAs that will become part of the ribosome. During processing the nontranscribed spacer sequences are removed.

Each pre-rRNA molecule moves away from the genomic material as it is processed in several steps. Processing of the pre-rRNA molecule appears to require many accessory proteins and other RNA molecules, called small, nucleolar RNAs (snoRNAs).

The nucleolus contains many proteins that function in rRNA transcription and processing as well as transport of ribosome components into and out of the nucleus.

One of these proteins, nucleolin, which is specific to the nucleolus, is found in the dense fibrillar center and appears to be involved in different stages of ribosome synthesis. Nucleolin travels between the nucleus and cytoplasm and therefore may also be involved in transport of ribosome components between the two cellular compartments.

For ribosome synthesis, ribosome proteins must be assembled with the three nucleolar rRNAs. The ribosomal proteins are synthesized, like other cellular proteins, on existing ribosomes in the cytoplasm.

These proteins must be transported into the nucleus, where they associate with the pre-rRNAin the nucleolus even while it is being processed. A fourth rRNA, the 5S RNA, is transcribed in a separate part of the nucleus and transported to the nucleolus to be assembled with the other ribosomal components.

The ribosome consists of a small subunit and a large subunit. The small subunit, which contains the 18s rRNA and many proteins, is produced and exported from the nucleus separately from the large subunit, which contains the 28S, 5.8S, and 5S rRNAs.

The two subunits continue to mature in the cytoplasm, and matured subunits recognize messenger RNA within the cytoplasm to assemble a functional protein-synthesizing ribosome.