Most Eukaryotic Genes Are Mosaics of Introns and Exons

Note: This table identifies the amino acid encoded by each triplet. For example, the codon 5 AUG 3 on mRNA specifies
methionine, whereas CAU specifies histidine, UAA, UAG, and UGA are termination signals. AUG is part of the initiation signal,
in addition to coding for internal methionine residues.
I. The Molecular Design of Life
5. DNA, RNA, and the Flow of Genetic Information
5.5. Amino Acids Are Encoded by Groups of Three Bases Starting from a Fixed Point
Figure 5.32. Initiation of Protein Synthesis. Start signals are required for the initiation of protein synthesis in (A)
prokaryotes and (B) eukaryotes.
I. The Molecular Design of Life
5. DNA, RNA, and the Flow of Genetic Information
5.5. Amino Acids Are Encoded by Groups of Three Bases Starting from a Fixed Point
Table 5.5. Distinctive codons of human mitochondria
Codon Standard code Mitochondrial code
UGA
UGG
AUA
AUG
AGA
AGG
I. The Molecular Design of Life
Stop
Trp
Ile
Met
Arg
Arg
Trp
Trp
Met
Met
Stop
Stop
5. DNA, RNA, and the Flow of Genetic Information
5.6. Most Eukaryotic Genes Are Mosaics of Introns and Exons
In bacteria, polypeptide chains are encoded by a continuous array of triplet codons in DNA. For many years, genes in
higher organisms also were assumed to be continuous. This view was unexpectedly shattered in 1977, when investigators
in several laboratories discovered that several genes are discontinuous. The mosaic nature of eukaryotic genes was
revealed by electron microscopic studies of hybrids formed between mRNA and a segment of DNA containing the
corresponding gene (Figure 5.33). For example, the gene for the β chain of hemoglobin is interrupted within its amino
acid-coding sequence by a long intervening sequence of 550 base pairs and a short one of 120 base pairs. Thus, the βglobin gene is split into three coding sequences.
5.6.1. RNA Processing Generates Mature RNA
At what stage in gene expression are intervening sequences removed? Newly synthesized RNA chains (pre-mRNA)
isolated from nuclei are much larger than the mRNA molecules derived from them: in the case of β-globin RNA, the
former sediment at 15S in zonal centrifugation experiments (Section 4.1.6) and the latter at 9S. In fact, the primary
transcript of the β-globin gene contains two regions that are not present in the mRNA. These intervening sequences in
the 15S primary transcript are excised, and the coding sequences are simultaneously linked by a precise splicing enzyme
to form the mature 9S mRNA (Figure 5.34). Regions that are removed from the primary transcript are called introns (for
intervening sequences), whereas those that are retained in the mature RNA are called exons (for expressed regions). A
common feature in the expression of split genes is that their exons are ordered in the same sequence in mRNA as in
DNA. Thus, split genes, like continuous genes, are colinear with their polypeptide products.
Splicing is a facile complex operation that is carried out by spliceosomes, which are assemblies of proteins and small
RNA molecules (Section 28.3.4). This enzymatic machinery recognizes signals in the nascent RNA that specify the
splice sites. Introns nearly always begin with GU and end with an AG that is preceded by a pyrimidine-rich tract (Figure
5.35). This consensus sequence is part of the signal for splicing.
5.6.2. Many Exons Encode Protein Domains
Most genes of higher eukaryotes, such as birds and mammals, are split. Lower eukaryotes, such as yeast, have a
much higher proportion of continuous genes. In prokaryotes, split genes are extremely rare. Have introns been
inserted into genes in the evolution of higher organisms? Or have introns been removed from genes to form the
streamlined genomes of prokaryotes and simple eukaryotes? Comparisons of the DNA sequences of genes encoding
proteins that are highly conserved in evolution suggest that introns were present in ancestral genes and were lost in the
evolution of organisms that have become optimized for very rapid growth, such as prokaryotes. The positions of introns
in some genes are at least 1 billion years old. Furthermore, a common mechanism of splicing developed before the
divergence of fungi, plants, and vertebrates, as shown by the finding that mammalian cell extracts can splice yeast RNA.
Many exons encode discrete structural and functional units of proteins. An attractive hypothesis is that new proteins
arose in evolution by the rearrangement of exons encoding discrete structural elements, binding sites, and catalytic sites,
a process called exon shuffling. Because it preserves functional units but allows them to interact in new ways, exon
shuffling is a rapid and efficient means of generating novel genes (Figure 5.36). Introns are extensive regions in which
DNA can break and recombine with no deleterious effect on encoded proteins. In contrast, the exchange of sequences
between different exons usually leads to loss of function.
Another advantage conferred by split genes is the potentiality for generating a series of related proteins by splicing a
nascent RNA transcript in different ways. For example, a precursor of an antibody-producing cell forms an antibody that
is anchored in the cell's plasma membrane (Figure 5.37). Stimulation of such a cell by a specific foreign antigen that is
recognized by the attached antibody leads to cell differentiation and proliferation. The activated antibody-producing cells
then splice their nascent RNA transcript in an alternative manner to form soluble antibody molecules that are secreted
rather than retained on the cell surface. We see here a clear-cut example of a benefit conferred by the complex
arrangement of introns and exons in higher organisms. Alternative splicing is a facile means of forming a set of proteins
that are variations of a basic motif according to a developmental program without requiring a gene for each protein.
I. The Molecular Design of Life
5. DNA, RNA, and the Flow of Genetic Information
5.6. Most Eukaryotic Genes Are Mosaics of Introns and Exons
Figure 5.33. Detection of Intervening Sequences by Electron Microscopy. An mRNA molecule (shown in red) is
hybridized to genomic DNA containing the corresponding gene. (A) A single loop of single-stranded DNA (shown in
blue) is seen if the gene is continuous. (B) Two loops of single-stranded DNA (blue) and a loop of double-stranded DNA
(blue and green) are seen if the gene contains an intervening sequence. Additional loops are evident if more than one
intervening sequence is present.
I. The Molecular Design of Life
5. DNA, RNA, and the Flow of Genetic Information
5.6. Most Eukaryotic Genes Are Mosaics of Introns and Exons
Figure 5.34. Transcription and Processing of the β -globin gene. The gene is transcribed to yield the primary
transcript, which is modified by cap and poly(A) addition. The intervening sequences in the primary RNA transcript are
removed to form the mRNA.
I. The Molecular Design of Life
5. DNA, RNA, and the Flow of Genetic Information
5.6. Most Eukaryotic Genes Are Mosaics of Introns and Exons
Figure 5.35. Consensus Sequence for the Splicing of mRNA Precursors.
I. The Molecular Design of Life
5. DNA, RNA, and the Flow of Genetic Information
5.6. Most Eukaryotic Genes Are Mosaics of Introns and Exons
Figure 5.36. Exon Shuffling. Exons can be readily shuffled by recombination of DNA to expand the genetic repertoire.
I. The Molecular Design of Life
5. DNA, RNA, and the Flow of Genetic Information
5.6. Most Eukaryotic Genes Are Mosaics of Introns and Exons
Figure 5.37. Alternative Splicing. Alternative splicing generates mRNAs that are templates for different forms of a
protein: (A) a membrane-bound antibody on the surface of a lymphocyte, and (B) its soluble counterpart, exported from
the cell. The membrane-bound antibody is anchored to the plasma membrane by a helical segment (highlighted in
yellow) that is encoded by its own exon.