14
2 Nucleic Acids and Nuclear Proteins
be dependent upon codon usage; in fact, in many
cases codon usage, tRNA frequency and gene
expression are correlated. Even where tRNA
availability is uniform, some codon-tRNA combinations are translated faster but less accurately,
e.g. in the cell-free systems of E. coli UUC (for
phenylalanine) is used twice as frequently as
UUU [109].
2.1.4 Introns
A basic difference between eukaryote and prokaryote genes is that the coding sequences of the
former are not continuous but are interrupted to
give partial sequences (exons) by non-coding,
intervening sequences (IVS or introns) (Fig. 2.1).
The introns are also initially transcribed but are
removed by slicing during processing of the RNA
(see Fig. 2.9). The presence of the introns dramatically increases the chances of successful
intrachromosomal recombination of genetic
information during crossing-over. Variations in
the splicing of particular genes allows the formation of different mRNAs and proteins from the
same gene (p. 40). Only in a very few eukaryotic
genes are introns absent, e.g. histone genes,
interferon genes, most heat-shock genes, and the
genes of the trypanosomes. In contrast, an exception to the rule that prokaryotes do not possess
introns has recently been found: the gene for the
23S ribosomal RNA of the archebacterium Desulfurococcus mobilis has a 622-bp intron that is
excised during r RNA processing [230].
Most genes contain one or just a few introns,
but there may be more than 10; e.g. there are 13
in the serum albumin gene of the rat, at least 14 in
the ~-crystallin gene and 16 in the ovtransferrin
gene of the chicken, 33 in the vitellogenin gene of
Xenopus, and more than 50 in the procollagen II
gene of the chicken [45, 317, 446]. Ciliate genes
are normally poor in introns. Recently, however,
a gene was found in Tetrahymena with about 30
introns within 15 kb [287]. A relationship exists
between the length of coding and non-coding sections such that protein-coding genes in excess of
550 bp are invariably interrupted by introns; the
intron: exon ratio greatly increases with increasing exon length [45, 317]. Extremes in exon size
are known: e.g. exon 17 in the troponin-T gene of
the chicken has 6 bp (equivalent to two amino
acid codons), and an exon in the human renin
gene is only 9 bp long [90]; in contrast, there is a
14000-bp exon in the fibroin gene of the silkworm
B. mori and one of 7572 bp (exon 26) in the
human apolipoprotein-B gene [37]. In general,
introns have lengths of up to 10000 bp, although
very large introns of 60 and 79 kb have been
found in the antp and dunce genes, respectively,
of Drosophila [69, 150]. In contrast to exon
lengths, mean intron lengths differ considerably
between the genomes of different groups of organisms. Introns in the middle of coding sequences
of vertebrates have a mean length of 1127 bp, in
insects 622 bp, in the lower fungi only 86 bp, and
in higher plants 249 bp [183]. Few introns are less
than 75 bp long [406]. Experiments with artificially modified globin genes have shown that
shortening the introns to 69 bp disturbs the splicing process [446].
Exons and introns, together with the nontranslated regions in front of and behind the coding sequences, make up the typical eukaryotic
transcription unit (Fig. 2.1). In addition, each
gene requires further regions on both sides to
ensure optimal expression. Thus, with the presence of introns, and non-translated and nontranscribed regions, eukaryotic genes require
stretches of DNA many times the length of the
actual protein-coding sequence. So, for example,
in the gene for the 28-kDa large ovomucoid of the
chicken, the sequence coding for the finished protein is 561 bp long, with another 260 bp for the
signal peptide, the 5' and 3' non-translated regions, and the initiation and termination signals;
these 0.82 kb, together with a total of 4.7 kb of
introns, make up a gene of 5.5 kb; with the addition of about 4 kb of territorial DNA on both
sides, it is seen that a coding sequence of 0.56 kb
requires not less that 13.5 kb of DNA [45, 317].
In Drosophila there are genes with even larger
introns; e.g. ubx, with a total length of 75 kb, or
antp, at 100 kb, both code for relatively small
proteins [189]. Introns lie mostly within coding
regions, sometimes in the 5' transcribed but not
translated region, and seldom in the 3' region. In
homologous genes of different species or in multiple genes resulting from duplication, they are
generally to be found at homologous positions;
they can, however, disappear or appear during
the course of evolution. Particularly large variation in intron position is found in the actin genes
(see Fig. 10.4; p.341). In length and sequence,
introns show especially rapid evolutionary change
and distinctive polymorphism. Thus, in the actin
genes, differences in the number, size and position of introns are found not only between different species but even between different members
of this multi-gene family in a single individual. In
Drosophila and other dipterans, introns are
2 Nucleic Acids and Nuclear Proteins
be dependent upon codon usage; in fact, in many
cases codon usage, tRNA frequency and gene
expression are correlated. Even where tRNA
availability is uniform, some codon-tRNA combinations are translated faster but less accurately,
e.g. in the cell-free systems of E. coli UUC (for
phenylalanine) is used twice as frequently as
UUU [109].
2.1.4 Introns
A basic difference between eukaryote and prokaryote genes is that the coding sequences of the
former are not continuous but are interrupted to
give partial sequences (exons) by non-coding,
intervening sequences (IVS or introns) (Fig. 2.1).
The introns are also initially transcribed but are
removed by slicing during processing of the RNA
(see Fig. 2.9). The presence of the introns dramatically increases the chances of successful
intrachromosomal recombination of genetic
information during crossing-over. Variations in
the splicing of particular genes allows the formation of different mRNAs and proteins from the
same gene (p. 40). Only in a very few eukaryotic
genes are introns absent, e.g. histone genes,
interferon genes, most heat-shock genes, and the
genes of the trypanosomes. In contrast, an exception to the rule that prokaryotes do not possess
introns has recently been found: the gene for the
23S ribosomal RNA of the archebacterium Desulfurococcus mobilis has a 622-bp intron that is
excised during r RNA processing [230].
Most genes contain one or just a few introns,
but there may be more than 10; e.g. there are 13
in the serum albumin gene of the rat, at least 14 in
the ~-crystallin gene and 16 in the ovtransferrin
gene of the chicken, 33 in the vitellogenin gene of
Xenopus, and more than 50 in the procollagen II
gene of the chicken [45, 317, 446]. Ciliate genes
are normally poor in introns. Recently, however,
a gene was found in Tetrahymena with about 30
introns within 15 kb [287]. A relationship exists
between the length of coding and non-coding sections such that protein-coding genes in excess of
550 bp are invariably interrupted by introns; the
intron: exon ratio greatly increases with increasing exon length [45, 317]. Extremes in exon size
are known: e.g. exon 17 in the troponin-T gene of
the chicken has 6 bp (equivalent to two amino
acid codons), and an exon in the human renin
gene is only 9 bp long [90]; in contrast, there is a
14000-bp exon in the fibroin gene of the silkworm
B. mori and one of 7572 bp (exon 26) in the
human apolipoprotein-B gene [37]. In general,
introns have lengths of up to 10000 bp, although
very large introns of 60 and 79 kb have been
found in the antp and dunce genes, respectively,
of Drosophila [69, 150]. In contrast to exon
lengths, mean intron lengths differ considerably
between the genomes of different groups of organisms. Introns in the middle of coding sequences
of vertebrates have a mean length of 1127 bp, in
insects 622 bp, in the lower fungi only 86 bp, and
in higher plants 249 bp [183]. Few introns are less
than 75 bp long [406]. Experiments with artificially modified globin genes have shown that
shortening the introns to 69 bp disturbs the splicing process [446].
Exons and introns, together with the nontranslated regions in front of and behind the coding sequences, make up the typical eukaryotic
transcription unit (Fig. 2.1). In addition, each
gene requires further regions on both sides to
ensure optimal expression. Thus, with the presence of introns, and non-translated and nontranscribed regions, eukaryotic genes require
stretches of DNA many times the length of the
actual protein-coding sequence. So, for example,
in the gene for the 28-kDa large ovomucoid of the
chicken, the sequence coding for the finished protein is 561 bp long, with another 260 bp for the
signal peptide, the 5' and 3' non-translated regions, and the initiation and termination signals;
these 0.82 kb, together with a total of 4.7 kb of
introns, make up a gene of 5.5 kb; with the addition of about 4 kb of territorial DNA on both
sides, it is seen that a coding sequence of 0.56 kb
requires not less that 13.5 kb of DNA [45, 317].
In Drosophila there are genes with even larger
introns; e.g. ubx, with a total length of 75 kb, or
antp, at 100 kb, both code for relatively small
proteins [189]. Introns lie mostly within coding
regions, sometimes in the 5' transcribed but not
translated region, and seldom in the 3' region. In
homologous genes of different species or in multiple genes resulting from duplication, they are
generally to be found at homologous positions;
they can, however, disappear or appear during
the course of evolution. Particularly large variation in intron position is found in the actin genes
(see Fig. 10.4; p.341). In length and sequence,
introns show especially rapid evolutionary change
and distinctive polymorphism. Thus, in the actin
genes, differences in the number, size and position of introns are found not only between different species but even between different members
of this multi-gene family in a single individual. In
Drosophila and other dipterans, introns are