during the evolution of the eukaryotic rRNA.
The 5 . . 8S rRNA is attached at both ends via
hydrogen bonds to the 28S rRNA: the 3' end
joins with the 5' terminus of the 28S rRNA, and
the 5' end attaches to a sequence 400 nt further
away. The lengths of the 5.8S rRNAs are around
160 nt; those of the flagellate Giardia lamblia
(140 nt) and the ciliate Tetrahymena (154 nt) are
the shortest, whereas those of the silkworm Bombyx mori (167 nt) and the trypanosomes (170 nt)
are the longest. Despite all the differences in
length and sequence, the secondary structure
always fits the same plan (Fig. 2.16a). The largest
differences between the various 5.8S rRNAs lie in
the (G+C)-rich region ne'ar the 3' end
(Fig. 2.16b). Compared with all the other 5.8S
rRNAs, approximately 15 nt are missing from the
3' end in Giardia lamblia; hence, the interaction
with the 5' end of the LS-rRNA is also absent
[39a]. In the dipterans Drosophila and Sciara, a
piece is cut out of the 5.8S rRNA after transcription, but the free ends are not spliced. Two short
rRNAs result and these are held together only by
base-pairing: 5.8Sa with 123 nt and 5.8Sb, or 2S
rRNA, with 30 nt (Figs. 2.14 & 2.16b) [419, 433].
The largest variety of products is shown by the
pre-rRNA of the flagellate Crithidia fasciculata,
where, in addition to 5S rRNA and 5.8S rRNA,
there are four further small rRNAs [49, 386].
In many animals, for example protozoans,
molluscs, annelids, crustaceans and insects, there
is a breakpoint in the middle of the 28S rRNA,
and under denaturing conditions this gives rise to
two fragments of about 18S ("28Sa and "28S~")
(Fig.2.14b). Investigations of Drosophila, the
fungus gnat Sciara coprophila and the silkworm
Bombyx mori have revealed not only the opening
of a bond but also the excision of a short,
extremely VA-rich, 19-nt fragment that forms a
stem-loop structure. In the pea aphid, Acyrtosiphon pisum, and other aphids, this characteristic
structure, and thus also the breakpoint, is missing
[329]. The 5.8S rRNA of the silkworm Bombyx
mori has an unusual length of 167 nt instead of
about 160 nt, and is perhaps specifically adapted
to form a stable complex with the 28S rRNA
[141]. In several carp-related fish, preformed
breakpoints that open under denaturing conditions are found in the majority of the 18S and 28S
rRNA molecules of somatic cells, but not in
germline cells. Ribosomes with such rRNAs have
reduced translation activity in vitro. It is remarkable that such aberrant rRNAs are found only in
tetraploid species, such as Barbus barb us, Cyprinus carpio and Carassius auratus, and do not
2.8.4 Ribosomal Proteins
49
occur in the diploid species of the family Cyprinidae or other fish [259, 260].
2.8.3 The 5S rRNAs and Their Genes
The 5S rRNA genes are organized in tandem
sequences outside of the nucleolus and are transcribed by polymerase III (p.37). In the clawed
frogs of the genus Xenopus, and also in the teleost Misgurnus fossilis, there are two sets of 5S
rRNA genes that are termed oocyte-specific or
somatic, according to the cell type in which they
are expressed; these differ in sequence by about
5 % [289, 323]. In the clawed frogs, the gene
family of the oocyte-specific 5S rRNA consists of
24000 copies (Xenopus laevis) or 9000 copies (X.
borealis) on chromosome 9, whereas that of the
somatic type consists of just a few hundred copies
dispersed over almost all the chromosomes (Table 2.4). Also, in the nemertean Emplectonema
gracile there are two types of 5S rRNAs that differ by no less than 22 (14 %) nucleotides [243].
Although in all other higher eukaryotes the 5S
rRNA genes are independent of the rDNA
repeats, in the plant-parasitic nematode Meloidogyne arenaria they are included [448]. The micronucleus of Tetrahymena contains, in fact, only one
gene for the larger rRNAs but has about 30 clusters of altogether approximately 150 genes for the
5S rRNA; the number is not significantly larger
in the macronucleus. In contrast, the macronucleus of the hypotrichous ciliate Euplotes eurystomus contains about 10 6 5S r RNA genes
[340, 363].
More than 350 5S rRNAs have been sequenced. There have been continuous attempts
to draw conclusions about phylogenetic relationships between the species from the speciesspecific differences amongst the 5S and 5.8S
rRNAs, and to draw up family trees [199, 330,
412]. The results are, however, contradictory or
even quite obviously absurd; clearly, these short
sequences do not provide sufficient information
for determining evolutionary distance [188]. Better results can be expected from comparisons of
the significantly longer SS-rRNA and LS-rRNA
sequences.
2.8.4 Ribosomal Proteins
The ribosomes of E. coli contain altogether 53
proteins in their two subunits; the number of
ribosomal proteins in the eukaryotes is known
The 5 . . 8S rRNA is attached at both ends via
hydrogen bonds to the 28S rRNA: the 3' end
joins with the 5' terminus of the 28S rRNA, and
the 5' end attaches to a sequence 400 nt further
away. The lengths of the 5.8S rRNAs are around
160 nt; those of the flagellate Giardia lamblia
(140 nt) and the ciliate Tetrahymena (154 nt) are
the shortest, whereas those of the silkworm Bombyx mori (167 nt) and the trypanosomes (170 nt)
are the longest. Despite all the differences in
length and sequence, the secondary structure
always fits the same plan (Fig. 2.16a). The largest
differences between the various 5.8S rRNAs lie in
the (G+C)-rich region ne'ar the 3' end
(Fig. 2.16b). Compared with all the other 5.8S
rRNAs, approximately 15 nt are missing from the
3' end in Giardia lamblia; hence, the interaction
with the 5' end of the LS-rRNA is also absent
[39a]. In the dipterans Drosophila and Sciara, a
piece is cut out of the 5.8S rRNA after transcription, but the free ends are not spliced. Two short
rRNAs result and these are held together only by
base-pairing: 5.8Sa with 123 nt and 5.8Sb, or 2S
rRNA, with 30 nt (Figs. 2.14 & 2.16b) [419, 433].
The largest variety of products is shown by the
pre-rRNA of the flagellate Crithidia fasciculata,
where, in addition to 5S rRNA and 5.8S rRNA,
there are four further small rRNAs [49, 386].
In many animals, for example protozoans,
molluscs, annelids, crustaceans and insects, there
is a breakpoint in the middle of the 28S rRNA,
and under denaturing conditions this gives rise to
two fragments of about 18S ("28Sa and "28S~")
(Fig.2.14b). Investigations of Drosophila, the
fungus gnat Sciara coprophila and the silkworm
Bombyx mori have revealed not only the opening
of a bond but also the excision of a short,
extremely VA-rich, 19-nt fragment that forms a
stem-loop structure. In the pea aphid, Acyrtosiphon pisum, and other aphids, this characteristic
structure, and thus also the breakpoint, is missing
[329]. The 5.8S rRNA of the silkworm Bombyx
mori has an unusual length of 167 nt instead of
about 160 nt, and is perhaps specifically adapted
to form a stable complex with the 28S rRNA
[141]. In several carp-related fish, preformed
breakpoints that open under denaturing conditions are found in the majority of the 18S and 28S
rRNA molecules of somatic cells, but not in
germline cells. Ribosomes with such rRNAs have
reduced translation activity in vitro. It is remarkable that such aberrant rRNAs are found only in
tetraploid species, such as Barbus barb us, Cyprinus carpio and Carassius auratus, and do not
2.8.4 Ribosomal Proteins
49
occur in the diploid species of the family Cyprinidae or other fish [259, 260].
2.8.3 The 5S rRNAs and Their Genes
The 5S rRNA genes are organized in tandem
sequences outside of the nucleolus and are transcribed by polymerase III (p.37). In the clawed
frogs of the genus Xenopus, and also in the teleost Misgurnus fossilis, there are two sets of 5S
rRNA genes that are termed oocyte-specific or
somatic, according to the cell type in which they
are expressed; these differ in sequence by about
5 % [289, 323]. In the clawed frogs, the gene
family of the oocyte-specific 5S rRNA consists of
24000 copies (Xenopus laevis) or 9000 copies (X.
borealis) on chromosome 9, whereas that of the
somatic type consists of just a few hundred copies
dispersed over almost all the chromosomes (Table 2.4). Also, in the nemertean Emplectonema
gracile there are two types of 5S rRNAs that differ by no less than 22 (14 %) nucleotides [243].
Although in all other higher eukaryotes the 5S
rRNA genes are independent of the rDNA
repeats, in the plant-parasitic nematode Meloidogyne arenaria they are included [448]. The micronucleus of Tetrahymena contains, in fact, only one
gene for the larger rRNAs but has about 30 clusters of altogether approximately 150 genes for the
5S rRNA; the number is not significantly larger
in the macronucleus. In contrast, the macronucleus of the hypotrichous ciliate Euplotes eurystomus contains about 10 6 5S r RNA genes
[340, 363].
More than 350 5S rRNAs have been sequenced. There have been continuous attempts
to draw conclusions about phylogenetic relationships between the species from the speciesspecific differences amongst the 5S and 5.8S
rRNAs, and to draw up family trees [199, 330,
412]. The results are, however, contradictory or
even quite obviously absurd; clearly, these short
sequences do not provide sufficient information
for determining evolutionary distance [188]. Better results can be expected from comparisons of
the significantly longer SS-rRNA and LS-rRNA
sequences.
2.8.4 Ribosomal Proteins
The ribosomes of E. coli contain altogether 53
proteins in their two subunits; the number of
ribosomal proteins in the eukaryotes is known