2.8.5 The Transfer RNAs and Their Genes
The cytoplasm of eukaryotic cells contains up to
10 8 tRNA molecules with lengths of 75-93 nt;
together these make up 10-15 % of the total
RNA. The number of different types of tRNA is
greater than that of the amino acids, so that severa~ different tRNAs (isoaccepting tRNAs) are
avaIlable for the same amino acid; on the other
hand, there is not a specific tRNA for each amino
acid codon as, in accordance with the "wobble
e~fect", the anticodon of some tRNAs recognizes
dIfferent co dons of the same amino acid. The
mitochondria contain a special set of tRNAs that
differ from those in the cytoplasm (p.53). The
homologous tRNAs of different animal species
show only minor differences; e.g., the sequence
identity between the tRNA LysJAAA of Drosophila
melanogaster and that of the rabbit is about 95 %
and the tRNALys/AAA of Drosophila and man ha~
in fact the same sequence [242]. Regardless ofthe
differences in length and sequence, tRNAs
always have a similar 3-D structure with four helical regions and three or four loops (Fig. 2.17).
In bacteria and yeast there are nonsense suppressor tRNAs that can read through stop
codons. The corresponding effect is achieved in
higher eukaryotes through false reading of stop
co dons by normal cytoplasmic tRNAs. Thus, in
rabbit reticulocytes the stop codon UGA (opal)
of the ~-globin mRNA is sometimes overlooked
in vivo and a "read through" protein, which is
l~nger than normal by 22 amino acids, is synthesIzed. The responsible tRNA here is either the
normal tRNATrp, as has been detected in vitro
or a specific suppressor tRNA Ser • Two opal:
suppressive tRNA Ser molecules are known in the
cow and chicken, and constitute about 1-3 % of
the total tRNA Ser population; they are probably
post-transcriptionally modified products of the
same gene. Their anticodon CmCA (mC represents methylcytosine) recognizes the stop codon
UGArather than, as expected, UGG = Trp [182].
I~ the nematode Caenorhabditis elegans, mutatIons of CCA ~ CTA in the anticodons of five
tRNATrp genes resulted in suppressor tRNAs for
the "amber" stop codon UAG [237].
All animals possess hundreds, if not thous~nds, of tRr:~A genes (Table 2.4) that are organ~sed very dIfferently between the various speCIes: they may occur as clusters of the same or different tRNA genes, e.g. in the clawed frog Xenopus, the salamander Taricha, Drosophila, Trypanos~ma and Tetrahymena; or are mainly dispersed III the genome as single genes, e.g. in man,
2.8.5 The Transfer RNAs and Their Genes
51
A-OH-3'
C
C
5'-p-0-8
0-0
0-0
0-0
0-0
00-0
.. 000008 0-000000000
I I I
11111
0
00000000
08 000 00 0
D-Loop
8=8 0 0 ~.
T'I'C-Loop
0-0
. variable Loop
0-0
0-0
o
0
~
~
Anticodon - Loop
Fig. 2.17. A model of a tRNA molecule. The amino acid is
attached to the 3' hydroxyl group by an ester bond
the nematode Caenorhabditis elegans and the
silkworm Bombyx mori. In Xenopus there are at
least 43 different tRNA genes, each with 200
copies that are mainly arranged in long tandem
clusters; in Drosophila there 12 copies each of
about 60 different genes that are dispersed in
many short clusters [58, 122,312, 417,437]. With
few exceptions, the tRNA genes of animals, in
contrast to those of yeast, contain no introns
[163]. The tRNA genes are transcribed by polymerase III, and the formation of mature tRNA
from the primary transcripts requires several
steps: the removal of superfluous nucleotides
from in front of the 5' end and after the 3' end
the addition of the sequence CCA to the 3' termi:
nus, and the modification of individual nucleoti~es [368]. The sequences of all the genes for a partlcular tRNA are kept constant by "horizontal
evolution", which at the same time hinders adaptive evolution. In place of the latter, there appears
to ~e. a~aptat~on through post-transcriptional
modIfIcatIons lIke methylation, acetylation and
pseudo-uridylation; however, in all eukaryotes
these are limited to about 20 specific positions.
As a result, the tRNAs of the eukaryotes contain
more unusual nucleotides than all other RNAs'
over 50 modified nucleotides have already bee~
discovered [242].
The cytoplasm of eukaryotic cells contains up to
10 8 tRNA molecules with lengths of 75-93 nt;
together these make up 10-15 % of the total
RNA. The number of different types of tRNA is
greater than that of the amino acids, so that severa~ different tRNAs (isoaccepting tRNAs) are
avaIlable for the same amino acid; on the other
hand, there is not a specific tRNA for each amino
acid codon as, in accordance with the "wobble
e~fect", the anticodon of some tRNAs recognizes
dIfferent co dons of the same amino acid. The
mitochondria contain a special set of tRNAs that
differ from those in the cytoplasm (p.53). The
homologous tRNAs of different animal species
show only minor differences; e.g., the sequence
identity between the tRNA LysJAAA of Drosophila
melanogaster and that of the rabbit is about 95 %
and the tRNALys/AAA of Drosophila and man ha~
in fact the same sequence [242]. Regardless ofthe
differences in length and sequence, tRNAs
always have a similar 3-D structure with four helical regions and three or four loops (Fig. 2.17).
In bacteria and yeast there are nonsense suppressor tRNAs that can read through stop
codons. The corresponding effect is achieved in
higher eukaryotes through false reading of stop
co dons by normal cytoplasmic tRNAs. Thus, in
rabbit reticulocytes the stop codon UGA (opal)
of the ~-globin mRNA is sometimes overlooked
in vivo and a "read through" protein, which is
l~nger than normal by 22 amino acids, is synthesIzed. The responsible tRNA here is either the
normal tRNATrp, as has been detected in vitro
or a specific suppressor tRNA Ser • Two opal:
suppressive tRNA Ser molecules are known in the
cow and chicken, and constitute about 1-3 % of
the total tRNA Ser population; they are probably
post-transcriptionally modified products of the
same gene. Their anticodon CmCA (mC represents methylcytosine) recognizes the stop codon
UGArather than, as expected, UGG = Trp [182].
I~ the nematode Caenorhabditis elegans, mutatIons of CCA ~ CTA in the anticodons of five
tRNATrp genes resulted in suppressor tRNAs for
the "amber" stop codon UAG [237].
All animals possess hundreds, if not thous~nds, of tRr:~A genes (Table 2.4) that are organ~sed very dIfferently between the various speCIes: they may occur as clusters of the same or different tRNA genes, e.g. in the clawed frog Xenopus, the salamander Taricha, Drosophila, Trypanos~ma and Tetrahymena; or are mainly dispersed III the genome as single genes, e.g. in man,
2.8.5 The Transfer RNAs and Their Genes
51
A-OH-3'
C
C
5'-p-0-8
0-0
0-0
0-0
0-0
00-0
.. 000008 0-000000000
I I I
11111
0
00000000
08 000 00 0
D-Loop
8=8 0 0 ~.
T'I'C-Loop
0-0
. variable Loop
0-0
0-0
o
0
~
~
Anticodon - Loop
Fig. 2.17. A model of a tRNA molecule. The amino acid is
attached to the 3' hydroxyl group by an ester bond
the nematode Caenorhabditis elegans and the
silkworm Bombyx mori. In Xenopus there are at
least 43 different tRNA genes, each with 200
copies that are mainly arranged in long tandem
clusters; in Drosophila there 12 copies each of
about 60 different genes that are dispersed in
many short clusters [58, 122,312, 417,437]. With
few exceptions, the tRNA genes of animals, in
contrast to those of yeast, contain no introns
[163]. The tRNA genes are transcribed by polymerase III, and the formation of mature tRNA
from the primary transcripts requires several
steps: the removal of superfluous nucleotides
from in front of the 5' end and after the 3' end
the addition of the sequence CCA to the 3' termi:
nus, and the modification of individual nucleoti~es [368]. The sequences of all the genes for a partlcular tRNA are kept constant by "horizontal
evolution", which at the same time hinders adaptive evolution. In place of the latter, there appears
to ~e. a~aptat~on through post-transcriptional
modIfIcatIons lIke methylation, acetylation and
pseudo-uridylation; however, in all eukaryotes
these are limited to about 20 specific positions.
As a result, the tRNAs of the eukaryotes contain
more unusual nucleotides than all other RNAs'
over 50 modified nucleotides have already bee~
discovered [242].