52
2 Nucleic Acids and Nuclear Proteins
2.8.6 The Small Nuclear RNAs
and Their Genes
A very important part of the spliceosome, the
complicated molecular complex in the cell nucleus
that converts the primary transcripts of proteincoding genes into mature, functional mRNAs in
all organisms from the ciliate Tetrahymena to man,
is the group of different types of small ribonucleoproteins (snRNPs). An snRNP is made up of one
molecule of an snRNA, 56-217 nt long, together
with about ten different proteins; some of these
proteins occur in all snRNPs and others are
limited to particular types. Thirteen different
snRNAs are known so far and are designated VI
to VB; however, results with yeast and plant cells
suggest that all eukaryotic cells probably contain
20-30 different snRNAs. VI to V6 are present in
about 10 5 copies per cell. The quantities of the
other snRNAs are much smaller, and as a consequence they were found only more recently. With
the exception of snRNA V6, the gene for which is
transcribed by Pol III, all other V-snRNAs are
products of Pol II. The functions of the individual
snRNAs in the spliceosome are only partly
known. The Vl-, V2-, V41U6- and V5-snRNPs
are essential components of the spliceosomes; V7
is required for the formation of the 3' end of histone mRNA [171,273]. The snRNA sequences are
apparently very conservative in terms of evolution. The partially sequenced snRNAs VI to V6
of the silkworm Bombyx mori are 66-81 % identical with the corresponding snRNAs of the vertebrates, and V6 of Trypanosoma brucei is 62 %
identical with that of the rat. In the nematodes,
which possess trans-splicing as well as normal spliceosomes, there are no overall peculiarities in the
snRNAs [4,438,441]. There are about 2000 genes
present for each snRNA in the higher vertebrates,
although the majority are actually pseudogenes.
In man, the rat and the chicken, and also in Drosophila, the snRNA genes are dispersed in the
genome, whereas in the sea urchin Lytechinus
they are arranged tandemly. Variants of particular
snRNAs occur in man and other mammals, and
also during sea urchin development [171, 274,
378].
2.9 Mitochondrial DNA
The mitochondria of the eukaryotes possess their
own system of protein synthesis, for which the
rRNAs and tRNAs are encoded in the mitochondrial genome, and the required enzymes and
protein components come from the cytoplasm
[232]. The genetic code involved here deviates
markedly from that of the chromosomalcytoplasmic system. The discovery of a unique
genetic apparatus in the mitochondria and plastids led to the idea that these organelles have
their origin in symbiotic prokaryotes that entered
primitive eukaryotic cells lacking mitochondria at
a very early stage of evolution [162, 169].
Although many characters of the mitochondrial
DNA (mtDNA) genome are identical in all eukaryotes, and they can be considered as homologues, there is a large variation in the molecular
structure. In the Eumetazoa, and apparently in
some Protozoa, the mtDNA has the form of a circular DNA double helix with a length of 15-20 kb
(in extreme cases, up to 42 kb); in the mitochondria of the Ciliophora, however, one finds
larger, linear molecules, and in the trypanosomes
and relatives a complicated network of linked circles exists. During evolution there has apparently
been a transfer of DNA between the mitochondria and the nucleus. At any rate, mtDNA-like
sequences have been detected in the nuclei of
many different kinds of eukaryotes (yeast, the
migratory locust, sea urchin, mammals and man)
and were probably integrated into the chromosomal DNA by illegitimate recombination [91].
As a rule, each mitochondrium contains about
five to ten mtDNA molecules associated with the
inner membrane; in the unfertilized eggs of Drosophila the number of mtDNA circles increases to
50 per organelle and declines again after fertilization [417]. Complete or nearly complete mtDNA
sequences are now known for more than a dozen
species of vertebrates, invertebrates and protozoans. Sequencing and restriction endonuclease
analysis clearly indicate a higher rate of evolution
of mtDNA than of chromosomal DNA. This may
be related to the fact that the mitochondria lack a
DNA repair system. As a result, mtDNA is a particularly useful system for molecular studies of
relationships between species and the study of
molecular evolution.
2.9.1 The mtDNA of Vertebrates
Human mtDNA will be used both as an example
of vertebrate mtDNA and to illustrate mtDNA
characteristics in general. It has a total length of
16569 nt and codes for 2 rRNAs, 22 tRNAs and
13 mitochondrial proteins (Fig. 2.18). Five of
these proteins were identified some time ago as
2 Nucleic Acids and Nuclear Proteins
2.8.6 The Small Nuclear RNAs
and Their Genes
A very important part of the spliceosome, the
complicated molecular complex in the cell nucleus
that converts the primary transcripts of proteincoding genes into mature, functional mRNAs in
all organisms from the ciliate Tetrahymena to man,
is the group of different types of small ribonucleoproteins (snRNPs). An snRNP is made up of one
molecule of an snRNA, 56-217 nt long, together
with about ten different proteins; some of these
proteins occur in all snRNPs and others are
limited to particular types. Thirteen different
snRNAs are known so far and are designated VI
to VB; however, results with yeast and plant cells
suggest that all eukaryotic cells probably contain
20-30 different snRNAs. VI to V6 are present in
about 10 5 copies per cell. The quantities of the
other snRNAs are much smaller, and as a consequence they were found only more recently. With
the exception of snRNA V6, the gene for which is
transcribed by Pol III, all other V-snRNAs are
products of Pol II. The functions of the individual
snRNAs in the spliceosome are only partly
known. The Vl-, V2-, V41U6- and V5-snRNPs
are essential components of the spliceosomes; V7
is required for the formation of the 3' end of histone mRNA [171,273]. The snRNA sequences are
apparently very conservative in terms of evolution. The partially sequenced snRNAs VI to V6
of the silkworm Bombyx mori are 66-81 % identical with the corresponding snRNAs of the vertebrates, and V6 of Trypanosoma brucei is 62 %
identical with that of the rat. In the nematodes,
which possess trans-splicing as well as normal spliceosomes, there are no overall peculiarities in the
snRNAs [4,438,441]. There are about 2000 genes
present for each snRNA in the higher vertebrates,
although the majority are actually pseudogenes.
In man, the rat and the chicken, and also in Drosophila, the snRNA genes are dispersed in the
genome, whereas in the sea urchin Lytechinus
they are arranged tandemly. Variants of particular
snRNAs occur in man and other mammals, and
also during sea urchin development [171, 274,
378].
2.9 Mitochondrial DNA
The mitochondria of the eukaryotes possess their
own system of protein synthesis, for which the
rRNAs and tRNAs are encoded in the mitochondrial genome, and the required enzymes and
protein components come from the cytoplasm
[232]. The genetic code involved here deviates
markedly from that of the chromosomalcytoplasmic system. The discovery of a unique
genetic apparatus in the mitochondria and plastids led to the idea that these organelles have
their origin in symbiotic prokaryotes that entered
primitive eukaryotic cells lacking mitochondria at
a very early stage of evolution [162, 169].
Although many characters of the mitochondrial
DNA (mtDNA) genome are identical in all eukaryotes, and they can be considered as homologues, there is a large variation in the molecular
structure. In the Eumetazoa, and apparently in
some Protozoa, the mtDNA has the form of a circular DNA double helix with a length of 15-20 kb
(in extreme cases, up to 42 kb); in the mitochondria of the Ciliophora, however, one finds
larger, linear molecules, and in the trypanosomes
and relatives a complicated network of linked circles exists. During evolution there has apparently
been a transfer of DNA between the mitochondria and the nucleus. At any rate, mtDNA-like
sequences have been detected in the nuclei of
many different kinds of eukaryotes (yeast, the
migratory locust, sea urchin, mammals and man)
and were probably integrated into the chromosomal DNA by illegitimate recombination [91].
As a rule, each mitochondrium contains about
five to ten mtDNA molecules associated with the
inner membrane; in the unfertilized eggs of Drosophila the number of mtDNA circles increases to
50 per organelle and declines again after fertilization [417]. Complete or nearly complete mtDNA
sequences are now known for more than a dozen
species of vertebrates, invertebrates and protozoans. Sequencing and restriction endonuclease
analysis clearly indicate a higher rate of evolution
of mtDNA than of chromosomal DNA. This may
be related to the fact that the mitochondria lack a
DNA repair system. As a result, mtDNA is a particularly useful system for molecular studies of
relationships between species and the study of
molecular evolution.
2.9.1 The mtDNA of Vertebrates
Human mtDNA will be used both as an example
of vertebrate mtDNA and to illustrate mtDNA
characteristics in general. It has a total length of
16569 nt and codes for 2 rRNAs, 22 tRNAs and
13 mitochondrial proteins (Fig. 2.18). Five of
these proteins were identified some time ago as