20
2 Nucleic Acids and Nuclear Proteins
parasite may become a symbiont. Non-functional
DNA, without the ability to transpose ("ignorant
DNA" or "junk DNA"), would, in contrast, be
relatively quickly eliminated during evolution. It
must be argued that the concept of "selfish DNA"
does not take sufficient account of the dynamic
flexibility of the genome: undoubtedly, the
genome is a mosaic of sequences that contribute
to the phenotype (genes) and those that do not;
however, there is a constant exchange between
these two compartments [470].
The mechanisms of transposition have not yet
been completely explained. Whereas transposition involving extrachromosomal DNA is important in the prokaryotes, transposition via RNA is
limited to the eukaryotes and is distinguished by
the term retroposition; sequences transposed in
this way are called retroposons. The direct transposition of DNA elements can happen either by
replication of the transposed element and insertion in the target site (replicative transposition),
or by excision of the element and its transfer to a
new site. Such a "cut-and-paste" mechanism is
assumed for the P element of Drosophila. The
enzyme required ("transposase") is coded by the
P element itself. The intermediate products of the
transposition are extrachromosomal, circular
DNA molecules, such as are often found, for
example, in tissue cultures of Drosophila and
various vertebrates [347].
Retroposition begins with the transcription of
the transposable elements. According to the type
of retroposon, this is apparently carried out with
RNA polymerase II or III; in any case, the ubiquitous, long LINEs contain a Pol II promoter,
and the shorter SINEs contain a Pol III promoter.
The RNA intermediate is temporarily included in
a ribonucleoprotein particle. Finally, a DNA copy
is produced from the RNA by reverse transcription and is reinserted into the genome [325, 353,
470]. A "staggered cut" occurs at the insertion
site, as does a short sequence duplication
(Fig. 2.3). All intact retroposons code for their
own reverse transcriptase, which has significant
homology to the enzyme of the retroviruses [488].
Little is known about the choice of the insertion
site, although several retroposons show definite
insertion specificity. Thus, the CRE-l elements of
the flagellates Trypanosoma and Crithidia are
found exclusively in the genes of the mini-exons
that are transpliced into all mRNAs [144]. The
insertion elements Rl and R2 in the rRNA genes
of several insects are site-specific mobile elements. In the silkworm, Bombyx mori, it has been
shown that the R2 element codes for an endonuclease that is highly specific for the 28S rRNA gene
and produces a staggered cut at the insertion site
with a 4-bp sticky end [325].
Two types of retroposons are recognized
according to structure and origin: "viral" and
"non-viral". The viral retroposons resemble the
tumorigenic RNA viruses (retroviruses) of mammals and birds. These are of special interest
because they are able to incorporate particular
host genes into their genome and then transfer
these to other regions of the host genome. The
host genes involved are known as cellular oncogenes, and their equivalents in the viral genome are
termed viral oncogenes. At present, about 20
viral oncogenes are known and these are named
after the virus in which they were found: v-src
(Rous sarcoma), v-myc (myelocytomatosa), v-ras
(sarcoma), etc.; the corresponding cellular oncogenes are accordingly termed c-src, c-myc and cras [89]. Sequences that are homologous to particular cellular oncogenes have been found
throughout all classes of vertebrates and in Drosophila, the nematode Caenorhabditis and yeast
[27, 157]. Most oncogenes are aberrant forms of
components of the intracellular signalling system,
i.e. growth hormones and their receptors, liganddependent protein tyrosine kinases, GTP-binding
proteins, cytoplasmic serine/threonine kinases,
and proteins involved in gene regulation. The
DNA of the non-transducing retroviruses carries
in its central region structural genes, in particular
for reverse transcriptase, integrase (pol) and viral
structural components (gag, env); it also carries
LTRs and short inverted repeats at both ends and
these are recognized by the mechanism for insertion into the genome (Fig. 2.4). The transcription
signals (promotor, enhancer, poly(A) signal) are
organized in the LTRs such that transcription
begins at the anterior LTR and ends at the posteTA
T}TTGCATGGC
ATAACGTtCCG
TTGCATGGC
=-_....:.===================. ATAACGT
ACCG
TATTGCA
TTGCATGGC
------------------ATAACGT
AACGTACCG
Fig. 2.3. During the insertion of a mobile element, the
strands of the DNA double helix are cut at slightly different
points (staggered cut), producing a short sequence duplication at the insertion site
2 Nucleic Acids and Nuclear Proteins
parasite may become a symbiont. Non-functional
DNA, without the ability to transpose ("ignorant
DNA" or "junk DNA"), would, in contrast, be
relatively quickly eliminated during evolution. It
must be argued that the concept of "selfish DNA"
does not take sufficient account of the dynamic
flexibility of the genome: undoubtedly, the
genome is a mosaic of sequences that contribute
to the phenotype (genes) and those that do not;
however, there is a constant exchange between
these two compartments [470].
The mechanisms of transposition have not yet
been completely explained. Whereas transposition involving extrachromosomal DNA is important in the prokaryotes, transposition via RNA is
limited to the eukaryotes and is distinguished by
the term retroposition; sequences transposed in
this way are called retroposons. The direct transposition of DNA elements can happen either by
replication of the transposed element and insertion in the target site (replicative transposition),
or by excision of the element and its transfer to a
new site. Such a "cut-and-paste" mechanism is
assumed for the P element of Drosophila. The
enzyme required ("transposase") is coded by the
P element itself. The intermediate products of the
transposition are extrachromosomal, circular
DNA molecules, such as are often found, for
example, in tissue cultures of Drosophila and
various vertebrates [347].
Retroposition begins with the transcription of
the transposable elements. According to the type
of retroposon, this is apparently carried out with
RNA polymerase II or III; in any case, the ubiquitous, long LINEs contain a Pol II promoter,
and the shorter SINEs contain a Pol III promoter.
The RNA intermediate is temporarily included in
a ribonucleoprotein particle. Finally, a DNA copy
is produced from the RNA by reverse transcription and is reinserted into the genome [325, 353,
470]. A "staggered cut" occurs at the insertion
site, as does a short sequence duplication
(Fig. 2.3). All intact retroposons code for their
own reverse transcriptase, which has significant
homology to the enzyme of the retroviruses [488].
Little is known about the choice of the insertion
site, although several retroposons show definite
insertion specificity. Thus, the CRE-l elements of
the flagellates Trypanosoma and Crithidia are
found exclusively in the genes of the mini-exons
that are transpliced into all mRNAs [144]. The
insertion elements Rl and R2 in the rRNA genes
of several insects are site-specific mobile elements. In the silkworm, Bombyx mori, it has been
shown that the R2 element codes for an endonuclease that is highly specific for the 28S rRNA gene
and produces a staggered cut at the insertion site
with a 4-bp sticky end [325].
Two types of retroposons are recognized
according to structure and origin: "viral" and
"non-viral". The viral retroposons resemble the
tumorigenic RNA viruses (retroviruses) of mammals and birds. These are of special interest
because they are able to incorporate particular
host genes into their genome and then transfer
these to other regions of the host genome. The
host genes involved are known as cellular oncogenes, and their equivalents in the viral genome are
termed viral oncogenes. At present, about 20
viral oncogenes are known and these are named
after the virus in which they were found: v-src
(Rous sarcoma), v-myc (myelocytomatosa), v-ras
(sarcoma), etc.; the corresponding cellular oncogenes are accordingly termed c-src, c-myc and cras [89]. Sequences that are homologous to particular cellular oncogenes have been found
throughout all classes of vertebrates and in Drosophila, the nematode Caenorhabditis and yeast
[27, 157]. Most oncogenes are aberrant forms of
components of the intracellular signalling system,
i.e. growth hormones and their receptors, liganddependent protein tyrosine kinases, GTP-binding
proteins, cytoplasmic serine/threonine kinases,
and proteins involved in gene regulation. The
DNA of the non-transducing retroviruses carries
in its central region structural genes, in particular
for reverse transcriptase, integrase (pol) and viral
structural components (gag, env); it also carries
LTRs and short inverted repeats at both ends and
these are recognized by the mechanism for insertion into the genome (Fig. 2.4). The transcription
signals (promotor, enhancer, poly(A) signal) are
organized in the LTRs such that transcription
begins at the anterior LTR and ends at the posteTA
T}TTGCATGGC
ATAACGTtCCG
TTGCATGGC
=-_....:.===================. ATAACGT
ACCG
TATTGCA
TTGCATGGC
------------------ATAACGT
AACGTACCG
Fig. 2.3. During the insertion of a mobile element, the
strands of the DNA double helix are cut at slightly different
points (staggered cut), producing a short sequence duplication at the insertion site