3
2
-
-
2
-
Fig. 2.4. Plan of retrovirus-provirus or retrotransposon
[136]. 1, Long sequence repeats with the same orientation
(direct repeats); 2, short repeats with the opposite orienrior LTR. Transducing retroviruses mostly have
defective viral genes which are partly substituted
by oncogenes; such viruses need non-transducing
helper viruses for their multiplication. Retroviruses are distributed throughout the vertebrates.
The best-known retroposons are "copia" and the
families similar to copia, which were discovered
in Drosophila but are also found in many other
animals and even in yeast and higher plants [461],
and the similarly ubiquitous foldback (FB) element, "THE1" in humans and "VL30" in rats and
mice [470]. The non-viral retroposons contain no
LTRs or flanking inverted repeats; they usually
have a 3' terminal poly(A) sequence, and also
cause a duplication of the target sequence that is
longer (7-21 bp) than with the viral type (46 bp). Such non-viral retroposons have their origin in various cellular RNAs, with the exception
of the rRNA and 5S rRNA, i.e. from mRNAs,
tRNAs, 7SL RNAs and snRNAs. They correspond almost always to the fully spliced RNA,
i.e. in contrast to the viral retroposons, they
never possess introns but they are quite often
shortened at the 5' or 3' end. With the exception
of these few structural similarities, the non-viral
retroposons show significant variation. Their
length may be anything from 33 bp (retropseudogenes of the U2 snRNA of humans) to over 6 kb
(unshortened L1). The processed pseudogenes,
and the long and short middle repetitive sequences (LINEs and SINEs) of the mammals belong
to this group. At first it was believed that nonviral retroposons were seldom to be found in
other groups of animals [470], but it has since
become clear that SINEs occur in fish, amphibians and reptiles [123], and LINE-like elements
are distributed amongst not only different ver2.3.4 Mobile Sequences of Invertebrates
21
2
-
•
2
-3 -
tation (inverted repeats); 3, duplicated sequence at the
insertion site. The arrows show the direction of reading
tebrate classes but also insects and unicellular
organisms [33, 301, 324, 325]. A large degree of
variability is seen in all families of retroposons;
mutations can spread and be present at high frequencies so long as they do not hinder transposition.
2.3.4 Mobile Sequences of Invertebrates
Approximately 12 % of the genome of Drosophila melanogaster consists of middle repetitive
sequences, of which about one-quarter concern
dispersed tRNA genes, tandem-repeated rRNA
and histone genes. The remaining three-quarters
consist of about 50 families of widely dispersed
elements, each with 10-100 copies and lengths of
5-10 kb. Other Drosophila species, such as D.
algonquin and D. affinis, apparently have fewer
repetitive elements but these have larger copy
numbers [68, 191]. The best known are "copia"
and the copia-like sequences (gipsy, 412, 297,
17.6, mdg1, B104, 3S18) [26, 179]. As shown by
hybridization with the relevant DNA probes,
copia and gipsy are widely distributed throughout
the whole Drosophila genus, although both the
sequence and number vary greatly between species [419]. Thus, in Drosophila melanogaster there
are 20-60 copies of copia, in the very similar sibling species D. simulans there are only 2-4, and
in D. hydei the element is not present [417]. The
copia-like sequences correspond to vertebrate
retroviruses in terms of their LTRs; they have
transcription signals and flanking, inverted
repeats (Fig. 2.4). The open reading frame (ORF)
within copia codes for a polyprotein 1409 amino
acids long that, like the retroviruses, encompas-
2
-
-
2
-
Fig. 2.4. Plan of retrovirus-provirus or retrotransposon
[136]. 1, Long sequence repeats with the same orientation
(direct repeats); 2, short repeats with the opposite orienrior LTR. Transducing retroviruses mostly have
defective viral genes which are partly substituted
by oncogenes; such viruses need non-transducing
helper viruses for their multiplication. Retroviruses are distributed throughout the vertebrates.
The best-known retroposons are "copia" and the
families similar to copia, which were discovered
in Drosophila but are also found in many other
animals and even in yeast and higher plants [461],
and the similarly ubiquitous foldback (FB) element, "THE1" in humans and "VL30" in rats and
mice [470]. The non-viral retroposons contain no
LTRs or flanking inverted repeats; they usually
have a 3' terminal poly(A) sequence, and also
cause a duplication of the target sequence that is
longer (7-21 bp) than with the viral type (46 bp). Such non-viral retroposons have their origin in various cellular RNAs, with the exception
of the rRNA and 5S rRNA, i.e. from mRNAs,
tRNAs, 7SL RNAs and snRNAs. They correspond almost always to the fully spliced RNA,
i.e. in contrast to the viral retroposons, they
never possess introns but they are quite often
shortened at the 5' or 3' end. With the exception
of these few structural similarities, the non-viral
retroposons show significant variation. Their
length may be anything from 33 bp (retropseudogenes of the U2 snRNA of humans) to over 6 kb
(unshortened L1). The processed pseudogenes,
and the long and short middle repetitive sequences (LINEs and SINEs) of the mammals belong
to this group. At first it was believed that nonviral retroposons were seldom to be found in
other groups of animals [470], but it has since
become clear that SINEs occur in fish, amphibians and reptiles [123], and LINE-like elements
are distributed amongst not only different ver2.3.4 Mobile Sequences of Invertebrates
21
2
-
•
2
-3 -
tation (inverted repeats); 3, duplicated sequence at the
insertion site. The arrows show the direction of reading
tebrate classes but also insects and unicellular
organisms [33, 301, 324, 325]. A large degree of
variability is seen in all families of retroposons;
mutations can spread and be present at high frequencies so long as they do not hinder transposition.
2.3.4 Mobile Sequences of Invertebrates
Approximately 12 % of the genome of Drosophila melanogaster consists of middle repetitive
sequences, of which about one-quarter concern
dispersed tRNA genes, tandem-repeated rRNA
and histone genes. The remaining three-quarters
consist of about 50 families of widely dispersed
elements, each with 10-100 copies and lengths of
5-10 kb. Other Drosophila species, such as D.
algonquin and D. affinis, apparently have fewer
repetitive elements but these have larger copy
numbers [68, 191]. The best known are "copia"
and the copia-like sequences (gipsy, 412, 297,
17.6, mdg1, B104, 3S18) [26, 179]. As shown by
hybridization with the relevant DNA probes,
copia and gipsy are widely distributed throughout
the whole Drosophila genus, although both the
sequence and number vary greatly between species [419]. Thus, in Drosophila melanogaster there
are 20-60 copies of copia, in the very similar sibling species D. simulans there are only 2-4, and
in D. hydei the element is not present [417]. The
copia-like sequences correspond to vertebrate
retroviruses in terms of their LTRs; they have
transcription signals and flanking, inverted
repeats (Fig. 2.4). The open reading frame (ORF)
within copia codes for a polyprotein 1409 amino
acids long that, like the retroviruses, encompas-