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noted that polyadenylation of the upstream mRNA in these operons almost always
occurs precisely at the AG of the trans-splice site, even though polyadenylation on G
residues is extremely rare in C. elegans (Blumenthal, unpublished observations.)
This observation suggests strongly that trans-splicing of the downstream gene
mRNA is actually the process responsible for 3
0
end formation of the upstream gene
mRNA. Upstream 3
0
end cleavage by trans-splicing would represent a novel RNA-
processing mechanism.
Incidental observations indicate that this mechanism could be employed occa-
sionally even in canonical SL2 operons. Indeed, during the initial characterization of
operons in C. elegans, RNA that terminated not at the polyadenylation sequence of
an upstream gene but at the downstream trans-splice site was detected (
Spieth et al.,
1993
). Furthermore, in cases where the upstream gene in an operon does not contain
a well-recognized polyadenylation signal, 3
0
end formation often fails to occur.
When this happens, trans-splicing of the downstream gene and polyadenylation of
the upstream gene occurs at the 3
0
end generated at the downstream trans-splice site,
effectively creating a long 3
0
UTR of the upstream gene (
Liu et al., 2003
).
6. How Widespread are Operons?
Although operons in metazoans were first discovered in C. elegans, they are by no
means unique to this group of nematodes or indeed to the nematode phylum. They
are also present in C. briggsae, as well as several other species in the rhabditid group.
Evidence for operons exists for more distantly related nematodes, including Brugia
malayi and Ascaris suum (
Guiliano and Blaxter, 2006; Liu et al., 2010;
). Although
operons have not yet been identified in the nematode species most distantly related
to C. elegans, such as Trichinella spiralis, the presence of a spliced leader in this
species makes their existence possible (
Pettitt et al., 2008
). It is reasonable to
suppose that operons evolved shortly after the arrival of trans-splicing and are
universal among nematodes. Once formed, operons are, of necessity, extremely
difficult to lose, evolutionarily. Since downstream genes are now separated from
their promoters, their duplication or transposition is less likely to result in a func-
tional gene (
Qian and Zhang, 2008
). Additionally, since processing of the polycis-
tronic RNA resulting from operons requires trans-splicing, out-of-frame start codons
can evolve in the DNA sequences upstream of a trans-splice site (
Blumenthal, 2005
).
For this reason, studies have concluded that, once formed, operons are not easily lost
through evolution. However, even in closely related species, such as C. elegans and
C. briggsae, separated by about 100 million years of evolution, operon content and
arrangement are notably different (
Qian and Zhang, 2008
). When more distantly
related nematodes were also examined, these authors documented numerous addi-
tional instances of operon loss and rearrangement.
Outside of the nematode phylum, operons have been reported in several additional
phyla. It appears that in all of these instances trans-splicing has arisen independently
(from cis-splicing), and that operons subsequently arose in the genome. In at least
two cases, arthropods and chordates, it appears that trans-splicing and possibly
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