RNA Processing in C. elegans - Caenorhabditis Elegans: Molecular Genetics and Development - page 199

has not been observed, so it is very likely that trans-splicing has arisen independently
numerous times ( Douris et al., 2010 ).
7. A Second Class of Spliced Leaders
Shortly after the discovery of trans-splicing in C. elegans and the characteri-
zation of the SL1 RNA, another spliced leader was found at the 5 0 ends of mRNA
molecules transcribed from specific genes ( Huang and Hirsh, 1989 ). This second
spliced leader, designated SL2, was found to be transcribed from several snRNA
genes scattered throughout the genome. It is also capped with trimethylguanosine,
contains an Sm protein binding site, and is predicted to fold into a structure
closely resembling that of SL1 RNA ( Fig. 3c ). Soon after, several additional SL
RNA genes were identified through characterization of their novel spliced leaders
on various mRNA molecules ( Ross et al., 1995 )( Kuwabara et al., 1992 ). Further
analysis indicated that these additional SL RNA genes are variants of SL2 RNA.
Eleven SL2 variants, SL2 to SL12, are encoded by 18 genes scattered throughout
the genome ( MacMorris et al., 2007 ).
An early examination of SL2 trans-spliced genes showed that the SL2 spliced
leader is exclusively attached to pre-mRNAs transcribed from genes located in
downstream positions in operons (discussed in the following section)
( Spieth et al., 1993 ). It is thought that the SL2 snRNP trans-splicing reaction occurs
analogously to that of the SL1 snRNP, although systematic studies of its mechanism
have not been reported. In vivo analysis using a marked SL2 RNA construct has
shown that the sequence of the first 20 nt of the spliced leader can be altered without
a significant drop in trans-splicing efficiency ( Evans and Blumenthal, 2000 ). In
contrast, the primary sequences of stem II and stem-loop III are necessary for trans-
splicing activity and/or specificity. Unlike the SL1 snRNP, the SL2 snRNP does not
associate with SNA-1 or SNA-2. It can potentially base-pair with the stem-loops of
SmY snRNPs, an observation that provides additional support for the idea that the
SmY snRNPs have a role in Sm recycling ( MacMorris et al., 2007 ). It has also been
found that SL2 RNA overexpression will partially rescue the lethality resulting from
deletion of the rrs-1 (SL1 RNA) locus ( Ferguson et al., 1996 ). Thus, when forced,
SL2 snRNP can function in place of SL1. Clearly, however, the two classes of SL
snRNP are not completely interchangeable, since the SL2 snRNP normally does not
donate a spliced leader to pre-mRNAs transcribed from nonoperon genes or first
genes in operons ( Hillier et al., 2009; Spieth et al., 1993 ).
Like the SL1 spliced leader, the SL2 spliced leader can be found in other species of
nematode ( Blumenthal, 2005; Evans et al., 1997; Lee and Sommer, 2003 ). All of
these nematode species are relatively closely related to C. elegans, indicating that
this second spliced leader evolved at some point subsequent to the divergence of the
rhabditid group of nematodes ( Guiliano and Blaxter, 2006 ). Furthermore, while the
SL1 spliced leader is largely invariant throughout most of the nematode phylum, SL2
sequence varies considerably between different species. In all cases, it is used to
trans-splice downstream genes in operons. However, operons have been discovered