trans

SL RNA AND U snRNA GENE TRANSCRIPTION IN NEMATODES AND TRYPANOSOMATIDS 63
in an RNA pol III-like manner. This view is
supported by an experiment conducted in
T. brucei in which transient transfection of an
SL RNA gene containing an RNA pol III termination
signal within the coding region prevented
the production of full-size molecules.
Interestingly, pre-mRNA synthesizing RNA pol
II must differ to some extent from the enzyme
complex transcribing SL RNA genes because it
does not recognize T-runs as termination signals
and reads through T-rich polypyrimidine
tracts which, as essential RNA processing signals,
are common motifs of polycistronic transcription
units.
Functional association of
tRNA genes and small nuclear or
small cytoplasmic RNA genes in
trypanosomatids
In trypanosomatids, low molecular weight
RNAs including U snRNAs are synthesized by
RNA pol III. The only exception appears to be
the SL RNA gene. In the genome, class III genes
are clustered and interspersed between RNA
pol II transcription units. In these clusters,
tRNA genes are associated head-to-head with
various U snRNA genes or the 7SL RNA gene
which encodes the RNA component of the signal
recognition particle. The first trypanosomatid
class III gene promoter analyzed was
that of the T. brucei U2 snRNA gene. It consists
of an intragenic control element comprising
the first 24 bp of the transcribed region and two
11 bp-long sequence blocks located 104 and
155 bp upstream of the TIS (Figure 3.3). A comparison
of the U2 promoter and corresponding
sequences of other U snRNA genes and the 7SL
RNA gene revealed that the upstream region
of these genes was occupied by a divergently
orientated tRNA gene. Promoters of tRNA
genes consist of two highly conserved intragenic
elements designated ‘A box’ and ‘B box’.
Interestingly, size, location, and sequence of
these elements in the upstream tRNA genes
corresponded to the two upstream promoter
elements of the U2 snRNA gene. Furthermore,
the sequence around the two U2 elements
resembles a tRNA sequence and may have originated
from a functional tRNA gene. Taken
together, these observations suggested that the
A and B boxes of the companion tRNA genes
promote transcription of both the tRNA gene
and the associated small RNA gene. This possibility
was confirmed by a detailed mutational
analysis of the linked U6 snRNA and threonine
tRNA genes in T. brucei. Furthermore, it was
found that in vivo expression and in vitro transcription
of the U6 snRNA gene depended, as in
the U2 snRNA gene, on an intragenic promoter
element comprising the first 21 nucleotides of
the U6 RNA coding region (Figure 3.3). The
FIGURE 3.3 Association of tRNA genes and small nuclear or small cytoplasmic RNA genes in trypanosomatids.
At the top, a schematic drawing to scale is shown of the Trypanosoma brucei U6, U2, and candidate U1 snRNA gene
promoters which represent the three types of U snRNA gene promoters characterized in trypanosomatids thus far.
The three genes have tRNA gene A and B box elements upstream of the TIS as indicated by striped rectangles. These
elements are in reverse orientation to the U snRNA transcription direction (arrows) and are either part of a functional
tRNA gene as in the U6 snRNA gene (tRNA Thr ) or inside a tRNA-like sequence as in the U2 and ‘U1’ snRNA
genes. The sequence immediately downstream of the TIS is an intragenic promoter element (IPE) in the U6 and U2
snRNA genes, but has no promoter function in the ‘U1 snRNA’ gene. At the bottom, a selection of U snRNA and 7SL
RNA genes of T. brucei, Leishmania pifanoi, Leishmania mexicana, Leptomonas seymouri, Leptomonas collosoma,
and Crithidia fasciculata is shown. For the listed genes, the upstream tRNA sequence and the location of A and B
box elements have been analyzed. For each gene, the position of the A box relative to the TIS and the nature of the
associated tRNA sequence is given.
MOLECULAR BIOLOGY