Gene expression in trypanosomatid parasites

Abstract

The parasites Leishmania spp., Trypanosoma brucei, and Trypanosoma cruzi are the trypanosomatid protozoa that cause the deadly human diseases leishmaniasis, African sleeping sickness, and Chagas disease, respectively. These organisms possess unique mechanisms for gene expression such as constitutive polycistronic transcription of protein-coding genes and trans-splicing. Little is known about either the DNA sequences or the proteins that are involved in the initiation and termination of transcription in trypanosomatids. In silico analyses of the genome databases of these parasites led to the identification of a small number of proteins involved in gene expression. However, functional studies have revealed that trypanosomatids have more general transcription factors than originally estimated. Many posttranslational histone modifications, histone variants, and chromatin modifying enzymes have been identified in trypanosomatids, and recent genome-wide studies showed that epigenetic regulation might play a very important role in gene expression in this group of parasites. Here, we review and comment on the most recent findings related to transcription initiation and termination in trypanosomatid protozoa.

Figure 1

Transcription and processing of mRNAs in trypanosomatids. The top part of the figure represents a hypothetical chromosome with three polycistronic gene clusters (PGC1-3). Pol II transcription initiates upstream of the first gene of the PGCs (arrows) [29, 38]. The G-run usually present at divergent strand-switch regions (SSR) is indicated. Nucleosomes located at the vicinity of transcription initiation regions contain histone variants H2AZ and H2BV [39]. The N-terminal tail of histone H3 in such nucleosomes are acetylated at K9/K14 (labeled as K9ac in the figure) and tri-methylated at K4 (K4me) [40, 41]. The N-terminal tail of histone H4 is acetylated at K10 (K10ac) [39], and at K5/K8/K12/K16 [41] (not shown in the figure). The bromodomain factor BDF3 [39], and transcription factors TRF4 and SNAP50 [40] also bind at transcription initiation regions. Pol II transcription of some PGCs terminates near tRNA genes (convergent strand-switch region between PGC2 and PGC3) [38], in regions of DNA that contain nucleosomes with histone variants H3V and H4V [39]. Transcription of a PGC produces a primary transcript (shown only for PGC2) that is processed by trans-splicing and polyadenylation to generate the mature mRNAs. By trans-splicing, a capped SL RNA (yellow box) is added to the 5′ end of every mRNA. In the spliced leader locus (located in a different chromosome) each gene possesses a Pol II promoter region (arrows). The cap in the SL RNA is indicated by an asterisk at the 5′ end of the RNA. The polycistronic transcript contains pyrimidine-rich regions (indicated by a striped box in the intergenic regions) that are needed for both trans-splicing and polyadenylation. The pyrimidine-rich regions are also present in the DNA, but they are not shown to simplify the figure. The four As located at the 3′ end of the mature mRNAs represent the poly-A tail.

Figure 2

Schematic representation of promoter regions in trypanosomatids. Transcription start sites are indicated by arrows. DNA sequence elements required for transcription initiation are denoted by dark blue boxes. Coding regions are shown as light blue boxes. The spliced leader RNA and chromosome 1 (transcribed by Pol II) correspond to L. tarentolae and L. major, respectively. The tRNA/U6snRNA locus and the 5S rRNA (transcribed by Pol III) correspond to T. brucei. The VSG, procyclin and rRNA transcription units (transcribed by Pol I) also correspond to T. brucei. The spliced leader RNA promoter contains the −30 and −60 elements [51]. In the divergent strand-switch region (SSR) from chromosome 1 several TSSs were mapped, in a ∼70 bp region, for both PGCs [29]. The tRNA gene possesses boxes A and B and the U6 snRNA an initiator element (Inr) [66]. The 5S rRNA gene contains boxes A and C and an intermediate element (IE). Domains I and II regulate transcription of the VSG expression site [69]. The VSG gene is located ~47 kb downstream of the expression-site-asociated-gene 7 (ESAG7). The procyclin promoter consists of four domains (I–IV) [70]. Procyclin genes EP1 and EP2 are followed by procyclin-associated genes (PAGs) 1 and 5. The rRNA promoter contains a bipartite core element (domains I and II), a distal element (domain III) and an upstream control region (UCR) [71]. Coding regions of the 18S, 5.8S and 24Sα rRNA genes are shown. Maps are drawn to scale. Please note that the scales are different upstream and downstream of the TSS in the VSG, procyclin and rRNA transcription units.