Expression site silencing and life-cycle progression appear normal in Argonaute1-deficient Trypanosoma brucei

TelAP1 links telomere complexes with developmental expression site silencing in African trypanosomes

During its life cycle, Trypanosoma brucei shuttles between a mammalian host and the tsetse fly vector. In the mammalian host, immune evasion of T. brucei bloodstream form (BSF) cells relies on antigenic variation, which includes monoallelic expression and periodic switching of variant surface glycoprotein (VSG) genes. The active VSG is transcribed from only 1 of the 15 subtelomeric expression sites (ESs). During differentiation from BSF to the insect-resident procyclic form (PCF), the active ES is transcriptionally silenced. We used mass spectrometry-based interactomics to determine the composition of telomere protein complexes in T. brucei BSF and PCF stages to learn more about the structure and functions of telomeres in trypanosomes. Our data suggest a different telomere complex composition in the two forms of the parasite. One of the novel telomere-associated proteins, TelAP1, forms a complex with telomeric proteins TbTRF, TbRAP1 and TbTIF2 and influences ES silencing kinetics during developmental differentiation.

Expression of the RNA-binding protein RBP10 promotes the bloodstream-form differentiation state in Trypanosoma brucei

In nearly all eukaryotes, cellular differentiation is governed by changes in transcription, and stabilized by chromatin and DNA modification. Gene expression control in the pathogen Trypanosoma brucei, in contrast, relies almost exclusively on post-transcriptional mechanisms, so RNA binding proteins must assume the burden that is usually borne by transcription factors. T. brucei multiply in the blood of mammals as bloodstream forms, and in the midgut of Tsetse flies as procyclic forms. We show here that a single RNA-binding protein, RBP10, promotes the bloodstream-form trypanosome differentiation state. Depletion of RBP10 from bloodstream-form trypanosomes gives cells that can grow only as procyclic forms; conversely, expression of RBP10 in procyclic forms converts them to bloodstream forms. RBP10 binds to procyclic-specific mRNAs containing an UAUUUUUU motif, targeting them for translation repression and destruction. Products of RBP10 target mRNAs include not only the major procyclic surface protein and enzymes of energy metabolism, but also protein kinases and stage-specific RNA-binding proteins: this suggests that alterations in RBP10 trigger a regulatory cascade.

VEX1 controls the allelic exclusion required for antigenic variation in trypanosomes

Allelic exclusion underpins antigenic variation and immune evasion in African trypanosomes. These bloodstream parasites use RNA polymerase-I (pol-I) to transcribe just one telomeric variant surface glycoprotein (VSG) gene at a time, producing superabundant and switchable VSG coats. We identified trypanosome VSG exclusion-1 (VEX1) using a genetic screen for defects in telomere-exclusive expression. VEX1 was sequestered by the active VSG and silencing of other VSGs failed when VEX1 was either ectopically expressed or depleted, indicating positive and negative regulation, respectively. Positive regulation affected VSGs and nontelomeric pol-I-transcribed genes, whereas negative regulation primarily affected VSGs. Negative regulation by VEX1 also affected telomeric pol-I-transcribed reporter constructs, but only when they contained blocks of sequence sharing homology with a pol-I-transcribed locus. We conclude that restricted positive regulation due to VEX1 sequestration, combined with VEX1-dependent, possibly homology-dependent silencing, drives a "winner-takes-all" mechanism of allelic exclusion.

Gene expression in Kinetoplastids

Kinetoplastid parasites adapt to different environments with wide-reaching control of gene expression, but transcription of nuclear protein-coding genes is polycistronic: there is no individual control of transcription initiation. Mature mRNAs are made by co-transcriptional trans splicing and polyadenylation, and competition between processing and nuclear degradation may contribute to regulation of mRNA levels. In the cytosol both the extent to which mRNAs are translated, and mRNA decay rates, vary enormously. I here highlight gaps in our knowledge: no measurements of transcription initiation or elongation rates; no measurements of how, precisely, mRNA processing and nuclear degradation control mRNA levels; and extremely limited understanding of the contributions of different translation initiation factors and RNA-binding proteins to mRNA fate.

The CAF1-NOT complex of trypanosomes

In African trypanosomes, there is no control of transcription initiation by RNA polymerase II at the level of individual protein-coding genes. Transcription is polycistronic, and individual mRNAs are excised by trans-splicing and polyadenylation. As a consequence, trypanosomes are uniquely reliant on post-transcriptional mechanisms for control of gene expression. Rates of mRNA decay vary over up to two orders of magnitude, making these organisms an excellent model system for the study of mRNA degradation processes. The trypanosome CAF1-NOT complex is simpler than that of other organisms, with no CCR4 or NOT4 homolog: it consists of CAF1, NOT1, NOT2, NOT5 NOT9, NOT10, and NOT11. It is important for the initiation of degradation of most, although not all, mRNAs. There is no homolog of NOT4, and Tho and TREX complexes are absent. Functions of the trypanosome NOT complex are therefore likely to be restricted mainly to deadenylation. Mechanisms that cause the NOT complex to deadenylate some mRNAs faster than others must exist, but have not yet been described.

Comparative transcriptome analysis of small noncoding RNAs in different stages of Trypanosoma brucei

Trypanosoma brucei, a pathogen of human and domestic animals, is an early evolved parasitic protozoan with a complex life cycle. Most genes of this parasite are post-transcriptionally regulated. However, the mechanisms and the molecules involved remain largely unknown. We have deep-sequenced the small RNAs of two life stages of this parasite--the bloodstream form and the procyclic form. Our results show that the small RNAs of T. brucei could derive from multiple sources, including NATs (natural antisense transcripts), tRNAs, and rRNAs. Most of these small RNAs in the two stages were found to share uniform characteristics. However, our results demonstrate that their variety and expression show significant differences between different stages, indicating possible functional differentiation. Dicer-knockdown evidence further proved that some of the small interfering RNAs (siRNAs) could regulate the expression of genes. Based on the genome-wide analysis of the small RNAs in the two stages of T. brucei, our results not only provide evidence to study their differentiation but also shed light on questions regarding the origins and evolution of small RNA-based mechanisms in early eukaryotes.

PRMT1 methylates the single Argonaute of Toxoplasma gondii and is important for the recruitment of Tudor nuclease for target RNA cleavage by antisense guide RNA

Argonaute (Ago) plays a central role in RNA interference in metazoans, but its status in lower organisms remains ill-defined. We report on the Ago complex of the unicellular protozoan, Toxoplasma gondii (Tg), an obligatory pathogen of mammalian hosts. The PIWI-like domain of TgAgo lacked the canonical DDE/H catalytic triad, explaining its weak target RNA cleavage activity. However, TgAgo associated with a stronger RNA slicer, a Tudor staphylococcal nuclease (TSN), and with a protein Arg methyl transferase, PRMT1. Mutational analysis suggested that the N-terminal RGG-repeat domain of TgAgo was methylated by PRMT1, correlating with the recruitment of TSN. The slicer activity of TgAgo was Mg(2+)-dependent and required perfect complementarity between the guide RNA and the target. In contrast, the TSN activity was Ca(2+) -dependent and required an imperfectly paired guide RNA. Ago knockout parasites showed essentially normal growth, but in contrast, the PRMT1 knockouts grew abnormally. Chemical inhibition of Arg-methylation also had an anti-parasitic effect. These results suggest that the parasitic PRMT1 plays multiple roles, and its loss affects the recruitment of a more potent second slicer to the parasitic RNA silencing complex, the exact mechanism of which remains to be determined.

Posttranscriptional control and the role of RNA-binding proteins in gene regulation in trypanosomatid protozoan parasites

Trypanosomatids are unicellular eukaryotes responsible for severe diseases in humans. They exhibit a number of remarkable biological phenomena, especially at the RNA level. During their life cycles, they alternate between a mammalian host and an insect vector and undergo profound biochemical and morphological transformations in order to adapt to the different environments they find within one or the other host species. These changes are orchestrated by specific gene expression programs. In contrast to other organisms, trypanosomatids do not regulate RNA polymerase II-dependent transcription initiation. Evidence so far indicates that the main control points in gene expression are mRNA degradation and translation. Recent studies have shown that RNA-binding proteins (RBPs) play a critical role in the developmental regulation of mRNA and protein abundance. RBPs seem to bind to specific subsets of mRNAs encoding functionally related proteins. These ribonucleoprotein complexes may represent posttranscriptional operons or regulons that are able to control the fate of multiple mRNAs simultaneously. We suggest that trypanosomatids transduce environmental signals into mRNA and protein abundance through posttranslational modification of RBPs.

The Argonaute protein TbAGO1 contributes to large and mini-chromosome segregation and is required for control of RIME retroposons and RHS pseudogene-associated transcripts

The protist Trypanosoma brucei possesses a single Argonaute gene called TbAGO1 that is necessary for RNAi silencing. We previously showed that in strain 427, TbAGO1 knock-out leads to a slow growth phenotype and to chromosome segregation defects. Here we report that the slow growth phenotype is linked to defects in segregation of both large and mini-chromosome populations, with large chromosomes being the most affected. These phenotypes are completely reversed upon inducible re-expression of TbAGO1 fused to GFP, demonstrating their link with TbAGO1. Trypanosomes that do not express TbAGO1 show a general increase in the abundance of transcripts derived from the short retroposon RIME (Ribosomal Interspersed Mobile Element). Supplementary large RIME transcripts emerge in the absence of RNAi, a phenomenon coupled to the disappearance of short transcripts. These fluctuations are reversed by inducible expression of GFP::TbAGO1. Furthermore, we use a combination of Northern blots, RT-PCR and sequencing to reveal that RNAi controls expression of transcripts derived from RHS (Retrotransposon Hot Spot) pseudogenes (RHS genes with retro-element(s) integrated within their coding sequence). Absence of RNAi also leads to an increase of steady-state transcripts from regular RHS genes (those without retro-element), indicating a role for pseudogene in control of gene expression. However, analysis of retroposon abundance and arrangement in the genome of multiple clonal cell lines of TbAGO1-/- failed to reveal movement of mobile elements despite the increased amounts of retroposon transcripts.

Shared epigenetic mechanisms control virulence factors in protozoan parasites

Protozoan pathogens have evolved countermeasures to avoid immune clearance and prolong the period of infection in their vertebrate hosts. The type and degree of immune escape strategies depends on the in vivo 'lifestyle' the pathogen has adopted. Here we describe how parasites use different strategies to coordinate their expression of phenotypic variation, which is used in many cases to fool the immune system, or to successfully invade new host cells. Recent insights using modern molecular biology techniques show that this is achieved via a coordinated manner of action of different epigenetic factors such as histone marks, subnuclear localization, or novel unknown mechanism(s). This emerging field may have an enormous impact on disease therapy.

The cell biology of Trypanosoma brucei differentiation

Developmental events in the life-cycle of the sleeping sickness parasite comprise integrated changes in cell morphology, metabolism, gene expression and signalling pathways. In each case these processes differ from the eukaryotic norm. In the past three years, understanding of these developmental processes has progressed from a description of the cytological events of differentiation to a discovery of its underlying molecular controls. With an expanding set of reagents for the identification of distinct parasite life-cycle stages in the tsetse, trypanosome differentiation is being studied from the molecular to the organismal and population level. Interestingly, the new molecular discoveries provide insights into the biology of the parasite in the field.

Antisense RNA and RNAi in protozoan parasites: working hard or hardly working?

The complex life cycles of many protozoan parasites require the ability to respond to environmental and developmental cues through regulated gene expression. Traditionally, parasitologists have investigated these mechanisms by identifying and characterizing proteins that are necessary for the regulated expression of the genetic material. Although often successful, it is clear that protein-mediated gene regulation is only part of a complex story in which RNA itself is endowed with regulatory functions. Herein, we review both the known and potential regulatory roles of two types of RNA pathways within protozoan parasites: the RNA interference pathway and natural antisense transcripts. A better understanding of the native role of these pathways will not only enhance our understanding of the biology of these organisms but also aid in the development of more robust tools for reverse genetic analysis in this post-genomic era.

Post-transcriptional regulation of gene expression in trypanosomes and leishmanias

Gene expression in Kinetoplastids is very unusual in that the open reading frames are arranged in long polycistronic arrays, monocistronic mRNAs being created by post-transcriptional processing. Thus the regulation of gene expression is post-transcriptional. We here discuss recent results concerning the enzymes required for mRNA degradation, and components of the translation initiation machinery, and how both are regulated.

Depletion of newly synthesized Argonaute1 impairs the RNAi response in Trypanosoma brucei

In Trypanosoma brucei, Argonaute1 (TbAGO1) is an essential component of the RNA interference (RNAi) pathway. While characterizing a TbAGO1 conditional knockout cell line, we discovered that, upon blockage of TbAGO1 transcription, the RNAi response to transfected double-stranded RNA was severely inhibited, although there was no change in the TbAGO1 protein level. This observation suggested that steady-state TbAGO1 was not sufficient to fully support the RNAi response to transfected dsRNA and implicated newly synthesized Argonaute in this phenomenon. Indeed, a translational blockade of TbAGO1 mRNA with an antisense morpholino oligonucleotide resulted in inhibition of the RNAi response, even though the steady-state level of TbAGO1 remained unchanged during the time of the assay. Thus, we concluded that in T. brucei, newly synthesized TbAGO1 is required to support an efficient RNAi response. We speculate that newly processed siRNAs may be preferentially loaded onto newly synthesized TbAGO1, and this mechanism may contribute to the homeostasis of the RNAi pathway.

Introducing histone modification in trypanosomes

Nuclear DNA is wrapped around histones. Vigorous research over the past decade has established a central role for histone post-translational modification in controlling the DNA-protein interactions that are required for successful growth and propagation. Recent work now provides a description of acetylated and methylated residues in the divergent trypanosome core histones. Future studies should provide insights into the genomic distribution of each modification and their roles in growth and pathogenesis.

Nuclear architecture underlying gene expression in Trypanosoma brucei

The influence of nuclear architecture on the regulation of developmental gene expression has recently become evident in many organisms ranging from yeast to humans. During interphase, chromosomes and nuclear structures are in constant motion; therefore, correct temporal association is needed to meet the requirements of gene expression. Trypanosoma brucei is an excellent model system in which to analyze nuclear spatial implications in the regulation of gene expression because the two main surface-protein genes (procyclin and VSG) are transcribed by the highly compartmentalized RNA polymerase I and undergo distinct transcriptional activation or downregulation during developmental differentiation. Furthermore, the infective bloodstream form of the parasite undergoes antigenic variation, displaying sequentially different types of VSG by allelic exclusion. Here, we discuss recent advances in understanding the role of chromosomal nuclear positioning in the regulation of gene expression in T. brucei.

Post-transcriptional control of nuclear-encoded cytochrome oxidase subunits in Trypanosoma brucei: evidence for genome-wide conservation of life-cycle stage-specific regulatory elements

Trypanosomes represent an excellent model for the post-transcriptional regulation of gene expression because their genome is organized into polycistronic transcription units. However, few signals governing developmental stage-specific expression have been identified, with there being no compelling evidence for widespread conservation of regulatory motifs. As a tool to search for common regulatory sequences we have used the nuclear-encoded components of the cytochrome oxidase (COX) complex of the trypanosome respiratory chain. Components of this complex represent a form of post-transcriptional operon because trypanosome mitochondrial activity is unusual in being developmentally programmed. By genome analysis we identified the genes for seven components of the COX complex. Each mRNA exhibits bloodstream stage-specific instability, which is not mediated by the RNA silencing pathway but which is alleviated by cycloheximide. Reporter assays have identified regulatory regions within the 3′-untranslated regions of three COX mRNAs operating principally at the translational level, but also via mRNA stability. Interrogation of the mapped regions via oligonucleotide frequency scoring provides evidence for genome-wide conservation of regulatory sequences among a large cohort of procyclic-enriched transcripts. Analysis of the co-regulated subunits of a stage-specific enzyme is therefore a novel approach to uncover cryptic regulatory sequences controlling gene expression at the post-transcriptional level.