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Trypanosoma cruzi: molecular characterization of an RNA binding protein differentially expressed in the parasite life cycle.

ABSTRACT: Molecular studies have shown several peculiarities in the regulatory mechanisms of gene expression in trypanosomatids. Protein coding genes are organized in long polycistronic units that seem to be constitutively transcribed. Therefore, post-transcriptional regulation of gene expression is considered to be the main point for control of transcript abundance and functionality. Here we describe the characterization of a 17 kDa RNA-binding protein from Trypanosoma cruzi (TcRBP19) containing an RNA recognition motive (RRM). This protein is coded by a single copy gene located in a high molecular weight chromosome of T. cruzi. Orthologous genes are present in the TriTryp genomes. TcRBP19 shows target selectivity since among the different homoribopolymers it preferentially binds polyC. TcRBP19 is a low expression protein only barely detected at the amastigote stage localizing in a diffuse pattern in the cytoplasm.

SUBMITTER: Perez-Diaz L

PROVIDER: S-EPMC2020836 | biostudies-literature | 2007 Sep

REPOSITORIES: biostudies-literature

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Trypanosoma cruzi: molecular characterization of an RNA binding protein differentially expressed in the parasite life cycle.

Pérez-Díaz Leticia L Duhagon María Ana MA Smircich Pablo P Sotelo-Silveira José J Robello Carlos C Krieger Marco Aurelio MA Goldenberg Samuel S Williams Noreen N Dallagiovanna Bruno B Garat Beatriz B

Experimental parasitology 20070327 1

Molecular studies have shown several peculiarities in the regulatory mechanisms of gene expression in trypanosomatids. Protein coding genes are organized in long polycistronic units that seem to be constitutively transcribed. Therefore, post-transcriptional regulation of gene expression is considered to be the main point for control of transcript abundance and functionality. Here we describe the characterization of a 17 kDa RNA-binding protein from Trypanosoma cruzi (TcRBP19) containing an RNA r ...[more]

PMID: 17475252

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Project description:BackgroundThe evolutionarily ancient parasite, Trypanosoma brucei, is unusual in that the majority of its genes are regulated post-transcriptionally, leading to the suggestion that transcript abundance of most genes does not vary significantly between different life cycle stages despite the fact that the parasite undergoes substantial cellular remodelling and metabolic changes throughout its complex life cycle. To investigate this in the clinically relevant sub-species, Trypanosoma brucei gambiense, which is the causative agent of the fatal human disease African sleeping sickness, we have compared the transcriptome of two different life cycle stages, the potentially human-infective bloodstream forms with the non-human-infective procyclic stage using digital gene expression (DGE) analysis.ResultsOver eleven million unique tags were generated, producing expression data for 7360 genes, covering 81% of the genes in the genome. Compared to microarray analysis of the related T. b. brucei parasite, approximately 10 times more genes with a 2.5-fold change in expression levels were detected. The transcriptome analysis revealed the existence of several differentially expressed gene clusters within the genome, indicating that contiguous genes, presumably from the same polycistronic unit, are co-regulated either at the level of transcription or transcript stability.ConclusionsDGE analysis is extremely sensitive for detecting gene expression differences, revealing firstly that a far greater number of genes are stage-regulated than had previously been identified and secondly and more importantly, this analysis has revealed the existence of several differentially expressed clusters of genes present on what appears to be the same polycistronic units, a phenomenon which had not previously been observed in microarray studies. These differentially regulated clusters of genes are in addition to the previously identified RNA polymerase I polycistronic units of variant surface glycoproteins and procyclin expression sites, which encode the major surface proteins of the parasite. This raises a number of questions regarding the function and regulation of the gene clusters that clearly warrant further study.

Project description:BackgroundTrypanosomatids are a group of protozoan parasites that includes the etiologic agents of important human illnesses as Chagas disease, sleeping sickness and leishmaniasis. These parasites have a significant distinction from other eukaryotes concerning mRNA structure, since all mature mRNAs have an identical species-specific sequence of 39 nucleotides at the 5' extremity, named spliced leader (SL). Considering this peculiar aspect of trypanosomatid mRNA, the aim of the present work was to develop a Trypanosoma cruzi specific in vitro transcription (IVT) linear mRNA amplification method in order to improve parasite transcriptomics analyses.MethodsWe designed an oligonucleotide complementary to the last 21 bases of T. cruzi SL sequence, bearing an upstream T7 promoter (T7SL primer), which was used to direct the synthesis of second-strand cDNA. Original mRNA was then amplified by IVT using T7 RNA polymerase. T7SL-amplified RNA from two distinct T. cruzi stages (epimastigotes and trypomastigotes) were deep sequenced in SOLiD platform. Usual poly(A) + RNA and and T7-oligo(dT) amplified RNA (Eberwine method) were also sequenced. RNA-Seq reads were aligned to our new and improved T. cruzi Dm28c genome assembly (PacBio technology) and resulting transcriptome pattern from these three RNA preparation methods were compared, mainly concerning the conservation of mRNA transcritional levels and DEGs detection between epimastigotes and trypomastigotes.ResultsT7SL IVT method detected more potential differentially expressed genes in comparison to either poly(A) + RNA or T7dT IVT, and was also able to produce reliable quantifications of the parasite transcriptome down to 3 ng of total RNA. Furthermore, amplification of parasite mRNA in HeLa/epimastigote RNA mixtures showed that T7SL IVT generates transcriptome quantification with similar detection of differentially expressed genes when parasite RNA mass was only 0.1% of the total mixture (R = 0.78 when compared to poly(A) + RNA).ConclusionsThe T7SL IVT amplification method presented here allows the detection of more potential parasite differentially expressed genes (in comparison to poly(A) + RNA) in host-parasite mixtures or samples with low amount of RNA. This method is especially useful for trypanosomatid transcriptomics because it produces less bias than PCR-based mRNA amplification. Additionally, by simply changing the complementary region of the T7SL primer, the present method can be applied to any trypanosomatid species.

Dataset Information

Trypanosoma cruzi: molecular characterization of an RNA binding protein differentially expressed in the parasite life cycle.

Publications

Trypanosoma cruzi: molecular characterization of an RNA binding protein differentially expressed in the parasite life cycle.

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