Spanish researchers probe role of protein RBP33 in trypanosome parasite

Understanding the mechanism of microscopic parasites that can sicken and kill humans and animals is essential for controlling their spread. 

Scientists at the Institute of Parasitology and Biomedicine in Grenada, Spain, have discovered an intricate process involved in one of these killer parasites which may provide new clues about how to inhibit the parasite. 

The researchers studied Trypanosoma brucei, one of the flagellate protozoans of the genus Trypanosoma, which causes sleeping sickness (trypanosomiasis) in sub-Saharan Africa. Other trypanosome parasites are responsible for causing sleeping sickness in other parts of Africa and Chagas disease in the Americas.

The trypanosomes are transmitted via tsetse fly bites. The disease is serious, but curable if treated with medication; if untreated, it can lead to death.

The new research made use of advances in sequencing technologies for transcriptomes, the total of an organism's messenger RNA molecules that encode information for making proteins. 

The work appears in the journal Nucleic Acids Research, Dec. 1, 2022.

Pervasive transcription

Improved sequencing technologies have allowed researchers to analyze transcriptomes in depth, revealing that there is pervasive transcription of genomes in the variety of organisms examined. In other words, all parts of the genome are transcribed (the process of copying a piece of DNA into RNA) at a low level. 

The authors note that the RNA in this pervasive transcription is degraded by surveillance mechanisms. These mechanisms are present in cells and are used to check the quality of messenger RNA molecules. Not much is known about the "repertoire of proteins" that is involved in the surveillance mechanisms, the authors state. 

Their specific research focused on how transcription begins and is terminated in trypanosomes. In particular, they examined the RNA-binding protein RBP33 in T. brucei cells, performing several cell line analyses.

Their results suggest how RBP33 functions, but they note that the "actual mechanisms by which RBP33 targets RNAs for destruction remains to be determined."

The RBP33 findings

The researchers found that when RBP33 is depleted, there is a "marked increase" in the level of antisense transcripts. Antisense RNA blocks messenger RNA from translating into a protein. RBP33 loss, they note, also resulted in the down-regulation of many essential genes.

They show that "depletion of RBP33 results in the overexpression of ~40% of all annotated genes in the genome...." The researchers also found that it resulted in an overall decrease of messenger RNA abundance.

The authors examined many aspects of RBP33: where the transcripts it regulated were derived from; how they were processed; its relationship with variant surface glycoprotein (VSG), another trypanosome protein; the role of chromatin in RBP33 cells; how RBP33 affects the stabilization of regulated transcripts; and how it interacts with other proteins.

RBP33 appears to be exclusive to trypanosomes, the researchers state. Although they note that more research is needed, the researchers conclude: "We hypothesize that RBP33 could act by inhibiting trans-splicing of pervasive transcripts, resulting in unprocessed RNAs that are rapidly degraded by the exosome [the structure inside a cell containing some proteins]; conversely, in the absence of RBP33, non-productive transcripts would be properly processed and thus be less prone to degradation." 

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Claudia Gómez-Liñán et al. "The RNA-binding protein RBP33 dampens non-productive transcription in trypanosomes." Nucleic Acids Research, Dec. 1, 2022.

https://doi.org/10.1093/nar/gkac1123