Dataset Information

Proteins interacting with ZC3H28 and DRBD18

ABSTRACT: ZC3H28 is a zinc-finger domain protein that is essential in bloodstream forms trypanosomes. Tethering ZC3H28 to a reporter mRNA results in an increase of the reporter mRNA levels but without a corresponding increase in protein expression levels. ZC3H28 associates with long RNAs that have low complexity in their 3’-untranslated regions. RNA immunoprecipitation results also showed that there was also a clear negative correlation between ZC3H28 mRNA binding and ribosome density. DRBD18 is a double RNA-binding domain protein that is essential in bloodstream forms and in procyclic forms. RNAi-mediated depletion of DRBD18 in bloodstream forms leads to reduction in RBP10 protein expression levels and caused accumulatio of several shortened RBP10 mRNA isoforms. DRBD18 depletion had similar effects on more than other 100 mRNAs including DRBD12. Binding of DRBD18 to mRNAs did not correlate with effects on the transcriptome, presumably because binding to mRNA precursors is not detected. We speculate that DRBD18 might bind to processing signals in the 3'-UTRs of mRNAs, thus preventing their use, and that this binding also serves to recruit mRNA export factors.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Trypanosoma Brucei

TISSUE(S): Permanent Cell Line Cell, Cell Culture

DISEASE(S): Trypanosomiasis

SUBMITTER: Tania Bishola

LAB HEAD: Christine Clayton

PROVIDER: PXD027792 | Pride | 2022-10-14

REPOSITORIES: Pride

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Publications

The Trypanosoma brucei RNA-binding protein DRBD18 ensures correct mRNA trans splicing and polyadenylation patterns.

Bishola Tshitenge Tania T Clayton Christine C

RNA (New York, N.Y.) 20220706 9

The parasite Trypanosoma brucei grows as bloodstream forms in mammals, and as procyclic forms in tsetse flies. Transcription is polycistronic, all mRNAs are trans spliced, and polyadenylation sites are defined by downstream splicing signals. Expression regulation therefore depends heavily on post-transcriptional mechanisms. The RNA-binding protein DRBD18 was previously implicated in the export of some mRNAs from the nucleus in procyclic forms. It copurifies the outer ring of the nu ...[more]

PMID: 35793904

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Project description:Trypanosoma brucei subspecies infect humans and animals in sub-Saharan Africa. This early diverging eukaryote shows many novel features in basic biological processes, including the use of polycistronic transcription to generate all protein-coding mRNAs. Therefore we hypothesized that translational control provides a means to tune gene expression during parasite development in mammalian and fly hosts. We used ribosome profiling to examine genome-wide protein production in animal-derived slender bloodstream forms and cultured procyclic (insect midgut) forms. About one-third of all CDSs showed statistically significant regulation of protein production between the two stages. Of these, more than two-thirds showed a change in translation efficiency, but few were controlled by this parameter alone. Ribosomal proteins were translated poorly, especially in animal-derived parasites. A disproportionate number of metabolic enzymes were up-regulated at the mRNA level in procyclic forms, as were variant surface glycoproteins in bloodstream forms. Comparison with cultured bloodstream forms from another strain identified stage-specific changes in protein production that transcend strain and growth conditions. Genes with upstream ORFs had a lower mean translation efficiency but no evidence was seen for involvement of these ORFs in stage-regulation. Ribosome profiling revealed that differences in the production of specific proteins in T. brucei slender bloodstream and procyclic forms are more common than anticipated from analysis of mRNA abundance. While in vivo and in vitro derived slender bloodstream forms of different strains are more similar to one another than to procyclic forms, they showed numerous differences at both the mRNA and protein production level. Ribosome profiling and mRNA libraries were constructed in triplicate from in vitro PCF and in vivo BF lifestages of theT. brucei Treu927 and in vitro T. brucei Lister427, to evaluate role of translational gene regulation

Dataset Information

Proteins interacting with ZC3H28 and DRBD18

Publications

The <i>Trypanosoma brucei</i> RNA-binding protein DRBD18 ensures correct mRNA <i>trans</i> splicing and polyadenylation patterns.

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