Assessing the partners of the RBP9-mRNP complex in Trypanosoma cruzi using shotgun proteomics and RNA-seq

RNA Biology
Helisa H WippelLysangela Ronalte Alves

Abstract

Gene expression regulation in trypanosomes differs from other eukaryotes due to absence of transcriptional regulation for most of their genes. RNA-binding proteins (RBPs) associate with mRNAs and other regulatory proteins to form ribonucleoprotein complexes (mRNPs), which play a major role in post-transcriptional regulation. Here, we show that RBP9 is a cytoplasmic RBP in Trypanosoma cruzi with one RNA-recognition motif (RRM). The RBP9 sedimentation profile in a sucrose gradient indicated its presence in cytoplasmic translational complexes, suggesting its involvement in translation regulation. Taking this result as a motivation, we used shotgun proteomics and RNA-seq approaches to assess the core of the RBP9-mRNP complex. In epimastigotes in exponential growth, the complex was composed mostly by RBPs involved in RNA metabolism, such as ZC3H39, UBP1/2, NRBD1, and ALBA3/4. When parasites were subjected to nutritional stress, our analysis identified regulatory RBPs and the translation initiation factors eIF4E5, eIF4G5, eIF4G1, and eIF4G4. The RNA-seq results showed that RBP9-mRNP complex regulates transcripts encoding some RBPs - e.g. RBP5, RBP6, and RBP10 -, and proteins involved in metabolic processes. Therefore, we argue that R...Continue Reading

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Citations

Mar 11, 2020·Frontiers in Cellular and Infection Microbiology·Bruno A A RomagnoliSamuel Goldenberg
Dec 8, 2020·Biochimica Et Biophysica Acta. Proteins and Proteomics·Emanuella de Castro AndreassaTatiana de Arruda Campos Brasil de Souza
May 22, 2021·Molecular Omics·Helisa H WippelJames E Bruce

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Datasets Mentioned

BETA
SRP051179

Methods Mentioned

BETA
RNA-seq
PCR
electrophoresis
confocal microscopy
immunoprecipitation
coimmunoprecipitation assay

Software Mentioned

BLASTP
PatternLab for proteomics
Psi
PatternLab
CLC Genomics Workbench
BioID
Leica AF6000
Figtree
PSIPRED
Comet

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