LeishmaniaRibosomal Protein (RP) paralogous genes compensate each other’s expression maintaining protein native levels

Abstract

In the protozoan parasite Leishmania, most of the genes encoding for ribosomal proteins (RPs) are present as two or more copies in the genome, their untranslated regions (UTRs) are predominantly divergent, and might be associated with a distinct regulation of the paralogous gene's expression. Here, we investigated the expression profiles of two RPs (S16 and L13a) encoded by duplicated genes in Leishmania major. The genes encoding for S16 protein have identical CDSs and divergent UTRs while the L13a CDSs diverge in two amino acids with divergent UTRs. Using CRISPR/Cas9 genomic editing system, we generated knockout (Delta) and tagged transfectants for each paralog of L13a and S16. Combining tagged and Delta cell lines we show that the expression of both RPS16 and RPL13a isoforms differ throughout the parasite development with one of the isoforms being always more abundant than its respective copy. Additionally, compensatory expression was observed for each paralog when one of the isoforms was deleted, evidencing functional conservation of these proteins. Such phenomenon is related to post-translational processes, since the compensation happened at the protein levels, with no alterations observed at the transcript levels. Ribosomal profiles for RPL13a point out a standard behavior for these paralogues as already reported for other RPs in trypanosomatids, showing its interaction with heavy RNA-protein complexes. The identification of sets of proteins binding specifically to the 3'UTRs of either the high or less abundant transcripts suggests a possible role of these proteins to differently control the levels of expression of these RP genes. In addition, conserved cis-elements were identified in the 3'UTRs of RPS16 or RPL13a; among these, exclusive cis-elements for the more or for the less expressed transcripts were identified.