Illuminating Parasite Protein Production by Ribosome Profiling

Abstract

While technologies for global enumeration of transcript abundance are well-developed, those that assess protein abundance require tailoring to penetrate to low abundance proteins. Ribosome profiling circumvents this challenge by measuring global protein production via sequencing small mRNA fragments protected by the assembled ribosome. This powerful approach is now being applied to protozoan parasites, including trypanosomes and Plasmodium. It has been used to identify new protein coding sequences (CDSs) and clarify the boundaries of previously annotated CDSs in Trypanosoma brucei. Ribosome profiling has demonstrated that translation efficiencies vary widely between genes and, for trypanosomes at least, for the same gene across stages. The ribosomal proteins are themselves subjected to translational control, suggesting a means of reinforcing global translational regulation.

The Role of Cytoplasmic mRNA Cap-Binding Protein Complexes in Trypanosoma brucei and Other Trypanosomatids

“…Although the lack of traditional control for the trypanosomatid polycistronic transcription suggests that adjacent genes would have the same levels of expression, it is known that, in fact, many show strikingly different steady-state levels [ 11 ]. Additionally, a large fraction of the proteomes of representative species exhibit changes according to their life stages, a likely consequence not only of changes in mRNA and protein stability [ 31 ], but also in translation efficiency rates, selectively targeting specific mRNAs that may play a significant role during the trypanosomatid complex life cycle [ 32 ]. Hence, it is believed that control of gene expression in trypanosomatids is based on mechanisms targeting post-transcriptional events, such as trans -splicing, mRNA transport, turnover, and translation [ 9 ].…”

Catalase and Ascorbate Peroxidase in Euglenozoan Protists

“…Surprisingly, in thermostable C. thermophila and L. seymouri, elevated temperature triggered an increase in respiration, but a decrease in the activities of both CAT and APX. That transcript abundance did not follow the same pattern as activity can be explained by the key role of post-transcriptional regulation in the gene expression of euglenids and trypanosomatids [54][55][56][57][58]. Indeed, weak-to-moderate correlation has been observed between transcript abundance and protein levels in both trypanosomatids and Euglena.…”

The GWIPS‐viz Browser

“…Depending on the approach used to arrest ribosomes, the Ribo‐seq technique can capture elongating ribosomes or initiating ribosomes (see Andreev et al., ; Aramayo & Polymenis, ; Bartholomaus, Del Campo, & Ignatova, ; Baudin‐Baillieu, Hatin, Legendre, & Namy, ; Brar & Weissman, ; Calviello & Ohler, ; Gobet & Naef, ; Ingolia, ; Michel & Baranov, ; Mumtaz & Couso, ; Parsons & Myler, ; Stern‐Ginossar, ; Stern‐Ginossar & Ingolia, , for a comprehensive overview of the technique, its applications and limitations). Data tracks for both initiating and elongating ribosomes are hosted on GWIPS‐viz.…”