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Open Access Research article

On the extent and role of the small proteome in the parasitic eukaryote Trypanosoma brucei

Megan Ericson1, Michael A Janes14, Falk Butter25, Matthias Mann2, Elisabetta Ullu3 and Christian Tschudi1*

Author Affiliations

1 Department of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, CT, USA

2 Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany

3 Department of Cell Biology and Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA

4 Current address: San Francisco General Hospital, Pulmonary & Critical Care, San Francisco, CA, USA

5 Current address: Institute of Molecular Biology gGmbH, Mainz, Germany

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BMC Biology 2014, 12:14  doi:10.1186/1741-7007-12-14

Published: 19 February 2014

Abstract

Background

Although technical advances in genomics and proteomics research have yielded a better understanding of the coding capacity of a genome, one major challenge remaining is the identification of all expressed proteins, especially those less than 100 amino acids in length. Such information can be particularly relevant to human pathogens, such as Trypanosoma brucei, the causative agent of African trypanosomiasis, since it will provide further insight into the parasite biology and life cycle.

Results

Starting with 993‚ÄČT. brucei transcripts, previously shown by RNA-Sequencing not to coincide with annotated coding sequences (CDS), homology searches revealed that 173 predicted short open reading frames in these transcripts are conserved across kinetoplastids with 13 also conserved in representative eukaryotes. Mining mass spectrometry data sets revealed 42 transcripts encoding at least one matching peptide. RNAi-induced down-regulation of these 42 transcripts revealed seven to be essential in insect-form trypanosomes with two also required for the bloodstream life cycle stage. To validate the specificity of the RNAi results, each lethal phenotype was rescued by co-expressing an RNAi-resistant construct of each corresponding CDS. These previously non-annotated essential small proteins localized to a variety of cell compartments, including the cell surface, mitochondria, nucleus and cytoplasm, inferring the diverse biological roles they are likely to play in T. brucei. We also provide evidence that one of these small proteins is required for replicating the kinetoplast (mitochondrial) DNA.

Conclusions

Our studies highlight the presence and significance of small proteins in a protist and expose potential new targets to block the survival of trypanosomes in the insect vector and/or the mammalian host.

Keywords:
Genomics; Proteomics; Mass spectrometry data; Non-coding RNA; Mitochondria