title: On the extent and role of the small proteome in the parasitic eukaryote Trypanosoma brucei.
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 T. 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.
authors.forename: Megan
authors.initials: M
authors.lastname: Ericson
authors.forename: Michael A
authors.initials: MA
authors.lastname: Janes
authors.forename: Falk
authors.initials: F
authors.lastname: Butter
authors.forename: Matthias
authors.initials: M
authors.lastname: Mann
authors.forename: Elisabetta
authors.initials: E
authors.lastname: Ullu
authors.affiliation: Department of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, CT, USA. christian.tschudi@yale.edu.
authors.forename: Christian
authors.initials: C
authors.lastname: Tschudi
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D002453:Cell Cycle; D017124:Conserved Sequence; D019143:Evolution, Molecular; D006801:Humans; D008018:Life Cycle Stages; D013058:Mass Spectrometry; D008565:Membrane Proteins / Q000378:metabolism; D024101:Mitochondrial Proteins / Q000378:metabolism; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D010271:Parasites / Q000254:growth & development / Q000378:metabolism*; D017434:Protein Structure, Tertiary; D020543:Proteome / Q000378:metabolism*; D040901:Proteomics; D015800:Protozoan Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D034622:RNA Interference; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D014346:Trypanosoma brucei brucei / Q000254:growth & development / Q000378:metabolism*
chemical_list: D008565:Membrane Proteins; D024101:Mitochondrial Proteins; D020543:Proteome; D015800:Protozoan Proteins; D012333:RNA, Messenger