title: Eukaryotic protein kinases (ePKs) of the helminth parasite Schistosoma mansoni.
abstract: BACKGROUND
  Schistosomiasis remains an important parasitic disease and a major economic problem in many countries. The Schistosoma mansoni genome and predicted proteome sequences were recently published providing the opportunity to identify new drug candidates. Eukaryotic protein kinases (ePKs) play a central role in mediating signal transduction through complex networks and are considered druggable targets from the medical and chemical viewpoints. Our work aimed at analyzing the S. mansoni predicted proteome in order to identify and classify all ePKs of this parasite through combined computational approaches. Functional annotation was performed mainly to yield insights into the parasite signaling processes relevant to its complex lifestyle and to select some ePKs as potential drug targets.
  
  
  RESULTS
  We have identified 252 ePKs, which corresponds to 1.9% of the S. mansoni predicted proteome, through sequence similarity searches using HMMs (Hidden Markov Models). Amino acid sequences corresponding to the conserved catalytic domain of ePKs were aligned by MAFFT and further used in distance-based phylogenetic analysis as implemented in PHYLIP. Our analysis also included the ePK homologs from six other eukaryotes. The results show that S. mansoni has proteins in all ePK groups. Most of them are clearly clustered with known ePKs in other eukaryotes according to the phylogenetic analysis. None of the ePKs are exclusively found in S. mansoni or belong to an expanded family in this parasite. Only 16 S. mansoni ePKs were experimentally studied, 12 proteins are predicted to be catalytically inactive and approximately 2% of the parasite ePKs remain unclassified. Some proteins were mentioned as good target for drug development since they have a predicted essential function for the parasite.
  
  
  CONCLUSIONS
  Our approach has improved the functional annotation of 40% of S. mansoni ePKs through combined similarity and phylogenetic-based approaches. As we continue this work, we will highlight the biochemical and physiological adaptations of S. mansoni in response to diverse environments during the parasite development, vector interaction, and host infection.
authors.affiliation: Genomics and Computational Biology Group, Instituto Nacional de Ciência e Tecnologia em Doenças Tropicais, Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz - FIOCRUZ, Belo Horizonte, MG- 30190-002, Brazil.
authors.forename: Luiza F
authors.initials: LF
authors.lastname: Andrade
authors.forename: Laila A
authors.initials: LA
authors.lastname: Nahum
authors.forename: Lívia G A
authors.initials: LG
authors.lastname: Avelar
authors.forename: Larissa L
authors.initials: LL
authors.lastname: Silva
authors.forename: Adhemar
authors.initials: A
authors.lastname: Zerlotini
authors.forename: Jerônimo C
authors.initials: JC
authors.lastname: Ruiz
authors.forename: Guilherme
authors.initials: G
authors.lastname: Oliveira
mesh_terms: D000818:Animals; D020134:Catalytic Domain; D008390:Markov Chains; D010802:Phylogeny; D011494:Protein Kinases / Q000737:chemistry / Q000145:classification* / Q000378:metabolism*; D020543:Proteome / Q000737:chemistry / Q000145:classification / Q000378:metabolism; D040901:Proteomics; D012550:Schistosoma mansoni / Q000166:cytology / Q000201:enzymology* / Q000469:parasitology*; D015398:Signal Transduction
chemical_list: D020543:Proteome; D011494:Protein Kinases