These molecules do not present all Dicer domains and, in some cases, they only show one Ribonuclease III domain instead of two. Additionally, by taking only the HCD of these protozoa proteins and performing a BLASTP against the Giardia assemblage A isolate WB database, we did not
find any significant homology with the described putative RNA helicases. Even when we generate a profile sequence from these five protozoan Small molecule library high throughput (the complete sequence or just the HCD sequence) and performed a more sensitive PSI-BLAST (iteration 5), the Giardia sequences presented low homology and corresponded to helicases already described in this work. We also used eight Dicer sequences from higher eukaryotes (S. pombe; M. truncatula; H. sapiens; M. musculus; X. laevis; A. thaliana; D. melanogaster and C. elegans), all of them presenting a helicase domain and almost all the others Dicer find more specific domains (a PAZ domain,
two Ribonuclease III domains and dsRNA binding motif). Considering only their HCD, we created a consensus sequence of 613 amino acids. A PSI-BLAST analysis (iteration 5) of the G. lamblia database using this consensus sequence give us 39 putative helicases already described and classified in this work. The best E-value was for the DEAD-box putative helicase GL50803_95898, with query coverage of only the 30%. To analyze the presence of patterns conserved in sets within this eight helicase domains, we performed a
pattern matching using the Pratt software [56]. We obtained a series of best sets and subsets patterns that could be divided into four groups, PTK6 two in the DEXDc domain, one in the HELICc domain and one in the region within this two. These four patterns were used again to search the Giardia database. First, we created a consensus sequence for each one of these patterns and used it to perform a PSI-BLAST analysis (iteration 5). Only with the best pattern, corresponding to the HELICc domain, our analysis gave a series of similar sequences, all of them already described as putative helicases. Again the putative DEAD-box helicase GL50803_95898 was at the top-five sequences with a 100% query coverage. The other patterns obtained provided no sequences producing significant alignments with E-value better than threshold. RNA helicases relative expression during encystation Based on in vitro experiments, the contribution of several DExD/H-box proteins in the accomplishment of crucial cellular functions has been revealed [30]. The fact that the entire life cycle of G. lamblia can be reproduced in vitro makes this species an attractive model to study cellular differentiation [57].