, 2011), pre-mRNA processing (Silva
et al., 2011), RNA editing (Hernandez et al., 2010; Li et al., 2011), regulation of gene expression (Holetz et al., 2007, 2010; Kramer et al., 2010), rRNA processing (Cristodero & Clayton, 2007), translation regulation (Dhalia et al., 2006), parasite stage differentiation (Diaz Anel et al., 2000; Kramer et al., 2010), kDNA replication (Klingbeil & Shapiro, 2009; Liu et al., 2009a, b, 2010), gDNA replication (Dang & Li, 2011), and DNA maintenance (Bochman et al., 2010). In addition, one protein that is involved in the selective Y-27632 order translation of developmentally regulated mRNAs is the DEAD-box RNA helicase DHH1 (Kramer, 2012). In this work, a systematic analysis of trypanosomatids’ helicases was performed, including the identification of those that are underrepresented in the human genome and could be used
as future therapeutic targets. All available amino acid sequences corresponding to helicases were recovered from the TriTryp database version 3.3 (http://tritrypdb.org/tritrypdb; Aslett et al., 2010) using different approaches including the TriTrypDB protein function predictions based on the InterPro protein sequence analysis and classification database (http://www.ebi.ac.uk/interpro/) or by similarity searching using helicase sequences from other organisms. The species http://www.selleckchem.com/products/abt-199.html and accession numbers of the sequences used are listed in Supporting information, Data S1. Only sequences isothipendyl corresponding to a single allelic copy per species were chosen to be included in the present analysis. The sequences were checked for similarities to helicases with the local and online version of blastp at the NCBI (http://www.ncbi.nlm.nih.gov/BLAST/)
under default parameters using the nonredundant protein sequence database. Further assemblies and analysis of the amino acid sequence data were carried out using the software package Vector nti v. 10.3.0 (Invitrogen, CA). The helicases classification system adopted was based on the previously described superfamilies SF1 and SF2 (Fairman-Williams et al., 2010). Phylogenetic analyses were performed using Molecular Evolutionary Genetics Analysis (mega) v5.05 (Kumar et al., 2008). Briefly, the evolutionary history was inferred with the maximum likelihood method with a JTT matrix-based model (Jones et al., 1992). The bootstrap consensus tree inferred from 500 replicates was taken to represent the evolutionary history of the sequences analyzed (Tamura et al., 2011). Branches corresponding to partitions reproduced in fewer than 50% of bootstrap replicates were collapsed. Initial trees for the heuristic search were obtained automatically as follows. When the number of common sites was lower than 100 or less than one-fourth of the total number of sites, the maximum parsimony method was used; otherwise, the BIONJ method with the MCL distance matrix was used.