Genetic profiling of the isoprenoid and sterol biosynthesis pathways of Trypanosoma cruzi
- Published
- Accepted
- Subject Areas
- Bioinformatics, Evolutionary Studies, Genetics, Genomics, Parasitology
- Keywords
- trypanosoma cruzi, genetic diversity, comparative genomics, sterol biosynthesis pathway, isoprenoid biosynthesis pathway, single-nucleotide polymorphisms, re-sequencing, mevalonate pathway, erg25, sterol methyl oxidase-like
- Copyright
- © 2013 Agüero et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
- Cite this article
- 2013. Genetic profiling of the isoprenoid and sterol biosynthesis pathways of Trypanosoma cruzi. PeerJ PrePrints 1:e44v1 https://doi.org/10.7287/peerj.preprints.44v1
Abstract
Background. Sterols such as cholesterol, are important components of cellular membranes. But unlike mammalian cells, the main sterols found in the membranes of trypanosomes and fungi are ergosterol, and other 24-methyl sterols, which are required for growth and viability. In spite of this strict requirement, this group of organisms have evolved different strategies to produce and/or obtain sterols. Trypanosoma cruzi is the causative agent of Chagas Disease. In this parasite, one of the few validated targets for chemotherapeutic intervention is the sterol biosynthesis pathway. In this work we present a study of the genetic diversity observed in genes of the isoprenoid and sterol biosynthesis pathways in T. cruzi, and a comparative analysis of the diversity found in other trypanosomatids.
Methodology/Principal Findings. Using a number of bioinformatic strategies, we first completed a number of holes in the pathway by identifying the sequences of genes that were missing and/or were truncated in the draft T. cruzi genome. Based on this analysis we identified a non-orthologous homolog of the yeast ERG25 gene (sterol methyl oxidase, SMO) and propose that the orthologs of ERG25 have been lost in trypanosomes (but not in leishmanias). Next, starting from a set of 16 T. cruzi strains representative of six major evolutionary lineages, we have amplified and sequenced ~ 24Kbp from 18 genes of the pathway, and identified a total of 975 SNPs or fixed differences, of which 28% represent nonsynonymous changes. We observed different patterns of accumulation of nucleotide changes for different genes of the pathway, from genes with a density of substitutions ranging from those close to the average (~2.5/100 bp) to some showing a high number of changes (11.4/100 bp, for a putative lathosterol oxidase gene). The majority of genes are under apparent purifying selection. However, two genes (TcPMK, TcSMO-like) have a ratio of nonsynonymous to synonymous changes that is close to neutrality. None of the nonsynonymous changes identified affect a catalytic or a ligand binding site residue. However, after mapping these changes on top of available structural data, we identified a number of changes that are in the close vicinity (7 Angstrom) of key residues, and that could therefore be functionally important. A comparative analysis of the corresponding T. brucei and Leishmania genes, obtained from available complete genomes highlights a high degree of conservation of the pathway, but with differences in the genes that are under apparent purifying selection in each case.
Conclusions/Significance. We have identified a number of genes of the sterol biosynthesis pathway that were missing from the T. cruzi genome assembly. Also, we have identified unequal apparent selection acting on these genes, which may provide essential information for the future of drug development studies focused on this pathway.
Supplemental Information
Distribution of observed SNPs in the TcSMO-like genes of T. cruzi.
Based on the prediction of trans-membrane spanning domains (see TMHMM probability plot at the bottom), we created two alternative representations, following Sperling, Ternes, Zank et al (2003). The distribution of synonymous and non- synonymous SNPs is shown according to these models. The representations differ in the presence/absence of the second (non-predicted) trans-membrane domain. In these two representations the location of the 3rd histidine box always lies on the opposite side of the membrane. Both topologies may be wrong and an in-depth study (similar to the one performed by Diaz, Mansilla, Vila et al., 2002) may be required to establish the correct topology of these proteins.
Reciprocal BLASTP searches between fungal and kinetoplastid ERG25/ERG3 homologs.
The file contains a summary of BLASTP searches against fungal and kinetoplastid protein databases. BLAST searches using the yeast ERG3/ERG25 protein sequences as query, were run at the TriTrypDB BLAST server against a database of Kinetoplastid proteomes from reference and draft genomes. BLAST searches using a number of putative T. cruzi orthologs of these yeast genes were run at the SGD Fungal BLAST Server, against a database containing a selection of fungal genomes. Each BLASTP search is shown in a separate tab in the Excel workbook.
List of nucleotide changes (SNPs, fixed differences) identified for each gene analyzed.
The excel file contains one spreadsheet per gene with information on the location of each SNP relative to the start codon, the PolyPhred score for the SNP, and the character state of the SNP in each strain/lineage.
List of oligonucleotide primers and amplification products analyzed in this study.
The table lists the oligonucleotide primers used to amplify each PCR product, the corresponding product size, and the number of products per gene/locus.