Comparative transcriptomics reveals striking similarities between the bovine and feline isolates of Tritrichomonas foetus: consequences for in silico drug-target identification.
| Title: | Comparative transcriptomics reveals striking similarities between the bovine and feline isolates of Tritrichomonas foetus: consequences for in silico drug-target identification. |
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| Authors: | Morin-Adeline V; Lomas R; O'Meally D; Stack C; Conesa A; Faculty of Veterinary Science, University of Sydney, New South Wales 2006, Australia. aconesa@cipf.es.; Šlapeta J |
| Source: | BMC genomics [BMC Genomics] 2014 Nov 05; Vol. 15, pp. 955. Date of Electronic Publication: 2014 Nov 05. |
| Publication Type: | Journal Article; Research Support, Non-U.S. Gov't |
| Language: | English |
| Journal Info: | Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164 (Electronic) Linking ISSN: 14712164 NLM ISO Abbreviation: BMC Genomics Subsets: MEDLINE |
| Imprint Name(s): | Original Publication: London : BioMed Central, [2000- |
| MeSH Terms: | Gene Expression Profiling* ; Transcriptome*; Tritrichomonas foetus/*genetics; Catalytic Domain/genetics ; Peptide Hydrolases/chemistry ; Peptide Hydrolases/genetics ; Protease Inhibitors/pharmacology ; Protozoan Infections, Animal/drug therapy ; Protozoan Infections, Animal/parasitology ; Tritrichomonas foetus/drug effects ; Animals ; Cats ; Cattle ; Computational Biology ; Computer Simulation ; Drug Discovery ; Genotype ; Molecular Sequence Annotation ; Nucleotide Motifs ; Untranslated Regions |
| Abstract: | Background: Few, if any, protozoan parasites are reported to exhibit extreme organ tropism like the flagellate Tritrichomonas foetus. In cattle, T. foetus infects the reproductive system causing abortion, whereas the infection in cats results in chronic large bowel diarrhoea. In the absence of a T. foetus genome, we utilized a de novo approach to assemble the transcriptome of the bovine and feline genotype to identify host-specific adaptations and virulence factors specific to each genotype. Furthermore, a subset of orthologs was used to characterize putative druggable targets and expose complications of in silico drug target mining in species with indefinite host-ranges.; Results: Illumina RNA-seq reads were assembled into two representative bovine and feline transcriptomes containing 42,363 and 36,559 contigs, respectively. Coding and non-coding regions of the genome libraries revealed striking similarities, with 24,620 shared homolog pairs reduced down to 7,547 coding orthologs between the two genotypes. The transcriptomes were near identical in functional category distribution; with no indication of selective pressure acting on orthologs despite differences in parasite origins/host. Orthologs formed a large proportion of highly expressed transcripts in both genotypes (bovine genotype: 76%, feline genotype: 56%). Mining the libraries for protease virulence factors revealed the cysteine proteases (CP) to be the most common. In total, 483 and 445 bovine and feline T. foetus transcripts were identified as putative proteases based on MEROPS database, with 9 hits to putative protease inhibitors. In bovine T. foetus, CP8 is the preferentially transcribed CP while in the feline genotype, transcription of CP7 showed higher abundance. In silico druggability analysis of the two genotypes revealed that when host sequences are taken into account, drug targets are genotype-specific.; Conclusion: Gene discovery analysis based on RNA-seq data analysis revealed prominent similarities between the bovine and feline T. foetus, suggesting recent adaptation to their respective host/niche. T. foetus represents a unique case of a mammalian protozoan expanding its parasitic grasp across distantly related host lineages. Consequences of the host-range for in silico drug targeting are exposed here, demonstrating that targets of the parasite in one host are not necessarily ideal for the same parasite in another host. |
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| Substance Nomenclature: | 0 (Protease Inhibitors); 0 (Untranslated Regions); EC 3.4.- (Peptide Hydrolases) |
| Entry Date(s): | Date Created: 20141107 Date Completed: 20150708 Latest Revision: 20240322 |
| Update Code: | 20260130 |
| PubMed Central ID: | PMC4247702 |
| DOI: | 10.1186/1471-2164-15-955 |
| PMID: | 25374366 |
| Database: | MEDLINE |
Journal Article; Research Support, Non-U.S. Gov't