IPRStats: visualization of the functional potential of an InterProScan run

Kelly, Ryan J; Vincent, David; Friedberg, Iddo

doi:10.1186/1471-2105-11-s12-s13

Cited by 12 publications

(7 citation statements)

References 15 publications

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“…Interpro consists of a collection of protein family and domain signatures and can be used for the automatic annotation of proteins [ 18 ]. The Interproscan software tool allows the scanning of protein sequences against the Interpro database using a range of profile-based hidden Markov models (pHMM) and positional specific score matrix protocols and in this way overcomes the problems inherent in single database searches [ 19 ]. Of the 961 ESTs with significant BLAST hits, Interpro was able to map 849, leaving 112 with no further protein domain mapping.…”

Section: Resultsmentioning

confidence: 99%

Generation, analysis and functional annotation of expressed sequence tags from the ectoparasitic mite Psoroptes ovis

et al. 2011

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BackgroundSheep scab is caused by Psoroptes ovis and is arguably the most important ectoparasitic disease affecting sheep in the UK. The disease is highly contagious and causes and considerable pruritis and irritation and is therefore a major welfare concern. Current methods of treatment are unsustainable and in order to elucidate novel methods of disease control a more comprehensive understanding of the parasite is required. To date, no full genomic DNA sequence or large scale transcript datasets are available and prior to this study only 484 P. ovis expressed sequence tags (ESTs) were accessible in public databases.ResultsIn order to further expand upon the transcriptomic coverage of P. ovis thus facilitating novel insights into the mite biology we undertook a larger scale EST approach, incorporating newly generated and previously described P. ovis transcript data and representing the largest collection of P. ovis ESTs to date. We sequenced 1,574 ESTs and assembled these along with 484 previously generated P. ovis ESTs, which resulted in the identification of 1,545 unique P. ovis sequences. BLASTX searches identified 961 ESTs with significant hits (E-value < 1E-04) and 584 novel P. ovis ESTs. Gene Ontology (GO) analysis allowed the functional annotation of 880 ESTs and included predictions of signal peptide and transmembrane domains; allowing the identification of potential P. ovis excreted/secreted factors, and mapping of metabolic pathways.ConclusionsThis dataset currently represents the largest collection of P. ovis ESTs, all of which are publicly available in the GenBank EST database (dbEST) (accession numbers FR748230 - FR749648). Functional analysis of this dataset identified important homologues, including house dust mite allergens and tick salivary factors. These findings offer new insights into the underlying biology of P. ovis, facilitating further investigations into mite biology and the identification of novel methods of intervention.

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Section: Resultsmentioning

confidence: 99%

Generation, analysis and functional annotation of expressed sequence tags from the ectoparasitic mite Psoroptes ovis

et al. 2011

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“…Enriched GO terms among DE gene products were established by Fisher’s exact test at a false discovery rate (FDR) P -value ≤ 0.05 [ 38 ]. Protein domains/signatures associated with putative products of the DE genes were determined through InterProScan analysis [ 41 ]. The DE genes encoding proteins with predicted cell-surface functions were retrieved from previously published data [ 42 ] and validated using PredGIP [ 43 ], FragAnchor [ 44 ] and BigPI [ 45 ] softwares for GPI-anchor motifs prediction, and TMHMM [ 46 ] software for trans -membrane helices prediction.…”

Section: Methodsmentioning

confidence: 99%

Expression profiling of Trypanosoma congolense genes during development in the tsetse fly vector Glossina morsitans morsitans

et al. 2018

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BackgroundThe tsetse transmitted parasitic flagellate Trypanosoma congolense causes animal African trypanosomosis (AAT) across sub-Saharan Africa. AAT negatively impacts agricultural, economic, nutritional and subsequently, health status of the affected populace. The molecular mechanisms that underlie T. congolense’s developmental program within tsetse are largely unknown due to considerable challenges with obtaining sufficient parasite cells to perform molecular studies.MethodsIn this study, we used RNA-seq to profile T. congolense gene expression during development in two distinct tsetse tissues, the cardia and proboscis. Indirect immunofluorescent antibody test (IFA) and confocal laser scanning microscope was used to localize the expression of a putative protein encoded by the hypothetical protein (TcIL3000_0_02370).ResultsConsistent with current knowledge, genes coding several variant surface glycoproteins (including metacyclic specific VSGs), and the surface coat protein, congolense epimastigote specific protein, were upregulated in parasites in the proboscis (PB-parasites). Additionally, our results indicate that parasites in tsetse’s cardia (C-parasites) and PB employ oxidative phosphorylation and amino acid metabolism for energy. Several genes upregulated in C-parasites encoded receptor-type adenylate cyclases, surface carboxylate transporter family proteins (or PADs), transport proteins, RNA-binding proteins and procyclin isoforms. Gene ontology analysis of products of genes upregulated in C-parasites showed enrichment of terms broadly associated with nucleotides, microtubules, cell membrane and its components, cell signaling, quorum sensing and several transport activities, suggesting that the parasites colonizing the cardia may monitor their environment and regulate their density and movement in this tissue. Additionally, cell surface protein (CSP) encoding genes associated with the Fam50 ‘GARP’, ‘iii’ and ‘i’ subfamilies were also significantly upregulated in C-parasites, suggesting that they are important for the long non-dividing trypomastigotes to colonize tsetse’s cardia. The putative products of genes that were upregulated in PB-parasites were linked to nucleosomes, cytoplasm and membrane-bound organelles, which suggest that parasites in this niche undergo cell division in line with prior findings. Most of the CSPs upregulated in PB-parasites were hypothetical, thus requiring further functional characterization. Expression of one such hypothetical protein (TcIL3000_0_02370) was analyzed using immunofluorescence and confocal laser scanning microscopy, which together revealed preferential expression of this protein on the entire surface coat of T. congolense parasite stages that colonize G. m. morsitans’ proboscis.ConclusionCollectively, our results provide insight into T. congolense gene expression profiles in distinct niches within the tsetse vector. Our results show that the hypothetical protein TcIL3000_0_02370, is expressed on the entire surface of the trypanosomes inhabiting tsetse’s probosci...

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“…Functional annotation of RNA derived contigs was carried out using a set of complementary tools: ESTscan [ 16 ], Blast2Go [ 17 ], InterProScan [ 18 ] and AnEnPi [ 19 ]. In the first place, to identify T .…”

Section: Methodsmentioning

confidence: 99%

Transcriptome analysis of the bloodstream stage from the parasite Trypanosoma vivax

et al. 2013

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BackgroundTrypanosoma vivax is the earliest branching African trypanosome. This crucial phylogenetic position makes T. vivax a fascinating model to tackle fundamental questions concerning the origin and evolution of several features that characterize African trypanosomes, such as the Variant Surface Glycoproteins (VSGs) upon which antibody clearing and antigenic variation are based. Other features like gene content and trans-splicing patterns are worth analyzing in this species for comparative purposes.ResultsWe present a RNA-seq analysis of the bloodstream stage of T. vivax from data obtained using two complementary sequencing technologies (454 Titanium and Illumina).Assembly of 454 reads yielded 13385 contigs corresponding to proteins coding genes (7800 of which were identified). These sequences, their annotation and other features are available through an online database presented herein. Among these sequences, about 1000 were found to be species specific and 50 exclusive of the T. vivax strain analyzed here. Expression patterns and levels were determined for VSGs and the remaining genes. Interestingly, VSG expression level, although being high, is considerably lower than in Trypanosoma brucei. Indeed, the comparison of surface protein composition between both African trypanosomes (as inferred from RNA-seq data), shows that they are substantially different, being VSG absolutely predominant in T. brucei, while in T. vivax it represents only about 55%. This raises the question concerning the protective role of VSGs in T. vivax, hence their ancestral role in immune evasion.It was also found that around 600 genes have their unique (or main) trans-splice site very close (sometimes immediately before) the start codon. Gene Ontology analysis shows that this group is enriched in proteins related to the translation machinery (e.g. ribosomal proteins, elongation factors).ConclusionsThis is the first RNA-seq data study in trypanosomes outside the model species T. brucei, hence it provides the possibility to conduct comparisons that allow drawing evolutionary and functional inferences. This analysis also provides several insights on the expression patterns and levels of protein coding sequences (such as VSG gene expression), trans-splicing, codon patterns and regulatory mechanisms. An online T. vivax RNA-seq database described herein could be a useful tool for parasitologists working with trypanosomes.

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IPRStats: visualization of the functional potential of an InterProScan run

Cited by 12 publications

References 15 publications

Generation, analysis and functional annotation of expressed sequence tags from the ectoparasitic mite Psoroptes ovis

Generation, analysis and functional annotation of expressed sequence tags from the ectoparasitic mite Psoroptes ovis

Expression profiling of Trypanosoma congolense genes during development in the tsetse fly vector Glossina morsitans morsitans

Transcriptome analysis of the bloodstream stage from the parasite Trypanosoma vivax

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