The tapeworm interactome: inferring confidence scored protein-protein interactions from the proteome of Hymenolepis microstoma.
In: BMC genomics, Jg. 21 (2020-05-07), Heft 1, S. 346
Online
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Zugriff:
Background: Reference genome and transcriptome assemblies of helminths have reached a level of completion whereby secondary analyses that rely on accurate gene estimation or syntenic relationships can be now conducted with a high level of confidence. Recent public release of the v.3 assembly of the mouse bile-duct tapeworm, Hymenolepis microstoma, provides chromosome-level characterisation of the genome and a stabilised set of protein coding gene models underpinned by bioinformatic and empirical data. However, interactome data have not been produced. Conserved protein-protein interactions in other organisms, termed interologs, can be used to transfer interactions between species, allowing systems-level analysis in non-model organisms.
Results: Here, we describe a probabilistic, integrated network of interologs for the H. microstoma proteome, based on conserved protein interactions found in eukaryote model species. Almost a third of the 10,139 gene models in the v.3 assembly could be assigned interaction data and assessment of the resulting network indicates that topologically-important proteins are related to essential cellular pathways, and that the network clusters into biologically meaningful components. Moreover, network parameters are similar to those of single-species interaction networks that we constructed in the same way for S. cerevisiae, C. elegans and H. sapiens, demonstrating that information-rich, system-level analyses can be conducted even on species separated by a large phylogenetic distance from the major model organisms from which most protein interaction evidence is based. Using the interolog network, we then focused on sub-networks of interactions assigned to discrete suites of genes of interest, including signalling components and transcription factors, germline multipotency genes, and genes differentially-expressed between larval and adult worms. Results show not only an expected bias toward highly-conserved proteins, such as components of intracellular signal transduction, but in some cases predicted interactions with transcription factors that aid in identifying their target genes.
Conclusions: With key helminth genomes now complete, systems-level analyses can provide an important predictive framework to guide basic and applied research on helminths and will become increasingly informative as new protein-protein interaction data accumulate.
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The tapeworm interactome: inferring confidence scored protein-protein interactions from the proteome of Hymenolepis microstoma.
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Autor/in / Beteiligte Person: | James, K ; Olson, PD |
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Zeitschrift: | BMC genomics, Jg. 21 (2020-05-07), Heft 1, S. 346 |
Veröffentlichung: | London : BioMed Central, [2000-, 2020 |
Medientyp: | academicJournal |
ISSN: | 1471-2164 (electronic) |
DOI: | 10.1186/s12864-020-6710-1 |
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