The tapeworm interactome: inferring confidence scored protein-protein interactions from the proteome of Hymenolepis microstoma
Abstract 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...
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| Format: | Article |
| Language: | English |
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BMC
2020-05-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-020-6710-1 |
| _version_ | 1818386365839048704 |
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| author | Katherine James Peter D. Olson |
| author_facet | Katherine James Peter D. Olson |
| author_sort | Katherine James |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-12-14T03:52:54Z |
| format | Article |
| id | doaj.art-639489fa39f344a1ae6c3836d1d57abd |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-14T03:52:54Z |
| publishDate | 2020-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-639489fa39f344a1ae6c3836d1d57abd2022-12-21T23:18:09ZengBMCBMC Genomics1471-21642020-05-0121112210.1186/s12864-020-6710-1The tapeworm interactome: inferring confidence scored protein-protein interactions from the proteome of Hymenolepis microstomaKatherine James0Peter D. Olson1Department of Applied Sciences, Northumbria UniversityDepartment of Life Sciences, The Natural History MuseumAbstract 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.http://link.springer.com/article/10.1186/s12864-020-6710-1Probabilistic networkData integrationInterologsTapewormsHymenolepis microstoma |
| spellingShingle | Katherine James Peter D. Olson The tapeworm interactome: inferring confidence scored protein-protein interactions from the proteome of Hymenolepis microstoma BMC Genomics Probabilistic network Data integration Interologs Tapeworms Hymenolepis microstoma |
| title | The tapeworm interactome: inferring confidence scored protein-protein interactions from the proteome of Hymenolepis microstoma |
| title_full | The tapeworm interactome: inferring confidence scored protein-protein interactions from the proteome of Hymenolepis microstoma |
| title_fullStr | The tapeworm interactome: inferring confidence scored protein-protein interactions from the proteome of Hymenolepis microstoma |
| title_full_unstemmed | The tapeworm interactome: inferring confidence scored protein-protein interactions from the proteome of Hymenolepis microstoma |
| title_short | The tapeworm interactome: inferring confidence scored protein-protein interactions from the proteome of Hymenolepis microstoma |
| title_sort | tapeworm interactome inferring confidence scored protein protein interactions from the proteome of hymenolepis microstoma |
| topic | Probabilistic network Data integration Interologs Tapeworms Hymenolepis microstoma |
| url | http://link.springer.com/article/10.1186/s12864-020-6710-1 |
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