論文 - 詳細
| RRC ID | 65271 |
|---|---|
| 著者 | James K, Olson PD. |
| タイトル | The tapeworm interactome: inferring confidence scored protein-protein interactions from the proteome of Hymenolepis microstoma. |
| ジャーナル | BMC Genomics |
| 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. |
| 巻・号 | 21(1) |
| ページ | 346 |
| 公開日 | 2020-5-7 |
| DOI | 10.1186/s12864-020-6710-1 |
| PII | 10.1186/s12864-020-6710-1 |
| PMID | 32380953 |
| PMC | PMC7204028 |
| MeSH | Animals Databases, Genetic Eukaryota / classification Eukaryota / genetics Eukaryota / metabolism Gene Regulatory Networks Genome, Helminth / genetics Helminth Proteins / genetics Helminth Proteins / metabolism Hymenolepis / classification Hymenolepis / genetics* Hymenolepis / metabolism Probability Protein Interaction Mapping* Proteome / genetics* |
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