Shared protein complex subunits contribute to explaining disrupted co-occurrence.
The gene composition of present-day genomes has been shaped by a complicated evolutionary history, resulting in diverse distributions of genes across genomes. The pattern of presence and absence of a gene in different genomes is called its phylogenetic profile. It has been shown that proteins whose...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2013-01-01
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| Series: | PLoS Computational Biology |
| Online Access: | http://europepmc.org/articles/PMC3715415?pdf=render |
| _version_ | 1819153392992256000 |
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| author | Adrian Schneider Michael F Seidl Berend Snel |
| author_facet | Adrian Schneider Michael F Seidl Berend Snel |
| author_sort | Adrian Schneider |
| collection | DOAJ |
| description | The gene composition of present-day genomes has been shaped by a complicated evolutionary history, resulting in diverse distributions of genes across genomes. The pattern of presence and absence of a gene in different genomes is called its phylogenetic profile. It has been shown that proteins whose encoding genes have highly similar profiles tend to be functionally related: As these genes were gained and lost together, their encoded proteins can probably only perform their full function if both are present. However, a large proportion of genes encoding interacting proteins do not have matching profiles. In this study, we analysed one possible reason for this, namely that phylogenetic profiles can be affected by multi-functional proteins such as shared subunits of two or more protein complexes. We found that by considering triplets of proteins, of which one protein is multi-functional, a large fraction of disturbed co-occurrence patterns can be explained. |
| first_indexed | 2024-12-22T15:04:28Z |
| format | Article |
| id | doaj.art-08125a6195a84cd6a6edce282a2d8278 |
| institution | Directory Open Access Journal |
| issn | 1553-734X 1553-7358 |
| language | English |
| last_indexed | 2024-12-22T15:04:28Z |
| publishDate | 2013-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj.art-08125a6195a84cd6a6edce282a2d82782022-12-21T18:22:01ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582013-01-0197e100312410.1371/journal.pcbi.1003124Shared protein complex subunits contribute to explaining disrupted co-occurrence.Adrian SchneiderMichael F SeidlBerend SnelThe gene composition of present-day genomes has been shaped by a complicated evolutionary history, resulting in diverse distributions of genes across genomes. The pattern of presence and absence of a gene in different genomes is called its phylogenetic profile. It has been shown that proteins whose encoding genes have highly similar profiles tend to be functionally related: As these genes were gained and lost together, their encoded proteins can probably only perform their full function if both are present. However, a large proportion of genes encoding interacting proteins do not have matching profiles. In this study, we analysed one possible reason for this, namely that phylogenetic profiles can be affected by multi-functional proteins such as shared subunits of two or more protein complexes. We found that by considering triplets of proteins, of which one protein is multi-functional, a large fraction of disturbed co-occurrence patterns can be explained.http://europepmc.org/articles/PMC3715415?pdf=render |
| spellingShingle | Adrian Schneider Michael F Seidl Berend Snel Shared protein complex subunits contribute to explaining disrupted co-occurrence. PLoS Computational Biology |
| title | Shared protein complex subunits contribute to explaining disrupted co-occurrence. |
| title_full | Shared protein complex subunits contribute to explaining disrupted co-occurrence. |
| title_fullStr | Shared protein complex subunits contribute to explaining disrupted co-occurrence. |
| title_full_unstemmed | Shared protein complex subunits contribute to explaining disrupted co-occurrence. |
| title_short | Shared protein complex subunits contribute to explaining disrupted co-occurrence. |
| title_sort | shared protein complex subunits contribute to explaining disrupted co occurrence |
| url | http://europepmc.org/articles/PMC3715415?pdf=render |
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