Spatiotemporal variation of mammalian protein complex stoichiometries
Background Recent large-scale studies revealed cell-type specific proteomes. However, protein complexes, the basic functional modules of a cell, have been so far mostly considered as static entities with well-defined structures. The co-expression of their members has not been systematically charted...
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Published in | Genome Biology Vol. 17; no. 1; p. 47 |
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Main Authors | , , , , , , , , |
Format | Journal Article |
Language | English |
Published |
London
BioMed Central
14.03.2016
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Subjects | |
Online Access | Get full text |
ISSN | 1474-760X 1474-7596 1474-760X |
DOI | 10.1186/s13059-016-0912-5 |
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Abstract | Background
Recent large-scale studies revealed cell-type specific proteomes. However, protein complexes, the basic functional modules of a cell, have been so far mostly considered as static entities with well-defined structures. The co-expression of their members has not been systematically charted at the protein level.
Results
We used measurements of protein abundance across 11 cell types and five temporal states to analyze the co-expression and the compositional variations of 182 well-characterized protein complexes. We show that although the abundance of protein complex members is generally co-regulated, a considerable fraction of all investigated protein complexes is subject to stoichiometric changes. Compositional variation is most frequently seen in complexes involved in chromatin regulation and cellular transport, and often involves paralog switching as a mechanism for the regulation of complex stoichiometry. We demonstrate that compositional signatures of variable protein complexes have discriminative power beyond individual cell states and can distinguish cancer cells from healthy ones.
Conclusions
Our work demonstrates that many protein complexes contain variable members that cause distinct stoichometries and functionally fine-tune complexes spatiotemporally. Only a fraction of these compositional variations is mediated by changes in transcription and other mechanisms regulating protein abundance contribute to determine protein complex stoichiometries. Our work highlights the superior power of proteome profiles to study protein complexes and their variants across cell states. |
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AbstractList | Recent large-scale studies revealed cell-type specific proteomes. However, protein complexes, the basic functional modules of a cell, have been so far mostly considered as static entities with well-defined structures. The co-expression of their members has not been systematically charted at the protein level.BACKGROUNDRecent large-scale studies revealed cell-type specific proteomes. However, protein complexes, the basic functional modules of a cell, have been so far mostly considered as static entities with well-defined structures. The co-expression of their members has not been systematically charted at the protein level.We used measurements of protein abundance across 11 cell types and five temporal states to analyze the co-expression and the compositional variations of 182 well-characterized protein complexes. We show that although the abundance of protein complex members is generally co-regulated, a considerable fraction of all investigated protein complexes is subject to stoichiometric changes. Compositional variation is most frequently seen in complexes involved in chromatin regulation and cellular transport, and often involves paralog switching as a mechanism for the regulation of complex stoichiometry. We demonstrate that compositional signatures of variable protein complexes have discriminative power beyond individual cell states and can distinguish cancer cells from healthy ones.RESULTSWe used measurements of protein abundance across 11 cell types and five temporal states to analyze the co-expression and the compositional variations of 182 well-characterized protein complexes. We show that although the abundance of protein complex members is generally co-regulated, a considerable fraction of all investigated protein complexes is subject to stoichiometric changes. Compositional variation is most frequently seen in complexes involved in chromatin regulation and cellular transport, and often involves paralog switching as a mechanism for the regulation of complex stoichiometry. We demonstrate that compositional signatures of variable protein complexes have discriminative power beyond individual cell states and can distinguish cancer cells from healthy ones.Our work demonstrates that many protein complexes contain variable members that cause distinct stoichometries and functionally fine-tune complexes spatiotemporally. Only a fraction of these compositional variations is mediated by changes in transcription and other mechanisms regulating protein abundance contribute to determine protein complex stoichiometries. Our work highlights the superior power of proteome profiles to study protein complexes and their variants across cell states.CONCLUSIONSOur work demonstrates that many protein complexes contain variable members that cause distinct stoichometries and functionally fine-tune complexes spatiotemporally. Only a fraction of these compositional variations is mediated by changes in transcription and other mechanisms regulating protein abundance contribute to determine protein complex stoichiometries. Our work highlights the superior power of proteome profiles to study protein complexes and their variants across cell states. Recent large-scale studies revealed cell-type specific proteomes. However, protein complexes, the basic functional modules of a cell, have been so far mostly considered as static entities with well-defined structures. The co-expression of their members has not been systematically charted at the protein level. We used measurements of protein abundance across 11 cell types and five temporal states to analyze the co-expression and the compositional variations of 182 well-characterized protein complexes. We show that although the abundance of protein complex members is generally co-regulated, a considerable fraction of all investigated protein complexes is subject to stoichiometric changes. Compositional variation is most frequently seen in complexes involved in chromatin regulation and cellular transport, and often involves paralog switching as a mechanism for the regulation of complex stoichiometry. We demonstrate that compositional signatures of variable protein complexes have discriminative power beyond individual cell states and can distinguish cancer cells from healthy ones. Our work demonstrates that many protein complexes contain variable members that cause distinct stoichometries and functionally fine-tune complexes spatiotemporally. Only a fraction of these compositional variations is mediated by changes in transcription and other mechanisms regulating protein abundance contribute to determine protein complex stoichiometries. Our work highlights the superior power of proteome profiles to study protein complexes and their variants across cell states. BACKGROUND: Recent large-scale studies revealed cell-type specific proteomes. However, protein complexes, the basic functional modules of a cell, have been so far mostly considered as static entities with well-defined structures. The co-expression of their members has not been systematically charted at the protein level. RESULTS: We used measurements of protein abundance across 11 cell types and five temporal states to analyze the co-expression and the compositional variations of 182 well-characterized protein complexes. We show that although the abundance of protein complex members is generally co-regulated, a considerable fraction of all investigated protein complexes is subject to stoichiometric changes. Compositional variation is most frequently seen in complexes involved in chromatin regulation and cellular transport, and often involves paralog switching as a mechanism for the regulation of complex stoichiometry. We demonstrate that compositional signatures of variable protein complexes have discriminative power beyond individual cell states and can distinguish cancer cells from healthy ones. CONCLUSIONS: Our work demonstrates that many protein complexes contain variable members that cause distinct stoichometries and functionally fine-tune complexes spatiotemporally. Only a fraction of these compositional variations is mediated by changes in transcription and other mechanisms regulating protein abundance contribute to determine protein complex stoichiometries. Our work highlights the superior power of proteome profiles to study protein complexes and their variants across cell states. Background Recent large-scale studies revealed cell-type specific proteomes. However, protein complexes, the basic functional modules of a cell, have been so far mostly considered as static entities with well-defined structures. The co-expression of their members has not been systematically charted at the protein level. Results We used measurements of protein abundance across 11 cell types and five temporal states to analyze the co-expression and the compositional variations of 182 well-characterized protein complexes. We show that although the abundance of protein complex members is generally co-regulated, a considerable fraction of all investigated protein complexes is subject to stoichiometric changes. Compositional variation is most frequently seen in complexes involved in chromatin regulation and cellular transport, and often involves paralog switching as a mechanism for the regulation of complex stoichiometry. We demonstrate that compositional signatures of variable protein complexes have discriminative power beyond individual cell states and can distinguish cancer cells from healthy ones. Conclusions Our work demonstrates that many protein complexes contain variable members that cause distinct stoichometries and functionally fine-tune complexes spatiotemporally. Only a fraction of these compositional variations is mediated by changes in transcription and other mechanisms regulating protein abundance contribute to determine protein complex stoichiometries. Our work highlights the superior power of proteome profiles to study protein complexes and their variants across cell states. |
ArticleNumber | 47 |
Author | Ori, Alessandro Buczak, Katarzyna Kastritis, Panagiotis Bork, Peer Parca, Luca Andrés-Pons, Amparo Iskar, Murat Singer, Stephan Beck, Martin |
Author_xml | – sequence: 1 givenname: Alessandro surname: Ori fullname: Ori, Alessandro organization: European Molecular Biology Laboratory, Structural and Computational Biology Unit, Present address: Leibniz Institute on Aging – Fritz Lipmann Institute (FLI) – sequence: 2 givenname: Murat surname: Iskar fullname: Iskar, Murat organization: European Molecular Biology Laboratory, Structural and Computational Biology Unit, Present address: Division of Molecular Genetics, German Cancer Research Center (DKFZ) – sequence: 3 givenname: Katarzyna surname: Buczak fullname: Buczak, Katarzyna organization: European Molecular Biology Laboratory, Structural and Computational Biology Unit – sequence: 4 givenname: Panagiotis surname: Kastritis fullname: Kastritis, Panagiotis organization: European Molecular Biology Laboratory, Structural and Computational Biology Unit – sequence: 5 givenname: Luca surname: Parca fullname: Parca, Luca organization: European Molecular Biology Laboratory, Structural and Computational Biology Unit – sequence: 6 givenname: Amparo surname: Andrés-Pons fullname: Andrés-Pons, Amparo organization: European Molecular Biology Laboratory, Structural and Computational Biology Unit – sequence: 7 givenname: Stephan surname: Singer fullname: Singer, Stephan organization: European Molecular Biology Laboratory, Structural and Computational Biology Unit, Institute of Pathology, University Hospital Heidelberg – sequence: 8 givenname: Peer surname: Bork fullname: Bork, Peer email: bork@embl.de organization: European Molecular Biology Laboratory, Structural and Computational Biology Unit, Max-Delbrück-Centre for Molecular Medicine – sequence: 9 givenname: Martin surname: Beck fullname: Beck, Martin email: martin.beck@embl.de organization: European Molecular Biology Laboratory, Structural and Computational Biology Unit |
BackLink | https://www.ncbi.nlm.nih.gov/pubmed/26975353$$D View this record in MEDLINE/PubMed |
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Keywords | Protein complex Stoichiometry Reprogramming Proteomics Paralog Epigenetic Transport Cancer |
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Recent large-scale studies revealed cell-type specific proteomes. However, protein complexes, the basic functional modules of a cell, have been so... Recent large-scale studies revealed cell-type specific proteomes. However, protein complexes, the basic functional modules of a cell, have been so far mostly... Background Recent large-scale studies revealed cell-type specific proteomes. However, protein complexes, the basic functional modules of a cell, have been so... BACKGROUND: Recent large-scale studies revealed cell-type specific proteomes. However, protein complexes, the basic functional modules of a cell, have been so... |
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SubjectTerms | Acids Animal Genetics and Genomics Animals Bioinformatics Biomedical and Life Sciences Cancer Cell cycle Cell Lineage - genetics Chromatin Chromatin - chemistry Chromatin - genetics Datasets Evolutionary Biology Gene expression Genomics Human Genetics Humans Life Sciences Mammals Microbial Genetics and Genomics Multiprotein Complexes - chemistry Multiprotein Complexes - genetics neoplasm cells neoplasms Plant Genetics and Genomics Protein expression Protein Structure, Tertiary Proteins proteome Proteome - genetics Proteomes Proteomics spatial variation Stem cells Stoichiometry temporal variation Transcription Transcription, Genetic Variation |
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Title | Spatiotemporal variation of mammalian protein complex stoichiometries |
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