Abstract
RNA-binding proteins (RBPs) form highly diverse and dynamic ribonucleoprotein complexes, whose functions determine the molecular fate of the bound RNA. In the model organism S. cerevisiae, the number of proteins identified as RBPs has largely increased over the last decade. However, the cellular function for most of these novel RBPs still remains largely unexplored. We use mass spectrometry-based quantitative proteomics to systematically identify protein-protein interactions (PPIs) and RNA-dependent interactions (RDIs) to create a novel data set for 40 RBPs that are associated with the mRNA life cycle. Domain, functional, and pathway enrichment analyses revealed an overrepresentation of RNA functionalities among the enriched interactors. Using our extensive PPI and RDI networks, we revealed putative new members of RNA-associated pathways, as well as highlighted potential new roles of several RBPs, such as within metabolism.
Experimental design
RBPs immunoprecipitation screen design. (A) The 40 selected target RBPs are shown under a schematic drawing of the broad RNA biology processes they are involved in.Proteins marked with (*) are associated to multiple processes. (B) Schematic representation of the immunoprecipitation screen experimental design.
KEGG analysis results
Heat map of the PPI and RDI KEGG terms. Each tile represents an overrepresented KEGG term (adjusted p-value < 0.05) and its colour gradient represents the gene ratio (enriched genes in term / total enriched genes). The first horizontal colour bar (Set) represent the PPI and RDI sets while the second (Bait) represents the bait RBP functional selection criteria. The vertical colour bar (Interactors) represents the global functionality the KEGG terms belong to.
Albert Fradera-Sola 1 , Emily Nischwitz 1 , Marie Elisabeth Bayer 1 , Katja Luck 2 , Falk Butter 1,#
# Indicates correspondance, 1 Quantitative Proteomics, Institute of Molecular Biology, Mainz, Germany, 2 Integrative systems biology, Institute of Molecular Biology, 55128 Mainz, GermanyApp created by Albert Fradera-Sola in June 2022
Comments and bug reports to the following e-mail: A.FraderaSola@imb-mainz.de
Last update: November 2022IP screen protein-protein interaction (PPI) network. RBP baits with a KEGG-associated function and their preys are depicted as a network. Functions is highlighted with the nodes and/or edges colour, while the number of preys per bait is highlighted with the nodes size. Finally, the network is further customized by choosing the nodes size, the edges thickness and the network layout.
IP screen RNA-dependent interactions (RDI) network. RBP baits with a KEGG-associated function and their preys are depicted as a network. Functions is highlighted with the nodes and/or edges colour, while the number of preys per bait is highlighted with the nodes size. Finally, the network is further customized by choosing the nodes size, the edges thickness and the network layout.
Splicing associated protein-protein interactors (PPI) sub-network. RBP baits associated to splicing and their preys are depicted as a network. Inclusion at interaction database and/or the RBP census is highlighted with the nodes colour, while the number of preys per bait is highlighted with the nodes size. Finally, the network is further customized by choosing the nodes size, the edges thickness and the network layout.
Splicing associated RNA-dependent interactors (RDI) sub-network. RBP baits associated to splicing and their preys are depicted as a network. Inclusion at interaction database and/or the RBP census is highlighted with the nodes colour, while the number of preys per bait is highlighted with the nodes size. Finally, the network is further customized by choosing the nodes size, the edges thickness and the network layout.
Splicing associated combined (PPI + RDI) sub-network. RBP baits associated to splicing and their preys are depicted as a network. Inclusion at interaction database and/or the RBP census is highlighted with the nodes colour, while the number of preys per bait is highlighted with the nodes size. The edge colour highlights which set the prey belongs to. Finally, the network is further customized by choosing the nodes size, the edges thickness and the network layout.
Complex filtering
Filtered complexes
Complex ratio dot plot
Complex selection
Node Attributes
Colour
Size
Edge Attributes
Colour
Thickness
Network layout
Download
Global network
Nodes EdgesInteractor network
Nodes EdgesGlobal network. RBP baits associated to the complex and their preys are depicted as a network. Node identity is highlighted with the colour, while the number of preys per bait is highlighted with the nodes size. The edge colour highlights which set the prey belongs to. Finally, the network is further customized by choosing the nodes size, the edges thickness and the network layout.
Interactor network. RBP baits associated to the complex and their preys are depicted as a network. Node identity is highlighted with the colour, while the number of preys per bait is highlighted with the nodes size. The edge colour highlights which set the prey belongs to. Finally, the network is further customized by choosing the nodes size, the edges thickness and the network layout.
Export associated protein-protein interactors (PPI) sub-network. RBP baits associated to export and their preys are depicted as a network. Inclusion at interaction database and/or the RBP census is highlighted with the nodes colour, while the number of preys per bait is highlighted with the nodes size. Finally, the network is further customized by choosing the nodes size, the edges thickness and the network layout.
Export associated RNA-dependent interactors (RDI) sub-network. RBP baits associated to export and their preys are depicted as a network. Inclusion at interaction database and/or the RBP census is highlighted with the nodes colour, while the number of preys per bait is highlighted with the nodes size. Finally, the network is further customized by choosing the nodes size, the edges thickness and the network layout.
Export associated combined (PPI + RDI) sub-network. RBP baits associated to export and their preys are depicted as a network. Inclusion at interaction database and/or the RBP census is highlighted with the nodes colour, while the number of preys per bait is highlighted with the nodes size. The edge colour highlights which set the prey belongs to. Finally, the network is further customized by choosing the nodes size, the edges thickness and the network layout.
Complex filtering
Filtered complexes
Complex ratio dot plot
Complex selection
Node Attributes
Colour
Size
Edge Attributes
Colour
Thickness
Network layout
Download
Global network
Nodes EdgesInteractor network
Nodes EdgesGlobal network. RBP baits associated to the complex and their preys are depicted as a network. Node identity is highlighted with the colour, while the number of preys per bait is highlighted with the nodes size. The edge colour highlights which set the prey belongs to. Finally, the network is further customized by choosing the nodes size, the edges thickness and the network layout.
Interactor network. RBP baits associated to the complex and their preys are depicted as a network. Node identity is highlighted with the colour, while the number of preys per bait is highlighted with the nodes size. The edge colour highlights which set the prey belongs to. Finally, the network is further customized by choosing the nodes size, the edges thickness and the network layout.
Ribosome associated protein-protein interactors (PPI) sub-network. RBP baits associated to ribosome and their preys are depicted as a network. Inclusion at interaction database and/or the RBP census is highlighted with the nodes colour, while the number of preys per bait is highlighted with the nodes size. Finally, the network is further customized by choosing the nodes size, the edges thickness and the network layout.
Ribosome associated RNA-dependent interactors (RDI) sub-network. RBP baits associated to ribosome and their preys are depicted as a network. Inclusion at interaction database and/or the RBP census is highlighted with the nodes colour, while the number of preys per bait is highlighted with the nodes size. Finally, the network is further customized by choosing the nodes size, the edges thickness and the network layout.
Ribosome associated combined (PPI + RDI) sub-network. RBP baits associated to ribosome and their preys are depicted as a network. Inclusion at interaction database and/or the RBP census is highlighted with the nodes colour, while the number of preys per bait is highlighted with the nodes size. The edge colour highlights which set the prey belongs to. Finally, the network is further customized by choosing the nodes size, the edges thickness and the network layout.
Complex filtering
Filtered complexes
Complex ratio dot plot
Complex selection
Node Attributes
Colour
Size
Edge Attributes
Colour
Thickness
Network layout
Download
Global network
Nodes EdgesInteractor network
Nodes EdgesGlobal network. RBP baits associated to the complex and their preys are depicted as a network. Node identity is highlighted with the colour, while the number of preys per bait is highlighted with the nodes size. The edge colour highlights which set the prey belongs to. Finally, the network is further customized by choosing the nodes size, the edges thickness and the network layout.
Interactor network. RBP baits associated to the complex and their preys are depicted as a network. Node identity is highlighted with the colour, while the number of preys per bait is highlighted with the nodes size. The edge colour highlights which set the prey belongs to. Finally, the network is further customized by choosing the nodes size, the edges thickness and the network layout.
Synthesis associated protein-protein interactors (PPI) sub-network. RBP baits associated to synthesis and their preys are depicted as a network. Inclusion at interaction database and/or the RBP census is highlighted with the nodes colour, while the number of preys per bait is highlighted with the nodes size. Finally, the network is further customized by choosing the nodes size, the edges thickness and the network layout.
Synthesis associated RNA-dependent interactors (RDI) sub-network. RBP baits associated to synthesis and their preys are depicted as a network. Inclusion at interaction database and/or the RBP census is highlighted with the nodes colour, while the number of preys per bait is highlighted with the nodes size. Finally, the network is further customized by choosing the nodes size, the edges thickness and the network layout.
Synthesis associated combined (PPI + RDI) sub-network. RBP baits associated to synthesis and their preys are depicted as a network. Inclusion at interaction database and/or the RBP census is highlighted with the nodes colour, while the number of preys per bait is highlighted with the nodes size. The edge colour highlights which set the prey belongs to. Finally, the network is further customized by choosing the nodes size, the edges thickness and the network layout.
Complex filtering
Filtered complexes
Complex ratio dot plot
Complex selection
Node Attributes
Colour
Size
Edge Attributes
Colour
Thickness
Network layout
Download
Global network
Nodes EdgesInteractor network
Nodes EdgesGlobal network. RBP baits associated to the complex and their preys are depicted as a network. Node identity is highlighted with the colour, while the number of preys per bait is highlighted with the nodes size. The edge colour highlights which set the prey belongs to. Finally, the network is further customized by choosing the nodes size, the edges thickness and the network layout.
Interactor network. RBP baits associated to the complex and their preys are depicted as a network. Node identity is highlighted with the colour, while the number of preys per bait is highlighted with the nodes size. The edge colour highlights which set the prey belongs to. Finally, the network is further customized by choosing the nodes size, the edges thickness and the network layout.
Metabolism associated protein-protein interactors (PPI) sub-network. RBP baits associated to metabolism and their preys are depicted as a network. Inclusion at interaction database and/or the RBP census is highlighted with the nodes colour, while the number of preys per bait is highlighted with the nodes size. Finally, the network is further customized by choosing the nodes size, the edges thickness and the network layout.
Metabolism associated RNA-dependent interactors (RDI) sub-network. RBP baits associated to metabolism and their preys are depicted as a network. Inclusion at interaction database and/or the RBP census is highlighted with the nodes colour, while the number of preys per bait is highlighted with the nodes size. Finally, the network is further customized by choosing the nodes size, the edges thickness and the network layout.
Metabolism associated combined (PPI + RDI) sub-network. RBP baits associated to metabolism and their preys are depicted as a network. Inclusion at interaction database and/or the RBP census is highlighted with the nodes colour, while the number of preys per bait is highlighted with the nodes size. The edge colour highlights which set the prey belongs to. Finally, the network is further customized by choosing the nodes size, the edges thickness and the network layout.
Complex filtering
Filtered complexes
Complex ratio dot plot
Complex selection
Node Attributes
Colour
Size
Edge Attributes
Colour
Thickness
Network layout
Download
Global network
Nodes EdgesInteractor network
Nodes EdgesGlobal network. RBP baits associated to the complex and their preys are depicted as a network. Node identity is highlighted with the colour, while the number of preys per bait is highlighted with the nodes size. The edge colour highlights which set the prey belongs to. Finally, the network is further customized by choosing the nodes size, the edges thickness and the network layout.
Interactor network. RBP baits associated to the complex and their preys are depicted as a network. Node identity is highlighted with the colour, while the number of preys per bait is highlighted with the nodes size. The edge colour highlights which set the prey belongs to. Finally, the network is further customized by choosing the nodes size, the edges thickness and the network layout.
Degradation associated protein-protein interactors (PPI) sub-network. RBP baits associated to degradation and their preys are depicted as a network. Inclusion at interaction database and/or the RBP census is highlighted with the nodes colour, while the number of preys per bait is highlighted with the nodes size. Finally, the network is further customized by choosing the nodes size, the edges thickness and the network layout.
Degradation associated RNA-dependent interactors (RDI) sub-network. RBP baits associated to degradation and their preys are depicted as a network. Inclusion at interaction database and/or the RBP census is highlighted with the nodes colour, while the number of preys per bait is highlighted with the nodes size. Finally, the network is further customized by choosing the nodes size, the edges thickness and the network layout.
Degradation associated combined (PPI + RDI) sub-network. RBP baits associated to degradation and their preys are depicted as a network. Inclusion at interaction database and/or the RBP census is highlighted with the nodes colour, while the number of preys per bait is highlighted with the nodes size. The edge colour highlights which set the prey belongs to. Finally, the network is further customized by choosing the nodes size, the edges thickness and the network layout.
Complex filtering
Filtered complexes
Complex ratio dot plot
Complex selection
Node Attributes
Colour
Size
Edge Attributes
Colour
Thickness
Network layout
Download
Global network
Nodes EdgesInteractor network
Nodes EdgesGlobal network. RBP baits associated to the complex and their preys are depicted as a network. Node identity is highlighted with the colour, while the number of preys per bait is highlighted with the nodes size. The edge colour highlights which set the prey belongs to. Finally, the network is further customized by choosing the nodes size, the edges thickness and the network layout.
Interactor network. RBP baits associated to the complex and their preys are depicted as a network. Node identity is highlighted with the colour, while the number of preys per bait is highlighted with the nodes size. The edge colour highlights which set the prey belongs to. Finally, the network is further customized by choosing the nodes size, the edges thickness and the network layout.