Synthetic protein interactions reveal a functional map of the cell

Abstract

To understand the function of eukaryotic cells, it is critical to understand the role of protein-protein interactions and protein localization. Currently, we do not know the importance of global protein localization nor do we understand to what extent the cell is permissive for new protein associations – a key requirement for the evolution of new protein functions. To answer this question, we fused every protein in the yeast Saccharomyces cerevisiae with a partner from each of the major cellular compartments and quantitatively assessed the effects upon growth. This analysis reveals that cells have a remarkable and unanticipated tolerance for forced protein associations, even if these associations lead to a proportion of the protein moving compartments within the cell. Furthermore, the interactions that do perturb growth provide a functional map of spatial protein regulation, identifying key regulatory complexes for the normal homeostasis of eukaryotic cells.DOI: http://dx.doi.org/10.7554/eLife.13053.001

A nanobody-based toolset to investigate the role of protein localization and dispersal inDrosophila

“…In line with observations made by Berry et al (Berry, Olafsson et al 2016), the GrabFP components were in some cases themselves mislocalized due to interaction with target proteins. This was particularly relevant for GrabFP-A Ext and GrabFP-B Int (Figure 2 Figure Supplement 1H), which were, presumably as a consequence, less efficient in causing target protein mislocalization.…”

“…Recently, it was reported that tethering of nanobodies to specific cellular compartments can result in protein relocalization (Berry, Olafsson et al 2016). In line with these observations, expression of the GrabFP constructs altered the subcellular localization along the apicalbasal axis of the 15 different GFP-tagged cytosolic or transmembrane proteins we tested.…”

“…Importantly, vhhGFP4 can be fused to other proteins without losing its activity and specificity in vivo (Rothbauer, Zolghadr et al 2008). As a consequence, vhhGFP4 has been functionalized by fusing it to different protein domains in order to visualize (Rothbauer, Zolghadr et al 2006), relocalize (Berry, Olafsson et al 2016) and degrade (Caussinus, Kanca et al 2012, Shin, Park et al 2015 GFP-tagged proteins of interest. More recently, GFP nanobodies were used to generate inducible tools that allow controlled transcription (Tang, Szikra et al 2013) and enzyme activity (Tang, Rudolph et al 2015), and to generate synthetic receptors (Harmansa, Hamaratoglu et al 2015, Morsut, Roybal et al 2016, to mention only a few examples.…”

Comparative analysis of Synthetic Physical Interactions with the yeast centrosome

“… Abstract The yeast centrosome or Spindle Pole Body (SPB) is situated in the nuclear membrane, where it nucleates spindle microtubules and acts as a signalling hub. Previously, we used Synthetic Physical Interactions to map the regions of the cell that are sensitive to forced relocalization of proteins across the proteome [Berry et al, 2016]. Here, we expand on this work to show that the SPB, in particular, is sensitive to the relocalization of many proteins.…”

“…Proteome-wide SPI screens have been used in the past to probe the regulation of the kinetochore [Ólafsson and Thorpe, 2015, 2016] and a set of 23 SPI screens was used to generate a cell-wide map of proteins sensitive to relocalization [Berry et al, 2016]. Relative to the screens of Berry et al our analysis shows that the SPB is particularly sensitive to forcible relocalization.…”