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A combined binary interaction and phenotypic map of C. elegans cell polarity proteins

Nature Cell Biology volume 18, pages 337–346 (2016)Cite this article

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Abstract

The establishment of cell polarity is an essential process for the development of multicellular organisms and the functioning of cells and tissues. Here, we combine large-scale protein interaction mapping with systematic phenotypic profiling to study the network of physical interactions that underlies polarity establishment and maintenance in the nematode Caenorhabditis elegans. Using a fragment-based yeast two-hybrid strategy, we identified 439 interactions between 296 proteins, as well as the protein regions that mediate these interactions. Phenotypic profiling of the network resulted in the identification of 100 physically interacting protein pairs for which RNAi-mediated depletion caused a defect in the same polarity-related process. We demonstrate the predictive capabilities of the network by showing that the physical interaction between the RhoGAP PAC-1 and PAR-6 is required for radial polarization of the C. elegans embryo. Our network represents a valuable resource of candidate interactions that can be used to further our insight into cell polarization.

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Figure 1: Identification and validation of a C. elegans polarity interaction network (CePIN).
Figure 2: Validation of the CePIN.
Figure 3: Identification and validation of minimal regions of interaction (MRIs).
Figure 4: Phenotypic analysis of the bait proteins.
Figure 5: Examples of RNAi phenotypes.
Figure 6: The PAR-6–PAC-1 interaction is required for radial polarization.

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Acknowledgements

We thank M. Zerial for providing the MZE1 strain, C. Bargmann for providing strain CX9797 and a strain carrying the Pdes-2::myristoyl::GFP extrachromosomal array, and M. Harterink for strain STR62. We thank S. de Rouck for technical assistance, and M. Vidal for permission to reanalyse MAPPIT data. We thank F. Zwartkruis, M. Gloerich and A. Thomas for critically reading the manuscript. Some nematode strains used in this work were provided by the Caenorhabditis Genetics Center, which is funded by the NIH National Center for Research Resources (NCRR). This work was supported by the Netherlands Organization for Scientific Research (NWO) ALW Innovational Research Incentives Scheme Vidi grant 864.09.008 to M.B., NWO-CW ECHO grant 711.014.005 to M.B., National Science Foundation Graduate Research Fellowship 12-A0-00-000165-01 to D.K., and NIH grants R01GM078341 and R01GM098492 to J.N. J.T. is the recipient of ERC Advanced Grant 340941.

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Author notes

  1. Monique van der Voet

    Present address: Present address: Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands.,

  2. Diana Klompstra and Monique van der Voet: These authors contributed equally to this work.

Authors and Affiliations

  1. Division of Developmental Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands

    Thijs Koorman, Monique van der Voet, João J. Ramalho, Susan Nieuwenhuize, Sander van den Heuvel & Mike Boxem

  2. Helen L. and Martin S. Kimmel Center for Biology and Medicine at the Skirball Institute of Biomolecular Medicine, NYU School of Medicine, New York, New York 10016, USA

    Diana Klompstra & Jeremy Nance

  3. Department of Cell Biology, NYU School of Medicine, New York, New York 10016, USA

    Diana Klompstra & Jeremy Nance

  4. Department of Medical Protein Research, VIB, 9000 Ghent, Belgium

    Irma Lemmens & Jan Tavernier

  5. Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium

    Irma Lemmens & Jan Tavernier

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Contributions

M.v.d.V. contributed to the cloning and Y2H screens. D.K. performed the PAC-1 rescue experiments. I.L. performed the MAPPIT experiments. J.J.R. and S.N. contributed to the RNAi screens. M.B. performed the computational analyses. All other experiments were performed by T.K. S.v.d.H. and T.K. contributed to the design of the study. J.N. contributed to the design of the PAC-1 PAR-6 experiments. J.T. contributed to the design of the MAPPIT experiments. T.K. and M.B. wrote the manuscript. M.B. guided all aspects of the study.

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Correspondence to Mike Boxem.

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Integrated supplementary information

Supplementary Figure 1 Enrichment of shared Gene Ontology (GO) terms and similar expression profiles in interacting protein pairs compared to control networks generated by replacing the prey proteins with random proteins from the search space.

(a) GO similarity scores for interacting protein pairs identified using the AD-cDNA library. Semantic similarity scores for the BP component of GO were calculated using the HRSS software package, which scores protein pairs on a scale of 0 (dissimilar GO terms) to 1 (similar GO terms)29. (b) Same as (a), but for interactions identified using the AD-Fragment scores. Due to the already high semantic similarity scores for pairs in the search space (749 genes involved in early embryonic development), enrichment scores are less high than for AD-cDNA derived interactions. Control network bars represent the mean of 100,000 control networks ± s.d. Statistical significance is the fraction of control networks that displayed the same or higher fraction of pairs with a particular GO similarity range as the actual interaction network. Protein pairs in the interaction network are depleted for pairs with a low semantic similarity score, and enriched for pairs with a high similarity score. (c–f) Average Pearson correlation coefficient (PCC) score of mRNAs corresponding to protein pairs in the indicated interaction datasets (red arrows), compared with the distribution of average PCC scores of 100,000 control networks generated by replacing the bait proteins with random proteins from the search space (blue line). PCC values were calculated using the compendium of expression microarray data collected in Wormbase release WS236. Statistical significance is the fraction of control networks that displayed an average PCC score identical or higher than the actual interaction network. As observed previously9, early embryogenesis genes already have such similar expression profiles that no further enrichment can be observed for interactions derived from the AD-Fragment library.

Supplementary Figure 2 Western blots for all protein pairs testing positive by co-affinity purification.

For every pair, three blots are shown. Top: detection of GFP-tagged proteins that co-purify with biotinylated mCherry-tagged proteins using an anti-GFP antibody. Middle: detection of GFP-tagged proteins in total lysates using an anti-GFP antibody. Bottom: detection of biotinylated Avi-mCherry tagged proteins in total lysates using streptavidin coupled to horse radish peroxidase. Protein pairs tested are indicated above the blots. The first protein listed is the Avi-mCherry tagged bait. Also indicated is whether the prey protein tested was full-length (f.l.) or corresponds to a shorter fragment (frag.). In all blots, lanes 1 and 2 are negative controls, and lane 3 is the actual affinity purification (1: Avi-mCherry-bait vs. EGFP alone, 2: Avi-mCherry alone vs. EGFP-tagged prey, 3: Avi-mCherry-bait versus EGFP-prey). The ∼35 kDa band in lanes 2 of the upper blots is due to cross-reactivity of the anti-GFP antibody with the highly abundant Avi-mCherry polypeptide. Asterisks indicate bands of expected molecular mass. Purifications were performed once. Unprocessed scans are shown in Supplementary Fig. 5.

Supplementary Figure 3 Graphical representation of every protein in the interaction network and the MRIs identified for that protein.

Grey boxes are full-length proteins. Predicted domains are shown as boxes of various colors and shapes. Identified MRIs are shown as yellow lines above the protein graphic. Protein names above each MRI indicate which proteins bind to that particular region.

Supplementary Figure 4 Analysis of MRIs.

(a–c) Distributions of MRI lengths expressed as the percentage of the corresponding full-length protein. (d–f) Distributions of absolute MRI lengths in amino acid residues. (a,d) MRIs identified for the bait proteins. (b,e) MRIs identified for the prey proteins from AD-Fragment library derived clones. (c,f) MRIs identified for the prey proteins from AD-cDNA library derived clones. (g) Graphical representations of all MRIs where interaction sites had previously been identified in the literature. Grey boxes are full-length proteins. Predicted domains are shown as boxes of various colors and shapes. Identified MRIs are shown as yellow lines above the protein graphic. Interaction sites from the literature are shown as blue lines above the protein graphic. In cases where the literature describes an interaction domain for a non-C. elegans protein, the corresponding site in the C. elegans protein is shown.

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Koorman, T., Klompstra, D., van der Voet, M. et al. A combined binary interaction and phenotypic map of C. elegans cell polarity proteins. Nat Cell Biol 18, 337–346 (2016). https://doi.org/10.1038/ncb3300

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