GPCRs in invertebrate innate immunity.
Biochemical Pharmacology 114:82 (2016)
G-protein coupled receptors (GPCRs) represent a privileged point of contact between cells and their surrounding environment. They have been widely adopted in vertebrates as mediators of signals involved in both innate and adaptive immunity. Invertebrates rely on innate immune defences to resist ...
Quantifying domain-ligand affinities and specificities by high-throughput holdup assay.
Nature Methods 12(8):787 (2015)
Many protein interactions are mediated by small linear motifs interacting specifically with defined families of globular domains. Quantifying the specificity of a motif requires measuring and comparing its binding affinities to all its putative target domains. To this end, we developed the high-...
The human PDZome: a gateway to PSD95-Disc large-zonula occludens (PDZ)-mediated functions.
Molecular & Cellular Proteomics 12(9):2587 (2013)
Protein-protein interactions organize the localization, clustering, signal transduction, and degradation of cellular proteins and are therefore implicated in numerous biological functions. These interactions are mediated by specialized domains able to bind to modified or unmodified peptides pres...
Prevalence, specificity and determinants of lipid-interacting PDZ domains from an in-cell screen and in vitro binding experiments.
PLoS ONE 8(2):e54581 (2013)
PDZ domains are highly abundant protein-protein interaction modules involved in the wiring of protein networks. Emerging evidence indicates that some PDZ domains also interact with phosphoinositides (PtdInsPs), important regulators of cell polarization and signaling. Yet our knowledge on the pre...
Gipc1 has a dual role in Vangl2 trafficking and hair bundle integrity in the inner ear.
Development 139(20):3775 (2012)
Vangl2 is one of the central proteins controlling the establishment of planar cell polarity in multiple tissues of different species. Previous studies suggest that the localization of the Vangl2 protein to specific intracellular microdomains is crucial for its function. However, the molecular me...
PP2A phosphatase acts upon SAS-5 to ensure centriole formation in C. elegans embryos.
Developmental Cell 20(4):550 (2011)
Centrosome duplication occurs once per cell cycle and ensures that the two resulting centrosomes assemble a bipolar mitotic spindle. Centriole formation is fundamental for centrosome duplication. In Caenorhabditis elegans, the evolutionarily conserved proteins SPD-2, ZYG-1, SAS-6, SAS-5, and SAS...
PAT-12, a potential anti-nematode target, is a new spectraplakin partner essential for Caenorhabditis elegans hemidesmosome integrity and embryonic morphogenesis.
Developmental Biology 350(2):267 (2011)
Caenorhabditis elegans embryonic elongation depends on both epidermal and muscle cells. The hemidesmosome-like junctions, commonly called fibrous organelles (FOs), that attach the epidermis to the extracellular matrix ensure muscle anchoring to the cuticular exoskeleton and play an essential rol...
A genome-wide study of PDZ-domain interactions in C. elegans reveals a high frequency of non-canonical binding.
BMC Genomics 11:671 (2010)
Proteins may evolve through the recruitment and modification of discrete domains, and in many cases, protein action can be dissected at the domain level. PDZ domains are found in many important structural and signaling complexes, and are generally thought to interact with their protein partners ...
High-throughput expression of C. elegans proteins.
Genome Research 14(10B):2102 (2004)
Proteome-scale studies of protein three-dimensional structures should provide valuable information for both investigating basic biology and developing therapeutics. Critical for these endeavors is the expression of recombinant proteins. We selected Caenorhabditis elegans as our model organism in...
TLR-independent control of innate immunity in Caenorhabditis elegans by the TIR domain adaptor protein TIR-1, an ortholog of human SARM.
Nature Immunology 5(5):488 (2004)
Both plants and animals respond to infection by synthesizing compounds that directly inhibit or kill invading pathogens. We report here the identification of infection-inducible antimicrobial peptides in Caenorhabditis elegans. Expression of two of these peptides, NLP-29 and NLP-31, was differen...
A map of the interactome network of the metazoan C. elegans.
Science 303(5657):540 (2004)
To initiate studies on how protein-protein interaction (or "interactome") networks relate to multicellular functions, we have mapped a large fraction of the Caenorhabditis elegans interactome network. Starting with a subset of metazoan-specific proteins, more than 4000 interactions were identifi...
BTB proteins are substrate-specific adaptors in an SCF-like modular ubiquitin ligase containing CUL-3.
Nature 425(6955):316 (2003)
Programmed destruction of regulatory proteins through the ubiquitin-proteasome system is a widely used mechanism for controlling signalling pathways. Cullins are proteins that function as scaffolds for modular ubiquitin ligases typified by the SCF (Skp1-Cul1-F-box) complex. The substrate selecti...
C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression.
Nature Genetics 34(1):35 (2003)
To verify the genome annotation and to create a resource to functionally characterize the proteome, we attempted to Gateway-clone all predicted protein-encoding open reading frames (ORFs), or the 'ORFeome,' of Caenorhabditis elegans. We successfully cloned approximately 12,000 ORFs (ORFeome 1.1)...
WorfDB: the Caenorhabditis elegans ORFeome Database.
Nucleic Acids Research 31(1):237 (2003)
WorfDB (Worm ORFeome DataBase; http://worfdb.dfci.harvard.edu) was created to integrate and disseminate the data from the cloning of complete set of approximately 19 000 predicted protein-encoding Open Reading Frames (ORFs) of Caenorhabditis elegans (also referred to as the 'worm ORFeome'). Worf...
Integrating interactome, phenome, and transcriptome mapping data for the C. elegans germline.
Current Biology 12(22):1952 (2002)
By integrating functional genomic and proteomic mapping approaches, biological hypotheses should be formulated with increasing levels of confidence. For example, yeast interactome and transcriptome data can be correlated in biologically meaningful ways. Here, we combine interactome mapping data ...
Combined functional genomic maps of the C. elegans DNA damage response.
Science 295(5552):127 (2002)
Many human cancers originate from defects in the DNA damage response (DDR). Although much is known about this process, it is likely that additional DDR genes remain to be discovered. To identify such genes, we used a strategy that combines protein-protein interaction mapping and large-scale phen...