scholarly journals A toolkit for tissue-specific protein degradation in C. elegans

2017 ◽  
Author(s):  
Shaohe Wang ◽  
Ngang Heok Tang ◽  
Pablo Lara-Gonzalez ◽  
Bram Prevo ◽  
Dhanya K. Cheerambathur ◽  
...  
Keyword(s):  
Protein Function ◽  
Specific Protein ◽  
Loss Of Function ◽  
Tissue Specific ◽  
C Elegans ◽  
Organismal Development ◽  
Mutant Phenotypes ◽  
Endogenous Locus ◽  
Socs Box ◽  
Production Cell

AbstractProteins essential for embryo production, cell division, and early embryonic events are frequently re-utilized later in embryogenesis, during organismal development, or in the adult. Examining protein function across these different biological contexts requires tissue-specific perturbation. Here, we describe a method that utilizes expression of a fusion between a GFP-targeting nanobody and SOCS-box containing ubiquitin ligase adaptor to target GFP tagged proteins for degradation. When combined with endogenous locus GFP tagging by CRISPR-Cas9 or rescue of a null mutant with a GFP fusion, this approach enables routine and efficient tissue-specific protein ablation. We show that this approach works in multiple tissues—the epidermis, intestine, body wall muscle, sensory neurons, and touch neurons—where it recapitulates expected loss-of-function mutant phenotypes. The transgene toolkit and the strain set described here will complement existing approaches to enable routine analysis of the tissue-specific roles of C. elegans proteins.

scholarly journals Goα Regulates Volatile Anesthetic Action in Caenorhabditis elegans

Genetics ◽  
2001 ◽  
Vol 158 (2) ◽  
pp. 643-655 ◽  
Author(s):  
Bruno van Swinderen ◽  
Laura B Metz ◽  
Laynie D Shebester ◽  
Jane E Mendel ◽  
Paul W Sternberg ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Novel Mutation ◽  
Volatile Anesthetic ◽  
Loss Of Function ◽  
Wild Type ◽  
Α Subunit ◽  
C Elegans ◽  
Missense Mutant ◽  
Anesthetic Action ◽  
Mutant Phenotypes

Abstract To identify genes controlling volatile anesthetic (VA) action, we have screened through existing Caenorhabditis elegans mutants and found that strains with a reduction in Go signaling are VA resistant. Loss-of-function mutants of the gene goa-1, which codes for the α-subunit of Go, have EC50s for the VA isoflurane of 1.7- to 2.4-fold that of wild type. Strains overexpressing egl-10, which codes for an RGS protein negatively regulating goa-1, are also isoflurane resistant. However, sensitivity to halothane, a structurally distinct VA, is differentially affected by Go pathway mutants. The RGS overexpressing strains, a goa-1 missense mutant found to carry a novel mutation near the GTP-binding domain, and eat-16(rf) mutants, which suppress goa-1(gf) mutations, are all halothane resistant; goa-1(null) mutants have wild-type sensitivities. Double mutant strains carrying mutations in both goa-1 and unc-64, which codes for a neuronal syntaxin previously found to regulate VA sensitivity, show that the syntaxin mutant phenotypes depend in part on goa-1 expression. Pharmacological assays using the cholinesterase inhibitor aldicarb suggest that VAs and GOA-1 similarly downregulate cholinergic neurotransmitter release in C. elegans. Thus, the mechanism of action of VAs in C. elegans is regulated by Goα, and presynaptic Goα-effectors are candidate VA molecular targets.

Two homologous regulatory genes, lin-12 and glp-1, have overlapping functions

Development ◽  
1991 ◽  
Vol 112 (1) ◽  
pp. 231-240 ◽  
Author(s):  
E.J. Lambie ◽  
J. Kimble
Keyword(s):  
Gene Expression ◽  
Double Mutant ◽  
Transmembrane Proteins ◽  
Cell Interactions ◽  
Loss Of Function ◽  
Cell Fates ◽  
Single Mutant ◽  
C Elegans ◽  
Homologous Genes ◽  
Mutant Phenotypes

Two homologous genes, lin-12 and glp-1, encode transmembrane proteins required for regulatory cell interactions during C. elegans development. Based on their single mutant phenotypes, each gene has been thought to govern a distinct set of cell fates. We show here that lin-12 and glp-1 are functionally redundant during embryogenesis: Unlike either single mutant, the lin-12 glp-1 double mutant dies soon after hatching. Numerous cellular defects can be observed in these Lag (for lin-12 and glp-1) double mutants. Furthermore, we have identified two genes, lag-1 and lag-2, that appear to be required for both lin-12 and glp-1-mediated cell interactions. Strong loss-of-function lag mutants are phenotypically indistinguishable from the lin-12 glp-1 double; weak lag mutants have phenotypes typical of lin-12 and glp-1 single mutants. We speculate that the lin-12 and glp-1 proteins are biochemically interchangeable and that their divergent roles in development may rely largely on differences in gene expression.

A Transmembrane Guanylyl Cyclase (DAF-11) and Hsp90 (DAF-21) Regulate a Common Set of Chemosensory Behaviors in Caenorhabditis elegans

Genetics ◽  
2000 ◽  
Vol 155 (1) ◽  
pp. 85-104 ◽  
Author(s):  
Deborah A Birnby ◽  
Elizabeth Malone Link ◽  
Jennifer J Vowels ◽  
Hong Tian ◽  
Patrick L Colacurcio ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Guanylyl Cyclase ◽  
Large Family ◽  
Heat Shock Protein 90 ◽  
Specific Protein ◽  
Single Amino Acid ◽  
C Elegans ◽  
Chemosensory Transduction ◽  
Chemosensory Pathways ◽  
Mutant Phenotypes

Abstract Caenorhabditis elegans daf-11 and daf-21 mutants share defects in specific chemosensory responses mediated by several classes of sensory neurons, indicating that these two genes have closely related functions in an assortment of chemosensory pathways. We report that daf-11 encodes one of a large family of C. elegans transmembrane guanylyl cyclases (TM-GCs). The cyclic GMP analogue 8-bromo-cGMP rescues a sensory defect in both daf-11 and daf-21 mutants, supporting a role for DAF-11 guanylyl cyclase activity in this process and further suggesting that daf-21 acts at a similar step. daf-11::gfp fusions are expressed in five identified pairs of chemosensory neurons in a pattern consistent with most daf-11 mutant phenotypes. We also show that daf-21 encodes the heat-shock protein 90 (Hsp90), a chaperone with numerous specific protein targets. We show that the viable chemosensory-deficient daf-21 mutation is an unusual allele resulting from a single amino acid substitution and that the daf-21 null phenotype is early larval lethality. These results demonstrate that cGMP is a prominent second messenger in C. elegans chemosensory transduction and suggest a previously unknown role for Hsp90 in regulating cGMP levels.

scholarly journals The Caenorhabditis elegans LIN-26 protein is required to specify and/or maintain all non-neuronal ectodermal cell fates

Development ◽  
1996 ◽  
Vol 122 (9) ◽  
pp. 2579-2588 ◽  
Author(s):  
M. Labouesse ◽  
E. Hartwieg ◽  
H.R. Horvitz
Keyword(s):  
Expression Patterns ◽  
Neuronal Cell ◽  
Loss Of Function ◽  
Cell Fates ◽  
Asymmetric Cell Divisions ◽  
Zinc Finger Transcription Factor ◽  
C Elegans ◽  
Cell Divisions ◽  
Mutant Phenotypes ◽  
Cell Expression

The C. elegans gene lin-26, which encodes a presumptive zinc-finger transcription factor, is required for hypodermal cells to acquire their proper fates. Here we show that lin-26 is expressed not only in all hypodermal cells but also in all glial-like cells. During asymmetric cell divisions that generate a neuronal cell and a non-neuronal cell, LIN-26 protein is symmetrically segregated and then lost from the neuronal cell. Expression in glial-like cells (socket and sheath cells) is biologically important, as some of these neuronal support cells die or seem sometimes to be transformed to neuron-like cells in embryos homozygous for strong loss-of-function mutations. In addition, most of these glial-like cells are structurally and functionally defective in animals carrying the weak loss-of-function mutation lin-26(n156). lin-26 mutant phenotypes and expression patterns together suggest that lin-26 is required to specify and/or maintain the fates not only of hypodermal cells but also of all other non-neuronal ectodermal cells in C. elegans. We speculate that lin-26 acts by repressing the expression of neuronal-specific genes in non-neuronal cells.

scholarly journals Augmenting protein network embeddings with sequence information

2019 ◽  
Author(s):  
Hassan Kané ◽  
Mohamed Coulibali ◽  
Ali Abdalla ◽  
Pelkins Ajanoh
Keyword(s):  
Protein Interactions ◽  
Protein Function ◽  
Quaternary Structure ◽  
Protein Function Prediction ◽  
Representation Learning ◽  
Specific Protein ◽  
Sequence Information ◽  
Protein Protein Interactions ◽  
Tissue Specific ◽  
Protein Protein Interaction

ABSTRACTComputational methods that infer the function of proteins are key to understanding life at the molecular level. In recent years, representation learning has emerged as a powerful paradigm to discover new patterns among entities as varied as images, words, speech, molecules. In typical representation learning, there is only one source of data or one level of abstraction at which the learned representation occurs. However, proteins can be described by their primary, secondary, tertiary, and quaternary structure or even as nodes in protein-protein interaction networks. Given that protein function is an emergent property of all these levels of interactions in this work, we learn joint representations from both amino acid sequence and multilayer networks representing tissue-specific protein-protein interactions. Using these hybrid representations, we show that simple machine learning models trained using these hybrid representations outperform existing network-based methods on the task of tissue-specific protein function prediction on 13 out of 13 tissues. Furthermore, these representations outperform existing ones by 14% on average.

scholarly journals NATF (Native And Tissue-specific Fluorescence): A strategy for bright, tissue-specific GFP labeling of native proteins

2018 ◽  
Author(s):  
Siwei He ◽  
Andrea Cuentas-Condori ◽  
David M. Miller
Keyword(s):  
Cell Types ◽  
Specific Protein ◽  
Target Protein ◽  
Specific Cell ◽  
Genomic Locus ◽  
Intracellular Location ◽  
Tissue Specific ◽  
Specific Fluorescence ◽  
C Elegans ◽  
Native Proteins

ABSTRACTGFP labeling by genome editing can reveal the authentic location of a native protein but is frequently hampered by weak GFP signals and broad expression across a range cell types in multicellular animals. To overcome these problems, we engineered a Native And Tissue-specific Fluorescence (NATF) strategy which combines CRISPR/Cas-9 and split-GFP to yield bright, cell-specific protein labeling. We use CRISPR/Cas9 to insert a tandem array of seven copies of the GFP11 β-strand (gfp11x7) at the genomic locus of each target protein. The resultant gfp11x7 knock-in strain is then crossed with separate reporter lines that express the complementing split-GFP fragment (gfp1-10) in specific cell types thus affording tissue-specific labeling of the target protein at its native level. We show that NATF reveals the otherwise undetectable intracellular location of the immunoglobulin protein, OIG-1, and demarcates a receptor auxiliary protein LEV-10 at cell-specific synaptic domains in the C. elegans nervous system.

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