Lu WX et al. (1990) J Biol Chem "Cloning, structure, and expression of the gene for a novel regulatory subunit of cAMP-dependent protein kinase in Caenorhabditis elegans."

Bagchi S, Lu WX, Rubin CS, Gross RE

[J Biol Chem, 1990]

The nematode Caenorhabditis elegans (C. elegans) expresses the regulatory subunit (R) of cAMP-dependent protein kinase at a level similar to the levels determined for R subunits in mammalian tissues. Approximately 60% of the C. elegans cAMP-binding protein is tightly associated with particulate structures by noncovalent interactions. Ionic detergents or 7 M urea solubilize particulate R. Solubilized and cytosolic R subunits have apparent Mr values of 52,000 and pI values of 5.5. cDNA and genomic DNA encoding a unique C. elegans R subunit were cloned and sequenced. The derived amino acid sequence contains 375 residues; carboxyl-terminal residues 145-375 are 69% identical with mammalian RI. However, residues 44-145 are markedly divergent from the corresponding regions of all other R sequences. This region might provide sufficient structural diversity to adapt a single R subunit for multiple functional roles in C. elegans. Antibodies directed against two epitopes in the deduced amino acid sequence of C. elegans R avidly bound nematode cytosolic and particulate R subunits on Western blots and precipitated dissociated R subunits and R2C2 complexes from solution. Immunofluorescence analysis revealed that the tip of the head, which contains chemosensory and mechanosensory neurons, and the pharyngeal nerve ring were enriched in R. The R subunit concentration is low during early embryogenesis in C. elegans. A sharp increase (approximately 6-fold) in R content begins several hours before the nematodes hatch and peaks during the first larval stage. Developmental regulation of R expression occurs at translational and/or post-translational levels. The 8-kilobase pair C. elegans R gene is divided into 8 exons by introns ranging from 46 to 4300 base pairs. The 5'-flanking region has no TATA box and contains preferred and minor transcription start sites.

Lu WX et al. (1998) Cell "lin-35 and lin-53, two genes that antagonize a C. elegans Ras pathway, encode proteins similar to Rb and its binding protein RbAp48."

Lu WX, Horvitz HR

[Cell, 1998]

The Ras signaling pathway for vulval induction in Caenorhabditis elegans is antagonized by the activity of the synthetic multivulva (synMuv) genes, which define two functionally redundant pathways. We have characterized two genes in one of these pathways. lin-35 encodes a protein similar to the tumor suppressor Rb and the closely related proteins p107 and p130. lin-53 encodes a protein similar to RbAp48, a mammalian protein that binds Rb. In mammals, Rb and related proteins act as regulators of E2F transcription factors, and RbAp48 may act with such proteins as a transcriptional corepressor. We propose that LIN-35 and LIN-53 antagonize the Ras signaling pathway in C. elegans by repressing transcription in the vulval precursor cells of genes required for the expression of vulval cell fates.

Walhout AJM et al. (2000) Science "Protein interaction mapping in C. elegans using proteins involved in vulval development."

Sordella R, Hartley JL, Lu WX, Thierry-Mieg N, Walhout AJM, Brasch MA, Temple GF, Vidal MI

[Science, 2000]

Protein interaction mapping using large-scale two-hybrid analysis has been proposed as a way to functionally annotate large numbers of uncharacterized proteins predicted by complete genome sequences. This approach was examined in Caenorhabditis elegans, starting with 27 proteins involved in vulval development. The resulting map reveals both known and new potential interactions and provides a functional annotation for approximately 100 uncharacterized gene products. A protein interaction mapping project is now feasible for C. elegans on a genome-wide scale and should contribute to the understanding of molecular mechanisms in this organism and in human diseases.AD - Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA.FAU - Walhout, A JAU - Walhout AJFAU - Sordella, RAU - Sordella RFAU - Lu, XAU - Lu XFAU - Hartley, J LAU - Hartley JLFAU - Temple, G FAU - Temple GFFAU - Brasch, M AAU - Brasch MAFAU - Thierry-Mieg, NAU - Thierry-Mieg NFAU - Vidal, MAU - Vidal MLA - engID - 1 R21 CA81658 A 01/CA/NCIID - 1 RO1 HG01715-01/HG/NHGRIPT - Journal ArticleCY - UNITED STATESTA - ScienceJID - 0404511RN - 0 (Genetic Vectors)RN - 0 (Helminth Proteins)RN - 0 (LIN-35 protein)RN - 0 (LIN-53 protein)RN - 0 (Repressor Proteins)RN - 0 (Retinoblastoma Protein)SB - IM

Clark SG et al. (1994) Genetics "The Caenorhabditis elegans locus lin-15, a negative regulator of a tyrosine kinase signaling pathway, encodes two different proteins."

Clark SG, Lu WX, Horvitz HR

[Genetics, 1994]

The Caenorhabditis elegans locus lin-15 negatively regulates an intercellular signaling process that induces formation of the hermaphrodite vulva. The lin-15 locus controls two separate genetic activities. Mutants that lack both activities have multiple, ectopic pseudo-vulvae resulting from the overproduction of vulval cells, whereas mutants defective in only one lin-15 activity appear wild-type. lin-15 acts non-cell-autonomously to prevent the activation of a receptor tyrosine kinase/ras signaling pathway. We report here the molecular characterization of the lin-15 locus. The two lin-15 activities are encoded by contiguous genomic regions and by two distinct, non-overlapping transcripts that may be processed from a single mRNA precursor by trans-splicing. Based on the DNA sequence, the 719- and 1,440-amino acid lin-15 proteins are not similar to each other or to known proteins. lin-15 multivulva mutants, which are defective in both lin-15 activities, contain deletions and insertions that affect the lin-15 genomic region.

Gross RE et al. (1990) J Biol Chem "Cloning, characterization, and expression of the gene for the catalytic subunit of cAMP-dependent protein kinase in Caenorhabditis elegans. Identification of highly conserved and unique isoforms generated by alternative splicing."

Lu WX, Bagchi S, Gross RE, Rubin CS

[J Biol Chem, 1990]

The nematode Caenorhabditis elegans expresses substantial amounts of several forms (Mr values = 39,000-41,000) of the catalytic subunit (C) of cAMP-dependent protein kinase. Approximately 65% of the total cAMP-dependent phosphotransferase activity is recovered in particulate fractions of homogenates prepared from asynchronous populations of C. elegans. The C subunit is expressed at a low level in cytosolic and particulate compartments during embryogenesis. As the nematodes progress from late embryonic stages to the newly hatched, first larval (L1) stage, C subunit content increases 15-fold. High levels of C subunits are observed in several subsequent larval and adult stages of development. Since the relative abundance of C subunit mRNA changes little with development, it appears that control of C expression is exerted the translational and/or post-translational levels. cDNAs for two types of C have been cloned and sequenced. The derived amino acid sequence of a major isoform (CeCAT alpha, 358 residues) is highly homologous (82% identical) with the murine C alpha subunit. A second, novel C subunit (CeCAT alpha', 374 residues) has a unique 56-residue carboxyl-terminal region that is generated by the alternative splicing of the C pre-mRNA. The splicing process that yields CeCAT alpha' is unusual because it converts the central portion of an apparent 1-kilobase (kb) intron to an exon. The alternative exon introduces the novel carboxyl terminus and a new translation stop signal, while simultaneously converting the coding sequence for 40 carboxyl-terminal residues in CeCAT alpha into 3'-untranslated nucleotides. The 5' end of the C. elegans C subunit mRNA is produced by the trans-splicing of the C gene transcript to a 22-base pair C. elegans leader sequence originally described by Krause, M., and Hirsh, D. [1987) Cell 49, 753-761). The 20-kb C. elegans C gene is divided into seven exons by introns ranging in size from 54 to 8000 bp. The sizes of the C. elegans C subunit gene, cytoplasmic mRNA (2.5 kb), and subunit protein are similar to the sizes of the murine C alpha gene, mRNA, and polypeptide. However, the nematode and murine C genes differ significantly in the organization of their introns and exons.

Shi D et al. (2019) Phys Rev E "Refined parcellation of the nervous system by algorithmic detection of hidden features within communities."

Noori HR, Levina A, Shi D

[Phys Rev E, 2019]

The nervous system can be represented as a multiscale network comprised by single cells or ensembles that are linked by physical or functional connections. Groups of morphologically and physiologically diverse neurons are wired as connectivity patterns with a certain degree of universality across species and individual variability. Thereby, community detection approaches are often used to characterize how neural units cluster into such densely interconnected groups. However, the communities may possess deeper structural features that remain undetected by current algorithms. We present a scheme for refined parcellation of neuronal networks, by identifying local integrator units (LU) that are contained in network communities. An LU is defined as a connected subnetwork in which all neuronal connections are constrained within this unit, and can be formed for instance by a set of interneurons. Our method uses the Louvain algorithm to detect communities and participation coefficients to discriminate local neurons from global hubs. The sensitivity of the algorithm for discovering LUs with respect to the choice of community detection algorithm and network parameters was tested by simulations of different synthetic networks. The appropriateness of the algorithm for real-world scenarios was demonstrated on weighted and binary Caenorhabditis elegans connectomes. The detected LUs are distinctly localized within the worm body and clearly define functional groups. This approach provides a robust, observer-independent parcellation strategy that is useful for functional structure confirmation and potentially contributes to the current efforts in quantitative whole-brain architectonics of different species as well as the analysis of functional connectivity networks.

Buddell, Tyler et al. (2021) MicroPubl Biol

Quinn, Christopher C, Buddell, Tyler

[MicroPubl Biol, 2021]

The egl-19 gene in C. elegans encodes the pore forming subunit for the L-type voltage gated calcium channel that is homologous to the CACNA1C gene in humans (Lee et al., 1997). Variants in CACNA1C are risk factors for autism and other neurodevelopmental disorders (Li et al., 2015; Lu et al., 2012; Strom, et al., 2010). Timothy syndrome is a syndromic form of autism that can be caused by either of three rare de novo mutations in CACNA1C. These mutations cause either a G402R, G402S or G406R mutation in the CACNA1C protein (Splawski et al., 2004; Bader et al., 2011). Our previous work demonstrated that PLM axon termination is disrupted by mutations equivalent to the G402R and G406R mutations in CACNA1C (Buddell et al., 2019). Our study also revealed behavioral defects in these mutant worms. Although the anatomical basis for these behavioral defects has not been determined, it is likely that they are caused by multiple defects within the mechanosensory system.

Neu AK et al. (2014) Appl Environ Microbiol "Toxicity of bioactive and probiotic marine bacteria and their secondary metabolites in Artemia sp. and Caenorhabditis elegans as eukaryotic model organisms."

Prol-Garcia MJ, Gram L, Neu AK, Mansson M

[Appl Environ Microbiol, 2014]

We have previously reported that some strains belonging to the marine Actinobacteria class, the Pseudoalteromonas genus, the Roseobacter clade, and the Photobacteriaceae and Vibrionaceae families produce both antibacterial and antivirulence compounds, and these organisms are interesting from an applied point of view as fish probiotics or as a source of pharmaceutical compounds. The application of either organisms or compounds requires that they do not cause any side effects, such as toxicity in eukaryotic organisms. The purpose of this study was to determine whether these bacteria or their compounds have any toxic side effects in the eukaryotic organisms Artemia sp. and Caenorhabditis elegans. Arthrobacter davidanieli WX-11, Pseudoalteromonas luteoviolacea S4060, P. piscicida S2049, P. rubra S2471, Photobacterium halotolerans S2753, and Vibrio coralliilyticus S2052 were lethal to either or both model eukaryotes. The toxicity of P. luteoviolacea S4060 could be related to the production of the antibacterial compound pentabromopseudilin, while the adverse effect observed in the presence of P. halotolerans S2753 and V. coralliilyticus S2052 could not be explained by the production of holomycin nor andrimid, the respective antibiotic compounds in these organisms. In contrast, the tropodithietic acid (TDA)-producing bacteria Phaeobacter inhibens DSM17395 and Ruegeria mobilis F1926 and TDA itself had no adverse effect on the target organisms. These results reaffirm TDA-producing Roseobacter bacteria as a promising group to be used as probiotics in aquaculture, whereas Actinobacteria, Pseudoalteromonas, Photobacteriaceae, and Vibrionaceae should be used with caution.

Tabish M et al. (1999) Biochem J "Organization and alternative splicing of the Caenorhabditis elegans cAMP-dependent protein kinase catalytic-subunit gene (kin-1)."

Tabish M, Clegg RA, Rees HH, Fisher MJ

[Biochem J, 1999]

The cAMP-dependent protein kinase (protein kinase A, PK-A) is multifunctional in nature, with key roles in the control of diverse aspects of eukaryotic cellular activity. In the case of the free-living nematode, Caenorhabditis elegans, a gene encoding the PK-A catalytic subunit has been identified and two isoforms of this subunit, arising from a C-terminal alternative-splicing event, have been characterized [Gross, Bagchi, Lu and Rubin (1990) J. Biol. Chem. 265, 6896-6907]. Here we report the occurrence of N-terminal alternative-splicing events that, in addition to generating a multiplicity of non-myristoylatable isoforms, also generate the myristoylated variant(s) of the catalytic subunit that we have recently characterized [Aspbury, Fisher, Rees and Clegg (1997) Biochem. Biophys. Res. Commun. 238, 523-527]. The gene spans more than 36 kb and is divided into a total of 13 exons. Each of the mature transcripts contains only 7 exons. In addition to the already characterized exon 1, the 5'-untranslated region and first intron actually contain 5 other exons, any one of which may be alternatively spliced on to exon 2 at the 5' end of the pre-mRNA. This N-terminal alternative splicing occurs in combination with either of the already characterized C-terminal alternative exons. Thus, C. elegans expresses at least 12 different isoforms of the catalytic subunit of PK-A. The significance of this unprecedented structural diversity in the family of PK-A catalytic subunits is discussed.

Rivera Gomez KA et al. (2018) MicroPubl Biol "Immobilization nematodes for live imaging using an agarose pad produced with a Vinyl Record"

Rivera Gomez KA, Schvarzstein M

[MicroPubl Biol, 2018]

Numerous microfluidic systems have been developed and used for live imaging of Caenorhabditis nematodes (Allen et al., 2008; Zhang et al., 2008; Krajniak and Lu, 2010; Krajniak et al., 2013; Cornaglia et al., 2015). These systems can be costly, complex to set up, or require high-maintenance between uses. In addition, microfluidic rigs can be thick, preventing live imaging of worms from strains expressing low fluorescence fusion proteins. In the absence of elaborate microfluidic rigs, most live imaging protocols utilize flat agarose pads along with anesthetics and/or microbeads to immobilize the nematodes (Kim et al., 2013). Since this method does not allow the user to maintain the nematode straight and does not prevent small movements that disturb live imaging, a higher number of worms need to be mounted to ensure that a some settle in an optimal position. This is especially problematic when trying to image nematodes genotypes that are scarce, since there is a very small number of nematodes with the desired genotype in a plate making it challenging to find enough animals to image. Here is a protocol, modified from Zhang, M. et al., 2008, to make grooved agarose pads utilizing a 12-inch vinyl Long Play (LP) record as a mold for agar pads in which nematodes can be positioned and immobilized for live imaging. This method is simple, effective, and allows long-term time-lapse imaging of young adult and adult hermaphrodites, and males expressing low fluorescence fusion proteins.