Kuang WW et al. (1998) Nucleic Acids Res "Differential screening and suppression subtractive hybridization identified genes differentially expressed in an estrogen receptor-positive breast carcinoma cell line."

Hoch RV, Thompson DA, Weigel RJ, Kuang WW

[Nucleic Acids Res, 1998]

Differences in gene expression are likely to explain the phenotypic differences between hormone-responsive and hormone-unresponsive breast cancer. We have identified differentially expressed cDNAs in the estrogen receptor (ER)-positive MCF7 breast carcinoma cell line compared with the ER-negative MDA-MB-231 breast carcinoma cell line. Differential screening isolated four differentially expressed genes: cytokeratin 8, cytokeratin 18, Hsp27 and GPCR -Br. To identify differentially expressed genes of lower abundance, suppression subtractive hybridization was utilized and 29 differentially expressed clones were isolated. Sequence analysis revealed that 11 clones were from previously described genes: HEK8, neuropeptide Y receptor Y1, p21 WAF-1, p55 PIK, cytokeratin 18 (cloned twice), fructose-1,6-biphosphatase, cytokeratin 8, TGFbeta1 binding protein, elongation factor 1alpha2 and pS2. The remaining 18 clones did not match sequences in the GenBank/EMBL database, indicating that they may be novel genes. Expression of pS2, neuropeptide Y receptor Y1 and three novel clones was induced by estradiol, indicating estrogen-responsiveness. The expression pattern of one novel gene, DEME -6, correlated with expression of ER and ERF -1/ AP -2gamma in a panel of breast carcinoma cell lines. A 2.6 kb cDNA of DEME -6 was sequenced and contains an open reading frame of 574 amino acids that demonstrates 62.4% similarity with a gene from Caenorhabditis elegans chromosome III. Expression of DEME -6 was also detected in primary breast carcinomas but not in normal breast tissue, as determined by RT-PCR. These findings support the hypothesis that a set of genes coordinately regulated with ER , but not necessarily estradiol-responsive, are characteristic of the hormone-responsive breast cancer phenotype.

Kato Y et al. (2002) J Biol Chem "Determinants of ligand specificity in groups I and IV WW domains as studied by surface plasmon resonance and model building."

Kato Y, Ito M, Tanokura M, Kawai K, Nagata K

[J Biol Chem, 2002]

WW domains are universal protein modules for binding Pro-rich ligands. They are classified into four groups according to their binding specificity. Arg-14 and Arg-17, on the WW domain of Pin1, are thought to be important for the binding of Group IV ligands that have (Ser(P)/Thr(P))-Pro sequences. We have applied surface plasmon resonance to determine the ligand specificity of several WW domains containing Arg-14. Among these WW domains, Rsp5.2 and mNedd4.3 bound only to the Group I ligand containing Pro-Pro-Xaa-Tyr with K(D) values of 11 and 55 microm, respectively. The WW domains of hPin1, Caenorhabditis elegans Pin1 homologue (Y110), PinA, and SspI bound to Group IV ligands with K(D) values ranging from 22 to 700 microm. PinA and SspI do not have Arg-17, unlike Pin1 and Y110. The modeled structures of the WW domains of PinA and SspI revealed that the structure and the network of hydrogen bonds of Loop I, which are also formed in Pin1 and Y110, are conserved. We propose that this configuration of Loop I (referred to as the "p patch") is necessary for binding Group IV ligands and that it can be used to predict the specificity and functions of other WW domains.

Wright GM et al. (2019) Nucleic Acids Res "The nucleosome position-encoding WW/SS sequence pattern is depleted in mammalian genes relative to other eukaryotes."

Cui F, Wright GM

[Nucleic Acids Res, 2019]

Nucleosomal DNA sequences generally follow a well-known pattern with 10-bp periodic WW (where W is A or T) dinucleotides that oscillate in phase with each other and out of phase with SS (where S is G or C) dinucleotides. However, nucleosomes with other DNA patterns have not been systematically analyzed. Here, we focus on an opposite pattern, namely anti-WW/SS pattern, in which WW dinucleotides preferentially occur at DNA sites that bend into major grooves and SS (where S is G or C) dinucleotides are often found at sites that bend into minor grooves. Nucleosomes with the anti-WW/SS pattern are widespread and exhibit a species- and context-specific distribution in eukaryotic genomes. Unlike non-mammals (yeast, nematode and fly), there is a positive correlation between the enrichment of anti-WW/SS nucleosomes and RNA Pol II transcriptional levels in mammals (mouse and human). Interestingly, such enrichment is not due to underlying DNA sequence. In addition, chromatin remodeling complexes have an impact on the abundance but not on the distribution of anti-WW/SS nucleosomes in yeast. Our data reveal distinct roles of cis- and trans-acting factors in the rotational positioning of nucleosomes between non-mammals and mammals. Implications of the anti-WW/SS sequence pattern for RNA Pol II transcription are discussed.

Serizay J et al. (2020) Genome Res "Distinctive regulatory architectures of germline-active and somatic genes in C. elegans."

Dong Y, Serizay J, Chesney M, Cerrato C, Ahringer J, Janes J

[Genome Res, 2020]

RNA profiling has provided increasingly detailed knowledge of gene expression patterns, yet the different regulatory architectures that drive them are not well understood. To address this, we profiled and compared transcriptional and regulatory element activities across five tissues of <i>C. elegans</i>, covering ~90% of cells. We find that the majority of promoters and enhancers have tissue-specific accessibility, and we discover regulatory grammars associated with ubiquitous, germline and somatic tissue-specific gene expression patterns. In addition, we find that germline-active and soma-specific promoters have distinct features. Germline-active promoters have well positioned +1 and -1 nucleosomes associated with a periodic 10-bp WW signal (W = A/T). Somatic tissue-specific promoters lack positioned nucleosomes and this signal, have wide nucleosome depleted regions, and are more enriched for core promoter elements, which differ between tissues. We observe the 10-bp periodic WW signal at ubiquitous promoters in other animals suggesting it is an ancient conserved signal. Our results demonstrate fundamental differences in regulatory architectures of germline and somatic tissue-specific genes, uncover regulatory rules for generating diverse gene expression patterns, and provide a tissue-specific resource for future studies.

Kuang, Xiangyu et al. (2021) International Worm Meeting "Computable early C. elegans embryo with a data-driven phase field model"

Tang, Chao, Zhao, Zhongying, Wong, Ming-Kin, Kuang, Xiangyu, Guan, Guoye, Zhang, Lei, Chan, Lu-Yan

[International Worm Meeting, 2021]

Morphogenesis is a precise and robust dynamic process during metazoan embryogenesis, consisting of both cell proliferation and cell migration. Despite the fact that much is known about specific regulations at the molecular level, how cell proliferation and migration together drive the morphogenesis at the cellular and organismic levels is not well understood. Here, using Caenorhabditis elegans as the model animal, we present a data-driven phase field model to compute the early embryonic morphogenesis within a confined eggshell. By using three-dimensional time-lapse cellular morphological information generated by imaging experiments to set the model parameters, we can not only reproduce the precise evolution of cell location, cell shape and cell-cell contact relationship in vivo, but also reveal the critical roles of cell division and cell-cell attraction in governing the early development of C. elegans embryo. In brief, we provide a generic approach to compute the embryonic morphogenesis and decipher the underlying mechanisms (Kuang&dagger;, Guan&dagger;, et al. bioRxiv, 2020, 422560).

Courbard JR et al. (2002) J Biol Chem "Interaction between two ubiquitin-protein isopeptide ligases of different classes, CBLC and AIP4/ITCH."

Birnbaum D, Fiore F, Borg JP, Ollendorff V, Courbard JR, Adelaide J

[J Biol Chem, 2002]

In metazoans, CBL proteins are RING finger type ubiquitin-protein isopeptide (E3) ligases involved in the down-regulation of epidermal growth factor tyrosine kinase receptors (EGFR). Among the three CBL proteins described in humans, CBLC (CBL3) remains poorly studied. By screening in parallel a human and a Caenorhabditis elegans library using the two-hybrid procedure in yeast, we found a novel interaction between Hsa-CBLC and Hsa-AIP4 or its C. elegans counterpart Cel-WWP1. Hsa-AIP4 and Cel-WWP1 are also ubiquitin E3 ligases. They contain a HECT (homologous to E6-AP C terminus) catalytic domain and four WW domains known to bind proline-rich regions. We confirmed the interaction between Hsa-CBLC and Hsa-AIP4 by a combination of glutathione S-transferase pull-down, co-immunoprecipitation, and colocalization experiments. We show that these two E3 ligases are involved in EGFR signaling because both become phosphorylated on tyrosine following epidermal growth factor stimulation. In addition, we observed that CBLC increases the ubiquitination of EGFR, and that coexpressing the WW domains of AIP4 exerts a dominant negative effect on EGFR ubiquitination. Finally, coexpressing CBLC and AIP4 induces a down-regulation of EGFR signaling. In conclusion, our data demonstrate that two E3 ligases of different classes can interact and cooperate to down-regulate EGFR signaling.

Huang K et al. (2000) Gene "A HECT domain ubiquitin ligase closely related to the mammalian protein WWP1 is essential for Caenorhabditis elegans embryogenesis."

Mosser EA, Bresnick EH, Petcherski AG, Johnson KD, Kimble JE, Vandergon T, Huang K, Jenkins NA, Copeland NG

[Gene, 2000]

The highly conserved ubiquitin/proteasome pathway controls the degradation of many critical regulatory proteins. Proteins are posttranslationally conjugated to ubiquitin through a concerted set of reactions involving activating (E1), conjugating (E2), and ligase (E3) enzymes. Ubiquitination targets proteins for proteolysis via the proteasome and may regulate protein function independent of proteolysis. We describe the cloning and functional analysis of new members of the HECT domain family of E3 ubiquitin ligases. Murine Wwp1 encoded a broadly expressed protein containing a C2 domain, four WW domains, and a catalytic HECT domain. A Caenorhabditis elegans gene was cloned encoding a HECT domain protein (CeWWP1), which was highly homologous to murine and human WWP1. Disruption of CeWwp1 via RNA interference yielded an embryonic lethal phenotype, despite the presence of at least six additional C. elegans genes encoding HECT domain proteins. The embryonic lethality was characterized by grossly abnormal morphogenesis during late embryogenesis, despite normal proliferation early in embryogenesis. CeWWP1 must therefore have unique and nonredundant functions critical for embryogenesis.

Attila Stetak et al. (2008) Development & Evolution Meeting "The MAGI-1 protein functions as an organizer of LET-23 localization the adherens junctions"

ALEX HAJNAL, Attila Stetak, Sander Van Den Heuvel

[Development & Evolution Meeting, 2008]

The C. elegans hermaphrodite vulva is formed by the descendents of three out of six equipotent vulval precursor cells (the VPCs P3.p through P8.p). The gonadal anchor cell produces the LIN3 EGF signal that activates the conserved EGFR/RAS/MAPK signaling pathway in the adjacent VPCs and specifies the primary cell fate in P6.p. The basolateral localization of LET-23 EGFR in the VPCs is essential for the efficient receptor activation and consequently for proper vulval induction. A ternary complex consisting of the PDZ-domain proteins LIN-7, LIN-2 and LIN-10 is required for the localization of the EGFR to the basolateral compartment. Interestingly, PDZ-domains are often found in adaptor proteins that are control the subcellular localization of other proteins such as receptors. Using a forward genetic approach, we have identified the magi-1 gene (K01A6.2) as a suppressor of the let-60(gf) Multivulva phenotype. MAGI-1 is a multi-PDZ domain protein consisting of an N-terminal guanylate kinase domain with two overlapping WW repeats followed by five PDZ domains. Mammalian MAGI is expressed in neurons and epidermal cells and is localized at the cell junctions where it interacts with several proteins including PTEN and beta-Catenin. The C. elegans magi-1 gene encodes two isoforms transcribed from alternative promoters. Using translational MAGI-1::GFP reporters, we found that the two MAGI-1 isoforms are widely expressed, however only the isoform encoded by the shorter transcript is expressed in the VPCs. Furthermore, the MAGI-1::GFP fusion protein is localized at the adherens junctions of the epidermal and gut cells. MAGI-1 interacts in GST-pull-down experiments with HMP-2 beta-Catenin via its fifth PDZ domain and with both LET-23 EGFR and LIN-7 via its guanylate kinase or WW domains. magi-1 deletion mutants display no obvious developmental phenotypes, but magi-1(lf) animals exhibit reduced basolateral LET-23 EGFR staining in the VPCs and enhanced embryonic lethality in combination with apr-1 RNAi. Thus, MAGI-1 might serve as a junctional organizer protein during embryogenesis and vulval development.

Chang-Shi Chen et al. (2010) East Asia Worm Meeting "DAF-2 Insulin-like signaling network is involved in Pore-Forming Toxin Cellular Defenses in C. elegans"

Huan-Da Chen, Audrey Bellier, Ferdinand C. O. Los, Chang-Shi Chen, Raffi V. Aroian, Ya-Luen Yang, Cheng-Yuan Kao

[East Asia Worm Meeting, 2010]

Cytolytic pore-forming toxins (PFTs) are a class of potent virulence factor of many disease-causing bacteria that convert from a soluble form to a membrane-integrated pore to intoxicate host cells. Although PFTs play important roles in the development of bacterial disease, we have enormous gaps in our knowledge and are only beginning to understand what these toxins do to the target cells and especially to the whole organism. The DAF-2 insulin/insulin-like growth factor-1 signaling pathway, which regulates lifespan and stress resistance in C. elegans, is known to mutate to resistance to pathogenic bacteria. Here we reveal that reduction of the DAF-2 insulin-like pathway signal cascade also confers the resistance of C. elegans to Crystal toxins, which are PFTs produced by Bacillus thuringiensis. Moreover, this resistance signal diverges at 3-phosphoinositide-dependent kinase 1 (PDK-1) and feeds into a novel signal arm defined by the WW domain Protein 1 (WWP-1). Taken together, our data suggest that WWP-1 and DAF-16 function in parallel within the fundamental DAF-2 signaling network to regulate fundamental cellular responses in C. elegans.

Plowman GD et al. (1999) Proc Natl Acad Sci U S A "The protein kinases of Caenorhabditis elegans: a model for signal transduction in multicellular organisms."

Sudarsanam S, Whyte D, Hunter T, Bingham J, Plowman GD

[Proc Natl Acad Sci U S A, 1999]

Caenorhabditis elegans should soon be the first multicellular organism whose complete genomic sequence has been determined. This achievement provides a unique opportunity for a comprehensive assessment of the signal transduction molecules required for the existence of a multicellular animal. Although the worm C. elegans may not much resemble humans, the molecules that regulate signal transduction in these two organisms prove to be quite similar. We focus here on the content and diversity of protein kinases present in worms, together with an assessment of other classes of proteins that regulate protein phosphorylation. By systematic analysis of the 19,099 predicted C. elegans proteins, and thorough analysis of the finished and unfinished genomic sequences, we have identified 411 full length protein kinases and 21 partial kinase fragments. We also describe 82 additional proteins that are predicted to be structurally similar to conventional protein kinases even though they share minimal primary sequence identity. Finally, the richness of phosphorylation-dependent signaling pathways in worms is further supported with the identification of 185 protein phosphatases and 128 phosphoprotein-binding domains (SH2, PTB, STYX, SBF, 14-3-3, FHA, and WW) in the worm genome.