Shen Z-Z et al. (1998) European Worm Meeting "Screen for body size mutants in C. elegans"

Leroi AM, Shen Z-Z, Patel MN

[European Worm Meeting, 1998]

Little is known about the molecular genetic specification of growth and body size in any metazoan. In C. elegans, a number of loci which influence the body size has been identified (Brenner, 1974). So far, these fall into three classes: First, genes involved in TGF-b signal transduction. Among them, daf-4 has been shown to encode a TGF-b receptor II (Estevez et al., 1993). Sma-2, sma-3 and sma-4 are TGF-b pathway components which are homologue to the Drosophila gene Mothers against Dpp (Savage et al., 1996). Second, genes involved in the control of cytoskeleton structure. he sequence from sma-1 has been shown to contain spectrin, a cytoskeleton component, and the sequence from lon-2 has been predicted to be regulatory proteins of cytoskeleton (Austin, pers comm.; Vellai pers comm). Finally, there are genes that affect cuticle structure. dpy-2, dpy-7 and dpy-10 encode collagen (Levy et al., 1993; Johnstone et al., 1992) and clearly are very small in size. How these pathways interact to control body size is unclear. In our attempt to understand the controls of body growth in C. elegans we conducted EMS mutagenesis for new body size loci. We are especially interested in giant mutants of which few have hitherto been found. We screened 50,000 genomes of Bristol N2 (table 1). We have begun measuring, backcrossing and mapping these mutants with a view towards cloning them. Some of the giants are 50-75% larger than wildtype (by volume). There may be a continuum between lons and giants.

Shen Z et al. (2023) Mol Biol Cell "Inhibition of the Chromatin Remodeling Factor NURF Rescued Sterility by a Clinic Variant of NuRD."

Ou G, Shen Z, Guo Z, Li W

[Mol Biol Cell, 2023]

The nucleosome remodeling and deacetylase (NuRD) complex is essential for gene expression and cell fate determination, and missense mutations of NuRD caused neurodevelopmental diseases. However, the molecular pathogenesis&#xa0;of clinic NuRD variants is unknown. Here, we introduced a clinic CHD3(L915F) variant into <i>C. elegans</i> homolog LET-418, impairing germline and vulva development and ultimately causing animal sterility. Our ATAC-seq and RNA-seq analyses revealed that this variant generated an abnormal open chromatin structure and disrupted the expression of developmental genes. Through genetic suppressor screens, we uncovered that intragenic mutations, likely renovating NuRD activity, restored animal viability. We also found that intergenic mutations in nucleosome remodeling factor NURF that counteracts NuRD rescued abnormal chromatin structure, gene expression, and animal sterility. We propose that two antagonistic chromatin-remodeling factors coordinate to establish the proper chromatin status and transcriptome and that inhibiting NURF may provide insights for treatment of NuRD mutation-related diseases.

Shen Z et al. (1998) J Biol Chem "A type I peritrophic matrix protein from the malaria vector Anopheles gambiae binds to chitin. Cloning, expression, and characterization."

Jacobs-Lorena M, Shen Z

[J Biol Chem, 1998]

Upon feeding, mosquito midguts secrete the peritrophic matrix (PM), an extracellular chitin-containing envelope that completely surrounds the blood meal. Because the malaria parasite must cross the PM to complete its life cycle in the mosquito, the PM is a potential barrier for malaria transmission. By antibody screening of an expression library we have identified and partially characterized a cDNA encoding a putative PM protein, termed Anopheles gambiae adult peritrophin 1 (Ag-Aper1). Ag-Aper1 is the first cloned PM gene from a disease vector. Northern analysis detected an abundant Ag-Aper1 transcript only in the adult gut, and not in any other tissues or at any other stages of development. The predicted amino acid sequence indicates that it has two tandem chitin-binding domains that share high sequence similarity with each other and also with the chitin-binding domain of an adult gut-specific chitinase from the same organism. The presumed ability of Ag-Aper1 to bind chitin was verified by a functional assay with the baculovirus-expressed recombinant protein. Ag-Aper1 did bind to chitin but not to cellulose, indicating that Ag-Aper1 binds chitin specifically. The double chitin-binding domain organization of Ag-Aper1 suggests that each protein molecule is able to link two chitin polymer chains. Hence, this protein is likely to act as a molecular linker that connects PM chitin fibrils into a three-dimensional network.

Shen Z et al. (2014) Dev Cell "Conditional knockouts generated by engineered CRISPR-Cas9 endonuclease reveal the roles of coronin in C. elegans neural development."

Feng G, Yi P, Chai Y, Ou G, Zhang X, Zhu Z, Li W, Shen Z

[Dev Cell, 2014]

Conditional gene knockout animals are valuable tools for studying the mechanisms underlying cell and developmental biology. We developed a conditional knockout strategy by spatiotemporally manipulating the expression of an RNA-guided DNA endonuclease, CRISPR-Cas9, in Caenorhabditis elegans somatic cell lineages. We showed that this somatic CRISPR-Cas9 technology provides a quick and efficient approach to generate conditional knockouts in various cell types at different developmental stages. Furthermore, we demonstrated that this method outperforms our recently developed somatic TALEN technique and enables the one-step generation of multiple conditional knockouts. By combining these techniques with live-cell imaging, we showed that an essential embryonic gene, Coronin, which is associated with human neurobehavioral dysfunction, regulates actin organization and cell morphology during C. elegans postembryonic neuroblast migration and neuritogenesis. We propose that the somatic CRISPR-Cas9 platform is uniquely suited for conditional gene editing-based biomedical research.

Ketel, CS et al. (2005) Mol Cell Biol "Subunit contributions to histone methyltransferase activities of fly and worm polycomb group complexes."

Vargas, ML, Andersen, EF, Strome, S, Ketel, CS, Suh, J, Simon, JA

[Mol Cell Biol, 2005]

The ESC-E(Z) complex of Drosophila melanogaster Polycomb group (PcG) repressors is a histone H3 methyltransferase (HMTase). This complex silences fly Hox genes, and related HMTases control germ line development in worms, flowering in plants, and X inactivation in mammals. The fly complex contains a catalytic SET domain subunit, E(Z), plus three noncatalytic subunits, SU(Z)12, ESC, and NURF-55. The four-subunit complex is > 1,000-fold more active than E(Z) alone. Here we show that ESC and SU(Z)12 play key roles in potentiating E(Z) HMTase activity. We also show that loss of ESC disrupts global methylation of histone H3-lysine 27 in fly embryos. Subunit mutations identify domains required for catalytic activity and/or binding to specific partners. We describe missense mutations in surface loops of ESC, in the CXC domain of E(Z), and in the conserved VEFS domain of SU(Z)12, which each disrupt HMTase activity but preserve complex assembly. Thus, the E(Z) SET domain requires multiple partner inputs to produce active HMTase. We also find that a recombinant worm complex containing the E(Z) homolog, MES-2, has robust HMTase activity, which depends upon both MES-6, an ESC homolog, and MES-3, a pioneer protein. Thus, although the fly and mammalian PcG complexes absolutely require SU(Z)12, the worm complex generates HMTase activity from a distinct partner set.

Wan G et al. (2021) EMBO J "ZSP-1 is a Z granule surface protein required for Z granule fluidity and germline immortality in Caenorhabditis elegans."

Pagano D, Dodson AE, Bajaj L, Kennedy S, Fei Y, Wan G, Fields B

[EMBO J, 2021]

Germ granules are biomolecular condensates that form in germ cells of all/most animals, where they regulate mRNA expression to promote germ cell function and totipotency. In the adult Caenorhabditis elegans germ cell, these granules are composed of at least four distinct sub-compartments, one of which is the Z granule. To better understand the role of the Z granule in germ cell biology, we conducted a genetic screen for genes specifically required for Z granule assembly or morphology. Here, we show that zsp-1, which encodes a low-complexity/polyampholyte-domain protein, is required for Z granule homeostasis. ZSP-1 localizes to the outer surface of Z granules. In the absence of ZSP-1, Z granules swell to an abnormal size, fail to segregate with germline blastomeres during development, and lose their liquid-like character. Finally, ZSP-1 promotes piRNA- and siRNA-directed gene regulation and germline immortality. Our data suggest that Z granules coordinate small RNA-based gene regulation to promote germ cell function and that ZSP-1 helps/is need to maintain Z granule morphology and liquidity.

Khan, Munzareen et al. (2021) International Worm Meeting "

Khan, Munzareen, Sengupta, Piali, Dwyer, Noelle, Hartmann, Anna, Bargmann, Cori, Piccione, Madeline

[International Worm Meeting, 2021]

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Krishna P et al. (1988) J Biol Chem "Yolk proteins from nematodes, chickens, and frogs bind strongly and preferentially to left-handed Z-DNA."

Krishna P, Kennedy BP, van de Sande JH, McGhee JD

[J Biol Chem, 1988]

Yolk proteins purified from the nematode Caenorhabditis elegans, from the frog Xenopus laevis, and from chicken eggs all have the unexpected property of binding strongly and preferentially to a left-handed Z-DNA probe, brominated poly(dG-dC). We estimate that the nematode proteins bind to Z-DNA with an association constant of at least 10(4) (M-1) and that this association constant is at least 40-50-fold higher than the association constant to B-DNA. Thus, yolk proteins have a higher Z-DNA specificity than most of the Z-DNA binding proteins previously isolated from other sources. Although yolk protein binding to Z-DNA is poorly competed by a wide variety of nucleic acids, the interaction is strongly competed by the phospholipids cardiolipin and phosphatidic acid (500-1000-fold better than by the same mass of B-DNA). We suggest that Z-DNA interacts with the yolk protein phospholipid binding site. In general, our results emphasize the danger of using physical properties to infer biological function. In particular, our results should raise serious questions about the biological relevance of previously isolated Z-DNA binding proteins.

Svendsen JM et al. (2018) Dev Cell "piRNA Rules of Engagement."

Svendsen JM, Montgomery TA

[Dev Cell, 2018]

piRNAs are known to silence transposable elements, but not all piRNAs match transposon sequences. Recent studies from Shen etal. (2018) and Zhang etal. (2018) identify rules for piRNA target recognition in Caenorhabditis elegans. Permissive pairing rules allow targeting of essentially all germline mRNAs, while protective mechanisms prevent silencing self-genes.

Davis E et al. (2007) Cell "Should I stay or should I go: Wnt signals at the synapse."

Davis E, Ghosh A

[Cell, 2007]

Several extracellular factors, including Wnt proteins, have been reported to induce synapse formation. In this issue, Klassen and Shen (2007) report that Wnt proteins can also act as antisynaptogenic signals to prevent synapse formation in certain parts of the worm Caenorhabditis elegans. The differential response of axon populations to local Wnt proteins may contribute to the patterning of synaptic connections.