Zhao C et al. (1993) Worm Breeder's Gazette "Cloning of the lin-32 Gene"

Emmons SW, Zhao C

[Worm Breeder's Gazette, 1993]

Cloning of the lin-32 gene Connie Zhao and Scott W. Emmons, Department of Molecular Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461

Bowerman B et al. (2019) Dev Cell "Breaking Symmetry: Worm Cue Finally Found."

Bowerman B, Sugioka K

[Dev Cell, 2019]

In this issue of Developmental Cell, Zhao etal. (2019) show that the Aurora A kinase AIR-1 is the long-sought cue that downregulates cortical actomyosin to establish anterior-posterior polarity in the C.elegans zygote, diffusing from centrosomes to the overlying cortex to phosphorylate yet to be identified target(s).

Shen, Yongquan et al. (2015) International Worm Meeting "Cubist biology - using evolutionary perspectives to define regulatory pathways."

Wei, Qing, Zhao, Yanmnei, Shen, Yongquan, Ellis, Ronald, Chen, Xiangmei, Lin, Shin-Yi

[International Worm Meeting, 2015]

One drawback of studying biology in a model organism is the difficulty of separating essential features from traits that are unique to one species but only of minor significance. We believe that evolutionary comparisons with close relatives provide the best way to address this problem, because each species provides a slightly different viewpoint. Combining these perspectives provides a richer, more complete picture, as in a cubist painting. Genome editing now makes this feasible.For example, our work with trr-1 (part of the Tip60 HAT complex) led us to focus on how chromatin regulators control the sperm/oocyte decision. We found that mutations in C. briggsae nurf-1 (part of the Nucleosome Remodeling Factor complex) favored oogenesis. Meanwhile, Li and Kelly showed that mutations in C. elegans wdr-5 genes (which act in an H3K4 trimethylation complex) favored spermatogenesis. Thus, we compared the functions of each gene in both species. Lowering NURF activity only favored oogenesis in C. briggsae, and had no effect on the sperm/oocyte decision in C. elegans or various male/female species. Hence, we conclude that its role in C. briggsae is a recent adaptation, rather than a general part of the sex-determination pathway. By contrast, we showed that wdr-5.1(RNAi); wdr-5.2(null) mutations promote oogenesis in C. briggsae, although they cause the opposite phenotype in C. elegans. Since these mutations affect the same decision, we suspect their biochemical interactions with TRA-1 are conserved; however, the context in which they act must have changed.Sperm activation also plays a critical role in the evolution of hermaphrodites. Five proteins mediate the hermaphrodite activation signal in C. elegans SPE-8, 12, 19, 27 and 29. Mutations in the C. briggsae SPE-8 kinase, the SPE-19 transmembrane protein, and SPE-27 prevent self-fertility, just like in C. elegans. However, null mutants for C. briggsae spe-29 and spe-12 appear wild type, which suggests that they do not play a central role in the signal transduction process. The zinc transporter HKE-4.1 also plays a major role in the activation of C. elegans sperm. However, C. elegans sperm can be activated by zinc in vitro, whereas C. briggsae sperm cannot, so we wondered if the role of HKE-4.1 was conserved. Null mutations in C. briggsae hke-4.1cause cold-sensitive sterility and those in C. tropicalis also cause sterility, so zinc transport plays a conserved role in sperm activation, and is an essential feature of this pathway.

Terskikh A et al. (2000) Science ""Fluorescent timer": protein that changes color with time."

Matz M, Ermakova G, Siebert P, Kim SK, Lukyanov S, Kajava AV, Weissman I, Zaraisky A, Terskikh A, Tan PBO, Fradkov A, Zhao X

[Science, 2000]

We generated a mutant of the red fluorescent protein drFP583. The mutant (E5) changes its fluorescence from green to red over time. The rate of color conversion is independent of protein concentration and therefore can be used to trace time-dependent expression. We used in vivo labeling with E5 to measure expression from the heat shock-dependent promoter in Caenorhabditis elegans and from the Otx-2 promoter in developing Xenopus embryos. Thus, E5 is a "fluorescent timer" that can be used to monitor both activation and down-regulation of target promoters on the whole-organism scale.AD - School of Medicine, Stanford University, Stanford, CA 94305, USA. Alexey.Terskikh@Stanford.eduFAU - Terskikh, AAU - Terskikh AFAU - Fradkov, AAU - Fradkov AFAU - Ermakova, GAU - Ermakova GFAU - Zaraisky, AAU - Zaraisky AFAU - Tan, PAU - Tan PFAU - Kajava, A VAU - Kajava AVFAU - Zhao, XAU - Zhao XFAU - Lukyanov, SAU - Lukyanov SFAU - Matz, MAU - Matz MFAU - Kim, SAU - Kim SFAU - Weissman, IAU - Weissman IFAU - Siebert, PAU - Siebert PLA - engID - 1 RO3 TW01362-01/TW/FICPT - Journal ArticleCY - UNITED STATESTA - ScienceJID - 0404511RN - 0 (Heat-Shock Proteins)RN - 0 (Luminescent Proteins)RN - 0 (Nerve Tissue Proteins)RN - 0 (Otx2 protein)RN - 0 (Trans-Activators)RN - 0 (red fluorescent protein)SB - IM

Memar, Nadin et al. (2009) International Worm Meeting "A view on the embryogenesis of the Caenorhabditis Family."

Martin, Katharina, Schnabel, Ralf, Memar, Nadin

[International Worm Meeting, 2009]

The molecular differences of the four Caenorhabditis species C. elegans, C. briggsae, C. remanei and C. brenneri are currently of great interest, however little is known about development. Zhao et al. (2008) reported an automatic lineage of C. briggsae and came - based mostly on the cleavage pattern and cell positions - to the conclusion that the embryogenesis of the two species is very similar. We now present detailed 4D analyses of the species including the terminal differentiation patterns. All analyses including bioinformatical quantifications of cell behaviour show a huge similarity between those species. Immunochemical analyses of the tissue distributions only reveal a difference in the intestinal differentiation of C. brenneri. Interestingly hybrid embryos always appear to fail in different ways in embryogenesis.

Duan, Ye et al. (2020) MicroPubl Biol

Ambros, Victor, Sun, Yongming, Duan, Ye

[MicroPubl Biol, 2020]

RNA-seq is widely used for the quantitative analysis of transcriptomes in the context of studies of gene expression and regulation (Mortazavi et al., 2008; Ozsolak and Milos, 2011; Wang et al., 2009). Generally, RNA-seq protocols employ poly(A) selection for mRNA enrichment. However, poly(A) based enrichment is subject to potential bias depending on the poly(A) status of various mRNAs, which could be particularly undesirable in the context of studying post-transcriptional gene regulatory mechanisms, such miRNA repression (Wu et al., 2006). Therefore, ribosomal RNA (rRNA) depletion is a desirable alternative strategy to enrich for mRNA sequences in RNA-seq sample preparation (Zhao et al., 2014). However, currently available rRNA depletion toolkits were designed for either mammals or bacteria, and hence do not offer an efficient option for rRNA depletion of RNA samples from certain experimental organisms, such as C. elegans.

Chu DS (2018) PLoS Biol "Zinc: A small molecule with a big impact on sperm function."

Chu DS

[PLoS Biol, 2018]

Zinc is an essential mineral, but our understanding of its uses in the body is limited. Capitalizing on approaches available in the model system Caenorhabditis elegans, Zhao and colleagues show that zinc transduces a signal that induces sperm to become motile. This is an enigmatic process because sperm in all sexually-reproducing animals are transcriptionally inactive. Zinc levels inside sperm are regulated by an evolutionarily conserved zinc transporter called Zrt- and Irt-like Protein Transporter 7.1 (ZIPT-7.1). This zinc transporter localizes to intracellular organelles, suggesting that it primarily controls zinc levels by releasing zinc into the cytoplasm from internal stores rather than importing it from the external environment. The zinc released within cells acts as a messenger in a signaling pathway to promote mobility acquisition. These studies reveal an important role for zinc as an intracellular second messenger that generates physiological changes vital for sperm motility and fertility.

Soo, Sonja K et al. (2021) MicroPubl Biol

Van Raamsdonk, Jeremy M, Soo, Sonja K

[MicroPubl Biol, 2021]

The mitochondrial unfolded protein response (mitoUPR) is a stress response pathway that promotes cell survival and restores mitochondrial function when mitochondrial health is compromised (Haynes et al. 2013; Jovaisaite et al. 2014; Shpilka and Haynes 2018). While a mitoUPR was first reported in mammalian cells (Zhao et al. 2002), the initial work on the mitoUPR in C. elegans was performed by Yoneda et al. who found that treatment with ethidium bromide, which affects the replication and expression of mitochondrial DNA, increased the expression of the mitochondrial chaperone gene hsp-6 (Yoneda et al. 2004). Based on this observation, they generated hsp-6p::gfp and hsp-60p::gfp reporter strains to further study the mitoUPR. They found that either RNA interference (RNAi) targeting spg-7, the worm homolog of paraplegin, or RNAi targeting other genes encoding mitochondrial proteins resulted in activation of the hsp-6p::gfp and hsp-60p::gfp reporter strains (Yoneda et al. 2004).

Weinreb, A. et al. (2017) International Worm Meeting "Analysis of activity-dependent synaptogenesis in the nematode Caenorhabditis elegans."

Jospin, M., Weinreb, A., Bessereau, JL.

[International Worm Meeting, 2017]

In various systems, activity of neurons or muscle leads to various forms of plasticity, thus shaping network connectivity and regulating synaptic strength. In C. elegans, activity was demonstrated in a few systems to play a role in synapse formation and function. We chose to analyze the development of the 3 cholinergic SAB motor neurons that are innervating the head muscles. In this system, electrical silencing of the muscle cells during development was demonstrated to regulate SAB morphology (Zhao and Nonet, 2000). Using fluorescently-tagged acetylcholine receptors (AChR), we observed SAB overgrowth and ectopic synapse formation in unc-13 and unc-18 mutant worms in which neuromuscular transmission was disrupted. We could confirm that this effect is not due to the loss of movement because there is no SAB overgrowth in the unc-54 myosin mutants that are paralyzed. To silence the electrical activity of muscle cells, we specifically expressed in muscles the Drosophila HisCl1 histamine-gated chloride channel and the TWK-18 temperature-dependent potassium channel. In both conditions, inhibition of muscle cell activity causes SAB overgrowth, suggesting that a retrograde factor(s) controls SAB development. We could further pinpoint a critical developmental window at the L1 stage during which SAB development is plastic. In addition, we demonstrated that chronic - but not acute - increase of synaptic transmission through acetylcholinesterase inhibition leads to a decrease in the number of synaptic AChRs, suggesting an activity-dependent regulation of AChR number during development. Through a transcriptomic approach, we expect to find genes involved in the overgrowth of the SAB and the regulation of AChR number. We are using RNA-Seq to detect genes differentially expressed upon electrical manipulation of the muscle cells. In parallel, we are using the tools that we developed to better define the conditions leading to SAB overgrowth and AChR downregulation, as well as testing a number of candidate genes. References: Zhao, H., and Nonet, M.L. (2000). A retrograde signal is involved in activity-dependent remodeling at a C. elegans neuromuscular junction. Development 127, 1253-1266.

Shuo Luo et al. (2005) International Worm Meeting "Dissection of the retrograde signal at C. elegans neuromuscular junctions"

Michael L Nonet, Shuo Luo

[International Worm Meeting, 2005]

Retrograde signals play important roles in regulating synapse plasticity during neural development. In the fruit fly D. melanogaster, the retrograde signal TGF modulates presynaptic morphology as well as synaptic transmission at both neuromuscular junctions (NMJs) and central synapses. In the nematode C. elegans, retrograde signal(s) also regulate the morphology of developing SAB head motor neurons (Zhao & Nonet, Development 127: 1253, 2000). Here we tested whether TGF-pathway could contribute to the retrograde signaling operating at SAB synapses. We examined a variety of TGF- pathway mutants for defects in SAB development but none exhibited SAB morphology defects. In addition, when synaptic transmission was disrupted in these mutants, all of them developed over-sprouted SAB axons, a phenotype similar to what has been observed in TGF normal animals. We conclude the TGF pathway does not play major roles in activity-dependent axon sprouting at SAB NMJs in worms. My current effort is to screen for the molecular components of retrograde signal at C. elegans NMJs. Various techniques including RNAi and chemical mutagenesis are being employed.