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).

Pop, C et al. (2005) Cell "The nematode death machine in 3D."

Pop, C, Salvesen, GS

[Cell, 2005]

Regulated apoptosis is part of the development of the nematode Caenorhabditis elegans. In a recent paper in Nature, Yan et al. (2005) describe the in vitro reconstitution of the core components of the worm apoptotic pathway. Based on a structural analysis of the complex between the death activator CED-4 and the antiapoptotic protein CED-9, the authors explain the regulation of activity of CED-4. Intriguingly, CED-4 comprises a AAA+ type ATPase domain yet does not seem to need ATP hydrolysis for activity.

Blazie, Stephen et al. (2021) International Worm Meeting "Eukaryotic initiation factor EIF-3.G augments mRNA translation efficiency to regulate neuronal activity"

Zhao, Yan, Blazie, Stephen, Jin, Yishi, McCulloch, Katherine, Takayanagi-Kiya, Seika

[International Worm Meeting, 2021]

Protein translation is principally regulated at the initiation phase, whereby six multi-subunit translation initiation factors (eIF1-6) ultimately engage elongation-competent 80S ribosomes with the mRNA open reading frame. eIF3 is the largest complex, consisting of 13 unique subunits. While each eIF3 subunit has vital roles in general protein synthesis, recent work has shown that some subunits can drive specialized cellular pathways that enforce when and where translation events occur. Moreover, human genetics studies have revealed prevalent dysregulation of different eIF3 subunits in disease, including neurological disorders. However, very few studies have examined how eIF3 regulates neuronal protein synthesis in living animals. Here, we report a selective role of the G subunit of C. elegans EIF-3 in shaping the motor neuron proteome to control locomotion. EIF-3.G contains an N-terminal domain that binds EIF-3.I, and a conserved zinc finger followed by an RNA-binding RRM at the C-terminus. We find that while EIF-3.G is essential for larval development, a missense mutation (C130Y) in its zinc finger exhibits a highly selective effect in cholinergic motor neurons to dampen overexcitation of the locomotor circuit. eif-3.G(C130Y) acts in a gain-of-function manner and requires its RNA binding domain. To systematically identify EIF-3.G mRNA targets in the cholinergic motor neurons, we performed cell-specific seCLIP analysis. Our data reveals that EIF-3.G preferentially occupies the GC-rich 5'UTRs of a specific cohort of mRNAs, many of which perform neuronal activity-dependent functions. We further demonstrate that EIF-3.G exerts translational control over two of its target genes, hlh-30 and ncs-2, through their GC-rich 5′UTRs. Finally, we carried out a genetic screen for genes interacting with EIF-3.G, and find that eif-3.G(C130Y) requires the putative phosphatase encoded by eat-9 and a regulatory factor LIN-66 to modify cholinergic activity. Our work provides the first insight into eIF3 selective translational control in neurons and establishes a system for unveiling protein translation pathways that regulate animal behavior.

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

Malinow, R.A. et al. (2019) International Worm Meeting "Functional dissection of C. elegans bZip-protein CEBP-1."

Kim, K.W., Koorman, T., Boxem, M., Ying, P., Malinow, R.A., Jin, Y.

[International Worm Meeting, 2019]

C. elegans CEBP-1 is a C/EBP bZIP transcription factor and essential for axon regeneration. Previous studies have focused on the role of bZIP domain at the C-terminus of CEBP-1 in axon regeneration (Yan et al., 2009 Cell). However, CEBP-1 also has a long N-terminal fragment that contains no known protein motifs and how it is involved in CEBP-1 function remains unknown. Here, we report novel structural motifs in the N-terminus of CEBP-1 for axon regeneration and nuclear import. Using two types of forward genetic screens, we have identified a unique domain in the N-terminus that is critical for CEBP-1's in vivo functions. This N' domain also has a predicted propensity to form alpha helices. Furthermore, using yeast two-hybrid screening with N-terminal CEBP-1 fragments as baits, we have identified IMA-3/Importin-? as a CEBP-1 binding partner. In transgenic expression studies, we characterized the subcellular localization of CEBP-1 fragments and identified three nuclear localization signals (NLS) in CEBP-1, one which interacts with IMA-3. Lastly, we showed that ima-3 is required for axon regeneration. Taken together, our findings uncover new protein structural elements for CEBP-1, and further reinforce the importance of Importin-mediated nuclear import system for promoting axon regeneration. Yan, D., Wu, Z., Chisholm, A.D., and Jin, Y. (2009). The DLK-1 kinase promotes mRNA stability and local translation in C. elegans synapses and axon regeneration. Cell 138, 1005-1018.

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).