S Kim et al. (1999) International C. elegans Meeting "A Telomere Binding Protein in the Nematode C. elegans."

J Lee, S Kim

[International C. elegans Meeting, 1999]

Telomeres are multifunctional elements that shield chromosome ends from degradation and end-to-end fusions, prevent activation of DNA damage checkpoints, and modulates the maintenance of telomeric DNA by telomerase. In normal cells, telomeres shorten with successive cell divisions, probably due to the terminal sequence loss that accompanies DNA replication. Telomeric DNA has been found to interact with proteins in many organisms. For example, hTRF1, a human telomeric-repeat binding factor, is involved in the telomere length regulation. We wanted to identify and elucidate functions of telomere binding proteins in the nematode C. elegans. Telomeric repeat of C. elegans consists of a long stretch of (TTAGGC)n. However, the mechanism that modulates telomere length in C. elegans has not been investigated. We have isolated Ceh-37, a novel homeotic protein in C. elegans, as double-stranded telomere binding factor by yeast one-hybrid screening. We found that Ceh-37 specifically binds C. elegans telomere in vitro. We generated and examined series of deletion constructs by gel retardation assay and yeast one-hybrid assay. We found that the N-terminal domain and the homeotic domain is sufficient for telomere binding. Since the homeodomain alone nor the N-terminal domain alone was not able to bind the telomere and the N-terminal domain could compete with the binding of telomere by the full length Ceh-37 protein, we purpose that Ceh-37 binds the telomere as dimers or higher complex, and that the N-terminal is required for the dimerization. Ceh-37 is expressed in the nuclei of embryos as shown by visualizing GFP reporter protein. We plan to generate dominant-negative mutant animals by overexpressing the N-terminal domain, and examine any phenotypes associated with the disruption of Ceh-37 function. We will present updated results.

S Kim et al. (1999) International C. elegans Meeting "alt-1, a Gene Required for Patterning Longitudinal Axon Tracts at the Midlines"

WG Wadsworth, S Kim

[International C. elegans Meeting, 1999]

During development, a simple scaffold of longitudinal and circumferential axon tracts forms. We undertook a genetic screen to identify genes required for this patterning and we have isolated 11 new mutants. One of these, alt-1 (ur41) , was identified because dorsal sublateral (DSL) nerves form along the dorsal midline and the ventral nerve cord is abnormally symmetric. By light or electron microscopy, there are no other obvious defects in morphology. The alt-1(ur41) animals have several novel features. First, alt-1 is required for patterning only a subset of neurons along the midlines. Second, mispositioned axons do not wander in alt-1(ur41) , instead they generally stay in the wrong tract. For example, DSL nerves are positioned to either the sublateral position or along side of the dorsal midline. In 45% of the mutants, either the left or right tract is mispositioned and in 45%, both are mispositioned. These results suggest that alt-1 is required to prevent these nerves from forming along the dorsal midline. Third, alt-1 (ur41) affects the ability of axons to initially select the right or left side of the midline, however it does not affect their ability to respond to the signals that keep axons to either side. At the ventral midline, the PVQL axon abnormally crosses to the right tract and the left fascicle from the nerve ring sometimes fails to cross to the right ventral cord tract. Ventral midline motoneurons often send their longitudinal axons to the left side of midline instead of to the right side. Furthermore, at the dorsal midline, the motor axons from the right side often fail to immediately cross to the left side and migrate instead along the right side of the midline. As a result of these defects, nerve cords become abnormally symmetric. This suggests that alt-1 is required for the asymmetric distribution of longitudinal axon tracts at the midlines. Interestingly, unc-40 and sax-3 partially suppress alt-1(ur41) phenotypes, indicating possible involvement of these genes in the same process. The alt-1(ur41) phenotypes are rescued by germ line transformation with a single cosmid DNA that is predicted to contain 3 genes.

Heon S Kim (2004) East Coast Worm Meeting "Roles of PAR-3 and PKC-3 in establishment and maintenance of epithelial cell polarity in C. elegans"

Heon S Kim

[East Coast Worm Meeting, 2004]

Cell polarity is required at many different stages of development, including early embryogenesis and organogenesis. Intercellular junctions are believed to be required to polarize epithelial cells. PAR-3/PKC-3/PAR-6 complex, which serves as one of the earlist polarity cues during the early embryogenesis in C. elegans , has been found to be localized at apical junctions of gut epithelium in C. elegans , Drosophila , and mammals. However, the function of PAR-3/PKC-3/PAR-6 in establishment and maintenance of epithelial cell polarity in C. elegans has not been studied, mainly because the loss of function of this protein complex perturbs early embryogenesis. I am trying to overcome this barrier in two different ways. Heat shock-induced par-3 RNAi, right after early embryogenesis will deplete par-3 mRNA and hopefully will result in par-3 knock-out phenotypes in late embryos or L1~L2 larvae. Alternatively, I am examining the effect of a mutation in pkc-3 on epitheial polarity. I have a pkc-3 mutant, which is newly generated by Vancouver Gene Knockout Lab. This mutant carries a 1.5kb deletion ( ok544 ) that removes kinase domain. Homozygotes undergo normal embryogenesis due to maternal contribution, but they are arrested as L2 larvae. Currently I am trying to optimize the heat shock conditions for par-3 RNAi, and to identify the phenotypes of arrested pkc-3 mutants.

Kim S et al. (2013) Adv Exp Med Biol "Control of oocyte growth and meiotic maturation in Caenorhabditis elegans."

Greenstein D, Kim S, Spike C

[Adv Exp Med Biol, 2013]

In sexually reproducing animals, oocytes arrest at diplotene or diakinesis and resume meiosis (meiotic maturation) in response to hormones. Chromosome segregation errors in female meiosis I are the leading cause of human birth defects, and age-related changes in the hormonal environment of the ovary are a suggested cause. Caenorhabditis elegans is emerging as a genetic paradigm for studying hormonal control of meiotic maturation. The meiotic maturation processes in C. elegans and mammals share a number of biological and molecular similarities. Major sperm protein (MSP) and luteinizing hormone (LH), though unrelated in sequence, both trigger meiotic resumption using somatic G(s)-adenylate cyclase pathways and soma-germline gap-junctional communication. At a molecular level, the oocyte responses apparently involve the control of conserved protein kinase pathways and post-transcriptional gene regulation in the oocyte. At a cellular level, the responses include cortical cytoskeletal rearrangement, nuclear envelope breakdown, assembly of the acentriolar meiotic spindle, chromosome segregation, and likely changes important for fertilization and the oocyte-to-embryo transition. This chapter focuses on signaling mechanisms required for oocyte growth and meiotic maturation in C. elegans and discusses how these mechanisms coordinate the completion of meiosis and the oocyte-to-embryo transition.

Kim S et al. (2008) Mol Cells "Thymidylate synthase and dihydropyrimidine dehydrogenase levels are associated with response to 5-fluorouracil in Caenorhabditis elegans."

Kim S, Park DH, Shim J

[Mol Cells, 2008]

5-Fluorouracil (5-FU), a pyrimidine antagonist, has a long history in cancer treatment. The targeted pyrimidine biosynthesis pathway includes dihydropyrimidine dehydrogenase (DPD), which converts 5-FU to an inactive metabolite, and thymidylate synthase (TS), which is a major target of 5-FU. Using Caenorhabditis elegans as a model system to study the functional and resistance mechanisms of anti-cancer drugs, we examined these two genes in order to determine the extent of molecular conservation between C. elegans and humans. Overexpression of the worm DPD and TS homologs (DPYD-1 and Y110A7A.4, respectively) suppressed germ cell death following 5-FU exposure. In addition, DPYD-1 depletion by RNAi resulted in 5-FU sensitivity, while treatment with Y110A7A.4 RNAi and 5-FU resulted in similar patterns of embryonic death. Thus, the pathway of 5-FU function appears to be highly conserved between C. elegans and humans at the molecular level.

Kim S et al. (2024) J Cell Biol "Regulation of proteostasis and innate immunity via mitochondria-nuclear communication."

Kim S, Haynes CM, Ramalho TR

[J Cell Biol, 2024]

Mitochondria are perhaps best known as the "powerhouse of the cell" for their role in ATP production required for numerous cellular activities. Mitochondria have emerged as an important signaling organelle. Here, we first focus on signaling pathways mediated by mitochondria-nuclear communication that promote protein homeostasis (proteostasis). We examine the mitochondrial unfolded protein response (UPRmt) in C. elegans, which is regulated by a transcription factor harboring both a mitochondrial- and nuclear-targeting sequence, the integrated stress response in mammals, as well as the regulation of chromatin by mitochondrial metabolites. In the second section, we explore the role of mitochondria-to-nuclear communication in the regulation of innate immunity and inflammation. Perhaps related to their prokaryotic origin, mitochondria harbor molecules also found in viruses and bacteria. If these molecules accumulate in the cytosol, they elicit the same innate immune responses as viral or bacterial infection.

Kim S et al. (2019) Genetics "FSHR-1/GPCR Regulates the Mitochondrial Unfolded Protein Response in Caenorhabditis elegans."

Kim S, Sieburth D

[Genetics, 2019]

The mitochondrial unfolded protein response (UPR^mt) is an evolutionarily conserved adaptive response that functions to maintain mitochondrial homeostasis following mitochondrial damage. In <i>Caenorhabditis elegans</i>, the nervous system plays a central role in responding to mitochondrial stress by releasing endocrine signals that act upon distal tissues to activate the UPR^mt The mechanisms by which mitochondrial stress is sensed by neurons and transmitted to distal tissues is not fully understood. Here, we identify a role for the conserved follicle-stimulating hormone G protein coupled receptor (GPCR), FSHR-1, in promoting UPR^mt activation. Genetic deficiency of <i>fshr-1</i> severely attenuates UPR^mt activation and organism-wide survival in response to mitochondrial stress. FSHR-1 functions in a common genetic pathway with SPHK-1/sphingosine kinase to promote UPR^mt activation, and FSHR-1 regulates the mitochondrial association of SPHK-1 in the intestine. Through tissue-specific rescue assays, we show that FSHR-1 functions in neurons to activate the UPR^mt, to promote mitochondrial association of SPHK-1 in the intestine, and to promote organism-wide survival in response to mitochondrial stress. We propose that FSHR-1 functions cell non-autonomously in neurons to activate UPR^mt upstream of SPHK-1 signaling in the intestine.

Kim S et al. (2016) PLoS Comput Biol "Vulnerability-Based Critical Neurons, Synapses, and Pathways in the Caenorhabditis elegans Connectome."

Jeong J, Kralik JD, Kim H, Kim S

[PLoS Comput Biol, 2016]

Determining the fundamental architectural design of complex nervous systems will lead to significant medical and technological advances. Yet it remains unclear how nervous systems evolved highly efficient networks with near optimal sharing of pathways that yet produce multiple distinct behaviors to reach the organism's goals. To determine this, the nematode roundworm Caenorhabditis elegans is an attractive model system. Progress has been made in delineating the behavioral circuits of the C. elegans, however, many details are unclear, including the specific functions of every neuron and synapse, as well as the extent the behavioral circuits are separate and parallel versus integrative and serial. Network analysis provides a normative approach to help specify the network design. We investigated the vulnerability of the Caenorhabditis elegans connectome by performing computational experiments that (a) &quot;attacked&quot; 279 individual neurons and 2,990 weighted synaptic connections (composed of 6,393 chemical synapses and 890 electrical junctions) and (b) quantified the effects of each removal on global network properties that influence information processing. The analysis identified 12 critical neurons and 29 critical synapses for establishing fundamental network properties. These critical constituents were found to be control elements-i.e., those with the most influence over multiple underlying pathways. Additionally, the critical synapses formed into circuit-level pathways. These emergent pathways provide evidence for (a) the importance of backward locomotion, avoidance behavior, and social feeding behavior to the organism; (b) the potential roles of specific neurons whose functions have been unclear; and

Kim S et al. (2018) Cell Rep "Sphingosine Kinase Activates the Mitochondrial Unfolded Protein Response and Is Targeted to Mitochondria by Stress."

Kim S, Sieburth D

[Cell Rep, 2018]

The mitochondrial unfolded protein response (UPR^mt) is critical for maintaining mitochondrial protein homeostasis in response to mitochondrial stress, but early steps in UPR^mt activation are not well understood. Here, we report a function for SPHK-1 sphingosine kinase in activating the UPR^mt in C.elegans. Genetic deficiency of sphk-1 in the intestine inhibits UPR^mt activation, whereas selective SPHK-1 intestinal overexpression is sufficient to activate the UPR^mt. Acute mitochondrial stress leads to rapid, reversible localization of SPHK-1::GFP fusion proteins with mitochondrial membranes before UPR^mt activation. SPHK-1 variants lacking kinase activity or mitochondrial targeting fail to rescue the stress-induced UPR^mt activation defects of sphk-1 mutants. Activation of the UPR^mt by the nervous system requires sphk-1 and elicits SPHK-1 mitochondrial association in the intestine. We propose that stress-regulated mitochondrial recruitment of SPHK-1 and subsequent S1P production are critical early events for both cell autonomous and cell non-autonomous UPR^mt activation.

Kim S et al. (2008) Mol Cells "Regulation of ERK1/2 by the C. elegans muscarinic acetylcholine receptor GAR-3 in Chinese hamster ovary cells."

Kim S, Cho NJ, Park YS, Shin Y

[Mol Cells, 2008]

Three G-protein-linked acetylcholine receptors (GARs) exist in the nematode C. elegans. GAR-3 is pharmacologically most similar to mammalian muscarinic acetylcholine receptors (mAChRs). We observed that carbachol stimulated ERK1/2 activation in Chinese hamster ovary (CHO) cells stably expressing GAR-3b, the predominant alternatively spliced isoform of GAR-3. This effect was substantially reduced by the phospholipase C (PLC) inhibitor U73122 and the protein kinase C (PKC) inhibitor GF109203X, implying that PLC and PKC are involved in this process. On the other hand, GAR-3b-mediated ERK1/2 activation was inhibited by treatment with forskolin, an adenylate cyclase (AC) activator. This inhibitory effect was blocked by H89, an inhibitor of cAMP-dependent protein kinase A (PKA). These results suggest that GAR-3b-mediated ERK1/2 activation is negatively regulated by cAMP through PKA. Together our data show that GAR-3b mediates ERK1/2 activation in CHO cells and that GAR-3b can couple to both stimulatory and inhibitory pathways to modulate ERK1/2.