Kim TY et al. (1996) West Coast Worm Meeting "A NON-NEURONAL SNAP-25-LIKE HOMOLOG IN C. ELEGANS?"

Lee JH, Kim TY

[West Coast Worm Meeting, 1996]

Vesicle fusion complexes are composed of cytosolic proteins such as NSF and SNAP, vesicle membrane proteins such as synaptobrevin, and target membrane proteins such as syntaxin and SNAP-25. Two of the membrane proteins, synaptobrevin and syntaxin, are known to be members of families of genes. SNAP-25, on the other hand, has not been shown to be a gene of a gene family. In yeast, there is only one SNAP-25, called Sec9, which acts at the Golgi to plasma membrane transport step. In higher organisms, only one SNAP-25 homolog has been identified, which acts at the nerve terminal. We wanted to know whether there are other homologs of SNAP-25 that act at other steps of transport and/or in other cells than neural cells. The C. elegans genome project has identified a cosmid (K02D10) that contains a genomic sequence similar to SNAP-25. According to the database, another putative transcript (similar to 4-nitrophenylphosphatase) lies upstream of the SNAP-25-like transcript in the same cosmid. To determine whether these two sequences make a single transcript, we performed a northern analysis with a probe made from the SNAP-25-like sequence. We found that the putative SNAP-25-like sequence makes a separate transcript about 1.1 kb long. We screened a cDNA library and isolated a few clones, none of which contained sequences of the upstream transcript, confirming that the two sequences are not a single gene. We do not know whether these two sequences are polycistronic. We were curious to know the expression pattern of this gene. We made antibodies in rabbits against the gene product and performed whole mount staining using the antibody. The antibody did not stain the nerve cords and nerve cells, which are stained with the antobodies against the genuine SNAP-25. It instead stains specific regions of the cuticle in early larvae. We think that this specific region is the alae of the L1 larvae. I. Hope's LacZ fusion expression data seem to agree with our antibody staining result (personal comm.; also from his home page at the C. elegans www server at UTSW). We plan to identify mutations to determine the defects associated with the disruption of this SNAP-25-like gene. We would like to call this gene nns-1 (Non-Neuronal Snap-25-like ). This work was initiated in Dr. Barbara Meyer's lab when J. Lee was a postdoctoral fellow in her lab.

Simske JS et al. (1994) Worm Breeder's Gazette "Specification of Vulval Cell Fates By Sequential Signalling Pathways."

Simske JS, Kim SK

[Worm Breeder's Gazette, 1994]

Specification of vulval cell fates by sequential signaling pathways Jeffrey S. Simske and Stuart K. Kim, Dept. of Developmental Biology, Stanford University Medical Center, Stanford CA 94305

Roque CG et al. (2018) Neuron "Wimpy Nerves: piRNA Pathway Curbs Axon Regrowth after Injury."

Roque CG, Hengst U

[Neuron, 2018]

While PIWI-interacting RNAs (piRNAs) are primarily recognized as guardians of genome integrity, new functions of these small non-coding RNAs are emerging. In this issue, Kim etal. (2018) describe a piRNA-based mechanism that limits axon regeneration in C.elegans.

Irazoqui JE (2014) Cell Host Microbe "DAF-tly depart stinky situations with elegans."

Irazoqui JE

[Cell Host Microbe, 2014]

During acute infection our behavior tends to change. Despite how common sickness behavior is, its molecular basis is not well understood. In a study published in Cell, Kim and colleagues (Meisel etal., 2014) implicate bacterial secondary metabolites as triggers of neural TGF-? signaling, which results in behavioral change during infection.

Vader G et al. (2014) Dev Cell "HORMA domains at the heart of meiotic chromosome dynamics."

Musacchio A, Vader G

[Dev Cell, 2014]

HORMA domain proteins are required for the careful orchestration of chromosomal organization during meiosis. Kim et al. (2014) and Silva et al. (2014) now provide structural and functional insights into the roles of C. elegans HORMA proteins, revealing parallels to the function of the HORMA protein MAD2 in mitotic checkpoint signaling.

Kim SW et al. (2020) Environ Sci Technol "Effects of Different Microplastics on Nematodes in the Soil Environment: Tracking the Extractable Additives Using an Ecotoxicological Approach."

Kim SW, Rillig MC, Waldman WR, Kim TY

[Environ Sci Technol, 2020]

With increasing interest in the effects of microplastics on the soil environment, there is a need to thoroughly evaluate the potential adverse effects of these particles as a function of their characteristics (size, shape, and composition). In addition, extractable chemical additives from microplastics have been identified as an important toxicity pathway in the aquatic environment. However, currently, little is known about the effects of such additives on the soil environment. In this study on nematodes (<i>Caenorhabditis elegans</i>), we adopted an ecotoxicological approach to assess the potential effects of 13 different microplastics (0.001-1% of soil dry weight) with different characteristics and extractable additives. We found that poly(ethylene terephthalate) (PET) fragments and polyacrylicnitrile (PAN) fibers show the highest toxicity, while high-density polyethylene (HDPE), polypropylene (PP), and polystyrene (PS) fragments induced relatively less adverse effects on nematodes. In addition, low-density polyethylene (LDPE) induced no toxicity within our test concentration range for the acute period. Acute toxicity was mainly attributed to the extractable additives: when the additives were extracted, the toxic effects of each microplastic disappeared in the acute soil toxicity test. The harmful effects of the LDPE films and PAN fibers increased when the microplastics were maintained in the soil for a long-term period with frequent wet-dry cycles. We here provide clear evidence that microplastic toxicity in the soil is highly related to extractable additives. Our results suggest that future experiments consider extractable additives as key explanatory variables.

Lee JH et al. (1997) International C. elegans Meeting "A SNAP-25 gene family in C. elegans?"

Kim TY, Lee Y, Lee JH, Kim HY

[International C. elegans Meeting, 1997]

Vesicle fusion complexes are composed of cytosolic proteins, vesicle membrane proteins such as synaptobrevin, and target membrane proteins such as syntaxin and SNAP-25. Synaptobrevin and syntaxin are known to be members of gene families. SNAP-25, on the other hand, has not been shown to belong to a gene family. In higher organisms, only one SNAP-25 has been identified, which is alternatively spliced. The nematode SNAP-25 is encoded by ric-4, which is not subject to alternative splicing. We wanted to know whether there is any other homolog of SNAP-25 that acts at other vesicle fusion steps and/or in other cells than neurons. The C. elegans genome project has identified two cosmids(K02D10 and T14G12) containing genomic sequences similar to SNAP-25. Both the sequences show limited homology (~30 %) to the nematode SNAP-25 gene (ric-4). We would like to call these genes nns-1 and nns-2 (Non-Neuronal Snap-25-like gene 1, 2). (1) nns-1 (K02D10.1): according to the database, there is another putative transcript (similar to 4-nitrophenyl- phosphatase) lies upstream of the SNAP-25-like transcript in K02D10. To determine whether these two sequences make a single transcript, we performed a northern analysis with a probe made from the SNAP-25-like sequence. From northern analysis and cDNA library screening, we found that the putative SNAP-25-like sequence makes a separate transcript about 1.1 kb long from the upstream transcript. We do not know whether these two sequences are polycistronic. Antibody against K02D10.1 gene product did not stain neural cells, which express the genuine SNAP-25. It instead stained specific regions of the cuticle in early larvae. I. Hope!s LacZ fusion expression data seem to agree with our antibody data. We will present our progress on the identification of mutations in this gene to find its biological functions. (2) nns-2 (T14G12.2) We will present the progress on the characterization of this gene at the meeting. This work was initiated in Dr. B. Meyer!s lab when J. Lee was a postdoctoral fellow in her lab. We would thank Dr. I. Hope for sharing staining data. Supported by a fund from Korean Ministry of Educaton.

DeGroot, Melisa et al. (2021) International Worm Meeting "The secreted modular calcium binding protein (SMOC-1) can function as both a long-range and a short-range modulator of BMP signaling in C. elegans"

Williams, Byron, Liu, Jun, DeGroot, Melisa

[International Worm Meeting, 2021]

The bone morphogenetic protein (BMP) pathway is a highly conserved signaling cascade that regulates key developmental and homeostatic processes in metazoans. The BMP pathway is conserved in Caenorhabditis elegans, and is known to regulate body size and mesoderm development. We have identified the C. elegans SMOC-1 (secreted modular calcium-binding protein-1) protein as a positive modulator of the BMP pathway. SMOC-1 is a predicted secreted matricellular protein with two predicted functional domains: the thyroglobulin-like type I repeat (TY) domain and the extracellular calcium binding (EC domain). Through a series of molecular genetic experiments, we have demonstrated that SMOC-1 functions in a positive feedback loop to promote BMP signaling: it acts through the BMP ligand DBL-1 to regulate BMP signaling, and its expression in the intestine is positively regulated by BMP signaling. smoc-1 is expressed in multiple tissues. Using cell type specific promoters to drive smoc-1 expression, we found that SMOC-1 functions cell non-autonomously to regulate body size. Surprisingly, a membrane-tethered SMOC-1 driven by the smoc-1 promoter can also partially function. These findings suggest that SMOC-1 can act both locally and over a distance to regulate BMP signaling. Intriguingly, the SMOC-1 EC domain alone is sufficient to regulate the BMP pathway when freely secreted, but not when membrane tethered. Conversely, the TY domain alone is not sufficient to promote BMP signaling, yet this domain is required for SMOC-1 to function locally. Together, these findings suggest that the SMOC-1 TY and EC domains contribute to different facets of SMOC-1 functions. We are using immunoprecipation/mass spectrometry (IP/MS) to identify interacting partners of the various functional forms of SMOC-1. Comparative analysis of the IP/MS results will yield molecular insights on how SMOC-1 promotes the BMP pathway.

Kim SW et al. (2023) Environ Sci Technol "Toxicity of Aged Paint Particles to Soil Ecosystems: Insights from Caenorhabditis elegans."

Kim SW, Song WY, Waldman WR, Rillig MC, Kim TY

[Environ Sci Technol, 2023]

Despite the extensive global consumption of architectural paint, the toxicological effects of aged exterior paint particles on terrestrial biota remain largely uncharacterized. Herein, we assessed the toxic effect of aged paint particles on soil environments using the nematode <i>Caenorhabditis elegans</i> (<i>C. elegans</i>) as a test organism. Various types of paint particles were generated by fragmentation and sequential sieving (500-1000, 250-500, 100-250, 50-100, 20-50 &#x3bc;m) of paint coatings collected from two old residential areas. The paint particles exerted different levels of toxicity, as indicated by a reduction in the number of <i>C. elegans</i> offspring, depending on their size, color, and layer structure. These physical characteristics were found to be closely associated with the chemical heterogeneity of additives present in the paint particles. Since the paint particle sizes were larger than what <i>C. elegans</i> typically consume, we attributed the toxicity to leachable additives present in the paint particles. To assess the toxicity of these leachable additives, we performed sequential washings of the paint particles with distilled water and ethanol. Ethanol washing of the paint particles significantly reduced the soil toxicity of the hydrophobic additives, indicating their potential environmental risk. Liquid chromatography-mass spectrometry analysis of the ethanol leachate revealed the presence of alkyl amines, which exhibited a high correlation with the toxicity of the paint particles. Further toxicity testing using an alkyl amine standard demonstrated that a paint particle concentration of 1.2% in soil could significantly reduce the number of <i>C. elegans</i> offspring. Our findings provide insights into the potential hazards posed by aged paint particles and their leachable additives in the terrestrial environment.

Sharrock WJ et al. (1990) J Biol Chem "Two distinct yolk lipoprotein complexes from Caenorhabditis elegans."

Sharrock WJ, Kim TY, Sutherlin ME, Cheng TK, Leske K

[J Biol Chem, 1990]

The four yolk polypeptides of the nematode Caenorhabditis elegans are found in two types of lipoprotein particle: 12 S particles with Mr estimated at 450,000 and 8 S particles with Mr estimated at 250,000. Both types of particle contain approximately 8% phospholipids, 3% triglycerides, and 3% other lipids by mass. All four C. elegans yolk polypeptides can be found in either 12 or 8 S particles, depending upon the conditions of isolation. While the properties of the 12 and 8 S lipoprotein particles are consistent with a dimermonomer relationship, the asymmetric distribution of the yolk polypeptides between 12 and 8 S fractions suggests that at least two different oligomeric lipoprotein complexes are present in C. elegans embryos. In order to clarify the subunit composition of the C. elegans yolk lipoproteins, the patterns of polypeptides retained in immunoaffinity binding procedures by immunoglobulins of different antigenic specificities have been compared. When immunoaffinity binding is performed in the absence of sodium dodecyl sulfate, three C. elegans yolk proteins (yp170A, yp115, and yp88) are retained together by polyclonal immunoglobulins directed against either yp115 or yp88. A monoclonal immunoglobulin also retains these three proteins together. In contrast, a second monoclonal immunoglobulin retains only the fourth yolk protein (yp170B). Aggregate species, evidently reflecting the spontaneous formation of interchain disulfide bonds, indicate that yp170A and yp88 are physically associated, whereas yp170B self-associates in dimers. It is concluded that there are two distinct lipoprotein complexes in C. elegans: the A complex, which consists of yp170A, yp115, and yp88 and is essentially heterodimeric and the B dimer, a simple dimer of yp170B.