Luth, E.S. et al. (2017) International Worm Meeting "The VER-4/VEGF receptor-related protein regulates GLR-1 glutamate receptors and related behaviors."

Luth, E.S., Riccio, C., Juo, P., Markoja, K.

[International Worm Meeting, 2017]

Glutamate synapses are highly dynamic, and their restructuring provides the cellular basis of learning and memory. Failure to properly form or maintain glutamate synapses can lead to a variety of neurological disorders, and controlling their abundance and activity is critical for maximizing functional recovery after stroke. However, the molecular mechanisms that regulate the formation and function of these connections in vivo during normal nervous system development are not well understood. Expression of channelrhodopsin in the glutamatergic sensory neuron ASH1 enabled us to combine optogenetic control of a simple glutamate-dependent behavior, the nose-touch response, with a focused RNAi screen to identify novel genes important for glutamate synapse function. RNAi knockdown of ver-4, a VEGF receptor homolog2, resulted in a strong defect in ASH-stimulated glutamate-dependent locomotor reversals, but did not affect overall glutamate-independent locomotion based on thrashing assays. Analysis of worms with loss of function mutations in ver-4 confirmed these RNAi results. The intensity and density of the presynaptic vesicle marker RAB-3::mCherry, expressed specifically in ASH, was unaltered in ver-4 mutants. In contrast, we observed widespread alterations in the size and intensity of GLR-1::GFP puncta in the nerve ring and ventral nerve cord of ver-4 mutants, suggesting that VER-4 globally affects GLR-1 levels. Confocal imaging of GLR-1 tagged with both mCherry and pH-sensitive superecliptic pHluorin (SEP::mCherry::GLR-1)3 indicated that ver-4 mutants exhibit a preferential loss of cell surface GLR-1. Consistent with this data, ver-4 mutants suppressed the increase in glutamate-dependent spontaneous reversals observed in animals expressing a constitutively-active form of GLR-14. Mutants lacking the VER-4 ligand PVF-15 also exhibited defects in the nose-touch response suggesting that ligand binding may be required for VER-4-mediated promotion of glutamate signaling. Together, our data identify VER-4 and its ligand as novel regulators of GLR-1 trafficking and signaling. Future experiments will identify the cellular and subcellular site of action of VER-4 and the mechanism by which PVF-1 and VER-4 regulate GLR-1 trafficking. References: 1. Ezcurra, M., et al. (2011) EMBO J 30:1110 2. Popovici, C., et al. (2002) Neurosci. Lett. 329:116 3. Hoerndli, F. J., et al. (2013) Neuron 80:1421 4. Zheng, Y., et al. (1999) Neuron 24:347-361 5. Dalpe, G., et al. (2013) Development 140:4020

Chun-Yi Huang et al. (2007) International Worm Meeting "eif-3.K is a pro-apoptotic gene in C. elegans."

Jia-Yun Chen, Yi-Chun Wu, Chun-Yi Huang

[International Worm Meeting, 2007]

Programmed cell death (or apoptosis) is an important feature of C. elegans development. Previous studies have identified pro-apoptotic genes egl-1, ced-3 and ced-4 and anti-apoptotic genes ced-9 and icd-1 that control programmed cell death.. We have identified and characterized a novel pro-apoptotic gene eif-3.K. Loss-of-function by mutation or RNAi inactivation in eif-3.K resulted in a decrease of cell corpses, whereas heatshock-induced over-expression of eif-3.K weakly but significantly increased cell corpses. Interestingly, the eif-3.K mutation partially suppressed ectopic cell deaths caused by over-expression of egl-1 or ced-4. This result suggests that eif-3.K may act downstream of or in parallel to egl-1 and ced-4 in the programmed cell death pathway. Using a cell-specific promoter to express eif-3.k in touch neurons, we showed that eif-3.K likely promoted cell death in a cell-autonomous manner. To further explore EIF-3.K function, we generated antibodies against bacterially expressed EIF-3.K protein. We found that EIF-3.K was ubiquitously expressed during embryogenesis and localized to the cytoplasm. As human eif-3.K can functionally substitute C. elegans eif-3.K in an eif-3.K mutant, the function of eif-3.K in apoptosis is likely conserved in evolution.

Chun-Yi Huang et al. (2006) East Asia C. elegans Meeting "eif-3.K is a pro-apoptotic gene in C. elegans"

Teng-Wei Huang, Chun-Yi Huang

[East Asia C. elegans Meeting, 2006]

Programmed cell death or apoptosis is an important feature during C. elegans development. The pro-apoptotic genes egl-1, ced-4 and ced-3 are required for the execution of cell death. We have identified and characterized a novel pro-apoptotic gene eif-3.K. A loss-of-function mutation or inactivation by RNA interference in eif-3.K resulted in a reduction of cell corpse number during embryogenesis, whereas heatshock-induced over-expression of eif-3.K weakly but significantly promoted programmed cell death. In addition, eif-3.K mutation partially suppressed ectopic cell deaths caused by over-expression of egl-1 and ced-4. This result suggests that eif-3.K may act downstream of or in parallel to egl-1 and ced-4 in the genetic pathway during programmed cell death. Using a cell-specific promoter we showed that eif-3.K likely promoted cell death in a cell-autonomous manner. We generated antibodies against bacterially expressed EIF-3.K protein. The immunostaining result showed that EIF-3.K was ubiquitously expressed during embryogenesis and localized to the cytoplasm. To better understand the cell-death defect of eif-3.K mutants, we are currently performing a 4D microscopic analysis of the cell death process in wild-type and eif-3.K mutants.

Huang CY et al. (2012) PLoS One "C. elegans EIF-3.K promotes programmed cell death through CED-3 caspase."

Tan CH, Huang CY, Wu SC, Chen JY, Wu YF, Wu YC, Chen RH, Lu PJ, Tzeng RY

[PLoS One, 2012]

Programmed cell death (apoptosis) is essential for the development and homeostasis of metazoans. The central step in the execution of programmed cell death is the activation of caspases. In C. elegans, the core cell death regulators EGL-1(a BH3 domain-containing protein), CED-9 (Bcl-2), and CED-4 (Apaf-1) act in an inhibitory cascade to activate the CED-3 caspase. Here we have identified an additional component eif-3.K (eukaryotic translation initiation factor 3 subunit k) that acts upstream of ced-3 to promote programmed cell death. The loss of eif-3.K reduced cell deaths in both somatic and germ cells, whereas the overexpression of eif-3.K resulted in a slight but significant increase in cell death. Using a cell-specific promoter, we show that eif-3.K promotes cell death in a cell-autonomous manner. In addition, the loss of eif-3.K significantly suppressed cell death-induced through the overexpression of ced-4, but not ced-3, indicating a distinct requirement for eif-3.K in apoptosis. Reciprocally, a loss of ced-3 suppressed cell death induced by the overexpression of eif-3.K. These results indicate that eif-3.K requires ced-3 to promote programmed cell death and that eif-3.K acts upstream of ced-3 to promote this process. The EIF-3.K protein is ubiquitously expressed in embryos and larvae and localizes to the cytoplasm. A structure-function analysis revealed that the 61 amino acid long WH domain of EIF-3.K, potentially involved in protein-DNA/RNA interactions, is both necessary and sufficient for the cell death-promoting activity of EIF-3.K. Because human eIF3k was able to partially substitute for C. elegans eif-3.K in the promotion of cell death, this WH domain-dependent EIF-3.K-mediated cell death process has potentially been conserved throughout evolution.

Wojtovich AP et al. (2011) PLoS One "SLO-2 is cytoprotective and contributes to mitochondrial potassium transport."

Sherman TA, Nehrke K, Urciuoli WR, Wojtovich AP, Nadtochiy SM, Brookes PS

[PLoS One, 2011]

Mitochondrial potassium channels are important mediators of cell protection against stress. The mitochondrial large-conductance "big" K(+) channel (mBK) mediates the evolutionarily-conserved process of anesthetic preconditioning (APC), wherein exposure to volatile anesthetics initiates protection against ischemic injury. Despite the role of the mBK in cardioprotection, the molecular identity of the channel remains unknown. We investigated the attributes of the mBK using C. elegans and mouse genetic models coupled with measurements of mitochondrial K(+) transport and APC. The canonical Ca(2+)-activated BK (or "maxi-K") channel SLO1 was dispensable for both mitochondrial K(+) transport and APC in both organisms. Instead, we found that the related but physiologically-distinct K(+) channel SLO2 was required, and that SLO2-dependent mitochondrial K(+) transport was triggered directly by volatile anesthetics. In addition, a SLO2 channel activator mimicked the protective effects of volatile anesthetics. These findings suggest that SLO2 contributes to protection from hypoxic injury by increasing the permeability of the mitochondrial inner membrane to K(+).

Johnson CK et al. (2020) J Neurophysiol "The Na+/K+-ATPase is needed in glia of touch receptors for responses to touch in C. elegans."

Wang Y, Bianchi L, Fernandez-Abascal J, Johnson CK, Wang L

[J Neurophysiol, 2020]

Four of the five types of mammalian mechanosensors are composed of nerve endings and accessory cells. In C. elegans we showed that glia supports the function of nose touch neurons via the activity of glial Na⁺ and K⁺channels. We show here that a third regulator of Na⁺ and K⁺, the Na⁺/K⁺-ATPase, is needed in glia of nose touch neurons for touch. Importantly, we show that the two Na⁺/K⁺-ATPase genes are needed for the function rather than structural integrity and that their ion transport activity is crucial for touch. Finally, when glial Na⁺/K⁺-ATPase genes are knocked-out, touch can be restored by activation of a third Na⁺/K⁺-ATPase. Taken together, these data show the requirement in glia of touch neurons of the function of the Na⁺/K⁺-ATPase. These data underscore the importance of the homeostasis of Na⁺ and K⁺, most likely in the space surrounding touch neurons, in touch sensation, a function that might be conserved across species.

Jospin M et al. (2002) J Physiol "Characterization of K(+) currents using an in situ patch clamp technique in body wall muscle cells from Caenorhabditis elegans."

Jospin M, Allard B, Segelat L, Mariol MC, Segalat L

[J Physiol, 2002]

The properties of K+ channels in body wall muscle cells acutely dissected from the nematode Caenorhabditis elegans were investigated at the macroscopic and unitary level using an in situ patch clamp technique. In the whole-cell configuration, depolarizations to potentials positive to -40 mV gave rise to outward currents resulting from the activation of two kinetically distinct voltage-dependent K+ currents: a fast activating and inactivating 4-aminopyridine-sensitive component and a slowly activating and maintained tetraethylammonium-sensitive component. In cell-attached patches, voltage-dependent K+ channels, with unitary conductances of 34 and 80 pS in the presence of 5 and 140 mm external K+, respectively, activated at membrane potentials positive to -40 mV. Excision revealed that these channels corresponded to Ca2+-activated K+ channels exhibiting an unusual sensitivity to internal Cl- and whose activity progressively decreased in inside-out conditions. After complete run-down of these channels, one third of inside-out patches displayed activity of another Ca2+-activated K+ channel of smaller unitary conductance (6 pS at 0 mV in the presence of 5 mm external K+). In providing a detailed description of native K+ currents in body wall muscle cells of C. elegans, this work lays the basis for further comparisons with mutants to assess the function of K+ channels in this model organism that is highly amenable to molecular and classical genetics.

Shibuya Y et al. (2022) Algorithms Mol Biol "Space-efficient representation of genomic k-mer count tables."

Kucherov G, Shibuya Y, Belazzougui D

[Algorithms Mol Biol, 2022]

MOTIVATION: k-mer counting is a common task in bioinformatic pipelines, with many dedicated tools available. Many of these tools produce in output k-mer count tables containing both k-mers and counts, easily reaching tens of GB. Furthermore, such tables do not support efficient random-access queries in general. RESULTS: In this work, we design an efficient representation of k-mer count tables supporting fast random-access queries. We propose to apply Compressed Static Functions (CSFs), with space proportional to the empirical zero-order entropy of the counts. For very skewed distributions, like those of k-mer counts in whole genomes, the only currently available implementation of CSFs does not provide a compact enough representation. By adding a Bloom filter to a CSF we obtain a Bloom-enhanced CSF (BCSF) effectively overcoming this limitation. Furthermore, by combining BCSFs with minimizer-based bucketing of k-mers, we build even smaller representations breaking the empirical entropy lower bound, for large enough k. We also extend these representations to the approximate case, gaining additional space. We experimentally validate these techniques on k-mer count tables of whole genomes (E. Coli and C. Elegans) and unassembled reads, as well as on k-mer document frequency tables for 29 E. Coli genomes. In the case of exact counts, our representation takes about a half of the space of the empirical entropy, for large enough k's.

Srivastava S et al. (2005) Mol Cell Biol "The phosphatidylinositol 3-phosphate phosphatase myotubularin- related protein 6 (MTMR6) is a negative regulator of the Ca2+-activated K+ channel KCa3.1."

Liu G, Li Z, Ko K, Skolnik EY, Coetzee WA, Srivastava S, Lin L

[Mol Cell Biol, 2005]

Myotubularins (MTMs) belong to a large subfamily of phosphatases that dephosphorylate the 3' position of phosphatidylinositol 3-phosphate [PI(3)P] and PI(3,5)P(2). MTM1 is mutated in X-linked myotubular myopathy, and MTMR2 and MTMR13 are mutated in Charcot-Marie-Tooth syndrome. However, little is known about the general mechanism(s) whereby MTMs are regulated or the specific biological processes regulated by the different MTMs. We identified a Ca(2+)-activated K channel, K(Ca)3.1 (also known as KCa4, IKCa1, hIK1, or SK4), that specifically interacts with the MTMR6 subfamily of MTMs via coiled coil (CC) domains on both proteins. Overexpression of MTMR6 inhibited K(Ca)3.1 channel activity, and this inhibition required MTMR6's CC and phosphatase domains. This inhibition is specific; MTM1, a closely related MTM, did not inhibit K(Ca)3.1. However, a chimeric MTM1 in which the MTM1 CC domain was swapped for the MTMR6 CC domain inhibited K(Ca)3.1, indicating that MTM CC domains are sufficient to confer target specificity. K(Ca)3.1 was also inhibited by the PI(3) kinase inhibitors LY294002 and wortmannin, and this inhibition was rescued by the addition of PI(3)P, but not other phosphoinositides, to the patch pipette solution. PI(3)P also rescued the inhibition of K(Ca)3.1 by MTMR6 overexpression. These data, when taken together, indicate that K(Ca)3.1 is regulated by PI(3)P and that MTMR6 inhibits K(Ca)3.1 by dephosphorylating the 3' position of PI(3)P, possibly leading to decreased PI(3)P in lipid microdomains adjacent to K(Ca)3.1. K(Ca)3.1 plays important roles in controlling proliferation by T cells, vascular smooth muscle cells, and some cancer cell lines. Thus, our findings not only provide unique insights into the regulation of K(Ca)3.1 channel activity but also raise the possibility that MTMs play important roles in the negative regulation of T cells and in conditions associated with pathological cell proliferation, such as cancer and atherosclerosis.

Holtzman EJ et al. (1998) Am J Physiol "Cloning, characterization, and gene organization of K-Cl cotransporter from pig and human kidney and C. elegans."

Dunham PB, Logue PJ, Kumar S, Holtzman EJ, Faaland CA, Waldman J, Ricken G, Erickson SJ, Warner F

[Am J Physiol, 1998]

We isolated and characterized the cDNAs far the human, pig, and Caenorhabditis elegans K-CI cotransporters. The pig and human homologs are 94% identical and contain 1,085 and 1,086 amino acids, respectively. The deduced protein of the C. elegans K-CI cotransporter clone (CE-KCC1) contains 1,003 amino acids. The mammalian K-CI cotransporters share similar to 45% similarity with CE-KCC1. Hydropathy analyses of the three clones indicate typical KCC topology patterns with 12 transmembrane segments, large extracellular loops between transmembrane domains 5 and 6 (unique to KCC), and large COOH-terminal domains. Human KCC1 is widely expressed among various tissues. This KCC1 gene spans 23 kb and is organized in 24 exons, whereas the CE-KCC1 gene spans 3.5 kb and contains ID exons. Transiently and stably transfected human embryonic kidney cells (HEK-293) expressing the human, pig, and C. elegans K-Cl cotransporter fulfilled two (pig) or five (human and C. elegans) criteria for increased expression of the K-Cl cotransporter. The criteria employed were basal K-CI cotransport; stimulation of cotransport by swelling, N-ethylmaleimide, staurosporine, and reduced cell Mg concentration; and secondary stimulation of Na-K-CI cotransport.