Smith J (2002) Trends Cell Biol "Human Sir2 and the 'silencing' of p53 activity."

Smith J

[Trends Cell Biol, 2002]

Members of the evolutionarily conserved silent information regulator 2 (Sir2) protein family are nicotinamide adenine dinucleotide (NAD(+))-dependent histone deacetylases. In yeast, the founding Sir2 protein is known to function in transcriptional silencing processes through the deacetylation of histones H3 and H4, thus setting up a repressive chromatin structure. Yeast and Caenorhabditis elegans Sir2 are also involved in regulating the life span of these organisms. Until recently, the function of mammalian Sir2 family members was completely unknown. However, several recent studies have now determined a remarkable function for the human SIRT1 protein, which is the closest human homolog of yeast Sir2. SIRT1 specifically associates with the p53 tumor suppressor protein and deacetylates it, resulting in negative regulation of p53-mediated transcriptional activation. Importantly, p53 deacetylation by SIRT1 also prevents cellular senescence and apoptosis induced by DNA damage and stress.

Smith J et al. (1998) West Coast Worm Meeting "A NEW FAMILY OF PROTEINS CONSERVED BETWEEN WORM NEURONS AND THE MAMMALIAN RETINA"

Smith J, Pilgrim DB, Chambers M

[West Coast Worm Meeting, 1998]

UNC-119 has a homologue expressed in the mammalian retina (HRG4/RRG4). We have noted a second UNC-119 homologue in C. elegans, C27H5.1, predicted from the Genome Sequencing Project. While only weakly similar to UNC-119, this gene is predicted to encode a 159 amino acid protein which is highly conserved throughout a number of other species. In particular, C27H5.1 is 70% identical and 85% similar to the rod phosphodiesterase delta subunit (PDE-delta) in mammalian retina. In turn, PDE-delta has been shown to be highly conserved throughout a number of vertebrates and invertebrates. Interestingly, two of the genes that share homology with C27H5.1, PDE-delta and HRG4, are retina specific while C. elegans has no demonstrated phototransduction ability. Therefore, it would seem that the role of this protein family (and specifically UNC-119/C27H5.1 in worms) is not specific to vision but is more fundamental in nature. The functions of PDE-delta, UNC-119, and HRG4 are known to varying degrees. PDE-delta has been shown to solubilize the rod phosphodiesterase complex, although the function or effect of this is not yet clear. UNC-119 is believed to play a role in development of the nervous system, particularly in axon guidance and growth cone outgrowth, while the function of its mammalian homologue RG4 is unknown. The function of C27H5.1 is not yet known, but based on its conserved relationship with PDE-delta, it is likely that C27H5.1 plays some role in signal transduction. We have identified, and are currently in the process of cloning out, a mutation in this gene. The in vivo expression of a green fluorescent protein: C27H5.1 promoter construct demonstrates that the gene is expressed throughout the nervous system in the same manner as UNC-119. Therefore, there appears to be a new family of proteins that are pan-neuronal in Caenorhabditis (and perhaps in other invertebrates) but retinal in mammals.

Smith J et al. (2016) Elife "Spatial patterning of P granules by RNA-induced phase separation of the intrinsically-disordered protein MEG-3."

Seydoux G, Rasoloson D, Schmidt H, Smith J, Lu T, Calidas D

[Elife, 2016]

RNA granules are non-membrane bound cellular compartments that contain RNA and RNA binding proteins. The molecular mechanisms that regulate the spatial distribution of RNA granules in cells are poorly understood. During polarization of the C. elegans zygote, germline RNA granules, called P granules, assemble preferentially in the posterior cytoplasm. We present evidence that P granule asymmetry depends on RNA-induced phase separation of the granule scaffold MEG-3. MEG-3 is an intrinsically disordered protein that binds and phase separates with RNA in vitro. In vivo, MEG-3 forms a posterior-rich concentration gradient that is anti-correlated with a gradient in the RNA-binding protein MEX-5. MEX-5 is necessary and sufficient to suppress MEG-3 granule formation in vivo, and suppresses RNA-induced MEG-3 phase separation in vitro. Our findings suggest that MEX-5 interferes with MEG-3's access to RNA, thus locally suppressing MEG-3 phase separation to drive P granule asymmetry. Regulated access to RNA, combined with RNA-induced phase separation of key scaffolding proteins, may be a general mechanism for controlling the formation of RNA granules in space and time.

Smith, Cody J. et al. (2009) International Worm Meeting "A combination of morphological landmarks and diffusible cues regulate dendritic arborization in PVD sensory neurons."

Cha, Byeong, Treinin, Millet, Watson, Joseph D., Miller, III, David M., Smith, Cody J., Spencer, Clay W.

[International Worm Meeting, 2009]

Sensory neurons that detect noxious stimuli (nociceptors) display highly branched dendritic arbors adjacent to the skin. The variable complexity of these structures has stymied efforts to identify molecular determinants of dendritic morphogenesis. To simplify this problem, we are using live-cell imaging and genetic methods in C. elegans to study a single type of nociceptive neuron with a stereotypical dendritic architecture. The PVD neuron (L+R) adopts a series of orthogonal branching decisions that envelops the animal in a net-like array of sensory processes directly beneath the hypodermis. Time-lapse imaging with fluorescent markers has revealed that PVD dendrites adopt a 90-degree turn to fasciculate with sub-lateral nerve cords. In contrast, PVD dendrites withdraw upon intracellular contact with an apparent self-avoidance mechanism that insures maximum coverage of the sensory field. These responses suggest that PVD dendritic outgrowth and branching are guided by extracellular signals. We generated a microarray profile of PVD to identify transcripts with potential roles in dendritic morphogenesis. Genetic ablation of the PVD-enriched axon guidance receptors UNC-5 (e152) and UNC-40/DCC (e271) disables the self-avoidance mechanism but does not perturb PVD fasciculation with sub-lateral nerve cords. A similar phenotype was obtained for the axon guidance cue UNC-6/netrin and its downstream effector UNC-34/ena (e315). On the basis of these results, we propose a novel mechanism in which extracellular UNC-6 interacts with UNC-5 and UNC-40 to mediate dendritic self-avoidance. Ongoing experiments are designed to establish the location of UNC-5 and UNC-40 receptors in growing PVD processes and to define the spatial origin of the UNC-6 cue.

Jessica J Smith et al. (2002) West Coast Worm Meeting "Investigating the role of pdl-1"

Dave B Pilgrim, Jessica J Smith

[West Coast Worm Meeting, 2002]

pdl-1 (phosphodiesterase 6 delta like) is the only known C. elegans homologue of unc-119, a gene involved in axon outgrowth and maintenance. Like unc-119, pdl-1 appears to be expressed throughout the nervous system beginning early in embryogenesis and continuing through adulthood. Both pdl-1 and unc-119 have highly conserved mammalian homologues which show enriched expression in the retina. We are studying pdl-1 in order to better understand the role(s) of this protein family.

Jessica J Smith et al. (2003) International Worm Meeting "pdl-1: redundant gene or evolutionary conundrum?"

Jessica J Smith, David B Pilgrim

[International Worm Meeting, 2003]

PDL-1 (phosphodiesterase 6 delta) is extremely well conserved among metazoans, showing 74-85% similarity between C. elegans, Drosophila, fish, and mammals. Despite their conservation, these proteins contain no characterized domains or motifs and until recently there were no known mutations. We have recently received a pdl-1 deletion from the C. elegans Knockout Consortium. The deletion removes the start site and should be a genetic null. To our surprise, the pdl-1 mutant lacks a readily observable phenotype. The only sequence homologue of pdl-1 is unc-119. In C. elegans, both genes show pan-neural expression beginning early in embryogenesis. We have long suspected that there might be functional overlap between the two genes. However, a pdl-1; unc-119 double mutant appears no worse than unc-119 alone. This raises a number of important questions. Why is this highly conserved protein seemingly dispensable? Is there a subtle phenotype that we have yet to identify, is there functional redundancy within the genome, or is pdl-1 truly without phenotype? We are working towards resolving these issues. As to whether PDE6D knockdown can produce a phenotype in any species, we have expanded our research to include the zebrafish Danio rerio. We are using morpholino oligos to block translation or splicing of PDE6D in the fish. RT-PCR shows that the PDE6D transcript is maternally provided and present in fish embryos for at least 72hpf. Thus there is hope that morpholino knock-down, which is only effective early in embryogenesis, could produce a phenotype. We are also using in situ hybridization to determine the expression pattern of PDE6D. The PDE6D transcript is ubiquitous, through retinally enriched, in mammals yet is restricted to the nervous system in C. elegans. It will be interesting to see whether there is specific or general localization in the zebrafish.

J A Smith et al. (2001) International C. elegans Meeting "GATA factor function and hypodermal development."

J S Gilleard, J A Smith, J D McGhee

[International C. elegans Meeting, 2001]

Smith ES et al. (2013) J Biol Chem "A chemoreceptor that detects molecular carbon dioxide."

Smith ES, Martinez-Velazquez LA, Ringstad N

[J Biol Chem, 2013]

Animals from diverse phyla possess neurons that are activated by the product of aerobic respiration, CO2. It has long been thought that such neurons primarily detect the CO2 metabolites protons and bicarbonate. We have determined the chemical tuning of isolated CO2 chemosensory BAG neurons of the nematode Caenorhabditis elegans. We show that BAG neurons are principally tuned to detect molecular CO2, although they can be activated by acid stimuli. One component of the BAG transduction pathway, the receptor-type guanylate cyclase GCY-9, suffices to confer cellular sensitivity to both molecular CO2 and acid, indicating that it is a bifunctional chemoreceptor. We speculate that in other animals, receptors similarly capable of detecting molecular CO2 might mediate effects of CO2 on neural circuits and behavior.

Smith-Vikos T et al. (2012) J Cell Sci "MicroRNAs and their roles in aging."

Smith-Vikos T, Slack FJ

[J Cell Sci, 2012]

MicroRNAs (miRNAs) are a class of short non-coding RNAs that bind mRNAs through partial base-pair complementarity with their target genes, resulting in post-transcriptional repression of gene expression. The role of miRNAs in controlling aging processes has been uncovered recently with the discovery of miRNAs that regulate lifespan in the nematode Caenorhabditis elegans through insulin and insulin-like growth factor-1 signaling and DNA damage checkpoint factors. Furthermore, numerous miRNAs are differentially expressed during aging in C. elegans, but the specific functions of many of these miRNAs are still unknown. Recently, various miRNAs have been identified that are up- or down-regulated during mammalian aging by comparing their tissue-specific expression in younger and older mice. In addition, many miRNAs have been implicated in governing senescence in a variety of human cell lines, and the precise functions of some of these miRNAs in regulating cellular senescence have helped to elucidate mechanisms underlying aging. In this Commentary, we review the various regulatory roles of miRNAs during aging processes. We highlight how certain miRNAs can regulate aging on the level of organism lifespan, tissue aging or cellular senescence. Finally, we discuss future approaches that might be used to investigate the mechanisms by which miRNAs govern aging processes.

Smith SA et al. (2011) ILAR J "Culture and maintenance of selected invertebrates in the laboratory and classroom."

Smith SA, Scimeca JM, Mainous ME

[ILAR J, 2011]

Invertebrate species have been used for many years in the laboratory and teaching environment. We discuss some of the most commonly maintained invertebrates--the nematode (Caenorhabditis elegans), the California sea hare (Aplysia californica), the fruit fly (Drosophila melanogaster), terrestrial hermit crabs, the horseshoe crab (Limulus polyphemus), and cephalopods--and briefly describe general techniques for culturing them in captivity. The aim of this article is to give potential users an idea of the materials, methods, and effort required to maintain each type of organism in a laboratory or classroom setting.