Miller DL (2019) J Gerontol A Biol Sci Med Sci "There Are Worms in My Aging Research!"

Miller DL

[J Gerontol A Biol Sci Med Sci, 2019]

Caenorhabditis elegans (the worm) has long been a key model organism for understanding the biological mechanisms that underlie life span, health span, and aging. The first mutations that modulate life span were identified in worms (14). Subsequent cloning of daf-2, an insulin-like receptor (5), and its downstream target daf-16, a FOXO transcription factor (6,7), opened up the field of aging research to genetic analysis. Since this time, there has been an explosion of aging research, much using worms, that has revealed many fundamental aspects of metabolism and cellular signaling that impinge on life span and health span. Today, the worm is still teaching us about fundamental aspects of aging, as highlighted by several recent publications in JGBS.

Miller RA (2009) J Gerontol A Biol Sci Med Sci "Cell stress and aging: new emphasis on multiplex resistance mechanisms."

Miller RA

[J Gerontol A Biol Sci Med Sci, 2009]

Work, initially in Caenorhabditis elegans and then more recently in fruit flies and mice, has suggested that anti-aging mutations extend life span by simultaneous activation of pathways that protect cells from multiple forms of injury. This "multiplex stress resistance" theory suggests a number of new avenues for investigation of the genetic and cellular controls that influence organismic longevity within and among species, and that might lead to the development of pharmaceuticals that retard the aging process and, therefore, the entire panoply of age-dependent diseases and disabilities.

Miller DM et al. (1992) Worm Breeder's Gazette "unc-4 LacZ Expression in A-Type Motor Neurons"

Miller DM, Niemeyer CJ

[Worm Breeder's Gazette, 1992]

unc-4 LacZ expression in A-type motor neurons David M. Miller and Charles J. Niemeyer, Dept. of Cell Biology, Duke Univ. Medical Ctr, Durham, NC 27710

Miller AC et al. (2005) J Neurosci "Step-response analysis of chemotaxis in Caenorhabditis elegans."

Moravec ML, Miller AC, Thiele TR, Faumont S, Lockery SR

[J Neurosci, 2005]

The sensorimotor transformation underlying Caenorhabditis elegans chemotaxis has been difficult to measure directly under normal assay conditions. Thus, key features of this transformation remain obscure, such as its time course and dependence on stimulus amplitude. Here, we present a comprehensive characterization of the transformation as obtained by inducing stepwise temporal changes in attractant concentration within the substrate as the worm crawls across it. We found that the step response is complex, with multiple phases and a nonlinear dependence on the sign and amplitude of the stimulus. Nevertheless, the step response could be reduced to a simple kinetic model that predicted the results of chemotaxis assays. Analysis of the model showed that chemotaxis results from the combined effects of approach and avoidance responses to concentration increases and decreases, respectively. Surprisingly, ablation of the ASE chemosensory neurons, known to be necessary for chemotaxis in chemical gradient assays, eliminated avoidance responses but left approach responses intact. These results indicate that the transformation can be dissected into components to which identified neurons can be assigned.

Miller D et al. (2022) FASEB J "RHY-1 Promotes Hydrogen Sulfide Tolerance."

Miller D, Swanson T, Hedman D

[FASEB J, 2022]

Once known best for its toxic effects, recent work has shown that hydrogen sulfide (H₂ S) has many roles as a cellular messenger. For example, both endogenously produced and exogenously supplied H₂ S protect against cellular damage and death associated with ischemia/reperfusion injury in mammals. The mechanistic relationship between beneficial and toxic effects of H₂ S is not understood. We have developed C. elegans as a model to understand the mechanistic basis of H₂ S effects in animals. In addition to facile genetic and genomic tools, using C. elegans provides the ability to precisely control both genotype and cellular H₂ S exposure. C. elegans grown in 50 ppm H₂ S are long-lived and resistant to hypoxia-induced disruption of protein homeostasis. The early transcriptional response to H₂ S requires the C. elegans orthologue of the hypoxia-inducible transcription factor, hif-1. HIF-1 promotes survival in H₂ S, at least in part, by upregulating expression of sqrd-1, which encodes the sulfide-quinone oxidoreductase. SQRD-1 catalyzes the first step in the mitochondrial oxidation of H₂ S. In an unbiased forward genetic screen, we found that expression of rhy-1 suppresses lethality of hif-1 mutant animals in 50 ppm H₂ S. RHY-1 is an integral-membrane ER protein with predicted acyltransferase (ACYL3) activity. The ACYL3 family is large and conserved across species from bacteria to primates, but the function of these enzymes is largely unstudied. RHY-1 was first characterized as a negative regulator of HIF-1, and our data indicate that it also promotes survival in H₂ S independently of HIF-1. To understand RHY-1 function we have used biotinylation by antibody recognition (BAR) to identify proteins that interact with RHY-1. We show that RHY-1 directly associates with CYSL proteins, which are orthologues of cystathionine -synthase. Mutations in cysl-1 abrogate RHY-1 function to regulate HIF-1 and to promote survival independently of HIF-1. We have also identified a novel methyltransferase, RIPS-1, that is required for RHY-1 to promote survival in H₂ S but which is dispensable for the proper regulation of HIF-1. Together, our data show that RHY-1 promotes survival in H₂ S through a novel mechanism which can bypass the only known catabolic pathway for H₂ S in vivo. Understanding the mechanism of RHY-1 activity in H₂ S will begin to elucidate the relationship between H₂ S signaling and toxicity, and could lead to new therapeutic strategies to modulate endogenous H₂ S levels.

Miller RK et al. (2006) J Cell Biol "UNC-98 links an integrin-associated complex to thick filaments in Caenorhabditis elegans muscle."

Benian GM, Landsverk ML, Miller RK, Qadota H, Epstein HF, Mercer KB

[J Cell Biol, 2006]

Focal adhesions are multiprotein assemblages that link cells to the extracellular matrix. The transmembrane protein, integrin, is a key component of these structures. In vertebrate muscle, focal adhesion-like structures called costameres attach myofibrils at the periphery of muscle cells to the cell membrane. In Caenorhabditis elegans muscle, all the myofibrils are attached to the cell membrane at both dense bodies (Z-disks) and M-lines. Clustered at the base of dense bodies and M-lines, and associated with the cytoplasmic tail of beta-integrin, is a complex of many proteins, including UNC-97 (vertebrate PINCH). Previously, we showed that UNC-97 interacts with UNC-98, a 37-kD protein, containing four C2H2 Zn fingers, that localizes to M-lines. We report that UNC-98 also interacts with the C-terminal portion of a myosin heavy chain. Multiple lines of evidence support a model in which UNC-98 links integrin-associated proteins to myosin in thick filaments at M-lines.

Miller RM et al. (2011) J Neurosci "The Wnt/beta-catenin asymmetry pathway patterns the atonal ortholog lin-32 to diversify cell fate in a Caenorhabditis elegans sensory lineage."

Portman DS, Miller RM

[J Neurosci, 2011]

Each sensory ray of the Caenorhabditis elegans male tail comprises three distinct neuroglial cell types. These three cells descend from a single progenitor, the ray precursor cell, through several rounds of asymmetric division called the ray sublineage. Ray development requires the conserved atonal-family bHLH gene lin-32, which specifies the ray neuroblast and promotes the differentiation of its progeny. However, the mechanisms that allocate specific cell fates among these progeny are unknown. Here we show that the distribution of LIN-32 during the ray sublineage is markedly asymmetric, localizing to anterior daughter cells in two successive cell divisions. The anterior-posterior patterning of LIN-32 expression and of differentiated ray neuroglial fates is brought about by the Wnt/-catenin asymmetry pathway, including the Wnt ligand LIN-44, its receptor LIN-17, and downstream components LIT-1 (NLK), SYS-1 (-catenin), and POP-1 (TCF). LIN-32 asymmetry itself has an important role in patterning ray cell fates, because the failure to silence lin-32 expression in posterior cells disrupts development of this branch of the ray sublineage. Together, our results illustrate a mechanism whereby the regulated function of a proneural-class gene in a single neural lineage can both specify a neural precursor and actively pattern the fates of its progeny. Moreover, they reveal a central role for the Wnt/-catenin asymmetry pathway in patterning neural and glial fates in a simple sensory lineage.

Miller-Fleming TW et al. (2021) J Neurosci "Transcriptional control of parallel-acting pathways that remove specific presynaptic proteins in remodeling neurons."

Miller-Fleming TW, Richmond JE, Manning L, Miller DM, Cuentas-Condori A, Palumbos S

[J Neurosci, 2021]

Synapses are actively dismantled to mediate circuit refinement, but the developmental pathways that regulate synaptic disassembly are largely unknown. We have previously shown that the epithelial sodium channel ENaC/UNC-8 triggers an activity-dependent mechanism that drives the removal of presynaptic proteins liprin-/SYD-2, Synaptobrevin/SNB-1, RAB-3 and Endophilin/UNC-57 in remodeling GABAergic neurons in <i>C. elegans</i> (Miller-Fleming et al., 2016). Here, we report that the conserved transcription factor Iroquois/IRX-1 regulates UNC-8 expression as well as an additional pathway, independent of UNC-8, that functions in parallel to dismantle functional presynaptic terminals. We show that the additional IRX-1-regulated pathway is selectively required for the removal of the presynaptic proteins, Munc13/UNC-13 and ELKS, which normally mediate synaptic vesicle fusion and neurotransmitter release. Our findings are notable because they highlight the key role of transcriptional regulation in synapse elimination during development and reveal parallel-acting pathways that coordinate synaptic disassembly by removing specific active zone proteins.<b>SIGNIFICANT STATEMENT:</b>Synaptic pruning is a conserved feature of developing neural circuits but the mechanisms that dismantle the presynaptic apparatus are largely unknown. We have determined that synaptic disassembly is orchestrated by parallel-acting mechanisms that target distinct components of the active zone. Thus, our finding suggests that synaptic disassembly is not accomplished by en masse destruction but depends on mechanisms that dismantle the structure in an organized process.

Johnson, Christina K. et al. (2021) MicroPubl Biol

Bianchi, Laura, Johnson, Christina K., Miller III, David M.

[MicroPubl Biol, 2021]

For Johnson, CK; Miller, DD; Bianchi, L (2021). Effect of the protease plasmin on C. elegans hyperactive DEG/ENaC channels MEC-4(d) and UNC-8(d). microPublication Biology. 10.17912/micropub.biology.000412.

McGhee JD (1987) Biochemistry "Purification and characterization of a carboxylesterase from the intestine of the nematode Caenorhabditis elegans."

McGhee JD

[Biochemistry, 1987]

The major intestinal esterase from the nematode Caenorhabditis elegans has been purified to essential homogeneity. Starting from whole worms, the overall purification is 9000-fold with a 10% recovery of activity. The esterase is a single polypeptide chain of Mr 60,000 and is stoichiometrically inhibited by organophosphates. Substrate preferences and inhibition patterns classify the enzyme as a carboxylesterase (EC 3.1.1.1), but the physiological function is unknown. The sequence of 13 amino acid residues at the esterase N- terminus has been determined. This partial sequence shows a surprisingly high degree of similarity to the N-terminal sequence of two carboxylesterases recently isolated from Drosophila mojavensis [Pen, J., van Beeumen, J., & Beintema, J. J. (1986) Biochem. J. 238, 691-699].