Yang P et al. (2011) Autophagy "The coiled-coil domain protein EPG-8 plays an essential role in the autophagy pathway in C. elegans."

Zhang H, Yang P

[Autophagy, 2011]

Macroautophagy (hereafter referred to as autophagy) involves the formation of a closed, double membrane structure, called the autophagosome. Most of the Atg proteins that are essential for autophagosome formation are evolutionarily conserved between yeast and higher eukaryotes. The functions of some Atg proteins, however, are mediated by highly divergent proteins in mammalian cells. In this study, we identified a novel coiled-coil domain protein, EPG-8, that plays an essential role in the autophagy pathway in C. elegans. Mutations in epg-8 cause defects in degradation of various autophagy substrates and also compromise survival of animals under nutrient-depletion conditions. In epg-8 mutants, lipidated LGG-1 (the C. elegans Atg8 homolog) accumulates but does not form distinct punctate structures. EPG-8 directly interacts with the C. elegans Beclin 1 homolog, BEC-1. Our study demonstrates that epg-8 may function as a highly divergent homolog of the yeast autophagy gene Atg14.

Yang P et al. (2013) Acta Biochim Biophys Sin (Shanghai) "A C-terminal truncated mutation of spr-3 gene extends lifespan in Caenorhabditis elegans."

Yao M, Fei J, Yang P, Chen W, Sun R, Wang Z

[Acta Biochim Biophys Sin (Shanghai), 2013]

The lifespan of Caenorhabditis elegans is determined by various genetic and environmental factors. In this paper, spr-3, a C. elegans homologous gene of the mammalian neural restrictive silencing factor (NRSF/REST), is reported to be an important gene regulating lifespan of C. elegans. A deletion mutation of spr-3, spr-3(ok2525), or RNAi inhibition of spr-3 expression led to the short lifespan phenotype in C. elegans. However, a nonsense mutation of spr-3, spr-3(by108), increased the lifespan by 26% when compared with that of wild-type nematode. The spr-3(by108) also showed increased resistance to environmental stress. The spr-3(by108) mutated gene encodes a C-terminal truncated protein with a structure comparable with the REST4, a splice variant of the NRSF/REST in mammalian. The long lifespan phenotype of spr-3(by108) mutant is confirmed as a gain of function and dependent on normal functions of daf-16 and glp-1. The lifespan of the spr-3(by108) can be synergistically enhanced by inducing a mutation in daf-2. Quantitative polymerase chain reaction results showed that the expression of daf-16 as well as its target gene sod-3, mtl-1, and sip-1 was up-regulated in the spr-3(by108) mutant. These results would be helpful to further understand the complex function of NRSF/REST gene in mammalian, especially in the aging process and longevity determination.

Fechner S et al. (2018) MicroPubl Biol "The bodies of dpy-10(e128) are twice as stiff as wild type"

Loizeau F, Pruitt B, Nekimken AL, Goodman MB, Fechner S

[MicroPubl Biol, 2018]

DPY-10 is a collagen protein in the nematodes cuticle. Mutations in the dpy-10 gene induce various morphological changes that lead to animals with a dumpy (Dpy) or roller (Rol) phenotype (Levy, Yang and Kramer, 1993).

Lu Q et al. (2011) Dev Cell "The WD40 repeat PtdIns(3)P-binding protein EPG-6 regulates progression of omegasomes to autophagosomes."

Wu F, Zhang H, Guo B, Yu L, Hu W, Kovacs AL, Lu Q, Huang X, Yang P, Lin L

[Dev Cell, 2011]

PtdIns(3)P plays critical roles in the autophagy pathway. However, little is known about how PtdIns(3)P effectors act with autophagy proteins in autophagosome formation. Here we identified an essential autophagy gene in C.elegans, epg-6, which encodes a WD40 repeat-containing protein with PtdIns(3)P-binding activity. EPG-6 directly interacts with ATG-2. epg-6 and atg-2 regulate progression of omegasomes to autophagosomes, and their loss of functioncauses accumulation of enlarged early autophagic structures. Another WD40 repeat PtdIns(3)P effector, ATG-18, plays a distinct role in autophagosome formation. We also established the hierarchical relationship of autophagy genes in degradation ofprotein aggregates and revealed that the UNC-51/Atg1 complex, EPG-8/Atg14, and binding of lipidated LGG-1 to protein aggregates are required foromegasome formation. Our study demonstrates that autophagic PtdIns(3)P effectors play distinct roles in autophagosome formation and also providesa framework for understanding the concerted action of autophagy genes in protein aggregate degradation.

Loo TW et al. (2013) Biochemistry "A salt bridge in intracellular loop 2 is essential for folding of human p-glycoprotein."

Clarke DM, Loo TW

[Biochemistry, 2013]

There is no high-resolution structure of the human P-glycoprotein (P-gp, ABCB1) drug pump. Homology models based on the crystal structures of mouse and Caenorhabditis elegans P-gps show extensive contacts between intracellular loop 2 (ICL2, in the first transmembrane domain) and the second nucleotide-binding domain. Human P-gp modeled on these P-gp structures yields different ICL2 structures. Only the model based on the C. elegans P-gp structure predicts the presence of a salt bridge. We show that the Glu256-Arg276 salt bridge was critical for P-gp folding.

Sun Y et al. (2011) Protein Cell "A genome-wide RNAi screen identifies genes regulating the formation of P bodies in C. elegans and their functions in NMD and RNAi."

Li J, Bao X, Hou W, Han J, Yang P, Zhang Y, Sun Y, Zhang H, Yao X

[Protein Cell, 2011]

Cytoplasmic processing bodies, termed P bodies, are involved in diverse post-transcriptional processes including mRNA decay, nonsense-mediated RNA decay (NMD), RNAi, miRNA-mediated translational repression and storage of translationally silenced mRNAs. Regulation of the formation of P bodies in the context of multicellular organisms is poorly understood. Here we describe a systematic RNAi screen in C. elegans that identified 224 genes with diverse cellular functions whose inactivations result in a dramatic increase in the number of P bodies. 83 of these genes form a complex functional interaction network regulating NMD. We demonstrate that NMD interfaces with many cellular processes including translation, ubiquitin-mediated protein degradation, intracellular trafficking and cytoskeleton structure.We also uncover an extensive link between translation and RNAi, with different steps in protein synthesis appearing to have distinct effects on RNAi efficiency. Moreover, the intracellular vesicular trafficking network plays an important role in the regulation of RNAi. A subset of genes enhancing P body formation also regulate the formation of stress granules in C. elegans. Our study offers insights into the cellular mechanisms that regulate the formation of P bodies and also provides a framework for system-level understanding of NMD and RNAi in the context of the development of multicellular organisms.

Ahmad W et al. (2020) Biochem Biophys Res Commun "Prediction of human tau 3D structure, and interplay between O--GlcNAc and phosphorylation modifications in Alzheimer's disease: C.elegans as a suitable model to study these interactions invivo."

Ahmad I, Ahmad W, Shabbiri K

[Biochem Biophys Res Commun, 2020]

Tau protein regulates, maintains and stabilizes microtubule assembly under normal physiological conditions. In certain pathological circumstances, tau is post-translationally modified predominantly via phosphorylation and glycosylation. Hyper-phosphorylation of tau in Alzheimer's disease (AD) resulted in aggregated neurofibrillary tangles (NFTs) formation. Unfortunately, absence of tau 3D structure makes difficult to understand exact mechanism involved in tau pathology. Here by using ab-initio modelling, we predicted a tau 3D structure that not only explains its binding with microtubules but also elucidates NFTs formation. O-linked -N-acetylglucosaminylation (O--GlcNAc) is thought to regulate tau phosphorylation on single or proximal Ser/Thr residues (called as Yin-Yang sites). In this study, we not only validate the previously described three-serine residues (208, 238 and 400) as Yin-Yang sites but also predicted 22 more possible Ser/Thr O-glycosylation sites. Among them seventeen residues were predicted as possible Yin-Yang sites and are proposed to mediate NFT formation in AD. These predicted Yin-Yang sites may act as attractive therapeutic targets for the drug development in AD. Predicted 3D structure of tau₄₄₁ was highly accessible for phosphorylation and hyperphosphorylation, and showed higher surface accessibility for interplay between O--GlcNAc and phosphorylation modifications. Kinases and phosphatases involved in tau phosphorylation are conserved in human and other organisms. Homology modelling revealed conserved catalytic domain for both human and C.elegans O-GlcNAc transferase (OGT), suggesting that transgenic C.elegans expressing human tau may be a suitable model system to study these modifications.

Simske JS et al. (1995) Nature "Sequential signalling during Caenorhabditis elegans vulval induction."

Simske JS, Kim SK

[Nature, 1995]

During the induction of the Caenorhabditis elegans vulva, cell signalling causes initially equipotent cells to express a reproducible pattern of cell fates(1,2). The position of the anchor cell determines the pattern of vulval precursor cell fates, such that the closest precursor cell (P6.p) expresses the primary cell fate, the next closest cells (P5.p and P7.p) both express the secondary cell fate, and each of the precursor cells located at a distance (P3.p, P4.p and P8.p) express the tertiary cell fate (Fig. 1a)(3-5). We present data indicating that this stereotypical pattern of cell fates can be generated by sequential signals. We identified genetic mosaic animals in which P5.p and P7.p were defective in the anchor-cell signal-transduction pathway and observed that these cells adopted the secondary cell fate, indicating that anchor-cell signal transduction is not required for the expression of the secondary cell fate. These results suggest that the anchor cell induces P6.p to express the primary cell fate, and that P6.p subsequently induces P5.p and P7.p to express the secondary cell fate.

Pitt JN et al. (2000) Dev Biol "P granules in the germ cells of Caenorhabditis elegans adults are associated with clusters of nuclear pores and contain RNA."

Priess JR, Schisa JA, Pitt JN

[Dev Biol, 2000]

The germ cells, and germ cell precursors, in the nematode Caenorhabditis elegans contain distinctive granules called P granules. During early embryogenesis, P granules are segregated asymmetrically into those blastomeres that eventually produce the germ line. Because of the correlation between P granule distribution and the development of the germ line, P granules are widely thought to function in some aspect of germ line specification or differentiation. Most of the analysis of P granule structure and localization has focused on the early embryo, when P granules are located in the cytoplasm. However, during most of development P granules are associated with germ cell nuclei. We report here an ultrastructural analysis of the nuclear-associated P granules in the germ cells of the adult hermaphrodite gonad. We show that P granules are tightly associated with nuclear pores and that the positions of certain structures within the P granules correspond to the positions of pores on the nuclear envelope. We present immunocytochemical and ultrastructural data suggesting that P granules can associate, or remain associated, with pore-like structures even after they detach from the nuclear envelope during oogenesis. Finally, we show that nuclear-associated P granules in the gonad contain RNA, complementing previous studies showing that cytoplasmic P granules in embryos contain RNA.

Berkowitz LA et al. (2000) Development "MES-1, a protein required for unequal divisions of the germline in early C. elegans embryos, resembles receptor tyrosine kinases and is localized to the boundary between the germline and gut cells."

Berkowitz LA, Strome S

[Development, 2000]

During Caenorhabditis elegans embryogenesis the primordial germ cell, P-4, is generated via a series of unequal divisions, These divisions produce germline blastomeres (P-1, P-2, P-3, P4) that differ from their somatic sisters in their size, fate and cytoplasmic content (e.g. germ granules), mes-1 mutant embryos display the striking phenotype of transformation of P-4 into a muscle precursor, like its somatic sister. A loss of polarity in P-2 and P-3 cell-specific events underlies the Mes-1 phenotype, In mes-1 embryos, P-2 and P-3 undergo symmetric divisions and partition germ granules to both daughters. This paper shows that mes-1 encodes a receptor tyrosine kinase-like protein, though it lacks several residues conserved in all kinases and therefore is predicted not to have kinase activity. Immunolocalization analysis shows that MES-1 is present in four- to 24-cell embryos, where it is localized in a crescent at the junction between the germline cell and its neighboring gut cell. This is the region of P-2 and P-3 to which the spindle and P granules must move to ensure normal division asymmetry and cytoplasmic partitioning. Indeed, during early stages of mitosis in P-2 and P-3, one centrosome is positioned adjacent to the MES-1 crescent. Staining of isolated blastomeres demonstrated that MES-1 was present in the membrane of the germline blastomeres, consistent with a cell-autonomous function. Analysis of MES-1 distribution in various cell-fate and patterning mutants suggests that its localization is not dependent on the correct fate of either the germline or the gut blastomere but is dependent upon correct spatial organization of the embryo. Our results suggest that MES-1 directly positions the developing mitotic spindle and its associated P granules within P-2 and P-3, or provides an orientation signal for P-2- and P-3-specific events.