Figure 5 - uploaded by Matt Crook
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A novel molting and excretory canal defect seen in a daf-7/+ larva carrying the daf-7T2 array at 25°C. DIC micrographs of (A) a larva showing multiple lateral constrictions and unshed cuticle (×40 magnification) and (B–D) close-ups of the same larva showing molting and excretory canal defects in greater detail, in particular the excretory canal course reversions that can be seen in each micrograph (×100 magnification). Molting and excretory canal defects are highlighted by black and white arrowheads, respectively. Images were taken using a Zeiss Axioplan 2 microscope and oil immersion DIC optics. Scale bars = 20 μm.
Source publication
Background:
TGF-β signaling pathways are involved in the control of development in every member of the animal kingdom. As such, TGF-β ligands are widely divergent yet retain a set of core conserved features, specifically, a pre-protein cleavage site and several conserved ligand domain residues, the disruption of which produces a dominant negative...
Context in source publication
Context 1
... we examined the arrested larvae by DIC, we found a molting defect, with constrictions caused by unshed cuticle present at variable locations along the worm, and defects in their excretory canals, including frequent course reversals (Fig. 5). The percentage of arrested larvae showing molting and excretory canal defects is shown in Table 1. One concern with using extrachromosomal arrays is that mosaicism will result in the array being lost from particular cell lineages, which is of particular importance given that daf-7 is expressed in only one cell type, the ASI neuron ...
Citations
... To identify candidates in C. elegans, we took advantage of previously performed transcriptional analysis of UPR in strains deficient for individual sensors/effectors 51 Downregulation of daf-7 mRNA by RIDD activity is partial, and thus it regulates DAF-7 signaling differently than a complete loss of function or gene deletion. Different degrees of DAF-7 loss lead to distinct phenotypes 55,93 . The worms without both daf-7 alleles enter only the pre-dauer L2d state if grown at 20°C with plentiful food, while they enter dauer at almost complete penetrance at 25°C 52,72 ; ...
Xbp1 splicing and regulated IRE1-dependent RNA decay (RIDD) are two RNase activities of the ER stress sensor IRE1. While Xbp1 splicing has important roles in stress responses and animal physiology, the physiological role(s) of RIDD remain enigmatic. Genetic evidence in C. elegans connects XBP1-independent IRE1 activity to organismal stress adaptation, but whether this is via RIDD, and what are the targets is yet unknown. We show that cytosolic kinase/RNase domain of C. elegans IRE1 is indeed capable of RIDD in human cells, and that sensory neurons use RIDD to signal environmental stress, by degrading mRNA of TGFβ-like growth factor DAF-7. daf-7 was degraded in human cells by both human and worm IRE1 RNAse activity with same efficiency and specificity as Blos1, confirming daf-7 as RIDD substrate. Surprisingly, daf-7 degradation in vivo was triggered by concentrations of ER stressor tunicamycin too low for xbp-1 splicing. Decrease in DAF-7 normally signals food limitation and harsh environment, triggering adaptive changes to promote population survival. Because C. elegans is a bacteriovore, and tunicamycin, like other common ER stressors, is an antibiotic secreted by Streptomyces spp. , we asked whether daf-7 degradation by RIDD could signal pending food deprivation. Indeed, pre-emptive tunicamycin exposure increased survival of C. elegans populations under food limiting/high temperature stress, and this protection was abrogated by overexpression of DAF-7. Thus, C. elegans uses stress-inducing metabolites in its environment as danger signals, and employs IRE1′s RIDD activity to modulate the neuroendocrine signaling for survival of upcoming environmental challenge.
... Similar results apply for genes neg-1, ced-4 and mec-8. It has been reported that daf-7 is closely related to the development of the nervous system in that it is a development-regulated growth factor that regulates the transcription and apoptotic processes [60], plays an important role in larval development, and has a greater impact on the development of molting and excretory ducts [61]. Several lines of evidence support that neg-1 [62], ced-4 [63], and mec-8 [64] play important roles in the developmental process. ...
Time-series single-cell RNA sequencing (scRNA-seq) provides a breakthrough in modern biology by enabling researchers to profile and study the dynamics of genes and cells based on samples obtained from multiple time points at an individual cell resolution. However, cell asynchrony and an additional dimension of multiple time points raises challenges in the effective use of time-series scRNA-seq data for identifying genes and cell subclusters that vary over time. However, no effective tools are available. Here, we propose scTITANS (https://github.com/ZJUFanLab/scTITANS), a method that takes full advantage of individual cells from all time points at the same time by correcting cell asynchrony using pseudotime from trajectory inference analysis. By introducing a time-dependent covariate based on time-series analysis method, scTITANS performed well in identifying differentially expressed genes and cell subclusters from time-series scRNA-seq data based on several example datasets. Compared to current attempts, scTITANS is more accurate, quantitative, and capable of dealing with heterogeneity among cells and making full use of the timing information hidden in biological processes. When extended to broader research areas, scTITANS will bring new breakthroughs in studies with time-series single cell RNA sequencing data.
... In Caenorhabditis elegans, the TGF-β signaling pathway has been demonstrated to regulate reproductive development by controlling dauer formation (Inoue and Thomas 2000a, b) and lifespan extension under unfavorable condition (Shaw et al. 2007). The TGF-β signaling pathway contains genes which encode a ligand (daf-7) (Crook and Grant 2013), type I (daf-1) and type II (daf-4) (Estevez et al. 1993) receptors, and three Smads (daf-8, daf-14, daf-3) (McGehee et al. 2015). The biochemical relationships of these gene products have not been determined; however, based on the vertebrate TGF-β signaling pathway system, it is thought that DAF-7 could bind to the type II receptor in order to activate the receptor complex DAF-1/DAF-4 and thus resulting in phosphorylation of the Smads. ...
The components of the transforming growth factor β (TGF-β) signaling pathway in parasitic nematodes remain unknown. In this research, a type I receptor for TGF-β was isolated from the hookworm Ancylostoma caninum. The new gene was designated as Acdaf-1, a Caenorhabditis elegans daf-1 homolog. The full-length cDNA of Acdaf-1 encodes a 595-amino-acid protein with an NH2-terminal signal peptide. This protein has a cytoplasm tail (209-595aa region) which corresponds to the type 1a membrane topology. Between amino acid position 295–500, the protein contains the ATP binding site, substrate binding sites, and PKC-kinase-like domain. Real-time RT-PCR showed that the transcript was expressed in three main stages of A. caninum. It reached the maximal level in the female adult worm stage with lower transcript level in the first and second larvae (L1/L2) and intermediate level in L3 stages as well as in the male worms. After serum activation, the activity of Acdaf-1 was decreased in L3 larvae. These data implied that Acdaf-1 might relate to the infection ability of the larvae. Immunolocalization revealed that AcDAF-1 was present in eggs, intestine, and epidermis cells of larvae (L1, L2, and L3 stages) with strong signal in primordium of the gonads in L3 and was abundant in epidermis, intestine, and ovary of adult worm. These results suggested that Acdaf-1 might be involved in the interaction of the parasite and host relationship and provide a potential target for parasite control.
... daf-1 encodes a TGF-beta type I receptor homolog, which together with the TGF-β-like type II receptor DAF-4, is required for the regulation of dauer formation by environmental signals [81][82][83][84]. Similarly, daf-7 encodes a member of the TGF-β superfamily; which is involved in signaling pathway that interprets environmental conditions to regulate energy balance pathways that affect dauer larval formation, fat metabolism, egg laying, feeding behavior and sperm motility [85][86][87][88]. Identification of several insulin-like peptide (ins) genes proved the role of insulin signaling in IJ formation and maintenance in H. indica. ...
Background
Nematodes are the most numerous animals in the soil. Insect parasitic nematodes of the genus Heterorhabditis are capable of selectively seeking, infecting and killing their insect-hosts in the soil. The infective juvenile (IJ) stage of the Heterorhabditis nematodes is analogous to Caenorhabditis elegans dauer juvenile stage, which remains in ‘arrested development’ till it finds and infects a new insect-host in the soil. H. indica is the most prevalent species of Heterorhabditis in India. To understand the genes and molecular processes that govern the biology of the IJ stage, and to create a resource to facilitate functional genomics and genetic exploration, we sequenced the transcriptome of H. indica IJs.
Results
The de-novo sequence assembly using Velvet-Oases pipeline resulted in 13,593 unique transcripts at N50 of 1,371 bp, of which 53 % were annotated by blastx. H. indica transcripts showed higher orthology with parasitic nematodes as compared to free living nematodes. In-silico expression analysis showed 30 % of transcripts expressing with ≥100 FPKM value. All the four canonical dauer formation pathways like cGMP-PKG, insulin, dafachronic acid and TGF-β were active in the IJ stage. Several other signaling pathways were highly represented in the transcriptome. Twenty-four orthologs of C. elegans RNAi pathway effector genes were discovered in H. indica, including nrde-3 that is reported for the first time in any of the parasitic nematodes. An ortholog of C. elegans tol-1 was also identified. Further, 272 kinases belonging to 137 groups, and several previously unidentified members of important gene classes were identified.
Conclusions
We generated high-quality transcriptome sequence data from H. indica IJs for the first time. The transcripts showed high similarity with the parasitic nematodes, M. hapla, and A. suum as opposed to C. elegans, a species to which H. indica is more closely related. The high representation of transcripts from several signaling pathways in the IJs indicates that despite being a developmentally arrested stage; IJs are a hotbed of signaling and are actively interacting with their environment.
Electronic supplementary material
The online version of this article (doi:10.1186/s12864-016-2510-z) contains supplementary material, which is available to authorized users.
... Lower levels of daf-7 signaling would be predicted to result in transient larval arrest or inappropriate resumption of development; higher levels of daf-7 signaling would be predicted to result in an inability to resume development. The use of dominant negative daf-7 transgenes, as with daf-16 and insulin signaling , offers one possible approach, although recent work in C. elegans suggests that this may not be straightforward (Crook and Grant, 2013). Another tantalizing approach would be the use of random insertional mutagenesis using the piggyBac transposon pioneered in S. stercoralis (Shao et al., 2012). ...
How any complex trait has evolved is a fascinating question, yet the evolution of parasitism among the nematodes is arguably one of the most arresting. How did free-living nematodes cross that seemingly insurmountable evolutionary chasm between soil dwelling and survival inside another organism? Which of the many finely honed responses to the varied and harsh environments of free-living nematodes provided the material upon which natural selection could act? Although several complementary theories explain this phenomenon, I will focus on the dauer hypothesis. The dauer hypothesis posits that the arrested third-stage dauer larvae of free-living nematodes such as Caenorhabditis elegans are, due to their manyphysiological similarities with infective third-stage larvae of parasitic nematodes, a pre-adaptation to parasitism. If so, then a logical extension of this hypothesis is that the molecular pathways which control entry into and recovery from dauer formation by free-living nematodes in response to environmental cues have been co-opted to control the processes of infective larval arrest and activation in parasitic nematodes. The molecular machinery that controls dauer entry and exit is present in a wide range of parasitic nematodes. However, the developmental outputs of the different pathways are both conserved and divergent, not only between populations of C. elegans or between C. elegans and parasitic nematodes but also between different species of parasitic nematodes. Thus the picture that emerges is more nuanced than originally predicted and may provide insights into the evolution of such an interesting and complex trait.
