scholarly journals Characterization of aminopeptidase encoding gene anp-1 and its association with development in Caenorhabditis elegans

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7944 ◽  
Author(s):  
Shanchun Su ◽  
Baoliang Pan ◽  
Yanxin Hu ◽  
Ming Wang
Keyword(s):  
Caenorhabditis Elegans ◽  
Transcriptome Sequencing ◽  
Adult Stage ◽  
Small Body ◽  
Enrichment Analysis ◽  
Functional Expression ◽  
C Elegans ◽  
Sequencing Method ◽  
Differential Expression Genes ◽  
Development And Aging

Background Aminopeptidases play important roles in various biological processes in nematodes including growth, development and reproduction. Although the aminopeptidases have been shown to regulate reproduction in Caenorhabditis elegans (C. elegans), the role of aminopeptidases in development and aging has not been reported. This study focused on the function of aminopeptidase AlaNyl aminopeptidase 1 (ANP-1) on development in C. elegans. Methods In the present study, we reported the identification of ANP-1 in C. elegans along with sequence analysis and its functional expression and characterization. The phenotype changes were observed when anp-1 mutated. Then, differential expression genes (DEGs) between wild type strain (N2) and anp-1 deletion strain (RB804) were identified using transcriptome sequencing method. Finally, DEGs were verified by qRT-PCR assay. Results Our observations suggested that anp-1 mutation induced small body size in the L4/young adult stage of C. elegans, however, there was no difference between N2 and RB804 in adult stage. Moreover, deletion of anp-1 resulted in shortening lifespan and laying fewer eggs. DEGs (184 genes) were observed between N2 groups and RB804 groups by transcriptome sequencing. According to GO annotations and KEGG enrichment analysis, these DEGs play vital roles in development regulation in C. elegans. These data demonstrate ANP-1 participates in development and aging of C. elegans and will considerably contribute to the existing knowledge of aminopeptidase function in C. elegans.

A Cuticle Collagen Encoded by the lon-3 Gene May Be a Target of TGF-β Signaling in Determining Caenorhabditis elegans Body Shape

Genetics ◽  
2002 ◽  
Vol 162 (4) ◽  
pp. 1631-1639
Author(s):  
Yo Suzuki ◽  
Gail A Morris ◽  
Min Han ◽  
William B Wood
Keyword(s):  
Caenorhabditis Elegans ◽  
Body Shape ◽  
Small Body ◽  
Dependent Manner ◽  
Loss Of Function ◽  
Cellular Mechanisms ◽  
C Elegans ◽  
Gene Expression Analyses ◽  
Dose Dependent

Abstract The signaling pathway initiated by the TGF-β family member DBL-1 in Caenorhabditis elegans controls body shape in a dose-dependent manner. Loss-of-function (lf) mutations in the dbl-1 gene cause a short, small body (Sma phenotype), whereas overexpression of dbl-1 causes a long body (Lon phenotype). To understand the cellular mechanisms underlying these phenotypes, we have isolated suppressors of the Sma phenotype resulting from a dbl-1(lf) mutation. Two of these suppressors are mutations in the lon-3 gene, of which four additional alleles are known. We show that lon-3 encodes a collagen that is a component of the C. elegans cuticle. Genetic and reporter-gene expression analyses suggest that lon-3 is involved in determination of body shape and is post-transcriptionally regulated by the dbl-1 pathway. These results support the possibility that TGF-β signaling controls C. elegans body shape by regulating cuticle composition.

Broad oxygen tolerance in the nematode Caenorhabditis elegans

2000 ◽  
Vol 203 (16) ◽  
pp. 2467-2478 ◽  
Author(s):  
W.A. Van Voorhies ◽  
S. Ward
Keyword(s):  
Caenorhabditis Elegans ◽  
Metabolic Rate ◽  
Developmental Stages ◽  
Small Body ◽  
Metabolic Cost ◽  
Soil Nematode ◽  
Nematode Caenorhabditis Elegans ◽  
Oxygen Levels ◽  
C Elegans ◽  
Short Period

This study examined the effects of oxygen tensions ranging from 0 to 90 kPa on the metabolic rate (rate of carbon dioxide production), movement and survivorship of the free-living soil nematode Caenorhabditis elegans. C. elegans requires oxygen to develop and survive. However, it can maintain a normal metabolic rate at oxygen levels of 3.6 kPa and has near-normal metabolic rates at oxygen levels as low as 2 kPa. The ability to withstand low ambient oxygen levels appears to be a consequence of the small body size of C. elegans, which allows diffusion to supply oxygen readily to the cells without requiring any specialized respiratory or metabolic adaptations. Thus, the small size of this organism pre-adapts C. elegans to living in soil environments that commonly become hypoxic. Movement in C. elegans appears to have a relatively minor metabolic cost. Several developmental stages of C. elegans were able to withstand up to 24 h of anoxia without major mortality. Longer periods of anoxia significantly increased mortality, particularly for eggs. Remarkably, long-term exposure to 100 % oxygen had no effect on the metabolic rate of C. elegans, and populations were able to survive for a least 50 generations in 100 % (90 kPa) oxygen. Such hyperoxic conditions are fatal to most organisms within a short period.

Measurements of Morphology and Locomotion of Caenorhabditis Elegans With Digital Holographic Microscopy

2020 ◽  
Author(s):  
Yijie Wang ◽  
Jun Chen ◽  
Yuan Zhang ◽  
Kee-Hong Kim
Keyword(s):  
Caenorhabditis Elegans ◽  
Zebrafish Embryo ◽  
Adult Stage ◽  
Experimental Studies ◽  
Digital Holographic Microscopy ◽  
Development Stages ◽  
C Elegans ◽  
Applied Development ◽  
Time Period ◽  
Holographic Microscopy

Abstract Digital holographic microscopy (DHM) enables 3D volumetric measurements of small objects with high magnification. DHM has been applied to measure a variety of experimental studies, including turbulent boundary layer, spray droplets, individual cells, development of zebrafish embryo, etc. In this study, a DHM system is applied to measure the morphology and locomotion of two groups of Caenorhabditis Elegans (C. Elegans) with different development conditions (ATGL-1 group and n2 group) in an 8-day time period from their hatching to the adult stage, whose body lengths range from hundreds of micrometers to one millimeter. The length and volume are determined to describe the morphology of the C. Elegans at different development stages. The locomotion of the C. Elegans is divided into linear motion and curl motion. The kinetic energy derived from the two types of motion describes the extent of how active the C. Elegans is. The statistics of morphology and locomotion of the two groups of C. Elegans are compared at different development stages to illustrate the influence of the applied development conditions.

scholarly journals Sublethal Effects of Ionic and Nanogold on the Nematode Caenorhabditis elegans

2018 ◽  
Vol 2018 ◽  
pp. 1-11 ◽  
Author(s):  
Suanne Bosch ◽  
Tarryn Lee Botha ◽  
Anine Jordaan ◽  
Mark Maboeta ◽  
Victor Wepener
Keyword(s):  
Caenorhabditis Elegans ◽  
Sublethal Effects ◽  
Low Cost ◽  
Small Body ◽  
Consumer Products ◽  
Ion Release ◽  
High Exposure ◽  
C Elegans ◽  
Short Period

The nematode Caenorhabditis elegans is used as an ecotoxicological model species in both aqueous medium and solid substrates. It is easy and of low cost to maintain in the laboratory and it produces hundreds of offspring within a short period of time. It also has a small body size (1 mm), making it possible for in vivo assays to be conducted in 12-well plates. Engineered nanomaterials (ENMs) are a class of emerging pollutants. Nanogold (nAu) is used in many consumer products and in vivo drug delivery. These materials can be released into the aquatic environment during production or discarding of consumer products. As nAu is insoluble in water, the sediment would become the final depository for the materials. It has become increasingly important to use sediment dwelling organisms to screen for possible toxicity of these ENMs. In this study C. elegans was exposed to a range of concentrations of nAu and ionic gold in M9-media, acting as a substitute for pore water. After 96-hour growth, fertility and reproduction were determined. Internal structure damage and internalisation of particles in C. elegans were determined by using SEM and CytoViva® Darkfield Imaging. From these images the nanomaterials are distributed around the oocytes in the reproductive organs, as well as the pharynx. Results obtained indicate that nAu affects reproduction more than growth due to internal gonad damage, albeit at very high exposure concentrations, indicating no toxicity at environmentally relevant concentrations. Ionic Au is more toxic than nAu and effects fertility and reproduction due to ion release. These results give more information regarding the toxicity and in vivo uptake of nAu and form part of an environmental risk assessment of ENMs.

Suppression of the ELO-2 FA Elongation Activity Results in Alterations of the Fatty Acid Composition and Multiple Physiological Defects, Including Abnormal Ultradian Rhythms, in Caenorhabditis elegans

Genetics ◽  
2003 ◽  
Vol 163 (1) ◽  
pp. 159-169 ◽  
Author(s):  
Marina Kniazeva ◽  
Matt Sieber ◽  
Scott McCauley ◽  
Kang Zhang ◽  
Jennifer L Watts ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Caenorhabditis Elegans ◽  
Small Body ◽  
Normal Growth ◽  
C Elegans ◽  
Physiological Importance ◽  
Pufa Biosynthesis ◽  
The Individual ◽  
Single Enzyme ◽  
Elongation Activity

Abstract While the general steps of fatty acid (FA) biosynthesis are well understood, the individual enzymes involved in the elongation of long chain saturated and polyunsaturated FA (PUFA) are largely unknown. Recent research indicates that these enzymes might be of considerable physiological importance for human health. We use Caenorhabditis elegans to study FA elongation activities and associated abnormal phenotypes. In this article we report that the predicted C. elegans F11E6.5/ELO-2 is a functional enzyme with the FA elongation activity. It is responsible for the elongation of palmitic acid and is involved in PUFA biosynthesis. RNAi-mediated suppression of ELO-2 causes an accumulation of palmitate and an associated decrease in the PUFA fraction in triacylglycerides and phospholipid classes. This imbalance in the FA composition results in multiple phenotypic defects such as slow growth, small body size, reproductive defects, and changes in rhythmic behavior. ELO-2 cooperates with the previously reported ELO-1 in 20-carbon PUFA production, and at least one of the enzymes must function to provide normal growth and development in C. elegans. The presented data indicate that suppression of a single enzyme of the FA elongation machinery is enough to affect various organs and systems in worms. This effect resembles syndromic disorders in humans.

scholarly journals Identification, functional expression and enzymic analysis of two distinct CaaX proteases from Caenorhabditis elegans

2003 ◽  
Vol 370 (3) ◽  
pp. 1047-1054 ◽  
Author(s):  
Juan CADIÑANOS ◽  
Walter K. SCHMIDT ◽  
Antonio FUEYO ◽  
Ignacio VARELA ◽  
Carlos LÓPEZ-OTÍN ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Model Organism ◽  
Functional Expression ◽  
Cysteine Residue ◽  
C Elegans ◽  
Ras Gtpases ◽  
Acid Protein ◽  
Bona Fide

Post-translational processing of proteins such as the Ras GTPases, which contain a C-terminal CaaX motif (where C stands for cysteine, a for aliphatic and X is one of several amino acids), includes prenylation, proteolytic removal of the C-terminal tripeptide and carboxy-methylation of the isoprenyl-cysteine residue. In the present study, we report the presence of two distinct CaaX-proteolytic activities in membrane extracts from Caenorhabditis elegans, which are sensitive to EDTA and Tos-Phe-CH2Cl (tosylphenylalanylchloromethane; ‘TPCK') respectively. A protein similar to the mammalian and yeast farnesylated-proteins converting enzyme-1 (FACE-1)/Ste24p CaaX metalloprotease, encoded by a hypothetical gene (CeFACE-1/C04F12.10) found in C. elegans chromosome I, probably accounts for the EDTA-sensitive activity. An orthologue of FACE-2/Rce1p, the enzyme responsible for the proteolytic maturation of Ras oncoproteins and other prenylated substrates, probably accounts for the Tos-Phe-CH2Cl-sensitive activity, even though the gene for FACE-2/Rce1 has not been previously identified in this model organism. We have identified a previously overlooked gene in C. elegans chromosome V, which codes for a 266-amino-acid protein (CeFACE-2) with 30% sequence identity to human FACE-2/Rce1. We show that both CeFACE-1 and CeFACE-2 have the ability to promote production of the farnesylated yeast pheromone a-factor in vivo and to cleave a farnesylated peptide in vitro. These results indicate that CeFACE-1 and CeFACE-2 are bona fide CaaX proteases and support the evolutionary conservation of this proteolytic system in eukaryotes.

scholarly journals WormPaths: Caenorhabditis elegans metabolic pathway annotation and visualization

Genetics ◽  
2021 ◽  
Author(s):  
Melissa D Walker ◽  
Gabrielle E Giese ◽  
Amy D Holdorf ◽  
Sushila Bhattacharya ◽  
Cédric Diot ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Metabolic Pathway ◽  
Enrichment Analysis ◽  
Pathway Enrichment Analysis ◽  
C Elegans ◽  
Therapeutic Drugs ◽  
Metabolic Genes ◽  
Pathway Annotation ◽  
Road Maps ◽  
Different Levels

Abstract In our group, we aim to understand metabolism in the nematode Caenorhabditis elegans and its relationships with gene expression, physiology and the response to therapeutic drugs. Visualization of the metabolic pathways that comprise the metabolic network is extremely useful for interpreting a wide variety of experiments. Detailed annotated metabolic pathway maps for C. elegans is mostly limited to pan-organismal maps, many with incomplete or inaccurate pathway and enzyme annotations. Here we present WormPaths, which is composed of two parts: 1) the careful manual annotation of metabolic genes into pathways, categories and levels, and 2) 62 pathway maps that include metabolites, metabolite structures, genes, reactions, and pathway connections between maps. These maps are available on the WormFlux website. We show that WormPaths provides easy-to-navigate maps and that the different levels in WormPaths can be used for metabolic pathway enrichment analysis of transcriptomic data. In the future we envision further developing these maps to be more interactive, with an analogy of road maps that are available on mobile devices.

An improved cryofixation technique for optimal orientation of Caenorhabditis elegans for cryosectioning and EPXMA

1995 ◽  
Vol 53 ◽  
pp. 1068-1069
Author(s):  
Edward Roberts ◽  
Nancy Wallace ◽  
Jonathan Freedman ◽  
Ann LeFurgey
Keyword(s):  
Caenorhabditis Elegans ◽  
Electron Probe ◽  
Intestinal Tract ◽  
Adult Stage ◽  
Elemental Distribution ◽  
Liquid Propane ◽  
X Ray ◽  
C Elegans ◽  
Optimal Orientation ◽  
Optimum Technique

INTRODUCTION: Plunge freezing into liquid cryogens has been frequently employed with success for cryofixation of biological specimens <lmm in size; however, positioning of cells or organisms with a precise orientation for subsequent cryosectioning is difficult. In these studies, a metal mirror cryofixation device, e.g. cryogun, has been tested to determine its applicability for cryofixation of small organisms such as nematodes or larval invertebrates with specific positioning. The objective of the experiments was to determine the optimum technique for rapid cryofixation and cryosectioning of the intestinal tract and lumen of the nematode Caenorhabditis elegans, prior to electron probe x-ray microanalysis (EPXMA) of subcellular elemental distribution.METHODS: Freezing and sectioning quality obtained using plunge freezing into -190°C liquid propane (Figure la) was compared with that obtained with -196°C metal mirror fixation using the cryogun (PS 1000, Delaware Diamond Knives, Wilmington, DE)(Figure lb). C. elegans were grown in culture to the adult stage, and individual nematodes were placed on either (1) a wooden specimen stub compatible with the plunge freezing device (Figure 2a) or (2) a cryogun specimen mount (Figure 2b).

scholarly journals WormPaths: Caenorhabditis elegans metabolic pathway annotation and visualization

2020 ◽  
Author(s):  
Melissa D. Walker ◽  
Gabrielle E. Giese ◽  
Amy D. Holdorf ◽  
Sushila Bhattacharya ◽  
Cédric Diot ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Metabolic Pathway ◽  
Enrichment Analysis ◽  
Pathway Enrichment Analysis ◽  
The Novel ◽  
C Elegans ◽  
Therapeutic Drugs ◽  
Metabolic Genes ◽  
Pathway Annotation ◽  
Road Maps

AbstractIn our group, we aim to understand metabolism in the nematode Caenorhabditis elegans and its relationships with gene expression, physiology and the response to therapeutic drugs. On March 15, 2020, a stay-at-home order was put into effect in the state of Massachusetts, USA, to flatten the curve of the spread of the novel SARS-CoV2 virus that causes COVID-19. For biomedical researchers in our state, this meant putting a hold on experiments for nine weeks until May 18, 2020. To keep the lab engaged and productive, and to enhance communication and collaboration, we embarked on an in-lab project that we all found important but that we never had the time for: the detailed annotation and drawing of C. elegans metabolic pathways. As a result, we present WormPaths, which is composed of two parts: 1) the careful manual annotation of metabolic genes into pathways, categories and levels, and 2) 66 pathway maps that include metabolites, metabolite structures, genes, reactions, and pathway connections between maps. These maps are available on our WormFlux website. We show that WormPaths provides easy-to-navigate maps and that the different levels in WormPaths can be used for metabolic pathway enrichment analysis of transcriptomic data. In the unfortunate event of additional lockdowns, we envision further developing these maps to be more interactive, with an analogy of road maps that are available on mobile devices.

The glycomes of Caenorhabditis elegans and other model organisms

2002 ◽  
Vol 69 ◽  
pp. 117-134 ◽  
Author(s):  
Stuart M. Haslam ◽  
David Gems ◽  
Howard R. Morris ◽  
Anne Dell
Keyword(s):  
Caenorhabditis Elegans ◽  
Current Knowledge ◽  
Structural Data ◽  
Model Organisms ◽  
Entire Genome ◽  
C Elegans ◽  
The Face ◽  
Area Of Concern ◽  
Nematode Worm

There is no doubt that the immense amount of information that is being generated by the initial sequencing and secondary interrogation of various genomes will change the face of glycobiological research. However, a major area of concern is that detailed structural knowledge of the ultimate products of genes that are identified as being involved in glycoconjugate biosynthesis is still limited. This is illustrated clearly by the nematode worm Caenorhabditis elegans, which was the first multicellular organism to have its entire genome sequenced. To date, only limited structural data on the glycosylated molecules of this organism have been reported. Our laboratory is addressing this problem by performing detailed MS structural characterization of the N-linked glycans of C. elegans; high-mannose structures dominate, with only minor amounts of complex-type structures. Novel, highly fucosylated truncated structures are also present which are difucosylated on the proximal N-acetylglucosamine of the chitobiose core as well as containing unusual Fucα1–2Gal1–2Man as peripheral structures. The implications of these results in terms of the identification of ligands for genomically predicted lectins and potential glycosyltransferases are discussed in this chapter. Current knowledge on the glycomes of other model organisms such as Dictyostelium discoideum, Saccharomyces cerevisiae and Drosophila melanogaster is also discussed briefly.

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