An unexpectedly high degree of specialization and a widespread involvement in sterol metabolism among the C. elegans putative aminophospholipid translocases

The nematode Caenorhabditis elegans was introduced as a model organism in biological research by Sydney Brenner in the 1970s. Since then, it has been increasingly used for investigating processes such as ageing, oxidative stress, neurodegeneration, or inflammation, for which there is a high degree of homology between C. elegans and human pathways, so that the worm offers promising possibilities to study mechanisms of action and effects of phytochemicals of foods and plants. In this paper, the genes and pathways regulating oxidative stress in C. elegans are discussed, as well as the methodological approaches used for their evaluation in the worm. In particular, the following aspects are reviewed: the use of stress assays, determination of chemical and biochemical markers (e.g., ROS, carbonylated proteins, lipid peroxides or altered DNA), influence on gene expression and the employment of mutant worm strains, either carrying loss-of-function mutations or fluorescent reporters, such as the GFP.

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C. elegans pharyngeal pumping provides a whole organism bio-assay to investigate anti-cholinesterase intoxication and antidotes

10.1101/2020.06.03.131490 ◽

2020 ◽

Author(s):

Patricia G. Izquierdo ◽

Vincent O’Connor ◽

Christopher Green ◽

Lindy Holden-Dye ◽

John Tattersall

Keyword(s):

Mode Of Action ◽

Neuromuscular Junctions ◽

Acetylcholinesterase Activity ◽

Cholinesterase Inhibition ◽

Genetic Determinants ◽

C Elegans ◽

Functional Conservation ◽

Wide Range ◽

High Degree ◽

Bio Assay

AbstractInhibition of acetylcholinesterase by either organophosphates or carbamates causes anti-cholinesterase poisoning. This arises through a wide range of neurotoxic effects triggered by the overstimulation of the cholinergic receptors at synapses and neuromuscular junctions. Without intervention, this poisoning can lead to profound toxic effects, including death, and the incomplete efficacy of the current treatments, particularly for oxime-insensitive agents, provokes the need to find better antidotes. Here we show how the non-parasitic nematode Caenorhabditis elegans offers an excellent tool for investigating the acetylcholinesterase intoxication. The C. elegans neuromuscular junctions show a high degree of molecular and functional conservation with the cholinergic transmission that operates in the autonomic, central and neuromuscular synapses in mammals. In fact, the anti-cholinesterase intoxication of the worm’s body wall neuromuscular junction has been unprecedented in understanding molecular determinants of cholinergic function in nematodes and other organisms. We extend the use of the model organism’s feeding behaviour as a tool to investigate carbamate and organophosphate mode of action. We show that inhibition of the cholinergic-dependent rhythmic pumping of the pharyngeal muscle correlates with the inhibition of the acetylcholinesterase activity caused by aldicarb, paraoxons and DFP exposure. Further, this bio-assay allows one to address oxime dependent reversal of cholinesterase inhibition in the context of whole organism recovery. Interestingly, the recovery of the pharyngeal function after such anti-cholinesterase poisoning represents a sensitive and easily quantifiable phenotype that is indicative of the spontaneous recovery or irreversible modification of the worm acetylcholinesterase after inhibition. These observations highlight the pharynx of C. elegans as a new tractable approach to explore anti-cholinesterase intoxication and recovery with the potential to resolve critical genetic determinants of these neurotoxins’ mode of action.

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C. elegans Models to Study the Propagation of Prions and Prion-Like Proteins

Biomolecules ◽

10.3390/biom10081188 ◽

2020 ◽

Vol 10 (8) ◽

pp. 1188 ◽

Cited By ~ 1

Author(s):

Carl Alexander Sandhof ◽

Simon Oliver Hoppe ◽

Jessica Tittelmeier ◽

Carmen Nussbaum-Krammer

Keyword(s):

Neurodegenerative Diseases ◽

Model Organism ◽

Model Systems ◽

Transmissible Spongiform Encephalopathies ◽

Spongiform Encephalopathies ◽

Population Demographics ◽

C Elegans ◽

Age Related ◽

Bona Fide ◽

High Degree

A hallmark common to many age-related neurodegenerative diseases, such as Alzheimer’s disease (AD), Parkinson’s disease (PD), and amyotrophic lateral sclerosis (ALS), is that patients develop proteinaceous deposits in their central nervous system (CNS). The progressive spreading of these inclusions from initially affected sites to interconnected brain areas is reminiscent of the behavior of bona fide prions in transmissible spongiform encephalopathies (TSEs), hence the term prion-like proteins has been coined. Despite intensive research, the exact mechanisms that facilitate the spreading of protein aggregation between cells, and the associated loss of neurons, remain poorly understood. As population demographics in many countries continue to shift to higher life expectancy, the incidence of neurodegenerative diseases is also rising. This represents a major challenge for healthcare systems and patients’ families, since patients require extensive support over several years and there is still no therapy to cure or stop these diseases. The model organism Caenorhabditis elegans offers unique opportunities to accelerate research and drug development due to its genetic amenability, its transparency, and the high degree of conservation of molecular pathways. Here, we will review how recent studies that utilize this soil dwelling nematode have proceeded to investigate the propagation and intercellular transmission of prions and prion-like proteins and discuss their relevance by comparing their findings to observations in other model systems and patients.

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FMRFamide-like peptides in root knot nematodes and their potential role in nematode physiology

Journal of Helminthology ◽

10.1017/s0022149x09990630 ◽

2009 ◽

Vol 84 (3) ◽

pp. 253-265 ◽

Cited By ~ 15

Author(s):

M.J.G. Johnston ◽

P. McVeigh ◽

S. McMaster ◽

C.C. Fleming ◽

A.G. Maule

Keyword(s):

Expression Patterns ◽

Single Copy ◽

The Novel ◽

Specific Expression ◽

Root Knot Nematodes ◽

C Elegans ◽

Free Living Nematode ◽

Rapid Amplification ◽

Race Pcr ◽

High Degree

AbstractFMRFamide-like peptides (FLPs) are a diverse group of neuropeptides that are expressed abundantly in nematodes. They exert potent physiological effects on locomotory, feeding and reproductive musculature and also act as neuromodulators. However, little is known about the specific expression patterns and functions of individual peptides. The current study employed rapid amplification of cDNA ends-polymerase chain reaction (RACE-PCR) to characterizeflpgenes from infective juveniles of the root knot nematodes,Meloidogyne incognitaandMeloidogyne minor. The peptides identified from these transcripts are sequelogs of FLPs from the free-living nematode,Caenorhabditis elegans; the genes have therefore been designated asMi-flp-1,Mi-flp-7,Mi-flp-12,Mm-flp-12andMi-flp-14.Mi-flp-1encodes five FLPs with the common C-terminal moiety, NFLRFamide.Mi-flp-7encodes two copies of APLDRSALVRFamide and APLDRAAMVRFamide and one copy of APFDRSSMVRFamide.Mi-flp-12andMm-flp-12encode the novel peptide KNNKFEFIRFamide (a longer version of RNKFEFIRFamide found inC. elegans).Mi-flp-14encodes a single copy of KHEYLRFamide (commonly known as AF2 and regarded as the most abundant nematode FLP), and a single copy of the novel peptide KHEFVRFamide. These FLPs share a high degree of conservation betweenMeloidogynespecies and nematodes from other clades, including those of humans and animals, perhaps suggesting a common neurophysiological role which may be exploited by novel drugs. FLP immunoreactivity was observed for the first time inMeloidogyne, in the circumpharyngeal nerve ring, pharyngeal nerves and ventral nerve cord. Additionally,in situhybridization revealedMi-flp-12expression in an RIR-like neuron andMi-flp-14expression in SMB-like neurons‡, respectively. These localizations imply physiological roles for FLP-12 and FLP-14 peptides, including locomotion and sensory perception.

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A sterol-defined system for quantitative studies of sterol metabolism in C. elegans

STAR Protocols ◽

10.1016/j.xpro.2021.100710 ◽

2021 ◽

Vol 2 (3) ◽

pp. 100710

Author(s):

Benjamin Trabelcy ◽

Yoram Gerchman ◽

Amir Sapir

Keyword(s):

Sterol Metabolism ◽

C Elegans ◽

Quantitative Studies

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Chromosome-level assembly of the Caenorhabditis remanei genome reveals conserved patterns of nematode genome organization

10.1101/2019.12.31.892059 ◽

2020 ◽

Cited By ~ 1

Author(s):

Anastasia A. Teterina ◽

John H. Willis ◽

Patrick C. Phillips

Keyword(s):

Population Variation ◽

Model Systems ◽

Total Size ◽

Opposite Pattern ◽

C Elegans ◽

Central Regions ◽

Long Read ◽

High Gene ◽

High Degree ◽

Chromosome Level

AbstractThe nematode Caenorhabditis elegans is one of the key model systems in biology, including possessing the first fully assembled animal genome. Whereas C. elegans is a self-reproducing hermaphrodite with fairly limited within-population variation, its relative C. remanei is an outcrossing species with much more extensive genetic variation, making it an ideal parallel model system for evolutionary genetic investigations. Here, we greatly improve on previous assemblies by generating a chromosome-level assembly of the entire C. remanei genome (124.8 Mb of total size) using long-read sequencing and chromatin conformation capture data. Like other fully assembled genomes in the genus, we find that the C. remanei genome displays a high degree of synteny with C. elegans despite multiple within-chromosome rearrangements. Both genomes have high gene density in central regions of chromosomes relative to chromosome ends and the opposite pattern for the accumulation of repetitive elements. C. elegans and C. remanei also show similar patterns of inter-chromosome interactions, with the central regions of chromosomes appearing to interact with one another more than the distal ends. The new C. remanei genome presented here greatly augments the use of the Caenorhabditis as a platform for comparative genomics and serves as a basis for molecular population genetics within this highly diverse species.

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The Fine Structure ofCaenorhabditis elegans N-Glycans

Journal of Biological Chemistry ◽

10.1074/jbc.m208020200 ◽

2002 ◽

Vol 277 (51) ◽

pp. 49143-49157 ◽

Cited By ~ 65

Author(s):

John F. Cipollo ◽

Catherine E. Costello ◽

Carlos B. Hirschberg

Keyword(s):

Fine Structure ◽

Biosynthetic Pathway ◽

Congenital Disorders ◽

Soil Nematode ◽

Congenital Disorders Of Glycosylation ◽

C Elegans ◽

Human Disorders ◽

High Mannose ◽

Trematode Infections ◽

High Degree

We report the fine structure of a nearly contiguous series ofN-glycans from the soil nematodeCaenorhabditis elegans.Five major classes are revealed including high mannose, mammalian-type complex, hybrid, fuco-pausimannosidic (five mannose residues or fewer substituted with fucose), and phosphocholine oligosaccharides. The high mannose, complex, and hybridN-glycan series show a high degree of conservation with the mammalian biosynthetic pathways. The fuco-pausimannosidic glycans contain a novel terminal fucose substitution of mannose. The phosphocholine oligosaccharides are high mannose type and are multiply substituted with phosphocholine. Although phosphocholine oligosaccharides are known immunomodulators in human nematode and trematode infections,C. elegansis unique as a non-parasitic nematode containing phosphocholineN-glycans. Therefore, studies inC. elegansshould aid in the elucidation of the biosynthetic pathway(s) of this class of biomedically relevant compounds. Results presented here show thatC. eleganshas a functional orthologue for nearly every known enzyme found to be deficient in congenital disorders of glycosylation types I and II. This nematode is well characterized genetically and developmentally. Therefore, elucidation of itsN-glycome, as shown in this report, may place it among the useful systems used to investigate human disorders of glycoconjugate synthesis such as the congenital disorders of glycosylation syndromes.

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Evolution of Developmental GATA Factors in Nematodes

Journal of Developmental Biology ◽

10.3390/jdb8040027 ◽

2020 ◽

Vol 8 (4) ◽

pp. 27

Author(s):

Ethan Eurmsirilerd ◽

Morris F. Maduro

Keyword(s):

Structural Similarity ◽

Model System ◽

Ecological Niches ◽

Free Living ◽

C Elegans ◽

Gata Factors ◽

Core Set ◽

Gata Transcription Factors ◽

Close Relatives ◽

High Degree

GATA transcription factors are found in animals, plants, and fungi. In animals, they have important developmental roles in controlling specification of cell identities and executing tissue-specific differentiation. The Phylum Nematoda is a diverse group of vermiform animals that inhabit ecological niches all over the world. Both free-living and parasitic species are known, including those that cause human infectious disease. To date, GATA factors in nematodes have been studied almost exclusively in the model system C. elegans and its close relatives. In this study, we use newly available sequences to identify GATA factors across the nematode phylum. We find that most species have fewer than six GATA factors, but some species have 10 or more. Comparisons of gene and protein structure suggest that there were at most two GATA factors at the base of the phylum, which expanded by duplication and modification to result in a core set of four factors. The high degree of structural similarity with the corresponding orthologues in C. elegans suggests that the nematode GATA factors share similar functions in development.

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Morphological and molecular characterization of Chalara elegans (Thielaviopsis basicola), cause of black root rot on diverse plant species

Canadian Journal of Botany ◽

10.1139/b99-164 ◽

2000 ◽

Vol 77 (12) ◽

pp. 1801-1812 ◽

Cited By ~ 3

Author(s):

Zamir K Punja ◽

Li-Juan Sun

Keyword(s):

British Columbia ◽

Random Amplified Polymorphic Dna ◽

Similarity Index ◽

Thielaviopsis Basicola ◽

Wild Type ◽

C Elegans ◽

Chalara Elegans ◽

Average Similarity ◽

High Degree ◽

Diverse Plant Species

The extent of variation in colony morphology and chlamydospore size, septation, and pigmentation was studied in 50 isolates of Chalara elegans Nag Raj et Kendrick (syn. Thielaviopsis basicola (Berk. et Br.) Ferr.) originating from 12 different geographic areas and substrates. In addition, the extent of genetic variation among these isolates was determined using random amplified polymorphic DNA (RAPD) analysis. Five general morphological groups could be distinguished among the isolates, two of which were aberrant phenotypes (albino and mycelial) that were derived upon continuous subculture of some wild-type isolates in the laboratory. The isolates with the most variation in phenotype originated from British Columbia and California. Six primers (10-mers) were used to generate 90 bands in RAPD-PCR, of which 75 were polymorphic. A high degree of diversity was apparent within C. elegans, and some banding patterns generated by specific primers were unique to certain isolates, thereby generating fingerprints. Distinct groups (clusters) were obtained following UPGMA analysis and, generally, these were composed of isolates from similar geographic regions or hosts. However, isolates from some areas, for example, British Columbia, were also found to belong to different clusters. There was generally a good relationship between groups assigned on the basis of morphology and those derived from cluster analysis, that is, isolates within a cluster tended to have similar morphology. In a few isolates, the aberrant phenotypes (albino and mycelial) could be distinguished using RAPDs from the wild type by the absence of 1 or 2 bands, indicating that changes in the nucleotide sequence had occurred, possibly through mutation. The average similarity index among all 50 isolates of C. elegans was 87%. An outgroup species (Chalara thielaviodes) had a similarity value of 40%.

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Alterations in the Conserved SL1trans-Spliced Leader of Caenorhabditis elegansDemonstrate Flexibility in Length and Sequence Requirements In Vivo

Molecular and Cellular Biology ◽

10.1128/mcb.19.3.1892 ◽

1999 ◽

Vol 19 (3) ◽

pp. 1892-1900 ◽

Cited By ~ 13

Author(s):

Kimberly C. Ferguson ◽

Joel H. Rothman

Keyword(s):

Dna Sequences ◽

Expression System ◽

Leader Sequence ◽

Critical Parameters ◽

Spliced Leader ◽

C Elegans ◽

The One ◽

High Degree ◽

Sequence Requirements

ABSTRACT Approximately 70% of mRNAs in Caenorhabditis elegansare trans spliced to conserved 21- to 23-nucleotide leader RNAs. While the function of SL1, the major C. elegans trans-spliced leader, is unknown, SL1 RNA, which contains this leader, is essential for embryogenesis. Efforts to characterize in vivo requirements of the SL1 leader sequence have been severely constrained by the essential role of the corresponding DNA sequences in SL1 RNA transcription. We devised a heterologous expression system that circumvents this problem, making it possible to probe the length and sequence requirements of the SL1 leader without interfering with its transcription. We report that expression of SL1 from a U2 snRNA promoter rescues mutants lacking the SL1-encoding genes and that the essential embryonic function of SL1 is retained when approximately one-third of the leader sequence and/or the length of the leader is significantly altered. In contrast, although all mutant SL1 RNAs were well expressed, more severe alterations eliminate this essential embryonic function. The one non-rescuing mutant leader tested was never detected on messages, demonstrating that part of the leader sequence is essential for trans splicing in vivo. Thus, in spite of the high degree of SL1 sequence conservation, its length, primary sequence, and composition are not critical parameters of its essential embryonic function. However, particular nucleotides in the leader are essential for the in vivo function of the SL1 RNA, perhaps for its assembly into a functional snRNP or for the trans-splicing reaction.

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