scholarly journals Evidence Suggesting That a Fifth of Annotated Caenorhabditis elegans Genes May Be Pseudogenes

2002 ◽  
Vol 12 (5) ◽  
pp. 770-775
Author(s):  
Andrew Mounsey ◽  
Petra Bauer ◽  
Ian A. Hope
Keyword(s):  
Caenorhabditis Elegans ◽  
Sequence Data ◽  
Expression Patterns ◽  
Lessons Learned ◽  
Gene Fusions ◽  
Duplicated Genes ◽  
C Elegans ◽  
Online Supplementary Material ◽  
High Figure ◽  
Supplementary Material

Only a minority of the genes, identified in theCaenorhabditis elegans genome sequence data by computer analysis, have been characterized experimentally. We attempted to determine the expression patterns for a random sample of the annotated genes using reporter gene fusions. A low success rate was obtained for evolutionarily recently duplicated genes. Analysis of the data suggests that this is not due to conditional or low-level expression. The remaining explanation is that most of the annotated genes in the recently duplicated category are pseudogenes, a proportion corresponding to 20% of all of the annotated C. elegansgenes. Further support for this surprisingly high figure was sought by comparing sequences for families of recently duplicated C. elegans genes. Although only a preliminary analysis, clear evidence for a gene having been recently inactivated by genetic drift was found for many genes in the recently duplicated category. At least 4% of the annotated C. elegans genes can be recognized as pseudogenes simply from closer inspection of the sequence data. Lessons learned in identifying pseudogenes in C. elegans could be of value in the annotation of the genomes of other species where, although there may be fewer pseudogenes, they may be harder to detect.[Online supplementary material available atwww.genome.org.]

Nematodes associated with terrestrial slugs in the Edmonton region of Alberta, Canada

2020 ◽  
Vol 94 ◽  
Author(s):  
T. Brophy ◽  
R.J. Mc Donnell ◽  
D.K. Howe ◽  
D.R. Denver ◽  
J.L. Ross ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Ribosomal Dna ◽  
Sequence Data ◽  
Nematode Species ◽  
Species Level ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
C Elegans ◽  
Facultative Parasite ◽  
Arion Rufus

Abstract A survey of nematodes associated with terrestrial slugs was conducted in residential gardens, nurseries, greenhouses and agricultural sites located in and around Edmonton, Alberta, Canada. A total of 2406 slugs were collected from 82 sites. Slugs were decapitated and cadavers were incubated for two weeks, with emerging nematodes removed and processed for identification. Nematodes were identified using molecular sequence data for the 18S ribosomal DNA. Nematodes were recovered from 20 of the 82 sites surveyed, with 24.4% of the slugs infected with nematodes. A total of seven nematodes were identified to species level, including Caenorhabditis elegans, Panagrolaimus papillosus, Pellioditis typica, Pelodera pseudoteres, Rhabditella axei, Rhabditoides inermiformis and Phasmarhabditis californica. An additional four specimens were identified to genus level, including Oscheius sp. (9), Pristionchus sp., Rhabditis sp. and Rhabditophanes sp. (1). The two most common nematode species were C. elegans and P. pseudoteres. The facultative parasite, P. californica, was recovered from a single Arion rufus specimen, collected from a seasonal nursery. To our knowledge, this study represents the first survey of slug-associated nematodes in Canada.

scholarly journals Tissue- and paralogue-specific functions of acyl-CoA-binding proteins in lipid metabolism in Caenorhabditis elegans

2011 ◽  
Vol 437 (2) ◽  
pp. 231-241 ◽  
Author(s):  
Ida C. Elle ◽  
Karina T. Simonsen ◽  
Louise C. B. Olsen ◽  
Pernille K. Birck ◽  
Sidse Ehmsen ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Unsaturated Fatty Acids ◽  
Expression Patterns ◽  
High Specificity ◽  
Tissue Expression ◽  
Yeast Cells ◽  
Loss Of Function ◽  
C Elegans ◽  
Eukaryotic Species ◽  
Quadruple Mutant

ACBP (acyl-CoA-binding protein) is a small primarily cytosolic protein that binds acyl-CoA esters with high specificity and affinity. ACBP has been identified in all eukaryotic species, indicating that it performs a basal cellular function. However, differential tissue expression and the existence of several ACBP paralogues in many eukaryotic species indicate that these proteins serve distinct functions. The nematode Caenorhabditis elegans expresses seven ACBPs: four basal forms and three ACBP domain proteins. We find that each of these paralogues is capable of complementing the growth of ACBP-deficient yeast cells, and that they exhibit distinct temporal and tissue expression patterns in C. elegans. We have obtained loss-of-function mutants for six of these forms. All single mutants display relatively subtle phenotypes; however, we find that functional loss of ACBP-1 leads to reduced triacylglycerol (triglyceride) levels and aberrant lipid droplet morphology and number in the intestine. We also show that worms lacking ACBP-2 show a severe decrease in the β-oxidation of unsaturated fatty acids. A quadruple mutant, lacking all basal ACBPs, is slightly developmentally delayed, displays abnormal intestinal lipid storage, and increased β-oxidation. Collectively, the present results suggest that each of the ACBP paralogues serves a distinct function in C. elegans.

scholarly journals Temporal and spatial expression patterns of the small heat shock (hsp16) genes in transgenic Caenorhabditis elegans.

1992 ◽  
Vol 3 (2) ◽  
pp. 221-233 ◽  
Author(s):  
E G Stringham ◽  
D K Dixon ◽  
D Jones ◽  
E P Candido
Keyword(s):  
Caenorhabditis Elegans ◽  
Heat Shock ◽  
Gene Pair ◽  
Expression Patterns ◽  
Developmentally Regulated ◽  
Noncoding Sequences ◽  
C Elegans ◽  
Gene Pairs ◽  
Temporal And Spatial ◽  
Beta Galactosidase

The expression of the hsp16 gene family in Caenorhabditis elegans has been examined by introducing hsp16-lacZ fusions into the nematode by transformation. Transcription of the hsp16-lacZ transgenes was totally heat-shock dependent and resulted in the rapid synthesis of detectable levels of beta-galactosidase. Although the two hsp16 gene pairs of C. elegans are highly similar within both their coding and noncoding sequences, quantitative and qualitative differences in the spatial pattern of expression between gene pairs were observed. The hsp16-48 promoter was shown to direct greater expression of beta-galactosidase in muscle and hypodermis, whereas the hsp16-41 promoter was more efficient in intestine and pharyngeal tissue. Transgenes that eliminated one promoter from a gene pair were expressed at reduced levels, particularly in postembryonic stages, suggesting that the heat shock elements in the intergenic region of an hsp16 gene pair may act cooperatively to achieve high levels of expression of both genes. Although the hsp16 gene pairs are never constitutively expressed, their heat inducibility is developmentally restricted; they are not heat inducible during gametogenesis or early embryogenesis. The hsp16 genes represent the first fully inducible system in C. elegans to be characterized in detail at the molecular level, and the promoters of these genes should find wide applicability in studies of tissue- and developmentally regulated genes in this experimental organism.

scholarly journals Untwisting the Caenorhabditis elegans embryo

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Ryan Patrick Christensen ◽  
Alexandra Bokinsky ◽  
Anthony Santella ◽  
Yicong Wu ◽  
Javier Marquina-Solis ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Cell Tracking ◽  
Positional Information ◽  
Supplementary File ◽  
Cell Nuclei ◽  
C Elegans ◽  
Seam Cell ◽  
Late Embryogenesis ◽  
Embryonic Nervous System ◽  
Supplementary Material

The nematode Caenorhabditis elegans possesses a simple embryonic nervous system with few enough neurons that the growth of each cell could be followed to provide a systems-level view of development. However, studies of single cell development have largely been conducted in fixed or pre-twitching live embryos, because of technical difficulties associated with embryo movement in late embryogenesis. We present open-source untwisting and annotation software (http://mipav.cit.nih.gov/plugin_jws/mipav_worm_plugin.php) that allows the investigation of neurodevelopmental events in late embryogenesis and apply it to track the 3D positions of seam cell nuclei, neurons, and neurites in multiple elongating embryos. We also provide a tutorial describing how to use the software (<xref ref-type="supplementary-material" rid="SD1-data">Supplementary file 1</xref>) and a detailed description of the untwisting algorithm (Appendix). The detailed positional information we obtained enabled us to develop a composite model showing movement of these cells and neurites in an 'average' worm embryo. The untwisting and cell tracking capabilities of our method provide a foundation on which to catalog C. elegans neurodevelopment, allowing interrogation of developmental events in previously inaccessible periods of embryogenesis.

scholarly journals Insect-Derived Cecropins Display Activity against Acinetobacter baumannii in a Whole-Animal High-Throughput Caenorhabditis elegans Model

2015 ◽  
Vol 59 (3) ◽  
pp. 1728-1737 ◽  
Author(s):  
Elamparithi Jayamani ◽  
Rajmohan Rajamuthiah ◽  
Jonah Larkins-Ford ◽  
Beth Burgwyn Fuchs ◽  
Annie L. Conery ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Acinetobacter Baumannii ◽  
High Throughput ◽  
Sequence Data ◽  
Treatment Options ◽  
Automated Image Analysis ◽  
Screening Assay ◽  
Content Type ◽  
C Elegans ◽  
Cecropin A

ABSTRACTThe rise of multidrug-resistantAcinetobacter baumanniiand a concomitant decrease in antibiotic treatment options warrants a search for new classes of antibacterial agents. We have found thatA. baumanniiis pathogenic and lethal to the model host organismCaenorhabditis elegansand have exploited this phenomenon to develop an automated, high-throughput, high-content screening assay in liquid culture that can be used to identify novel antibiotics effective againstA. baumannii. The screening assay involves coincubatingC. eleganswithA. baumanniiin 384-well plates containing potential antibacterial compounds. At the end of the incubation period, worms are stained with a dye that stains only dead animals, and images are acquired using automated microscopy and then analyzed using an automated image analysis program. This robust assay yields a Z′ factor consistently greater than 0.7. In a pilot experiment to test the efficacy of the assay, we screened a small custom library of synthetic antimicrobial peptides (AMPs) that were synthesized using publicly available sequence data and/or transcriptomic data from immune-challenged insects. We identified cecropin A and 14 other cecropin or cecropin-like peptides that were able to enhanceC. eleganssurvival in the presence ofA. baumannii. Interestingly, one particular hit, BR003-cecropin A, a cationic peptide synthesized by the mosquitoAedes aegypti, showed antibiotic activity against a panel of Gram-negative bacteria and exhibited a low MIC (5 μg/ml) againstA. baumannii. BR003-cecropin A causes membrane permeability inA. baumannii, which could be the underlying mechanism of its lethality.

scholarly journals Caenorhabditis elegans β-G Spectrin Is Dispensable for Establishment of Epithelial Polarity, but Essential for Muscular and Neuronal Function

2000 ◽  
Vol 149 (4) ◽  
pp. 915-930 ◽  
Author(s):  
Suraj Moorthy ◽  
Lihsia Chen ◽  
Vann Bennett
Keyword(s):  
Nervous System ◽  
Caenorhabditis Elegans ◽  
Plasma Membranes ◽  
Striated Muscle ◽  
Expression Patterns ◽  
Cell Contact ◽  
Epithelial Polarity ◽  
Cell Stage ◽  
C Elegans ◽  
Cell Cell

The Caenorhabditis elegans genome encodes one α spectrin subunit, a β spectrin subunit (β-G), and a β-H spectrin subunit. Our experiments show that the phenotype resulting from the loss of the C. elegans α spectrin is reproduced by tandem depletion of both β-G and β-H spectrins. We propose that α spectrin combines with the β-G and β-H subunits to form α/β-G and α/β-H heteromers that perform the entire repertoire of spectrin function in the nematode. The expression patterns of nematode β-G spectrin and vertebrate β spectrins exhibit three striking parallels including: (1) β spectrins are associated with the sites of cell–cell contact in epithelial tissues; (2) the highest levels of β-G spectrin occur in the nervous system; and (3) β spec-trin-G in striated muscle is associated with points of attachment of the myofilament apparatus to adjacent cells. Nematode β-G spectrin associates with plasma membranes at sites of cell–cell contact, beginning at the two-cell stage, and with a dramatic increase in intensity after gastrulation when most cell proliferation has been completed. Strikingly, depletion of nematode β-G spectrin by RNA-mediated interference to undetectable levels does not affect the establishment of structural and functional polarity in epidermis and intestine. Contrary to recent speculation, β-G spectrin is not associated with internal membranes and depletion of β-G spectrin was not associated with any detectable defects in secretion. Instead β-G spectrin-deficient nematodes arrest as early larvae with progressive defects in the musculature and nervous system. Therefore, C. elegans β-G spectrin is required for normal muscle and neuron function, but is dispensable for embryonic elongation and establishment of early epithelial polarity. We hypothesize that heteromeric spectrin evolved in metazoans in response to the needs of cells in the context of mechanically integrated tissues that can withstand the rigors imposed by an active organism.

‘Promoter trapping’ in Caenorhabditis elegans

Development ◽  
1991 ◽  
Vol 113 (2) ◽  
pp. 399-408 ◽  
Author(s):  
I.A. Hope
Keyword(s):  
Caenorhabditis Elegans ◽  
Expression Patterns ◽  
Cell Types ◽  
Histochemical Staining ◽  
Lacz Gene ◽  
Dna Fragments ◽  
C Elegans ◽  
Active Expression ◽  
Beta Galactosidase

A screen of gene expression patterns has been developed for the nematode Caenorhabditis elegans. Promoter-reporter gene fusions were constructed in vitro by ligating C. elegans genomic DNA fragments upstream of a lacZ gene. Patterns of beta-galactosidase expression were examined by histochemical staining of C. elegans lines transformed with the constructs. beta-galactosidase expression depended on translational fusion, so constructs were assayed in large pools to expedite detection of the low proportion that were active. Expression in a variety of cell types and temporal patterns was observed with different construct pools. The most striking expression patterns were obtained when the beta-galactosidase activity was localized to subcellular structures by the C. elegans portion of the fusion protein. The active constructs of three selected pools were identified subsequently by an efficient combinatorial procedure. The genomic locations of the DNA fragments from the active constructs were determined and appear to define previously uncharacterized genetic loci.

scholarly journals Suppression of transcriptional drift extends C. elegans lifespan by postponing the onset of mortality

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Sunitha Rangaraju ◽  
Gregory M Solis ◽  
Ryan C Thompson ◽  
Rafael L Gomez-Amaro ◽  
Leo Kurian ◽  
...  
Keyword(s):  
Young Adults ◽  
Caenorhabditis Elegans ◽  
Functional Groups ◽  
Expression Patterns ◽  
Older Age ◽  
C Elegans ◽  
Age Dependent ◽  
Effects Of Aging

Longevity mechanisms increase lifespan by counteracting the effects of aging. However, whether longevity mechanisms counteract the effects of aging continually throughout life, or whether they act during specific periods of life, preventing changes that precede mortality is unclear. Here, we uncover transcriptional drift, a phenomenon that describes how aging causes genes within functional groups to change expression in opposing directions. These changes cause a transcriptome-wide loss in mRNA stoichiometry and loss of co-expression patterns in aging animals, as compared to young adults. Using Caenorhabditis elegans as a model, we show that extending lifespan by inhibiting serotonergic signals by the antidepressant mianserin attenuates transcriptional drift, allowing the preservation of a younger transcriptome into an older age. Our data are consistent with a model in which inhibition of serotonergic signals slows age-dependent physiological decline and the associated rise in mortality levels exclusively in young adults, thereby postponing the onset of major mortality.

scholarly journals Whole genome sequencing and assembly of a Caenorhabditis elegans genome with complex genomic rearrangements using the MinION sequencing device

2017 ◽  
Author(s):  
JR Tyson ◽  
NJ O’Neil ◽  
M Jain ◽  
HE Olsen ◽  
P Hieter ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genome Assembly ◽  
De Novo ◽  
Sequence Data ◽  
Genomic Rearrangements ◽  
Whole Genome ◽  
C Elegans ◽  
Long Reads

ABSTRACTAdvances in 3rd generation sequencing have opened new possibilities for ‘benchtop’ whole genome sequencing. The MinION is a portable device that uses nanopore technology and can sequence long DNA molecules. MinION long reads are well suited for sequencing and de novo assembly of complex genomes with large repetitive elements. Long reads also facilitate the identification of complex genomic rearrangements such as those observed in tumor genomes. To assess the feasibility of the de novo assembly of large complex genomes using both MinION and Illumina platforms, we sequenced the genome of a Caenorhabditis elegans strain that contains a complex acetaldehyde-induced rearrangement and a biolistic bombardment-mediated insertion of a GFP containing plasmid. Using ∼5.8 gigabases of MinION sequence data, we were able to assemble a C. elegans genome containing 145 contigs (N50 contig length = 1.22 Mb) that covered >99% of the 100,286,401 bp reference genome. In contrast, using ∼8.04 gigabases of Illumina sequence data, we were able to assemble a C. elegans genome in 38,645 contigs (N50 contig length = ∼26 kb) containing 117 Mb. From the MinION genome assembly we identified the complex structures of both the acetaldehyde-induced mutation and the biolistic-mediated insertion. To date, this is the largest genome to be assembled exclusively from MinION data and is the first demonstration that the long reads of MinION sequencing can be used for whole genome assembly of large (100 Mb) genomes and the elucidation of complex genomic rearrangements.

scholarly journals Regulation of fatty acid desaturase- and immunity gene-expression by mbk-1/DYRK1A in Caenorhabditis elegans

BMC Genomics ◽  
2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Hildegard I. D. Mack ◽  
Jennifer Kremer ◽  
Eva Albertini ◽  
Elisabeth K. M. Mack ◽  
Pidder Jansen-Dürr
Keyword(s):  
Fatty Acid ◽  
Caenorhabditis Elegans ◽  
Insulin Receptor ◽  
Genetic Background ◽  
Expression Patterns ◽  
Fatty Acid Desaturase ◽  
Pathogen Resistance ◽  
Global Changes ◽  
C Elegans ◽  
Receptor Mutant

Abstract Background In the nematode Caenorhabditis elegans, longevity in response to germline ablation, but not in response to reduced insulin/IGF1-like signaling, is strongly dependent on the conserved protein kinase minibrain-related kinase 1 (MBK-1). In humans, the MBK-1 ortholog DYRK1A is associated with a variety of disorders, most prominently with neurological defects observed in Down syndrome. To better understand mbk-1’s physiological roles and their dependence on genetic background, we analyzed the influence of mbk-1 loss on the transcriptomes of wildtype and long-lived, germline-deficient or insulin-receptor defective, C. elegans strains by RNA-sequencing. Results mbk-1 loss elicited global changes in transcription that were less pronounced in insulin-receptor mutant than in germline-deficient or wildtype C. elegans. Irrespective of genetic background, mbk-1 regulated genes were enriched for functions in biological processes related to organic acid metabolism and pathogen defense. qPCR-studies confirmed mbk-1 dependent induction of all three C. elegans Δ9-fatty acid desaturases, fat-5, fat-6 and fat-7, in wildtype, germline-deficient and insulin-receptor mutant strains. Conversely, mbk-1 dependent expression patterns of selected pathogen resistance genes, including asp-12, dod-24 and drd-50, differed across the genetic backgrounds examined. Finally, cth-1 and cysl-2, two genes which connect pathogen resistance to the metabolism of the gaseous messenger and lifespan regulator hydrogen sulfide (H2S), were commonly suppressed by mbk-1 loss only in wildtype and germline-deficient, but not in insulin-receptor mutant C. elegans. Conclusion Our work reveals previously unknown roles of C. elegans mbk-1 in the regulation of fatty acid desaturase- and H2S metabolic-genes. These roles are only partially dependent on genetic background. Considering the particular importance of fatty acid desaturation and H2S for longevity of germline-deficient C. elegans, we propose that these processes at least in part account for the previous observation that mbk-1 preferentially regulates lifespan in these worms.

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