c elegans human ortholog

The WormCoolKit website was devised to streamline the process of modeling human genetic diseases in C. elegans (figure 1), starting by identifying the most likely worm ortholog of the human gene of interest, checking whether a given amino acid variation in the human gene is in a residue conserved in worms and finally designing the CRISPR . We then obtained 61 common genes between the 1,320 human reproductive genes obtained using AmiGO2 and the 1,419 one-to-one human and C. elegans orthologs ( Fig. We found that a PDEdelta ortholog from the eyeless nematode Caenorhabditis elegans (termed CEdelta) solubilizes bovine PDE in vitro with an EC50 very similar to PDEdelta. Strain Validation Service Its evolutionary connection to MFAP1 reduces this number to four, raising . Figure 2: Schematic diagram of the presumed role for C. elegans autophagy proteins involved in the formation of an autophagosome.. A) Regulation of induction: In yeast, the Tor kinase and its effectors regulate the induction of autophagy. Gene names (gene) as well as WormBase sequence names (ORF) are given. Increased sensitivity to MMS has been observed for several other C. elegans DNA radiation-repair (rad) mutants . Check the variants A service that aims to provide you with information regarding a specific variant you'd like to CRISPR. Using the nematode Caenorhabditis elegans ( C. elegans) as a model, we study the role of the RNA-binding protein, ATX-2, a C. elegans homolog of Human Ataxin-2 in early cell division. A number of RNAs and RNA-binding proteins are shown to be associated with centrosomes and MTs, and influence the assembly of mitotic spindles. By combining bioinformatics and C. elegans experiments on orthologs, we provide functional insights on twelve previously uncharacterized human genes. The main components of the C. elegans IIS pathway include insulin-like peptides (ILPs), at least one of which can bind to and activate the human insulin receptor (Hua et al., 2003).DAF-2/IGFR activation results in recruitment and activation of the phosphoinositide 3-kinase AGE-1/PI3K. 2. By generating loss-of-function mutants of the sole TMEM132 ortholog in C. 7 elegans, we identify abnormal morphologic . The Swiss-Prot accession numbers are given for the worm sequences and their human orthologs. Little is known about the role of ROS1, however in vertebrates it has been implicated in promoting differentiation programs in specialized epithelial tissues. TDP-1 is the Caenorhabditis elegans ortholog of mammalian TDP-43, which is strongly implicated in the etiology of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS). The orphan receptor ROS1 is a human proto‐oncogene, mutations of which are found in an increasing number of cancers. In Vivo Studies Menu Toggle. ScSpp381, hsMFAP1 and the two previously known MFAP1 orthologs ctMFAP1 and C. elegans (ce) MFAP1 also share a number of physicochemical and biochemical properties, i.e. Strain Validation Service There is a 97.6% amino acid identity between human and mouse A2BP1. C. elegans Solutions Menu Toggle. In the absence of ATX-2, proliferation of stem cells is reduced, and the . open reading frame T10H9.2, which encodes the C. elegans ortholog of the human proto-oncogene ALK. @article{osti_1019675, title = {Structural Characterization of the E2 Domain of APL-1, a C. Elegans Homolog of Human Amyloid Precursor Protein, and its Heparin Binding Site}, author = {Hoopes, J and Liu, X and Xu, X and Demeler, B and Folta-Stogniew, E and Li, C and Ha, Y}, abstractNote = {The amyloid {beta}-peptide deposit found in the brain tissue of patients with Alzheimer disease is . ATX-2 is the C. elegans ortholog of human Ataxin-2 that is implicated in human neurodegenerative disease (Lastres-Becker et al., 2008). Belonging to a conserved family of 5 transmembrane proteins, TMEM132D and its homologs are still of unknown molecular 6 functions. Functional genomic analysis of C. elegans chromosome I by systematic RNA interference. The human ALK family of RTKs is part of the insulin-receptor superfamily It is possible that EXO-3 may perform its . We previously identified the C. elegans dnj-27 gene as the ortholog of human ERdj5 by an in silico approach . For example, saturation genetic analysis of lin-12 receptor signaling revealed that a C. elegans ortholog of the human PS1 multipass transmembrane protein, which had been implicated by human pedigree analysis in predisposition to Alzheimer's disease, . Statement of Significance. C. elegans DNJ-27 and human ERdj5 proteins display a high amino acid sequence homology consisting of an N-terminal DnaJ/Hsp-40 domain followed by four Trx-like domains, with different CXXC redox active site motifs . 3. Identification of casy-1, a Calsyntenin/Alcadein Homolog, as a Learning-Related Gene.. We previously reported that C. elegans learns to avoid NaCl after being exposed to NaCl under starvation conditions (salt chemotaxis learning) (4, 8).To identify unknown molecules involved in salt chemotaxis learning, we performed an EMS mutagenesis screen ().We screened for mutants that failed to avoid NaCl . The hermaphrodite germ line is the only tissue in C. elegans that can lead to bona fide tumors caused by germline hyper-proliferation and the only tissue capable of undergoing apoptosis throughout adulthood. Scale bar Along . In this study, we examined both acute and long-term exposure studies of CBD at . We identified Caenorhabditis elegans chd-7 in a screen for suppressors of dauer formation, an alternative larval stage that develops under harsh environmental conditions. We found that the C. elegans ortholog of ataxin 2, ATX-2, forms a complex with PAB-1, a cytoplasmic poly(A)-binding protein, and that ATX-2 is required for development of the germline. Computer searches identified previously two Caenorhabditis elegans genes, C15H11.3 and C15H11.6, that encode putative homologs of hTAP and Mex67p (Segref et al., EMBO J, 1997, 16:3256-3271).Using RNA interference experiments in C. elegans, we found that functional knockout of C15H11.3 . C. elegans dnj-27 is the ortholog of mammalian ERdj5 We previously identified the C. elegans dnj-27 gene as the ortholog of human ERdj5 by an in silico approach (11). We applied this strategy to C. elegans CED-9 (ref. Q92504 probably transports zinc out of the endoplasmic . In this study, we identified 1,419 one-to-one orthologs in C. elegans and humans using Ensembl Compara ( Fig. Regulation of C. elegans DAF-16 and its human ortholog FKHRL1 by the daf-2 insulin-like signaling pathway. In this study we show that the C. elegans ortholog of ROS1, the receptor tyrosine kinase ROL‐3, has an essential . Moreover, the ATD deficiency example highlights the possibility of studying dominant mutations in human genes that do not have a C. elegans ortholog. Compound Effects Testing; Phenotype-based Drug Discovery; Neuro Disease Models; Custom Analytical Services; In Vivo Models Menu Toggle. We have uncovered an additional role for this enzyme in the DNA damage checkpoint. . Boxed alignment shows individual amino acid conser-vation. This study used an experimental approach that combined human sleep studies and epigenome-wide methylation analysis, with assessment of gene function in a model organism, Caenorhabditis elegans. Regulation of the Caenorhabditis elegans longevity protein DAF-16 by insulin/IGF-1 and germline signaling. As both H2S and reactive oxygen species (such as H2O2) are major regulators of Caenorhabditis elegans lifespan and stress resistance, we hypothesized that a SELENBP1 ortholog in C. elegans would likely be involved in regulating these aspects.Here we characterize Y37A1B.5, a putative selenium-binding protein 1 ortholog in C. elegans with 52% . We previously generated OrthoList, a compendium of C. elegans genes with human orthologs, by a meta-analysis of the results of four different orthology-prediction programs (Shaye and Greenwald, 2011.Through compiling OrthoList, we found that 7,663 genes have predicted human orthologs, corresponding to about 38% of the . In turn, the serine/threonine kinases PDK-1, AKT-1, and AKT-2 are activated, resulting in phosphorylation of . SZY-20. Although we find that updates to the orthology-prediction methods significantly changed the landscape of C. elegans -human orthologs predicted by individual programs and—unexpectedly—reduced agreement among them, we also show that our meta-analysis approach "buffered" against changes in gene content. Check the variants Bioinformatic searches for GAA ortholog in C. elegans genome revealed four acid alpha-glucosidase-related (aagr-1-4) genes. Spp381 was suggested to be one of only five yeast splicing factors without a human ortholog. Reporter analysis revealed that HUT-1 is an ER protein ubiquitously expressed in tissues, including the intestine. Results: Various assessments indicate that OrthoList has extensive coverage with low false-positive and false-negative rates. This signaling pathway negatively regulates the activity of the forkhead transcription factor DAF-16. At the bottom of the list under the "No HD" heading are genes related to homeobox genes that lack a HD. Introduction: Despite widespread use of cannabidiol (CBD), no lifelong toxicity study has been published to date.Caenorhabditis elegans is often used in preclinical lifelong toxicity studies, due to an estimated 60-80% of their genes having a human ortholog, and their short lifespan of ∼2-3 weeks. psa-3 is a TALE homeobox gene with a MEIS domain that secondarily lost its HD. UNC-51 is the C. elegans Atg1 ortholog, however, it is not clear if there are similar regulatory proteins to Atg17 or Atg13. C. elegans measures one millimeter in length and lives in dirt. A number of To identify candidate regulatory sequences in the 5′ non-coding regions of differentially regulated genes identified in this study were putative C. elegans homologs of p107/p130-target genes, 1 kilobase of sequence homologous to mammalian genes also regulated by pocket pro- data upstream of the start codon of each gene was . Background The nematode Caenorhabditis elegans has been used as a simple model for understanding animal biology for nearly four decades. Find the Human orthologs: A service that aims to find the best Human orthologs for your Caenorhabditis elegans genes. Caenorhabditis elegans as a transgenic model for AD and other neurodegenerative diseases. Hence, C. elegans has many excellent advantages as an in vivo model for the study of AD and other neurodegenerative diseases. C. elegans Solutions Menu Toggle. For many rare diseases, C. elegans has an ortholog that can be edited to contain the analogous mutation observed in the individuals affected. Of the 88 human proteins, 61 were matched to 73 (68 unique) predicted protein orthologs in C. elegans; ortholog assignment criteria and mapping can be found in Supplementary File 2 and . Title:Selenite-induced Expression of a Caenorhabditis elegans Pro-aging Factor and Ortholog of Human Selenium-binding Protein 1 Volume: 1 Issue: 1 Author(s): Karl Köhnlein, Nadine Urban, Holger Steinbrenner, David Guerrero-Gómez, Antonio Miranda-Vizuete, Christoph Kaether and Lars-Oliver Klotz* Defining a conserved family of transmembrane proteins, TMEM132D and its homologs are still of unknown molecular functions. C. elegans DNJ-27 and human ERdj5 proteins display a high amino acid sequence homology consisting of an N-terminal DnaJ/Hsp-40 domain followed by four Trx-like domains, with different CXXC redox active site motifs . It was the first animal - complete with nervous and digestive systems and a system for reproducing sexually - to have its genome deciphered. WormBase is supported by grant #U24 HG002223 from the National Human Genome Research Institute at the US National Institutes of Health, the UK Medical Research Council and the UK Biotechnology and Biological Sciences Research Council. . These results indicate important roles for hut-1 in development and maintenance of ER homeostasis in C. elegans. . Immobilized PDEdelta and CEdelta both bind, in addition to bovine PDE, an N-terminal fragment of human retinitis pigmentosa GTPase regulator, but not rhodopsin kinase and Ran . 1 A and Supplementary Table S3). Description of C. elegans - human orthologs. We efficiently identified edgetic alleles with various interaction defects caused by specific perturbations of CED-9 binding sites. The C. elegans gene pme-5: molecular cloning and role in the DNA-damage response of a tankyrase orthologue By Serge Desnoyers Evolution of the PP2C Family in Caenorhabditis: Rapid Divergence of the Sex-Determining Protein FEM-2 SZY-20. ALK is a receptor tyrosine kinase (RTK), a member of a di-verse group of receptors for intercellular signal transduction that share basic topological and catalytic features. Specifically, human spinocerebellar ataxia type 2 is shown to be associated with an extended poly-glutamine (Q) tract in Ataxin-2 (Elden et al., 2010; Huynh et al., 1999; Lastres-Becker et al., 2008). We also sought to assess the in vivo functions and potential genetic interactions of CeTRAP240 with C. elegans TRAP230 and Srb8 ortholog, CeTRAP230/dpy-22 . US National Institutes of Health, the UK Medical Research Council and the UK Biotechnology and Thus, we sought to determine whether CeTRAP240/let-19 interacts during C. elegans development with other components of its orthologous subcomplex. C. elegans fox-1 is closest to the putative ancient sequence. Predicted to be part of receptor complex. Human TAP and Saccharomyces cerevisiae Mex67p belong to a family of proteins that mediate mRNA export. The predicted human ortholog (Q92504) to H13N06.5 in C. elegans has been shown to be a zinc transporter localized to intracellular membranes . daf-16 encodes multiple isoforms that are expressed in distinct tissue types and are probable orthologs of human FKHRL1, FKHR, and AFX. The C. elegans genome encodes a single GPHR family member, FSHR-1, which shares equal identity to the FSH, LH, and TSH receptors from mammals. Worm Book. TMEM132D is a human gene identified with multiple risk alleles for panic disorders, anxiety and major depressive disorders. pp 1-17. Our studies have revealed a role for FSHR-1, a structural ortholog of the human glycopeptide hormone receptors, in the control of germ-cell differentiation, . 1 A, Table 1, Supplementary Tables S1 and S3). Identifying a subset of C. elegans genes with human orthologs would be especially useful for gene discovery with translational potential to human disease, because the effort spent on screening and analysis could be cut significantly by eliminating genes for which counterparts in humans do not exist or cannot be recognized by primary sequence data. An RNAi screen for modifiers of protein aggregation in C. elegans identified only one gene, moag-4 (the nematode ortholog of human SERF1), for which knockdown protected nematodes against Q40::YFP . psa-3 is a TALE homeobox gene with a MEIS domain that secondarily lost its HD. Curr Biol 11, 1950-1957.Lin, K., Hsin, H., Libina, N., and Kenyon, C. (2001). Identifying a subset of C. elegans genes with human orthologs would be especially useful for gene discovery with translational potential to human disease, because the effort spent on screening and analysis could be cut significantly by eliminating genes for which counterparts in humans do not exist or cannot be recognized by primary sequence data. . The Ortholog Finder project is consisted of three sub services: 1. Identifying a subset of C. elegans genes with human orthologs would be especially useful for gene discovery with translational potential to human disease, because the effort spent on screening and analysis could be cut significantly by eliminating genes for which counterparts in humans do not exist or cannot be recognized by primary sequence data. the C. elegans ortholog of mammalian ku-70 and ku-80 have phenotypes consistent with roles in DNA repair. C. elegans is widely accepted as a simple model system for elucidating key aspects of stem cell biology (3). (1) a . C. elegans DNJ-27 and human ERdj5 proteins display a high amino acid sequence homology consisting of an N-terminal DnaJ/Hsp-40 domain followed by four Trx-like domains, Expressed in several structures, including P3.p hermaphrodite; P4.p hermaphrodite; apoptotic cell; epithelial cell; and neurons. 12), an ortholog of the human antiapoptotic oncoprotein BCL2. Located in cell-cell junction and plasma membrane. Completion of the C. elegans genome sequence in 1998 ( C. elegans Sequencing Consortium, 1998) demonstrated that roughly 38% of worm genes have a human ortholog, such as APP and tau ( Shaye and Greenwald, 2011 ). The results are deposited in the Caenorhabditis elegans Glycogene Database (CGGDB) at AIST, Tsukuba, Japan. CHARGE syndrome is a complex developmental disorder caused by mutations in CHD7 (chromodomain helicase DNA-binding protein-7). Check The Variants This online tool: Allows input of one or more worm genes (even large sets) to retrieve the resulting human ortholog(s) 2 1 SUMMARY 2 3 TMEM132D is a human gene identified with multiple risk alleles for panic disorders, 4 anxiety and major depressive disorders. The aim of this study was to assess GH31 proteins in Caenorhabditis elegans (C. elegans) to identify the ortholog of human GAA. 3. Previous work had been done on the C. elegans ortholog of Srb8, CeTRAP230/dpy-22; several mutant alleles of that gene, such as sop-1, suppress a mutant male tail phenotype of pal-1(e2091) Gene names (gene) as well as WormBase sequence names (ORF) are given. . We sought to assess the orthology between C. elegans and human genes to understand better the. Location of RNP-1 and RNP-2 motifs are indicated as lines above . • Y37A1B.5 enhances selenite resistance but sensitizes towards oxidative stress. Compound Effects Testing; Phenotype-based Drug Discovery; Neuro Disease Models; Custom Analytical Services; In Vivo Models Menu Toggle. We identified five conserved genes with previously unsuspected roles in sleep in C. elegans.An ortholog of one of these genes showed consistent differential DNA methylation in . identify novel mechanisms by which HP1 homologs can be recruited to chromatin and by which nuclear depletion of human TDP-43 may lead to changes in RNA . exo-3 encodes the C. elegans ortholog of human APEX/REF1, a bifunctional enzyme that has been implicated previously in both DNA excision repair and a redox-dependent activity that stimulates transcription factor binding . We previously identified the C. elegans dnj-27 gene as the ortholog of human ERdj5 by an in silico approach . Find the Human orthologs: A service that aims to find the best Human orthologs for your Caenorhabditis elegans genes. Lethality and the ER stress phenotype of the mutant were rescued with the human hut-1 ortholog UGTrel1. egl-38, pax-1, pax-2 encode a Paired (PRD) domain only (Pax genes in vertebrates encode a PRD domain and may or may not encode a HD), and . • Y37A1B.5 is a cytoplasmic protein predominantly expressed in hypodermal cells. Y37A1B.5 is a C. elegans ortholog of human selenium binding protein 1 (SELENBP-1). There are about 20,000 protein-coding genes in C. elegans (WormBase WS238). A number of To identify candidate regulatory sequences in the 5′ non-coding regions of differentially regulated genes identified in this study were putative C. elegans homologs of p107/p130-target genes, 1 kilobase of sequence homologous to mammalian genes also regulated by pocket pro- data upstream of the start codon of each gene was . By generating loss-of-function mutants of the sole TMEM132 ortholog in C. elegans, we identify abnormal morphologic phenotypes in the dopaminergic . Such studies also reveal the utility of high . A subset of ced-9 edgetic alleles reintroduced in vivo caused phenotypes clearly dis- we focused on the C. elegans ortholog of TRAP240 and Srb9, CeTRAP240/let-19.1 We set out to isolate the full-length Ce-TRAP240/let-19 cDNA and to characterize its expression pat-tern. C. elegans is an important model for genetic studies relevant to human biology and disease. Benchmarking ortholog identification methods using functional genomics data. • Y37A1B.5 knockdown by RNAi causes C. elegans (mean and maximum) lifespan extension. The C. elegans ortholog of the Zn finger transcriptional output of hh signaling, . Furthermore, human HSP70 can bind and enhance the specific endonuclease activity of human apurinic/apyrimidinic endonuclease . View C.elegans and Bioinformatics.docx from BIOL 111L at Duquesne University. In Vivo Studies Menu Toggle. egl-38, pax-1, pax-2 encode a Paired (PRD) domain only (Pax genes in vertebrates encode a PRD domain and may or may not encode a HD), and . One of the worm orthologs of human A2BP1 is the numerator element FOX-1, with an overall 29.8% aa identity. C. elegans C. elegans Gene Protein Possible C. elegans Human Protein Possible Human Possible The single FOXO ortholog in C. elegans, daf-16, promotes entry into a quiescent and stress-resistant larval stage called dauer in response to adverse environmental cues. Multiple sequence alignment of AAGRs with other GH31 proteins demonstrated their . The human WRN gene encodes a 1432 amino acid protein that possesses an N-terminal 3′−5′ exonuclease domain and three C-terminal helicase domains ().Two different nematode proteins are orthologous to the functional domains of human WRN: C. elegans MUT-7 contains a 3′−5′ exonuclease and CeWRN-1 has three helicase domains ().Our previous studies demonstrated that MUT-7 is also . ATX-2 is the C. elegans ortholog of human Ataxin-2 that is implicated in human neurodegenerative disease (Lastres-Becker et al., 2008). The most prominent RNAi phenotypes observed are disruptions of cell cycle progression in germline mitosis/meiosis and in early embryonic cell mitosis. mouse ortholog, the human homolog RBM9, a Drosophila and two C. elegans orthologs. Human ataxin 2 is a protein of unknown function that is implicated in the neurodegenerative disorder spinocerebellar ataxia type 2. In December 1998, the first genome sequence of a multicellular organism, the roundworm Caenorhabditis elegans, was completed. C. elegans Genes with Human Orthologs PLoS To submit an update or takedown request for this paper, . As a control, we selected 59 C. elegans genes (25 HCOs and 34 RPs) based on orthology to randomly selected human genes - the 'Random gene set' (Tables 1 and S3, Supporting information). Human ataxin-2 has 20.1% amino acid identity and 43.9% similarity to its C. elegans ortholog, designated ATX-2, that encodes a predicted 1026 aa protein. In this study, we selected 181 nematode glycogenes that are orthologous to human glycogenes and examined their RNAi phenotypes. OrthoList is a compendium of C. elegans genes with human orthologs derived from a meta-analysis of results from four orthology prediction programs (Shaye and Greenwald, 2011).. By 1998, scientists established the completed genome sequencing of C. elegans ( C. elegans sequencing consortium, 1998). 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