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[
Evolutionary Biology of Caenorhabditis and Other Nematodes,
2010]
Parasitic nematodes have a major impact on human and animal health and crop productivity. Many of the most important parasitic nematodes are endoparasites, which makes them generally inaccessible to molecular techniques once they are inside their hosts. With the exception of RNA interference, forward and reverse genetics and transgenesis have so far proven to be impossible with parasitic nematodes, which represents a significant technological hurdle. Comparative genomics between the model nematode Caenorhabditis elegans and parasitic species is a powerful approach to circumvent some of these problems and to gain insights into fundamental biological processes that are conserved in the Nematoda. We have conducted a comparative analysis between C. elegans and the plant-parasitic nematode Heterodera glycines. Using microarrays and sequence analyses we identified 788 H. glycines candidate genes with putative roles in parasitism for further studies. Furthermore, we found that a significant number of genes that are enriched for the dauer stage in C. elegans have putative orthologs in H. glycines but that their expression signatures were not uniformly conserved when the developmentally arrested infective stage of H. glycines and the C. elegans dauer stage were compared. This suggests that the molecular mechanisms governing developmental arrest in C. elegans and H. glycines might have undergone more divergent evolution than previously thought and points at the need for more detailed analyses of parasitic species. Sequencing the genomes of more non-parasitic and parasitic nematodes to capture the enormous diversity in trophic ecology, habitats and life styles found in the phylum Nematoda will allow a better understanding of the evolutionary changes that have occurred between the dauer stage in C. elegans and the infective stage of parasitic nematodes.
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Mitreva M, Baum TJ, Martin J, Gai X, McK Bird D, McCarter JP, McDermott JP, Davis EL, Nettleton D, Elling AA, Maier TR, Recknor J, Hussey RS, Hewezi T
[
Genome Biol,
2007]
ABSTRACT: BACKGROUND: The soybean cyst nematode Heterodera glycines is the most important parasite in soybean production worldwide. A comprehensive analysis of large-scale gene expression changes throughout the development of plant-parasitic nematodes has been lacking to date. RESULTS: We report an extensive genomic analysis of Heterodera glycines, beginning with the generation of 20,100 expressed sequence tags (EST). In-depth analysis of these EST plus approximately 1,900 previously published sequences predicted 6,860 unique H. glycines genes and allowed a classification by function using InterProScan. Expression profiling of all 6,860 genes throughout the H. glycines life cycle was undertaken using the Affymetrix Soybean Genome Array GeneChip. Our data sets and results represent a comprehensive resource for molecular studies of H. glycines. Demonstrating the power of this resource, we were able to address whether arrested development in the Caenorhabditis elegans dauer larva and the H. glycines infective second-stage juvenile (J2) exhibits shared gene expression profiles. We determined that the gene expression profiles associated with the C. elegans dauer pathway are not uniformly conserved in H. glycines and that the expression profiles of genes for metabolic enzymes of C. elegans dauer larvae and H. glycines infective J2 are dissimilar. CONCLUSIONS: Our results indicate that hallmark gene expression patterns and metabolism features are not shared in the developmentally arrested life stages of C. elegans and H. glycines, suggesting that developmental arrest in these two nematode species has undergone more divergent evolution than previously thought and pointing to the need for detailed genomic analyses of individual parasite species.
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[
Genomics,
1997]
The Caenorhabditis elegans genome sequencing project has completed over half of this nematode's 100-Mb genome. Proteins predicted in the finished sequence have been compiled and released in the data-base Wormpep. Presented here is a comprehensive analysis of protein domain families in Wormpep 11, which comprises 7299 proteins. The relative abundance of common protein domain families was counted by comparing all Wormpep proteins to the Pfam collection of protein families, which is based on recognition by hidden Markov models. This analysis also identified a number of previously unannotated domains. To investigate new apparently nematode-specific protein families, Wormpep was clustered into domain families on the basis of sequence similarity using the Domainer program. The largest clusters that lacked clear homology to proteins outside Nematoda were analyzed in further detail, after which some could be assigned a putative function. We compared all proteins in Wormpep 11 to proteins in the human, Saccharomyces cerevisiae, and Haemophilus influenzae genomes. Among the results are the estimation that over two-thirds of the currently known human proteins are likely to have a homologue in the whole C. elegans genome and that a significant number of proteins are well conserved between C. elegans and H. influenzae, that are not found in S. cerevisiae.
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[
Worm,
2012]
The nematode C. elegans has during the past decade proven to be a valuable model organism to identify and examine molecular mechanisms regulating lipid storage and metabolism. While the primary approach has been to identify genes and pathways conferring alterations in lipid accumulation, only a few recent studies have recognized the central role of fatty acid degradation in cellular lipid homeostasis. In the present study, we show how complete oxidation of fatty acids can be determined in live C. elegans by examining oxidation of tritium-labeled fatty acids to tritiated H2O that can be measured by scintillation counting. Treating animals with sodium azide, an inhibitor of the electron transport chain, reduced (3)H2O production to approximately 15%, while boiling of animals prior to assay completely blocked the production of labeled water. We demonstrate that worms fed different bacterial strains exhibit different fatty acid oxidation rates. We show that starvation results in increased fatty acid oxidation, which is independent of the transcription factor NHR-49. On the contrary, fatty acid oxidation is reduced to approximately 70% in animals lacking the worm homolog of the insulin receptor, DAF-2. Hence, the present methodology can be used to delineate the role of specific genes and pathways in the regulation of -oxidation in C. elegans.
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[
Comput Appl Biosci,
1994]
When routinely analysing very long stretches of DNA sequences produced by genome sequencing projects, detailed analysis of database search results becomes exceedingly time consuming. To reduce the tedious browsing of large quantities of protein similarities, two programs, MSPcrunch and Blixem, were developed, which assist in processing the results from the database search programs in the BLAST suite. MSPcrunch removes biased composition and redundant matches while keeping weak matches that are consistent with a larger gapped alignment. This makes BLAST searching in practice more sensitive and reduces the risk of overlooking distant similarities. Blixem is a multiple sequence alignment viewer for X-windows which makes it significantly easier to scan and evaluate the matches ratified by MSPcrunch. In Blixem, matches to the translated DNA query sequence are simultaneously aligned in three frames. Also, the distribution of matches over the whole DNA query is displayed. Examples of usage are drawn from 36 C. elegans cosmid clones totalling 1.2 megabases, to which these tools were applied.
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[
Proteins,
1997]
Databases of multiple sequence alignments are a valuable aid to protein sequence classification and analysis. One of the main challenges when constructing such a database is to simultaneously satisfy the conflicting demands of completeness on the one hand and quality of alignment and domain definitions on the other. The latter properties are best dealt with by manual approaches, whereas completeness in practice is only amenable to automatic methods. Herein we present a database based on hidden Markov model profiles (HMMs), which combines high quality and completeness. Our database, Pfam, consists of parts A and B. Pfam-A is curated and contains well-characterized protein domain families with high quality alignments, which are maintained by using manually checked seed alignments and HMMs to find and align all members. Pfam-B contains sequence families that were generated automatically by applying the Domainer algorithm to cluster and align the remaining protein sequences after removal of Pfam-A domains. By using Pfam, a large number of previously unannotated proteins from the Caenorhabditis elegans genome project were classified. We have also identified many novel family memberships in known proteins, including new kazal, Fibronectin type III, and response regulator receiver domains. Pfam-A families have permanent accession numbers and form a library of HMMs available for searching and automatic annotation of new protein sequences.
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[
Nucleic Acids Res,
1998]
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[
International Worm Meeting,
2011]
Acyl-CoA esters, the metabolically active form of fatty acids, are important intermediates in both anabolic and catabolic processes, but have also been identified as regulators of ion channels, enzymes, membrane fusion, and gene expression. Acyl-CoA binding protein (ACBP) is a small, primarily cytosolic protein, which binds acyl-CoA esters with high specificity and affinity. ACBP has been identified in all eukaryotic species, and the gene encoding the basal form displays all the hallmarks of a housekeeping gene, indicating that ACBP performs a basal cellular function. However, the existence of several ACBP paralogues in many eukaryotic species and differential tissue expression indicate that these proteins serve distinct functions. Studies in other model organisms have implicated ACBPs in triglyceride storage, lipid synthesis, autophagy, cold tolerance, and skin barrier function. C. elegans expresses seven functional ACBPs; four basal forms and three ACBP domain proteins. In the present study, we have obtained mutants with functional loss of each of six of the ACBPs and characterized their macroscopic and biochemical phenotypes. The seventh paralogue Membrane-Associated ACBP-1 has been shown to be involved in endosomal vesicle transport. We find that each of the six paralogues is capable of complementing growth of ACBP-deficient yeast cells, and that they exhibit distinct temporal and tissue expression patterns. All acbp single mutants display only subtle phenotypes, likely due to compensatory mechanisms and some extent of functional redundancy. ACBP-1 is shown to be involved in triglyceride storage and lipid droplet morphology. ACBP-2, containing an enoyl-CoA hydratase domain, is necessary for b-oxidation of unsaturated fatty acids, and ACBP-3 is needed for normal skin barrier function. We have generated a quadruple mutant, which we are currently investigating. This mutant is developmentally delayed compared to N2, and preliminary data suggest that it increases its b-oxidation of exogenous fatty acids, suggesting that lack of all basal ACBPs elicits a starvation-like phenotype.
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[
FEBS Lett,
2010]
The nematode Caenorhabditis elegans (C. elegans) has during the last decade emerged as an invaluable eukaryotic model organism to understand the metabolic and neuro-endocrine regulation of lipid accumulation. The fundamental pathways of food intake, digestion, metabolism, and signalling are evolutionary conserved between mammals and worms making C. elegans a genetically and metabolically extremely tractable model to decipher new regulatory mechanisms of lipid storage and to understand how nutritional and genetic perturbations can lead to obesity and other metabolic diseases. Besides providing an overview of the most important regulatory mechanisms of lipid accumulation in C. elegans, we also critically assess the current methodologies to monitor lipid storage and content as various methods differ in their applicability, consistency, and simplicity.
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[
International C. elegans Meeting,
1995]
The proteins predicted in the sequence generated by the genome project are released as a protein sequence database called Wormpep, which is incorporated into Swissprot. Release 8 (March 95) of Wormpep contains the translations of 1965 predicted genes in 12 megabases of genomic DNA from a total of 398 cosmids on chromosome II, III and X. About 50% of the predicted proteins can be classified based on sequence homology with other proteins. Examples of the most common domains are: EGF (125), IG superfamily (60, 45 in one protein), protein kinase (54), RNA-binding (32), fibronectin type III (20), homeobox (18) and reverse transcriptase (10). Of the proteins that don't show homology, many are similar to each other, thus forming new families. This often involves neighboring proteins or repeated domains within one protein. We have extracted such families by clustering Wormpep based on sequence similarity with the Domainer algorithm (Sonnhammer and Kahn, Prot. Sci. 3:482). The largest families were analysed in more detail by constructing the multiple alignment and using it to search for homology more sensitively. We also looked for Prosite motifs, transmembrane features and coiled-coil regions. The poster describes 10 new protein families, each comprising 5-15 members. In some cases searching with the whole family revealed previously undetected similarities. Examples of this are: TPR domains and a 7-helix transmembrane family possibly interacting with G-proteins. Two other families are likely transmembrane proteins.