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At least 145 records · Page 8Linked to original sources
PubMed1995

Most mRNAs in the nematode Ascaris lumbricoides are trans-spliced: a role for spliced leader addition in translational efficiency.

Some pre-mRNAs in nematodes are processed by trans-splicing. In this reaction, a 22-nt 5' terminal exon (the spliced leader, SL) and its associated 2,2,7-trimethylguanosine cap are acquired from a specialized Sm snRNP, the SL RNP. Although it has been evident for many years that not all nematode mRNAs contain the SL sequence, the prevalence of trans-spliced mRNAs has, with the exception of Caenorhabditis elegans, not been determined. To address this question in an organism amenable to biochemical analysis, we have prepared a message-dependent protein synthesis system from developing embryos of the parasitic nematode, Ascaris lumbricoides. Using this system, we have used both hybrid-arrest and hybrid-selection approaches to show that the vast majority (80-90%) of A. lumbricoides mRNAs contain the SL sequence and therefore are processed by trans-splicing. Furthermore, to examine the effect of SL addition on translation, we have measured levels of protein synthesis in extracts programmed with a variety of synthetic mRNAs. We find that the SL sequence itself and its associated hypermethylated cap functionally collaborate to enhance translational efficiency, presumably at the level of initiation of protein synthesis. These results indicate that trans-splicing plays a larger role in nematode gene expression than previously suspected.

Animals↗
PubMed1996

Molecular phylogeny of Schistosoma species supports traditional groupings within the genus.

Phylogenetic relationships among 9 blood flukes (7 schistosome species, a spirorchid, and a sanguinicolid) were inferred from nucleotide sequences of the D1 domain of large subunit rRNA and the V4 region of small subunit rRNA. These sequences were more conserved than those examined by previous authors and thus may provide insight into deeper-level relationships. Analyzed separately and combined by 3 methods, these data yielded congruent trees that were well supported by bootstrap resampling. The traditional groups of schistosome species based on egg type were supported. Schistosoma japonicum and Schistosoma mekongi were distinct from the remaining Schistosoma species. Schistosoma spindale (from India and southeast Asia) clustered strongly with the African species to the exclusion of the other Asian species, S. japonicum and S. mekongi. Schistosoma spindale may have been brought to India and southeast Asia from Africa by early humans. Statistical tests revealed only weak evidence for the operation of a molecular clock in the V4 sequence; no evidence was found for this in the D1 domain.

Africa↗
PubMed1998

Regulation of the Caenorhabditis elegans gut cysteine protease gene cpr-1: requirement for GATA motifs.

Expression of the Caenorhabditis elegans cysteine protease gene cpr-1 is regulated both spatially and temporally. In situ hybridisation and Northern blot analysis have shown that this gene is expressed exclusively in gut cells of all developmental stages except the embryo. We now show by transgenic transformation with cpr-1/lac Z reporter gene constructs that a sequence contained within the cpr-1 5' flanking region can direct this spatial and temporal expression. Deletion analysis of the cpr-1 promoter indicates that as little as 212 bp of upstream sequence is sufficient for this expression, although more upstream sequence may be involved in quantitative regulation of expression. Mutation of two GATA-like sequence elements at positions -51 and -147 upstream of the transcription start site ablates all expression, indicating an essential role in cpr-1 regulation. A concatemer of the cpr-1 -147 GATA motif placed upstream of minimal promoter/lac Z reporter gene constructs results in strong reporter gene expression in gut cells of larval stages and also in embryos. Weak expression is also detected in hypodermal cells. This pattern is reversed in the adult stage with strong expression in hypodermal cells and weaker expression in gut cells. Our findings suggest that spatial and temporal regulation of the cpr-1 gene is complex and involves activation by a GATA-like transcription factor.

Animals↗
PubMed1997

Isolation and characterization of five actin cDNAs from the cestode Diphyllobothrium dendriticum: a phylogenetic study of the multigene family.

Five cDNAs (pDidact2-pDidact6), representing different actin genes, were isolated from a Diphyllobothrium dendriticum cDNA library, and the DNA as well as the putative amino acid sequences were determined. The corresponding Didact2 and Didact4 genes code for peptides 376 amino acids long, with molecular weights 41,772 and 41,744 Da, respectively, while the deduced Didact3 protein is 377 amino acids long and weighs 41,912 Da. The pDidact5 and -6 cDNAs lack nucleotides corresponding to three to six amino acids at the amino-terminus. Two of the five cDNAs contain the conventional AATAAA as the putative polyadenylation signal, one has the common variant ATTAAA, whereas the hexanucleotide AATAGA is found 15 and 18 nucleotides, respectively, upstream of the poly(A) site in two of the cDNAs. Phylogenetic studies including 102 actin protein sequences revealed that there are at least four different types of cestode actins. In this study three of these types were found to be expressed in the adult D. dendriticum tapeworm. Structurally the cestode actin groupings differ from each other to an extent seen only among the metazoan actins between the vertebrate muscle and cytoplasmic isoforms. In the phylogenetic trees constructed, cestode actins were seen to map to two different regions, one on the border of the metazoan actins and the other within this group. It is, however, difficult to say whether the cestode actins branched off early in the metazoan evolution or if this position in the phylogenetic tree only reflects upon differences in evolutionary rate.

Actins↗
PubMed2004

Characterisation of a beta-tubulin gene from the monogenean parasite, Gyrodactylus salaris Malmberg, 1957.

The cDNA and two partial genomic sequences of beta-tubulin genes have been isolated from the monogenean parasite Gyrodactylus salaris. The cDNA sequence is not represented by either of the genomic sequences, implying that at least three isotypes of the gene exist in G. salaris. The sequences show regions of high homology with other helminth beta-tubulin genes. This represents the first isolation of a beta-tubulin gene from a monogenean and contributes to the overall characterisation of these genes within the helminths. This is an important area, as anthelmintic resistance is increasing against benzimidazole drugs that target the beta-tubulin gene. Benzimidazole drugs have been tested successfully against Gyrodactylus parasites, but their use is not widespread. Should it increase, analysis of the beta-tubulin gene may provide a tool for monitoring resistance development and improving management practises. Use of the beta-tubulin gene in the identification of Gyrodactylus species may prove complex due to the presence of different isotypes.

Amino Acid Sequence↗
PubMed1994

The role of dityrosine formation in the crosslinking of CUT-2, the product of a second cuticlin gene of Caenorhabditis elegans.

A second cuticlin gene, cut-2, of the nematode Caenorhabditis elegans, has been isolated and its genomic and cDNA sequences determined. The gene codes for a component of cuticlin, the insoluble residue of nematode cuticles. Conceptual translation of cut-2 reveals a 231-amino acid secreted protein which, like CUT-1, begins with a putative signal peptide of 16 residues. The central part of the protein consists of 13 repetitions of a short hydrophobic motif, which is often degenerated with substitutions and deletions. Parts of this motif are present also in CUT-1 (Caenorhabditis elegans) as well as in several protein components of the larval cuticle and of the eggshell layers of various insects (Locusta migratoria, Ceratitis capitata and Drosophila species). These sequence similarities are related to the similar functions of these proteins: they are all components of extracellular insoluble protective layers. Immunolocalisation and transcription analysis suggest that CUT-2 contributes to the cuticles of all larval stages and that it is not stage-specific. Analysis by reverse transcriptase-PCR suggests that it is not stage-specific. Analysis by reverse transcriptase-PCR suggests that transcription is not continuous throughout larval development but occurs in peaks which precede the moults. Dityrosine has been detected in the cuticle of nematodes and of insects; formation of dityrosine bridges may be one of the cross-linking mechanisms contributing to the insolubility of cuticlins. Recombinant, soluble CUT-2 is shown to be an excellent substrate for an in vitro cross-linking reaction, catalysed by horseradish peroxidase in the presence of H2O2, which results in the formation of insoluble, high-molecular weight CUT-2 and of dityrosine.

Amino Acid Sequence↗
PubMed1995

Extensive diversity in repeat unit sequences of the cDNA encoding the polyprotein antigen/allergen from the bovine lungworm Dictyocaulus viviparus.

The complete sequence of the cDNA encoding the nematode polyprotein allergen/antigen (NPA) of the bovine lungworm Dictyocaulus viviparus was obtained by immunoscreening of cDNA expression libraries and by 5' RACE (rapid amplification of cDNA ends). The encoded polypeptide is similar in sequence to the ABA-1 allergen of Ascaris, the gp15/400 'ladder' protein of Brugia malayi, Brugia pahangi and Wuchereria bancrofti, and a 15-kDa antigen of Dirofilaria immitis. As with these, the predicted amino-acid sequence comprises a head-to-tail array of similar polypeptides with regularly spaced consensus proteinase cleavage sites. The D. viviparus protein was designated DvA-1 (D. viviparus antigen-1) and the gene dva-1. The deduced amino-acid sequence of DvA-1 showed features not observed before in other NPAs: (i) a hydrophobic leader peptide is present, (ii) none of the 12 units in the array are identical and the sequences diverge to a degree hitherto unseen in the NPAs of other nematode parasites, (iii) the predicted proteinase cleavage sites are also diverse in sequence and, in two instances, no consensus cleavage site was identifiable at the expected position, (iv) a short repeat unit is present, which is the only one containing a consensus N-glycosylation site and (v) a C-terminal extension peptide is encoded which shows no similarity to that from A. suum ABA-1. Comparison of independent cDNAs revealed slight variations in the sequence of the gene within the parasite population. Antisera to recombinant DvA-1 polypeptide identified 14-15-kDa antigens in both parasite somatic and excretory-secretory material. DvA-1 is the only NPA for which the complete coding sequence is available and the new principles which it illustrates may lie unsuspected in the NPA-encoding genes of all nematode parasites.

Amino Acid Sequence↗
PubMed2002

Transcriptional profile of aging in C. elegans.

BACKGROUND: Numerous gerontogene mutants leading to dramatic life extensions have been identified in the nematode Caenorhabditis elegans over the last 20 years. Analysis of these mutants has provided a basis for understanding the mechanisms driving the aging process(es). Several distinct mechanisms including an altered rate of aging, increased resistance to stress, decreased metabolic rate, or alterations in a program causing organismic aging and death have been proposed to underlie these mutants. RESULTS: Whole-genome analysis of gene expression during chronological aging of the worm provides a rich database of age-specific changes in gene expression and represents one way to distinguish among these models. Using a rigorous statistical model with multiple replicates, we find that a relatively small number of genes (only 164) show statistically significant changes in transcript levels as aging occurs (<1% of the genome). Expression of heat shock proteins decreases, while expression of certain transposases increases in older worms, and these findings are consistent with a higher mortality risk due to a failure in homeostenosis and destabilization of the genome in older animals. Finally, a specific subset of genes is coordinately altered both during chronological aging and in the transition from the reproductive form to the dauer, demonstrating a mechanistic overlap in aging between these two processes. CONCLUSIONS: We have performed a whole-genome analysis of changes in gene expression during aging in C. elegans that provides a molecular description of C. elegans senescence.

Aging↗
PubMed2001

A small fortune.

Explore the source record for details and available documents.

Animals↗
PubMed1998

A robust molecular phylogeny of the Tricladida (Platyhelminthes: Seriata) with a discussion on morphological synapomorphies.

The suborder Tricladida (Platyhelminthes: Turbellaria, Seriata) comprises most well-known species of free-living flatworms. Four infraorders are recognized: (i) the Maricola (marine planarians); (ii) the Cavernicola (a group of primarily cavernicolan planarians); (iii) the Paludicola (freshwater planarians); and (iv) the Terricola (land planarians). The phylogenetic relationships among these infraorders have been analysed using morphological characters, but they remain uncertain. Here we analyse the phylogeny and classification of the Tricladida, with additional, independent, molecular data from complete sequences of 18S rDNA and 18S rRNA. We use maximum parsimony and neighbour-joining methods and the characterization of a unique gene duplication event involving the Terricola and the dugesiids to reconstruct the phylogeny. The results show that the Maricola is monophyletic and is the primitive sister group to the rest of the Tricladida (the Paludicola plus the Terricola). The Paludicola are paraphyletic since the Terricola and one paludicolan family, the Dugesiidae, share a more recent common ancestor than the dugesiids with other paludicolans (dendrocoelids and planariids). A reassessment of morphological evidence may confirm the apparent redundancy of the existing infraorders Paludicola and Terricola. In the meantime, we suggest replacing the Paludicola and Terricola with a new clade, the Continenticola, which comprises the families Dugesiidae, Planariidae, Dendrocoelidae and the Terricola.

Animals↗
PubMed2005

Organization of the Caenorhabditis elegans small non-coding transcriptome: genomic features, biogenesis, and expression.

Recent evidence points to considerable transcription occurring in non-protein-coding regions of eukaryote genomes. However, their lack of conservation and demonstrated function have created controversy over whether these transcripts are functional. Applying a novel cloning strategy, we have cloned 100 novel and 61 known or predicted Caenorhabditis elegans full-length ncRNAs. Studying the genomic environment and transcriptional characteristics have shown that two-thirds of all ncRNAs, including many intronic snoRNAs, are independently transcribed under the control of ncRNA-specific upstream promoter elements. Furthermore, the transcription levels of at least 60% of the ncRNAs vary with developmental stages. We identified two new classes of ncRNAs, stem-bulge RNAs (sbRNAs) and snRNA-like RNAs (snlRNAs), both featuring distinct internal motifs, secondary structures, upstream elements, and high and developmentally variable expression. Most of the novel ncRNAs are conserved in Caenorhabditis briggsae, but only one homolog was found outside the nematodes. Preliminary estimates indicate that the C. elegans transcriptome contains approximately 2700 small non-coding RNAs, potentially acting as regulatory elements in nematode development.

Animals↗
PubMed1996

Sex-specific assembly of a dosage compensation complex on the nematode X chromosome.

In nematodes, flies, and mammals, dosage compensation equalizes X-chromosome gene expression between the sexes through chromosome-wide regulatory mechanisms that function in one sex to adjust the levels of X-linked transcripts. Here, a dosage compensation complex was identified in the nematode Caenorhabditis elegans that reduces transcript levels from the two X chromosomes in hermaphrodites. This complex contains at least four proteins, including products of the dosage compensation genes dpy-26 and dpy-27. Specific localization of the complex to the hermaphrodite X chromosomes is conferred by XX-specific regulatory genes that coordinately control both sex determination and dosage compensation.

Animals↗
PubMed2001

Exposure of Caenorhabditis elegans to extremely low frequency high magnetic fields induces stress responses.

Responses of the small heat shock protein gene, hsp-16, were examined in transgenic Caenorhabditis elegans exposed to electromagnetic fields. Expression of the hsp-16-lacZ gene was enhanced when transgenic animals were exposed to magnetic fields up to 0.5 T at 60 Hz. The hsp-16 promoter was more efficiently expressed at the embryonic than at the post-embryonic stage irrespective of exposure. Promoter activity was more sensitive to the stimulus in the intestine at the post-embryonic stage. Evidence is presented that the induction occurs at the transcriptional step of hsp-16.

Animals↗
PubMed1995

Characterization of a novel non-muscle myosin-related protein from Onchocerca gibsoni.

A cDNA library was constructed in lambda gt11 using poly(A)+ mRNA from early larvae of Onchocerca gibsoni. Screening of the library using serum from a single onchocerciasis patient yielded several strongly immunoreactive clones, one of which (OGK2) was found to encode a novel myosin-related protein. cDNA clone OGK2 contained an insert of 2017 bp, consisting of continuous open reading frame in frame with the vector, hence this clone encodes 671 amino acid residues of a larger protein. A fragment (619 nt) of the OGK2 cDNA was subcloned into the expression vector pGEX-1N to generate a glutathione S-transferase fusion protein. Polyclonal antiserum raised to this fusion protein strongly recognised an O. gibsoni protein of approximately 220 kDa. Immunolocalization studies indicated that this protein was associated predominantly with the hypodermis and a number of other specific membrane layers in the adult parasite. Myosin-related proteins are frequently immunodominant parasite antigens and in a number of studies have been shown to confer a degree of protective immunity against the corresponding parasite. Evaluation of the protective potential of the OGK2 protein, therefore, appears to be warranted.

Amino Acid Sequence↗
PubMed1995

The ksr-1 gene encodes a novel protein kinase involved in Ras-mediated signaling in C. elegans.

By screening for mutations that suppress the vulval defects caused by a constitutively active let-60 ras gene, we identified six loss-of-function alleles of ksr-1, a novel C. elegans gene. Our genetic analysis showed ksr-1 positively mediates Ras signaling and functions downstream of or in parallel to let-60. In the absence of ksr-1 function, normal Ras signaling is impaired only slightly, suggesting ksr-1 may act to modulate, or in a branch that diverges from, the main signaling pathway. The predicted KSR-1 protein has a protein kinase domain and is most similar to a recently identified Drosophila protein involved in Ras signaling. We propose that the function of ksr-1 is evolutionarily conserved.

Amino Acid Sequence↗
PubMed2005

The complete mitochondrial genome of Anisakis simplex (Ascaridida: Nematoda) and phylogenetic implications.

We determined the nucleotide sequence of the complete mitochondrial genome of the nematode species Anisakis simplex. The genome is circular, 13,916 bp in size and conforms to the general characteristics of nematode mitochondrial DNAs. The gene arrangement of A. simplex is the same as that of Ascaris suum and almost identical to those of rhabditid species with a minor exception concerning the relative position of the AT-rich and non-coding regions and radically different from those of spirurid species. Along with comparisons of gene arrangement, phylogenetic analyses (maximum parsimony, neighbour joining and maximum likelihood methods) based on concatenated amino acid sequences of 12 protein-coding genes from 13 nematode species provided strong support for the sister-group relationship between Ascaridida and Rhabditida. The Shimodaira-Hasegawa and Templeton's tests both rejected the alternative hypothesis of a closer relationship between Ascaridida and Spirurida. These results contradicted the traditional view of nematode classification and a recent molecular phylogenetic study of 18S rDNA data that assigned Ascaridida and Spirurida as being a sister-group. Mapping of gene arrangement across the phylogenetic tree lead to the assumption that the conserved gene arrangement found in Ascaridida-Rhabditida members might have been acquired after the most recent common ancestor of ascaridid/rhabditid members branched off from the basal stock of the rhabditid lineage.

Amino Acid Sequence↗
PubMed2004

Gender-associated gene expression in two related strains of Schistosoma japonicum.

Host inflammatory responses directed against eggs laid by sexually-mature Schistosoma japonicum female worms instigate lesion formation and associated clinical pathologies during infection. To identify parasite gene transcripts that associate with egg production and to characterise sexually-mature adult gene expression profiles of two related Chinese strains, S. japonicum cDNA microarrays were fabricated using 457 ESTs originating from three parasite developmental stages. Twenty-two female-associated and 8 male-associated gene transcripts were identified in the adult Anhui strain whereas 21 female-associated and 7 male-associated gene transcripts were revealed in the adult Zhejiang strain. RT-PCR analysis, in situ enzyme localisation studies and enzymatic assays confirmed the cDNA microarray results, and importantly, provided information previously unappreciated in schistosome conjugal biology. Specifically, our novel findings include the female-specific expression of genes putatively involved in haemoglobin digestion and eggshell formation including extracellular superoxide dismutase, two histidine-rich proteins, a large blood-brain barrier amino acid transporter and two tyrosinase orthologues. In contrast, transcripts involved in mechanical support (actin), cytoskeletal infrastructure (e.g. dynein light chain 3 and myosin regulatory light chain) and tegumental biology (e.g. TM4SF and Sj25) were more highly represented in adult male schistosomes. Together these data establish a transcriptional basis for adult schistosome labour division and expands the list of novel S. japonicum gender-associated gene transcripts that may be considered targets for improved intervention strategies.

Animals↗