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PubMed2004

Developmental regulation and secretion of nematode-specific cysteine-glycine domain proteins in Trichinella spiralis.

The muscle larva of Trichinella spiralis is an intracellular parasite of mammalian skeletal muscle, encapsulating within a portion of the myofiber and resulting in muscle de-differentiation. Parasite-derived factors secreted or excreted by the muscle larva are thought to play a role in the formation of the host-parasite complex and in the induction of changes in the host cell. We screened a library enriched for T. spiralis-specific cDNAs and identified a clone encoding a protein with similarity to a predicted secreted or extracellular Caenorhabditis elegans protein. The region of similarity included a conserved cysteine-glycine (CCG) domain, which we have identified as being nematode-specific. This domain is present in the predicted T. spiralis protein, Ts-CCG-1, and in a second protein, Ts-CCG-2, which we identified from subsequent analysis. We showed that while the Ts-ccg-1 gene is constitutively expressed, Ts-ccg-2 gene expression is restricted to the muscle L1 larva. Both predicted proteins contain an N-terminal signal peptide and we subsequently confirmed by MALDI-TOF mass spectrometric analyses of excretory/secretory peptide spots excised from two-dimensional gels that Ts-CCG-2 is secreted.

Amino Acid Motifs↗
PubMed1997

A member of the TGF-beta receptor gene family in the parasitic nematode Brugia pahangi.

The full length cDNA sequence of a Type I transforming growth factor-beta (TGF-beta) receptor has been isolated from the filarial parasitic nematode Brugia pahangi. This new gene, designated Bp-trk-1, encodes a predicted 645 amino acid sequence with an N-terminal hydrophobic stretch which may act as a signal peptide. The extracellular portion (residues 15-187) is cysteine-rich and has three potential N-glycosylation sites. At positions 250-255 the protein contains the glycine-serine rich motif characteristic of Type I receptors. The closest homologue is a Caenorhabditis elegans gene (Q09488) in cosmid C32D5.2 which shares 67% amino acid identity with Bp-trk-1 in the most conserved kinase domain (aa 259-482). Other type I receptors such as C. elegans daf-1 and Drosophila tkv show 38-53% identity in the same region. Some residues conserved in Drosophila and vertebrates are not present in the B. pahangi sequence. RT-PCR amplification has been used to show that the transcript is expressed in the three main stages of the B. pahangi life cycle: microfilariae, infective larvae and adults. The ligand remains unknown at this time but is likely to be most similar to that for C. elegans Q09488.

Amino Acid Sequence↗
PubMed2005

A stage-specific open reading frame from three-day old adult worms of Trichinella spiralis encodes zinc-finger motifs.

The aim of the study was to isolate genes coding for stage-specific antigens of T. spiralis. Such antigens may then be associated with local and systemic immune responses against adult T. spiralis. Recombinant clones were obtained with an adult stage specific probe from a cDNA library of three-day old adult T. spiralis. Several cDNA clones encoding the same peptide were identified and their stage specificity was confirmed by northern blot analysis. Three independent clones were fully sequenced, and the resulting sequence found to code for a 487 amino acid peptide with a deduced molecular weight of approximately 55 kDa. Sequence analysis showed that the 55 kDa peptide contained putative DNA binding motifs, suggesting that this protein may be involved in transcriptional regulation during the early development of the parasite.

Amino Acid Sequence↗
PubMed1994

Nucleotide correlations that suggest tertiary interactions in the TV-replacement loop-containing mitochondrial tRNAs of the nematodes, Caenorhabditis elegans and Ascaris suum.

In the predicted secondary structures of 20 of the 22 tRNAs encoded in mitochondrial DNA (mtDNA) molecules of the nematodes, Caenorhabditis elegans and Ascaris suum, the T psi C arm and variable loop are replaced with a loop of 6 to 12 nucleotides: the TV-replacement loop. From considerations of patterns of nucleotide correlations in the central regions of these tRNAs, it seems highly likely that tertiary interactions occur within five sets of binary and ternary combinations of nucleotides that correspond in location to nucleotides known to be involved in tertiary interactions in yeast tRNA(Phe) and other standard tRNAs. These observations are consistent with the nematode TV-replacement loop-containing mt-tRNAs being folded into a similar L-shaped functional form to that demonstrated for standard tRNAs, and for the bovine DHU (dihydrouridine) arm replacement-loop-containing mt-tRNA(Ser(AGY)). However, the apparent occurrence in nematode mt-tRNAs of tertiary bonds common to standard tRNAs contrasts with the situation in bovine mt-tRNA(Ser(AGY)) where the functional form is dependent on an almost unique set of tertiary interactions. Because three of the proposed conserved tertiary interactions in the nematode mt-tRNAs involve nucleotides that occur in the variable loop in standard tRNAs, it seems more likely that in nematode mt-tRNAs it is the T psi C arm rather than the variable loop that has undergone the greatest proportional decrease in nucleotide number.

Animals↗
PubMed1996

Posterior patterning by the Caenorhabditis elegans even-skipped homolog vab-7.

Patterning of the posterior end in animals is not well understood. Homologs of Drosophila even-skipped (eve) have a similar posterior expression pattern in many animals, and in vertebrates they are linked physically to the "posterior" ends of homeotic clusters (HOM-C), suggesting a conserved role in posterior development. However, the function of this posterior expression is not known. Here I show that the Caenorhabditis elegans gene vab-7 encodes an eve homolog that is required for posterior development and expressed in a pattern strikingly similar to that of vertebrate eve genes. Using a four-dimensional recording system, I found that posterior body muscles and the posterior epidermis are patterned abnormally in vab-7 mutants, but commitment to muscle and epidermal fates is normal. Furthermore, vab-7 activity is required for the complete expression of the most posterior HOM-C gene egl-5 in muscle cells, supporting the idea that eve homologs may act with the HOM-C to determine posterior cell fates. The conservation of sequence and expression pattern between vab-7 and eve homologs in other animals argues that most eve genes have posterior mesodermal and ectodermal patterning functions.

Amino Acid Sequence↗
PubMed2001

An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans.

Two small temporal RNAs (stRNAs), lin-4 and let-7, control developmental timing in Caenorhabditis elegans. We find that these two regulatory RNAs are members of a large class of 21- to 24-nucleotide noncoding RNAs, called microRNAs (miRNAs). We report on 55 previously unknown miRNAs in C. elegans. The miRNAs have diverse expression patterns during development: a let-7 paralog is temporally coexpressed with let-7; miRNAs encoded in a single genomic cluster are coexpressed during embryogenesis; and still other miRNAs are expressed constitutively throughout development. Potential orthologs of several of these miRNA genes were identified in Drosophila and human genomes. The abundance of these tiny RNAs, their expression patterns, and their evolutionary conservation imply that, as a class, miRNAs have broad regulatory functions in animals.

Animals↗
PubMed2006

A real-time PCR method for quantifying viable ascaris eggs using the first internally transcribed spacer region of ribosomal DNA.

Worldwide, 1.4 billion people are infected with the intestinal worm Ascaris lumbricoides. As a result, Ascaris eggs are commonly found in wastewater and sludges. The current microscopy method for detecting viable Ascaris eggs is time- and labor-intensive. The goal of this study was to develop a real-time quantitative PCR (qPCR) method to determine the levels of total and viable Ascaris eggs in laboratory solutions using the first internally transcribed spacer (ITS-1) region of ribosomal DNA (rDNA) and rRNA. ITS-1 rDNA levels were proportional to Ascaris egg cell numbers, increasing as eggs developed from single cells to mature larvae and ultimately reaching a constant level per egg. Treatments causing >99% inactivation (high heat, moderate heat, ammonia, and UV) eliminated this increase in ITS-1 rDNA levels and caused decreases that were dependent on the treatment type. By taking advantage of this difference in ITS-1 rDNA level between viable, larvated eggs and inactivated, single-celled eggs, qPCR results were used to develop inactivation profiles for the different treatments. No statistical difference from the standard microscopy method was found in 75% of the samples (12 of 16). ITS-1 rRNA was detected only in samples containing viable eggs, but the levels were more variable than rDNA levels and ITS-1 rRNA could not be used for quantification. The detection limit of the rDNA-based method was approximately one larvated egg or 90 single-celled eggs; the detection limit for the rRNA-based method was several orders of magnitude higher. The rDNA qPCR method is promising for both research and regulatory applications.

Animals↗
PubMed1997

Detection of Schistosoma mansoni in Biomphalaria using nested PCR.

A nested polymerase chain reaction (PCR) protocol was developed for detecting the presence of Schistosoma mansoni sporocysts in intermediate host snails of the genus Biomphalaria. To accomplish this, rDNA genes encoding the 18S rRNA of S. mansoni and Biomphalaria alexandrina from Egypt were sequenced, as were 18S-encoding genes of the 13-16-R1 and Salvador strains of Biomphalaria glabrata. Based on a comparison of host and parasite sequences, a nested set of PCR primers was designed to allow specific amplification of portions of S. mansoni 18S rDNA. These primers allowed detection of as little as 10 fg of S. mansoni DNA diluted in 100 ng of snail DNA and did not allow amplification of snail 18S sequences. Using nested PCR, the presence of a single S. mansoni sporocyst within an adult snail could be detected at 1 day postexposure. In DNA samples extracted from each of 74 snails of the M-line strain of B. glabrata exposed to from 1 to 10 S. mansoni miracidia for intervals ranging from 1 to 44 days, use of the outside primer pair alone detected the parasite's presence in 51% of the snails, whereas the sequential use of outside and nested primer pairs detected parasites in 92% of the snails. This approach has utility in determining if snails in endemic areas bear prepatent or inactive infections and in assessing the degree of compatibility between local snail and schistosome populations. It will also facilitate studies of resistance of snails to infection.

Animals↗
PubMed1995

The tpa-1 gene of Caenorhabditis elegans encodes two proteins similar to Ca(2+)-independent protein kinase Cs: evidence by complete genomic and complementary DNA sequences of the tpa-1 gene.

The gene tpa-1 on chromosome IV of the nematode Caenorhabditis elegans plays a major and definitive role in the adversary action of tumour-promoting phorbol esters, which induce growth arrest and locomotory distress in the animal. The gene was deduced to code for a protein kinase C (PKC) homologue by molecular cloning. We have now sequenced the complete genomic and complementary DNAs for tpa-1 and have analysed their structural features in detail: (1) tpa-1 spans over 20 kb consisting of eleven exons and ten introns; (2) two different-sized mRNAs are generated from the tpa-1 locus; (3) both mRNAs are trans-spliced to the trans-spliced leader SL1; (4) both mRNAs encode PKC isoforms, which are most similar to Ca(2+)-independent novel PKC0; (5) the two PKC isoforms differ from each other in that the smaller lacks the amino-terminal region of the larger corresponding to the first four exons and a portion of the fifth exon; and (6) three introns are located at; identical positions in the polypeptide sequences aligned between the C. elegans tpa-1 product and a PKC of the fruit fly Drosophila melanogaster.

Amino Acid Sequence↗
PubMedDate not supplied

Echinococcus multilocularis: identification and molecular characterization of a Ral-like small GTP-binding protein.

In mammals, Ral (Ras-like) GTPases have been implicated in the regulation of several cellular key processes such as oncogenic transformation, endocytosis, and actin-cytoskeleton dynamics. Here we provide, for the first time, molecular data on a Ral homologue from a parasitic helminth. We have cloned and characterized the complete cDNA molecule and the chromosomal locus encoding a novel GTP binding protein, EmRal, of the human parasite Echinococcus multilocularis. The encoded protein contained all highly conserved amino acid residues of the protein family at corresponding positions and shared significant sequence homologies with human RalA (53% identity) and RalB (54%). Upon heterologous expression of EmRal in Escherichia coli, the recombinant protein was able to bind GTP, thus indicating functionality of the Echinococcus factor. Using an in vitro prenylation assay, the purified protein was shown to be geranylgernylated, but not farnesylated, in both rabbit reticulocyte and Echinococcus cell extracts. The EmRal mRNA was found to be processed via trans-splicing and, using RT-PCR and virtual Northern blot experiments, expression of the factor could be demonstrated for the larval stages metacestode and protoscolex during an infection of the intermediate host. The data presented herein provide a solid basis for further investigations on Ras-Ral signaling mechanisms in Echinococcus.

Amino Acid Sequence↗
PubMed1997

Molecular characterization of a partial sequence encoding a novel Schistosoma mansoni serine protease.

A PCR strategy using degenerate oligonucleotide primers based upon consensus sequences of the active site of serine proteases yielded a 467 bp fragment from genomic DNA from Schistosoma mansoni cercariae. The sequence presented a continuous open reading frame and the deduced amino acid sequence (156 aa) presented homologies with various serine proteases, in particular the highest percentage identity was observed with a mammalian plasma kallikrein. The expression of this serine protease was studied first at the mRNA level and it was only detected by RT-PCR in cercariae and in adult worms. At the protein level we were able to detect it by Western blotting and by using antigen extracts from metabolically radio-isotope labelled worms. The absence of any positive signal in Northern blot and the detection of the protein suggest that the mRNA has a very short half-life, however the protein may be accumulated in the parasite. The significance of identity with mammalian kallikrein was confirmed by cross-immunoreactivity with a native porcine pancreatic kallikrein. However, no cross-reactivity was observed with S. mansoni elastase, another serine protease. Thus, we suggest that the serine protease described in this paper is a kallikrein-like protease.

Amino Acid Sequence↗
PubMed2003

Analysis and functional classification of transcripts from the nematode Meloidogyne incognita.

BACKGROUND: Plant parasitic nematodes are major pathogens of most crops. Molecular characterization of these species as well as the development of new techniques for control can benefit from genomic approaches. As an entrée to characterizing plant parasitic nematode genomes, we analyzed 5,700 expressed sequence tags (ESTs) from second-stage larvae (L2) of the root-knot nematode Meloidogyne incognita. RESULTS: From these, 1,625 EST clusters were formed and classified by function using the Gene Ontology (GO) hierarchy and the Kyoto KEGG database. L2 larvae, which represent the infective stage of the life cycle before plant invasion, express a diverse array of ligand-binding proteins and abundant cytoskeletal proteins. L2 are structurally similar to Caenorhabditis elegans dauer larva and the presence of transcripts encoding glyoxylate pathway enzymes in the M. incognita clusters suggests that root-knot nematode larvae metabolize lipid stores while in search of a host. Homology to other species was observed in 79% of translated cluster sequences, with the C. elegans genome providing more information than any other source. In addition to identifying putative nematode-specific and Tylenchida-specific genes, sequencing revealed previously uncharacterized horizontal gene transfer candidates in Meloidogyne with high identity to rhizobacterial genes including homologs of nodL acetyltransferase and novel cellulases. CONCLUSIONS: With sequencing from plant parasitic nematodes accelerating, the approaches to transcript characterization described here can be applied to more extensive datasets and also provide a foundation for more complex genome analyses.

Animals↗
PubMed1997

Hexosaminidase in Trichinella spiralis is a single protein with alpha- and beta-subunits catalytic activities.

Beta-N-acetylhexosaminidase is expressed as a single protein in Trichinella spiralis and has catalytic properties similar to the alpha- and beta-subunits of human and mouse isoenzymes A and B. It can hydrolyze the artificial substrates, 4-methylumbelliferyl-beta-D-glucosamine and 4-methylumbelliferyl-beta-D-glucosamine-6-sulphate which are respectively hydrolyzed by the beta- and alpha-subunits. The enzyme is thermostable, has a basic isoelectric point, and thus is similar to the B isoenzyme. Northern blotting experiments indicate that the enzyme is encoded by a single gene. Hexosaminidase from Trichinella spiralis shows that the substrate specificities of alpha- and beta-subunits precede the duplication of their genes.

Animals↗
PubMed1996

Cuticular collagen genes from the parasitic nematode Ostertagia circumcincta.

The nematode cuticle is a multifunctional structure whose roles include exoskeleton and barrier between the animal and its environment. It is an extracellular matrix which consists predominantly of small collagen-like proteins. For those species studied, these cuticular collagens are encoded by a multigene family. In the free living nematode Caenorhabditis elegans, this family has approximately 100 members. Our data indicate a gene family of similar size in the parasitic nematode Ostertagia circumcincta. We have characterised a pair of tandemly duplicated collagen genes from O. circumcincta, colost-1 and colost-2, which we believe to be the direct homologues of col-12 and col-13, a tandemly duplicated pair previously identified in C. elegans. The interspecies comparison of these homologues indicates regions of extreme conservation. We conclude that the gene duplication event that resulted in the creation of col-12 and col-13 in C. elegans is most likely the same duplication that generated colost-1 and colost-2 in O. circumcincta, and thus this particular gene duplication precedes the divergence of the two species. These two nematode species are deeply diverged, O. circumcincta belonging to the order Strongylata and C. elegans to Rhabditata. The ability to identify direct homologues of individual cuticular collagen genes between deeply diverged species provides a powerful method for determining regions of structural importance in these small collagens. Characteristics that are conserved between homologues in divergent species, but not conserved with other members of the multigene family within one species, must relate to the specific function of that particular cuticular collagen.

Amino Acid Sequence↗
PubMed2006

Schistosoma mansoni CBP/p300 has a conserved domain structure and interacts functionally with the nuclear receptor SmFtz-F1.

Metazoan species diversification in general and the adaptation of parasites to their life-style in particular are due, not only to the evolution of different structural or metabolic proteins, but also to changes in the expression patterns of the corresponding genes. In order to explore the conservation/divergence of transcriptional regulation in the platyhelminth parasite Schistosoma mansoni, we are studying the structures and functions of transcriptional mediators. CREB-binding protein (CBP) and p300 are closely related transcriptional coactivators that possess histone acetyltransferase (HAT) activity that can modify chromatin to an active relaxed state. They are also thought to link transcription factors to the basic transcriptional machinery and to act as integrators for different regulatory pathways. Here we describe the cloning and functional characterization of S. mansoni CBP. SmCBP1 comprises 2093 amino acids and displays a conserved modular domain structure. The HAT domain was shown to acetylate histones with a marked activity toward H4. Functional studies showed that SmCBP1 could interact physically with the nuclear receptor SmFtz-F1 and also potentiated its transcriptional activity in the CV-1 cell line. Screening of the EST and genomic sequence databases with the SmCBP1 sequence allowed us to characterize a second CBP gene in S. mansoni. SmCBP2 shows a high degree of sequence identity to SmCBP1, particularly in the HAT domain. Phylogenetic studies show that these peptides are more closely related to each other than to either mammalian CBP or p300, suggesting that they derive from a platyhelminth-specific duplication event. Both genes are expressed at all life-cycle stages, but differences in their relative expression and structural variations suggest that they play distinct roles in schistosome gene regulation.

Acetylation↗