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PubMed2005

The nicotinic acetylcholine receptor gene family of the malaria mosquito, Anopheles gambiae.

Nicotinic acetylcholine receptors (nAChRs) mediate fast cholinergic synaptic transmission in the insect nervous system and are targets of widely selling insecticides. We have identified the nAChR gene family from the genome of the malaria mosquito vector, Anopheles gambiae, to be the second complete insect nAChR gene family described following that of Drosophila melanogaster. Like Drosophila, Anopheles possesses 10 nAChR subunits with orthologous relationships evident between the two insects. Interestingly, the Anopheles orthologues of Dbeta2 and Dbeta3 possess the vicinal cysteines that define alpha subunits. As with Dalpha4 and Dalpha6, the Anopheles orthologues are alternatively spliced at equivalent exons. Reverse transcription-polymerase chain reaction analysis shows that RNA A-to-I editing sites conserved between Dalpha6 of Drosophila and alpha7-2 of the tobacco budworm, Heliothis virescens, are not shared with the equivalent nAChR subunit of Anopheles. Indeed, RNA-editing sites identified in functionally significant regions of Dbeta1, Dalpha5, and Dalpha6 are not conserved in the mosquito orthologues, indicating considerable divergence of RNA molecules targeted for editing within the insect order Diptera. These findings shed further light on the diversity of nAChR subunits and may present a useful basis for the development of improved malaria control agents by enhancing our understanding of a validated mosquito insecticide target.

Alternative Splicing↗

PubMed2002

Analysis of the complete genome sequence of the Hz-1 virus suggests that it is related to members of the Baculoviridae.

We report the complete sequence of a large rod-shaped DNA virus, called the Hz-1 virus. This virus persistently infects the Heliothis zea cell lines. The Hz-1 virus has a double-stranded circular DNA genome of 228,089 bp encoding 154 open reading frames (ORFs) and also expresses a persistence-associated transcript 1, PAT1. The G+C content of the Hz-1 virus genome is 41.8%, with a gene density of one gene per 1.47 kb. Sequence analysis revealed that a 9.6-kb region at 43.6 to 47.8 map units harbors five cellular genes encoding proteins with homology to dUTP pyrophosphatase, matrix metalloproteinase, deoxynucleoside kinase, glycine hydroxymethyltransferase, and ribonucleotide reductase large subunit. Other cellular homologs were also detected dispersed in the viral genome. Several baculovirus homologs were detected in the Hz-1 virus genome. These include PxOrf-70, PxOrf-29, AcOrf-81, AcOrf-96, AcOrf-22, VLF-1, RNA polymerase LEF-8 (orf50), and two structural proteins, p74 and p91. The Hz-1 virus p74 homolog shows high structural conservation with a double transmembrane domain at its C terminus. Phylogenetic analysis of the p74 revealed that the Hz-1 virus is evolutionarily distant from the baculoviruses. Another distinctive feature of the Hz-1 virus genome is a gene that is involved in insect development. However, the remainder of the ORFs (81%) encoded proteins that bear no homology to any known proteins. In conclusion, the sequence differences between the Hz-1 virus and the baculoviruses outnumber the similarities and suggest that the Hz-1 virus may form a new family of viruses distantly related to the Baculoviridae:

Amino Acid Sequence↗

PubMed2005

In silico characterization of the family of PARP-like poly(ADP-ribosyl)transferases (pARTs).

BACKGROUND: ADP-ribosylation is an enzyme-catalyzed posttranslational protein modification in which mono(ADP-ribosyl)transferases (mARTs) and poly(ADP-ribosyl)transferases (pARTs) transfer the ADP-ribose moiety from NAD onto specific amino acid side chains and/or ADP-ribose units on target proteins. RESULTS: Using a combination of database search tools we identified the genes encoding recognizable pART domains in the public genome databases. In humans, the pART family encompasses 17 members. For 16 of these genes, an orthologue exists also in the mouse, rat, and pufferfish. Based on the degree of amino acid sequence similarity in the catalytic domain, conserved intron positions, and fused protein domains, pARTs can be divided into five major subgroups. All six members of groups 1 and 2 contain the H-Y-E trias of amino acid residues found also in the active sites of Diphtheria toxin and Pseudomonas exotoxin A, while the eleven members of groups 3 - 5 carry variations of this motif. The pART catalytic domain is found associated in Lego-like fashion with a variety of domains, including nucleic acid-binding, protein-protein interaction, and ubiquitylation domains. Some of these domain associations appear to be very ancient since they are observed also in insects, fungi, amoebae, and plants. The recently completed genome of the pufferfish T. nigroviridis contains recognizable orthologues for all pARTs except for pART7. The nearly completed albeit still fragmentary chicken genome contains recognizable orthologues for twelve pARTs. Simpler eucaryotes generally contain fewer pARTs: two in the fly D. melanogaster, three each in the mosquito A. gambiae, the nematode C. elegans, and the ascomycete microfungus G. zeae, six in the amoeba E. histolytica, nine in the slime mold D. discoideum, and ten in the cress plant A. thaliana. GenBank contains two pART homologues from the large double stranded DNA viruses Chilo iridescent virus and Bacteriophage Aeh1 and only a single entry (from V. cholerae) showing recognizable homology to the pART-like catalytic domains of Diphtheria toxin and Pseudomonas exotoxin A. CONCLUSION: The pART family, which encompasses 17 members in the human and 16 members in the mouse, can be divided into five subgroups on the basis of sequence similarity, phylogeny, conserved intron positions, and patterns of genetically fused protein domains.

Adenosine Diphosphate↗

PubMed2004

The PhoP-PhoQ two-component regulatory system of Photorhabdus luminescens is essential for virulence in insects.

Photorhabdus luminescens is a symbiont of entomopathogenic nematodes. Analysis of the genome sequence of this organism revealed a homologue of PhoP-PhoQ, a two-component system associated with virulence in intracellular bacterial pathogens. This organism was shown to respond to the availability of environmental magnesium. A mutant with a knockout mutation in the regulatory component of this system (phoP) had no obvious growth defect. It was, however, more motile and more sensitive to antimicrobial peptides than its wild-type parent. Remarkably, the mutation eliminated virulence in an insect model. No insect mortality was observed after injection of a large number of the phoP bacteria, while very small amounts of parental cells killed insect larvae in less than 48 h. At the molecular level, the PhoPQ system mediated Mg(2+)-dependent modifications in lipopolysaccharides and controlled a locus (pbgPE) required for incorporation of 4-aminoarabinose into lipid A. Mg(2+)-regulated gene expression of pbgP1 was absent in the mutant and was restored when phoPQ was complemented in trans. This finding highlights the essential role played by PhoPQ in the virulence of an entomopathogen.

Amino Acid Sequence↗

PubMed2026

A high-quality chromosome-level genome assembly of apple of Peru (Nicandra physalodes).

Nicandra physalodes, a member of the Solanaceae family, is known for its medicinal potential and strong natural insect-repellent properties, which are mainly attributed to its bioactive withanolides and alkaloids. Despite its ecological and pharmacological significance, genomic information for this species has remained limited. Here, we generated a chromosome-level reference genome for N. physalodes based on PacBio high-fidelity (HiFi) long-read sequencing and Hi-C scaffolding. The assembled genome is 933.97 Mb in size, with a contig N50 of 87.37 Mb, and 99.95% (933.54 Mb) of the sequences anchored to 10 pseudochromosomes. Repetitive elements account for 73.06% of the genome, and 27,925 protein-coding genes were predicted, 97.81% of which were functionally annotated. This genomic resource provides a valuable foundation for investigating the genetic basis of specialized metabolite biosynthesis, insect resistance, and environmental adaptation in N. physalodes, as well as for comparative studies within the Solanaceae family.

Genome, Plant↗

PubMed2000

Analysis of Drosophila yellow-B cDNA reveals a new family of proteins related to the royal jelly proteins in the honeybee and to an orphan protein in an unusual bacterium Deinococcus radiodurans.

The yellow locus in Drosophila is involved in both cuticle development and behaviour. However, the function of the encoded protein is unknown. Here we have characterised the sequence and expression pattern of a new Drosophila gene, designated yellow-B, encoding a 453-amino-acid protein that is 57% identical to Yellow. High levels of yellow-B mRNA are present in the larval-pupal stages, but the gene is also expressed in the head. Bioinformatics analysis indicates that the Drosophila genome encodes at least 7 members of the Yellow family distributed among chromosomes 2, 3, and X. The Yellow proteins are related to the Royal Jelly proteins and have no relatives in other non-insect metazoan species. Interestingly, a Yellow-like protein is encoded by the genome of a radiation tolerant bacterium, Deinococcus radiodurans.

Amino Acid Sequence↗

PubMed2004

Gene finding in novel genomes.

BACKGROUND: Computational gene prediction continues to be an important problem, especially for genomes with little experimental data. RESULTS: I introduce the SNAP gene finder which has been designed to be easily adaptable to a variety of genomes. In novel genomes without an appropriate gene finder, I demonstrate that employing a foreign gene finder can produce highly inaccurate results, and that the most compatible parameters may not come from the nearest phylogenetic neighbor. I find that foreign gene finders are more usefully employed to bootstrap parameter estimation and that the resulting parameters can be highly accurate. CONCLUSION: Since gene prediction is sensitive to species-specific parameters, every genome needs a dedicated gene finder.

Animals↗

PubMed1999

Molecular characterization of a new excitatory insect neurotoxin with an analgesic effect on mice from the scorpion Buthus martensi Karsch.

Besides the neurotoxins active on mammals, a new excitatory insect selective toxin with a mice analgesic activity was found and purified from the venom of the scorpion Buthus martensi Karsch (BmK) (Ji, Y.H., Mansuelle, P., Terakawa, S., Kopeyan, C., Yanaihara, N., Hsu, K., Rochat, H., 1996. Toxicon 34, 987; Luo, M.J., Xiong, Y.M., Wang, M., Wang, D.C., Chi, C.W., 1997. Toxicon 35, 723.). This peptide (designated as BmK IT-AP) is composed of 72 amino acid residues. Its primary structure was determined by automated Edman degradation of the N-terminal part of the reduced and S-carboxamidemethylated protein and its lysylendopeptidase degraded fragments. Based on the determined sequence, the gene specific primers were designed and synthesized for 3' and 5' RACE (rapid amplification of cDNA ends). Their partial cDNA fragments obtained by 3' and 5' RACEwere cloned and sequenced and the full length cDNA sequence of BmK IT-AP was then completed by overlapping their two partial cDNA sequences. It encodes a precursor of 90 amino acid residues: a signal peptide of 18 residues and a mature peptide of 72 residues which are consistent with the determined protein sequence of BmK IT-AP. The genomic DNA of the peptide was also amplified by PCR from the scorpion genomic DNA and sequenced, which is a first report on the genomic structure of a scorpion toxin specific for insects. Its sequence revealed an intron of 590 bp inserted in the end part of the signal peptide. The peptide caused a fast excitatory contraction paralysis on house fly larvae. Furthermore, the peptide also showed an obvious analgesic effect on mice, as assayed by using a twisting test model. This effect of BmK IT-AP well characterized at molecular level is first reported among the known scorpion insect neurotoxins.

Amino Acid Sequence↗

PubMed2005

Expression and function of two nicotinic subunits in insect neurons.

Nicotinic acetylcholine receptors (nAChRs) in insects are neuron-specific oligomeric proteins essential for the central transmission of sensory information. Little is known about their subunit composition because it is difficult to express functional insect nAChRs in heterologous systems. As an alternative approach we have examined the native expression of two subunits in neurons of the nicotinic-resistant, tobacco-feeding insect Manduca sexta. Both the alpha-subunit MARA1 and the beta-subunit MARB can be detected by in situ hybridization in the majority of cultured neurons with an overlapping, but not identical, distribution. Changes in intracellular Ca(2+) evoked by nicotinic stimulation are more strongly correlated to the expression of MARA1 than MARB and are independent of cell size. Unlike the previously reported critical role of MARA1 in mediating nicotinic Ca(2+) responses, down-regulation of MARB by RNA interference (RNAi) did not reduce the number of responding neurons or the size of evoked responses, suggesting that additional subunits remain to be identified in Manduca.

Acetylcholine↗

PubMedDate not supplied

[Host specificity of homoxenous trypanosomatids].

Some problems in a correct using of the term "host specificity" for parasitic protozoans and specifically for the trypanosomatids are discussed. Results of investigation the host specificity of the trypanosomatids obtained by traditional methods are summarized. Host specificity data of some insect-associated trypanosomatids based on the identification of parasites by means of molecular methods is discussed. The subjectivity is an imminent distinctive feature of host specificity investigation in parasitic protozoans--trypanosomatids, especially in parasites of insects and plants. There is a vicious circle, when the conclusions about specificity are related with the necessity of taxonomic identification of the parasites during the process of biodiversity and ecological studies. The taxonomic position of parasite is often determined based on a data of observed hosts specificity. This is quite common in cases, when reliable morphological characters are absent, and it indeed takes place in the homoxenous trypanosomatids. The using of molecular markers only allows to reliably identify and compare the parasites, without involving the properly taxonomic data, and finally to make more objective conclusions about their host specificity. A crucial question in this kind of investigation is an obtaining of adequate and wide set of laboratory cultures (isolates) correctly reflecting the diversity of the hosts. It is always necessary to take in attention a possibility of occasional infections, which could misrepresent obtained results. About 50 cultures isolated from different hosts (mostly Hemiptera: Heteroptera) and places (mostly North Russia) have been examined by means of RAPD, UP-PCR, MLEE and cross DNA hybridization. Some of them were placed in rRNA-based molecular phylogeny. As it was found out, none natural groups of homoxenous trypanosomatids (groups of similar genomes) demonstrated a clear preferential distribution on certain insect taxon of any taxonomic rank,--species, genera, family and even order. It is postulated that the host specificity of insect-associated trypanosomatids is extremely wide.

Animals↗

PubMed2004

Biosynthesis of human-type N-glycans in heterologous systems.

Insects, yeasts and plants generate widely different N-glycans, the structures of which differ significantly from those produced by mammals. The processing of the initial Glc2Man9GlcNAc2 oligosaccharide to Man8GlcNAc2 in the endoplasmic reticulum shows significant similarities among these species and with mammals, whereas very different processing events occur in the Golgi compartments. For example, yeasts can add 50 or even more Man residues to Man(8-9)GlcNAc2, whereas insect cells typically remove most or all Man residues to generate paucimannosidic Man(3-1)GlcNAc2N-glycans. Plant cells also remove Man residues to yield Man(4-5)GlcNAc2, with occasional complex GlcNAc or Gal modifications, but often add potentially allergenic beta(1,2)-linked Xyl and, together with insect cells, core alpha(1,3)-linked Fuc residues. However, genomic efforts, such as expression of exogenous glycosyltransferases, have revealed more complex processing capabilities in these hosts that are not usually observed in native cell lines. In addition, metabolic engineering efforts undertaken to modify insect, yeast and plant N-glycan processing pathways have yielded sialylated complex-type N-glycans in insect cells, and galactosylated N-glycans in yeasts and plants, indicating that cell lines can be engineered to produce mammalian-like glycoproteins of potential therapeutic value.

Animals↗

PubMed2003

Construction of two BAC libraries from the wild Mexican diploid potato, Solanum pinnatisectum, and the identification of clones near the late blight and Colorado potato beetle resistance loci.

To facilitate isolation and characterization of disease and insect resistance genes important to potato, two bacterial artificial chromosome (BAC) libraries were constructed from genomic DNA of the Mexican wild diploid species, Solanum pinnatisectum, which carries high levels of resistance to the most important potato pathogen and pest, the late blight and the Colorado potato beetle (CPB). One of the libraries was constructed from the DNA, partially digested with BamHI, and it consists of 40328 clones with an average insert size of 125 kb. The other library was constructed from the DNA partially digested with EcoRI, and it consists of 17280 clones with an average insert size of 135 kb. The two libraries, together, represent approximately six equivalents of the wild potato haploid genome. Both libraries were evaluated for contamination with organellar DNA sequences and were shown to have a very low percentage (0.65-0.91%) of clones derived from the chloroplast genome. High-density filters, prepared from the two libraries, were screened with ten restriction fragment length polymorphism (RFLP) markers linked to the resistance genes for late blight, CPB, Verticillium wilt and potato cyst nematodes, and the gene Sr1 for the self-incompatibility S-locus. Thirty nine positive clones were identified and at least two positive BAC clones were detected for each RFLP marker. Four markers that are linked to the late blight resistance gene Rpi1 hybridized to 14 BAC clones. Fifteen BAC clones were shown to harbor the PPO (polyphenol oxidase) locus for the CPB resistance by three RFLP probes. Two RFLP markers detected five BAC clones that were linked to the Sr1 gene for self-incompatibility. These results agree with the library's predicted extent of coverage of the potato genome, and indicated that the libraries are useful resources for the molecular isolation of disease and insect resistance genes, as well as other economically important genes in the wild potato species. The development of the two potato BAC libraries provides a starting point, and landmarks for BAC contig construction and chromosome walking towards the map-based cloning of agronomically important target genes in the species.

Animals↗

PubMedDate not supplied

Comparison of the effects of pyrokinins and related peptides identified from arthropods on pupariation behaviour in flesh fly (Sarcophaga bullata) larvae (Diptera: Sarcophagidae).

Peptides from the pyrokinin/PBAN family and some structurally related compounds identified in various arthropods were tested for acceleration of puparial contraction in flesh fly larvae. Modifications of behavioural patterns of pupariation were further studied for the active compounds using a behavioural analysis based on the recording of changes in tension of the cuticle. Nine peptides belonging to the pyrokinin/PBAN family (Lem-PK, Pea-PK-5, Lom-PK II, Hez-PBAN, Bom-DH-I), identified in five different insect species, two pyrokinin peptides derived from the genome of Drosophila melanogaster (capa-3, and hugin), and two pyrokinins identified from the white shrimp Penaeus vannamei were very active in the pupariation assay, with threshold doses within the range of 0.1-5.0 pmol larva(-1). High activity was also detected for a related peptide ETH1 from Drosophila. All of these peptides share a C-terminal PRLamide, which is essential and sufficient for the activity. Interestingly, two other structurally related peptides from Drosophila--ETH2 and capa-1--which feature conservative changes (Ile and Val, respectively) at the C-terminal Leu position, were inactive within a physiological range of concentrations. It is clear that the receptor mediating the acceleration of puparial contraction behaviour is sensitive to the introduction of greater steric bulk at the C-terminal Leu position. The peptides that accelerated pupariation showed very similar patterns of muscular and cuticular activity.

Animals↗

PubMed2002

Genome-wide analysis of the odorant-binding protein gene family in Drosophila melanogaster.

Olfaction is of considerable importance to many insects in behaviors critical for survival and reproduction, including location of food sources, selection of mates, recognition of colony con-specifics, and determination of oviposition sites. An ubiquitous, but poorly understood, component of the insect's olfactory system is a group of odorant-binding proteins (OBPs) that are present at high concentrations in the aqueous lymph surrounding the dendrites of olfactory receptor neurons. OBPs are believed to shuttle odorants from the environment to the underlying odorant receptors, for which they could potentially serve as odorant presenters. Here we show that the Drosophila genome carries 51 potential OBP genes, a number comparable to that of its odorant-receptor genes. We find that the majority (73%) of these OBP-like genes occur in clusters of as many as nine genes, in contrast to what has been observed for the Drosophila odorant-receptor genes. Two of the presumptive OBP gene clusters each carries an odorant-receptor gene. We also report an intriguing subfamily of 12 putative OBPs that share a unique C-terminal structure with three conserved cysteines and a conserved proline. Members of this subfamily have not previously been described for any insect. We have performed phylogenetic analyses of the OBP-related proteins in Drosophila as well as other insects, and we discuss the duplication and divergence of the genes for this large family. [The sequence data from this study have been submitted to FlyBase. Annotations for these sequences are available as supplementary material at http://www.genome.org.]

Amino Acid Sequence↗

PubMed2004

Evolutionary conservation and selection of human disease gene orthologs in the rat and mouse genomes.

BACKGROUND: Model organisms have contributed substantially to our understanding of the etiology of human disease as well as having assisted with the development of new treatment modalities. The availability of the human, mouse and, most recently, the rat genome sequences now permit the comprehensive investigation of the rodent orthologs of genes associated with human disease. Here, we investigate whether human disease genes differ significantly from their rodent orthologs with respect to their overall levels of conservation and their rates of evolutionary change. RESULTS: Human disease genes are unevenly distributed among human chromosomes and are highly represented (99.5%) among human-rodent ortholog sets. Differences are revealed in evolutionary conservation and selection between different categories of human disease genes. Although selection appears not to have greatly discriminated between disease and non-disease genes, synonymous substitution rates are significantly higher for disease genes. In neurological and malformation syndrome disease systems, associated genes have evolved slowly whereas genes of the immune, hematological and pulmonary disease systems have changed more rapidly. Amino-acid substitutions associated with human inherited disease occur at sites that are more highly conserved than the average; nevertheless, 15 substituting amino acids associated with human disease were identified as wild-type amino acids in the rat. Rodent orthologs of human trinucleotide repeat-expansion disease genes were found to contain substantially fewer of such repeats. Six human genes that share the same characteristics as triplet repeat-expansion disease-associated genes were identified; although four of these genes are expressed in the brain, none is currently known to be associated with disease. CONCLUSIONS: Most human disease genes have been retained in rodent genomes. Synonymous nucleotide substitutions occur at a higher rate in disease genes, a finding that may reflect increased mutation rates in the chromosomal regions in which disease genes are found. Rodent orthologs associated with neurological function exhibit the greatest evolutionary conservation; this suggests that rodent models of human neurological disease are likely to most faithfully represent human disease processes. However, with regard to neurological triplet repeat expansion-associated human disease genes, the contraction, relative to human, of rodent trinucleotide repeats suggests that rodent loci may not achieve a 'critical repeat threshold' necessary to undergo spontaneous pathological repeat expansions. The identification of six genes in this study that have multiple characteristics associated with repeat expansion-disease genes raises the possibility that not all human loci capable of facilitating neurological disease by repeat expansion have as yet been identified.

Animals↗

PubMed2000

Evidence for phosphorylation and ubiquitinylation of the turnip yellow mosaic virus RNA-dependent RNA polymerase domain expressed in a baculovirus-insect cell system.

All RNA viruses known to date encode an RNA-dependent RNA polymerase (RdRp) that is required for replication of the viral genome. We have expressed and purified the turnip yellow mosaic virus (TYMV) RdRp in insect cells using a recombinant baculovirus, either in its native form, or fused to an hexa-histidine tag. Phosphorylation of the protein was demonstrated by labelling experiments in vivo, as well as phosphatase treatment of the purified protein in vitro. Phospho amino acid analysis and immunoblotting experiments identified serine and threonine residues as being the subject of phosphorylation. Peptide mass mapping using MS analysis of a protein digest revealed that phosphorylation sites are localized within a putative PEST sequence [a sequence rich in proline (P), glutamic acid (E), serine (S) and threonine (T) residues] in the N-terminal region of the protein. Using monoclonal antibodies specific for ubiquitin conjugates, we were able to demonstrate that the TYMV RdRp is conjugated to ubiquitin molecules when expressed in insect cells. These observations suggest that the TYMV RdRp may be processed selectively by the ubiquitin/proteasome degradation system upon phosphorylation of the PEST sequence.

Amino Acid Motifs↗

PubMed2006

Clusters of diverse genes existing as multiple, sequence-variable mosaics in a phytoplasma genome.

Phytoplasmas are cell wall-less prokaryotes living as obligate parasites and pathogens of plants and insects, making them attractive subjects for studies to gain a greater understanding of transkingdom parasitism and pathogenicity. During a study of two phytoplasma genomes, we obtained evidence for previously unreported clustering of genes, pseudogenes, mobile genetic elements, intergenic repeat units, and repetitive extragenic palindromes that occur in multiple, homologous clusters in some phytoplasma genomes. The clusters represent previously unrecognized mosaics, possibly assembled through multiple events of targeted mobile element attack, duplication, recombination, and rearrangement. Multiple clusters could conceivably afford potential for genome reduction through homologous recombination. Differences in the sizes and multiplicity of such clusters possibly account for some of the previously reported but unexplained variations in genome size among closely related phytoplasma strains.

Base Sequence↗

PubMed1983

The gene organisation of a small RNA-containing insect virus: comparison with that of mammalian picornaviruses.

The coding regions of an insect virus, cricket paralysis virus, have been mapped using pactamycin. The results suggest that the genome of this virus functions as a polycistronic mRNA, the structural proteins being encoded by the 5' end of the RNA in an order similar to those of mammalian picornaviruses. High-molecular-weight proteins of unknown function map at the 3' end of the genome.

Animals↗