Bioinformatic Approaches to the Identification of Novel Neuropeptide Precursors

Clynen, Elke; Liu, Feng; Husson, Steven; Landuyt, Bart; Hayakawa, Eisuke; Baggerman, Geert; Wets, Geert; Schoofs, Liliane

doi:10.1007/978-1-60761-535-4_25

Cited by 19 publications

(17 citation statements)

References 36 publications

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“…Similarly, the visceral ganglia expressed numerous genes related to its function in the regulation of neurotransmitter release and hormone secretion ( syt7, mrp, syt12, at5g38780, npy, cex-1, sspo, acr-2, takr86C, cmd-1, pcsk2, nAcRalpha, dbh, unc-64 and pin ). Interestingly, in addition to well-characterized neuropeptide encoding genes ( neuropeptide Y [CU983945], PRQFV-amide-related peptides [CU986397], orcokinin-like peptides [AM854447] and pedal peptide [CU988369, CX069323]), some of the non-annotated ganglia-specific contigs were found to encode the precursors of putative novel neuropeptides [CU995163, CU992964, AM868259] that the BLAST tool did not identify, probably due to limited sequence conservation between peptides or their precursors [37]. These putative novel neuropeptides displayed the conventional dibasic (KR, RR) cleavage sites for prohormone convertases and potentially downstream GKR sequencing serving as combined amidation and proteolytic signals.…”

Section: Resultsmentioning

confidence: 99%

Development of a Pacific oyster (Crassostrea gigas) 31,918-feature microarray: identification of reference genes and tissue-enriched expression patterns

et al. 2011

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BackgroundResearch using the Pacific oyster Crassostrea gigas as a model organism has experienced rapid growth in recent years due to the development of high-throughput molecular technologies. As many as 56,268 EST sequences have been sequenced to date, representing a genome-wide resource that can be used for transcriptomic investigations.ResultsIn this paper, we developed a Pacific oyster microarray containing oligonucleotides representing 31,918 transcribed sequences selected from the publicly accessible GigasDatabase. This newly designed microarray was used to study the transcriptome of male and female gonads, mantle, gills, posterior adductor muscle, visceral ganglia, hemocytes, labial palps and digestive gland. Statistical analyses identified genes differentially expressed among tissues and clusters of tissue-enriched genes. These genes reflect major tissue-specific functions at the molecular level, such as tissue formation in the mantle, filtering in the gills and labial palps, and reproduction in the gonads. Hierarchical clustering predicted the involvement of unannotated genes in specific functional pathways such as the insulin/NPY pathway, an important pathway under study in our model species. Microarray data also accurately identified reference genes whose mRNA level appeared stable across all the analyzed tissues. Adp-ribosylation factor 1 (arf1) appeared to be the most robust reference for normalizing gene expression data across different tissues and is therefore proposed as a relevant reference gene for further gene expression analysis in the Pacific oyster.ConclusionsThis study provides a new transcriptomic tool for studies of oyster biology, which will help in the annotation of its genome and which identifies candidate reference genes for gene expression analysis.

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Section: Resultsmentioning

confidence: 99%

Development of a Pacific oyster (Crassostrea gigas) 31,918-feature microarray: identification of reference genes and tissue-enriched expression patterns

et al. 2011

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“…There are several possible peptidomics methods available to provide in these needs, all based on mass spectrometry. The most common tool is a combination of liquid chromatography, tandem mass spectrometry and database mining, which allows the detection and sequencing of low concentrations of neuropeptides from complex mixtures (Clynen et al, 2010b). Mass spectrometry applications led to the discovery of hundreds of neuropeptides.…”

Section: Neuropeptides and Peptidomicsmentioning

confidence: 99%

More than two decades of research on insect neuropeptide GPCRs: an overview

Caers¹,

Verlinden²,

Zels³

et al. 2012

Front. Endocrin.

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155

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This review focuses on the state of the art on neuropeptide receptors in insects. Most of these receptors are G protein-coupled receptors (GPCRs) and are involved in the regulation of virtually all physiological processes during an insect's life. More than 20 years ago a milestone in invertebrate endocrinology was achieved with the characterization of the first insect neuropeptide receptor, i.e., the Drosophila tachykinin-like receptor. However, it took until the release of the Drosophila genome in 2000 that research on neuropeptide receptors boosted. In the last decade a plethora of genomic information of other insect species also became available, leading to a better insight in the functions and evolution of the neuropeptide signaling systems and their intracellular pathways. It became clear that some of these systems are conserved among all insect species, indicating that they fulfill crucial roles in their physiological processes. Meanwhile, other signaling systems seem to be lost in several insect orders or species, suggesting that their actions were superfluous in those insects, or that other neuropeptides have taken over their functions. It is striking that the deorphanization of neuropeptide GPCRs gets much attention, but the subsequent unraveling of the intracellular pathways they elicit, or their physiological functions are often hardly examined. Especially in insects besides Drosophila this information is scarce if not absent. And although great progress made in characterizing neuropeptide signaling systems, even in Drosophila several predicted neuropeptide receptors remain orphan, awaiting for their endogenous ligand to be determined. The present review gives a précis of the insect neuropeptide receptor research of the last two decades. But it has to be emphasized that the work done so far is only the tip of the iceberg and our comprehensive understanding of these important signaling systems will still increase substantially in the coming years.

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“…Nowadays, in many insect species, neuropeptides are identified either by a combination of well-developed bioinformatics prediction tools and de novo sequencing or mass match approaches (Southey et al 2006;Liu et al 2006aLiu et al , 2006bLiu et al , 2008Amare and Sweedler 2007;Southey et al 2008;Clynen et al 2010a).…”

Section: Peptidomicsmentioning

confidence: 99%

Insect omics research coming of age¹This review is part of a virtual symposium on recent advances in understanding a variety of complex regulatory processes in insect physiology and endocrinology, including development, metabolism, cold hardiness, food intake and digestion, and diuresis, through the use of omics technologies in the postgenomic era.

et al. 2012

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As more and more insect genomes are fully sequenced and annotated, omics technologies, including transcriptomic, proteomic, peptidomics, and metobolomic profiling, as well as bioinformatics, can be used to exploit this huge amount of sequence information for the study of different biological aspects of insect model organisms. Omics experiments are an elegant way to deliver candidate genes, the function of which can be further explored by genetic tools for functional inactivation or overexpression of the genes of interest. Such tools include mainly RNA interference and are currently being developed in diverse insect species. In this manuscript, we have reviewed how omics technologies were integrated and applied in insect biology.Résumé : À mesure que de plus en plus de génomes d'insectes sont complètement séquencés et annotés, les technologies « omiques », en particulier la transcriptomique, la protéomique, la peptidomique et le profilage métobolomique, de même que la bioinformatique, peuvent servir à exploiter cet immense quantité d'information séquencée pour l'étude de différents aspects biologiques des organismes modèles entomologiques. Les expériences omiques représentent une voie élégante pour fournir des gènes candidats dont la fonction peut être encore explorée plus avant à l'aide des outils génétiques d'inactivation fonctionnelle ou de surexpression des gènes retenus. Ces outils comprennent surtout l'ARN interférent et sont en train d'être mis au point pour diverses espèces d'insectes. Nous passons en revue dans notre présentation comment les technologies omiques ont été intégrées dans la biologie des insectes et comment on les a utilisées.

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Bioinformatic Approaches to the Identification of Novel Neuropeptide Precursors

Cited by 19 publications

References 36 publications

Development of a Pacific oyster (Crassostrea gigas) 31,918-feature microarray: identification of reference genes and tissue-enriched expression patterns

Development of a Pacific oyster (Crassostrea gigas) 31,918-feature microarray: identification of reference genes and tissue-enriched expression patterns

More than two decades of research on insect neuropeptide GPCRs: an overview

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