Transcriptome and Peptidome Characterisation of the Main Neuropeptides and Peptidic Hormones of a Euphausiid: The Ice Krill, Euphausia crystallorophias

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Abstract

Background

The Ice krill, Euphausia crystallorophias is one of the species at the base of the Southern Ocean food chain. Given their significant contribution to the biomass of the Southern Ocean, it is vitally important to gain a better understanding of their physiology and, in particular, anticipate their responses to climate change effects in the warming seas around Antarctica.

Methodology/Principal Findings

Illumina sequencing was used to produce a transcriptome of the ice krill. Analysis of the assembled contigs via two different methods, produced 36 new pre-pro-peptides, coding for 61 neuropeptides or peptide hormones belonging to the following families: Allatostatins (A, B et C), Bursicon (α and β), Crustacean Hyperglycemic Hormones (CHH and MIH/VIHs), Crustacean Cardioactive Peptide (CCAP), Corazonin, Diuretic Hormones (DH), the Eclosion Hormone (EH), Neuroparsin, Neuropeptide F (NPF), small Neuropeptide F (sNPF), Pigment Dispersing Hormone (PDH), Red Pigment Concentrating Hormone (RPCH) and finally Tachykinin. LC/MS/MS proteomics was also carried out on eyestalk extracts, which are the major site of neuropeptide synthesis in decapod crustaceans. Results confirmed the presence of six neuropeptides and six precursor-related peptides previously identified in the transcriptome analyses.

Conclusions

This study represents the first comprehensive analysis of neuropeptide hormones in a Eucarida non-decapod Malacostraca, several of which are described for the first time in a non-decapod crustacean. Additionally, there is a potential expansion of PDH and Neuropeptide F family members, which may reflect certain life history traits such as circadian rhythms associated with diurnal migrations and also the confirmation via mass spectrometry of several novel pre-pro-peptides, of unknown function. Knowledge of these essential hormones provides a vital framework for understanding the physiological response of this key Southern Ocean species to climate change and provides a valuable resource for studies into the molecular phylogeny of these organisms and the evolution of neuropeptide hormones.

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Identification and removal of ribosomal RNA sequences from metatranscriptomes

Robert Schmieder, Yan Wei Lim, Robert Edwards (2011)

Summary: Here, we present riboPicker, a robust framework for the rapid, automated identification and removal of ribosomal RNA sequences from metatranscriptomic datasets. The results can be exported for subsequent analysis, and the databases used for the web-based version are updated on a regular basis. riboPicker categorizes rRNA-like sequences and provides graphical visualizations and tabular outputs of ribosomal coverage, alignment results and taxonomic classifications. Availability and implementation: This open-source application was implemented in Perl and can be used as stand-alone version or accessed online through a user-friendly web interface. The source code, user help and additional information is available at http://ribopicker.sourceforge.net/. Contact: rschmied@sciences.sdsu.edu; rschmied@sciences.sdsu.edu Supplementary information: Supplementary data are available at Bioinformatics online.

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Genomics, transcriptomics, and peptidomics of neuropeptides and protein hormones in the red flour beetle Tribolium castaneum.

Bin Li, Reinhard Predel, Susanne Neupert … (2008)

Neuropeptides and protein hormones are ancient molecules that mediate cell-to-cell communication. The whole genome sequence from the red flour beetle Tribolium castaneum, along with those from other insect species, provides an opportunity to study the evolution of the genes encoding neuropeptide and protein hormones. We identified 41 of these genes in the Tribolium genome by using a combination of bioinformatic and peptidomic approaches. These genes encode >80 mature neuropeptides and protein hormones, 49 peptides of which were experimentally identified by peptidomics of the central nervous system and other neuroendocrine organs. Twenty-three genes have orthologs in Drosophila melanogaster: Sixteen genes in five different groups are likely the result of recent gene expansions during beetle evolution. These five groups contain peptides related to antidiuretic factor-b (ADF-b), CRF-like diuretic hormone (DH37 and DH47 of Tribolium), adipokinetic hormone (AKH), eclosion hormone, and insulin-like peptide. In addition, we found a gene encoding an arginine-vasopressin-like (AVPL) peptide and one for its receptor. Both genes occur only in Tribolium and not in other holometabolous insects with a sequenced genome. The presence of many additional osmoregulatory peptides in Tribolium agrees well with its ability to live in very dry surroundings. In contrast to these extra genes, there are at least nine neuropeptide genes missing in Tribolium, including the genes encoding the prepropeptides for corazonin, kinin, and allatostatin-A. The cognate receptor genes for these three peptides also appear to be absent in the Tribolium genome. Our analysis of Tribolium indicates that, during insect evolution, genes for neuropeptides and protein hormones are often duplicated or lost.

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A comparative review of short and long neuropeptide F signaling in invertebrates: Any similarities to vertebrate neuropeptide Y signaling?

Dick Nässel, Christian Wegener (2011)

Neuropeptides referred to as neuropeptide F (NPF) and short neuropeptide F (sNPF) have been identified in numerous invertebrate species. Sequence information has expanded tremendously due to recent genome sequencing and EST projects. Analysis of sequences of the peptides and prepropeptides strongly suggest that NPFs and sNPFs are not closely related. However, the NPFs are likely to be ancestrally related to the vertebrate family of neuropeptide Y (NPY) peptides. Peptide diversification may have been accomplished by different mechanisms in NPFs and sNPFs; in the former by gene duplications followed by diversification and in the sNPFs by internal duplications resulting in paracopies of peptides. We discuss the distribution and functions of NPFs and their receptors in several model invertebrates. Signaling with sNPF, however, has been investigated mainly in insects, especially in Drosophila. Both in invertebrates and in mammals NPF/NPY play roles in feeding, metabolism, reproduction and stress responses. Several other NPF functions have been studied in Drosophila that may be shared with mammals. In Drosophila sNPFs are widely distributed in numerous neurons of the CNS and some gut endocrines and their functions may be truly pleiotropic. Peptide distribution and experiments suggest roles of sNPF in feeding and growth, stress responses, modulation of locomotion and olfactory inputs, hormone release, as well as learning and memory. Available data indicate that NPF and sNPF signaling systems are distinct and not likely to play redundant roles. Copyright © 2011 Elsevier Inc. All rights reserved.

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Author and article information

Contributors

Frederique Lisacek: Role: Editor

Journal

Journal ID (nlm-ta): PLoS One

Journal ID (iso-abbrev): PLoS ONE

Journal ID (publisher-id): plos

Journal ID (pmc): plosone

Title: PLoS ONE

Publisher: Public Library of Science (San Francisco, USA )

ISSN (Electronic): 1932-6203

Publication date Collection: 2013

Publication date (Electronic): 21 August 2013

Volume: 8

Issue: 8

Electronic Location Identifier: e71609

Affiliations

[1 ]UPMC University of Paris 06, UMR 7144 CNRS, Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France

[2 ]UPMC University of Paris 06, FR 2424 CNRS, ABiMS, Analysis and Bioinformatics for Marine Science, Station Biologique de Roscoff, Roscoff, France

[3 ]UPMC University of Paris 06, UMR 7150 CNRS, Mer et Santé, Station Biologique de Roscoff, Roscoff, France

[4 ]Centre National de la Recherche Scientifique, UMR 7144, Station Biologique de Roscoff, Roscoff, France

[5 ]Centre National de la Recherche Scientifique, UMR 7150, Station Biologique de Roscoff, Roscoff, France

[6 ]Université Européenne de Bretagne, UEB, France

[7 ]University of Caen Basse Normandie, FRE 3484 CNRS, Biologie des Mollusques Marins et des Ecosystèmes Associés, Caen, France

[8 ]University of Caen Basse Normandie, Plateforme PROTEOGEN, Caen, France, SF ICORE 4206

[9 ]British Antarctic Survey, Natural Environment Research Council, High Cross, Cambridge, United Kingdom

Swiss Institute of Bioinformatics, Switzerland

Author notes

* E-mail: jean-yves.toullec@ 123456sb-roscoff.fr

Competing Interests: The authors have declared that no competing interests exist.

Conceived and designed the experiments: JYT JH. Performed the experiments: JYT BB KC JH. Analyzed the data: JYT EC CO MAST MSC. Contributed reagents/materials/analysis tools: JYT EC BB JH. Wrote the paper: JYT MSC EC CO.

Article

Publisher ID: PONE-D-13-07312

DOI: 10.1371/journal.pone.0071609

PMC ID: 3749230

PubMed ID: 23990964

SO-VID: 376a4629-9c74-4ea5-835c-6b18d88cc4c3

License:

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

History

Date received : 15 February 2013

Date accepted : 1 July 2013

Page count

Pages: 20

Funding

KC received a PhD grant by the Émergence-UPMC 2011 research program and the «Région Bretagne». JYT benefits from funding provided by Institut Paul Emile Victor (KREVET program) and also by la Région Bretagne (SAD-1 – DRAKAR program). MSC and MAST were funded by Natural Environment Research Council core funding to the British Antarctic Survey. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.