True Lies: Using Proteomics to Assess the Accuracy of Transcriptome-Based Venomics in Centipedes Uncovers False Positives and Reveals Startling Intraspecific Variation in Scolopendra Subspinipes

Toxins
Jennifer J Smith, Eivind A B Undheim

Abstract

Centipede venoms have emerged as a rich source of novel bioactive compounds. However, most centipede species are commonly considered too small for venom extraction and transcriptomics is likely to be an attractive way of probing the molecular diversity of these venoms. Examining the venom composition of Scolopendra subspinipes, we test the accuracy of this approach. We compared the proteomically determined venom profile with four common toxin transcriptomic toxin annotation approaches: BLAST search against toxins in UniProt, lineage-specific toxins, or species-specific toxins and comparative expression analyses of venom and non-venom producing tissues. This demonstrated that even toxin annotation based on lineage-specific homology searches is prone to substantial errors compared to a proteomic approach. However, combined comparative transcriptomics and phylogenetic analysis of putative toxin families substantially improves annotation accuracy. Furthermore, comparison of the venom composition of S. subspinipes with the closely related S. subspinipes mutilans revealed a surprising lack of overlap. This first insight into the intraspecific venom variability of centipedes contrasts the sequence conservation expected from previous f...Continue Reading

References

Jun 1, 2005·Toxicon : Official Journal of the International Society on Toxinology·Takashi Morita
Jul 1, 2008·Toxicon : Official Journal of the International Society on Toxinology·Marília B MaltaKatia C Barbaro
Oct 29, 2009·BMC Bioinformatics·Mira V Han, Christian M Zmasek
Dec 17, 2009·BMC Bioinformatics·Christiam CamachoThomas L Madden
Jan 25, 2011·Toxicon : Official Journal of the International Society on Toxinology·Eivind A B Undheim, Glenn F King
May 17, 2011·Nature Biotechnology·Manfred G GrabherrAviv Regev
Oct 1, 2011·Nature Methods·Thomas Nordahl PetersenHenrik Nielsen
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Apr 3, 2012·Toxicon : Official Journal of the International Society on Toxinology·Florence JungoSylvain Poux
May 19, 2012·Molecular & Cellular Proteomics : MCP·Shilong YangRen Lai
Nov 15, 2012·Journal of Proteome Research·Zi-Chao LiuYun Zhang
Jan 19, 2013·Molecular Biology and Evolution·Kazutaka Katoh, Daron M Standley
Feb 19, 2013·Molecular Biology and Evolution·Bui Quang MinhArndt von Haeseler
Mar 26, 2013·Cellular and Molecular Life Sciences : CMLS·Jennifer J SmithPaul F Alewood
Apr 4, 2014·Bioinformatics·Anthony M BolgerBjoern Usadel
May 23, 2014·Molecular Biology and Evolution·Eivind A B UndheimBryan G Fry
Aug 5, 2014·Journal of Molecular Biology·Jeet KaliaFrank Bosmans
Sep 7, 2014·Genome Biology and Evolution·Björn M von ReumontChristoph Bleidorn
Nov 6, 2014·Molecular Biology and Evolution·Lam-Tung NguyenBui Quang Minh
Nov 19, 2014·Future Medicinal Chemistry·Sandy S PinedaGlenn F King
Nov 30, 2014·Genome Biology and Evolution·Nathan V WhelanKenneth M Halanych
Dec 3, 2014·Journal of Proteomics·Mingqiang RongRen Lai
Dec 17, 2014·Molecular Biology and Evolution·Inácio L M Junqueira-de-AzevedoNicholas R Casewell
Feb 28, 2015·Toxins·Eivind A B UndheimGlenn F King
Aug 21, 2016·Integrative and Comparative Biology·Ricardo C Rodríguez de la Vega, Tatiana Giraud
Sep 10, 2016·Expert Opinion on Drug Discovery·Eivind A B UndheimGlenn F King
Oct 30, 2016·Toxicon : Official Journal of the International Society on Toxinology·Maria P IkonomopoulouGlenn F King
Dec 3, 2016·Nucleic Acids Research·UNKNOWN The UniProt Consortium
Mar 23, 2017·Proceedings of the National Academy of Sciences of the United States of America·Irène R ChassagnonGlenn F King
May 10, 2017·Nature Methods·Subha KalyaanamoorthyLars S Jermiin
Sep 8, 2017·Expert Review of Proteomics·Samuel D RobinsonGlenn F King

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Citations

Aug 10, 2019·Molecular Biology and Evolution·Ronald A JennerEivind A B Undheim
Nov 28, 2019·Proceedings of the National Academy of Sciences of the United States of America·Nicholas R CasewellSamuel T Turvey
Aug 21, 2020·Proteomics·Andrew A WalkerGlenn F King
May 14, 2020·Proceedings of the National Academy of Sciences of the United States of America·Sandy S PinedaGlenn F King
Jun 24, 2019·Toxicon : Official Journal of the International Society on Toxinology·Schyler A EllsworthDarin R Rokyta
Apr 19, 2021·Briefings in Bioinformatics·Pedro G NachtigallInácio L M Junqueira-de-Azevedo
Aug 8, 2018·Toxicon : Official Journal of the International Society on Toxinology·Micaiah J Ward, Darin R Rokyta
Sep 18, 2018·Journal of Proteome Research·Legana C H W FingerhutIra R Cooke
Aug 21, 2021·Toxicon : Official Journal of the International Society on Toxinology·Jonas KrämerReinhard Predel

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Datasets Mentioned

BETA
PRJNA422449

Software Mentioned

GraphPad
bowtie
Galaxy
MAFFT
SignalP
BLAST
RSEM
Prism
Protein Pilot
Trinity

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