Gene duplications are extensive and contribute significantly to the toxic proteome of nematocysts isolated from Acropora digitifera (Cnidaria: Anthozoa: Scleractinia)

BMC Genomics

Research Article

Simon R. Dunn¹  Adrian Jaimes-Becerra²  André C. Morandini²  Antonio C. Marques³  Ranko Gacesa⁴  Paul F. Long⁵  Andrew J. Weston⁶  Ray Chung⁷  Malcolm Ward⁷  Antonio Starcevic⁸  Daslav Hranueli⁸ 

[1] Coral Reefs Ecosystems Laboratory, School of Biological Sciences, The University of Queensland, 4072, St. Lucia, QLD, Australia;Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, Rua Matao, Trav. 14, 101, 05508-090, São Paulo, SP, Brazil;Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, Rua Matao, Trav. 14, 101, 05508-090, São Paulo, SP, Brazil;Centro de Biologia Marinha, Universidade de São Paulo, Rodovia Manoel Hypólito do Rego, km. 131,5, 11600-000, São Sebastião, Brazil;Institute of Pharmaceutical Science, King’s College London, 150 Stamford Street, SE1 9NH, London, UK;Institute of Pharmaceutical Science, King’s College London, 150 Stamford Street, SE1 9NH, London, UK;Department of Chemistry, King’s College London, Strand, WC2R 2LS, London, UK;Brazil Institute, King’s College London, Strand, WC2R 2LS, London, UK;Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, Av. Prof. Lineu Prestes, 580, B16, 05508-000, São Paulo, SP, Brazil;Mass Spectrometry Laboratory, UCL School of Pharmacy, 29/39 Brunswick Square, WC1N 1AX, London, UK;Proteomics Facility, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, 16 De Crespigny Park, SE5 8AF, London, UK;Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000, Zagreb, Croatia;

关键词: Coral;    Nematocyst;    Venom;    Proteome;    Evolution;    Hidden Markov model (HMM);   

DOI  :  10.1186/s12864-015-1976-4

 received in 2015-07-22, accepted in 2015-10-03,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundGene duplication followed by adaptive selection is a well-accepted process leading to toxin diversification in venoms. However, emergent genomic, transcriptomic and proteomic evidence now challenges this role to be at best equivocal to other processess . Cnidaria are arguably the most ancient phylum of the extant metazoa that are venomous and such provide a definitive ancestral anchor to examine the evolution of this trait.MethodsHere we compare predicted toxins from the translated genome of the coral Acropora digitifera to putative toxins revealed by proteomic analysis of soluble proteins discharged from nematocysts, to determine the extent to which gene duplications contribute to venom innovation in this reef-building coral species. A new bioinformatics tool called HHCompare was developed to detect potential gene duplications in the genomic data, which is made freely available (https://github.com/rgacesa/HHCompare).ResultsA total of 55 potential toxin encoding genes could be predicted from the A. digitifera genome, of which 36 (65 %) had likely arisen by gene duplication as evinced using the HHCompare tool and verified using two standard phylogeny methods. Surprisingly, only 22 % (12/55) of the potential toxin repertoire could be detected following rigorous proteomic analysis, for which only half (6/12) of the toxin proteome could be accounted for as peptides encoded by the gene duplicates. Biological activities of these toxins are dominatedby putative phospholipases and toxic peptidases.ConclusionsGene expansions in A. digitifera venom are the most extensive yet described in any venomous animal, and gene duplication plays a significant role leading to toxin diversification in this coral species. Since such low numbers of toxins were detected in the proteome, it is unlikely that the venom is evolving rapidly by prey-driven positive natural selection. Rather we contend that the venom has a defensive role deterring predation or harm from interspecific competition and overgrowth by fouling organisms. Factors influencing translation of toxin encoding genes perhaps warrants more profound experimental consideration.

【 授权许可】

CC BY   
© Gacesa et al. 2015