Proteomics informed by transcriptomics for characterising active transposable elements and genome annotation in Aedes aegypti

BMC Genomics

Research Article

Ana Fernandez-Sesma¹  Kate J. Heesom²  Jun Fan³  Conrad Bessant³  Andrew D. Davidson⁴  David Lee⁴  David A. Matthews⁴  Amjad Yousuf⁵  Kevin Maringer⁶ 

[1] Department of Microbiology, Icahn School of Medicine at Mount Sinai, 10029, New York, NY, USA;School of Biochemistry, University of Bristol, BS8 1TD, Bristol, UK;School of Biological and Chemical Sciences, Queen Mary University of London, E1 4NS, London, UK;School of Cellular and Molecular Medicine, University of Bristol, BS8 1TD, Bristol, UK;School of Cellular and Molecular Medicine, University of Bristol, BS8 1TD, Bristol, UK;College of Applied Medical Sciences, Taibah University, Medina, Kingdom of Saudi Arabia;School of Cellular and Molecular Medicine, University of Bristol, BS8 1TD, Bristol, UK;Department of Microbiology, Icahn School of Medicine at Mount Sinai, 10029, New York, NY, USA;Present address: Department of Microbial Sciences, University of Surrey, GU2 7XH, Guildford, UK;

关键词: Aedes aegypti;    Genome annotation;    Non-model organism;    PIT;    Proteomics informed by transcriptomics;    Transposon;   

DOI  :  10.1186/s12864-016-3432-5

 received in 2016-06-22, accepted in 2016-12-19,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundAedes aegypti is a vector for the (re-)emerging human pathogens dengue, chikungunya, yellow fever and Zika viruses. Almost half of the Ae. aegypti genome is comprised of transposable elements (TEs). Transposons have been linked to diverse cellular processes, including the establishment of viral persistence in insects, an essential step in the transmission of vector-borne viruses. However, up until now it has not been possible to study the overall proteome derived from an organism’s mobile genetic elements, partly due to the highly divergent nature of TEs. Furthermore, as for many non-model organisms, incomplete genome annotation has hampered proteomic studies on Ae. aegypti.ResultsWe analysed the Ae. aegypti proteome using our new proteomics informed by transcriptomics (PIT) technique, which bypasses the need for genome annotation by identifying proteins through matched transcriptomic (rather than genomic) data. Our data vastly increase the number of experimentally confirmed Ae. aegypti proteins. The PIT analysis also identified hotspots of incomplete genome annotation, and showed that poor sequence and assembly quality do not explain all annotation gaps. Finally, in a proof-of-principle study, we developed criteria for the characterisation of proteomically active TEs. Protein expression did not correlate with a TE’s genomic abundance at different levels of classification. Most notably, long terminal repeat (LTR) retrotransposons were markedly enriched compared to other elements. PIT was superior to ‘conventional’ proteomic approaches in both our transposon and genome annotation analyses.ConclusionsWe present the first proteomic characterisation of an organism’s repertoire of mobile genetic elements, which will open new avenues of research into the function of transposon proteins in health and disease. Furthermore, our study provides a proof-of-concept that PIT can be used to evaluate a genome’s annotation to guide annotation efforts which has the potential to improve the efficiency of annotation projects in non-model organisms. PIT therefore represents a valuable new tool to study the biology of the important vector species Ae. aegypti, including its role in transmitting emerging viruses of global public health concern.

【 授权许可】

CC BY   
© The Author(s). 2017