title: Proteomics informed by transcriptomics for characterising active transposable elements and genome annotation in Aedes aegypti.
abstract: Aedes 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.
  
  
  
  We 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.
  
  
  
  We 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.
authors.affiliation: School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK. K.Maringer@surrey.ac.uk.|Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, USA. K.Maringer@surrey.ac.uk.|Present address: Department of Microbial Sciences, University of Surrey, Guildford, GU2 7XH, UK. K.Maringer@surrey.ac.uk.
authors.forename: Kevin
authors.initials: K
authors.lastname: Maringer
authors.affiliation: School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK.|College of Applied Medical Sciences, Taibah University, Medina, Kingdom of Saudi Arabia.
authors.forename: Amjad
authors.initials: A
authors.lastname: Yousuf
authors.affiliation: School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK.
authors.forename: Kate J
authors.initials: KJ
authors.lastname: Heesom
authors.affiliation: School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK.
authors.forename: Jun
authors.initials: J
authors.lastname: Fan
authors.affiliation: School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK.
authors.forename: David
authors.initials: D
authors.lastname: Lee
authors.affiliation: Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, USA.
authors.forename: Ana
authors.initials: A
authors.lastname: Fernandez-Sesma
authors.affiliation: School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK.
authors.forename: Conrad
authors.initials: C
authors.lastname: Bessant
authors.affiliation: School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK.
authors.forename: David A
authors.initials: DA
authors.lastname: Matthews
authors.affiliation: School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK. Andrew.Davidson@bristol.ac.uk.
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Davidson
mesh_terms: D000330:Aedes / Q000235:genetics / Q000378:metabolism*; D000818:Animals; D002460:Cell Line; D002851:Chromatography, High Pressure Liquid; D020451:Contig Mapping; D004251:DNA Transposable Elements / Q000235:genetics*; D016678:Genome; D019476:Insect Proteins / Q000032:analysis / Q000302:isolation & purification; D020543:Proteome / Q000032:analysis*; D040901:Proteomics / Q000379:methods*; D012313:RNA / Q000302:isolation & purification / Q000378:metabolism; D017423:Sequence Analysis, RNA; D053719:Tandem Mass Spectrometry
chemical_list: D004251:DNA Transposable Elements; D019476:Insect Proteins; D020543:Proteome; D012313:RNA
keywords: Aedes aegypti; Genome annotation; Non-model organism; PIT; Proteomics informed by transcriptomics; Transposon