Dataset Information

Proteomics Informed by Transcriptomics for Characterising Active Transposable Elements and Genome Annotation in Aedes aegypti

ABSTRACT: The incomplete genome annotation of non-model organisms hampers molecular and proteomic studies. Proteomics informed by transcriptomics (PIT) is suited to non-model organisms because peptides are identified using transcriptomic, not genomic, data. Aedes aegypti is the mosquito vector for the (re-)emerging dengue, chikungunya, yellow fever and Zika viruses. An Ae. aegypti genome sequence is available, however experimental evidence for >90% of the Ae. aegypti proteome or the activity of transposable elements (TEs) that constitute 50% of the Ae. aegypti genome is lacking. We used PIT to characterise the proteome of the Aedes aegypti derived cell line Aag2. Hotspots of incomplete genome annotation were identified which are not explained by poor sequence and assembly quality. We developed criteria for the characterisation of proteomically active TEs and demonstrate that protein expression does not correlate with a TE’s genomic abundance. Finally, we identify Phasi Charoen-like virus as an unrecognised contaminant of Aag2 cells. We therefore present the first proteomic characterisation of mobile genetic elements, and provide proof-of-principle that PIT can evaluate a genome’s annotation to guide annotation efforts.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Aedes Aegypti Aegypti

TISSUE(S): Cell Culture, Early Embryonic Cell

SUBMITTER: Andrew Davidson

LAB HEAD: Andrew Davidson

PROVIDER: PXD003799 | Pride | 2017-02-15

REPOSITORIES: pride

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

Maringer Kevin K Yousuf Amjad A Heesom Kate J KJ Fan Jun J Lee David D Fernandez-Sesma Ana A Bessant Conrad C Matthews David A DA Davidson Andrew D AD

BMC genomics 20170119 1

<h4>Background</h4>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 organ ...[more]

PMID: 28103802

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Project description:Globally invasive Aedes aegypti mosquitoes disseminate numerous arboviruses that impact human health. One promising method to control Ae. aegypti populations is transinfection with the intracellular bacterium Wolbachia pipientis, a symbiont that naturally infects ~40-52% of insects but is normally absent from Ae. aegypti. Transinfection of Ae. aegypti with the wMel Wolbachia strain induces cytoplasmic incompatibility (CI), allowing infected individuals to rapidly invade native populations. Further, wMel Wolbachia-infected females display refractoriness to medically relevant arboviruses. Thus, wMel Wolbachia-infected Ae. aegypti are being released in several areas to replace native populations, thereby suppressing disease transmission by this species. Wolbachia is reported to have minimal effects on Ae. aegypti fertility, but its influence on other reproductive processes is unknown. Female insects undergo several post-mating physiological and behavioral changes required for optimal fertility. Post-mating responses (PMRs) in female insects are typically elicited by receipt of male seminal fluid proteins (SFPs) transferred with sperm during mating, but can be modified by other factors, such as adult age, nutritional status, and microbiome composition. To assess how Wolbachia infection influences Ae. aegypti female PMRs, we collected wMel Wolbachia-infected Ae. aegypti from the field in Medellín, Colombia and introduced the bacterium into our laboratory strain. We found that Wolbachia influences female fecundity, fertility, and re-mating incidence. Further, we observed that Wolbachia significantly extends longevity of virgin females. Changes in female PMRs are not due to defects in sperm transfer by infected males, or sperm storage by infected females. Using proteomic methods to examine the seminal proteome of infected males, we found that Wolbachia infection has a moderate effect on SFP composition. However, we identified 125 Wolbachia proteins that are paternally transferred to females by infected males. Surprisingly, the CI factor proteins (Cifs), were not detected in the ejaculates of Wolbachia-infected males. Our findings indicate that Wolbachia infection of Ae. aegypti alters female post-mating responses, potentially influencing control programs that utilize Wolbachia-infected individuals.

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