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

Abstract

Background 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.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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3432-5) contains supplementary material, which is available to authorized users.

The Diversity, Structure, and Function of Heritable Adaptive Immunity Sequences in the Aedes aegypti Genome

“…LTRs show a pronounced peak at the origin, indicating recent activity. This is consistent with reports that LTR-retrotransposon transcripts and proteins are readily detected in Aag2 cells [25]. …”

“…Aag2 cells are known to be persistently infected with cell-fusing agent virus (CFAV; flaviviridae ), and were recently shown to also be persistently infected with Phasi Charoen-like virus (PCLV), a bunyavirus [25]. These viruses constitute available targets for recognition by EVE-derived piRNAs and subsequent processing.…”

“…Whether EVEs integrate into transcriptionally active piRNA clusters, or whether selection drives EVE-containing piRNA clusters to become more active is unknown. However, LTRs (and specifically Ty3 elements) located in piRNA clusters without EVEs produce, on average, more piRNAs per bp than other classes of TEs (Figure S3B,C), likely reflecting the increased LTR activity in Aag2 cells [25]. The regulation of the transcriptional activity of piRNA clusters is mediated by epigenetic changes that respond, in part, to active ping-pong processing of target transcripts in the cytoplasm [40].…”

Rift Valley Fever Virus: Propagation, Quantification, and Storage

“…Other mosquito cell lines such as the A. aegypti AAG2 cell line have also been used in RVFV propagation (Leger et al, 2013). However, the AAG2 culture methods are less defined and the cells are persistently infected with two insect-specific viruses, cell fusing agent virus (a flavivirus) and Phasi Charoen-like virus (a bunyavirus; Maringer et al, 2017). Therefore, we recommend the use of C6/36 cells.…”

Multi-omics Visualization Platform: An extensible Galaxy plug-in for multi-omics data visualization and exploration

“…Galaxy [10] has proven a highly capable platform for meeting the requirements of multi-omic informatics, including proteogenomics, as described by us and others [11][12][13][14][15]. Its amenability to integration of disparate software in a unified, user-friendly environment, along with a variety of useful features including complex workflow creation, provenance tracking and reproducibility, address the challenges of proteogenomics.…”