Large scale RNAi screen in Tribolium reveals novel target genes for pest control and the proteasome as prime target.
BACKGROUND
Insect pest control is challenged by insecticide resistance and negative impact on ecology and health. One promising pest specific alternative is the generation of transgenic plants, which express double stranded RNAs targeting essential genes of a pest species. Upon feeding, the dsRNA induces gene silencing in the pest resulting in its death. However, the identification of efficient RNAi target genes remains a major challenge as genomic tools and breeding capacity is limited in most pest insects impeding whole-animal-high-throughput-screening.


RESULTS
We use the red flour beetle Tribolium castaneum as a screening platform in order to identify the most efficient RNAi target genes. From about 5,000 randomly screened genes of the iBeetle RNAi screen we identify 11 novel and highly efficient RNAi targets. Our data allowed us to determine GO term combinations that are predictive for efficient RNAi target genes with proteasomal genes being most predictive. Finally, we show that RNAi target genes do not appear to act synergistically and that protein sequence conservation does not correlate with the number of potential off target sites.


CONCLUSIONS
Our results will aid the identification of RNAi target genes in many pest species by providing a manageable number of excellent candidate genes to be tested and the proteasome as prime target. Further, the identified GO term combinations will help to identify efficient target genes from organ specific transcriptomes. Our off target analysis is relevant for the sequence selection used in transgenic plants.
Johann-Friedrich-Blumenbach-Institut, GZMB, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany. julia.ulrich@biologie.uni-goettingen.de.
Julia
J
Ulrich
Institut für Entwicklungsbiologie, Universität zu Köln, Zülpicher Straße 47b, 50674, Cologne, Germany. daovananh.bio@gmail.com.
Van Anh
VA
Dao
Department Biologie, Entwicklungsbiologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstraße 5, 91058, Erlangen, Germany. majumdar.upalparna@gmail.com.
Upalparna
U
Majumdar
Johann-Friedrich-Blumenbach-Institut, GZMB, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany. christian.schmitt-engel@gmx.de.
Christian
C
Schmitt-Engel
Johann-Friedrich-Blumenbach-Institut, GZMB, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany. Jonas_Schwirz@web.de.
Jonas
J
Schwirz
Department Biologie, Entwicklungsbiologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstraße 5, 91058, Erlangen, Germany. dorothea.schultheis@gmx.de.
Dorothea
D
Schultheis
Department Biologie, Entwicklungsbiologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstraße 5, 91058, Erlangen, Germany. nadi.stroehlein@fau.de.
Nadi
N
Ströhlein
Department Biologie, Entwicklungsbiologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstraße 5, 91058, Erlangen, Germany. Nicole.Troelenberg@gmx.de.
Nicole
N
Troelenberg
Johann-Friedrich-Blumenbach-Institut, GZMB, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany. DaniCory@aol.com.
Daniela
D
Grossmann
Department Biologie, Entwicklungsbiologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstraße 5, 91058, Erlangen, Germany. trichter@biologie.uni-erlangen.de.
Tobias
T
Richter
Johann-Friedrich-Blumenbach-Institut, GZMB, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany. juergen.doenitz@ibeetle-base.uni-goettingen.de.
Jürgen
J
Dönitz
Institut für Mathematik und Informatik, Ernst Moritz Arndt Universität Greifswald, Walther-Rathenau-Straße 47, 17487, Greifswald, Germany. lizzy.gerischer@gmail.com.
Lizzy
L
Gerischer
Institut für Biologie, Neurobiologie, Freie Universität Berlin, Königin-Luise-Str. 28/30, 14195, Berlin, Germany. gerleb@zedat.fu-berlin.de.
Gérard
G
Leboulle
Institut für Phytopathologie und Angewandte Zoologie, Justus-Liebig-Universität Gießen, Heinrich-Buff-Ring 26-32, D-35392, Gießen, Germany. Andreas.Vilcinskas@agrar.uni-giessen.de.
Andreas
A
Vilcinskas
Institut für Mathematik und Informatik, Ernst Moritz Arndt Universität Greifswald, Walther-Rathenau-Straße 47, 17487, Greifswald, Germany. mario.stanke@uni-greifswald.de.
Mario
M
Stanke
Johann-Friedrich-Blumenbach-Institut, GZMB, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany. gbucher1@uni-goettingen.de.
Gregor
G
Bucher
D000818:Animals; D001483:Base Sequence; D016000:Cluster Analysis; D017124:Conserved Sequence; D063990:Gene Ontology; D017344:Genes, Insect; D010572:Pest Control, Biological; D046988:Proteasome Endopeptidase Complex / Q000378:metabolism*; D034622:RNA Interference; D014231:Tribolium / Q000235:genetics*
D046988:Proteasome Endopeptidase Complex