TEXT S7: RNAi GENES
Shu Tao, Monica C. Muñoz-Torres, and Christine G. Elsik
Department of Biology, Georgetown University, Washington, DC, United States of America
The RNA interference (RNAi) pathway [1,2] is broadly defined as a doublestranded RNA (dsRNA)-mediated process through which expression of target RNAs
(e.g., mRNA, transposon/retrotransposon or other types of transcripts) are inhibited by
transcript cleavage or translational repression. These can be categorized into the
microRNA (miRNA) pathway, small interfering RNA (siRNA) pathway and piwiinteracting RNA (piRNA) pathway depending on the source of dsRNA molecules and
the type of transcripts to be targeted. Based on the manual annotation results of RNAi
pathway genes, this pathway seems to be intact in leaf-cutter ant Atta cephalotes.
A total of 29 RNAi pathway-related genes have been manually annotated in Atta
cephalotes, including almost all the genes potentially involved in stepwise processing
and normal functioning of miRNAs, siRNAs and piRNAs. All those genes occur as a
single copy except Loquacious (Loq), which seems to be duplicated in Atta cephalotes.
The two Loq copies have three and two dsRNA binding domains (dsRBDs),
respectively, as indicated by the InterProScan [3] analysis. The biological function of
these two Loq copies remains to be investigated, and it could be possible that the
difference in the number of dsRBDs would determine their distinct involvement in
miRNA or siRNA pathway.
Noticeably, not all the piRNA pathway-related genes in Drosophila melanogaster
are present in Atta cephalotes. This might be due either to the long evolutionary
distance (around 350 million years [4]) between Diptera and Hymenoptera, which
makes sequence homology analysis an ineffective method for orthologous gene
identification, or to lineage-specific gene loss during the evolutionary history of Atta
cephalotes. The piRNA pathway related genes absent in the current manual annotation
include Krimp (Krimper), which encodes a Tudor-domain protein that has very
pronounced impact on piRNA levels in germline compartments of the Drosophila ovary
[5], and Zuc (Zucchini) and Squ (Squash), each encoding a putative nuclease required
for the production of rasiRNA (repeat-associated siRNA, a subclass of piRNA) in the
Drosophila germline [6]. Thanks to a closer phylogenetic relationship within the
Hymenopterta, as more genes from Apis mellifera and Nasonia vitripennis become
available and curated, they will be of help to further annotate genes in different species
of ants.
References
1. Meister G, Tuschl T (2004) Mechanisms of gene silencing by double-stranded RNA.
Nature 431: 343.
2. Hannon GJ (2002) RNA interference. Nature 418: 244.
3. Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, et al. (2005) InterProScan:
protein domains identifier. Nucleic Acids Research 33: W116.
4. Douzery EJP, Snell EA, Bapteste E, Delsuc Fdr, Philippe H (2004) The timing of
eukaryotic evolution: Does a relaxed molecular clock reconcile proteins and
fossils? Proceedings of the National Academy of Sciences of the United States of
America 101: 15386.
5. Malone CD, Brennecke J, Dus M, Stark A, McCombie WR, et al. (2009) Specialized
piRNA Pathways Act in Germline and Somatic Tissues of the Drosophila Ovary.
Cell 137: 522.
6. Pane A, Wehr K, Schüpbach T (2007) zucchini and squash Encode Two Putative
Nucleases Required for rasiRNA Production in the Drosophila Germline.
Developmental cell 12: 851.