Experimental increase in fecundity causes upregulation of fecundity and body maintenance genes in the fat body of ant queens
Foitzik, Susanne (2021), Experimental increase in fecundity causes upregulation of fecundity and body maintenance genes in the fat body of ant queens, Dryad, Dataset, https://doi.org/10.5061/dryad.sxksn0322
In most organisms, fecundity and longevity are negatively associated and the molecular regulation of these two life history traits is highly interconnected. In addition, nutrient intake often has opposing effects on lifespan and reproduction. In contrast to solitary insects, the main reproductive individual of social hymenopterans, the queen, is also the most long-lived. During development, queen larvae are well-nourished, but we are only beginning to understand the impact of nutrition on the queens’ adult life and the molecular regulation and connectivity of fecundity and longevity. Here, we used two experimental manipulations to alter queen fecundity in the ant Temnothorax rugatulus and investigated associated changes in fat body gene expression. Egg removal triggered a fecundity increase, leading to expression changes in genes with functions in fecundity such as oogenesis and body maintenance. Dietary restriction lowered the egg production of queens and altered the expression of genes linked to autophagy, Toll signalling, cellular homeostasis, and immunity. Our study reveals that an experimental increase in fecundity causes the co-activation of reproduction and body maintenance mechanisms, shedding light on the molecular regulation of the link between longevity and fecundity in social insects.
Temnothorax rugatulus is a small ant with colonies of a few hundred workers and one to several queens. Two queen morphs can occur and we only used colonies of the common larger queen morph (19). These ants reside in rock crevices in forests throughout Western North America. We collected 105 T. rugatulus colonies in the Chiricahua Mountains, Arizona in August 2015 (Table S1). In our laboratory, colonies were transferred to artificial nest boxes and kept at 22°C and 12h light / 12h dark in a climate chamber.
For the dietary-restriction experiment, we limited the queens’ access to workers, as these might buffer food restrictions imposed on the queen. The queen was isolated with five workers to ensure food provisioning in the upper part of an artificial nestsite (queenright part, QR), while the reminder of the colony inhabited the lower section (queenless, QL). Both parts were separated by a metal grid, allowing the exchange of volatiles, but not food (Fig. S1). The QR-parts of the dietary-restriction treatment were provided with two cricket legs and a droplet of honey every 2nd week (N = 32 colonies, Fig. S1), while the QR-parts of the control (N = 30 colonies) and the QL-parts of both treatments the received the same amount of food twice weekly. At each feeding session, all nests were opened and any remaining food was removed. Food was replaced with fresh food at every session for the QL-parts and the QR-part control, but only at every 4th time for the QR-part of dietary-restriction treatment. Thus, these ants had food available only a quarter of the time, whereas all others had continuous access to food. All colonies had continuous access to water. Worker survival was monitored weekly. Queens reduced egg-laying over time in both treatments, as eggs laid at the beginning developed into larvae. In order to increase the likelihood to detect an treatment effect, all eggs and young larvae were removed from the QR parts at week eight (Figure S2). The experiment ended after 13 weeks. All eggs were counted. All queens were dissected.
For the egg-removal experiment, 44 polygynous colonies were used to create 58 experimental colonies. 14 colonies were split and colony fragments were allocated to different treatments. We standardized the number of queen, workers, and larvae to 2, 50 and 12 respectively, and removed all eggs. In the egg-removal treatment (N = 29 colonies) all eggs were removed once per week, while in the control treatment (N = 39 colonies) eggs were just moved around with forceps. Colonies were anesthetized with CO2 to remove or simulate egg removal. Queen survival was recorded weekly. The experiment was performed over six weeks. All queens were dissected two weeks after the experiments’ end.
Ovaries and fat bodies of eight queens per treatment were dissected on ice (N = 32). The fat body was individually homogenized in 50μL TRIZOL (Invitrogen) and stored at -20°C. RNA was extracted using the RNeasy mini kit (Qiagen) with a preceding chloroform step. Library preparation and sequencing of 100bp paired-end reads on an Illumina HiSeq 2000/2500 was conducted at BGI Hong Kong. The ovaries of all remaining queens were dissected and photographed for fertility measurements (Leica DFC425 20x; LAS version 4.5). Ovary length in the dietary-restriction experiment was analysed by using a Wilcoxon test. We used generalized-linear models with a poisson distribution (link function = log) to investigate the effect of treatment on the number of white eggs in the ovaries and in the colony as dependent variables. For the egg-removal experiment, fecundity differences were analysed with a linear-mixed model with ovary length (in mm) as dependant variable, and a generalized linear-mixed model with a poisson distribution (link function = log) with the number of white eggs in the ovaries as dependent variable. Experimental fragment ID and colony ID were added as random factors. For both experiments, we separately analysed queen survival by running survival models, with treatment as explanatory variable. As all queens were independent in the dietary-restriction experiment, we used the R package survival (), while we used the package coxme() for the analysis of the egg removal data by adding colony ID as random factor. The statistical analyses were conducted in R v. 3.0.2 (R Development Core Team 2008).
For the transcriptome analyses, raw reads from all 32 samples were trimmed with Trimmomatic-v0.36 (20), quality checked using FastQC-v0.11.5 (21). Paired reads were de-novo assembled using Trinity v.2.4.8 (22), resulting in 328,731 transcripts. For annotation, we conducted a BlastX homology search (23) against the non-redundant invertebrate protein database (June 2018) with an E-value cut-off of E-05. Read count estimates per transcript and sample were obtained using RSEM-v1.3.0 (24) with Bowtie2 aligner for each experiment separately. To eliminate low read counts likely representing noise, we removed transcripts with less than 10 reads in less than four samples (25). The differential expression analyses were performed with R package Deseq2-v1.2.10 (26) (contrast function) by comparing treatment to control for each experiment. We added colonyID as random factor in the egg-removal treatment as some samples were dependent. Nucleotide sequences were translated into amino-acid sequences with Transdecoder-v5.5.0 (22), before conducting a gene ontology (GO) annotation using InterProScan-v5.34-73.0 (27). We performed GO term enrichment analyses based on subsets of DEGs using the R package TopGo-v-3.6 (28), with the “weight01” algorithm. For each DEG, we extracted the geneID from the BlastX results to retrieve additional GO and biological functions from the Uniprot database (www.uniprot.org) with Homo sapiens, Mus musculus, and Drosophila melanogaster as query organisms using an in-house python script (Supplement: maintenance_test.R). Thereafter, we searched for terms associated with fecundity (fecund, fertile, meiosis, meiotic, zygote, reproductive, reproduction, embryo, pregnancy, mating, foetal, sexual, brood, egg, ovule, ovary, ovarian), body maintenance (Toll, response to oxidative stress, apoptosis, TOR, tumour repressor, transposable element, response to UV damages, DNA repair, stress response, aging, autophagy, cellular homeostasis), epigenetics (chromatin, histone), fatty acid metabolism (fatty), and immunity (immune). χ²-tests were used to contrast the frequency of DEGs with these functions between treatment and controls. We conducted these additional analyses to obtain insights into putative functions of DEGs in fecundity, longevity (body maintenance, immunity), food processing (fatty acid metabolism) and gene regulation (epigenetics).
Deutsche Forschungsgemeinschaft, Award: FE 1333/6-1
Deutsche Forschungsgemeinschaft, Award: FO 298/19-1