Inhibition of histone acetylation and deacetylation enzymes affects longevity, development, and fecundity in the pea aphid (Acyrthosiphon pisum)

Epigenomic Changes in Ostrinia Moths Under Elevated Pupal and Adult Temperature

Epigenetic changes in the methylation of DNA may occur in response to environmental stressors, including warming climates. DNA methylation may also play an important role in regulating gene expression during both male and female reproduction in many insect species. However, it is currently unknown how DNA methylation shifts when individuals are reproducing under warmer temperatures. We exposed European corn borer moths (Ostrinia nubilalis) to heat during the pupal and adult life stages then investigated changes in DNA methylation across the genome using enzymatic methyl-seq (EM-seq). We compared methylation patterns in reproductive males and females exposed to heat (28°C) to those that experienced an ambient temperature (23°C). We found that heat exposure led to a small but significant increase in the percentage of methylated CpG sites throughout the genome in both sexes. However, DNA methylation rates were higher in females and differential methylation following heat exposure localised to unique regions in each sex. In males, methylation shifted within genes belonging to pathways including Hippo signalling, ubiquitin-mediated proteolysis, DNA damage repair and spermatogenesis. In females, differential methylation occurred in genes related to histone modification and oogenesis. Our results suggest that DNA methylation patterns respond to moderate heat exposure in Lepidoptera and provide insight into epigenetic responses to heatwaves, suggesting novel pathways that may be involved in responding to heat stress during metamorphosis and reproduction.

Annotation of transcription factors, chromatin-associated factors, and basal transcription machinery in the pea aphid, Acyrthosiphon pisum, and development of the ATFdb database, a resource for studies of transcriptional regulation

The pea aphid, Acyrthosiphon pisum, is an emerging model system in functional and comparative genomics, in part due to the availability of new genomic approaches and the different sequencing and annotation efforts that the community has dedicated to this important crop pest insect. The pea aphid is also used as a model to study fascinating biological traits of aphids, such as their extensive polyphenisms, their bacteriocyte-confined nutritional symbiosis, or their adaptation to the highly unbalanced diet represented by phloem sap. To get insights into the molecular basis of all these processes, it is important to have an appropriate annotation of transcription factors (TFs), which would enable the reconstruction/inference of gene regulatory networks in aphids. Using the latest version of the A. pisum genome assembly and annotation, which represents the first chromosome-level pea aphid genome, we annotated the complete repertoire of A. pisum TFs and complemented this information by annotating genes encoding chromatin-associated and basal transcription machinery proteins. These annotations were done combining information from the model Drosophila melanogaster, for which we also provide a revisited list of these proteins, and de novo prediction. The comparison between the two model systems allowed the identification of major losses or expansions in each genome, while a deeper analysis was made of ZNF TFs (with certain families expanded in the pea aphid), and the Hox gene cluster (showing reorganization in gene position in the pea aphid compared to D. melanogaster). All annotations are available to the community through the Aphid Transcription Factors database (ATFdb), consolidating the various annotations we generated. ATFdb serves as a valuable resource for gene regulation studies in aphids.

Accessory gland protein regulates pairing process and oviposition in the subterranean termite Reticulitermes chinensis after swarming

Swarming and pairing behaviors are significant to population dispersal of termites. Tandem running is a key process in pairing behavior of dealates to find a mate. Succinylation can lead to significant changes in protein structure and function, which is widely involved in metabolism and behavior regulation in many organisms. However, whether succinylation modification regulates termites' tandem running is currently unknown. In this research, we performed quantitative modified proteomics of the subterranean termite Reticulitermes chinensis Snyder before and after alate swarming. The succinylation levels of accessory gland protein (ACP) were significantly altered after alate swarming. We found that ACP is enriched in male accessory gland and female oocytes of termites. The acetylation and succinylation sites of ACP affected tandem running of dealates. The transcriptome and metabolome analyses of alates injected with ACP and its mutant proteins showed that β-alanine metabolism pathway was the major downstream pathway of ACP. Silencing the significantly differentially expressed genes in the β-alanine metabolic pathway (acyl-CoA dehydrogenase, enoyl-CoA hydratase, 3-hydroxyisobutyrate dehydrogenase, methylmalonate-semialdehyde dehydrogenase) suppressed tandem running and altered oviposition of paired dealates. These findings demonstrate that protein translation modification is an important regulator of tandem running behavior of termites, which implies that the succinylation and acetylation modification sites of ACP could be potential targets for insecticide action. Our research offers a potential approach for developing novel dispersal inhibitors against social insect pests.

Transcriptomic analysis reveals the key role of histone deacetylation via mediating different phytohormone signalings in fiber initiation of cotton

Background

Histone deacetylation is one of the most important epigenetic modifications and plays diverse roles in plant development. However, the detailed functions and mechanisms of histone deacetylation in fiber development of cotton are still unclear. HDAC inhibitors (HDACi) have been commonly used to study the molecular mechanism underlying histone deacetylation or to facilitate disease therapy in humans through hindering the histone deacetylase catalytic activity. Trichostatin A (TSA)—the most widely used HDACi has been extensively employed to determine the role of histone deacetylation on different developmental stages of plants.

Results

Through in vitro culture of ovules, we observed that exogenous application of TSA was able to inhibit the fiber initiation development. Subsequently, we performed a transcriptomic analysis to reveal the underlying mechanisms. The data showed that TSA treatment resulted in 4209 differentially expressed genes, which were mostly enriched in plant hormone signal transduction, phenylpropanoid biosynthesis, photosynthesis, and carbon metabolism pathways. The phytohormone signal transduction pathways harbor the most differentially expressed genes. Deeper studies showed that some genes promoting auxin, Gibberellic Acid (GA) signaling were down-regulated, while some genes facilitating Abscisic Acid (ABA) and inhibiting Jasmonic Acid (JA) signaling were up-regulated after the TSA treatments. Further analysis of plant hormone contents proved that TSA significantly promoted the accumulation of ABA, JA and GA₃.

Conclusions

Collectively, histone deacetylation can regulate some key genes involved in different phytohormone pathways, and consequently promoting the auxin, GA, and JA signaling, whereas repressing the ABA synthesis and signaling to improve the fiber cell initiation. Moreover, the genes associated with energy metabolism, phenylpropanoid, and glutathione metabolism were also regulated by histone deacetylation. The above results provided novel clues to illuminate the underlying mechanisms of epigenetic modifications as well as related different phytohormones in fiber cell differentiation, which is also very valuable for the molecular breeding of higher quality cotton.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13578-022-00840-4.

The emerging role of epigenetic mechanisms in insect defense against pathogens

Insects resist infection by natural selection that favors the survival and reproduction of the fittest phenotypes. Although the genetic mechanisms mediating the evolution of insect resistance have been investigated, little is known about the contribution of epigenetic mechanisms. Gene expression in response to a pathogen selection pressure is regulated by different mechanisms affecting chromatin plasticity. Whether transgenerational inheritance of genome-wide epigenetic marks contributes to the heritable manifestation of insect resistance is presently debated. Here, we review the latest works on the contributions of chromatin remodeling to insect immunity and adaptation to pathogens. We highlight DNA methylation, histone acetylation, and microRNAs in mediating the transgenerational inherited transcriptional reprogramming of defense-related gene expression and the evolution of insect resistance.

Histone acetylation regulates the expression of genes involved in worker reproduction in the ant Temnothorax rugatulus

Background

In insect societies, queens monopolize reproduction while workers perform tasks such as brood care or foraging. Queen loss leads to ovary development and lifespan extension in workers of many ant species. However, the underlying molecular mechanisms of this phenotypic plasticity remain unclear. Recent studies highlight the importance of epigenetics in regulating plastic traits in social insects. Thus, we investigated the role of histone acetylation in regulating worker reproduction in the ant Temnothorax rugatulus. We removed queens from their colonies to induce worker fecundity, and either fed workers with chemical inhibitors of histone acetylation (C646), deacetylation (TSA), or the solvent (DMSO) as control. We monitored worker number for six weeks after which we assessed ovary development and sequenced fat body mRNA.

Results

Workers survived better in queenless colonies. They also developed their ovaries after queen removal in control colonies as expected, but not in colonies treated with the chemical inhibitors. Both inhibitors affected gene expression, although the inhibition of histone acetylation using C646 altered the expression of more genes with immunity, fecundity, and longevity functionalities. Interestingly, these C646-treated workers shared many upregulated genes with infertile workers from queenright colonies. We also identified one gene with antioxidant properties commonly downregulated in infertile workers from queenright colonies and both C646 and TSA-treated workers from queenless colonies.

Conclusion

Our results suggest that histone acetylation is involved in the molecular regulation of worker reproduction, and thus point to an important role of histone modifications in modulating phenotypic plasticity of life history traits in social insects.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08196-8.

Epigenetic Regulation and Environmental Sex Determination in Cichlid Fishes

Studying environmental sex determination (ESD) in cichlids provides a phylogenetic and comparative approach to understand the evolution of the underlying mechanisms, their impact on the evolution of the overlying systems, and the neuroethology of life history strategies. Natural selection normally favors parents who invest equally in the development of male and female offspring, but evolution may favor deviations from this 50:50 ratio when environmental conditions produce an advantage for doing so. Many species of cichlids demonstrate ESD in response to water chemistry (temperature, pH, and oxygen concentration). The relative strengths of and the exact interactions between these factors vary between congeners, demonstrating genetic variation in sensitivity. The presence of sizable proportions of the less common sex towards the environmental extremes in most species strongly suggests the presence of some genetic sex-determining loci acting in parallel with the ESD factors. Sex determination and differentiation in these species does not seem to result in the organization of a final and irreversible sexual fate, so much as a life-long ongoing battle between competing male- and female-determining genetic and hormonal networks governed by epigenetic factors. We discuss what is and is not known about the epigenetic mechanism behind the differentiation of both gonads and sex differences in the brain. Beyond the well-studied tilapia species, the 2 best-studied dwarf cichlid systems showing ESD are the South American genus Apistogramma and the West African genus Pelvicachromis. Both species demonstrate male morphs with alternative reproductive tactics. We discuss the further neuroethology opportunities such systems provide to the study of epigenetics of alternative life history strategies and other behavioral variation.

10-hydroxy-2E-decenoic acid (10HDA) does not promote caste differentiation in Melipona scutellaris stingless bees

In bees from genus Melipona, differential feeding is not enough to fully explain female polyphenism. In these bees, there is a hypothesis that in addition to the environmental component (food), a genetic component is also involved in caste differentiation. This mechanism has not yet been fully elucidated and may involve epigenetic and metabolic regulation. Here, we verified that the genes encoding histone deacetylases HDAC1 and HDAC4 and histone acetyltransferase KAT2A were expressed at all stages of Melipona scutellaris, with fluctuations between developmental stages and castes. In larvae, the HDAC genes showed the same profile of Juvenile Hormone titers-previous reported-whereas the HAT gene exhibited the opposite profile. We also investigated the larvae and larval food metabolomes, but we did not identify the putative queen-fate inducing compounds, geraniol and 10-hydroxy-2E-decenoic acid (10HDA). Finally, we demonstrated that the histone deacetylase inhibitor 10HDA-the major lipid component of royal jelly and hence a putative regulator of honeybee caste differentiation-was unable to promote differentiation in queens in Melipona scutellaris. Our results suggest that epigenetic and hormonal regulations may act synergistically to drive caste differentiation in Melipona and that 10HDA is not a caste-differentiation factor in Melipona scutellaris.

Transcriptomic changes in the pea aphid, Acyrthosiphon pisum: Effects of the seasonal timer and photoperiod

Many insect species use photoperiod as a cue for induction of seasonal responses, including seasonal polyphenism. Although most aphid species viviparously produce parthenogenetic and sexual morphs under long and short days, respectively, a seasonal timer suppresses the sexual morph production over several successive generations during a few months following hatching of a sexually produced diapause egg. To reveal the relative influences of photoperiod and the seasonal timer on the reproductive polyphenism at the gene expression level, we performed RNA sequencing-based transcriptome analyses in the pea aphid, Acyrthosiphon pisum (Hemiptera: Aphididae). Under short days, aphids with an expired seasonal timer showed a higher expression level in hundreds of genes than those with an operative seasonal timer. In contrast, aphids with an operative seasonal timer did not show upregulation in most of these genes. Functional annotations based on gene ontology showed that histone modifications and small non-coding RNA pathways were enriched in aphids with an expired seasonal timer under short-day conditions, suggesting that these epigenetic regulations on gene expression might be involved in a mechanism of maternal switching from the parthenogenetic to sexual morph production.

Lysine Acetyltransferase p300/CBP Plays an Important Role in Reproduction, Embryogenesis and Longevity of the Pea Aphid Acyrthosiphon pisum

CREB-binding protein (p300/CBP) is a universal transcriptional co-regulator with lysine acetyltransferase activity. Drosophila melanogaster p300/CBP is a well-known regulator of embryogenesis, and recent studies in beetles and cockroaches have revealed the importance of this protein during post-embryonic development and endocrine signaling. In pest insects, p300/CBP may therefore offer a useful target for control methods based on RNA interference (RNAi). We investigated the role of p300/CBP in the pea aphid (Acyrthosiphon pisum), a notorious pest insect used as a laboratory model for the analysis of complex life-history traits. The RNAi-based attenuation of A. pisum p300/CBP significantly reduced the aphid lifespan and number of offspring, as well as shortening the reproductive phase, suggesting the manipulation of this gene contributes to accelerated senescence. Furthermore, injection of p300/CBP dsRNA also reduced the number of viable offspring and increased the number of premature nymphs, which developed in abnormally structured ovaries. Our data confirm the evolutionarily conserved function of p300/CBP during insect embryogenesis and show that the protein has a critical effect on longevity, reproduction and development in A. pisum. The potent effect of p300/CBP silencing indicates that this regulatory protein is an ideal target for RNAi-based aphid control.