Gene silencing in non-model insects: Overcoming hurdles using symbiotic bacteria for trauma-free sustainable delivery of RNA interference

The thrips gut pH and implications for symbiont-mediated RNAi

The gut pH plays crucial roles in diet preference, habitat choice, insect fitness, and insect-microbial relationships. It significantly impacts enzyme activity efficiency, as well as the internalisation and efficacy of pesticides. Without a comprehensive understanding of the gut environment, potential pest management strategies cannot be fully optimised.This study investigates the gut pH of the globally invasive pest insect Western flower thrips Frankliniella occidentalis, and the effect its Gram-negative symbiotic gut bacterium BFo2 has on pH modulation. Indicator dyes were fed to F. occidentalis and the gut pH was found to vary between 6 and 7. In general, the larval and adult guts appear to have a pH of between 6 and 6.5; however, the posterior gut of some adults appears to be closer to 7. This almost neutral pH offers a favourable environment for the neutrophilic symbiotic BFo2. The ability of BFo2 isolates to buffer pH towards neutral was also observed during in vitro culture using broths at different pH values.This paper also discusses the implications of this gut environment on dsRNAi delivery. By laying the foundation for understanding how gut pH can be leveraged to enhance current pest management strategies, this study particularly benefits research aimed at optimising the delivery of lethal dsRNA through symbiont-mediated RNAi to Western flower thrips in pest management programs.

RNAi targeting Nav and CPR via leaf delivery reduces adult emergence and increases the susceptibility to λ-cyholthin in Tuta absoluta (Meyrick)

The tomato leafminer, Tuta absoluta (Meyrick), one of the most economically destructive pests of tomato, causes severe yields losses of tomato production globally. Rapid evolution of insecticide resistance requires the development of alternative control strategy for this pest. RNA interference (RNAi) represents a promising, innovative control strategy against key agricultural insect pests, which has recently been licensed for Colorado Potato Beetle control. Here two essential genes, voltage-gated sodium channel (Nav) and NADPH-cytochrome P450 reductase (CPR) were evaluated as targets for RNAi using an ex vivo tomato leaf delivery system. Developmental stage-dependent expression profiles showed TaNav was most abundant in adult stages, whereas TaCPR was highly expressed in larval and adult stages. T. absoluta larvae feeding on tomato leaflets treated with dsRNA targeting TaNav and TaCPR showed significant knockdown of gene expression, leading to reduction in adult emergence. Additionally, tomato leaves treated with dsRNA targeting these two genes were significantly less damaged by larval feeding and mining. Furthermore, bioassay with LC30 doses of λ-cyholthin showed that silencing TaNav and TaCPR increased T. absoluta mortality about 32.2 and 17.4%, respectively, thus indicating that RNAi targeting TaNav and TaCPR could increase the susceptibility to λ-cyholthin in T. absoluta. This study demonstrates the potential of using RNAi targeting key genes, like TaNav and TaCPR, as an alternative technology for the control of this most destructive tomato pests in the future.

A narrow host-range and lack of persistence in two non-target insect species of a bacterial symbiont exploited to deliver insecticidal RNAi in Western Flower Thrips

Introduction

Insecticidal RNAi is a targeted pest insect population control measure. The specificity of insecticidal RNAi can theoretically be enhanced by using symbiotic bacteria with a narrow host range to deliver RNAi, an approach termed symbiont-mediated RNAi (SMR), a technology we have previously demonstrated in the globally-invasive pest species Western Flower Thrips (WFT).

Methods

Here we examine distribution of the two predominant bacterial symbionts of WFT, BFo1 and BFo2, among genome-sequenced insects. Moreover, we have challenged two non-target insect species with both bacterial species, namely the pollinating European bumblebee, Bombus terrestris, and an insect predator of WFT, the pirate bug Orius laevigatus.

Results

Our data indicate a very limited distribution of either symbiont among insects other than WFT. Moreover, whereas BFo1 could establish itself in both bees and pirate bugs, albeit with no significant effects on insect fitness, BFo2 was unable to persist in either species.

Discussion

In terms of biosafety, these data, together with its more specific growth requirements, vindicate the choice of BFo2 for delivery of RNAi and precision pest management of WFT.

Honey bee functional genomics using symbiont-mediated RNAi

Honey bees are indispensable pollinators and model organisms for studying social behavior, development and cognition. However, their eusociality makes it difficult to use standard forward genetic approaches to study gene function. Most functional genomics studies in bees currently utilize double-stranded RNA (dsRNA) injection or feeding to induce RNAi-mediated knockdown of a gene of interest. However, dsRNA injection is laborious and harmful, and dsRNA feeding is difficult to scale cheaply. Further, both methods require repeated dsRNA administration to ensure a continued RNAi response. To fill this gap, we engineered the bee gut bacterium Snodgrassella alvi to induce a sustained host RNA interference response that reduces expression of a targeted gene. To employ this functional genomics using engineered symbionts (FUGUES) procedure, a dsRNA expression plasmid is cloned in Escherichia coli using Golden Gate assembly and then transferred to S. alvi. Adult worker bees are then colonized with engineered S. alvi. Finally, gene knockdown is verified through qRT-PCR, and bee phenotypes of interest can be further assessed. Expression of targeted genes is reduced by as much as 50-75% throughout the entire bee body by 5 d after colonization. This protocol can be accomplished in 4 weeks by bee researchers with microbiology and molecular cloning skills. FUGUES currently offers a streamlined and scalable approach for studying the biology of honey bees. Engineering other microbial symbionts to influence their hosts in ways that are similar to those described in this protocol may prove useful for studying additional insect and animal species in the future.

Current Scenario of Exogenously Induced RNAi for Lepidopteran Agricultural Pest Control: From dsRNA Design to Topical Application

Invasive insects cost the global economy around USD 70 billion per year. Moreover, increasing agricultural insect pests raise concerns about global food security constraining and infestation rising after climate changes. Current agricultural pest management largely relies on plant breeding-with or without transgenes-and chemical pesticides. Both approaches face serious technological obsolescence in the field due to plant resistance breakdown or development of insecticide resistance. The need for new modes of action (MoA) for managing crop health is growing each year, driven by market demands to reduce economic losses and by consumer demand for phytosanitary measures. The disabling of pest genes through sequence-specific expression silencing is a promising tool in the development of environmentally-friendly and safe biopesticides. The specificity conferred by long dsRNA-base solutions helps minimize effects on off-target genes in the insect pest genome and the target gene in non-target organisms (NTOs). In this review, we summarize the status of gene silencing by RNA interference (RNAi) for agricultural control. More specifically, we focus on the engineering, development and application of gene silencing to control Lepidoptera through non-transforming dsRNA technologies. Despite some delivery and stability drawbacks of topical applications, we reviewed works showing convincing proof-of-concept results that point to innovative solutions. Considerations about the regulation of the ongoing research on dsRNA-based pesticides to produce commercialized products for exogenous application are discussed. Academic and industry initiatives have revealed a worthy effort to control Lepidoptera pests with this new mode of action, which provides more sustainable and reliable technologies for field management. New data on the genomics of this taxon may contribute to a future customized target gene portfolio. As a case study, we illustrate how dsRNA and associated methodologies could be applied to control an important lepidopteran coffee pest.

Facultative symbionts are potential agents of symbiont-mediated RNAi in aphids

Aphids are major crop pests, and they can be controlled through the application of the promising RNA interference (RNAi) techniques. However, chemical synthesis yield of dsRNA for RNAi is low and costly. Another sustainable aphid pest control strategy takes advantage of symbiont-mediated RNAi (SMR), which can generate dsRNA by engineered microbes. Aphid host the obligate endosymbiont Buchnera aphidicola and various facultative symbionts that not only have a wide host range but are also vertically and horizontally transmitted. Thus, we described the potential of facultative symbionts in aphid pest control by SMR. We summarized the community and host range of these facultative symbionts, and then reviewed their probable horizontal transmitted routes and ecological functions. Moreover, recent advances in the cultivation and genetic engineering of aphid facultative symbionts were discussed. In addition, current legislation of dsRNA-based pest control strategies and their safety assessments were reviewed.

Bacterial Competition Influences the Ability of Symbiotic Bacteria to Colonize Western Flower Thrips

Symbiont mediated RNAi (SMR) is a promising method for precision control of pest insect species such as Western Flower Thrips (WFT). Two species of bacteria are known to be dominant symbiotic bacteria in WFT, namely BFo1 and BFo2 (Bacteria from Frankliniella occidentalis 1 and 2), as we here confirm by analysis of next-generation sequence data derived to obtain a reference WFT genome sequence. Our first demonstration of SMR in WFT used BFo2, related to Pantoea, isolated from a domesticated Dutch thrips population. However, for successful use of SMR as a thrips control measure, these bacteria need to successfully colonize different environmental thrips populations. Here, we describe a United Kingdom thrips population that does not harbour BFo2, but does contain BFo1, a species related to Erwinia. Attempts to introduce BFo2 indicate that this bacterium is unable to establish itself in the United Kingdom thrips, in contrast to successful colonization by a strain of BFo1 expressing green fluorescent protein. Fluorescence microscopy indicates that BFo1 occupies similar regions of the thrips posterior midgut and hindgut as BFo2. Bacterial competition assays revealed that a barrier to BFo2 establishing itself in thrips is the identity of the resident BFo1; BFo1 isolated from the United Kingdom thrips suppresses growth of BFo2 to a greater extent than BFo1 from the Dutch thrips that is permissive for BFo2 colonization. The ability of the latter strain of BFo1 to colonize the United Kingdom thrips is also likely attributable to its ability to out-compete the resident BFo1. Lastly, we observed that United Kingdom thrips pre-exposed to the Dutch BFo1 could then be successfully colonized by BFo2. These results indicate, for the first time, that microbial competition and strain differences can have a large influence on how symbiotic bacteria can colonize different populations of an insect species.

Characterisation of the symbionts in the Mediterranean fruit fly gut

Symbioses between bacteria and their insect hosts can range from loose associations through to obligate interdependence. While fundamental evolutionary insights have been gained from the in-depth study of obligate mutualisms, there is increasing interest in the evolutionary potential of flexible symbiotic associations between hosts and their gut microbiomes. Understanding relationships between microbes and hosts also offers the potential for exploitation for insect control. Here, we investigate the gut microbiome of a global agricultural pest, the Mediterranean fruit fly (Ceratitis capitata). We used 16S rRNA profiling to compare the gut microbiomes of laboratory and wild strains raised on different diets and from flies collected from various natural plant hosts. The results showed that medfly guts harbour a simple microbiome that is primarily determined by the larval diet. However, regardless of the laboratory diet or natural plant host on which flies were raised, Klebsiella spp. dominated medfly microbiomes and were resistant to removal by antibiotic treatment. We sequenced the genome of the dominant putative Klebsiella spp. (‘Medkleb’) isolated from the gut of the Toliman wild-type strain. Genome-wide ANI analysis placed Medkleb within the K. oxytoca / michiganensis group. Species level taxonomy for Medkleb was resolved using a mutli-locus phylogenetic approach - and molecular, sequence and phenotypic analyses all supported its identity as K. michiganensis. Medkleb has a genome size (5825435 bp) which is 1.6 standard deviations smaller than the mean genome size of free-living Klebsiella spp. Medkleb also lacks some genes involved in environmental sensing. Moreover, the Medkleb genome contains at least two recently acquired unique genomic islands as well as genes that encode pectinolytic enzymes capable of degrading plant cell walls. This may be advantageous given that the medfly diet includes unripe fruits containing high proportions of pectin. The results suggest that the medfly harbours a commensal gut bacterium that may have developed a mutualistic association with its host and provide nutritional benefits.

Overview of paratransgenesis as a strategy to control pathogen transmission by insect vectors

This article presents an overview of paratransgenesis as a strategy to control pathogen transmission by insect vectors. It first briefly summarises some of the disease-causing pathogens vectored by insects and emphasises the need for innovative control methods to counter the threat of resistance by both the vector insect to pesticides and the pathogens to therapeutic drugs. Subsequently, the state of art of paratransgenesis is described, which is a particularly ingenious method currently under development in many important vector insects that could provide an additional powerful tool for use in integrated pest control programmes. The requirements and recent advances of the paratransgenesis technique are detailed and an overview is given of the microorganisms selected for genetic modification, the effector molecules to be expressed and the environmental spread of the transgenic bacteria into wild insect populations. The results of experimental models of paratransgenesis developed with triatomines, mosquitoes, sandflies and tsetse flies are analysed. Finally, the regulatory and safety rules to be satisfied for the successful environmental release of the genetically engineered organisms produced in paratransgenesis are considered.

Increased RNAi Efficiency by dsEGFP-Induced Up-Regulation of Two Core RNAi Pathway Genes (OfDicer2 and OfAgo2) in the Asian Corn Borer (Ostrinia furnacalis)

Simple Summary

RNA interference (RNAi) has shown great potentials as a novel technology for insect pest management. However, numerous studies have shown that the efficiency of RNAi varies substantially among different insect species. For example, as a major insect pest of corn, the Asian corn borer (Ostrinia furnacalis) showed very low RNAi efficiency. Therefore, it is necessary to develop new strategies for enhancing RNAi efficiency in insects with low RNAi efficiency. In this study, six core RNAi pathway genes were identified and characterized from O. furnacalis transcriptome database. After dsEGFP was injected into O. furnacalis, the expression of the core RNAi pathway genes (OfDicer2 and OfAgo2) was significantly up-regulated in response to the exposure of dsEGFP. As a result, the RNAi efficiency against the target genes in certain tissues of O. furnacalis was significantly improved. These results suggest that RNAi efficiency can be improved by inducing the expression of key RNAi pathway genes in O. furnacalis.

Abstract

RNA interference (RNAi) is a sequence-specific gene silencing mechanism that holds great promise for effective management of agricultural pests. Previous studies have shown that the efficacy of RNAi varies among different insect species, which limits its wide spread application in the field of crop protection. In this study, we identified and characterized six core RNAi pathway genes including OfDicer1, OfDicer2, OfR2D2, OfAgo1, OfAgo2, and OfAgo3 from the transcriptomic database of the Asian corn borer (Ostrinia furnacalis). Domain analysis showed that the six deduced proteins contained the necessary functional domains. Insect developmental stage- and tissue-specific expression analysis showed that five genes were expressed in all the stages and tissues examined except OfAgo3, which showed low expression in larvae, and high expression in pupae and adults and in the midgut. RT-qPCR was performed to examine the response of these six genes to exogenous double-stranded RNA (dsRNA). Interestingly, the transcript levels of OfDicer2 and OfAgo2 were significantly enhanced after the injection of dsEGFP at different time points and tissues investigated. Consequently, the RNAi efficiency in targeting the insect endogenous genes can be greatly enhanced in the hemolymph or midgut. Taken together, our investigations suggest that RNAi efficiency can be enhanced by pre-injection of dsRNA to induce the RNAi core machinery genes, which could be a useful strategy to improving RNAi efficiency for studying gene functions under laboratory conditions.

Molecular Rationale of Insect-Microbes Symbiosis-From Insect Behaviour to Mechanism

Insects nurture a panoply of microbial populations that are often obligatory and exist mutually with their hosts. Symbionts not only impact their host fitness but also shape the trajectory of their phenotype. This co-constructed niche successfully evolved long in the past to mark advanced ecological specialization. The resident microbes regulate insect nutrition by controlling their host plant specialization and immunity. It enhances the host fitness and performance by detoxifying toxins secreted by the predators and abstains them. The profound effect of a microbial population on insect physiology and behaviour is exploited to understand the host–microbial system in diverse taxa. Emergent research of insect-associated microbes has revealed their potential to modulate insect brain functions and, ultimately, control their behaviours, including social interactions. The revelation of the gut microbiota–brain axis has now unravelled insects as a cost-effective potential model to study neurodegenerative disorders and behavioural dysfunctions in humans. This article reviewed our knowledge about the insect–microbial system, an exquisite network of interactions operating between insects and microbes, its mechanistic insight that holds intricate multi-organismal systems in harmony, and its future perspectives. The demystification of molecular networks governing insect–microbial symbiosis will reveal the perplexing behaviours of insects that could be utilized in managing insect pests.

Lab-to-Field Transition of RNA Spray Applications - How Far Are We?

The drastic loss of biodiversity has alarmed the public and raised sociopolitical demand for chemical pesticide-free plant production, which is now treated by governments worldwide as a top priority. Given this global challenge, RNAi-based technologies are rapidly evolving as a promising substitute to conventional chemical pesticides. Primarily, genetically modified (GM) crops expressing double-stranded (ds)RNA-mediating gene silencing of foreign transcripts have been developed. However, since the cultivation of GM RNAi crops is viewed negatively in numerous countries, GM-free exogenous RNA spray applications attract tremendous scientific and political interest. The sudden rise in demand for pesticide alternatives has boosted research on sprayable RNA biopesticides, generating significant technological developments and advancing the potential for field applications in the near future. Here we review the latest advances that could pave the way for a quick lab-to-field transition for RNA sprays, which, as safe, selective, broadly applicable, and cost-effective biopesticides, represent an innovation in sustainable crop production. Given these latest advances, we further discuss technological limitations, knowledge gaps in the research, safety concerns and regulatory requirements that need to be considered and addressed before RNA sprays can become a reliable and realistic agricultural approach.

Biotechnological interventions for the sustainable management of a global pest, whitefly (Bemisia tabaci)

Whiteflies (Bemisia tabaci) are polyphagous invasive hemipteran insects that cause serious losses of important crops by directly feeding on phloem sap and transmitting pathogenic viruses. These insects have emerged as a major threat to global agriculture and food security. Chemically synthesized insecticides are currently the only option to control whiteflies, but the ability of whiteflies to evolve resistance against insecticides has made the management of these insects very difficult. Natural host-plant resistance against whiteflies identified in some crop plants has not been exploited to a great extent. Genetic engineering approaches, such as transgenics and RNA interference (RNAi), are potentially useful for the control of whiteflies. Transgenic plants harboring insecticidal toxins/lectins developed via nuclear or chloroplast transformation are a promising vehicle for whitefly control. Double-stranded RNAs (dsRNAs) of several insect genes, delivered either through microinjection into the insect body cavity or orally via an artificial diet and transiently or stably expressed in transgenic plants, have controlled whiteflies in model plants and in some crops at the laboratory level, but not at the field level. In this review, we highlight the merits and demerits of each delivery method along with strategies for sustained delivery of dsRNAs via fungal entomopathogen/endosymbiont or nontransgenic RNAi approaches, foliar sprays, root absorption or nanocarriers as well as the factors affecting efficient RNAi and their biosafety issues. Genome sequencing and transcriptome studies of whitefly species are facilitating the selection of appropriate genes for RNAi and gene-editing technology for the efficient and resilient management of whiteflies and their transmitted viruses.

Advances in the Development of Microbial Double-Stranded RNA Production Systems for Application of RNA Interference in Agricultural Pest Control

RNA interference (RNAi) is a valuable and revolutionary technology that has been widely applied in medicine and agriculture. The application of RNAi in various industries requires large amounts of low-cost double-stranded RNA (dsRNA). Chemical synthesis can only produce short dsRNAs; long dsRNAs need to be synthesized biologically. Several microbial chassis cells, such as Escherichia coli, Saccharomyces cerevisiae, and Bacillus species, have been used for dsRNA synthesis. However, the titer, rate of production, and yield of dsRNA obtained by these microorganism-based strategies is still low. In this review, we summarize advances in microbial dsRNA production, and analyze the merits and faults of different microbial dsRNA production systems. This review provides a guide for dsRNA production system selection. Future development of efficient microbial dsRNA production systems is also discussed.

Engineering insects from the endosymbiont out

Insects are an incredibly diverse group of animals with species that benefit and harm natural ecosystems, agriculture, and human health. Many insects have consequential associations with microbes: bacterial symbionts may be embedded in different insect tissues and cell types, inherited across insect generations, and required for insect survival and reproduction. Genetically engineering insect symbionts is key to understanding and harnessing these associations. We summarize different types of insect-bacteria relationships and review methods used to genetically modify endosymbiont and gut symbiont species. Finally, we discuss recent studies that use this approach to study symbioses, manipulate insect-microbe interactions, and influence insect biology. Further progress in insect symbiont engineering promises to solve societal challenges, ranging from controlling pests to protecting pollinator health.

The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control

Background

The stable fly, Stomoxys calcitrans, is a major blood-feeding pest of livestock that has near worldwide distribution, causing an annual cost of over $2 billion for control and product loss in the USA alone. Control of these flies has been limited to increased sanitary management practices and insecticide application for suppressing larval stages. Few genetic and molecular resources are available to help in developing novel methods for controlling stable flies.

Results

This study examines stable fly biology by utilizing a combination of high-quality genome sequencing and RNA-Seq analyses targeting multiple developmental stages and tissues. In conjunction, 1600 genes were manually curated to characterize genetic features related to stable fly reproduction, vector host interactions, host-microbe dynamics, and putative targets for control. Most notable was characterization of genes associated with reproduction and identification of expanded gene families with functional associations to vision, chemosensation, immunity, and metabolic detoxification pathways.

Conclusions

The combined sequencing, assembly, and curation of the male stable fly genome followed by RNA-Seq and downstream analyses provide insights necessary to understand the biology of this important pest. These resources and new data will provide the groundwork for expanding the tools available to control stable fly infestations. The close relationship of Stomoxys to other blood-feeding (horn flies and Glossina) and non-blood-feeding flies (house flies, medflies, Drosophila) will facilitate understanding of the evolutionary processes associated with development of blood feeding among the Cyclorrhapha.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-021-00975-9.

RNAi-Based Functional Genomics in Hemiptera

RNA interference (RNAi) is a powerful approach for sequence-specific gene silencing, displaying tremendous potential for functional genomics studies in hemipteran insects. Exploiting RNAi allows the biological roles of critical genes to be defined and aids the development of RNAi-based biopesticides. In this review, we provide context to the rapidly expanding field of RNAi-based functional genomics studies in hemipteran insects. We highlight the most widely used RNAi delivery strategies, including microinjection, oral ingestion and topical application. Additionally, we discuss the key variables affecting RNAi efficacy in hemipteran insects, including insect life-stage, gene selection, the presence of nucleases, and the role of core RNAi machinery. In conclusion, we summarise the application of RNAi in functional genomics studies in Hemiptera, focusing on genes involved in reproduction, behaviour, metabolism, immunity and chemical resistance across 33 species belonging to 14 families.

Going wild for functional genomics: RNA interference as a tool to study gene-behavior associations in diverse species and ecological contexts

Identifying the genetic basis of behavior has remained a challenge for biologists. A major obstacle to this goal is the difficulty of examining gene function in an ecologically relevant context. New tools such as CRISPR/Cas9, which alter the germline of an organism, have taken center stage in functional genomics in non-model organisms. However, germline modifications of this nature cannot be ethically implemented in the wild as a part of field experiments. This impediment is more than technical. Gene function is intimately tied to the environment in which the gene is expressed, especially for behavior. Most lab-based studies fail to recapitulate an organism's ecological niche, thus most published functional genomics studies of gene-behavior relationships may provide an incomplete or even inaccurate assessment of gene function. In this review, we highlight RNA interference as an especially effective experimental method to deepen our understanding of the interplay between genes, behavior, and the environment. We highlight the utility of RNAi for researchers investigating behavioral genetics, noting unique attributes of RNAi including transience of effect and the feasibility of releasing treated animals into the wild, that make it especially useful for studying the function of behavior-related genes. Furthermore, we provide guidelines for planning and executing an RNAi experiment to study behavior, including challenges to consider. We urge behavioral ecologists and functional genomicists to adopt a more fully integrated approach which we call "ethological genomics". We advocate this approach, utilizing tools such as RNAi, to study gene-behavior relationships in their natural context, arguing that such studies can provide a deeper understanding of how genes can influence behavior, as well as ecological aspects beyond the organism that houses them.

An integrative approach to symbiont-mediated vector control for agricultural pathogens

Vector-borne pathogens pose significant threats to agricultural productivity. Methods that exploit associations between insects and their symbiotic microbes, dubbed symbiont-mediated vector control, are emerging as viable alternatives to insecticides for the control of vector-borne agricultural plant pathogens. The development of methods for effective microbial manipulation, such as RNA interference and paratransgenesis, may facilitate symbiont-mediated vector control tactics aimed at either suppressing insect populations or at manipulating vector competence, an insect vector's ability to acquire, harbor, and transmit pathogens. As suppression strategies transition from the laboratory to the field, the need for methods to evaluate their viability and predict their outcomes is apparent. Mathematical models of symbiont impact on agricultural disease can inform the development of symbiont-mediated vector control. We propose an integrative approach, combining theoretical and empirical experiments to identify the best practices for achieving meaningful improvements to crop health and productivity.

Double-Stranded RNA Technology to Control Insect Pests: Current Status and Challenges

Exploiting the RNA interference (RNAi) gene mechanism to silence essential genes in pest insects, leading to toxic effects, has surfaced as a promising new control strategy in the past decade. While the first commercial RNAi-based products are currently coming to market, the application against a wide range of insect species is still hindered by a number of challenges. In this review, we discuss the current status of these RNAi-based products and the different delivery strategies by which insects can be targeted by the RNAi-triggering double-stranded RNA (dsRNA) molecules. Furthermore, this review also addresses a number of physiological and cellular barriers, which can lead to decreased RNAi efficacy in insects. Finally, novel non-transgenic delivery technologies, such as polymer or liposomic nanoparticles, peptide-based delivery vehicles and viral-like particles, are also discussed, as these could overcome these barriers and lead to effective RNAi-based pest control.

Optimization of dietary RNA interference delivery to western flower thrips Frankliniella occidentalis and onion thrips Thrips tabaci

In insect reverse genetics, dietary delivery of interfering RNAs is a practical approach in nonmodel species, such as thrips, whose small size, and feeding behavior restricts the use of other delivery methods. In a laboratory context, an unsuitable diet could confound the interpretation of an RNA interference (RNAi) phenotype, however well-formulated artificial diets can minimize experimental variability, reduce the need for insect handling, and can further be used for roles, such as delivering double-strand RNA (dsRNA)-expressing recombinant bacteria. In this study, artificial diets for oral delivery of dsRNA were developed for two important pest thrips species, western flower thrips (Frankliniella occidentalis) and onion thrips (Thrips tabaci), with the goal of (a) stimulating feeding behavior, (b) supporting optimal growth rates of dsRNA-expressing symbiotic bacteria, and (c) nutritionally supporting the thrips for sufficient periods to observe RNAi phenotypes. The efficacy of artificial diets for ingesting "naked" dsRNA or dsRNA-expressing symbionts and dsRNA delivery via host plant uptake was evaluated. Compared with previously published diet formulations, new combinations based on tryptone, yeast, and soy were superior for enhancing feeding and longevity. However, simply adding "naked" dsRNA to an artificial diet was an unreliable form of RNAi delivery in our hands due to dsRNA degradation. Delivery via host plants was more successful, and the new diet formulation was suitable for symbiont-mediated dsRNA delivery, which we believe is the most convenient approach for large-scale knockdown experiments. This study, therefore, provides alternative methodologies for thrips rearing, dietary RNAi delivery, and insights into the challenges of performing dietary RNAi in nonmodel insects.

Mechanisms, Applications, and Challenges of Insect RNA Interference

The RNA interference (RNAi) triggered by short/small interfering RNA (siRNA) was discovered in nematodes and found to function in most living organisms. RNAi has been widely used as a research tool to study gene functions and has shown great potential for the development of novel pest management strategies. RNAi is highly efficient and systemic in coleopterans but highly variable or inefficient in many other insects. Differences in double-stranded RNA (dsRNA) degradation, cellular uptake, inter- and intracellular transports, processing of dsRNA to siRNA, and RNA-induced silencing complex formation influence RNAi efficiency. The basic dsRNA delivery methods include microinjection, feeding, and soaking. To improve dsRNA delivery, various new technologies, including cationic liposome-assisted, nanoparticle-enabled, symbiont-mediated, and plant-mediated deliveries, have been developed. Major challenges to widespread use of RNAi in insect pest management include variable RNAi efficiency among insects, lack of reliable dsRNA delivery methods, off-target and nontarget effects, and potential development of resistance in insect populations.

Gene silencing by RNAi via oral delivery of dsRNA by bacteria in the South American tomato pinworm, Tuta absoluta

BACKGROUND

RNA interference (RNAi) has been evaluated in several insect pests as a novel strategy to be included in integrated pest management. Lepidopterans are recognized to be recalcitrant to gene silencing by RNAi. As such, double-stranded RNA (dsRNA) delivery needs to be adjusted to assure its stability until it reaches the target gene transcript for silencing. Gene silencing by RNAi offers the potential to be used in the control of Tuta absoluta (Meyrick), one of the main insect pests of tomato (Solanum lycopersicum) worldwide. Here, we tested the delivery of dsRNA expressed in Escherichia coli HT115(DE3) and supplied to larvae in an artificial diet by screening target genes for silencing. We tested six target genes: juvenile hormone inducible protein (JHP); juvenile hormone epoxide hydrolase protein (JHEH); ecdysteroid 25-hydroxylase (PHM); chitin synthase A (CHI); carboxylesterase (COE); and arginine kinase (AK).

RESULTS

Based on larval mortality, the duration of the larval stage in days, pupal weight, and the accumulation of the target gene transcript, we demonstrated the efficacy of bacterial dsRNA delivery for the functional effects on larval development. Providing dsRNA targeted to JHP, CHI, COE and AK by bacteria led to a significant decrease in transcript accumulation and an increase in larval mortality.

CONCLUSION

Bacteria expressing dsRNA targeting essential T. absoluta genes supplied in artificial diet are efficient to screen RNAi target-genes. The oral delivery of dsRNA by bacteria is a novel potential alternative for the control of T. absoluta based on RNAi. © 2019 Society of Chemical Industry.

Prospects, challenges and current status of RNAi through insect feeding

RNA interference is a phenomenon in which the introduction of double-stranded RNA (dsRNA) into cells triggers the degradation of the complementary messenger RNA in a sequence-specific manner. Suppressing expression of vital genes could lead to insect death, therefore this technology has been considered as a potential strategy for insect pest control. There are three main routes of dsRNA administration into insects: (i) injections to the hemolymph, (ii) topical, and (iii) feeding. In this review, we focus on dsRNA administration through feeding. We summarize novel strategies that have been developed to improve the efficacy of this method, such as the use of nano-based formulations, engineered microorganisms, and transgenic plants. We also expose the hurdles that have to be overcome in order to use this technique as a reliable pest management method. © 2019 Society of Chemical Industry.

Symbiosis in Sustainable Agriculture: Can Olive Fruit Fly Bacterial Microbiome Be Useful in Pest Management?

The applied importance of symbiosis has been gaining recognition. The relevance of symbiosis has been increasing in agriculture, in developing sustainable practices, including pest management. Insect symbiotic microorganisms' taxonomical and functional diversity is high, and so is the potential of manipulation of these microbial partners in suppressing pest populations. These strategies, which rely on functional organisms inhabiting the insect, are intrinsically less susceptible to external environmental variations and hence likely to overcome some of the challenges posed by climate change. Rates of climate change in the Mediterranean Basin are expected to exceed global trends for most variables, and this warming will also affect olive production and impact the interactions of olives and their main pest, the obligate olive fruit fly (Bactrocera oleae). This work summarizes the current knowledge on olive fly symbiotic bacteria towards the potential development of symbiosis-based strategies for olive fruit fly control. Particular emphasis is given to Candidatus Erwinia dacicola, an obligate, vertically transmitted endosymbiont that allows the insect to cope with the olive-plant produced defensive compound oleuropein, as a most promising target for a symbiosis disruption approach.

Novel RNAi delivery systems in the control of medical and veterinary pests

RNA interference (RNAi) is a transformative technology with great potential to control, study or even protect insects and acarines through the knockdown of target gene expression. RNAi offers unprecedented levels of control, but fundamental to its successful deployment is the need to deliver 'trigger' RNA in an appropriate fashion giving due consideration to potential barriers of RNAi efficiency, safety, and the intended purpose of the knockdown. This short review focusses on recent innovations in RNAi delivery that are designed for, or could be adapted for use with, insect and acarine pests of medical or veterinary importance.

Arboviruses and the Challenge to Establish Systemic and Persistent Infections in Competent Mosquito Vectors: The Interaction With the RNAi Mechanism

Arboviruses are capable to establish long-term persistent infections in mosquitoes that do not affect significantly the physiology of the insect vectors. Arbovirus infections are controlled by the RNAi machinery via the production of viral siRNAs and the formation of RISC complexes targeting viral genomes and mRNAs. Engineered arboviruses that contain cellular gene sequences can therefore be transformed to "viral silencing vectors" for studies of gene function in reverse genetics approaches. More specifically, "ideal" viral silencing vectors must be competent to induce robust RNAi effects while other interactions with the host immune system should be kept at a minimum to reduce non-specific effects. Because of their inconspicuous nature, arboviruses may approach the "ideal" viral silencing vectors in insects and it is therefore worthwhile to study the mechanisms by which the interactions with the RNAi machinery occur. In this review, an analysis is presented of the antiviral RNAi response in mosquito vectors with respect to the major types of arboviruses (alphaviruses, flaviviruses, bunyaviruses, and others). With respect to antiviral defense, the exo-RNAi pathway constitutes the major mechanism while the contribution of both miRNAs and viral piRNAs remains a contentious issue. However, additional mechanisms exist in mosquitoes that are capable to enhance or restrict the efficiency of viral silencing vectors such as the amplification of RNAi effects by DNA forms, the existence of incorporated viral elements in the genome and the induction of a non-specific systemic response by Dicer-2. Of significance is the observation that no major "viral suppressors of RNAi" (VSRs) seem to be encoded by arboviral genomes, indicating that relatively tight control of the activity of the RNA-dependent RNA polymerase (RdRp) may be sufficient to maintain the persistent character of arbovirus infections. Major strategies for improvement of viral silencing vectors therefore are proposed to involve engineering of VSRs and modifying of the properties of the RdRp. Because of safety issues (pathogen status), however, arbovirus-based silencing vectors are not well suited for practical applications, such as RNAi-based mosquito control. In that case, related mosquito-specific viruses that also establish persistent infections and may cause similar RNAi responses may represent a valuable alternative solution.

Molecular mechanisms influencing efficiency of RNA interference in insects

RNA interference (RNAi) is an endogenous, sequence-specific gene-silencing mechanism elicited by small RNA molecules. RNAi is a powerful reverse genetic tool, and is currently being utilized for managing insects and viruses. Widespread implementation of RNAi-based pest management strategies is currently hindered by inefficient and highly variable results when different insect species, strains, developmental stages, tissues, and genes are targeted. Mechanistic studies have shown that double-stranded ribonucleases (dsRNases), endosomal entrapment, deficient function of the core machinery, and inadequate immune stimulation contribute to limited RNAi efficiency. However, a comprehensive understanding of the molecular mechanisms limiting RNAi efficiency remains elusive. Recent advances in dsRNA stability in physiological tissues, dsRNA internalization into cells, the composition and function of the core RNAi machinery, as well as small-interfering RNA/double-stranded RNA amplification and spreading mechanisms are reviewed to establish a global understanding of the obstacles impeding wider understanding of RNAi mechanisms in insects. © 2018 Society of Chemical Industry.

Management of Pest Insects and Plant Diseases by Non-Transformative RNAi

Since the discovery of RNA interference (RNAi), scientists have made significant progress towards the development of this unique technology for crop protection. The RNAi mechanism works at the mRNA level by exploiting a sequence-dependent mode of action with high target specificity due to the design of complementary dsRNA molecules, allowing growers to target pests more precisely compared to conventional agrochemicals. The delivery of RNAi through transgenic plants is now a reality with some products currently in the market. Conversely, it is also expected that more RNA-based products reach the market as non-transformative alternatives. For instance, topically applied dsRNA/siRNA (SIGS - Spray Induced Gene Silencing) has attracted attention due to its feasibility and low cost compared to transgenic plants. Once on the leaf surface, dsRNAs can move directly to target pest cells (e.g., insects or pathogens) or can be taken up indirectly by plant cells to then be transferred into the pest cells. Water-soluble formulations containing pesticidal dsRNA provide alternatives, especially in some cases where plant transformation is not possible or takes years and cost millions to be developed (e.g., perennial crops). The ever-growing understanding of the RNAi mechanism and its limitations has allowed scientists to develop non-transgenic approaches such as trunk injection, soaking, and irrigation. While the technology has been considered promising for pest management, some issues such as RNAi efficiency, dsRNA degradation, environmental risk assessments, and resistance evolution still need to be addressed. Here, our main goal is to review some possible strategies for non-transgenic delivery systems, addressing important issues related to the use of this technology.

Strategies for Enhanced Crop Resistance to Insect Pests

Insect pests are responsible for substantial crop losses worldwide through direct damage and transmission of plant diseases, and novel approaches that complement or replace broad-spectrum chemical insecticides will facilitate the sustainable intensification of food production in the coming decades. Multiple strategies for improved crop resistance to insect pests, especially strategies relating to plant secondary metabolism and immunity and microbiome science, are becoming available. Recent advances in metabolic engineering of plant secondary chemistry offer the promise of specific toxicity or deterrence to insect pests; improved understanding of plant immunity against insects provides routes to optimize plant defenses against insects; and the microbiomes of insect pests can be exploited, either as a target or as a vehicle for delivery of insecticidal agents. Implementation of these advances will be facilitated by ongoing advances in plant breeding and genetic technologies.

Hype or opportunity? Using microbial symbionts in novel strategies for insect pest control

All insects, including pest species, are colonized by microorganisms, variously located in the gut and within insect tissues. Manipulation of these microbial partners can reduce the pest status of insects, either by modifying insect traits (e.g. altering the host range or tolerance of abiotic conditions, reducing insect competence to vector disease agents) or by reducing fitness. Strategies utilizing heterologous microorganisms (i.e. derived from different insect species) and genetically-modified microbial symbionts are under development, particularly in relation to insect vectors of human disease agents. There is also the potential to target microorganisms absolutely required by the insect, resulting in insect mortality or suppression of insect growth or fecundity. This latter approach is particularly valuable for insect pests that depend on nutrients from symbiotic microorganisms to supplement their nutritionally-inadequate diet, e.g. insects feeding through the life cycle on vertebrate blood (cimicid bugs, anopluran lice, tsetse flies), plant sap (whiteflies, aphids, psyllids, planthoppers, leafhoppers/sharpshooters) and sound wood (various xylophagous beetles and some termites). Further research will facilitate implementation of these novel insect pest control strategies, particularly to ensure specificity of control agents to the pest insect without dissemination of bio-active compounds, novel microorganisms or their genes into the wider environment.

Comparative Genomics of Facultative Bacterial Symbionts Isolated from European Orius Species Reveals an Ancestral Symbiotic Association

Pest control in agriculture employs diverse strategies, among which the use of predatory insects has steadily increased. The use of several species within the genus Orius in pest control is widely spread, particularly in Mediterranean Europe. Commercial mass rearing of predatory insects is costly, and research efforts have concentrated on diet manipulation and selective breeding to reduce costs and improve efficacy. The characterisation and contribution of microbial symbionts to Orius sp. fitness, behaviour, and potential impact on human health has been neglected. This paper provides the first genome sequence level description of the predominant culturable facultative bacterial symbionts associated with five Orius species (O. laevigatus, O. niger, O. pallidicornis, O. majusculus, and O. albidipennis) from several geographical locations. Two types of symbionts were broadly classified as members of the genera Serratia and Leucobacter, while a third constitutes a new genus within the Erwiniaceae. These symbionts were found to colonise all the insect specimens tested, which evidenced an ancestral symbiotic association between these bacteria and the genus Orius. Pangenome analyses of the Serratia sp. isolates offered clues linking Type VI secretion system effector–immunity proteins from the Tai4 sub-family to the symbiotic lifestyle.

Re-evaluation of insect melanogenesis research: Views from the dark side

Melanins (eumelanin and pheomelanin) are synthesized in insects for several purposes including cuticle sclerotization and color patterning, clot formation, organogenesis, and innate immunity. Traditional views of insect immunity detail the storage of pro-phenoloxidases inside specialized blood cells (hemocytes) and their release upon recognition of foreign bodies. Activated phenoloxidases convert monophenols into reactive quinones in a two-step enzymatic reaction, and until recently, the mechanism of tyrosine hydroxylation remained a mystery. Herein, we present our interpretations of these enzyme-substrate complexes. The resultant melanins are deposited onto the surface of microbes to immobilize, agglutinate, and suffocate them. Phenoloxidase activity and melanin production are not limited to the blood (hemolymph) or cuticle, as recent evidence points to more diverse, sophisticated interactions in the gut and with the resident symbionts. This review offers insight into the somewhat neglected areas of insect melanogenesis research, particularly in innate immunity, its role in beneficial insects such as pollinators, the functional versatility of phenoloxidases, and the limitations of common experimental approaches that may impede progress inadvertently.