BMP signaling dynamics in the follicle cells of multiple Drosophila species

Diversity of Drosophila egg patterning: The missing tools to explore embryonic axis formation

Focusing on selected model organisms to establish scientific communities and resources has greatly advanced our understanding of biological processes, including embryogenesis, and facilitated the translation of these data into developing human remedies. However, by restricting our research to a small number of model organisms, we risk overlooking the underlying mechanisms controlling animal diversity and speciation. Changes in cell signaling, protein compatibility, and genetic tinkering are often neglected due to the lack of molecular tools in non-traditional model organisms. The era of high-throughput genome sequencing, computational gene prediction, and emerging genome editing and imaging tools, offers an opportunity to explore novel mechanisms of organismal development and homeostasis. As we develop new model platforms, it is imperative to prioritize resources effectively. What criteria make an organism a "good" candidate for becoming a new model organism for exploring embryogenesis? The axis of the Drosophila embryo is set during eggshell patterning. Although species with a dorsal ridge exhibit dramatically different patterns of the dorsalization signal, epidermal growth factor receptor activation, compared to Drosophila melanogaster, the embryonic dorsal-ventral axis remains consistent. Despite the increasing number of sequenced fly species' genomes, the experimental tools necessary to study these species are still lagging. Here, we emphasize the need to further develop genetic and molecular tools for studying nontraditional model organisms to understand complex processes like evolution of maternal contribution and correct embryonic body axis. We address current challenges in achieving these goals, such as genetic markers, selectable markers, and the efficiency of CRISPR/Cas9 mediated genomic editing.

Germ Granule Evolution Provides Mechanistic Insight into Drosophila Germline Development

The copackaging of mRNAs into biomolecular condensates called germ granules is a conserved strategy to posttranscriptionally regulate germline mRNAs. In Drosophila melanogaster, mRNAs accumulate in germ granules by forming homotypic clusters, aggregates containing multiple transcripts from the same gene. Nucleated by Oskar (Osk), homotypic clusters are generated through a stochastic seeding and self-recruitment process that requires the 3' untranslated region (UTR) of germ granule mRNAs. Interestingly, the 3' UTR belonging to germ granule mRNAs, such as nanos (nos), have considerable sequence variations among Drosophila species and we hypothesized that this diversity influences homotypic clustering. To test our hypothesis, we investigated the homotypic clustering of nos and polar granule component (pgc) in four Drosophila species and concluded that clustering is a conserved process used to enrich germ granule mRNAs. However, we discovered germ granule phenotypes that included significant changes in the abundance of transcripts present in species' homotypic clusters, which also reflected diversity in the number of coalesced primordial germ cells within their embryonic gonads. By integrating biological data with computational modeling, we found that multiple mechanisms underlie naturally occurring germ granule diversity, including changes in nos, pgc, osk levels and/or homotypic clustering efficacy. Furthermore, we demonstrated how the nos 3' UTR from different species influences nos clustering, causing granules to have ∼70% less nos and increasing the presence of defective primordial germ cells. Our results highlight the impact that evolution has on germ granules, which should provide broader insight into processes that modify compositions and activities of other classes of biomolecular condensate.

Evolutionary changes in germ granule mRNA content are driven by multiple mechanisms in Drosophila

The co-packaging of mRNAs into biomolecular condensates called germ granules is a conserved strategy to post-transcriptionally regulate mRNAs that function in germline development and maintenance. In D. melanogaster, mRNAs accumulate in germ granules by forming homotypic clusters, aggregates that contain multiple transcripts from a specific gene. Nucleated by Oskar (Osk), homotypic clusters in D. melanogaster are generated through a stochastic seeding and self-recruitment process that requires the 3' UTR of germ granule mRNAs. Interestingly, the 3' UTR belonging to germ granule mRNAs, such as nanos (nos), have considerable sequence variations among Drosophila species. Thus, we hypothesized that evolutionary changes in the 3' UTR influences germ granule development. To test our hypothesis, we investigated the homotypic clustering of nos and polar granule component (pgc) in four Drosophila species and concluded that homotypic clustering is a conserved developmental process used to enrich germ granule mRNAs. Additionally, we discovered that the number of transcripts found in nos and/or pgc clusters could vary significantly among species. By integrating biological data with computational modeling, we determined that multiple mechanisms underlie naturally occurring germ granule diversity, including changes in nos, pgc, osk levels, and/or homotypic clustering efficacy. Finally, we found that the nos 3' UTR from different species can alter the efficacy of nos homotypic clustering, resulting in germ granules with reduced nos accumulation. Our findings highlight the impact that evolution has on the development of germ granules and may provide insight into processes that modify the content of other classes of biomolecular condensates.

Nebulous without white: annotated long-read genome assembly and CRISPR/Cas9 genome engineering in Drosophila nebulosa

The diversity among Drosophila species presents an opportunity to study the molecular mechanisms underlying the evolution of biological phenomena. A challenge to investigating these species is that, unlike the plethora of molecular and genetics tools available for D. melanogaster research, many other species do not have sequenced genomes; a requirement for employing these tools. Selecting transgenic flies through white (w) complementation has been commonly practiced in numerous Drosophila species. While tolerated, the disruption of w is associated with impaired vision, among other effects in D. melanogaster. The D. nebulosa fly has a unique mating behavior which requires vision, and is thus unable to successfully mate in dark conditions. Here, we hypothesized that the disruption of w will impede mating success. As a first step, using PacBio long-read sequencing, we assembled a high-quality annotated genome of D. nebulosa. Using these data, we employed CRISPR/Cas9 to successfully disrupt the w gene. As expected, D. nebulosa males null for w did not court females, unlike several other mutant strains of Drosophila species whose w gene has been disrupted. In the absence of mating, no females became homozygous null for w. We conclude that gene disruption via CRISPR/Cas9 genome engineering is a successful tool in D. nebulosa, and that the w gene is necessary for mating. Thus, an alternative selectable marker unrelated to vision is desirable.

In locus analysis of patterning evolution of the BMP type II receptor Wishful thinking

Proper tissue patterning is an essential step during organ formation. During this process, genes are expressed in distinct patterns, defining boundaries for future functional domains. The bone morphogenetic protein (BMP) signaling pathway sets the anterior domain during eggshell patterning. Previously, the Drosophila melanogaster homolog of BMPR2, Wishful thinking (WIT), was shown to be required for BMP signaling and patterning during eggshell formation. Expressed in a conserved anterior pattern, the width of wit patterning in the follicular epithelium is evolutionarily divergent between Drosophila species. We used genome editing to demonstrate how the gene pattern divergence is controlled in cis within the wit locus of D. virilis Furthermore, unlike direct targets of BMP signaling, we demonstrate how one transcription factor binding site shapes the pattern of WIT in D. melanogaster by negative regulation. However, changes in this site are not sufficient to explain the evolution of wit patterning, suggesting that a positive regulatory element that controls pattern divergence remains to be discovered.

Gene regulation during Drosophila eggshell patterning

A common path to the formation of complex 3D structures starts with an epithelial sheet that is patterned by inductive cues that control the spatiotemporal activities of transcription factors. These activities are then interpreted by the cis-regulatory regions of the genes involved in cell differentiation and tissue morphogenesis. Although this general strategy has been documented in multiple developmental contexts, the range of experimental models in which each of the steps can be examined in detail and evaluated in its effect on the final structure remains very limited. Studies of the Drosophila eggshell patterning provide unique insights into the multiscale mechanisms that connect gene regulation and 3D epithelial morphogenesis. Here we review the current understanding of this system, emphasizing how the recent identification of cis-regulatory regions of genes within the eggshell patterning network enables mechanistic analysis of its spatiotemporal dynamics and evolutionary diversification. It appears that cis-regulatory changes can account for only some aspects of the morphological diversity of Drosophila eggshells, such as the prominent differences in the number of the respiratory dorsal appendages. Other changes, such as the appearance of the respiratory eggshell ridges, are caused by changes in the spatial distribution of inductive signals. Both types of mechanisms are at play in this rapidly evolving system, which provides an excellent model of developmental patterning and morphogenesis.

Two Drosophilids exhibit distinct EGF pathway patterns in oogenesis

Deciphering the evolution of morphological structures is a remaining challenge in the field of developmental biology. The respiratory structures of insect eggshells, called the dorsal appendages, provide an outstanding system for exploring these processes since considerable information is known about their patterning and morphogenesis in Drosophila melanogaster and dorsal appendage number and morphology vary widely across Drosophilid species. We investigated the patterning differences that might facilitate morphogenetic differences between D. melanogaster, which produces two oar-like structures first by wrapping and then elongating the tubes via cell intercalation and cell crawling, and Scaptodrosophila lebanonensis, which produces a variable number of appendages simply by cell intercalation and crawling. Analyses of BMP pathway components thickveins and P-Mad demonstrate that anterior patterning is conserved between these species. In contrast, EGF signaling exhibits significant differences. Transcripts for the ligand encoded by gurken localize similarly in the two species, but this morphogen creates a single dorsolateral primordium in S. lebanonensis as defined by activated MAP kinase and the downstream marker broad. Expression patterns of pointed, argos, and Capicua, early steps in the EGF pathway, exhibit a heterochronic shift in S. lebanonensis relative to those seen in D. melanogaster. We demonstrate that the S. lebanonensis Gurken homolog is active in D. melanogaster but is insufficient to alter downstream patterning responses, indicating that Gurken-EGF receptor interactions do not distinguish the two species' patterning. Altogether, these results differentiate EGF signaling patterns between species and shed light on how changes to the regulation of patterning genes may contribute to different tube-forming mechanisms.

Epithelial Patterning, Morphogenesis, and Evolution: Drosophila Eggshell as a Model

Understanding the mechanisms driving tissue and organ formation requires knowledge across scales. How do signaling pathways specify distinct tissue types? How does the patterning system control morphogenesis? How do these processes evolve? The Drosophila egg chamber, where EGF and BMP signaling intersect to specify unique cell types that construct epithelial tubes for specialized eggshell structures, has provided a tractable system to ask these questions. Work there has elucidated connections between scales of development, including across evolutionary scales, and fostered the development of quantitative modeling tools. These tools and general principles can be applied to the understanding of other developmental processes across organisms.

Simple Expression Domains Are Regulated by Discrete CRMs During Drosophila Oogenesis

Eggshell patterning has been extensively studied in Drosophila melanogaster. However, the cis-regulatory modules (CRMs), which control spatiotemporal expression of these patterns, are vastly unexplored. The FlyLight collection contains >7000 intergenic and intronic DNA fragments that, if containing CRMs, can drive the transcription factor GAL4. We cross-listed the 84 genes known to be expressed during D. melanogaster oogenesis with the ∼1200 listed genes of the FlyLight collection, and found 22 common genes that are represented by 281 FlyLight fly lines. Of these lines, 54 show expression patterns during oogenesis when crossed to an UAS-GFP reporter. Of the 54 lines, 16 recapitulate the full or partial pattern of the associated gene pattern. Interestingly, while the average DNA fragment size is ∼3 kb in length, the vast majority of fragments show one type of spatiotemporal pattern in oogenesis. Mapping the distribution of all 54 lines, we found a significant enrichment of CRMs in the first intron of the associated genes’ model. In addition, we demonstrate the use of different anteriorly active FlyLight lines as tools to disrupt eggshell patterning in a targeted manner. Our screen provides further evidence that complex gene patterns are assembled combinatorially by different CRMs controlling the expression of genes in simple domains.

The repertoire of epithelial morphogenesis on display: Progressive elaboration of Drosophila egg structure

Epithelial structures are foundational for tissue organization in all metazoans. Sheets of epithelial cells form lateral adhesive junctions and acquire apico-basal polarity perpendicular to the surface of the sheet. Genetic analyses in the insect model, Drosophila melanogaster, have greatly advanced our understanding of how epithelial organization is established, and how it is modulated during tissue morphogenesis. Major insights into collective cell migrations have come from analyses of morphogenetic movements within the adult follicular epithelium that cooperates with female germ cells to build a mature egg. Epithelial follicle cells progress through tightly choreographed phases of proliferation, patterning, reorganization and migrations, before they differentiate to form the elaborate structures of the eggshell. Distinct structural domains are organized by differential adhesion, within which lateral junctions are remodeled to further shape the organized epithelia. During collective cell migrations, adhesive interactions mediate supracellular organization of planar polarized macromolecules, and facilitate crawling over the basement membrane or traction against adjacent cell surfaces. Comparative studies with other insects are revealing the diversification of morphogenetic movements for elaboration of epithelial structures. This review surveys the repertoire of follicle cell morphogenesis, to highlight the coordination of epithelial plasticity with progressive differentiation of a secretory epithelium. Technological advances will keep this tissue at the leading edge for interrogating the precise spatiotemporal regulation of normal epithelial reorganization events, and provide a framework for understanding pathological tissue dysplasia.

Diversity of epithelial morphogenesis during eggshell formation in drosophilids

The eggshells of drosophilid species provide a powerful model for studying the origins of morphological diversity. The dorsal appendages, or respiratory filaments, of these eggshells display a remarkable interspecies variation in number and shape, and the epithelial patterning underlying the formation of these structures is an area of active research. To extend the analysis of dorsal appendage formation to include morphogenesis, we developed an improved 3D image reconstruction approach. This approach revealed considerable interspecies variation in the cell shape changes and neighbor exchanges underlying appendage formation. Specifically, although the appendage floor in Drosophila melanogaster is formed through spatially ordered neighbor exchanges, the same structure in Scaptodrosophila pattersoni is formed through extreme changes in cell shape, whereas Drosophila funebris appears to display a combination of both cellular mechanisms. Furthermore, localization patterns of Par3/Bazooka suggest a self-organized, cell polarity-based origin for the variability of appendage number in S. pattersoni. Our results suggest that species deploy different combinations of apically and basally driven mechanisms to convert a two-dimensional primordium into a three-dimensional structure, and provide new directions for exploring the molecular origins of interspecies morphological variation.

Evolutionary changes in TGFα distribution underlie morphological diversity in eggshells from Drosophila species

Drosophila eggshells display remarkable morphological diversity among species; however, the molecular origin of this structural diversification is mostly unknown. Here, we analyzed the dorsal ridge (DR), a lumen-like structure along the dorsal side of eggshells, from numerous Drosophila species. This structure varies in length and width across species, and is absent from D. melanogaster eggshells. We associated DR formation with distinct spatiotemporal changes in epidermal growth factor receptor (EGFR) activation, which acts as a key receptor in eggshell patterning. We show that changes in the distribution of the TGFα-like ligand Gurken (GRK), a crucial ligand for axis formation, underlies EGFR activation and DR formation in D. willistoni. Furthermore, we demonstrate that GRK from D. willistoni rescues a grk-null D. melanogaster fly and, remarkably, it is also sufficient to generate a DR-like structure on its eggshell.

Zfrp8/PDCD2 is required in ovarian stem cells and interacts with the piRNA pathway machinery

The maintenance of stem cells is central to generating diverse cell populations in many tissues throughout the life of an animal. Elucidating the mechanisms involved in how stem cells are formed and maintained is crucial to understanding both normal developmental processes and the growth of many cancers. Previously, we showed that Zfrp8/PDCD2 is essential for the maintenance of Drosophila hematopoietic stem cells. Here, we show that Zfrp8/PDCD2 is also required in both germline and follicle stem cells in the Drosophila ovary. Expression of human PDCD2 fully rescues the Zfrp8 phenotype, underlining the functional conservation of Zfrp8/PDCD2. The piRNA pathway is essential in early oogenesis, and we find that nuclear localization of Zfrp8 in germline stem cells and their offspring is regulated by some piRNA pathway genes. We also show that Zfrp8 forms a complex with the piRNA pathway protein Maelstrom and controls the accumulation of Maelstrom in the nuage. Furthermore, Zfrp8 regulates the activity of specific transposable elements also controlled by Maelstrom and Piwi. Our results suggest that Zfrp8/PDCD2 is not an integral member of the piRNA pathway, but has an overlapping function, possibly competing with Maelstrom and Piwi.

Methods for studying oogenesis

Drosophila oogenesis is an excellent system for the study of developmental cell biology. Active areas of research include stem cell maintenance, gamete development, pattern formation, cytoskeletal regulation, intercellular communication, intercellular transport, cell polarity, cell migration, cell death, morphogenesis, cell cycle control, and many more. The large size and relatively simple organization of egg chambers make them ideally suited for microscopy of both living and fixed whole mount tissue. A wide range of tools is available for oogenesis research. Newly available shRNA transgenic lines provide an alternative to classic loss-of-function F2 screens and clonal screens. Gene expression can be specifically controlled in either germline or somatic cells using the Gal4/UAS system. Protein trap lines provide fluorescent tags of proteins expressed at endogenous levels for live imaging and screening backgrounds. This review provides information on many available reagents and key methods for research in oogenesis.

Chorion patterning: a window into gene regulation and Drosophila species' relatedness

Changes in gene regulation are associated with the evolution of morphologies. However, the specific sequence information controlling gene expression is largely unknown and discovery is time and labor consuming. We use the intricate patterning of follicle cells to probe species' relatedness in the absence of sequence information. We focus on one of the major families of genes that pattern the Drosophila eggshell, the Chorion protein (Cp). Systematically screening for the spatiotemporal patterning of all nine Cp genes in three species (Drosophila melanogaster, D. nebulosa, and D. willistoni), we found that most genes are expressed dynamically during mid and late stages of oogenesis. Applying an annotation code, we transformed the data into binary matrices that capture the complexity of gene expression. Gene patterning is sufficient to predict species' relatedness, consistent with their phylogeny. Surprisingly, we found that expression domains of most genes are different among species, suggesting that Cp regulation is rapidly evolving. In addition, we found a morphological novelty along the dorsalmost side of the eggshell, the dorsal ridge. Our matrix analysis placed the dorsal ridge domain in a cluster of epidermal growth factor receptor associated domains, which was validated through genetic and chemical perturbations. Expression domains are regulated cooperatively or independently by signaling pathways, supporting that complex patterns are combinatorially assembled from simple domains.

Co-option of a coordinate system defined by the EGFr and Dpp pathways in the evolution of a morphological novelty

Background

Morphological innovation is an elusive and fascinating concept in evolutionary biology. A novel structure may open up an array of possibilities for adaptation, and thus is fundamental to the evolution of complex multicellular life. We use the respiratory appendages on the dorsal-anterior side of the Drosophila eggshell as a model system for morphological novelty. To study the co-option of genetic pathways in the evolution of this novelty we have compared oogenesis and eggshell patterning in Drosophila melanogaster with Ceratitis capitata, a dipteran whose eggs do not bear dorsal appendages.

Results

During the final stages of oogenesis, the appendages are formed by specific groups of cells in the follicular epithelium of the egg chamber. These cells are defined via signaling activity of the Dpp and EGFr pathways, and we find that both pathways are active in C. capitata oogenesis. The transcription factor gene mirror is expressed downstream of EGFr activation in a dorsolateral domain in the D. melanogaster egg chamber, but could not be detected during C. capitata oogenesis. In D. melanogaster, mirror regulates the expression of two important genes: broad, which defines the appendage primordia, and pipe, involved in embryonic dorsoventral polarity. In C. capitata, broad remains expressed ubiquitously throughout the follicular epithelium, and is not restricted to the appendage primordia. Interestingly pipe expression did not differ between the two species.

Conclusions

Our analysis identifies both broad and mirror as important nodes that have been redeployed in the Drosophila egg chamber patterning network in the evolution of a morphologically novel feature. Further, our results show how pre-existing signals can provide an epithelium with a spatial coordinate system, which can be co-opted for novel patterns.

The Drosophila BMPRII, wishful thinking, is required for eggshell patterning

The Drosophila eggshell is an elaborate structure that is derived from a monolayer of follicular epithelium surrounding the developing oocyte within the female ovary. The bone morphogenetic protein (BMP) signaling pathway is essential for controlling the patterning and morphogenesis of the eggshell. During oogenesis, the roles of patterning and morphogenesis by the BMP type I receptor thickveins (tkv) have been studied extensively. However, signaling through this pathway requires both type I and II receptors, and the latter has yet to be established in oogenesis. We focus on wishful thinking (wit), the Drosophila homolog to the mammalian BMP type II receptor, BMPRII. We found that wit is expressed dynamically in the FCs of D. melanogaster in an evolutionary conserved pattern. The expression patterns are highly correlated with the dynamics of the BMP signaling, which is consistent with our finding that wit is a target of BMP signaling. Furthermore, we established that WIT is necessary for BMP signaling, and loss of WIT is associated with cell autonomous loss of BMP responses. Of importance, we demonstrated that perturbations in WIT led to changes in eggshell morphologies in domains that are patterned by BMP signaling. Previous studies have shown a role for WIT in BMP signaling during neurogenesis; however, our results reveal a role for WIT in epithelial cells' development.

Evolution of BMP signaling in Drosophila oogenesis: a receptor-based mechanism

The bone morphogenetic protein (BMP) signaling pathway is a conserved regulator of cellular and developmental processes in animals. The mechanisms underlying BMP signaling activation differ among tissues and mostly reflect changes in the expression of pathway components. BMP signaling is one of the major pathways responsible for the patterning of the Drosophila eggshell, a complex structure derived from a layer of follicle cells (FCs) surrounding the developing oocyte. Activation of BMP signaling in the FCs is dynamic. Initially, signaling is along the anterior-posterior (A/P) axis; later, signaling acquires dorsal-ventral (D/V) polarity. These dynamics are regulated by changes in the expression pattern of the type I BMP receptor thickveins (tkv). We recently found that signaling dynamics and TKV patterning are highly correlated in the FCs of multiple Drosophila species. In addition, we showed that signaling patterns are spatially different among species. Here, we use a mathematical model to simulate the dynamics and differences of BMP signaling in numerous species. This model predicts that qualitative and quantitative changes in receptor expression can lead to differences in the spatial pattern of BMP signaling. We tested these predications experimentally in three different Drosophila species and through genetic perturbations of BMP signaling in D. melanogaster. On the basis of our results, we concluded that changes in tkv patterning can account for the experimentally observed differences in the patterns of BMP signaling in multiple Drosophila species.

Position matters: variability in the spatial pattern of BMP modulators generates functional diversity

Bone morphogenetic proteins (BMPs) perform a variety of functions during development. Considering a single BMP, what enables its multiple roles in tissues of varied sizes and shapes? What regulates the spatial distribution and activity patterns of the BMP in these different developmental contexts? Some BMP functions require controlling spread of the BMP morphogen, while others require formation of localized, high concentration peaks of BMP activity. Here we review work in Drosophila that describes spatial regulation of the BMP encoded by decapentaplegic (dpp) in different developmental contexts. We concentrate on extracellular modulation of BMP function and discuss the mechanisms that generate concentrated peaks of Dpp activity, subdivide territories of different activity levels or regulate spread of the Dpp morphogen from a point source. We compare these findings with data from vertebrates and non-model organisms to discuss how changes in the regulation of Dpp distribution by extracellular modulators may lead to variability in dpp function in different species.

Regulation of BMP activity and range in Drosophila wing development

Bone morphogenetic protein (BMP) signaling controls development and maintenance of many tissues. Genetic and quantitative approaches in Drosophila reveal that ligand isoforms show distinct function in wing development. Spatiotemporal control of BMP patterning depends on a network of extracellular proteins Pent, Ltl and Dally that regulate BMP signaling strength and morphogen range. BMP-mediated feedback regulation of Pent, Ltl, and Dally expression provides a system where cells actively respond to, and modify, the extracellular morphogen landscape to form a gradient that exhibits remarkable properties, including proportional scaling of BMP patterning with tissue size and the modulation of uniform tissue growth. This system provides valuable insights into mechanisms that mitigate the influence of variability to regulate cell-cell interactions and maintain organ function.