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1.  Delivery of circulating lipoproteins to specific neurons in the Drosophila brain regulates systemic insulin signaling 
eLife  2014;3:e02862.
The Insulin signaling pathway couples growth, development and lifespan to nutritional conditions. Here, we demonstrate a function for the Drosophila lipoprotein LTP in conveying information about dietary lipid composition to the brain to regulate Insulin signaling. When yeast lipids are present in the diet, free calcium levels rise in Blood Brain Barrier glial cells. This induces transport of LTP across the Blood Brain Barrier by two LDL receptor-related proteins: LRP1 and Megalin. LTP accumulates on specific neurons that connect to cells that produce Insulin-like peptides, and induces their release into the circulation. This increases systemic Insulin signaling and the rate of larval development on yeast-containing food compared with a plant-based food of similar nutritional content.
DOI: http://dx.doi.org/10.7554/eLife.02862.001
eLife digest
How does an animal sense if it is well nourished or not, and then regulate its metabolism appropriately? This process largely relies on the animal's body deciphering signals that that are transmitted between different organs in the form of molecules and hormones. Many animals—ranging from insects to mammals (including humans)—also use their brains to sense and decipher these nutritional signals.
A signaling pathway involving the hormone insulin controls how various different animals grow and develop—and how long they will live—based on these animals' food intake. Insulin is produced in mammals by an organ called the pancreas. But in the fruit fly Drosophila, this hormone is produced by cells within different tissues, including the insect’s brain.
The fruit fly is used to study many biological processes because it is easy to work with in a laboratory. Insulin-producing cells make and release insulin-like molecules into the insect's hemolymph (a blood-like fluid) in response to sugar and to other nutrients (which are detected via molecules generated in a fruit fly organ called the fat body). The fat body produces lipophorin, a protein which carries fat molecules in the hemolymph, and which is known to be able to move from the hemolymph to the brain and accumulate within the brain. The fat body also produces lipid transfer protein (or LTP), which transfers fats absorbed or made within the insect's gut onto lipophorin, and can also unload fat molecules to other insect cells. If LTP can also enter the brain, and what it might do there, was unclear.
Brankatschk et al.now discover that LTP can cross the ‘blood brain barrier’ in fruit fly larvae and can accumulate over time on their insulin-producing cells and the neurons in direct contact with these cells. This accumulation depends on the flies’ diet: flies fed a diet made from yeast cells accumulated LTP on these neurons, while those fed only on sugar and proteins did not.
Furthermore Brankatschk et al. found that when they switched flies from a yeast-based to a plant-based diet, the larvae grew more slowly and the flies lived longer. Both of the diets contained abundant calories and nutrients, but contained slightly different kinds of fat molecules. The fly larvae on the plant-based diet also accumulated less LTP on their insulin-pathway neurons, and insulin signaling was reduced.
Branskatschk et al. also found that fat molecules from the yeast-based diet activated the cells of the blood brain barrier, and that this encouraged LTP to be transported the brain. Blocking LTP from crossing the blood brain barrier reduced insulin signaling, slowed the growth of the fly larvae, and extended the lifespan of the flies.
These findings of Brankatschk et al. thus reveal that fat-containing molecules carry information about specific nutrients to the brain. The extent to which these mechanisms operate in other animals—such as mammals—remains to be explored.
DOI: http://dx.doi.org/10.7554/eLife.02862.002
doi:10.7554/eLife.02862
PMCID: PMC4210815  PMID: 25275323
lipoprotein; insulin; blood brain barrier; D. melanogaster
2.  Integrating Body and Organ Size in Drosophila: Recent Advances and Outstanding Problems 
Over the past two decades, fundamental strides in physiology and genetics have allowed us to finally grasp the developmental mechanisms regulating body size, primarily in one model organism: the fruit fly Drosophila melanogaster. In Drosophila, as in all animals, final body size is regulated by the rate and duration of growth. These studies have identified important roles for the insulin and the target of rapamycin (TOR) signaling pathways in regulating the growth rate of the larva, the stage most important in determining final adult size. Furthermore, they have shown that the insulin/TOR pathway interacts with hormonal systems, like ecdysone and juvenile hormone, to regulate the timing of development and hence the duration of growth. This interaction allows the growing larvae to integrate cues from the environment with environmentally sensitive developmental windows to ensure that optimal size and proportions are reached given the larval rearing conditions. Results from this work have opened up new avenues of studies, including how environmental cues are integrated to regulate developmental time and how organs maintain proportional growth. Other researchers interested in the evolution of body size are beginning to apply these results to studies of body size evolution and the generation of allometry. With these new findings, and with the developments to come, the field of size control finds itself in the fortunate position of finally being able to tackle century old questions of how organisms achieve final adult size and proportions. This review discusses the state of the art of size control from a Drosophila perspective, and outlines an approach to resolving outstanding issues.
doi:10.3389/fendo.2012.00049
PMCID: PMC3356080  PMID: 22654869
environmental effects on body size; insulin/target of rapamycin signaling; ecdysone; juvenile hormone; regulation of organ growth; growth rates; developmental timing; genetics of body size and proportions
3.  Genome-wide dFOXO targets and topology of the transcriptomic response to stress and insulin signalling 
Over 700 direct transcriptional targets of the dFOXO transcription factor are identified in the adult fruit fly. dFOXO-bound genes are conserved between worm and fly, but dFOXO is not the sole mediator of the transcriptional response to changes in insulin signalling in the fly.
More than 700 direct transcriptional targets of dFOXO were determined in the adult Drosophila female, in the wild-type or an insulin-signalling mutant.dFOXO has an important role in the wild-type fly and is important for transcription of numerous signalling components including TOR and Sos.While dFOXO is an important effector of the insulin signalling pathway, it is required for only a portion of the transcriptional changes that occur in response to alterations in the pathway in the fly, and in many cases indirectly.There is strong evolutionary conservation of dFOXO-bound genes between the worm and the fly, specifically enriched in regulatory genes.
Forkhead Box-O (FoxO) transcription factors are crucial players in numerous cellular and organismal processes including metabolism, stress protection, cellular differentiation, cell-cycle arrest, apoptosis and lifespan. FoxOs are regulated by a number of signalling pathways, including negative regulation by insulin/insulin-like growth factor signalling (IIS) (Partridge and Bruning, 2008; Salih and Brunet, 2008). The fruit fly Drosophila melanogaster has a single FoxO orthologue—dFOXO. dFOXO is capable of extending fly lifespan, as well as being required for lifespan extension in response to downregulation of IIS (Giannakou et al, 2004; Hwangbo et al, 2004; Slack et al, 2011). To further our understanding of dFOXO biology, we uncover over 700 direct dFOXO targets in the adult female fly, both in the wild-type fly and in a mutant with reduced IIS activity.
dFOXO is directly required for transcription of several components of IIS and interacting pathways, such as the gene encoding the target of rapamycin (TOR) kinase, in the wild-type fly. Indeed, the removal of dFOXO results in reduced signal through these pathways. The genomic locations occupied by dFOXO in adults are different from those observed by others in larvae or cultured cells (Puig et al, 2003; Teleman et al, 2008), indicating that dFOXO binding is influenced by developmental stage and/or cell type. These locations remain unchanged upon activation of dFOXO by stresses or reduced IIS in the adult, but the binding of dFOXO to the same sites is increased. Genetically induced reduction in IIS results in activation/repression of a greater number of direct dFOXO targets than observed in the wild-type fly.
To determine the relationship between dFOXO and IIS in the adult fly, we identify the part of the IIS transcriptional response that is controlled by dFOXO, both directly and indirectly. We observe that aspects of the transcriptional response to changes in IIS can take place in the absence of dFOXO, indicating that other transcriptional regulators must be involved. This is different to the situation in the worm Caenorhabditis elegans where the worm FoxO, encoded by the daf-16 gene, is required for all the effects of a reduction in IIS (Kenyon et al, 1993; Gems et al, 1998; Murphy et al, 2003). On the other hand, the existence of dFOXO-independent effects is in accordance with genetic experiments in the fly where lifespan extension and xenobiotic resistance caused by a reduction in IIS are dependent on dFOXO, while lowered fecundity and body size, delayed development and resistance to paraquat are not (Slack et al, 2011). Promoter analyses revealed GATA and other forkhead factors as candidate mediators of the dFOXO-independent effects in the fly.
Despite the different topology of the transcriptomic response to IIS changes in the two organisms, there is genome-wide evolutionary conservation of dFOXO targets between the fly and the worm (Figure 9), enriched for a second tier of regulators including the dHR96/daf-12 nuclear hormone receptor.
FoxO transcription factors, inhibited by insulin/insulin-like growth factor signalling (IIS), are crucial players in numerous organismal processes including lifespan. Using genomic tools, we uncover over 700 direct dFOXO targets in adult female Drosophila. dFOXO is directly required for transcription of several IIS components and interacting pathways, such as TOR, in the wild-type fly. The genomic locations occupied by dFOXO in adults are different from those observed in larvae or cultured cells. These locations remain unchanged upon activation by stresses or reduced IIS, but the binding is increased and additional targets activated upon genetic reduction in IIS. We identify the part of the IIS transcriptional response directly controlled by dFOXO and the indirect effects and show that parts of the transcriptional response to IIS reduction do not require dfoxo. Promoter analyses revealed GATA and other forkhead factors as candidate mediators of the indirect and dfoxo-independent effects. We demonstrate genome-wide evolutionary conservation of dFOXO targets between the fly and the worm Caenorhabditis elegans, enriched for a second tier of regulators including the dHR96/daf-12 nuclear hormone receptor.
doi:10.1038/msb.2011.36
PMCID: PMC3159968  PMID: 21694719
dFOXO; Drosophila; insulin/insulin-like growth factor signalling; transcription
4.  FOXO Regulates Organ-Specific Phenotypic Plasticity In Drosophila 
PLoS Genetics  2011;7(11):e1002373.
Phenotypic plasticity, the ability for a single genotype to generate different phenotypes in response to environmental conditions, is biologically ubiquitous, and yet almost nothing is known of the developmental mechanisms that regulate the extent of a plastic response. In particular, it is unclear why some traits or individuals are highly sensitive to an environmental variable while other traits or individuals are less so. Here we elucidate the developmental mechanisms that regulate the expression of a particularly important form of phenotypic plasticity: the effect of developmental nutrition on organ size. In all animals, developmental nutrition is signaled to growing organs via the insulin-signaling pathway. Drosophila organs differ in their size response to developmental nutrition and this reflects differences in organ-specific insulin-sensitivity. We show that this variation in insulin-sensitivity is regulated at the level of the forkhead transcription factor FOXO, a negative growth regulator that is activated when nutrition and insulin signaling are low. Individual organs appear to attenuate growth suppression in response to low nutrition through an organ-specific reduction in FOXO expression, thereby reducing their nutritional plasticity. We show that FOXO expression is necessary to maintain organ-specific differences in nutritional-plasticity and insulin-sensitivity, while organ-autonomous changes in FOXO expression are sufficient to autonomously alter an organ's nutritional-plasticity and insulin-sensitivity. These data identify a gene (FOXO) that modulates a plastic response through variation in its expression. FOXO is recognized as a key player in the response of size, immunity, and longevity to changes in developmental nutrition, stress, and oxygen levels. FOXO may therefore act as a more general regulator of plasticity. These data indicate that the extent of phenotypic plasticity may be modified by changes in the expression of genes involved in signaling environmental information to developmental processes.
Author Summary
The ability of an organism to respond to its environment is a defining quality of life. However, why are some characteristics or individuals sensitive to environmental change while others are not? We identified the mechanism that controls the response of growing organs to a particularly important environmental factor—developmental nutrition. In all animals, a decrease in developmental nutrition reduces final body and organ size. However, the size of some organs is less responsive to changes in nutrition than others. In a male fruit fly, it is the size of the genitals that is resistant to dietary restriction. This is achieved by the male fruit fly reducing expression of a key gene in their genitalia. This gene, FOXO, forms part of the insulin signaling system, which signals food levels to tissues in all animals. By lowering the production of FOXO, the genitalia are able to “ignore” hormonal signals that tell the rest of the body to grow slowly due to limited food. The ability of tissues to become insensitive to nutritional information is a characteristic of many tumors and also underlies type 2 diabetes. Our data may therefore provide insight into the origin and treatment of both conditions.
doi:10.1371/journal.pgen.1002373
PMCID: PMC3213149  PMID: 22102829
5.  Dopamine drives Drosophila sechellia adaptation to its toxic host 
eLife  null;3:e03785.
Many insect species are host-obligate specialists. The evolutionary mechanism driving the adaptation of a species to a toxic host is, however, intriguing. We analyzed the tight association of Drosophila sechellia to its sole host, the fruit of Morinda citrifolia, which is toxic to other members of the melanogaster species group. Molecular polymorphisms in the dopamine regulatory protein Catsup cause infertility in D. sechellia due to maternal arrest of oogenesis. In its natural host, the fruit compensates for the impaired maternal dopamine metabolism with the precursor l-DOPA, resuming oogenesis and stimulating egg production. l-DOPA present in morinda additionally increases the size of D. sechellia eggs, what in turn enhances early fitness. We argue that the need of l-DOPA for successful reproduction has driven D. sechellia to become an M. citrifolia obligate specialist. This study illustrates how an insect's dopaminergic system can sustain ecological adaptations by modulating ontogenesis and development.
DOI: http://dx.doi.org/10.7554/eLife.03785.001
eLife digest
Many insect species rely on another animal or plant species for their own reproduction. For example, a fruit fly called Drosophila sechellia—which is found in the Seychelles—will only feed and lay its eggs on the fruit of a species of tree called Morinda citrifolia. This pairing is particularly unusual because these fruits, commonly called morinda, are toxic to all other Drosophila species.
Female Drosophila sechellia flies produce fewer eggs than other Drosophila species, which makes it difficult to raise this species in the laboratory. However providing these flies with morinda fruit, or chemicals from this fruit, was known to increase the expression of many genes involved in egg production and stimulate the flies to lay more eggs. Nevertheless, the reasons why this species of fruit fly depends on the toxic morinda fruit were unclear.
Now Lavista-Llanos et al. have confirmed that feeding Drosophila sechellia flies a diet of morinda fruit—instead of a typical laboratory diet—causes these flies to produce six-times as many eggs. Furthermore, this morinda diet had effects that went beyond the previously reported stimulatory effects of acidic chemicals in the fruits triggering the flies to lay more eggs.
Egg production in flies is controlled by dopamine, and a lack of this hormone is known to reduce the size of other fruit flies' ovaries and the number of eggs that they produce. Lavista-Llanos et al. went on to feed female Drosophila sechellia flies the chemical building blocks that make up the dopamine hormone, and one such chemical (called l-DOPA) caused the flies to produce more eggs. This did not occur when the flies were fed dopamine itself.
Lavista-Llanos et al. discovered that Drosophila sechellia flies have very high levels of dopamine but much lower levels of l-DOPA than other Drosophila fly species; and revealed that this was because a gene called Catsup is mutated in Drosophila sechellia. When Lavista-Llanos et al. mutated the same gene in another Drosophila species, the mutant flies produced fewer eggs and abnormally accumulated an enzyme (which makes l-DOPA) inside their developing eggs—just like Drosophila sechellia.
The presence of l-DOPA in morinda fruit partly compensates for the reduced fertility of Drosophila sechellia and the other flies with mutations in the Catsup gene. Lavista-Llanos et al. discovered that removing or replacing l-DOPA in the morinda fruit caused the flies to produce fewer eggs. Furthermore, the l-DOPA present in morinda increases the size of Drosophila sechellia eggs, which in turn helps them to survive their toxic environment.
Lavista-Llanos et al. also discovered that feeding dopamine to vulnerable Drosophila species helps them to cope with the toxic effects of a morinda diet. One of the next challenges will be to uncover how chemicals from the morinda fruit affect the dopamine system of the flies. It is also unknown if the dopamine hormone also influences the strong attraction that Drosophila sechellia feels towards its only host, the morinda fruit.
DOI: http://dx.doi.org/10.7554/eLife.03785.002
doi:10.7554/eLife.03785
PMCID: PMC4270095  PMID: 25487989
Drosophila sechellia; Morinda citrifolia; dopamine; oogenesis; evolution; tyrosine hydroxilase; D. melanogaster; other
6.  The Drosophila F-box protein Fbxl7 binds to the protocadherin Fat and regulates Dachs localization and Hippo signaling 
eLife  2014;3:e03383.
The Drosophila protocadherin Fat (Ft) regulates growth, planar cell polarity (PCP) and proximodistal patterning. A key downstream component of Ft signaling is the atypical myosin Dachs (D). Multiple regions of the intracellular domain of Ft have been implicated in regulating growth and PCP but how Ft regulates D is not known. Mutations in Fbxl7, which encodes an F-box protein, result in tissue overgrowth and abnormalities in proximodistal patterning that phenocopy deleting a specific portion of the intracellular domain (ICD) of Ft that regulates both growth and PCP. Fbxl7 binds to this same portion of the Ft ICD, co-localizes with Ft to the proximal edge of cells and regulates the levels and asymmetry of D at the apical membrane. Fbxl7 can also regulate the trafficking of proteins between the apical membrane and intracellular vesicles. Thus Fbxl7 functions in a subset of pathways downstream of Ft and links Ft to D localization.
DOI: http://dx.doi.org/10.7554/eLife.03383.001
eLife digest
Multi-cellular organisms are made up of cells that are organized into tissues and organs that reach a predictable size and shape at the end of their development. To do this, cells must be able to sense their position and orientation within the body and know when to stop growing.
Epithelial cells—which make up the outer surface of an animal's body and line the cavities of its internal organs—connect to each other to form flat sheets. These sheets of cells contain structures that are oriented along the plane of the sheet. However, how this so-called ‘planar cell polarity’ coordinates with cell growth in order to build complex tissues and organs remains to be discovered.
A protein called Fat is a major player in both planar cell polarity and the Hippo signaling pathway, which controls cell growth. As such, the Fat protein appears to be crucial for controlling the size and shape of organs. Mutations in the Fat protein cause massive tissue overgrowth, prevent planar cell polarity being established correctly, and stop the legs and wings of fruit flies developing normally.
The Fat protein also plays a role in distributing another protein called Dachs—which is also part of the Hippo signaling pathway. In epithelial cells of the developing wing, Dachs is mostly located on the side of the cell that is closest to the tip of the developing wing (the so-called ‘distal surface’). How Fat and Dachs work together is not understood, but it is known that they do not bind to each other directly.
Now, Bosch et al. show that in the fruit fly Drosophila, the Fat protein binds to another protein called Fbxl7. Flies that cannot produce working Fbxl7 have defects in some aspects of planar cell polarity and a modest increase in tissue growth. Fbxl7 seems to account for part, but not all, of the ability of Fat to restrict tissue growth. Furthermore, a lack of the Fbxl7 protein results in a spreading of Dachs protein across the apical surface—which faces out of the epithelial sheet—of epithelial cells. On the other hand, if Fbxl7 is over-expressed, Dachs is driven to the interior of each cell. Hence, a normal level of Fbxl7 protein restricts the Dachs protein to the correct parts of the cell surface.
Together, the findings of Bosch et al. show that the Fbxl7 protein is a key link between the Fat and Dachs proteins. These results also provide an understanding of how growth and planar cell polarity—two processes that are essential for normal development of all multi-cellular organisms—are coordinated.
DOI: http://dx.doi.org/10.7554/eLife.03383.002
doi:10.7554/eLife.03383
PMCID: PMC4144329  PMID: 25107277
Hippo pathway; cell proliferation; planar cell polarity; cadherin; vesicle; ubiquitin; D. melanogaster
7.  The neuronal architecture of the mushroom body provides a logic for associative learning 
eLife  null;3:e04577.
We identified the neurons comprising the Drosophila mushroom body (MB), an associative center in invertebrate brains, and provide a comprehensive map describing their potential connections. Each of the 21 MB output neuron (MBON) types elaborates segregated dendritic arbors along the parallel axons of ∼2000 Kenyon cells, forming 15 compartments that collectively tile the MB lobes. MBON axons project to five discrete neuropils outside of the MB and three MBON types form a feedforward network in the lobes. Each of the 20 dopaminergic neuron (DAN) types projects axons to one, or at most two, of the MBON compartments. Convergence of DAN axons on compartmentalized Kenyon cell–MBON synapses creates a highly ordered unit that can support learning to impose valence on sensory representations. The elucidation of the complement of neurons of the MB provides a comprehensive anatomical substrate from which one can infer a functional logic of associative olfactory learning and memory.
DOI: http://dx.doi.org/10.7554/eLife.04577.001
eLife digest
One of the key goals of neuroscience is to understand how specific circuits of brain cells enable animals to respond optimally to the constantly changing world around them. Such processes are more easily studied in simpler brains, and the fruit fly—with its small size, short life cycle, and well-developed genetic toolkit—is widely used to study the genes and circuits that underlie learning and behavior.
Fruit flies can learn to approach odors that have previously been paired with food, and also to avoid any odors that have been paired with an electric shock, and a part of the brain called the mushroom body has a central role in this process. When odorant molecules bind to receptors on the fly's antennae, they activate neurons in the antennal lobe of the brain, which in turn activate cells called Kenyon cells within the mushroom body. The Kenyon cells then activate output neurons that convey signals to other parts of the brain.
It is known that relatively few Kenyon cells are activated by any given odor. Moreover, it seems that a given odor activates different sets of Kenyon cells in different flies. Because the association between an odor and the Kenyon cells it activates is unique to each fly, each fly needs to learn through its own experiences what a particular pattern of Kenyon cell activation means.
Aso et al. have now applied sophisticated molecular genetic and anatomical techniques to thousands of different transgenic flies to identify the neurons of the mushroom body. The resulting map reveals that the mushroom body contains roughly 2200 neurons, including seven types of Kenyon cells and 21 types of output cells, as well as 20 types of neurons that use the neurotransmitter dopamine. Moreover, this map provides insights into the circuits that support odor-based learning. It reveals, for example, that the mushroom body can be divided into 15 anatomical compartments that are each defined by the presence of a specific set of output and dopaminergic neuron cell types. Since the dopaminergic neurons help to shape a fly's response to odors on the basis of previous experience, this organization suggests that these compartments may be semi-autonomous information processing units.
In contrast to the rest of the insect brain, the mushroom body has a flexible organization that is similar to that of the mammalian brain. Elucidating the circuits that support associative learning in fruit flies should therefore make it easier to identify the equivalent mechanisms in vertebrate animals.
DOI: http://dx.doi.org/10.7554/eLife.04577.002
doi:10.7554/eLife.04577
PMCID: PMC4273437  PMID: 25535793
mushroom body; olfactory learning; associative memory; neuronal circuits; dopamine; plasticity; D. melanogaster
8.  Identification of a new stem cell population that generates Drosophila flight muscles 
eLife  2014;3:e03126.
How myoblast populations are regulated for the formation of muscles of different sizes is an essentially unanswered question. The large flight muscles of Drosophila develop from adult muscle progenitor (AMP) cells set-aside embryonically. The thoracic segments are all allotted the same small AMP number, while those associated with the wing-disc proliferate extensively to give rise to over 2500 myoblasts. An initial amplification occurs through symmetric divisions and is followed by a switch to asymmetric divisions in which the AMPs self-renew and generate post-mitotic myoblasts. Notch signaling controls the initial amplification of AMPs, while the switch to asymmetric division additionally requires Wingless, which regulates Numb expression in the AMP lineage. In both cases, the epidermal tissue of the wing imaginal disc acts as a niche expressing the ligands Serrate and Wingless. The disc-associated AMPs are a novel muscle stem cell population that orchestrates the early phases of adult flight muscle development.
DOI: http://dx.doi.org/10.7554/eLife.03126.001
eLife digest
Muscle tissues must grow and change to accommodate the needs of an animal at various stages in its life. For example, fruit flies begin life as larvae and their muscles must help them move their soft bodies. Later, when the flies mature into adults, the muscles must provide power for flight and support for the insects' external skeletons.
Like other animal tissues, muscles develop from non-specialized stem cells which at first have the potential to become almost any cell type, but later change to become more specialized. Studies of fruit flies, in particular, have yielded insights on how pools of stem cell are created and regulated. Fruit flies are small and easier to study than larger organisms, and as a result, scientists have learned a lot about their genetics and cell biology. Gunage et al. have now identified the stem cell pools that develop into flight muscle tissue, and found that these cells were set aside for the muscles when the fruit fly embryo was still developing.
Fruit flies have large forewings that power flight, and small modified hindwings (called halteres) that help the insect to balance when flying. Gunage et al. reveal that a small, but similar, number of cells are set aside to make both both the tiny muscles that will move the halteres and the much larger flight muscles that move the forewings. However, the cells that contribute to the flight muscles divide to give far more muscle progenitor cells than their haltere counterparts, and make a couple of thousand cells that eventually fuse to form muscle fibers.
Gunage et al. looked at how the flight muscle progenitors multiplied by genetically engineering some of the stem cells in fruit fly larvae so that when each cell divided, its two daughter cells would fluoresce with different colors. One daughter cell would glow green and the other glow red. Gunage et al. found that at first the cells multiply equally, with half the new cells coming from a ‘red’ stem cell and the other half from a ‘green’ cell—meaning that the number of cells increases exponentially. Later, the balance shifted so that either more red cells than green cells were produced, or vice versa. This results in a ‘linear’ increase in number of muscle progenitor cells. Furthermore, Gunage et al. identified the proteins that orchestrate the switch from equal to unequal multiplying of these cells at the different times points in the fruit flies’ development.
The next challenge is to see if these stem cells that form the muscles are also available for repair of mature muscle tissue after it is damaged. If this is so, these stems cells might perform a similar function to muscle satellite cells, which are found in the mature muscles of mammals and other vertebrates.
DOI: http://dx.doi.org/10.7554/eLife.03126.002
doi:10.7554/eLife.03126
PMCID: PMC4171707  PMID: 25135939
stem cells; muscles; numb; Wnt; Notch; niche; D. melanogaster
9.  Regulation of branching dynamics by axon-intrinsic asymmetries in Tyrosine Kinase Receptor signaling 
eLife  2014;3:e01699.
Axonal branching allows a neuron to connect to several targets, increasing neuronal circuit complexity. While axonal branching is well described, the mechanisms that control it remain largely unknown. We find that in the Drosophila CNS branches develop through a process of excessive growth followed by pruning. In vivo high-resolution live imaging of developing brains as well as loss and gain of function experiments show that activation of Epidermal Growth Factor Receptor (EGFR) is necessary for branch dynamics and the final branching pattern. Live imaging also reveals that intrinsic asymmetry in EGFR localization regulates the balance between dynamic and static filopodia. Elimination of signaling asymmetry by either loss or gain of EGFR function results in reduced dynamics leading to excessive branch formation. In summary, we propose that the dynamic process of axon branch development is mediated by differential local distribution of signaling receptors.
DOI: http://dx.doi.org/10.7554/eLife.01699.001
eLife digest
In the human brain, 100 billion neurons form 100 trillion connections. Each neuron consists of a cell body with numerous small branch-like projections known as dendrites (from the Greek word for ‘tree’), plus a long cable-like structure called the axon. Neurons receive electrical inputs from neighboring cells via their dendrites, and then relay these signals onto other cells in their network via their axons.
The development of the brain relies on new neurons integrating successfully into existing networks. Axon branching helps with this by enabling a single neuron to establish connections with several cells, but it is unclear how individual neurons decide when and where to form branches. Now, Zschätzsch et al. have revealed the mechanism behind this process in the fruit fly, Drosophila.
Mutant flies that lack a protein called EGFR produce abnormal numbers of axon branches, suggesting that this molecule regulates branch formation. Indeed in fruit flies, just as in mammals, the developing brain initially produces excessive numbers of branches, which are subsequently pruned to leave only those that have formed appropriate connections. In Drosophila, an uneven distribution of EGFR between branches belonging to the same axon acts as a signal to regulate this pruning process.
To examine this mechanism in more detail, high-resolution four-dimensional imaging was used to study brains that had been removed from Drosophila pupae and kept alive in special culture chambers. Axon branching and loss could now be followed in real time, and were found to occur more slowly in brains that lacked EGFR. The receptor controlled the branching of axons by influencing the distribution of another protein called actin, which is a key component of the internal skeleton that gives cells their structure.
In addition to providing new insights into a fundamental aspect of brain development, the work of Zschätzsch et al. also highlights the importance of stochastic events in shaping the network of connections within the developing brain. These findings may well be relevant to ongoing efforts to map the human brain ‘connectome’.
DOI: http://dx.doi.org/10.7554/eLife.01699.002
doi:10.7554/eLife.01699
PMCID: PMC3990184  PMID: 24755286
axonal branching; brain development; signaling; D. melanogaster
10.  Molecular mechanism of size control in development and human diseases 
Cell Research  2011;21(5):715-729.
How multicellular organisms control their size is a fundamental question that fascinated generations of biologists. In the past 10 years, tremendous progress has been made toward our understanding of the molecular mechanism underlying size control. Original studies from Drosophila showed that in addition to extrinsic nutritional and hormonal cues, intrinsic mechanisms also play important roles in the control of organ size during development. Several novel signaling pathways such as insulin and Hippo-LATS signaling pathways have been identified that control organ size by regulating cell size and/or cell number through modulation of cell growth, cell division, and cell death. Later studies using mammalian cell and mouse models also demonstrated that the signaling pathways identified in flies are also conserved in mammals. Significantly, recent studies showed that dysregulation of size control plays important roles in the development of many human diseases such as cancer, diabetes, and hypertrophy.
doi:10.1038/cr.2011.63
PMCID: PMC3203678  PMID: 21483452
size control; cell proliferation; cell size; insulin signaling; Hippo-LATS signaling
11.  Dual mode of embryonic development is highlighted by expression and function of Nasonia pair-rule genes 
eLife  2014;3:e01440.
Embryonic anterior–posterior patterning is well understood in Drosophila, which uses ‘long germ’ embryogenesis, in which all segments are patterned before cellularization. In contrast, most insects use ‘short germ’ embryogenesis, wherein only head and thorax are patterned in a syncytial environment while the remainder of the embryo is generated after cellularization. We use the wasp Nasonia (Nv) to address how the transition from short to long germ embryogenesis occurred. Maternal and gap gene expression in Nasonia suggest long germ embryogenesis. However, the Nasonia pair-rule genes even-skipped, odd-skipped, runt and hairy are all expressed as early blastoderm pair-rule stripes and late-forming posterior stripes. Knockdown of Nv eve, odd or h causes loss of alternate segments at the anterior and complete loss of abdominal segments. We propose that Nasonia uses a mixed mode of segmentation wherein pair-rule genes pattern the embryo in a manner resembling Drosophila at the anterior and ancestral Tribolium at the posterior.
DOI: http://dx.doi.org/10.7554/eLife.01440.001
eLife digest
Networks of genes that work together are widespread in nature. The conservation of individual genes across species and the tendency of their networks to stick together is a sign that they are working efficiently. Furthermore, it is common for existing gene networks to be adapted to perform new tasks, instead of new networks being invented every time a similar but distinct demand arises. One important question is: how can evolution use the same building blocks—such as the genes in a functioning network—in different ways to achieve new outcomes?
The gene network that sets up the ‘body plan’ of insects during development has been well studied, most deeply in the fruit fly, Drosophila. Like all insects, the body of a fruit fly is divided into three main parts—the head, the thorax and the abdomen—and each of these parts is made up of several smaller segments. There is a remarkable diversity of insect body plans in nature, and yet, these seem to arise from the same gene networks in the embryo.
When a Drosophila embryo is growing into a larva, all the different body segments develop at the same time. In most other insects, however, segments of the abdomen emerge later and sequentially during the development process. The ancestors of most insects are also thought to have developed in this way, which is known as ‘short germ embryogenesis’. So how did the so-called ‘long germ embryogenesis’, as observed in Drosophila, evolve from the short germ embryogenesis that is observed in most other insects?
The gene network that controls development includes the ‘pair-rule genes’ that are expressed in a pattern of alternating stripes that wrap around, top to bottom, along most of the length of the embryo. These stripes mark where the edges of each body segment will eventually develop. In fruit flies, this pattern extends along the entire length of the embryo and the stripes all appear at one time. However, in the abdominal region of short germ insects, the pair-rule genes are expressed in waves that pass through the posterior region as it grows, with new segments being added one behind the other.
Now, Rosenberg et al. have attempted to explain how the same genes can be used to direct the segmentation process in such different ways by studying another long germ insect species, the jewel wasp. Analysis of the expression of pair-rule genes in the jewel wasp shows that it uses a mixed strategy to control segmentation. The development of segments at the front of its body is directed in the same way as the fruit fly, with all these segments laid down together. However, the segments at the rear of the body are only patterned later, one after the other, like most other insects.
The work of Rosenberg et al. suggests that the jewel wasp represents an intermediate step between ancestral insects and Drosophila in the evolution of the gene network that patterns the ‘body plan’. Identifying and studying these intermediate forms allows us to understand the ways in which evolution can innovate by building upon what has come before.
DOI: http://dx.doi.org/10.7554/eLife.01440.002
doi:10.7554/eLife.01440
PMCID: PMC3941026  PMID: 24599282
Nasonia vitripennis; Tribolium; embryonic patterning; evolution; segmentation; pair-rule genes; D. melanogaster; other
12.  A Caenorhabditis elegans Wild Type Defies the Temperature–Size Rule Owing to a Single Nucleotide Polymorphism in tra-3 
PLoS Genetics  2007;3(3):e34.
Ectotherms rely for their body heat on surrounding temperatures. A key question in biology is why most ectotherms mature at a larger size at lower temperatures, a phenomenon known as the temperature–size rule. Since temperature affects virtually all processes in a living organism, current theories to explain this phenomenon are diverse and complex and assert often from opposing assumptions. Although widely studied, the molecular genetic control of the temperature–size rule is unknown. We found that the Caenorhabditis elegans wild-type N2 complied with the temperature–size rule, whereas wild-type CB4856 defied it. Using a candidate gene approach based on an N2 × CB4856 recombinant inbred panel in combination with mutant analysis, complementation, and transgenic studies, we show that a single nucleotide polymorphism in tra-3 leads to mutation F96L in the encoded calpain-like protease. This mutation attenuates the ability of CB4856 to grow larger at low temperature. Homology modelling predicts that F96L reduces TRA-3 activity by destabilizing the DII-A domain. The data show that size adaptation of ectotherms to temperature changes may be less complex than previously thought because a subtle wild-type polymorphism modulates the temperature responsiveness of body size. These findings provide a novel step toward the molecular understanding of the temperature–size rule, which has puzzled biologists for decades.
Author Summary
Biologists are fascinated by variation in body size, which is hardly surprising, considering that the range of body sizes spans orders of magnitude from bacteria to blue whales. Even within species, body sizes can vary dramatically. This intraspecies variation is intriguing because it suggests strong associations between body size and environment. Already in 1847, Bergmann noticed that mammals tend to be larger in colder environments. More recently similar relationships were found for ectotherms, which rely for their body heat on the temperature of their surroundings, where more than 85% of the species studied grew larger at lower temperatures. This phenomenon, dubbed the temperature–size rule, has caused a renewed interest to understand how temperature affects body size. Yet the control of the temperature–size rule remains enigmatic, and the hypotheses proposed have been inconclusive. In this paper the authors show that a single nucleic acid change in one gene is required for regulation of the temperature–size rule in the nematode C. elegans. Using protein modelling they also show that this subtle change in DNA decreases the function of the encoded protein. The data suggest that temperature adaptation can be simple and far less complex than previously thought.
doi:10.1371/journal.pgen.0030034
PMCID: PMC1808073  PMID: 17335351
13.  Quantification of gait parameters in freely walking wild type and sensory deprived Drosophila melanogaster 
eLife  2013;2:e00231.
Coordinated walking in vertebrates and multi-legged invertebrates such as Drosophila melanogaster requires a complex neural network coupled to sensory feedback. An understanding of this network will benefit from systems such as Drosophila that have the ability to genetically manipulate neural activities. However, the fly's small size makes it challenging to analyze walking in this system. In order to overcome this limitation, we developed an optical method coupled with high-speed imaging that allows the tracking and quantification of gait parameters in freely walking flies with high temporal and spatial resolution. Using this method, we present a comprehensive description of many locomotion parameters, such as gait, tarsal positioning, and intersegmental and left-right coordination for wild type fruit flies. Surprisingly, we find that inactivation of sensory neurons in the fly's legs, to block proprioceptive feedback, led to deficient step precision, but interleg coordination and the ability to execute a tripod gait were unaffected.
DOI: http://dx.doi.org/10.7554/eLife.00231.001
eLife digest
Most animals need to be able to move to survive. Animals without limbs, such as snakes, move by generating by wave-like contractions along their bodies, whereas limbed animals, such as vertebrates and arthropods, walk by coordinating the movements of multi-jointed arms and legs. Locomotion in limbed animals involves bending each joint within each arm or leg in a coordinated manner, while also ensuring that the movements of all the limbs are coordinated with each other. In bipeds such as humans, for example, it is critical that one leg is in the stance phase when the other leg is in the swing phase. The rules that govern the coordination of limbs also depend on the gait, so the rules for walking are not the same as the rules for running.
The nervous systems of bipeds and other animals that walk solve these problems by using complex neural circuits that coordinate the firing of the relevant motor neurons. Two general mechanisms are used to coordinate the firing of motor neurons. In one mechanism, local interneurons within the central nervous system coordinate motor neuron activities: in vertebrates these interneurons are found in the spinal cord. A second mechanism, termed proprioception, relies on sensory neurons that report the load and joint angles from the arms and legs back to the central nervous system, and thereby influence the firing of the motor neurons. Remarkably, both of these mechanisms, and also the types of neurons that comprise motor neuron circuits, are conserved from arthropods to vertebrates.
Mendes et al. describe a new approach that can be used to analyze how the fruit fly, D. melanogaster, walks on surfaces. They use a combination of an optical touch sensor and high-speed video imaging to follow the body of the fly as it walks, and also to record when and where it places each of its six feet on the surface as it moves. Then, using a software package called FlyWalker, they are able to extract a large of number of parameters that can be used to describe locomotion in adult fruit flies with high temporal and spatial resolution. Many of these parameters have never been measured or studied before.
Mendes et al. show that fruit flies do not display the abrupt transitions in gait that are typically observed in vertebrates. However, they do modify their neural circuits depending on their speed: indeed it appears that flies use subtly different neural circuitry for walking at slow, medium and fast speeds. Moreover, when genetic methods are used to block sensory feedback, the fly is still able to walk, albeit with reduced coordination and precision. Further, the data suggest that proprioception is less important when flies walk faster compared to when they walk more slowly. The next step in this research will be to combine this new method for analyzing locomotion in flies with the wide range of genetic tools that are available for the study of Drosophila: this will allow researchers to explore in greater detail the components of the motor neuron circuitry and their role in coordinated walking.
DOI: http://dx.doi.org/10.7554/eLife.00231.002
doi:10.7554/eLife.00231
PMCID: PMC3545443  PMID: 23326642
walking behavior; coordination; proprioception; sensory feedback; gait analysis; motor neuron; D. melanogaster
14.  A Model of Bacterial Intestinal Infections in Drosophila melanogaster 
PLoS Pathogens  2007;3(11):e173.
Serratia marcescens is an entomopathogenic bacterium that opportunistically infects a wide range of hosts, including humans. In a model of septic injury, if directly introduced into the body cavity of Drosophila, this pathogen is insensitive to the host's systemic immune response and kills flies in a day. We find that S. marcescens resistance to the Drosophila immune deficiency (imd)-mediated humoral response requires the bacterial lipopolysaccharide O-antigen. If ingested by Drosophila, bacteria cross the gut and penetrate the body cavity. During this passage, the bacteria can be observed within the cells of the intestinal epithelium. In such an oral infection model, the flies succumb to infection only after 6 days. We demonstrate that two complementary host defense mechanisms act together against such food-borne infection: an antimicrobial response in the intestine that is regulated by the imd pathway and phagocytosis by hemocytes of bacteria that have escaped into the hemolymph. Interestingly, bacteria present in the hemolymph elicit a systemic immune response only when phagocytosis is blocked. Our observations support a model wherein peptidoglycan fragments released during bacterial growth activate the imd pathway and do not back a proposed role for phagocytosis in the immune activation of the fat body. Thanks to the genetic tools available in both host and pathogen, the molecular dissection of the interactions between S. marcescens and Drosophila will provide a useful paradigm for deciphering intestinal pathogenesis.
Author Summary
The gut is a crucial interface of the host with its environment and represents an important portal of entry for pathogens. Here, we have developed a novel model of intestinal infections in the genetic model organism Drosophila melanogaster using the potent entomopathogen bacterium Serratia marcescens. In contrast to other enteropathogens, this bacterium traverses the intestinal epithelium despite a local immune response and gains access to the body cavity of the fruit fly. The cellular arm of innate immunity controls its proliferation in the hemocoele. Interestingly, ingested bacteria that have moved to the hemolymph compartment are not detected by the humoral immune system of the fly unless phagocytosis is blocked. In a septic injury model, S. marcescens kills its host in a day. In contrast, the flies succumb slowly to an intestinal infection, even though the bacterium is present in the hemolymph. We surmise that the bacterium expresses distinct virulence programs according to the mode of infection. Thanks to the genetic tools available in both host and pathogen, the molecular dissection of the interactions between S. marcescens and Drosophila will provide a useful paradigm to decipher intestinal pathogenesis.
doi:10.1371/journal.ppat.0030173
PMCID: PMC2094306  PMID: 18039029
15.  H3K27 modifications define segmental regulatory domains in the Drosophila bithorax complex 
eLife  2014;3:e02833.
The bithorax complex (BX-C) in Drosophila melanogaster is a cluster of homeotic genes that determine body segment identity. Expression of these genes is governed by cis-regulatory domains, one for each parasegment. Stable repression of these domains depends on Polycomb Group (PcG) functions, which include trimethylation of lysine 27 of histone H3 (H3K27me3). To search for parasegment-specific signatures that reflect PcG function, chromatin from single parasegments was isolated and profiled. The H3K27me3 profiles across the BX-C in successive parasegments showed a ‘stairstep’ pattern that revealed sharp boundaries of the BX-C regulatory domains. Acetylated H3K27 was broadly enriched across active domains, in a pattern complementary to H3K27me3. The CCCTC-binding protein (CTCF) bound the borders between H3K27 modification domains; it was retained even in parasegments where adjacent domains lack H3K27me3. These findings provide a molecular definition of the homeotic domains, and implicate precisely positioned H3K27 modifications as a central determinant of segment identity.
DOI: http://dx.doi.org/10.7554/eLife.02833.001
eLife digest
Like other insects, the body of the fruit fly is divided into three main parts—the head, the thorax and the abdomen—and each part, in turn, is made up of several smaller segments. The bithorax complex is a cluster of three genes that together control the identity of the segments that make up the back half of the fruit fly's body. This gene cluster has been studied for several decades and these studies have helped to further our understanding of how genetic information is accessed and used to make an animal’s body plan.
Early on in a fruit fly embryo, stretches of DNA within the bithorax complex regulate where the complex's genes are switched on, and where they are switched off. Proteins called Polycomb group proteins then keep the silenced genes off, in part by adding small chemical marks to other proteins called histones. Most DNA in a cell is wrapped around histones, and the addition of such chemical marks causes the DNA to become more tightly packed. This prevents the bithorax complex genes from being accessed and switched on. It had previously been suggested that each segment might have a unique pattern of chemical marks on the bithorax complex histones, but evidence to support this idea was lacking.
Bowman et al. have now undertaken the technically challenging task of purifying the DNA and its histones from individual segments of fruit fly embryos. This revealed that segments closer to the embryo's head contain larger stretches of bithorax complex DNA covered with histones marked by the Polycomb group proteins. Bowman et al. also found that the coverage of chemical marks on the histones changed dramatically when one segment was compared to its neighboring segments. These sharp boundaries clearly outline which regulatory regions of the DNA are switched on and which are switch off; however the same pattern is not seen for the Polycomb group proteins themselves. Instead, within the bithorax complex, the pattern of these proteins is almost identical in different segments.
The challenge now is to understand how the chemical marks and the Polycomb group proteins work together to restrict access to DNA in such precise patterns. Also—since similar gene clusters control the development of the body plans of mammals—this, in turn, might help us to understand how the Polycomb group proteins perform similar functions in human development and disease.
DOI: http://dx.doi.org/10.7554/eLife.02833.002
doi:10.7554/eLife.02833
PMCID: PMC4139060  PMID: 25082344
chromatin; Polycomb; bithorax complex; CTCF; D. melanogaster
16.  Canalization of Gene Expression and Domain Shifts in the Drosophila Blastoderm by Dynamical Attractors 
PLoS Computational Biology  2009;5(3):e1000303.
The variation in the expression patterns of the gap genes in the blastoderm of the fruit fly Drosophila melanogaster reduces over time as a result of cross regulation between these genes, a fact that we have demonstrated in an accompanying article in PLoS Biology (see Manu et al., doi:10.1371/journal.pbio.1000049). This biologically essential process is an example of the phenomenon known as canalization. It has been suggested that the developmental trajectory of a wild-type organism is inherently stable, and that canalization is a manifestation of this property. Although the role of gap genes in the canalization process was established by correctly predicting the response of the system to particular perturbations, the stability of the developmental trajectory remains to be investigated. For many years, it has been speculated that stability against perturbations during development can be described by dynamical systems having attracting sets that drive reductions of volume in phase space. In this paper, we show that both the reduction in variability of gap gene expression as well as shifts in the position of posterior gap gene domains are the result of the actions of attractors in the gap gene dynamical system. Two biologically distinct dynamical regions exist in the early embryo, separated by a bifurcation at 53% egg length. In the anterior region, reduction in variation occurs because of stability induced by point attractors, while in the posterior, the stability of the developmental trajectory arises from a one-dimensional attracting manifold. This manifold also controls a previously characterized anterior shift of posterior region gap domains. Our analysis shows that the complex phenomena of canalization and pattern formation in the Drosophila blastoderm can be understood in terms of the qualitative features of the dynamical system. The result confirms the idea that attractors are important for developmental stability and shows a richer variety of dynamical attractors in developmental systems than has been previously recognized.
Author Summary
C. H. Waddington predicted in 1942 that networks of chemical reactions in embryos can counteract the effects of variable developmental conditions to produce reliable outcomes. The experimental signature of this process, called “canalization,” is the reduction of the variation of the concentrations of molecular determinants between individuals over time. Recently, Waddington's prediction was confirmed in embryos of the fruit fly Drosophila by observing the expression of a network of genes involved in generating the basic segmented body plan of this animal. Nevertheless, the details of how interactions within this genetic network reduced variation were still not understood. We use an accurate mathematical model of a part of this genetic network to demonstrate how canalization comes about. Our results show that coupled chemical reactions having multiple steady states, or attractors, can account for the reduction of variation in development. The variation reduction process can be driven not only by chemical steady states, but also by special pathways of motion through chemical concentration space to which neighboring pathways converge. These results constitute a precise mathematical characterization of a healing process in the fruit fly embryo.
doi:10.1371/journal.pcbi.1000303
PMCID: PMC2646127  PMID: 19282965
17.  The Temporal Requirements for Insulin Signaling During Development in Drosophila 
PLoS Biology  2005;3(9):e289.
Recent studies have indicated that the insulin-signaling pathway controls body and organ size in Drosophila, and most metazoans, by signaling nutritional conditions to the growing organs. The temporal requirements for insulin signaling during development are, however, unknown. Using a temperature-sensitive insulin receptor (Inr) mutation in Drosophila, we show that the developmental requirements for Inr activity are organ specific and vary in time. Early in development, before larvae reach the “critical size” (the size at which they commit to metamorphosis and can complete development without further feeding), Inr activity influences total development time but not final body and organ size. After critical size, Inr activity no longer affects total development time but does influence final body and organ size. Final body size is affected by Inr activity from critical size until pupariation, whereas final organ size is sensitive to Inr activity from critical size until early pupal development. In addition, different organs show different sensitivities to changes in Inr activity for different periods of development, implicating the insulin pathway in the control of organ allometry. The reduction in Inr activity is accompanied by a two-fold increase in free-sugar levels, similar to the effect of reduced insulin signaling in mammals. Finally, we find that varying the magnitude of Inr activity has different effects on cell size and cell number in the fly wing, providing a potential linkage between the mode of action of insulin signaling and the distinct downstream controls of cell size and number. We present a model that incorporates the effects of the insulin-signaling pathway into the Drosophila life cycle. We hypothesize that the insulin-signaling pathway controls such diverse effects as total developmental time, total body size and organ size through its effects on the rate of cell growth, and proliferation in different organs.
Studies using a temperature-sensitive insulin receptor elucidate the temporal requirements for insulin signaling in Drosophila; insulin signaling at different times during development affects many characters, such as total developmental time, total body size and organ size.
doi:10.1371/journal.pbio.0030289
PMCID: PMC1184592  PMID: 16086608
18.  Cellular resolution models for even skipped regulation in the entire Drosophila embryo 
eLife  2013;2:e00522.
Transcriptional control ensures genes are expressed in the right amounts at the correct times and locations. Understanding quantitatively how regulatory systems convert input signals to appropriate outputs remains a challenge. For the first time, we successfully model even skipped (eve) stripes 2 and 3+7 across the entire fly embryo at cellular resolution. A straightforward statistical relationship explains how transcription factor (TF) concentrations define eve’s complex spatial expression, without the need for pairwise interactions or cross-regulatory dynamics. Simulating thousands of TF combinations, we recover known regulators and suggest new candidates. Finally, we accurately predict the intricate effects of perturbations including TF mutations and misexpression. Our approach imposes minimal assumptions about regulatory function; instead we infer underlying mechanisms from models that best fit the data, like the lack of TF-specific thresholds and the positional value of homotypic interactions. Our study provides a general and quantitative method for elucidating the regulation of diverse biological systems.
DOI: http://dx.doi.org/10.7554/eLife.00522.001
eLife digest
The transcription of genes into messenger RNA (mRNA) molecules is one of the most important processes in biology, but our present understanding of this process is largely qualitative. Molecules such as transcription factors and regions of DNA other than the region that codes for the mRNA are known to interact with each other to influence the onset of transcription, and also the rate at which it occurs. However, given the cellular concentrations of transcription factors in a developing organism, it is not known if it is possible to accurately predict their effects on transcription. Being able to make such predictions would greatly improve our understanding of how transcription and the development of an organism are controlled.
Ilsley et al. have tackled this problem by analysing a large volume of data called the Virtual Embryo dataset: produced by the Berkeley Drosophila Transcription Network Project, this dataset includes the results of mRNA expression measurements on 95 different genes at six different times during the early development of Drosophila melanogaster, a species of fruit fly. In particular, Ilsley et al. focussed on the expression at one point in time of the even skipped (eve) gene, a widely studied gene that is important for embryo development in these fruit flies. The eve gene is one of the genes responsible for dividing the fly into segments which form part of its body plan.
Without making any assumptions about the biological mechanisms that might be involved, Ilsley et al. built a statistical model that was able to predict the pattern of gene expression for a fruit fly, given the concentrations of the relevant transcription factors in the various cells within the embryo as input. The model was also able to predict the patterns of gene expression observed in other experiments involving mutations and the misexpression of fruit fly genes. Moreover, Ilsley et al. have made various predictions involving the genes Bicoid and Hunchback that can be tested experimentally in future studies.
DOI: http://dx.doi.org/10.7554/eLife.00522.002
doi:10.7554/eLife.00522
PMCID: PMC3736529  PMID: 23930223
transcriptional regulation; logistic regression; fly embryo; developmental patterning; positional information; even skipped; D. melanogaster
19.  Noninvasive Analysis of Microbiome Dynamics in the Fruit Fly Drosophila melanogaster 
Applied and Environmental Microbiology  2013;79(22):6984-6988.
The diversity and structure of the intestinal microbial community has a strong influence on life history. To understand how hosts and microbes interact, model organisms with comparatively simple microbial communities, such as the fruit fly (Drosophila melanogaster), offer key advantages. However, studies of the Drosophila microbiome are limited to a single point in time, because flies are typically sacrificed for DNA extraction. In order to test whether noninvasive approaches, such as sampling of fly feces, could be a means to assess fly-associated communities over time on the same cohort of flies, we compared the microbial communities of fly feces, dissected fly intestines, and whole flies across three different Drosophila strains. Bacterial species identified in either whole flies or isolated intestines were reproducibly found in feces samples. Although the bacterial communities of feces and intestinal samples were not identical, they shared similarities and obviously the same origin. In contrast to material from whole flies and intestines, feces samples were not compromised by Wolbachia spp. infections, which are widespread in laboratory and wild strains. In a proof-of-principle experiment, we showed that simple nutritional interventions, such as a high-fat diet or short-term starvation, had drastic and long-lasting effects on the micobiome. Thus, the analysis of feces can supplement the toolbox for microbiome studies in Drosophila, unleashing the full potential of such studies in time course experiments where multiple samples from single populations are obtained during aging, development, or experimental manipulations.
doi:10.1128/AEM.01903-13
PMCID: PMC3811555  PMID: 24014528
20.  Modularity and hormone sensitivity of the Drosophila melanogaster insulin receptor/target of rapamycin interaction proteome 
First systematic analysis of the evolutionary conserved InR/TOR pathway interaction proteome in Drosophila.Quantitative mass spectrometry revealed that 22% of identified protein interactions are regulated by the growth hormone insulin affecting membrane proximal as well as intracellular signaling complexes.Systematic RNA interference linked a significant fraction of network components to the control of dTOR kinase activity.Combined biochemical and genetic data suggest dTTT, a dTOR-containing complex required for cell growth control by dTORC1 and dTORC2 in vivo.
Cellular growth is a fundamental process that requires constant adaptations to changing environmental conditions, like growth factor and nutrient availability, energy levels and more. Over the years, the insulin receptor/target of rapamycin pathway (InR/TOR) emerged as a key signaling system for the control of metazoan cell growth. Genetic screens carried out in the fruit fly Drosophila melanogaster identified key InR/TOR pathway components and their relationships. Phenotypes such as altered cell growth are likely to emerge from perturbed dynamic networks containing InR/TOR pathway components, which stably or transiently interact with other cellular proteins to form complexes and networks thereof. Systematic studies on the topology and dynamics of protein interaction networks become therefore highly relevant to gain systems level understanding of deregulated cell growth. Despite much progress in genetic analysis only few systematic protein interaction studies have been reported for Drosophila, which in most cases lack quantitative information representing the dynamic nature of such networks. Here, we present the first quantitative affinity purification mass spectrometry (AP–MS/MS) analysis on the evolutionary conserved InR/TOR signaling network in Drosophila. Systematic RNAi-based functional analysis of identified network components revealed key components linked to the regulation of the central effector kinase dTOR. This includes also dTTT, a novel dTOR-containing complex required for the control of dTORC1 and dTORC2 in vivo.
For systematic AP–MS analysis, we generated Drosophila Kc167 cell lines inducibly expressing affinity-tagged bait proteins previously linked to InR/TOR signaling. Bait expressing Kc167 cell lines were harvested before and after insulin stimulation for subsequent affinity purification. Following LC–MS/MS analysis and probabilistic data filtering using SAINT (Choi et al, 2010), we generated a quantitative network model from 97 high confidence protein–protein interactions and 58 network components (Figure 2). The presented network displayed a high degree of orthologous interactions conserved also in human cells and identified a number of novel molecular interactions with InR/TOR signaling components for future hypothesis driven analysis.
To measure insulin-induced changes within the InR/TOR interaction proteome, we applied a recently introduced label-free quantitative MS approach (Rinner et al, 2007). The obtained quantitative data suggest that 22% of all interactions in the network are regulated by insulin. Major changes could be observed within the membrane proximal InR/chico/PI3K signaling complexes, and also in 14-3-3 protein containing signaling complexes and dTORC1, a complex that contains besides dTOR all major orthologous proteins found also in human mTORC1 including the two dTORC1 substrates d4E-BP (Thor) and S6 Kinase (S6K). Insulin triggered both, dissociation and association of dTORC1 proteins. Among the proteins that showed enhanced binding to dTORC1 upon insulin stimulation we found Unkempt, a RING-finger protein with a proposed role in ubiquitin-mediated protein degradation (Lores et al, 2010). Besides dTORC1 our systematic AP–MS analysis also revealed the presence of dTORC2, the second major TOR complex in Drosophila. dTORC2 contains the Drosophila orthologous of human mTORC2 proteins, but in contrast to dTORC1 was not affected upon insulin stimulation. Interestingly, we also found a specific set of proteins that were not linked to the canonical TOR complexes TORC1 and TORC2 in dTOR purifications. These include LqfR (liquid facets related), Pontin, Reptin, Spaghetti and the gene product of CG16908. We found the same set of proteins when we used CG16908 as a bait, suggesting complex formation among the identified proteins. None of the dTORC1/2 components besides dTOR was identified in CG16908 purifications, indicating that these proteins form dTOR complexes distinct from dTORC1 and dTORC2. Based on known interaction information from other species and data obtained from this study we refer to this complex as dTTT (Drosophila TOR, TELO2, TTI1) (Horejsi et al, 2010; [18]Hurov et al, 2010; [20]Kaizuka et al, 2010). A directed quantitative MS analysis of dTOR complex components suggests that dTORC1 is the most abundant dTOR complex we identified in Kc167 cells.
We next studied the potential roles of the identified network components for controlling the activity of the dInR/TOR pathway using systematic RNAi depletion and quantitative western blotting to measure the changes in abundance of phosphorylated substrates of dTORC1 (Thor/d4E-BP, dS6K) and dTORC2 (dPKB) in RNAi-treated cells (Figure 5). Overall, we could identify 16 proteins (out of 58) whose depletion caused an at least 50% increase or decrease in the levels of phosphorylated d4E-BP, S6K and/or PKB compared with control GFP RNAi. Besides established pathway components, we found several novel regulators within the dInR/TOR interaction network. For example, RNAi against the novel insulin-regulated dTORC1 component Unkempt resulted in enhanced phosphorylation of the dTORC1 substrate d4E-BP, which suggests a negative role for Unkempt on dTORC1 activity. In contrast, depletion of CG16908 and LqfR caused hypo-phosphorylation of all dTOR substrates similar to dTOR itself, suggesting a positive role for the dTTT complex on dTOR activity. Subsequently, we tested whether dTTT components also plays a role in dTOR-mediated cell growth in vivo. Depletion of both dTTT components, CG16908 and LqfR, in the Drosophila eye resulted in a substantial decrease in eye size. Likewise, FLP-FRT-mediated mitotic recombination resulted in CG16908 and LqfR mutant clones with a similar reduced growth phenotype as observed in dTOR mutant clones. Hence, the combined biochemical and genetic analysis revealed dTTT as a dTOR-containing complex required for the activity of both dTORC1 and dTORC2 and thus plays a critical role in controlling cell growth.
Taken together, these results illustrate how a systematic quantitative AP–MS approach when combined with systematic functional analysis in Drosophila can reveal novel insights into the dynamic organization of regulatory networks for cell growth control in metazoans.
Using quantitative mass spectrometry, this study reports how insulin affects the modularity of the interaction proteome of the Drosophila InR/TOR pathway, an evolutionary conserved signaling system for the control of metazoan cell growth. Systematic functional analysis linked a significant number of identified network components to the control of dTOR activity and revealed dTTT, a dTOR complex required for in vivo cell growth control by dTORC1 and dTORC2.
Genetic analysis in Drosophila melanogaster has been widely used to identify a system of genes that control cell growth in response to insulin and nutrients. Many of these genes encode components of the insulin receptor/target of rapamycin (InR/TOR) pathway. However, the biochemical context of this regulatory system is still poorly characterized in Drosophila. Here, we present the first quantitative study that systematically characterizes the modularity and hormone sensitivity of the interaction proteome underlying growth control by the dInR/TOR pathway. Applying quantitative affinity purification and mass spectrometry, we identified 97 high confidence protein interactions among 58 network components. In all, 22% of the detected interactions were regulated by insulin affecting membrane proximal as well as intracellular signaling complexes. Systematic functional analysis linked a subset of network components to the control of dTORC1 and dTORC2 activity. Furthermore, our data suggest the presence of three distinct dTOR kinase complexes, including the evolutionary conserved dTTT complex (Drosophila TOR, TELO2, TTI1). Subsequent genetic studies in flies suggest a role for dTTT in controlling cell growth via a dTORC1- and dTORC2-dependent mechanism.
doi:10.1038/msb.2011.79
PMCID: PMC3261712  PMID: 22068330
cell growth; InR/TOR pathway; interaction proteome; quantitative mass spectrometry; signaling
21.  Dpp Signaling Activity Requires Pentagone to Scale with Tissue Size in the Growing Drosophila Wing Imaginal Disc 
PLoS Biology  2011;9(10):e1001182.
The activity of the Dpp morphogen adapts to tissue size in the growing Drosophila wing imaginal disc, and Pentagone, an important secreted feedback regulator of the Dpp pathway, is required for this adaptation.
The wing of the fruit fly, Drosophila melanogaster, with its simple, two-dimensional structure, is a model organ well suited for a systems biology approach. The wing arises from an epithelial sac referred to as the wing imaginal disc, which undergoes a phase of massive growth and concomitant patterning during larval stages. The Decapentaplegic (Dpp) morphogen plays a central role in wing formation with its ability to co-coordinately regulate patterning and growth. Here, we asked whether the Dpp signaling activity scales, i.e. expands proportionally, with the growing wing imaginal disc. Using new methods for spatial and temporal quantification of Dpp activity and its scaling properties, we found that the Dpp response scales with the size of the growing tissue. Notably, scaling is not perfect at all positions in the field and the scaling of target gene domains is ensured specifically where they define vein positions. We also found that the target gene domains are not defined at constant concentration thresholds of the downstream Dpp activity gradients P-Mad and Brinker. Most interestingly, Pentagone, an important secreted feedback regulator of the pathway, plays a central role in scaling and acts as an expander of the Dpp gradient during disc growth.
Author Summary
Scaling, the fitting of pattern to size, manifests itself in numerous examples around us. During development, individual body parts scale up to fit the overall body size. Starved animals form smaller adults with proportionally smaller parts, and amphibian embryos can form normally proportioned adults after extreme surgical operations. How scaling is achieved is not well understood. Here, we establish the Drosophila wing imaginal disc, the precursor tissue of the adult wing, as a model to study scaling quantitatively during growth. In this model, we define scaling as the preservation of proportions of gene expression domains with tissue size during disc growth. The Decapentaplegic (Dpp) morphogen is known to play a central role in Drosophila wing formation and co-coordinately regulates growth and patterning. We found that as the disc grows, the Dpp response expands and scales with the tissue size. Interestingly, scaling is not perfect at all positions in the field. The scaling of the target gene domains is best where they have a function; Spalt, for example, scales best at the position in the anterior compartment where it helps to form one of the anterior veins of the wing. Analysis of mutants for pentagone, a transcriptional target of Dpp that encodes a secreted feedback regulator of the pathway, indicates that Pentagone plays a key role in scaling the Dpp gradient activity.
doi:10.1371/journal.pbio.1001182
PMCID: PMC3201923  PMID: 22039350
22.  Insulin/IGF-Regulated Size Scaling of Neuroendocrine Cells Expressing the bHLH Transcription Factor Dimmed in Drosophila 
PLoS Genetics  2013;9(12):e1004052.
Neurons and other cells display a large variation in size in an organism. Thus, a fundamental question is how growth of individual cells and their organelles is regulated. Is size scaling of individual neurons regulated post-mitotically, independent of growth of the entire CNS? Although the role of insulin/IGF-signaling (IIS) in growth of tissues and whole organisms is well established, it is not known whether it regulates the size of individual neurons. We therefore studied the role of IIS in the size scaling of neurons in the Drosophila CNS. By targeted genetic manipulations of insulin receptor (dInR) expression in a variety of neuron types we demonstrate that the cell size is affected only in neuroendocrine cells specified by the bHLH transcription factor DIMMED (DIMM). Several populations of DIMM-positive neurons tested displayed enlarged cell bodies after overexpression of the dInR, as well as PI3 kinase and Akt1 (protein kinase B), whereas DIMM-negative neurons did not respond to dInR manipulations. Knockdown of these components produce the opposite phenotype. Increased growth can also be induced by targeted overexpression of nutrient-dependent TOR (target of rapamycin) signaling components, such as Rheb (small GTPase), TOR and S6K (S6 kinase). After Dimm-knockdown in neuroendocrine cells manipulations of dInR expression have significantly less effects on cell size. We also show that dInR expression in neuroendocrine cells can be altered by up or down-regulation of Dimm. This novel dInR-regulated size scaling is seen during postembryonic development, continues in the aging adult and is diet dependent. The increase in cell size includes cell body, axon terminations, nucleus and Golgi apparatus. We suggest that the dInR-mediated scaling of neuroendocrine cells is part of a plasticity that adapts the secretory capacity to changing physiological conditions and nutrient-dependent organismal growth.
Author Summary
Nerve cells display a large variation in size in an organism. Thus, a fundamental question is how growth of individual cells and their organelles is regulated. We ask if there is a regulatory mechanism for scaling the size of individual nerve cells, independent of the growth of the entire central nervous system (CNS). Growth of tissues and whole organisms depends on insulin/insulin-like growth factor signaling (IIS), but it is not known whether IIS regulates the size of individual nerve cells. We therefore studied the role of IIS in the size scaling of neurons in the CNS of the fruitfly Drosophila. By targeted genetic manipulations of insulin receptor (dInR) expression in a variety of neuron types we demonstrate that the cell size is affected only in neuroendocrine cells specified by the transcription factor DIMMED (DIMM). DIMM-positive neurons displayed enlarged cell bodies after overexpression of the dInR and downstream signaling components, whereas DIMM-negative neurons did not. Knockdown of these components results in smaller neurons. This novel dInR-regulated size scaling is seen during postembryonic development, continues in the aging adult and is diet dependent. We suggest that the dInR-mediated scaling of neuroendocrine cells is part of a plasticity that adapts the secretory capacity (neurohormone production) to changing physiological conditions and nutrient-dependent organismal growth.
doi:10.1371/journal.pgen.1004052
PMCID: PMC3873260  PMID: 24385933
23.  Drosophila as a genetic and cellular model for studies on axonal growth 
Neural Development  2007;2:9.
One of the most fascinating processes during nervous system development is the establishment of stereotypic neuronal networks. An essential step in this process is the outgrowth and precise navigation (pathfinding) of axons and dendrites towards their synaptic partner cells. This phenomenon was first described more than a century ago and, over the past decades, increasing insights have been gained into the cellular and molecular mechanisms regulating neuronal growth and navigation. Progress in this area has been greatly assisted by the use of simple and genetically tractable invertebrate model systems, such as the fruit fly Drosophila melanogaster. This review is dedicated to Drosophila as a genetic and cellular model to study axonal growth and demonstrates how it can and has been used for this research. We describe the various cellular systems of Drosophila used for such studies, insights into axonal growth cones and their cytoskeletal dynamics, and summarise identified molecular signalling pathways required for growth cone navigation, with particular focus on pathfinding decisions in the ventral nerve cord of Drosophila embryos. These Drosophila-specific aspects are viewed in the general context of our current knowledge about neuronal growth.
doi:10.1186/1749-8104-2-9
PMCID: PMC1876224  PMID: 17475018
24.  Functional Evolution of cis-Regulatory Modules at a Homeotic Gene in Drosophila 
PLoS Genetics  2009;5(11):e1000709.
It is a long-held belief in evolutionary biology that the rate of molecular evolution for a given DNA sequence is inversely related to the level of functional constraint. This belief holds true for the protein-coding homeotic (Hox) genes originally discovered in Drosophila melanogaster. Expression of the Hox genes in Drosophila embryos is essential for body patterning and is controlled by an extensive array of cis-regulatory modules (CRMs). How the regulatory modules functionally evolve in different species is not clear. A comparison of the CRMs for the Abdominal-B gene from different Drosophila species reveals relatively low levels of overall sequence conservation. However, embryonic enhancer CRMs from other Drosophila species direct transgenic reporter gene expression in the same spatial and temporal patterns during development as their D. melanogaster orthologs. Bioinformatic analysis reveals the presence of short conserved sequences within defined CRMs, representing gap and pair-rule transcription factor binding sites. One predicted binding site for the gap transcription factor KRUPPEL in the IAB5 CRM was found to be altered in Superabdominal (Sab) mutations. In Sab mutant flies, the third abdominal segment is transformed into a copy of the fifth abdominal segment. A model for KRUPPEL-mediated repression at this binding site is presented. These findings challenge our current understanding of the relationship between sequence evolution at the molecular level and functional activity of a CRM. While the overall sequence conservation at Drosophila CRMs is not distinctive from neighboring genomic regions, functionally critical transcription factor binding sites within embryonic enhancer CRMs are highly conserved. These results have implications for understanding mechanisms of gene expression during embryonic development, enhancer function, and the molecular evolution of eukaryotic regulatory modules.
Author Summary
The fertilized animal embryo is a mass of uniform cells that becomes a complex, segmented, and highly organized structure of differentiated cells through the process of development. This vital process is controlled by networks of developmental genes interacting with each other on the molecular level. Because these genes are crucial for animal development, they are conserved both in function and at the DNA sequence level in related species. We have examined critical DNA sequence modules which regulate genes that pattern the early embryo in different species of the fruit fly. We found that despite rapid evolution of the DNA sequences, the regulatory sequences from one fruit fly species are able to operate when tested in another fruit fly species. Further analysis reveals that there are sequences within these regulatory DNA modules which are conserved across different species and which are critical for regulatory function. These conserved sequences represent critical binding sites for protein transcription factors. These findings have important implications for our understanding of gene regulation during development and evolution across diverse animal species ranging from the fruit fly to humans.
doi:10.1371/journal.pgen.1000709
PMCID: PMC2763271  PMID: 19893611
25.  Polarized Secretion of Drosophila EGFR Ligand from Photoreceptor Neurons Is Controlled by ER Localization of the Ligand-Processing Machinery 
PLoS Biology  2010;8(10):e1000505.
Trafficking within the endoplasmic reticulum and specialized localization of the intra-membrane protease Rhomboid regulate EGF ligand-dependent signaling in Drosophila photoreceptor axon termini.
The release of signaling molecules from neurons must be regulated, to accommodate their highly polarized structure. In the developing Drosophila visual system, photoreceptor neurons secrete the epidermal growth factor receptor ligand Spitz (Spi) from their cell bodies, as well as from their axonal termini. Here we show that subcellular localization of Rhomboid proteases, which process Spi, determines the site of Spi release from neurons. Endoplasmic reticulum (ER) localization of Rhomboid 3 is essential for its ability to promote Spi secretion from axons, but not from cell bodies. We demonstrate that the ER extends throughout photoreceptor axons, and show that this feature facilitates the trafficking of the Spi precursor, the ligand chaperone Star, and Rhomboid 3 to axonal termini. Following this trafficking step, secretion from the axons is regulated in a manner similar to secretion from cell bodies. These findings uncover a role for the ER in trafficking proteins from the neuronal cell body to axon terminus.
Author Summary
Cells secrete signaling molecules that trigger a variety of responses in neighboring cells by activating their respective cell-surface receptors. Because many cells in an organism are polarized, regulating the precise location of ligand secretion is important for controlling the position and nature of the response. During the development of the compound eye of the fruit fly Drosophila, for example, a ligand of the epidermal growth factor family called Spitz (Spi) is secreted from both the apical and basal (axonal) poles of photoreceptor cells but with different outcomes. Photoreceptor cells are recruited to the developing eye following apical secretion of Spi. Conversely, basal secretion of this same ligand, at a significant distance from the cell body, triggers differentiation of cells in the outer layer of the brain. Although secretion of Spi is known to occur at both poles of the cell, one important question is how Spi and its processing machinery are trafficked throughout the length of the photoreceptor axon to achieve basal secretion. In this study we show that the key to axonal trafficking is the regulated localization of Spi and its processing machinery, including the intramembrane protease Rhomboid, to sites within the endoplasmic reticulum (ER), which extends along the length of the axon. Two different Rhomboid proteins are expressed in photoreceptor cells, but only one of them is localized to the ER. We show that this ER-localized Rhomboid is indeed necessary and sufficient for Spi processing at axon termini. Our work therefore demonstrates how variations in intracellular localization of conserved signaling components can alter signaling outcomes dramatically. It also highlights the importance of the ER in trafficking proteins along the axon.
doi:10.1371/journal.pbio.1000505
PMCID: PMC2950126  PMID: 20957186

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