Nutrigenomic regulation of sensory plasticity
Curation statements for this article:-
Curated by eLife
eLife assessment
This important work identifies new proteins and outlines the interactions between molecular players that control diet-induced plasticity in sensory neuron function in the Drosophila taste system. The authors provide solid evidence in support of their working model and open clear avenues to follow up on downstream molecular mechanisms.
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (eLife)
- Neuroscience (eLife)
Abstract
Diet profoundly influences brain physiology, but how metabolic information is transmuted into neural activity and behavior changes remains elusive. Here, we show that the metabolic enzyme O-GlcNAc Transferase (OGT) moonlights on the chromatin of the D. melanogaster gustatory neurons to instruct changes in chromatin accessibility and transcription that underlie sensory adaptations to a high-sugar diet. OGT works synergistically with the Mitogen Activated Kinase/Extracellular signal Regulated Kinase (MAPK/ERK) rolled and its effector stripe (also known as EGR2 or Krox20) to integrate activity information. OGT also cooperates with the epigenetic silencer Polycomb Repressive Complex 2.1 (PRC2.1) to decrease chromatin accessibility and repress transcription in the high-sugar diet. This integration of nutritional and activity information changes the taste neurons’ responses to sugar and the flies’ ability to sense sweetness. Our findings reveal how nutrigenomic signaling generates neural activity and behavior in response to dietary changes in the sensory neurons.
Article activity feed
-
-
Author Response
Reviewer #1 (Public Review):
The study's primary motivating goal of understanding how nutrigenomic signaling works in different contexts. The authors propose that OGT- a sugar-sensing enzyme- connects sugar levels to chromatin accessibility. Specifically, the authors hypothesize that the OGT/Plc-PRC axis in sweet taste neurons interprets the sugar levels and alters chromatin accessibility in sugar-activated neurons. However, the detailed model presented by authors on OGT/PRC/Pcl Rolled in regulating nutrigenomic signaling relies on pharmacological treatments and overexpression of transgenes to derive genetic interactions and pathways; these approaches provide speculative rather than convincing evidence. Secondly, evidence is absent to show that PRC occupancy remains the same in other neurons (non-sweet taste neurons) …
Author Response
Reviewer #1 (Public Review):
The study's primary motivating goal of understanding how nutrigenomic signaling works in different contexts. The authors propose that OGT- a sugar-sensing enzyme- connects sugar levels to chromatin accessibility. Specifically, the authors hypothesize that the OGT/Plc-PRC axis in sweet taste neurons interprets the sugar levels and alters chromatin accessibility in sugar-activated neurons. However, the detailed model presented by authors on OGT/PRC/Pcl Rolled in regulating nutrigenomic signaling relies on pharmacological treatments and overexpression of transgenes to derive genetic interactions and pathways; these approaches provide speculative rather than convincing evidence. Secondly, evidence is absent to show that PRC occupancy remains the same in other neurons (non-sweet taste neurons) under varied sugar levels or OGT manipulations. Hence, the claim that OGT-mediated access to chromatin via PRC-Plc is a key regulatory arm of nutrigenomic signaling needs further substantiation.
We thank the reviewer for their thoughtful reading of the manuscript and their suggestions. We disagree with the reviewer’s assessment that our work only relies solely on overexpression and pharmacological treatments and that this provides only “speculative” evidence. Indeed, both of the other two reviewers praised our approach:
Reviewer 2: “This is an elegant group of experiments revealing mechanisms for how nutrigenomic signaling triggers cellular responses to nutrients”
Reviewer 3: “Strengths: Good genetically targeted interventions; Thorough exploration of the epistatic relationships between different players in the system … The conclusions in this manuscript are mostly well or at least reasonably supported by data.
All of our experiments combine genetic manipulations in combination with dietary and/or pharmacological treatments to show that molecular, neural, and behavioral taste phenotypes arise only in specific contexts, so no single phenotype occurs due to nonspecific manipulations. Without this approach, most of these epistatic relationships would be largely inaccessible in this system. We have also used a combination of both genetic and pharmacological tools to implicate not only genes but also their function (i.e., enzymatic activity) to nutrient-specific effects. Third, we established causality and relationship by inducing and rescuing the molecular, behavioral, and electrophysiological phenotypes. Thus, our model is based on a combination of direct and indirect data (genetic manipulations are by nature inferential) obtained from a controlled and careful set of experiments. Limitations of our approach were laid out under the “Limitation” section of the discussion, as well as alternative interpretations or possibilities. In the manuscript's revised version, we added additional genetic experiments to further support and validate our model and expanded data analyses as suggested by the reviewer.
Reviewer #2 (Public Review):
Nutrigenomics has advanced in recent years, with studies identifying how the food environment influences gene expression in multiple model organisms. The molecular mechanisms mediating these food-gene interactions are poorly understood. Previous work identified the enzyme O-GlcNAC (OGT) in mediating the decreased sensitivity in sweet-taste cells when exposed to a high-sugar diet. The present study, using fly gustatory neurons as a model, provides mechanistic insight into how nutrigenomic signaling encodes nutritional information into cellular changes. The authors expand previous work by showing that OGT is associated with neural chromatin at introns and transcriptional start sites, and that diet-induced changes in chromatin accessibility were amplified at loci with presence of both OGT and PRC2.1. The work also identifies Mitogen Activated Kinase as a critical mediator in this pathway. This is an elegant group of experiments revealing mechanisms for how nutrigenomic signaling triggers cellular responses to nutrients.
We thank the reviewer for their thoughtful reading of the manuscript and their positive and actionable suggestions. We have addressed these in the revised manuscript.
Reviewer #3 (Public Review):
This paper dissects the molecular mechanisms of diet induced taste plasticity in Drosophila. The authors had previously identified two proteins essential for sugar-diet derived reduction of sweet taste sensitivity - OGT and PRC2.1. Here, they showed that OGT, an enzyme implicated in metabolic signaling with chromatin binding functions, also binds a range of genomic loci in the fly sweet gustatory receptor neurons where binding in a subset of those sites is diet composition dependent. Furthermore, a minority of OGT binding sites overlapped with PRC2.1 recruiter Pcl, where collectively binding of both proteins increased under sugar-diet while chromatin accessibility decreased. The authors demonstrate, that the observed taste plasticity requires catalytic activity of OGT, which impacts chromatin accessibility at shared OGT x Pcl but not diet induced occupancy. In an effort to identify transcriptional mechanisms that instantiate the plastic changes in sensory neuron functions the authors looked for transcription factors with enriched motifs around OGT binding sites and identified Stripe (Sr) as a transcription factor that yielded sugar taste phenotypes upon gain and loss of function experiments. In follow-up overexpression experiments, they show that this results in reduced taste sensitivity and reduced taste evoked spiking in gustatory receptor neurons. Notably the effects of Sr on taste sensitivity also depend on OGT catalytic activity as well as PRC2.1 function. Finally, they explore the function of rolled (rl) - an extracellular-signal regulated kinase (ERK) ortholog in Drosophila, suggested to function upstream of Sr - in diet induced gustatory plasticity. The authors showed that the overexpression of the constitutively active form of rl kinase results in reduced neuronal and behavioral responses to sucrose which was dependent on OGT catalytic activity. In sum, these findings reveal several new players that link dietary experience to sensory neuron plasticity and open up clear avenues to explore up- and downstream mechanisms mediating this phenomenon.
Strengths:
• Good genetically targeted interventions
• Thorough exploration of the epistatic relationships between different players in the system• Identification of several new signaling systems and proteins regulating diet derived gustatory plasticity
Weaknesses:
• The GO term enrichment analyses with little functional follow up has limited explanatory power• ERK/rl data is a bit hard to interpret since any imbalance in this system appears to reduce gustatory sensitivity.
The conclusions in this manuscript are mostly well or at least reasonably supported by data.
We appreciate the reviewer’s thoughtful read of the manuscript and their feedback. We were pleased to read the reviewer’s positive comments on the experimental treatment of epistatic relationships and the identification of new pathways; we have addressed the reviewer’s comments and suggestions in the revised manuscript.
We agree with the reviewer about the limited explanatory power of the GO term analysis. We have expanded our computation analysis of the OGT/PRC2 genes in Figure 5 and selected several of these genes for functional analysis. In the revised version of the manuscript, we show that several of the genes affected by diet via this nutrigenomic pathway impact sugar taste sensation as measured by PER. We also agree with the reviewer that the Erk data are harder to interpret than those from OGT or PRC2; this effect is somewhat expected, given the reported action of this kinase in neural activity and plasticity. Importantly, the epistatic interactions between ERK/Sr and OGT/PRC2 we discovered are intriguing and may be involved in other cellular processes beyond taste.
Below are a few recommendations for improvement:
• The paper claims to address cell-type-specific nutrigenomic regulatory mechanisms. However, this work only explores nutrigenomic mechanisms in a single cell type (Gr5a+ sweet sensing cells) and we don't really learn whether these nutrigenomic mechanisms exist in all other cell types or just Gr5a+ cells. It would be valuable to see how specific OGT and PRC2.1 binding locations and effects on chromatin accessibility are in a different cell type - e.g. bitter sensing Gr66a. This would reveal how global in nature these findings are and or which aspects of nutrigenomic signaling are specific for sweet sensory cells.
This study is a cell-specific investigation of nutrigenomic mechanisms in the Gr5a+ sweet taste neurons, which is what we outlined to do. It was not our intention for this study to examine mechanisms across different cell types. However, we can understand the reviewer’s comment after rereading the abstract and introduction. As such, we have rewritten part of the manuscript to better introduce the rationale behind the study as the integration of metabolic signaling and cellular contexts. We hope this is now an improved framing for the study rationale.
(As in response to the author’s recommendations): About analyzing the effects of diet on other cells; no doubt this is an interesting question. However, this also signifies embarking on a completely separate project that would take, optimistically speaking, at least one year to complete and require a budget of ~ $130,000 (see breakdown). Thus, this suggestion doesn’t seem in line with the peer review and editorial philosophy of eLife. Carrying out this new project would result in an additional 6-7 figures but would not fundamentally change the conclusion of the current work; in fact, it may even take away from the targeted integration of molecular biology and neuroscience we have tried to achieve. Beyond this, we do not have such an unallocated budget, and so this new project would require us first to generate preliminary data on the bitter neurons to write then a grant proposal to fund it; as you can appreciate, this would take longer than a year, especially since we do not even know if the bitter gustatory neurons are affected by a high-sugar diet. Beyond this, looking at the bitter neurons would do little to prove specificity. If we found no effects of this pathway on the activity of the bitter neurons, it wouldn’t establish that the changes in the sweet taste neurons are specific. In fact, the same pathway could be acting in some of the other thousands of fly circuits that were not investigated (Black swan effect). If we did find that OGT/PRC2/Sr play a role in the bitter neurons, it would also do little to disprove specificity since their targets would likely be different because the sets of genes expressed in these two sensory neurons are different. By analogy, the protein sensor mTOR is expressed and active in every cell, where it modulates some of the same targets (i.e., S6K); however, the effects of the pathway may be different due to the distinct metabolic and genetic idiosyncrasies of cells, as well as cellular compartments. This lack of specificity doesn’t mean that mTOR is not important. Finally, we would like to note that we have tested the effects of manipulating OGT levels in other neurons (dopamine and Mushroom Body Output Neurons) without effects on behavior or neural responses (May et al. 2020; Pardo-Garcia et al. 2022); based on these, OGT doesn’t seem to affect neurons indiscriminately.
Budget = $129,000
Salary and benefit for PD for 10 calendar months: (2 months behavior experiments, 2 months training for molecular biology experiments and troubleshooting in new neurons, 4 months growing flies and conducting experiments, 2 months data analysis and visualization)= $75,000. DAM ID: Pcl:dam and OGT:dam in CD and SD, with and without OSMI x 4 biological replicates per condition= 32 samples @ $500 per sample (UM Genomics core) $16,0000
TRAP: Pcl mutant and OSMI in CD and SD x 4 biological replicates per condition + sequencing input = 32 samples @ $500 per sample (UM Genomics core) $16,0000
Animals: $500 per person/10 months = $5,000
Reagents: including sequencing kit (32 reactions =$6,000) x 2 = $12,000, and other reagents such as drugs and plastic = $17,000
Note that this PD would have to be hired and retrained. The first author of the manuscript who carried out the molecular experiments graduated in Dec 2021 but failed to pass on the technical knowledge due to COVID restrictions at the UM: we were completely shut down until July 2020, and at 20% capacity from March 2020 to July 2021 (people couldn’t also work together to show techniques), and no new people joined the lab in 2020-2022 (most of the 2021 grad student class deferred to 2022).
● Behavioral data from the screen identifying Sr is missing. Which other candidates were screened and what were the phenotypes?
We have now added the screen data in Fig. 5-Supplemental Fig. 1C. We targeted RNAi and OE transgenes against the candidate transcription factors (or control RNAi) to the Gr5a+ neurons and measured PER to 30, 20, and 5% sucrose in fasted flies on a control diet.
● Go terms analysis for Figure 4
We selected a dozen DEGs dependent on OGT and PRC2.1 (purple circle in Fig. 4E) and tested the effects on PER when these were overexpressed or knocked down (depending on the direction of changes in the SD). In Fig. 4F we show the effects of a handful of them on proboscis responses to sucrose.
-
eLife assessment
This important work identifies new proteins and outlines the interactions between molecular players that control diet-induced plasticity in sensory neuron function in the Drosophila taste system. The authors provide solid evidence in support of their working model and open clear avenues to follow up on downstream molecular mechanisms.
-
Reviewer #1 (Public Review):
The study's primary motivating goal of understanding how nutrigenomic signaling works in different contexts. The authors propose that OGT- a sugar-sensing enzyme- connects sugar levels to chromatin accessibility. Specifically, the authors hypothesize that the OGT/Plc-PRC axis in sweet taste neurons interprets the sugar levels and alters chromatin accessibility in sugar-activated neurons. However, the detailed model presented by authors on OGT/PRC/Pcl Rolled in regulating nutrigenomic signaling relies on pharmacological treatments and overexpression of transgenes to derive genetic interactions and pathways; these approaches provide speculative rather than convincing evidence. Secondly, evidence is absent to show that PRC occupancy remains the same in other neurons (non-sweet taste neurons) under varied sugar …
Reviewer #1 (Public Review):
The study's primary motivating goal of understanding how nutrigenomic signaling works in different contexts. The authors propose that OGT- a sugar-sensing enzyme- connects sugar levels to chromatin accessibility. Specifically, the authors hypothesize that the OGT/Plc-PRC axis in sweet taste neurons interprets the sugar levels and alters chromatin accessibility in sugar-activated neurons. However, the detailed model presented by authors on OGT/PRC/Pcl Rolled in regulating nutrigenomic signaling relies on pharmacological treatments and overexpression of transgenes to derive genetic interactions and pathways; these approaches provide speculative rather than convincing evidence. Secondly, evidence is absent to show that PRC occupancy remains the same in other neurons (non-sweet taste neurons) under varied sugar levels or OGT manipulations. Hence, the claim that OGT-mediated access to chromatin via PRC-Plc is a key regulatory arm of nutrigenomic signaling needs further substantiation.
-
Reviewer #2 (Public Review):
Nutrigenomics has advanced in recent years, with studies identifying how the food environment influences gene expression in multiple model organisms. The molecular mechanisms mediating these food-gene interactions are poorly understood. Previous work identified the enzyme O-GlcNAC (OGT) in mediating the decreased sensitivity in sweet-taste cells when exposed to a high-sugar diet. The present study, using fly gustatory neurons as a model, provides mechanistic insight into how nutrigenomic signaling encodes nutritional information into cellular changes. The authors expand previous work by showing that OGT is associated with neural chromatin at introns and transcriptional start sites, and that diet-induced changes in chromatin accessibility were amplified at loci with presence of both OGT and PRC2.1. The work …
Reviewer #2 (Public Review):
Nutrigenomics has advanced in recent years, with studies identifying how the food environment influences gene expression in multiple model organisms. The molecular mechanisms mediating these food-gene interactions are poorly understood. Previous work identified the enzyme O-GlcNAC (OGT) in mediating the decreased sensitivity in sweet-taste cells when exposed to a high-sugar diet. The present study, using fly gustatory neurons as a model, provides mechanistic insight into how nutrigenomic signaling encodes nutritional information into cellular changes. The authors expand previous work by showing that OGT is associated with neural chromatin at introns and transcriptional start sites, and that diet-induced changes in chromatin accessibility were amplified at loci with presence of both OGT and PRC2.1. The work also identifies Mitogen Activated Kinase as a critical mediator in this pathway. This is an elegant group of experiments revealing mechanisms for how nutrigenomic signaling triggers cellular responses to nutrients.
-
Reviewer #3 (Public Review):
This paper dissects the molecular mechanisms of diet induced taste plasticity in Drosophila. The authors had previously identified two proteins essential for sugar-diet derived reduction of sweet taste sensitivity - OGT and PRC2.1. Here, they showed that OGT, an enzyme implicated in metabolic signaling with chromatin binding functions, also binds a range of genomic loci in the fly sweet gustatory receptor neurons where binding in a subset of those sites is diet composition dependent. Furthermore, a minority of OGT binding sites overlapped with PRC2.1 recruiter Pcl, where collectively binding of both proteins increased under sugar-diet while chromatin accessibility decreased. The authors demonstrate, that the observed taste plasticity requires catalytic activity of OGT, which impacts chromatin accessibility …
Reviewer #3 (Public Review):
This paper dissects the molecular mechanisms of diet induced taste plasticity in Drosophila. The authors had previously identified two proteins essential for sugar-diet derived reduction of sweet taste sensitivity - OGT and PRC2.1. Here, they showed that OGT, an enzyme implicated in metabolic signaling with chromatin binding functions, also binds a range of genomic loci in the fly sweet gustatory receptor neurons where binding in a subset of those sites is diet composition dependent. Furthermore, a minority of OGT binding sites overlapped with PRC2.1 recruiter Pcl, where collectively binding of both proteins increased under sugar-diet while chromatin accessibility decreased. The authors demonstrate, that the observed taste plasticity requires catalytic activity of OGT, which impacts chromatin accessibility at shared OGT x Pcl but not diet induced occupancy. In an effort to identify transcriptional mechanisms that instantiate the plastic changes in sensory neuron functions the authors looked for transcription factors with enriched motifs around OGT binding sites and identified Stripe (Sr) as a transcription factor that yielded sugar taste phenotypes upon gain and loss of function experiments. In follow-up overexpression experiments, they show that this results in reduced taste sensitivity and reduced taste evoked spiking in gustatory receptor neurons. Notably the effects of Sr on taste sensitivity also depend on OGT catalytic activity as well as PRC2.1 function. Finally, they explore the function of rolled (rl) - an extracellular-signal regulated kinase (ERK) ortholog in Drosophila, suggested to function upstream of Sr - in diet induced gustatory plasticity. The authors showed that the overexpression of the constitutively active form of rl kinase results in reduced neuronal and behavioral responses to sucrose which was dependent on OGT catalytic activity. In sum, these findings reveal several new players that link dietary experience to sensory neuron plasticity and open up clear avenues to explore up- and downstream mechanisms mediating this phenomenon.
Strengths:
• Good genetically targeted interventions
• Thorough exploration of the epistatic relationships between different players in the system
• Identification of several new signaling systems and proteins regulating diet derived gustatory plasticityWeaknesses:
• The GO term enrichment analyses with little functional follow up has limited explanatory power
• ERK/rl data is a bit hard to interpret since any imbalance in this system appears to reduce gustatory sensitivity.The conclusions in this manuscript are mostly well or at least reasonably supported by data. Below are a few recommendations for improvement:
• The paper claims to address cell-type-specific nutrigenomic regulatory mechanisms. However, this work only explores nutrigenomic mechanisms in a single cell type (Gr5a+ sweet sensing cells) and we don't really learn whether these nutrigenomic mechanisms exist in all other cell types or just Gr5a+ cells. It would be valuable to see how specific OGT and PRC2.1 binding locations and effects on chromatin accessibility are in a different cell type - e.g. bitter sensing Gr66a. This would reveal how global in nature these findings are and or which aspects of nutrigenomic signaling are specific for sweet sensory cells.
• Behavioral data from the screen identifying Sr is missing. Which other candidates were screened and what were the phenotypes? -
-