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Qiao S, Bernasek S, Gallagher KD, O'Connell J, Yamada S, Bagheri N, Amaral LAN, Carthew RW. Energy metabolism modulates the regulatory impact of activators on gene expression. Development 2024; 151:dev201986. [PMID: 38063847 PMCID: PMC10820824 DOI: 10.1242/dev.201986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 11/29/2023] [Indexed: 12/19/2023]
Abstract
Gene expression is a regulated process fueled by ATP consumption. Therefore, regulation must be coupled to constraints imposed by the level of energy metabolism. Here, we explore this relationship both theoretically and experimentally. A stylized mathematical model predicts that activators of gene expression have variable impact depending on metabolic rate. Activators become less essential when metabolic rate is reduced and more essential when metabolic rate is enhanced. We find that, in the Drosophila eye, expression dynamics of the yan gene are less affected by loss of EGFR-mediated activation when metabolism is reduced, and the opposite effect is seen when metabolism is enhanced. The effects are also seen at the level of pattern regularity in the adult eye, where loss of EGFR-mediated activation is mitigated by lower metabolism. We propose that gene activation is tuned by energy metabolism to allow for faithful expression dynamics in the face of variable metabolic conditions.
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Affiliation(s)
- Sha Qiao
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Sebastian Bernasek
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Kevin D. Gallagher
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, USA
| | - Jessica O'Connell
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Shigehiro Yamada
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Neda Bagheri
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, USA
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL 60208, USA
| | - Luis A. N. Amaral
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, USA
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL 60208, USA
- Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208, USA
| | - Richard W. Carthew
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, USA
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2
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Valamparamban GF, Spéder P. Homemade: building the structure of the neurogenic niche. Front Cell Dev Biol 2023; 11:1275963. [PMID: 38107074 PMCID: PMC10722289 DOI: 10.3389/fcell.2023.1275963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/16/2023] [Indexed: 12/19/2023] Open
Abstract
Neural stem/progenitor cells live in an intricate cellular environment, the neurogenic niche, which supports their function and enables neurogenesis. The niche is made of a diversity of cell types, including neurons, glia and the vasculature, which are able to signal to and are structurally organised around neural stem/progenitor cells. While the focus has been on how individual cell types signal to and influence the behaviour of neural stem/progenitor cells, very little is actually known on how the niche is assembled during development from multiple cellular origins, and on the role of the resulting topology on these cells. This review proposes to draw a state-of-the art picture of this emerging field of research, with the aim to expose our knowledge on niche architecture and formation from different animal models (mouse, zebrafish and fruit fly). We will span its multiple aspects, from the existence and importance of local, adhesive interactions to the potential emergence of larger-scale topological properties through the careful assembly of diverse cellular and acellular components.
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Affiliation(s)
| | - Pauline Spéder
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Structure and Signals in the Neurogenic Niche, Paris, France
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Qiao S, Bernasek S, Gallagher KD, Yamada S, Bagheri N, Amaral LA, Carthew RW. Energy metabolism modulates the regulatory impact of activators on gene expression. bioRxiv 2023:2023.10.24.563842. [PMID: 37961620 PMCID: PMC10634812 DOI: 10.1101/2023.10.24.563842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Gene expression is a regulated process fueled by ATP consumption. Therefore, regulation must be coupled to constraints imposed by the level of energy metabolism. Here, we explore this relationship both theoretically and experimentally. A stylized mathematical model predicts that activators of gene expression have variable impact depending on metabolic rate. Activators become less essential when metabolic rate is reduced and more essential when metabolic rate is enhanced. We find that in the Drosophila eye, expression dynamics of the yan gene are less affected by loss of EGFR-mediated activation when metabolism is reduced, and the opposite effect is seen when metabolism is enhanced. The effects are also seen at the level of pattern regularity in the adult eye, where loss of EGFR-mediated activation is mitigated by lower metabolism. We propose that gene activation is tuned by energy metabolism to allow for faithful expression dynamics in the face of variable metabolic conditions.
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Affiliation(s)
- Sha Qiao
- Department of Molecular Biosciences, Northwestern University, Evanston, IL
| | - Sebastian Bernasek
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL
| | - Kevin D. Gallagher
- Department of Molecular Biosciences, Northwestern University, Evanston, IL
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL
| | - Shigehiro Yamada
- Department of Molecular Biosciences, Northwestern University, Evanston, IL
| | - Neda Bagheri
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL
| | - Luis A.N. Amaral
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL
- Department of Physics and Astronomy, Northwestern University, Evanston, IL
| | - Richard W. Carthew
- Department of Molecular Biosciences, Northwestern University, Evanston, IL
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL
- Lead Contact
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Casas Gimeno G, Dvorianinova E, Lembke CS, Dijkstra ESC, Abbas H, Liu Y, Paridaen JTML. A quantitative characterization of early neuron generation in the developing zebrafish telencephalon. Dev Neurobiol 2023; 83:237-254. [PMID: 37679904 DOI: 10.1002/dneu.22926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/28/2023] [Accepted: 08/24/2023] [Indexed: 09/09/2023]
Abstract
The adult brain is made up of anatomically and functionally distinct regions with specific neuronal compositions. At the root of this neuronal diversity are neural stem and progenitor cells (NPCs) that produce many neurons throughout embryonic development. During development, NPCs switch from initial expanding divisions to neurogenic divisions, which marks the onset of neurogenesis. Here, we aimed to understand when NPCs switch division modes to generate the first neurons in the anterior-most part of the zebrafish brain, the telencephalon. To this end, we used the deep learning-based segmentation method Cellpose and clonal analysis of individual NPCs to assess the production of neurons by NPCs in the first 24 h of zebrafish telencephalon development. Our results provide a quantitative atlas detailing the production of telencephalic neurons and NPC division modes between 14 and 24 h postfertilization. We find that within this timeframe, the switch to neurogenesis is gradual, with considerable heterogeneity in individual NPC neurogenic potential and division rates. This quantitative characterization of initial neurogenesis in the zebrafish telencephalon establishes a basis for future studies aimed at illuminating the molecular mechanisms and regulators of early neurogenesis.
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Affiliation(s)
- Glòria Casas Gimeno
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands
| | - Ekaterina Dvorianinova
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands
| | - Carla-Sophie Lembke
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands
| | - Emma S C Dijkstra
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands
| | - Hussam Abbas
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands
| | - Yuanyuan Liu
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands
| | - Judith T M L Paridaen
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands
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Stewart RK, Nguyen P, Laederach A, Volkan PC, Sawyer JK, Fox DT. Orb2 enables rare-codon-enriched mRNA expression during Drosophila neuron differentiation. bioRxiv 2023:2023.07.26.550700. [PMID: 37546801 PMCID: PMC10402044 DOI: 10.1101/2023.07.26.550700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Regulation of codon optimality is an increasingly appreciated layer of cell- and tissue-specific protein expression control. Here, we use codon-modified reporters to show that differentiation of Drosophila neural stem cells into neurons enables protein expression from rare-codon-enriched genes. From a candidate screen, we identify the cytoplasmic polyadenylation element binding (CPEB) protein Orb2 as a positive regulator of rare-codon-dependent expression in neurons. Using RNA sequencing, we reveal that Orb2-upregulated mRNAs in the brain with abundant Orb2 binding sites have a rare-codon bias. From these Orb2-regulated mRNAs, we demonstrate that rare-codon enrichment is important for expression control and social behavior function of the metabotropic glutamate receptor (mGluR). Our findings reveal a molecular mechanism by which neural stem cell differentiation shifts genetic code regulation to enable critical mRNA and protein expression.
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Segura RC, Cabernard C. Live-Cell Imaging of Drosophila melanogaster Third Instar Larval Brains. J Vis Exp 2023:10.3791/65538. [PMID: 37427933 PMCID: PMC10655794 DOI: 10.3791/65538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2023] Open
Abstract
Drosophila neural stem cells (neuroblasts, NBs hereafter) undergo asymmetric divisions, regenerating the self-renewing neuroblast, while also forming a differentiating ganglion mother cell (GMC), which will undergo one additional division to give rise to two neurons or glia. Studies in NBs have uncovered the molecular mechanisms underlying cell polarity, spindle orientation, neural stem cell self-renewal, and differentiation. These asymmetric cell divisions are readily observable via live-cell imaging, making larval NBs ideally suited for investigating the spatiotemporal dynamics of asymmetric cell division in living tissue. When properly dissected and imaged in nutrient-supplemented medium, NBs in explant brains robustly divide for 12-20 h. Previously described methods are technically difficult and may be challenging to those new to the field. Here, a protocol is described for the preparation, dissection, mounting, and imaging of live third-instar larval brain explants using fat body supplements. Potential problems are also discussed, and examples are provided for how this technique can be used.
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Li X, Syed MH. Time, space, and diversity. Semin Cell Dev Biol 2023; 142:1-3. [PMID: 36100475 DOI: 10.1016/j.semcdb.2022.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Xin Li
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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Abstract
Fish eyes require high Zn levels to support their early development. Although numerous studies have been conducted on the nutritional and toxic effects of Zn on the eye, the Zn requirement for retinal cell development is still debatable. Moreover, due to the complexity of the retinal structure, it is difficult to clearly visualize each retinal layer and accurately separate cell morphology in vivo by conventional methods. In the present study, we for the first time have achieved nanoscale imaging of retinal anatomy affected by dietary and waterborne Zn exposure by novel expansion microscopy. We demonstrated that the fish retina showed different developmental strategies in response to dietary and aqueous Zn exposures. Excess dietary Zn produced toxicity to retinal photoreceptor cells, resulting in a reduction in cell number and cell area, and this toxicity became severe with biological development. In contrast, waterborne Zn in the natural environment probably failed to meet the Zn requirements of retinal development. Overall, our results indicated that during early development, the Zn requirement of the fish eyes was sensitive, and oversupplementation led to impaired photoreceptor cell development. Our study has provided new perspectives using the powerful and novel expansion microscopy technique in toxicity assessment, enabling ultra-clear visualization of small but complex organ development.
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Affiliation(s)
- Mengyu Wang
- School of Energy and Environment, State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong 518057, China
- Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China
| | - Wen-Xiong Wang
- School of Energy and Environment, State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong 518057, China
- Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China
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