1
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Merle M, Friedman L, Chureau C, Shoushtarizadeh A, Gregor T. Precise and scalable self-organization in mammalian pseudo-embryos. Nat Struct Mol Biol 2024; 31:896-902. [PMID: 38491138 DOI: 10.1038/s41594-024-01251-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 02/08/2024] [Indexed: 03/18/2024]
Abstract
Gene expression is inherently noisy, posing a challenge to understanding how precise and reproducible patterns of gene expression emerge in mammals. Here we investigate this phenomenon using gastruloids, a three-dimensional in vitro model for early mammalian development. Our study reveals intrinsic reproducibility in the self-organization of gastruloids, encompassing growth dynamics and gene expression patterns. We observe a remarkable degree of control over gene expression along the main body axis, with pattern boundaries positioned with single-cell precision. Furthermore, as gastruloids grow, both their physical proportions and gene expression patterns scale proportionally with system size. Notably, these properties emerge spontaneously in self-organizing cell aggregates, distinct from many in vivo systems constrained by fixed boundary conditions. Our findings shed light on the intricacies of developmental precision, reproducibility and size scaling within a mammalian system, suggesting that these phenomena might constitute fundamental features of multicellularity.
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Affiliation(s)
- Mélody Merle
- Department of Developmental and Stem Cell Biology, CNRS UMR3738 Paris Cité, Institut Pasteur, Paris, France
| | - Leah Friedman
- Department of Developmental and Stem Cell Biology, CNRS UMR3738 Paris Cité, Institut Pasteur, Paris, France
| | - Corinne Chureau
- Department of Developmental and Stem Cell Biology, CNRS UMR3738 Paris Cité, Institut Pasteur, Paris, France
| | - Armin Shoushtarizadeh
- Department of Developmental and Stem Cell Biology, CNRS UMR3738 Paris Cité, Institut Pasteur, Paris, France
| | - Thomas Gregor
- Department of Developmental and Stem Cell Biology, CNRS UMR3738 Paris Cité, Institut Pasteur, Paris, France.
- Joseph Henry Laboratories of Physics & Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
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2
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Li XC, Gandara L, Ekelöf M, Richter K, Alexandrov T, Crocker J. Rapid response of fly populations to gene dosage across development and generations. Nat Commun 2024; 15:4551. [PMID: 38811562 PMCID: PMC11137061 DOI: 10.1038/s41467-024-48960-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 05/17/2024] [Indexed: 05/31/2024] Open
Abstract
Although the effects of genetic and environmental perturbations on multicellular organisms are rarely restricted to single phenotypic layers, our current understanding of how developmental programs react to these challenges remains limited. Here, we have examined the phenotypic consequences of disturbing the bicoid regulatory network in early Drosophila embryos. We generated flies with two extra copies of bicoid, which causes a posterior shift of the network's regulatory outputs and a decrease in fitness. We subjected these flies to EMS mutagenesis, followed by experimental evolution. After only 8-15 generations, experimental populations have normalized patterns of gene expression and increased survival. Using a phenomics approach, we find that populations were normalized through rapid increases in embryo size driven by maternal changes in metabolism and ovariole development. We extend our results to additional populations of flies, demonstrating predictability. Together, our results necessitate a broader view of regulatory network evolution at the systems level.
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Affiliation(s)
- Xueying C Li
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
- College of Life Sciences, Beijing Normal University, Beijing, China.
| | - Lautaro Gandara
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Måns Ekelöf
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Kerstin Richter
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Theodore Alexandrov
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Molecular Medicine Partnership Unit between EMBL and Heidelberg University, Heidelberg, Germany
- BioInnovation Institute, Copenhagen, Denmark
| | - Justin Crocker
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
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3
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Athilingam T, Nelanuthala AVS, Breen C, Karedla N, Fritzsche M, Wohland T, Saunders TE. Long-range formation of the Bicoid gradient requires multiple dynamic modes that spatially vary across the embryo. Development 2024; 151:dev202128. [PMID: 38345326 PMCID: PMC10911119 DOI: 10.1242/dev.202128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 01/03/2024] [Indexed: 02/15/2024]
Abstract
Morphogen gradients provide essential positional information to gene networks through their spatially heterogeneous distribution, yet how they form is still hotly contested, with multiple models proposed for different systems. Here, we focus on the transcription factor Bicoid (Bcd), a morphogen that forms an exponential gradient across the anterior-posterior (AP) axis of the early Drosophila embryo. Using fluorescence correlation spectroscopy we find there are spatial differences in Bcd diffusivity along the AP axis, with Bcd diffusing more rapidly in the posterior. We establish that such spatially varying differences in Bcd dynamics are sufficient to explain how Bcd can have a steep exponential gradient in the anterior half of the embryo and yet still have an observable fraction of Bcd near the posterior pole. In the nucleus, we demonstrate that Bcd dynamics are impacted by binding to DNA. Addition of the Bcd homeodomain to eGFP::NLS qualitatively replicates the Bcd concentration profile, suggesting this domain regulates Bcd dynamics. Our results reveal how a long-range gradient can form while retaining a steep profile through much of its range.
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Affiliation(s)
- Thamarailingam Athilingam
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
- Mechanobiology Institute, National University of Singapore, Singapore117411
| | - Ashwin V. S. Nelanuthala
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, Singapore117558
| | | | - Narain Karedla
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, OX3 7LF, UK
| | - Marco Fritzsche
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, OX3 7LF, UK
| | - Thorsten Wohland
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, Singapore117558
- Department of Chemistry, National University of Singapore, Singapore117558
| | - Timothy E. Saunders
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
- Mechanobiology Institute, National University of Singapore, Singapore117411
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, Singapore117558
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4
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Baumgartner S. Revisiting bicoid function: complete inactivation reveals an additional fundamental role in Drosophila egg geometry specification. Hereditas 2024; 161:1. [PMID: 38167241 PMCID: PMC10759373 DOI: 10.1186/s41065-023-00305-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
INTRODUCTION The bicoid (bcd) gene in Drosophila has served as a paradigm for a morphogen in textbooks for decades. Discovered in 1986 as a mutation affecting anterior development in the embryo, its expression pattern as a protein gradient later confirmed the prediction from transplantation experiments. These experiments suggested that the protein fulfills the criteria of a true morphogen, with the existence of a homeodomain crucial for activation of genes along the anterior-posterior axis, based on the concentration of the morphogen. The bcd gene undergoes alternative splicing, resulting in, among other isoforms, a small and often neglected isoform with low abundance, which lacks the homeodomain, termed small bicoid (smbcd). Most importantly, all known classical strong bcd alleles used in the past to determine bcd function apparently do not affect the function of this isoform. RESULTS To overcome the uncertainty regarding which isoform regulates what, I removed the bcd locus entirely using CRISPR technology. bcdCRISPR eggs exhibited a short and round appearance. The phenotype could be ascribed to smbcd because all bcd alleles affecting the function of the major transcript, termed large bicoid (lgbcd) showed normally sized eggs. Several patterning genes for the embryo showed expression in the oocyte, and their expression patterns were altered in bcdCRISPR oocytes. In bcdCRISPR embryos, all downstream segmentation genes showed altered expression patterns, consistent with the expression patterns in "classical" alleles; however, due to the altered egg geometry resulting in fewer blastoderm nuclei, additional constraints came into play, further affecting their expression patterns. CONCLUSIONS This study unveils a novel and fundamental role of bcd in shaping the egg's geometry. This discovery demands a comprehensive revision of our understanding of this important patterning gene and prompts a reevaluation of past experiments conducted under the assumption that bcd mutants were bcdnull-mutants.
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Affiliation(s)
- Stefan Baumgartner
- Dept. of Experimental Medical Sciences, Lund University, Lund, S-22184, Sweden.
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5
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A high throughput method for egg size measurement in Drosophila. Sci Rep 2023; 13:3791. [PMID: 36882448 PMCID: PMC9992389 DOI: 10.1038/s41598-023-30472-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/23/2023] [Indexed: 03/09/2023] Open
Abstract
Life-history traits are used as proxies of fitness in insects including Drosophila. Egg size is an adaptive and ecologically important trait potentially with genetic variation across different populations. However, the low throughput of manual measurement of egg size has hampered the widespread use of this trait in evolutionary biology and population genetics. We established a method for accurate and high throughput measurement of Drosophila egg size using large particle flow cytometry (LPFC). The size estimates using LPFC are accurate and highly correlated with the manual measurements. The measurement of egg size is high throughput (average of 214 eggs measured per minute) and viable eggs of a specific size can be sorted rapidly (average of 70 eggs per minute). Sorting by LPFC does not reduce the survival of eggs making it a suitable approach for sorting eggs for downstream analyses. This protocol can be applied to any organism within the detectable size range (10-1500 µm) of the large particle flow cytometers. We discuss the potential applications of this method and provide recommendations for optimizing the protocol for other organisms.
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6
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Villedieu A, Alpar L, Gaugué I, Joudat A, Graner F, Bosveld F, Bellaïche Y. Homeotic compartment curvature and tension control spatiotemporal folding dynamics. Nat Commun 2023; 14:594. [PMID: 36737611 PMCID: PMC9898526 DOI: 10.1038/s41467-023-36305-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 01/25/2023] [Indexed: 02/05/2023] Open
Abstract
Shape is a conspicuous and fundamental property of biological systems entailing the function of organs and tissues. While much emphasis has been put on how tissue tension and mechanical properties drive shape changes, whether and how a given tissue geometry influences subsequent morphogenesis remains poorly characterized. Here, we explored how curvature, a key descriptor of tissue geometry, impinges on the dynamics of epithelial tissue invagination. We found that the morphogenesis of the fold separating the adult Drosophila head and thorax segments is driven by the invagination of the Deformed (Dfd) homeotic compartment. Dfd controls invagination by modulating actomyosin organization and in-plane epithelial tension via the Tollo and Dystroglycan receptors. By experimentally introducing curvature heterogeneity within the homeotic compartment, we established that a curved tissue geometry converts the Dfd-dependent in-plane tension into an inward force driving folding. Accordingly, the interplay between in-plane tension and tissue curvature quantitatively explains the spatiotemporal folding dynamics. Collectively, our work highlights how genetic patterning and tissue geometry provide a simple design principle driving folding morphogenesis during development.
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Affiliation(s)
- Aurélien Villedieu
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, F-75248 Paris Cedex 05, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, CNRS UMR 3215, INSERM U934, F-75005, Paris, France
| | - Lale Alpar
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, F-75248 Paris Cedex 05, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, CNRS UMR 3215, INSERM U934, F-75005, Paris, France
| | - Isabelle Gaugué
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, F-75248 Paris Cedex 05, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, CNRS UMR 3215, INSERM U934, F-75005, Paris, France
| | - Amina Joudat
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, F-75248 Paris Cedex 05, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, CNRS UMR 3215, INSERM U934, F-75005, Paris, France
| | - François Graner
- Université Paris Cité, CNRS, Matière et Systèmes Complexes, F-75006, Paris, France
| | - Floris Bosveld
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, F-75248 Paris Cedex 05, Paris, France. .,Sorbonne Universités, UPMC Univ Paris 06, CNRS, CNRS UMR 3215, INSERM U934, F-75005, Paris, France.
| | - Yohanns Bellaïche
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, F-75248 Paris Cedex 05, Paris, France. .,Sorbonne Universités, UPMC Univ Paris 06, CNRS, CNRS UMR 3215, INSERM U934, F-75005, Paris, France.
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7
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Xu R, Dai F, Wu H, Jiao R, He F, Ma J. Shaping the scaling characteristics of gap gene expression patterns in Drosophila. Heliyon 2023; 9:e13623. [PMID: 36879745 PMCID: PMC9984453 DOI: 10.1016/j.heliyon.2023.e13623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 01/25/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
How patterns are formed to scale with tissue size remains an unresolved problem. Here we investigate embryonic patterns of gap gene expression along the anterior-posterior (AP) axis in Drosophila. We use embryos that greatly differ in length and, importantly, possess distinct length-scaling characteristics of the Bicoid (Bcd) gradient. We systematically analyze the dynamic movements of gap gene expression boundaries in relation to both embryo length and Bcd input as a function of time. We document the process through which such dynamic movements drive both an emergence of a global scaling landscape and evolution of boundary-specific scaling characteristics. We show that, despite initial differences in pattern scaling characteristics that mimic those of Bcd in the anterior, such characteristics of final patterns converge. Our study thus partitions the contributions of Bcd input and regulatory dynamics inherent to the AP patterning network in shaping embryonic pattern's scaling characteristics.
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Affiliation(s)
- Ruoqing Xu
- Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Fei Dai
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Honggang Wu
- Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou 510182, China
- Key Laboratory of Interdisciplinary Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Renjie Jiao
- Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou 510182, China
- Key Laboratory of Interdisciplinary Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Feng He
- Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Corresponding author. Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.
| | - Jun Ma
- Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Joint Institute of Genetics and Genome Medicine between Zhejiang University and University of Toronto, Hangzhou, Zhejiang, China
- Corresponding author. Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.
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8
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Clark E, Battistara M, Benton MA. A timer gene network is spatially regulated by the terminal system in the Drosophila embryo. eLife 2022; 11:e78902. [PMID: 36524728 PMCID: PMC10065802 DOI: 10.7554/elife.78902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
In insect embryos, anteroposterior patterning is coordinated by the sequential expression of the 'timer' genes caudal, Dichaete, and odd-paired, whose expression dynamics correlate with the mode of segmentation. In Drosophila, the timer genes are expressed broadly across much of the blastoderm, which segments simultaneously, but their expression is delayed in a small 'tail' region, just anterior to the hindgut, which segments during germband extension. Specification of the tail and the hindgut depends on the terminal gap gene tailless, but beyond this the regulation of the timer genes is poorly understood. We used a combination of multiplexed imaging, mutant analysis, and gene network modelling to resolve the regulation of the timer genes, identifying 11 new regulatory interactions and clarifying the mechanism of posterior terminal patterning. We propose that a dynamic Tailless expression gradient modulates the intrinsic dynamics of a timer gene cross-regulatory module, delineating the tail region and delaying its developmental maturation.
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Affiliation(s)
- Erik Clark
- Department of Zoology, University of CambridgeCambridgeUnited Kingdom
- Department of Systems Biology, Harvard Medical SchoolBostonUnited States
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
| | - Margherita Battistara
- Department of Zoology, University of CambridgeCambridgeUnited Kingdom
- Department of Physiology, Development and Neuroscience, University of CambridgeCambridgeUnited Kingdom
| | - Matthew A Benton
- Department of Zoology, University of CambridgeCambridgeUnited Kingdom
- Developmental Biology Unit, EMBLHeidelbergGermany
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9
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Abstract
Metazoan embryos develop from a single cell into three-dimensional structured organisms while groups of genetically identical cells attain specialized identities. Cells of the developing embryo both create and accurately interpret morphogen gradients to determine their positions and make specific decisions in response. Here, we first cover intellectual roots of morphogen and positional information concepts. Focusing on animal embryos, we then provide a review of current understanding on how morphogen gradients are established and how their spans are controlled. Lastly, we cover how gradients evolve in time and space during development, and how they encode information to control patterning. In sum, we provide a list of patterning principles for morphogen gradients and review recent advances in quantitative methodologies elucidating information provided by morphogens.
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Affiliation(s)
- M. Fethullah Simsek
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Ertuğrul M. Özbudak
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
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10
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Shen J, Liu F, Tang C. Scaling dictates the decoder structure. Sci Bull (Beijing) 2022; 67:1486-1495. [PMID: 36546192 DOI: 10.1016/j.scib.2022.06.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/06/2022] [Accepted: 06/13/2022] [Indexed: 01/07/2023]
Abstract
Despite fluctuations in embryo size within a species, the spatial gene expression pattern and hence the embryonic structure can nonetheless maintain the correct proportion to the embryo size. This is known as the scaling phenomenon. For morphogen-induced patterning of gene expression, the positional information encoded in the local morphogen concentrations is decoded by the downstream genetic network (the decoder). In this paper, we show that the requirement of scaling sets severe constraints on the geometric structure of such a local decoder, which in turn enables deduction of mutants' behavior and extraction of regulation information without going into any molecular details. We demonstrate that the Drosophila gap gene system achieves scaling in the way consistent with our theory-the decoder geometry required by scaling correctly accounts for the observed gap gene expression pattern in nearly all maternal morphogen mutants. Furthermore, the regulation logic and the coding/decoding strategy of the gap gene system can also be revealed from the decoder geometry. Our work provides a general theoretical framework for a large class of problems where scaling output is achieved by non-scaling inputs and a local decoder, as well as a unified understanding of scaling, mutants' behavior, and gene regulation for the Drosophila gap gene system.
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Affiliation(s)
- Jingxiang Shen
- Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Feng Liu
- Center for Quantitative Biology, Peking University, Beijing 100871, China; School of Physics, Peking University, Beijing 100871, China
| | - Chao Tang
- Center for Quantitative Biology, Peking University, Beijing 100871, China; School of Physics, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
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11
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Kumar PP, Bawani SS, Anandhi DU, Prashanth KVH. Rotenone mediated developmental toxicity in Drosophila melanogaster. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2022; 93:103892. [PMID: 35654372 DOI: 10.1016/j.etap.2022.103892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/21/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
Rotenone (ROT) is a widely used natural pesticide, and its effect on growth and developmental toxicity remain unclear. In the present study, the effects of ROT exposure on the reproductive structure and function of the female Drosophila melanogaster and third instar larvae were investigated. ROT exposure on female Drosophila melanogaster resulted in developmental inhibition and ovarian abnormality, which were evident from the disruptive growth of border cells as well as morphological changes in the orientation of nurse cells during the 9th-10th stage of developing egg chamber of in the Drosophila ovary. Other abnormalities, such as, altered developmental gene expression (Osk, Grk, Nos, Bic-d), inhibition in the kinesin motor protein level (KIF-5B), increased caspases activities (Caspase 3, 8, & 9) and apoptosis were also observed. Subsequently, ROT treated larvae exhibited behavioral deficits and delay in developmental time. The above findings demonstrate that the exposure of ROT causes developmental toxicity in Drosophila melanogaster.
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Affiliation(s)
- P Pramod Kumar
- Functional Biopolymer Lab, Department of Biochemistry, CSIR-Central Food Technological Research Institute, Mysuru 570020, Karnataka, India
| | - Saliya S Bawani
- Reproductive Physiology Unit, Department of Zoology, Bangalore University, 560056 Karnataka, India
| | - Duraiswamy Usha Anandhi
- Reproductive Physiology Unit, Department of Zoology, Bangalore University, 560056 Karnataka, India
| | - K V Harish Prashanth
- Functional Biopolymer Lab, Department of Biochemistry, CSIR-Central Food Technological Research Institute, Mysuru 570020, Karnataka, India.
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12
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Iber D, Vetter R. Relationship between epithelial organization and morphogen interpretation. Curr Opin Genet Dev 2022; 75:101916. [PMID: 35605527 DOI: 10.1016/j.gde.2022.101916] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 04/10/2022] [Accepted: 04/22/2022] [Indexed: 11/18/2022]
Abstract
Despite molecular noise and genetic differences between individuals, developmental outcomes are remarkably constant. Decades of research has focused on the underlying mechanisms that ensure this precision and robustness. Recent quantifications of chemical gradients and epithelial cell shapes provide novel insights into the basis of precise development. In this review, we argue that these two aspects may be linked in epithelial morphogenesis.
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Affiliation(s)
- Dagmar Iber
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland; Swiss Institute of Bioinformatics, Mattenstrasse 26, 4058 Basel, Switzerland.
| | - Roman Vetter
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland; Swiss Institute of Bioinformatics, Mattenstrasse 26, 4058 Basel, Switzerland
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13
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Singh AP, Wu P, Ryabichko S, Raimundo J, Swan M, Wieschaus E, Gregor T, Toettcher JE. Optogenetic control of the Bicoid morphogen reveals fast and slow modes of gap gene regulation. Cell Rep 2022; 38:110543. [PMID: 35320726 PMCID: PMC9019726 DOI: 10.1016/j.celrep.2022.110543] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/10/2022] [Accepted: 02/28/2022] [Indexed: 11/29/2022] Open
Abstract
Developmental patterning networks are regulated by multiple inputs and feedback connections that rapidly reshape gene expression, limiting the information that can be gained solely from slow genetic perturbations. Here we show that fast optogenetic stimuli, real-time transcriptional reporters, and a simplified genetic background can be combined to reveal the kinetics of gene expression downstream of a developmental transcription factor in vivo. We engineer light-controlled versions of the Bicoid transcription factor and study their effects on downstream gap genes in embryos. Our results recapitulate known relationships, including rapid Bicoid-dependent transcription of giant and hunchback and delayed repression of Krüppel. In addition, we find that the posterior pattern of knirps exhibits a quick but inverted response to Bicoid perturbation, suggesting a noncanonical role for Bicoid in directly suppressing knirps transcription. Acute modulation of transcription factor concentration while recording output gene activity represents a powerful approach for studying developmental gene networks in vivo.
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Affiliation(s)
- Anand P Singh
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Ping Wu
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Sergey Ryabichko
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - João Raimundo
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Michael Swan
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Eric Wieschaus
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
| | - Thomas Gregor
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Physics, Princeton University, Princeton, NJ 08544, USA.
| | - Jared E Toettcher
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
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14
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Lepeta K, Bauer M, Aguilar G, Vigano MA, Matsuda S, Affolter M. Studying Protein Function Using Nanobodies and Other Protein Binders in Drosophila. Methods Mol Biol 2022; 2540:219-237. [PMID: 35980580 DOI: 10.1007/978-1-0716-2541-5_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The direct manipulation of proteins by nanobodies and other protein binders has become an additional and valuable approach to investigate development and homeostasis in Drosophila. In contrast to other techniques, that indirectly interfere with proteins via their nucleic acids (CRISPR, RNAi, etc.), protein binders permit direct and acute protein manipulation. Since the first use of a nanobody in Drosophila a decade ago, many different applications exploiting protein binders have been introduced. Most of these applications use nanobodies against GFP to regulate GFP fusion proteins. In order to exert specific protein manipulations, protein binders are linked to domains that confer them precise biochemical functions. Here, we reflect on the use of tools based on protein binders in Drosophila. We describe their key features and provide an overview of the available reagents. Finally, we briefly explore the future avenues that protein binders might open up and thus further contribute to better understand development and homeostasis of multicellular organisms.
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Affiliation(s)
| | - Milena Bauer
- Biozentrum der Universität Basel, Basel, Switzerland
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15
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Guglielmi L, Heliot C, Kumar S, Alexandrov Y, Gori I, Papaleonidopoulou F, Barrington C, East P, Economou AD, French PMW, McGinty J, Hill CS. Smad4 controls signaling robustness and morphogenesis by differentially contributing to the Nodal and BMP pathways. Nat Commun 2021; 12:6374. [PMID: 34737283 PMCID: PMC8569018 DOI: 10.1038/s41467-021-26486-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 10/07/2021] [Indexed: 12/25/2022] Open
Abstract
The transcriptional effector SMAD4 is a core component of the TGF-β family signaling pathways. However, its role in vertebrate embryo development remains unresolved. To address this, we deleted Smad4 in zebrafish and investigated the consequences of this on signaling by the TGF-β family morphogens, BMPs and Nodal. We demonstrate that in the absence of Smad4, dorsal/ventral embryo patterning is disrupted due to the loss of BMP signaling. However, unexpectedly, Nodal signaling is maintained, but lacks robustness. This Smad4-independent Nodal signaling is sufficient for mesoderm specification, but not for optimal endoderm specification. Furthermore, using Optical Projection Tomography in combination with 3D embryo morphometry, we have generated a BMP morphospace and demonstrate that Smad4 mutants are morphologically indistinguishable from embryos in which BMP signaling has been genetically/pharmacologically perturbed. Smad4 is thus differentially required for signaling by different TGF-β family ligands, which has implications for diseases where Smad4 is mutated or deleted.
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Affiliation(s)
- Luca Guglielmi
- Developmental Signalling Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Claire Heliot
- Developmental Signalling Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Sunil Kumar
- Advanced Light Microscopy, The Francis Crick Institute, London, NW1 1AT, UK
| | - Yuriy Alexandrov
- Advanced Light Microscopy, The Francis Crick Institute, London, NW1 1AT, UK
| | - Ilaria Gori
- Developmental Signalling Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | | | - Christopher Barrington
- Bioinformatics and Biostatistics Facility, The Francis Crick Institute, London, NW1 1AT, UK
| | - Philip East
- Bioinformatics and Biostatistics Facility, The Francis Crick Institute, London, NW1 1AT, UK
| | - Andrew D Economou
- Developmental Signalling Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Paul M W French
- Department of Physics, Imperial College London, SW7 2AZ, London, UK
| | - James McGinty
- Department of Physics, Imperial College London, SW7 2AZ, London, UK
| | - Caroline S Hill
- Developmental Signalling Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.
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16
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Tiwari P, Rengarajan H, Saunders TE. Scaling of internal organs during Drosophila embryonic development. Biophys J 2021; 120:4264-4276. [PMID: 34087212 PMCID: PMC8516638 DOI: 10.1016/j.bpj.2021.05.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 05/04/2021] [Accepted: 05/27/2021] [Indexed: 11/20/2022] Open
Abstract
Many species show a diverse range of sizes; for example, domestic dogs have large variation in body mass. Yet, the internal structure of the organism remains similar, i.e., the system scales to organism size. Drosophila melanogaster has been a powerful model system for exploring scaling mechanisms. In the early embryo, gene expression boundaries scale very precisely to embryo length. Later in development, the adult wings grow with remarkable symmetry and scale well with animal size. Yet, our knowledge of whether internal organs initially scale to embryo size remains largely unknown. Here, we utilize artificially small Drosophila embryos to explore how three critical internal organs-the heart, hindgut, and ventral nerve cord (VNC)-adapt to changes in embryo morphology. We find that the heart scales precisely with embryo length. Intriguingly, reduction in cardiac cell length, rather than number, appears to be important in controlling heart length. The hindgut, which is the first chiral organ to form, displays scaling with embryo size under large-scale changes in the artificially smaller embryos but shows few hallmarks of scaling within wild-type size variation. Finally, the VNC only displays weak scaling behavior; even large changes in embryo geometry result in only small shifts in VNC length. This suggests that the VNC may have an intrinsic minimal length that is largely independent of embryo length. Overall, our work shows that internal organs can adapt to embryo size changes in Drosophila, but the extent to which they scale varies significantly between organs.
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Affiliation(s)
- Prabhat Tiwari
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | | | - Timothy E Saunders
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore; Department of Biological Sciences, National University of Singapore, Singapore, Singapore; Institute of Molecular and Cell Biology, A(∗)Star, Singapore, Singapore; Warwick Medical School, University of Warwick, Coventry, United Kingdom.
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17
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The early Drosophila embryo as a model system for quantitative biology. Cells Dev 2021; 168:203722. [PMID: 34298230 DOI: 10.1016/j.cdev.2021.203722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 06/03/2021] [Accepted: 07/13/2021] [Indexed: 11/20/2022]
Abstract
With the rise of new tools, from controlled genetic manipulations and optogenetics to improved microscopy, it is now possible to make clear, quantitative and reproducible measurements of biological processes. The humble fruit fly Drosophila melanogaster, with its ease of genetic manipulation combined with excellent imaging accessibility, has become a major model system for performing quantitative in vivo measurements. Such measurements are driving a new wave of interest from physicists and engineers, who are developing a range of testable dynamic models of active systems to understand fundamental biological processes. The reproducibility of the early Drosophila embryo has been crucial for understanding how biological systems are robust to unavoidable noise during development. Insights from quantitative in vivo experiments in the Drosophila embryo are having an impact on our understanding of critical biological processes, such as how cells make decisions and how complex tissue shape emerges. Here, to highlight the power of using Drosophila embryogenesis for quantitative biology, I focus on three main areas: (1) formation and robustness of morphogen gradients; (2) how gene regulatory networks ensure precise boundary formation; and (3) how mechanical interactions drive packing and tissue folding. I further discuss how such data has driven advances in modelling.
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18
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Abstract
Arthropod segmentation and vertebrate somitogenesis are leading fields in the experimental and theoretical interrogation of developmental patterning. However, despite the sophistication of current research, basic conceptual issues remain unresolved. These include: (i) the mechanistic origins of spatial organization within the segment addition zone (SAZ); (ii) the mechanistic origins of segment polarization; (iii) the mechanistic origins of axial variation; and (iv) the evolutionary origins of simultaneous patterning. Here, I explore these problems using coarse-grained models of cross-regulating dynamical processes. In the morphogenetic framework of a row of cells undergoing axial elongation, I simulate interactions between an 'oscillator', a 'switch' and up to three 'timers', successfully reproducing essential patterning behaviours of segmenting systems. By comparing the output of these largely cell-autonomous models to variants that incorporate positional information, I find that scaling relationships, wave patterns and patterning dynamics all depend on whether the SAZ is regulated by temporal or spatial information. I also identify three mechanisms for polarizing oscillator output, all of which functionally implicate the oscillator frequency profile. Finally, I demonstrate significant dynamical and regulatory continuity between sequential and simultaneous modes of segmentation. I discuss these results in the context of the experimental literature.
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Affiliation(s)
- Erik Clark
- Department of Systems Biology, Harvard Medical School, 210 Longwood Ave, Boston, MA 02115, USA
- Trinity College Cambridge, University of Cambridge, Trinity Street, Cambridge CB2 1TQ, UK
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19
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Perkins ML. Implications of diffusion and time-varying morphogen gradients for the dynamic positioning and precision of bistable gene expression boundaries. PLoS Comput Biol 2021; 17:e1008589. [PMID: 34061823 PMCID: PMC8195430 DOI: 10.1371/journal.pcbi.1008589] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 06/11/2021] [Accepted: 05/11/2021] [Indexed: 11/19/2022] Open
Abstract
The earliest models for how morphogen gradients guide embryonic patterning failed to account for experimental observations of temporal refinement in gene expression domains. Following theoretical and experimental work in this area, dynamic positional information has emerged as a conceptual framework to discuss how cells process spatiotemporal inputs into downstream patterns. Here, we show that diffusion determines the mathematical means by which bistable gene expression boundaries shift over time, and therefore how cells interpret positional information conferred from morphogen concentration. First, we introduce a metric for assessing reproducibility in boundary placement or precision in systems where gene products do not diffuse, but where morphogen concentrations are permitted to change in time. We show that the dynamics of the gradient affect the sensitivity of the final pattern to variation in initial conditions, with slower gradients reducing the sensitivity. Second, we allow gene products to diffuse and consider gene expression boundaries as propagating wavefronts with velocity modulated by local morphogen concentration. We harness this perspective to approximate a PDE model as an ODE that captures the position of the boundary in time, and demonstrate the approach with a preexisting model for Hunchback patterning in fruit fly embryos. We then propose a design that employs antiparallel morphogen gradients to achieve accurate boundary placement that is robust to scaling. Throughout our work we draw attention to tradeoffs among initial conditions, boundary positioning, and the relative timescales of network and gradient evolution. We conclude by suggesting that mathematical theory should serve to clarify not just our quantitative, but also our intuitive understanding of patterning processes.
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Affiliation(s)
- Melinda Liu Perkins
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- * E-mail:
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20
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Hernandez-Lagana E, Mosca G, Mendocilla-Sato E, Pires N, Frey A, Giraldo-Fonseca A, Michaud C, Grossniklaus U, Hamant O, Godin C, Boudaoud A, Grimanelli D, Autran D, Baroux C. Organ geometry channels reproductive cell fate in the Arabidopsis ovule primordium. eLife 2021; 10:e66031. [PMID: 33960300 PMCID: PMC8219382 DOI: 10.7554/elife.66031] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 05/03/2021] [Indexed: 12/13/2022] Open
Abstract
In multicellular organisms, sexual reproduction requires the separation of the germline from the soma. In flowering plants, the female germline precursor differentiates as a single spore mother cell (SMC) as the ovule primordium forms. Here, we explored how organ growth contributes to SMC differentiation. We generated 92 annotated 3D images at cellular resolution in Arabidopsis. We identified the spatio-temporal pattern of cell division that acts in a domain-specific manner as the primordium forms. Tissue growth models uncovered plausible morphogenetic principles involving a spatially confined growth signal, differential mechanical properties, and cell growth anisotropy. Our analysis revealed that SMC characteristics first arise in more than one cell but SMC fate becomes progressively restricted to a single cell during organ growth. Altered primordium geometry coincided with a delay in the fate restriction process in katanin mutants. Altogether, our study suggests that tissue geometry channels reproductive cell fate in the Arabidopsis ovule primordium.
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Affiliation(s)
| | - Gabriella Mosca
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of ZürichZürichSwitzerland
| | - Ethel Mendocilla-Sato
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of ZürichZürichSwitzerland
| | - Nuno Pires
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of ZürichZürichSwitzerland
| | - Anja Frey
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of ZürichZürichSwitzerland
| | - Alejandro Giraldo-Fonseca
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of ZürichZürichSwitzerland
| | | | - Ueli Grossniklaus
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of ZürichZürichSwitzerland
| | - Olivier Hamant
- Laboratoire Reproduction et Développement des Plantes, University of Lyon, ENS Lyon, UCB Lyon 1, CNRS, INRAE, INRIALyonFrance
| | - Christophe Godin
- Laboratoire Reproduction et Développement des Plantes, University of Lyon, ENS Lyon, UCB Lyon 1, CNRS, INRAE, INRIALyonFrance
| | - Arezki Boudaoud
- Laboratoire Reproduction et Développement des Plantes, University of Lyon, ENS Lyon, UCB Lyon 1, CNRS, INRAE, INRIALyonFrance
| | | | - Daphné Autran
- DIADE, University of Montpellier, CIRAD, IRDMontpellierFrance
- Laboratoire Reproduction et Développement des Plantes, University of Lyon, ENS Lyon, UCB Lyon 1, CNRS, INRAE, INRIALyonFrance
| | - Célia Baroux
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of ZürichZürichSwitzerland
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21
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Mirth CK, Saunders TE, Amourda C. Growing Up in a Changing World: Environmental Regulation of Development in Insects. ANNUAL REVIEW OF ENTOMOLOGY 2021; 66:81-99. [PMID: 32822557 DOI: 10.1146/annurev-ento-041620-083838] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
All organisms are exposed to changes in their environment throughout their life cycle. When confronted with these changes, they adjust their development and physiology to ensure that they can produce the functional structures necessary for survival and reproduction. While some traits are remarkably invariant, or robust, across environmental conditions, others show high degrees of variation, known as plasticity. Generally, developmental processes that establish cell identity are thought to be robust to environmental perturbation, while those relating to body and organ growth show greater degrees of plasticity. However, examples of plastic patterning and robust organ growth demonstrate that this is not a hard-and-fast rule.In this review, we explore how the developmental context and the gene regulatory mechanisms underlying trait formation determine the impacts of the environment on development in insects. Furthermore, we outline future issues that need to be resolved to understand how the structure of signaling networks defines whether a trait displays plasticity or robustness.
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Affiliation(s)
- Christen K Mirth
- School of Biological Sciences, Monash University, Melbourne 3800, Victoria, Australia;
| | - Timothy E Saunders
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Republic of Singapore
- Department of Biological Sciences, National University of Singapore, Singapore 117588, Republic of Singapore
- Institute of Molecular and Cell Biology, A*Star, Proteos, Singapore 138673, Republic of Singapore
| | - Christopher Amourda
- MRC London Institute of Medical Sciences, Imperial College London, London W12 0NN, United Kingdom
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