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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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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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Shlemov A, Alexandrov T, Golyandina N, Holloway D, Baumgartner S, Spirov AV. Quantification reveals early dynamics in Drosophila maternal gradients. PLoS One 2021; 16:e0244701. [PMID: 34411119 PMCID: PMC8376041 DOI: 10.1371/journal.pone.0244701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 07/16/2021] [Indexed: 11/18/2022] Open
Abstract
The Bicoid (Bcd) protein is a primary determinant of early anterior-posterior (AP) axis specification in Drosophila embryogenesis. This morphogen is spatially distributed in an anterior-high gradient, and affects particular AP cell fates in a concentration-dependent manner. The early distribution and dynamics of the bicoid (bcd) mRNA, the source for the Bcd protein gradient, is not well understood, leaving a number of open questions for how Bcd positional information develops and is regulated. Confocal microscope images of whole early embryos, stained for bcd mRNA or the Staufen (Stau) protein involved in its transport, were processed to extract quantitative AP intensity profiles at two depths (apical-under the embryo surface but above the nuclear layer; and basal-below the nuclei). Each profile was quantified by a two- (or three-) exponential equation. The parameters of these equations were used to analyze the early developmental dynamics of bcd. Analysis of 1D profiles was compared with 2D intensity surfaces from the same images. This approach reveals strong early changes in bcd and Stau, which appear to be coordinated. We can unambiguously discriminate three stages in early development using the exponential parameters: pre-blastoderm (1-9 cleavage cycle, cc), syncytial blastoderm (10-13 cc) and cellularization (from 14A cc). Key features which differ in this period are how fast the first exponential (anterior component) of the apical profile drops with distance and whether it is higher or lower than the basal first exponential. We can further discriminate early and late embryos within the pre-blastoderm stage, depending on how quickly the anterior exponential drops. This relates to the posterior-wards spread of bcd in the first hour of development. Both bcd and Stau show several redistributions in the head cytoplasm, quite probably related to nuclear activity: first shifting inwards towards the core plasm, forming either protrusions (early pre-blastoderm) or round aggregations (early nuclear cleavage cycles, cc, 13 and 14), then moving to the embryo surface and spreading posteriorly. These movements are seen both with the 2D surface study and the 1D profile analysis. The continued spreading of bcd can be tracked from the time of nuclear layer formation (later pre-blastoderm) to the later syncytial blastoderm stages by the progressive loss of steepness of the apical anterior exponential (for both bcd and Stau). Finally, at the beginning of cc14 (cellularization stage) we see a distinctive flip from the basal anterior gradient being higher to the apical gradient being higher (for both bcd and Stau). Quantitative analysis reveals substantial (and correlated) bcd and Stau redistributions during early development, supporting that the distribution and dynamics of bcd mRNA are key factors in the formation and maintenance of the Bcd protein morphogenetic gradient. This analysis reveals the complex and dynamic nature of bcd redistribution, particularly in the head cytoplasm. These resemble observations in oogenesis; their role and significance have yet to be clarified. The observed co-localization during redistribution of bcd and Stau may indicate the involvement of active transport.
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Affiliation(s)
- Alex Shlemov
- Laboratory for Algorithmic Biology, St. Petersburg State University, St. Petersburg, Russia
| | - Theodore Alexandrov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Nina Golyandina
- Faculty of Mathematics and Mechanics, St. Petersburg State University, St. Petersburg, Russia
| | - David Holloway
- Mathematics Department, British Columbia Institute of Technology, Burnaby, British Columbia, Canada
| | - Stefan Baumgartner
- Department of Experimental Medical Sciences, Lund University, Lund, Sweden
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Alexander V. Spirov
- Computer Science and CEWIT, SUNY Stony Brook, Stony Brook, New York, United States of America
- Lab Modelling Evolution, The I.M. Sechenov Institute of Evolutionary Physiology & Biochemistry, St. Petersburg, Russia
- * E-mail:
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Cai X, Rondeel I, Baumgartner S. Modulating the bicoid gradient in space and time. Hereditas 2021; 158:29. [PMID: 34404481 PMCID: PMC8371787 DOI: 10.1186/s41065-021-00192-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 07/19/2021] [Indexed: 11/15/2022] Open
Abstract
Background The formation of the Bicoid (Bcd) gradient in the early Drosophila is one of the most fascinating observations in biology and serves as a paradigm for gradient formation, yet its mechanism is still not fully understood. Two distinct models were proposed in the past, the SDD and the ARTS model. Results We define novel cis- and trans-acting factors that are indispensable for gradient formation. The first one is the poly A tail length of the bcd mRNA where we demonstrate that it changes not only in time, but also in space. We show that posterior bcd mRNAs possess a longer poly tail than anterior ones and this elongation is likely mediated by wispy (wisp), a poly A polymerase. Consequently, modulating the activity of Wisp results in changes of the Bcd gradient, in controlling downstream targets such as the gap and pair-rule genes, and also in influencing the cuticular pattern. Attempts to modulate the Bcd gradient by subjecting the egg to an extra nuclear cycle, i.e. a 15th nuclear cycle by means of the maternal haploid (mh) mutation showed no effect, neither on the appearance of the gradient nor on the control of downstream target. This suggests that the segmental anlagen are determined during the first 14 nuclear cycles. Finally, we identify the Cyclin B (CycB) gene as a trans-acting factor that modulates the movement of Bcd such that Bcd movement is allowed to move through the interior of the egg. Conclusions Our analysis demonstrates that Bcd gradient formation is far more complex than previously thought requiring a revision of the models of how the gradient is formed.
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Affiliation(s)
- Xiaoli Cai
- Departmentof Experimental Medical Sciences, Lund University, BMC D10, 22184, Lund, Sweden
| | - Inge Rondeel
- Departmentof Experimental Medical Sciences, Lund University, BMC D10, 22184, Lund, Sweden.,Present address: Hubrecht Institute, 3584 CT, Utrecht, The Netherlands
| | - Stefan Baumgartner
- Departmentof Experimental Medical Sciences, Lund University, BMC D10, 22184, Lund, Sweden. .,Department of Biology, University of Konstanz, 78457, Konstanz, Germany.
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Myasnikova EM, Sabirov MA, Spirov AV. Quantitative Analysis of the Dynamics of Maternal Gradients in the Early Drosophila Embryo. J Comput Biol 2021; 28:747-757. [PMID: 34152850 DOI: 10.1089/cmb.2020.0571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Predetermination, formation, and maintenance of the primary morphogenetic gradient (bicoid, bcd) of the early Drosophila embryo involves many interrelated processes. Here we focus on the biological systems analysis of the bcd mRNA redistribution in an early embryo. The results of the quantitative analysis of experimental data, together with the results of their dynamic modeling, substantiate the role of active transport in the redistribution of the bcd mRNA. The role of the nonlinearity of degradation mechanisms in the mRNA pattern robustness is discussed.
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Affiliation(s)
- Ekaterina M Myasnikova
- Lab Modeling Evolution, I.M. Sechenov Institute of Evolutionary Physiology and Biochemistry of the Russian Academy of Sciences, St-Petersburg, Russia.,Center for Advanced Studies, Peter the Great St. Petersburg Polytechnical University, St-Petersburg, Russia
| | - Marat A Sabirov
- Lab Modeling Evolution, I.M. Sechenov Institute of Evolutionary Physiology and Biochemistry of the Russian Academy of Sciences, St-Petersburg, Russia
| | - Alexander V Spirov
- Lab Modeling Evolution, I.M. Sechenov Institute of Evolutionary Physiology and Biochemistry of the Russian Academy of Sciences, St-Petersburg, Russia
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Saternos H, Ley S, AbouAlaiwi W. Primary Cilia and Calcium Signaling Interactions. Int J Mol Sci 2020; 21:E7109. [PMID: 32993148 PMCID: PMC7583801 DOI: 10.3390/ijms21197109] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/23/2020] [Accepted: 09/24/2020] [Indexed: 02/06/2023] Open
Abstract
The calcium ion (Ca2+) is a diverse secondary messenger with a near-ubiquitous role in a vast array of cellular processes. Cilia are present on nearly every cell type in either a motile or non-motile form; motile cilia generate fluid flow needed for a variety of biological processes, such as left-right body patterning during development, while non-motile cilia serve as the signaling powerhouses of the cell, with vital singling receptors localized to their ciliary membranes. Much of the research currently available on Ca2+-dependent cellular actions and primary cilia are tissue-specific processes. However, basic stimuli-sensing pathways, such as mechanosensation, chemosensation, and electrical sensation (electrosensation), are complex processes entangled in many intersecting pathways; an overview of proposed functions involving cilia and Ca2+ interplay will be briefly summarized here. Next, we will focus on summarizing the evidence for their interactions in basic cellular activities, including the cell cycle, cell polarity and migration, neuronal pattering, glucose-mediated insulin secretion, biliary regulation, and bone formation. Literature investigating the role of cilia and Ca2+-dependent processes at a single-cellular level appears to be scarce, though overlapping signaling pathways imply that cilia and Ca2+ interact with each other on this level in widespread and varied ways on a perpetual basis. Vastly different cellular functions across many different cell types depend on context-specific Ca2+ and cilia interactions to trigger the correct physiological responses, and abnormalities in these interactions, whether at the tissue or the single-cell level, can result in diseases known as ciliopathies; due to their clinical relevance, pathological alterations of cilia function and Ca2+ signaling will also be briefly touched upon throughout this review.
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Affiliation(s)
| | | | - Wissam AbouAlaiwi
- Department of Pharmacology and Experimental Therapeutics, University of Toledo Health Science Campus, Toledo, OH 43614, USA; (H.S.); (S.L.)
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Abstract
Spatially distributed signaling molecules, known as morphogens, provide spatial information during development. A host of different morphogens have now been identified, from subcellular gradients through to morphogens that act across a whole embryo. These gradients form over a wide-range of timescales, from seconds to hours, and their time windows for interpretation are also highly variable; the processes of morphogen gradient formation and interpretation are highly dynamic. The morphogen Bicoid (Bcd), present in the early Drosophila embryo, is essential for setting up the future Drosophila body segments. Due to its accessibility for both genetic perturbations and imaging, this system has provided key insights into how precise patterning can occur within a highly dynamic system. Here, we review the temporal scales of Bcd gradient formation and interpretation. In particular, we discuss the quantitative evidence for different models of Bcd gradient formation, outline the time windows for Bcd interpretation, and describe how Bcd temporally adapts its own ability to be interpreted. The utilization of temporal information in morphogen readout may provide crucial inputs to ensure precise spatial patterning, particularly in rapidly developing systems.
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Cai X, Fahmy K, Baumgartner S. bicoid RNA localization requires the trans-Golgi network. Hereditas 2019; 156:30. [PMID: 31528161 PMCID: PMC6737670 DOI: 10.1186/s41065-019-0106-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 08/26/2019] [Indexed: 11/10/2022] Open
Abstract
Background The formation of the bicoid (bcd) mRNA gradient is a crucial step for Bcd protein gradient formation in Drosophila. In the past, a microtubule (MT)-based cortical network had been shown to be indispensable for bcd mRNA transport to the posterior. Results We report the identification of a MT-binding protein CLASP/Chb as the first component associated with this cortical MT network. Since CLASPs in vertebrates were shown to serve as an acentriolar microtubule organization center (aMTOC) in concert with trans-Golgi proteins, we examined the effect of the Drosophila trans-Golgins on bcd localization and gradient formation. Using a genetic approach, we demonstrate that the Drosophila trans-Golgins dGCC88, dGolgin97 and dGCC185 indeed affect bcd mRNA localization during oocyte development. Consequently, the bcd mRNA is already mislocalized before the egg is fertilized. The expression domains of genes downstream of the hierarchy of bcd, e.g. of the gap gene empty spiracles or of the pair-rule gene even-skipped are changed, indicating an altered segmental anlagen, due to a faulty bcd gradient. Thus, at the end of embryogenesis, trans-Golgin mutants show bcd-like cuticle phenotypes. Conclusions Our data provides evidence that the Golgi as a cellular member of the secretory pathway exerts control on bcd localization which indicates that bcd gradient formation is probably more intricate than previously presumed.
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Affiliation(s)
- Xiaoli Cai
- 1Department of Experimental Medical Sciences, Lund University, BMC D10, S-22184 Lund, Sweden
| | - Khalid Fahmy
- 2Present Address: Department of Genetics, Ain Shams University, Cairo, Egypt
| | - Stefan Baumgartner
- 1Department of Experimental Medical Sciences, Lund University, BMC D10, S-22184 Lund, Sweden.,3Department of Biology, University of Konstanz, D-78457 Constance, Germany
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Baumgartner S. Seeing is believing: the Bicoid protein reveals its path. Hereditas 2018; 155:28. [PMID: 30220899 PMCID: PMC6134762 DOI: 10.1186/s41065-018-0067-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 09/04/2018] [Indexed: 11/30/2022] Open
Abstract
In this commentary, I will review the latest findings on the Bicoid (Bcd) morphogen in Drosophila, a paradigm for gradient formation taught to biology students for more than two decades. “Seeing is believing” also summarizes the erroneous steps that were needed to elucidate the mechanisms of gradient formation and the path of movement of Bcd. Initially proclaimed as a dogma in 1988 and later incorporated into the SDD model where the broad diffusion of Bcd throughout the embryo was the predominant step leading to gradient formation, the SDD model was irrefutable for more than two decades until first doubts were raised in 2007 regarding the diffusion properties of Bcd associated with the SDD model. This led to re-thinking of the issue and the definition of a new model, termed the ARTS model which could explain most of the physical constraints that were inherently associated with the SDD model. In the ARTS model, gradient formation is mediated by the mRNA which is redistributed along cortical microtubules to form a mRNA gradient which is translated to form the protein gradient. Contrary to the SDD model, there is no Bcd diffusion from the tip. The ARTS model is also compatible with the observed cortical movement of Bcd. I will critically compare the SDD and the ARTS models as well as other models, analyze the major differences, and highlight the path where Bcd is localized during early nuclear cycles.
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Affiliation(s)
- Stefan Baumgartner
- Department of Experimental Medical Sciences, Lund University, BMC D10, S-22184 Lund, Sweden
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Cai X, Akber M, Spirov A, Baumgartner S. Correction: Cortical movement of Bicoid in early Drosophila embryos is actin- and microtubule-dependent and disagrees with the SDD diffusion model. PLoS One 2018; 13:e0196144. [PMID: 29668742 PMCID: PMC5906000 DOI: 10.1371/journal.pone.0196144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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