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Aldrich JC, Vanderlinden LA, Jacobsen TL, Wood C, Saba LM, Britt SG. Genome-Wide Association Study and transcriptome analysis reveals a complex gene network that regulates opsin gene expression and cell fate determination in Drosophila R7 photoreceptor cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.05.606616. [PMID: 39149333 PMCID: PMC11326169 DOI: 10.1101/2024.08.05.606616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Background An animal's ability to discriminate between differing wavelengths of light (i.e., color vision) is mediated, in part, by a subset of photoreceptor cells that express opsins with distinct absorption spectra. In Drosophila R7 photoreceptors, expression of the rhodopsin molecules, Rh3 or Rh4, is determined by a stochastic process mediated by the transcription factor spineless. The goal of this study was to identify additional factors that regulate R7 cell fate and opsin choice using a Genome Wide Association Study (GWAS) paired with transcriptome analysis via RNA-Seq. Results We examined Rh3 and Rh4 expression in a subset of fully-sequenced inbred strains from the Drosophila Genetic Reference Panel and performed a GWAS to identify 42 naturally-occurring polymorphisms-in proximity to 28 candidate genes-that significantly influence R7 opsin expression. Network analysis revealed multiple potential interactions between the associated candidate genes, spineless and its partners. GWAS candidates were further validated in a secondary RNAi screen which identified 12 lines that significantly reduce the proportion of Rh3 expressing R7 photoreceptors. Finally, using RNA-Seq, we demonstrated that all but four of the GWAS candidates are expressed in the pupal retina at a critical developmental time point and that five are among the 917 differentially expressed genes in sevenless mutants, which lack R7 cells. Conclusions Collectively, these results suggest that the relatively simple, binary cell fate decision underlying R7 opsin expression is modulated by a larger, more complex network of regulatory factors. Of particular interest are a subset of candidate genes with previously characterized neuronal functions including neurogenesis, neurodegeneration, photoreceptor development, axon growth and guidance, synaptogenesis, and synaptic function.
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Affiliation(s)
- John C. Aldrich
- Department of Neurology, Department of Ophthalmology, Dell Medical School; University of Texas at Austin, Austin, TX 78712
- Department of Psychology, University of Texas at Austin, Austin, TX 78712
| | - Lauren A. Vanderlinden
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Thomas L. Jacobsen
- Department of Neurology, Department of Ophthalmology, Dell Medical School; University of Texas at Austin, Austin, TX 78712
| | - Cheyret Wood
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Laura M. Saba
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Steven G. Britt
- Department of Neurology, Department of Ophthalmology, Dell Medical School; University of Texas at Austin, Austin, TX 78712
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Lloyd VJ, Burg SL, Harizanova J, Garcia E, Hill O, Enciso-Romero J, Cooper RL, Flenner S, Longo E, Greving I, Nadeau NJ, Parnell AJ. The actin cytoskeleton plays multiple roles in structural colour formation in butterfly wing scales. Nat Commun 2024; 15:4073. [PMID: 38769302 PMCID: PMC11106069 DOI: 10.1038/s41467-024-48060-3] [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: 10/18/2023] [Accepted: 04/19/2024] [Indexed: 05/22/2024] Open
Abstract
Vivid structural colours in butterflies are caused by photonic nanostructures scattering light. Structural colours evolved for numerous biological signalling functions and have important technological applications. Optically, such structures are well understood, however insight into their development in vivo remains scarce. We show that actin is intimately involved in structural colour formation in butterfly wing scales. Using comparisons between iridescent (structurally coloured) and non-iridescent scales in adult and developing H. sara, we show that iridescent scales have more densely packed actin bundles leading to an increased density of reflective ridges. Super-resolution microscopy across three distantly related butterfly species reveals that actin is repeatedly re-arranged during scale development and crucially when the optical nanostructures are forming. Furthermore, actin perturbation experiments at these later developmental stages resulted in near total loss of structural colour in H. sara. Overall, this shows that actin plays a vital and direct templating role during structural colour formation in butterfly scales, providing ridge patterning mechanisms that are likely universal across lepidoptera.
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Affiliation(s)
- Victoria J Lloyd
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Alfred Denny Building, Western bank, Sheffield, S10 2TN, UK.
| | - Stephanie L Burg
- Department of Physics and Astronomy, University of Sheffield, Hicks Building, Hounsfield Road, Sheffield, S3 7RH, UK
| | - Jana Harizanova
- Central Laser Facility-Science & Technology Facility Council, The Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot, Oxfordshire, OX11 0FA, UK
- Core Facility for Integrated Microscopy, Department of Biomedical Sciences, University of Copenhagen, 2200N, Copenhagen, Denmark
| | - Esther Garcia
- Central Laser Facility-Science & Technology Facility Council, The Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot, Oxfordshire, OX11 0FA, UK
| | - Olivia Hill
- Department of Physics and Astronomy, University of Sheffield, Hicks Building, Hounsfield Road, Sheffield, S3 7RH, UK
| | - Juan Enciso-Romero
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Alfred Denny Building, Western bank, Sheffield, S10 2TN, UK
- Department of Biological Sciences, University of Lethbridge, 4401 University Drive, Lethbridge, AB, T1K 3M4, Canada
| | - Rory L Cooper
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Alfred Denny Building, Western bank, Sheffield, S10 2TN, UK
- Department of Genetics and Evolution, University of Geneva, Sciences III, Geneva, 1205, Switzerland
| | - Silja Flenner
- Helmholtz-Zentrum Hereon, Max-Planck-Strasse 1, 21502, Geesthacht, Germany
| | - Elena Longo
- Elettra-Sincrotrone Trieste S.C.p.A., 34149, Basovizza, Trieste, Italy
| | - Imke Greving
- Helmholtz-Zentrum Hereon, Max-Planck-Strasse 1, 21502, Geesthacht, Germany
| | - Nicola J Nadeau
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Alfred Denny Building, Western bank, Sheffield, S10 2TN, UK.
| | - Andrew J Parnell
- Department of Physics and Astronomy, University of Sheffield, Hicks Building, Hounsfield Road, Sheffield, S3 7RH, UK.
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Hopkins BR, Barmina O, Kopp A. A single-cell atlas of the sexually dimorphic Drosophila foreleg and its sensory organs during development. PLoS Biol 2023; 21:e3002148. [PMID: 37379332 DOI: 10.1371/journal.pbio.3002148] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 05/03/2023] [Indexed: 06/30/2023] Open
Abstract
To respond to the world around them, animals rely on the input of a network of sensory organs distributed throughout the body. Distinct classes of sensory organs are specialized for the detection of specific stimuli such as strain, pressure, or taste. The features that underlie this specialization relate both to the neurons that innervate sensory organs and the accessory cells they comprise. To understand the genetic basis of this diversity of cell types, both within and between sensory organs, we performed single-cell RNA sequencing on the first tarsal segment of the male Drosophila melanogaster foreleg during pupal development. This tissue displays a wide variety of functionally and structurally distinct sensory organs, including campaniform sensilla, mechanosensory bristles, and chemosensory taste bristles, as well as the sex comb, a recently evolved male-specific structure. In this study, we characterize the cellular landscape in which the sensory organs reside, identify a novel cell type that contributes to the construction of the neural lamella, and resolve the transcriptomic differences among support cells within and between sensory organs. We identify the genes that distinguish between mechanosensory and chemosensory neurons, resolve a combinatorial transcription factor code that defines 4 distinct classes of gustatory neurons and several types of mechanosensory neurons, and match the expression of sensory receptor genes to specific neuron classes. Collectively, our work identifies core genetic features of a variety of sensory organs and provides a rich, annotated resource for studying their development and function.
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Affiliation(s)
- Ben R Hopkins
- Department of Evolution and Ecology, University of California, Davis, California, United States of America
| | - Olga Barmina
- Department of Evolution and Ecology, University of California, Davis, California, United States of America
| | - Artyom Kopp
- Department of Evolution and Ecology, University of California, Davis, California, United States of America
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4
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Djokic S, Bakhrat A, Li M, Akbari OS, Abdu U. Scale-type-specific requirement for the mosquito Aedes aegypti Spindle-F homologue by regulating microtubule organization. INSECT MOLECULAR BIOLOGY 2022; 31:216-224. [PMID: 34919304 PMCID: PMC10537241 DOI: 10.1111/imb.12752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 11/11/2021] [Accepted: 12/12/2021] [Indexed: 06/14/2023]
Abstract
Insect epithelial cells contain unique cellular extensions such as bristles, hairs, and scales. In contrast to bristle and hair, which are not divergent in their shape, scale morphology shows high diversity. In our attempt to characterize the role of the insect-specific gene, Spindle-F (spn-F), in mosquito development, we revealed a scale-type specific requirement for the mosquito Aedes aegypti spn-F homologue. Using CRISPR-Cas9, we generated Ae-spn-F mutants and found that Ae-spn-F is an essential gene, but we were able to recover a few adult escapers. These escapers could not fly nor move, and died after 3 to 4 days. We found that in Ae-spn-F mutants, only the tip part of the bristle was affected with bulbous with misoriented ribs. We also show that in Ae-spn-F mutants, only in falcate scales, which are curved with a sharp or narrowly rounded apex, and not in other scale types, the tip region is strongly affected. Our analysis also revealed that in contrast to Drosophila spn-F, which show strong defects in both the actin and microtubule (MT) network in the bristle, the Ae-spn-F gene is required only for MT organization in scales and bristles. In summary, our results reveal that Ae-spn-F is required for shaping tapered epithelial cellular extension structures, namely, the bristle and falcate scales by affecting MT organization.
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Affiliation(s)
- Sanja Djokic
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Anna Bakhrat
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Ming Li
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, San Diego, CA, USA
| | - Omar S. Akbari
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, San Diego, CA, USA
| | - Uri Abdu
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
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5
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Krishnan RK, Baskar R, Anna B, Elia N, Boermel M, Bausch AR, Abdu U. Recapitulating Actin Module Organization in the Drosophila Oocyte Reveals New Roles for Bristle-Actin-Modulating Proteins. Int J Mol Sci 2021; 22:ijms22084006. [PMID: 33924532 PMCID: PMC8070096 DOI: 10.3390/ijms22084006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/05/2021] [Accepted: 04/06/2021] [Indexed: 11/16/2022] Open
Abstract
The generation of F-actin bundles is controlled by the action of actin-binding proteins. In Drosophila bristle development, two major actin-bundling proteins—Forked and Fascin—were identified, but still the molecular mechanism by which these actin-bundling proteins and other proteins generate bristle actin bundles is unknown. In this study, we developed a technique that allows recapitulation of bristle actin module organization using the Drosophila ovary by a combination of confocal microscopy, super-resolution structured illumination microscopy, and correlative light and electron microscope analysis. Since Forked generated a distinct ectopic network of actin bundles in the oocyte, the additive effect of two other actin-associated proteins, namely, Fascin and Javelin (Jv), was studied. We found that co-expression of Fascin and Forked demonstrated that the number of actin filaments within the actin bundles dramatically increased, and in their geometric organization, they resembled bristle-like actin bundles. On the other hand, co-expression of Jv with Forked increased the length and density of the actin bundles. When all three proteins co-expressed, the actin bundles were longer and denser, and contained a high number of actin filaments in the bundle. Thus, our results demonstrate that the Drosophila oocyte could serve as a test tube for actin bundle analysis.
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Affiliation(s)
- Ramesh Kumar Krishnan
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel; (R.K.K.); (R.B.); (B.A.); (N.E.)
| | - Raju Baskar
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel; (R.K.K.); (R.B.); (B.A.); (N.E.)
| | - Bakhrat Anna
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel; (R.K.K.); (R.B.); (B.A.); (N.E.)
| | - Natalie Elia
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel; (R.K.K.); (R.B.); (B.A.); (N.E.)
- National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Mandy Boermel
- Electron Microscopy Core Facility, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany;
| | - Andreas R. Bausch
- Lehrstuhl für Zellbiophysik E27, Technische Universität München, James-Franck-Str. 1, 85748 Garching, Germany;
- Center for Protein Assemblies (CPA), Ernst-Otto-Fischer Str. 8, 85747 Garching, Germany
| | - Uri Abdu
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel; (R.K.K.); (R.B.); (B.A.); (N.E.)
- Correspondence:
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Gershman BW, Pritchard CE, Chaney KP, Ware VC. Tissue-specific expression of ribosomal protein paralogue eRpL22-like in Drosophila melanogaster eye development. Dev Dyn 2020; 249:1147-1165. [PMID: 32353187 PMCID: PMC8109839 DOI: 10.1002/dvdy.185] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 03/24/2020] [Accepted: 04/23/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Differences in core or tissue-specific ribosomal protein (Rp) composition within ribosomes contribute to ribosome heterogeneity and functional variability. Yet, the degree to which ribosome heterogeneity modulates development is unknown. The Drosophila melanogaster eRpL22 family contains structurally diverse paralogues, eRpL22 and eRpL22-like. Unlike ubiquitously expressed eRpL22, eRpL22-like expression is tissue-specific, notably within the male germline and the eye. We investigated expression within the developing eye to uncover tissue/cell types where specific paralogue roles might be defined. RESULTS Immunohistochemistry analysis confirms ubiquitous eRpL22 expression throughout eye development. In larvae, eRpL22-like is ubiquitously expressed, but highly enriched in the peripodial epithelium (PE). In early pupae, eRpL22-like is broadly distributed in multiple cell types, but later, is primarily enriched in interommatidial hair cells (IoHC). Adult patterns include the ring of accessory cells around ommatidia. Adult retinae IoHC patterning phenotypes (shown by scanning electron microscopy) may be linked to RNAi-mediated eRpL22-like depletion within larval PE. Immunoblots and polysome profile analyses show multiple variants of eRpL22-like across development, with the variant at the expected molecular mass co-sedimenting with active ribosomes. CONCLUSION Our data reveal differential patterns of eRpL22-like expression relative to eRpL22 and suggest a specific role for eRpL22-like in developmental patterning of the eye.
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Affiliation(s)
- Brett W. Gershman
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania
| | | | - Kenneth P. Chaney
- Department of Computer and Information Science, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Vassie C. Ware
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania
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7
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Day CR, Hanly JJ, Ren A, Martin A. Sub-micrometer insights into the cytoskeletal dynamics and ultrastructural diversity of butterfly wing scales. Dev Dyn 2019; 248:657-670. [PMID: 31107575 DOI: 10.1002/dvdy.63] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/13/2019] [Accepted: 05/16/2019] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND The color patterns that adorn lepidopteran wings are ideal for studying cell type diversity using a phenomics approach. Color patterns are made of chitinous scales that are each the product of a single precursor cell, offering a 2D system where phenotypic diversity can be studied cell by cell, both within and between species. Those scales reveal complex ultrastructures in the sub-micrometer range that are often connected to a photonic function, including iridescent blues and greens, highly reflective whites, or light-trapping blacks. RESULTS We found that during scale development, Fascin immunostainings reveal punctate distributions consistent with a role in the control of actin patterning. We quantified the cytoskeleton regularity as well as its relationship to chitin deposition sites, and confirmed a role in the patterning of the ultrastructures of the adults scales. Then, in an attempt to characterize the range and variation in lepidopteran scale ultrastructures, we devised a high-throughput method to quickly derive multiple morphological measurements from fluorescence images and scanning electron micrographs. We imaged a multicolor eyespot element from the butterfly Vanessa cardui (V. cardui), taking approximately 200 000 individual measurements from 1161 scales. Principal component analyses revealed that scale structural features cluster by color type, and detected the divergence of non-reflective scales characterized by tighter cross-rib distances and increased orderedness. CONCLUSION We developed descriptive methods that advance the potential of butterfly wing scales as a model system for studying how a single cell type can differentiate into a multifaceted spectrum of complex morphologies. Our data suggest that specific color scales undergo a tight regulation of their ultrastructures, and that this involves cytoskeletal dynamics during scale growth.
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Affiliation(s)
- Christopher R Day
- Department of Biological Sciences, The George Washington University, Washington, District of Columbia.,Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina
| | - Joseph J Hanly
- Department of Biological Sciences, The George Washington University, Washington, District of Columbia
| | - Anna Ren
- Department of Biological Sciences, The George Washington University, Washington, District of Columbia
| | - Arnaud Martin
- Department of Biological Sciences, The George Washington University, Washington, District of Columbia
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Do KK, Hoàng KL, Endow SA. The kinesin-13 KLP10A motor regulates oocyte spindle length and affects EB1 binding without altering microtubule growth rates. Biol Open 2014; 3:561-70. [PMID: 24907370 PMCID: PMC4154291 DOI: 10.1242/bio.20148276] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Kinesin-13 motors are unusual in that they do not walk along microtubules, but instead diffuse to the ends, where they remove tubulin dimers, regulating microtubule dynamics. Here we show that Drosophila kinesin-13 klp10A regulates oocyte meiosis I spindle length and is haplo-insufficient – KLP10A, reduced by RNAi or a loss-of-function P element insertion mutant, results in elongated and mispositioned oocyte spindles, and abnormal cortical microtubule asters and aggregates. KLP10A knockdown by RNAi does not significantly affect microtubule growth rates in oocyte spindles, but, unexpectedly, EB1 binding and unbinding are slowed, suggesting a previously unobserved role for kinesin-13 in mediating EB1 binding interactions with microtubules. Kinesin-13 may regulate spindle length both by disassembling subunits from microtubule ends and facilitating EB1 binding to plus ends. We also observe an increased number of paused microtubules in klp10A RNAi knockdown spindles, consistent with a reduced frequency of microtubule catastrophes. Overall, our findings indicate that reduced kinesin-13 decreases microtubule disassembly rates and affects EB1 interactions with microtubules, rather than altering microtubule growth rates, causing spindles to elongate and abnormal cortical microtubule asters and aggregates to form.
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Affiliation(s)
- Kevin K Do
- Department of Cell Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Kim Liên Hoàng
- Department of Cell Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Sharyn A Endow
- Department of Cell Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
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