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Kang J, Zhang C, Wang Y, Peng J, Berger B, Perrimon N, Shen J. Lipophorin receptors genetically modulate neurodegeneration caused by reduction of Psn expression in the aging Drosophila brain. Genetics 2024; 226:iyad202. [PMID: 37996068 PMCID: PMC10763532 DOI: 10.1093/genetics/iyad202] [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: 10/11/2023] [Revised: 11/01/2023] [Accepted: 11/12/2023] [Indexed: 11/25/2023] Open
Abstract
Mutations in the Presenilin (PSEN) genes are the most common cause of early-onset familial Alzheimer's disease (FAD). Studies in cell culture, in vitro biochemical systems, and knockin mice showed that PSEN mutations are loss-of-function mutations, impairing γ-secretase activity. Mouse genetic analysis highlighted the importance of Presenilin (PS) in learning and memory, synaptic plasticity and neurotransmitter release, and neuronal survival, and Drosophila studies further demonstrated an evolutionarily conserved role of PS in neuronal survival during aging. However, molecular pathways that interact with PS in neuronal survival remain unclear. To identify genetic modifiers that modulate PS-dependent neuronal survival, we developed a new DrosophilaPsn model that exhibits age-dependent neurodegeneration and increases of apoptosis. Following a bioinformatic analysis, we tested top ranked candidate genes by selective knockdown (KD) of each gene in neurons using two independent RNAi lines in Psn KD models. Interestingly, 4 of the 9 genes enhancing neurodegeneration in Psn KD flies are involved in lipid transport and metabolism. Specifically, neuron-specific KD of lipophorin receptors, lpr1 and lpr2, dramatically worsens neurodegeneration in Psn KD flies, and overexpression of lpr1 or lpr2 does not alleviate Psn KD-induced neurodegeneration. Furthermore, lpr1 or lpr2 KD alone also leads to neurodegeneration, increased apoptosis, climbing defects, and shortened lifespan. Lastly, heterozygotic deletions of lpr1 and lpr2 or homozygotic deletions of lpr1 or lpr2 similarly lead to age-dependent neurodegeneration and further exacerbate neurodegeneration in Psn KD flies. These findings show that LpRs modulate Psn-dependent neuronal survival and are critically important for neuronal integrity in the aging brain.
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Affiliation(s)
- Jongkyun Kang
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Chen Zhang
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Yuhao Wang
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jian Peng
- Department of Computer Science, University of Illinois at Urbana-Champaign, Champaign, IL 61801, USA
| | - Bonnie Berger
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Jie Shen
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA
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Mannino MC, Cassidy MB, Florez S, Rusan Z, Chakraborty S, Schoborg T. Mutations in abnormal spindle disrupt temporal transcription factor expression and trigger immune responses in the Drosophila brain. Genetics 2023; 225:iyad188. [PMID: 37831641 PMCID: PMC10697820 DOI: 10.1093/genetics/iyad188] [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: 08/30/2023] [Revised: 08/30/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
The coordination of cellular behaviors during neurodevelopment is critical for determining the form, function, and size of the central nervous system (CNS). Mutations in the vertebrate Abnormal Spindle-Like, Microcephaly Associated (ASPM) gene and its Drosophila melanogaster ortholog abnormal spindle (asp) lead to microcephaly (MCPH), a reduction in overall brain size whose etiology remains poorly defined. Here, we provide the neurodevelopmental transcriptional landscape for a Drosophila model for autosomal recessive primary microcephaly-5 (MCPH5) and extend our findings into the functional realm to identify the key cellular mechanisms responsible for Asp-dependent brain growth and development. We identify multiple transcriptomic signatures, including new patterns of coexpressed genes in the developing CNS. Defects in optic lobe neurogenesis were detected in larval brains through downregulation of temporal transcription factors (tTFs) and Notch signaling targets, which correlated with a significant reduction in brain size and total cell numbers during the neurogenic window of development. We also found inflammation as a hallmark of asp mutant brains, detectable throughout every stage of CNS development, which also contributes to the brain size phenotype. Finally, we show that apoptosis is not a primary driver of the asp mutant brain phenotypes, further highlighting an intrinsic Asp-dependent neurogenesis promotion mechanism that is independent of cell death. Collectively, our results suggest that the etiology of the asp mutant brain phenotype is complex and that a comprehensive view of the cellular basis of the disorder requires an understanding of how multiple pathway inputs collectively determine tissue size and architecture.
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Affiliation(s)
- Maria C Mannino
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
| | | | - Steven Florez
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
| | - Zeid Rusan
- Personalis, Inc., Fremont, CA 94555, USA
| | - Shalini Chakraborty
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
| | - Todd Schoborg
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
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3
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Chen Y, Li H, Yi TC, Shen J, Zhang J. Notch Signaling in Insect Development: A Simple Pathway with Diverse Functions. Int J Mol Sci 2023; 24:14028. [PMID: 37762331 PMCID: PMC10530718 DOI: 10.3390/ijms241814028] [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: 07/31/2023] [Revised: 09/05/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Notch signaling is an evolutionarily conserved pathway which functions between adjacent cells to establish their distinct identities. Despite operating in a simple mechanism, Notch signaling plays remarkably diverse roles in development to regulate cell fate determination, organ growth and tissue patterning. While initially discovered and characterized in the model insect Drosophila melanogaster, recent studies across various insect species have revealed the broad involvement of Notch signaling in shaping insect tissues. This review focuses on providing a comprehensive picture regarding the roles of the Notch pathway in insect development. The roles of Notch in the formation and patterning of the insect embryo, wing, leg, ovary and several specific structures, as well as in physiological responses, are summarized. These results are discussed within the developmental context, aiming to deepen our understanding of the diversified functions of the Notch signaling pathway in different insect species.
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Affiliation(s)
- Yao Chen
- Department of Plant Biosecurity and MOA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing 100193, China; (Y.C.)
| | - Haomiao Li
- Department of Plant Biosecurity and MOA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing 100193, China; (Y.C.)
| | - Tian-Ci Yi
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of Mountainous Regions, Institute of Entomology, Guizhou University, Guiyang 550025, China
| | - Jie Shen
- Department of Plant Biosecurity and MOA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing 100193, China; (Y.C.)
| | - Junzheng Zhang
- Department of Plant Biosecurity and MOA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing 100193, China; (Y.C.)
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4
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Rocha JJ, Jayaram SA, Stevens TJ, Muschalik N, Shah RD, Emran S, Robles C, Freeman M, Munro S. Functional unknomics: Systematic screening of conserved genes of unknown function. PLoS Biol 2023; 21:e3002222. [PMID: 37552676 PMCID: PMC10409296 DOI: 10.1371/journal.pbio.3002222] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 06/27/2023] [Indexed: 08/10/2023] Open
Abstract
The human genome encodes approximately 20,000 proteins, many still uncharacterised. It has become clear that scientific research tends to focus on well-studied proteins, leading to a concern that poorly understood genes are unjustifiably neglected. To address this, we have developed a publicly available and customisable "Unknome database" that ranks proteins based on how little is known about them. We applied RNA interference (RNAi) in Drosophila to 260 unknown genes that are conserved between flies and humans. Knockdown of some genes resulted in loss of viability, and functional screening of the rest revealed hits for fertility, development, locomotion, protein quality control, and resilience to stress. CRISPR/Cas9 gene disruption validated a component of Notch signalling and 2 genes contributing to male fertility. Our work illustrates the importance of poorly understood genes, provides a resource to accelerate future research, and highlights a need to support database curation to ensure that misannotation does not erode our awareness of our own ignorance.
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Affiliation(s)
- João J. Rocha
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | | | - Tim J. Stevens
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | | | - Rajen D. Shah
- Centre for Mathematical Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Sahar Emran
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Cristina Robles
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Matthew Freeman
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Sean Munro
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
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5
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Jejina A, Ayala Y, Hernández G, Suter B. Role of BicDR in bristle shaft construction, tracheal development, and support of BicD functions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.16.545245. [PMID: 37398393 PMCID: PMC10312712 DOI: 10.1101/2023.06.16.545245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Cell polarization requires asymmetric localization of numerous mRNAs, proteins, and organelles. The movement of cargo towards the minus end of microtubules mostly depends on cytoplasmic dynein motors, which function as multiprotein complexes. In the dynein/dynactin/Bicaudal-D (DDB) transport machinery, Bicaudal-D (BicD) links the cargo to the motor. Here we focus on the role of BicD-related (BicDR) and its contribution to microtubule-dependent transport processes. Drosophila BicDR is required for the normal development of bristles and dorsal trunk tracheae. Together with BicD, it contributes to the organization and stability of the actin cytoskeleton in the not-yet-chitinized bristle shaft and the localization of Spn-F and Rab6 at the distal tip. We show that BicDR supports the function of BicD in bristle development and our results suggest that BicDR transports cargo more locally whereas BicD is more responsible for delivering functional cargo over the long distance to the distal tip. We identified the proteins that interact with BicDR and appear to be BicDR cargo in embryonic tissues. For one of them, EF1γ, we showed that EF1γ genetically interacts with BicD and BicDR in the construction of the bristles.
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Affiliation(s)
- Aleksandra Jejina
- Institute of Cell Biology, University of Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Switzerland
| | - Yeniffer Ayala
- Laboratory of Translation and Cancer, Unit of Biomedical Research on Cancer, Instituto Nacional de Cancerologıá (INCan), Mexico City, Mexico
| | - Greco Hernández
- Laboratory of Translation and Cancer, Unit of Biomedical Research on Cancer, Instituto Nacional de Cancerologıá (INCan), Mexico City, Mexico
| | - Beat Suter
- Institute of Cell Biology, University of Bern, Switzerland
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6
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Oddsson A, Sulem P, Sveinbjornsson G, Arnadottir GA, Steinthorsdottir V, Halldorsson GH, Atlason BA, Oskarsson GR, Helgason H, Nielsen HS, Westergaard D, Karjalainen JM, Katrinardottir H, Fridriksdottir R, Jensson BO, Tragante V, Ferkingstad E, Jonsson H, Gudjonsson SA, Beyter D, Moore KHS, Thordardottir HB, Kristmundsdottir S, Stefansson OA, Rantapää-Dahlqvist S, Sonderby IE, Didriksen M, Stridh P, Haavik J, Tryggvadottir L, Frei O, Walters GB, Kockum I, Hjalgrim H, Olafsdottir TA, Selbaek G, Nyegaard M, Erikstrup C, Brodersen T, Saevarsdottir S, Olsson T, Nielsen KR, Haraldsson A, Bruun MT, Hansen TF, Steingrimsdottir T, Jacobsen RL, Lie RT, Djurovic S, Alfredsson L, Lopez de Lapuente Portilla A, Brunak S, Melsted P, Halldorsson BV, Saemundsdottir J, Magnusson OT, Padyukov L, Banasik K, Rafnar T, Askling J, Klareskog L, Pedersen OB, Masson G, Havdahl A, Nilsson B, Andreassen OA, Daly M, Ostrowski SR, Jonsdottir I, Stefansson H, Holm H, Helgason A, Thorsteinsdottir U, Stefansson K, Gudbjartsson DF. Deficit of homozygosity among 1.52 million individuals and genetic causes of recessive lethality. Nat Commun 2023; 14:3453. [PMID: 37301908 PMCID: PMC10257723 DOI: 10.1038/s41467-023-38951-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
Genotypes causing pregnancy loss and perinatal mortality are depleted among living individuals and are therefore difficult to find. To explore genetic causes of recessive lethality, we searched for sequence variants with deficit of homozygosity among 1.52 million individuals from six European populations. In this study, we identified 25 genes harboring protein-altering sequence variants with a strong deficit of homozygosity (10% or less of predicted homozygotes). Sequence variants in 12 of the genes cause Mendelian disease under a recessive mode of inheritance, two under a dominant mode, but variants in the remaining 11 have not been reported to cause disease. Sequence variants with a strong deficit of homozygosity are over-represented among genes essential for growth of human cell lines and genes orthologous to mouse genes known to affect viability. The function of these genes gives insight into the genetics of intrauterine lethality. We also identified 1077 genes with homozygous predicted loss-of-function genotypes not previously described, bringing the total set of genes completely knocked out in humans to 4785.
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Affiliation(s)
| | | | | | - Gudny A Arnadottir
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | | | | | - Henriette Svarre Nielsen
- Deptartment of Obstetrics and Gynecology, Copenhagen University Hospital, Hvidovre, Denmark
- Department of Clinical Medicine, Faculty of Health, University of Copenhagen, Copenhagen, Denmark
| | - David Westergaard
- Deptartment of Obstetrics and Gynecology, Copenhagen University Hospital, Hvidovre, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Methods and Analysis, Statistics Denmark, Copenhagen, Denmark
| | - Juha M Karjalainen
- Institute for Molecular Medicine, Finland, University of Helsinki, Helsinki, Finland
| | | | | | | | | | | | | | | | | | - Kristjan H S Moore
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | - Helga B Thordardottir
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | - Ida Elken Sonderby
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
- NORMENT Centre, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental disorders, University of Oslo, Oslo, Norway
| | - Maria Didriksen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Pernilla Stridh
- Neuroimmunology Unit, Department of Clinical Neuroscience, Center of Molecular Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Jan Haavik
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Bergen Center of Brain Plasticity, Division of Psychiatry, Haukeland University Hospital, Bergen, Norway
| | - Laufey Tryggvadottir
- Icelandic Cancer Registry, Icelandic Cancer Society, Reykjavik, Iceland
- Faculty of Medicine, BMC, Laeknagardur, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Oleksandr Frei
- NORMENT Centre, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | | | - Ingrid Kockum
- Neuroimmunology Unit, Department of Clinical Neuroscience, Center of Molecular Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Henrik Hjalgrim
- Department of Clinical Medicine, Faculty of Health, University of Copenhagen, Copenhagen, Denmark
- Danish Cancer Society Research Center, Copenhagen, Denmark
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | | | - Geir Selbaek
- Norwegian National Centre of Ageing and Health, Vestfold Hospital Trust, Tonsberg, Norway
- Department of Geriatric Medicine, Oslo University Hospital, Oslo, Norway
- Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Mette Nyegaard
- Deptartment of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Thorsten Brodersen
- Department of Clinical Immunology, Zealand University Hospital, Koge, Denmark
| | - Saedis Saevarsdottir
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Tomas Olsson
- Neuroimmunology Unit, Department of Clinical Neuroscience, Center of Molecular Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Kaspar Rene Nielsen
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
| | - Asgeir Haraldsson
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
- Children's Hospital Iceland, Landspitali University Hospital, Reykjavik, Iceland
| | - Mie Topholm Bruun
- Department of Clinical Immunology, Odense University Hospital, Odense, Denmark
| | - Thomas Folkmann Hansen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Neurology, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Thora Steingrimsdottir
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Rikke Louise Jacobsen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Rolv T Lie
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Srdjan Djurovic
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
- NORMENT Centre, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental disorders, University of Oslo, Oslo, Norway
| | - Lars Alfredsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Soren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Pall Melsted
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Bjarni V Halldorsson
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- School of Science and Engineering, Reykjavik University, Reykjavik, Iceland
| | | | | | - Leonid Padyukov
- Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
| | - Karina Banasik
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Johan Askling
- Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
| | - Lars Klareskog
- Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
| | - Ole Birger Pedersen
- Department of Clinical Medicine, Faculty of Health, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Immunology, Zealand University Hospital, Koge, Denmark
| | | | - Alexandra Havdahl
- Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway
- Nic Waals Institute, Lovisenberg Diaconal Hospital, Oslo, Norway
- PROMENTA Research Center, Department of Psychology, University of Oslo, Oslo, Norway
| | - Bjorn Nilsson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund, Sweden
| | - Ole A Andreassen
- NORMENT Centre, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental disorders, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Mark Daly
- Institute for Molecular Medicine, Finland, University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sisse Rye Ostrowski
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Deptartment of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ingileif Jonsdottir
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Hilma Holm
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
| | - Agnar Helgason
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Kari Stefansson
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland.
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.
| | - Daniel F Gudbjartsson
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- School of Science and Engineering, Reykjavik University, Reykjavik, Iceland
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7
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Vaikakkara Chithran A, Allan DW, O'Connor TP. Adult expression of Semaphorins and Plexins is essential for motor neuron survival. Sci Rep 2023; 13:5894. [PMID: 37041188 PMCID: PMC10090137 DOI: 10.1038/s41598-023-32943-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/05/2023] [Indexed: 04/13/2023] Open
Abstract
Axon guidance cues direct the growth and steering of neuronal growth cones, thus guiding the axons to their targets during development. Nonetheless, after axons have reached their targets and established functional circuits, many mature neurons continue to express these developmental cues. The role of axon guidance cues in the adult nervous system has not been fully elucidated. Using the expression pattern data available on FlyBase, we found that more than 96% of the guidance genes that are expressed in the Drosophila melanogaster embryo continue to be expressed in adults. We utilized the GeneSwitch and TARGET systems to spatiotemporally knockdown the expression of these guidance genes selectively in the adult neurons, once the development was completed. We performed an RNA interference (RNAi) screen against 44 guidance genes in the adult Drosophila nervous system and identified 14 genes that are required for adult survival and normal motility. Additionally, we show that adult expression of Semaphorins and Plexins in motor neurons is necessary for neuronal survival, indicating that guidance genes have critical functions in the mature nervous system.
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Affiliation(s)
- Aarya Vaikakkara Chithran
- Graduate Program in Neuroscience, University of British Columbia, 3402-2215 Wesbrook Mall, Vancouver, BC, V6T 1Z3, Canada
- Department of Cellular and Physiological Sciences, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Douglas W Allan
- Department of Cellular and Physiological Sciences, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2215 Wesbrook Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Timothy P O'Connor
- Department of Cellular and Physiological Sciences, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada.
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2215 Wesbrook Mall, Vancouver, BC, V6T 1Z3, Canada.
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8
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Pueyo JI, Salazar J, Grincho C, Berni J, Towler BP, Newbury SF. Purriato is a conserved small open reading frame gene that interacts with the CASA pathway to regulate muscle homeostasis and epithelial tissue growth in Drosophila. Front Cell Dev Biol 2023; 11:1117454. [PMID: 36968202 PMCID: PMC10036370 DOI: 10.3389/fcell.2023.1117454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 02/24/2023] [Indexed: 03/12/2023] Open
Abstract
Recent advances in proteogenomic techniques and bioinformatic pipelines have permitted the detection of thousands of translated small Open Reading Frames (smORFs), which contain less than 100 codons, in eukaryotic genomes. Hundreds of these actively translated smORFs display conserved sequence, structure and evolutionary signatures indicating that the translated peptides could fulfil important biological roles. Despite their abundance, only tens of smORF genes have been fully characterised; these act mainly as regulators of canonical proteins involved in essential cellular processes. Importantly, some of these smORFs display conserved functions with their mutations being associated with pathogenesis. Thus, investigating smORF roles in Drosophila will not only expand our understanding of their functions but it may have an impact in human health. Here we describe the function of a novel and essential Drosophila smORF gene named purriato (prto). prto belongs to an ancient gene family whose members have expanded throughout the Protostomia clade. prto encodes a transmembrane peptide which is localized in endo-lysosomes and perinuclear and plasma membranes. prto is dynamically expressed in mesodermal tissues and imaginal discs. Targeted prto knockdown (KD) in these organs results in changes in nuclear morphology and endo-lysosomal distributions correlating with the loss of sarcomeric homeostasis in muscles and reduction of mitosis in wing discs. Consequently, prto KD mutants display severe reduction of motility, and shorter wings. Finally, our genetic interaction experiments show that prto function is closely associated to the CASA pathway, a conserved mechanism involved in turnover of mis-folded proteins and linked to muscle dystrophies and neurodegenerative diseases. Thus, this study shows the relevance of smORFs in regulating important cellular functions and supports the systematic characterisation of this class of genes to understand their functions and evolution.
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Affiliation(s)
- Jose I. Pueyo
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
| | - Jorge Salazar
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
| | - Carolina Grincho
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
| | - Jimena Berni
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
| | - Benjamin P. Towler
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Sarah F. Newbury
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
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9
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The function and evolution of a genetic switch controlling sexually dimorphic eye differentiation in honeybees. Nat Commun 2023; 14:463. [PMID: 36709321 PMCID: PMC9884244 DOI: 10.1038/s41467-023-36153-4] [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: 01/29/2022] [Accepted: 01/18/2023] [Indexed: 01/30/2023] Open
Abstract
Animals develop sex-specific morphological structures that are diverse between organisms. However, understanding the developmental and evolutionary mechanisms governing these traits is still limited and largely restricted to DM domain genes, which are conserved, sex-specific developmental regulators identified in genetic models. Here, we report a sex-specific developmental regulator gene, glubschauge (glu) that selectively regulates sexually dimorphic eye differentiation in honeybees. We found that the sex determination gene feminizer (fem) controls sex-specific splicing of glu transcripts, establishing a genetic switch in which Glu proteins with a zinc finger (ZnF) domain are only expressed in females. We showed that female coding sequence was essential and sufficient for partial feminization. Comparative sequence and functional studies revealed that the evolutionary origination of the genetic switch was followed by the mutational origin of the essential ZnF domain. Our results demonstrate that glu is a newly evolved sex-specific genetic switch for region-specific regulation of a dimorphic character.
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10
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Mannino MC, Bartels Cassidy M, Florez S, Rusan Z, Chakraborty S, Schoborg T. The neurodevelopmental transcriptome of the Drosophila melanogaster microcephaly gene abnormal spindle reveals a role for temporal transcription factors and the immune system in regulating brain size. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.09.523369. [PMID: 36711768 PMCID: PMC9882087 DOI: 10.1101/2023.01.09.523369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The coordination of cellular behaviors during neurodevelopment is critical for determining the form, function, and size of the central nervous system. Mutations in the vertebrate Abnormal Spindle-Like, Microcephaly Associated (ASPM) gene and its Drosophila melanogaster ortholog abnormal spindle (asp) lead to microcephaly, a reduction in overall brain size whose etiology remains poorly defined. Here we provide the neurodevelopmental transcriptional landscape for a Drosophila model for autosomal recessive primary microcephaly (MCPH) and extend our findings into the functional realm in an attempt to identify the key cellular mechanisms responsible for Asp-dependent brain growth and development. We identify multiple transcriptomic signatures, including new patterns of co-expressed genes in the developing CNS. Defects in optic lobe neurogenesis were detected in larval brains through downregulation of temporal transcription factors (tTFs) and Notch signaling targets, which correlated with a significant reduction in brain size and total cell numbers during the neurogenic window of development. We also found inflammation as a hallmark of asp MCPH brains, detectable throughout every stage of CNS development, which also contributes to the brain size phenotype. Finally, we show that apoptosis is not a primary driver of the asp MCPH phenotype, further highlighting an intrinsic Asp-dependent neurogenesis promotion mechanism that is independent of cell death. Collectively, our results suggest that the etiology of asp MCPH is complex and that a comprehensive view of the cellular basis of the disorder requires an understanding of how multiple pathway inputs collectively determine the microcephaly phenotype.
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Affiliation(s)
- Maria C. Mannino
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
| | | | - Steven Florez
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
| | | | - Shalini Chakraborty
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
| | - Todd Schoborg
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
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11
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Chen Q, Sasikala-Appukuttan AK, Husain Z, Shrivastava A, Spain M, Sendler ED, Daines B, Fischer S, Chen R, Cook TA, Friedrich M. Global Gene Expression Analysis Reveals Complex Cuticle Organization of the Tribolium Compound Eye. Genome Biol Evol 2023; 15:evac181. [PMID: 36575057 PMCID: PMC9866248 DOI: 10.1093/gbe/evac181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/08/2022] [Accepted: 12/17/2022] [Indexed: 12/29/2022] Open
Abstract
The red flour beetle Tribolium castaneum is a resource-rich model for genomic and developmental studies. To extend previous studies on Tribolium eye development, we produced transcriptomes for normal-eyed and eye-depleted heads of pupae and adults to identify differentially transcript-enriched (DE) genes in the visual system. Unexpectedly, cuticle-related genes were the largest functional class in the pupal compound eye DE gene population, indicating differential enrichment in three distinct cuticle components: clear lens facet cuticle, highly melanized cuticle of the ocular diaphragm, which surrounds the Tribolium compound eye for internal fortification, and newly identified facet margins of the tanned cuticle, possibly enhancing external fortification. Phylogenetic, linkage, and high-throughput gene knockdown data suggest that most cuticle proteins (CPs) expressed in the Tribolium compound eye stem from the deployment of ancient CP genes. Consistent with this, TcasCPR15, which we identified as the major lens CP gene in Tribolium, is a beetle-specific but pleiotropic paralog of the ancient CPR RR-2 CP gene family. The less abundant yet most likely even more lens-specific TcasCP63 is a member of a sprawling family of noncanonical CP genes, documenting a role of local gene family expansions in the emergence of the Tribolium compound eye CP repertoire. Comparisons with Drosophila and the mosquito Anopheles gambiae reveal a steady turnover of lens-enriched CP genes during insect evolution.
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Affiliation(s)
- Qing Chen
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | | | - Zahabiya Husain
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Anura Shrivastava
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Marla Spain
- Center of Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Edward D Sendler
- Center of Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Bryce Daines
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Stefan Fischer
- Evolutionary Biology of Invertebrates, Institute of Evolution and Ecology, University of Tübingen, Germany
| | - Rui Chen
- Evolutionary Biology of Invertebrates, Institute of Evolution and Ecology, University of Tübingen, Germany
| | - Tiffany A Cook
- Center of Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA
- Department of Ophthalmological, Visual, and Anatomical Sciences, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
- Department of Ophthalmological, Visual, and Anatomical Sciences, Wayne State University School of Medicine, Detroit, Michigan, USA
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12
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Li M, Kasan K, Saha Z, Yoon Y, Schmidt-Ott U. Twenty-seven ZAD-ZNF genes of Drosophila melanogaster are orthologous to the embryo polarity determining mosquito gene cucoid. PLoS One 2023; 18:e0274716. [PMID: 36595500 PMCID: PMC9810180 DOI: 10.1371/journal.pone.0274716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/16/2022] [Indexed: 01/04/2023] Open
Abstract
The C2H2 zinc finger gene cucoid establishes anterior-posterior (AP) polarity in the early embryo of culicine mosquitoes. This gene is unrelated to genes that establish embryo polarity in other fly species (Diptera), such as the homeobox gene bicoid, which serves this function in the traditional model organism Drosophila melanogaster. The cucoid gene is a conserved single copy gene across lower dipterans but nothing is known about its function in other species, and its evolution in higher dipterans, including Drosophila, is unresolved. We found that cucoid is a member of the ZAD-containing C2H2 zinc finger (ZAD-ZNF) gene family and is orthologous to 27 of the 91 members of this family in D. melanogaster, including M1BP, ranshi, ouib, nom, zaf1, odj, Nnk, trem, Zif, and eighteen uncharacterized genes. Available knowledge of the functions of cucoid orthologs in Drosophila melanogaster suggest that the progenitor of this lineage specific expansion may have played a role in regulating chromatin. We also describe many aspects of the gene duplication history of cucoid in the brachyceran lineage of D. melanogaster, thereby providing a framework for predicting potential redundancies among these genes in D. melanogaster.
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Affiliation(s)
- Muzi Li
- Dept. of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, United States of America
| | - Koray Kasan
- Dept. of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, United States of America
| | - Zinnia Saha
- Dept. of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, United States of America
| | - Yoseop Yoon
- Dept. of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, United States of America
| | - Urs Schmidt-Ott
- Dept. of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, United States of America
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13
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Elongator stabilizes microtubules to control central spindle asymmetry and polarized trafficking of cell fate determinants. Nat Cell Biol 2022; 24:1606-1616. [PMID: 36302967 PMCID: PMC7613801 DOI: 10.1038/s41556-022-01020-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 09/19/2022] [Indexed: 01/18/2023]
Abstract
Asymmetric cell division gives rise to two daughter cells that inherit different determinants, thereby acquiring different fates. Polarized trafficking of endosomes containing fate determinants recently emerged as an evolutionarily conserved feature of asymmetric cell division to enhance the robustness of asymmetric cell fate determination in flies, fish and mammals. In particular, polarized sorting of signalling endosomes by an asymmetric central spindle contributes to asymmetric cell division in Drosophila melanogaster. However, how central spindle asymmetry arises remains elusive. Here we identify a moonlighting function of the Elongator complex-an established protein acetylase and tRNA methylase involved in the fidelity of protein translation-as a key factor for central spindle asymmetry. Elongator controls spindle asymmetry by stabilizing microtubules differentially on the anterior side of the central spindle. Accordingly, lowering the activity of Elongator on the anterior side using nanobodies mistargets endosomes to the wrong cell. Molecularly, Elongator regulates microtubule dynamics independently of its acetylation and methylation enzymatic activities. Instead, Elongator directly binds to microtubules and increases their polymerization speed while decreasing their catastrophe frequency. Our data establish a non-canonical role of Elongator at the core of cytoskeleton polarity and asymmetric signalling.
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14
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Liu J, Jin T, Ran L, Zhao Z, Zhu R, Xie G, Bi X. Profiling ATM regulated genes in Drosophila at physiological condition and after ionizing radiation. Hereditas 2022; 159:41. [PMID: 36271387 PMCID: PMC9587650 DOI: 10.1186/s41065-022-00254-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 10/06/2022] [Indexed: 11/17/2022] Open
Abstract
Background ATM (ataxia-telangiectasia mutated) protein kinase is highly conserved in metazoan, and plays a critical role at DNA damage response, oxidative stress, metabolic stress, immunity, RNA biogenesis etc. Systemic profiling of ATM regulated genes, including protein-coding genes, miRNAs, and long non-coding RNAs, will greatly improve our understanding of ATM functions and its regulation. Results 1) differentially expressed protein-coding genes, miRNAs, and long non-coding RNAs in atm mutated flies were identified at physiological condition and after X-ray irradiation. 2) functions of differentially expressed genes in atm mutated flies, regardless of protein-coding genes or non-coding RNAs, are closely related with metabolic process, immune response, DNA damage response or oxidative stress. 3) these phenomena are persistent after irradiation. 4) there is a cross-talk regulation towards miRNAs by ATM, E2f1, and p53 during development and after irradiation. 5) knock-out flies or knock-down flies of most irradiation-induced miRNAs were sensitive to ionizing radiation. Conclusions We provide a valuable resource of protein-coding genes, miRNAs, and long non-coding RNAs, for understanding ATM functions and regulations. Our work provides the new evidence of inter-dependence among ATM-E2F1-p53 for the regulation of miRNAs. Supplementary Information The online version contains supplementary material available at 10.1186/s41065-022-00254-9.
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Affiliation(s)
- Jun Liu
- School of Medicine, Nantong University, Nantong, 226001, China
| | - Tianyu Jin
- College of Basic Medical Medicine, Dalian Medical University, Dalian, 116044, China
| | - Lanxi Ran
- College of Basic Medical Medicine, Dalian Medical University, Dalian, 116044, China
| | - Ze Zhao
- College of Basic Medical Medicine, Dalian Medical University, Dalian, 116044, China
| | - Rui Zhu
- College of Basic Medical Medicine, Dalian Medical University, Dalian, 116044, China
| | - Gangcai Xie
- School of Medicine, Nantong University, Nantong, 226001, China.
| | - Xiaolin Bi
- School of Medicine, Nantong University, Nantong, 226001, China. .,College of Basic Medical Medicine, Dalian Medical University, Dalian, 116044, China.
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15
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Ayukawa T, Akiyama M, Hozumi Y, Ishimoto K, Sasaki J, Senoo H, Sasaki T, Yamazaki M. Tissue flow regulates planar cell polarity independently of the Frizzled core pathway. Cell Rep 2022; 40:111388. [PMID: 36130497 DOI: 10.1016/j.celrep.2022.111388] [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: 08/24/2021] [Revised: 07/16/2022] [Accepted: 08/29/2022] [Indexed: 11/27/2022] Open
Abstract
Planar cell polarity (PCP) regulates the orientation of external structures. A core group of proteins that includes Frizzled forms the heart of the PCP regulatory system. Other PCP mechanisms that are independent of the core group likely exist, but their underlying mechanisms are elusive. Here, we show that tissue flow is a mechanism governing core group-independent PCP on the Drosophila notum. Loss of core group function only slightly affects bristle orientation in the adult central notum. This near-normal PCP results from tissue flow-mediated rescue of random bristle orientation during the pupal stage. Manipulation studies suggest that tissue flow can orient bristles in the opposite direction to the flow. This process is independent of the core group and implies that the apical extracellular matrix functions like a "comb" to align bristles. Our results reveal the significance of cooperation between tissue dynamics and extracellular substances in PCP establishment.
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Affiliation(s)
- Tomonori Ayukawa
- Department of Cell Biology and Morphology, Akita University Graduate School of Medicine, Akita 010-8543, Japan
| | - Masakazu Akiyama
- Meiji Institute for Advanced Study of Mathematical Sciences, Meiji University, Tokyo 164-8525, Japan; Faculty of Science, Academic Assembly, University of Toyama, Toyama 930-8555, Japan
| | - Yasukazu Hozumi
- Department of Cell Biology and Morphology, Akita University Graduate School of Medicine, Akita 010-8543, Japan
| | - Kenta Ishimoto
- Research Institute for Mathematical Sciences, Kyoto University, Kyoto 606-8502, Japan
| | - Junko Sasaki
- Department of Biochemical Pathophysiology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Haruki Senoo
- Department of Cell Biology and Morphology, Akita University Graduate School of Medicine, Akita 010-8543, Japan
| | - Takehiko Sasaki
- Department of Biochemical Pathophysiology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Masakazu Yamazaki
- Department of Cell Biology and Morphology, Akita University Graduate School of Medicine, Akita 010-8543, Japan; Japan Science and Technology Agency, PRESTO, Saitama 332-0012, Japan.
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16
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Chen S, Venkatesan A, Lin YQ, Xie J, Neely G, Banerjee S, Bhat MA. Drosophila Homolog of the Human Carpenter Syndrome Linked Gene, MEGF8, Is Required for Synapse Development and Function. J Neurosci 2022; 42:7016-7030. [PMID: 35944997 PMCID: PMC9480877 DOI: 10.1523/jneurosci.0442-22.2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 07/29/2022] [Accepted: 08/03/2022] [Indexed: 11/21/2022] Open
Abstract
Drosophila multiple epidermal growth factor-like domains 8 (dMegf8) is a homolog of human MEGF8 MEGF8 encodes a multidomain transmembrane protein which is highly conserved across species. In humans, MEGF8 mutations cause a rare genetic disorder called Carpenter syndrome, which is frequently associated with abnormal left-right patterning, cardiac defects, and learning disabilities. MEGF8 is also associated with psychiatric disorders. Despite its clinical relevance, MEGF8 remains poorly characterized; and although it is highly conserved, studies on animal models of Megf8 are also very limited. The presence of intellectual disabilities in Carpenter syndrome patients and association of MEGF8 with psychiatric disorders indicate that mutations in MEGF8 cause underlying defects in synaptic structure and functions. In this study, we investigated the role of Drosophila dMegf8 in glutamatergic synapses of the larval neuromuscular junctions (NMJ) in both males and females. We show that dMegf8 localizes to NMJ synapses and is required for proper synaptic growth. dMegf8 mutant larvae and adults show severe motor coordination deficits. At the NMJ, dMegf8 mutants show altered localization of presynaptic and postsynaptic proteins, defects in synaptic ultrastructure, and neurotransmission. Interestingly, dMegf8 mutants have reduced levels of the Type II BMP receptor Wishful thinking (Wit). dMegf8 displays genetic interactions with neurexin-1 (dnrx) and wit, and in association with Dnrx and Wit plays an essential role in synapse organization. Our studies provide insights into human MEGF8 functions and potentially into mechanisms that may underlie intellectual disabilities observed in Carpenter syndrome as well as MEGF8-related synaptic structural and/or functional deficits in psychiatric disorders.SIGNIFICANCE STATEMENT Carpenter syndrome, known for over a century now, is a genetic disorder linked to mutations in Multiple Epidermal Growth Factor-like Domains 8 (MEGF8) gene and associated with intellectual disabilities among other symptoms. MEGF8 is also associated with psychiatric disorders. Despite the high genetic conservation and clinical relevance, the functions of MEGF8 remain largely uncharacterized. Patients with intellectual disabilities and psychiatric diseases often have an underlying defect in synaptic structure and function. This work defines the role of the fly homolog of human MEGF8, dMegf8, in glutamatergic synapse growth, organization, and function and provide insights into potential functions of MEGF8 in human central synapses and synaptic mechanisms that may underlie psychiatric disorders and intellectual disabilities seen in Carpenter syndrome.
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Affiliation(s)
- Shuting Chen
- Department of Cellular and Integrative Physiology, Joe R. and Teresa Lozano Long School of Medicine, University of Texas Health Science Center San Antonio, San Antonio, Texas 78229
- Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Anand Venkatesan
- Department of Cellular and Integrative Physiology, Joe R. and Teresa Lozano Long School of Medicine, University of Texas Health Science Center San Antonio, San Antonio, Texas 78229
| | - Yong Qi Lin
- Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre and School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales Australia 2006
| | - Jing Xie
- Department of Cellular and Integrative Physiology, Joe R. and Teresa Lozano Long School of Medicine, University of Texas Health Science Center San Antonio, San Antonio, Texas 78229
- Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Gregory Neely
- Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre and School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales Australia 2006
| | - Swati Banerjee
- Department of Cellular and Integrative Physiology, Joe R. and Teresa Lozano Long School of Medicine, University of Texas Health Science Center San Antonio, San Antonio, Texas 78229
| | - Manzoor A Bhat
- Department of Cellular and Integrative Physiology, Joe R. and Teresa Lozano Long School of Medicine, University of Texas Health Science Center San Antonio, San Antonio, Texas 78229
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17
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Hu DB, Xiao S, Wang Y, Hua HX. Notch is an alternative splicing gene in brown planthopper, Nilaparvata lugens. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2022; 110:e21894. [PMID: 35362159 DOI: 10.1002/arch.21894] [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: 10/17/2021] [Revised: 03/01/2022] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
Much research has assumed that Notch codes one protein. Then the protein will be cleaved into two parts and regenerates a heterodimers receptor to construct Notch signal pathways to regulate development in the past three decades. Here, we show that Notch in brown planthopper is a complex alternatively spliced gene has at least three transcriptional start sites, four exon skips, and 21 transcriptional endpoints that uses these to form variants and codes a series of proteins. When used dsRNAs to suppression different regions of the full-length variant NlNF resulted in a similar phenotype. Insects were molting after treatment, sensation circles on antennas near to root decayed, bristles on wings shortened, thickened or disappeared, accompanied by thickening veins and blades of fore-wing apex regions thickened. These results suggested that Notch influenced developmental of sensation circles, bristles, veins, and blades in nymph late periods. This study has deepened our understanding of Notch.
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Affiliation(s)
- Ding-Bang Hu
- College of life Science, State Key Laboratory of Virology, College of Life Science, Wuhan University, Wuhan, China
- School of Ethnic-Minority Medicine, Guizhou Minzu University, Guiyang, China
| | - Shuai Xiao
- College of life Science, State Key Laboratory of Virology, College of Life Science, Wuhan University, Wuhan, China
| | - Yefu Wang
- College of life Science, State Key Laboratory of Virology, College of Life Science, Wuhan University, Wuhan, China
| | - Hong-Xia Hua
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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18
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Dean DM, Deitcher DL, Paster CO, Xu M, Loehlin DW. "A fly appeared": sable, a classic Drosophila mutation, maps to Yippee, a gene affecting body color, wings, and bristles. G3 (BETHESDA, MD.) 2022; 12:jkac058. [PMID: 35266526 PMCID: PMC9073688 DOI: 10.1093/g3journal/jkac058] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/04/2022] [Indexed: 11/12/2022]
Abstract
Insect body color is an easily assessed and visually engaging trait that is informative on a broad range of topics including speciation, biomaterial science, and ecdysis. Mutants of the fruit fly Drosophila melanogaster have been an integral part of body color research for more than a century. As a result of this long tenure, backlogs of body color mutations have remained unmapped to their genes, all while their strains have been dutifully maintained, used for recombination mapping, and part of genetics education. Stemming from a lesson plan in our undergraduate genetics class, we have mapped sable1, a dark body mutation originally described by Morgan and Bridges, to Yippee, a gene encoding a predicted member of the E3 ubiquitin ligase complex. Deficiency/duplication mapping, genetic rescue, DNA and cDNA sequencing, RT-qPCR, and 2 new CRISPR alleles indicated that sable1 is a hypomorphic Yippee mutation due to an mdg4 element insertion in the Yippee 5'-UTR. Further analysis revealed additional Yippee mutant phenotypes including curved wings, ectopic/missing bristles, delayed development, and failed adult emergence. RNAi of Yippee in the ectoderm phenocopied sable body color and most other Yippee phenotypes. Although Yippee remains functionally uncharacterized, the results presented here suggest possible connections between melanin biosynthesis, copper homeostasis, and Notch/Delta signaling; in addition, they provide insight into past studies of sable cell nonautonomy and of the genetic modifier suppressor of sable.
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Affiliation(s)
- Derek M Dean
- Department of Biology, Williams College, Williamstown, MA 01267, USA
| | - David L Deitcher
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA
| | - Caleigh O Paster
- Department of Biology, Williams College, Williamstown, MA 01267, USA
| | - Manting Xu
- Department of Biology, Williams College, Williamstown, MA 01267, USA
| | - David W Loehlin
- Department of Biology, Williams College, Williamstown, MA 01267, USA
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19
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Känel P, Noll GA, Schroedter K, Naffin E, Kronenberg J, Busswinkel F, Twyman RM, Klämbt C, Prüfer D. The tobacco phosphatidylethanolamine-binding protein NtFT4 increases the lifespan of Drosophila melanogaster by interacting with the proteostasis network. Aging (Albany NY) 2022; 14:2989-3029. [PMID: 35396341 PMCID: PMC9037272 DOI: 10.18632/aging.204005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 03/24/2022] [Indexed: 11/25/2022]
Abstract
Proteostasis reflects the well-balanced synthesis, trafficking and degradation of cellular proteins. This is a fundamental aspect of the dynamic cellular proteome, which integrates multiple signaling pathways, but it becomes increasingly error-prone during aging. Phosphatidylethanolamine-binding proteins (PEBPs) are highly conserved regulators of signaling networks and could therefore affect aging-related processes. To test this hypothesis, we expressed PEPBs in a heterologous context to determine their ectopic activity. We found that heterologous expression of the tobacco (Nicotiana tabacum) PEBP NtFT4 in Drosophila melanogaster significantly increased the lifespan of adult flies and reduced age-related locomotor decline. Similarly, overexpression of the Drosophila ortholog CG7054 increased longevity, whereas its suppression by RNA interference had the opposite effect. In tobacco, NtFT4 acts as a floral regulator by integrating environmental and intrinsic stimuli to promote the transition to reproductive growth. In Drosophila, NtFT4 engaged distinct targets related to proteostasis, such as HSP26. In older flies, it also prolonged Hsp26 gene expression, which promotes longevity by maintaining protein integrity. In NtFT4-transgenic flies, we identified deregulated genes encoding proteases that may contribute to proteome stability at equilibrium. Our results demonstrate that the expression of NtFT4 influences multiple aspects of the proteome maintenance system via both physical interactions and transcriptional regulation, potentially explaining the aging-related phenotypes we observed.
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Affiliation(s)
- Philip Känel
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Münster, Germany
| | - Gundula A. Noll
- Institute of Plant Biology and Biotechnology, University of Münster, Münster, Germany
| | - Katrin Schroedter
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Münster, Germany
| | - Elke Naffin
- Institute of Neuro- and Behavioral Biology, University of Münster, Münster, Germany
| | - Julia Kronenberg
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Münster, Germany
| | - Franziska Busswinkel
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Münster, Germany
| | | | - Christian Klämbt
- Institute of Neuro- and Behavioral Biology, University of Münster, Münster, Germany
| | - Dirk Prüfer
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Münster, Germany
- Institute of Plant Biology and Biotechnology, University of Münster, Münster, Germany
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20
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Vandhana TM, Reyre JL, Sushmaa D, Berrin JG, Bissaro B, Madhuprakash J. On the expansion of biological functions of lytic polysaccharide monooxygenases. THE NEW PHYTOLOGIST 2022; 233:2380-2396. [PMID: 34918344 DOI: 10.1111/nph.17921] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/19/2021] [Indexed: 05/21/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) constitute an enigmatic class of enzymes, the discovery of which has opened up a new arena of riveting research. LPMOs can oxidatively cleave the glycosidic bonds found in carbohydrate polymers enabling the depolymerisation of recalcitrant biomasses, such as cellulose or chitin. While most studies have so far mainly explored the role of LPMOs in a (plant) biomass conversion context, alternative roles and paradigms begin to emerge. In the present review, we propose a historical perspective of LPMO research providing a succinct overview of the major achievements of LPMO research over the past decade. This journey through LPMOs landscape leads us to dive into the emerging biological functions of LPMOs and LPMO-like proteins. We notably highlight roles in fungal and oomycete plant pathogenesis (e.g. potato late blight), but also in mutualistic/commensalism symbiosis (e.g. ectomycorrhizae). We further present the potential importance of LPMOs in other microbial pathogenesis including diseases caused by bacteria (e.g. pneumonia), fungi (e.g. human meningitis), oomycetes and viruses (e.g. entomopox), as well as in (micro)organism development (including several plant pests). Our assessment of the literature leads to the formulation of outstanding questions, promising for the coming years exciting research and discoveries on these moonlighting proteins.
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Affiliation(s)
- Theruvothu Madathil Vandhana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, 500046, India
| | - Jean-Lou Reyre
- INRAE, UMR1163 Biodiversité et Biotechnologie Fongiques, Aix Marseille University, 13009, Marseille, France
- IFP Energies Nouvelles, 1 et 4 avenue de Bois-Préau, 92852, Rueil-Malmaison, France
| | - Dangudubiyyam Sushmaa
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, 500046, India
| | - Jean-Guy Berrin
- INRAE, UMR1163 Biodiversité et Biotechnologie Fongiques, Aix Marseille University, 13009, Marseille, France
| | - Bastien Bissaro
- INRAE, UMR1163 Biodiversité et Biotechnologie Fongiques, Aix Marseille University, 13009, Marseille, France
| | - Jogi Madhuprakash
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, 500046, India
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21
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Leg length and bristle density, both necessary for water surface locomotion, are genetically correlated in water striders. Proc Natl Acad Sci U S A 2022; 119:2119210119. [PMID: 35193982 PMCID: PMC8892508 DOI: 10.1073/pnas.2119210119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2022] [Indexed: 11/18/2022] Open
Abstract
Access to hitherto unexploited ecological opportunities is associated with phenotypic evolution and often results in significant lineage diversification. Yet our understanding of the mechanisms underlying such adaptive traits remains limited. Water striders have been able to exploit the water-air interface, primarily facilitated by changes in the density of hydrophobic bristles and a significant increase in leg length. These two traits are functionally correlated and are both necessary for generating efficient locomotion on the water surface. Whether bristle density and leg length have any cellular or developmental genetic mechanisms in common is unknown. Here, we combine comparative genomics and transcriptomics with functional RNA interference assays to examine the developmental genetic and cellular mechanisms underlying the patterning of the bristles and the legs in Gerris buenoi and Mesovelia mulsanti, two species of water striders. We found that two duplication events in the genes beadex and taxi led to a functional expansion of the paralogs, which affected bristle density and leg length. We also identified genes for which no function in bristle development has been previously described in other insects. Interestingly, most of these genes play a dual role in regulating bristle development and leg length. In addition, these genes play a role in regulating cell division. This result suggests that cell division may be a common mechanism through which these genes can simultaneously regulate leg length and bristle density. We propose that pleiotropy, through which gene function affects the development of multiple traits, may play a prominent role in facilitating access to unexploited ecological opportunities and species diversification.
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22
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Aranjuez GF, Kim J, Jewett TJ. The Chlamydia trachomatis Early Effector Tarp Outcompetes Fascin in Forming F-Actin Bundles In Vivo. Front Cell Infect Microbiol 2022; 12:811407. [PMID: 35300377 PMCID: PMC8921475 DOI: 10.3389/fcimb.2022.811407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/10/2022] [Indexed: 11/13/2022] Open
Abstract
The intracellular pathogen Chlamydia trachomatis secretes multiple early effectors into the host cell to promote invasion. A key early effector during host cell entry, Tarp (translocated actin-recruiting phosphoprotein) is comprised of multiple protein domains known to have roles in cell signaling, G-actin nucleation and F-actin bundle formation. In vitro, the actin bundles generated by Tarp are uncharacteristically flexible, however, in vivo, the biological significance of Tarp-mediated actin bundles remains unknown. We hypothesize that Tarp's ability to generate unique actin bundles, in part, facilitates chlamydial entry into epithelial cells. To study the in vivo interaction between Tarp and F-actin, we transgenically expressed Tarp in Drosophila melanogaster tissues. Tarp expressed in Drosophila is phosphorylated and forms F-actin-enriched aggregates in tissues. To gain insight into the significance of Tarp actin bundles in vivo, we utilized the well-characterized model system of mechanosensory bristle development in Drosophila melanogaster. Tarp expression in wild type flies produced curved bristles, indicating a perturbation in F-actin dynamics during bristle development. Two F-actin bundlers, Singed/Fascin and Forked/Espin, are important for normal bristle shape. Surprisingly, Tarp expression in the bristles displaced Singed/Fascin away from F-actin bundles. Tarp's competitive behavior against Fascin during F-actin bundling was confirmed in vitro. Loss of either singed or forked in flies leads to highly deformed bristles. Strikingly, Tarp partially rescued the loss of singed, reducing the severity of the bristle morphology defect. This work provides in vivo confirmation of Tarp's F-actin bundling activity and further uncovers a competitive behavior against the host bundler Singed/Fascin during bundle assembly. Also, we demonstrate the utility of Drosophila melanogaster as an in vivo cell biological platform to study bacterial effector function.
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Affiliation(s)
- George F. Aranjuez
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, Orlando, FL, United States
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23
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Yang Q, De Schutter K, Chen P, Van Damme EJM, Smagghe G. RNAi of the N-glycosylation-related genes confirms their importance in insect development and α-1,6-fucosyltransferase plays a role in the ecdysis event for the hemimetabolous pest insect Nilaparvata lugens. INSECT SCIENCE 2022; 29:91-99. [PMID: 33860636 DOI: 10.1111/1744-7917.12920] [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: 11/26/2020] [Revised: 02/16/2021] [Accepted: 03/13/2021] [Indexed: 06/12/2023]
Abstract
Recently N-glycosylation was found to be required for the postembryonic development and metamorphosis of the holometabolous beetle Tribolium castaneum. However, the role of N-glycosylation in the development of hemimetabolous insects is unknown. To further elucidate the role of N-glycosylation in the development of insects, a functional characterization of the N-glycosylation-related genes (NGRGs) was performed in a model insect for hemimetabolous development, namely the brown planthopper Nilaparvata lugens. In this project, we report the effects of RNAi-mediated silencing of 15 NGRGs on the postembryonic development of N. lugens. Two major observations were made. First, interruption of the early steps of N-glycan processing led to a lethal phenotype during the transition from nymph to adult as was observed in T. castaneum. Second, we report here on an essential function for the α-1,6-fucosyl transferase in the ecdysis event of N. lugens between nymphal instars, since gene-silencing by RNAi led to failure of ecdysis and subsequent mortality of the treated insect.
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Affiliation(s)
- Qun Yang
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, Ghent, 9000, Belgium
| | - Kristof De Schutter
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, Ghent, 9000, Belgium
| | - Pengyu Chen
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, Ghent, 9000, Belgium
- Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, Ghent, 9000, Belgium
| | - Els J M Van Damme
- Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, Ghent, 9000, Belgium
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, Ghent, 9000, Belgium
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24
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Gao Q, Lin Y, Wang X, Jing D, Wang Z, He K, Bai S, Zhang Y, Zhang T. Knockout of ABC Transporter ABCG4 Gene Confers Resistance to Cry1 Proteins in Ostrinia furnacalis. Toxins (Basel) 2022; 14:toxins14010052. [PMID: 35051029 PMCID: PMC8780026 DOI: 10.3390/toxins14010052] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/07/2022] [Accepted: 01/08/2022] [Indexed: 12/16/2022] Open
Abstract
Ostrinia furnacalis is an important borer on maize. Long-term and large-scale planting of transgenic corn has led O. furnacalis evolving resistance and reducing the control effect. Recently, high levels of resistance to Bt Cry1 toxins have been reported to be genetically linked to the mutation or down-regulation of ABC transporter subfamily G gene ABCG4 in O. furnacalis. In order to further determine the relationship between ABCG4 gene and the resistance to Cry1 toxins in O. furnacalis, the novel CRISPR/Cas9 genome engineering system was utilized to successfully construct ABCG4-KO knockout homozygous strain. Bioassay results indicated that an ABCG4-KO strain had a higher resistance to Cry1 proteins compared with a susceptible strain (ACB-BtS). The result indicates that the ABCG4 gene may act as a receptor of the Bt Cry1 toxin in O. furnacalis. Furthermore, the development time was significantly changed in the early stage ABCG4-KO larvae, and the population parameters were also significantly changed. In summary, our CRISPR/Cas9-mediated genome editing study presents evidence that ABCG4 gene is a functional receptor for Bt Cry1 toxins, laying the foundation for further clarification of the Bt resistance mechanism.
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Affiliation(s)
- Qing Gao
- State Key Laboratory for the Biology of the Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Q.G.); (Y.L.); (D.J.); (Z.W.); (K.H.); (S.B.); (Y.Z.)
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao 066000, China
| | - Yaling Lin
- State Key Laboratory for the Biology of the Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Q.G.); (Y.L.); (D.J.); (Z.W.); (K.H.); (S.B.); (Y.Z.)
- College of Plant Protection, Gansu Agriculture University, Lanzhou 730070, China
| | - Xiuping Wang
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao 066000, China
- Correspondence: (X.W.); (T.Z.)
| | - Dapeng Jing
- State Key Laboratory for the Biology of the Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Q.G.); (Y.L.); (D.J.); (Z.W.); (K.H.); (S.B.); (Y.Z.)
| | - Zhenying Wang
- State Key Laboratory for the Biology of the Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Q.G.); (Y.L.); (D.J.); (Z.W.); (K.H.); (S.B.); (Y.Z.)
| | - Kanglai He
- State Key Laboratory for the Biology of the Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Q.G.); (Y.L.); (D.J.); (Z.W.); (K.H.); (S.B.); (Y.Z.)
| | - Shuxiong Bai
- State Key Laboratory for the Biology of the Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Q.G.); (Y.L.); (D.J.); (Z.W.); (K.H.); (S.B.); (Y.Z.)
| | - Yongjun Zhang
- State Key Laboratory for the Biology of the Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Q.G.); (Y.L.); (D.J.); (Z.W.); (K.H.); (S.B.); (Y.Z.)
| | - Tiantao Zhang
- State Key Laboratory for the Biology of the Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Q.G.); (Y.L.); (D.J.); (Z.W.); (K.H.); (S.B.); (Y.Z.)
- Correspondence: (X.W.); (T.Z.)
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25
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Sokolov VV, Georgiev PG, Kyrchanova OV. The Piragua Gene Is not Essential for Drosophila Development. DOKLADY BIOLOGICAL SCIENCES : PROCEEDINGS OF THE ACADEMY OF SCIENCES OF THE USSR, BIOLOGICAL SCIENCES SECTIONS 2021; 501:197-200. [PMID: 34962606 DOI: 10.1134/s0012496621060089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/03/2021] [Accepted: 09/03/2021] [Indexed: 06/14/2023]
Abstract
Proteins with clusters of C2H2 zinc finger domains (C2H2-proteins) constitute the most abundant class of transcription factors in higher eukaryotes. N-terminal ZAD (zinc finger-associated domain) dimerization domain has been identified in a large group of C2H2-proteins mostly in insects. The piragua gene encodes one of these proteins, Fu2. We have generated CRISPR/Cas9-mediated deletion of the piragua gene that has no phenotype. We have used φC31-mediated attP/attB recombination to generate a transgenic line expressing Fu2 protein fused with HA epitope. This line will be useful for analysis of DNA binding profile and functions of Fu2 protein.
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Affiliation(s)
- V V Sokolov
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia.
| | - P G Georgiev
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia
| | - O V Kyrchanova
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia
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26
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Bian W, Tang M, Jiang H, Xu W, Hao W, Sui Y, Hou Y, Nie L, Zhang H, Wang C, Li N, Wang J, Qin J, Wu L, Ma X, Chen J, Wang W, Li X. Low-density-lipoprotein-receptor-related protein 1 mediates Notch pathway activation. Dev Cell 2021; 56:2902-2919.e8. [PMID: 34626540 DOI: 10.1016/j.devcel.2021.09.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 08/18/2021] [Accepted: 09/14/2021] [Indexed: 12/12/2022]
Abstract
The Notch signaling pathway controls cell growth, differentiation, and fate decisions, and its dysregulation has been linked to various human genetic disorders and cancers. To comprehensively understand the global organization of the Notch pathway and identify potential drug targets for Notch-related diseases, we established a protein interaction landscape for the human Notch pathway. By combining and analyzing genetic and phenotypic data with bioinformatics analysis, we greatly expanded this pathway and identified many key regulators, including low-density-lipoprotein-receptor-related protein 1 (LRP1). We demonstrated that LRP1 mediates the ubiquitination chain linkage switching of Delta ligands, which further affects ligand recycling, membrane localization, and stability. LRP1 inhibition led to Notch signaling inhibition and decreased tumorigenesis in leukemia models. Our study provides a glimpse into the Notch pathway interaction network and uncovers LRP1 as one critical regulator of the Notch pathway, as well as a possible therapeutic target for Notch-related cancers.
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Affiliation(s)
- Weixiang Bian
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang, China
| | - Mengfan Tang
- Department of Experimental Radiation Oncology, the University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA
| | - Hua Jiang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang, China
| | - Wenyan Xu
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Wanyu Hao
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Institute of Basic Medical Science, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Yue Sui
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang, China
| | - Yingnan Hou
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang, China
| | - Litong Nie
- Department of Experimental Radiation Oncology, the University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA
| | - Huimin Zhang
- Department of Experimental Radiation Oncology, the University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA
| | - Chao Wang
- Department of Experimental Radiation Oncology, the University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA
| | - Nan Li
- Department of Experimental Radiation Oncology, the University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA
| | - Jiadong Wang
- Institute of Systems Biomedicine, Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, People's Republic of China
| | - Jun Qin
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Lianfeng Wu
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Institute of Basic Medical Science, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China.
| | - Xianjue Ma
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
| | - Junjie Chen
- Department of Experimental Radiation Oncology, the University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA.
| | - Wenqi Wang
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA 92697, USA.
| | - Xu Li
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang, China.
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27
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López-Varea A, Ostalé CM, Vega-Cuesta P, Ruiz-Gómez A, Organista MF, Martín M, Hevia CF, Molnar C, de Celis J, Culi J, Esteban N, de Celis JF. Genome-wide Phenotypic RNAi Screen in the Drosophila Wing: Global Parameters. G3-GENES GENOMES GENETICS 2021; 11:6380435. [PMID: 34599819 PMCID: PMC8962446 DOI: 10.1093/g3journal/jkab351] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 08/27/2021] [Indexed: 11/17/2022]
Abstract
We have screened a collection of UAS-RNAi lines targeting 10,920 Drosophila protein-coding genes for phenotypes in the adult wing. We identified 3653 genes (33%) whose knockdown causes either larval/pupal lethality or a mutant phenotype affecting the formation of a normal wing. The most frequent phenotypes consist of changes in wing size, vein differentiation, and patterning, defects in the wing margin and in the apposition of the dorsal and ventral wing surfaces. We also defined 16 functional categories encompassing the most relevant aspect of each protein function and assigned each Drosophila gene to one of these functional groups. This allowed us to identify which mutant phenotypes are enriched within each functional group. Finally, we used previously published gene expression datasets to determine which genes are or are not expressed in the wing disc. Integrating expression, phenotypic and molecular information offers considerable precision to identify the relevant genes affecting wing formation and the biological processes regulated by them.
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Affiliation(s)
- Ana López-Varea
- Centro de Biología Molecular "Severo Ochoa", CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Cristina M Ostalé
- Centro de Biología Molecular "Severo Ochoa", CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Patricia Vega-Cuesta
- Centro de Biología Molecular "Severo Ochoa", CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Ana Ruiz-Gómez
- Centro de Biología Molecular "Severo Ochoa", CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - María F Organista
- Centro de Biología Molecular "Severo Ochoa", CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Mercedes Martín
- Centro de Biología Molecular "Severo Ochoa", CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Covadonga F Hevia
- Centro de Biología Molecular "Severo Ochoa", CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Cristina Molnar
- Centro de Biología Molecular "Severo Ochoa", CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Jesús de Celis
- Centro de Biología Molecular "Severo Ochoa", CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Joaquim Culi
- Centro de Biología Molecular "Severo Ochoa", CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Nuria Esteban
- Centro de Biología Molecular "Severo Ochoa", CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Jose F de Celis
- Centro de Biología Molecular "Severo Ochoa", CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
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28
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Rusu AD, Cornhill ZE, Coutiño BC, Uribe MC, Lourdusamy A, Markus Z, May ST, Rahman R, Georgiou M. CG7379 and ING1 suppress cancer cell invasion by maintaining cell-cell junction integrity. Open Biol 2021; 11:210077. [PMID: 34493070 PMCID: PMC8424350 DOI: 10.1098/rsob.210077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Approximately 90% of cancer-related deaths can be attributed to a tumour's ability to spread. We have identified CG7379, the fly orthologue of human ING1, as a potent invasion suppressor. ING1 is a type II tumour suppressor with well-established roles in the transcriptional regulation of genes that control cell proliferation, response to DNA damage, oncogene-induced senescence and apoptosis. Recent work suggests a possible role for ING1 in cancer cell invasion and metastasis, but the molecular mechanism underlying this observation is lacking. Our results show that reduced expression of CG7379 promotes invasion in vivo in Drosophila, reduces the junctional localization of several adherens and septate junction components, and severely disrupts cell-cell junction architecture. Similarly, ING1 knockdown significantly enhances invasion in vitro and disrupts E-cadherin distribution at cell-cell junctions. A transcriptome analysis reveals that loss of ING1 affects the expression of several junctional and cytoskeletal modulators, confirming ING1 as an invasion suppressor and a key regulator of cell-cell junction integrity.
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Affiliation(s)
- Alexandra D. Rusu
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK,Leicester Institute for Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 9HN, UK
| | - Zoe E. Cornhill
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
| | - Brenda Canales Coutiño
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK,Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
| | | | - Anbarasu Lourdusamy
- School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK
| | - Zsuzsa Markus
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
| | - Sean T. May
- School of Biosciences, University of Nottingham, Sutton Bonington, Leicestershire LE12 5RD, UK
| | - Ruman Rahman
- School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK
| | - Marios Georgiou
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
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29
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Prakash P, Roychowdhury-Sinha A, Goto A. Verloren negatively regulates the expression of IMD pathway dependent antimicrobial peptides in Drosophila. Sci Rep 2021; 11:15549. [PMID: 34330981 PMCID: PMC8324896 DOI: 10.1038/s41598-021-94973-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 07/16/2021] [Indexed: 11/08/2022] Open
Abstract
Drosophila immune deficiency (IMD) pathway is similar to the human tumor necrosis factor receptor (TNFR) signaling pathway and is preferentially activated by Gram-negative bacterial infection. Recent studies highlighted the importance of IMD pathway regulation as it is tightly controlled by numbers of negative regulators at multiple levels. Here, we report a new negative regulator of the IMD pathway, Verloren (Velo). Silencing of Velo led to constitutive expression of the IMD pathway dependent antimicrobial peptides (AMPs), and Escherichia coli stimulation further enhanced the AMP expression. Epistatic analysis indicated that Velo knock-down mediated AMP upregulation is dependent on the canonical members of the IMD pathway. The immune fluorescent study using overexpression constructs revealed that Velo resides both in the nucleus and cytoplasm, but the majority (~ 75%) is localized in the nucleus. We also observed from in vivo analysis that Velo knock-down flies exhibit significant upregulation of the AMP expression and reduced bacterial load. Survival experiments showed that Velo knock-down flies have a short lifespan and are susceptible to the infection of pathogenic Gram-negative bacteria, P. aeruginosa. Taken together, these data suggest that Velo is an additional new negative regulator of the IMD pathway, possibly acting in both the nucleus and cytoplasm.
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Affiliation(s)
- Pragya Prakash
- INSERM, Université de Strasbourg, CNRS, Insect Models of Innate Immunity (M3I; UPR9022), 67084, Strasbourg, France
| | | | - Akira Goto
- INSERM, Université de Strasbourg, CNRS, Insect Models of Innate Immunity (M3I; UPR9022), 67084, Strasbourg, France.
- Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, 511436, China.
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30
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Nalamalapu RR, Yue M, Stone AR, Murphy S, Saha MS. The tweety Gene Family: From Embryo to Disease. Front Mol Neurosci 2021; 14:672511. [PMID: 34262434 PMCID: PMC8273234 DOI: 10.3389/fnmol.2021.672511] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 05/18/2021] [Indexed: 12/31/2022] Open
Abstract
The tweety genes encode gated chloride channels that are found in animals, plants, and even simple eukaryotes, signifying their deep evolutionary origin. In vertebrates, the tweety gene family is highly conserved and consists of three members—ttyh1, ttyh2, and ttyh3—that are important for the regulation of cell volume. While research has elucidated potential physiological functions of ttyh1 in neural stem cell maintenance, proliferation, and filopodia formation during neural development, the roles of ttyh2 and ttyh3 are less characterized, though their expression patterns during embryonic and fetal development suggest potential roles in the development of a wide range of tissues including a role in the immune system in response to pathogen-associated molecules. Additionally, members of the tweety gene family have been implicated in various pathologies including cancers, particularly pediatric brain tumors, and neurodegenerative diseases such as Alzheimer’s and Parkinson’s disease. Here, we review the current state of research using information from published articles and open-source databases on the tweety gene family with regard to its structure, evolution, expression during development and adulthood, biochemical and cellular functions, and role in human disease. We also identify promising areas for further research to advance our understanding of this important, yet still understudied, family of genes.
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Affiliation(s)
- Rithvik R Nalamalapu
- Department of Biology, College of William and Mary, Williamsburg, VA, United States
| | - Michelle Yue
- Department of Biology, College of William and Mary, Williamsburg, VA, United States
| | - Aaron R Stone
- Department of Biology, College of William and Mary, Williamsburg, VA, United States
| | - Samantha Murphy
- Department of Biology, College of William and Mary, Williamsburg, VA, United States
| | - Margaret S Saha
- Department of Biology, College of William and Mary, Williamsburg, VA, United States
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31
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Li W, De Schutter K, Van Damme EJM, Smagghe G. RNAi-Mediated Silencing of Pgants Shows Core 1 O-Glycans Are Required for Pupation in Tribolium castaneum. Front Physiol 2021; 12:629682. [PMID: 33841170 PMCID: PMC8024498 DOI: 10.3389/fphys.2021.629682] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 03/01/2021] [Indexed: 01/08/2023] Open
Abstract
Protein glycosylation is one of the most common and most important post-translational modifications. Despite the growing knowledge on N-glycosylation, the research on O-glycosylation is lagging behind. This study investigates the importance of O-glycosylation in the post-embryonic development of insects using the red flour beetle, Tribolium castaneum, as a model. We identified 28 O-glycosylation-related genes (OGRGs) in the genome of the red flour beetle. 14 OGRGs were selected for functional analysis based on their involvement in the initial attachment of the carbohydrate in the different O-glycosylation pathways or the further elongation of the most abundant O-glycans and, in addition, showing severe RNAi-induced phenotypes in Drosophila melanogaster. The expression profile of these OGRGs was mapped throughout the developmental stages of the insect and in the different tissues of the pupa and adult. Subsequently, these genes were silenced using RNA interference (RNAi) to analyze their role in development. A broad spectrum of phenotypes was observed: from subtle effects and disrupted wing formation when silencing the genes involved in O-mannosylation, to blockage of pupation and high mortality after silencing of the genes involved in O-GalNAc and core 1 O-glycan (O-GalNAc-Gal) synthesis. RNAi experiments were also performed to assess the effects of blocking multiple pathways of O-glycosylation. However, the observed phenotypes induced by multiple RNAi were similar to those of the single gene RNAi experiments. The silencing of OGRGs often resulted in high mortality and wing phenotypes, indicating the importance of O-glycosylation for the survival of the insect and the formation of wings during the post-embryonic development of T. castaneum.
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Affiliation(s)
- Weidong Li
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.,Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Kristof De Schutter
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Els J M Van Damme
- Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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32
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Spierer AN, Mossman JA, Smith SP, Crawford L, Ramachandran S, Rand DM. Natural variation in the regulation of neurodevelopmental genes modifies flight performance in Drosophila. PLoS Genet 2021; 17:e1008887. [PMID: 33735180 PMCID: PMC7971549 DOI: 10.1371/journal.pgen.1008887] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 01/26/2021] [Indexed: 12/28/2022] Open
Abstract
The winged insects of the order Diptera are colloquially named for their most recognizable phenotype: flight. These insects rely on flight for a number of important life history traits, such as dispersal, foraging, and courtship. Despite the importance of flight, relatively little is known about the genetic architecture of flight performance. Accordingly, we sought to uncover the genetic modifiers of flight using a measure of flies’ reaction and response to an abrupt drop in a vertical flight column. We conducted a genome wide association study (GWAS) using 197 of the Drosophila Genetic Reference Panel (DGRP) lines, and identified a combination of additive and marginal variants, epistatic interactions, whole genes, and enrichment across interaction networks. Egfr, a highly pleiotropic developmental gene, was among the most significant additive variants identified. We functionally validated 13 of the additive candidate genes’ (Adgf-A/Adgf-A2/CG32181, bru1, CadN, flapper (CG11073), CG15236, flippy (CG9766), CREG, Dscam4, form3, fry, Lasp/CG9692, Pde6, Snoo), and introduce a novel approach to whole gene significance screens: PEGASUS_flies. Additionally, we identified ppk23, an Acid Sensing Ion Channel (ASIC) homolog, as an important hub for epistatic interactions. We propose a model that suggests genetic modifiers of wing and muscle morphology, nervous system development and function, BMP signaling, sexually dimorphic neural wiring, and gene regulation are all important for the observed differences flight performance in a natural population. Additionally, these results represent a snapshot of the genetic modifiers affecting drop-response flight performance in Drosophila, with implications for other insects. Insect flight is a widely recognizable phenotype of many winged insects, hence the name: flies. While fruit flies, or Drosophila melanogaster, are a genetically tractable model, flight performance is a highly integrative phenotype, and therefore challenging to identify comprehensively which genetic modifiers contribute to its genetic architecture. Accordingly, we screened 197 Drosophila Genetic Reference Panel lines for their ability to react and respond to an abrupt drop. Using several computational approaches, we identified additive, marginal, and epistatic variants, as well as whole genes and altered sub-networks of gene-gene and protein-protein interaction networks that contribute to variation in flight performance. More generally, we demonstrate the benefits of employing multiple methodologies to elucidate the genetic architecture of complex traits. Many variants and genes mapped to regions of the genome that affect neurodevelopment, wing and muscle development, and regulation of gene expression. We also introduce PEGASUS_flies, a Drosophila-adapted version of the PEGASUS platform first used in human studies, to infer gene-level significance of association based on the gene’s distribution of individual variant P-values. Our results contribute to the debate over the relative importance of individual, additive factors and epistatic, or higher order, interactions, in the mapping of genotype to phenotype.
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Affiliation(s)
- Adam N Spierer
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
| | - Jim A Mossman
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
| | - Samuel Pattillo Smith
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
| | - Lorin Crawford
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
- Microsoft Research New England, Cambridge, Massachusetts, United States of America
| | - Sohini Ramachandran
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
| | - David M Rand
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
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33
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Srivastava P, Kane A, Harrison C, Levin M. A Meta-Analysis of Bioelectric Data in Cancer, Embryogenesis, and Regeneration. Bioelectricity 2021; 3:42-67. [PMID: 34476377 DOI: 10.1089/bioe.2019.0034] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Developmental bioelectricity is the study of the endogenous role of bioelectrical signaling in all cell types. Resting potentials and other aspects of ionic cell physiology are known to be important regulatory parameters in embryogenesis, regeneration, and cancer. However, relevant quantitative measurement and genetic phenotyping data are distributed throughout wide-ranging literature, hampering experimental design and hypothesis generation. Here, we analyze published studies on bioelectrics and transcriptomic and genomic/phenotypic databases to provide a novel synthesis of what is known in three important aspects of bioelectrics research. First, we provide a comprehensive list of channelopathies-ion channel and pump gene mutations-in a range of important model systems with developmental patterning phenotypes, illustrating the breadth of channel types, tissues, and phyla (including man) in which bioelectric signaling is a critical endogenous aspect of embryogenesis. Second, we perform a novel bioinformatic analysis of transcriptomic data during regeneration in diverse taxa that reveals an electrogenic protein to be the one common factor specifically expressed in regeneration blastemas across Kingdoms. Finally, we analyze data on distinct Vmem signatures in normal and cancer cells, revealing a specific bioelectrical signature corresponding to some types of malignancies. These analyses shed light on fundamental questions in developmental bioelectricity and suggest new avenues for research in this exciting field.
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Affiliation(s)
- Pranjal Srivastava
- Rye High School, Rye, New York, USA; Current Affiliation: College of Chemistry, University of California, Berkeley, Berkeley, California, USA
| | - Anna Kane
- Department of Biology, Allen Discovery Center, Tufts University, Medford, Massachusetts, USA
| | - Christina Harrison
- Department of Biology, Allen Discovery Center, Tufts University, Medford, Massachusetts, USA
| | - Michael Levin
- Department of Biology, Allen Discovery Center, Tufts University, Medford, Massachusetts, USA
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34
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Sun J, Wang X, Xu RG, Mao D, Shen D, Wang X, Qiu Y, Han Y, Lu X, Li Y, Che Q, Zheng L, Peng P, Kang X, Zhu R, Jia Y, Wang Y, Liu LP, Chang Z, Ji JY, Wang Z, Liu Q, Li S, Sun FL, Ni JQ. HP1c regulates development and gut homeostasis by suppressing Notch signaling through Su(H). EMBO Rep 2021; 22:e51298. [PMID: 33594776 DOI: 10.15252/embr.202051298] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 01/01/2021] [Accepted: 01/13/2021] [Indexed: 12/30/2022] Open
Abstract
Notch signaling and epigenetic factors are known to play critical roles in regulating tissue homeostasis in most multicellular organisms, but how Notch signaling coordinates with epigenetic modulators to control differentiation remains poorly understood. Here, we identify heterochromatin protein 1c (HP1c) as an essential epigenetic regulator of gut homeostasis in Drosophila. Specifically, we observe that HP1c loss-of-function phenotypes resemble those observed after Notch signaling perturbation and that HP1c interacts genetically with components of the Notch pathway. HP1c represses the transcription of Notch target genes by directly interacting with Suppressor of Hairless (Su(H)), the key transcription factor of Notch signaling. Moreover, phenotypes caused by depletion of HP1c in Drosophila can be rescued by expressing human HP1γ, suggesting that HP1γ functions similar to HP1c in Drosophila. Taken together, our findings reveal an essential role of HP1c in normal development and gut homeostasis by suppressing Notch signaling.
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Affiliation(s)
- Jin Sun
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China.,Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Xia Wang
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Rong-Gang Xu
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China
| | - Decai Mao
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China.,Sichuan Academy of Grassland Science, Chengdu, China
| | - Da Shen
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China
| | - Xin Wang
- Institute for TCM-X, MOE Key Laboratory of Bioinformatics/Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, Beijing, China
| | - Yuhao Qiu
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China.,Tsinghua University-Peking University Joint Center for Life Sciences, Beijing, China
| | - Yuting Han
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China
| | - Xinyi Lu
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China
| | - Yutong Li
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China
| | - Qinyun Che
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China
| | - Li Zheng
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China
| | - Ping Peng
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China.,Tsinghua University-Peking University Joint Center for Life Sciences, Beijing, China
| | - Xuan Kang
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Advanced Institute of Translational Medicine, Tongji University, Shanghai, China
| | - Ruibao Zhu
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China.,Tsinghua University-Peking University Joint Center for Life Sciences, Beijing, China
| | - Yu Jia
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China.,Tsinghua University-Peking University Joint Center for Life Sciences, Beijing, China
| | - Yinyin Wang
- State Key Laboratory of Membrane Biology, School of Medicine and the School of Life Sciences, Tsinghua University, Beijing, China
| | - Lu-Ping Liu
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China
| | - Zhijie Chang
- State Key Laboratory of Membrane Biology, School of Medicine and the School of Life Sciences, Tsinghua University, Beijing, China
| | - Jun-Yuan Ji
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Science Center, College Station, TX, USA
| | - Zhao Wang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Qingfei Liu
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Shao Li
- Institute for TCM-X, MOE Key Laboratory of Bioinformatics/Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, Beijing, China
| | - Fang-Lin Sun
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Advanced Institute of Translational Medicine, Tongji University, Shanghai, China
| | - Jian-Quan Ni
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China.,Tsingdao Advanced Research Institute, Tongji University, Qingdao, China
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35
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The Drosophila Forkhead/Fox transcription factor Jumeau mediates specific cardiac progenitor cell divisions by regulating expression of the kinesin Nebbish. Sci Rep 2021; 11:3221. [PMID: 33547352 PMCID: PMC7864957 DOI: 10.1038/s41598-021-81894-1] [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: 05/24/2020] [Accepted: 12/28/2020] [Indexed: 11/16/2022] Open
Abstract
Forkhead (Fkh/Fox) domain transcription factors (TFs) mediate multiple cardiogenic processes in both mammals and Drosophila. We showed previously that the Drosophila Fox gene jumeau (jumu) controls three categories of cardiac progenitor cell division—asymmetric, symmetric, and cell division at an earlier stage—by regulating Polo kinase activity, and mediates the latter two categories in concert with the TF Myb. Those observations raised the question of whether other jumu-regulated genes also mediate all three categories of cardiac progenitor cell division or a subset thereof. By comparing microarray-based expression profiles of wild-type and jumu loss-of-function mesodermal cells, we identified nebbish (neb), a kinesin-encoding gene activated by jumu. Phenotypic analysis shows that neb is required for only two categories of jumu-regulated cardiac progenitor cell division: symmetric and cell division at an earlier stage. Synergistic genetic interactions between neb, jumu, Myb, and polo and the rescue of jumu mutations by ectopic cardiac mesoderm-specific expression of neb demonstrate that neb is an integral component of a jumu-regulated subnetwork mediating cardiac progenitor cell divisions. Our results emphasize the central role of Fox TFs in cardiogenesis and illustrate how a single TF can utilize different combinations of other regulators and downstream effectors to control distinct developmental processes.
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36
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Chen J, Peng Y, Zhang H, Wang K, Zhao C, Zhu G, Reddy Palli S, Han Z. Off-target effects of RNAi correlate with the mismatch rate between dsRNA and non-target mRNA. RNA Biol 2021; 18:1747-1759. [PMID: 33397184 DOI: 10.1080/15476286.2020.1868680] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
RNAi is a potent technique for the knockdown of target genes. However, its potential off-target effects limit the widespread applications in both reverse genetic analysis and genetic manipulation. Previous efforts have uncovered rules underlying specificity of siRNA-based silencing, which has broad applications in humans, but the basis for specificity of dsRNAs, which are better suited for use as insecticides, is poorly understood. Here, we investigated the rules governing dsRNA specificity. Mutational analyses showed that dsRNAs with >80% sequence identity with target genes triggered RNAi efficiently. dsRNAs with ≥16 bp segments of perfectly matched sequence or >26 bp segments of almost perfectly matched sequence with one or two mismatches scarcely distributed (single mismatches inserted between ≥5 bp matching segments or mismatched couplets inserted between ≥8 bp matching segments) also able to trigger RNAi. Using these parameters to predict off-target risk, dsRNAs can be designed to optimize specificity and efficiency, paving the way to the widespread, rational application of RNAi in pest control.
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Affiliation(s)
- Jiasheng Chen
- The Key Laboratory of Monitoring and Management of Plant Diseases and Insects/Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Yingchuan Peng
- The Key Laboratory of Monitoring and Management of Plant Diseases and Insects/Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China.,Institute of Entomology, Jiangxi Agricultural University, Nanchang, China
| | - Hainan Zhang
- The Key Laboratory of Monitoring and Management of Plant Diseases and Insects/Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Kangxu Wang
- The Key Laboratory of Monitoring and Management of Plant Diseases and Insects/Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China.,Key Laboratory of Grains and Oils Quality Control and Processing, College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing, China
| | - Chunqing Zhao
- The Key Laboratory of Monitoring and Management of Plant Diseases and Insects/Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Guanheng Zhu
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, USA
| | - Subba Reddy Palli
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, USA
| | - Zhaojun Han
- The Key Laboratory of Monitoring and Management of Plant Diseases and Insects/Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
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37
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Wang H, Liu S, Xun X, Li M, Lou J, Zhang Y, Shi J, Hu J, Bao Z, Hu X. Toxin- and species-dependent regulation of ATP-binding cassette (ABC) transporters in scallops after exposure to paralytic shellfish toxin-producing dinoflagellates. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2021; 230:105697. [PMID: 33254068 DOI: 10.1016/j.aquatox.2020.105697] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 11/12/2020] [Accepted: 11/18/2020] [Indexed: 06/12/2023]
Abstract
ATP-binding cassette (ABC) transporters are membrane-bound proteins involved in exporting various xenobiotic compounds from living cells. Bivalve mollusks can accumulate large amounts of paralytic shellfish toxins (PSTs) from marine dinoflagellates. For aquatic invertebrates, the importance of ABC proteins in multi-xenobiotic resistance has been demonstrated, however, the systematic identification of ABC transporters is very limited. In this study, 64 and 67 ABC genes containing all eight described subfamilies (A to H) were identified in Yesso scallop (Patinopecten yessoensis) and Zhikong scallop (Chlamys farreri), respectively, with massive gene expansion being observed in the ABCC and ABCG subfamilies. The kidney harbored more specifically expressed ABC genes than other organs/tissues, most of which belonged to ABCB, ABCC, and ABCG subfamilies. After feeding the scallops with PST-producing dinoflagellates, the expression of scallop ABC genes in the kidney was regulated in toxin- and species-dependent manners. In total, 20 and 24 ABC genes in Zhikong scallop (CfABCs) were induced after exposure to Alexandrium minutum and A. catenella, with the up-regulated members from both ABCC and ABCG subfamilies mainly showing acute and chronic induction by A. minutum and A. catenella, respectively, while the up-regulated CfABCBs mainly showing chronic induction by both dinoflagellates. In Yesso scallop, only eight ABC genes (PyABCs) were regulated after A. catenella exposure, and all the five up-regulated PyABCs were acutely induced. Our findings imply the functional diversity of scallop ABC genes in coping with PST accumulation, which may contribute to the lineage-specific adaptation of scallops for dealing with algal toxins challenge.
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Affiliation(s)
- Huizhen Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Shiqi Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Xiaogang Xun
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Moli Li
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Jiarun Lou
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Yihan Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Jiaoxia Shi
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Jingjie Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Xiaoli Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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38
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Phosphatidic acid increases Notch signalling by affecting Sanpodo trafficking during Drosophila sensory organ development. Sci Rep 2020; 10:21731. [PMID: 33303974 PMCID: PMC7729928 DOI: 10.1038/s41598-020-78831-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 11/27/2020] [Indexed: 11/08/2022] Open
Abstract
Organ cell diversity depends on binary cell-fate decisions mediated by the Notch signalling pathway during development and tissue homeostasis. A clear example is the series of binary cell-fate decisions that take place during asymmetric cell divisions that give rise to the sensory organs of Drosophila melanogaster. The regulated trafficking of Sanpodo, a transmembrane protein that potentiates receptor activity, plays a pivotal role in this process. Membrane lipids can regulate many signalling pathways by affecting receptor and ligand trafficking. It remains unknown, however, whether phosphatidic acid regulates Notch-mediated binary cell-fate decisions during asymmetric cell divisions, and what are the cellular mechanisms involved. Here we show that increased phosphatidic acid derived from Phospholipase D leads to defects in binary cell-fate decisions that are compatible with ectopic Notch activation in precursor cells, where it is normally inactive. Null mutants of numb or the α-subunit of Adaptor Protein complex-2 enhance dominantly this phenotype while removing a copy of Notch or sanpodo suppresses it. In vivo analyses show that Sanpodo localization decreases at acidic compartments, associated with increased internalization of Notch. We propose that Phospholipase D-derived phosphatidic acid promotes ectopic Notch signalling by increasing receptor endocytosis and inhibiting Sanpodo trafficking towards acidic endosomes.
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39
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Bordet G, Lodhi N, Guo D, Kossenkov A, Tulin AV. Poly(ADP-ribose) polymerase 1 in genome-wide expression control in Drosophila. Sci Rep 2020; 10:21151. [PMID: 33273587 PMCID: PMC7712786 DOI: 10.1038/s41598-020-78116-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 11/20/2020] [Indexed: 11/13/2022] Open
Abstract
Poly(ADP-ribose) polymerase 1 (PARP-1) is a nuclear enzyme involved in DNA repair and transcription regulation, among other processes. Malignant transformations, tumor progression, the onset of some neuropathies and other disorders have been linked to misregulation of PARP-1 activity. Despite intensive studies during the last few decades, the role of PARP-1 in transcription regulation is still not well understood. In this study, a transcriptomic analysis in Drosophila melanogaster third instar larvae was carried out. A total of 602 genes were identified, showing large-scale changes in their expression levels in the absence of PARP-1 in vivo. Among these genes, several functional gene groups were present, including transcription factors and cytochrome family members. The transcription levels of genes from the same functional group were affected by the absence of PARP-1 in a similar manner. In the absence of PARP-1, all misregulated genes coding for transcription factors were downregulated, whereas all genes coding for members of the cytochrome P450 family were upregulated. The cytochrome P450 proteins contain heme as a cofactor and are involved in oxidoreduction. Significant changes were also observed in the expression of several mobile elements in the absence of PARP-1, suggesting that PARP-1 may be involved in regulating the expression of mobile elements.
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Affiliation(s)
- Guillaume Bordet
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, 501 North Columbia Road, Stop 9061, Grand Forks, ND, 58202, USA
| | - Niraj Lodhi
- Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Danping Guo
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, 501 North Columbia Road, Stop 9061, Grand Forks, ND, 58202, USA
| | | | - Alexei V Tulin
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, 501 North Columbia Road, Stop 9061, Grand Forks, ND, 58202, USA.
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40
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Kasinathan B, Colmenares SU, McConnell H, Young JM, Karpen GH, Malik HS. Innovation of heterochromatin functions drives rapid evolution of essential ZAD-ZNF genes in Drosophila. eLife 2020; 9:e63368. [PMID: 33169670 PMCID: PMC7655104 DOI: 10.7554/elife.63368] [Citation(s) in RCA: 17] [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: 09/23/2020] [Accepted: 10/12/2020] [Indexed: 12/12/2022] Open
Abstract
Contrary to dogma, evolutionarily young and dynamic genes can encode essential functions. We find that evolutionarily dynamic ZAD-ZNF genes, which encode the most abundant class of insect transcription factors, are more likely to encode essential functions in Drosophila melanogaster than ancient, conserved ZAD-ZNF genes. We focus on the Nicknack ZAD-ZNF gene, which is evolutionarily young, poorly retained in Drosophila species, and evolves under strong positive selection. Yet we find that it is necessary for larval development in D. melanogaster. We show that Nicknack encodes a heterochromatin-localizing protein like its paralog Oddjob, also an evolutionarily dynamic yet essential ZAD-ZNF gene. We find that the divergent D. simulans Nicknack protein can still localize to D. melanogaster heterochromatin and rescue viability of female but not male Nicknack-null D. melanogaster. Our findings suggest that innovation for rapidly changing heterochromatin functions might generally explain the essentiality of many evolutionarily dynamic ZAD-ZNF genes in insects.
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Affiliation(s)
- Bhavatharini Kasinathan
- Medical Scientist Training Program, University of Washington School of MedicineSeattleUnited States
- Molecular and Cellular Biology Graduate program, University of Washington School of MedicineSeattleUnited States
- Division of Basic Sciences, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Serafin U Colmenares
- Biological Systems and Engineering Division, Lawrence Berkeley National LaboratoryBerkeleyUnited States
- Department of Molecular and Cell Biology, University of California at BerkeleyBerkeleyUnited States
- Innovative Genomics InstituteBerkeleyUnited States
| | - Hannah McConnell
- Division of Basic Sciences, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Janet M Young
- Division of Basic Sciences, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Gary H Karpen
- Biological Systems and Engineering Division, Lawrence Berkeley National LaboratoryBerkeleyUnited States
- Department of Molecular and Cell Biology, University of California at BerkeleyBerkeleyUnited States
- Innovative Genomics InstituteBerkeleyUnited States
| | - Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research CenterSeattleUnited States
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research CenterSeattleUnited States
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41
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Meng X, Yang X, Wu Z, Shen Q, Miao L, Zheng Y, Qian K, Wang J. Identification and transcriptional response of ATP-binding cassette transporters to chlorantraniliprole in the rice striped stem borer, Chilo suppressalis. PEST MANAGEMENT SCIENCE 2020; 76:3626-3635. [PMID: 32406167 DOI: 10.1002/ps.5897] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 04/14/2020] [Accepted: 05/13/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND As the largest transporter gene family in metazoans, ATP-binding cassette (ABC) transporters regulate the efflux of a broad spectrum of substrates from the cytoplasm to the outside of the cell. In arthropods, ABC transporters are involved in phase III of the detoxification process, and play important roles in the metabolism and transport of insecticides. RESULTS We identified 54 ABC transporters from the genome and transcriptome of Chilo suppressalis, one of the most damaging pests of rice in China. The identified ABC transporters were classified into eight subfamilies (ABCA to ABCH) based on NCBI BLAST and phylogenetic analysis. Synergism studies showed that treatment with verapamil, a potent inhibitor of ABC transporters, resulted in significantly increased toxicity of chlorantraniliprole against C. suppressalis larvae. Among the 21 tested ABC genes, three ABC transporter genes including CsABCC8, CsABCG1C and CsABCH1 were significantly upregulated after chlorantraniliprole treatment. CONCLUSION ABC transporters play important roles in the detoxification and transport of chlorantraniliprole in C. suppressalis. The results from our study provide valuable information on C. suppressalis ABC transporters, and are helpful in understanding the roles of ABC transporters in chlorantraniliprole resistance mechanisms in C. suppressalis and other insect pests. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Xiangkun Meng
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Xuemei Yang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Zhaolu Wu
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Qinwen Shen
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Lijun Miao
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Yang Zheng
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Kun Qian
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Jianjun Wang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
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42
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López-Gay JM, Nunley H, Spencer M, di Pietro F, Guirao B, Bosveld F, Markova O, Gaugue I, Pelletier S, Lubensky DK, Bellaïche Y. Apical stress fibers enable a scaling between cell mechanical response and area in epithelial tissue. Science 2020; 370:370/6514/eabb2169. [PMID: 33060329 DOI: 10.1126/science.abb2169] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 08/13/2020] [Indexed: 12/14/2022]
Abstract
Biological systems tailor their properties and behavior to their size throughout development and in numerous aspects of physiology. However, such size scaling remains poorly understood as it applies to cell mechanics and mechanosensing. By examining how the Drosophila pupal dorsal thorax epithelium responds to morphogenetic forces, we found that the number of apical stress fibers (aSFs) anchored to adherens junctions scales with cell apical area to limit larger cell elongation under mechanical stress. aSFs cluster Hippo pathway components, thereby scaling Hippo signaling and proliferation with area. This scaling is promoted by tricellular junctions mediating an increase in aSF nucleation rate and lifetime in larger cells. Development, homeostasis, and repair entail epithelial cell size changes driven by mechanical forces; our work highlights how, in turn, mechanosensitivity scales with cell size.
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Affiliation(s)
- Jesús M López-Gay
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, F-75248 Paris Cedex 05, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, CNRS UMR 3215, INSERM U934, F-75005 Paris, France
| | - Hayden Nunley
- Biophysics Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Meryl Spencer
- Department of Physics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Florencia di Pietro
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, F-75248 Paris Cedex 05, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, CNRS UMR 3215, INSERM U934, F-75005 Paris, France
| | - Boris Guirao
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, F-75248 Paris Cedex 05, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, CNRS UMR 3215, INSERM U934, F-75005 Paris, France
| | - Floris Bosveld
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, F-75248 Paris Cedex 05, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, CNRS UMR 3215, INSERM U934, F-75005 Paris, France
| | - Olga Markova
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, F-75248 Paris Cedex 05, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, CNRS UMR 3215, INSERM U934, F-75005 Paris, France
| | - Isabelle Gaugue
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, F-75248 Paris Cedex 05, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, CNRS UMR 3215, INSERM U934, F-75005 Paris, France
| | - Stéphane Pelletier
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, F-75248 Paris Cedex 05, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, CNRS UMR 3215, INSERM U934, F-75005 Paris, France
| | - David K Lubensky
- Biophysics Program, University of Michigan, Ann Arbor, MI 48109, USA. .,Department of Physics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yohanns Bellaïche
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, F-75248 Paris Cedex 05, France. .,Sorbonne Universités, UPMC Univ Paris 06, CNRS, CNRS UMR 3215, INSERM U934, F-75005 Paris, France
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43
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Zhang B, Binks T, Burke R. The E3 ubiquitin ligase Slimb/β-TrCP is required for normal copper homeostasis in Drosophila. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118768. [DOI: 10.1016/j.bbamcr.2020.118768] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 04/27/2020] [Accepted: 05/29/2020] [Indexed: 12/21/2022]
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44
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Dutta P, Nath S, Li J, Li WX. Drosophila SERTAD domain protein Taranis is required in somatic cells for maintenance of male germline stem cells. Dev Dyn 2020; 250:237-248. [PMID: 32969117 DOI: 10.1002/dvdy.255] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/15/2020] [Accepted: 09/21/2020] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND Polycomb proteins are essential for maintaining stem cell identity across different stem cell niches. However, how they function to maintain stem cell niches is not fully understood. RESULTS Here we show that the SERTAD protein Taranis (Tara), which is a Polycomb-trithorax group protein, is expressed in the adult testis niche and plays a role in its maintenance in Drosophila. We found that tara is expressed in early cyst cells, likely including somatic cyst stem cells (CySCs) of Drosophila male testis tip region, which houses both germline and somatic cyst stem cells along with the hub cells, forming the stem cell niche. Consistent with its expression, we found that, while loss of tara in germline cells only had minimal effects, tara knockdown in all cells or only in somatic cells of the niche reduced the number of not only somatic cells, but also germline stem cells (GSCs). We further found that Tara might antagonize Notch signaling in CySCs to maintain the stem cell niche. CONCLUSIONS Our studies suggest that Tara might function in somatic CySCs for GSC maintenance in the Drosophila testis.
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Affiliation(s)
- Pranabananda Dutta
- Department of Medicine, University of California San Diego, La Jolla, California, USA.,Division of Cancer Research and Training, Department of Medicine, Charles R. Drew University of Medicine and Science, Los Angeles, California, USA
| | - Soma Nath
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Jinghong Li
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Willis X Li
- Department of Medicine, University of California San Diego, La Jolla, California, USA
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45
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Lewis JJ, Van Belleghem SM, Papa R, Danko CG, Reed RD. Many functionally connected loci foster adaptive diversification along a neotropical hybrid zone. SCIENCE ADVANCES 2020; 6:6/39/eabb8617. [PMID: 32978147 PMCID: PMC7518860 DOI: 10.1126/sciadv.abb8617] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 08/11/2020] [Indexed: 05/02/2023]
Abstract
Characterizing the genetic complexity of adaptation and trait evolution is a major emphasis of evolutionary biology and genetics. Incongruent findings from genetic studies have resulted in conceptual models ranging from a few large-effect loci to massively polygenic architectures. Here, we combine chromatin immunoprecipitation sequencing, Hi-C, RNA sequencing, and 40 whole-genome sequences from Heliconius butterflies to show that red color pattern diversification occurred via many genomic loci. We find that the red wing pattern master regulatory transcription factor Optix binds dozens of loci also under selection, which frequently form three-dimensional adaptive hubs with selection acting on multiple physically interacting genes. Many Optix-bound genes under selection are tied to pigmentation and wing development, and these loci collectively maintain separation between adaptive red color pattern phenotypes in natural populations. We propose a model of trait evolution where functional connections between loci may resolve much of the disparity between large-effect and polygenic evolutionary models.
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Affiliation(s)
- James J Lewis
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA.
- Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
| | | | - Riccardo Papa
- Department of Biology, University of Puerto Rico-Rio Piedras, San Juan, Puerto Rico
- Molecular Sciences and Research Center, University of Puerto Rico, San Juan, Puerto Rico
| | - Charles G Danko
- Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
| | - Robert D Reed
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
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46
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Pridie C, Ueda K, Simmonds AJ. Rosy Beginnings: Studying Peroxisomes in Drosophila. Front Cell Dev Biol 2020; 8:835. [PMID: 32984330 PMCID: PMC7477296 DOI: 10.3389/fcell.2020.00835] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 08/04/2020] [Indexed: 12/19/2022] Open
Abstract
Research using the fruit fly Drosophila melanogaster has traditionally focused on understanding how mutations affecting gene regulation or function affect processes linked to animal development. Accordingly, flies have become an essential foundation of modern medical research through repeated contributions to our fundamental understanding of how their homologs of human genes function. Peroxisomes are organelles that metabolize lipids and reactive oxygen species like peroxides. However, despite clear linkage of mutations in human genes affecting peroxisomes to developmental defects, for many years fly models were conspicuously absent from the study of peroxisomes. Now, the few early studies linking the Rosy eye color phenotype to peroxisomes in flies have been joined by a growing body of research establishing novel roles for peroxisomes during the development or function of specific tissues or cell types. Similarly, unique properties of cultured fly Schneider 2 cells have advanced our understanding of how peroxisomes move on the cytoskeleton. Here, we profile how those past and more recent Drosophila studies started to link specific effects of peroxisome dysfunction to organ development and highlight the utility of flies as a model for human peroxisomal diseases. We also identify key differences in the function and proliferation of fly peroxisomes compared to yeast or mammals. Finally, we discuss the future of the fly model system for peroxisome research including new techniques that should support identification of additional tissue specific regulation of and roles for peroxisomes.
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Affiliation(s)
- C Pridie
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Kazuki Ueda
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Andrew J Simmonds
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
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47
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Wilson KA, Beck JN, Nelson CS, Hilsabeck TA, Promislow D, Brem RB, Kapahi P. GWAS for Lifespan and Decline in Climbing Ability in Flies upon Dietary Restriction Reveal decima as a Mediator of Insulin-like Peptide Production. Curr Biol 2020; 30:2749-2760.e3. [PMID: 32502405 DOI: 10.1016/j.cub.2020.05.020] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 03/17/2020] [Accepted: 05/06/2020] [Indexed: 12/16/2022]
Abstract
Dietary restriction (DR) is the most robust means to extend lifespan and delay age-related diseases across species. An underlying assumption in the aging field is that DR enhances both lifespan and physical activity through similar mechanisms, but this has not been rigorously tested in different genetic backgrounds. Furthermore, nutrient response genes responsible for lifespan extension or age-related decline in functionality remain underexplored in natural populations. To address this, we measured nutrient-dependent changes in lifespan and age-related decline in climbing ability in the Drosophila Genetic Reference Panel fly strains. On average, DR extended lifespan and delayed decline in climbing ability, but there was a lack of correlation between these traits across individual strains, suggesting that distinct genetic factors modulate these traits independently and that genotype determines response to diet. Only 50% of strains showed positive response to DR for both lifespan and climbing ability, 14% showed a negative response for one trait but not both, and 35% showed no change in one or both traits. Through GWAS, we uncovered a number of genes previously not known to be diet responsive nor to influence lifespan or climbing ability. We validated decima as a gene that alters lifespan and daedalus as one that influences age-related decline in climbing ability. We found that decima influences insulin-like peptide transcription in the GABA receptor neurons downstream of short neuropeptide F precursor (sNPF) signaling. Modulating these genes produced independent effects on lifespan and physical activity decline, which suggests that these age-related traits can be regulated through distinct mechanisms.
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Affiliation(s)
- Kenneth A Wilson
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945, USA; Davis School of Gerontology, University of Southern California, University Park, Los Angeles, CA 90007, USA
| | - Jennifer N Beck
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945, USA; Department of Urology, University of California, San Francisco, 400 Parnassus Avenue, Room A-632, San Francisco, CA 94143, USA
| | | | - Tyler A Hilsabeck
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945, USA; Davis School of Gerontology, University of Southern California, University Park, Los Angeles, CA 90007, USA
| | - Daniel Promislow
- Department of Pathology, University of Washington, Seattle, WA 98195, USA; Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Rachel B Brem
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945, USA; Davis School of Gerontology, University of Southern California, University Park, Los Angeles, CA 90007, USA; Department of Plant and Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA 94720, USA.
| | - Pankaj Kapahi
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945, USA; Davis School of Gerontology, University of Southern California, University Park, Los Angeles, CA 90007, USA; Department of Urology, University of California, San Francisco, 400 Parnassus Avenue, Room A-632, San Francisco, CA 94143, USA.
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48
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Hapairai LK, Mysore K, Sun L, Li P, Wang CW, Scheel ND, Lesnik A, Scheel MP, Igiede J, Wei N, Severson DW, Duman-Scheel M. Characterization of an adulticidal and larvicidal interfering RNA pesticide that targets a conserved sequence in mosquito G protein-coupled dopamine 1 receptor genes. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020; 120:103359. [PMID: 32169582 PMCID: PMC8744133 DOI: 10.1016/j.ibmb.2020.103359] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/29/2020] [Accepted: 02/27/2020] [Indexed: 05/14/2023]
Abstract
G protein-coupled receptors (GPCRs), key regulators of a variety of critical biological processes, are attractive targets for insecticide development. Given the importance of these receptors in many organisms, including humans, it is critical that novel pesticides directed against GPCRs are designed to be species-specific. Here, we present characterization of an interfering RNA pesticide (IRP) targeting the mosquito GPCR-encoding dopamine 1 receptor (dop1) genes. A small interfering RNA corresponding to dop1 was identified in a screen for IRPs that kill Aedes aegypti during both the adult and larval stages. The 25 bp sequence targeted by this IRP is conserved in the dop1 genes of multiple mosquito species, but not in non-target organisms, indicating that it could function as a biorational mosquito insecticide. Aedes aegypti adults treated through microinjection or attractive toxic sugar bait delivery of small interfering RNA corresponding to the target site exhibited severe neural and behavioral defects and high levels of adult mortality. Likewise, A. aegypti larval consumption of dried inactivated yeast tablets prepared from a Saccharomyces cerevisiae strain engineered to express short hairpin RNA corresponding to the dop1 target site resulted in severe neural defects and larval mortality. Aedes albopictus and Anopheles gambiae adult and larval mortality was also observed following treatment with dop1 IRPs, which were not toxic to non-target arthropods. The results of this investigation indicate that dop1 IRPs can be used for species-specific targeting of dop1 GPCRs and may represent a new biorational strategy for control of both adult and larval mosquitoes.
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Affiliation(s)
- Limb K Hapairai
- Indiana University School of Medicine, Department of Medical and Molecular Genetics, Raclin-Carmichael Hall, 1234 Notre Dame Ave., South Bend, IN, 46617, USA; The University of Notre Dame Eck Institute for Global Health, Notre Dame, IN, 46556, USA.
| | - Keshava Mysore
- Indiana University School of Medicine, Department of Medical and Molecular Genetics, Raclin-Carmichael Hall, 1234 Notre Dame Ave., South Bend, IN, 46617, USA; The University of Notre Dame Eck Institute for Global Health, Notre Dame, IN, 46556, USA.
| | - Longhua Sun
- Indiana University School of Medicine, Department of Medical and Molecular Genetics, Raclin-Carmichael Hall, 1234 Notre Dame Ave., South Bend, IN, 46617, USA; The University of Notre Dame Eck Institute for Global Health, Notre Dame, IN, 46556, USA.
| | - Ping Li
- Indiana University School of Medicine, Department of Medical and Molecular Genetics, Raclin-Carmichael Hall, 1234 Notre Dame Ave., South Bend, IN, 46617, USA; The University of Notre Dame Eck Institute for Global Health, Notre Dame, IN, 46556, USA.
| | - Chien-Wei Wang
- The University of Notre Dame Eck Institute for Global Health, Notre Dame, IN, 46556, USA; The University of Notre Dame Department of Civil and Environmental Engineering and Earth Sciences, Cushing Hall, Notre Dame, IN, 46556, USA.
| | - Nicholas D Scheel
- The University of Notre Dame Eck Institute for Global Health, Notre Dame, IN, 46556, USA; The University of Notre Dame Department of Biological Sciences, Galvin Life Sciences, Notre Dame, IN, 46556, USA.
| | - Alexandra Lesnik
- The University of Notre Dame Eck Institute for Global Health, Notre Dame, IN, 46556, USA.
| | - Max P Scheel
- Indiana University School of Medicine, Department of Medical and Molecular Genetics, Raclin-Carmichael Hall, 1234 Notre Dame Ave., South Bend, IN, 46617, USA; The University of Notre Dame Eck Institute for Global Health, Notre Dame, IN, 46556, USA.
| | - Jessica Igiede
- The University of Notre Dame Eck Institute for Global Health, Notre Dame, IN, 46556, USA; The University of Notre Dame Department of Biological Sciences, Galvin Life Sciences, Notre Dame, IN, 46556, USA.
| | - Na Wei
- The University of Notre Dame Eck Institute for Global Health, Notre Dame, IN, 46556, USA; The University of Notre Dame Department of Civil and Environmental Engineering and Earth Sciences, Cushing Hall, Notre Dame, IN, 46556, USA.
| | - David W Severson
- Indiana University School of Medicine, Department of Medical and Molecular Genetics, Raclin-Carmichael Hall, 1234 Notre Dame Ave., South Bend, IN, 46617, USA; The University of Notre Dame Eck Institute for Global Health, Notre Dame, IN, 46556, USA; The University of Notre Dame Department of Biological Sciences, Galvin Life Sciences, Notre Dame, IN, 46556, USA; The University of the West Indies, Department of Life Sciences, St. Augustine, Trinidad, Trinidad and Tobago.
| | - Molly Duman-Scheel
- Indiana University School of Medicine, Department of Medical and Molecular Genetics, Raclin-Carmichael Hall, 1234 Notre Dame Ave., South Bend, IN, 46617, USA; The University of Notre Dame Eck Institute for Global Health, Notre Dame, IN, 46556, USA; The University of Notre Dame Department of Biological Sciences, Galvin Life Sciences, Notre Dame, IN, 46556, USA.
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49
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Koshikawa S. Evolution of wing pigmentation in Drosophila: Diversity, physiological regulation, and cis-regulatory evolution. Dev Growth Differ 2020; 62:269-278. [PMID: 32171022 PMCID: PMC7384037 DOI: 10.1111/dgd.12661] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 03/04/2020] [Accepted: 03/04/2020] [Indexed: 12/20/2022]
Abstract
Fruit flies (Drosophila and its close relatives, or “drosophilids”) are a group that includes an important model organism, Drosophila melanogaster, and also very diverse species distributed worldwide. Many of these species have black or brown pigmentation patterns on their wings, and have been used as material for evo‐devo research. Pigmentation patterns are thought to have evolved rapidly compared with body plans or body shapes; hence they are advantageous model systems for studying evolutionary gains of traits and parallel evolution. Various groups of drosophilids, including genus Idiomyia (Hawaiian Drosophila), have a variety of pigmentations, ranging from simple black pigmentations around crossveins to a single antero‐distal spot and a more complex mottled pattern. Pigmentation patterns are sometimes obviously used for sexual displays; however, in some cases they may have other functions. The process of wing formation in Drosophila, the general mechanism of pigmentation formation, and the transport of substances necessary for pigmentation, including melanin precursors, through wing veins are summarized here. Lastly, the evolution of the expression of genes regulating pigmentation patterns, the role of cis‐regulatory regions, and the conditions required for the evolutionary emergence of pigmentation patterns are discussed. Future prospects for research on the evolution of wing pigmentation pattern formation in drosophilids are presented, particularly from the point of view of how they compare with other studies of the evolution of new traits.
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Affiliation(s)
- Shigeyuki Koshikawa
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Japan.,Graduate School of Environmental Science, Hokkaido University, Sapporo, Japan
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Lee YCG, Ventura IM, Rice GR, Chen DY, Colmenares SU, Long M. Rapid Evolution of Gained Essential Developmental Functions of a Young Gene via Interactions with Other Essential Genes. Mol Biol Evol 2020; 36:2212-2226. [PMID: 31187122 DOI: 10.1093/molbev/msz137] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
New genes are of recent origin and only present in a subset of species in a phylogeny. Accumulated evidence suggests that new genes, like old genes that are conserved across species, can also take on important functions and be essential for the survival and reproductive success of organisms. Although there are detailed analyses of the mechanisms underlying new genes' gaining fertility functions, how new genes rapidly become essential for viability remains unclear. We focused on a young retro-duplicated gene (CG7804, which we named Cocoon) in Drosophila that originated between 4 and 10 Ma. We found that, unlike its evolutionarily conserved parental gene, Cocoon has evolved under positive selection and accumulated many amino acid differences at functional sites from the parental gene. Despite its young age, Cocoon is essential for the survival of Drosophila melanogaster at multiple developmental stages, including the critical embryonic stage, and its expression is essential in different tissues from those of its parental gene. Functional genomic analyses found that Cocoon acquired unique DNA-binding sites and has a contrasting effect on gene expression to that of its parental gene. Importantly, Cocoon binding predominantly locates at genes that have other essential functions and/or have multiple gene-gene interactions, suggesting that Cocoon acquired novel essential function to survival through forming interactions that have large impacts on the gene interaction network. Our study is an important step toward deciphering the evolutionary trajectory by which new genes functionally diverge from parental genes and become essential.
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Affiliation(s)
- Yuh Chwen G Lee
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL.,Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA
| | - Iuri M Ventura
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL.,CAPES Foundation, Ministry of Education of Brazil, Brasília, DF, Brazil
| | - Gavin R Rice
- Department of Evolution and Ecology, University of California, Davis, Davis, CA.,Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA
| | - Dong-Yuan Chen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA
| | - Serafin U Colmenares
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA
| | - Manyuan Long
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL
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