1
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Fujimori H, Shima-Nakamura M, Kanno SI, Shibuya-Takahashi R, Mochizuki M, Mizuma M, Unno M, Wakui Y, Abue M, Iwai W, Fukushi D, Satoh K, Yamaguchi K, Shindo N, Yasuda J, Tamai K. FAXC interacts with ANXA2 and SRC in mitochondria and promotes tumorigenesis in cholangiocarcinoma. Cancer Sci 2024; 115:1896-1909. [PMID: 38480477 DOI: 10.1111/cas.16140] [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: 02/13/2024] [Accepted: 02/22/2024] [Indexed: 06/04/2024] Open
Abstract
Cholangiocarcinoma (CCA) is one of the most difficult malignancies to treat as the therapeutic options are limited. Although several driver genes have been identified, most remain unknown. In this study, we identified a failed axon connection homolog (FAXC), whose function is unknown in mammals, by analyzing serially passaged CCA xenograft models. Knockdown of FAXC reduced subcutaneous tumorigenicity in mice. FAXC was bound to annexin A2 (ANXA2) and c-SRC, which are tumor-promoting genes. The FAXC/ANXA2/c-SRC complex forms in the mitochondria. FAXC enhances SRC-dependent ANXA2 phosphorylation at tyrosine-24, and the C-terminal amino acid residues (351-375) of FAXC are required for ANXA2 phosphorylation. Transcriptome data from a xenografted CCA cell line revealed that FAXC correlated with epithelial-mesenchymal transition, hypoxia, and KRAS signaling genes. Collectively, these findings advance our understanding of CCA tumorigenesis and provide candidate therapeutic targets.
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Affiliation(s)
- Haruna Fujimori
- Division of Cancer Stem Cell, Miyagi Cancer Center Research Institute, Natori, Japan
| | - Mao Shima-Nakamura
- Division of Cancer Stem Cell, Miyagi Cancer Center Research Institute, Natori, Japan
| | - Shin-Ichiro Kanno
- IDAC Fellow Research Group for DNA Repair and Dynamic Proteome Institute of Development, Aging and Cancer (IDAC), Tohoku University, Sendai, Japan
| | - Rie Shibuya-Takahashi
- Division of Cancer Stem Cell, Miyagi Cancer Center Research Institute, Natori, Japan
| | - Mai Mochizuki
- Division of Cancer Stem Cell, Miyagi Cancer Center Research Institute, Natori, Japan
| | - Masamichi Mizuma
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Michiaki Unno
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yuta Wakui
- Department of Gastroenterology, Miyagi Cancer Center, Natori, Japan
| | - Makoto Abue
- Department of Gastroenterology, Miyagi Cancer Center, Natori, Japan
| | - Wataru Iwai
- Department of Gastroenterology, Miyagi Cancer Center, Natori, Japan
| | - Daisuke Fukushi
- Division of Gastroenterology, Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Kennich Satoh
- Division of Gastroenterology, Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Kazunori Yamaguchi
- Division of Molecular and Cellular Oncology, Miyagi Cancer Center Research Institute, Natori, Japan
| | - Norihisa Shindo
- Cancer Chromosome Biology Unit, Miyagi Cancer Center Research Institute, Natori, Japan
| | - Jun Yasuda
- Division of Molecular and Cellular Oncology, Miyagi Cancer Center Research Institute, Natori, Japan
| | - Keiichi Tamai
- Division of Cancer Stem Cell, Miyagi Cancer Center Research Institute, Natori, Japan
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2
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Gilbert G, Renaud Y, Teste C, Anglaret N, Bertrand R, Hoehn S, Jurkowski TP, Schuettengruber B, Cavalli G, Waltzer L, Vandel L. Drosophila TET acts with PRC1 to activate gene expression independently of its catalytic activity. SCIENCE ADVANCES 2024; 10:eadn5861. [PMID: 38701218 PMCID: PMC11068012 DOI: 10.1126/sciadv.adn5861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 04/03/2024] [Indexed: 05/05/2024]
Abstract
Enzymes of the ten-eleven translocation (TET) family play a key role in the regulation of gene expression by oxidizing 5-methylcytosine (5mC), a prominent epigenetic mark in many species. Yet, TET proteins also have less characterized noncanonical modes of action, notably in Drosophila, whose genome is devoid of 5mC. Here, we show that Drosophila TET activates the expression of genes required for larval central nervous system (CNS) development mainly in a catalytic-independent manner. Genome-wide profiling shows that TET is recruited to enhancer and promoter regions bound by Polycomb group complex (PcG) proteins. We found that TET interacts and colocalizes on chromatin preferentially with Polycomb repressor complex 1 (PRC1) rather than PRC2. Furthermore, PRC1 but not PRC2 is required for the activation of TET target genes. Last, our results suggest that TET and PRC1 binding to activated genes is interdependent. These data highlight the importance of TET noncatalytic function and the role of PRC1 for gene activation in the Drosophila larval CNS.
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Affiliation(s)
- Guerric Gilbert
- Université Clermont Auvergne, CNRS, INSERM, iGReD, F-63000 Clermont-Ferrand, France
| | - Yoan Renaud
- Université Clermont Auvergne, CNRS, INSERM, iGReD, F-63000 Clermont-Ferrand, France
| | - Camille Teste
- Université Clermont Auvergne, CNRS, INSERM, iGReD, F-63000 Clermont-Ferrand, France
| | - Nadège Anglaret
- Université Clermont Auvergne, CNRS, INSERM, iGReD, F-63000 Clermont-Ferrand, France
| | - Romane Bertrand
- Université Clermont Auvergne, CNRS, INSERM, iGReD, F-63000 Clermont-Ferrand, France
| | - Sven Hoehn
- Cardiff University, School of Biosciences, Museum Avenue, CF10 3AX Cardiff, Wales, UK
| | - Tomasz P. Jurkowski
- Cardiff University, School of Biosciences, Museum Avenue, CF10 3AX Cardiff, Wales, UK
| | - Bernd Schuettengruber
- Institute of Human Genetics, UMR9002, CNRS and University of Montpellier, Montpellier, France
| | - Giacomo Cavalli
- Institute of Human Genetics, UMR9002, CNRS and University of Montpellier, Montpellier, France
| | - Lucas Waltzer
- Université Clermont Auvergne, CNRS, INSERM, iGReD, F-63000 Clermont-Ferrand, France
| | - Laurence Vandel
- Université Clermont Auvergne, CNRS, INSERM, iGReD, F-63000 Clermont-Ferrand, France
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3
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Ozcelik G, Koca MS, Sunbul B, Yilmaz-Atay F, Demirhan F, Tiryaki B, Cilenk K, Selvi S, Ozturk N. Interactions of drosophila cryptochrome. Photochem Photobiol 2024. [PMID: 38314442 DOI: 10.1111/php.13916] [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: 09/14/2023] [Revised: 01/20/2024] [Accepted: 01/23/2024] [Indexed: 02/06/2024]
Abstract
In this study, we investigate the intricate regulatory mechanisms underlying the circadian clock in Drosophila, focusing on the light-induced conformational changes in the cryptochrome (DmCry). Upon light exposure, DmCry undergoes conformational changes that prompt its binding to Timeless and Jetlag proteins, initiating a cascade crucial for the starting of a new circadian cycle. DmCry is subsequently degraded, contributing to the desensitization of the resetting mechanism. The transient and short-lived nature of DmCry protein-protein interactions (PPIs), leading to DmCry degradation within an hour of light exposure, presents a challenge for comprehensive exploration. To address this, we employed proximity-dependent biotinylation techniques, combining engineered BioID (TurboID) and APEX (APEX2) enzymes with mass spectrometry. This approach enabled the identification of the in vitro DmCry interactome in Drosophila S2 cells, uncovering several novel PPIs associated with DmCry. Validation of these interactions through a novel co-immunoprecipitation technique enhances the reliability of our findings. Importantly, our study suggests the potential of this method to reveal additional circadian clock- or magnetic field-dependent PPIs involving DmCry. This exploration of the DmCry interactome not only advances our understanding of circadian clock regulation but also establishes a versatile framework for future investigations into light- and time-dependent protein interactions in Drosophila.
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Affiliation(s)
- Gozde Ozcelik
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Mehmet Serdar Koca
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Buket Sunbul
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Fatma Yilmaz-Atay
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Feride Demirhan
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Busra Tiryaki
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Kevser Cilenk
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Saba Selvi
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Nuri Ozturk
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey
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4
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Stanhope SC, Brandwine-Shemmer T, Blum HR, Doud EH, Jannasch A, Mosley AL, Minke B, Weake VM. Proteome-wide quantitative analysis of redox cysteine availability in the Drosophila melanogaster eye reveals oxidation of phototransduction machinery during blue light exposure and age. Redox Biol 2023; 63:102723. [PMID: 37146512 DOI: 10.1016/j.redox.2023.102723] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/20/2023] [Accepted: 04/26/2023] [Indexed: 05/07/2023] Open
Abstract
The retina is one of the highest oxygen-consuming tissues because visual transduction and light signaling processes require large amounts of ATP. Thus, because of the high energy demand, oxygen-rich environment, and tissue transparency, the eye is susceptible to excess production of reactive oxygen species (ROS) resulting in oxidative stress. Oxidative stress in the eye is associated with the development and progression of ocular diseases including cataracts, glaucoma, age-related macular degeneration, and diabetic retinopathy. ROS can modify and damage cellular proteins, but can also be involved in redox signaling. In particular, the thiol groups of cysteines can undergo reversible or irreversible oxidative post-translational modifications (PTMs). Identifying the redox-sensitive cysteines on a proteome-wide scale provides insight into those proteins that act as redox sensors or become irreversibly damaged upon exposure to oxidative stress. In this study, we profiled the redox proteome of the Drosophila eye under prolonged, high intensity blue light exposure and age using iodoacetamide isobaric label sixplex reagents (iodo-TMT) to identify changes in cysteine availability. Although redox metabolite analysis of the major antioxidant, glutathione, revealed similar ratios of its oxidized and reduced form in aged or light-stressed eyes, we observed different changes in the redox proteome under these conditions. Both conditions resulted in significant oxidation of proteins involved in phototransduction and photoreceptor maintenance but affected distinct targets and cysteine residues. Moreover, redox changes induced by blue light exposure were accompanied by a large reduction in light sensitivity that did not arise from a reduction in the photopigment level, suggesting that the redox-sensitive cysteines we identified in the phototransduction machinery might contribute to light adaptation. Our data provide a comprehensive description of the redox proteome of Drosophila eye tissue under light stress and aging and suggest how redox signaling might contribute to light adaptation in response to acute light stress.
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Affiliation(s)
- Sarah C Stanhope
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Tal Brandwine-Shemmer
- Department of Medical Neurobiology, Institute for Medical Research Israel-Canada (IMRIC), Edmond and Lily Safra Center for Brain Sciences (ELSC), Faculty of Medicine, The Hebrew University, Jerusalem, 91120, Israel
| | - Hannah R Blum
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Emma H Doud
- Center for Proteome Analysis, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Amber Jannasch
- Bindley Bioscience Center, Purdue University, West Lafayette, IN, 47907, USA
| | - Amber L Mosley
- Center for Proteome Analysis, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Baruch Minke
- Department of Medical Neurobiology, Institute for Medical Research Israel-Canada (IMRIC), Edmond and Lily Safra Center for Brain Sciences (ELSC), Faculty of Medicine, The Hebrew University, Jerusalem, 91120, Israel
| | - Vikki M Weake
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA; Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, 47907, USA.
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5
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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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6
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Mendoza-Garcia P, Basu S, Sukumar SK, Arefin B, Wolfstetter G, Anthonydhason V, Molander L, Uçkun E, Lindehell H, Lebrero-Fernandez C, Larsson J, Larsson E, Bemark M, Palmer RH. DamID transcriptional profiling identifies the Snail/Scratch transcription factor Kahuli as an Alk target in the Drosophila visceral mesoderm. Development 2021; 148:dev199465. [PMID: 34905617 PMCID: PMC8722224 DOI: 10.1242/dev.199465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 10/26/2021] [Indexed: 12/19/2022]
Abstract
Development of the Drosophila visceral muscle depends on Anaplastic Lymphoma Kinase (Alk) receptor tyrosine kinase (RTK) signaling, which specifies founder cells (FCs) in the circular visceral mesoderm (VM). Although Alk activation by its ligand Jelly Belly (Jeb) is well characterized, few target molecules have been identified. Here, we used targeted DamID (TaDa) to identify Alk targets in embryos overexpressing Jeb versus embryos with abrogated Alk activity, revealing differentially expressed genes, including the Snail/Scratch family transcription factor Kahuli (Kah). We confirmed Kah mRNA and protein expression in the VM, and identified midgut constriction defects in Kah mutants similar to those of pointed (pnt). ChIP and RNA-Seq data analysis defined a Kah target-binding site similar to that of Snail, and identified a set of common target genes putatively regulated by Kah and Pnt during midgut constriction. Taken together, we report a rich dataset of Alk-responsive loci in the embryonic VM and functionally characterize the role of Kah in the regulation of embryonic midgut morphogenesis.
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Affiliation(s)
- Patricia Mendoza-Garcia
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Swaraj Basu
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Sanjay Kumar Sukumar
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Badrul Arefin
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Georg Wolfstetter
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Vimala Anthonydhason
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Linnea Molander
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Ezgi Uçkun
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Henrik Lindehell
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden
| | - Cristina Lebrero-Fernandez
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Jan Larsson
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden
| | - Erik Larsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Mats Bemark
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, SE-405 30 Gothenburg, Sweden
- Department of Clinical Immunology and Transfusion Medicine, Sahlgrenska University Hospital, Region Västra Götaland, SE-41346 Gothenburg, Sweden
| | - Ruth H. Palmer
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, SE-405 30 Gothenburg, Sweden
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7
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Lin KY, Hsu HJ. Regulation of adult female germline stem cells by nutrient-responsive signaling. CURRENT OPINION IN INSECT SCIENCE 2020; 37:16-22. [PMID: 32070932 DOI: 10.1016/j.cois.2019.10.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 10/10/2019] [Accepted: 10/14/2019] [Indexed: 06/10/2023]
Abstract
Insect oogenesis is greatly affected by nutrient availability. When nutrients are abundant, oocytes are rapidly generated, but the process is slowed to conserve energy under nutrient-deficient conditions. To properly allocate limited resources toward oogenesis, systemic factors coordinate the behavioral response of ovarian germline stem cells (GSCs) to nutritional inputs by acting on the GSC itself, GSC supporting cells (the niche), or the adipose tissue surrounding the ovary. In this review, we describe current knowledge of the Drosophila ovarian GSC-niche-adipocyte system and major nutrient sensing pathways (insulin/IGF signaling, TOR signaling, and GCN2-dependent amino acid sensing) that intrinsically or extrinsically regulate GSC responses to nutrient signals.
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Affiliation(s)
- Kun-Yang Lin
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei 11529, Taiwan; Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan; Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Hwei-Jan Hsu
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei 11529, Taiwan; Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan; Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan.
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8
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Generation of Inducible Gene-Switched GAL4 Expressed in the Drosophila Female Germline Stem Cell Niche. G3-GENES GENOMES GENETICS 2019; 9:2007-2016. [PMID: 31018943 PMCID: PMC6553524 DOI: 10.1534/g3.119.400246] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The stem cell niche, a regulatory microenvironment, houses and regulates stem cells for maintenance of tissues throughout an organism's lifespan. While it is known that stem cell function declines with age, the role of niche cells in this decline is not completely understood. Drosophila exhibits a short lifespan with well-characterized ovarian germline stem cells (GSCs) and niche compartments, providing a good model with which to study stem cell biology. However, no inducible tools for temporal and spatial control of gene expression in the GSC-niche unit have been previously developed for aging studies. The current UAS-GAL4 systems are not ideal for aging studies because fly physiological aging may be affected by the temperature shifts used to manipulate GAL4 activity. Additionally, the actual needs of the aged niche may be masked by continuously driven gene expression. Since GeneSwitch GAL4 is conveniently activated by the steroid RU486 (mifepristone), we conducted an enhancer-trap screen to isolate GeneSwitch GAL4 lines with expression in the GSC-niche unit. We identified six lines with expression in germarial somatic cells, and two lines (#2305 and #2261) with expression in niche cap cells, the major constituent of the GSC niche. The use of lines #2305 or #2261 to overexpress Drosophila insulin-like peptide 2, which maintains GSC lifespan, in aged niche cap cells significantly delayed age-dependent GSC loss. These results support the notion that insulin signaling is beneficial for maintaining aged stem cells and also validate the utility of our GeneSwitch GAL4 lines for studying stem cell aging.
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9
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Koskimäki J, Girard R, Li Y, Saadat L, Zeineddine HA, Lightle R, Moore T, Lyne S, Avner K, Shenkar R, Cao Y, Shi C, Polster SP, Zhang D, Carrión-Penagos J, Romanos S, Fonseca G, Lopez-Ramirez MA, Chapman EM, Popiel E, Tang AT, Akers A, Faber P, Andrade J, Ginsberg M, Derry WB, Kahn ML, Marchuk DA, Awad IA. Comprehensive transcriptome analysis of cerebral cavernous malformation across multiple species and genotypes. JCI Insight 2019; 4:126167. [PMID: 30728328 DOI: 10.1172/jci.insight.126167] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 01/03/2019] [Indexed: 12/18/2022] Open
Abstract
The purpose of this study was to determine important genes, functions, and networks contributing to the pathobiology of cerebral cavernous malformation (CCM) from transcriptomic analyses across 3 species and 2 disease genotypes. Sequencing of RNA from laser microdissected neurovascular units of 5 human surgically resected CCM lesions, mouse brain microvascular endothelial cells, Caenorhabditis elegans with induced Ccm gene loss, and their respective controls provided differentially expressed genes (DEGs). DEGs from mouse and C. elegans were annotated into human homologous genes. Cross-comparisons of DEGs between species and genotypes, as well as network and gene ontology (GO) enrichment analyses, were performed. Among hundreds of DEGs identified in each model, common genes and 1 GO term (GO:0051656, establishment of organelle localization) were commonly identified across the different species and genotypes. In addition, 24 GO functions were present in 4 of 5 models and were related to cell-to-cell adhesion, neutrophil-mediated immunity, ion transmembrane transporter activity, and responses to oxidative stress. We have provided a comprehensive transcriptome library of CCM disease across species and for the first time to our knowledge in Ccm1/Krit1 versus Ccm3/Pdcd10 genotypes. We have provided examples of how results can be used in hypothesis generation or mechanistic confirmatory studies.
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Affiliation(s)
- Janne Koskimäki
- Neurovascular Surgery Program, Section of Neurosurgery, The University of Chicago Medicine and Biological Sciences, Chicago, Illinois, USA
| | - Romuald Girard
- Neurovascular Surgery Program, Section of Neurosurgery, The University of Chicago Medicine and Biological Sciences, Chicago, Illinois, USA
| | - Yan Li
- Center for Research Informatics, The University of Chicago, Chicago, Illinois, USA
| | - Laleh Saadat
- Neurovascular Surgery Program, Section of Neurosurgery, The University of Chicago Medicine and Biological Sciences, Chicago, Illinois, USA
| | - Hussein A Zeineddine
- Neurovascular Surgery Program, Section of Neurosurgery, The University of Chicago Medicine and Biological Sciences, Chicago, Illinois, USA
| | - Rhonda Lightle
- Neurovascular Surgery Program, Section of Neurosurgery, The University of Chicago Medicine and Biological Sciences, Chicago, Illinois, USA
| | - Thomas Moore
- Neurovascular Surgery Program, Section of Neurosurgery, The University of Chicago Medicine and Biological Sciences, Chicago, Illinois, USA
| | - Seán Lyne
- Neurovascular Surgery Program, Section of Neurosurgery, The University of Chicago Medicine and Biological Sciences, Chicago, Illinois, USA
| | - Kenneth Avner
- Neurovascular Surgery Program, Section of Neurosurgery, The University of Chicago Medicine and Biological Sciences, Chicago, Illinois, USA
| | - Robert Shenkar
- Neurovascular Surgery Program, Section of Neurosurgery, The University of Chicago Medicine and Biological Sciences, Chicago, Illinois, USA
| | - Ying Cao
- Neurovascular Surgery Program, Section of Neurosurgery, The University of Chicago Medicine and Biological Sciences, Chicago, Illinois, USA
| | - Changbin Shi
- Neurovascular Surgery Program, Section of Neurosurgery, The University of Chicago Medicine and Biological Sciences, Chicago, Illinois, USA
| | - Sean P Polster
- Neurovascular Surgery Program, Section of Neurosurgery, The University of Chicago Medicine and Biological Sciences, Chicago, Illinois, USA
| | - Dongdong Zhang
- Neurovascular Surgery Program, Section of Neurosurgery, The University of Chicago Medicine and Biological Sciences, Chicago, Illinois, USA
| | - Julián Carrión-Penagos
- Neurovascular Surgery Program, Section of Neurosurgery, The University of Chicago Medicine and Biological Sciences, Chicago, Illinois, USA
| | - Sharbel Romanos
- Neurovascular Surgery Program, Section of Neurosurgery, The University of Chicago Medicine and Biological Sciences, Chicago, Illinois, USA
| | | | | | - Eric M Chapman
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Evelyn Popiel
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Alan T Tang
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Amy Akers
- Angioma Alliance, Norfolk, Virginia, USA
| | - Pieter Faber
- University of Chicago Genomics Facility, The University of Chicago, Chicago, Illinois, USA
| | - Jorge Andrade
- Center for Research Informatics, The University of Chicago, Chicago, Illinois, USA
| | - Mark Ginsberg
- Department of Medicine, UCSD, La Jolla, California, USA
| | - W Brent Derry
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Mark L Kahn
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Douglas A Marchuk
- The Molecular Genetics and Microbiology Department, Duke University Medical Center, Durham, North Carolina, USA
| | - Issam A Awad
- Neurovascular Surgery Program, Section of Neurosurgery, The University of Chicago Medicine and Biological Sciences, Chicago, Illinois, USA
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10
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Bernardoni R, Giordani G, Signorino E, Monticelli S, Messa F, Pradotto M, Rosso V, Bracco E, Giangrande A, Perini G, Saglio G, Cilloni D. A new BCR-ABL1 Drosophila model as a powerful tool to elucidate the pathogenesis and progression of chronic myeloid leukemia. Haematologica 2018; 104:717-728. [PMID: 30409797 PMCID: PMC6442973 DOI: 10.3324/haematol.2018.198267] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 11/08/2018] [Indexed: 01/10/2023] Open
Abstract
The oncoprotein BCR-ABL1 triggers chronic myeloid leukemia. It is clear that the disease relies on constitutive BCR-ABL1 kinase activity, but not all the interactors and regulators of the oncoprotein are known. We describe and validate a Drosophila leukemia model based on inducible human BCR-ABL1 expression controlled by tissue-specific promoters. The model was conceived to be a versatile tool for performing genetic screens. BCR-ABL1 expression in the developing eye interferes with ommatidia differentiation and expression in the hematopoietic precursors increases the number of circulating blood cells. We show that BCR-ABL1 interferes with the pathway of endogenous dAbl with which it shares the target protein Ena. Loss of function of ena or Dab, an upstream regulator of dAbl, respectively suppresses or enhances both the BCR-ABL1-dependent phenotypes. Importantly, in patients with leukemia decreased human Dab1 and Dab2 expression correlates with more severe disease and Dab1 expression reduces the proliferation of leukemia cells. Globally, these observations validate our Drosophila model, which promises to be an excellent system for performing unbiased genetic screens aimed at identifying new BCR-ABL1 interactors and regulators in order to better elucidate the mechanism of leukemia onset and progression.
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Affiliation(s)
- Roberto Bernardoni
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Italy .,Health Sciences and Technology - Interdepartmental Center for Industrial Research (HST-ICIR), University of Bologna, Ozzano Emilia, Italy
| | - Giorgia Giordani
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Italy.,Department of Clinical and Biological Sciences, University of Turin, Italy.,Present address: Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, UK
| | | | - Sara Monticelli
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Italy
| | - Francesca Messa
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Italy
| | - Monica Pradotto
- Department of Clinical and Biological Sciences, University of Turin, Italy
| | - Valentina Rosso
- Department of Clinical and Biological Sciences, University of Turin, Italy
| | | | - Angela Giangrande
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP 67404 Illkirch, France
| | - Giovanni Perini
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Italy.,Health Sciences and Technology - Interdepartmental Center for Industrial Research (HST-ICIR), University of Bologna, Ozzano Emilia, Italy
| | - Giuseppe Saglio
- Department of Clinical and Biological Sciences, University of Turin, Italy
| | - Daniela Cilloni
- Department of Clinical and Biological Sciences, University of Turin, Italy
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11
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Su YH, Rastegri E, Kao SH, Lai CM, Lin KY, Liao HY, Wang MH, Hsu HJ. Diet regulates membrane extension and survival of niche escort cells for germline homeostasis via insulin signaling. Development 2018; 145:dev.159186. [DOI: 10.1242/dev.159186] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Accepted: 03/09/2018] [Indexed: 12/29/2022]
Abstract
Diet is an important regulator of stem cell homeostasis, however, the underlying mechanisms of this regulation are not fully known. Here, we report that insulin signaling mediates dietary maintenance of Drosophila ovarian germline stem cells (GSCs) by promoting the extension of niche escort cell (EC) membranes to wrap around GSCs. This wrapping may facilitate the delivery of BMP stemness factors from ECs in the niche to GSCs. In addition to the effects on GSCs, insulin signaling-mediated regulation of EC number and protrusions controls the division and growth of GSC progeny. The effects of insulin signaling on EC membrane extension are, at least in part, driven by enhanced translation of Failed axon connections (Fax) via Ribosomal protein S6 kinase. Fax is a membrane protein that may participate in Abl-regulated cytoskeletal dynamics and is known to be involved in axon bundle formation. Therefore, we conclude that dietary cues stimulate insulin signaling in the niche to regulate EC cellular structure, probably via Fax-dependent cytoskeleton remodeling. This mechanism enhances intercellular contact and facilitates homeostatic interactions between somatic and germline cells in response to diet.
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Affiliation(s)
- Yu-Han Su
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Elham Rastegri
- Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and Graduate Institute of Life Science, National Defense Medical Center, Taipei 11529, Taiwan
| | - Shih-Han Kao
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Chun-Min Lai
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung-Hsing University, Taipei, 11529, Taiwan
- Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung 40227, Taiwan
- Biotechnology Center, National Chung-Hsing University, Taichung 40227, Taiwan
| | - Kun-Yang Lin
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung-Hsing University, Taipei, 11529, Taiwan
- Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung 40227, Taiwan
- Biotechnology Center, National Chung-Hsing University, Taichung 40227, Taiwan
| | - Hung-Yu Liao
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Mu-Hsiang Wang
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Hwei-Jan Hsu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
- Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and Graduate Institute of Life Science, National Defense Medical Center, Taipei 11529, Taiwan
- Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung 40227, Taiwan
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12
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Hsu HJ, Drummond-Barbosa D. A visual screen for diet-regulated proteins in the Drosophila ovary using GFP protein trap lines. Gene Expr Patterns 2017; 23-24:13-21. [PMID: 28093350 DOI: 10.1016/j.gep.2017.01.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 01/06/2017] [Accepted: 01/12/2017] [Indexed: 02/06/2023]
Abstract
The effect of diet on reproduction is well documented in a large number of organisms; however, much remains to be learned about the molecular mechanisms underlying this connection. The Drosophila ovary has a well described, fast and largely reversible response to diet. Ovarian stem cells and their progeny proliferate and grow faster on a yeast-rich diet than on a yeast-free (poor) diet, and death of early germline cysts, degeneration of early vitellogenic follicles and partial block in ovulation further contribute to the ∼60-fold decrease in egg laying observed on a poor diet. Multiple diet-dependent factors, including insulin-like peptides, the steroid ecdysone, the nutrient sensor Target of Rapamycin, AMP-dependent kinase, and adipocyte factors mediate this complex response. Here, we describe the results of a visual screen using a collection of green fluorescent protein (GFP) protein trap lines to identify additional factors potentially involved in this response. In each GFP protein trap line, an artificial GFP exon is fused in frame to an endogenous protein, such that the GFP fusion pattern parallels the levels and subcellular localization of the corresponding native protein. We identified 53 GFP-tagged proteins that exhibit changes in levels and/or subcellular localization in the ovary at 12-16 hours after switching females from rich to poor diets, suggesting them as potential candidates for future functional studies.
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Affiliation(s)
- Hwei-Jan Hsu
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Daniela Drummond-Barbosa
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA.
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13
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Kannan R, Song JK, Karpova T, Clarke A, Shivalkar M, Wang B, Kotlyanskaya L, Kuzina I, Gu Q, Giniger E. The Abl pathway bifurcates to balance Enabled and Rac signaling in axon patterning in Drosophila. Development 2017; 144:487-498. [PMID: 28087633 DOI: 10.1242/dev.143776] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 12/15/2016] [Indexed: 01/31/2023]
Abstract
The Abl tyrosine kinase signaling network controls cell migration, epithelial organization, axon patterning and other aspects of development. Although individual components are known, the relationships among them remain unresolved. We now use FRET measurements of pathway activity, analysis of protein localization and genetic epistasis to dissect the structure of this network in Drosophila We find that the adaptor protein Disabled stimulates Abl kinase activity. Abl suppresses the actin-regulatory factor Enabled, and we find that Abl also acts through the GEF Trio to stimulate the signaling activity of Rac GTPase: Abl gates the activity of the spectrin repeats of Trio, allowing them to relieve intramolecular repression of Trio GEF activity by the Trio N-terminal domain. Finally, we show that a key target of Abl signaling in axons is the WAVE complex that promotes the formation of branched actin networks. Thus, we show that Abl constitutes a bifurcating network, suppressing Ena activity in parallel with stimulation of WAVE. We suggest that the balancing of linear and branched actin networks by Abl is likely to be central to its regulation of axon patterning.
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Affiliation(s)
- Ramakrishnan Kannan
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jeong-Kuen Song
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tatiana Karpova
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Akanni Clarke
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Madhuri Shivalkar
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Benjamin Wang
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lyudmila Kotlyanskaya
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Irina Kuzina
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Qun Gu
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Edward Giniger
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
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14
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Fabre B, Korona D, Groen A, Vowinckel J, Gatto L, Deery MJ, Ralser M, Russell S, Lilley KS. Analysis of Drosophila melanogaster proteome dynamics during embryonic development by a combination of label-free proteomics approaches. Proteomics 2016; 16:2068-80. [PMID: 27029218 PMCID: PMC5737838 DOI: 10.1002/pmic.201500482] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 02/23/2016] [Accepted: 03/24/2016] [Indexed: 12/22/2022]
Abstract
During embryogenesis, organisms undergo considerable cellular remodelling requiring the combined action of thousands of proteins. In case of the well-studied model Drosophila melanogaster, transcriptomic studies, most notably from the modENCODE project, have described in detail changes in gene expression at the mRNA level across development. Although such data are clearly very useful to understand how the genome is regulated during embryogenesis, it is important to understand how changes in gene expression are reflected at the level of the proteome. In this study, we describe a combination of two quantitative label-free approaches, SWATH and data-dependent acquisition, to monitor changes in protein expression across a timecourse of D. melanogaster embryonic development. We demonstrate that both approaches provide robust and reproducible methods for the analysis of proteome changes. In a preliminary analysis of Drosophila embryogenesis, we identified several pathways, including the heat-shock response, nuclear protein import and energy production that are regulated during embryo development. In some cases changes in protein expression mirrored transcript levels across development, whereas other proteins showed signatures of post-transcriptional regulation. Taken together, our pilot study provides a solid platform for a more detailed exploration of the embryonic proteome.
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Affiliation(s)
- Bertrand Fabre
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, University of Cambridge, Cambridge, UK
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Dagmara Korona
- Department of Genetics, University of Cambridge, University of Cambridge, Cambridge, UK
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Arnoud Groen
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, University of Cambridge, Cambridge, UK
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Jakob Vowinckel
- Department of Biochemistry, University of Cambridge, University of Cambridge, Cambridge, UK
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Laurent Gatto
- Department of Biochemistry, University of Cambridge, University of Cambridge, Cambridge, UK
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
- Computational Proteomics Unit, Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Michael J Deery
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, University of Cambridge, Cambridge, UK
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Markus Ralser
- Department of Biochemistry, University of Cambridge, University of Cambridge, Cambridge, UK
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London, UK
| | - Steven Russell
- Department of Genetics, University of Cambridge, University of Cambridge, Cambridge, UK
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, University of Cambridge, Cambridge, UK
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
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15
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Huynen MA, Mühlmeister M, Gotthardt K, Guerrero-Castillo S, Brandt U. Evolution and structural organization of the mitochondrial contact site (MICOS) complex and the mitochondrial intermembrane space bridging (MIB) complex. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:91-101. [DOI: 10.1016/j.bbamcr.2015.10.009] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 09/25/2015] [Accepted: 10/14/2015] [Indexed: 02/03/2023]
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16
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Crombie AT, Khawand ME, Rhodius VA, Fengler KA, Miller MC, Whited GM, McGenity TJ, Murrell JC. Regulation of plasmid-encoded isoprene metabolism in Rhodococcus, a representative of an important link in the global isoprene cycle. Environ Microbiol 2015; 17:3314-29. [PMID: 25727256 PMCID: PMC4676930 DOI: 10.1111/1462-2920.12793] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 01/26/2015] [Indexed: 01/25/2023]
Abstract
Emissions of biogenic volatile organic compounds (VOCs) form an important part of the global carbon cycle, comprising a significant proportion of net ecosystem productivity. They impact atmospheric chemistry and contribute directly and indirectly to greenhouse gases. Isoprene, emitted largely from plants, comprises one third of total VOCs, yet in contrast to methane, which is released in similar quantities, we know little of its biodegradation. Here, we report the genome of an isoprene degrading isolate, Rhodococcus sp. AD45, and, using mutagenesis shows that a plasmid-encoded soluble di-iron centre isoprene monooxygenase (IsoMO) is essential for isoprene metabolism. Using RNA sequencing (RNAseq) to analyse cells exposed to isoprene or epoxyisoprene in a substrate-switch time-course experiment, we show that transcripts from 22 contiguous genes, including those encoding IsoMO, were highly upregulated, becoming among the most abundant in the cell and comprising over 25% of the entire transcriptome. Analysis of gene transcription in the wild type and an IsoMO-disrupted mutant strain showed that epoxyisoprene, or a subsequent product of isoprene metabolism, rather than isoprene itself, was the inducing molecule. We provide a foundation of molecular data for future research on the environmental biological consumption of this important, climate-active compound.
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Affiliation(s)
| | | | - Virgil A Rhodius
- DuPont Industrial Biosciences925 Page Mill Road, Palo Alto, CA, 94304, USA
| | | | - Michael C Miller
- DuPont Industrial Biosciences925 Page Mill Road, Palo Alto, CA, 94304, USA
| | - Gregg M Whited
- DuPont Industrial Biosciences925 Page Mill Road, Palo Alto, CA, 94304, USA
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17
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Reemann P, Reimann E, Ilmjärv S, Porosaar O, Silm H, Jaks V, Vasar E, Kingo K, Kõks S. Melanocytes in the skin--comparative whole transcriptome analysis of main skin cell types. PLoS One 2014; 9:e115717. [PMID: 25545474 PMCID: PMC4278762 DOI: 10.1371/journal.pone.0115717] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 11/27/2014] [Indexed: 12/13/2022] Open
Abstract
Melanocytes possess several functions besides a role in pigment synthesis, but detailed characteristics of the cells are still unclear. We used whole transcriptome sequencing (RNA-Seq) to assess differential gene expression of cultivated normal human melanocytes with respect to keratinocytes, fibroblasts and whole skin. The present results reveal cultivated melanocytes as highly proliferative cells with possible stem cell-like properties. The enhanced readiness to regenerate makes melanocytes the most vulnerable cells in the skin and explains their high risk of developing into malignant melanoma.
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Affiliation(s)
- Paula Reemann
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
- * E-mail:
| | - Ene Reimann
- Core Facility of Clinical Genomics, Department of Pathophysiology, Department of Biomedicine, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
- The Institute of Veterinary Medicine and Animal Sciences of the Estonian University of Life Sciences, Competence Centre on Reproductive Medicine and Biology, Tartu, Estonia
| | - Sten Ilmjärv
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu and Quretec Ltd (private limited company), Tartu, Estonia
| | - Orm Porosaar
- Department of Pediatric Surgery, Tallinn Children's Hospital, Tallinn, Estonia
| | - Helgi Silm
- Clinic of Dermatology, Tartu University Hospital, Department of Dermatology, University of Tartu, Tartu, Estonia
| | - Viljar Jaks
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Eero Vasar
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu and Centre of Translational Medicine, University of Tartu, Tartu, Estonia
| | - Külli Kingo
- Clinic of Dermatology, Tartu University Hospital, Department of Dermatology, University of Tartu, Tartu, Estonia
| | - Sulev Kõks
- The Institute of Veterinary Medicine and Animal Sciences of the Estonian University of Life Sciences, Competence Centre on Reproductive Medicine and Biology, Tartu, Estonia
- Department of Pathophysiology, Institute of Biomedicine and Translational Medicine, University of Tartu and Centre of Translational Medicine, University of Tartu, Tartu, Estonia
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18
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Hughes CS, Foehr S, Garfield DA, Furlong EE, Steinmetz LM, Krijgsveld J. Ultrasensitive proteome analysis using paramagnetic bead technology. Mol Syst Biol 2014; 10:757. [PMID: 25358341 PMCID: PMC4299378 DOI: 10.15252/msb.20145625] [Citation(s) in RCA: 669] [Impact Index Per Article: 66.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
In order to obtain a systems-level understanding of a complex biological system, detailed
proteome information is essential. Despite great progress in proteomics technologies, thorough
interrogation of the proteome from quantity-limited biological samples is hampered by inefficiencies
during processing. To address these challenges, here we introduce a novel protocol using
paramagnetic beads, termed Single-Pot Solid-Phase-enhanced Sample Preparation (SP3). SP3 provides a
rapid and unbiased means of proteomic sample preparation in a single tube that facilitates
ultrasensitive analysis by outperforming existing protocols in terms of efficiency, scalability,
speed, throughput, and flexibility. To illustrate these benefits, characterization of 1,000 HeLa
cells and single Drosophila embryos is used to establish that SP3 provides an
enhanced platform for profiling proteomes derived from sub-microgram amounts of material. These data
present a first view of developmental stage-specific proteome dynamics in
Drosophila at a single-embryo resolution, permitting characterization of
inter-individual expression variation. Together, the findings of this work position SP3 as a
superior protocol that facilitates exciting new directions in multiple areas of proteomics ranging
from developmental biology to clinical applications.
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Affiliation(s)
| | - Sophia Foehr
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - David A Garfield
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Eileen E Furlong
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Lars M Steinmetz
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Jeroen Krijgsveld
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
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19
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unfulfilled interacting genes display branch-specific roles in the development of mushroom body axons in Drosophila melanogaster. G3-GENES GENOMES GENETICS 2014; 4:693-706. [PMID: 24558265 PMCID: PMC4577660 DOI: 10.1534/g3.113.009829] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The mushroom body (MB) of Drosophila melanogaster is an organized collection of interneurons that is required for learning and memory. Each of the three subtypes of MB neurons, γ, α´/β´, and α/β, branch at some point during their development, providing an excellent model in which to study the genetic regulation of axon branching. Given the sequential birth order and the unique patterning of MB neurons, it is likely that specific gene cascades are required for the different guidance events that form the characteristic lobes of the MB. The nuclear receptor UNFULFILLED (UNF), a transcription factor, is required for the differentiation of all MB neurons. We have developed and used a classical genetic suppressor screen that takes advantage of the fact that ectopic expression of unf causes lethality to identify candidate genes that act downstream of UNF. We hypothesized that reducing the copy number of unf-interacting genes will suppress the unf-induced lethality. We have identified 19 candidate genes that when mutated suppress the unf-induced lethality. To test whether candidate genes impact MB development, we performed a secondary phenotypic screen in which the morphologies of the MBs in animals heterozygous for unf and a specific candidate gene were analyzed. Medial MB lobes were thin, missing, or misguided dorsally in five double heterozygote combinations (;unf/+;axin/+, unf/+;Fps85D/+, ;unf/+;Tsc1/+, ;unf/+;Rheb/+, ;unf/+;msn/+). Dorsal MB lobes were missing in ;unf/+;DopR2/+ or misprojecting beyond the termination point in ;unf/+;Sytβ double heterozygotes. These data suggest that unf and unf-interacting genes play specific roles in axon development in a branch-specific manner.
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20
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Dean KE, Fields A, Geer MJ, King EC, Lynch BT, Manohar RR, McCall JR, Palozola KC, Zhang Y, Liebl EC. An allele of sequoia dominantly enhances a trio mutant phenotype to influence Drosophila larval behavior. PLoS One 2014; 8:e84149. [PMID: 24376789 PMCID: PMC3869853 DOI: 10.1371/journal.pone.0084149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Accepted: 11/20/2013] [Indexed: 11/18/2022] Open
Abstract
The transition of Drosophila third instar larvae from feeding, photo-phobic foragers to non-feeding, photo-neutral wanderers is a classic behavioral switch that precedes pupariation. The neuronal network responsible for this behavior has recently begun to be defined. Previous genetic analyses have identified signaling components for food and light sensory inputs and neuropeptide hormonal outputs as being critical for the forager to wanderer transition. Trio is a Rho-Guanine Nucleotide Exchange Factor integrated into a variety of signaling networks including those governing axon pathfinding in early development. Sequoia is a pan-neuronally expressed zinc-finger transcription factor that governs dendrite and axon outgrowth. Using pre-pupal lethality as an endpoint, we have screened for dominant second-site enhancers of a weakly lethal trio mutant background. In these screens, an allele of sequoia has been identified. While these mutants have no obvious disruption of embryonic central nervous system architecture and survive to third instar larvae similar to controls, they retain forager behavior and thus fail to pupariate at high frequency.
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Affiliation(s)
- Kathryn E. Dean
- Department of Biology, Denison University, Talbot Hall of Biological Science, Granville, Ohio, United States of America
| | - April Fields
- Department of Biology, Denison University, Talbot Hall of Biological Science, Granville, Ohio, United States of America
| | - Marcus J. Geer
- Department of Biology, Denison University, Talbot Hall of Biological Science, Granville, Ohio, United States of America
| | - Eric C. King
- Department of Biology, Denison University, Talbot Hall of Biological Science, Granville, Ohio, United States of America
| | - Brian T. Lynch
- Department of Biology, Denison University, Talbot Hall of Biological Science, Granville, Ohio, United States of America
| | - Rohan R. Manohar
- Department of Biology, Denison University, Talbot Hall of Biological Science, Granville, Ohio, United States of America
| | - Julianne R. McCall
- Department of Biology, Denison University, Talbot Hall of Biological Science, Granville, Ohio, United States of America
| | - Katherine C. Palozola
- Department of Biology, Denison University, Talbot Hall of Biological Science, Granville, Ohio, United States of America
| | - Yan Zhang
- Department of Biology, Denison University, Talbot Hall of Biological Science, Granville, Ohio, United States of America
| | - Eric C. Liebl
- Department of Biology, Denison University, Talbot Hall of Biological Science, Granville, Ohio, United States of America
- * E-mail:
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21
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Moda LM, Vieira J, Guimarães Freire AC, Bonatti V, Bomtorin AD, Barchuk AR, Simões ZLP. Nutritionally driven differential gene expression leads to heterochronic brain development in honeybee castes. PLoS One 2013; 8:e64815. [PMID: 23738002 PMCID: PMC3667793 DOI: 10.1371/journal.pone.0064815] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 04/16/2013] [Indexed: 11/19/2022] Open
Abstract
The differential feeding regimes experienced by the queen and worker larvae of the honeybee Apis mellifera shape a complex endocrine response cascade that ultimately gives rise to differences in brain morphologies. Brain development analyzed at the morphological level from the third (L3) through fifth (L5) larval instars revealed an asynchrony between queens and workers. In the feeding phase of the last larval instar (L5F), two well-formed structures, pedunculi and calyces, are identifiable in the mushroom bodies of queens, both of which are not present in workers until a later phase (spinning phase, L5S). Genome-wide expression analyses and normalized transcript expression experiments monitoring specific genes revealed that this differential brain development starts earlier, during L3. Analyzing brains from L3 through L5S1 larvae, we identified 21 genes with caste-specific transcription patterns (e.g., APC-4, GlcAT-P, fax, kr-h1 and shot), which encode proteins that are potentially involved in the development of brain tissues through controlling the cell proliferation rate (APC4, kr-h1) and fasciculation (GlcAT-P, fax, and shot). Shot, whose expression is known to be required for axon extension and cell proliferation, was found to be transcribed at significantly higher levels in L4 queens compared with worker larvae. Moreover, the protein encoded by this gene was immunolocalized to the cytoplasm of cells near the antennal lobe neuropiles and proximal to the Kenyon cells in the brains of L4 queens. In conclusion, during the larval period, the brains of queens are larger and develop more rapidly than workers’ brains, which represents a developmental heterochrony reflecting the effect of the differential feeding regime of the two castes on nervous system development. Furthermore, this differential development is characterized by caste-specific transcriptional profiles of a set of genes, thus pointing to a link between differential nutrition and differential neurogenesis via genes that control cell proliferation and fasciculation.
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Affiliation(s)
- Lívia Maria Moda
- Departamento de Genética, Universidade de São Paulo-FMRP, Ribeirão Preto, São Paulo, Brazil
- Departamento de Biologia Celular, Tecidual e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, UNIFAL-MG, Alfenas, Minas Gerais, Brazil
| | - Joseana Vieira
- Departamento de Biologia Celular, Tecidual e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, UNIFAL-MG, Alfenas, Minas Gerais, Brazil
| | - Anna Cláudia Guimarães Freire
- Departamento de Biologia Celular, Tecidual e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, UNIFAL-MG, Alfenas, Minas Gerais, Brazil
| | - Vanessa Bonatti
- Departamento de Genética, Universidade de São Paulo-FMRP, Ribeirão Preto, São Paulo, Brazil
- Departamento de Biologia Celular, Tecidual e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, UNIFAL-MG, Alfenas, Minas Gerais, Brazil
| | - Ana Durvalina Bomtorin
- Departamento de Genética, Universidade de São Paulo-FMRP, Ribeirão Preto, São Paulo, Brazil
| | - Angel Roberto Barchuk
- Departamento de Biologia Celular, Tecidual e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, UNIFAL-MG, Alfenas, Minas Gerais, Brazil
- * E-mail:
| | - Zilá Luz Paulino Simões
- Departamento de Biologia, Universidade de São Paulo-FFCLRP, Ribeirão Preto, São Paulo, Brazil
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Chen C, Samuel TK, Krause M, Dailey HA, Hamza I. Heme utilization in the Caenorhabditis elegans hypodermal cells is facilitated by heme-responsive gene-2. J Biol Chem 2012; 287:9601-12. [PMID: 22303006 DOI: 10.1074/jbc.m111.307694] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The roundworm Caenorhabditis elegans is a heme auxotroph that requires the coordinated actions of HRG-1 heme permeases to transport environmental heme into the intestine and HRG-3, a secreted protein, to deliver intestinal heme to other tissues including the embryo. Here we show that heme homeostasis in the extraintestinal hypodermal tissue was facilitated by the transmembrane protein HRG-2. Systemic heme deficiency up-regulated hrg-2 mRNA expression over 200-fold in the main body hypodermal syncytium, hyp 7. HRG-2 is a type I membrane protein that binds heme and localizes to the endoplasmic reticulum and apical plasma membrane. Cytochrome heme profiles are aberrant in HRG-2-deficient worms, a phenotype that was partially suppressed by heme supplementation. A heme-deficient yeast strain, ectopically expressing worm HRG-2, revealed significantly improved growth at submicromolar concentrations of exogenous heme. Taken together, our results implicate HRG-2 as a facilitator of heme utilization in the Caenorhabditis elegans hypodermis and provide a mechanism for the regulation of heme homeostasis in an extraintestinal tissue.
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Affiliation(s)
- Caiyong Chen
- Department of Animal & Avian Sciences, University of Maryland, College Park, Maryland 20742, USA
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23
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Schlatterer SD, Acker CM, Davies P. c-Abl in neurodegenerative disease. J Mol Neurosci 2011; 45:445-52. [PMID: 21728062 DOI: 10.1007/s12031-011-9588-1] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Accepted: 06/21/2011] [Indexed: 12/30/2022]
Abstract
The c-Abl tyrosine kinase participates in a variety of cellular functions, including regulation of the actin cytoskeleton, regulation of the cell cycle, and the apoptotic/cell cycle arrest response to stress, and the Abl family of kinases has been shown to play a crucial role in development of the central nervous system. Recent studies have shown c-Abl activation in human Alzheimer's and Parkinson's diseases and c-Abl activation in mouse models and neuronal culture in response to amyloid beta fibrils and oxidative stress. Overexpression of active c-Abl in adult mouse neurons results in neurodegeneration and neuroinflammation. Based on this evidence, a potential role for c-Abl in the pathogenesis of neurodegenerative disease is discussed, and we attempt to place activation of c-Abl in context with other known contributors to neurodegenerative pathology.
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Affiliation(s)
- Sarah D Schlatterer
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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24
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Song JK, Giniger E. Noncanonical Notch function in motor axon guidance is mediated by Rac GTPase and the GEF1 domain of Trio. Dev Dyn 2011; 240:324-32. [PMID: 21246649 DOI: 10.1002/dvdy.22525] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The receptor Notch interacts with the Abl tyrosine kinase signaling pathway to control axon growth and guidance in Drosophila motor neurons. In part, this is mediated by binding to Trio, a guanine nucleotide exchange factor (GEF) for Rho GTPases. We show here that one of the two GEF domains of Trio, the Rac-specific GEF1, is essential for Trio-dependent motor axon guidance and for the genetic suppression of Notch function in motor axon patterning, but the Rho-specific GEF2 domain is not. Consistent with this, we show that Rac, and not Rho1 or Cdc42, interacts genetically with Notch in a manner indistinguishable from that of bona fide Abl signaling components. We infer, therefore, that Rac is a key component of Abl signaling in Drosophila motor axons, and specifically that it is the crucial Rho GTPase in "noncanonical" Notch/Abl signaling.
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Affiliation(s)
- Jeong K Song
- Axon Guidance and Neural Connectivity Unit, Basic Neuroscience Program, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
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25
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Song JK, Kannan R, Merdes G, Singh J, Mlodzik M, Giniger E. Disabled is a bona fide component of the Abl signaling network. Development 2010; 137:3719-27. [PMID: 20940230 DOI: 10.1242/dev.050948] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abl is an essential regulator of cell migration and morphogenesis in both vertebrates and invertebrates. It has long been speculated that the adaptor protein Disabled (Dab), which is a key regulator of neuronal migration in the vertebrate brain, might be a component of this signaling pathway, but this idea has been controversial. We now demonstrate that null mutations of Drosophila Dab result in phenotypes that mimic Abl mutant phenotypes, both in axon guidance and epithelial morphogenesis. The Dab mutant interacts genetically with mutations in Abl, and with mutations in the Abl accessory factors trio and enabled (ena). Genetic epistasis tests show that Dab functions upstream of Abl and ena, and, consistent with this, we show that Dab is required for the subcellular localization of these two proteins. We therefore infer that Dab is a bona fide component of the core Abl signaling pathway in Drosophila.
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Affiliation(s)
- Jeong K Song
- Axon Guidance and Neural Connectivity Unit, Basic Neuroscience Program, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
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26
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Franco M, Seyfried NT, Brand AH, Peng J, Mayor U. A novel strategy to isolate ubiquitin conjugates reveals wide role for ubiquitination during neural development. Mol Cell Proteomics 2010; 10:M110.002188. [PMID: 20861518 PMCID: PMC3098581 DOI: 10.1074/mcp.m110.002188] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Ubiquitination has essential roles in neuronal development and function. Ubiquitin proteomics studies on yeast and HeLa cells have proven very informative, but there still is a gap regarding neuronal tissue-specific ubiquitination. In an organism context, direct evidence for the ubiquitination of neuronal proteins is even scarcer. Here, we report a novel proteomics strategy based on the in vivo biotinylation of ubiquitin to isolate ubiquitin conjugates from the neurons of Drosophila melanogaster embryos. We confidently identified 48 neuronal ubiquitin substrates, none of which was yet known to be ubiquitinated. Earlier proteomics and biochemical studies in non-neuronal cell types had identified orthologs to some of those but not to others. The identification here of novel ubiquitin substrates, those with no known ubiquitinated ortholog, suggests that proteomics studies must be performed on neuronal cells to identify ubiquitination pathways not shared by other cell types. Importantly, several of those newly found neuronal ubiquitin substrates are key players in synaptogenesis. Mass spectrometry results were validated by Western blotting to confirm that those proteins are indeed ubiquitinated in the Drosophila embryonic nervous system and to elucidate whether they are mono- or polyubiquitinated. In addition to the ubiquitin substrates, we also identified the ubiquitin carriers that are active during synaptogenesis. Identifying endogenously ubiquitinated proteins in specific cell types, at specific developmental stages, and within the context of a living organism will allow understanding how the tissue-specific function of those proteins is regulated by the ubiquitin system.
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Affiliation(s)
- Maribel Franco
- CIC Biogune, Bizkaia Teknologi Parkea, 48160 Derio, Spain
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27
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Rinehart JP, Robich RM, Denlinger DL. Isolation of diapause-regulated genes from the flesh fly, Sarcophaga crassipalpis by suppressive subtractive hybridization. JOURNAL OF INSECT PHYSIOLOGY 2010; 56:603-609. [PMID: 20026067 DOI: 10.1016/j.jinsphys.2009.12.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Revised: 11/30/2009] [Accepted: 12/09/2009] [Indexed: 05/28/2023]
Abstract
Subtractive suppressive hybridization (SSH) was used to characterize the diapause transcriptome of the flesh fly Sarcophaga crassipalpis. Through these efforts, we isolated 97 unique clones which were used as probes in northern hybridization to assess their expression during diapause. Of these, 17 were confirmed to be diapause upregulated and 1 was diapause downregulated, while 12 were shown to be unaffected by diapause in this species. The diapause upregulated genes fall into several broad categories including heat shock proteins, heavy metal responsive genes, neuropeptides, structural genes, regulatory elements, and several genes of unknown function. In combination with other large-scale analyses of gene expression during diapause, this study assists in the characterization of the S. crassipalpis diapause transcriptome, and begins to identify common elements involved in diapause across diverse taxa.
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Affiliation(s)
- Joseph P Rinehart
- Ohio State University, Department of Entomology, 318 W. 12th Ave., Columbus, OH, USA.
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28
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Organization of F-actin via concerted regulation of Kette by PTP61F and dAbl. Mol Cell Biol 2009; 29:3623-32. [PMID: 19398577 DOI: 10.1128/mcb.00229-09] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We identify Kette, a key regulator of actin polymerization, as a substrate for Drosophila protein tyrosine phosphatase PTP61F, as well as for dAbl tyrosine kinase. We further show that dAbl is a direct substrate for PTP61F. Therefore, Kette phosphotyrosine levels are regulated both directly and indirectly by PTP61F. Kette and PTP61F genetically interact in the regulation of F-actin organization in pupal eye discs, suggesting that tyrosine phosphorylation is essential for the proper regulation of Kette-mediated actin dynamics. This hypothesis was confirmed by demonstrating the loss of Kette-mediated F-actin organization and lamella formation in S2 cells in a Kette Y482F mutant in which the dAbl phosphorylation site was eliminated. Our results establish for the first time that PTP61F and dAbl ensure proper actin organization through the coordinated and reversible tyrosine phosphorylation of Kette.
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29
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Le Gall M, De Mattei C, Giniger E. Molecular separation of two signaling pathways for the receptor, Notch. Dev Biol 2007; 313:556-67. [PMID: 18062953 DOI: 10.1016/j.ydbio.2007.10.030] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2007] [Revised: 10/18/2007] [Accepted: 10/23/2007] [Indexed: 10/22/2022]
Abstract
Notch is required for many aspects of cell fate specification and morphogenesis during development, including neurogenesis and axon guidance. We here provide genetic and biochemical evidence that Notch directs axon growth and guidance in Drosophila via a "non-canonical", i.e. non-Su(H)-mediated, signaling pathway, characterized by association with the adaptor protein, Disabled, and Trio, an accessory factor of the Abl tyrosine kinase. We find that forms of Notch lacking the binding sites for its canonical effector, Su(H), are nearly inactive for the cell fate function of the receptor, but largely or fully active in axon patterning. Conversely, deletion from Notch of the binding site for Disabled impairs its action in axon patterning without disturbing cell fate control. Finally, we show by co-immunoprecipitation that Notch protein is physically associated in vivo with both Disabled and Trio. Together, these data provide evidence for an alternate Notch signaling pathway that mediates a postmitotic, morphogenetic function of the receptor.
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Affiliation(s)
- Maude Le Gall
- Axon Guidance and Neural Connectivity Unit, Basic Neuroscience Program, National Institute of Neurological Disorders and Stroke (NINDS), National Institutes of Health, Bldg. 37, Rm. 1016, 37 Convent Drive, Bethesda, MD 20892, USA
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30
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Stepanyan R, Day K, Urban J, Hardin DL, Shetty RS, Derby CD, Ache BW, McClintock TS. Gene expression and specificity in the mature zone of the lobster olfactory organ. Physiol Genomics 2006; 25:224-33. [PMID: 16614458 DOI: 10.1152/physiolgenomics.00276.2005] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The lobster olfactory organ is an important model for investigating many aspects of the olfactory system. To facilitate study of the molecular basis of olfaction in lobsters, we made a subtracted cDNA library from the mature zone of the olfactory organ of Homarus americanus, the American lobster. Sequencing of the 5′-end of 5,184 cDNA clones produced 2,389 distinct high-quality sequences consisting of 1,944 singlets and 445 contigs. Matches to known sequences corresponded with the types of cells present in the olfactory organ, including specific markers of olfactory sensory neurons, auxiliary cells, secretory cells of the aesthetasc tegumental gland, and epithelial cells. The wealth of neuronal mRNAs represented among the sequences reflected the preponderance of neurons in the tissue. The sequences identified candidate genes responsible for known functions and suggested new functions not previously recognized in the olfactory organ. A cDNA microarray was designed and tested by assessing mRNA abundance differences between two of the lobster's major chemosensory structures: the mature zone of the olfactory organ and the dactyl of the walking legs, a taste organ. The 115 differences detected again emphasized the abundance of neurons in the olfactory organ, especially a cluster of mRNAs encoding cytoskeletal-associated proteins and cell adhesion molecules such as 14-3-3ζ, actins, tubulins, trophinin, Fax, Yel077cp, suppressor of profilin 2, and gelsolin.
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Affiliation(s)
- Ruben Stepanyan
- Department of Physiology, Cellular and Molecular Neuroscience of Sensory Systems Training Program, University of Kentucky, Lexington, Kentucky 40536-0298, USA
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31
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Dong J, Song MO, Freedman JH. Identification and characterization of a family of Caenorhabditis elegans genes that is homologous to the cadmium-responsive gene cdr-1. ACTA ACUST UNITED AC 2005; 1727:16-26. [PMID: 15652154 DOI: 10.1016/j.bbaexp.2004.11.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2004] [Revised: 11/03/2004] [Accepted: 11/09/2004] [Indexed: 11/16/2022]
Abstract
Six Caenorhabditis elegans genes that are homologous to the novel, cadmium-responsive gene cdr-1 have been identified and characterized. Nucleotide and amino acid sequence comparisons among the CDR family, which includes cdr-1, cdr-2, cdr-3, cdr-4, cdr-5, cdr-6, and cdr-7, reveals a high degree of identity among the seven members in this family. There are high levels of amino acid and nucleotide sequence similarity in the lengths of the open reading frames, predicted sizes, and protein characteristics. The seven proteins are predicted to be extremely hydrophobic, and are classified as integral membrane proteins. Structural analysis of the predicted proteins suggests that they may have similar biological functions. In response to cadmium exposure, cdr-1, cdr-2, cdr-3, and cdr-4 transcription significantly increases. In contrast, the levels of cdr-5, cdr-6, and cdr-7 transcription are not significantly affected or inhibited by cadmium exposure. Further, in non-exposed C. elegans, cdr-2, cdr-4, cdr-6, and cdr-7 are constitutively expressed. When CDR-1 expression was inhibited using RNAi, numerous fluid droplets were observed throughout the nematode body cavity. This phenotype became more pronounced in the presence of hypotonic stress. This suggests that CDR-1 may function in osmoregulation to maintain salt balance in C. elegans.
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Affiliation(s)
- Jie Dong
- Nicholas School of the Environment and Earth Sciences, Duke University, Durham, NC 27708, USA
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32
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Liebl EC, Rowe RG, Forsthoefel DJ, Stammler AL, Schmidt ER, Turski M, Seeger MA. Interactions between the secreted protein Amalgam, its transmembrane receptor Neurotactin and the Abelson tyrosine kinase affect axon pathfinding. Development 2003; 130:3217-26. [PMID: 12783792 DOI: 10.1242/dev.00545] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Two novel dosage-sensitive modifiers of the Abelson tyrosine kinase (Abl) mutant phenotype have been identified. Amalgam (Ama) is a secreted protein that interacts with the transmembrane protein Neurotactin (Nrt) to promote cell:cell adhesion. We have identified an unusual missense ama allele, ama(M109), which dominantly enhances the Abl mutant phenotype, affecting axon pathfinding. Heterozygous null alleles of ama do not show this dominant enhancement, but animals homozygous mutant for both ama and Abl show abnormal axon outgrowth. Cell culture experiments demonstrate the Ama(M109) mutant protein binds to Nrt, but is defective in mediating Ama/Nrt cell adhesion. Heterozygous null alleles of nrt dominantly enhance the Abl mutant phenotype, also affecting axon pathfinding. Furthermore, we have found that all five mutations originally attributed to disabled are in fact alleles of nrt. These results suggest Ama/Nrt-mediated adhesion may be part of signaling networks involving the Abl tyrosine kinase in the growth cone.
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Affiliation(s)
- Eric C Liebl
- Department of Biology, Denison University, Granville, OH 43023, USA.
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33
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Crowner D, Le Gall M, Gates MA, Giniger E. Notch steers Drosophila ISNb motor axons by regulating the Abl signaling pathway. Curr Biol 2003; 13:967-72. [PMID: 12781136 DOI: 10.1016/s0960-9822(03)00325-7] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The central problem in axon guidance is to understand how guidance signals interact to determine where an axon will grow. Here we investigate a specific axon guidance decision in Drosophila embryos, the sharp inward turn taken by the ISNb motor nerve to approach its muscle targets. We find that this turn requires Notch and its ligand Delta. We show that Delta is expressed on cells adjacent to the ISNb turning point, and we know from previous work that Notch is present on axonal growth cones, suggesting that Delta and Notch might provide a guidance signal to ISNb. To induce the turning of ISNb axons, Notch interacts genetically with multiple components of a signal transduction pathway that includes the Abl tyrosine kinase and its affiliated accessory proteins. In contrast, genetic interaction experiments fail to provide evidence for a major role of the "canonical" Notch/Su(H) signaling pathway in this process. We suggest that the Notch/Abl interaction promotes the turning of ISNb axons by attenuating the Abl-dependent adhesion of ISNb axons to their substratum, thus releasing the axons to respond to attraction from target muscles.
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Affiliation(s)
- Daniel Crowner
- Division of Basic Sciences and Program in Developmental Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue, North, Seattle, WA 98109, USA
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34
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Liao VHC, Dong J, Freedman JH. Molecular characterization of a novel, cadmium-inducible gene from the nematode Caenorhabditis elegans. A new gene that contributes to the resistance to cadmium toxicity. J Biol Chem 2002; 277:42049-59. [PMID: 12189149 DOI: 10.1074/jbc.m206740200] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cadmium is an environmental contaminant that is both a human toxicant and carcinogen. To inhibit cadmium-induced damage, cells respond by increasing the expression of genes that encode stress-response proteins. We previously reported the identification of 48 cadmium-inducible mRNAs in the nematode Caenorhabditis elegans. Here we describe a new cadmium-responsive gene, designated cdr-1, whose rate and level of inducible expression parallel those of the C. elegans metallothioneins. The CDR-1 mRNA contains an open reading frame of 831 bp and encodes a predicted 32-kDa, integral membrane protein. Following cadmium exposure, cdr-1 is transcribed exclusively in intestinal cells of post-embryonic C. elegans. In vivo, the CDR-1 protein is targeted specifically to the intestinal cell lysosomes. cdr-1 transcription is significantly induced by cadmium but not by other tested stressors. These results indicate that cdr-1 expression is regulated by cadmium and in a cell-specific fashion. Inhibition of CDR-1 expression renders C. elegans susceptible to cadmium toxicity. In conclusion, cdr-1 defines a new class of cadmium-inducible genes and encodes an integral membrane, lysosomal protein. This protein functions to protect against cadmium toxicity.
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Affiliation(s)
- Vivian Hsiu-Chuan Liao
- Nicholas School of the Environment and Earth Sciences, Duke University, Durham, North Carolina 27708, USA
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35
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Woodring PJ, Litwack ED, O'Leary DDM, Lucero GR, Wang JYJ, Hunter T. Modulation of the F-actin cytoskeleton by c-Abl tyrosine kinase in cell spreading and neurite extension. J Cell Biol 2002; 156:879-92. [PMID: 11864995 PMCID: PMC2173320 DOI: 10.1083/jcb.200110014] [Citation(s) in RCA: 133] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The nonreceptor tyrosine kinase encoded by the c-Abl gene has the unique feature of an F-actin binding domain (FABD). Purified c-Abl tyrosine kinase is inhibited by F-actin, and this inhibition can be relieved through mutation of its FABD. The c-Abl kinase is activated by physiological signals that also regulate the actin cytoskeleton. We show here that c-Abl stimulated the formation of actin microspikes in fibroblasts spreading on fibronectin. This function of c-Abl is dependent on kinase activity and is not shared by c-Src tyrosine kinase. The Abl-dependent F-actin microspikes occurred under conditions where the Rho-family GTPases were inhibited. The FABD-mutated c-Abl, which is active in detached fibroblasts, stimulated F-actin microspikes independent of cell attachment. Moreover, FABD-mutated c-Abl stimulated the formation of F-actin branches in neurites of rat embryonic cortical neurons. The reciprocal regulation between F-actin and the c-Abl tyrosine kinase may provide a self-limiting mechanism in the control of actin cytoskeleton dynamics.
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36
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Yu HH, Zisch AH, Dodelet VC, Pasquale EB. Multiple signaling interactions of Abl and Arg kinases with the EphB2 receptor. Oncogene 2001; 20:3995-4006. [PMID: 11494128 DOI: 10.1038/sj.onc.1204524] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2000] [Revised: 04/02/2001] [Accepted: 04/09/2001] [Indexed: 11/08/2022]
Abstract
The Eph family of receptor tyrosine kinases and the Abl family of non-receptor tyrosine kinases have both been implicated in tissue morphogenesis. They regulate the organization of the actin cytoskeleton in the developing nervous system and participate in signaling pathways involved in axon growth. Both Eph receptors and Abl are localized in the neuronal growth cone, suggesting that they play a role in axon pathfinding. Two-hybrid screens identified regions of Abl and Arg that bind to the EphB2 and EphA4 receptors, suggesting a novel signaling connection involving the two kinase families. The association of full-length Abl and Arg with EphB2 was confirmed by co-immunoprecipitation and found to involve several distinct protein interactions. The SH2 domains of Abl and Arg bind to tyrosine-phosphorylated motifs in the juxtamembrane region of EphB2. A second, phosphorylation-independent interaction with EphB2 involves non-conserved sequences in the C-terminal tails of Abl and Arg. A third interaction between Abl and EphB2 is probably mediated by an intermediary protein because it requires tyrosine phosphorylation of EphB2, but not the binding sites for the Abl SH2 domain. The connection between EphB2 and Abl/Arg appears to be reciprocal. Activated EphB2 causes tyrosine phosphorylation of Abl and Arg, and vice versa. Interestingly, treatment of COS cells and B35 neuronal-like cells with ephrin-B1 to activate endogenous EphB2 decreased the kinase activity of endogenous Abl. These data are consistent with the opposite effects that Eph receptors and Abl have on neurite ougrowth and suggest that Eph receptors and Abl family kinases have shared signaling activities.
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Affiliation(s)
- H H Yu
- The Burnham Institute, 10901 N. Torrey Pines Road, La Jolla, California, CA 92037, USA
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Yook KJ, Proulx SR, Jorgensen EM. Rules of nonallelic noncomplementation at the synapse in Caenorhabditis elegans. Genetics 2001; 158:209-20. [PMID: 11333231 PMCID: PMC1461624 DOI: 10.1093/genetics/158.1.209] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Nonallelic noncomplementation occurs when recessive mutations in two different loci fail to complement one another, in other words, the double heterozygote exhibits a phenotype. We observed that mutations in the genes encoding the physically interacting synaptic proteins UNC-13 and syntaxin/UNC-64 failed to complement one another in the nematode Caenorhabditis elegans. Noncomplementation was not observed between null alleles of these genes and thus this genetic interaction does not occur with a simple decrease in dosage at the two loci. However, noncomplementation was observed if at least one gene encoded a partially functional gene product. Thus, this genetic interaction requires a poisonous gene product to sensitize the genetic background. Nonallelic noncomplementation was not limited to interacting proteins: Although the strongest effects were observed between loci encoding gene products that bind to one another, interactions were also observed between proteins that do not directly interact but are members of the same complex. We also observed noncomplementation between genes that function at distant points in the same pathway, implying that physical interactions are not required for nonallelic noncomplementation. Finally, we observed that mutations in genes that function in different processes such as neurotransmitter synthesis or synaptic development complement one another. Thus, this genetic interaction is specific for genes acting in the same pathway, that is, for genes acting in synaptic vesicle trafficking.
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Affiliation(s)
- K J Yook
- Department of Biology, University of Utah, 257 S. 1400 East, Salt Lake City, UT 84112-0840, USA
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38
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Glover RT, Angiolieri M, Kelly S, Monaghan DT, Wang JY, Smithgall TE, Buller AL. Interaction of the N-methyl-D-aspartic acid receptor NR2D subunit with the c-Abl tyrosine kinase. J Biol Chem 2000; 275:12725-9. [PMID: 10777567 DOI: 10.1074/jbc.275.17.12725] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The COOH-terminal domain of the NR2D subunit of the NMDA receptor contains proline-rich regions that show striking homology to sequences known to bind to Src homology 3 (SH3) domains. To determine whether the proline-rich region of the NR2D subunit interacts with specific SH3 domains, in vitro SH3 domain binding assays were performed. A proline-rich fragment of the NR2D subunit (2D(866-1064)) bound to the Abl SH3 domain but not to the SH3 domains from Src, Fyn, Grb2, GAP, or phospholipase C-gamma (PLCgamma). Co-immunoprecipitation of NR2D with Abl suggests stable association of NR2D and Abl in transfected cells. The SH3 domain plays an important role in the negative regulation of Abl kinase activity. To determine whether the interaction of NR2D with the Abl SH3 domain alters Abl kinase activity, Abl was expressed alone or with NR2D in 293T cells. Autophosphorylation of Abl was readily observed when Abl was expressed alone. However, co-expression of Abl with 2D(866-1064) or full-length NR2D inhibited autophosphorylation. 2D(866-1064) did not inhibit DeltaSH3 Abl, indicating a requirement for the Abl SH3 domain in the inhibitory effect. Similarly, 2D(866-1064) did not inhibit the catalytic activity of Abl-PP, which contains two point mutations in the SH2-kinase linker domain that release the negative kinase regulation by the SH3 domain. In contrast, the full-length NR2D subunit partially inhibited the autokinase activity of both DeltaSH3 Abl and Abl-PP, suggesting that NR2D and Abl may interact at multiple sites. Taken together, the data in this report provide the first evidence for a novel inhibitory interaction between the NR2D subunit of the NMDA receptor and the Abl tyrosine kinase.
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Affiliation(s)
- R T Glover
- Department of Pharmacology, University of Nebraska Medical Center, Omaha, Nebraska 68198, USA
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39
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Liebl EC, Forsthoefel DJ, Franco LS, Sample SH, Hess JE, Cowger JA, Chandler MP, Shupert AM, Seeger MA. Dosage-sensitive, reciprocal genetic interactions between the Abl tyrosine kinase and the putative GEF trio reveal trio's role in axon pathfinding. Neuron 2000; 26:107-18. [PMID: 10798396 DOI: 10.1016/s0896-6273(00)81142-3] [Citation(s) in RCA: 161] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The Abelson tyrosine kinase (Abl) is integrated into signal transduction networks regulating axon outgrowth. We have identified the Drosophila trio gene through a mutation that exacerbates the Abl mutant phenotype. Drosophila Trio is an ortholog of mammalian Trio, a protein that contains multiple spectrin-like repeats and two Dbl homology (DH) domains that affect actin cytoskeletal dynamics via the small GTPases Rho and Rac. Phenotypic analysis demonstrates that trio and Abl cooperate in regulating axon outgrowth in the embryonic central nervous system (CNS). Dosage-sensitive interactions between trio and Abl, failed axon connections (fax), and enabled (ena) indicate that Trio is integrated into common signaling networks with these gene products. These observations suggest a mechanism by which Abl-mediated signaling networks influence the actin cytoskeleton in neuronal growth cones.
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Affiliation(s)
- E C Liebl
- Department of Biology, Denison University, Granville, Ohio 43023, USA.
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40
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Grossman TR, Luque JM, Nelson N. Identification of a ubiquitous family of membrane proteins and their expression in mouse brain. J Exp Biol 2000; 203:447-57. [PMID: 10637174 DOI: 10.1242/jeb.203.3.447] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A family of genes encoding membrane proteins with a unique structure has been identified in DNA and cDNA clones of various eukaryotes ranging from yeast to human. The nucleotide sequences of three novel cDNAs from Drosophila melanogaster and mouse were determined. The amino acid sequences of the two mouse proteins have human homologs. The gene (TMS1) encoding the yeast member of this family was disrupted, and the resulting mutant showed no significant phenotype under several stress conditions. The expression of the mouse genes TMS-1 and TMS-2 was examined by in situ hybridization of sections from brain, liver, kidney, heart and testis of an adult mouse as well as in a 1-day-old whole mouse. While the expression of TMS-2 was found to be restricted to the central nervous system, TMS-1 was also expressed in kidney and testis. The expression of TMS-1 and TMS-2 in the brain overlapped and was localized to areas associated with glutamatergic excitatory neurons, such as the hippocampus and cerebral cortex. High-magnification analysis indicated that both mRNAs are expressed in neurons. Semiquantitative analysis of mRNA expression was performed in various parts of the brain. The conservation, unique structure and localization in the mammalian brain of this novel protein family suggest an important biological role.
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Affiliation(s)
- T R Grossman
- Department of Biochemistry, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Israel
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41
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Lanier LM, Gertler FB. From Abl to actin: Abl tyrosine kinase and associated proteins in growth cone motility. Curr Opin Neurobiol 2000; 10:80-7. [PMID: 10679439 DOI: 10.1016/s0959-4388(99)00058-6] [Citation(s) in RCA: 170] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The Abl tyrosine kinase plays an important role in axonogenesis. Recent reports indicate that this role involves interaction with several different protein families, including LAR phosphatases, catenin/cadherin cell adhesion complexes, Trio family GEFs, and Ena/VASP family actin regulatory proteins. These findings suggest that Abl and its associated proteins may regulate cell adhesion and actin polymerization, thereby regulating growth cone motility during axonogenesis.
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Affiliation(s)
- L M Lanier
- Biology Department, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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42
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Armstrong LC, Saenz AJ, Bornstein P. Metaxin 1 interacts with metaxin 2, a novel related protein associated with the mammalian mitochondrial outer membrane. J Cell Biochem 1999. [DOI: 10.1002/(sici)1097-4644(19990701)74:1<11::aid-jcb2>3.0.co;2-v] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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43
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Wills Z, Bateman J, Korey CA, Comer A, Van Vactor D. The tyrosine kinase Abl and its substrate enabled collaborate with the receptor phosphatase Dlar to control motor axon guidance. Neuron 1999; 22:301-12. [PMID: 10069336 DOI: 10.1016/s0896-6273(00)81091-0] [Citation(s) in RCA: 256] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Genetic analysis of growth cone guidance choice points in Drosophila identified neuronal receptor protein tyrosine phosphatases (RPTPs) as key determinants of axon pathfinding behavior. We now demonstrate that the Drosophila Abl tyrosine kinase functions in the intersegmental nerve b (ISNb) motor choice point pathway as an antagonist of the RPTP Dlar. The function of Abl in this pathway is dependent on an intact catalytic domain. We also show that the Abl phosphoprotein substrate Enabled (Ena) is required for choice point navigation. Both Abl and Ena proteins associate with the Dlar cytoplasmic domain and serve as substrates for Dlar in vitro, suggesting that they play a direct role in the Dlar pathway. These data suggest that Dlar, Abl, and Ena define a phosphorylation state-dependent switch that controls growth cone behavior by transmitting signals at the cell surface to the actin cytoskeleton.
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Affiliation(s)
- Z Wills
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
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44
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Wills Z, Marr L, Zinn K, Goodman CS, Van Vactor D. Profilin and the Abl tyrosine kinase are required for motor axon outgrowth in the Drosophila embryo. Neuron 1999; 22:291-9. [PMID: 10069335 DOI: 10.1016/s0896-6273(00)81090-9] [Citation(s) in RCA: 172] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The ability of neuronal growth cones to be guided by extracellular cues requires intimate communication between signal transduction systems and the dynamic actin-based cytoskeleton at the leading edge. Profilin, a small, actin-binding protein, has been proposed to be a regulator of the cell motility machinery at leading edge membranes. However, its requirement in the developing nervous system has been unknown. Profilin associates with members of the Enabled family of proteins, suggesting that Profilin might link Abl function to the cytoskeleton. Here, genetic analysis in Drosophila is used to demonstrate that mutations in Profilin (chickadee) and Abl (abl) display an identical growth cone arrest phenotype for axons of intersegmental nerve b (ISNb). Moreover, the phenotype of a double mutant suggests that these components function together to control axonal outgrowth.
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Affiliation(s)
- Z Wills
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
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45
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Fogerty FJ, Juang JL, Petersen J, Clark MJ, Hoffmann FM, Mosher DF. Dominant effects of the bcr-abl oncogene on Drosophila morphogenesis. Oncogene 1999; 18:219-32. [PMID: 9926937 DOI: 10.1038/sj.onc.1202239] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We targeted expression of human/fly chimeric Bcr-Abl proteins to the developing central nervous system (CNS) and eye imaginal disc of Drosophila melanogaster. Neural expression of human/fly chimeric P210 Bcr-Abl or P185 Bcr-Abl rescued abl mutant flies from pupal lethality, indicating that P210 and P185 Bcr-Abl can substitute functionally for Drosophila Abl during axonogenesis. However, increased levels of neurally expressed P210 or P185 Bcr-Abl but not Drosophila Abl produced CNS defects and lethality. Expression of P210 or P185 in the eye imaginal disc produced a dominant rough eye phenotype that was dependent on dosage of the transgene. Drosophila Enabled, previously identified as a suppressor of the abl mutant phenotype and substrate for Drosophila Abl kinase, had markedly increased phosphotyrosine levels in Bcr-Abl expressing Drosophila, indicating that it is a substrate for Bcr-Abl as well. Drosophila, therefore, is a suitable model system to identify Bcr-Abl interactions important for signal transduction and oncogenesis.
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Affiliation(s)
- F J Fogerty
- Department of Medicine, University of Wisconsin Comprehensive Cancer Center, Madison 53706, USA
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46
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Ahern-Djamali SM, Comer AR, Bachmann C, Kastenmeier AS, Reddy SK, Beckerle MC, Walter U, Hoffmann FM. Mutations in Drosophila enabled and rescue by human vasodilator-stimulated phosphoprotein (VASP) indicate important functional roles for Ena/VASP homology domain 1 (EVH1) and EVH2 domains. Mol Biol Cell 1998; 9:2157-71. [PMID: 9693373 PMCID: PMC25470 DOI: 10.1091/mbc.9.8.2157] [Citation(s) in RCA: 100] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/1998] [Accepted: 06/05/1998] [Indexed: 12/19/2022] Open
Abstract
Drosophila Enabled (Ena) was initially identified as a dominant genetic suppressor of mutations in the Abelson tyrosine kinase and, more recently, as a member of the Ena/human vasodilator-stimulated phosphoprotein (VASP) family of proteins. We have used genetic, biochemical, and cell biological approaches to demonstrate the functional relationship between Ena and human VASP. In addition, we have defined the roles of Ena domains identified as essential for its activity in vivo. We have demonstrated that VASP rescues the embryonic lethality associated with loss of Ena function in Drosophila and have shown that Ena, like VASP, is associated with actin filaments and focal adhesions when expressed in cultured cells. To define sequences that are central to Ena function, we have characterized the molecular lesions present in two lethal ena mutant alleles that affected the Ena/VASP homology domain 1 (EVH1) and EVH2. A missense mutation that resulted in an amino acid substitution in the EVH1 domain eliminated in vitro binding of Ena to the cytoskeletal protein zyxin, a previously reported binding partner of VASP. A nonsense mutation that resulted in a C-terminally truncated Ena protein lacking the EVH2 domain failed to form multimeric complexes and exhibited reduced binding to zyxin and the Abelson Src homology 3 domain. Our analysis demonstrates that Ena and VASP are functionally homologous and defines the conserved EVH1 and EVH2 domains as central to the physiological activity of Ena.
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Affiliation(s)
- S M Ahern-Djamali
- McArdle Laboratory for Cancer Research and Laboratory of Genetics University of Wisconsin Medical School, Madison, Wisconsin 53706, USA
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Ogura K, Shirakawa M, Barnes TM, Hekimi S, Ohshima Y. The UNC-14 protein required for axonal elongation and guidance in Caenorhabditis elegans interacts with the serine/threonine kinase UNC-51. Genes Dev 1997; 11:1801-11. [PMID: 9242488 DOI: 10.1101/gad.11.14.1801] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Certain unc mutants in the nematode Caenorhabditis elegans, such as unc-14 and unc-51, show abnormal axonal elongation and axonal structures. We cloned the unc-51 gene previously and predicted that it encodes a novel serine/threonine protein kinase. In this study, we precisely localized the activity to rescue an unc-14 mutation. Also, we identified four cDNA clones encoded by the unc-14 rescuing region, in screens for proteins that bind to UNC-51 using a yeast two-hybrid system. A mutation site in the cDNA was identified for each of the six unc-14 mutants, establishing that the unc-14 gene was cloned. The unc-14 gene encodes a novel protein of 665 amino acids, and is coexpressed with the unc-51 gene in the cell bodies and axons of almost all neurons including DD/VD and hermaphrodite-specific neurons. Another clone recovered in the two-hybrid screen encodes a carboxy-terminal region of UNC-51. Analysis using the yeast two-hybrid system suggested that a central region of UNC-14 bound to a carboxy-terminal region of UNC-51, and that the UNC-51 carboxy-terminal region oligomerized. In in vitro binding studies using recombinant fusion proteins, UNC-14 interacted with UNC-51 directly. We propose that UNC-51 protein kinase acts as an oligomer, and that UNC-14 is a regulator of UNC-51, in axonal elongation and guidance.
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Affiliation(s)
- K Ogura
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka, Japan
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48
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Becker KG, Mattson DH, Powers JM, Gado AM, Biddison WE. Analysis of a sequenced cDNA library from multiple sclerosis lesions. J Neuroimmunol 1997; 77:27-38. [PMID: 9209265 DOI: 10.1016/s0165-5728(97)00045-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
To identify genes that are expressed in MS pathogenesis, we have analyzed a normalized cDNA library made from mRNA obtained from CNS lesions of a patient with primary progressive MS. Complementary DNA clones obtained from this library were subjected to automated DNA sequencing to generate expressed sequence tags. Analysis of this MS cDNA library revealed the presence of 54 cDNAs that were associated with immune activation and indicated the presence of an ongoing inflammatory response with evidence of both cell-mediated and humoral immune responses. The surprising finding was that 16 of the cDNAs encoded autoantigens associated with seven other autoimmune disorders, while only three of these 16 autoantigen cDNAs were present in a similarly constructed adult brain library. Such aberrant autoantigen expression could provide a source of secondary autoimmune stimulation that could contribute to the ongoing inflammatory response in MS. In addition, two cDNAs were found that mapped to a known MS susceptibility locus (5p14-p12): one encoded an excitatory amino acid transporter and the other a human homologue of the Drosophila disabled gene. This approach to the molecular biology of MS pathogenesis may help to illuminate previously unappreciated aspects of this disease.
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Affiliation(s)
- K G Becker
- Molecular Immunology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda MD, USA
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Armstrong LC, Komiya T, Bergman BE, Mihara K, Bornstein P. Metaxin is a component of a preprotein import complex in the outer membrane of the mammalian mitochondrion. J Biol Chem 1997; 272:6510-8. [PMID: 9045676 DOI: 10.1074/jbc.272.10.6510] [Citation(s) in RCA: 110] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Metaxin, a novel gene located between the glucocerebrosidase and thrombospondin 3 genes in the mouse, is essential for survival of the postimplantation mouse embryo. In this study, the subcellular location, domain structure, and biochemical function of metaxin were investigated. Anti-recombinant metaxin antibodies recognized 35- and 70-kDa proteins in mitochondria from various tissues; the 35-kDa protein is consistent in size with the predicted translation product of metaxin cDNA. When metaxin cDNA was transfected into COS cells, immunofluorescence staining demonstrated that the protein is located in mitochondria. Metaxin contains a putative mitochondrial outer membrane signal anchor domain at its C terminus, and a truncated form of metaxin lacking this signal anchor domain had a reduced association with mitochondria. In addition, metaxin was highly susceptible to proteases in intact mitochondria. We therefore conclude that metaxin is a mitochondrial protein that extends into the cytosol while anchored into the outer membrane at its C terminus. In its N-terminal region, metaxin shows significant sequence identity to Tom37, a component of the outer membrane portion of the mitochondrial preprotein translocation apparatus in Saccharomyces cerevisiae, but important structural differences, including apparently different mechanisms of targeting to membranes, also exist between the two proteins. Given the similar subcellular locations of metaxin and Tom37, the possible role of metaxin in mitochondrial preprotein import was investigated. Antibodies against metaxin, when preincubated with mitochondria, partially inhibited the uptake of radiolabeled preadrenodoxin into mitochondria. Metaxin is therefore the second mammalian component of the protein translocation apparatus of the mitochondrial outer membrane to be characterized at the molecular level and the first for which an inherited mutation has been described. The early embryonic lethal phenotype of mice lacking metaxin demonstrates that efficient import of proteins into mitochondria is crucial for cellular survival. The characterization of metaxin provides an opportunity to elucidate similarities and possible differences in the mechanisms of protein import between fungi and mammals and in the phenotypes of fungi and mammals lacking mitochondrial import receptors.
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Affiliation(s)
- L C Armstrong
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
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50
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Genetic interaction ofDrosophila homologue ofabelson (abl) proto-oncogene (D-abl) andlethal(2)giant larvae (lgl) tumour suppressor gene during embryonic development. J Genet 1996. [DOI: 10.1007/bf02931759] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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