1
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Martinez MAQ, Zhao CZ, Moore FEQ, Yee C, Zhang W, Shen K, Martin BL, Matus DQ. Cell cycle perturbation uncouples mitotic progression and invasive behavior in a post-mitotic cell. Differentiation 2024; 137:100765. [PMID: 38522217 DOI: 10.1016/j.diff.2024.100765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 03/05/2024] [Accepted: 03/09/2024] [Indexed: 03/26/2024]
Abstract
The acquisition of the post-mitotic state is crucial for the execution of many terminally differentiated cell behaviors during organismal development. However, the mechanisms that maintain the post-mitotic state in this context remain poorly understood. To gain insight into these mechanisms, we used the genetically and visually accessible model of C. elegans anchor cell (AC) invasion into the vulval epithelium. The AC is a terminally differentiated uterine cell that normally exits the cell cycle and enters a post-mitotic state before initiating contact between the uterus and vulva through a cell invasion event. Here, we set out to identify the set of negative cell cycle regulators that maintain the AC in this post-mitotic, invasive state. Our findings revealed a critical role for CKI-1 (p21CIP1/p27KIP1) in redundantly maintaining the post-mitotic state of the AC, as loss of CKI-1 in combination with other negative cell cycle regulators-including CKI-2 (p21CIP1/p27KIP1), LIN-35 (pRb/p107/p130), FZR-1 (Cdh1/Hct1), and LIN-23 (β-TrCP)-resulted in proliferating ACs. Remarkably, time-lapse imaging revealed that these ACs retain their ability to invade. Upon examination of a node in the gene regulatory network controlling AC invasion, we determined that proliferating, invasive ACs do so by maintaining aspects of pro-invasive gene expression. We therefore report that the requirement for a post-mitotic state for invasive cell behavior can be bypassed following direct cell cycle perturbation.
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Affiliation(s)
- Michael A Q Martinez
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Chris Z Zhao
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Frances E Q Moore
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Callista Yee
- Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Wan Zhang
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Kang Shen
- Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Benjamin L Martin
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, 11794, USA
| | - David Q Matus
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, 11794, USA.
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2
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Martinez MAQ, Zhao CZ, Moore FEQ, Yee C, Zhang W, Shen K, Martin BL, Matus DQ. Cell cycle perturbation uncouples mitotic progression and invasive behavior in a post-mitotic cell. bioRxiv 2024:2023.03.16.533034. [PMID: 38370624 PMCID: PMC10871222 DOI: 10.1101/2023.03.16.533034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
The acquisition of the post-mitotic state is crucial for the execution of many terminally differentiated cell behaviors during organismal development. However, the mechanisms that maintain the post-mitotic state in this context remain poorly understood. To gain insight into these mechanisms, we used the genetically and visually accessible model of C. elegans anchor cell (AC) invasion into the vulval epithelium. The AC is a terminally differentiated uterine cell that normally exits the cell cycle and enters a post-mitotic state, initiating contact between the uterus and vulva through a cell invasion event. Here, we set out to identify the set of negative cell cycle regulators that maintain the AC in this post-mitotic, invasive state. Our findings revealed a critical role for CKI-1 (p21CIP1/p27KIP1) in redundantly maintaining the post-mitotic state of the AC, as loss of CKI-1 in combination with other negative cell cycle regulators-including CKI-2 (p21CIP1/p27KIP1), LIN-35 (pRb/p107/p130), FZR-1 (Cdh1/Hct1), and LIN-23 (β-TrCP)-resulted in proliferating ACs. Remarkably, time-lapse imaging revealed that these ACs retain their ability to invade. Upon examination of a node in the gene regulatory network controlling AC invasion, we determined that proliferating, invasive ACs do so by maintaining aspects of pro-invasive gene expression. We therefore report that the requirement for a post-mitotic state for invasive cell behavior can be bypassed following direct cell cycle perturbation.
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Affiliation(s)
- Michael A Q Martinez
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Chris Z Zhao
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Frances E Q Moore
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Callista Yee
- Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Wan Zhang
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Kang Shen
- Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Benjamin L Martin
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - David Q Matus
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
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3
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Medwig-Kinney TN, Kinney BA, Martinez MAQ, Yee C, Sirota SS, Mullarkey AA, Somineni N, Hippler J, Zhang W, Shen K, Hammell C, Pani AM, Matus DQ. Dynamic compartmentalization of the pro-invasive transcription factor NHR-67 reveals a role for Groucho in regulating a proliferative-invasive cellular switch in C. elegans. eLife 2023; 12:RP84355. [PMID: 38038410 PMCID: PMC10691804 DOI: 10.7554/elife.84355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023] Open
Abstract
A growing body of evidence suggests that cell division and basement membrane invasion are mutually exclusive cellular behaviors. How cells switch between proliferative and invasive states is not well understood. Here, we investigated this dichotomy in vivo by examining two cell types in the developing Caenorhabditis elegans somatic gonad that derive from equipotent progenitors, but exhibit distinct cell behaviors: the post-mitotic, invasive anchor cell and the neighboring proliferative, non-invasive ventral uterine (VU) cells. We show that the fates of these cells post-specification are more plastic than previously appreciated and that levels of NHR-67 are important for discriminating between invasive and proliferative behavior. Transcription of NHR-67 is downregulated following post-translational degradation of its direct upstream regulator, HLH-2 (E/Daughterless) in VU cells. In the nuclei of VU cells, residual NHR-67 protein is compartmentalized into discrete punctae that are dynamic over the cell cycle and exhibit liquid-like properties. By screening for proteins that colocalize with NHR-67 punctae, we identified new regulators of uterine cell fate maintenance: homologs of the transcriptional co-repressor Groucho (UNC-37 and LSY-22), as well as the TCF/LEF homolog POP-1. We propose a model in which the association of NHR-67 with the Groucho/TCF complex suppresses the default invasive state in non-invasive cells, which complements transcriptional regulation to add robustness to the proliferative-invasive cellular switch in vivo.
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Affiliation(s)
- Taylor N Medwig-Kinney
- Department of Biochemistry and Cell Biology, Stony Brook UniversityStony BrookUnited States
| | - Brian A Kinney
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
| | - Michael AQ Martinez
- Department of Biochemistry and Cell Biology, Stony Brook UniversityStony BrookUnited States
| | - Callista Yee
- Howard Hughes Medical Institute, Department of Biology, Stanford UniversityStanfordUnited States
| | - Sydney S Sirota
- Department of Biochemistry and Cell Biology, Stony Brook UniversityStony BrookUnited States
| | - Angelina A Mullarkey
- Department of Biochemistry and Cell Biology, Stony Brook UniversityStony BrookUnited States
| | - Neha Somineni
- Department of Biochemistry and Cell Biology, Stony Brook UniversityStony BrookUnited States
| | - Justin Hippler
- Department of Biochemistry and Cell Biology, Stony Brook UniversityStony BrookUnited States
- Science and Technology Research Program, Smithtown High School EastSt. JamesUnited States
| | - Wan Zhang
- Department of Biochemistry and Cell Biology, Stony Brook UniversityStony BrookUnited States
| | - Kang Shen
- Howard Hughes Medical Institute, Department of Biology, Stanford UniversityStanfordUnited States
| | | | - Ariel M Pani
- Departments of Biology and Cell Biology, University of VirginiaCharlottesvilleUnited States
| | - David Q Matus
- Department of Biochemistry and Cell Biology, Stony Brook UniversityStony BrookUnited States
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4
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Gibney TV, Favichia M, Latifi L, Medwig-Kinney TN, Matus DQ, McIntyre DC, Arrigo AB, Branham KR, Bubrig LT, Ghaddar A, Jiranek JA, Liu KE, Marcucci CG, Porter RJ, Pani AM. A simple method to dramatically increase C. elegans germline microinjection efficiency. Dev Biol 2023; 502:63-67. [PMID: 37433390 PMCID: PMC10559938 DOI: 10.1016/j.ydbio.2023.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 07/13/2023]
Abstract
Genome manipulation methods in C. elegans require microinjecting DNA or ribonucleoprotein complexes into the microscopic core of the gonadal syncytium. These microinjections are technically demanding and represent a key bottleneck for all genome engineering and transgenic approaches in C. elegans. While there have been steady improvements in the ease and efficiency of genetic methods for C. elegans genome manipulation, there have not been comparable advances in the physical process of microinjection. Here, we report a simple and inexpensive method for handling worms using a paintbrush during the injection process that nearly tripled average microinjection rates compared to traditional worm handling methods. We found that the paintbrush increased injection throughput by substantially increasing both injection speeds and post-injection survival rates. In addition to dramatically and universally increasing injection efficiency for experienced personnel, the paintbrush method also significantly improved the abilities of novice investigators to perform key steps in the microinjection process. We expect that this method will benefit the C. elegans community by increasing the speed at which new strains can be generated and will also make microinjection-based approaches less challenging and more accessible to personnel and labs without extensive experience.
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Affiliation(s)
- Theresa V Gibney
- Department of Biology, University of Virginia, Charlottesville, VA, USA.
| | - Michelle Favichia
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Laila Latifi
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | | | - David Q Matus
- Department of Biochemistry & Cell Biology, Stony Brook University, Stony Brook, NY, USA
| | - Daniel C McIntyre
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Angelo B Arrigo
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Kendall R Branham
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Louis T Bubrig
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Abbas Ghaddar
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Juliana A Jiranek
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Kendra E Liu
- Department of Cell Biology, University of Virginia, Charlottesville, VA, USA
| | - Charles G Marcucci
- Neuroscience Graduate Program, University of Virginia, Charlottesville, VA, USA
| | - Robert J Porter
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Ariel M Pani
- Department of Biology, University of Virginia, Charlottesville, VA, USA; Department of Cell Biology, University of Virginia, Charlottesville, VA, USA.
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5
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Costa DS, Kenny-Ganzert IW, Chi Q, Park K, Kelley LC, Garde A, Matus DQ, Park J, Yogev S, Goldstein B, Gibney TV, Pani AM, Sherwood DR. The Caenorhabditis elegans anchor cell transcriptome: ribosome biogenesis drives cell invasion through basement membrane. Development 2023; 150:dev201570. [PMID: 37039075 PMCID: PMC10259517 DOI: 10.1242/dev.201570] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 03/27/2023] [Indexed: 04/12/2023]
Abstract
Cell invasion through basement membrane (BM) barriers is important in development, immune function and cancer progression. As invasion through BM is often stochastic, capturing gene expression profiles of actively invading cells in vivo remains elusive. Using the stereotyped timing of Caenorhabditis elegans anchor cell (AC) invasion, we generated an AC transcriptome during BM breaching. Through a focused RNAi screen of transcriptionally enriched genes, we identified new invasion regulators, including translationally controlled tumor protein (TCTP). We also discovered gene enrichment of ribosomal proteins. AC-specific RNAi, endogenous ribosome labeling and ribosome biogenesis analysis revealed that a burst of ribosome production occurs shortly after AC specification, which drives the translation of proteins mediating BM removal. Ribosomes also enrich near the AC endoplasmic reticulum (ER) Sec61 translocon and the endomembrane system expands before invasion. We show that AC invasion is sensitive to ER stress, indicating a heightened requirement for translation of ER-trafficked proteins. These studies reveal key roles for ribosome biogenesis and endomembrane expansion in cell invasion through BM and establish the AC transcriptome as a resource to identify mechanisms underlying BM transmigration.
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Affiliation(s)
- Daniel S. Costa
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27708, USA
| | | | - Qiuyi Chi
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
| | - Kieop Park
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
| | - Laura C. Kelley
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
| | - Aastha Garde
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
- Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08544, USA
| | - David Q. Matus
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Junhyun Park
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Shaul Yogev
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Bob Goldstein
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Theresa V. Gibney
- Department of Biology, University of Virginia, Charlottesville, VA 29903, USA
| | - Ariel M. Pani
- Department of Biology, University of Virginia, Charlottesville, VA 29903, USA
- Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, VA 29904, USA
| | - David R. Sherwood
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
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6
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Xiao Y, Yee C, Zhao CZ, Martinez MAQ, Zhang W, Shen K, Matus DQ, Hammell C. An expandable FLP-ON::TIR1 system for precise spatiotemporal protein degradation in Caenorhabditis elegans. Genetics 2023; 223:iyad013. [PMID: 36722258 PMCID: PMC10319979 DOI: 10.1093/genetics/iyad013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/16/2023] [Indexed: 02/02/2023] Open
Abstract
The auxin-inducible degradation system has been widely adopted in the Caenorhabditis elegans research community for its ability to empirically control the spatiotemporal expression of target proteins. This system can efficiently degrade auxin-inducible degron (AID)-tagged proteins via the expression of a ligand-activatable AtTIR1 protein derived from A. thaliana that adapts target proteins to the endogenous C. elegans proteasome. While broad expression of AtTIR1 using strong, ubiquitous promoters can lead to rapid degradation of AID-tagged proteins, cell type-specific expression of AtTIR1 using spatially restricted promoters often results in less efficient target protein degradation. To circumvent this limitation, we have developed an FLP/FRT3-based system that functions to reanimate a dormant, high-powered promoter that can drive sufficient AtTIR1 expression in a cell type-specific manner. We benchmark the utility of this system by generating a number of tissue-specific FLP-ON::TIR1 drivers to reveal genetically separable cell type-specific phenotypes for several target proteins. We also demonstrate that the FLP-ON::TIR1 system is compatible with enhanced degron epitopes. Finally, we provide an expandable toolkit utilizing the basic FLP-ON::TIR1 system that can be adapted to drive optimized AtTIR1 expression in any tissue or cell type of interest.
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Affiliation(s)
- Yutong Xiao
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Callista Yee
- Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Chris Z Zhao
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Michael A Q Martinez
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Wan Zhang
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Kang Shen
- Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - David Q Matus
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
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7
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Gibney TV, Favichia M, Latifi L, Medwig-Kinney TN, Matus DQ, McIntyre DC, Arrigo AB, Branham KR, Bubrig LT, Ghaddar A, Jiranek JA, Liu KE, Marcucci CG, Porter RJ, Pani AM. A simple method to dramatically increase C. elegans germline microinjection efficiency. bioRxiv 2023:2023.03.23.533855. [PMID: 36993165 PMCID: PMC10055348 DOI: 10.1101/2023.03.23.533855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Genome manipulation methods in C. elegans require microinjecting DNA or ribonucleoprotein complexes into the microscopic core of the gonadal syncytium. These microinjections are technically demanding and represent a key bottleneck for all genome engineering and transgenic approaches in C. elegans . While there have been steady improvements in the ease and efficiency of genetic methods for C. elegans genome manipulation, there have not been comparable advances in the physical process of microinjection. Here, we report a simple and inexpensive method for handling worms using a paintbrush during the injection process that nearly tripled average microinjection rates compared to traditional worm handling methods. We found that the paintbrush increased injection throughput by substantially increasing both injection speeds and post-injection survival rates. In addition to dramatically and universally increasing injection efficiency for experienced personnel, the paintbrush method also significantly improved the abilities of novice investigators to perform key steps in the microinjection process. We expect that this method will benefit the C. elegans community by increasing the speed at which new strains can be generated and will also make microinjection-based approaches less challenging and more accessible to personnel and labs without extensive experience.
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Affiliation(s)
- Theresa V. Gibney
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Michelle Favichia
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Laila Latifi
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | | | - David Q. Matus
- Department of Biochemistry & Cell Biology, Stony Brook University, Stony Brook, NY, USA
- David Matus is a paid consultant of Arcadia Science
| | | | - Angelo B. Arrigo
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | | | - Louis T. Bubrig
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Abbas Ghaddar
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | | | - Kendra E. Liu
- Neuroscience Graduate Program, University of Virginia, Charlottesville, VA, USA
| | - Charles G. Marcucci
- Neuroscience Graduate Program, University of Virginia, Charlottesville, VA, USA
| | - Robert J. Porter
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Ariel M. Pani
- Department of Biology, University of Virginia, Charlottesville, VA, USA
- Department of Cell Biology, University of Virginia, Charlottesville, VA, USA
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8
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Maheshwari R, Rahman MM, Drey S, Onyundo M, Fabig G, Martinez MAQ, Matus DQ, Müller-Reichert T, Cohen-Fix O. A membrane reticulum, the centriculum, affects centrosome size and function in Caenorhabditis elegans. Curr Biol 2023; 33:791-806.e7. [PMID: 36693370 PMCID: PMC10023444 DOI: 10.1016/j.cub.2022.12.059] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 11/21/2022] [Accepted: 12/21/2022] [Indexed: 01/24/2023]
Abstract
Centrosomes are cellular structures that nucleate microtubules. At their core is a pair of centrioles that recruit pericentriolar material (PCM). Although centrosomes are considered membraneless organelles, in many cell types, including human cells, centrosomes are surrounded by endoplasmic reticulum (ER)-derived membranes of unknown structure and function. Using volume electron microscopy (vEM), we show that centrosomes in the Caenorhabditis elegans (C. elegans) early embryo are surrounded by a three-dimensional (3D), ER-derived membrane reticulum that we call the centriculum, for centrosome-associated membrane reticulum. The centriculum is adjacent to the nuclear envelope in interphase and early mitosis and fuses with the fenestrated nuclear membrane at metaphase. Centriculum formation is dependent on the presence of an underlying centrosome and on microtubules. Conversely, increasing centriculum size by genetic means led to the expansion of the PCM, increased microtubule nucleation capacity, and altered spindle width. The effect of the centriculum on centrosome function suggests that in the C. elegans early embryo, the centrosome is not membraneless. Rather, it is encased in a membrane meshwork that affects its properties. We provide evidence that the centriculum serves as a microtubule "filter," preventing the elongation of a subset of microtubules past the centriculum. Finally, we propose that the fusion between the centriculum and the nuclear membrane contributes to nuclear envelope breakdown by coupling spindle elongation to nuclear membrane fenestration.
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Affiliation(s)
- Richa Maheshwari
- The Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mohammad M Rahman
- The Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Bethesda, MD 20892, USA
| | - Seth Drey
- The Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Bethesda, MD 20892, USA
| | - Megan Onyundo
- The Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gunar Fabig
- Experimental Center, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany
| | - Michael A Q Martinez
- Department of Biochemistry and Cell Biology, Stony Brook University, 450 Life Sciences Building, Stony Brook, NY 11794, USA
| | - David Q Matus
- Department of Biochemistry and Cell Biology, Stony Brook University, 450 Life Sciences Building, Stony Brook, NY 11794, USA
| | - Thomas Müller-Reichert
- Experimental Center, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany
| | - Orna Cohen-Fix
- The Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Bethesda, MD 20892, USA.
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9
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Lampersberger L, Conte F, Ghosh S, Xiao Y, Price J, Jordan D, Matus DQ, Sarkies P, Beli P, Miska EA, Burton NO. Loss of the E3 ubiquitin ligases UBR-5 or HECD-1 restores Caenorhabditis elegans development in the absence of SWI/SNF function. Proc Natl Acad Sci U S A 2023; 120:e2217992120. [PMID: 36689659 PMCID: PMC9945973 DOI: 10.1073/pnas.2217992120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 12/15/2022] [Indexed: 01/25/2023] Open
Abstract
SWItch/sucrose non-fermenting (SWI/SNF) complexes are a family of chromatin remodelers that are conserved across eukaryotes. Mutations in subunits of SWI/SNF cause a multitude of different developmental disorders in humans, most of which have no current treatment options. Here, we identify an alanine-to-valine-causing mutation in the SWI/SNF subunit snfc-5 (SMARCB1 in humans) that prevents embryonic lethality in Caenorhabditis elegans nematodes harboring a loss-of-function mutation in the SWI/SNF subunit swsn-1 (SMARCC1/2 in humans). Furthermore, we found that the combination of this specific mutation in snfc-5 and a loss-of-function mutation in either of the E3 ubiquitin ligases ubr-5 (UBR5 in humans) or hecd-1 (HECTD1 in humans) can restore development to adulthood in swsn-1 loss-of-function mutants that otherwise die as embryos. Using these mutant models, we established a set of 335 genes that are dysregulated in SWI/SNF mutants that arrest their development embryonically but exhibit near wild-type levels of expression in the presence of suppressor mutations that prevent embryonic lethality, suggesting that SWI/SNF promotes development by regulating some subset of these 335 genes. In addition, we show that SWI/SNF protein levels are reduced in swsn-1; snfc-5 double mutants and partly restored to wild-type levels in swsn-1; snfc-5; ubr-5 triple mutants, consistent with a model in which UBR-5 regulates SWI/SNF levels by tagging the complex for proteasomal degradation. Our findings establish a link between two E3 ubiquitin ligases and SWI/SNF function and suggest that UBR5 and HECTD1 could be potential therapeutic targets for the many developmental disorders caused by missense mutations in SWI/SNF subunits.
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Affiliation(s)
- Lisa Lampersberger
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, CambridgeCB2 1QN, UK
- Department of Genetics, University of Cambridge, CambridgeCB2 3EH, UK
| | | | - Subhanita Ghosh
- Medical Research Council London Institute of Medical Sciences, LondonW12 0NN, UK
| | - Yutong Xiao
- Department of Biochemistry and Cell Biology, Stony Brook University, NY11790
| | - Jonathan Price
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, CambridgeCB2 1QN, UK
- Department of Genetics, University of Cambridge, CambridgeCB2 3EH, UK
| | - David Jordan
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, CambridgeCB2 1QN, UK
- Department of Genetics, University of Cambridge, CambridgeCB2 3EH, UK
| | - David Q. Matus
- Department of Biochemistry and Cell Biology, Stony Brook University, NY11790
| | - Peter Sarkies
- Medical Research Council London Institute of Medical Sciences, LondonW12 0NN, UK
- Department of Biochemistry, University of Oxford, OxfordOX1 3QU, UK
| | - Petra Beli
- Institute of Molecular Biology, Mainz55128, Germany
| | - Eric A. Miska
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, CambridgeCB2 1QN, UK
- Department of Genetics, University of Cambridge, CambridgeCB2 3EH, UK
- Department of Biochemistry, University of Cambridge, CambridgeCB2 1QW, UK
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, CambridgeCB10 1SA, UK
| | - Nicholas O. Burton
- Department of Epigenetics, Van Andel Research Institute, Grand Rapids, MI49503
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10
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Martinez MAQ, Mullarkey AA, Yee C, Zhao CZ, Zhang W, Shen K, Matus DQ. Reevaluating the relationship between EGL-43 (EVI1) and LIN-12 (Notch) during C. elegans anchor cell invasion. Biol Open 2022; 11:bio059668. [PMID: 36445013 PMCID: PMC9751802 DOI: 10.1242/bio.059668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 11/16/2022] [Indexed: 11/30/2022] Open
Abstract
Development of the Caenorhabditis elegans reproductive tract is orchestrated by the anchor cell (AC). This occurs in part through a cell invasion event that connects the uterine and vulval tissues. Several key transcription factors regulate AC invasion, such as EGL-43, HLH-2, and NHR-67. Specifically, these transcription factors function together to maintain the post-mitotic state of the AC, a requirement for AC invasion. Recently, a mechanistic connection has been made between loss of EGL-43 and AC cell-cycle entry. The current model states that EGL-43 represses LIN-12 (Notch) expression to prevent AC proliferation, suggesting that Notch signaling has mitogenic effects in the invasive AC. To reexamine the relationship between EGL-43 and LIN-12, we first designed and implemented a heterologous co-expression system called AIDHB that combines the auxin-inducible degron (AID) system of plants with a live cell-cycle sensor based on human DNA helicase B (DHB). After validating AIDHB using AID-tagged GFP, we sought to test it by using AID-tagged alleles of egl-43 and lin-12. Auxin-induced degradation of either EGL-43 or LIN-12 resulted in the expected AC phenotypes. Lastly, we seized the opportunity to pair AIDHB with RNAi to co-deplete LIN-12 and EGL-43, respectively, which revealed that LIN-12 is not required for AC proliferation following loss of EGL-43.
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Affiliation(s)
- Michael A. Q. Martinez
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Angelina A. Mullarkey
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Callista Yee
- Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Chris Z. Zhao
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Wan Zhang
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Kang Shen
- Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - David Q. Matus
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
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11
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Smith JJ, Kenny IW, Wolff C, Cray R, Kumar A, Sherwood DR, Matus DQ. A light sheet fluorescence microscopy protocol for Caenorhabditis elegans larvae and adults. Front Cell Dev Biol 2022; 10:1012820. [PMID: 36274853 PMCID: PMC9586288 DOI: 10.3389/fcell.2022.1012820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/20/2022] [Indexed: 01/07/2023] Open
Abstract
Light sheet fluorescence microscopy (LSFM) has become a method of choice for live imaging because of its fast acquisition and reduced photobleaching and phototoxicity. Despite the strengths and growing availability of LSFM systems, no generalized LSFM mounting protocol has been adapted for live imaging of post-embryonic stages of C. elegans. A major challenge has been to develop methods to limit animal movement using a mounting media that matches the refractive index of the optical system. Here, we describe a simple mounting and immobilization protocol using a refractive-index matched UV-curable hydrogel within fluorinated ethylene propylene (FEP) tubes for efficient and reliable imaging of larval and adult C. elegans stages.
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Affiliation(s)
- Jayson J. Smith
- Department of Neurobiology, University of Chicago, Chicago, IL, United States,University of Chicago Neuroscience Institute, Chicago, IL, United States,Embryology: Modern Concepts and Techniques, Marine Biological Laboratory, Woods Hole, MA, United States
| | - Isabel W. Kenny
- Embryology: Modern Concepts and Techniques, Marine Biological Laboratory, Woods Hole, MA, United States,Department of Biology, Duke University, Durham, NC, United States
| | - Carsten Wolff
- Embryology: Modern Concepts and Techniques, Marine Biological Laboratory, Woods Hole, MA, United States,Marine Biological Laboratory, Woods Hole, MA, United States
| | - Rachel Cray
- Marine Biological Laboratory, Woods Hole, MA, United States
| | - Abhishek Kumar
- Embryology: Modern Concepts and Techniques, Marine Biological Laboratory, Woods Hole, MA, United States,Marine Biological Laboratory, Woods Hole, MA, United States
| | - David R. Sherwood
- Embryology: Modern Concepts and Techniques, Marine Biological Laboratory, Woods Hole, MA, United States,Department of Biology, Duke University, Durham, NC, United States,*Correspondence: David R. Sherwood, ; David Q. Matus,
| | - David Q. Matus
- Embryology: Modern Concepts and Techniques, Marine Biological Laboratory, Woods Hole, MA, United States,Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, United States,*Correspondence: David R. Sherwood, ; David Q. Matus,
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12
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Mondal C, Gacha-Garay MJ, Larkin KA, Adikes RC, Di Martino JS, Chien CC, Fraser M, Eni-Aganga I, Agullo-Pascual E, Cialowicz K, Ozbek U, Naba A, Gaitas A, Fu TM, Upadhyayula S, Betzig E, Matus DQ, Martin BL, Bravo-Cordero JJ. A proliferative to invasive switch is mediated by srGAP1 downregulation through the activation of TGF-β2 signaling. Cell Rep 2022; 40:111358. [PMID: 36130489 PMCID: PMC9596226 DOI: 10.1016/j.celrep.2022.111358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 05/06/2022] [Accepted: 08/24/2022] [Indexed: 11/28/2022] Open
Abstract
Many breast cancer (BC) patients suffer from complications of metastatic disease. To form metastases, cancer cells must become migratory and coordinate both invasive and proliferative programs at distant organs. Here, we identify srGAP1 as a regulator of a proliferative-to-invasive switch in BC cells. High-resolution light-sheet microscopy demonstrates that BC cells can form actin-rich protrusions during extravasation. srGA-P1low cells display a motile and invasive phenotype that facilitates their extravasation from blood vessels, as shown in zebrafish and mouse models, while attenuating tumor growth. Interestingly, a population of srGAP1low cells remain as solitary disseminated tumor cells in the lungs of mice bearing BC tumors. Overall, srGAP1low cells have increased Smad2 activation and TGF-β2 secretion, resulting in increased invasion and p27 levels to sustain quiescence. These findings identify srGAP1 as a mediator of a proliferative to invasive phenotypic switch in BC cells in vivo through a TGF-β2-mediated signaling axis. Disseminated tumor cells can remain quiescent or actively proliferate in distant organs, contributing to aggressive disease. Mondal et al. identify srGAP1 as a regulator of a proliferative-to-invasive decision by breast cancer (BC) cells through a TGF-β2-mediated signaling axis.
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Affiliation(s)
- Chandrani Mondal
- Department of Medicine, Division of Hematology and Oncology, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Majo J Gacha-Garay
- Biochemistry and Cell Biology Department, Stony Brook University, Stony Brook, NY 11794, USA
| | - Kathryn A Larkin
- Biochemistry and Cell Biology Department, Stony Brook University, Stony Brook, NY 11794, USA
| | - Rebecca C Adikes
- Biochemistry and Cell Biology Department, Stony Brook University, Stony Brook, NY 11794, USA
| | - Julie S Di Martino
- Department of Medicine, Division of Hematology and Oncology, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Chen-Chi Chien
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Madison Fraser
- Department of Medicine, Division of Hematology and Oncology, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ireti Eni-Aganga
- Department of Medicine, Division of Hematology and Oncology, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Esperanza Agullo-Pascual
- Microscopy and Advanced Bioimaging Core, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Katarzyna Cialowicz
- Microscopy and Advanced Bioimaging Core, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Umut Ozbek
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alexandra Naba
- Department of Physiology & Biophysics, University of Illinois at Chicago, Chicago, IL 60612, USA; University of Illinois Cancer Center, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Angelo Gaitas
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Tian-Ming Fu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | | | - Eric Betzig
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA; Department of Molecular and Cellular Biology, UC Berkeley, CA 94720, USA
| | - David Q Matus
- Biochemistry and Cell Biology Department, Stony Brook University, Stony Brook, NY 11794, USA
| | - Benjamin L Martin
- Biochemistry and Cell Biology Department, Stony Brook University, Stony Brook, NY 11794, USA
| | - Jose Javier Bravo-Cordero
- Department of Medicine, Division of Hematology and Oncology, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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13
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Pani AM, Gibney TV, Medwig-Kinney TN, Matus DQ, Goldstein B. A new toolkit to visualize and perturb endogenous LIN-12/Notch signaling in C. elegans. MicroPubl Biol 2022; 2022:10.17912/micropub.biology.000603. [PMID: 35966394 PMCID: PMC9372766 DOI: 10.17912/micropub.biology.000603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/12/2022] [Accepted: 07/24/2022] [Indexed: 11/05/2022]
Abstract
Notch signaling mediates cell-cell interactions during development and homeostasis. Methods for visualizing and manipulating Notch activity in vivo are essential to elucidate how the Notch pathway functions. Here, we provide new tools for use in C. elegans to visualize and perturb Notch signaling in vivo using endogenously tagged alleles of the Notch receptor lin-12 . Tagging the endogenous LIN-12 intracellular domain with the fluorescent protein mNeonGreen (mNG) allowed for visualization of both its membrane-localized state and translocation of the Notch intracellular domain into the nucleus upon ligand activation. LIN-12::mNG localized to the nucleus in cells where and when Notch signaling is known to be active and provided a real-time readout of Notch activity in vivo that complements existing biosensors and transcriptional reporters. We also report an allele of endogenous lin-12 that we tagged with both mNG and an auxin-inducible degron, to facilitate conditional LIN-12 protein degradation. This toolkit provides novel reagents for the C. elegans research community to investigate mechanisms of Notch signaling and its functions in vivo .
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Affiliation(s)
- Ariel M Pani
- Department of Biology, University of Virginia, Charlottesville, VA, USA
,
Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, VA, USA
,
Correspondence to: Ariel M Pani (
)
| | - Theresa V Gibney
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | | | - David Q Matus
- Department of Biochemistry & Cell Biology, Stony Brook University, Stony Brook, NY, USA
,
D.Q.M. is a paid consultant of Arcadia Science
| | - Bob Goldstein
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
,
Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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14
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Medwig-Kinney TN, Sirota SS, Gibney TV, Pani AM, Matus DQ. An in vivo toolkit to visualize endogenous LAG-2/Delta and LIN-12/Notch signaling in C. elegans. MicroPubl Biol 2022; 2022:10.17912/micropub.biology.000602. [PMID: 35966395 PMCID: PMC9372767 DOI: 10.17912/micropub.biology.000602] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/21/2022] [Accepted: 07/24/2022] [Indexed: 11/05/2022]
Abstract
Notch/Delta signaling regulates numerous cell-cell interactions that occur during development, homeostasis, and in disease states. In many cases, the Notch/Delta pathway mediates lateral inhibition between cells to specify alternative fates. Here, we provide new tools for use in C. elegans to investigate feedback between the Notch receptor LIN-12 and the ligand LAG-2 (Delta) in vivo . We report new, endogenously tagged strains to visualize LAG-2 protein and lag-2 transcription, which we combined with endogenously tagged LIN-12 to visualize Notch and Delta dynamics over the course of a stochastic Notch-mediated cell fate decision. To validate these tools in a functional context, we demonstrated that our endogenous lag-2 transcriptional reporter was expressed in ectopic anchor and primary vulval precursor cells after auxin-mediated depletion of LIN-12. This toolkit provides new reagents for the C. elegans research community to further investigate Notch/Delta signaling mechanisms and functions for this pathway in vivo .
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Affiliation(s)
- Taylor N Medwig-Kinney
- Department of Biochemistry & Cell Biology, Stony Brook University, Stony Brook, NY, USA
,
Correspondence to: Taylor N Medwig-Kinney (
)
| | - Sydney S Sirota
- Department of Biochemistry & Cell Biology, Stony Brook University, Stony Brook, NY, USA
,
current address, Touro College of Osteopathic Medicine, Middletown, NY, USA
| | - Theresa V Gibney
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Ariel M Pani
- Department of Biology, University of Virginia, Charlottesville, VA, USA
,
Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, VA, USA
,
Correspondence to: Ariel M Pani (
)
| | - David Q Matus
- Department of Biochemistry & Cell Biology, Stony Brook University, Stony Brook, NY, USA
,
D.Q.M. is a paid consultant of Arcadia Science
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15
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Hills-Muckey K, Martinez MAQ, Stec N, Hebbar S, Saldanha J, Medwig-Kinney TN, Moore FEQ, Ivanova M, Morao A, Ward JD, Moss EG, Ercan S, Zinovyeva AY, Matus DQ, Hammell CM. An engineered, orthogonal auxin analog/AtTIR1(F79G) pairing improves both specificity and efficacy of the auxin degradation system in Caenorhabditis elegans. Genetics 2022; 220:iyab174. [PMID: 34739048 PMCID: PMC9097248 DOI: 10.1093/genetics/iyab174] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/17/2021] [Indexed: 02/06/2023] Open
Abstract
The auxin-inducible degradation system in C. elegans allows for spatial and temporal control of protein degradation via heterologous expression of a single Arabidopsis thaliana F-box protein, transport inhibitor response 1 (AtTIR1). In this system, exogenous auxin (Indole-3-acetic acid; IAA) enhances the ability of AtTIR1 to function as a substrate recognition component that adapts engineered degron-tagged proteins to the endogenous C. elegans E3 ubiquitin ligases complex [SKR-1/2-CUL-1-F-box (SCF)], targeting them for degradation by the proteosome. While this system has been employed to dissect the developmental functions of many C. elegans proteins, we have found that several auxin-inducible degron (AID)-tagged proteins are constitutively degraded by AtTIR1 in the absence of auxin, leading to undesired loss-of-function phenotypes. In this manuscript, we adapt an orthogonal auxin derivative/mutant AtTIR1 pair [C. elegans AID version 2 (C.e.AIDv2)] that transforms the specificity of allosteric regulation of TIR1 from IAA to one that is dependent on an auxin derivative harboring a bulky aryl group (5-Ph-IAA). We find that a mutant AtTIR1(F79G) allele that alters the ligand-binding interface of TIR1 dramatically reduces ligand-independent degradation of multiple AID*-tagged proteins. In addition to solving the ectopic degradation problem for some AID-targets, the addition of 5-Ph-IAA to culture media of animals expressing AtTIR1(F79G) leads to more penetrant loss-of-function phenotypes for AID*-tagged proteins than those elicited by the AtTIR1-IAA pairing at similar auxin analog concentrations. The improved specificity and efficacy afforded by the mutant AtTIR1(F79G) allele expand the utility of the AID system and broaden the number of proteins that can be effectively targeted with it.
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Affiliation(s)
| | - Michael A Q Martinez
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Natalia Stec
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Shilpa Hebbar
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Joanne Saldanha
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Taylor N Medwig-Kinney
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Frances E Q Moore
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Maria Ivanova
- Department of Molecular Biology, Rowan University, Stratford, NJ 08084, USA
| | - Ana Morao
- Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - J D Ward
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Eric G Moss
- Department of Molecular Biology, Rowan University, Stratford, NJ 08084, USA
| | - Sevinc Ercan
- Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Anna Y Zinovyeva
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - David Q Matus
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
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16
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Smith JJ, Xiao Y, Parsan N, Medwig-Kinney TN, Martinez MAQ, Moore FEQ, Palmisano NJ, Kohrman AQ, Chandhok Delos Reyes M, Adikes RC, Liu S, Bracht SA, Zhang W, Wen K, Kratsios P, Matus DQ. The SWI/SNF chromatin remodeling assemblies BAF and PBAF differentially regulate cell cycle exit and cellular invasion in vivo. PLoS Genet 2022; 18:e1009981. [PMID: 34982771 PMCID: PMC8759636 DOI: 10.1371/journal.pgen.1009981] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 01/14/2022] [Accepted: 12/07/2021] [Indexed: 12/15/2022] Open
Abstract
Chromatin remodelers such as the SWI/SNF complex coordinate metazoan development through broad regulation of chromatin accessibility and transcription, ensuring normal cell cycle control and cellular differentiation in a lineage-specific and temporally restricted manner. Mutations in genes encoding the structural subunits of chromatin, such as histone subunits, and chromatin regulating factors are associated with a variety of disease mechanisms including cancer metastasis, in which cancer co-opts cellular invasion programs functioning in healthy cells during development. Here we utilize Caenorhabditis elegans anchor cell (AC) invasion as an in vivo model to identify the suite of chromatin agents and chromatin regulating factors that promote cellular invasiveness. We demonstrate that the SWI/SNF ATP-dependent chromatin remodeling complex is a critical regulator of AC invasion, with pleiotropic effects on both G0 cell cycle arrest and activation of invasive machinery. Using targeted protein degradation and enhanced RNA interference (RNAi) vectors, we show that SWI/SNF contributes to AC invasion in a dose-dependent fashion, with lower levels of activity in the AC corresponding to aberrant cell cycle entry and increased loss of invasion. Our data specifically implicate the SWI/SNF BAF assembly in the regulation of the G0 cell cycle arrest in the AC, whereas the SWI/SNF PBAF assembly promotes AC invasion via cell cycle-independent mechanisms, including attachment to the basement membrane (BM) and activation of the pro-invasive fos-1/FOS gene. Together these findings demonstrate that the SWI/SNF complex is necessary for two essential components of AC invasion: arresting cell cycle progression and remodeling the BM. The work here provides valuable single-cell mechanistic insight into how the SWI/SNF assemblies differentially contribute to cellular invasion and how SWI/SNF subunit-specific disruptions may contribute to tumorigeneses and cancer metastasis. Cellular invasion is required for animal development and homeostasis. Inappropriate activation of invasion however can result in cancer metastasis. Invasion programs are orchestrated by complex gene regulatory networks (GRN) that function in a coordinated fashion to turn on and off pro-invasive genes. While the core of GRNs are DNA binding transcription factors, they require aid from chromatin remodelers to access the genome. To identify the suite of pro-invasive chromatin remodelers, we paired high resolution imaging with RNA interference to individually knockdown 269 chromatin factors, identifying the evolutionarily conserved SWItching defective/Sucrose Non-Fermenting (SWI/SNF) ATP-dependent chromatin remodeling complex as a new regulator of Caenorhabditis elegans anchor cell (AC) invasion. Using a combination of CRISPR/Cas9 genome engineering and targeted protein degradation we demonstrate that the core SWI/SNF complex functions in a dose-dependent manner to control invasion. Further, we determine that the accessory SWI/SNF complexes, BAF and PBAF, contribute to invasion via distinctive mechanisms: BAF is required to prevent inappropriate proliferation while PBAF promotes AC attachment and remodeling of the basement membrane. Together, our data provide insights into how the SWI/SNF complex, which is mutated in many human cancers, can function in a dose-dependent fashion to regulate switching from invasive to proliferative fates.
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Affiliation(s)
- Jayson J. Smith
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Yutong Xiao
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Nithin Parsan
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
- Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Taylor N. Medwig-Kinney
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Michael A. Q. Martinez
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Frances E. Q. Moore
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Nicholas J. Palmisano
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Abraham Q. Kohrman
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Mana Chandhok Delos Reyes
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Rebecca C. Adikes
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
- Biology Department, Siena College, Loudonville, New York, United States of America
| | - Simeiyun Liu
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
- Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Sydney A. Bracht
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
- Department of Cell Biology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Wan Zhang
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Kailong Wen
- The Grossman Institute for Neuroscience, Quantitative Biology, and Human Behavior, University of Chicago, Chicago, Illinois, United States of America
- Department of Neurobiology, University of Chicago, Chicago, Illinois, United States of America
| | - Paschalis Kratsios
- The Grossman Institute for Neuroscience, Quantitative Biology, and Human Behavior, University of Chicago, Chicago, Illinois, United States of America
- Department of Neurobiology, University of Chicago, Chicago, Illinois, United States of America
| | - David Q. Matus
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
- * E-mail:
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17
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Morabito RD, Adikes RC, Matus DQ, Martin BL. Cyclin-Dependent Kinase Sensor Transgenic Zebrafish Lines for Improved Cell Cycle State Visualization in Live Animals. Zebrafish 2021; 18:374-375. [PMID: 34669514 DOI: 10.1089/zeb.2021.0059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Robert D Morabito
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, USA
| | - Rebecca C Adikes
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, USA
| | - David Q Matus
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, USA
| | - Benjamin L Martin
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, USA
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18
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Medwig-Kinney TN, Palmisano NJ, Matus DQ. Deletion of a putative HDA-1 binding site in the hlh-2 promoter eliminates expression in C. elegans dorsal uterine cells. MicroPubl Biol 2021; 2021:10.17912/micropub.biology.000449. [PMID: 34514358 PMCID: PMC8414078 DOI: 10.17912/micropub.biology.000449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 01/04/2023]
Abstract
The helix-loop-helix transcription factor hlh-2 (E/Daughterless) has been shown to play an important role in regulating cell fate patterning, cell cycle, and basement membrane invasion in the context of the development of the C. elegans somatic gonad. Here, using CRISPR/Cas9 genome engineering, we generated a new hlh-2 allele (hlh-2(Δ-1303-702)) in the endogenous, GFP-tagged hlh-2 locus. This allele represents a deletion of a 601 bp region in the hlh-2 promoter that contains a putative binding site of the histone deacetylase hda-1 (HDAC) according to publicly available ChIP-sequencing data. Strikingly, we find that HLH-2 expression is virtually absent in the dorsal uterine cells of hlh-2(Δ-1303-702) animals compared to wild type controls. Levels of HLH-2 in the anchor cell and ventral uterine cells are only modestly reduced in the mutant; however, this does not seem to be functionally significant based on the lack of relevant phenotypes and expression levels of a downstream gene, NHR-67 (TLX/Tailless/NR2E1), in these cells. Taken together, these results support growing evidence that HDACs can potentially positively regulate transcription and provide a new reagent for studying hlh-2 regulation.
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Affiliation(s)
| | | | - David Q Matus
- Stony Brook University,
Correspondence to: David Q Matus ()
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19
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Ashley GE, Duong T, Levenson MT, Martinez MAQ, Johnson LC, Hibshman JD, Saeger HN, Palmisano NJ, Doonan R, Martinez-Mendez R, Davidson BR, Zhang W, Ragle JM, Medwig-Kinney TN, Sirota SS, Goldstein B, Matus DQ, Dickinson DJ, Reiner DJ, Ward JD. An expanded auxin-inducible degron toolkit for Caenorhabditis elegans. Genetics 2021; 217:iyab006. [PMID: 33677541 PMCID: PMC8045686 DOI: 10.1093/genetics/iyab006] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/10/2021] [Indexed: 12/30/2022] Open
Abstract
The auxin-inducible degron (AID) system has emerged as a powerful tool to conditionally deplete proteins in a range of organisms and cell types. Here, we describe a toolkit to augment the use of the AID system in Caenorhabditis elegans. We have generated a set of single-copy, tissue-specific (germline, intestine, neuron, muscle, pharynx, hypodermis, seam cell, anchor cell) and pan-somatic TIR1-expressing strains carrying a co-expressed blue fluorescent reporter to enable use of both red and green channels in experiments. These transgenes are inserted into commonly used, well-characterized genetic loci. We confirmed that our TIR1-expressing strains produce the expected depletion phenotype for several nuclear and cytoplasmic AID-tagged endogenous substrates. We have also constructed a set of plasmids for constructing repair templates to generate fluorescent protein::AID fusions through CRISPR/Cas9-mediated genome editing. These plasmids are compatible with commonly used genome editing approaches in the C. elegans community (Gibson or SapTrap assembly of plasmid repair templates or PCR-derived linear repair templates). Together these reagents will complement existing TIR1 strains and facilitate rapid and high-throughput fluorescent protein::AID tagging of genes. This battery of new TIR1-expressing strains and modular, efficient cloning vectors serves as a platform for straightforward assembly of CRISPR/Cas9 repair templates for conditional protein depletion.
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Affiliation(s)
- Guinevere E Ashley
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Tam Duong
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M Health Science Center, Texas A&M University, Houston, TX 77030, USA
| | - Max T Levenson
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Michael A Q Martinez
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Londen C Johnson
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jonathan D Hibshman
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Hannah N Saeger
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Nicholas J Palmisano
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Ryan Doonan
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Raquel Martinez-Mendez
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Brittany R Davidson
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Wan Zhang
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - James Matthew Ragle
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Taylor N Medwig-Kinney
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Sydney S Sirota
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Bob Goldstein
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - David Q Matus
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Daniel J Dickinson
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - David J Reiner
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M Health Science Center, Texas A&M University, Houston, TX 77030, USA
| | - Jordan D Ward
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
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20
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Adikes RC, Kohrman AQ, Martinez MAQ, Palmisano NJ, Smith JJ, Medwig-Kinney TN, Min M, Sallee MD, Ahmed OB, Kim N, Liu S, Morabito RD, Weeks N, Zhao Q, Zhang W, Feldman JL, Barkoulas M, Pani AM, Spencer SL, Martin BL, Matus DQ. Visualizing the metazoan proliferation-quiescence decision in vivo. eLife 2020; 9:e63265. [PMID: 33350383 PMCID: PMC7880687 DOI: 10.7554/elife.63265] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/21/2020] [Indexed: 12/15/2022] Open
Abstract
Cell proliferation and quiescence are intimately coordinated during metazoan development. Here, we adapt a cyclin-dependent kinase (CDK) sensor to uncouple these key events of the cell cycle in Caenorhabditis elegans and zebrafish through live-cell imaging. The CDK sensor consists of a fluorescently tagged CDK substrate that steadily translocates from the nucleus to the cytoplasm in response to increasing CDK activity and consequent sensor phosphorylation. We show that the CDK sensor can distinguish cycling cells in G1 from quiescent cells in G0, revealing a possible commitment point and a cryptic stochasticity in an otherwise invariant C. elegans cell lineage. Finally, we derive a predictive model of future proliferation behavior in C. elegans based on a snapshot of CDK activity in newly born cells. Thus, we introduce a live-cell imaging tool to facilitate in vivo studies of cell-cycle control in a wide-range of developmental contexts.
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Affiliation(s)
- Rebecca C Adikes
- Department of Biochemistry and Cell Biology, Stony Brook UniversityStony BrookUnited States
| | - Abraham Q Kohrman
- Department of Biochemistry and Cell Biology, Stony Brook UniversityStony BrookUnited States
| | - Michael A Q Martinez
- Department of Biochemistry and Cell Biology, Stony Brook UniversityStony BrookUnited States
| | - Nicholas J Palmisano
- Department of Biochemistry and Cell Biology, Stony Brook UniversityStony BrookUnited States
| | - Jayson J Smith
- Department of Biochemistry and Cell Biology, Stony Brook UniversityStony BrookUnited States
| | - Taylor N Medwig-Kinney
- Department of Biochemistry and Cell Biology, Stony Brook UniversityStony BrookUnited States
| | - Mingwei Min
- Department of Biochemistry and BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
| | - Maria D Sallee
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Ononnah B Ahmed
- Department of Biochemistry and Cell Biology, Stony Brook UniversityStony BrookUnited States
| | - Nuri Kim
- Department of Biochemistry and Cell Biology, Stony Brook UniversityStony BrookUnited States
| | - Simeiyun Liu
- Department of Biochemistry and Cell Biology, Stony Brook UniversityStony BrookUnited States
| | - Robert D Morabito
- Department of Biochemistry and Cell Biology, Stony Brook UniversityStony BrookUnited States
| | - Nicholas Weeks
- Department of Biochemistry and Cell Biology, Stony Brook UniversityStony BrookUnited States
| | - Qinyun Zhao
- Department of Biochemistry and Cell Biology, Stony Brook UniversityStony BrookUnited States
| | - Wan Zhang
- Department of Biochemistry and Cell Biology, Stony Brook UniversityStony BrookUnited States
| | | | | | - Ariel M Pani
- Department of Biology, University of VirginiaCharlottesvilleUnited States
| | - Sabrina L Spencer
- Department of Biochemistry and BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
| | - Benjamin L Martin
- Department of Biochemistry and Cell Biology, Stony Brook UniversityStony BrookUnited States
| | - David Q Matus
- Department of Biochemistry and Cell Biology, Stony Brook UniversityStony BrookUnited States
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21
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Martinez MAQ, Kinney BA, Medwig-Kinney TN, Ashley G, Ragle JM, Johnson L, Aguilera J, Hammell CM, Ward JD, Matus DQ. Rapid Degradation of Caenorhabditis elegans Proteins at Single-Cell Resolution with a Synthetic Auxin. G3 (Bethesda) 2020; 10:267-280. [PMID: 31727633 PMCID: PMC6945041 DOI: 10.1534/g3.119.400781] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 11/12/2019] [Indexed: 12/20/2022]
Abstract
As developmental biologists in the age of genome editing, we now have access to an ever-increasing array of tools to manipulate endogenous gene expression. The auxin-inducible degradation system allows for spatial and temporal control of protein degradation via a hormone-inducible Arabidopsis F-box protein, transport inhibitor response 1 (TIR1). In the presence of auxin, TIR1 serves as a substrate-recognition component of the E3 ubiquitin ligase complex SKP1-CUL1-F-box (SCF), ubiquitinating auxin-inducible degron (AID)-tagged proteins for proteasomal degradation. Here, we optimize the Caenorhabditis elegans AID system by utilizing 1-naphthaleneacetic acid (NAA), an indole-free synthetic analog of the natural auxin indole-3-acetic acid (IAA). We take advantage of the photostability of NAA to demonstrate via quantitative high-resolution microscopy that rapid degradation of target proteins can be detected in single cells within 30 min of exposure. Additionally, we show that NAA works robustly in both standard growth media and physiological buffer. We also demonstrate that K-NAA, the water-soluble, potassium salt of NAA, can be combined with microfluidics for targeted protein degradation in C. elegans larvae. We provide insight into how the AID system functions in C. elegans by determining that TIR1 depends on C. elegans SKR-1/2, CUL-1, and RBX-1 to degrade target proteins. Finally, we present highly penetrant defects from NAA-mediated degradation of the FTZ-F1 nuclear hormone receptor, NHR-25, during C. elegans uterine-vulval development. Together, this work improves our use and understanding of the AID system for dissecting gene function at the single-cell level during C. elegans development.
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Affiliation(s)
- Michael A Q Martinez
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794
| | - Brian A Kinney
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, and
| | - Taylor N Medwig-Kinney
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794
| | - Guinevere Ashley
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064
| | - James M Ragle
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064
| | - Londen Johnson
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064
| | - Joseph Aguilera
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064
| | | | - Jordan D Ward
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064
| | - David Q Matus
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794,
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22
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Medwig-Kinney TN, Smith JJ, Palmisano NJ, Tank S, Zhang W, Matus DQ. A developmental gene regulatory network for C. elegans anchor cell invasion. Development 2020; 147:dev185850. [PMID: 31806663 PMCID: PMC6983719 DOI: 10.1242/dev.185850] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 11/25/2019] [Indexed: 01/02/2023]
Abstract
Cellular invasion is a key part of development, immunity and disease. Using an in vivo model of Caenorhabditis elegans anchor cell invasion, we characterize the gene regulatory network that promotes cell invasion. The anchor cell is initially specified in a stochastic cell fate decision mediated by Notch signaling. Previous research has identified four conserved transcription factors, fos-1 (Fos), egl-43 (EVI1/MEL), hlh-2 (E/Daughterless) and nhr-67 (NR2E1/TLX), that mediate anchor cell specification and/or invasive behavior. Connections between these transcription factors and the underlying cell biology that they regulate are poorly understood. Here, using genome editing and RNA interference, we examine transcription factor interactions before and after anchor cell specification. Initially, these transcription factors function independently of one another to regulate LIN-12 (Notch) activity. Following anchor cell specification, egl-43, hlh-2 and nhr-67 function largely parallel to fos-1 in a type I coherent feed-forward loop with positive feedback to promote invasion. Together, these results demonstrate that the same transcription factors can function in cell fate specification and differentiated cell behavior, and that a gene regulatory network can be rapidly assembled to reinforce a post-mitotic, pro-invasive state.
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Affiliation(s)
- Taylor N Medwig-Kinney
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Jayson J Smith
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Nicholas J Palmisano
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Sujata Tank
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
- Science and Technology Research Program, Smithtown High School East, St. James, NY 11780-1833, USA
| | - Wan Zhang
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - David Q Matus
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
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23
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Abstract
The auxin-inducible degron (AID) technology was recently adapted for use in the nematode Caenorhabditis elegans. Rapid degradation of C. elegans proteins tagged with an AID is mediated by a plant-specific F-box protein, transport inhibitor response 1 (TIR1), and occurs only in the presence of the phytohormone auxin. The first iteration of this technology elicited protein degradation in C. elegans through a naturally occurring form of auxin, indole-3-acetic acid (IAA). Here, we present a protocol that uses 1-naphthaleneacetic acid, potassium salt (K-NAA), an indole-free synthetic auxin analog. At equal concentration, K-NAA is as effective as IAA in standard nematode growth media (NGM). K-NAA is also effective in physiological buffer (M9), allowing for high-throughput experimentation. The main advantages of K-NAA are twofold: first, its photostability prevents light-induced compound degradation during storage and the production of toxic indole-derivatives during fluorescence microscopy of live cells; and second, its water solubility eliminates the need of using ethanol to dissolve the auxin compound, a solvent that may confound C. elegans lifespan and behavioral assays. In this protocol, we describe our method of degrading C. elegans proteins using K-NAA on solid and in liquid media, as well as our method of analyzing protein degradation.
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Affiliation(s)
- Michael A Q Martinez
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA
| | - David Q Matus
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA
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24
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Kelley LC, Chi Q, Cáceres R, Hastie E, Schindler AJ, Jiang Y, Matus DQ, Plastino J, Sherwood DR. Adaptive F-Actin Polymerization and Localized ATP Production Drive Basement Membrane Invasion in the Absence of MMPs. Dev Cell 2019; 48:313-328.e8. [PMID: 30686527 PMCID: PMC6372315 DOI: 10.1016/j.devcel.2018.12.018] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 11/07/2018] [Accepted: 12/20/2018] [Indexed: 12/21/2022]
Abstract
Matrix metalloproteinases (MMPs) are associated with decreased patient prognosis but have failed as anti-invasive drug targets despite promoting cancer cell invasion. Through time-lapse imaging, optical highlighting, and combined genetic removal of the five MMPs expressed during anchor cell (AC) invasion in C. elegans, we find that MMPs hasten invasion by degrading basement membrane (BM). Though irregular and delayed, AC invasion persists in MMP- animals via adaptive enrichment of the Arp2/3 complex at the invasive cell membrane, which drives formation of an F-actin-rich protrusion that physically breaches and displaces BM. Using a large-scale RNAi synergistic screen and a genetically encoded ATP FRET sensor, we discover that mitochondria enrich within the protrusion and provide localized ATP that fuels F-actin network growth. Thus, without MMPs, an invasive cell can alter its BM-breaching tactics, suggesting that targeting adaptive mechanisms will be necessary to mitigate BM invasion in human pathologies.
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Affiliation(s)
- Laura C Kelley
- Department of Biology, Regeneration Next, Duke University, Box 90338, Durham, NC 27708, USA
| | - Qiuyi Chi
- Department of Biology, Regeneration Next, Duke University, Box 90338, Durham, NC 27708, USA
| | - Rodrigo Cáceres
- CNRS, Laboratoire Physico Chimie Curie, Institut Curie, PSL Research Université, Paris 75005, France; Sorbonne Université, Paris 75005, France; Université Paris Descartes, Sorbonne Paris Cité, Paris 75005, France
| | - Eric Hastie
- Department of Biology, Regeneration Next, Duke University, Box 90338, Durham, NC 27708, USA
| | - Adam J Schindler
- Department of Biology, Regeneration Next, Duke University, Box 90338, Durham, NC 27708, USA
| | - Yue Jiang
- Department of Biology, Regeneration Next, Duke University, Box 90338, Durham, NC 27708, USA
| | - David Q Matus
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Julie Plastino
- CNRS, Laboratoire Physico Chimie Curie, Institut Curie, PSL Research Université, Paris 75005, France; Sorbonne Université, Paris 75005, France
| | - David R Sherwood
- Department of Biology, Regeneration Next, Duke University, Box 90338, Durham, NC 27708, USA.
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25
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Liu TL, Upadhyayula S, Milkie DE, Singh V, Wang K, Swinburne IA, Mosaliganti KR, Collins ZM, Hiscock TW, Shea J, Kohrman AQ, Medwig TN, Dambournet D, Forster R, Cunniff B, Ruan Y, Yashiro H, Scholpp S, Meyerowitz EM, Hockemeyer D, Drubin DG, Martin BL, Matus DQ, Koyama M, Megason SG, Kirchhausen T, Betzig E. Observing the cell in its native state: Imaging subcellular dynamics in multicellular organisms. Science 2018; 360:eaaq1392. [PMID: 29674564 PMCID: PMC6040645 DOI: 10.1126/science.aaq1392] [Citation(s) in RCA: 289] [Impact Index Per Article: 48.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 02/19/2018] [Indexed: 01/10/2023]
Abstract
True physiological imaging of subcellular dynamics requires studying cells within their parent organisms, where all the environmental cues that drive gene expression, and hence the phenotypes that we actually observe, are present. A complete understanding also requires volumetric imaging of the cell and its surroundings at high spatiotemporal resolution, without inducing undue stress on either. We combined lattice light-sheet microscopy with adaptive optics to achieve, across large multicellular volumes, noninvasive aberration-free imaging of subcellular processes, including endocytosis, organelle remodeling during mitosis, and the migration of axons, immune cells, and metastatic cancer cells in vivo. The technology reveals the phenotypic diversity within cells across different organisms and developmental stages and may offer insights into how cells harness their intrinsic variability to adapt to different physiological environments.
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Affiliation(s)
- Tsung-Li Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Srigokul Upadhyayula
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
- Department of Cell Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, 200 Longwood Avenue, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Daniel E Milkie
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Ved Singh
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Kai Wang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Ian A Swinburne
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Kishore R Mosaliganti
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Zach M Collins
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Tom W Hiscock
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Jamien Shea
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Abraham Q Kohrman
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Taylor N Medwig
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Daphne Dambournet
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ryan Forster
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Brian Cunniff
- Department of Cell Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Yuan Ruan
- Howard Hughes Medical Institute and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Hanako Yashiro
- Howard Hughes Medical Institute and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Steffen Scholpp
- Living Systems Institute, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, 76021 Karlsruhe, Germany
| | - Elliot M Meyerowitz
- Howard Hughes Medical Institute and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Dirk Hockemeyer
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - David G Drubin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Benjamin L Martin
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - David Q Matus
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Minoru Koyama
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Sean G Megason
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Tom Kirchhausen
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
- Department of Cell Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, 200 Longwood Avenue, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Eric Betzig
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.
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26
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Medwig TN, Matus DQ. Breaking down barriers: the evolution of cell invasion. Curr Opin Genet Dev 2017; 47:33-40. [PMID: 28881331 DOI: 10.1016/j.gde.2017.08.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 08/02/2017] [Accepted: 08/11/2017] [Indexed: 12/12/2022]
Abstract
Cell invasion is a specialized cell behavior that likely co-evolved with the emergence of basement membranes in metazoans as a mechanism to break down the barriers that separate tissues. A variety of conserved and lineage-specific biological processes that occur during development and homeostasis rely on cell invasive behavior. Recent innovations in genome editing and live-cell imaging have shed some light on the programs that mediate acquisition of an invasive phenotype; however, comparative approaches among species are necessary to understand how this cell behavior evolved. Here, we discuss the contexts of cell invasion, highlighting both established and emerging model systems, and underscore gaps in our understanding of the evolution of this key cellular behavior.
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Affiliation(s)
- Taylor N Medwig
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - David Q Matus
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA.
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27
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Goto H, Kimmey SC, Row RH, Matus DQ, Martin BL. FGF and canonical Wnt signaling cooperate to induce paraxial mesoderm from tailbud neuromesodermal progenitors through regulation of a two-step epithelial to mesenchymal transition. Development 2017; 144:1412-1424. [PMID: 28242612 DOI: 10.1242/dev.143578] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 02/16/2017] [Indexed: 12/17/2022]
Abstract
Mesoderm induction begins during gastrulation. Recent evidence from several vertebrate species indicates that mesoderm induction continues after gastrulation in neuromesodermal progenitors (NMPs) within the posteriormost embryonic structure, the tailbud. It is unclear to what extent the molecular mechanisms of mesoderm induction are conserved between gastrula and post-gastrula stages of development. Fibroblast growth factor (FGF) signaling is required for mesoderm induction during gastrulation through positive transcriptional regulation of the T-box transcription factor brachyury We find in zebrafish that FGF is continuously required for paraxial mesoderm (PM) induction in post-gastrula NMPs. FGF signaling represses the NMP markers brachyury (ntla) and sox2 through regulation of tbx16 and msgn1, thereby committing cells to a PM fate. FGF-mediated PM induction in NMPs functions in tight coordination with canonical Wnt signaling during the epithelial to mesenchymal transition (EMT) from NMP to mesodermal progenitor. Wnt signaling initiates EMT, whereas FGF signaling terminates this event. Our results indicate that germ layer induction in the zebrafish tailbud is not a simple continuation of gastrulation events.
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Affiliation(s)
- Hana Goto
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Samuel C Kimmey
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Richard H Row
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - David Q Matus
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Benjamin L Martin
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
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28
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Abstract
Cell invasion through the basement membrane (BM) occurs during normal embryonic development and is a fundamental feature of cancer metastasis. The underlying cellular and genetic machinery required for invasion has been difficult to identify, due to a lack of adequate in vivo models to accurately examine invasion in single cells at subcellular resolution. Recent evidence has documented a functional link between cell cycle arrest and invasive activity. While cancer progression is traditionally thought of as a disease of uncontrolled cell proliferation, cancer cell dissemination, a critical aspect of metastasis, may require a switch from a proliferative to an invasive state. In this work, we review evidence that BM invasion requires cell cycle arrest and discuss the implications of this concept with regard to limiting the lethality associated with cancer metastasis.
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Affiliation(s)
- Abraham Q Kohrman
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - David Q Matus
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA.
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Kohrman AQ, Chandhok M, Zhang W, Matus DQ. Abstract A18: G1 cell cycle arrest is required for invasive behavior. Mol Cancer Res 2016. [DOI: 10.1158/1557-3125.cellcycle16-a18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The ability for a cell to breach the surrounding basement membrane and adopt an invasive phenotype is a critical, but poorly understood step in the progression of cancer. Like many aspects of cancer cell behavior, the genetic programs that regulate invasive behavior are likely shared with normal cell biological processes, as invasion occurs during embryonic development and immune surveillance. Due to difficulties of studying this dynamic behavior in vivo, elucidating the genetic and epigenetic controls of cell invasive activity has been difficult. Our laboratory uses a unique in vivo model to examine cell invasion that combines functional genomic and genetic tools with single-cell high resolution visual analyses. We examine anchor cell (AC) invasion into the vulval epithelium during the larval development of the model roundworm, C. elegans. Our data functionally links G1 cell cycle arrest to acquisition of invasive behavior. Previously we have identified that a single transcription factor, the conserved nuclear hormone receptor nhr-67 (NR2E1/TLX) is required in the AC to prevent the invasive AC from entering the cell cycle. NHR-67 maintains the AC in G1 cell cycle arrest, in part through upregulation of the cyclin-dependent kinase inhibitor cki-1 (p21CIP1/p27Kip1). Loss of nhr-67 results in non-invasive mitotic ACs that fail to express matrix metalloproteinases (MMPs) and actin regulators or form invadopodia, F-actin rich membrane-localized protrusions that are required for invasion. Strikingly, AC invasion can be rescued through induction of G1 arrest, preventing cell division and promoting differentiation. Downstream of G1 arrest, the AC requires the activity of the conserved histone deacetylase HDA-1, a key regulator of cell differentiation, to regulate the expression of pro-invasive genes and localize invadopodia. Through loss-of-function RNA interference (RNAi) screening, we have identified new cell cycle regulatory components (lin-35/RB, skr-2/SKP1, cdc-14/CDC14A, cul-1/ Cullin-1 and cul-4/ Cullin-4B) and epigenetic modifiers (let-418/Mi-2/CHD3 and Swi/snf-components) that function with cki-1 and hda-1, respectively, to maintain G1 cell cycle arrest and differentiate the invasive phenotype. Together our results suggest that the acquisition of the invasive phenotype is a post-mitotic differentiated state, which may help explain the paradoxical reports that the invasive fronts of many metastatic cancers are non-proliferative.
Citation Format: Abraham Q. Kohrman, Mana Chandhok, Wan Zhang, David Q. Matus. G1 cell cycle arrest is required for invasive behavior. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Cancer Cell Cycle - Tumor Progression and Therapeutic Response; Feb 28-Mar 2, 2016; Orlando, FL. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(11_Suppl):Abstract nr A18.
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Affiliation(s)
| | | | - Wan Zhang
- Stony Brook University, Stony Brook, NY
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Matus DQ, Lohmer LL, Kelley LC, Schindler AJ, Kohrman AQ, Barkoulas M, Zhang W, Chi Q, Sherwood DR. Invasive Cell Fate Requires G1 Cell-Cycle Arrest and Histone Deacetylase-Mediated Changes in Gene Expression. Dev Cell 2016; 35:162-74. [PMID: 26506306 DOI: 10.1016/j.devcel.2015.10.002] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 10/01/2015] [Accepted: 10/02/2015] [Indexed: 12/19/2022]
Abstract
Despite critical roles in development and cancer, the mechanisms that specify invasive cellular behavior are poorly understood. Through a screen of transcription factors in Caenorhabditis elegans, we identified G1 cell-cycle arrest as a precisely regulated requirement of the anchor cell (AC) invasion program. We show that the nuclear receptor nhr-67/tlx directs the AC into G1 arrest in part through regulation of the cyclin-dependent kinase inhibitor cki-1. Loss of nhr-67 resulted in non-invasive, mitotic ACs that failed to express matrix metalloproteinases or actin regulators and lack invadopodia, F-actin-rich membrane protrusions that facilitate invasion. We further show that G1 arrest is necessary for the histone deacetylase HDA-1, a key regulator of differentiation, to promote pro-invasive gene expression and invadopodia formation. Together, these results suggest that invasive cell fate requires G1 arrest and that strategies targeting both G1-arrested and actively cycling cells may be needed to halt metastatic cancer.
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Affiliation(s)
- David Q Matus
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA; Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA.
| | - Lauren L Lohmer
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
| | - Laura C Kelley
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
| | - Adam J Schindler
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
| | - Abraham Q Kohrman
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Michalis Barkoulas
- Department of Life Sciences, Imperial College London, Imperial College Road SAF Building, London SW7 2AZ, UK
| | - Wan Zhang
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Qiuyi Chi
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
| | - David R Sherwood
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA.
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Moczek AP, Sears KE, Stollewerk A, Wittkopp PJ, Diggle P, Dworkin I, Ledon-Rettig C, Matus DQ, Roth S, Abouheif E, Brown FD, Chiu CH, Cohen CS, Tomaso AWD, Gilbert SF, Hall B, Love AC, Lyons DC, Sanger TJ, Smith J, Specht C, Vallejo-Marin M, Extavour CG. The significance and scope of evolutionary developmental biology: a vision for the 21st century. Evol Dev 2015; 17:198-219. [PMID: 25963198 DOI: 10.1111/ede.12125] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Evolutionary developmental biology (evo-devo) has undergone dramatic transformations since its emergence as a distinct discipline. This paper aims to highlight the scope, power, and future promise of evo-devo to transform and unify diverse aspects of biology. We articulate key questions at the core of eleven biological disciplines-from Evolution, Development, Paleontology, and Neurobiology to Cellular and Molecular Biology, Quantitative Genetics, Human Diseases, Ecology, Agriculture and Science Education, and lastly, Evolutionary Developmental Biology itself-and discuss why evo-devo is uniquely situated to substantially improve our ability to find meaningful answers to these fundamental questions. We posit that the tools, concepts, and ways of thinking developed by evo-devo have profound potential to advance, integrate, and unify biological sciences as well as inform policy decisions and illuminate science education. We look to the next generation of evolutionary developmental biologists to help shape this process as we confront the scientific challenges of the 21st century.
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Affiliation(s)
- Armin P Moczek
- Department of Biology, Indiana University, 915 East 3rd Street, Bloomington, IN 47405, USA
| | - Karen E Sears
- School of Integrative Biology and Institute for Genomic Biology, University of Illinois, 505 South Goodwin Avenue, Urbana, IL, 61801, USA
| | - Angelika Stollewerk
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London, E1 4NS, UK
| | - Patricia J Wittkopp
- Department of Ecology and Evolutionary Biology, Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Pamela Diggle
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - Ian Dworkin
- Department of Biology, McMaster University, 1280 Main St. West Hamilton, Ontario, L8S 4K1, Canada
| | - Cristina Ledon-Rettig
- Department of Biology, Indiana University, 915 East 3rd Street, Bloomington, IN 47405, USA
| | - David Q Matus
- Department of Biochemistry and Cell Biology, Stony Brook University, 412 Life Sciences Building, Stony Brook, NY, 11794-5215, USA
| | - Siegfried Roth
- University of Cologne, Institute of Developmental Biology, Biocenter, Zülpicher Straße 47b, D-50674, Cologne, Germany
| | - Ehab Abouheif
- Department of Biology, McGill University, 1205 Avenue Docteur Penfield, Montréal Québec, H3A 1B1, Canada
| | - Federico D Brown
- Departamento de Zoologia, Instituto Biociências, Universidade de São Paulo, Rua do Matão, Travessa 14, no. 101, 05508-090, São Paulo, Brazil
| | - Chi-Hua Chiu
- Department of Biological Sciences, Kent State University, OH, USA
| | - C Sarah Cohen
- Biology Department, Romberg Tiburon Center for Environmental Studies, San Francisco State University, 3150 Paradise Drive, Tiburon, CA, 94920, USA
| | | | - Scott F Gilbert
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania 19081, USA and Biotechnology Institute, University of Helsinki, 00014, Helsinki, Finland
| | - Brian Hall
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, CA, B3H 4R2, USA
| | - Alan C Love
- Department of Philosophy, Minnesota Center for Philosophy of Science, University of Minnesota, USA
| | - Deirdre C Lyons
- Department of Biology, Duke University, Box 90338, Durham, NC, 27708, USA
| | - Thomas J Sanger
- Department of Molecular Genetics and Microbiology, University of Florida, P.O. Box 103610, Gainesville, FL, 32610, USA
| | - Joel Smith
- Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA, 02543, USA
| | - Chelsea Specht
- Plant and Microbial Biology, Department of Integrative Biology, University and Jepson Herbaria, University of California, Berkeley, CA, USA
| | - Mario Vallejo-Marin
- Biological and Environmental Sciences, University of Stirling, FK9 4LA, Scotland, UK
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, BioLabs 4103, Cambridge, MA, 02138, USA
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Matus DQ, Chang E, Makohon-Moore SC, Hagedorn MA, Chi Q, Sherwood DR. Cell division and targeted cell cycle arrest opens and stabilizes basement membrane gaps. Nat Commun 2014; 5:4184. [PMID: 24924309 PMCID: PMC4138880 DOI: 10.1038/ncomms5184] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Accepted: 05/21/2014] [Indexed: 12/13/2022] Open
Abstract
Large gaps in basement membrane (BM) occur during organ remodelling and cancer cell invasion. Whether dividing cells, which temporarily reduce their attachment to BM, influence these breaches is unknown. Here we analyse uterine-vulval attachment during development across 21 species of rhabditid nematodes and find that the BM gap that forms between these organs is always bounded by a non-dividing vulval cell. Through cell cycle manipulation and live cell imaging in Caenorhabditis elegans, we show that actively dividing vulval cells facilitate enlargement of this breach by promoting BM movement. In contrast, targeted cell cycle arrest halts BM movement and limits gap opening. Further, we demonstrate that the BM component laminin accumulates at the BM gap edge and promotes increased integrin levels in non-dividing vulval cells, stabilizing gap position. Together, these studies reveal that cell division can be used as a mechanism to regulate BM breaches, thus controlling the exchange of cells between tissues.
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Affiliation(s)
- David Q Matus
- 1] Department of Biology, Duke University, Durham, North Carolina 27705, USA [2]
| | - Emily Chang
- 1] Department of Biology, Duke University, Durham, North Carolina 27705, USA [2]
| | | | - Mary A Hagedorn
- Department of Biology, Duke University, Durham, North Carolina 27705, USA
| | - Qiuyi Chi
- Department of Biology, Duke University, Durham, North Carolina 27705, USA
| | - David R Sherwood
- Department of Biology, Duke University, Durham, North Carolina 27705, USA
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Marlow H, Matus DQ, Martindale MQ. Ectopic activation of the canonical wnt signaling pathway affects ectodermal patterning along the primary axis during larval development in the anthozoan Nematostella vectensis. Dev Biol 2013; 380:324-34. [PMID: 23722001 DOI: 10.1016/j.ydbio.2013.05.022] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 04/22/2013] [Accepted: 05/20/2013] [Indexed: 10/26/2022]
Abstract
The primary axis of cnidarians runs from the oral pole to the apical tuft and defines the major body axis of both the planula larva and adult polyp. In the anthozoan cnidarian Nematostella vectensis, the primary oral-aboral (O-Ab) axis first develops during the early embryonic stage. Here, we present evidence that pharmaceutical activators of canonical wnt signaling affect molecular patterning along the primary axis of Nematostella. Although not overtly morphologically complex, molecular investigations in Nematostella reveal that the O-Ab axis is demarcated by the expression of differentially localized signaling molecules and transcription factors that may serve roles in establishing distinct ectodermal domains. We have further characterized the larval epithelium by determining the position of a nested set of molecular boundaries, utilizing several newly characterized as well as previously reported epithelial markers along the primary axis. We have assayed shifts in their position in control embryos and in embryos treated with the pharmacological agents alsterpaullone and azakenpaullone, Gsk3β inhibitors that act as canonical wnt agonists, and the Wnt antagonist iCRT14, following gastrulation. Agonist drug treatments result in an absence of aboral markers, a shift in the expression boundaries of oral markers toward the aboral pole, and changes in the position of differentially localized populations of neurons in a dose-dependent manner, while antagonist treatment had the opposite effect. These experiments are consistent with canonical wnt signaling playing a role in an orally localized wnt signaling center. These findings suggest that in Nematostella, wnt signaling mediates O-Ab ectodermal patterning across a surprisingly complex epithelium in planula stages following gastrulation in addition to previously described roles for the wnt signaling pathway in endomesoderm specification during gastrulation and overall animal-vegetal patterning at earlier stages of anthozoan development.
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Affiliation(s)
- Heather Marlow
- Kewalo Marine Laboratory, University of Hawaii, 41 Ahui Street, Honolulu, HI 96813, USA
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Matus DQ, Sherwood DR, VanHook AM. Science Signaling
Podcast: 11 May 2010. Sci Signal 2010. [DOI: 10.1126/scisignal.3121pc10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Genes that affect development of the nematode gonad are implicated in cell invasion and metastasis.
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Affiliation(s)
- David Q. Matus
- Biology Department, Duke University, Durham, NC 27708, USA
| | | | - Annalisa M. VanHook
- Associate Online Editor of Science Signaling, American Association for the Advancement of Science, 1200 New York Avenue, N.W., Washington, DC 20005, USA
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Matus DQ, Li XY, Durbin S, Agarwal D, Chi Q, Weiss SJ, Sherwood DR. In vivo identification of regulators of cell invasion across basement membranes. Sci Signal 2010; 3:ra35. [PMID: 20442418 DOI: 10.1126/scisignal.2000654] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Cell invasion through basement membranes during development, immune surveillance, and metastasis remains poorly understood. To gain further insight into this key cellular behavior, we performed an in vivo screen for regulators of cell invasion through basement membranes, using the simple model of Caenorhabditis elegans anchor cell invasion, and identified 99 genes that promote invasion, including the genes encoding the chaperonin complex cct. Notably, most of these genes have not been previously implicated in invasive cell behavior. We characterized members of the cct complex and 11 other gene products, determining the distinct aspects of the invasive cascade that they regulate, including formation of a specialized invasive cell membrane and its ability to breach the basement membrane. RNA interference-mediated knockdown of the human orthologs of cct-5 and lit-1, which had not previously been implicated in cell invasion, reduced the invasiveness of metastatic carcinoma cells, suggesting that a conserved genetic program underlies cell invasion. These results increase our understanding of the genetic underpinnings of cell invasion and also provide new potential therapeutic targets to limit this behavior.
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Affiliation(s)
- David Q Matus
- Biology Department, Duke University, Durham, NC 27708, USA
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Ziel JW, Matus DQ, Sherwood DR. An expression screen for RhoGEF genes involved in C. elegans gonadogenesis. Gene Expr Patterns 2009; 9:397-403. [PMID: 19540360 DOI: 10.1016/j.gep.2009.06.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2009] [Revised: 06/04/2009] [Accepted: 06/12/2009] [Indexed: 11/18/2022]
Abstract
The gonad in Caenorhabditis elegans is an important model system for understanding complex morphogenetic processes including cellular movement, cell fusion, cell invasion and cell polarity during development. One class of signaling proteins known to be critical for the cellular events underlying morphogenesis is the Rho family GTPases, particularly RhoA, Rac and Cdc42. In C. elegans orthologues of these genes have been shown to be important for gonad development. In our current study we have extended those findings by examining the patterns of 5'cis-regulatory element (5'CRE) activity associated with nineteen putative guanine nucleotide exchange factors (GEFs) encoded by the C. elegans genome predicted to activate Rho family GTPases. Here we identify 13 RhoGEF genes that are expressed during gonadogenesis and characterize the cells in which their 5'CREs are active. These data provide the basis for designing experiments to examine Rho GTPase activation during morphogenetic processes central to normal gonad development.
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Affiliation(s)
- Joshua W Ziel
- Department of Biology, Duke University, Durham, NC 27708, USA
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Marlow HQ, Srivastava M, Matus DQ, Rokhsar D, Martindale MQ. Anatomy and development of the nervous system of Nematostella vectensis, an anthozoan cnidarian. Dev Neurobiol 2009; 69:235-54. [PMID: 19170043 DOI: 10.1002/dneu.20698] [Citation(s) in RCA: 158] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Nematostella vectensis, an anthozoan cnidarian, whose genome has been sequenced and is suitable for developmental and ecological studies, has a complex neural morphology that is modified during development from the larval to adult form. N. vectensis' nervous system is a diffuse nerve net with both ectodermal sensory and effector cells and endodermal multipolar ganglion cells. This nerve net consists of several distinct neural territories along the oral-aboral axis including the pharyngeal and oral nerve rings, and the larval apical tuft. These neuralized regions correspond to expression of conserved bilaterian neural developmental regulatory genes including homeodomain transcription factors and NCAMs. Early neurons and stem cell populations identified with NvMsi, NvELAV, and NvGCM, indicate that neural differentiation occurs throughout the animal and initiates prior to the conclusion of gastrulation. Neural specification in N. vectensis appears to occur through an independent mechanism from that in the classical cnidarian model Hydra.
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Affiliation(s)
- Heather Q Marlow
- Kewalo Marine Laboratory, Pacific Biomedical Research Center, University of Hawaii, Honolulu, Hawaii 96813, USA
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Fröbius AC, Matus DQ, Seaver EC. Genomic organization and expression demonstrate spatial and temporal Hox gene colinearity in the lophotrochozoan Capitella sp. I. PLoS One 2008; 3:e4004. [PMID: 19104667 PMCID: PMC2603591 DOI: 10.1371/journal.pone.0004004] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2008] [Accepted: 11/21/2008] [Indexed: 11/29/2022] Open
Abstract
Hox genes define regional identities along the anterior–posterior axis in many animals. In a number of species, Hox genes are clustered in the genome, and the relative order of genes corresponds with position of expression in the body. Previous Hox gene studies in lophotrochozoans have reported expression for only a subset of the Hox gene complement and/or lack detailed genomic organization information, limiting interpretations of spatial and temporal colinearity in this diverse animal clade. We studied expression and genomic organization of the single Hox gene complement in the segmented polychaete annelid Capitella sp. I. Total genome searches identified 11 Hox genes in Capitella, representing 11 distinct paralog groups thought to represent the ancestral lophotrochozoan complement. At least 8 of the 11 Capitella Hox genes are genomically linked in a single cluster, have the same transcriptional orientation, and lack interspersed non-Hox genes. Studying their expression by situ hybridization, we find that the 11 Capitella Hox genes generally exhibit spatial and temporal colinearity. With the exception of CapI-Post1, Capitella Hox genes are all expressed in broad ectodermal domains during larval development, consistent with providing positional information along the anterior–posterior axis. The anterior genes CapI-lab, CapI-pb, and CapI-Hox3 initiate expression prior to the appearance of segments, while more posterior genes appear at or soon after segments appear. Many of the Capitella Hox genes have either an anterior or posterior expression boundary coinciding with the thoracic–abdomen transition, a major body tagma boundary. Following metamorphosis, several expression patterns change, including appearance of distinct posterior boundaries and restriction to the central nervous system. Capitella Hox genes have maintained a clustered organization, are expressed in the canonical anterior–posterior order found in other metazoans, and exhibit spatial and temporal colinearity, reflecting Hox gene characteristics that likely existed in the protostome–deuterostome ancestor.
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Affiliation(s)
- Andreas C. Fröbius
- Kewalo Marine Lab, Pacific Biosciences Research Center, University of Hawaii, Honolulu, Hawaii, United States of America
| | - David Q. Matus
- Kewalo Marine Lab, Pacific Biosciences Research Center, University of Hawaii, Honolulu, Hawaii, United States of America
| | - Elaine C. Seaver
- Kewalo Marine Lab, Pacific Biosciences Research Center, University of Hawaii, Honolulu, Hawaii, United States of America
- * E-mail:
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Dunn CW, Hejnol A, Matus DQ, Pang K, Browne WE, Smith SA, Seaver E, Rouse GW, Obst M, Edgecombe GD, Sørensen MV, Haddock SHD, Schmidt-Rhaesa A, Okusu A, Kristensen RM, Wheeler WC, Martindale MQ, Giribet G. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 2008; 452:745-9. [PMID: 18322464 DOI: 10.1038/nature06614] [Citation(s) in RCA: 1252] [Impact Index Per Article: 78.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2007] [Accepted: 12/20/2007] [Indexed: 11/09/2022]
Abstract
Long-held ideas regarding the evolutionary relationships among animals have recently been upended by sometimes controversial hypotheses based largely on insights from molecular data. These new hypotheses include a clade of moulting animals (Ecdysozoa) and the close relationship of the lophophorates to molluscs and annelids (Lophotrochozoa). Many relationships remain disputed, including those that are required to polarize key features of character evolution, and support for deep nodes is often low. Phylogenomic approaches, which use data from many genes, have shown promise for resolving deep animal relationships, but are hindered by a lack of data from many important groups. Here we report a total of 39.9 Mb of expressed sequence tags from 29 animals belonging to 21 phyla, including 11 phyla previously lacking genomic or expressed-sequence-tag data. Analysed in combination with existing sequences, our data reinforce several previously identified clades that split deeply in the animal tree (including Protostomia, Ecdysozoa and Lophotrochozoa), unambiguously resolve multiple long-standing issues for which there was strong conflicting support in earlier studies with less data (such as velvet worms rather than tardigrades as the sister group of arthropods), and provide molecular support for the monophyly of molluscs, a group long recognized by morphologists. In addition, we find strong support for several new hypotheses. These include a clade that unites annelids (including sipunculans and echiurans) with nemerteans, phoronids and brachiopods, molluscs as sister to that assemblage, and the placement of ctenophores as the earliest diverging extant multicellular animals. A single origin of spiral cleavage (with subsequent losses) is inferred from well-supported nodes. Many relationships between a stable subset of taxa find strong support, and a diminishing number of lineages remain recalcitrant to placement on the tree.
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Affiliation(s)
- Casey W Dunn
- Kewalo Marine Laboratory, PBRC, University of Hawaii, 41 Ahui Street, Honolulu, Hawaii 96813, USA.
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Affiliation(s)
- Maja Adamska
- School of Integrative Biology, The University of Queensland, Brisbane Queensland 4072, Australia
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Abstract
Chaetognaths are transparent marine animals that are ubiquitous and abundant members of oceanic zooplanktonic communities. Their phylogenetic position within the Metazoa, however, has remained obscure since their discovery. Morphology and embryology have traditionally allied chaetognaths with deuterostomes, but molecular evidence suggests otherwise. Two recent multigene expressed sequence tag (EST) molecular phylogenomic studies suggest that chaetognaths are either sister to the Lophotrochozoa (Matus et al. 2006) or to all protostomes (Marlétaz et al. 2006). We have isolated eight Hox genes, one Parahox gene, and Mox, a related homeodomain gene, from the pelagic chaetognath, Flaccisagitta enflata. Although chaetognath central class Hox genes lack the Lox5 or "spiralian" parapeptide, a diagnostic amino-acid motif that has been utilized previously to assign lophotrochozoan affinity, they do possess a central class Hox gene that has a partial "Ubd-A peptide" found in both ecdysozoan and lophotrochozoan Ubx/Abd-A/Lox2/Lox4 genes. Additionally, we report the presence of two distinct chaetognath posterior Hox genes that possess both ecdysozoan and lophotrochozoan signature amino-acid motifs. The phylogenetic position of chaetognaths, as well as the evolution of the Hox cluster, is discussed in light of these data.
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Affiliation(s)
- David Q Matus
- *Kewalo Marine Laboratory, University of Hawaii, 41 Ahui Street, Honolulu, HI 96813, USA; Biological Sciences, Auburn University, 101 Rouse, Auburn, AL 36830, USA
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Abstract
Pax genes are a family of homeodomain transcription factors that have been isolated from protostomes (e.g., eight in Drosophilia) and deuterostomes (e.g., nine in vertebrates) as well as outside the Bilateria, from sponges, a placozoan, and several classes of cnidarians. The genome of an anthozoan cnidarian, the starlet sea anemone, Nematostella vectensis, has been surveyed by both degenerate polymerase chain reaction and in silico for the presence of Pax genes. N. vectensis possesses seven Pax genes, which are orthologous to cnidarian Pax genes (A,B,C, and D) previously identified in another anthozoan, a coral, Acropora millepora. Phylogenetic analyses including data from nonchordate deuterostomes indicates that there were five Pax gene classes in the protostome-deuterostome ancestor, but only three in the cnidarian-bilaterian ancestor, with PaxD class genes lost in medusozoan cnidarians. Pax genes play diverse roles in bilaterians, including eye formation (e.g., Pax6), segmentation (e.g., Pax3/7 class genes), and neural patterning (e.g., Pox-neuro, Pax2/5/8). We show the first expression data for members of all four Pax classes in a single species of cnidarian. N. vectensis Pax genes are expressed in both a cell-type and region-specific manner during embryogenesis, and likely play a role in patterning specific components of the cnidarian ectodermal nerve net. The results of these patterns are discussed with respect to Pax gene evolution in the Bilateria.
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Affiliation(s)
- David Q Matus
- Kewalo Marine Lab, Pacific Bioscience Research Center, University of Hawaii, Honolulu, HI 96813, USA
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Matus DQ, Thomsen GH, Martindale MQ. FGF signaling in gastrulation and neural development in Nematostella vectensis, an anthozoan cnidarian. Dev Genes Evol 2007; 217:137-48. [PMID: 17237944 PMCID: PMC4580332 DOI: 10.1007/s00427-006-0122-3] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2006] [Accepted: 11/03/2006] [Indexed: 11/26/2022]
Abstract
The fibroblast growth factor (FGF) signal transduction pathway serves as one of the key regulators of early metazoan development, displaying conserved roles in the specification of endodermal, mesodermal, and neural fates during vertebrate development. FGF signals also regulate gastrulation, in part, by triggering epithelial to mesenchymal transitions in embryos of both vertebrates and invertebrates. Thus, FGF signals coordinate gastrulation movements across many different phyla. To help understand the breadth of FGF signaling deployment across the animal kingdom, we have examined the presence and expression of genes encoding FGF pathway components in the anthozoan cnidarian Nematostella vectensis. We isolated three FGF ligands (NvFGF8A, NvFGF8B, and NvFGF1A), two FGF receptors (NvFGFRa and NvFGFRb), and two orthologs of vertebrate FGF responsive genes, Sprouty (NvSprouty), an inhibitor of FGF signaling, and Churchill (NvChurchill), a Zn finger transcription factor. We found these FGF ligands, receptors, and response gene expressed asymmetrically along the oral/aboral axis during gastrulation and in a developing chemosensory structure of planula stages known as the apical tuft. These results suggest a conserved role for FGF signaling molecules in coordinating both gastrulation and neural induction that predates the Cambrian explosion and the origins of the Bilateria.
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Affiliation(s)
- David Q. Matus
- Kewalo Marine Lab, Pacific Bioscience Research Centre, University of Hawai'i, 41 Ahui Street, Honolulu, HI 96813, USA
| | - Gerald H. Thomsen
- Department of Biochemistry and Cell Biology, Center for Developmental Genetics, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Mark Q. Martindale
- Kewalo Marine Lab, Pacific Bioscience Research Centre, University of Hawai'i, 41 Ahui Street, Honolulu, HI 96813, USA
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Ryan JF, Mazza ME, Pang K, Matus DQ, Baxevanis AD, Martindale MQ, Finnerty JR. Pre-bilaterian origins of the Hox cluster and the Hox code: evidence from the sea anemone, Nematostella vectensis. PLoS One 2007; 2:e153. [PMID: 17252055 PMCID: PMC1779807 DOI: 10.1371/journal.pone.0000153] [Citation(s) in RCA: 153] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2006] [Accepted: 11/30/2006] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Hox genes were critical to many morphological innovations of bilaterian animals. However, early Hox evolution remains obscure. Phylogenetic, developmental, and genomic analyses on the cnidarian sea anemone Nematostella vectensis challenge recent claims that the Hox code is a bilaterian invention and that no "true" Hox genes exist in the phylum Cnidaria. METHODOLOGY/PRINCIPAL FINDINGS Phylogenetic analyses of 18 Hox-related genes from Nematostella identify putative Hox1, Hox2, and Hox9+ genes. Statistical comparisons among competing hypotheses bolster these findings, including an explicit consideration of the gene losses implied by alternate topologies. In situ hybridization studies of 20 Hox-related genes reveal that multiple Hox genes are expressed in distinct regions along the primary body axis, supporting the existence of a pre-bilaterian Hox code. Additionally, several Hox genes are expressed in nested domains along the secondary body axis, suggesting a role in "dorsoventral" patterning. CONCLUSIONS/SIGNIFICANCE A cluster of anterior and posterior Hox genes, as well as ParaHox cluster of genes evolved prior to the cnidarian-bilaterian split. There is evidence to suggest that these clusters were formed from a series of tandem gene duplication events and played a role in patterning both the primary and secondary body axes in a bilaterally symmetrical common ancestor. Cnidarians and bilaterians shared a common ancestor some 570 to 700 million years ago, and as such, are derived from a common body plan. Our work reveals several conserved genetic components that are found in both of these diverse lineages. This finding is consistent with the hypothesis that a set of developmental rules established in the common ancestor of cnidarians and bilaterians is still at work today.
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Affiliation(s)
- Joseph F. Ryan
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Maureen E. Mazza
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
| | - Kevin Pang
- Kewalo Marine Laboratory, Pacific Bioscience Research Center, University of Hawaii, Honolulu, Hawaii, United States of America
| | - David Q. Matus
- Kewalo Marine Laboratory, Pacific Bioscience Research Center, University of Hawaii, Honolulu, Hawaii, United States of America
| | - Andreas D. Baxevanis
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Mark Q. Martindale
- Kewalo Marine Laboratory, Pacific Bioscience Research Center, University of Hawaii, Honolulu, Hawaii, United States of America
| | - John R. Finnerty
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
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Matus DQ, Copley RR, Dunn CW, Hejnol A, Eccleston H, Halanych KM, Martindale MQ, Telford MJ. Broad taxon and gene sampling indicate that chaetognaths are protostomes. Curr Biol 2006; 16:R575-6. [PMID: 16890509 DOI: 10.1016/j.cub.2006.07.017] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Matus DQ, Pang K, Marlow H, Dunn CW, Thomsen GH, Martindale MQ. Molecular evidence for deep evolutionary roots of bilaterality in animal development. Proc Natl Acad Sci U S A 2006; 103:11195-200. [PMID: 16837574 PMCID: PMC1544064 DOI: 10.1073/pnas.0601257103] [Citation(s) in RCA: 129] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2006] [Indexed: 11/18/2022] Open
Abstract
Nearly all metazoans show signs of bilaterality, yet it is believed the bilaterians arose from radially symmetric forms hundreds of millions of years ago. Cnidarians (corals, sea anemones, and "jellyfish") diverged from other animals before the radiation of the Bilateria. They are diploblastic and are often characterized as being radially symmetrical around their longitudinal (oral-aboral) axis. We have studied the deployment of orthologs of a number of family members of developmental regulatory genes that are expressed asymmetrically during bilaterian embryogenesis from the sea anemone, Nematostella vectensis. The secreted TGF-beta genes Nv-dpp, Nv-BMP5-8, six TGF-beta antagonists (NvChordin, NvNoggin1, NvNoggin2, NvGremlin, NvFollistatin, and NvFollistatin-like), the homeodomain proteins NvGoosecoid (NvGsc) and NvGbx, and the secreted guidance factor, NvNetrin, were studied. NvDpp, NvChordin, NvNoggin1, NvGsc, and NvNetrin are expressed asymmetrically along the axis perpendicular to the oral-aboral axis, the directive axis. Furthermore, NvGbx, and NvChordin are expressed in restricted domains on the left and right sides of the body, suggesting that the directive axis is homologous with the bilaterian dorsal-ventral axis. The asymmetric expression of NvNoggin1 and NvGsc appear to be maintained by the canonical Wnt signaling pathway. The asymmetric expression of NvNoggin1, NvNetrin, and Hox orthologs NvAnthox7, NvAnthox8, NvAnthox1a, and NvAnthox6, in conjunction with the observation that NvNoggin1 is able to induce a secondary axis in Xenopus embryos argues that N. vectensis could possess antecedents of the organization of the bilaterian central nervous system.
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Affiliation(s)
- David Q. Matus
- *Kewalo Marine Laboratory, Pacific Bioscience Research Center, University of Hawaii, 41 Ahui Street, Honolulu, HI 96813; and
| | - Kevin Pang
- *Kewalo Marine Laboratory, Pacific Bioscience Research Center, University of Hawaii, 41 Ahui Street, Honolulu, HI 96813; and
| | - Heather Marlow
- *Kewalo Marine Laboratory, Pacific Bioscience Research Center, University of Hawaii, 41 Ahui Street, Honolulu, HI 96813; and
| | - Casey W. Dunn
- *Kewalo Marine Laboratory, Pacific Bioscience Research Center, University of Hawaii, 41 Ahui Street, Honolulu, HI 96813; and
| | - Gerald H. Thomsen
- Department of Biochemistry and Cell Biology, Center for Developmental Genetics, Stony Brook University, Stony Brook, NY 11794-5215
| | - Mark Q. Martindale
- *Kewalo Marine Laboratory, Pacific Bioscience Research Center, University of Hawaii, 41 Ahui Street, Honolulu, HI 96813; and
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Abstract
The conserved family of Wnt signaling molecules mediates various developmental processes including governing cell fate, proliferation, and polarity. The diverse developmental functions of the Wnt genes in bilaterians have obscured the evolutionary origin of this important signaling pathway. Recent work in the Cnidaria has shown the diversity of Wnt genes, and regulatory components of Wnt signaling, evolved early in metazoan evolution, prior to the divergence of cnidarians and bilaterians. Evidence from Hydra and the sea anemone, Nematostella, demonstrates a role for Wnt signaling in axis formation and patterning, as well as gastrulation and germ-layer specification. In this review, we examine what is currently known about Wnt signaling in cnidarians, and discuss what this group of "simple" animals may reveal about the evolution of Wnt signaling and polarity.
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Affiliation(s)
- Patricia N Lee
- Kewalo Marine Lab/Pacific Biosciences Research Center, University of Hawaii, 41 Ahui Street, Honolulu, 96813, USA.
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Matus DQ, Thomsen GH, Martindale MQ. Dorso/ventral genes are asymmetrically expressed and involved in germ-layer demarcation during cnidarian gastrulation. Curr Biol 2006; 16:499-505. [PMID: 16527745 DOI: 10.1016/j.cub.2006.01.052] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2005] [Revised: 01/11/2006] [Accepted: 01/19/2006] [Indexed: 11/28/2022]
Abstract
Cnidarians (corals, sea anemones, hydroids, and jellyfish) are a basal taxon closely related to bilaterally symmetrical animals and have been characterized as diploblastic and as radially symmetrical around their longitudinal axis. We show that some orthologs of key bilaterian dorso/ventral (D/V) patterning genes, including the TGFbeta signaling molecules NvDpp and NvBMP5-8 and their antagonist NvChordin, are initially expressed asymmetrically at the onset of gastrulation in the anthozoan sea anemone Nematostella vectensis. Surprisingly, unlike flies and vertebrates, the TGFbeta ligands and their antagonist are colocalized at the onset of gastrulation but then segregate by germ layer as gastrulation proceeds. TGFbeta ligands, their extracellular enhancer, NvTolloid, and components of their downstream signaling pathway (NvSmad1/5 and NvSmad4) are all coexpressed in presumptive endoderm, indicating that only planar TGFbeta signaling operates at these stages. NvChordin expression forms a boundary between TGFbeta-expressing endodermal cells and aboral ectoderm. Manipulation of nuclear beta-catenin localization affects TGFbeta ligand and antagonist expression, suggesting that the ancestral role of the dpp/chordin antagonism during gastrulation may have been in germ-layer segregation and/or epithelial patterning rather than dorsal/ventral patterning.
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Affiliation(s)
- David Q Matus
- Kewalo Marine Lab, Pacific Bioscience Research Center, University of Hawaii, 41 Ahui Street, Honolulu, Hawaii 96813, USA
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Extavour CG, Pang K, Matus DQ, Martindale MQ. vasa and nanos expression patterns in a sea anemone and the evolution of bilaterian germ cell specification mechanisms. Evol Dev 2005; 7:201-15. [PMID: 15876193 DOI: 10.1111/j.1525-142x.2005.05023.x] [Citation(s) in RCA: 113] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Most bilaterians specify primordial germ cells (PGCs) during early embryogenesis using either inherited cytoplasmic germ line determinants (preformation) or induction of germ cell fate through signaling pathways (epigenesis). However, data from nonbilaterian animals suggest that ancestral metazoans may have specified germ cells very differently from most extant bilaterians. Cnidarians and sponges have been reported to generate germ cells continuously throughout reproductive life, but previous studies on members of these basal phyla have not examined embryonic germ cell origin. To try to define the embryonic origin of PGCs in the sea anemone Nematostella vectensis, we examined the expression of members of the vasa and nanos gene families, which are critical genes in bilaterian germ cell specification and development. We found that vasa and nanos family genes are expressed not only in presumptive PGCs late in embryonic development, but also in multiple somatic cell types during early embryogenesis. These results suggest one way in which preformation in germ cell development might have evolved from the ancestral epigenetic mechanism that was probably used by a metazoan ancestor.
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Affiliation(s)
- Cassandra G Extavour
- Laboratory for Development and Evolution, Department of Zoology, University of Cambridge, Cambridge, UK.
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Pang K, Matus DQ, Martindale MQ. The ancestral role of COE genes may have been in chemoreception: evidence from the development of the sea anemone, Nematostella vectensis (Phylum Cnidaria; Class Anthozoa). Dev Genes Evol 2004; 214:134-8. [PMID: 14752662 DOI: 10.1007/s00427-004-0383-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2003] [Accepted: 11/29/2003] [Indexed: 11/26/2022]
Abstract
An orthologue of the COE family of helix-loop-helix transcription factors was recovered from the anthozoan Nematostella vectensis (Cnidaria). NvCOE has high sequence similarity to vertebrate and invertebrate orthologues in all three major functional domains of the protein. In situ hybridization studies show early expression through the cleavage period but transcripts are down regulated at gastrulation while remaining expressed at high levels only in the apical tuft of cilia at the aboral end of the planula larva. It is likely that one of the ancestral roles of the COE family of genes may have been in the development of chemosensory neurons.
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Affiliation(s)
- Kevin Pang
- Kewalo Marine Laboratory, Pacific Biomedical Research Center, University of Hawaii, 41 Ahui St., Honolulu, HI 96813, USA
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