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Wang W, Hu CK, Zeng A, Alegre D, Hu D, Gotting K, Ortega Granillo A, Wang Y, Robb S, Schnittker R, Zhang S, Alegre D, Li H, Ross E, Zhang N, Brunet A, Sánchez Alvarado A. Changes in regeneration-responsive enhancers shape regenerative capacities in vertebrates. Science 2020; 369:369/6508/eaaz3090. [PMID: 32883834 DOI: 10.1126/science.aaz3090] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 03/05/2020] [Accepted: 07/07/2020] [Indexed: 12/13/2022]
Abstract
Vertebrates vary in their ability to regenerate, and the genetic mechanisms underlying such disparity remain elusive. Comparative epigenomic profiling and single-cell sequencing of two related teleost fish uncovered species-specific and evolutionarily conserved genomic responses to regeneration. The conserved response revealed several regeneration-responsive enhancers (RREs), including an element upstream to inhibin beta A (inhba), a known effector of vertebrate regeneration. This element activated expression in regenerating transgenic fish, and its genomic deletion perturbed caudal fin regeneration and abrogated cardiac regeneration altogether. The enhancer is present in mammals, shares functionally essential activator protein 1 (AP-1)-binding motifs, and responds to injury, but it cannot rescue regeneration in fish. This work suggests that changes in AP-1-enriched RREs are likely a crucial source of loss of regenerative capacities in vertebrates.
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Affiliation(s)
- Wei Wang
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA.,Howard Hughes Medical Institute, Kansas City, MO 64110, USA
| | - Chi-Kuo Hu
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - An Zeng
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Dana Alegre
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Deqing Hu
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Kirsten Gotting
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | | | - Yongfu Wang
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Sofia Robb
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | | | - Shasha Zhang
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Dillon Alegre
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Hua Li
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Eric Ross
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA.,Howard Hughes Medical Institute, Kansas City, MO 64110, USA
| | - Ning Zhang
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Anne Brunet
- Department of Genetics, Stanford University, Stanford, CA 94305, USA.,Glenn Laboratories for the Biology of Aging. Stanford University, Stanford, CA 94305, USA
| | - Alejandro Sánchez Alvarado
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA. .,Howard Hughes Medical Institute, Kansas City, MO 64110, USA
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Klocko AD, Summers CA, Glover ML, Parrish R, Storck WK, McNaught KJ, Moss ND, Gotting K, Stewart A, Morrison AM, Payne L, Hatakeyama S, Selker EU. Selection and Characterization of Mutants Defective in DNA Methylation in Neurospora crassa. Genetics 2020; 216:671-688. [PMID: 32873602 PMCID: PMC7648584 DOI: 10.1534/genetics.120.303471] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 06/24/2020] [Accepted: 08/25/2020] [Indexed: 01/05/2023] Open
Abstract
DNA methylation, a prototypical epigenetic modification implicated in gene silencing, occurs in many eukaryotes and plays a significant role in the etiology of diseases such as cancer. The filamentous fungus Neurospora crassa places DNA methylation at regions of constitutive heterochromatin such as in centromeres and in other A:T-rich regions of the genome, but this modification is dispensable for normal growth and development. This and other features render N. crassa an excellent model to genetically dissect elements of the DNA methylation pathway. We implemented a forward genetic selection on a massive scale, utilizing two engineered antibiotic-resistance genes silenced by DNA methylation, to isolate mutants d efective i n m ethylation (dim). Hundreds of potential mutants were characterized, yielding a rich collection of informative alleles of 11 genes important for DNA methylation, most of which were already reported. In parallel, we characterized the pairwise interactions in nuclei of the DCDC, the only histone H3 lysine 9 methyltransferase complex in Neurospora, including those between the DIM-5 catalytic subunit and other complex members. We also dissected the N- and C-termini of the key protein DIM-7, required for DIM-5 histone methyltransferase localization and activation. Lastly, we identified two alleles of a novel gene, dim-10 - a homolog of Clr5 in Schizosaccharomyces pombe - that is not essential for DNA methylation, but is necessary for repression of the antibiotic-resistance genes used in the selection, which suggests that both DIM-10 and DNA methylation promote silencing of constitutive heterochromatin.
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Affiliation(s)
- Andrew D Klocko
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Calvin A Summers
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Marissa L Glover
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Robert Parrish
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - William K Storck
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Kevin J McNaught
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Nicole D Moss
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Kirsten Gotting
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Aurelian Stewart
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Ariel M Morrison
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Laurel Payne
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Shin Hatakeyama
- Laboratory of Genetics, Faculty of Science, Shimo-ohkubo 255, Saitama University, Sakura-ward, 338-8570, JAPAN
| | - Eric U Selker
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
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Francoeur CB, Khadempour L, Moreira-Soto RD, Gotting K, Book AJ, Pinto-Tomás AA, Keefover-Ring K, Currie CR. Bacteria Contribute to Plant Secondary Compound Degradation in a Generalist Herbivore System. mBio 2020; 11:e02146-20. [PMID: 32934088 PMCID: PMC7492740 DOI: 10.1128/mbio.02146-20] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 08/11/2020] [Indexed: 02/07/2023] Open
Abstract
Herbivores must overcome a variety of plant defenses, including coping with plant secondary compounds (PSCs). To help detoxify these defensive chemicals, several insect herbivores are known to harbor gut microbiota with the metabolic capacity to degrade PSCs. Leaf-cutter ants are generalist herbivores, obtaining sustenance from specialized fungus gardens that act as external digestive systems and which degrade the diverse collection of plants foraged by the ants. There is in vitro evidence that certain PSCs harm Leucoagaricus gongylophorus, the fungal cultivar of leaf-cutter ants, suggesting a role for the Proteobacteria-dominant bacterial community present within fungus gardens. In this study, we investigated the ability of symbiotic bacteria present within fungus gardens of leaf-cutter ants to degrade PSCs. We cultured fungus garden bacteria, sequenced the genomes of 42 isolates, and identified genes involved in PSC degradation, including genes encoding cytochrome P450 enzymes and genes in geraniol, cumate, cinnamate, and α-pinene/limonene degradation pathways. Using metatranscriptomic analysis, we showed that some of these degradation genes are expressed in situ Most of the bacterial isolates grew unhindered in the presence of PSCs and, using gas chromatography-mass spectrometry (GC-MS), we determined that isolates from the genera Bacillus, Burkholderia, Enterobacter, Klebsiella, and Pseudomonas degrade α-pinene, β-caryophyllene, or linalool. Using a headspace sampler, we show that subcolonies of fungus gardens reduced α-pinene and linalool over a 36-h period, while L. gongylophorus strains alone reduced only linalool. Overall, our results reveal that the bacterial communities in fungus gardens play a pivotal role in alleviating the effect of PSCs on the leaf-cutter ant system.IMPORTANCE Leaf-cutter ants are dominant neotropical herbivores capable of deriving energy from a wide range of plant substrates. The success of leaf-cutter ants is largely due to their external gut, composed of key microbial symbionts, specifically, the fungal mutualist L. gongylophorus and a consistent bacterial community. Both symbionts are known to have critical roles in extracting energy from plant material, yet comparatively little is known about their roles in the detoxification of plant secondary compounds. In this study, we assessed if the bacterial communities associated with leaf-cutter ant fungus gardens can degrade harmful plant chemicals. We identify plant secondary compound detoxification in leaf-cutter ant gardens as a process that depends on the degradative potential of both the bacterial community and L. gongylophorus Our findings suggest that the fungus garden and its associated microbial community influence the generalist foraging abilities of the ants, underscoring the importance of microbial symbionts in plant substrate suitability for herbivores.
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Affiliation(s)
- Charlotte B Francoeur
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Lily Khadempour
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Rolando D Moreira-Soto
- Sección de Entomología Medica, Departamento de Parasitología, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Kirsten Gotting
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Adam J Book
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Adrián A Pinto-Tomás
- Centro de Investigación en Estructuras Microscópicas, Universidad de Costa Rica, San José, Costa Rica
- Departamento de Bioquímica, Facultad de Medicina, Universidad de Costa Rica, San José, Costa Rica
- Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica, San José, Costa Rica
| | - Ken Keefover-Ring
- Departments of Botany and Geography, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Davies EL, Lei K, Seidel CW, Kroesen AE, McKinney SA, Guo L, Robb SM, Ross EJ, Gotting K, Alvarado AS. Embryonic origin of adult stem cells required for tissue homeostasis and regeneration. eLife 2017; 6:21052. [PMID: 28072387 PMCID: PMC5293490 DOI: 10.7554/elife.21052] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [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: 08/30/2016] [Accepted: 01/04/2017] [Indexed: 11/13/2022] Open
Abstract
Planarian neoblasts are pluripotent, adult somatic stem cells and lineage-primed progenitors that are required for the production and maintenance of all differentiated cell types, including the germline. Neoblasts, originally defined as undifferentiated cells residing in the adult parenchyma, are frequently compared to embryonic stem cells yet their developmental origin remains obscure. We investigated the provenance of neoblasts during Schmidtea mediterranea embryogenesis, and report that neoblasts arise from an anarchic, cycling piwi-1+ population wholly responsible for production of all temporary and definitive organs during embryogenesis. Early embryonic piwi-1+ cells are molecularly and functionally distinct from neoblasts: they express unique cohorts of early embryo enriched transcripts and behave differently than neoblasts in cell transplantation assays. Neoblast lineages arise as organogenesis begins and are required for construction of all major organ systems during embryogenesis. These subpopulations are continuously generated during adulthood, where they act as agents of tissue homeostasis and regeneration.
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Affiliation(s)
- Erin L Davies
- Howard Hughes Medical Institute, Stowers Institute for Medical Research, Kansas City, United States
| | - Kai Lei
- Howard Hughes Medical Institute, Stowers Institute for Medical Research, Kansas City, United States
| | - Christopher W Seidel
- Howard Hughes Medical Institute, Stowers Institute for Medical Research, Kansas City, United States
| | - Amanda E Kroesen
- Howard Hughes Medical Institute, Stowers Institute for Medical Research, Kansas City, United States
| | - Sean A McKinney
- Howard Hughes Medical Institute, Stowers Institute for Medical Research, Kansas City, United States
| | - Longhua Guo
- Howard Hughes Medical Institute, Stowers Institute for Medical Research, Kansas City, United States
| | - Sofia Mc Robb
- Howard Hughes Medical Institute, Stowers Institute for Medical Research, Kansas City, United States
| | - Eric J Ross
- Howard Hughes Medical Institute, Stowers Institute for Medical Research, Kansas City, United States
| | - Kirsten Gotting
- Howard Hughes Medical Institute, Stowers Institute for Medical Research, Kansas City, United States
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Luttrell SM, Gotting K, Ross E, Alvarado AS, Swalla BJ. Head regeneration in hemichordates is not a strict recapitulation of development. Dev Dyn 2016; 245:1159-1175. [PMID: 27649280 PMCID: PMC5129524 DOI: 10.1002/dvdy.24457] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [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: 01/15/2016] [Revised: 09/04/2016] [Accepted: 09/05/2016] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Head or anterior body part regeneration is commonly associated with protostome, but not deuterostome invertebrates. However, it has been shown that the solitary hemichordate Ptychodera flava possesses the remarkable capacity to regenerate their entire nervous system, including their dorsal neural tube and their anterior head-like structure, or proboscis. Hemichordates, also known as acorn worms, are marine invertebrate deuterostomes that have retained chordate traits that were likely present in the deuterostome ancestor, placing these animals in a vital position to study regeneration and chordate evolution. All acorn worms have a tripartite body plan, with an anterior proboscis, middle collar region, and a posterior trunk. The collar houses a hollow, dorsal neural tube in ptychoderid hemichordates and numerous chordate genes involved in brain and spinal cord development are expressed in a similar anterior-posterior spatial arrangement along the body axis. RESULTS We have examined anterior regeneration in the hemichordate Ptychodera flava and report the spatial and temporal morphological changes that occur. Additionally, we have sequenced, assembled, and analyzed the transcriptome for eight stages of regenerating P. flava, revealing significant differential gene expression between regenerating and control animals. CONCLUSIONS Importantly, we have uncovered developmental steps that are regeneration-specific and do not strictly follow the embryonic program. Developmental Dynamics 245:1159-1175, 2016. © 2016 The Authors. Developmental Dynamics published by Wiley Periodicals, Inc. on behalf of American Association of Anatomists.
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Affiliation(s)
- Shawn M. Luttrell
- Biology DepartmentUniversity of WashingtonSeattleWashington
- Friday Harbor LaboratoriesUniversity of WashingtonFriday HarborWashington
| | | | - Eric Ross
- Stowers Institute for Medical ResearchKansas CityMissouri
- Howard Hughes Medical InstituteStowers Institute for Medical ResearchKansas CityMissouri
| | - Alejandro Sánchez Alvarado
- Stowers Institute for Medical ResearchKansas CityMissouri
- Howard Hughes Medical InstituteStowers Institute for Medical ResearchKansas CityMissouri
| | - Billie J. Swalla
- Biology DepartmentUniversity of WashingtonSeattleWashington
- Friday Harbor LaboratoriesUniversity of WashingtonFriday HarborWashington
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Lei K, Thi-Kim Vu H, Mohan RD, McKinney SA, Seidel CW, Alexander R, Gotting K, Workman JL, Sánchez Alvarado A. Egf Signaling Directs Neoblast Repopulation by Regulating Asymmetric Cell Division in Planarians. Dev Cell 2016; 38:413-29. [PMID: 27523733 DOI: 10.1016/j.devcel.2016.07.012] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [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: 12/14/2015] [Revised: 06/01/2016] [Accepted: 07/15/2016] [Indexed: 12/27/2022]
Abstract
A large population of proliferative stem cells (neoblasts) is required for physiological tissue homeostasis and post-injury regeneration in planarians. Recent studies indicate that survival of a few neoblasts after sublethal irradiation results in the clonal expansion of the surviving stem cells and the eventual restoration of tissue homeostasis and regenerative capacity. However, the precise mechanisms regulating the population dynamics of neoblasts remain largely unknown. Here, we uncovered a central role for epidermal growth factor (EGF) signaling during in vivo neoblast expansion mediated by Smed-egfr-3 (egfr-3) and its putative ligand Smed-neuregulin-7 (nrg-7). Furthermore, the EGF receptor-3 protein localizes asymmetrically on the cytoplasmic membrane of neoblasts, and the ratio of asymmetric to symmetric cell divisions decreases significantly in egfr-3(RNAi) worms. Our results not only provide the first molecular evidence of asymmetric stem cell divisions in planarians, but also demonstrate that EGF signaling likely functions as an essential regulator of neoblast clonal expansion.
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Affiliation(s)
- Kai Lei
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA.
| | - Hanh Thi-Kim Vu
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Ryan D Mohan
- Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO 64110, USA
| | - Sean A McKinney
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Chris W Seidel
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | | | - Kirsten Gotting
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Jerry L Workman
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Alejandro Sánchez Alvarado
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Howard Hughes Medical Institute, Stowers Institute for Medical Research, Kansas City, MO 64110, USA.
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Robb SMC, Gotting K, Ross E, Sánchez Alvarado A. SmedGD 2.0: The Schmidtea mediterranea genome database. Genesis 2015; 53:535-46. [PMID: 26138588 DOI: 10.1002/dvg.22872] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [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: 05/22/2015] [Revised: 06/29/2015] [Accepted: 06/30/2015] [Indexed: 12/13/2022]
Abstract
Planarians have emerged as excellent models for the study of key biological processes such as stem cell function and regulation, axial polarity specification, regeneration, and tissue homeostasis among others. The most widely used organism for these studies is the free-living flatworm Schmidtea mediterranea. In 2007, the Schmidtea mediterranea Genome Database (SmedGD) was first released to provide a much needed resource for the small, but growing planarian community. SmedGD 1.0 has been a depository for genome sequence, a draft assembly, and related experimental data (e.g., RNAi phenotypes, in situ hybridization images, and differential gene expression results). We report here a comprehensive update to SmedGD (SmedGD 2.0) that aims to expand its role as an interactive community resource. The new database includes more recent, and up-to-date transcription data, provides tools that enhance interconnectivity between different genome assemblies and transcriptomes, including next-generation assemblies for both the sexual and asexual biotypes of S. mediterranea. SmedGD 2.0 (http://smedgd.stowers.org) not only provides significantly improved gene annotations, but also tools for data sharing, attributes that will help both the planarian and biomedical communities to more efficiently mine the genomics and transcriptomics of S. mediterranea.
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Affiliation(s)
- Sofia M C Robb
- Stowers Institute for Medical Research, Howard Hughes Medical Institute, Kansas City, Missouri, 64110
| | - Kirsten Gotting
- Stowers Institute for Medical Research, Howard Hughes Medical Institute, Kansas City, Missouri, 64110
| | - Eric Ross
- Stowers Institute for Medical Research, Howard Hughes Medical Institute, Kansas City, Missouri, 64110
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