1
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Harry CJ, Hibshman JD, Damatac A, Davidson PL, Estermann MA, Flores-Flores M, Holmes CM, Lázaro J, Legere EA, Leyhr J, Thendral SB, Vincent BA, Goldstein B. Protocol for fluorescent live-cell staining of tardigrades. STAR Protoc 2024; 5:103232. [PMID: 39128009 DOI: 10.1016/j.xpro.2024.103232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/31/2024] [Accepted: 07/10/2024] [Indexed: 08/13/2024] Open
Abstract
Tardigrades are microscopic organisms with exceptional resilience to environmental extremes. Most protocols to visualize the internal anatomy of tardigrades rely on fixation, hampering our understanding of dynamic changes to organelles and other subcellular components. Here, we provide protocols for staining live tardigrade adults and other postembryonic stages, facilitating real-time visualization of structures including lipid droplets, mitochondria, lysosomes, and DNA.
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Affiliation(s)
- Clayton J Harry
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jonathan D Hibshman
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Embryology Course, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Amor Damatac
- Embryology Course, Marine Biological Laboratory, Woods Hole, MA 02543, USA; Max Planck Institute for Evolutionary Biology, 24306 Ploen, Germany
| | - Phillip L Davidson
- Embryology Course, Marine Biological Laboratory, Woods Hole, MA 02543, USA; Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Martin Andres Estermann
- Embryology Course, Marine Biological Laboratory, Woods Hole, MA 02543, USA; Reproductive Developmental Biology Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Marycruz Flores-Flores
- Embryology Course, Marine Biological Laboratory, Woods Hole, MA 02543, USA; University of Colorado, School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Caroline M Holmes
- Embryology Course, Marine Biological Laboratory, Woods Hole, MA 02543, USA; Department of Organismal and Evolutionary Biology, Harvard University, Boston, MA, USA
| | - Jorge Lázaro
- Embryology Course, Marine Biological Laboratory, Woods Hole, MA 02543, USA; European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Elizabeth-Ann Legere
- Embryology Course, Marine Biological Laboratory, Woods Hole, MA 02543, USA; Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Jake Leyhr
- Embryology Course, Marine Biological Laboratory, Woods Hole, MA 02543, USA; Department of Organismal Biology, Uppsala University, Uppsala, Sweden; Department of Biology, Duke University, Durham, NC 27708, USA
| | - Siddharthan Balachandar Thendral
- Embryology Course, Marine Biological Laboratory, Woods Hole, MA 02543, USA; Department of Biology, Duke University, Durham, NC 27708, USA
| | - Bridget A Vincent
- Embryology Course, Marine Biological Laboratory, Woods Hole, MA 02543, USA; Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Bob Goldstein
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Embryology Course, Marine Biological Laboratory, Woods Hole, MA 02543, USA.
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2
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Sadowska-Bartosz I, Bartosz G. Antioxidant Defense in the Toughest Animals on the Earth: Its Contribution to the Extreme Resistance of Tardigrades. Int J Mol Sci 2024; 25:8393. [PMID: 39125965 PMCID: PMC11313143 DOI: 10.3390/ijms25158393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Revised: 07/23/2024] [Accepted: 07/29/2024] [Indexed: 08/12/2024] Open
Abstract
Tardigrades are unique among animals in their resistance to dehydration, mainly due to anhydrobiosis and tun formation. They are also very resistant to high-energy radiation, low and high temperatures, low and high pressure, and various chemical agents, Interestingly, they are resistant to ionizing radiation both in the hydrated and dehydrated states to a similar extent. They are able to survive in the cosmic space. Apparently, many mechanisms contribute to the resistance of tardigrades to harmful factors, including the presence of trehalose (though not common to all tardigrades), heat shock proteins, late embryogenesis-abundant proteins, tardigrade-unique proteins, DNA repair proteins, proteins directly protecting DNA (Dsup and TDR1), and efficient antioxidant system. Antioxidant enzymes and small-molecular-weight antioxidants are an important element in the tardigrade resistance. The levels and activities of many antioxidant proteins is elevated by anhydrobiosis and UV radiation; one explanation for their induction during dehydration is provided by the theory of "preparation for oxidative stress", which occurs during rehydration. Genes coding for some antioxidant proteins are expanded in tardigrades; some genes (especially those coding for catalases) were hypothesized to be of bacterial origin, acquired by horizontal gene transfer. An interesting antioxidant protein found in tardigrades is the new Mn-dependent peroxidase.
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Affiliation(s)
- Izabela Sadowska-Bartosz
- Laboratory of Analytical Biochemistry, Institute of Food Technology and Nutrition, College of Natural Sciences, University of Rzeszów, 4 Zelwerowicza Street, 35-601 Rzeszow, Poland;
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3
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Li C, Yang Z, Xu X, Meng L, Liu S, Yang D. Conserved and specific gene expression patterns in the embryonic development of tardigrades. Evol Dev 2024; 26:e12476. [PMID: 38654704 DOI: 10.1111/ede.12476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 02/18/2024] [Accepted: 04/03/2024] [Indexed: 04/26/2024]
Abstract
Tardigrades, commonly known as water bears, are enigmatic organisms characterized by their remarkable resilience to extreme environments despite their simple and compact body structure. To date, there is still much to understand about their evolutionary and developmental features contributing to their special body plan and abilities. This research provides preliminary insights on the conserved and specific gene expression patterns during embryonic development of water bears, focusing on the species Hypsibius exemplaris. The developmental dynamic expression analysis of the genes with various evolutionary age grades indicated that the mid-conserved stage of H. exemplaris corresponds to the period of ganglia and midgut development, with the late embryonic stage showing a transition from non-conserved to conserved state. Additionally, a comparison with Drosophila melanogaster highlighted the absence of certain pathway nodes in development-related pathways, such as Maml and Hairless, which are respectively the transcriptional co-activator and co-repressor of NOTCH regulated genes. We also employed Weighted Gene Co-expression Network Analysis (WGCNA) to investigate the expression patterns of tardigrade-specific genes during embryo development. Our findings indicated that the module containing the highest proportion of tardigrade-specific genes (TSGs) exhibits high expression levels before the mid-conserved stage, potentially playing a role in glutathione and lipid metabolism. These functions may be associated to the ecdysone synthesis and storage cell formation, which is unique to tardigrades.
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Affiliation(s)
- Chaoran Li
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Zhixiang Yang
- School of Life Sciences, Hebei University, Baoding, China
| | - Xiaofang Xu
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Lingling Meng
- School of Life Sciences, Hebei University, Baoding, China
| | - Shihao Liu
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Dong Yang
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
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4
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Kirk MJ, Xu C, Rothman JH. Single-animal, single-tube RNA extraction for quantitative analysis of transcripts in the tardigrade Hypsibius exemplaris. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.15.585302. [PMID: 38559134 PMCID: PMC10979942 DOI: 10.1101/2024.03.15.585302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The tardigrade Hypsibius exemplaris is an emerging model organism renowned for its ability to survive environmental extremes.1-3 To explore the molecular mechanisms and genetic basis of such extremotolerance, many studies rely on transcriptional profiling4, 5 and RNA interference (RNAi)6 to define molecular targets. Such studies require efficient, accurate, and robust RNA extraction methods; however, obtaining high-quality quantitative levels of RNA from H. exemplaris has been challenging6, 7. Possessing a layer of firm chitinous cuticle, tardigrade tissues are difficult to disrupt by chemical or mechanical means8. Here we present an efficient single-tardigrade, single-tube RNA extraction method (STST) that not only reliably isolates RNA from individual tardigrades but dramatically reduces the time required for extraction. We show that this RNA extraction method yields robust quantities of cDNA and can be used to amplify multiple transcripts by qRT-PCR. To validate the method, we use it to compare dynamic changes in expression of genes encoding two heat-shock-regulated proteins, Heat-Shock Protein 70 β2 (HSP70β2) and Heat-Shock Protein 90α (HSP90α) by quantifying their expression levels in heat-exposed and cold-exposed individuals using qRT-PCR across long-term and short-term heat stressors. Our method effectively complements existing bulk RNA extraction methods7, permitting rapid examination of individual tardigrade transcriptional data and quantification of phenotypic variations in expression profiles amongst individuals.
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Affiliation(s)
- Molly J. Kirk
- Department of Molecular Cellular and Developmental Biology University of California, Santa Barbara, Santa Barbara, CA
| | - Chaoming Xu
- Department of Molecular Cellular and Developmental Biology University of California, Santa Barbara, Santa Barbara, CA
| | - Joel H. Rothman
- Department of Molecular Cellular and Developmental Biology University of California, Santa Barbara, Santa Barbara, CA
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA
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5
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Heikes KL, Goldstein B. Expression patterns of FGF and BMP pathway genes in the tardigrade Hypsibius exemplaris. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.577774. [PMID: 38352320 PMCID: PMC10862696 DOI: 10.1101/2024.01.29.577774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
A small number of conserved signaling pathways regulate development of most animals, yet we do not know where these pathways are deployed in most embryos. This includes tardigrades, a phylum with a unique body shape. We examined expression patterns of components of the BMP and FGF signaling pathways during embryonic segmentation and mesoderm development of the tardigrade Hypsibius exemplaris. Among the patterns examined, we found that an FGF ligand gene is expressed in ectodermal segment posteriors and an FGF receptor gene is expressed in underlying endomesodermal pouches, suggesting possible FGF signaling between these developing germ layers. We found that a BMP ligand gene is expressed in lateral ectoderm and dorsolateral bands along segment posteriors, while the BMP antagonist Sog gene is expressed in lateral ectoderm and also in a subset of endomesodermal cells, suggesting a possible role of BMP signaling in dorsal-ventral patterning of lateral ectoderm. In combination with known roles of these pathways during development of common model systems, we developed hypotheses for how the BMP and FGF pathways might regulate embryo segmentation and mesoderm formation of the tardigrade H. exemplaris. These results identify the expression patterns of genes from two conserved signaling pathways for the first time in the tardigrade phylum.
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Affiliation(s)
- Kira L. Heikes
- Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bob Goldstein
- Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular 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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6
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Smythers AL, Joseph KM, O'Dell HM, Clark TA, Crislip JR, Flinn BB, Daughtridge MH, Stair ER, Mubarek SN, Lewis HC, Salas AA, Hnilica ME, Kolling DRJ, Hicks LM. Chemobiosis reveals tardigrade tun formation is dependent on reversible cysteine oxidation. PLoS One 2024; 19:e0295062. [PMID: 38232097 DOI: 10.1371/journal.pone.0295062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/14/2023] [Indexed: 01/19/2024] Open
Abstract
Tardigrades, commonly known as 'waterbears', are eight-legged microscopic invertebrates renowned for their ability to withstand extreme stressors, including high osmotic pressure, freezing temperatures, and complete desiccation. Limb retraction and substantial decreases to their internal water stores results in the tun state, greatly increasing their ability to survive. Emergence from the tun state and/or activity regain follows stress removal, where resumption of life cycle occurs as if stasis never occurred. However, the mechanism(s) through which tardigrades initiate tun formation is yet to be uncovered. Herein, we use chemobiosis to demonstrate that tardigrade tun formation is mediated by reactive oxygen species (ROS). We further reveal that tuns are dependent on reversible cysteine oxidation, and that this reversible cysteine oxidation is facilitated by the release of intracellular reactive oxygen species (ROS). We provide the first empirical evidence of chemobiosis and map the initiation and survival of tardigrades via osmobiosis, chemobiosis, and cryobiosis. In vivo electron paramagnetic spectrometry suggests an intracellular release of reactive oxygen species following stress induction; when this release is quenched through the application of exogenous antioxidants, the tardigrades can no longer survive osmotic stress. Together, this work suggests a conserved dependence of reversible cysteine oxidation across distinct tardigrade cryptobioses.
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Affiliation(s)
- Amanda L Smythers
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Kara M Joseph
- Department of Chemistry, Marshall University, Huntington, WV, United States of America
| | - Hayden M O'Dell
- Department of Chemistry, Marshall University, Huntington, WV, United States of America
| | - Trace A Clark
- Department of Chemistry, Marshall University, Huntington, WV, United States of America
| | - Jessica R Crislip
- Department of Chemistry, Marshall University, Huntington, WV, United States of America
| | - Brendin B Flinn
- Department of Chemistry, Marshall University, Huntington, WV, United States of America
| | - Meredith H Daughtridge
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Evan R Stair
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Saher N Mubarek
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Hailey C Lewis
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Abel A Salas
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Megan E Hnilica
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Derrick R J Kolling
- Department of Chemistry, Marshall University, Huntington, WV, United States of America
| | - Leslie M Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
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7
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Sim KS, Inoue T. Structure of a superoxide dismutase from a tardigrade: Ramazzottius varieornatus strain YOKOZUNA-1. Acta Crystallogr F Struct Biol Commun 2023; 79:169-179. [PMID: 37358501 PMCID: PMC10327573 DOI: 10.1107/s2053230x2300523x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 06/12/2023] [Indexed: 06/27/2023] Open
Abstract
Superoxide dismutase (SOD) is an essential and ubiquitous antioxidant protein that is widely present in biological systems. The anhydrobiotic tardigrades are some of the toughest micro-animals. They have an expanded set of genes for antioxidant proteins such as SODs. These proteins are thought to play an essential role in oxidative stress resistance in critical situations such as desiccation, although their functions at the molecular level have yet to be explored. Here, crystal structures of a copper/zinc-containing SOD (RvSOD15) from an anhydrobiotic tardigrade, Ramazzottius varieornatus strain YOKOZUNA-1, are reported. In RvSOD15, one of the histidine ligands of the catalytic copper center is replaced by a valine (Val87). The crystal structures of the wild type and the V87H mutant show that even though a histidine is placed at position 87, a nearby flexible loop can destabilize the coordination of His87 to the Cu atom. Model structures of other RvSODs were investigated and it was found that some of them are also unusual SODs, with features such as deletion of the electrostatic loop or β3 sheet and unusual metal-binding residues. These studies show that RvSOD15 and some other RvSODs may have evolved to lose the SOD function, suggesting that gene duplications of antioxidant proteins do not solely explain the high stress tolerance of anhydrobiotic tardigrades.
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Affiliation(s)
- Kee-Shin Sim
- Graduate School of Pharmaceutical Science, Osaka University, Suita City, Osaka 565-0871, Japan
| | - Tsuyoshi Inoue
- Graduate School of Pharmaceutical Science, Osaka University, Suita City, Osaka 565-0871, Japan
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8
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Escarcega RD, Patil AA, Meyer MD, Moruno-Manchon JF, Silvagnoli AD, McCullough LD, Tsvetkov AS. The Tardigrade damage suppressor protein Dsup promotes DNA damage in neurons. Mol Cell Neurosci 2023; 125:103826. [PMID: 36858083 PMCID: PMC10247392 DOI: 10.1016/j.mcn.2023.103826] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 02/18/2023] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
Tardigrades are microscopic invertebrates, which are capable of withstanding extreme environmental conditions, including high levels of radiation. A Tardigrade protein, Dsup (Damage Suppressor), protects the Tardigrade's DNA during harsh environmental stress and X-rays. When expressed in cancer cells, Dsup protects DNA from single- and double-strand breaks (DSBs) induced by radiation, increases survival of irradiated cells, and protects DNA from reactive oxygen species. These unusual properties of Dsup suggested that understanding how the protein functions may help in the design of small molecules that could protect humans during radiotherapy or space travel. Here, we investigated if Dsup is protective in cortical neurons cultured from rat embryos. We discovered that, in cortical neurons, the codon-optimized Dsup localizes to the nucleus and, surprisingly, promotes neurotoxicity, leading to neurodegeneration. Unexpectedly, we found that Dsup expression results in the formation of DNA DSBs in cultured neurons. With electron microscopy, we discovered that Dsup promotes chromatin condensation. Unlike Dsup's protective properties in cancerous cells, in neurons, Dsup promotes neurotoxicity, induces DNA damage, and rearranges chromatin. Neurons are sensitive to Dsup, and Dsup is a doubtful surrogate for DNA protection in neuronal cells.
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Affiliation(s)
- Rocio Diaz Escarcega
- Department of Neurology, The University of Texas McGovern Medical School at Houston, TX 77030, United States of America
| | - Abhijeet A Patil
- Department of Neurology, The University of Texas McGovern Medical School at Houston, TX 77030, United States of America
| | - Matthew D Meyer
- Shared Equipment Authority, Rice University, Houston, TX 77005, United States of America
| | - Jose F Moruno-Manchon
- Department of Neurology, The University of Texas McGovern Medical School at Houston, TX 77030, United States of America
| | - Alexander D Silvagnoli
- Department of Neurology, The University of Texas McGovern Medical School at Houston, TX 77030, United States of America
| | - Louise D McCullough
- Department of Neurology, The University of Texas McGovern Medical School at Houston, TX 77030, United States of America; The University of Texas Graduate School of Biomedical Sciences, Houston, TX 77030, United States of America
| | - Andrey S Tsvetkov
- Department of Neurology, The University of Texas McGovern Medical School at Houston, TX 77030, United States of America; The University of Texas Graduate School of Biomedical Sciences, Houston, TX 77030, United States of America; UTHealth Consortium on Aging, The University of Texas McGovern Medical School, Houston, TX 77030, United States of America.
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9
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Heikes KL, Game M, Smith FW, Goldstein B. The Embryonic Origin of Primordial Germ Cells in the Tardigrade Hypsibius exemplaris. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.02.522500. [PMID: 36824831 PMCID: PMC9948961 DOI: 10.1101/2023.01.02.522500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Primordial germ cells (PGCs) give rise to gametes â€" cells necessary for the propagation and fertility of diverse organisms. Current understanding of PGC development is limited to the small number of organisms whose PGCs have been identified and studied. Expanding the field to include little-studied taxa and emerging model organisms is important to understand the full breadth of the evolution of PGC development. In the phylum Tardigrada, no early cell lineages have been identified to date using molecular markers. This includes the PGC lineage. Here, we describe PGC development in the model tardigrade Hypsibius exemplaris . The four earliest-internalizing cells (EICs) exhibit PGC-like behavior and nuclear morphology. The location of the EICs is enriched for mRNAs of conserved PGC markers wiwi1 (water bear piwi 1) and vasa . At early stages, both wiwi1 and vasa mRNAs are detectable uniformly in embryos, which suggests that these mRNAs do not serve as localized determinants for PGC specification. Only later are wiwi1 and vasa enriched in the EICs. Finally, we traced the cells that give rise to the four PGCs. Our results reveal the embryonic origin of the PGCs of H. exemplaris and provide the first molecular characterization of an early cell lineage in the tardigrade phylum. We anticipate that these observations will serve as a basis for characterizing the mechanisms of PGC development in this animal.
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Affiliation(s)
- Kira L. Heikes
- Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mandy Game
- Biology Department, University of North Florida, Jacksonville, FL, USA
| | - Frank W. Smith
- Biology Department, University of North Florida, Jacksonville, FL, USA
| | - Bob Goldstein
- Biology Department, 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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10
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Goldstein B. Tardigrades. Nat Methods 2022; 19:904-905. [PMID: 35927483 DOI: 10.1038/s41592-022-01573-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Bob Goldstein
- Department of Biology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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11
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Abstract
Experimentally tractable organisms like C. elegans, Drosophila, zebrafish, and mouse are popular models for addressing diverse questions in biology. In 1997, two of the most valuable invertebrate model organisms to date-C. elegans and Drosophila-were found to be much more closely related to each other than expected. C. elegans and Drosophila belong to the nematodes and arthropods, respectively, and these two phyla and six other phyla make up a clade of molting animals referred to as the Ecdysozoa. The other ecdysozoan phyla could be valuable models for comparative biology, taking advantage of the rich and continual sources of research findings as well as tools from both C. elegans and Drosophila. But when the Ecdysozoa was first recognized, few tools were available for laboratory studies in any of these six other ecdysozoan phyla. In 1999 I began an effort to develop tools for studying one such phylum, the tardigrades. Here, I describe how the tardigrade species Hypsibius exemplaris and tardigrades more generally have emerged over the past two decades as valuable new models for answering diverse questions. To date, these questions have included how animal body plans evolve and how biological materials can survive some remarkably extreme conditions.
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Affiliation(s)
- Bob Goldstein
- Department of Biology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States.
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12
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Transgenesis in the acoel worm Hofstenia miamia. Dev Cell 2021; 56:3160-3170.e4. [PMID: 34752780 DOI: 10.1016/j.devcel.2021.10.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 07/20/2021] [Accepted: 10/12/2021] [Indexed: 12/27/2022]
Abstract
The acoel worm Hofstenia miamia, which can replace tissue lost to injury via differentiation of a population of stem cells, has emerged as a new research organism for studying regeneration. To enhance the depth of mechanistic studies in this system, we devised a protocol for microinjection into embryonic cells that resulted in stable transgene integration into the genome and generated animals with tissue-specific fluorescent transgene expression in epidermis, gut, and muscle. We demonstrate that transgenic Hofstenia are amenable to the isolation of specific cell types, investigations of regeneration, tracking of photoconverted molecules, and live imaging. Further, our stable transgenic lines revealed insights into the biology of Hofstenia, including a high-resolution three-dimensional view of cell morphology and the organization of muscle as a cellular scaffold for other tissues. Our work positions Hofstenia as a powerful system with multiple toolkits for mechanistic investigations of development, whole-body regeneration, and stem cell biology.
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13
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Ramsay BP, Marley NJ, Bilton DT, Rundle SD, Ramsay PM. The structure of tardigrade communities at fine spatial scales in an Andean Polylepis forest. NEOTROPICAL BIODIVERSITY 2021. [DOI: 10.1080/23766808.2021.1943216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Affiliation(s)
- Balbina P.L. Ramsay
- Departamento de Ciencias Químico Biológicas, Universidad de las Américas Puebla, Puebla, México
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, UK
| | - Nigel J. Marley
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, UK
| | - David T. Bilton
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, UK
| | - Simon D. Rundle
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, UK
| | - Paul M. Ramsay
- Departamento de Ciencias Químico Biológicas, Universidad de las Américas Puebla, Puebla, México
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, UK
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14
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Luo Y, Wan G, Zhou X, Wang Q, Zhang Y, Bao J, Cong Y, Zhao Y, Li D. Architecture of Dispatched, a Transmembrane Protein Responsible for Hedgehog Release. Front Mol Biosci 2021; 8:701826. [PMID: 34557519 PMCID: PMC8453165 DOI: 10.3389/fmolb.2021.701826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 08/11/2021] [Indexed: 11/30/2022] Open
Abstract
The evolutionarily conserved Hedgehog (Hh) signaling pathway is crucial for programmed cell differentiation and proliferation. Dispatched (Disp) is a 12-transmembrane protein that plays a critical role in the Hedgehog (Hh) signaling pathway by releasing the dually lipidated ligand HhN from the membrane, a prerequisite step to the downstream signaling cascade. In this study, we focus on the Disp from water bear, a primitive animal known as the most indestructible on Earth. Using a zebrafish model, we show that the water bear homolog possesses the function of Disp. We have solved its structure to a 6.5-Å resolution using single-particle cryogenic electron microscopy. Consistent with the evolutional conservation of the pathway, the water bear Disp structure is overall similar to the previously reported structures of the fruit fly and human homologs. Although not revealing much detail at this resolution, the water bear Disp shows a different conformation compared to published structures, suggesting that they represent different functional snapshots.
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Affiliation(s)
- Yitian Luo
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Guoyue Wan
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xuan Zhou
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Qiuwen Wang
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yunbin Zhang
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Juan Bao
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yao Cong
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yun Zhao
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Dianfan Li
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
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15
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Hibshman JD, Clegg JS, Goldstein B. Mechanisms of Desiccation Tolerance: Themes and Variations in Brine Shrimp, Roundworms, and Tardigrades. Front Physiol 2020; 11:592016. [PMID: 33192606 PMCID: PMC7649794 DOI: 10.3389/fphys.2020.592016] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 09/25/2020] [Indexed: 01/05/2023] Open
Abstract
Water is critical for the survival of most cells and organisms. Remarkably, a small number of multicellular animals are able to survive nearly complete drying. The phenomenon of anhydrobiosis, or life without water, has been of interest to researchers for over 300 years. In this review we discuss advances in our understanding of protectants and mechanisms of desiccation tolerance that have emerged from research in three anhydrobiotic invertebrates: brine shrimp (Artemia), roundworms (nematodes), and tardigrades (water bears). Discovery of molecular protectants that allow each of these three animals to survive drying diversifies our understanding of desiccation tolerance, and convergent themes suggest mechanisms that may offer a general model for engineering desiccation tolerance in other contexts.
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Affiliation(s)
- Jonathan D. Hibshman
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - James S. Clegg
- Bodega Marine Laboratory, University of California, Davis, Davis, CA, United States
| | - Bob Goldstein
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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16
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Shih PY, Lee JS, Shinya R, Kanzaki N, Pires-daSilva A, Badroos JM, Goetz E, Sapir A, Sternberg PW. Newly Identified Nematodes from Mono Lake Exhibit Extreme Arsenic Resistance. Curr Biol 2019; 29:3339-3344.e4. [PMID: 31564490 DOI: 10.1016/j.cub.2019.08.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/24/2019] [Accepted: 08/09/2019] [Indexed: 01/26/2023]
Abstract
Extremophiles have much to reveal about the biology of resilience, yet their study is limited by sampling and culturing difficulties [1-3]. The broad success and small size of nematodes make them advantageous for tackling these problems [4-6]. We investigated the arsenic-rich, alkaline, and hypersaline Mono Lake (CA, US) [7-9] for extremophile nematodes. Though Mono Lake has previously been described to contain only two animal species (brine shrimp and alkali flies) in its water and sediments [10], we report the discovery of eight nematode species from the lake, including microbe grazers, parasites, and predators. Thus, nematodes are the dominant animals of Mono Lake in species richness. Phylogenetic analysis suggests that the nematodes originated from multiple colonization events, which is striking, given the young history of extreme conditions at Mono Lake [7, 11]. One species, Auanema sp., is new, culturable, and survives 500 times the human lethal dose of arsenic. Comparisons to two non-extremophile sister species [12] reveal that arsenic resistance is a common feature of the genus and a preadaptive trait that likely allowed Auanema to inhabit Mono Lake. This preadaptation may be partly explained by a variant in the gene dbt-1 shared with some Caenorhabditis elegans natural populations and known to confer arsenic resistance [13]. Our findings expand Mono Lake's ecosystem from two known animal species to ten, and they provide a new system for studying arsenic resistance. The dominance of nematodes in Mono Lake and other extreme environments and our findings of preadaptation to arsenic raise the intriguing possibility that nematodes are widely pre-adapted to be extremophiles.
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Affiliation(s)
- Pei-Yin Shih
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E California Blvd, Pasadena, CA 91125, USA
| | - James Siho Lee
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E California Blvd, Pasadena, CA 91125, USA
| | - Ryoji Shinya
- Department of Agriculture, Meiji University and JST PRESTO, 1-1-1, Higashimita, Tama-ku, Kawasaki-shi, Kanagawa 214-8571, Japan
| | - Natsumi Kanzaki
- Kansai Research Center, Forestry and Forest Products Research Institute, 68 Nagaikyutaroh, Momoyama, Fushimi, Kyoto, Kyoto 612-0855, Japan
| | - Andre Pires-daSilva
- School of Life Sciences, University of Warwick, Gibbet Hill, Coventry CV4 7AL, UK
| | - Jean Marie Badroos
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Elizabeth Goetz
- Department of Biology and the Environment, Faculty of Natural Sciences, University of Haifa, Derch Kiryat Amal, Oranim, Tivon 3600600, Israel
| | - Amir Sapir
- Department of Biology and the Environment, Faculty of Natural Sciences, University of Haifa, Derch Kiryat Amal, Oranim, Tivon 3600600, Israel.
| | - Paul W Sternberg
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E California Blvd, Pasadena, CA 91125, USA.
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17
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Gross V, Treffkorn S, Reichelt J, Epple L, Lüter C, Mayer G. Miniaturization of tardigrades (water bears): Morphological and genomic perspectives. ARTHROPOD STRUCTURE & DEVELOPMENT 2019; 48:12-19. [PMID: 30447338 DOI: 10.1016/j.asd.2018.11.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/08/2018] [Accepted: 11/13/2018] [Indexed: 05/03/2023]
Abstract
Tardigrades form a monophyletic group of microscopic ecdysozoans best known for surviving extreme environmental conditions. Due to their key phylogenetic position as a subgroup of the Panarthropoda, understanding tardigrade biology is important for comparative studies with related groups like Arthropoda. Panarthropods - and Ecdysozoa as a whole - likely evolved from macroscopic ancestors, with several taxa becoming secondarily miniaturized. Morphological and genomic evidence likewise points to a miniaturized tardigrade ancestor. The five-segmented tardigrade body typically measures less than 1 mm in length and consists of only about 1000 cells. Most organs comprise a relatively small number of cells, with the highest proportion belonging to the central nervous system, while muscles are reduced to a single cell each. Similarly, fully sequenced genomes of three tardigrade species - together with Hox gene expression data - point to extensive modifications, rearrangements, and major losses of genes and even a large body region. Parallels are evident with related ecdysozoans that may have also undergone genomic reductions, such as the nematode Caenorhabditis elegans. We interpret these data together as evidence of miniaturization in the tardigrade lineage, while cautioning that the effects of miniaturization may manifest in different ways depending on the organ or organ system under examination.
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Affiliation(s)
- Vladimir Gross
- Department of Zoology, Institute of Biology, University of Kassel, Heinrich-Plett-Straße 40, Kassel, D-34132, Germany
| | - Sandra Treffkorn
- Department of Zoology, Institute of Biology, University of Kassel, Heinrich-Plett-Straße 40, Kassel, D-34132, Germany
| | - Julian Reichelt
- Department of Zoology, Institute of Biology, University of Kassel, Heinrich-Plett-Straße 40, Kassel, D-34132, Germany
| | - Lisa Epple
- Department of Zoology, Institute of Biology, University of Kassel, Heinrich-Plett-Straße 40, Kassel, D-34132, Germany
| | - Carsten Lüter
- Museum für Naturkunde, Leibniz-Institute for Evolution and Biodiversity Science, Invalidenstraße 43, Berlin, D-10115, Germany
| | - Georg Mayer
- Department of Zoology, Institute of Biology, University of Kassel, Heinrich-Plett-Straße 40, Kassel, D-34132, Germany.
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18
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Gross V, Müller M, Hehn L, Ferstl S, Allner S, Dierolf M, Achterhold K, Mayer G, Pfeiffer F. X-ray imaging of a water bear offers a new look at tardigrade internal anatomy. ZOOLOGICAL LETTERS 2019; 5:14. [PMID: 31110777 PMCID: PMC6511223 DOI: 10.1186/s40851-019-0130-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 04/09/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND Tardigrades (water bears) are microscopic invertebrates of which the anatomy has been well studied using traditional techniques, but a comprehensive three-dimensional reconstruction has never been performed. In order to close this gap, we employed X-ray computed tomography (CT), a technique that is becoming increasingly popular in zoology for producing high-resolution, three-dimensional (3D) scans of whole specimens. While CT has long been used to scan larger samples, its use in some microscopic animals can be problematic, as they are often too small for conventional CT yet too large for high-resolution, optics-based soft X-ray microscopy. This size gap continues to be narrowed with advancements in technology, with high-resolution imaging now being possible using both large synchrotron devices and, more recently, laboratory-based instruments. RESULTS Here we use a recently developed prototype lab-based nano-computed tomography device to image a 152 μm-long tardigrade at high resolution (200-270 nm pixel size). The resulting dataset allowed us to visualize the anatomy of the tardigrade in 3D and analyze the spatial relationships of the internal structures. Segmentation of the major structures of the body enabled the direct measurement of their respective volumes. Furthermore, we segmented every storage cell individually and quantified their volume distribution. We compare our measurements to those from published studies in which other techniques were used. CONCLUSIONS The data presented herein demonstrate the utility of CT imaging as a powerful supplementary tool for studies of tardigrade anatomy, especially for quantitative volume measurements. This nanoCT study represents the smallest complete animal ever imaged using CT, and offers new 3D insights into the spatial relationships of the internal organs of water bears.
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Affiliation(s)
- Vladimir Gross
- Department of Zoology, Institute of Biology, University of Kassel, Heinrich-Plett-Straße 40, 34132 Kassel, Germany
| | - Mark Müller
- Department of Physics and Munich School of BioEngineering, Technical University of Munich, 85748 Garching, Germany
| | - Lorenz Hehn
- Department of Physics and Munich School of BioEngineering, Technical University of Munich, 85748 Garching, Germany
| | - Simone Ferstl
- Department of Physics and Munich School of BioEngineering, Technical University of Munich, 85748 Garching, Germany
| | - Sebastian Allner
- Department of Physics and Munich School of BioEngineering, Technical University of Munich, 85748 Garching, Germany
| | - Martin Dierolf
- Department of Physics and Munich School of BioEngineering, Technical University of Munich, 85748 Garching, Germany
| | - Klaus Achterhold
- Department of Physics and Munich School of BioEngineering, Technical University of Munich, 85748 Garching, Germany
| | - Georg Mayer
- Department of Zoology, Institute of Biology, University of Kassel, Heinrich-Plett-Straße 40, 34132 Kassel, Germany
| | - Franz Pfeiffer
- Department of Physics and Munich School of BioEngineering, Technical University of Munich, 85748 Garching, Germany
- Department of Diagnostic and Interventional Radiology, Klinikum rechts der Isar, Technical University of Munich, 81675 Munich, Germany
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19
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Heikes KL, Goldstein B. Live Imaging of Tardigrade Embryonic Development by Differential Interference Contrast Microscopy. Cold Spring Harb Protoc 2018; 2018:2018/11/pdb.prot102335. [PMID: 30385671 DOI: 10.1101/pdb.prot102335] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The tardigrade Hypsibius exemplaris was chosen as a model system in part because embryos and animals are optically clear at all stages, facilitating the viewing and filming of internal processes. Multiplane video recordings under differential interference contrast (DIC) microscopy have allowed early embryonic cell lineages to be reconstructed through seven rounds of division and have revealed invariant patterns of asymmetric cell divisions, nuclear migrations, and cell migrations. Here, we present a protocol for filming embryonic development of H. exemplaris by DIC microscopy.
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Affiliation(s)
- Kira L Heikes
- Biology Department, University of North Carolina, Chapel Hill, North Carolina 27599.,Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Bob Goldstein
- Biology Department, University of North Carolina, Chapel Hill, North Carolina 27599; .,Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
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