1
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Ma F, Lau CY, Zheng C. Young duplicate genes show developmental stage- and cell type-specific expression and function in Caenorhabditis elegans. CELL GENOMICS 2024; 4:100467. [PMID: 38190105 PMCID: PMC10794840 DOI: 10.1016/j.xgen.2023.100467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 10/06/2023] [Accepted: 11/23/2023] [Indexed: 01/09/2024]
Abstract
Gene duplication produces the material that fuels evolutionary innovation. The "out-of-testis" hypothesis suggests that sperm competition creates selective pressure encouraging the emergence of new genes in male germline, but the somatic expression and function of the newly evolved genes are not well understood. We systematically mapped the expression of young duplicate genes throughout development in Caenorhabditis elegans using both whole-organism and single-cell transcriptomic data. Based on the expression dynamics across developmental stages, young duplicate genes fall into three clusters that are preferentially expressed in early embryos, mid-stage embryos, and late-stage larvae. Early embryonic genes are involved in protein degradation and develop essentiality comparable to the genomic average. In mid-to-late embryos and L4-stage larvae, young genes are enriched in intestine, epidermal cells, coelomocytes, and amphid chemosensory neurons. Their molecular functions and inducible expression indicate potential roles in innate immune response and chemosensory perceptions, which may contribute to adaptation outside of the sperm.
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Affiliation(s)
- Fuqiang Ma
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Chun Yin Lau
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Chaogu Zheng
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China.
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2
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Tandingan De Ley I, Kiontke K, Bert W, Sudhaus W, Fitch DHA. Pellioditis pelhamensis n. sp. (Nematoda: Rhabditidae) and Pellioditis pellio (Schneider, 1866), earthworm associates from different subclades within Pellioditis (syn. Phasmarhabditis Andrássy, 1976). PLoS One 2023; 18:e0288196. [PMID: 37672545 PMCID: PMC10482300 DOI: 10.1371/journal.pone.0288196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 07/27/2023] [Indexed: 09/08/2023] Open
Abstract
Recently, much attention has been focused on a group of rhabditid nematodes called Phasmarhabditis, a junior synonym of Pellioditis, as a promising source of biocontrol agents for invasive slugs. Pellioditis pelhamensis n. sp. was first isolated from earthworms near Pelham Bay Park in Bronx, New York, USA, in 1990 and has been found to be pathogenic to slugs as well as some earthworms. It has also been used in several comparative developmental studies. Here, we provide a description of this species, as well as a redescription of a similar earthworm-associated nematode, Pellioditis pellio Schneider, 1866, re-isolated from the type locality. Although P. pelhamensis n. sp. and P. pellio are morphologically similar, they are reproductively isolated. Molecular phylogenetic analysis places both species in a clade that includes all species previously described as Phasmarhabditis which are associated with gastropods. Phasmarhabditis Andrássy, 1976 is therefore a junior synonym of Pellioditis Dougherty, 1953. Also, Pellioditis bohemica Nermut', Půža, Mekete & Mráček, 2017, described to be a facultative parasite of slugs, is found to be a junior synonym of Pellioditis pellio (Schneider, 1866), adding to evidence that P. pellio is associated with both slugs and earthworms. The earthworm-associated species P. pelhamensis n. sp. and P. pellio represent different subclades within Pellioditis, suggesting that Pellioditis species in general have a broader host range than just slugs. Because of this, caution is warranted in using these species as biological control agents until more is understood about their ecology.
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Affiliation(s)
- Irma Tandingan De Ley
- Department of Nematology, University of California, Riverside, CA, United States of America
| | - Karin Kiontke
- Department of Biology, New York University, New York, NY, United States of America
| | - Wim Bert
- Nematology Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - Walter Sudhaus
- Institut für Biologie/Zoologie, Freie Universität Berlin, Berlin, Germany
| | - David H. A. Fitch
- Department of Biology, New York University, New York, NY, United States of America
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3
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Broitman-Maduro G, Maduro MF. Evolutionary Change in Gut Specification in Caenorhabditis Centers on the GATA Factor ELT-3 in an Example of Developmental System Drift. J Dev Biol 2023; 11:32. [PMID: 37489333 PMCID: PMC10366740 DOI: 10.3390/jdb11030032] [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: 06/02/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/26/2023] Open
Abstract
Cells in a developing animal embryo become specified by the activation of cell-type-specific gene regulatory networks. The network that specifies the gut in the nematode Caenorhabditis elegans has been the subject of study for more than two decades. In this network, the maternal factors SKN-1/Nrf and POP-1/TCF activate a zygotic GATA factor cascade consisting of the regulators MED-1,2 → END-1,3 → ELT-2,7, leading to the specification of the gut in early embryos. Paradoxically, the MED, END, and ELT-7 regulators are present only in species closely related to C. elegans, raising the question of how the gut can be specified without them. Recent work found that ELT-3, a GATA factor without an endodermal role in C. elegans, acts in a simpler ELT-3 → ELT-2 network to specify gut in more distant species. The simpler ELT-3 → ELT-2 network may thus represent an ancestral pathway. In this review, we describe the elucidation of the gut specification network in C. elegans and related species and propose a model by which the more complex network might have formed. Because the evolution of this network occurred without a change in phenotype, it is an example of the phenomenon of Developmental System Drift.
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Affiliation(s)
- Gina Broitman-Maduro
- Department of Molecular, Cell, and Systems Biology, University of California-Riverside, Riverside, CA 92521, USA
| | - Morris F Maduro
- Department of Molecular, Cell, and Systems Biology, University of California-Riverside, Riverside, CA 92521, USA
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4
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Ma F, Zheng C. Transcriptome age of individual cell types in Caenorhabditis elegans. Proc Natl Acad Sci U S A 2023; 120:e2216351120. [PMID: 36812209 PMCID: PMC9992843 DOI: 10.1073/pnas.2216351120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/27/2023] [Indexed: 02/24/2023] Open
Abstract
The phylotranscriptomic analysis of development in several species revealed the expression of older and more conserved genes in midembryonic stages and younger and more divergent genes in early and late embryonic stages, which supported the hourglass mode of development. However, previous work only studied the transcriptome age of whole embryos or embryonic sublineages, leaving the cellular basis of the hourglass pattern and the variation of transcriptome ages among cell types unexplored. By analyzing both bulk and single-cell transcriptomic data, we studied the transcriptome age of the nematode Caenorhabditis elegans throughout development. Using the bulk RNA-seq data, we identified the morphogenesis phase in midembryonic development as the phylotypic stage with the oldest transcriptome and confirmed the results using whole-embryo transcriptome assembled from single-cell RNA-seq data. The variation in transcriptome ages among individual cell types remained small in early and midembryonic development and grew bigger in late embryonic and larval stages as cells and tissues differentiate. Lineages that give rise to certain tissues (e.g., hypodermis and some neurons) but not all recapitulated the hourglass pattern across development at the single-cell transcriptome level. Further analysis of the variation in transcriptome ages among the 128 neuron types in C. elegans nervous system found that a group of chemosensory neurons and their downstream interneurons expressed very young transcriptomes and may contribute to adaptation in recent evolution. Finally, the variation in transcriptome age among the neuron types, as well as the age of their cell fate regulators, led us to hypothesize the evolutionary history of some neuron types.
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Affiliation(s)
- Fuqiang Ma
- School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Chaogu Zheng
- School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
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5
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Broitman-Maduro G, Sun S, Kikuchi T, Maduro MF. The GATA factor ELT-3 specifies endoderm in Caenorhabditis angaria in an ancestral gene network. Development 2022; 149:277064. [PMID: 36196618 PMCID: PMC9720673 DOI: 10.1242/dev.200984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/20/2022] [Indexed: 11/07/2022]
Abstract
ABSTRACT
Endoderm specification in Caenorhabditis elegans occurs through a network in which maternally provided SKN-1/Nrf, with additional input from POP-1/TCF, activates the GATA factor cascade MED-1,2→END-1,3→ELT-2,7. Orthologues of the MED, END and ELT-7 factors are found only among nematodes closely related to C. elegans, raising the question of how gut is specified in their absence in more distant species in the genus. We find that the C. angaria, C. portoensis and C. monodelphis orthologues of the GATA factor gene elt-3 are expressed in the early E lineage, just before their elt-2 orthologues. In C. angaria, Can-pop-1(RNAi), Can-elt-3(RNAi) and a Can-elt-3 null mutation result in a penetrant ‘gutless’ phenotype. Can-pop-1 is necessary for Can-elt-3 activation, showing that it acts upstream. Forced early E lineage expression of Can-elt-3 in C. elegans can direct the expression of a Can-elt-2 transgene and rescue an elt-7 end-1 end-3; elt-2 quadruple mutant strain to viability. Our results demonstrate an ancestral mechanism for gut specification and differentiation in Caenorhabditis involving a simpler POP-1→ELT-3→ELT-2 gene network.
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Affiliation(s)
- Gina Broitman-Maduro
- University of California 1 Department of Molecular, Cell and Systems Biology , , Riverside, CA 92521 , USA
| | - Simo Sun
- Faculty of Medicine, University of Miyazaki 2 Department of Infectious Diseases , , 5200 Kihara, Miyazaki 889-1692 , Japan
- Graduate School of Frontier Sciences, The University of Tokyo 3 Department of Integrated Biosciences , , Chiba 277-8562 , Japan
| | - Taisei Kikuchi
- Faculty of Medicine, University of Miyazaki 2 Department of Infectious Diseases , , 5200 Kihara, Miyazaki 889-1692 , Japan
- Graduate School of Frontier Sciences, The University of Tokyo 3 Department of Integrated Biosciences , , Chiba 277-8562 , Japan
| | - Morris F. Maduro
- University of California 1 Department of Molecular, Cell and Systems Biology , , Riverside, CA 92521 , USA
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6
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Eweis DS, Delattre M, Plastino J. Asymmetry is defined during meiosis in the oocyte of the parthenogenetic nematode Diploscapter pachys. Dev Biol 2021; 483:13-21. [PMID: 34971598 DOI: 10.1016/j.ydbio.2021.12.013] [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: 07/09/2021] [Revised: 12/16/2021] [Accepted: 12/23/2021] [Indexed: 11/03/2022]
Abstract
Asymmetric cell division is an essential feature of normal development and certain pathologies. The process and its regulation have been studied extensively in the Caenorhabditis elegans embryo, particularly how symmetry of the actomyosin cortical cytoskeleton is broken by a sperm-derived signal at fertilization, upstream of polarity establishment. Diploscapter pachys is the closest parthenogenetic relative to C. elegans, and D. pachys one-cell embryos also divide asymmetrically. However how polarity is triggered in the absence of sperm remains unknown. In post-meiotic embryos, we find that the nucleus inhabits principally one embryo hemisphere, the future posterior pole. When forced to one pole by centrifugation, the nucleus returns to its preferred pole, although poles appear identical as concerns cortical ruffling and actin cytoskeleton. The location of the meiotic spindle also correlates with the future posterior pole and slight actin enrichment is observed at that pole in some early embryos along with microtubule structures emanating from the meiotic spindle. Polarized location of the nucleus is not observed in pre-meiotic D. pachys oocytes. All together our results are consistent with the idea that polarity of the D. pachys embryo is attained during meiosis, seemingly based on the location of the meiotic spindle, by a mechanism that may be present but suppressed in C. elegans.
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Affiliation(s)
- Dureen Samandar Eweis
- Physico Chimie Curie, Institut Curie, Université PSL, CNRS, Sorbonne Université, 75005, Paris, France
| | - Marie Delattre
- Laboratory of Biology and Modeling of the Cell, Ecole Normale Supérieure de Lyon, CNRS, Inserm, UCBL, 69007, Lyon, France
| | - Julie Plastino
- Physico Chimie Curie, Institut Curie, Université PSL, CNRS, Sorbonne Université, 75005, Paris, France.
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7
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Jankele R, Jelier R, Gönczy P. Physically asymmetric division of the C. elegans zygote ensures invariably successful embryogenesis. eLife 2021; 10:e61714. [PMID: 33620314 PMCID: PMC7972452 DOI: 10.7554/elife.61714] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 02/22/2021] [Indexed: 12/17/2022] Open
Abstract
Asymmetric divisions that yield daughter cells of different sizes are frequent during early embryogenesis, but the importance of such a physical difference for successful development remains poorly understood. Here, we investigated this question using the first division of Caenorhabditis elegans embryos, which yields a large AB cell and a small P1 cell. We equalized AB and P1 sizes using acute genetic inactivation or optogenetic manipulation of the spindle positioning protein LIN-5. We uncovered that only some embryos tolerated equalization, and that there was a size asymmetry threshold for viability. Cell lineage analysis of equalized embryos revealed an array of defects, including faster cell cycle progression in P1 descendants, as well as defects in cell positioning, division orientation, and cell fate. Moreover, equalized embryos were more susceptible to external compression. Overall, we conclude that unequal first cleavage is essential for invariably successful embryonic development of C. elegans.
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Affiliation(s)
- Radek Jankele
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL)LausanneSwitzerland
| | - Rob Jelier
- Centre of Microbial and Plant Genetics, Katholieke Universiteit LeuvenLeuvenBelgium
| | - Pierre Gönczy
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL)LausanneSwitzerland
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8
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Delattre M, Goehring NW. The first steps in the life of a worm: Themes and variations in asymmetric division in C. elegans and other nematodes. Curr Top Dev Biol 2021; 144:269-308. [PMID: 33992156 DOI: 10.1016/bs.ctdb.2020.12.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Starting with Boveri in the 1870s, microscopic investigation of early embryogenesis in a broad swath of nematode species revealed the central role of asymmetric cell division in embryonic axis specification, blastomere positioning, and cell fate specification. Notably, across the class Chromadorea, a conserved theme emerges-asymmetry is first established in the zygote and specifies its asymmetric division, giving rise to an anterior somatic daughter cell and a posterior germline daughter cell. Beginning in the 1980s, the emergence of Caenorhabditis elegans as a model organism saw the advent of genetic tools that enabled rapid progress in our understanding of the molecular mechanisms underlying asymmetric division, in many cases defining key paradigms that turn out to regulate asymmetric division in a wide range of systems. Yet, the consequence of this focus on C. elegans came at the expense of exploring the extant diversity of developmental variation exhibited across nematode species. Given the resurgent interest in evolutionary studies facilitated in part by new tools, here we revisit the diversity in this asymmetric first division, juxtaposing molecular insight into mechanisms of symmetry-breaking, spindle positioning and fate specification, with a consideration of plasticity and variability within and between species. In the process, we hope to highlight questions of evolutionary forces and molecular variation that may have shaped the extant diversity of developmental mechanisms observed across Nematoda.
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Affiliation(s)
- Marie Delattre
- Laboratory of Biology and Modeling of the Cell, Ecole Normale Supérieure de Lyon, CNRS, Inserm, UCBL, Lyon, France.
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9
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Strausfeld N, Sayre ME. Shore crabs reveal novel evolutionary attributes of the mushroom body. eLife 2021; 10:65167. [PMID: 33559601 PMCID: PMC7872517 DOI: 10.7554/elife.65167] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 01/14/2021] [Indexed: 11/13/2022] Open
Abstract
Neural organization of mushroom bodies is largely consistent across insects, whereas the ancestral ground pattern diverges broadly across crustacean lineages resulting in successive loss of columns and the acquisition of domed centers retaining ancestral Hebbian-like networks and aminergic connections. We demonstrate here a major departure from this evolutionary trend in Brachyura, the most recent malacostracan lineage. In the shore crab Hemigrapsus nudus, instead of occupying the rostral surface of the lateral protocerebrum, mushroom body calyces are buried deep within it with their columns extending outwards to an expansive system of gyri on the brain’s surface. The organization amongst mushroom body neurons reaches extreme elaboration throughout its constituent neuropils. The calyces, columns, and especially the gyri show DC0 immunoreactivity, an indicator of extensive circuits involved in learning and memory.
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Affiliation(s)
| | - Marcel E Sayre
- Lund Vision Group, Department of Biology, Lund University, Lund, Sweden.,Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
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10
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Strausfeld NJ, Wolff GH, Sayre ME. Mushroom body evolution demonstrates homology and divergence across Pancrustacea. eLife 2020; 9:e52411. [PMID: 32124731 PMCID: PMC7054004 DOI: 10.7554/elife.52411] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 02/03/2020] [Indexed: 02/06/2023] Open
Abstract
Descriptions of crustacean brains have focused mainly on three highly derived lineages of malacostracans: the reptantian infraorders represented by spiny lobsters, lobsters, and crayfish. Those descriptions advocate the view that dome- or cap-like neuropils, referred to as 'hemiellipsoid bodies,' are the ground pattern organization of centers that are comparable to insect mushroom bodies in processing olfactory information. Here we challenge the doctrine that hemiellipsoid bodies are a derived trait of crustaceans, whereas mushroom bodies are a derived trait of hexapods. We demonstrate that mushroom bodies typify lineages that arose before Reptantia and exist in Reptantia thereby indicating that the mushroom body, not the hemiellipsoid body, provides the ground pattern for both crustaceans and hexapods. We show that evolved variations of the mushroom body ground pattern are, in some lineages, defined by extreme diminution or loss and, in others, by the incorporation of mushroom body circuits into lobeless centers. Such transformations are ascribed to modifications of the columnar organization of mushroom body lobes that, as shown in Drosophila and other hexapods, contain networks essential for learning and memory.
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Affiliation(s)
- Nicholas James Strausfeld
- Department of Neuroscience, School of Mind, Brain and BehaviorUniversity of ArizonaTucsonUnited States
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11
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Thoen HH, Wolff GH, Marshall J, Sayre ME, Strausfeld NJ. The reniform body: An integrative lateral protocerebral neuropil complex of Eumalacostraca identified in Stomatopoda and Brachyura. J Comp Neurol 2019; 528:1079-1094. [PMID: 31621907 DOI: 10.1002/cne.24788] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 09/27/2019] [Accepted: 10/02/2019] [Indexed: 11/10/2022]
Abstract
Mantis shrimps (Stomatopoda) possess in common with other crustaceans, and with Hexapoda, specific neuroanatomical attributes of the protocerebrum, the most anterior part of the arthropod brain. These attributes include assemblages of interconnected centers called the central body complex and in the lateral protocerebra, situated in the eyestalks, paired mushroom bodies. The phenotypic homologues of these centers across Panarthropoda support the view that ancestral integrative circuits crucial to action selection and memory have persisted since the early Cambrian or late Ediacaran. However, the discovery of another prominent integrative neuropil in the stomatopod lateral protocerebrum raises the question whether it is unique to Stomatopoda or at least most developed in this lineage, which may have originated in the upper Ordovician or early Devonian. Here, we describe the neuroanatomical structure of this center, called the reniform body. Using confocal microscopy and classical silver staining, we demonstrate that the reniform body receives inputs from multiple sources, including the optic lobe's lobula. Although the mushroom body also receives projections from the lobula, it is entirely distinct from the reniform body, albeit connected to it by discrete tracts. We discuss the implications of their coexistence in Stomatopoda, the occurrence of the reniform body in another eumalacostracan lineage and what this may mean for our understanding of brain functionality in Pancrustacea.
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Affiliation(s)
- Hanne Halkinrud Thoen
- Sensory Neurobiology Group, Queensland Brain Institute, University of Queensland, Brisbane, Australia
| | | | - Justin Marshall
- Sensory Neurobiology Group, Queensland Brain Institute, University of Queensland, Brisbane, Australia
| | - Marcel E Sayre
- Lund Vision Group, Department of Biology, Lund University, Lund, Sweden
| | - Nicholas James Strausfeld
- Department of Neuroscience, School of Mind, Brain and Behavior, University of Arizona, Tucson, Arizona
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12
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Strausfeld NJ, Sayre ME. Mushroom bodies in Reptantia reflect a major transition in crustacean brain evolution. J Comp Neurol 2019; 528:261-282. [PMID: 31376285 DOI: 10.1002/cne.24752] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/27/2019] [Accepted: 07/30/2019] [Indexed: 11/11/2022]
Abstract
Brain centers possessing a suite of neuroanatomical characters that define mushroom bodies of dicondylic insects have been identified in mantis shrimps, which are basal malacostracan crustaceans. Recent studies of the caridean shrimp Lebbeus groenlandicus further demonstrate the existence of mushroom bodies in Malacostraca. Nevertheless, received opinion promulgates the hypothesis that domed centers called hemiellipsoid bodies typifying reptantian crustaceans, such as lobsters and crayfish, represent the malacostracan cerebral ground pattern. Here, we provide evidence from the marine hermit crab Pagurus hirsutiusculus that refutes this view. P. hirsutiusculus, which is a member of the infraorder Anomura, reveals a chimeric morphology that incorporates features of a domed hemiellipsoid body and a columnar mushroom body. These attributes indicate that a mushroom body morphology is the ancestral ground pattern, from which the domed hemiellipsoid body derives and that the "standard" reptantian hemiellipsoid bodies that typify Astacidea and Achelata are extreme examples of divergence from this ground pattern. This interpretation is underpinned by comparing the lateral protocerebrum of Pagurus with that of the crayfish Procambarus clarkii and Orconectes immunis, members of the reptantian infraorder Astacidea.
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Affiliation(s)
- Nicholas J Strausfeld
- Department of Neuroscience, School of Mind, Brain and Behavior, University of Arizona, Tucson, Arizona
| | - Marcel E Sayre
- Lund Vision Group, Department of Biology, Lund University, Lund, Sweden
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13
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Sayre ME, Strausfeld NJ. Mushroom bodies in crustaceans: Insect-like organization in the caridid shrimp Lebbeus groenlandicus. J Comp Neurol 2019; 527:2371-2387. [PMID: 30861118 DOI: 10.1002/cne.24678] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 02/27/2019] [Accepted: 02/28/2019] [Indexed: 11/11/2022]
Abstract
Paired centers in the forebrain of insects, called the mushroom bodies, have become the most investigated brain region of any invertebrate due to novel genetic strategies that relate unique morphological attributes of these centers to their functional roles in learning and memory. Mushroom bodies possessing all the morphological attributes of those in dicondylic insects have been identified in mantis shrimps, basal hoplocarid crustaceans that are sister to Eumalacostraca, the most species-rich group of Crustacea. However, unless other examples of mushroom bodies can be identified in Eumalacostraca, the possibility is that mushroom body-like centers may have undergone convergent evolution in Hoplocarida and are unique to this crustacean lineage. Here, we provide evidence that speaks against convergent evolution, describing in detail the paired mushroom bodies in the lateral protocerebrum of a decapod crustacean, Lebbeus groenlandicus, a species belonging to the infraorder Caridea, an ancient lineage of Eumalacostraca.
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Affiliation(s)
- Marcel E Sayre
- Lund Vision Group, Department of Biology, Lund University, Lund, Sweden
| | - Nicholas J Strausfeld
- Department of Neuroscience, School of Mind, Brain and Behavior, University of Arizona, Tucson, Arizona
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14
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Haag ES, Fitch DHA, Delattre M. From "the Worm" to "the Worms" and Back Again: The Evolutionary Developmental Biology of Nematodes. Genetics 2018; 210:397-433. [PMID: 30287515 PMCID: PMC6216592 DOI: 10.1534/genetics.118.300243] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 08/03/2018] [Indexed: 12/13/2022] Open
Abstract
Since the earliest days of research on nematodes, scientists have noted the developmental and morphological variation that exists within and between species. As various cellular and developmental processes were revealed through intense focus on Caenorhabditis elegans, these comparative studies have expanded. Within the genus Caenorhabditis, they include characterization of intraspecific polymorphisms and comparisons of distinct species, all generally amenable to the same laboratory culture methods and supported by robust genomic and experimental tools. The C. elegans paradigm has also motivated studies with more distantly related nematodes and animals. Combined with improved phylogenies, this work has led to important insights about the evolution of nematode development. First, while many aspects of C. elegans development are representative of Caenorhabditis, and of terrestrial nematodes more generally, others vary in ways both obvious and cryptic. Second, the system has revealed several clear examples of developmental flexibility in achieving a particular trait. This includes developmental system drift, in which the developmental control of homologous traits has diverged in different lineages, and cases of convergent evolution. Overall, the wealth of information and experimental techniques developed in C. elegans is being leveraged to make nematodes a powerful system for evolutionary cellular and developmental biology.
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Affiliation(s)
- Eric S Haag
- Department of Biology, University of Maryland, College Park, Maryland 20742
| | | | - Marie Delattre
- Laboratoire de Biologie Moléculaire de la Cellule, CNRS, INSERM, Ecole Normale Supérieure de Lyon, 69007, France
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15
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Valfort AC, Launay C, Sémon M, Delattre M. Evolution of mitotic spindle behavior during the first asymmetric embryonic division of nematodes. PLoS Biol 2018; 16:e2005099. [PMID: 29357348 PMCID: PMC5794175 DOI: 10.1371/journal.pbio.2005099] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 02/01/2018] [Accepted: 01/03/2018] [Indexed: 01/08/2023] Open
Abstract
Asymmetric cell division is essential to generate cellular diversity. In many animal cells, the cleavage plane lies perpendicular to the mitotic spindle, and it is the spindle positioning that dictates the size of the daughter cells. Although some properties of spindle positioning are conserved between distantly related model species and different cell types, little is known of the evolutionary robustness of the mechanisms underlying this event. We recorded the first embryonic division of 42 species of nematodes closely related to Caenorhabditis elegans, which is an excellent model system to study the biophysical properties of asymmetric spindle positioning. Our recordings, corresponding to 128 strains from 27 Caenorhabditis and 15 non-Caenorhabditis species (accessible at http://www.ens-lyon.fr/LBMC/NematodeCell/videos/), constitute a powerful collection of subcellular phenotypes to study the evolution of various cellular processes across species. In the present work, we analyzed our collection to the study of asymmetric spindle positioning. Although all the strains underwent an asymmetric first cell division, they exhibited large intra- and inter-species variations in the degree of cell asymmetry and in several parameters controlling spindle movement, including spindle oscillation, elongation, and displacement. Notably, these parameters changed frequently during evolution with no apparent directionality in the species phylogeny, with the exception of spindle transverse oscillations, which were an evolutionary innovation at the base of the Caenorhabditis genus. These changes were also unrelated to evolutionary variations in embryo size. Importantly, spindle elongation, displacement, and oscillation each evolved independently. This finding contrasts starkly with expectations based on C. elegans studies and reveals previously unrecognized evolutionary changes in spindle mechanics. Collectively, these data demonstrate that, while the essential process of asymmetric cell division has been conserved over the course of nematode evolution, the underlying spindle movement parameters can combine in various ways. Like other developmental processes, asymmetric cell division is subject to system drift.
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Affiliation(s)
- Aurore-Cécile Valfort
- Department of Pharmacology & Physiology (Colin Flaveny lab), Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Caroline Launay
- UnivLyon, ENS de Lyon, Univ Claude Bernard, Laboratory of Biology and Modelling of the Cell, Lyon University, Lyon, France
| | - Marie Sémon
- UnivLyon, ENS de Lyon, Univ Claude Bernard, Laboratory of Biology and Modelling of the Cell, Lyon University, Lyon, France
| | - Marie Delattre
- UnivLyon, ENS de Lyon, Univ Claude Bernard, Laboratory of Biology and Modelling of the Cell, Lyon University, Lyon, France
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16
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Kraus C, Schiffer PH, Kagoshima H, Hiraki H, Vogt T, Kroiher M, Kohara Y, Schierenberg E. Differences in the genetic control of early egg development and reproduction between C. elegans and its parthenogenetic relative D. coronatus. EvoDevo 2017; 8:16. [PMID: 29075433 PMCID: PMC5648466 DOI: 10.1186/s13227-017-0081-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 10/10/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The free-living nematode Diploscapter coronatus is the closest known relative of Caenorhabditis elegans with parthenogenetic reproduction. It shows several developmental idiosyncracies, for example concerning the mode of reproduction, embryonic axis formation and early cleavage pattern (Lahl et al. in Int J Dev Biol 50:393-397, 2006). Our recent genome analysis (Hiraki et al. in BMC Genomics 18:478, 2017) provides a solid foundation to better understand the molecular basis of developmental idiosyncrasies in this species in an evolutionary context by comparison with selected other nematodes. Our genomic data also yielded indications for the view that D. coronatus is a product of interspecies hybridization. RESULTS In a genomic comparison between D. coronatus, C. elegans, other representatives of the genus Caenorhabditis and the more distantly related Pristionchus pacificus and Panagrellus redivivus, certain genes required for central developmental processes in C. elegans like control of meiosis and establishment of embryonic polarity were found to be restricted to the genus Caenorhabditis. The mRNA content of early D. coronatus embryos was sequenced and compared with similar stages in C. elegans and Ascaris suum. We identified 350 gene families transcribed in the early embryo of D. coronatus but not in the other two nematodes. Looking at individual genes transcribed early in D. coronatus but not in C. elegans and A. suum, we found that orthologs of most of these are present in the genomes of the latter species as well, suggesting heterochronic shifts with respect to expression behavior. Considerable genomic heterozygosity and allelic divergence lend further support to the view that D. coronatus may be the result of an interspecies hybridization. Expression analysis of early acting single-copy genes yields no indication for silencing of one parental genome. CONCLUSIONS Our comparative cellular and molecular studies support the view that the genus Caenorhabditis differs considerably from the other studied nematodes in its control of development and reproduction. The easy-to-culture parthenogenetic D. coronatus, with its high-quality draft genome and only a single chromosome when haploid, offers many new starting points on the cellular, molecular and genomic level to explore alternative routes of nematode development and reproduction.
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Affiliation(s)
- Christopher Kraus
- Zoologisches Institut, Universität zu Köln, Cologne, NRW Germany
- Present Address: Institute for Genetics, Universität zu Köln, Cologne, NRW Germany
| | - Philipp H. Schiffer
- Zoologisches Institut, Universität zu Köln, Cologne, NRW Germany
- Genetics, Evolution and Environment, University College London, London, WC16BT UK
| | | | | | - Theresa Vogt
- Zoologisches Institut, Universität zu Köln, Cologne, NRW Germany
- Present Address: Molecular Cell Biology, Institute I for Anatomy University Clinic Cologne, University of Cologne, Cologne, Germany
| | - Michael Kroiher
- Zoologisches Institut, Universität zu Köln, Cologne, NRW Germany
| | - Yuji Kohara
- National Institute of Genetics, Mishima, Japan
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17
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Fradin H, Kiontke K, Zegar C, Gutwein M, Lucas J, Kovtun M, Corcoran DL, Baugh LR, Fitch DHA, Piano F, Gunsalus KC. Genome Architecture and Evolution of a Unichromosomal Asexual Nematode. Curr Biol 2017; 27:2928-2939.e6. [PMID: 28943090 PMCID: PMC5659720 DOI: 10.1016/j.cub.2017.08.038] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/14/2017] [Accepted: 08/15/2017] [Indexed: 10/24/2022]
Abstract
Asexual reproduction in animals, though rare, is the main or exclusive mode of reproduction in some long-lived lineages. The longevity of asexual clades may be correlated with the maintenance of heterozygosity by mechanisms that rearrange genomes and reduce recombination. Asexual species thus provide an opportunity to gain insight into the relationship between molecular changes, genome architecture, and cellular processes. Here we report the genome sequence of the parthenogenetic nematode Diploscapter pachys with only one chromosome pair. We show that this unichromosomal architecture is shared by a long-lived clade of asexual nematodes closely related to the genetic model organism Caenorhabditis elegans. Analysis of the genome assembly reveals that the unitary chromosome arose through fusion of six ancestral chromosomes, with extensive rearrangement among neighboring regions. Typical nematode telomeres and telomeric protection-encoding genes are lacking. Most regions show significant heterozygosity; homozygosity is largely concentrated to one region and attributed to gene conversion. Cell-biological and molecular evidence is consistent with the absence of key features of meiosis I, including synapsis and recombination. We propose that D. pachys preserves heterozygosity and produces diploid embryos without fertilization through a truncated meiosis. As a prelude to functional studies, we demonstrate that D. pachys is amenable to experimental manipulation by RNA interference.
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Affiliation(s)
- Hélène Fradin
- Department of Biology, New York University, New York, NY 10003, USA; Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Karin Kiontke
- Department of Biology, New York University, New York, NY 10003, USA
| | - Charles Zegar
- Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Michelle Gutwein
- Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Jessica Lucas
- Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Mikhail Kovtun
- Duke Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
| | - David L Corcoran
- Duke Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
| | - L Ryan Baugh
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - David H A Fitch
- Department of Biology, New York University, New York, NY 10003, USA.
| | - Fabio Piano
- Department of Biology, New York University, New York, NY 10003, USA; Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA; Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.
| | - Kristin C Gunsalus
- Department of Biology, New York University, New York, NY 10003, USA; Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA; Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.
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18
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Kanzaki N, Kiontke K, Tanaka R, Hirooka Y, Schwarz A, Müller-Reichert T, Chaudhuri J, Pires-daSilva A. Description of two three-gendered nematode species in the new genus Auanema (Rhabditina) that are models for reproductive mode evolution. Sci Rep 2017; 7:11135. [PMID: 28894108 PMCID: PMC5593846 DOI: 10.1038/s41598-017-09871-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 08/01/2017] [Indexed: 01/05/2023] Open
Abstract
The co-existence of males, females and hermaphrodites, a rare mating system known as trioecy, has been considered as an evolutionarily transient state. In nematodes, androdioecy (males/hermaphrodites) as found in Caenorhabditis elegans, is thought to have evolved from dioecy (males/females) through a trioecious intermediate. Thus, trioecious species are good models to understand the steps and requirements for the evolution of new mating systems. Here we describe two new species of nematodes with trioecy, Auanema rhodensis and A. freiburgensis. Along with molecular barcodes, we provide a detailed analysis of the morphology of these species, and document it with drawings and light and SEM micrographs. Based on morphological data, these free-living nematodes were assigned to a new genus, Auanema, together with three other species described previously. Auanema species display convergent evolution in some features with parasitic nematodes with complex life cycles, such as the production of few males after outcrossing and the obligatory development of dauers into self-propagating adults.
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Affiliation(s)
- Natsumi Kanzaki
- Forest Pathology Laboratory, Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan
| | - Karin Kiontke
- Department of Biology, New York University, 100 Washington Square E., New York, NY, 10003, USA
| | - Ryusei Tanaka
- Forest Pathology Laboratory, Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan.,Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki, 889-1692, Japan
| | - Yuuri Hirooka
- Forest Pathology Laboratory, Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan.,Department of Clinical Plant Science, Faculty of Bioscience and Applied Chemistry, Hosei University, Kajino-cho 3-7-2, Koganei, Tokyo, 184-8584, Japan
| | - Anna Schwarz
- Experimental Center, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Fiedlerstraße 42, 01307, Dresden, Germany
| | - Thomas Müller-Reichert
- Experimental Center, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Fiedlerstraße 42, 01307, Dresden, Germany
| | - Jyotiska Chaudhuri
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, CA, 94945, USA
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19
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Abstract
Gametogenesis in animal oocytes reduces the diploid genome content of germline precursors to a haploid state in gametes by discarding ¾ of the duplicated chromosomes through a sequence of two meiotic cell divisions called meiosis I and II. The assembly of the microtubule-based spindle structure that mediates this reduction in genome content remains poorly understood compared to our knowledge of mitotic spindle assembly and function. In this review, we consider the diversity of oocyte meiotic spindle assembly and structure across animal phylogeny, review recent advances in our understanding of how animal oocytes assemble spindles in the absence of the centriole-based microtubule-organizing centers that dominate mitotic spindle assembly, and discuss different models for how chromosomes are captured and moved to achieve chromosome segregation during oocyte meiotic cell division.
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Affiliation(s)
- Aaron F Severson
- Department of Biological, Geological, and Environmental Sciences, Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, Ohio, USA
| | - George von Dassow
- Oregon Institute of Marine Biology, University of Oregon, Charleston, Oregon, USA
| | - Bruce Bowerman
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA.
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20
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Farhadifar R, Baer CF, Valfort AC, Andersen EC, Müller-Reichert T, Delattre M, Needleman DJ. Scaling, selection, and evolutionary dynamics of the mitotic spindle. Curr Biol 2015; 25:732-740. [PMID: 25683802 PMCID: PMC10504684 DOI: 10.1016/j.cub.2014.12.060] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 12/24/2014] [Accepted: 12/24/2014] [Indexed: 12/20/2022]
Abstract
BACKGROUND Cellular structures such as the nucleus, Golgi, centrioles, and spindle show remarkable diversity between species, but the mechanisms that produce these variations in cell biology are not known. RESULTS Here we investigate the mechanisms that contribute to variations in morphology and dynamics of the mitotic spindle, which orchestrates chromosome segregation in all Eukaryotes and positions the division plane in many organisms. We use high-throughput imaging of the first division in nematodes to demonstrate that the measured effects of spontaneous mutations, combined with stabilizing selection on cell size, are sufficient to quantitatively explain both the levels of within-species variation in the spindle and its diversity over ∼100 million years of evolution. Furthermore, our finding of extensive within-species variation for the spindle demonstrates that there is not just one "wild-type" form, rather that cellular structures can exhibit a surprisingly broad diversity of naturally occurring behaviors. CONCLUSIONS Our results argue that natural selection acts predominantly on cell size and indirectly influences the spindle through the scaling of the spindle with cell size. Previous studies have shown that the spindle also scales with cell size during early development. Thus, the scaling of the spindle with cell size controls its variation over both ontogeny and phylogeny.
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Affiliation(s)
- Reza Farhadifar
- School of Engineering and Applied Sciences, Department of Molecular and Cellular Biology, FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Charles F Baer
- Department of Biology and University of Florida Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - Aurore-Cécile Valfort
- Laboratory of Molecular Biology of the Cell, UMR 5239, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, 69007 Lyon, France
| | - Erik C Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Thomas Müller-Reichert
- Experimental Center, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fiedlerstrasse 42, 01307 Dresden, Germany
| | - Marie Delattre
- Laboratory of Molecular Biology of the Cell, UMR 5239, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, 69007 Lyon, France
| | - Daniel J Needleman
- School of Engineering and Applied Sciences, Department of Molecular and Cellular Biology, FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
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21
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Liu Y, Wang C, Destin G, Szaro BG. Microtubule-associated protein tau promotes neuronal class II β-tubulin microtubule formation and axon elongation in embryonic Xenopus laevis. Eur J Neurosci 2015; 41:1263-75. [PMID: 25656701 DOI: 10.1111/ejn.12848] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 12/13/2014] [Accepted: 01/07/2015] [Indexed: 01/06/2023]
Abstract
Compared with its roles in neurodegeneration, much less is known about microtubule-associated protein tau's normal functions in vivo, especially during development. The external development and ease of manipulating gene expression of Xenopus laevis embryos make them especially useful for studying gene function during early development. To study tau's functions in axon outgrowth, we characterized the most prominent tau isoforms of Xenopus embryos and manipulated their expression. None of these four isoforms were strictly analogous to those commonly studied in mammals, as all constitutively contained exon 10, which is preferentially removed from mammalian fetal tau isoforms, as well as exon 8, which in mammals is rare. Nonetheless, like mammalian tau, Xenopus tau exhibited alternative splicing of exon 4a, which in mammals distinguishes 'big' tau of peripheral neurons, and exon 6. Strongly suppressing tau expression with antisense morpholino oligonucleotides only modestly compromised peripheral nerve outgrowth of intact tadpoles, but severely disrupted neuronal microtubules containing class II β-tubulins while leaving other microtubules largely unperturbed. Thus, the relatively mild dependence of axon development on tau likely resulted from having only a single class of microtubules disrupted by its loss. Also, consistent with its greater expression in long peripheral axons, boosting expression of 'big' tau increased neurite outgrowth significantly and enhanced tubulin acetylation more so than did the smaller isoform. These data demonstrate the utility of Xenopus as a tool to gain new insights into tau's functions in vivo.
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Affiliation(s)
- Yuanyuan Liu
- Department of Biological Sciences and the Center for Neuroscience Research, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Chen Wang
- Department of Biological Sciences and the Center for Neuroscience Research, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Giovanny Destin
- Department of Biological Sciences and the Center for Neuroscience Research, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Ben G Szaro
- Department of Biological Sciences and the Center for Neuroscience Research, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
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22
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Huang RE, Ren X, Qiu Y, Zhao Z. Description of Caenorhabditis sinica sp. n. (Nematoda: Rhabditidae), a nematode species used in comparative biology for C. elegans. PLoS One 2014; 9:e110957. [PMID: 25375770 PMCID: PMC4222906 DOI: 10.1371/journal.pone.0110957] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 07/20/2014] [Indexed: 02/06/2023] Open
Abstract
We re-isolated in China a relative of the nematode model Caenorhabditis elegans that was previously referred to informally as C. sp. 5. In spite of its importance for comparative biology, C. sp. 5 has remained morphologically uncharacterized. Therefore, we now provide detailed description of morphology and anatomy, assigning the name of Caenorhabditis sinica sp. n. to this nematode that is found frequently in China. C. sinica sp. n. belongs to the Elegans group in the genus Caenorhabditis, being phylogenetically close to C. briggsae although differing in reproductive mode. The gonochoristic C. sinica sp. n. displays two significantly larger distal parts of uteri filled with sperms in the female/hermaphroditic gonad than does the androdioecious C. briggsae. The new species can be differentiated morphologically from all known Caenorhabditis species within the Elegans group by presenting a uniquely shaped, three-pointed hook structure on the male precloacal lip. The lateral field of C. sinica sp. n. is marked by three ridges that are flanked by two additional incisures, sometimes appearing as five ridges in total. This study ends the prolonged period of the 'undescribed' anonymity for C. sinica sp. n. since its discovery and use in comparative biological research. Significant and crossing-direction dependent hybrid incompatibilities in F1 and F2 crossing progeny make C. sinica sp. n. an excellent model for studies of population and speciation genetics. The abundance of nematode species lacking detailed taxonomic characterization deserves renewed attention to address the species description gap for this important yet morphologically 'difficult' group of animals.
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Affiliation(s)
- Ren-E Huang
- School of Life Sciences, Tsinghua University, Beijing, China
- Department of Biology, Faculty of Science, Hong Kong Baptist University, Hong Kong, China
| | - Xiaoliang Ren
- Department of Biology, Faculty of Science, Hong Kong Baptist University, Hong Kong, China
| | - Yifei Qiu
- Department of Biology, Faculty of Science, Hong Kong Baptist University, Hong Kong, China
| | - Zhongying Zhao
- Department of Biology, Faculty of Science, Hong Kong Baptist University, Hong Kong, China
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23
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Landmann F, Foster JM, Michalski ML, Slatko BE, Sullivan W. Co-evolution between an endosymbiont and its nematode host: Wolbachia asymmetric posterior localization and AP polarity establishment. PLoS Negl Trop Dis 2014; 8:e3096. [PMID: 25165813 PMCID: PMC4148215 DOI: 10.1371/journal.pntd.0003096] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 07/03/2014] [Indexed: 01/07/2023] Open
Abstract
While bacterial symbionts influence a variety of host cellular responses throughout development, there are no documented instances in which symbionts influence early embryogenesis. Here we demonstrate that Wolbachia, an obligate endosymbiont of the parasitic filarial nematodes, is required for proper anterior-posterior polarity establishment in the filarial nematode B. malayi. Characterization of pre- and post-fertilization events in B. malayi reveals that, unlike C. elegans, the centrosomes are maternally derived and produce a cortical-based microtubule organizing center prior to fertilization. We establish that Wolbachia rely on these cortical microtubules and dynein to concentrate at the posterior cortex. Wolbachia also rely on PAR-1 and PAR-3 polarity cues for normal concentration at the posterior cortex. Finally, we demonstrate that Wolbachia depletion results in distinct anterior-posterior polarity defects. These results provide a striking example of endosymbiont-host co-evolution operating on the core initial developmental event of axis determination. Filarial nematodes are responsible for a number of neglected tropical diseases. The vast majority of these human parasites harbor the bacterial endosymbiont Wolbachia. Wolbachia are essential for filarial nematode survival and reproduction, and thus are a promising anti-filarial drug target. Understanding the molecular and cellular basis of Wolbachia-nematode interactions will facilitate the development of a new class of drugs that specifically disrupt these interactions. Here we focus on Wolbachia segregation patterns and interactions with the host cytoskeleton during early embryogenesis. Our studies indicate that centrosomes are maternally inherited in filarial nematodes resulting in a posterior microtubule-organizing center of maternal origin, unique to filarial nematodes. This microtubule-organizing center facilitates the concentration of Wolbachia at the posterior pole. We find that the microtubule motor dynein is required for the proper posterior Wolbachia localization. In addition, we demonstrate that Wolbachia rely on polarity signals in the egg for their preferential localization at the posterior pole. Conversely, Wolbachia are required for normal embryonic axis determination and Wolbachia removal leads to distinct anterior-posterior embryonic polarity defects. To our knowledge, this is the first example of a bacterial endosymbiont required for normal host embryogenesis.
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Affiliation(s)
- Frederic Landmann
- Department of Molecular, Cell and Developmental Biology, Sinsheimer Labs, University of California, Santa Cruz, California, United States of America
- Centre de Recherche de Biochimie Macromoléculaire, CNRS, Montpellier, France
- * E-mail:
| | - Jeremy M. Foster
- Molecular Parasitology, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Michelle L. Michalski
- Department of Biology and Microbiology, University of Wisconsin Oshkosh, Oshkosh, Wisconsin, United States of America
| | - Barton E. Slatko
- Molecular Parasitology, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - William Sullivan
- Department of Molecular, Cell and Developmental Biology, Sinsheimer Labs, University of California, Santa Cruz, California, United States of America
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Abstract
SUMMARY Strongyloides venezuelensis is a parasitic nematode that infects rodents. Although Strongyloides species described to date are known to exhibit parthenogenetic reproduction in the parasitic stage of their life cycle and sexual reproduction in the free-living stage, we did not observe any free-living males in S. venezuelensis in our strain, suggesting that the nematode is likely to depend on parthenogenetic reproduction. We confirmed by cytological analysis that S. venezuelensis produces eggs by parthenogenesis during the parasitic stage of its life cycle. Phylogenetic analysis using nearly the full length of 18S and D3 region of 28S ribosomal RNA gene suggested that S. venezuelensis is distantly related to another rodent parasite, namely Strongyloides ratti, but more closely related to a ruminant parasite, Strongyloides papillosus. Karyotype analysis revealed S. venezuelensis reproduces with mitotic parthenogenesis, and has the same number of chromosomes as S. papillosus (2n = 4), but differs from S. ratti (2n = 6) in this regard. These results, taken together, suggest that S. venezuelensis evolved its parasitism for rodents independently from S. ratti and, therefore, is likely to have a different reproductive strategy.
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Cluet D, Stébé PN, Riche S, Spichty M, Delattre M. Automated high-throughput quantification of mitotic spindle positioning from DIC movies of Caenorhabditis embryos. PLoS One 2014; 9:e93718. [PMID: 24763198 PMCID: PMC3998942 DOI: 10.1371/journal.pone.0093718] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 03/05/2014] [Indexed: 01/19/2023] Open
Abstract
The mitotic spindle is a microtubule-based structure that elongates to accurately segregate chromosomes during anaphase. Its position within the cell also dictates the future cell cleavage plan, thereby determining daughter cell orientation within a tissue or cell fate adoption for polarized cells. Therefore, the mitotic spindle ensures at the same time proper cell division and developmental precision. Consequently, spindle dynamics is the matter of intensive research. Among the different cellular models that have been explored, the one-cell stage C. elegans embryo has been an essential and powerful system to dissect the molecular and biophysical basis of spindle elongation and positioning. Indeed, in this large and transparent cell, spindle poles (or centrosomes) can be easily detected from simple DIC microscopy by human eyes. To perform quantitative and high-throughput analysis of spindle motion, we developed a computer program ACT for Automated-Centrosome-Tracking from DIC movies of C. elegans embryos. We therefore offer an alternative to the image acquisition and processing of transgenic lines expressing fluorescent spindle markers. Consequently, experiments on large sets of cells can be performed with a simple setup using inexpensive microscopes. Moreover, analysis of any mutant or wild-type backgrounds is accessible because laborious rounds of crosses with transgenic lines become unnecessary. Last, our program allows spindle detection in other nematode species, offering the same quality of DIC images but for which techniques of transgenesis are not accessible. Thus, our program also opens the way towards a quantitative evolutionary approach of spindle dynamics. Overall, our computer program is a unique macro for the image- and movie-processing platform ImageJ. It is user-friendly and freely available under an open-source licence. ACT allows batch-wise analysis of large sets of mitosis events. Within 2 minutes, a single movie is processed and the accuracy of the automated tracking matches the precision of the human eye.
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Affiliation(s)
- David Cluet
- Laboratory of Molecular Biology of the Cell, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Lyon, France
| | - Pierre-Nicolas Stébé
- Laboratory of Molecular Biology of the Cell, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Lyon, France
| | - Soizic Riche
- Laboratory of Molecular Biology of the Cell, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Lyon, France
| | - Martin Spichty
- Laboratory of Molecular Biology of the Cell, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Lyon, France
- * E-mail: (MS); (MD)
| | - Marie Delattre
- Laboratory of Molecular Biology of the Cell, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Lyon, France
- * E-mail: (MS); (MD)
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Schiffer PH, Kroiher M, Kraus C, Koutsovoulos GD, Kumar S, R Camps JI, Nsah NA, Stappert D, Morris K, Heger P, Altmüller J, Frommolt P, Nürnberg P, Thomas WK, Blaxter ML, Schierenberg E. The genome of Romanomermis culicivorax: revealing fundamental changes in the core developmental genetic toolkit in Nematoda. BMC Genomics 2013; 14:923. [PMID: 24373391 PMCID: PMC3890508 DOI: 10.1186/1471-2164-14-923] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 12/17/2013] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The genetics of development in the nematode Caenorhabditis elegans has been described in exquisite detail. The phylum Nematoda has two classes: Chromadorea (which includes C. elegans) and the Enoplea. While the development of many chromadorean species resembles closely that of C. elegans, enoplean nematodes show markedly different patterns of early cell division and cell fate assignment. Embryogenesis of the enoplean Romanomermis culicivorax has been studied in detail, but the genetic circuitry underpinning development in this species has not been explored. RESULTS We generated a draft genome for R. culicivorax and compared its gene content with that of C. elegans, a second enoplean, the vertebrate parasite Trichinella spiralis, and a representative arthropod, Tribolium castaneum. This comparison revealed that R. culicivorax has retained components of the conserved ecdysozoan developmental gene toolkit lost in C. elegans. T. spiralis has independently lost even more of this toolkit than has C. elegans. However, the C. elegans toolkit is not simply depauperate, as many novel genes essential for embryogenesis in C. elegans are not found in, or have only extremely divergent homologues in R. culicivorax and T. spiralis. Our data imply fundamental differences in the genetic programmes not only for early cell specification but also others such as vulva formation and sex determination. CONCLUSIONS Despite the apparent morphological conservatism, major differences in the molecular logic of development have evolved within the phylum Nematoda. R. culicivorax serves as a tractable system to contrast C. elegans and understand how divergent genomic and thus regulatory backgrounds nevertheless generate a conserved phenotype. The R. culicivorax draft genome will promote use of this species as a research model.
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Affiliation(s)
| | - Michael Kroiher
- Zoologisches Institut, Universität zu Köln, Cologne, NRW, Germany
| | | | - Georgios D Koutsovoulos
- Institute of Evolutionary Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, Scotland, UK
| | - Sujai Kumar
- Institute of Evolutionary Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, Scotland, UK
| | - Julia I R Camps
- Zoologisches Institut, Universität zu Köln, Cologne, NRW, Germany
| | - Ndifon A Nsah
- Zoologisches Institut, Universität zu Köln, Cologne, NRW, Germany
| | - Dominik Stappert
- Institute für Entwicklungsbiologie, Universität zu Köln, Cologne, NRW, Germany
| | - Krystalynne Morris
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, USA
| | - Peter Heger
- Zoologisches Institut, Universität zu Köln, Cologne, NRW, Germany
| | - Janine Altmüller
- Cologne Center for Genomics, Universität zu Köln, Cologne, NRW, Germany
| | - Peter Frommolt
- Cologne Center for Genomics, Universität zu Köln, Cologne, NRW, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics, Universität zu Köln, Cologne, NRW, Germany
| | - W Kelley Thomas
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, USA
| | - Mark L Blaxter
- Institute of Evolutionary Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, Scotland, UK
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Riche S, Zouak M, Argoul F, Arneodo A, Pecreaux J, Delattre M. Evolutionary comparisons reveal a positional switch for spindle pole oscillations in Caenorhabditis embryos. ACTA ACUST UNITED AC 2013; 201:653-62. [PMID: 23690175 PMCID: PMC3664713 DOI: 10.1083/jcb.201210110] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In one-cell stage embryos of different worm species, a conserved positional switch controls the onset of mitotic spindle oscillations, whereas the maximum amplitude of oscillations is determined by the time spent in the oscillating phase. During the first embryonic division in Caenorhabditis elegans, the mitotic spindle is pulled toward the posterior pole of the cell and undergoes vigorous transverse oscillations. We identified variations in spindle trajectories by analyzing the outwardly similar one-cell stage embryo of its close relative Caenorhabditis briggsae. Compared with C. elegans, C. briggsae embryos exhibit an anterior shifting of nuclei in prophase and reduced anaphase spindle oscillations. By combining physical perturbations and mutant analysis in both species, we show that differences can be explained by interspecies changes in the regulation of the cortical Gα–GPR–LIN-5 complex. However, we found that in both species (1) a conserved positional switch controls the onset of spindle oscillations, (2) GPR posterior localization may set this positional switch, and (3) the maximum amplitude of spindle oscillations is determined by the time spent in the oscillating phase. By investigating microevolution of a subcellular process, we identify new mechanisms that are instrumental to decipher spindle positioning.
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Affiliation(s)
- Soizic Riche
- Laboratory of Molecular Biology of the Cell, UMR5239, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, 69007 Lyon, France
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Pohl C, Tiongson M, Moore JL, Santella A, Bao Z. Actomyosin-based self-organization of cell internalization during C. elegans gastrulation. BMC Biol 2012; 10:94. [PMID: 23198792 PMCID: PMC3583717 DOI: 10.1186/1741-7007-10-94] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Accepted: 11/30/2012] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Gastrulation is a key transition in embryogenesis; it requires self-organized cellular coordination, which has to be both robust to allow efficient development and plastic to provide adaptability. Despite the conservation of gastrulation as a key event in Metazoan embryogenesis, the morphogenetic mechanisms of self-organization (how global order or coordination can arise from local interactions) are poorly understood. RESULTS We report a modular structure of cell internalization in Caenorhabditis elegans gastrulation that reveals mechanisms of self-organization. Cells that internalize during gastrulation show apical contractile flows, which are correlated with centripetal extensions from surrounding cells. These extensions converge to seal over the internalizing cells in the form of rosettes. This process represents a distinct mode of monolayer remodeling, with gradual extrusion of the internalizing cells and simultaneous tissue closure without an actin purse-string. We further report that this self-organizing module can adapt to severe topological alterations, providing evidence of scalability and plasticity of actomyosin-based patterning. Finally, we show that globally, the surface cell layer undergoes coplanar division to thin out and spread over the internalizing mass, which resembles epiboly. CONCLUSIONS The combination of coplanar division-based spreading and recurrent local modules for piecemeal internalization constitutes a system-level solution of gradual volume rearrangement under spatial constraint. Our results suggest that the mode of C. elegans gastrulation can be unified with the general notions of monolayer remodeling and with distinct cellular mechanisms of actomyosin-based morphogenesis.
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Affiliation(s)
- Christian Pohl
- Developmental Biology Program, Sloan-Kettering Institute, 1275 York Avenue, New York, NY, 10065, USA
- Buchmann Institute for Molecular Life Sciences, Institute of Biochemistry II, Goethe University, Max-von-Laue-Strasse 15, 60438 Frankfurt, Germany
| | - Michael Tiongson
- Developmental Biology Program, Sloan-Kettering Institute, 1275 York Avenue, New York, NY, 10065, USA
| | - Julia L Moore
- Developmental Biology Program, Sloan-Kettering Institute, 1275 York Avenue, New York, NY, 10065, USA
- Program in Computational Biology and Medicine, Cornell University, 1300 York Avenue, New York, NY, 10065, USA
| | - Anthony Santella
- Developmental Biology Program, Sloan-Kettering Institute, 1275 York Avenue, New York, NY, 10065, USA
| | - Zhirong Bao
- Developmental Biology Program, Sloan-Kettering Institute, 1275 York Avenue, New York, NY, 10065, USA
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Tse YC, Werner M, Longhini KM, Labbe JC, Goldstein B, Glotzer M. RhoA activation during polarization and cytokinesis of the early Caenorhabditis elegans embryo is differentially dependent on NOP-1 and CYK-4. Mol Biol Cell 2012; 23:4020-31. [PMID: 22918944 PMCID: PMC3469517 DOI: 10.1091/mbc.e12-04-0268] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
RhoA and the Rho guanine nucleotide exchange factor ECT-2 are involved in both polarization and cytokinesis. During cytokinesis, interactions of ECT-2 with the Rho GTPase-activating protein CYK-4 promote RhoA activation. A novel protein, NOP-1, acts in parallel with CYK-4 to promote RhoA activation during polarization and cytokinesis. The GTPase RhoA is a central regulator of cellular contractility in a wide variety of biological processes. During these events, RhoA is activated by guanine nucleotide exchange factors (GEFs). These molecules are highly regulated to ensure that RhoA activation occurs at the proper time and place. During cytokinesis, RhoA is activated by the RhoGEF ECT-2. In human cells, ECT-2 activity requires its association with CYK-4, which is a component of the centralspindlin complex. In contrast, in early Caenorhabditis elegans embryos, not all ECT-2–dependent functions require CYK-4. In this study, we identify a novel protein, NOP-1, that functions in parallel with CYK-4 to promote RhoA activation. We use mutations in nop-1 and cyk-4 to dissect cytokinesis and cell polarization. NOP-1 makes a significant, albeit largely redundant, contribution to cytokinesis. In contrast, NOP-1 is required for the preponderance of RhoA activation during the establishment phase of polarization.
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Affiliation(s)
- Yu Chung Tse
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
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Sommer RJ, Bumbarger DJ. Nematode model systems in evolution and development. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2012; 1:389-400. [PMID: 23801489 DOI: 10.1002/wdev.33] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The free-living nematode Caenorhabditis elegans is one of the most important model organisms in all areas of modern biology. Using the knowledge about C. elegans as a baseline, nematodes are now intensively studied in evolution and development. Evolutionary developmental biology or for short, 'evo-devo' has been developed as a new research discipline during the last two decades to investigate how changes in developmental processes and mechanisms result in the modification of morphological structures and phenotypic novelty. In this article, we review the concepts that make nematode evo-devo a successful approach to evolutionary biology. We introduce selected model systems for nematode evo-devo and provide a detailed discussion of four selected case studies. The most striking finding of nematode evo-devo is the magnitude of developmental variation in the context of a conserved body plan. Detailed investigation of early embryogenesis, gonad formation, vulva development, and sex determination revealed that molecular mechanisms evolve rapidly, often in the context of a conserved body plan. These studies highlight the importance of developmental systems drift and neutrality in evolution.
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Affiliation(s)
- Ralf J Sommer
- Department Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany.
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31
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Kiontke KC, Félix MA, Ailion M, Rockman MV, Braendle C, Pénigault JB, Fitch DHA. A phylogeny and molecular barcodes for Caenorhabditis, with numerous new species from rotting fruits. BMC Evol Biol 2011; 11:339. [PMID: 22103856 PMCID: PMC3277298 DOI: 10.1186/1471-2148-11-339] [Citation(s) in RCA: 256] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2011] [Accepted: 11/21/2011] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The nematode Caenorhabditis elegans is a major laboratory model in biology. Only ten Caenorhabditis species were available in culture at the onset of this study. Many of them, like C. elegans, were mostly isolated from artificial compost heaps, and their more natural habitat was unknown. RESULTS Caenorhabditis nematodes were found to be proliferating in rotten fruits, flowers and stems. By collecting a large worldwide set of such samples, 16 new Caenorhabditis species were discovered. We performed mating tests to establish biological species status and found some instances of semi-fertile or sterile hybrid progeny. We established barcodes for all species using ITS2 rDNA sequences. By obtaining sequence data for two rRNA and nine protein-coding genes, we determined the likely phylogenetic relationships among the 26 species in culture. The new species are part of two well-resolved sister clades that we call the Elegans super-group and the Drosophilae super-group. We further scored phenotypic characters such as reproductive mode, mating behavior and male tail morphology, and discuss their congruence with the phylogeny. A small space between rays 2 and 3 evolved once in the stem species of the Elegans super-group; a narrow fan and spiral copulation evolved once in the stem species of C. angaria, C. sp. 8 and C. sp. 12. Several other character changes occurred convergently. For example, hermaphroditism evolved three times independently in C. elegans, C. briggsae and C. sp. 11. Several species can co-occur in the same location or even the same fruit. At the global level, some species have a cosmopolitan distribution: C. briggsae is particularly widespread, while C. elegans and C. remanei are found mostly or exclusively in temperate regions, and C. brenneri and C. sp. 11 exclusively in tropical zones. Other species have limited distributions, for example C. sp. 5 appears to be restricted to China, C. sp. 7 to West Africa and C. sp. 8 to the Eastern United States. CONCLUSIONS Caenorhabditis are "fruit worms", not soil nematodes. The 16 new species provide a resource and their phylogeny offers a framework for further studies into the evolution of genomic and phenotypic characters.
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Affiliation(s)
- Karin C Kiontke
- Department of Biology, New York University, 100 Washington Square East New York, New York 10003, USA
| | - Marie-Anne Félix
- CNRS-Institut Jacques Monod, 15 rue Hélène Brion, 75205 Paris cedex 13, France
| | - Michael Ailion
- Department of Biology, University of Utah, Salt Lake City, Utah 84112, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Matthew V Rockman
- Department of Biology, New York University, 100 Washington Square East New York, New York 10003, USA
- Center for Genomics and Systems Biology, New York University, New York, USA
| | - Christian Braendle
- Institute of Developmental Biology and Cancer, CNRS-University of Nice, Sophia-Antipolis, Parc Valrose, 06108 NICE cedex 2, France
| | | | - David HA Fitch
- Department of Biology, New York University, 100 Washington Square East New York, New York 10003, USA
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32
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Gunsalus KC, Rhrissorrakrai K. Networks in Caenorhabditis elegans. Curr Opin Genet Dev 2011; 21:787-98. [PMID: 22054717 DOI: 10.1016/j.gde.2011.10.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 10/11/2011] [Indexed: 10/15/2022]
Abstract
The network paradigm has become a pervasive theme in biology over the last decade, as increasingly large functional genomic datasets are being collected to interrogate regulatory influences, physical interactions, and genetic dependencies between genes, transcripts, and proteins. These 'molecular interaction' networks can be analyzed collectively and individually to define their global architecture and local patterns of connectivity. These structural features ultimately underlie functional properties such as robustness, modularity, component circuitry (e.g. feedback loops), dynamics, and responses to perturbations. This review focuses on recent progress in elucidating molecular interaction networks using different kinds of functional assays in the classical genetic model for animal development, the roundworm Caenorhabditis elegans, with representative examples to illustrate current directions in different areas of network biology.
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Affiliation(s)
- Kristin C Gunsalus
- Center for Genomics and Systems Biology and Department of Biology, New York University, 12 Waverly Place, 8th floor, New York, NY 10012, USA.
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Schulze J, Schierenberg E. Evolution of embryonic development in nematodes. EvoDevo 2011; 2:18. [PMID: 21929824 PMCID: PMC3195109 DOI: 10.1186/2041-9139-2-18] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Accepted: 09/20/2011] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Nematodes can be subdivided into basal Enoplea (clades 1 and 2) and more derived Chromadorea (clades 3 to 12). Embryogenesis of Caenorhabditis elegans (clade 9) has been analyzed in most detail. Their establishment of polarity and asymmetric cleavage requires the differential localization of PAR proteins. Earlier studies on selected other nematodes revealed that embryonic development of nematodes is more diverse than the essentially invariant development of C. elegans and the classic study object Ascaris had suggested. To obtain a more detailed picture of variations and evolutionary trends we compared embryonic cell lineages and pattern formation in embryos of all 12 nematode clades. METHODS The study was conducted using 4-D microscopy and 3-D modeling of developing embryos. RESULTS We found dramatic differences compared to C. elegans in Enoplea but also considerable variations among Chromadorea. We discovered 'Polarity Organizing Centers' (POCs) that orient cleavage spindles along the anterior-posterior axis in distinct cells over consecutive cell generations. The resulting lineally arranged blastomeres represent a starting point for the establishment of bilateral symmetry within individual lineages. We can discern six different early cleavage types and suggest that these variations are due to modifications in the activity of the POCs in conjunction with changes in the distribution of PAR proteins. In addition, our studies indicate that lineage complexity advanced considerably during evolution, that is we observe trends towards an increase of somatic founder cells, from monoclonal to polyclonal lineages and from a variable (position-dependent) to an invariable (lineage-dependent) way of cell fate specification. In contrast to the early phase of embryogenesis, the second half ('morphogenesis') appears similar in all studied nematodes. Comparison of early cleavage between the basal nematode Tobrilus stefanskii and the tardigrade Hypsibius dujardini revealed surprising similarities indicating that the presence of POCs is not restricted to nematode embryos. CONCLUSIONS The pattern of cleavage, spatial arrangement and differentiation of cells diverged dramatically during the history of the phylum Nematoda without corresponding changes in the phenotype. While in all studied representatives the same distinctive developmental steps need to be taken, cell behavior leading to these is not conserved.
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Affiliation(s)
- Jens Schulze
- University of Cologne, Biocenter, Zuelpicher Str. 47b 50967 Köln, Germany
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Abstract
Cell specification requires that particular subsets of cells adopt unique expression patterns that ultimately define the fates of their descendants. In C. elegans, cell fate specification involves the combinatorial action of multiple signals that produce activation of a small number of "blastomere specification" factors. These initiate expression of gene regulatory networks that drive development forward, leading to activation of "tissue specification" factors. In this review, the C. elegans embryo is considered as a model system for studies of cell specification. The techniques used to study cell fate in this species, and the themes that have emerged, are described.
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Affiliation(s)
- Morris F Maduro
- Department of Biology, University of California, Riverside, Riverside, California 92521, USA.
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Zhou K, Hanna-Rose W. Movers and shakers or anchored: Caenorhabditis elegans nuclei achieve it with KASH/SUN. Dev Dyn 2010; 239:1352-64. [PMID: 20108325 DOI: 10.1002/dvdy.22226] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
The invariant cell division patterns that characterize Caenorhabditis elegans development make it an ideal system to study the mechanisms that control nuclear movement and positioning. Forward genetic screens in this system allowed identification of the key molecular machinery for connecting the nucleus to the cytoskeleton; pairs of protein partners, consisting of a KASH domain protein and a SUN domain protein, bridge the nuclear envelope to connect the nucleus to cytoskeletal components. The C. elegans genome encodes several KASH/SUN pairs, and mutant phenotypes as well as tissue-specific expression patterns suggest a diversity of functions. These functions include moving the nucleus but have been extended to effects on the chromosomes inside the nucleus as well. We review the impact of the C. elegans system in pioneering this field as well as the functions of these KASH/SUN protein pairs across spatial and temporal C. elegans development.
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Affiliation(s)
- Kang Zhou
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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Abstract
Recent studies have demonstrated a correlation between cell size and the behaviors of the cytoskeletal division machinery during embryogenesis, giving insight into how a core cellular process is modulated over the course of development.
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Affiliation(s)
- Daniel J Needleman
- Harvard University, 52 Oxford Street, Room 365.10, Cambridge, MA 02138, USA.
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