1
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Pamula MC, Lehmann R. How germ granules promote germ cell fate. Nat Rev Genet 2024:10.1038/s41576-024-00744-8. [PMID: 38890558 DOI: 10.1038/s41576-024-00744-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/08/2024] [Indexed: 06/20/2024]
Abstract
Germ cells are the only cells in the body capable of giving rise to a new organism, and this totipotency hinges on their ability to assemble membraneless germ granules. These specialized RNA and protein complexes are hallmarks of germ cells throughout their life cycle: as embryonic germ granules in late oocytes and zygotes, Balbiani bodies in immature oocytes, and nuage in maturing gametes. Decades of developmental, genetic and biochemical studies have identified protein and RNA constituents unique to germ granules and have implicated these in germ cell identity, genome integrity and gamete differentiation. Now, emerging research is defining germ granules as biomolecular condensates that achieve high molecular concentrations by phase separation, and it is assigning distinct roles to germ granules during different stages of germline development. This organization of the germ cell cytoplasm into cellular subcompartments seems to be critical not only for the flawless continuity through the germline life cycle within the developing organism but also for the success of the next generation.
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Affiliation(s)
| | - Ruth Lehmann
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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2
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Simpson LA, Crowley D, Forey T, Acosta H, Ferjentsik Z, Chatfield J, Payne A, Simpson BS, Redwood C, Dixon JE, Holmes N, Sang F, Alberio R, Loose M, Johnson AD. NANOG is required to establish the competence for germ-layer differentiation in the basal tetrapod axolotl. PLoS Biol 2023; 21:e3002121. [PMID: 37315073 PMCID: PMC10599592 DOI: 10.1371/journal.pbio.3002121] [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: 06/10/2022] [Revised: 10/25/2023] [Accepted: 04/13/2023] [Indexed: 06/16/2023] Open
Abstract
Pluripotency defines the unlimited potential of individual cells of vertebrate embryos, from which all adult somatic cells and germ cells are derived. Understanding how the programming of pluripotency evolved has been obscured in part by a lack of data from lower vertebrates; in model systems such as frogs and zebrafish, the function of the pluripotency genes NANOG and POU5F1 have diverged. Here, we investigated how the axolotl ortholog of NANOG programs pluripotency during development. Axolotl NANOG is absolutely required for gastrulation and germ-layer commitment. We show that in axolotl primitive ectoderm (animal caps; ACs) NANOG and NODAL activity, as well as the epigenetic modifying enzyme DPY30, are required for the mass deposition of H3K4me3 in pluripotent chromatin. We also demonstrate that all 3 protein activities are required for ACs to establish the competency to differentiate toward mesoderm. Our results suggest the ancient function of NANOG may be establishing the competence for lineage differentiation in early cells. These observations provide insights into embryonic development in the tetrapod ancestor from which terrestrial vertebrates evolved.
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Affiliation(s)
- Luke A. Simpson
- School of Life Sciences, University of Nottingham, Queens Medical Centre, Nottingham, United Kingdom
| | - Darren Crowley
- School of Life Sciences, University of Nottingham, Queens Medical Centre, Nottingham, United Kingdom
| | - Teri Forey
- School of Life Sciences, University of Nottingham, Queens Medical Centre, Nottingham, United Kingdom
| | - Helena Acosta
- School of Life Sciences, University of Nottingham, Queens Medical Centre, Nottingham, United Kingdom
| | - Zoltan Ferjentsik
- School of Life Sciences, University of Nottingham, Queens Medical Centre, Nottingham, United Kingdom
| | - Jodie Chatfield
- School of Life Sciences, University of Nottingham, Queens Medical Centre, Nottingham, United Kingdom
| | - Alexander Payne
- School of Life Sciences, University of Nottingham, Queens Medical Centre, Nottingham, United Kingdom
| | - Benjamin S. Simpson
- Tumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, United Kingdom
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Catherine Redwood
- School of Life Sciences, University of Nottingham, Queens Medical Centre, Nottingham, United Kingdom
| | - James E. Dixon
- School of Life Sciences, University of Nottingham, Queens Medical Centre, Nottingham, United Kingdom
| | - Nadine Holmes
- School of Life Sciences, University of Nottingham, Queens Medical Centre, Nottingham, United Kingdom
| | - Fei Sang
- School of Life Sciences, University of Nottingham, Queens Medical Centre, Nottingham, United Kingdom
| | - Ramiro Alberio
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Matthew Loose
- School of Life Sciences, University of Nottingham, Queens Medical Centre, Nottingham, United Kingdom
| | - Andrew D. Johnson
- School of Life Sciences, University of Nottingham, Queens Medical Centre, Nottingham, United Kingdom
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3
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Roelen BAJ, Chuva de Sousa Lopes SM. Stay on the road: from germ cell specification to gonadal colonization in mammals. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210259. [PMID: 36252219 PMCID: PMC9574628 DOI: 10.1098/rstb.2021.0259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The founder cells of the gametes are primordial germ cells (PGCs). In mammals, PGCs are specified early during embryonic development, at the boundary between embryonic and extraembryonic tissue, long before their later residences, the gonads, have developed. Despite the differences in form and behaviour when differentiated into oocytes or sperm cells, in the period between specification and gonadal colonization, male and female PGCs are morphologically indistinct and largely regulated by similar mechanisms. Here, we compare different modes and mechanisms that lead to the formation of PGCs, putting in context protocols that are in place to differentiate both human and mouse pluripotent stem cells into PGC-like cells. In addition, we review important aspects of the migration of PGCs to the gonadal ridges, where they undergo further sex-specific differentiation. Defects in migration need to be effectively corrected, as misplaced PGCs can become tumorigenic. Concluding, a combination of in vivo studies and the development of adequate innovative in vitro models, ensuring both robustness and standardization, are providing us with the tools for a greater understanding of the first steps of gametogenesis and to develop disease models to study the origin of germ cell tumours. This article is part of the theme issue ‘Extraembryonic tissues: exploring concepts, definitions and functions across the animal kingdom’.
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Affiliation(s)
- Bernard A J Roelen
- Anatomy and Physiology, Department Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584CL Utrecht, The Netherlands.,Department of Biosciences, Biotechnologies & Biopharmaceutics, University of Bari Aldo Moro, Bari, Italy
| | - Susana M Chuva de Sousa Lopes
- Department of Biosciences, Biotechnologies & Biopharmaceutics, University of Bari Aldo Moro, Bari, Italy.,Department of Anatomy and Embryology, Leiden University Medical Centre, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
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4
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Razmi K, Patil JG. Primordial Germ Cell Development in the Poeciliid, Gambusia holbrooki, Reveals Shared Features Between Lecithotrophs and Matrotrophs. Front Cell Dev Biol 2022; 10:793498. [PMID: 35300414 PMCID: PMC8920993 DOI: 10.3389/fcell.2022.793498] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/03/2022] [Indexed: 12/02/2022] Open
Abstract
Metazoans exhibit two modes of primordial germ cell (PGC) specification that are interspersed across taxa. However, the evolutionary link between the two modes and the reproductive strategies of lecithotrophy and matrotrophy is poorly understood. As a first step to understand this, the spatio-temporal expression of teleostean germ plasm markers was investigated in Gambusia holbrooki, a poecilid with shared lecitho- and matrotrophy. A group of germ plasm components was detected in the ovum suggesting maternal inheritance mode of PGC specification. However, the strictly zygotic activation of dnd-β and nanos1 occurred relatively early, reminiscent of models with induction mode (e.g., mice). The PGC clustering, migration and colonisation patterns of G. holbrooki resembled those of zebrafish, medaka and mice at blastula, gastrula and somitogenesis, respectively—recapitulating features of advancing evolutionary nodes with progressive developmental stages. Moreover, the expression domains of PGC markers in G. holbrooki were either specific to teleost (vasa expression in developing PGCs), murine models (dnd spliced variants) or shared between the two taxa (germline and somatic expression of piwi and nanos1). Collectively, the results suggest that the reproductive developmental adaptations may reflect a transition from lecithotrophy to matrotrophy.
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Affiliation(s)
- Komeil Razmi
- Laboratory of Molecular Biology, Fisheries and Aquaculture Centre, Institute for Marine and Antarctic Studies, University of Tasmania, Taroona, TAS, Australia
| | - Jawahar G Patil
- Laboratory of Molecular Biology, Fisheries and Aquaculture Centre, Institute for Marine and Antarctic Studies, University of Tasmania, Taroona, TAS, Australia
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5
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Seemann SE, Mirza AH, Bang-Berthelsen CH, Garde C, Christensen-Dalsgaard M, Workman CT, Pociot F, Tommerup N, Gorodkin J, Ruzzo WL. OUP accepted manuscript. Nucleic Acids Res 2022; 50:2452-2463. [PMID: 35188540 PMCID: PMC8934657 DOI: 10.1093/nar/gkac067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 01/07/2022] [Accepted: 01/25/2022] [Indexed: 12/01/2022] Open
Abstract
Accelerated evolution of any portion of the genome is of significant interest, potentially signaling positive selection of phenotypic traits and adaptation. Accelerated evolution remains understudied for structured RNAs, despite the fact that an RNA’s structure is often key to its function. RNA structures are typically characterized by compensatory (structure-preserving) basepair changes that are unexpected given the underlying sequence variation, i.e., they have evolved through negative selection on structure. We address the question of how fast the primary sequence of an RNA can change through evolution while conserving its structure. Specifically, we consider predicted and known structures in vertebrate genomes. After careful control of false discovery rates, we obtain 13 de novo structures (and three known Rfam structures) that we predict to have rapidly evolving sequences—defined as structures where the primary sequences of human and mouse have diverged at least twice as fast (1.5 times for Rfam) as nearby neutrally evolving sequences. Two of the three known structures function in translation inhibition related to infection and immune response. We conclude that rapid sequence divergence does not preclude RNA structure conservation in vertebrates, although these events are relatively rare.
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Affiliation(s)
| | - Aashiq H Mirza
- Center for non-coding RNA in Technology and Health (RTH), University of Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
| | - Claus H Bang-Berthelsen
- Center for non-coding RNA in Technology and Health (RTH), University of Copenhagen, Denmark
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Christian Garde
- Center for non-coding RNA in Technology and Health (RTH), University of Copenhagen, Denmark
| | | | - Christopher T Workman
- Center for non-coding RNA in Technology and Health (RTH), University of Copenhagen, Denmark
- Center for Biological Sequence Analysis, Technical University of Denmark, Denmark
| | - Flemming Pociot
- Center for non-coding RNA in Technology and Health (RTH), University of Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
| | - Niels Tommerup
- Center for non-coding RNA in Technology and Health (RTH), University of Copenhagen, Denmark
- Department of Cellular and Molecular Medicine (ICMM), University of Copenhagen, Denmark
| | - Jan Gorodkin
- Center for non-coding RNA in Technology and Health (RTH), University of Copenhagen, Denmark
- Department of Veterinary and Animal Sciences, University of Copenhagen, Denmark
| | - Walter L Ruzzo
- Center for non-coding RNA in Technology and Health (RTH), University of Copenhagen, Denmark
- Computer Science and Engineering and Genome Sciences, University of Washington, USA
- Fred Hutchinson Cancer Research Center, Seattle, USA
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6
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Ramakrishna NB, Murison K, Miska EA, Leitch HG. Epigenetic Regulation during Primordial Germ Cell Development and Differentiation. Sex Dev 2021; 15:411-431. [PMID: 34847550 DOI: 10.1159/000520412] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/10/2021] [Indexed: 11/19/2022] Open
Abstract
Germline development varies significantly across metazoans. However, mammalian primordial germ cell (PGC) development has key conserved landmarks, including a critical period of epigenetic reprogramming that precedes sex-specific differentiation and gametogenesis. Epigenetic alterations in the germline are of unique importance due to their potential to impact the next generation. Therefore, regulation of, and by, the non-coding genome is of utmost importance during these epigenomic events. Here, we detail the key chromatin changes that occur during mammalian PGC development and how these interact with the expression of non-coding RNAs alongside broader epitranscriptomic changes. We identify gaps in our current knowledge, in particular regarding epigenetic regulation in the human germline, and we highlight important areas of future research.
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Affiliation(s)
- Navin B Ramakrishna
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Genome Institute of Singapore, A*STAR, Biopolis, Singapore, Singapore
| | - Keir Murison
- MRC London Institute of Medical Sciences, London, United Kingdom
- Institute of Clinical Sciences, Imperial College London, London, United Kingdom
| | - Eric A Miska
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Harry G Leitch
- MRC London Institute of Medical Sciences, London, United Kingdom
- Institute of Clinical Sciences, Imperial College London, London, United Kingdom
- Centre for Paediatrics and Child Health, Faculty of Medicine, Imperial College London, London, United Kingdom
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7
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Lloyd R, Alberio R, Crother BI. Andrew Johnson (1958-2021). Development 2021. [DOI: 10.1242/dev.200333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
ABSTRACT
Andrew Johnson, a pioneer in the development of the amphibian axolotl as a model to study the early stages of metazoan development, died 15th September 2021. Known as ‘AJ’ by his family, and by his friends and colleagues, his older sister Pam referred to him as an unstoppable ‘force of nature’ who at the age of 9 or 10 said to her, ‘I'm going to become a professor’. Here, we reflect on AJ's life and work, paying particular attention to his studies on the establishment of primordial germ cells in vertebrates.
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Affiliation(s)
- Robert Lloyd
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Ramiro Alberio
- School of Biosciences, Sutton Bonington Campus, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Brian I. Crother
- Department of Biology, Southeastern Louisiana University, Hammond, LA 70402, USA
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8
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Cooney CR, Mank JE, Wright AE. Constraint and divergence in the evolution of male and female recombination rates in fishes. Evolution 2021; 75:2857-2866. [PMID: 34533208 DOI: 10.1111/evo.14357] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 08/09/2021] [Accepted: 08/19/2021] [Indexed: 12/28/2022]
Abstract
Recombination is a fundamental feature of sexual reproduction across eukaryotes, yet recombination rates are highly variable both within and between species. In particular, sex differences in recombination rate between males and females (heterochiasmy) are more often the rule than the exception, but despite the prevalence of heterochiasmy the ultimate causes of global patterns of heterochiasmy remain unclear. Here, we assemble a comprehensive dataset of sex-specific recombination rate estimates for 61 fish species, and combine this with information on sex determination, fertilization mode, and sexual dimorphism to test competing theories for the causes and evolution of heterochiasmy. We find that sex differences in recombination rate are evolutionary labile, with frequent shifts in the direction and magnitude of heterochiasmy. This rapid turnover does not appear to be driven by simple neutral processes and is inconsistent with nonadaptive explanations for heterochiasmy, including biological sex differences in meiosis. Although patterns of heterochiasmy across the phylogeny indicate a potential role for adaptive processes, we are unable to directly link variation in heterochiasmy with proxies for sexual selection or sexual conflict across species, indicating that these effects-if present-are either subtle or complex. Finally, we show evidence for correlated rates of recombination rate evolution between males and females, indicating the potential for genetic constraints and sexual conflict over the recombination landscape.
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Affiliation(s)
- Christopher R Cooney
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Judith E Mank
- Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.,Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.,Biosciences, University of Exeter, Penryn, TR10 9FE, United Kingdom
| | - Alison E Wright
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom
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9
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Hansen CL, Pelegri F. Primordial Germ Cell Specification in Vertebrate Embryos: Phylogenetic Distribution and Conserved Molecular Features of Preformation and Induction. Front Cell Dev Biol 2021; 9:730332. [PMID: 34604230 PMCID: PMC8481613 DOI: 10.3389/fcell.2021.730332] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/25/2021] [Indexed: 11/24/2022] Open
Abstract
The differentiation of primordial germ cells (PGCs) occurs during early embryonic development and is critical for the survival and fitness of sexually reproducing species. Here, we review the two main mechanisms of PGC specification, induction, and preformation, in the context of four model vertebrate species: mouse, axolotl, Xenopus frogs, and zebrafish. We additionally discuss some notable molecular characteristics shared across PGC specification pathways, including the shared expression of products from three conserved germline gene families, DAZ (Deleted in Azoospermia) genes, nanos-related genes, and DEAD-box RNA helicases. Then, we summarize the current state of knowledge of the distribution of germ cell determination systems across kingdom Animalia, with particular attention to vertebrate species, but include several categories of invertebrates - ranging from the "proto-vertebrate" cephalochordates to arthropods, cnidarians, and ctenophores. We also briefly highlight ongoing investigations and potential lines of inquiry that aim to understand the evolutionary relationships between these modes of specification.
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Affiliation(s)
| | - Francisco Pelegri
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, United States
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10
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Nakao H. Early embryonic development of Bombyx. Dev Genes Evol 2021; 231:95-107. [PMID: 34296338 DOI: 10.1007/s00427-021-00679-8] [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: 12/03/2020] [Accepted: 07/09/2021] [Indexed: 11/25/2022]
Abstract
Decades have passed since the early molecular embryogenesis of Drosophila melanogaster was outlined. During this period, the molecular mechanisms underlying early embryonic development in other insects, particularly the flour beetle, Tribolium castaneum, have been described in more detail. The information clearly demonstrated that Drosophila embryogenesis is not representative of other insects and has highly distinctive characteristics. At the same time, this new data has been gradually clarifying ancestral operating mechanisms. The silk moth, Bombyx mori, is a lepidopteran insect and, as a representative of the order, has many unique characteristics found in early embryonic development that have not been identified in other insect groups. Herein, some of these characteristics are introduced and discussed in the context of recent information obtained from other insects.
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Affiliation(s)
- Hajime Nakao
- Insect Genome Research and Engineering Unit, Division of Applied Genetics, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Oowashi, Tsukuba, Ibaraki, 305-8634, Japan.
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11
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Abstract
Primordial germ cells (PGCs) must complete a complex and dynamic developmental program during embryogenesis to establish the germline. This process is highly conserved and involves a diverse array of tasks required of PGCs, including migration, survival, sex differentiation, and extensive epigenetic reprogramming. A common theme across many organisms is that PGC success is heterogeneous: only a portion of all PGCs complete all these steps while many other PGCs are eliminated from further germline contribution. The differences that distinguish successful PGCs as a population are not well understood. Here, we examine variation that exists in PGCs as they navigate the many stages of this developmental journey. We explore potential sources of PGC heterogeneity and their potential implications in affecting germ cell behaviors. Lastly, we discuss the potential for PGC development to function as a multistage selection process that assesses heterogeneity in PGCs to refine germline quality.
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Affiliation(s)
- Daniel H Nguyen
- Department of Obstetrics, Gynecology and Reproductive Science, Center for Reproductive Sciences, Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, United States
| | - Rebecca G Jaszczak
- Department of Obstetrics, Gynecology and Reproductive Science, Center for Reproductive Sciences, Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, United States
| | - Diana J Laird
- Department of Obstetrics, Gynecology and Reproductive Science, Center for Reproductive Sciences, Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, United States.
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12
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Whittle CA, Extavour CG. Contrasting patterns of molecular evolution in metazoan germ line genes. BMC Evol Biol 2019; 19:53. [PMID: 30744572 PMCID: PMC6371493 DOI: 10.1186/s12862-019-1363-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 01/14/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Germ lines are the cell lineages that give rise to the sperm and eggs in animals. The germ lines first arise from primordial germ cells (PGCs) during embryogenesis: these form from either a presumed derived mode of preformed germ plasm (inheritance) or from an ancestral mechanism of inductive cell-cell signalling (induction). Numerous genes involved in germ line specification and development have been identified and functionally studied. However, little is known about the molecular evolutionary dynamics of germ line genes in metazoan model systems. RESULTS Here, we studied the molecular evolution of germ line genes within three metazoan model systems. These include the genus Drosophila (N=34 genes, inheritance), the fellow insect Apis (N=30, induction), and their more distant relative Caenorhabditis (N=23, inheritance). Using multiple species and established phylogenies in each genus, we report that germ line genes exhibited marked variation in the constraint on protein sequence divergence (dN/dS) and codon usage bias (CUB) within each genus. Importantly, we found that de novo lineage-specific inheritance (LSI) genes in Drosophila (osk, pgc) and in Caenorhabditis (pie-1, pgl-1), which are essential to germ plasm functions under the derived inheritance mode, displayed rapid protein sequence divergence relative to the other germ line genes within each respective genus. We show this may reflect the evolution of specialized germ plasm functions and/or low pleiotropy of LSI genes, features not shared with other germ line genes. In addition, we observed that the relative ranking of dN/dS and of CUB between genera were each more strongly correlated between Drosophila and Caenorhabditis, from different phyla, than between Drosophila and its insect relative Apis, suggesting taxonomic differences in how germ line genes have evolved. CONCLUSIONS Taken together, the present results advance our understanding of the evolution of animal germ line genes within three well-known metazoan models. Further, the findings provide insights to the molecular evolution of germ line genes with respect to LSI status, pleiotropy, adaptive evolution as well as PGC-specification mode.
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Affiliation(s)
- Carrie A Whittle
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA, 02138, USA
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA, 02138, USA.
- Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA, 02138, USA.
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13
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Smith JJ, Timoshevskaya N, Timoshevskiy VA, Keinath MC, Hardy D, Voss SR. A chromosome-scale assembly of the axolotl genome. Genome Res 2019; 29:317-324. [PMID: 30679309 PMCID: PMC6360810 DOI: 10.1101/gr.241901.118] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/26/2018] [Indexed: 01/14/2023]
Abstract
The axolotl (Ambystoma mexicanum) provides critical models for studying regeneration, evolution, and development. However, its large genome (∼32 Gb) presents a formidable barrier to genetic analyses. Recent efforts have yielded genome assemblies consisting of thousands of unordered scaffolds that resolve gene structures, but do not yet permit large-scale analyses of genome structure and function. We adapted an established mapping approach to leverage dense SNP typing information and for the first time assemble the axolotl genome into 14 chromosomes. Moreover, we used fluorescence in situ hybridization to verify the structure of these 14 scaffolds and assign each to its corresponding physical chromosome. This new assembly covers 27.3 Gb and encompasses 94% of annotated gene models on chromosomal scaffolds. We show the assembly's utility by resolving genome-wide orthologies between the axolotl and other vertebrates, identifying the footprints of historical introgression events that occurred during the development of axolotl genetic stocks, and precisely mapping several phenotypes including a large deletion underlying the cardiac mutant. This chromosome-scale assembly will greatly facilitate studies of the axolotl in biological research.
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Affiliation(s)
- Jeramiah J Smith
- Department of Biology, University of Kentucky, Lexington, Kentucky 40506, USA
| | | | | | - Melissa C Keinath
- Department of Biology, University of Kentucky, Lexington, Kentucky 40506, USA.,Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA
| | - Drew Hardy
- Department of Neuroscience, University of Kentucky, Lexington, Kentucky 40506, USA.,Ambystoma Genetic Stock Center, University of Kentucky, Lexington, Kentucky 40506, USA
| | - S Randal Voss
- Department of Neuroscience, University of Kentucky, Lexington, Kentucky 40506, USA.,Ambystoma Genetic Stock Center, University of Kentucky, Lexington, Kentucky 40506, USA.,Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, Kentucky 40506, USA
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14
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Nakao H, Takasu Y. Complexities in Bombyx germ cell formation process revealed by Bm-nosO (a Bombyx homolog of nanos) knockout. Dev Biol 2018; 445:29-36. [PMID: 30367845 DOI: 10.1016/j.ydbio.2018.10.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 09/11/2018] [Accepted: 10/17/2018] [Indexed: 11/25/2022]
Abstract
Inheritance (sequestration of a localized determinant: germplasm) and zygotic induction are two modes of metazoan primordial germ cell (PGC) specification. vasa and nanos homologs are evolutionarily conserved germline marker genes that have been used to examine the ontogeny of germ cells in various animals. In the lepidopteran insect Bombyx mori, although the lack of vasa homolog (BmVLG) protein localization as well as microscopic observation suggested the lack of germplasm, classical embryo manipulation studies and the localization pattern of Bm-nosO (one of the four nanos genes in Bombyx) maternal mRNA in the egg raised the possibility that an inheritance mode is operating in Bombyx. Here, we generated Bm-nosO knockouts to examine whether the localized mRNA acts as a localized germ cell determinant. Contrary to our expectations, Bm-nosO knockout lines could be established. However, these lines frequently produced abnormal eggs, which failed to hatch, to various extent depending on the individuals. We also found that Bm-nosO positively regulated BmVLG expression at least during embryonic stage, directly or indirectly, indicating that these genes were on the same developmental pathway for germ cell formation in Bombyx. These results suggest that these conserved genes are concerned with stable germ cell production. On the other hand, from the aspect of BmVLG as a PGC marker, we showed that maternal Bm-nosO product(s) as well as early zygotic Bm-nosO activity were redundantly involved in PGC specification; elimination of both maternal and zygotic gene activities (as in knockout lines) resulted in the apparent lack of PGCs, indicating that an inheritance mechanism indeed operates in Bombyx. This, however, together with the fact that germ cells are produced at all in Bm-nosO knockout lines, also suggests the possibility that, in Bombyx, not only this inheritance mechanism but also an inductive mechanism acts in concert to form germ cells or that loss of early PGCs are compensated for by germline regeneration: mechanisms that could enable the evolution of preformation. Thus, Bombyx could serve as an important organism in understanding the evolution of germ cell formation mechanisms; transition between preformation and inductive modes.
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Affiliation(s)
- Hajime Nakao
- Insect Genome Research and Engineering Unit, Division of Applied Genetics, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Oowashi, Tsukuba, Ibaraki 305-8634, Japan.
| | - Yoko Takasu
- Silk Materials Research Unit, Division of Biotechnology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Oowashi, Tsukuba, Ibaraki 305-8634, Japan
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15
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Liedtke HC, Gower DJ, Wilkinson M, Gomez-Mestre I. Macroevolutionary shift in the size of amphibian genomes and the role of life history and climate. Nat Ecol Evol 2018; 2:1792-1799. [PMID: 30250158 DOI: 10.1038/s41559-018-0674-4] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 08/17/2018] [Indexed: 11/09/2022]
Abstract
The evolution and great diversity of genome size has been of long-standing interest to biologists, but has seldom been investigated on a broad phylogenetic scale. Here we present a comparative quantitative analysis of factors shaping genome size evolution in amphibians, the extant class of vertebrates with the largest variation in genome size. We find that amphibian genomes have undergone saltations in size, although these are rare and the evolutionary history of genome size in amphibians has otherwise been one of gradual, time-dependent variation (that is, Brownian motion). This macroevolutionary homogeneity is remarkable given the evolutionary and ecological diversity of most other aspects of the natural history of amphibians. Contrary to previous claims, we find no evidence for associations between life cycle complexity and genome size despite the high diversity of reproductive modes and the multiple events of independent evolution of divergent life cycles in the group. Climate (temperature and humidity) affects genome size indirectly, at least in frogs, as a consequence of its effect on premetamorphic developmental period, although directionality of the relationship between developmental period and genome size is not unequivocal.
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Affiliation(s)
- H Christoph Liedtke
- Ecology, Evolution and Developmental Group, Department of Wetland Ecology, Estación Biológica de Doñana (CSIC), Sevilla, Spain
| | - David J Gower
- Department of Life Sciences, Natural History Museum, London, UK
| | - Mark Wilkinson
- Department of Life Sciences, Natural History Museum, London, UK
| | - Ivan Gomez-Mestre
- Ecology, Evolution and Developmental Group, Department of Wetland Ecology, Estación Biológica de Doñana (CSIC), Sevilla, Spain.
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16
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Causes and evolutionary consequences of primordial germ-cell specification mode in metazoans. Proc Natl Acad Sci U S A 2018; 114:5784-5791. [PMID: 28584112 DOI: 10.1073/pnas.1610600114] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
In animals, primordial germ cells (PGCs) give rise to the germ lines, the cell lineages that produce sperm and eggs. PGCs form in embryogenesis, typically by one of two modes: a likely ancestral mode wherein germ cells are induced during embryogenesis by cell-cell signaling (induction) or a derived mechanism whereby germ cells are specified by using germ plasm-that is, maternally specified germ-line determinants (inheritance). The causes of the shift to germ plasm for PGC specification in some animal clades remain largely unknown, but its repeated convergent evolution raises the question of whether it may result from or confer an innate selective advantage. It has been hypothesized that the acquisition of germ plasm confers enhanced evolvability, resulting from the release of selective constraint on somatic gene networks in embryogenesis, thus leading to acceleration of an organism's protein-sequence evolution, particularly for genes expressed at early developmental stages, and resulting in high speciation rates in germ plasm-containing lineages (denoted herein as the "PGC-specification hypothesis"). Although that hypothesis, if supported, could have major implications for animal evolution, our recent large-scale coding-sequence analyses from vertebrates and invertebrates provided important examples of genera that do not support the hypothesis of liberated constraint under germ plasm. Here, we consider reasons why germ plasm might be neither a direct target of selection nor causally linked to accelerated animal evolution. We explore alternate scenarios that could explain the repeated evolution of germ plasm and propose potential consequences of the inheritance and induction modes to animal evolutionary biology.
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17
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Evans T, Johnson AD, Loose M. Virtual Genome Walking across the 32 Gb Ambystoma mexicanum genome; assembling gene models and intronic sequence. Sci Rep 2018; 8:618. [PMID: 29330416 PMCID: PMC5766544 DOI: 10.1038/s41598-017-19128-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 12/19/2017] [Indexed: 11/09/2022] Open
Abstract
Large repeat rich genomes present challenges for assembly using short read technologies. The 32 Gb axolotl genome is estimated to contain ~19 Gb of repetitive DNA making an assembly from short reads alone effectively impossible. Indeed, this model species has been sequenced to 20× coverage but the reads could not be conventionally assembled. Using an alternative strategy, we have assembled subsets of these reads into scaffolds describing over 19,000 gene models. We call this method Virtual Genome Walking as it locally assembles whole genome reads based on a reference transcriptome, identifying exons and iteratively extending them into surrounding genomic sequence. These assemblies are then linked and refined to generate gene models including upstream and downstream genomic, and intronic, sequence. Our assemblies are validated by comparison with previously published axolotl bacterial artificial chromosome (BAC) sequences. Our analyses of axolotl intron length, intron-exon structure, repeat content and synteny provide novel insights into the genic structure of this model species. This resource will enable new experimental approaches in axolotl, such as ChIP-Seq and CRISPR and aid in future whole genome sequencing efforts. The assembled sequences and annotations presented here are freely available for download from https://tinyurl.com/y8gydc6n . The software pipeline is available from https://github.com/LooseLab/iterassemble .
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Affiliation(s)
- Teri Evans
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Andrew D Johnson
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Matthew Loose
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK.
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18
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Hurd TR, Herrmann B, Sauerwald J, Sanny J, Grosch M, Lehmann R. Long Oskar Controls Mitochondrial Inheritance in Drosophila melanogaster. Dev Cell 2017; 39:560-571. [PMID: 27923120 DOI: 10.1016/j.devcel.2016.11.004] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 09/21/2016] [Accepted: 11/07/2016] [Indexed: 12/11/2022]
Abstract
Inherited mtDNA mutations cause severe human disease. In most species, mitochondria are inherited maternally through mechanisms that are poorly understood. Genes that specifically control the inheritance of mitochondria in the germline are unknown. Here, we show that the long isoform of the protein Oskar regulates the maternal inheritance of mitochondria in Drosophila melanogaster. We show that, during oogenesis, mitochondria accumulate at the oocyte posterior, concurrent with the bulk streaming and churning of the oocyte cytoplasm. Long Oskar traps and maintains mitochondria at the posterior at the site of primordial germ cell (PGC) formation through an actin-dependent mechanism. Mutating long oskar strongly reduces the number of mtDNA molecules inherited by PGCs. Therefore, Long Oskar ensures germline transmission of mitochondria to the next generation. These results provide molecular insight into how mitochondria are passed from mother to offspring, as well as how they are positioned and asymmetrically partitioned within polarized cells.
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Affiliation(s)
- Thomas Ryan Hurd
- Department of Cell Biology, HHMI and Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA
| | - Beate Herrmann
- Department of Cell Biology, HHMI and Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA
| | - Julia Sauerwald
- Department of Cell Biology, HHMI and Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA
| | - Justina Sanny
- Department of Cell Biology, HHMI and Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA
| | - Markus Grosch
- Department of Cell Biology, HHMI and Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA
| | - Ruth Lehmann
- Department of Cell Biology, HHMI and Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA.
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19
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Levy Karin E, Wicke S, Pupko T, Mayrose I. An Integrated Model of Phenotypic Trait Changes and Site-Specific Sequence Evolution. Syst Biol 2017; 66:917-933. [DOI: 10.1093/sysbio/syx032] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 01/24/2017] [Indexed: 02/05/2023] Open
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20
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Mohlhenrich ER, Mueller RL. Genetic drift and mutational hazard in the evolution of salamander genomic gigantism. Evolution 2016; 70:2865-2878. [DOI: 10.1111/evo.13084] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 09/27/2016] [Accepted: 09/27/2016] [Indexed: 12/25/2022]
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21
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Neuhof M, Levin M, Rechavi O. Vertically- and horizontally-transmitted memories - the fading boundaries between regeneration and inheritance in planaria. Biol Open 2016; 5:1177-88. [PMID: 27565761 PMCID: PMC5051648 DOI: 10.1242/bio.020149] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The Weismann barrier postulates that genetic information passes only from the germline to the soma and not in reverse, thus providing an obstacle to the inheritance of acquired traits. Certain organisms such as planaria – flatworms that can reproduce through asymmetric fission – avoid the limitations of this barrier, thus blurring the distinction between the processes of inheritance and development. In this paper, we re-evaluate canonical ideas about the interaction between developmental, genetic and evolutionary processes through the lens of planaria. Biased distribution of epigenetic effects in asymmetrically produced parts of a regenerating organism could increase variation and therefore affect the species' evolution. The maintenance and fixing of somatic experiences, encoded via stable biochemical or physiological states, may contribute to evolutionary processes in the absence of classically defined generations. We discuss different mechanisms that could induce asymmetry between the two organisms that eventually develop from the regenerating parts, including one particularly fascinating source – the potential capacity of the brain to produce long-lasting epigenetic changes. Summary: In this hypothesis paper we re-evaluate canonical ideas about the interaction between developmental, genetic and evolutionary processes through the lens of planaria, an invertebrate model organism which challenges fundamental assumptions regarding reproduction.
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Affiliation(s)
- Moran Neuhof
- Department of Neurobiology, Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Michael Levin
- Allen Discovery Center, Tufts University, 200 Boston Avenue, Suite 4600, Medford, MA 02155, USA
| | - Oded Rechavi
- Department of Neurobiology, Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel Allen Discovery Center, Tufts University, 200 Boston Avenue, Suite 4600, Medford, MA 02155, USA Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
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22
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Whittle CA, Extavour CG. Refuting the hypothesis that the acquisition of germ plasm accelerates animal evolution. Nat Commun 2016; 7:12637. [PMID: 27577604 PMCID: PMC5013649 DOI: 10.1038/ncomms12637] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 07/20/2016] [Indexed: 02/04/2023] Open
Abstract
Primordial germ cells (PGCs) give rise to the germ line in animals. PGCs are specified during embryogenesis either by an ancestral mechanism of cell-cell signalling (induction) or by a derived mechanism of maternally provided germ plasm (preformation). Recently, a hypothesis was set forth purporting that germ plasm liberates selective constraint and accelerates an organism's protein sequence evolution, especially for genes from early developmental stages, thereby leading to animal species radiations; empirical validation has been claimed in vertebrates. Here we present findings from global rates of protein evolution in vertebrates and invertebrates refuting this hypothesis. Contrary to assertions of the hypothesis, we find no effect of preformation on protein sequence evolution, the evolutionary rates of early-stage developmental genes, or on species diversification. We conclude that the hypothesis is mechanistically implausible, and our multi-faceted analysis shows no empirical support for any of its predictions.
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Affiliation(s)
- Carrie A. Whittle
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts 02138, USA
| | - Cassandra G. Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts 02138, USA
- Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts 02138, USA
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23
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Fresques T, Swartz SZ, Juliano C, Morino Y, Kikuchi M, Akasaka K, Wada H, Yajima M, Wessel GM. The diversity of nanos expression in echinoderm embryos supports different mechanisms in germ cell specification. Evol Dev 2016; 18:267-78. [PMID: 27402572 PMCID: PMC4943673 DOI: 10.1111/ede.12197] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Specification of the germ cell lineage is required for sexual reproduction in all animals. However, the timing and mechanisms of germ cell specification is remarkably diverse in animal development. Echinoderms, such as sea urchins and sea stars, are excellent model systems to study the molecular and cellular mechanisms that contribute to germ cell specification. In several echinoderm embryos tested, the germ cell factor Vasa accumulates broadly during early development and is restricted after gastrulation to cells that contribute to the germ cell lineage. In the sea urchin, however, the germ cell factor Vasa is restricted to a specific lineage by the 32-cell stage. We therefore hypothesized that the germ cell specification program in the sea urchin/Euechinoid lineage has evolved to an earlier developmental time point. To test this hypothesis we determined the expression pattern of a second germ cell factor, Nanos, in four out of five extant echinoderm clades. Here we find that Nanos mRNA does not accumulate until the blastula stage or later during the development of all other echinoderm embryos except those that belong to the Echinoid lineage. Instead, Nanos is expressed in a restricted domain at the 32-128 cell stage in Echinoid embryos. Our results support the model that the germ cell specification program underwent a heterochronic shift in the Echinoid lineage. A comparison of Echinoid and non-Echinoid germ cell specification mechanisms will contribute to our understanding of how these mechanisms have changed during animal evolution.
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Affiliation(s)
- Tara Fresques
- Department of Molecular Biology, Cell Biology and Biochemistry, 185 Meeting Street, Brown University, Providence RI 02912
| | - S. Zachary Swartz
- Department of Molecular Biology, Cell Biology and Biochemistry, 185 Meeting Street, Brown University, Providence RI 02912
| | - Celina Juliano
- Department of Molecular Biology, Cell Biology and Biochemistry, 185 Meeting Street, Brown University, Providence RI 02912
- Department of Molecular and Cellular Biology, College of Biological Sciences, One Shields Avenue, University of California, Davis, Davis CA 95616
| | - Yoshiaki Morino
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan
| | - Mani Kikuchi
- Misaki Marine Biological Station, Graduate School of Science, University of Tokyo, Koajiro 1024, Misaki, Miura 238-0225, Japan
| | - Koji Akasaka
- Misaki Marine Biological Station, Graduate School of Science, University of Tokyo, Koajiro 1024, Misaki, Miura 238-0225, Japan
| | - Hiroshi Wada
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan
| | - Mamiko Yajima
- Department of Molecular Biology, Cell Biology and Biochemistry, 185 Meeting Street, Brown University, Providence RI 02912
| | - Gary M. Wessel
- Department of Molecular Biology, Cell Biology and Biochemistry, 185 Meeting Street, Brown University, Providence RI 02912
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24
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Tworzydlo W, Kisiel E, Jankowska W, Witwicka A, Bilinski SM. Exclusion of dysfunctional mitochondria from Balbiani body during early oogenesis of Thermobia. Cell Tissue Res 2016; 366:191-201. [PMID: 27164893 PMCID: PMC5031756 DOI: 10.1007/s00441-016-2414-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 04/12/2016] [Indexed: 01/08/2023]
Abstract
Oocytes of many invertebrate and vertebrate species contain a characteristic organelle complex known as the Balbiani body (Bb). Until now, three principal functions have been ascribed to this complex: delivery of germ cell determinants and localized RNAs to the vegetal cortex/posterior pole of the oocyte, transport of the mitochondria towards the germ plasm, and participation in the formation of lipid droplets. Here, we present the results of a computer-aided 3D reconstruction of the Bb in the growing oocytes of an insect, Thermobia domestica. Our analyses have shown that, in Thermobia, the central part of each fully developed Bb comprises a single intricate mitochondrial network. This “core” network is surrounded by several isolated bean-shaped mitochondrial units that display lowered membrane potential and clear signs of degeneration. In light of the above results and recent theoretical models of mitochondrial quality control, the role of the Bb is discussed. We suggest that, in addition to the aforementioned functions, the Bb is implicated in the selective elimination of dysfunctional mitochondria during oogenesis.
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Affiliation(s)
- Waclaw Tworzydlo
- Department of Developmental Biology and Morphology of Invertebrates, Institute of Zoology, Jagiellonian University, Krakow, Poland.
| | - Elzbieta Kisiel
- Department of Developmental Biology and Morphology of Invertebrates, Institute of Zoology, Jagiellonian University, Krakow, Poland
| | - Wladyslawa Jankowska
- Department of Developmental Biology and Morphology of Invertebrates, Institute of Zoology, Jagiellonian University, Krakow, Poland
| | - Alicja Witwicka
- Department of Developmental Biology and Morphology of Invertebrates, Institute of Zoology, Jagiellonian University, Krakow, Poland
| | - Szczepan M Bilinski
- Department of Developmental Biology and Morphology of Invertebrates, Institute of Zoology, Jagiellonian University, Krakow, Poland
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25
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Crother BI, White ME, Johnson AD. Diversification and Germ-Line Determination Revisited: Linking Developmental Mechanism with Species Richness. Front Ecol Evol 2016. [DOI: 10.3389/fevo.2016.00026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
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26
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Kaufman OH, Marlow FL. Methods to study maternal regulation of germ cell specification in zebrafish. Methods Cell Biol 2016; 134:1-32. [PMID: 27312489 DOI: 10.1016/bs.mcb.2016.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
The process by which the germ line is specified in the zebrafish embryo is under the control of maternal gene products that were produced during oogenesis. Zebrafish are highly amenable to microscopic observation of the processes governing maternal germ cell specification because early embryos are transparent, and the germ line is specified rapidly (within 4-5h post fertilization). Advantages of zebrafish over other models used to study vertebrate germ cell formation include their genetic tractability, the large numbers of progeny, and the easily manipulable genome, all of which make zebrafish an ideal system for studying the genetic regulators and cellular basis of germ cell formation and maintenance. Classical molecular biology techniques, including expression analysis through in situ hybridization and forward genetic screens, have laid the foundation for our understanding of germ cell development in zebrafish. In this chapter, we discuss some of these classic techniques, as well as recent cutting-edge methodologies that have improved our ability to visualize the process of germ cell specification and differentiation, and the tracking of specific molecules involved in these processes. Additionally, we discuss traditional and novel technologies for manipulating the zebrafish genome to identify new components through loss-of-function studies of putative germ cell regulators. Together with the numerous aforementioned advantages of zebrafish as a genetic model for studying development, we believe these new techniques will continue to advance zebrafish to the forefront for investigation of the molecular regulators of germ cell specification and germ line biology.
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Affiliation(s)
- O H Kaufman
- Albert Einstein College of Medicine, Bronx, NY, United States
| | - F L Marlow
- Albert Einstein College of Medicine, Bronx, NY, United States
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27
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Quan H, Lynch JA. The evolution of insect germline specification strategies. CURRENT OPINION IN INSECT SCIENCE 2016; 13:99-105. [PMID: 27088076 PMCID: PMC4827259 DOI: 10.1016/j.cois.2016.02.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The establishment of the germline is essential for sexually reproducing organisms. In animals, there are two major strategies to specify the germline: maternal provision and zygotic induction. The molecular basis of the maternal provision mode has been well characterized in several model organisms (fly, frog, fish, and nematode), while that of the zygotic induction mode has mainly been studied in mammalian models such as the mouse. Shifts in germline determination modes occur unexpectedly frequently and many such shifts have occurred several times among insects. Given their general tractability and rapidly increasing genomic and genetic tools applicable to many species, the insects present a uniquely powerful model system for understanding major transitions in reproductive strategies, and developmental processes in general.
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Affiliation(s)
- Honghu Quan
- Department of Biological Sciences, University of Illinois at Chicago, United States
| | - Jeremy A Lynch
- Department of Biological Sciences, University of Illinois at Chicago, United States.
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28
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Dailey SC, Febrero Planas R, Rossell Espier A, Garcia-Fernàndez J, Somorjai IML. Asymmetric Distribution of pl10 and bruno2, New Members of a Conserved Core of Early Germline Determinants in Cephalochordates. Front Ecol Evol 2016. [DOI: 10.3389/fevo.2015.00156] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
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29
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Abstract
Primordial germ cells are the progenitor cells that give rise to the gametes. In some animals, the germline is induced by zygotic transcription factors, whereas in others, primordial germ cell specification occurs via inheritance of maternally provided gene products known as germ plasm. Once specified, the primordial germ cells of some animals must acquire motility and migrate to the gonad in order to survive. In all animals examined, perinuclear structures called germ granules form within germ cells. This review focuses on some of the recent studies, conducted by several groups using diverse systems, from invertebrates to vertebrates, which have provided mechanistic insight into the molecular regulation of germ cell specification and migration.
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Affiliation(s)
- Florence Marlow
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY, 10461, USA; Department of Neuroscience, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY, 10461, USA
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30
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Evans T, Loose M. AlignWise: a tool for identifying protein-coding sequence and correcting frame-shifts. BMC Bioinformatics 2015; 16:376. [PMID: 26553107 PMCID: PMC4640205 DOI: 10.1186/s12859-015-0813-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 10/31/2015] [Indexed: 11/22/2022] Open
Abstract
Background Identifying protein-coding genes from species without a reference genome sequence can be complicated by the presence of sequencing errors, particularly insertions and deletions. A number of tools capable of correcting erroneous frame-shifts within assembled transcripts are available but often do not report back DNA sequences required for subsequent phylogenetic analysis. Amongst those that do, the Genewise algorithm is the most effective. However, it requires a homology wrapper to be used in this way, and here we demonstrate it perfectly corrects frame-shifts only 60 % of the time. Results We therefore created AlignWise, a tool that combines Genewise with our own homology-based method, AlignFS, to identify protein-coding regions and correct erroneous frame-shifts, suitable for subsequent phylogenetic analysis. We compared AlignWise against other open reading frame finding software and demonstrate that the AlignFS algorithm is more accurate than Genewise at correcting frame-shifts within an order. We show that AlignWise provides the greatest accuracy at higher evolutionary distances, out-performing both AlignFS and Genewise individually. Conclusions AlignWise produces a single ORF per transcript and identifies and corrects frame-shifts with high accuracy. It is therefore well suited for analysing novel transcriptome assemblies and EST sequences in the absence of a reference genome.
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Affiliation(s)
- Teri Evans
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK.
| | - Matthew Loose
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK.
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31
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Abstract
Germ cells are the special cells in the body that undergo meiosis to generate gametes and subsequently entire new organisms after fertilization, a process that continues generation after generation. Recent studies have expanded our understanding of the factors and mechanisms that specify germ cell fate, including the partitioning of maternally supplied 'germ plasm', inheritance of epigenetic memory and expression of transcription factors crucial for primordial germ cell (PGC) development. Even after PGCs are specified, germline fate is labile and thus requires protective mechanisms, such as global transcriptional repression, chromatin state alteration and translation of only germline-appropriate transcripts. Findings from diverse species continue to provide insights into the shared and divergent needs of these special reproductive cells.
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Affiliation(s)
- Susan Strome
- Molecular, Cell &Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA
| | - Dustin Updike
- Kathryn W. Davis Center for Regenerative Biology &Medicine, Mount Desert Island Biological Laboratory, Bar Harbor, Maine 04672, USA
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Abstract
With few exceptions, all animals acquire the ability to produce eggs or sperm at some point in their life cycle. Despite this near-universal requirement for sexual reproduction, there exists an incredible diversity in germ line development. For example, animals exhibit a vast range of differences in the timing at which the germ line, which retains reproductive potential, separates from the soma, or terminally differentiated, nonreproductive cells. This separation may occur during embryonic development, after gastrulation, or even in adults, depending on the organism. The molecular mechanisms of germ line segregation are also highly diverse, and intimately intertwined with the overall transition from a fertilized egg to an embryo. The earliest embryonic stages of many species are largely controlled by maternally supplied factors. Later in development, patterning control shifts to the embryonic genome and, concomitantly with this transition, the maternally supplied factors are broadly degraded. This chapter attempts to integrate these processes--germ line segregation, and how the divergence of germ line and soma may utilize the egg to embryo transitions differently. In some embryos, this difference is subtle or maybe lacking altogether, whereas in other embryos, this difference in utilization may be a key step in the divergence of the two lineages. Here, we will focus our discussion on the echinoderms, and in particular the sea urchins, in which recent studies have provided mechanistic understanding in germ line determination. We propose that the germ line in sea urchins requires an acquisition of maternal factors from the egg and, when compared to other members of the taxon, this appears to be a derived mechanism. The acquisition is early--at the 32-cell stage--and involves active protection of maternal mRNAs, which are instead degraded in somatic cells with the maternal-to-embryonic transition. We collectively refer to this model as the Time Capsule method for germ line determination.
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Affiliation(s)
- S Zachary Swartz
- Department of Molecular and Cellular Biology, Brown University, Providence, Rhode Island, USA
| | - Gary M Wessel
- Department of Molecular and Cellular Biology, Brown University, Providence, Rhode Island, USA.
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Abstract
Embryos of many animal models express germ line determinants that suppress transcription and mediate early germ line commitment, which occurs before the somatic cell lineages are established. However, not all animals segregate their germ line in this manner. The 'last cell standing' model describes primordial germ cell (PGC) development in axolotls, in which PGCs are maintained by an extracellular signalling niche, and germ line commitment occurs after gastrulation. Here, we propose that this 'stochastic' mode of PGC specification is conserved in vertebrates, including non-rodent mammals. We postulate that early germ line segregation liberates genetic regulatory networks for somatic development to evolve, and that it therefore emerged repeatedly in the animal kingdom in response to natural selection.
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Affiliation(s)
- Andrew D Johnson
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | - Ramiro Alberio
- School of Biosciences, Sutton Bonington Campus, University of Nottingham, Loughborough LE12 5RD, UK
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Niklas KJ, Kutschera U. Historical revisionism and the inheritance theories of Darwin and Weismann. Naturwissenschaften 2015; 102:27. [PMID: 25917381 DOI: 10.1007/s00114-015-1279-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 04/17/2015] [Indexed: 11/25/2022]
Affiliation(s)
- Karl J Niklas
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14893, USA,
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35
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Kumano G. Evolution of germline segregation processes in animal development. Dev Growth Differ 2015; 57:324-32. [DOI: 10.1111/dgd.12211] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 03/05/2015] [Accepted: 03/05/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Gaku Kumano
- Asamushi Research Center for Marine Biology; Graduate School of Life Science; Tohoku University; 9 Sakamoto Asamushi Aomori 039-3501 Japan
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36
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Anava S, Posner R, Rechavi O. The soft genome. WORM 2015; 3:e989798. [PMID: 26430554 DOI: 10.4161/21624054.2014.989798] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Accepted: 11/14/2014] [Indexed: 11/19/2022]
Abstract
Caenorhabditis elegans (C. elegans) nematodes transmit small RNAs across generations, a process that enables transgenerational regulation of genes. In contrast to changes to the DNA sequence, transgenerational transmission of small RNA-mediated responses is reversible, and thus enables "soft" or "flexible" inheritance of acquired characteristics. Until very recently only introduction of foreign genetic material (viruses, transposons, transgenes) was shown to directly lead to inheritance of small RNAs. New discoveries however, demonstrate that starvation also triggers inheritance of endogenous small RNAs in C.elegans. Multiple generations of worms inherit starvation-responsive endogenous small RNAs, and starvation also results in heritable extension of the progeny's lifespan. In this Commentary paper we explore the intriguing possibility that large parts of the genome and many additional traits are similarly subjected to heritable small RNA-mediated regulation, and focus on the potential influence of transgenerational RNAi on the worm's physiology. While the universal relevance of this mechanism remains to be discovered, we will examine how the discoveries made in worms already challenge long held dogmas in genetics and evolution.
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Affiliation(s)
- Sarit Anava
- Department of Neurobiology; Wise Faculty of Life Sciences & Sagol School of Neuroscience; Tel Aviv University ; Tel Aviv, Israel
| | - Rachel Posner
- Department of Neurobiology; Wise Faculty of Life Sciences & Sagol School of Neuroscience; Tel Aviv University ; Tel Aviv, Israel
| | - Oded Rechavi
- Department of Neurobiology; Wise Faculty of Life Sciences & Sagol School of Neuroscience; Tel Aviv University ; Tel Aviv, Israel
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37
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Chatfield J, O'Reilly MA, Bachvarova RF, Ferjentsik Z, Redwood C, Walmsley M, Patient R, Loose M, Johnson AD. Stochastic specification of primordial germ cells from mesoderm precursors in axolotl embryos. Development 2014; 141:2429-40. [PMID: 24917499 PMCID: PMC4050694 DOI: 10.1242/dev.105346] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 04/22/2014] [Indexed: 01/18/2023]
Abstract
A common feature of development in most vertebrate models is the early segregation of the germ line from the soma. For example, in Xenopus and zebrafish embryos primordial germ cells (PGCs) are specified by germ plasm that is inherited from the egg; in mice, Blimp1 expression in the epiblast mediates the commitment of cells to the germ line. How these disparate mechanisms of PGC specification evolved is unknown. Here, in order to identify the ancestral mechanism of PGC specification in vertebrates, we studied PGC specification in embryos from the axolotl (Mexican salamander), a model for the tetrapod ancestor. In the axolotl, PGCs develop within mesoderm, and classic studies have reported their induction from primitive ectoderm (animal cap). We used an axolotl animal cap system to demonstrate that signalling through FGF and BMP4 induces PGCs. The role of FGF was then confirmed in vivo. We also showed PGC induction by Brachyury, in the presence of BMP4. These conditions induced pluripotent mesodermal precursors that give rise to a variety of somatic cell types, in addition to PGCs. Irreversible restriction of the germ line did not occur until the mid-tailbud stage, days after the somatic germ layers are established. Before this, germline potential was maintained by MAP kinase signalling. We propose that this stochastic mechanism of PGC specification, from mesodermal precursors, is conserved in vertebrates.
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Affiliation(s)
- Jodie Chatfield
- School of Life Sciences, University of Nottingham, Queens Medical Centre, Nottingham NG7 2UH, UK
| | - Marie-Anne O'Reilly
- School of Life Sciences, University of Nottingham, Queens Medical Centre, Nottingham NG7 2UH, UK
| | - Rosemary F Bachvarova
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Zoltan Ferjentsik
- School of Life Sciences, University of Nottingham, Queens Medical Centre, Nottingham NG7 2UH, UK
| | - Catherine Redwood
- School of Life Sciences, University of Nottingham, Queens Medical Centre, Nottingham NG7 2UH, UK
| | - Maggie Walmsley
- Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, UK
| | - Roger Patient
- Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, UK
| | - Mathew Loose
- School of Life Sciences, University of Nottingham, Queens Medical Centre, Nottingham NG7 2UH, UK
| | - Andrew D Johnson
- School of Life Sciences, University of Nottingham, Queens Medical Centre, Nottingham NG7 2UH, UK
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38
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Development: Germ plasm 'fuels' vertebrate evolution. Nat Rev Genet 2014; 15:364. [PMID: 24759329 DOI: 10.1038/nrg3737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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