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Jacobs J, Nakamoto A, Mastoras M, Loucks H, Mirchandani C, Karim L, Penunuri G, Wanket C, Russell SL. Complete de novo assembly of Wolbachia endosymbiont of Drosophila willistoni using long-read genome sequencing. Sci Rep 2024; 14:17770. [PMID: 39090271 PMCID: PMC11294445 DOI: 10.1038/s41598-024-68716-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Accepted: 07/25/2024] [Indexed: 08/04/2024] Open
Abstract
Wolbachia is an obligate intracellular α-proteobacterium, which commonly infects arthropods and filarial nematodes. Different strains of Wolbachia are capable of a wide range of regulatory manipulations in their diverse hosts, including the modulation of host cellular differentiation to influence host reproduction. The genetic basis for the majority of these phenotypes is unknown. The wWil strain from the neotropical fruit fly, Drosophila willistoni, exhibits a remarkably high affinity for host germline-derived cells relative to the somatic cells. This trait could be leveraged for understanding how Wolbachia influences the host germline and for controlling host populations in the field. To further the use of this strain in biological and biomedical research, we sequenced the genome of the wWil strain isolated from host cell culture cells. Here, we present the first high quality Nanopore assembly of wWil, the Wolbachia endosymbiont of D. willistoni. Our assembly resulted in a circular genome of 1.27 Mb with a BUSCO completeness score of 99.7%. Consistent with other insect-associated Wolbachia strains, comparative genomic analysis revealed that wWil has a highly mosaic genome relative to the closely related wMel and wAu strains from Drosophila melanogaster and Drosophila simulans, respectively.
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Affiliation(s)
- Jodie Jacobs
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Anne Nakamoto
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Mira Mastoras
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Hailey Loucks
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Cade Mirchandani
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Lily Karim
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Gabriel Penunuri
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Ciara Wanket
- Genomics Institute, University of California, Santa Cruz, CA, USA
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Shelbi L Russell
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA.
- Genomics Institute, University of California, Santa Cruz, CA, USA.
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Jacobs J, Nakamoto A, Mastoras M, Loucks H, Mirchandani C, Karim L, Penunuri G, Wanket C, Russell SL. Complete de novo assembly of Wolbachia endosymbiont of Drosophila willistoni using long-read genome sequencing. RESEARCH SQUARE 2024:rs.3.rs-4510571. [PMID: 38946980 PMCID: PMC11213192 DOI: 10.21203/rs.3.rs-4510571/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Wolbachia is an obligate intracellular α-proteobacterium which commonly infects arthropods and filarial nematodes. Different strains of Wolbachia are capable of a wide range of regulatory manipulations in many hosts and modulate host cellular differentiation to influence host reproduction. The genetic basis for the majority of these phenotypes is unknown. The wWil strain from the neotropical fruit fly, Drosophila willistoni, exhibits a remarkably high affinity for host germline-derived cells relative to the soma. This trait could be leveraged for understanding how Wolbachia influences the host germline and for controlling host populations in the field. To further the use of this strain in biological and biomedical research, we sequenced the genome of the wWil strain isolated from host cell culture cells. Here, we present the first high quality nanopore assembly of wWil, the Wolbachia endosymbiont of D. willistoni. Our assembly resulted in a circular genome of 1.27 Mb with a BUSCO completeness score of 99.7%. Consistent with other insect-associated Wolbachia strains, comparative genomic analysis revealed that wWil has a highly mosaic genome relative to the closely related wMel strain from Drosophila melanogaster.
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Affiliation(s)
- Jodie Jacobs
- Department of Biomolecular Engineering, University of California Santa Cruz
| | - Anne Nakamoto
- Department of Biomolecular Engineering, University of California Santa Cruz
| | - Mira Mastoras
- Department of Biomolecular Engineering, University of California Santa Cruz
| | - Hailey Loucks
- Department of Biomolecular Engineering, University of California Santa Cruz
| | - Cade Mirchandani
- Department of Biomolecular Engineering, University of California Santa Cruz
| | - Lily Karim
- Department of Biomolecular Engineering, University of California Santa Cruz
| | - Gabriel Penunuri
- Department of Biomolecular Engineering, University of California Santa Cruz
| | - Ciara Wanket
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz
| | - Shelbi L Russell
- Department of Biomolecular Engineering, University of California Santa Cruz
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Russell SL, Castillo JR, Sullivan WT. Wolbachia endosymbionts manipulate the self-renewal and differentiation of germline stem cells to reinforce fertility of their fruit fly host. PLoS Biol 2023; 21:e3002335. [PMID: 37874788 PMCID: PMC10597519 DOI: 10.1371/journal.pbio.3002335] [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: 01/18/2023] [Accepted: 09/14/2023] [Indexed: 10/26/2023] Open
Abstract
The alphaproteobacterium Wolbachia pipientis infects arthropod and nematode species worldwide, making it a key target for host biological control. Wolbachia-driven host reproductive manipulations, such as cytoplasmic incompatibility (CI), are credited for catapulting these intracellular bacteria to high frequencies in host populations. Positive, perhaps mutualistic, reproductive manipulations also increase infection frequencies, but are not well understood. Here, we identify molecular and cellular mechanisms by which Wolbachia influences the molecularly distinct processes of germline stem cell (GSC) self-renewal and differentiation. We demonstrate that wMel infection rescues the fertility of flies lacking the translational regulator mei-P26 and is sufficient to sustain infertile homozygous mei-P26-knockdown stocks indefinitely. Cytology revealed that wMel mitigates the impact of mei-P26 loss through restoring proper pMad, Bam, Sxl, and Orb expression. In Oregon R files with wild-type fertility, wMel infection elevates lifetime egg hatch rates. Exploring these phenotypes through dual-RNAseq quantification of eukaryotic and bacterial transcripts revealed that wMel infection rescues and offsets many gene expression changes induced by mei-P26 loss at the mRNA level. Overall, we show that wMel infection beneficially reinforces host fertility at mRNA, protein, and phenotypic levels, and these mechanisms may promote the emergence of mutualism and the breakdown of host reproductive manipulations.
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Affiliation(s)
- Shelbi L. Russell
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Jennie Ruelas Castillo
- Division of Infectious Diseases, Department of Medicine, The Johns Hopkins Hospital, Baltimore, Maryland, United States of America
| | - William T. Sullivan
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
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Marangon E, Uthicke S, Patel F, Marzinelli EM, Bourne DG, Webster NS, Laffy PW. Life-stage specificity and cross-generational climate effects on the microbiome of a tropical sea urchin (Echinodermata: Echinoidea). Mol Ecol 2023; 32:5645-5660. [PMID: 37724851 DOI: 10.1111/mec.17124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 08/23/2023] [Accepted: 08/30/2023] [Indexed: 09/21/2023]
Abstract
Microbes play a critical role in the development and health of marine invertebrates, though microbial dynamics across life stages and host generations remain poorly understood in most reef species, especially in the context of climate change. Here, we use a 4-year multigenerational experiment to explore microbe-host interactions under the Intergovernmental Panel on Climate Change (IPCC)-forecast climate scenarios in the rock-boring tropical urchin Echinometra sp. A. Adult urchins (F0 ) were exposed for 18 months to increased temperature and pCO2 levels predicted for years 2050 and 2100 under RCP 8.5, a period which encompassed spawning. After rearing F1 offspring for a further 2 years, spawning was induced, and F2 larvae were raised under current day and 2100 conditions. Cross-generational climate effects were also explored in the microbiome of F1 offspring through a transplant experiment. Using 16S rRNA gene sequence analysis, we determined that each life stage and generation was associated with a distinct microbiome, with higher microbial diversity observed in juveniles compared to larval stages. Although life-stage specificity was conserved under climate conditions projected for 2050 and 2100, we observed changes in the urchin microbial community structure within life stages. Furthermore, we detected a climate-mediated parental effect when juveniles were transplanted among climate treatments, with the parental climate treatment influencing the offspring microbiome. Our findings reveal a potential for cross-generational impacts of climate change on the microbiome of a tropical invertebrate species.
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Affiliation(s)
- Emma Marangon
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- AIMS@JCU, Townsville, Queensland, Australia
| | - Sven Uthicke
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Frances Patel
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Ezequiel M Marzinelli
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - David G Bourne
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- AIMS@JCU, Townsville, Queensland, Australia
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, Queensland, Australia
- Australian Antarctic Division, Kingston, Tasmania, Australia
| | - Patrick W Laffy
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- AIMS@JCU, Townsville, Queensland, Australia
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Abstract
Animal development is an inherently complex process that is regulated by highly conserved genomic networks, and the resulting phenotype may remain plastic in response to environmental signals. Despite development having been studied in a more natural setting for the past few decades, this framework often precludes the role of microbial prokaryotes in these processes. Here, we address how microbial symbioses impact animal development from the onset of gametogenesis through adulthood. We then provide a first assessment of which developmental processes may or may not be influenced by microbial symbioses and, in doing so, provide a holistic view of the budding discipline of developmental symbiosis.
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Affiliation(s)
- Tyler J Carrier
- GEOMAR Helmholtz Centre for Ocean Research, Kiel 24105, Germany.,Zoological Institute, Christian-Albrechts University of Kiel, Kiel 24118, Germany
| | - Thomas C G Bosch
- Zoological Institute, Christian-Albrechts University of Kiel, Kiel 24118, Germany
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Bubnell JE, Fernandez-Begne P, Ulbing CKS, Aquadro CF. Diverse wMel variants of Wolbachia pipientis differentially rescue fertility and cytological defects of the bag of marbles partial loss of function mutation in Drosophila melanogaster. G3-GENES GENOMES GENETICS 2021; 11:6365939. [PMID: 34580706 PMCID: PMC8664471 DOI: 10.1093/g3journal/jkab312] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 08/16/2021] [Indexed: 11/13/2022]
Abstract
In Drosophila melanogaster, the maternally inherited endosymbiont Wolbachia pipientis interacts with germline stem cell genes during oogenesis. One such gene, bag of marbles (bam) is the key switch for differentiation and also shows signals of adaptive evolution for protein diversification. These observations have led us to hypothesize that W. pipientis could be driving the adaptive evolution of bam for control of oogenesis. To test this hypothesis, we must understand the specificity of the genetic interaction between bam and W. pipientis. Previously, we documented that the W. pipientis variant, wMel, rescued the fertility of the bamBW hypomorphic mutant as a transheterozygote over a bam null. However, bamBW was generated more than 20 years ago in an uncontrolled genetic background and maintained over a balancer chromosome. Consequently, the chromosome carrying bamBW accumulated mutations that have prevented controlled experiments to further assess the interaction. Here, we used CRISPR/Cas9 to engineer the same single amino acid bam hypomorphic mutation (bamL255F) and a new bam null disruption mutation into the w1118 isogenic background. We assess the fertility of wildtype bam, bamL255F/bamnull hypomorphic, and bamL255F/bamL255F mutant females, each infected individually with 10 W. pipientis wMel variants representing three phylogenetic clades. Overall, we find that all of the W. pipientis variants tested here rescue bam hypomorphic fertility defects with wMelCS-like variants exhibiting the strongest rescue effects. In addition, these variants did not increase wildtype bam female fertility. Therefore, both bam and W. pipientis interact in genotype-specific ways to modulate female fertility, a critical fitness phenotype.
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Affiliation(s)
- Jaclyn E Bubnell
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Paula Fernandez-Begne
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Cynthia K S Ulbing
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Charles F Aquadro
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
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Hanford HE, Von Dwingelo J, Abu Kwaik Y. Bacterial nucleomodulins: A coevolutionary adaptation to the eukaryotic command center. PLoS Pathog 2021; 17:e1009184. [PMID: 33476322 PMCID: PMC7819608 DOI: 10.1371/journal.ppat.1009184] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Through long-term interactions with their hosts, bacterial pathogens have evolved unique arsenals of effector proteins that interact with specific host targets and reprogram the host cell into a permissive niche for pathogen proliferation. The targeting of effector proteins into the host cell nucleus for modulation of nuclear processes is an emerging theme among bacterial pathogens. These unique pathogen effector proteins have been termed in recent years as "nucleomodulins." The first nucleomodulins were discovered in the phytopathogens Agrobacterium and Xanthomonas, where their nucleomodulins functioned as eukaryotic transcription factors or integrated themselves into host cell DNA to promote tumor induction, respectively. Numerous nucleomodulins were recently identified in mammalian pathogens. Bacterial nucleomodulins are an emerging family of pathogen effector proteins that evolved to target specific components of the host cell command center through various mechanisms. These mechanisms include: chromatin dynamics, histone modification, DNA methylation, RNA splicing, DNA replication, cell cycle, and cell signaling pathways. Nucleomodulins may induce short- or long-term epigenetic modifications of the host cell. In this extensive review, we discuss the current knowledge of nucleomodulins from plant and mammalian pathogens. While many nucleomodulins are already identified, continued research is instrumental in understanding their mechanisms of action and the role they play during the progression of pathogenesis. The continued study of nucleomodulins will enhance our knowledge of their effects on nuclear chromatin dynamics, protein homeostasis, transcriptional landscapes, and the overall host cell epigenome.
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Affiliation(s)
- Hannah E. Hanford
- Department of Microbiology and Immunology, University of Louisville, Kentucky, United States of America
| | - Juanita Von Dwingelo
- Department of Microbiology and Immunology, University of Louisville, Kentucky, United States of America
| | - Yousef Abu Kwaik
- Department of Microbiology and Immunology, University of Louisville, Kentucky, United States of America
- Center for Predicative Medicine, College of Medicine, University of Louisville, Kentucky, United States of America
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