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Jia H, Tan S, Cai Y, Guo Y, Shen J, Zhang Y, Ma H, Zhang Q, Chen J, Qiao G, Ruan J, Zhang YE. Low-input PacBio sequencing generates high-quality individual fly genomes and characterizes mutational processes. Nat Commun 2024; 15:5644. [PMID: 38969648 PMCID: PMC11226609 DOI: 10.1038/s41467-024-49992-6] [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: 11/01/2023] [Accepted: 06/20/2024] [Indexed: 07/07/2024] Open
Abstract
Long-read sequencing, exemplified by PacBio, revolutionizes genomics, overcoming challenges like repetitive sequences. However, the high DNA requirement ( > 1 µg) is prohibitive for small organisms. We develop a low-input (100 ng), low-cost, and amplification-free library-generation method for PacBio sequencing (LILAP) using Tn5-based tagmentation and DNA circularization within one tube. We test LILAP with two Drosophila melanogaster individuals, and generate near-complete genomes, surpassing preexisting single-fly genomes. By analyzing variations in these two genomes, we characterize mutational processes: complex transpositions (transposon insertions together with extra duplications and/or deletions) prefer regions characterized by non-B DNA structures, and gene conversion of transposons occurs on both DNA and RNA levels. Concurrently, we generate two complete assemblies for the endosymbiotic bacterium Wolbachia in these flies and similarly detect transposon conversion. Thus, LILAP promises a broad PacBio sequencing adoption for not only mutational studies of flies and their symbionts but also explorations of other small organisms or precious samples.
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Affiliation(s)
- Hangxing Jia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Shengjun Tan
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Yingao Cai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanyan Guo
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jieyu Shen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yaqiong Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Huijing Ma
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qingzhu Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jinfeng Chen
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Gexia Qiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jue Ruan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
| | - Yong E Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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Martin M, Newton ILG. The Wolbachia WalE1 effector alters Drosophila endocytosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.26.530160. [PMID: 36909520 PMCID: PMC10002650 DOI: 10.1101/2023.02.26.530160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
The most common intracellular bacterial infection is Wolbachia pipientis, a microbe that manipulates host reproduction and is used in control of insect vectors. Phenotypes induced by Wolbachia have been studied for decades and range from sperm-egg incompatibility to male killing. How Wolbachia alters host biology is less well understood. Previously, we characterized the first Wolbachia effector - WalE1, which encodes a synuclein domain at the N terminus. Purified WalE1 sediments with and bundles actin and when heterologously expressed in flies, increases Wolbachia titer in the developing oocyte. In this work, we first identify the native expression WalE1 by Wolbachia infecting both fly cells and whole animals. WalE1 appears as aggregates, separate from Wolbachia cells. We next show that WalE1 co-immunoprecipitates with the host protein Past1 and that WalE1 manipulates host endocytosis. Yeast expressing WalE1 show deficiency in uptake of FM4-64 dye, and flies harboring mutations in Past1 or overexpressing WalE1 are sensitive to AgNO3, a hallmark of endocytosis defects. Finally, we also show that Past1 null flies harbor more Wolbachia overall and in late egg chambers. Our results identify interactions between a Wolbachia secreted effector and a host protein and point to yet another important host cell process impinged upon by Wolbachia.
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Affiliation(s)
- MaryAnn Martin
- Department of Biology, Indiana University, Bloomington, IN USA
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3
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Differential viral RNA methylation contributes to pathogen blocking in Wolbachia-colonized arthropods. PLoS Pathog 2022; 18:e1010393. [PMID: 35294495 PMCID: PMC8959158 DOI: 10.1371/journal.ppat.1010393] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 03/28/2022] [Accepted: 02/24/2022] [Indexed: 02/06/2023] Open
Abstract
Arthropod endosymbiont Wolbachia pipientis is part of a global biocontrol strategy to reduce the replication of mosquito-borne RNA viruses such as alphaviruses. We previously demonstrated the importance of a host cytosine methyltransferase, DNMT2, in Drosophila and viral RNA as a cellular target during pathogen-blocking. Here we report a role for DNMT2 in Wolbachia-induced alphavirus inhibition in Aedes species. Expression of DNMT2 in mosquito tissues, including the salivary glands, is elevated upon virus infection. Notably, this is suppressed in Wolbachia-colonized animals, coincident with reduced virus replication and decreased infectivity of progeny virus. Ectopic expression of DNMT2 in cultured Aedes cells is proviral, increasing progeny virus infectivity, and this effect of DNMT2 on virus replication and infectivity is dependent on its methyltransferase activity. Finally, examining the effects of Wolbachia on modifications of viral RNA by LC-MS show a decrease in the amount of 5-methylcytosine modification consistent with the down-regulation of DNMT2 in Wolbachia colonized mosquito cells and animals. Collectively, our findings support the conclusion that disruption of 5-methylcytosine modification of viral RNA is a vital mechanism operative in pathogen blocking. These data also emphasize the essential role of epitranscriptomic modifications in regulating fundamental alphavirus replication and transmission processes.
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Leitner M, Bishop C, Asgari S. Transcriptional Response of Wolbachia to Dengue Virus Infection in Cells of the Mosquito Aedes aegypti. mSphere 2021; 6:e0043321. [PMID: 34190587 PMCID: PMC8265661 DOI: 10.1128/msphere.00433-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/07/2021] [Indexed: 11/20/2022] Open
Abstract
Aedes aegypti transmits one of the most significant mosquito-borne viruses, dengue virus (DENV). The absence of effective vaccines and clinical treatments and the emergence of insecticide resistance in A. aegypti necessitate novel vector control strategies. A new approach uses the endosymbiotic bacterium Wolbachia pipientis to reduce the spread of arboviruses. However, the Wolbachia-mediated antiviral mechanism is not well understood. To shed light on this mechanism, we investigated an unexplored aspect of Wolbachia-virus-mosquito interaction. We used RNA sequencing to examine the transcriptional response of Wolbachia to DENV infection in A. aegypti Aag2 cells transinfected with the wAlbB strain of Wolbachia. Our results suggest that genes encoding an endoribonuclease (RNase HI), a regulator of sigma 70-dependent gene transcription (6S RNA), essential cellular, transmembrane, and stress response functions and primary type I and IV secretion systems were upregulated, while a number of transport and binding proteins of Wolbachia, ribosome structure, and elongation factor-associated genes were downregulated due to DENV infection. Furthermore, bacterial retrotransposon, transposable, and phage-related elements were found among the up- and downregulated genes. We show that Wolbachia elicits a transcriptional response to virus infection and identify differentially expressed Wolbachia genes mostly at the early stages of virus infection. These findings highlight Wolbachia's ability to alter its gene expression in response to DENV infection of the host cell. IMPORTANCE Aedes aegypti is a vector of several pathogenic viruses, including dengue, Zika, chikungunya, and yellow fever viruses, which are of importance to human health. Wolbachia is an endosymbiotic bacterium currently used in transinfected mosquitoes to suppress replication and transmission of dengue viruses. However, the mechanism of Wolbachia-mediated virus inhibition is not fully understood. While several studies have shown mosquitoes' transcriptional responses to dengue virus infection, none have investigated these responses in Wolbachia, which may provide clues to the inhibition mechanism. Our results suggest changes in the expression of a number of functionally important Wolbachia genes upon dengue virus infection, including those involved in stress responses, providing insights into the endosymbiont's reaction to virus infection.
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Affiliation(s)
- Michael Leitner
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, Australia
| | - Cameron Bishop
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, Australia
| | - Sassan Asgari
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, Australia
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5
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Vera-Ponce León A, Dominguez-Mirazo M, Bustamante-Brito R, Higareda-Alvear V, Rosenblueth M, Martínez-Romero E. Functional genomics of a Spiroplasma associated with the carmine cochineals Dactylopius coccus and Dactylopius opuntiae. BMC Genomics 2021; 22:240. [PMID: 33823812 PMCID: PMC8025503 DOI: 10.1186/s12864-021-07540-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 03/18/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Spiroplasma is a widely distributed endosymbiont of insects, arthropods, and plants. In insects, Spiroplasma colonizes the gut, hemolymph, and reproductive organs of the host. Previous metagenomic surveys of the domesticated carmine cochineal Dactylopius coccus and the wild cochineal D. opuntiae reported sequences of Spiroplasma associated with these insects. However, there is no analysis of the genomic capabilities and the interaction of this Spiroplasma with Dactylopius. RESULTS Here we present three Spiroplasma genomes independently recovered from metagenomes of adult males and females of D. coccus, from two different populations, as well as from adult females of D. opuntiae. Single-copy gene analysis showed that these genomes were > 92% complete. Phylogenomic analyses classified these genomes as new members of Spiroplasma ixodetis. Comparative genome analysis indicated that they exhibit fewer genes involved in amino acid and carbon catabolism compared to other spiroplasmas. Moreover, virulence factor-encoding genes (i.e., glpO, spaid and rip2) were found incomplete in these S. ixodetis genomes. We also detected an enrichment of genes encoding the type IV secretion system (T4SS) in S. ixodetis genomes of Dactylopius. A metratranscriptomic analysis of D. coccus showed that some of these T4SS genes (i.e., traG, virB4 and virD4) in addition to the superoxide dismutase sodA of S. ixodetis were overexpressed in the ovaries. CONCLUSION The symbiont S. ixodetis is a new member of the bacterial community of D. coccus and D. opuntiae. The recovery of incomplete virulence factor-encoding genes in S. ixodetis of Dactylopius suggests that this bacterium is a non-pathogenic symbiont. A high number of genes encoding the T4SS, in the S. ixodetis genomes and the overexpression of these genes in the ovary and hemolymph of the host suggest that S. ixodetis use the T4SS to interact with the Dactylopius cells. Moreover, the transcriptional differences of S. ixodetis among the gut, hemolymph and ovary tissues of D. coccus indicate that this bacterium can respond and adapt to the different conditions (e.g., oxidative stress) present within the host. All this evidence proposes that there is a strong interaction and molecular signaling in the symbiosis between S. ixodetis and the carmine cochineal Dactylopius.
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Affiliation(s)
- Arturo Vera-Ponce León
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico. .,Present Address: Faculty of Biotechnology, Chemistry and Food Science, Norwegian University of Life Sciences, 1433, Ås, Norway.
| | - Marian Dominguez-Mirazo
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.,Present Address: School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
| | - Rafael Bustamante-Brito
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Víctor Higareda-Alvear
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Mónica Rosenblueth
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Esperanza Martínez-Romero
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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6
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Salje J. Cells within cells: Rickettsiales and the obligate intracellular bacterial lifestyle. Nat Rev Microbiol 2021; 19:375-390. [PMID: 33564174 DOI: 10.1038/s41579-020-00507-2] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2020] [Indexed: 01/01/2023]
Abstract
The Rickettsiales are a group of obligate intracellular vector-borne Gram-negative bacteria that include many organisms of clinical and agricultural importance, including Anaplasma spp., Ehrlichia chaffeensis, Wolbachia, Rickettsia spp. and Orientia tsutsugamushi. This Review provides an overview of the current state of knowledge of the biology of these bacteria and their interactions with host cells, with a focus on pathogenic species or those that are otherwise important for human health. This includes a description of rickettsial genomics, bacterial cell biology, the intracellular lifestyles of Rickettsiales and the mechanisms by which they induce and evade the innate immune response.
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Affiliation(s)
- Jeanne Salje
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK. .,Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand. .,Public Health Research Institute, Rutgers University, Newark, NJ, USA.
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7
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Lindsey ARI. Sensing, Signaling, and Secretion: A Review and Analysis of Systems for Regulating Host Interaction in Wolbachia. Genes (Basel) 2020; 11:E813. [PMID: 32708808 PMCID: PMC7397232 DOI: 10.3390/genes11070813] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 07/12/2020] [Accepted: 07/13/2020] [Indexed: 12/18/2022] Open
Abstract
Wolbachia (Anaplasmataceae) is an endosymbiont of arthropods and nematodes that resides within host cells and is well known for manipulating host biology to facilitate transmission via the female germline. The effects Wolbachia has on host physiology, combined with reproductive manipulations, make this bacterium a promising candidate for use in biological- and vector-control. While it is becoming increasingly clear that Wolbachia's effects on host biology are numerous and vary according to the host and the environment, we know very little about the molecular mechanisms behind Wolbachia's interactions with its host. Here, I analyze 29 Wolbachia genomes for the presence of systems that are likely central to the ability of Wolbachia to respond to and interface with its host, including proteins for sensing, signaling, gene regulation, and secretion. Second, I review conditions under which Wolbachia alters gene expression in response to changes in its environment and discuss other instances where we might hypothesize Wolbachia to regulate gene expression. Findings will direct mechanistic investigations into gene regulation and host-interaction that will deepen our understanding of intracellular infections and enhance applied management efforts that leverage Wolbachia.
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Affiliation(s)
- Amelia R I Lindsey
- Department of Entomology, University of Minnesota, St. Paul, MN 55108, USA
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8
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Herran B, Geniez S, Delaunay C, Raimond M, Lesobre J, Bertaux J, Slatko B, Grève P. The shutting down of the insulin pathway: a developmental window for Wolbachia load and feminization. Sci Rep 2020; 10:10551. [PMID: 32601334 PMCID: PMC7324399 DOI: 10.1038/s41598-020-67428-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 06/04/2020] [Indexed: 02/08/2023] Open
Abstract
Using the isopod Armadillidium vulgare as a case study, we review the significance of the "bacterial dosage model", which connects the expression of the extended phenotype to the rise of the Wolbachia load. In isopods, the Insulin-like Androgenic Gland hormone (IAG) induces male differentiation: Wolbachia feminizes males through insulin resistance, presumably through defunct insulin receptors. This should prevent an autocrine development of the androgenic glands so that females differentiate instead: feminization should translate as IAG silencing and increased Wolbachia load in the same developmental window. In line with the autocrine model, uninfected males expressed IAG from the first larval stage on, long before the androgenic gland primordia begin to differentiate, and exponentially throughout development. In contrast in infected males, expression fully stopped at stage 4 (juvenile), when male differentiation begins. This co-occurred with the only significant rise in the Wolbachia load throughout the life-stages. Concurrently, the raw expression of the bacterial Secretion Systems co-increased, but they were not over-expressed relative to the number of bacteria. The isopod model leads to formulate the "bacterial dosage model" throughout extended phenotypes as the conjunction between bacterial load as the mode of action, timing of multiplication (pre/post-zygotic), and site of action (soma vs. germen).
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Affiliation(s)
- Benjamin Herran
- Laboratoire Ecologie et Biologie des Interactions - UMR CNRS 7267 - Equipe Ecologie, Evolution, Symbiose - Université de Poitiers, 5 rue Albert Turpain, TSA 51106, 86073, Poitiers Cedex 9, France
| | - Sandrine Geniez
- Laboratoire Ecologie et Biologie des Interactions - UMR CNRS 7267 - Equipe Ecologie, Evolution, Symbiose - Université de Poitiers, 5 rue Albert Turpain, TSA 51106, 86073, Poitiers Cedex 9, France
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, USA
| | - Carine Delaunay
- Laboratoire Ecologie et Biologie des Interactions - UMR CNRS 7267 - Equipe Ecologie, Evolution, Symbiose - Université de Poitiers, 5 rue Albert Turpain, TSA 51106, 86073, Poitiers Cedex 9, France
| | - Maryline Raimond
- Laboratoire Ecologie et Biologie des Interactions - UMR CNRS 7267 - Equipe Ecologie, Evolution, Symbiose - Université de Poitiers, 5 rue Albert Turpain, TSA 51106, 86073, Poitiers Cedex 9, France
| | - Jérôme Lesobre
- Laboratoire Ecologie et Biologie des Interactions - UMR CNRS 7267 - Equipe Ecologie, Evolution, Symbiose - Université de Poitiers, 5 rue Albert Turpain, TSA 51106, 86073, Poitiers Cedex 9, France
- Laboratoire Microorganismes: Génome et Environnement, UMR CNRS 6023, Université Clermont Auvergne, 63178, Aubière, France
| | - Joanne Bertaux
- Laboratoire Ecologie et Biologie des Interactions - UMR CNRS 7267 - Equipe Ecologie, Evolution, Symbiose - Université de Poitiers, 5 rue Albert Turpain, TSA 51106, 86073, Poitiers Cedex 9, France.
| | - Barton Slatko
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, USA
| | - Pierre Grève
- Laboratoire Ecologie et Biologie des Interactions - UMR CNRS 7267 - Equipe Ecologie, Evolution, Symbiose - Université de Poitiers, 5 rue Albert Turpain, TSA 51106, 86073, Poitiers Cedex 9, France.
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Weisskopf L, Newton ILG, Berry D, Webster NS. Spotlight on how microbes influence their host's behavior. Environ Microbiol 2019; 21:3185-3187. [PMID: 31342631 DOI: 10.1111/1462-2920.14757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 07/21/2019] [Indexed: 10/26/2022]
Affiliation(s)
- Laure Weisskopf
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Irene L G Newton
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - David Berry
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, Australia.,Australian Centre for Ecogenomics, University of Queensland, Brisbane, Australia
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Sinha A, Li Z, Sun L, Carlow CKS. Complete Genome Sequence of the Wolbachia wAlbB Endosymbiont of Aedes albopictus. Genome Biol Evol 2019; 11:706-720. [PMID: 30715337 PMCID: PMC6414309 DOI: 10.1093/gbe/evz025] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/29/2019] [Indexed: 12/21/2022] Open
Abstract
Wolbachia, an alpha-proteobacterium closely related to Rickettsia, is a maternally transmitted, intracellular symbiont of arthropods and nematodes. Aedes albopictus mosquitoes are naturally infected with Wolbachia strains wAlbA and wAlbB. Cell line Aa23 established from Ae. albopictus embryos retains only wAlbB and is a key model to study host–endosymbiont interactions. We have assembled the complete circular genome of wAlbB from the Aa23 cell line using long-read PacBio sequencing at 500× median coverage. The assembled circular chromosome is 1.48 megabases in size, an increase of more than 300 kb over the published draft wAlbB genome. The annotation of the genome identified 1,205 protein coding genes, 34 tRNA, 3 rRNA, 1 tmRNA, and 3 other ncRNA loci. The long reads enabled sequencing over complex repeat regions which are difficult to resolve with short-read sequencing. Thirteen percent of the genome comprised insertion sequence elements distributed throughout the genome, some of which cause pseudogenization. Prophage WO genes encoding some essential components of phage particle assembly are missing, while the remainder are found in five prophage regions/WO-like islands or scattered around the genome. Orthology analysis identified a core proteome of 535 orthogroups across all completed Wolbachia genomes. The majority of proteins could be annotated using Pfam and eggNOG analyses, including ankyrins and components of the Type IV secretion system. KEGG analysis revealed the absence of five genes in wAlbB which are present in other Wolbachia. The availability of a complete circular chromosome from wAlbB will enable further biochemical, molecular, and genetic analyses on this strain and related Wolbachia.
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Affiliation(s)
- Amit Sinha
- New England Biolabs, Ipswich, Massachusetts
| | - Zhiru Li
- New England Biolabs, Ipswich, Massachusetts
| | - Luo Sun
- New England Biolabs, Ipswich, Massachusetts
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11
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Newton ILG, Slatko BE. Symbiosis Comes of age at the 10 th Biennial Meeting of Wolbachia Researchers. Appl Environ Microbiol 2019; 85:AEM.03071-18. [PMID: 30796064 PMCID: PMC6450017 DOI: 10.1128/aem.03071-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Wolbachia pipientis is an alpha-proteobacterial, obligate intracellular microbe and arguably the most successful infection on our planet, colonizing 40-60% of insect species. Wolbachia are also present in most, but not all, filarial nematodes where they are obligate mutualists and are the targets for anti-filarial drug discovery. Although Wolbachia are related to important human pathogens they do not infect mammals, but instead are well known for their reproductive manipulations of insect populations, inducing the following phenotypes: male-killing, feminization, parthenogenesis induction, or cytoplasmic incompatibility (CI). The most common of these, CI, results in a sperm-egg incompatibility and increases the relative fecundity of infected females in a population. In the last decade, Wolbachia have also been shown to provide a benefit to insects, where the infection can inhibit RNA virus replication within the host. Wolbachia cannot be cultivated outside of host cells and no genetic tools are available in the symbiont, limiting approaches available to its study. This means that many questions fundamental to our understanding of Wolbachia basic biology remained unknown for decades. The tenth biennial international Wolbachia conference, "Wolbachia Evolution, Ecology, Genomics and Cell Biology: A Chronicle of the Most Ubiquitous Symbiont", was held on June 17-22, 2018, Salem, MA USA. In the review below we highlight the new science presented at the meeting, link it to prior efforts to answer these questions across the Wolbachia genus, and the importance to the field of symbiosis. The topics covered in this review are based on the presentations at the conference.
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Affiliation(s)
| | - Barton E. Slatko
- Molecular Parasitology Group, New England BioLabs, Ipswich, Massachusetts, USA
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12
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Martínez-Rodríguez P, Bella JL. Chorthippus parallelus and Wolbachia: Overlapping Orthopteroid and Bacterial Hybrid Zones. Front Genet 2018; 9:604. [PMID: 30564272 PMCID: PMC6288197 DOI: 10.3389/fgene.2018.00604] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 11/19/2018] [Indexed: 11/25/2022] Open
Abstract
Wolbachia is a well-known endosymbiotic, strictly cytoplasmic bacterium. It establishes complex cytonuclear relations that are not necessarily deleterious to its host, but that often result in reproductive alterations favoring bacterial transmission. Among these alterations, a common one is the cytoplasmic incompatibility (CI) that reduces the number of descendants in certain crosses between infected and non-infected individuals. This CI induced by Wolbachia appears in the hybrid zone that the grasshoppers Chorthippus parallelus parallelus (Cpp) and C. p. erythropus (Cpe) form in the Pyrenees: a reputed model in evolutionary biology. However, this cytonuclear incompatibility is the result of sophisticated processes of the co-divergence of the genomes of the bacterial strains and the host after generations of selection and coevolution. Here we show how these genome conflicts have resulted in a finely tuned adjustment of the bacterial strain to each pure orthopteroid taxon, and the striking appearance of another, newly identified recombinant Wolbachia strain that only occurs in hybrid grasshoppers. We propose the existence of two superimposed hybrid zones: one organized by the grasshoppers, which overlaps with a second, bacterial hybrid zone. The two hybrid zones counterbalance one another and have evolved together since the origin of the grasshopper's hybrid zone.
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Affiliation(s)
- Paloma Martínez-Rodríguez
- Departamento de Biología (Genética), Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - José L Bella
- Departamento de Biología (Genética), Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
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Molina‐Santiago C. Insights in a novel gram‐positive type IV secretion system. Environ Microbiol 2018; 20:2334-2336. [DOI: 10.1111/1462-2920.14296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 05/24/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Carlos Molina‐Santiago
- Departamento de MicrobiologíaInstituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de teatinos) Málaga Spain
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Badawi M, Moumen B, Giraud I, Grève P, Cordaux R. Investigating the Molecular Genetic Basis of Cytoplasmic Sex Determination Caused by Wolbachia Endosymbionts in Terrestrial Isopods. Genes (Basel) 2018; 9:genes9060290. [PMID: 29890648 PMCID: PMC6026926 DOI: 10.3390/genes9060290] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 05/29/2018] [Accepted: 06/05/2018] [Indexed: 12/24/2022] Open
Abstract
In animals, sexual differences between males and females are usually determined by sex chromosomes. Alternatively, sex may also be determined by vertically transmitted intracellular microbial endosymbionts. The best known cytoplasmic sex manipulative endosymbiont is Wolbachia which can, for instance, feminize genetic males into phenotypic females in the terrestrial isopod Armadillidium vulgare. However, the molecular genetic basis of cytoplasmic sex determination is unknown. To identify candidate genes of feminization induced by Wolbachia strain wVulC from A. vulgare, we sequenced the genome of Wolbachia strain wCon from Cylisticus convexus, the most closely related known Wolbachia strain to wVulC that does not induce feminization, and compared it to the wVulC genome. Then, we performed gene expression profiling of the 216 resulting wVulC candidate genes throughout host developmental stages in A. vulgare and the heterologous host C. convexus. We identified a set of 35 feminization candidate genes showing differential expression during host sexual development. Interestingly, 27 of the 35 genes are present in the f element, which is a piece of a feminizing Wolbachia genome horizontally transferred into the nuclear genome of A. vulgare and involved in female sex determination. Assuming that the molecular genetic basis of feminization by Wolbachia and the f element is the same, the 27 genes are candidates for acting as master sex determination genes in A. vulgare females carrying the f element.
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Affiliation(s)
- Myriam Badawi
- Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Université de Poitiers, UMR CNRS 7267, Bât. B8, 5 rue Albert Turpin, TSA 51106, 86073 Poitiers CEDEX 9, France.
| | - Bouziane Moumen
- Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Université de Poitiers, UMR CNRS 7267, Bât. B8, 5 rue Albert Turpin, TSA 51106, 86073 Poitiers CEDEX 9, France.
| | - Isabelle Giraud
- Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Université de Poitiers, UMR CNRS 7267, Bât. B8, 5 rue Albert Turpin, TSA 51106, 86073 Poitiers CEDEX 9, France.
| | - Pierre Grève
- Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Université de Poitiers, UMR CNRS 7267, Bât. B8, 5 rue Albert Turpin, TSA 51106, 86073 Poitiers CEDEX 9, France.
| | - Richard Cordaux
- Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Université de Poitiers, UMR CNRS 7267, Bât. B8, 5 rue Albert Turpin, TSA 51106, 86073 Poitiers CEDEX 9, France.
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Conflict in the Intracellular Lives of Endosymbionts and Viruses: A Mechanistic Look at Wolbachia-Mediated Pathogen-blocking. Viruses 2018; 10:v10040141. [PMID: 29561780 PMCID: PMC5923435 DOI: 10.3390/v10040141] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 03/14/2018] [Accepted: 03/20/2018] [Indexed: 12/16/2022] Open
Abstract
At the forefront of vector control efforts are strategies that leverage host-microbe associations to reduce vectorial capacity. The most promising of these efforts employs Wolbachia, a maternally transmitted endosymbiotic bacterium naturally found in 40% of insects. Wolbachia can spread through a population of insects while simultaneously inhibiting the replication of viruses within its host. Despite successes in using Wolbachia-transfected mosquitoes to limit dengue, Zika, and chikungunya transmission, the mechanisms behind pathogen-blocking have not been fully characterized. Firstly, we discuss how Wolbachia and viruses both require specific host-derived structures, compounds, and processes to initiate and maintain infection. There is significant overlap in these requirements, and infection with either microbe often manifests as cellular stress, which may be a key component of Wolbachia’s anti-viral effect. Secondly, we discuss the current understanding of pathogen-blocking through this lens of cellular stress and develop a comprehensive view of how the lives of Wolbachia and viruses are fundamentally in conflict with each other. A thorough understanding of the genetic and cellular determinants of pathogen-blocking will significantly enhance the ability of vector control programs to deploy and maintain effective Wolbachia-mediated control measures.
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