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Wannassi T, Sayadi A, Abbes K, Djebbi S, Naccache C, Khemakhem MM, Chermiti B. Prevalence of Wolbachia infection in field natural population of the apricot seed wasp Eurytoma samsonowi (Hymenoptera: Eurytomidae). Int Microbiol 2024:10.1007/s10123-024-00593-9. [PMID: 39264544 DOI: 10.1007/s10123-024-00593-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 08/27/2024] [Accepted: 09/06/2024] [Indexed: 09/13/2024]
Abstract
Obligate endosymbiont bacteria associated with insects are naturally providing their hosts with essential nutrients such as vitamins and amino acids and biological services including protection from pathogens. In this study, we aimed to investigate the presence of Wolbachia infection among males and females of the parasitic apricot seed wasp (ASW) Eurytoma samsonowi Vassiliev (Vassiliev Petrograd 11: 1-15, 1915) (Hymenoptera: Eurytomidae), a very harmful pest of apricot (Prunus armeniaca), in the oasis of Gafsa, Southern-West of Tunisia. The detection of Wolbachia infection was assessed based on the amplification of the Wolbachia surface protein (wsp) gene and a multilocus sequence typing (MLST) as a universal genotyping tool for Wolbachia involving the analyses of genes gatB, coxA, hcpA, fbpA, and ftsz. Confirming the screening results, Wolbachia was detected in the natural apricot wasp for the first time, with a significant difference between males (5%) and females (59%) based on wsp gene. All Wolbachia strains identified in E. samsonowi were clustered among supergroups B of Wolbachia.
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Affiliation(s)
- Takwa Wannassi
- Department of Biological Sciences and Plant Protection, High Agronomic Institute of Chott-Mariem, University of Sousse, 4042, Sousse, Tunisia.
| | - Ahmed Sayadi
- Department of Biological Sciences and Plant Protection, High Agronomic Institute of Chott-Mariem, University of Sousse, 4042, Sousse, Tunisia
| | - Khaled Abbes
- Department of Biological Sciences and Plant Protection, High Agronomic Institute of Chott-Mariem, University of Sousse, 4042, Sousse, Tunisia
| | - Salma Djebbi
- Laboratory of Biochemistry and Biotechnology (LR01ES05), Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Chahnez Naccache
- Laboratory of Biochemistry and Biotechnology (LR01ES05), Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Maha Mezghani Khemakhem
- Laboratory of Biochemistry and Biotechnology (LR01ES05), Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Brahim Chermiti
- Department of Biological Sciences and Plant Protection, High Agronomic Institute of Chott-Mariem, University of Sousse, 4042, Sousse, Tunisia
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2
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Hamilton WC, Newton ILG. crANKing up the infection: ankyrin domains in Rickettsiales and their role in host manipulation. Infect Immun 2024:e0005924. [PMID: 39212405 DOI: 10.1128/iai.00059-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024] Open
Abstract
Intracellular bacteria use secreted effector proteins to modify host biology and facilitate infection. For many of these microbes, a particular eukaryotic domain-the ankyrin repeat (ANK)-plays a central role in specifying the host proteins and pathways targeted by the microbe. While we understand much of how some ANKs function in model organisms like Legionella and Coxiella, the understudied Rickettsiales species harbor many proteins with ANKs, some of which play critical roles during infection. This minireview is meant to organize and summarize the research progress made in understanding some of these Rickettsiales ANKs as well as document some of the techniques that have driven much of this progress.
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Affiliation(s)
| | - Irene L G Newton
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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3
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Kohnehrouz BB, Ehsasatvatan M. Redesigning amino/carboxyl ends of DARPin G3 for high thermostability and production in tobacco transplastomic plants. PLANT CELL REPORTS 2024; 43:210. [PMID: 39126530 DOI: 10.1007/s00299-024-03307-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 08/02/2024] [Indexed: 08/12/2024]
Abstract
KEY MESSAGE Redesigning the N- and C-capping repeats of the native DARPin G3 significantly improved its stability, and may facilitate its purification from the total soluble proteins of high-temperature dried leaf materials of transplastomic plants. Designed ankyrin repeat proteins (DARPins) constitute a promising class of binding molecules that can overcome the limitations of monoclonal antibodies and enable the development of novel therapeutic approaches. Despite their inherent stability, detailed studies have revealed that the original capping repeats derived from natural ankyrin repeat proteins impair the stability of the initial DARPin design. Consequently, the development of thermodynamically stabilized antibody mimetics may facilitate the development of innovative drugs in the future. In this study, we replaced the original N- and C-capping repeats with improved caps to enhance the thermostability of native DARPin G3. Computational analyses suggested that the redesigned thermostable DARPin G3 structure possessed optimal quality and stability. Molecular dynamics simulations verified the stability of the redesigned thermostable DARPin G3 at high temperatures. The redesigned thermostable DARPin G3 was expressed at high levels in tobacco transplastomic plants and subsequently purified from high-temperature dried leaf materials. Thermal denaturation results revealed that the redesigned thermostable DARPin G3 had a higher Tm value than the native DARPin G3, with a Tm of 35.51 °C greater than that of native DARPin G3. The results of the in vitro bioassays confirmed that the purified thermostable DARPin G3 from high-temperature dried leaf materials maintained its binding activity without any loss of affinity and specifically bound to the HER2 receptor on the cell surface. These findings demonstrate the successful improvement in the thermostability of DARPin G3 without compromising its biological activity.
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Affiliation(s)
- Bahram Baghban Kohnehrouz
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Tabriz, Tabriz, 51666, Iran.
| | - Maryam Ehsasatvatan
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Tabriz, Tabriz, 51666, Iran
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4
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Zhang J, Liu Q, Dai L, Zhang Z, Wang Y. Pan-Genome Analysis of Wolbachia, Endosymbiont of Diaphorina citri, Reveals Independent Origin in Asia and North America. Int J Mol Sci 2024; 25:4851. [PMID: 38732070 PMCID: PMC11084931 DOI: 10.3390/ijms25094851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 04/25/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024] Open
Abstract
Wolbachia, a group of Gram-negative symbiotic bacteria, infects nematodes and a wide range of arthropods. Diaphorina citri Kuwayama, the vector of Candidatus Liberibacter asiaticus (CLas) that causes citrus greening disease, is naturally infected with Wolbachia (wDi). However, the interaction between wDi and D. citri remains poorly understood. In this study, we performed a pan-genome analysis using 65 wDi genomes to gain a comprehensive understanding of wDi. Based on average nucleotide identity (ANI) analysis, we classified the wDi strains into Asia and North America strains. The ANI analysis, principal coordinates analysis (PCoA), and phylogenetic tree analysis supported that the D. citri in Florida did not originate from China. Furthermore, we found that a significant number of core genes were associated with metabolic pathways. Pathways such as thiamine metabolism, type I secretion system, biotin transport, and phospholipid transport were highly conserved across all analyzed wDi genomes. The variation analysis between Asia and North America wDi showed that there were 39,625 single-nucleotide polymorphisms (SNPs), 2153 indels, 10 inversions, 29 translocations, 65 duplications, 10 SV-based insertions, and 4 SV-based deletions. The SV-based insertions and deletions involved genes encoding transposase, phage tail tube protein, ankyrin repeat (ANK) protein, and group II intron-encoded protein. Pan-genome analysis of wDi contributes to our understanding of the geographical population of wDi, the origin of hosts of D. citri, and the interaction between wDi and its host, thus facilitating the development of strategies to control the insects and huanglongbing (HLB).
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Affiliation(s)
- Jiahui Zhang
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (Q.L.); (L.D.)
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Qian Liu
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (Q.L.); (L.D.)
| | - Liangying Dai
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (Q.L.); (L.D.)
| | - Zhijun Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yunsheng Wang
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (Q.L.); (L.D.)
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Wallace BA, Varona NS, Hesketh-Best PJ, Stiffler AK, Silveira CB. Globally distributed bacteriophage genomes reveal mechanisms of tripartite phage-bacteria-coral interactions. THE ISME JOURNAL 2024; 18:wrae132. [PMID: 39030686 PMCID: PMC11309003 DOI: 10.1093/ismejo/wrae132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 05/23/2024] [Accepted: 07/18/2024] [Indexed: 07/21/2024]
Abstract
Reef-building corals depend on an intricate community of microorganisms for functioning and resilience. The infection of coral-associated bacteria by bacteriophages can modify bacterial ecological interactions, yet very little is known about phage functions in the holobiont. This gap stems from methodological limitations that have prevented the recovery of high-quality viral genomes and bacterial host assignment from coral samples. Here, we introduce a size fractionation approach that increased bacterial and viral recovery in coral metagenomes by 9-fold and 2-fold, respectively, and enabled the assembly and binning of bacterial and viral genomes at relatively low sequencing coverage. We combined these viral genomes with those derived from 677 publicly available metagenomes, viromes, and bacterial isolates from stony corals to build a global coral virus database of over 20,000 viral genomic sequences spanning four viral realms. The tailed bacteriophage families Kyanoviridae and Autographiviridae were the most abundant, replacing groups formerly referred to as Myoviridae and Podoviridae, respectively. Prophage and CRISPR spacer linkages between these viruses and 626 bacterial metagenome-assembled genomes and bacterial isolates showed that most viruses infected Alphaproteobacteria, the most abundant class, and less abundant taxa like Halanaerobiia and Bacteroidia. A host-phage-gene network identified keystone viruses with the genomic capacity to modulate bacterial metabolic pathways and direct molecular interactions with eukaryotic cells. This study reveals the genomic basis of nested symbioses between bacteriophage, bacteria, and the coral host and its endosymbiotic algae.
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Affiliation(s)
- Bailey A Wallace
- Department of Biology, University of Miami, Coral Gables, FL 33146, United States
| | - Natascha S Varona
- Department of Biology, University of Miami, Coral Gables, FL 33146, United States
| | - Poppy J Hesketh-Best
- Department of Biology, University of Miami, Coral Gables, FL 33146, United States
- Department Veterinary Population Medicine, University of Minnesota, St. Paul, MN 55108, United States
| | - Alexandra K Stiffler
- Department of Biology, University of Miami, Coral Gables, FL 33146, United States
| | - Cynthia B Silveira
- Department of Biology, University of Miami, Coral Gables, FL 33146, United States
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL 33149, United States
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6
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Trouche B, Schrieke H, Duron O, Eren AM, Reveillaud J. Wolbachia populations across organs of individual Culex pipiens: highly conserved intra-individual core pangenome with inter-individual polymorphisms. ISME COMMUNICATIONS 2024; 4:ycae078. [PMID: 38915450 PMCID: PMC11195471 DOI: 10.1093/ismeco/ycae078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 04/26/2024] [Accepted: 06/06/2024] [Indexed: 06/26/2024]
Abstract
Wolbachia is a maternally inherited intracellular bacterium that infects a wide range of arthropods including mosquitoes. The endosymbiont is widely used in biocontrol strategies due to its capacity to modulate arthropod reproduction and limit pathogen transmission. Wolbachia infections in Culex spp. are generally assumed to be monoclonal but the potential presence of genetically distinct Wolbachia subpopulations within and between individual organs has not been investigated using whole genome sequencing. Here we reconstructed Wolbachia genomes from ovary and midgut metagenomes of single naturally infected Culex pipiens mosquitoes from Southern France to investigate patterns of intra- and inter-individual differences across mosquito organs. Our analyses revealed a remarkable degree of intra-individual conservancy among Wolbachia genomes from distinct organs of the same mosquito both at the level of gene presence-absence signal and single-nucleotide polymorphisms (SNPs). Yet, we identified several synonymous and non-synonymous substitutions between individuals, demonstrating the presence of some level of genomic heterogeneity among Wolbachia that infect the same C. pipiens field population. Overall, the absence of genetic heterogeneity within Wolbachia populations in a single individual confirms the presence of a dominant Wolbachia that is maintained under strong purifying forces of evolution.
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Affiliation(s)
- Blandine Trouche
- IRD, MIVEGEC, University of Montpellier, INRAE, CNRS, 34394 Montpellier, France
| | - Hans Schrieke
- IRD, MIVEGEC, University of Montpellier, INRAE, CNRS, 34394 Montpellier, France
| | - Olivier Duron
- IRD, MIVEGEC, University of Montpellier, INRAE, CNRS, 34394 Montpellier, France
| | - A Murat Eren
- Marine Biological Laboratory, Woods Hole, MA 02543, United States
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg, 26129 Oldenburg, Germany
| | - Julie Reveillaud
- IRD, MIVEGEC, University of Montpellier, INRAE, CNRS, 34394 Montpellier, France
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7
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Davison HR, Crozier J, Pirro S, Kampen H, Werner D, Hurst GDD. 'Candidatus Tisiphia' is a widespread Rickettsiaceae symbiont in the mosquito Anopheles plumbeus (Diptera: Culicidae). Environ Microbiol 2023; 25:3064-3074. [PMID: 37658745 PMCID: PMC10947512 DOI: 10.1111/1462-2920.16486] [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: 03/02/2023] [Accepted: 08/08/2023] [Indexed: 09/05/2023]
Abstract
Symbiotic bacteria can alter host biology by providing protection from natural enemies, or alter reproduction or vectoral competence. Symbiont-linked control of vector-borne disease in Anopheles has been hampered by a lack of symbioses that can establish stable vertical transmission in the host. Previous screening found the symbiont 'Candidatus Tisiphia' in Anopheles plumbeus, an aggressive biter and potential secondary vector of malaria parasites and West Nile virus. We screened samples collected over 10-years across Germany and used climate databases to assess environmental influence on incidence. We observed a 95% infection rate, and that the frequency of infection did not fluctuate with broad environmental factors. Maternal inheritance is indicated by presence in the ovaries through FISH microscopy. Finally, we assembled a high-quality 1.6 Mbp draft genome of 'Ca. Tisiphia' to explore its phylogeny and potential metabolic competence. The infection is closely related to strains found in Culicoides biting midges and shows similar patterns of metabolism, providing no evidence of the capacity to synthesize B-vitamins. This infection offers avenues for onward research in anopheline mosquito symbioses. Additionally, it provides future opportunity to study the impact of 'Ca. Tisiphia' on natural and transinfected hosts, especially in relation to reproductive fitness and vectorial competence and capacity.
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Affiliation(s)
- Helen R. Davison
- Institute of Infection, Veterinary and Ecological Sciences (IVES)University of LiverpoolLiverpoolUK
| | - Jessica Crozier
- Institute of Infection, Veterinary and Ecological Sciences (IVES)University of LiverpoolLiverpoolUK
| | | | - Helge Kampen
- Institute of Infectology (IMED)Friedrich‐Loeffler‐Institut, Federal Research Institute for Animal HealthGreifswaldIsle of RiemsGermany
| | - Doreen Werner
- Land Use and GovernanceLeibniz Centre for Agricultural Landscape Research (ZALF)MünchebergGermany
| | - Gregory D. D. Hurst
- Institute of Infection, Veterinary and Ecological Sciences (IVES)University of LiverpoolLiverpoolUK
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8
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Shikov AE, Savina IA, Nizhnikov AA, Antonets KS. Recombination in Bacterial Genomes: Evolutionary Trends. Toxins (Basel) 2023; 15:568. [PMID: 37755994 PMCID: PMC10534446 DOI: 10.3390/toxins15090568] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/02/2023] [Accepted: 09/07/2023] [Indexed: 09/28/2023] Open
Abstract
Bacterial organisms have undergone homologous recombination (HR) and horizontal gene transfer (HGT) multiple times during their history. These processes could increase fitness to new environments, cause specialization, the emergence of new species, and changes in virulence. Therefore, comprehensive knowledge of the impact and intensity of genetic exchanges and the location of recombination hotspots on the genome is necessary for understanding the dynamics of adaptation to various conditions. To this end, we aimed to characterize the functional impact and genomic context of computationally detected recombination events by analyzing genomic studies of any bacterial species, for which events have been detected in the last 30 years. Genomic loci where the transfer of DNA was detected pertained to mobile genetic elements (MGEs) housing genes that code for proteins engaged in distinct cellular processes, such as secretion systems, toxins, infection effectors, biosynthesis enzymes, etc. We found that all inferences fall into three main lifestyle categories, namely, ecological diversification, pathogenesis, and symbiosis. The latter primarily exhibits ancestral events, thus, possibly indicating that adaptation appears to be governed by similar recombination-dependent mechanisms.
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Affiliation(s)
- Anton E. Shikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (I.A.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
| | - Iuliia A. Savina
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (I.A.S.); (A.A.N.)
| | - Anton A. Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (I.A.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
| | - Kirill S. Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (I.A.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
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9
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Archer J, Hurst GDD, Hornett EA. Male-killer symbiont screening reveals novel associations in Adalia ladybirds. Access Microbiol 2023; 5:acmi000585.v3. [PMID: 37601442 PMCID: PMC10436010 DOI: 10.1099/acmi.0.000585.v3] [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: 02/15/2023] [Accepted: 05/18/2023] [Indexed: 08/22/2023] Open
Abstract
While male-killing bacteria are known to infect across arthropods, ladybird beetles represent a hotspot for these symbioses. In some host species, there are multiple different symbionts that vary in presence and frequency between populations. To further our understanding of spatial and frequency variation, we tested for the presence of three male-killing bacteria: Wolbachia , Rickettsia and Spiroplasma , in two Adalia ladybird species from a previously unexplored UK population. The two-spot ladybird, A. bipunctata, is known to harbour all three male-killers, and we identified Spiroplasma infection in the Merseyside population for the first time. However, in contrast to previous studies on two-spot ladybirds from continental Europe, evidence from egg-hatch rates indicates the Spiroplasma strain present in the Merseyside population does not cause embryonic male-killing. In the related ten-spot ladybird, A. decempunctata, there is only one previous record of a male-killing symbiont, a Rickettsia , which we did not detect in the Merseyside sample. However, PCR assays indicated the presence of a Spiroplasma in a single A. decempunctata specimen. Marker sequence indicated that this Spiroplasma was divergent from that found in sympatric A. bipunctata. Genome sequencing of the Spiroplasma -infected A. decempunctata additionally revealed the presence of cobionts in the form of a Centistes parasitoid wasp and the parasitic fungi Beauveria. Further study of A. decempunctata from this population is needed to resolve whether it is the ladybird or wasp cobiont that harbours Spiroplasma , and to establish the phenotype of this strain. These data indicate first that microbial symbiont phenotype should not be assumed from past studies conducted in different locations, and second that cobiont presence may confound screening studies aimed to detect the frequency of a symbiont in field collected material from a focal host species.
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Affiliation(s)
- Jack Archer
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Gregory D. D. Hurst
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Emily A. Hornett
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
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Feng H, Chen W, Hussain S, Shakir S, Tzin V, Adegbayi F, Ugine T, Fei Z, Jander G. Horizontally transferred genes as RNA interference targets for aphid and whitefly control. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:754-768. [PMID: 36577653 PMCID: PMC10037149 DOI: 10.1111/pbi.13992] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/14/2022] [Accepted: 12/22/2022] [Indexed: 06/01/2023]
Abstract
RNA interference (RNAi)-based technologies are starting to be commercialized as a new approach for agricultural pest control. Horizontally transferred genes (HTGs), which have been transferred into insect genomes from viruses, bacteria, fungi or plants, are attractive targets for RNAi-mediated pest control. HTGs are often unique to a specific insect family or even genus, making it unlikely that RNAi constructs targeting such genes will have negative effects on ladybugs, lacewings and other beneficial predatory insect species. In this study, we sequenced the genome of a red, tobacco-adapted isolate of Myzus persicae (green peach aphid) and bioinformatically identified 30 HTGs. We then used plant-mediated virus-induced gene silencing (VIGS) to show that several HTGs of bacterial and plant origin are important for aphid growth and/or survival. Silencing the expression of fungal-origin HTGs did not affect aphid survivorship but decreased aphid reproduction. Importantly, although there was uptake of plant-expressed RNA by Coccinella septempunctata (seven-spotted ladybugs) via the aphids that they consumed, we did not observe negative effects on ladybugs from aphid-targeted VIGS constructs. To demonstrate that this approach is more broadly applicable, we also targeted five Bemisia tabaci (whitefly) HTGs using VIGS and demonstrated that knockdown of some of these genes affected whitefly survival. As functional HTGs have been identified in the genomes of numerous pest species, we propose that these HTGs should be explored further as efficient and safe targets for control of insect pests using plant-mediated RNA interference.
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Affiliation(s)
| | - Wenbo Chen
- Boyce Thompson InstituteIthacaNYUSA
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative BiologyZhejiang UniversityHangzhouChina
| | - Sonia Hussain
- Boyce Thompson InstituteIthacaNYUSA
- Present address:
National Institute for Biotechnology and Genetic Engineering CollegePakistan Institute of Engineering and Applied SciencesFaisalabadPakistan
| | - Sara Shakir
- Boyce Thompson InstituteIthacaNYUSA
- Present address:
Gembloux Agro‐Bio Tech InstituteThe University of LiegeGemblouxBelgium
| | - Vered Tzin
- Boyce Thompson InstituteIthacaNYUSA
- Present address:
Jacob Blaustein Institutes for Desert ResearchBen‐Gurion University of the NegevSede BoqerIsrael
| | - Femi Adegbayi
- Boyce Thompson InstituteIthacaNYUSA
- Present address:
Drexel University College of MedicinePhiladelphiaPAUSA
| | - Todd Ugine
- Department of EntomologyCornell UniversityIthacaNYUSA
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11
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Halter T, Köstlbacher S, Rattei T, Hendrickx F, Manzano-Marín A, Horn M. One to host them all: genomics of the diverse bacterial endosymbionts of the spider Oedothorax gibbosus. Microb Genom 2023; 9:mgen000943. [PMID: 36757767 PMCID: PMC9997750 DOI: 10.1099/mgen.0.000943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 12/04/2022] [Indexed: 02/10/2023] Open
Abstract
Bacterial endosymbionts of the groups Wolbachia, Cardinium and Rickettsiaceae are well known for their diverse effects on their arthropod hosts, ranging from mutualistic relationships to reproductive phenotypes. Here, we analysed a unique system in which the dwarf spider Oedothorax gibbosus is co-infected with up to five different endosymbionts affiliated with Wolbachia, 'Candidatus Tisiphia' (formerly Torix group Rickettsia), Cardinium and Rhabdochlamydia. Using short-read genome sequencing data, we show that the endosymbionts are heterogeneously distributed among O. gibbosus populations and are frequently found co-infecting spider individuals. To study this intricate host-endosymbiont system on a genome-resolved level, we used long-read sequencing to reconstruct closed genomes of the Wolbachia, 'Ca. Tisiphia' and Cardinium endosymbionts. We provide insights into the ecology and evolution of the endosymbionts and shed light on the interactions with their spider host. We detected high quantities of transposable elements in all endosymbiont genomes and provide evidence that ancestors of the Cardinium, 'Ca. Tisiphia' and Wolbachia endosymbionts have co-infected the same hosts in the past. Our findings contribute to broadening our knowledge about endosymbionts infecting one of the largest animal phyla on Earth and show the usefulness of transposable elements as an evolutionary 'contact-tracing' tool.
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Affiliation(s)
- Tamara Halter
- Centre for Microbiology and Environmental Systems Science, University of Vienna. Djerassiplatz 1, 1030 Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna. Universitätsring 1, 1010 Vienna, Austria
| | - Stephan Köstlbacher
- Centre for Microbiology and Environmental Systems Science, University of Vienna. Djerassiplatz 1, 1030 Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna. Universitätsring 1, 1010 Vienna, Austria
- Current address: Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6700 EH Wageningen, The Netherlands
| | - Thomas Rattei
- Centre for Microbiology and Environmental Systems Science, University of Vienna. Djerassiplatz 1, 1030 Vienna, Austria
| | - Frederik Hendrickx
- OD Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences. Rue Vautier/Vautierstraat 29,, 1000 Brussels, Belgium
| | - Alejandro Manzano-Marín
- Centre for Microbiology and Environmental Systems Science, University of Vienna. Djerassiplatz 1, 1030 Vienna, Austria
| | - Matthias Horn
- Centre for Microbiology and Environmental Systems Science, University of Vienna. Djerassiplatz 1, 1030 Vienna, Austria
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Martinez J, Ross PA, Gu X, Ant TH, Murdochy SM, Tong L, da Silva Filipe A, Hoffmann AA, Sinkins SP. Genomic and Phenotypic Comparisons Reveal Distinct Variants of Wolbachia Strain wAlbB. Appl Environ Microbiol 2022; 88:e0141222. [PMID: 36318064 PMCID: PMC9680635 DOI: 10.1128/aem.01412-22] [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: 08/19/2022] [Accepted: 09/26/2022] [Indexed: 11/23/2022] Open
Abstract
The intracellular bacterium Wolbachia inhibits virus replication and is being harnessed around the world to fight mosquito-borne diseases through releases of mosquitoes carrying the symbiont. Wolbachia strains vary in their ability to invade mosquito populations and suppress viruses in part due to differences in their density within the insect and associated fitness costs. Using whole-genome sequencing, we demonstrate the existence of two variants in wAlbB, a Wolbachia strain being released in natural populations of Aedes aegypti mosquitoes. The two variants display striking differences in genome architecture and gene content. Differences in the presence/absence of 52 genes between variants include genes located in prophage regions and others potentially involved in controlling the symbiont's density. Importantly, we show that these genetic differences correlate with variation in wAlbB density and its tolerance to heat stress, suggesting that different wAlbB variants may be better suited for field deployment depending on local environmental conditions. Finally, we found that the wAlbB genome remained stable following its introduction in a Malaysian mosquito population. Our results highlight the need for further genomic and phenotypic characterization of Wolbachia strains in order to inform ongoing Wolbachia-based programs and improve the selection of optimal strains in future field interventions. IMPORTANCE Dengue is a viral disease transmitted by Aedes mosquitoes that threatens around half of the world population. Recent advances in dengue control involve the introduction of Wolbachia bacterial symbionts with antiviral properties into mosquito populations, which can lead to dramatic decreases in the incidence of the disease. In light of these promising results, there is a crucial need to better understand the factors affecting the success of such strategies, in particular the choice of Wolbachia strain for field releases and the potential for evolutionary changes. Here, we characterized two variants of a Wolbachia strain used for dengue control that differ at the genomic level and in their ability to replicate within the mosquito. We also found no evidence for the evolution of the symbiont within the 2 years following its deployment in Malaysia. Our results have implications for current and future Wolbachia-based health interventions.
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Affiliation(s)
- Julien Martinez
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Perran A. Ross
- Pest and Environmental Adaptation Research Group, Bio21 Institute, the University of Melbourne, Parkville, VIC, Australia
| | - Xinyue Gu
- Pest and Environmental Adaptation Research Group, Bio21 Institute, the University of Melbourne, Parkville, VIC, Australia
| | - Thomas H. Ant
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Shivan M. Murdochy
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Lily Tong
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Ana da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Ary A. Hoffmann
- Pest and Environmental Adaptation Research Group, Bio21 Institute, the University of Melbourne, Parkville, VIC, Australia
| | - Steven P. Sinkins
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
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Bordenstein SR, Bordenstein SR. Widespread phages of endosymbionts: Phage WO genomics and the proposed taxonomic classification of Symbioviridae. PLoS Genet 2022; 18:e1010227. [PMID: 35666732 PMCID: PMC9203015 DOI: 10.1371/journal.pgen.1010227] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 06/16/2022] [Accepted: 04/29/2022] [Indexed: 11/19/2022] Open
Abstract
Wolbachia are the most common obligate, intracellular bacteria in animals. They exist worldwide in arthropod and nematode hosts in which they commonly act as reproductive parasites or mutualists, respectively. Bacteriophage WO, the largest of Wolbachia’s mobile elements, includes reproductive parasitism genes, serves as a hotspot for genetic divergence and genomic rearrangement of the bacterial chromosome, and uniquely encodes a Eukaryotic Association Module with eukaryotic-like genes and an ensemble of putative host interaction genes. Despite WO’s relevance to genome evolution, selfish genetics, and symbiotic applications, relatively little is known about its origin, host range, diversification, and taxonomic classification. Here we analyze the most comprehensive set of 150 Wolbachia and phage WO assemblies to provide a framework for discretely organizing and naming integrated phage WO genomes. We demonstrate that WO is principally in arthropod Wolbachia with relatives in diverse endosymbionts and metagenomes, organized into four variants related by gene synteny, often oriented opposite the putative origin of replication in the Wolbachia chromosome, and the large serine recombinase is an ideal typing tool to distinguish the four variants. We identify a novel, putative lytic cassette and WO’s association with a conserved eleven gene island, termed Undecim Cluster, that is enriched with virulence-like genes. Finally, we evaluate WO-like Islands in the Wolbachia genome and discuss a new model in which Octomom, a notable WO-like Island, arose from a split with WO. Together, these findings establish the first comprehensive Linnaean taxonomic classification of endosymbiont phages, including non-Wolbachia phages from aquatic environments, that includes a new family and two new genera to capture the collective relatedness of these viruses.
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Affiliation(s)
- Sarah R. Bordenstein
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Microbiome Innovation Center, Vanderbilt University, Nashville, Tennessee, United States of America
- * E-mail:
| | - Seth R. Bordenstein
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Microbiome Innovation Center, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Institute of Infection, Immunology, and Inflammation, Vanderbilt University, Nashville, Tennessee, United States of America
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Temperature effects on cellular host-microbe interactions explain continent-wide endosymbiont prevalence. Curr Biol 2022; 32:878-888.e8. [PMID: 34919808 PMCID: PMC8891084 DOI: 10.1016/j.cub.2021.11.065] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 11/09/2021] [Accepted: 11/26/2021] [Indexed: 01/03/2023]
Abstract
Endosymbioses influence host physiology, reproduction, and fitness, but these relationships require efficient microbe transmission between host generations to persist. Maternally transmitted Wolbachia are the most common known endosymbionts,1 but their frequencies vary widely within and among host populations for unknown reasons.2,3 Here, we integrate genomic, cellular, and phenotypic analyses with mathematical models to provide an unexpectedly simple explanation for global wMel Wolbachia prevalence in Drosophila melanogaster. Cooling temperatures decrease wMel cellular abundance at a key stage of host oogenesis, producing temperature-dependent variation in maternal transmission that plausibly explains latitudinal clines of wMel frequencies on multiple continents. wMel sampled from a temperate climate targets the germline more efficiently in the cold than a recently differentiated tropical variant (∼2,200 years ago), indicative of rapid wMel adaptation to climate. Genomic analyses identify a very narrow list of wMel alleles-most notably, a derived stop codon in the major Wolbachia surface protein WspB-that underlie thermal sensitivity of cellular Wolbachia abundance and covary with temperature globally. Decoupling temperate wMel and host genomes further reduces transmission in the cold, a pattern that is characteristic of host-microbe co-adaptation to a temperate climate. Complex interactions among Wolbachia, hosts, and the environment (GxGxE) mediate wMel cellular abundance and maternal transmission, implicating temperature as a key determinant of Wolbachia spread and equilibrium frequencies, in conjunction with Wolbachia effects on host fitness and reproduction.4,5 Our results motivate the strategic use of locally selected wMel variants for Wolbachia-based biocontrol efforts, which protect millions of individuals from arboviruses that cause human disease.6.
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15
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Feng L, Xu L, Li X, Xue J, Li T, Duan X. A Combined Analysis of Transcriptome and Proteome Reveals the Inhibitory Mechanism of a Novel Oligosaccharide Ester against Penicillium italicum. J Fungi (Basel) 2022; 8:jof8020111. [PMID: 35205865 PMCID: PMC8877838 DOI: 10.3390/jof8020111] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/21/2022] [Accepted: 01/21/2022] [Indexed: 02/08/2023] Open
Abstract
Blue mold caused by Penicillium italicum is one of the most serious postharvest diseases of citrus fruit. The aim of this study was to investigate the inhibitory effect of a novel oligosaccharide ester, 6-O-β-L-mannopyranosyl-3-O-(2-methylbutanoyl)-4-O-(8-methyldecanoyl)-2-O-(4-methyl-hexanoyl) trehalose (MTE-1), against P. italicum. Scanning electron microscopy (SEM) and transmission electron microscopy (TEM), along with transcriptome and proteome analysis also, were conducted to illuminate the underlying mechanism. Results showed that MTE-1 significantly inhibited P. italicum growth in vitro in a dose-dependent manner. Moreover, MTE-1 suppressed the disease development of citrus fruit inoculated with P. italicum. Furthermore, ultrastructure observation, as well as transcriptome and proteome analysis, indicated that MTE-1 treatment damaged the cell wall and plasma membrane in spores and mycelia of P. italicum. In addition, MTE-1 regulated genes or proteins involved in primary metabolism, cell-wall metabolism, and pathogenicity. These results demonstrate that MTE-1 inhibited P. italicum by damaging cell walls and membranes and disrupting normal cellular metabolism. These findings contribute to the understanding of the possible molecular action of MTE-1. Finally, MTE-1 also provides a new natural strategy for controlling diseases in postharvest fruit.
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Affiliation(s)
- Linyan Feng
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (L.F.); (J.X.)
| | - Liangxiong Xu
- School of Life Sciences, Huizhou University, Huizhou 510607, China; (L.X.); (X.L.)
| | - Xiaojie Li
- School of Life Sciences, Huizhou University, Huizhou 510607, China; (L.X.); (X.L.)
| | - Jinghua Xue
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (L.F.); (J.X.)
| | - Taotao Li
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (L.F.); (J.X.)
- Correspondence: (T.L.); (X.D.)
| | - Xuewu Duan
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (L.F.); (J.X.)
- Agro-Food Science and Technology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
- Correspondence: (T.L.); (X.D.)
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16
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Erban T, Klimov PB, Harant K, Talacko P, Nesvorna M, Hubert J. Label-free proteomic analysis reveals differentially expressed Wolbachia proteins in Tyrophagus putrescentiae: Mite allergens and markers reflecting population-related proteome differences. J Proteomics 2021; 249:104356. [PMID: 34438106 DOI: 10.1016/j.jprot.2021.104356] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 08/12/2021] [Accepted: 08/19/2021] [Indexed: 12/21/2022]
Abstract
Tyrophagus putrescentiae is an astigmatid mite of great economic, medical and veterinary importance. The microbiome, especially intracellular bacteria, may affect allergy/allergen expression. We targeted Wolbachia proteins, allergen comparisons and markers in Wolbachia-mite interactions in three mite populations. A decoy database was constructed by proteogenomics using the T. putrescentiae draft genome, Wolbachia transcriptome assembly and current T. putrescentiae-related sequences in GenBank. Among thousands of mite-derived proteins, 18 Wolbachia proteins were reliably identified. We suggest that peroxiredoxin, bacterioferritin, ankyrin repeat domain-containing protein and DegQ family serine endoprotease indicate a higher-level bacterium-bacterium-host interaction. We produced evidence that the host-Wolbachia interaction is modulated through pattern recognition receptors (PRRs), mannose-binding lectins/mannose receptors, the cholinergic anti-inflammatory pathway with TNF-α, and others. We observed Tyr p 3 suppression in mites with Wolbachia, linking trypsin to PRR modulation. Nine out of the 12 current WHO/IUIS official allergens were reliably identified, but the remaining three allergens, Tyr p 1, 8 and 35, were detected as only trace hits. This study provides numerous markers for further Wolbachia-host interaction research. For accuracy, mite allergens should be considered according to abundance in species, but mite populations/strains, as well as their microbiome structure, may be key factors. SIGNIFICANCE: The astigmatid mites occurring in homes are significant producers of allergens that are highly dangerous to humans and domesticated animals. Mites are tightly associated with microorganisms that affect their biology and consequently allergy signatures. Mite populations were found to be infected with certain intracellular bacteria, but some populations lacked an intracellular bacterium. Our previous research showed that some populations of Tyrophagus putrescentiae are infected with Wolbachia, but some populations host additional bacteria of interest. Thus, there are not only interactions between the mites and Wolbachia but also likely an additional level of interaction that can be found in the interaction between different bacteria in the mites. These "higher-level" signatures and consequences that bacteria affect, including allergen production, are not understood in mites. In this study, we identified Wolbachia-specific proteins in mites for the first time. This study provides Wolbachia- and mite-derived markers that can be clues for describing "higher-level" mite-bacterium-bacterium interactions. Indeed, the microbiome contribution to allergies can potentially be derived directly from bacterial proteins, especially if they are abundant.
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Affiliation(s)
- Tomas Erban
- Crop Research Institute, Drnovska 507/73, Prague 6-Ruzyne CZ-16106, Czechia.
| | - Pavel B Klimov
- School of Natural Sciences, Bangor University, Bangor LL57 2 UW, UK; Institute of Biology, University of Tyumen, Pirogova 3, 625043 Tyumen, Russia
| | - Karel Harant
- Proteomics Core Facility, Faculty of Science, Charles University, BIOCEV, Prumyslova 595, Vestec CZ-25242, Czechia; Institute for Environmental Studies, Faculty of Science, Charles University, Benatska 2, Prague 2 CZ-128 01, Czechia
| | - Pavel Talacko
- Proteomics Core Facility, Faculty of Science, Charles University, BIOCEV, Prumyslova 595, Vestec CZ-25242, Czechia
| | - Marta Nesvorna
- Crop Research Institute, Drnovska 507/73, Prague 6-Ruzyne CZ-16106, Czechia
| | - Jan Hubert
- Crop Research Institute, Drnovska 507/73, Prague 6-Ruzyne CZ-16106, Czechia
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17
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Kupritz J, Martin J, Fischer K, Curtis KC, Fauver JR, Huang Y, Choi YJ, Beatty WL, Mitreva M, Fischer PU. Isolation and characterization of a novel bacteriophage WO from Allonemobius socius crickets in Missouri. PLoS One 2021; 16:e0250051. [PMID: 34197460 PMCID: PMC8248633 DOI: 10.1371/journal.pone.0250051] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 06/15/2021] [Indexed: 11/19/2022] Open
Abstract
Wolbachia are endosymbionts of numerous arthropod and some nematode species, are important for their development and if present can cause distinct phenotypes of their hosts. Prophage DNA has been frequently detected in Wolbachia, but particles of Wolbachia bacteriophages (phage WO) have been only occasionally isolated. Here, we report the characterization and isolation of a phage WO of the southern ground cricket, Allonemobius socius, and provided the first whole-genome sequence of phage WO from this arthropod family outside of Asia. We screened A. socius abdomen DNA extracts from a cricket population in eastern Missouri by quantitative PCR for Wolbachia surface protein and phage WO capsid protein and found a prevalence of 55% and 50%, respectively, with many crickets positive for both. Immunohistochemistry using antibodies against Wolbachia surface protein showed many Wolbachia clusters in the reproductive system of female crickets. Whole-genome sequencing using Oxford Nanopore MinION and Illumina technology allowed for the assembly of a high-quality, 55 kb phage genome containing 63 open reading frames (ORF) encoding for phage WO structural proteins and host lysis and transcriptional manipulation. Taxonomically important regions of the assembled phage genome were validated by Sanger sequencing of PCR amplicons. Analysis of the nucleotides sequences of the ORFs encoding the large terminase subunit (ORF2) and minor capsid (ORF7) frequently used for phage WO phylogenetics showed highest homology to phage WOAu of Drosophila simulans (94.46% identity) and WOCin2USA1 of the cherry fruit fly, Rhagoletis cingulata (99.33% identity), respectively. Transmission electron microscopy examination of cricket ovaries showed a high density of phage particles within Wolbachia cells. Isolation of phage WO revealed particles characterized by 40–62 nm diameter heads and up to 190 nm long tails. This study provides the first detailed description and genomic characterization of phage WO from North America that is easily accessible in a widely distributed cricket species.
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Affiliation(s)
- Jonah Kupritz
- Infectious Disease Division, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - John Martin
- Infectious Disease Division, Washington University School of Medicine, St. Louis, Missouri, United States of America
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Kerstin Fischer
- Infectious Disease Division, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Kurt C. Curtis
- Infectious Disease Division, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Joseph R. Fauver
- Infectious Disease Division, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Yuefang Huang
- Infectious Disease Division, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Young-Jun Choi
- Infectious Disease Division, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Wandy L. Beatty
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Makedonka Mitreva
- Infectious Disease Division, Washington University School of Medicine, St. Louis, Missouri, United States of America
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Peter U. Fischer
- Infectious Disease Division, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
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18
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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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19
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Genome Features of Asaia sp. W12 Isolated from the Mosquito Anopheles stephensi Reveal Symbiotic Traits. Genes (Basel) 2021; 12:genes12050752. [PMID: 34067621 PMCID: PMC8156966 DOI: 10.3390/genes12050752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 05/04/2021] [Accepted: 05/06/2021] [Indexed: 01/29/2023] Open
Abstract
Asaia bacteria commonly comprise part of the microbiome of many mosquito species in the genera Anopheles and Aedes, including important vectors of infectious agents. Their close association with multiple organs and tissues of their mosquito hosts enhances the potential for paratransgenesis for the delivery of antimalaria or antivirus effectors. The molecular mechanisms involved in the interactions between Asaia and mosquito hosts, as well as Asaia and other bacterial members of the mosquito microbiome, remain underexplored. Here, we determined the genome sequence of Asaia strain W12 isolated from Anopheles stephensi mosquitoes, compared it to other Asaia species associated with plants or insects, and investigated the properties of the bacteria relevant to their symbiosis with mosquitoes. The assembled genome of strain W12 had a size of 3.94 MB, the largest among Asaia spp. studied so far. At least 3585 coding sequences were predicted. Insect-associated Asaia carried more glycoside hydrolase (GH)-encoding genes than those isolated from plants, showing their high plant biomass-degrading capacity in the insect gut. W12 had the most predicted regulatory protein components comparatively among the selected Asaia, indicating its capacity to adapt to frequent environmental changes in the mosquito gut. Two complete operons encoding cytochrome bo3-type ubiquinol terminal oxidases (cyoABCD-1 and cyoABCD-2) were found in most Asaia genomes, possibly offering alternative terminal oxidases and allowing the flexible transition of respiratory pathways. Genes involved in the production of 2,3-butandiol and inositol have been found in Asaia sp. W12, possibly contributing to biofilm formation and stress tolerance.
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20
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Transmission of the wMel Wolbachia strain is modulated by its titre and by immune genes in Drosophila melanogaster (Wolbachia density and transmission). J Invertebr Pathol 2021; 181:107591. [PMID: 33882275 DOI: 10.1016/j.jip.2021.107591] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/21/2021] [Accepted: 03/25/2021] [Indexed: 11/21/2022]
Abstract
Wolbachia are common intracellular endosymbionts of arthropods, but the interactions between Wolbachia and arthropods are only partially understood. The fruit fly Drosophila melanogaster is a model insect for understanding Wolbachia-host interactions. Here the native wMel strain of D. melanogaster was isolated and then different initial titres of wMel were artificially transferred back into antibiotics-treated fruit flies. Our purpose was to examine the interactions between the injected wMel in a density gradient and the recipient host during trans-generational transmission. The results showed that the trans-generational transmission rates of wMel and titres of wMel exhibited a fluctuating trend over nine generations, and the titres of wMel displayed a similar fluctuating trans-generational trend. There was a significant positive correlation between the transmission rate and the titre of wMel. Reciprocal crossings between wMel-transinfected and uninfected fruit flies revealed that wMel could induce cytoplasmic incompatibility (CI) at different initial titres, but the intensity of CI was not significantly correlated with the initial titre of wMel. Quantitative PCR analysis showed that the immune genes Drsl5 and Spn38F displayed a significant transcriptional response to wMel transfection, with an obvious negative correlation with the titre of wMel at the 3rd and 4th generations. Furthermore, RNA interference-mediated knockdown of Drsl5 and Spn38F elicited a drastic increase in the titre of wMel. In combination, our study suggests that the trans-generational transmission of wMel is modulated by its density, and the immune genes are involved in the regulation of Wolbachia density.
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21
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Lefoulon E, Clark T, Guerrero R, Cañizales I, Cardenas-Callirgos JM, Junker K, Vallarino-Lhermitte N, Makepeace BL, Darby AC, Foster JM, Martin C, Slatko BE. Diminutive, degraded but dissimilar: Wolbachia genomes from filarial nematodes do not conform to a single paradigm. Microb Genom 2020; 6:mgen000487. [PMID: 33295865 PMCID: PMC8116671 DOI: 10.1099/mgen.0.000487] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/14/2020] [Indexed: 01/13/2023] Open
Abstract
Wolbachia are alpha-proteobacteria symbionts infecting a large range of arthropod species and two different families of nematodes. Interestingly, these endosymbionts are able to induce diverse phenotypes in their hosts: they are reproductive parasites within many arthropods, nutritional mutualists within some insects and obligate mutualists within their filarial nematode hosts. Defining Wolbachia 'species' is controversial and so they are commonly classified into 17 different phylogenetic lineages, termed supergroups, named A-F, H-Q and S. However, available genomic data remain limited and not representative of the full Wolbachia diversity; indeed, of the 24 complete genomes and 55 draft genomes of Wolbachia available to date, 84 % belong to supergroups A and B, exclusively composed of Wolbachia from arthropods. For the current study, we took advantage of a recently developed DNA-enrichment method to produce four complete genomes and two draft genomes of Wolbachia from filarial nematodes. Two complete genomes, wCtub and wDcau, are the smallest Wolbachia genomes sequenced to date (863 988 bp and 863 427 bp, respectively), as well as the first genomes representing supergroup J. These genomes confirm the validity of this supergroup, a controversial clade due to weaknesses of the multilocus sequence typing approach. We also produced the first draft Wolbachia genome from a supergroup F filarial nematode representative (wMhie), two genomes from supergroup D (wLsig and wLbra) and the complete genome of wDimm from supergroup C. Our new data confirm the paradigm of smaller Wolbachia genomes from filarial nematodes containing low levels of transposable elements and the absence of intact bacteriophage sequences, unlike many Wolbachia from arthropods, where both are more abundant. However, we observe differences among the Wolbachia genomes from filarial nematodes: no global co-evolutionary pattern, strong synteny between supergroup C and supergroup J Wolbachia, and more transposable elements observed in supergroup D Wolbachia compared to the other supergroups. Metabolic pathway analysis indicates several highly conserved pathways (haem and nucleotide biosynthesis, for example) as opposed to more variable pathways, such as vitamin B biosynthesis, which might be specific to certain host-symbiont associations. Overall, there appears to be no single Wolbachia-filarial nematode pattern of co-evolution or symbiotic relationship.
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Affiliation(s)
- Emilie Lefoulon
- Molecular Parasitology Group, New England Biolabs, Ipswich, MA, USA
- Present address: School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, USA
| | - Travis Clark
- Molecular Parasitology Group, New England Biolabs, Ipswich, MA, USA
| | - Ricardo Guerrero
- Instituto de Zoología y Ecología Tropical, Universidad Central de Venezuela, Caracas, Venezuela
| | - Israel Cañizales
- Instituto de Zoología y Ecología Tropical, Universidad Central de Venezuela, Caracas, Venezuela
- Ediciones La Fauna KPT SL, Madrid, Spain
| | - Jorge Manuel Cardenas-Callirgos
- Neotropical Parasitology Research Network - NEOPARNET, Asociación Peruana de Helmintología e Invertebrados Afines – APHIA, Peru
| | - Kerstin Junker
- Epidemiology, Parasites and Vectors, ARC-Onderstepoort Veterinary Institute, Onderstepoort 0110, South Africa
| | - Nathaly Vallarino-Lhermitte
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR7245), Muséum National d’Histoire Naturelle, CNRS, Paris, France
| | - Benjamin L. Makepeace
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Alistair C. Darby
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Jeremy M. Foster
- Molecular Parasitology Group, New England Biolabs, Ipswich, MA, USA
| | - Coralie Martin
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR7245), Muséum National d’Histoire Naturelle, CNRS, Paris, France
| | - Barton E. Slatko
- Molecular Parasitology Group, New England Biolabs, Ipswich, MA, USA
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Debarba JA, Sehabiague MPC, Monteiro KM, Gerber AL, Vasconcelos ATR, Ferreira HB, Zaha A. Transcriptomic Analysis of the Early Strobilar Development of Echinococcus granulosus. Pathogens 2020; 9:E465. [PMID: 32545493 PMCID: PMC7350322 DOI: 10.3390/pathogens9060465] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/07/2020] [Accepted: 06/10/2020] [Indexed: 11/29/2022] Open
Abstract
Echinococcus granulosus has a complex life cycle involving two mammalian hosts. The transition from one host to another is accompanied by changes in gene expression, and the transcriptional events that underlie this transition have not yet been fully characterized. In this study, RNA-seq was used to compare the transcription profiles of samples from E. granulosus protoscoleces induced in vitro to strobilar development at three time points. We identified 818 differentially expressed genes, which were divided into eight expression clusters formed over the entire 24 h period. An enrichment of gene transcripts with molecular functions of signal transduction, enzymes, and protein modifications was observed upon induction and developmental progression. This transcriptomic study provides insights for understanding the complex life cycle of E. granulosus and contributes for searching for the key genes correlating with the strobilar development, which can be used to identify potential candidates for the development of anthelmintic drugs.
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Affiliation(s)
- João Antonio Debarba
- Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil; (J.A.D.); (M.P.C.S.); (K.M.M.); (H.B.F.)
- Laboratório de Biologia Molecular de Cestódeos, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil
| | - Martín Pablo Cancela Sehabiague
- Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil; (J.A.D.); (M.P.C.S.); (K.M.M.); (H.B.F.)
- Laboratório de Biologia Molecular de Cestódeos, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil
| | - Karina Mariante Monteiro
- Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil; (J.A.D.); (M.P.C.S.); (K.M.M.); (H.B.F.)
- Laboratório de Biologia Molecular de Cestódeos, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil
| | - Alexandra Lehmkuhl Gerber
- Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro 25651-075, Brazil; (A.L.G.); (A.T.R.V.)
| | | | - Henrique Bunselmeyer Ferreira
- Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil; (J.A.D.); (M.P.C.S.); (K.M.M.); (H.B.F.)
- Laboratório de Biologia Molecular de Cestódeos, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil
| | - Arnaldo Zaha
- Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil; (J.A.D.); (M.P.C.S.); (K.M.M.); (H.B.F.)
- Laboratório de Biologia Molecular de Cestódeos, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil
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Wolbachia Endosymbiont of the Horn Fly (Haematobia irritans irritans): a Supergroup A Strain with Multiple Horizontally Acquired Cytoplasmic Incompatibility Genes. Appl Environ Microbiol 2020; 86:AEM.02589-19. [PMID: 31900308 DOI: 10.1128/aem.02589-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 12/20/2019] [Indexed: 11/20/2022] Open
Abstract
The horn fly, Haematobia irritans irritans, is a hematophagous parasite of livestock distributed throughout Europe, Africa, Asia, and the Americas. Welfare losses on livestock due to horn fly infestation are estimated to cost between $1 billion and $2.5 billion (U.S. dollars) annually in North America and Brazil. The endosymbiotic bacterium Wolbachia pipientis is a maternally inherited manipulator of reproductive biology in arthropods and naturally infects laboratory colonies of horn flies from Kerrville, TX, and Alberta, Canada, but it has also been identified in wild-caught samples from Canada, the United States, Mexico, and Hungary. Reassembly of PacBio long-read and Illumina genomic DNA libraries from the Kerrville H. i. irritans genome project allowed for a complete and circularized 1.3-Mb Wolbachia genome (wIrr). Annotation of wIrr yielded 1,249 coding genes, 34 tRNAs, 3 rRNAs, and 5 prophage regions. Comparative genomics and whole-genome Bayesian evolutionary analysis of wIrr compared to published Wolbachia genomes suggested that wIrr is most closely related to and diverged from Wolbachia supergroup A strains known to infect Drosophila spp. Whole-genome synteny analyses between wIrr and closely related genomes indicated that wIrr has undergone significant genome rearrangements while maintaining high nucleotide identity. Comparative analysis of the cytoplasmic incompatibility (CI) genes of wIrr suggested two phylogenetically distinct CI loci and acquisition of another cifB homolog from phylogenetically distant supergroup A Wolbachia strains, suggesting horizontal acquisition of these loci. The wIrr genome provides a resource for future examination of the impact Wolbachia may have in both biocontrol and potential insecticide resistance of horn flies.IMPORTANCE Horn flies, Haematobia irritans irritans, are obligate hematophagous parasites of cattle having significant effects on production and animal welfare. Control of horn flies mainly relies on the use of insecticides, but issues with resistance have increased interest in development of alternative means of control. Wolbachia pipientis is an endosymbiont bacterium known to have a range of effects on host reproduction, such as induction of cytoplasmic incompatibility, feminization, male killing, and also impacts vector transmission. These characteristics of Wolbachia have been exploited in biological control approaches for a range of insect pests. Here we report the assembly and annotation of the circular genome of the Wolbachia strain of the Kerrville, TX, horn fly (wIrr). Annotation of wIrr suggests its unique features, including the horizontal acquisition of additional transcriptionally active cytoplasmic incompatibility loci. This study provides the foundation for future studies of Wolbachia-induced biological effects for control of horn flies.
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Transgenic Testing Does Not Support a Role for Additional Candidate Genes in Wolbachia Male Killing or Cytoplasmic Incompatibility. mSystems 2020; 5:5/1/e00658-19. [PMID: 31937677 PMCID: PMC6967388 DOI: 10.1128/msystems.00658-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Wolbachia are widespread bacterial endosymbionts that manipulate the reproduction of diverse arthropods to spread through a population and can substantially shape host evolution. Recently, reports identified three prophage WO genes (wmk, cifA, and cifB) that transgenically recapitulate many aspects of reproductive manipulation in Drosophila melanogaster. Here, we transgenically tested 10 additional gene candidates for CI and/or male killing in flies. The results yield no evidence for the involvement of these gene candidates in reproductive parasitism, bolstering the evidence for identification of the cif and wmk genes as the major factors involved in their phenotypes. In addition, evidence supports new hypotheses for prediction of male-killing phenotypes or lack thereof based on wmk transcript length and copy number. These experiments inform efforts to understand the full basis of reproductive parasitism for basic and applied purposes and lay the foundation for future work on the function of an interesting group of Wolbachia and phage WO genes. Endosymbiotic bacteria in the genus Wolbachia remarkably infect nearly half of all arthropod species. They spread in part because of manipulations of host sexual reproduction that enhance the maternal transmission of the bacteria, including male killing (death of infected males) and unidirectional cytoplasmic incompatibility (CI; death of offspring from infected fathers and uninfected mothers). Recent discoveries identified several genes in prophage WO of Wolbachia (wmk, cifA, and cifB) that fully or partially recapitulate male killing or CI when transgenically expressed in Drosophila melanogaster. However, it is not yet fully resolved if other gene candidates contribute to these phenotypes. Here, we transgenically tested 10 additional gene candidates for their involvement in male killing and/or CI. The results show that despite sequence and protein architecture similarities or comparative associations with reproductive parasitism, transgenic expression of the candidates does not recapitulate male killing or CI. Sequence analysis across Wmk and its closest relatives reveals amino acids that may be important to its function. In addition, evidence is presented to propose new hypotheses regarding the relationship between wmk transcript length and its ability to kill a given host, as well as copy number of wmk homologs within a bacterial strain, which may be predictive of host resistance. Together, these analyses continue to build the evidence for identification of wmk, cifA, and cifB as the major genes that have thus far been shown to cause reproductive parasitism in Wolbachia, and the transgenic resources provide a basis for further functional study of phage WO genes. IMPORTANCEWolbachia are widespread bacterial endosymbionts that manipulate the reproduction of diverse arthropods to spread through a population and can substantially shape host evolution. Recently, reports identified three prophage WO genes (wmk, cifA, and cifB) that transgenically recapitulate many aspects of reproductive manipulation in Drosophila melanogaster. Here, we transgenically tested 10 additional gene candidates for CI and/or male killing in flies. The results yield no evidence for the involvement of these gene candidates in reproductive parasitism, bolstering the evidence for identification of the cif and wmk genes as the major factors involved in their phenotypes. In addition, evidence supports new hypotheses for prediction of male-killing phenotypes or lack thereof based on wmk transcript length and copy number. These experiments inform efforts to understand the full basis of reproductive parasitism for basic and applied purposes and lay the foundation for future work on the function of an interesting group of Wolbachia and phage WO genes.
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Abstract
Bacteria participate in a wide diversity of symbiotic associations with eukaryotic hosts that require precise interactions for bacterial recognition and persistence. Most commonly, host-associated bacteria interfere with host gene expression to modulate the immune response to the infection. However, many of these bacteria also interfere with host cellular differentiation pathways to create a hospitable niche, resulting in the formation of novel cell types, tissues, and organs. In both of these situations, bacterial symbionts must interact with eukaryotic regulatory pathways. Here, we detail what is known about how bacterial symbionts, from pathogens to mutualists, control host cellular differentiation across the central dogma, from epigenetic chromatin modifications, to transcription and mRNA processing, to translation and protein modifications. We identify four main trends from this survey. First, mechanisms for controlling host gene expression appear to evolve from symbionts co-opting cross-talk between host signaling pathways. Second, symbiont regulatory capacity is constrained by the processes that drive reductive genome evolution in host-associated bacteria. Third, the regulatory mechanisms symbionts exhibit correlate with the cost/benefit nature of the association. And, fourth, symbiont mechanisms for interacting with host genetic regulatory elements are not bound by native bacterial capabilities. Using this knowledge, we explore how the ubiquitous intracellular Wolbachia symbiont of arthropods and nematodes may modulate host cellular differentiation to manipulate host reproduction. Our survey of the literature on how infection alters gene expression in Wolbachia and its hosts revealed that, despite their intermediate-sized genomes, different strains appear capable of a wide diversity of regulatory manipulations. Given this and Wolbachia's diversity of phenotypes and eukaryotic-like proteins, we expect that many symbiont-induced host differentiation mechanisms will be discovered in this system.
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Affiliation(s)
- Shelbi L Russell
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA.
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26
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Frank AC. Molecular host mimicry and manipulation in bacterial symbionts. FEMS Microbiol Lett 2019; 366:5342066. [PMID: 30877310 DOI: 10.1093/femsle/fnz038] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 02/18/2019] [Indexed: 12/17/2022] Open
Abstract
It is common among intracellular bacterial pathogens to use eukaryotic-like proteins that mimic and manipulate host cellular processes to promote colonization and intracellular survival. Eukaryotic-like proteins are bacterial proteins with domains that are rare in bacteria, and known to function in the context of a eukaryotic cell. Such proteins can originate through horizontal gene transfer from eukaryotes or, in the case of simple repeat proteins, through convergent evolution. Recent studies of microbiomes associated with several eukaryotic hosts suggest that similar molecular strategies are deployed by cooperative bacteria that interact closely with eukaryotic cells. Some mimics, like ankyrin repeats, leucine rich repeats and tetratricopeptide repeats are shared across diverse symbiotic systems ranging from amoebae to plants, and may have originated early, or evolved independently in multiple systems. Others, like plant-mimicking domains in members of the plant microbiome are likely to be more recent innovations resulting from horizontal gene transfer from the host, or from microbial eukaryotes occupying the same host. Host protein mimics have only been described in a limited set of symbiotic systems, but are likely to be more widespread. Systematic searches for eukaryote-like proteins in symbiont genomes could lead to the discovery of novel mechanisms underlying host-symbiont interactions.
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Affiliation(s)
- A Carolin Frank
- Life and Environmental Sciences, 5200 North Lake Rd, University of California Merced, Merced, CA 95343, USA.,Sierra Nevada Research Institute, School of Natural Sciences, 5200 North Lake Rd, University of California Merced, Merced, CA 95343, USA
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27
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Tolley SJA, Nonacs P, Sapountzis P. Wolbachia Horizontal Transmission Events in Ants: What Do We Know and What Can We Learn? Front Microbiol 2019; 10:296. [PMID: 30894837 PMCID: PMC6414450 DOI: 10.3389/fmicb.2019.00296] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 02/04/2019] [Indexed: 11/17/2022] Open
Abstract
While strict vertical transmission insures the durability of intracellular symbioses, phylogenetic incongruences between hosts and endosymbionts suggest horizontal transmission must also occur. These horizontal acquisitions can have important implications for the biology of the host. Wolbachia is one of the most ecologically successful prokaryotes in arthropods, infecting an estimated 50–70% of all insect species. Much of this success is likely due to the fact that, in arthropods, Wolbachia is notorious for manipulating host reproduction to favor transmission through the female germline. However, its natural potential for horizontal transmission remains poorly understood. Here we evaluate the fundamental prerequisites for successful horizontal transfer, including necessary environmental conditions, genetic potential of bacterial strains, and means of mediating transfers. Furthermore, we revisit the relatedness of Wolbachia strains infecting the Panamanian leaf-cutting ant, Acromyrmex echinatior, and its inquiline social parasite, Acromyrmex insinuator, and compare our results to a study published more than 15 years ago by Van Borm et al. (2003). The results of this pilot study prompt us to reevaluate previous notions that obligate social parasitism reliably facilitates horizontal transfer and suggest that not all Wolbachia strains associated with ants have the same genetic potential for horizontal transmission.
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Affiliation(s)
- Sarah J A Tolley
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Peter Nonacs
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States
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28
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Genome organisation and comparative genomics of four novel Wolbachia genome assemblies from Indian Drosophila host. Funct Integr Genomics 2019; 19:617-632. [PMID: 30798391 DOI: 10.1007/s10142-019-00664-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Revised: 11/12/2018] [Accepted: 02/04/2019] [Indexed: 10/27/2022]
Abstract
Wolbachia has long been known to share an endosymbiotic relationship with its host as an obligate intracellular organism. Wolbachia diversity as different supergroups is found to be host-specific in most cases except a few, where the host species is seen to accommodate multiple strains. Besides, the Wolbachia genome must have undergone several changes in response to the evolving host genome in order to adapt and establish a strong association with its host, thus making a distinctive Wolbachia-host alliance. The present study focusses on four novel genome assembly and genome-wide sequence variations of Indian Wolbachia strains, i.e. wMel and wRi isolated from two different Drosophila hosts. The genome assembly has an average size of ~ 1.1 Mb and contains ~ 1100 genes, which is comparable with the previously sequenced Wolbachia genomes. The comparative genomics analysis of these genomes and sequence-wide comparison of some functionally significant genes, i.e. ankyrin repeats, Wsp and T4SS, highlight their sequence similarities and dissimilarities, further supporting the strain-specific association of Wolbachia to its host. Interestingly, some of the sequence variations are also found to be restricted to only Indian Wolbachia strains. Further analysis of prophage and their flanking regions in the Wolbachia genome reveals the presence of several functional genes which may assist the phage to reside inside the bacterial host, thus providing a trade-off for the endosymbiont-host association. Understanding this endosymbiont genome in different eco-geographical conditions has become imperative for the recent use of Wolbachia in medical entomology as a vector-control agent.
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Siozios S, Pilgrim J, Darby AC, Baylis M, Hurst GD. The draft genome of strain cCpun from biting midges confirms insect Cardinium are not a monophyletic group and reveals a novel gene family expansion in a symbiont. PeerJ 2019; 7:e6448. [PMID: 30809447 PMCID: PMC6387759 DOI: 10.7717/peerj.6448] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 01/15/2019] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND It is estimated that 13% of arthropod species carry the heritable symbiont Cardinium hertigii. 16S rRNA and gyrB sequence divides this species into at least four groups (A-D), with the A group infecting a range of arthropods, the B group infecting nematode worms, the C group infecting Culicoides biting midges, and the D group associated with the marine copepod Nitocra spinipes. To date, genome sequence has only been available for strains from groups A and B, impeding general understanding of the evolutionary history of the radiation. We present a draft genome sequence for a C group Cardinium, motivated both by the paucity of genomic information outside of the A and B group, and the importance of Culicoides biting midge hosts as arbovirus vectors. METHODS We reconstructed the genome of cCpun, a Cardinium strain from group C that naturally infects Culicoides punctatus, through Illumina sequencing of infected host specimens. RESULTS The draft genome presented has high completeness, with BUSCO scores comparable to closed group A Cardinium genomes. Phylogenomic analysis based on concatenated single copy core proteins do not support Cardinium from arthropod hosts as a monophyletic group, with nematode Cardinium strains nested within the two groups infecting arthropod hosts. Analysis of the genome of cCpun revealed expansion of a variety of gene families classically considered important in symbiosis (e.g., ankyrin domain containing genes), and one set-characterized by DUF1703 domains-not previously associated with symbiotic lifestyle. This protein group encodes putative secreted nucleases, and the cCpun genome carried at least 25 widely divergent paralogs, 24 of which shared a common ancestor in the C group. The genome revealed no evidence in support of B vitamin provisioning to its haematophagous host, and indeed suggests Cardinium may be a net importer of biotin. DISCUSSION These data indicate strains of Cardinium within nematodes cluster within Cardinium strains found in insects. The draft genome of cCpun further produces new hypotheses as to the interaction of the symbiont with the midge host, in particular the biological role of DUF1703 nuclease proteins that are predicted as being secreted by cCpun. In contrast, the coding content of this genome provides no support for a role for the symbiont in provisioning the host with B vitamins.
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Affiliation(s)
- Stefanos Siozios
- Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Jack Pilgrim
- Institute of Infection and Global Health, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Alistair C. Darby
- Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Matthew Baylis
- Institute of Infection and Global Health, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections (HPRU-EZI), University of Liverpool, Liverpool, UK
| | - Gregory D.D. Hurst
- Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
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Kampfraath AA, Klasson L, Anvar SY, Vossen RHAM, Roelofs D, Kraaijeveld K, Ellers J. Genome expansion of an obligate parthenogenesis-associated Wolbachia poses an exception to the symbiont reduction model. BMC Genomics 2019; 20:106. [PMID: 30727958 PMCID: PMC6364476 DOI: 10.1186/s12864-019-5492-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 01/29/2019] [Indexed: 12/11/2022] Open
Abstract
Background Theory predicts that dependency within host-endosymbiont interactions results in endosymbiont genome size reduction. Unexpectedly, the largest Wolbachia genome was found in the obligate, parthenogenesis-associated wFol. In this study, we investigate possible processes underlying this genome expansion by comparing a re-annotated wFol genome to other Wolbachia genomes. In addition, we also search for candidate genes related to parthenogenesis induction (PI). Results Within wFol, we found five phage WO regions representing 25.4% of the complete genome, few pseudogenized genes, and an expansion of DNA-repair genes in comparison to other Wolbachia. These signs of genome conservation were mirrored in the wFol host, the springtail F. candida, which also had an expanded DNA-repair gene family and many horizontally transferred genes. Across all Wolbachia genomes, there was a strong correlation between gene numbers of Wolbachia strains and their hosts. In order to identify genes with a potential link to PI, we assembled the genome of an additional PI strain, wLcla. Comparisons between four PI Wolbachia, including wFol and wLcla, and fourteen non-PI Wolbachia yielded a small set of potential candidate genes for further investigation. Conclusions The strong similarities in genome content of wFol and its host, as well as the correlation between host and Wolbachia gene numbers suggest that there may be some form of convergent evolution between endosymbiont and host genomes. If such convergent evolution would be strong enough to overcome the evolutionary forces causing genome reduction, it would enable expanded genomes within long-term obligate endosymbionts. Electronic supplementary material The online version of this article (10.1186/s12864-019-5492-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- A A Kampfraath
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
| | - L Klasson
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - S Y Anvar
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.,Leiden Genome Technology Center, Leiden University Medical Center, Leiden, The Netherlands
| | - R H A M Vossen
- Leiden Genome Technology Center, Leiden University Medical Center, Leiden, The Netherlands
| | - D Roelofs
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - K Kraaijeveld
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - J Ellers
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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31
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Abstract
Several lineages of symbiotic bacteria in insects selfishly manipulate host reproduction to spread in a population 1 , often by distorting host sex ratios. Spiroplasma poulsonii2,3 is a helical and motile, Gram-positive symbiotic bacterium that resides in a wide range of Drosophila species 4 . A notable feature of S. poulsonii is male killing, whereby the sons of infected female hosts are selectively killed during development1,2. Although male killing caused by S. poulsonii has been studied since the 1950s, its underlying mechanism is unknown. Here we identify an S. poulsonii protein, designated Spaid, whose expression induces male killing. Overexpression of Spaid in D. melanogaster kills males but not females, and induces massive apoptosis and neural defects, recapitulating the pathology observed in S. poulsonii-infected male embryos5-11. Our data suggest that Spaid targets the dosage compensation machinery on the male X chromosome to mediate its effects. Spaid contains ankyrin repeats and a deubiquitinase domain, which are required for its subcellular localization and activity. Moreover, we found a laboratory mutant strain of S. poulsonii with reduced male-killing ability and a large deletion in the spaid locus. Our study has uncovered a bacterial protein that affects host cellular machinery in a sex-specific way, which is likely to be the long-searched-for factor responsible for S. poulsonii-induced male killing.
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In Vitro Culture of the Insect Endosymbiont Spiroplasma poulsonii Highlights Bacterial Genes Involved in Host-Symbiont Interaction. mBio 2018; 9:mBio.00024-18. [PMID: 29559567 PMCID: PMC5874924 DOI: 10.1128/mbio.00024-18] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Endosymbiotic bacteria associated with eukaryotic hosts are omnipresent in nature, particularly in insects. Studying the bacterial side of host-symbiont interactions is, however, often limited by the unculturability and genetic intractability of the symbionts. Spiroplasma poulsonii is a maternally transmitted bacterial endosymbiont that is naturally associated with several Drosophila species. S. poulsonii strongly affects its host’s physiology, for example by causing male killing or by protecting it against various parasites. Despite intense work on this model since the 1950s, attempts to cultivate endosymbiotic Spiroplasma in vitro have failed so far. Here, we developed a method to sustain the in vitro culture of S. poulsonii by optimizing a commercially accessible medium. We also provide a complete genome assembly, including the first sequence of a natural plasmid of an endosymbiotic Spiroplasma species. Last, by comparing the transcriptome of the in vitro culture to the transcriptome of bacteria extracted from the host, we identified genes putatively involved in host-symbiont interactions. This work provides new opportunities to study the physiology of endosymbiotic Spiroplasma and paves the way to dissect insect-endosymbiont interactions with two genetically tractable partners. The discovery of insect bacterial endosymbionts (maternally transmitted bacteria) has revolutionized the study of insects, suggesting novel strategies for their control. Most endosymbionts are strongly dependent on their host to survive, making them uncultivable in artificial systems and genetically intractable. Spiroplasma poulsonii is an endosymbiont of Drosophila that affects host metabolism, reproduction, and defense against parasites. By providing the first reliable culture medium that allows a long-lasting in vitro culture of Spiroplasma and by elucidating its complete genome, this work lays the foundation for the development of genetic engineering tools to dissect endosymbiosis with two partners amenable to molecular study. Furthermore, the optimization method that we describe can be used on other yet uncultivable symbionts, opening new technical opportunities in the field of host-microbes interactions.
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Bonneau M, Atyame C, Beji M, Justy F, Cohen-Gonsaud M, Sicard M, Weill M. Culex pipiens crossing type diversity is governed by an amplified and polymorphic operon of Wolbachia. Nat Commun 2018; 9:319. [PMID: 29358578 PMCID: PMC5778026 DOI: 10.1038/s41467-017-02749-w] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 12/21/2017] [Indexed: 12/17/2022] Open
Abstract
Culex pipiens mosquitoes are infected with Wolbachia (wPip) that cause an important diversity of cytoplasmic incompatibilities (CIs). Functional transgenic studies have implicated the cidA-cidB operon from wPip and its homolog in wMel in CI between infected Drosophila males and uninfected females. However, the genetic basis of the CI diversity induced by different Wolbachia strains was unknown. We show here that the remarkable diversity of CI in the C. pipiens complex is due to the presence, in all tested wPip genomes, of several copies of the cidA-cidB operon, which undergoes diversification through recombination events. In 183 isofemale lines of C. pipiens collected worldwide, specific variations of the cidA-cidB gene repertoires are found to match crossing types. The diversification of cidA-cidB is consistent with the hypothesis of a toxin–antitoxin system in which the gene cidB co-diversifies with the gene cidA, particularly in putative domains of reciprocal interactions. Wolbachia causes cytoplasmic incompatibility (CI) between mosquitoes infected with different strains, but the genetic basis of observed CI diversity is unknown. Here, Bonneau et al. sequence Wolbachia from over 100 Culex pipiens lines and show that crossing types match variations of the toxin-antitoxin cidA-cidB genes.
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Affiliation(s)
- Manon Bonneau
- Institut des Sciences de l'Evolution de Montpellier (ISEM), UMR CNRS-IRD-EPHE-Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, France
| | - Celestine Atyame
- Institut des Sciences de l'Evolution de Montpellier (ISEM), UMR CNRS-IRD-EPHE-Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, France.,Processus Infectieux en Milieu Insulaire Tropical (PIMIT), UMR CNRS-INSERM-IRD-Université de La Réunion, Sainte-Clotilde, Ile de La Réunion, 97490, France
| | - Marwa Beji
- Institut Pasteur Tunis, Laboratory of Epidemiology and Veterinary Microbiology, University of Tunis El Manar, 1068, Tunis, Tunisia
| | - Fabienne Justy
- Institut des Sciences de l'Evolution de Montpellier (ISEM), UMR CNRS-IRD-EPHE-Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, France
| | - Martin Cohen-Gonsaud
- Centre de Biochimie Structurale (CBS), UMR CNRS-INSERM-Université de Montpellier, 29 rue de Navacelles, 34090, Montpellier, France
| | - Mathieu Sicard
- Institut des Sciences de l'Evolution de Montpellier (ISEM), UMR CNRS-IRD-EPHE-Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, France.
| | - Mylène Weill
- Institut des Sciences de l'Evolution de Montpellier (ISEM), UMR CNRS-IRD-EPHE-Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, France.
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Shukla A, Chatterjee A, Kondabagil K. The number of genes encoding repeat domain-containing proteins positively correlates with genome size in amoebal giant viruses. Virus Evol 2018; 4:vex039. [PMID: 29308275 PMCID: PMC5753266 DOI: 10.1093/ve/vex039] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Curiously, in viruses, the virion volume appears to be predominantly driven by genome length rather than the number of proteins it encodes or geometric constraints. With their large genome and giant particle size, amoebal viruses (AVs) are ideally suited to study the relationship between genome and virion size and explore the role of genome plasticity in their evolutionary success. Different genomic regions of AVs exhibit distinct genealogies. Although the vertically transferred core genes and their functions are universally conserved across the nucleocytoplasmic large DNA virus (NCLDV) families and are essential for their replication, the horizontally acquired genes are variable across families and are lineage-specific. When compared with other giant virus families, we observed a near–linear increase in the number of genes encoding repeat domain-containing proteins (RDCPs) with the increase in the genome size of AVs. From what is known about the functions of RDCPs in bacteria and eukaryotes and their prevalence in the AV genomes, we envisage important roles for RDCPs in the life cycle of AVs, their genome expansion, and plasticity. This observation also supports the evolution of AVs from a smaller viral ancestor by the acquisition of diverse gene families from the environment including RDCPs that might have helped in host adaption.
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Affiliation(s)
- Avi Shukla
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076, India
| | - Anirvan Chatterjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076, India
| | - Kiran Kondabagil
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076, India
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Rice DW, Sheehan KB, Newton ILG. Large-Scale Identification of Wolbachia pipientis Effectors. Genome Biol Evol 2017; 9:1925-1937. [PMID: 28854601 PMCID: PMC5544941 DOI: 10.1093/gbe/evx139] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2017] [Indexed: 12/13/2022] Open
Abstract
Wolbachia pipientis is an intracellular symbiont of arthropods well known for the reproductive manipulations induced in the host and, more recently, for the ability of Wolbachia to block virus replication in insect vectors. Since Wolbachia cannot yet be genetically manipulated, and due to the constraints imposed when working with an intracellular symbiont, little is known about mechanisms used by Wolbachia for host interaction. Here we employed a bioinformatics pipeline and identified 163 candidate effectors, potentially secreted by Wolbachia into the host cell. A total of 84 of these candidates were then subjected to a screen of growth defects induced in yeast upon heterologous expression which identified 14 top candidates likely secreted by Wolbachia. These predicted secreted effectors may function in concert as we find that their native expression is correlated and is highly upregulated at specific time points during Drosophila development. In addition, the evolutionary histories of some of these predicted effectors are also correlated, suggesting they may function together, or in the same pathway, during host infection. Similarly, most of these predicted effectors are limited to one or two Wolbachia strains—perhaps reflecting shared evolutionary history and strain specific functions in host manipulation. Identification of these Wolbachia candidate effectors is the first step in dissecting the mechanisms of symbiont–host interaction in this important system.
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Affiliation(s)
- Danny W Rice
- Department of Biology, Indiana University, Bloomington
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Bleidorn C, Gerth M. A critical re-evaluation of multilocus sequence typing (MLST) efforts in Wolbachia. FEMS Microbiol Ecol 2017; 94:4654844. [DOI: 10.1093/femsec/fix163] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 11/22/2017] [Indexed: 01/10/2023] Open
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Islam Z, Nagampalli RSK, Fatima MT, Ashraf GM. New paradigm in ankyrin repeats: Beyond protein-protein interaction module. Int J Biol Macromol 2017; 109:1164-1173. [PMID: 29157912 DOI: 10.1016/j.ijbiomac.2017.11.101] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 11/13/2017] [Accepted: 11/16/2017] [Indexed: 01/06/2023]
Abstract
Classically, ankyrin repeat (ANK) proteins are built from tandems of two or more repeats and form curved solenoid structures that are associated with protein-protein interactions. These are short, widespread structural motif of around 33 amino acids repeats in tandem, having a canonical helix-loop-helix fold, found individually or in combination with other domains. The multiplicity of structural pattern enables it to form assemblies of diverse sizes, required for their abilities to confer multiple binding and structural roles of proteins. Three-dimensional structures of these repeats determined to date reveal a degree of structural variability that translates into the considerable functional versatility of this protein superfamily. Recent work on the ANK has proposed novel structural information, especially protein-lipid, protein-sugar and protein-protein interaction. Self-assembly of these repeats was also shown to prevent the associated protein in forming filaments. In this review, we summarize the latest findings and how the new structural information has increased our understanding of the structural determinants of ANK proteins. We discussed latest findings on how these proteins participate in various interactions to diversify the ANK roles in numerous biological processes, and explored the emerging and evolving field of designer ankyrins and its framework for protein engineering emphasizing on biotechnological applications.
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Affiliation(s)
- Zeyaul Islam
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, 13083-100, Brazil.
| | | | - Munazza Tamkeen Fatima
- Department of Biochemistry and Tissue Biology, Institute of Biology, State University of Campinas (UNICAMP), Campinas, SP, 13083-862, Brazil
| | - Ghulam Md Ashraf
- King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah, 21589, Saudi Arabia.
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Kaur R, Siozios S, Miller WJ, Rota-Stabelli O. Insertion sequence polymorphism and genomic rearrangements uncover hidden Wolbachia diversity in Drosophila suzukii and D. subpulchrella. Sci Rep 2017; 7:14815. [PMID: 29093474 PMCID: PMC5665950 DOI: 10.1038/s41598-017-13808-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 10/03/2017] [Indexed: 11/09/2022] Open
Abstract
Ability to distinguish between closely related Wolbachia strains is crucial for understanding the evolution of Wolbachia-host interactions and the diversity of Wolbachia-induced phenotypes. A useful model to tackle these issues is the Drosophila suzukii - Wolbachia association. D. suzukii, a destructive insect pest, harbor a non-CI inducing Wolbachia 'wSuz' closely related to the strong CI-inducing wRi strain. Multi locus sequence typing (MLST) suggests presence of genetic homogeneity across wSuz strains infecting European and American D. suzukii populations, although different Wolbachia infection frequencies and host fecundity levels have been observed in both populations. Currently, it is not clear if these differences are due to cryptic wSuz polymorphism, host background, geographical factors or a combination of all of them. Here, we have identified geographical diversity in wSuz in D. suzukii populations from different continents using a highly diagnostic set of markers based on insertion sequence (IS) site polymorphism and genomic rearrangements (GR). We further identified inter-strain diversity between Wolbachia infecting D. suzukii and its sister species D. subpulchrella (wSpc). Based on our results, we speculate that discernible wSuz variants may associate with different observed host phenotypes, a hypothesis that demands future investigation. More generally, our results demonstrate the utility of IS and GRs in discriminating closely related Wolbachia strains.
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Affiliation(s)
- Rupinder Kaur
- Department of Sustainable Agro-Ecosystems and Bioresources, Fondazione Edmund Mach, San Michele all'Adige, Italy
- Centre of Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Stefanos Siozios
- Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Wolfgang J Miller
- Centre of Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Omar Rota-Stabelli
- Department of Sustainable Agro-Ecosystems and Bioresources, Fondazione Edmund Mach, San Michele all'Adige, Italy.
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Bhattacharya T, Newton ILG. Mi Casa es Su Casa: how an intracellular symbiont manipulates host biology. Environ Microbiol 2017; 21:10.1111/1462-2920.13964. [PMID: 29076641 PMCID: PMC5924462 DOI: 10.1111/1462-2920.13964] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 10/16/2017] [Accepted: 10/19/2017] [Indexed: 12/17/2022]
Abstract
Wolbachia pipientis, the most common intracellular infection on the planet, infects 40% of insects as well as nematodes, isopods and arachnids. Wolbachia are obligately intracellular and challenging to study; there are no genetic tools for manipulating Wolbachia nor can they be cultured outside of host cells. Despite these roadblocks, the research community has defined a set of Wolbachia loci involved in host interaction: Wolbachia effectors. Through the use of Drosophila genetics, surrogate systems and biochemistry, the field has begun to define the toolkit Wolbachia use for host manipulation. Below we review recent findings identifying these Wolbachia effectors and point to potential, as yet uncharacterized, links between known phenotypes induced by Wolbachia infection and predicted effectors.
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Affiliation(s)
| | - Irene L G Newton
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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Signor S. Population genomics of Wolbachia and mtDNA in Drosophila simulans from California. Sci Rep 2017; 7:13369. [PMID: 29042606 PMCID: PMC5645465 DOI: 10.1038/s41598-017-13901-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 10/02/2017] [Indexed: 12/21/2022] Open
Abstract
Wolbachia pipientis is an intracellular endosymbiont infecting many arthropods and filarial nematodes. Little is known about the short-term evolution of Wolbachia or its interaction with its host. Wolbachia is maternally inherited, resulting in co-inheritance of mitochondrial organelles such as mtDNA. Here I explore the evolution of Wolbachia, and the relationship between Wolbachia and mtDNA, using a large inbred panel of Drosophila simulans. I compare this to the only other large population genomic Wolbachia dataset from D. melanogaster. I find reduced diversity relative to expectation in both Wolbachia and mtDNA, but only mtDNA shows evidence of a recent selective sweep or population bottleneck. I estimate Wolbachia and mtDNA titre in each genotype, and I find considerable variation in both phenotypes, despite low genetic diversity in Wolbachia and mtDNA. A phylogeny of Wolbachia and of mtDNA suggest a recent origin of the infection derived from a single origin. Using Wolbachia and mtDNA titre as a phenotype, I perform the first association analysis using this phenotype with the nuclear genome and find several implicated regions, including one which contains four CAAX-box protein processing genes. CAAX-box protein processing can be an important part of host-pathogen interactions in other systems, suggesting interesting directions for future research.
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Affiliation(s)
- Sarah Signor
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA.
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Genomes of Candidatus Wolbachia bourtzisii wDacA and Candidatus Wolbachia pipientis wDacB from the Cochineal Insect Dactylopius coccus (Hemiptera: Dactylopiidae). G3-GENES GENOMES GENETICS 2016; 6:3343-3349. [PMID: 27543297 PMCID: PMC5068953 DOI: 10.1534/g3.116.031237] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dactylopius species, known as cochineal insects, are the source of the carminic acid dye used worldwide. The presence of two Wolbachia strains in Dactylopius coccus from Mexico was revealed by PCR amplification of wsp and sequencing of 16S rRNA genes. A metagenome analysis recovered the genome sequences of Candidatus Wolbachia bourtzisii wDacA (supergroup A) and Candidatus Wolbachia pipientis wDacB (supergroup B). Genome read coverage, as well as 16S rRNA clone sequencing, revealed that wDacB was more abundant than wDacA. The strains shared similar predicted metabolic capabilities that are common to Wolbachia, including riboflavin, ubiquinone, and heme biosynthesis, but lacked other vitamin and cofactor biosynthesis as well as glycolysis, the oxidative pentose phosphate pathway, and sugar uptake systems. A complete tricarboxylic acid cycle and gluconeogenesis were predicted as well as limited amino acid biosynthesis. Uptake and catabolism of proline were evidenced in Dactylopius Wolbachia strains. Both strains possessed WO-like phage regions and type I and type IV secretion systems. Several efflux systems found suggested the existence of metal toxicity within their host. Besides already described putative virulence factors like ankyrin domain proteins, VlrC homologs, and patatin-like proteins, putative novel virulence factors related to those found in intracellular pathogens like Legionella and Mycobacterium are highlighted for the first time in Wolbachia. Candidate genes identified in other Wolbachia that are likely involved in cytoplasmic incompatibility were found in wDacB but not in wDacA.
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Brown AMV, Wasala SK, Howe DK, Peetz AB, Zasada IA, Denver DR. Genomic evidence for plant-parasitic nematodes as the earliest Wolbachia hosts. Sci Rep 2016; 6:34955. [PMID: 27734894 PMCID: PMC5062116 DOI: 10.1038/srep34955] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 09/21/2016] [Indexed: 12/31/2022] Open
Abstract
Wolbachia, one of the most widespread endosymbionts, is a target for biological control of mosquito-borne diseases (malaria and dengue virus), and antibiotic elimination of infectious filarial nematodes. We sequenced and analyzed the genome of a new Wolbachia strain (wPpe) in the plant-parasitic nematode Pratylenchus penetrans. Phylogenomic analyses placed wPpe as the earliest diverging Wolbachia, suggesting two evolutionary invasions into nematodes. The next branches comprised strains in sap-feeding insects, suggesting Wolbachia may have first evolved as a nutritional mutualist. Genome size, protein content, %GC, and repetitive DNA allied wPpe with mutualistic Wolbachia, whereas gene repertoire analyses placed it between parasite (A, B) and mutualist (C, D, F) groups. Conservation of iron metabolism genes across Wolbachia suggests iron homeostasis as a potential factor in its success. This study enhances our understanding of this globally pandemic endosymbiont, highlighting genetic patterns associated with host changes. Combined with future work on this strain, these genomic data could help provide potential new targets for plant-parasitic nematode control.
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Affiliation(s)
- Amanda M V Brown
- Department of Integrative Biology, 3029 Cordley Hall, Oregon State University, Corvallis, OR 97331 USA
| | - Sulochana K Wasala
- Department of Integrative Biology, 3029 Cordley Hall, Oregon State University, Corvallis, OR 97331 USA
| | - Dana K Howe
- Department of Integrative Biology, 3029 Cordley Hall, Oregon State University, Corvallis, OR 97331 USA
| | - Amy B Peetz
- USDA-ARS Horticultural Crops Research Laboratory, 3420 NW Orchard Avenue, Corvallis, OR 97330, USA
| | - Inga A Zasada
- USDA-ARS Horticultural Crops Research Laboratory, 3420 NW Orchard Avenue, Corvallis, OR 97330, USA
| | - Dee R Denver
- Department of Integrative Biology, 3029 Cordley Hall, Oregon State University, Corvallis, OR 97331 USA
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Reynolds D, Thomas T. Evolution and function of eukaryotic-like proteins from sponge symbionts. Mol Ecol 2016; 25:5242-5253. [PMID: 27543954 DOI: 10.1111/mec.13812] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 08/08/2016] [Accepted: 08/18/2016] [Indexed: 12/25/2022]
Abstract
Sponges (Porifera) are ancient metazoans that harbour diverse microorganisms, whose symbiotic interactions are essential for the host's health and function. Although symbiosis between bacteria and sponges are ubiquitous, the molecular mechanisms that control these associations are largely unknown. Recent (meta-) genomic analyses discovered an abundance of genes encoding for eukaryotic-like proteins (ELPs) in bacterial symbionts from different sponge species. ELPs belonging to the ankyrin repeat (AR) class from a bacterial symbiont of the sponge Cymbastela concentrica were subsequently found to modulate amoebal phagocytosis. This might be a molecular mechanism, by which symbionts can control their interaction with the sponge. In this study, we investigated the evolution and function of ELPs from other classes and from symbionts found in other sponges to better understand the importance of ELPs for bacteria-eukaryote interactions. Phylogenetic analyses showed that all of the nine ELPs investigated were most closely related to proteins found either in eukaryotes or in bacteria that can live in association with eukaryotes. ELPs were then recombinantly expressed in Escherichia coli and exposed to the amoeba Acanthamoeba castellanii, which is functionally analogous to phagocytic cells in sponges. Phagocytosis assays with E. coli containing three ELP classes (AR, TPR-SEL1 and NHL) showed a significantly higher percentage of amoeba containing bacteria and average number of intracellular bacteria per amoeba when compared to negative controls. The result that various classes of ELPs found in symbionts of different sponges can modulate phagocytosis indicates that they have a broader function in mediating bacteria-sponge interactions.
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Affiliation(s)
- David Reynolds
- Centre for Marine Bio-Innovation and School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Torsten Thomas
- Centre for Marine Bio-Innovation and School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia.
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Sun B, Li T, Xiao J, Liu L, Zhang P, Murphy RW, He S, Huang D. Contribution of Multiple Inter-Kingdom Horizontal Gene Transfers to Evolution and Adaptation of Amphibian-Killing Chytrid, Batrachochytrium dendrobatidis. Front Microbiol 2016; 7:1360. [PMID: 27630622 PMCID: PMC5005798 DOI: 10.3389/fmicb.2016.01360] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 08/17/2016] [Indexed: 01/30/2023] Open
Abstract
Amphibian populations are experiencing catastrophic declines driven by the fungal pathogen Batrachochytrium dendrobatidis (Bd). Although horizontal gene transfer (HGT) facilitates the evolution and adaptation in many fungi by conferring novel function genes to the recipient fungi, inter-kingdom HGT in Bd remains largely unexplored. In this study, our investigation detects 19 bacterial genes transferred to Bd, including metallo-beta-lactamase and arsenate reductase that play important roles in the resistance to antibiotics and arsenates. Moreover, three probable HGT gene families in Bd are from plants and one gene family coding the ankyrin repeat-containing protein appears to come from oomycetes. The observed multi-copy gene families associated with HGT are probably due to the independent transfer events or gene duplications. Five HGT genes with extracellular locations may relate to infection, and some other genes may participate in a variety of metabolic pathways, and in doing so add important metabolic traits to the recipient. The evolutionary analysis indicates that all the transferred genes evolved under purifying selection, suggesting that their functions in Bd are similar to those of the donors. Collectively, our results indicate that HGT from diverse donors may be an important evolutionary driver of Bd, and improve its adaptations for infecting and colonizing host amphibians.
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Affiliation(s)
- Baofa Sun
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of SciencesBeijing, China; CAS Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of SciencesBeijing, China
| | - Tong Li
- Key Laboratory of Crop Pests Control of Henan Province, Institute of Plant Protection, Henan Academy of Agricultural Sciences Zhengzhou, China
| | - Jinhua Xiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences Beijing, China
| | - Li Liu
- Network & Information Center, Institute of Microbiology, Chinese Academy of Sciences Beijing, China
| | - Peng Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences Beijing, China
| | - Robert W Murphy
- Department of Natural History, Royal Ontario Museum Toronto, ON, Canada
| | - Shunmin He
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences Beijing, China
| | - Dawei Huang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of SciencesBeijing, China; Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural UniversityTai'an, China
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Abstract
Wolbachia is an intracellular symbiont of invertebrates responsible for inducing a wide variety of phenotypes in its host. These host-Wolbachia relationships span the continuum from reproductive parasitism to obligate mutualism, and provide a unique system to study genomic changes associated with the evolution of symbiosis. We present the genome sequence from a parthenogenesis-inducing Wolbachia strain (wTpre) infecting the minute parasitoid wasp Trichogramma pretiosum. The wTpre genome is the most complete parthenogenesis-inducing Wolbachia genome available to date. We used comparative genomics across 16 Wolbachia strains, representing five supergroups, to identify a core Wolbachia genome of 496 sets of orthologous genes. Only 14 of these sets are unique to Wolbachia when compared to other bacteria from the Rickettsiales. We show that the B supergroup of Wolbachia, of which wTpre is a member, contains a significantly higher number of ankyrin repeat-containing genes than other supergroups. In the wTpre genome, there is evidence for truncation of the protein coding sequences in 20% of ORFs, mostly as a result of frameshift mutations. The wTpre strain represents a conversion from cytoplasmic incompatibility to a parthenogenesis-inducing lifestyle, and is required for reproduction in the Trichogramma host it infects. We hypothesize that the large number of coding frame truncations has accompanied the change in reproductive mode of the wTpre strain.
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Qi W, Vaughan L, Katharios P, Schlapbach R, Seth-Smith HMB. Host-Associated Genomic Features of the Novel Uncultured Intracellular Pathogen Ca. Ichthyocystis Revealed by Direct Sequencing of Epitheliocysts. Genome Biol Evol 2016; 8:1672-89. [PMID: 27190004 PMCID: PMC4943182 DOI: 10.1093/gbe/evw111] [Citation(s) in RCA: 12] [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] [Accepted: 05/05/2016] [Indexed: 12/24/2022] Open
Abstract
Advances in single-cell and mini-metagenome sequencing have enabled important investigations into uncultured bacteria. In this study, we applied the mini-metagenome sequencing method to assemble genome drafts of the uncultured causative agents of epitheliocystis, an emerging infectious disease in the Mediterranean aquaculture species gilthead seabream. We sequenced multiple cyst samples and constructed 11 genome drafts from a novel beta-proteobacterial lineage, Candidatus Ichthyocystis. The draft genomes demonstrate features typical of pathogenic bacteria with an obligate intracellular lifestyle: a reduced genome of up to 2.6 Mb, reduced G + C content, and reduced metabolic capacity. Reconstruction of metabolic pathways reveals that Ca Ichthyocystis genomes lack all amino acid synthesis pathways, compelling them to scavenge from the fish host. All genomes encode type II, III, and IV secretion systems, a large repertoire of predicted effectors, and a type IV pilus. These are all considered to be virulence factors, required for adherence, invasion, and host manipulation. However, no evidence of lipopolysaccharide synthesis could be found. Beyond the core functions shared within the genus, alignments showed distinction into different species, characterized by alternative large gene families. These comprise up to a third of each genome, appear to have arisen through duplication and diversification, encode many effector proteins, and are seemingly critical for virulence. Thus, Ca Ichthyocystis represents a novel obligatory intracellular pathogenic beta-proteobacterial lineage. The methods used: mini-metagenome analysis and manual annotation, have generated important insights into the lifestyle and evolution of the novel, uncultured pathogens, elucidating many putative virulence factors including an unprecedented array of novel gene families.
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Affiliation(s)
- Weihong Qi
- Functional Genomics Center Zurich, University of Zurich, Switzerland
| | - Lloyd Vaughan
- Vetsuisse Faculty, Institute for Veterinary Pathology, University of Zurich, Switzerland
| | - Pantelis Katharios
- Hellenic Center for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Heraklion, Greece
| | - Ralph Schlapbach
- Functional Genomics Center Zurich, University of Zurich, Switzerland
| | - Helena M B Seth-Smith
- Functional Genomics Center Zurich, University of Zurich, Switzerland Vetsuisse Faculty, Institute for Veterinary Pathology, University of Zurich, Switzerland
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Newton ILG, Clark ME, Kent BN, Bordenstein SR, Qu J, Richards S, Kelkar YD, Werren JH. Comparative Genomics of Two Closely Related Wolbachia with Different Reproductive Effects on Hosts. Genome Biol Evol 2016; 8:1526-42. [PMID: 27189996 PMCID: PMC4898810 DOI: 10.1093/gbe/evw096] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Wolbachia pipientis are obligate intracellular bacteria commonly found in many arthropods. They can induce various reproductive alterations in hosts, including cytoplasmic incompatibility, male-killing, feminization, and parthenogenetic development, and can provide host protection against some viruses and other pathogens. Wolbachia differ from many other primary endosymbionts in arthropods because they undergo frequent horizontal transmission between hosts and are well known for an abundance of mobile elements and relatively high recombination rates. Here, we compare the genomes of two closely related Wolbachia (with 0.57% genome-wide synonymous divergence) that differ in their reproductive effects on hosts. wVitA induces a sperm-egg incompatibility (also known as cytoplasmic incompatibility) in the parasitoid insect Nasonia vitripennis, whereas wUni causes parthenogenetic development in a different parasitoid, Muscidifurax uniraptor Although these bacteria are closely related, the genomic comparison reveals rampant rearrangements, protein truncations (particularly in proteins predicted to be secreted), and elevated substitution rates. These changes occur predominantly in the wUni lineage, and may be due in part to adaptations by wUni to a new host environment, or its phenotypic shift to parthenogenesis induction. However, we conclude that the approximately 8-fold elevated synonymous substitution rate in wUni is due to a either an elevated mutation rate or a greater number of generations per year in wUni, which occurs in semitropical host species. We identify a set of genes whose loss or pseudogenization in the wUni lineage implicates them in the phenotypic shift from cytoplasmic incompatibility to parthenogenesis induction. Finally, comparison of these closely related strains allows us to determine the fine-scale mutation patterns in Wolbachia Although Wolbachia are AT rich, mutation probabilities estimated from 4-fold degenerate sites are not AT biased, and predict an equilibrium AT content much less biased than observed (57-50% AT predicted vs. 76% current content at degenerate sites genome wide). The contrast suggests selection for increased AT content within Wolbachia genomes.
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Affiliation(s)
| | | | - Bethany N Kent
- Department of Biological Sciences, Vanderbilt University
| | - Seth R Bordenstein
- Department of Biological Sciences, Vanderbilt University Department of Pathology, Microbiology and Immunology, Vanderbilt University
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Yogeshwar D Kelkar
- Department of Biostatistics and Computational Biology, University of Rochester
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Longevity-modulating effects of symbiosis: insights from Drosophila–Wolbachia interaction. Biogerontology 2016; 17:785-803. [DOI: 10.1007/s10522-016-9653-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Accepted: 05/18/2016] [Indexed: 01/30/2023]
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Sun JX, Guo Y, Zhang X, Zhu WC, Chen YT, Hong XY. Effects of host interaction withWolbachiaon cytoplasmic incompatibility in the two-spotted spider miteTetranychus urticae. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12804] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Jian-Xin Sun
- Department of Entomology; Nanjing Agricultural University; No.1, Weigang Nanjing Jiangsu 210095 China
| | - Yan Guo
- Department of Entomology; Nanjing Agricultural University; No.1, Weigang Nanjing Jiangsu 210095 China
| | - Xu Zhang
- Department of Entomology; Nanjing Agricultural University; No.1, Weigang Nanjing Jiangsu 210095 China
| | - Wen-Chao Zhu
- Department of Entomology; Nanjing Agricultural University; No.1, Weigang Nanjing Jiangsu 210095 China
| | - Ya-Ting Chen
- Department of Entomology; Nanjing Agricultural University; No.1, Weigang Nanjing Jiangsu 210095 China
| | - Xiao-Yue Hong
- Department of Entomology; Nanjing Agricultural University; No.1, Weigang Nanjing Jiangsu 210095 China
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Yeoh YK, Sekiguchi Y, Parks DH, Hugenholtz P. Comparative Genomics of Candidate Phylum TM6 Suggests That Parasitism Is Widespread and Ancestral in This Lineage. Mol Biol Evol 2015; 33:915-27. [PMID: 26615204 PMCID: PMC4776705 DOI: 10.1093/molbev/msv281] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Candidate phylum TM6 is a major bacterial lineage recognized through culture-independent rRNA surveys to be low abundance members in a wide range of habitats; however, they are poorly characterized due to a lack of pure culture representatives. Two recent genomic studies of TM6 bacteria revealed small genomes and limited gene repertoire, consistent with known or inferred dependence on eukaryotic hosts for their metabolic needs. Here, we obtained additional near-complete genomes of TM6 populations from agricultural soil and upflow anaerobic sludge blanket reactor metagenomes which, together with the two publicly available TM6 genomes, represent seven distinct family level lineages in the TM6 phylum. Genome-based phylogenetic analysis confirms that TM6 is an independent phylum level lineage in the bacterial domain, possibly affiliated with the Patescibacteria superphylum. All seven genomes are small (1.0–1.5 Mb) and lack complete biosynthetic pathways for various essential cellular building blocks including amino acids, lipids, and nucleotides. These and other features identified in the TM6 genomes such as a degenerated cell envelope, ATP/ADP translocases for parasitizing host ATP pools, and protein motifs to facilitate eukaryotic host interactions indicate that parasitism is widespread in this phylum. Phylogenetic analysis of ATP/ADP translocase genes suggests that the ancestral TM6 lineage was also parasitic. We propose the name Dependentiae (phyl. nov.) to reflect dependence of TM6 bacteria on host organisms.
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Affiliation(s)
- Yun Kit Yeoh
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia
| | - Yuji Sekiguchi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia
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