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Klose SM, Legione AR, Bushell RN, Browning GF, Vaz PK. Unveiling genome plasticity and a novel phage in Mycoplasma felis: Genomic investigations of four feline isolates. Microb Genom 2024; 10:001227. [PMID: 38546735 PMCID: PMC11004492 DOI: 10.1099/mgen.0.001227] [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: 01/09/2024] [Accepted: 03/18/2024] [Indexed: 04/12/2024] Open
Abstract
Mycoplasma felis has been isolated from diseased cats and horses, but to date only a single fully assembled genome of this species, of an isolate from a horse, has been characterized. This study aimed to characterize and compare the completely assembled genomes of four clinical isolates of M. felis from three domestic cats, assembled with the aid of short- and long-read sequencing methods. The completed genomes encoded a median of 759 ORFs (range 743-777) and had a median average nucleotide identity of 98.2 % with the genome of the available equid origin reference strain. Comparative genomic analysis revealed the occurrence of multiple horizontal gene transfer events and significant genome reassortment. This had resulted in the acquisition or loss of numerous genes within the Australian felid isolate genomes, encoding putative proteins involved in DNA transfer, metabolism, DNA replication, host cell interaction and restriction modification systems. Additionally, a novel mycoplasma phage was detected in one Australian felid M. felis isolate by genomic analysis and visualized using cryo-transmission electron microscopy. This study has highlighted the complex genomic dynamics in different host environments. Furthermore, the sequences obtained in this work will enable the development of new diagnostic tools, and identification of future infection control and treatment options for the respiratory disease complex in cats.
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Affiliation(s)
- Sara M. Klose
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, VIC, Australia
- Institute of Molecular Medicine and Experimental Immunology, Faculty of Medicine, University of Bonn, NRW, Germany
| | - Alistair R. Legione
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, VIC, Australia
| | - Rhys N. Bushell
- Department of Veterinary Clinical Sciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, VIC, Australia
| | - Glenn F. Browning
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, VIC, Australia
| | - Paola K. Vaz
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, VIC, Australia
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2
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Moore LD, Ballinger MJ. The toxins of vertically transmitted Spiroplasma. Front Microbiol 2023; 14:1148263. [PMID: 37275155 PMCID: PMC10232968 DOI: 10.3389/fmicb.2023.1148263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 04/19/2023] [Indexed: 06/07/2023] Open
Abstract
Vertically transmitted (VT) microbial symbionts play a vital role in the evolution of their insect hosts. A longstanding question in symbiont research is what genes help promote long-term stability of vertically transmitted lifestyles. Symbiont success in insect hosts is due in part to expression of beneficial or manipulative phenotypes that favor symbiont persistence in host populations. In Spiroplasma, these phenotypes have been linked to toxin and virulence domains among a few related strains. However, these domains also appear frequently in phylogenetically distant Spiroplasma, and little is known about their distribution across the Spiroplasma genus. In this study, we present the complete genome sequence of the Spiroplasma symbiont of Drosophila atripex, a non-manipulating member of the Ixodetis clade of Spiroplasma, for which genomic data are still limited. We perform a genus-wide comparative analysis of toxin domains implicated in defensive and reproductive phenotypes. From 12 VT and 31 non-VT Spiroplasma genomes, ribosome-inactivating proteins (RIPs), OTU-like cysteine proteases (OTUs), ankyrins, and ETX/MTX2 domains show high propensity for VT Spiroplasma compared to non-VT Spiroplasma. Specifically, OTU and ankyrin domains can be found only in VT-Spiroplasma, and RIP domains are found in all VT Spiroplasma and three non-VT Spiroplasma. These domains are frequently associated with Spiroplasma plasmids, suggesting a possible mechanism for dispersal and maintenance among heritable strains. Searching insect genome assemblies available on public databases uncovered uncharacterized Spiroplasma genomes from which we identified several spaid-like genes encoding RIP, OTU, and ankyrin domains, suggesting functional interactions among those domain types. Our results suggest a conserved core of symbiont domains play an important role in the evolution and persistence of VT Spiroplasma in insects.
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Affiliation(s)
- Logan D. Moore
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, United States
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3
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Arai H, Inoue MN, Kageyama D. Male-killing mechanisms vary between Spiroplasma species. Front Microbiol 2022; 13:1075199. [PMID: 36519169 PMCID: PMC9742256 DOI: 10.3389/fmicb.2022.1075199] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 11/08/2022] [Indexed: 03/11/2024] Open
Abstract
Male-killing, a male-specific death of arthropod hosts during development, is induced by Spiroplasma (Mollicutes) endosymbionts of the Citri-Poulsonii and the Ixodetis groups, which are phylogenetically distant groups. Spiroplasma poulsonii induces male-killing in Drosophila melanogaster (Diptera) using the Spaid toxin that harbors ankyrin repeats, whereas little is known about the origin and mechanisms of male-killing induced by Spiroplasma ixodetis. Here, we analyzed the genome and the biological characteristics of a male-killing S. ixodetis strain sHm in the moth Homona magnanima (Tortricidae, Lepidoptera). Strain sHm harbored a 2.1 Mb chromosome and two potential plasmids encoding Type IV effectors, putatively involved in virulence and host-symbiont interactions. Moreover, sHm did not harbor the spaid gene but harbored 10 ankyrin genes that were homologous to those in other S. ixodetis strains. In contrast to the predominant existence of S. poulsonii in hemolymph, our quantitative PCR assays revealed a systemic distribution of strain sHm in H. magnanima, with particularly high titers in Malpighian tubules but low titers in hemolymph. Furthermore, transinfection assays confirmed that strain sHm can infect cultured cells derived from distantly related insects, namely Aedes albopictus (Diptera) and Bombyx mori (Lepidoptera). These results suggest different origins and characteristics of S. ixodetis- and S. poulsonii-induced male-killing.
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Affiliation(s)
- Hiroshi Arai
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu, Japan
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Maki N. Inoue
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Daisuke Kageyama
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
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4
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Cytoskeletal components can turn wall-less spherical bacteria into kinking helices. Nat Commun 2022; 13:6930. [PMID: 36376306 PMCID: PMC9663586 DOI: 10.1038/s41467-022-34478-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 10/26/2022] [Indexed: 11/16/2022] Open
Abstract
Bacterial cell shape is generally determined through an interplay between the peptidoglycan cell wall and cytoplasmic filaments made of polymerized MreB. Indeed, some bacteria (e.g., Mycoplasma) that lack both a cell wall and mreB genes consist of non-motile cells that are spherical or pleomorphic. However, other members of the same class Mollicutes (e.g., Spiroplasma, also lacking a cell wall) display a helical cell shape and kink-based motility, which is thought to rely on the presence of five MreB isoforms and a specific fibril protein. Here, we show that heterologous expression of Spiroplasma fibril and MreB proteins confers helical shape and kinking ability to Mycoplasma capricolum cells. Isoform MreB5 is sufficient to confer helicity and kink propagation to mycoplasma cells. Cryoelectron microscopy confirms the association of cytoplasmic MreB filaments with the plasma membrane, suggesting a direct effect on membrane curvature. However, in our experiments, the heterologous expression of MreBs and fibril did not result in efficient motility in culture broth, indicating that additional, unknown Spiroplasma components are required for swimming.
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Shimooka M, Sakurai Y, Muramatsu Y, Uchida L. Isolation and Characterization of Mosquito-Associated Spiroplasma cantharicola from Aedes japonicus Collected in Hokkaido, Japan. INSECTS 2021; 12:insects12121056. [PMID: 34940145 PMCID: PMC8703607 DOI: 10.3390/insects12121056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/18/2021] [Accepted: 11/23/2021] [Indexed: 11/16/2022]
Abstract
Species of the genus Spiroplasma are common within arthropods and plants worldwide. Mosquito-associated Spiroplasma spp. have been reported to show pathogenicity toward mosquitoes, which serve as vectors of several infectious diseases that have detrimental effects on public health. Although Spiroplasma spp. are expected to have potential use as biological vector-control tools, characteristics such as their distribution, host species, and cytopathogenic effects (CPEs) are not well understood. In this study, we isolated a Spiroplasma sp. from a female Aedes japonicus collected in Hokkaido, northern Japan. Phylogenetic analysis based on the 16S rRNA gene sequence indicated our isolate was closely related to S. cantharicola. We screened 103 mosquito pools consisting of 3 genera and 9 species, but only detected S. cantharicola in the first isolation. In an in vitro assay, our isolate grew well at 28 °C, but no propagation was observed at 37 °C. Furthermore, the isolate showed strong CPE on a mosquito-derived cultured cell line (C6/36), and its propagation slightly increased when co-cultured with C6/36 cells. To our knowledge, this is the third report of the isolation of S. cantharicola from mosquitoes and the first case in Asia. Our findings provide epidemiological data on S. cantharicola distribution in the region.
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Vera-Ponce León A, Dominguez-Mirazo M, Bustamante-Brito R, Higareda-Alvear V, Rosenblueth M, Martínez-Romero E. Functional genomics of a Spiroplasma associated with the carmine cochineals Dactylopius coccus and Dactylopius opuntiae. BMC Genomics 2021; 22:240. [PMID: 33823812 PMCID: PMC8025503 DOI: 10.1186/s12864-021-07540-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 03/18/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Spiroplasma is a widely distributed endosymbiont of insects, arthropods, and plants. In insects, Spiroplasma colonizes the gut, hemolymph, and reproductive organs of the host. Previous metagenomic surveys of the domesticated carmine cochineal Dactylopius coccus and the wild cochineal D. opuntiae reported sequences of Spiroplasma associated with these insects. However, there is no analysis of the genomic capabilities and the interaction of this Spiroplasma with Dactylopius. RESULTS Here we present three Spiroplasma genomes independently recovered from metagenomes of adult males and females of D. coccus, from two different populations, as well as from adult females of D. opuntiae. Single-copy gene analysis showed that these genomes were > 92% complete. Phylogenomic analyses classified these genomes as new members of Spiroplasma ixodetis. Comparative genome analysis indicated that they exhibit fewer genes involved in amino acid and carbon catabolism compared to other spiroplasmas. Moreover, virulence factor-encoding genes (i.e., glpO, spaid and rip2) were found incomplete in these S. ixodetis genomes. We also detected an enrichment of genes encoding the type IV secretion system (T4SS) in S. ixodetis genomes of Dactylopius. A metratranscriptomic analysis of D. coccus showed that some of these T4SS genes (i.e., traG, virB4 and virD4) in addition to the superoxide dismutase sodA of S. ixodetis were overexpressed in the ovaries. CONCLUSION The symbiont S. ixodetis is a new member of the bacterial community of D. coccus and D. opuntiae. The recovery of incomplete virulence factor-encoding genes in S. ixodetis of Dactylopius suggests that this bacterium is a non-pathogenic symbiont. A high number of genes encoding the T4SS, in the S. ixodetis genomes and the overexpression of these genes in the ovary and hemolymph of the host suggest that S. ixodetis use the T4SS to interact with the Dactylopius cells. Moreover, the transcriptional differences of S. ixodetis among the gut, hemolymph and ovary tissues of D. coccus indicate that this bacterium can respond and adapt to the different conditions (e.g., oxidative stress) present within the host. All this evidence proposes that there is a strong interaction and molecular signaling in the symbiosis between S. ixodetis and the carmine cochineal Dactylopius.
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Affiliation(s)
- Arturo Vera-Ponce León
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico. .,Present Address: Faculty of Biotechnology, Chemistry and Food Science, Norwegian University of Life Sciences, 1433, Ås, Norway.
| | - Marian Dominguez-Mirazo
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.,Present Address: School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
| | - Rafael Bustamante-Brito
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Víctor Higareda-Alvear
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Mónica Rosenblueth
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Esperanza Martínez-Romero
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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Harne S, Gayathri P, Béven L. Exploring Spiroplasma Biology: Opportunities and Challenges. Front Microbiol 2020; 11:589279. [PMID: 33193251 PMCID: PMC7609405 DOI: 10.3389/fmicb.2020.589279] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/28/2020] [Indexed: 11/13/2022] Open
Abstract
Spiroplasmas are cell-wall-deficient helical bacteria belonging to the class Mollicutes. Their ability to maintain a helical shape in the absence of cell wall and their motility in the absence of external appendages have attracted attention from the scientific community for a long time. In this review we compare and contrast motility, shape determination and cytokinesis mechanisms of Spiroplasma with those of other Mollicutes and cell-walled bacteria. The current models for rod-shape determination and cytokinesis in cell-walled bacteria propose a prominent role for the cell wall synthesis machinery. These models also involve the cooperation of the actin-like protein MreB and FtsZ, the bacterial homolog of tubulin. However the exact role of the cytoskeletal proteins is still under much debate. Spiroplasma possess MreBs, exhibit a rod-shape dependent helical morphology, and divide by an FtsZ-dependent mechanism. Hence, spiroplasmas represent model organisms for deciphering the roles of MreBs and FtsZ in fundamental mechanisms of non-spherical shape determination and cytokinesis in bacteria, in the absence of a cell wall. Identification of components implicated in these processes and deciphering their functions would require genetic experiments. Challenges in genetic manipulations in spiroplasmas are a major bottleneck in understanding their biology. We discuss advancements in genome sequencing, gene editing technologies, super-resolution microscopy and electron cryomicroscopy and tomography, which can be employed for addressing long-standing questions related to Spiroplasma biology.
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Affiliation(s)
- Shrikant Harne
- Indian Institute of Science Education and Research, Pune, India
| | | | - Laure Béven
- INRAE, UMR 1332, Biologie du Fruit et Pathologie, University of Bordeaux, Bordeaux, France
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8
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Yeoman CJ, Brutscher LM, Esen ÖC, Ibaoglu F, Fowler C, Eren AM, Wanner K, Weaver DK. Genome-resolved insights into a novel Spiroplasma symbiont of the Wheat Stem Sawfly ( Cephus cinctus). PeerJ 2019; 7:e7548. [PMID: 31523509 PMCID: PMC6716498 DOI: 10.7717/peerj.7548] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 07/25/2019] [Indexed: 12/24/2022] Open
Abstract
Arthropods often have obligate relationships with symbiotic microbes, and recent investigations have demonstrated that such host-microbe relationships could be exploited to suppress natural populations of vector carrying mosquitos. Strategies that target the interplay between agricultural pests and their symbionts could decrease the burden caused by agricultural pests; however, the lack of comprehensive genomic insights into naturally occurring microbial symbionts presents a significant bottleneck. Here we employed amplicon surveys, genome-resolved metagenomics, and scanning electron microscopy to investigate symbionts of the wheat stem sawfly (Cephus cinctus), a major pest that causes an estimated $350 million dollars or more in wheat yield losses in the northwestern United States annually. Through 16S rRNA gene sequencing of two major haplotypes and life stages of wheat stem sawfly, we show a novel Spiroplasma species is ever-present and predominant, with phylogenomic analyses placing it as a member of the ixodetis clade of mollicutes. Using state-of-the-art metagenomic assembly and binning strategies we were able to reconstruct a 714 Kb, 72.7%-complete Spiroplasma genome, which represents just the second draft genome from the ixodetis clade of mollicutes. Functional annotation of the Spiroplasma genome indicated carbohydrate-metabolism involved PTS-mediated import of glucose and fructose followed by glycolysis to lactate, acetate, and propionoate. The bacterium also encoded biosynthetic pathways for essential vitamins B2, B3, and B9. We identified putative Spiroplasma virulence genes: cardiolipin and chitinase. These results identify a previously undescribed symbiosis between wheat stem sawfly and a novel Spiroplasma sp., availing insight into their molecular relationship, and may yield new opportunities for microbially-mediated pest control strategies.
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Affiliation(s)
- Carl J Yeoman
- Department of Animal & Range Sciences, Montana State University, Bozeman, MT, United States of America
| | - Laura M Brutscher
- Department of Animal & Range Sciences, Montana State University, Bozeman, MT, United States of America.,Department of Microbiology & Immunology, Montana State University, Bozeman, MT, United States of America
| | - Özcan C Esen
- Department of Medicine, University of Chicago, Chicago, IL, United States of America
| | - Furkan Ibaoglu
- Department of Animal & Range Sciences, Montana State University, Bozeman, MT, United States of America.,Department of Microbiology & Immunology, Montana State University, Bozeman, MT, United States of America
| | - Curtis Fowler
- Department of Animal & Range Sciences, Montana State University, Bozeman, MT, United States of America
| | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL, United States of America.,Marine Biological Laboratory, The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Woods Hole, Massachuetts, United States of America
| | - Kevin Wanner
- Department of Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT, United States of America
| | - David K Weaver
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, United States of America
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9
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Schumacher M, Nicholson P, Stoffel MH, Chandran S, D’Mello A, Ma L, Vashee S, Jores J, Labroussaa F. Evidence for the Cytoplasmic Localization of the L-α-Glycerophosphate Oxidase in Members of the " Mycoplasma mycoides Cluster". Front Microbiol 2019; 10:1344. [PMID: 31275271 PMCID: PMC6593217 DOI: 10.3389/fmicb.2019.01344] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 05/29/2019] [Indexed: 12/15/2022] Open
Abstract
Members of the "Mycoplasma mycoides cluster" are important animal pathogens causing diseases including contagious bovine pleuropneumonia and contagious caprine pleuropneumonia, which are of utmost importance in Africa or Asia. Even if all existing vaccines have shortcomings, vaccination of herds is still considered the best way to fight mycoplasma diseases, especially with the recent and dramatic increase of antimicrobial resistance observed in many mycoplasma species. A new generation of vaccines will benefit from a better understanding of the pathogenesis of mycoplasmas, which is very patchy up to now. In particular, surface-exposed virulence traits are likely to induce a protective immune response when formulated in a vaccine. The candidate virulence factor L-α-glycerophosphate oxidase (GlpO), shared by many mycoplasmas including Mycoplasma pneumoniae, was suggested to be a surface-exposed enzyme in Mycoplasma mycoides subsp. mycoides responsible for the production of hydrogen peroxide directly into the host cells. We produced a glpO isogenic mutant GM12::YCpMmyc1.1-ΔglpO using in-yeast synthetic genomics tools including the tandem-repeat endonuclease cleavage (TREC) technique followed by the back-transplantation of the engineered genome into a mycoplasma recipient cell. GlpO localization in the mutant and its parental strain was assessed using scanning electron microscopy (SEM). We obtained conflicting results and this led us to re-evaluate the localization of GlpO using a combination of in silico and in vitro techniques, such as Triton X-114 fractionation or tryptic shaving followed by immunoblotting. Our in vitro results unambiguously support the finding that GlpO is a cytoplasmic protein throughout the "Mycoplasma mycoides cluster." Thus, the use of GlpO as a candidate vaccine antigen is unlikely to induce a protective immune response.
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Affiliation(s)
- Melanie Schumacher
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Pamela Nicholson
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | | | | | - Adonis D’Mello
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Li Ma
- J. Craig Venter Institute, Rockville, MD, United States
| | - Sanjay Vashee
- J. Craig Venter Institute, Rockville, MD, United States
| | - Joerg Jores
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Fabien Labroussaa
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
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10
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Duguma D, Hall MW, Smartt CT, Debboun M, Neufeld JD. Microbiota variations in Culex nigripalpus disease vector mosquito of West Nile virus and Saint Louis Encephalitis from different geographic origins. PeerJ 2019; 6:e6168. [PMID: 30643680 PMCID: PMC6330035 DOI: 10.7717/peerj.6168] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 11/27/2018] [Indexed: 12/24/2022] Open
Abstract
Although mosquito microbiota are known to influence reproduction, nutrition, disease transmission, and pesticide resistance, the relationship between host-associated microbial community composition and geographical location is poorly understood. To begin addressing this knowledge gap, we characterized microbiota associated with adult females of Culex nigripalpus mosquito vectors of Saint Louis Encephalitis and West Nile viruses sampled from three locations in Florida (Vero Beach, Palmetto Inland, and Palmetto Coast). High-throughput sequencing of PCR-amplified 16S rRNA genes demonstrated significant differences among microbial communities of mosquitoes sampled from the three locations. Mosquitoes from Vero Beach (east coast Florida) were dominated by uncultivated Asaia sp. (Alphaproteobacteria), whereas microbiota associated with mosquitoes collected from two mosquito populations at Palmetto (west coast Florida) sites were dominated by uncultured Spironema culicis (Spirochaetes), Salinisphaera hydrothermalis (Gammaproteobacteria), Spiroplasma (Mollicutes), uncultured Enterobacteriaceae, Candidatus Megaira (Alphaproteobacteria; Rickettsiae), and Zymobacter (Gammaproteobacteria). The variation in taxonomic profiles of Cx. nigripalpus gut microbial communities, especially with respect to dominating taxa, is a potentially critical factor in understanding disease transmission and mosquito susceptibility to insecticides among different mosquito populations.
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Affiliation(s)
- Dagne Duguma
- Florida Medical Entomology Laboratory, Institute of Food and Agricultural Sciences, University of Florida, Vero Beach, FL, USA.,Mosquito and Vector Control Division, Harris County Public Health, Houston, TX, USA
| | - Michael W Hall
- Faculty of Graduate Studies, Dalhousie University, Halifax, NS, Canada
| | - Chelsea T Smartt
- Florida Medical Entomology Laboratory, Institute of Food and Agricultural Sciences, University of Florida, Vero Beach, FL, USA
| | - Mustapha Debboun
- Mosquito and Vector Control Division, Harris County Public Health, Houston, TX, USA
| | - Josh D Neufeld
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
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11
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Alonso DP, Mancini MV, Damiani C, Cappelli A, Ricci I, Alvarez MVN, Bandi C, Ribolla PEM, Favia G. Genome Reduction in the Mosquito Symbiont Asaia. Genome Biol Evol 2019; 11:1-10. [PMID: 30476071 PMCID: PMC6317953 DOI: 10.1093/gbe/evy255] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2018] [Indexed: 12/31/2022] Open
Abstract
Symbiosis is now recognized as a driving force in evolution, a role that finds its ultimate expression in the variety of associations bonding insects with microbial symbionts. These associations have contributed to the evolutionary success of insects, with the hosts acquiring the capacity to exploit novel ecological niches, and the symbionts passing from facultative associations to obligate, mutualistic symbioses. In bacterial symbiont of insects, the transition from the free-living life style to mutualistic symbiosis often resulted in a reduction in the genome size, with the generation of the smallest bacterial genomes thus far described. Here, we show that the process of genome reduction is still occurring in Asaia, a group of bacterial symbionts associated with a variety of insects. Indeed, comparative genomics of Asaia isolated from different mosquito species revealed a substantial genome size and gene content reduction in Asaia from Anopheles darlingi, a South-American malaria vector. We thus propose Asaia as a novel model to study genome reduction dynamics, within a single bacterial taxon, evolving in a common biological niche.
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Affiliation(s)
- Diego Peres Alonso
- Biotechnology Institute (IBTEC) & Biosciences Institute at Botucatu (IBB), Sao Paulo State University (UNESP), Sao Paulo, Brazil
| | - Maria Vittoria Mancini
- School of Biosciences and Veterinary Medicine, University of Camerino, Italy.,MRC-University of Glasgow-Centre for Virus Research, Glasgow, United Kingdom
| | - Claudia Damiani
- School of Biosciences and Veterinary Medicine, University of Camerino, Italy
| | - Alessia Cappelli
- School of Biosciences and Veterinary Medicine, University of Camerino, Italy
| | - Irene Ricci
- School of Biosciences and Veterinary Medicine, University of Camerino, Italy
| | - Marcus Vinicius Niz Alvarez
- Biotechnology Institute (IBTEC) & Biosciences Institute at Botucatu (IBB), Sao Paulo State University (UNESP), Sao Paulo, Brazil
| | - Claudio Bandi
- Clinical Pediatric Research Center Romeo and Enrica Invernizzi, Department of Biosciences, University of Milan, Italy
| | - Paulo Eduardo Martins Ribolla
- Biotechnology Institute (IBTEC) & Biosciences Institute at Botucatu (IBB), Sao Paulo State University (UNESP), Sao Paulo, Brazil
| | - Guido Favia
- School of Biosciences and Veterinary Medicine, University of Camerino, Italy
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12
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Sapountzis P, Zhukova M, Shik JZ, Schiott M, Boomsma JJ. Reconstructing the functions of endosymbiotic Mollicutes in fungus-growing ants. eLife 2018; 7:e39209. [PMID: 30454555 PMCID: PMC6245734 DOI: 10.7554/elife.39209] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 10/16/2018] [Indexed: 12/25/2022] Open
Abstract
Mollicutes, a widespread class of bacteria associated with animals and plants, were recently identified as abundant abdominal endosymbionts in healthy workers of attine fungus-farming leaf-cutting ants. We obtained draft genomes of the two most common strains harbored by Panamanian fungus-growing ants. Reconstructions of their functional significance showed that they are independently acquired symbionts, most likely to decompose excess arginine consistent with the farmed fungal cultivars providing this nitrogen-rich amino-acid in variable quantities. Across the attine lineages, the relative abundances of the two Mollicutes strains are associated with the substrate types that foraging workers offer to fungus gardens. One of the symbionts is specific to the leaf-cutting ants and has special genomic machinery to catabolize citrate/glucose into acetate, which appears to deliver direct metabolic energy to the ant workers. Unlike other Mollicutes associated with insect hosts, both attine ant strains have complete phage-defense systems, underlining that they are actively maintained as mutualistic symbionts.
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Affiliation(s)
- Panagiotis Sapountzis
- Centre for Social Evolution, Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Mariya Zhukova
- Centre for Social Evolution, Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Jonathan Z Shik
- Centre for Social Evolution, Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Morten Schiott
- Centre for Social Evolution, Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Jacobus J Boomsma
- Centre for Social Evolution, Department of BiologyUniversity of CopenhagenCopenhagenDenmark
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13
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Tsai YM, Chang A, Kuo CH. Horizontal Gene Acquisitions Contributed to Genome Expansion in Insect-Symbiotic Spiroplasma clarkii. Genome Biol Evol 2018; 10:1526-1532. [PMID: 29860283 PMCID: PMC6007557 DOI: 10.1093/gbe/evy113] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2018] [Indexed: 12/21/2022] Open
Abstract
Genome reduction is a recurring theme of symbiont evolution. The genus Spiroplasma contains species that are mostly facultative insect symbionts. The typical genome sizes of those species within the Apis clade were estimated to be ∼1.0–1.4 Mb. Intriguingly, Spiroplasma clarkii was found to have a genome size that is >30% larger than the median of other species within the same clade. To investigate the molecular evolution events that led to the genome expansion of this bacterium, we determined its complete genome sequence and inferred the evolutionary origin of each protein-coding gene based on the phylogenetic distribution of homologs. Among the 1,346 annotated protein-coding genes, 641 were originated from within the Apis clade while 233 were putatively acquired from outside of the clade (including 91 high-confidence candidates). Additionally, 472 were specific to S. clarkii without homologs in the current database (i.e., the origins remained unknown). The acquisition of protein-coding genes, rather than mobile genetic elements, appeared to be a major contributing factor of genome expansion. Notably, >50% of the high-confidence acquired genes are related to carbohydrate transport and metabolism, suggesting that these acquired genes contributed to the expansion of both genome size and metabolic capability. The findings of this work provided an interesting case against the general evolutionary trend observed among symbiotic bacteria and further demonstrated the flexibility of Spiroplasma genomes. For future studies, investigation on the functional integration of these acquired genes, as well as the inference of their contribution to fitness could improve our knowledge of symbiont evolution.
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Affiliation(s)
- Yi-Ming Tsai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - An Chang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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14
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Lo WS, Gasparich GE, Kuo CH. Convergent Evolution among Ruminant-Pathogenic Mycoplasma Involved Extensive Gene Content Changes. Genome Biol Evol 2018; 10:2130-2139. [PMID: 30102350 PMCID: PMC6117150 DOI: 10.1093/gbe/evy172] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/07/2018] [Indexed: 01/21/2023] Open
Abstract
Convergent evolution, a process by which organisms evolved independently to have similar traits, provides opportunities to understand adaptation. The bacterial genus Mycoplasma contains multiple species that evolved independently to become ruminant pathogens, which represents an interesting study system for investigating the process. In this work, we determined the genome sequences of 11 Entomoplasma/Mesoplasma species. This new data set, together with the other available Mollicutes genomes, provided comprehensive taxon sampling for inferring the gene content evolution that led to the emergence of Mycoplasma Mycoides cluster. Our results indicated that the most recent common ancestor (MRCA) of the Mycoides-Entomoplasmataceae clade lost ∼15% of the core genes when it diverged from the Spiroplasma Apis clade. After this initial wave of genome reduction, relatively few gene gains or losses were inferred until the emergence of the Mycoides cluster. Compared with those Entomoplasmataceae lineages that maintained the association with insects, the MRCA of the Mycoides cluster experienced a second wave of gene losses, as well as acquiring >100 novel genes through horizontal gene transfer. These gene acquisitions involved many with the Mycoplasma Hominis/Pneumoniae lineages as the putative donors, suggesting that gene exchanges among these vertebrate symbionts with distinct phylogenetic affiliations may be important in the emergence of the Mycoides cluster. These findings demonstrated that the gene content of bacterial genomes could be exceedingly dynamic, even for those symbionts with highly reduced genomes. Moreover, the emergence of novel pathogens may involve extensive remodeling of gene content, rather than acquisition of few virulence genes.
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Affiliation(s)
- Wen-Sui Lo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Department for Evolutionary Biology, Max-Planck Institute for Developmental Biology, Tuebingen, Germany
| | | | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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15
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Lo WS, Kuo CH. Horizontal Acquisition and Transcriptional Integration of Novel Genes in Mosquito-Associated Spiroplasma. Genome Biol Evol 2018; 9:3246-3259. [PMID: 29177479 PMCID: PMC5726471 DOI: 10.1093/gbe/evx244] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2017] [Indexed: 12/20/2022] Open
Abstract
Genetic differentiation among symbiotic bacteria is important in shaping biodiversity. The genus Spiroplasma contains species occupying diverse niches and is a model system for symbiont evolution. Previous studies have established that two mosquito-associated species have diverged extensively in their carbohydrate metabolism genes despite having a close phylogenetic relationship. Notably, although the commensal Spiroplasma diminutum lacks identifiable pathogenicity factors, the pathogenic Spiroplasma taiwanense was found to have acquired a virulence factor glpO and its associated genes through horizontal transfer. However, it is unclear if these acquired genes have been integrated into the regulatory network. In this study, we inferred the gene content evolution in these bacteria, as well as examined their transcriptomes in response to glucose availability. The results indicated that both species have many more gene acquisitions from the Mycoides-Entomoplasmataceae clade, which contains several important pathogens of ruminants, than previously thought. Moreover, several acquired genes have higher expression levels than the vertically inherited homologs, indicating possible functional replacement. Finally, the virulence factor and its functionally linked genes in S. taiwanense were up-regulated in response to glucose starvation, suggesting that these acquired genes are under expression regulation and the pathogenicity may be a stress response. In summary, although differential gene losses are a major process for symbiont divergence, gene gains are critical in counteracting genome degradation and driving diversification among facultative symbionts.
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Affiliation(s)
- Wen-Sui Lo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.,Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, Taiwan.,Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.,Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, Taiwan.,Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
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16
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Tsai YM, Lo WS, Wu PS, Cho ST, Kuo CH. Complete Genome Sequence of Spiroplasma monobiae MQ-1 T (ATCC 33825), a Bacterium Isolated from the Vespid Wasp (Monobia quadridens). GENOME ANNOUNCEMENTS 2018; 6:e00347-18. [PMID: 29724836 PMCID: PMC5940939 DOI: 10.1128/genomea.00347-18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 03/24/2018] [Indexed: 11/23/2022]
Abstract
Spiroplasma monobiae MQ-1T (ATCC 33825) was isolated from the hemolymph of an adult vespid wasp (Monobia quadridens) collected in Maryland. Here, we report the complete genome sequence of this bacterium to facilitate the investigation of its biology and the comparative genomics among Spiroplasma species.
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Affiliation(s)
- Yi-Ming Tsai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Wen-Sui Lo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Pei-Shan Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Shu-Ting Cho
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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17
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Complete Genome Sequence of Spiroplasma floricola 23-6
T
(ATCC 29989), a Bacterium Isolated from a Tulip Tree (Liriodendron tulipifera L.). GENOME ANNOUNCEMENTS 2018; 6:6/16/e00302-18. [PMID: 29674553 PMCID: PMC5908944 DOI: 10.1128/genomea.00302-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Spiroplasma floricola 23-6T (ATCC 29989) was isolated from the flower surface of a tulip tree (Liriodendron tulipifera L.). Here, we report the complete genome sequence of this bacterium to facilitate the investigation of its biology and the comparative genomics among Spiroplasma species.
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18
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Lo WS, Huang YY, Kuo CH. Winding paths to simplicity: genome evolution in facultative insect symbionts. FEMS Microbiol Rev 2018; 40:855-874. [PMID: 28204477 PMCID: PMC5091035 DOI: 10.1093/femsre/fuw028] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/28/2016] [Accepted: 07/10/2016] [Indexed: 02/07/2023] Open
Abstract
Symbiosis between organisms is an important driving force in evolution. Among the diverse relationships described, extensive progress has been made in insect–bacteria symbiosis, which improved our understanding of the genome evolution in host-associated bacteria. Particularly, investigations on several obligate mutualists have pushed the limits of what we know about the minimal genomes for sustaining cellular life. To bridge the gap between those obligate symbionts with extremely reduced genomes and their non-host-restricted ancestors, this review focuses on the recent progress in genome characterization of facultative insect symbionts. Notable cases representing various types and stages of host associations, including those from multiple genera in the family Enterobacteriaceae (class Gammaproteobacteria), Wolbachia (Alphaproteobacteria) and Spiroplasma (Mollicutes), are discussed. Although several general patterns of genome reduction associated with the adoption of symbiotic relationships could be identified, extensive variation was found among these facultative symbionts. These findings are incorporated into the established conceptual frameworks to develop a more detailed evolutionary model for the discussion of possible trajectories. In summary, transitions from facultative to obligate symbiosis do not appear to be a universal one-way street; switches between hosts and lifestyles (e.g. commensalism, parasitism or mutualism) occur frequently and could be facilitated by horizontal gene transfer. This review synthesizes the recent progress in genome characterization of insect-symbiotic bacteria, the emphases include (i) patterns of genome organization, (ii) evolutionary models and trajectories, and (iii) comparisons between facultative and obligate symbionts.
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Affiliation(s)
- Wen-Sui Lo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.,Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei 11529, Taiwan.,Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Ya-Yi Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.,Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei 11529, Taiwan.,Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
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19
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Blötz C, Stülke J. Glycerol metabolism and its implication in virulence in Mycoplasma. FEMS Microbiol Rev 2017; 41:640-652. [PMID: 28961963 DOI: 10.1093/femsre/fux033] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 06/09/2017] [Indexed: 12/11/2022] Open
Abstract
Glycerol and glycerol-containing compounds such as lipids belong to the most abundant organic compounds that may serve as nutrient for many bacteria. For the cell wall-less bacteria of the genus Mycoplasma, glycerol derived from phospholipids of their human or animal hosts is the major source of carbon and energy. The lipids are first degraded by lipases, and the resulting glycerophosphodiesters are transported into the cell and cleaved to release glycerol-3-phosphate. Alternatively, free glycerol can be transported, and then become phosphorylated. The oxidation of glycerol-3-phosphate in Mycoplasma spp. as well as in related firmicutes involves a hydrogen peroxide-generating glycerol-3-phosphate oxidase. This enzyme is a key player in the virulence of Mycoplasma spp. as the produced hydrogen peroxide is one of the major virulence factors of these bacteria. In this review, the different components involved in the utilization of lipids and glycerol in Mycoplasma pneumoniae and related bacteria are discussed.
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Affiliation(s)
- Cedric Blötz
- Department for General Microbiology, Georg-August-University Göttingen, 37077 Göttingen, Germany
| | - Jörg Stülke
- Department for General Microbiology, Georg-August-University Göttingen, 37077 Göttingen, Germany
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20
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Complete Genome Sequence of Spiroplasma corruscae EC-1
T
(DSM 19793), a Bacterium Isolated from a Lampyrid Beetle (Ellychnia corrusca). GENOME ANNOUNCEMENTS 2017; 5:5/37/e00964-17. [PMID: 28912320 PMCID: PMC5597761 DOI: 10.1128/genomea.00964-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Spiroplasma corruscae EC-1T (DSM 19793) was isolated from the gut of a lampryid beetle (Ellychnia corrusca) collected in Beltsville, MD, USA, in 1983. Here, we report the complete genome sequence of this bacterium to facilitate the investigation of its biology and the comparative genomics among Spiroplasma species.
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21
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Abstract
Spiroplasma sp. TU-14 was isolated from a contaminated sample of Entomoplasma lucivorax PIPN-2T obtained from the International Organization for Mycoplasmology collection. Here, we report the complete genome sequence of this bacterium to facilitate the investigation of its biology and the comparative genomics among Spiroplasma spp.
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22
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Complete Genome Sequence of Spiroplasma turonicum Tab4c
T
, a Bacterium Isolated from Horse Flies (
Haematopota
sp.). GENOME ANNOUNCEMENTS 2016; 4:4/5/e01010-16. [PMID: 27660788 PMCID: PMC5034139 DOI: 10.1128/genomea.01010-16] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Spiroplasma turonicum Tab4cT was isolated from a horse fly (Haematopota sp.; probably Haematopota pluvialis) collected at Champchevrier, Indre-et-Loire, Touraine, France, in 1991. Here, we report the complete genome sequence of this bacterium to facilitate the investigation of its biology and the comparative genomics among Spiroplasma spp.
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23
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Complete Genome Sequence of Spiroplasma helicoides TABS-2T (DSM 22551), a Bacterium Isolated from a Horsefly (Tabanus abactor). GENOME ANNOUNCEMENTS 2016; 4:4/5/e01201-16. [PMID: 27795290 PMCID: PMC5073277 DOI: 10.1128/genomea.01201-16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Spiroplasma helicoides TABS-2T (DSM 22551) was isolated from the gut of a horsefly (Tabanus abactor) collected near Ardmore, Oklahoma, USA, in 1987. Here, we report the complete genome sequence of this bacterium to facilitate the investigation of its biology and the comparative genomics among Spiroplasma species.
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24
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Complete Genome Sequence of Spiroplasma cantharicola CC-1
T
(DSM 21588), a Bacterium Isolated from Soldier Beetle (
Cantharis carolinus
). GENOME ANNOUNCEMENTS 2015; 3:3/5/e01253-15. [PMID: 26494686 PMCID: PMC4616193 DOI: 10.1128/genomea.01253-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Spiroplasma cantharicola CC-1T (DSM 21588) was isolated from the gut of a soldier beetle (Cantharis carolinus) collected in Maryland, USA. Here, we report the complete genome sequence of this bacterium to facilitate the investigation of its biology.
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25
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Cho ST, Chang HH, Egamberdieva D, Kamilova F, Lugtenberg B, Kuo CH. Genome Analysis of Pseudomonas fluorescens PCL1751: A Rhizobacterium that Controls Root Diseases and Alleviates Salt Stress for Its Plant Host. PLoS One 2015; 10:e0140231. [PMID: 26452056 PMCID: PMC4599888 DOI: 10.1371/journal.pone.0140231] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 09/22/2015] [Indexed: 01/05/2023] Open
Abstract
Pseudomonas fluorescens PCL1751 is a rod-shaped Gram-negative bacterium isolated from the rhizosphere of a greenhouse-grown tomato plant in Uzbekistan. It controls several plant root diseases caused by Fusarium fungi through the mechanism of competition for nutrients and niches (CNN). This mechanism does not rely on the production of antibiotics, so it avoids the concerns of resistance development and is environmentally safe. Additionally, this bacterium promotes plant growth by alleviating salt stress for its plant host. To investigate the genetic mechanisms that may explain these observations, we determined the complete genome sequence of this bacterium, examined its gene content, and performed comparative genomics analysis with other Pseudomonas strains. The genome of P. fluorescens PCL1751 consisted of one circular chromosome that is 6,143,950 base-pairs (bp) in size; no plasmid was found. The annotation included 19 rRNA, 70 tRNA, and 5,534 protein-coding genes. The gene content analysis identified a large number of genes involved in chemotaxis and motility, colonization of the rhizosphere, siderophore biosynthesis, and osmoprotectant production. In contrast, the pathways involved in the biosynthesis of phytohormones or antibiotics were not found. Comparison with other Pseudomonas genomes revealed extensive variations in their genome size and gene content. The presence and absence of secretion system genes were highly variable. As expected, the synteny conservation among strains decreased as a function of phylogenetic divergence. The integration of prophages appeared to be an important driver for genome rearrangements. The whole-genome gene content analysis of this plant growth-promoting rhizobacterium (PGPR) provided some genetic explanations to its phenotypic characteristics. The extensive and versatile substrate utilization pathways, together with the presence of many genes involved in competitive root colonization, provided further support for the finding that this strain achieves biological control of pathogens through effective competition for nutrients and niches.
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Affiliation(s)
- Shu-Ting Cho
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Hsing-Hua Chang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Dilfuza Egamberdieva
- Institute for Landscape Biogeochemistry, Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder str. 84, Müncheberg, Germany
| | - Faina Kamilova
- Koppert Biological Systems, Veilingweg 14, 2651 BE Berkel en Rodenrijs, the Netherlands
| | - Ben Lugtenberg
- Institute of Biology, Sylvius Laboratory, Leiden University, Leiden, the Netherlands
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
- * E-mail:
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26
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Complete Genome Sequence of Spiroplasma litorale TN-1T (DSM 21781), a Bacterium Isolated from a Green-Eyed Horsefly (Tabanus nigrovittatus). GENOME ANNOUNCEMENTS 2015; 3:3/5/e01116-15. [PMID: 26430038 PMCID: PMC4591310 DOI: 10.1128/genomea.01116-15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Spiroplasma litorale TN-1T (DSM 21781) was isolated from the gut of a green-eyed horsefly (Tabanus nigrovittatus), collected at Ocracoke Island in North Carolina in 1983. Here, we report the complete genome sequence of this bacterium to facilitate the investigation of its biology.
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27
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Lo WS, Gasparich GE, Kuo CH. Found and Lost: The Fates of Horizontally Acquired Genes in Arthropod-Symbiotic Spiroplasma. Genome Biol Evol 2015; 7:2458-72. [PMID: 26254485 PMCID: PMC4607517 DOI: 10.1093/gbe/evv160] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Horizontal gene transfer (HGT) is an important mechanism that contributed to biological diversity, particularly in bacteria. Through acquisition of novel genes, the recipient cell may change its ecological preference and the process could promote speciation. In this study, we determined the complete genome sequence of two Spiroplasma species for comparative analyses and inferred the putative gene gains and losses. Although most Spiroplasma species are symbionts of terrestrial insects, Spiroplasma eriocheiris has evolved to be a lethal pathogen of freshwater crustaceans. We found that approximately 7% of the genes in this genome may have originated from HGT and these genes expanded the metabolic capacity of this organism. Through comparison with the closely related Spiroplasma atrichopogonis, as well as other more divergent lineages, our results indicated that these HGT events could be traced back to the most recent common ancestor of these two species. However, most of these horizontally acquired genes have been pseudogenized in S. atrichopogonis, suggesting that they did not contribute to the fitness of this lineage that maintained the association with terrestrial insects. Thus, accumulation of small deletions that disrupted these foreign genes was not countered by natural selection. On the other hand, the long-term survival of these horizontally acquired genes in the S. eriocheiris genome hinted that they might play a role in the ecological shift of this species. Finally, the implications of these findings and the conflicts among gene content, 16S rRNA gene sequencing, and serological typing, are discussed in light of defining bacterial species.
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Affiliation(s)
- Wen-Sui Lo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, NationalChung Hsing University and Academia Sinica, Taipei, Taiwan Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | | | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, NationalChung Hsing University and Academia Sinica, Taipei, Taiwan Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
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28
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Abstract
Agrobacterium tumefaciens is a phytopathogenic bacterium that causes crown gall disease. The strain Ach5 was isolated from yarrow (Achillea ptarmica L.) and is the wild-type progenitor of other derived strains widely used for plant transformation. Here, we report the complete genome sequence of this bacterium.
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29
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Genome sequence of the Drosophila melanogaster male-killing Spiroplasma strain MSRO endosymbiont. mBio 2015; 6:mBio.02437-14. [PMID: 25827421 PMCID: PMC4453565 DOI: 10.1128/mbio.02437-14] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Spiroplasmas are helical and motile members of a cell wall-less eubacterial group called Mollicutes. Although all spiroplasmas are associated with arthropods, they exhibit great diversity with respect to both their modes of transmission and their effects on their hosts; ranging from horizontally transmitted pathogens and commensals to endosymbionts that are transmitted transovarially (i.e., from mother to offspring). Here we provide the first genome sequence, along with proteomic validation, of an endosymbiotic inherited Spiroplasma bacterium, the Spiroplasma poulsonii MSRO strain harbored by Drosophila melanogaster. Comparison of the genome content of S. poulsonii with that of horizontally transmitted spiroplasmas indicates that S. poulsonii has lost many metabolic pathways and transporters, demonstrating a high level of interdependence with its insect host. Consistent with genome analysis, experimental studies showed that S. poulsonii metabolizes glucose but not trehalose. Notably, trehalose is more abundant than glucose in Drosophila hemolymph, and the inability to metabolize trehalose may prevent S. poulsonii from overproliferating. Our study identifies putative virulence genes, notably, those for a chitinase, the H2O2-producing glycerol-3-phosphate oxidase, and enzymes involved in the synthesis of the eukaryote-toxic lipid cardiolipin. S. poulsonii also expresses on the cell membrane one functional adhesion-related protein and two divergent spiralin proteins that have been implicated in insect cell invasion in other spiroplasmas. These lipoproteins may be involved in the colonization of the Drosophila germ line, ensuring S. poulsonii vertical transmission. The S. poulsonii genome is a valuable resource to explore the mechanisms of male killing and symbiont-mediated protection, two cardinal features of many facultative endosymbionts. Most insect species, including important disease vectors and crop pests, harbor vertically transmitted endosymbiotic bacteria. These endosymbionts play key roles in their hosts’ fitness, including protecting them against natural enemies and manipulating their reproduction in ways that increase the frequency of symbiont infection. Little is known about the molecular mechanisms that underlie these processes. Here, we provide the first genome draft of a vertically transmitted male-killing Spiroplasma bacterium, the S. poulsonii MSRO strain harbored by D. melanogaster. Analysis of the S. poulsonii genome was complemented by proteomics and ex vivo metabolic experiments. Our results indicate that S. poulsonii has reduced metabolic capabilities and expresses divergent membrane lipoproteins and potential virulence factors that likely participate in Spiroplasma-host interactions. This work fills a gap in our knowledge of insect endosymbionts and provides tools with which to decipher the interaction between Spiroplasma bacteria and their well-characterized host D. melanogaster, which is emerging as a model of endosymbiosis.
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Draft Genome Sequences of Two Strains of Serratia spp. from the Midgut of the Malaria Mosquito Anopheles gambiae. GENOME ANNOUNCEMENTS 2015; 3:3/2/e00090-15. [PMID: 25767231 PMCID: PMC4357753 DOI: 10.1128/genomea.00090-15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Here, we report the annotated draft genome sequences of two strains of Serratia spp., Ag1 and Ag2, isolated from the midgut of two different strains of Anopheles gambiae. The genomes of these two strains are almost identical.
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Complete Genome Sequence of "Candidatus Sulcia muelleri" ML, an Obligate Nutritional Symbiont of Maize Leafhopper (Dalbulus maidis). GENOME ANNOUNCEMENTS 2015; 3:3/1/e01483-14. [PMID: 25635014 PMCID: PMC4319508 DOI: 10.1128/genomea.01483-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
“Candidatus Sulcia muelleri” is a symbiont of sap-feeding insects in the suborder Auchenorrhyncha. The strain “Ca. Sulcia muelleri” ML is associated with the maize leafhopper (Dalbulus maidis), collected in Brazil, which is a disease vector that affects corn production. Here, we report the complete genome sequence of this bacterium.
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Bolaños LM, Servín-Garcidueñas LE, Martínez-Romero E. Arthropod-Spiroplasma relationship in the genomic era. FEMS Microbiol Ecol 2014; 91:1-8. [PMID: 25764543 DOI: 10.1093/femsec/fiu008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The genus Spiroplasma comprises wall-less, low-GC bacteria that establish pathogenic, mutualistic and commensal symbiotic associations with arthropods and plants. This review focuses on the symbiotic relationships between Spiroplasma bacteria and arthropod hosts in the context of the available genomic sequences. Spiroplasma genomes are reduced and some contain highly repetitive plectrovirus-related sequences. Spiroplasma's diversity in viral invasion susceptibility, virulence factors, substrate utilization, genome dynamics and symbiotic associations with arthropods make this bacterial genus a biological model that provides insights about the evolutionary traits that shape bacterial symbiotic relationships with eukaryotes.
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Affiliation(s)
- Luis M Bolaños
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, México
| | - Luis E Servín-Garcidueñas
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, México
| | - Esperanza Martínez-Romero
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, México
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Complete Genome Sequence of Vibrio vulnificus 93U204, a Bacterium Isolated from Diseased Tilapia in Taiwan. GENOME ANNOUNCEMENTS 2014; 2:2/5/e01005-14. [PMID: 25278541 PMCID: PMC4183885 DOI: 10.1128/genomea.01005-14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Vibrio vulnificus 93U204 is a bacterium isolated from a moribund tilapia collected in Kaohsiung, Taiwan. Here, we report the complete genome sequence of this bacterium to facilitate the investigation of its pathogenicity and for comparative analyses with human-pathogenic strains within the same species.
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Ku C, Lo WS, Kuo CH. Molecular evolution of the actin-like MreB protein gene family in wall-less bacteria. Biochem Biophys Res Commun 2014; 446:927-32. [DOI: 10.1016/j.bbrc.2014.03.039] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 03/10/2014] [Indexed: 01/01/2023]
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