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Thia JA, Zhan D, Robinson K, Umina PA, Hoffmann AA, Yang Q. 'Drifting' Buchnera genomes track the microevolutionary trajectories of their aphid hosts. INSECT MOLECULAR BIOLOGY 2024. [PMID: 39031957 DOI: 10.1111/imb.12946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 07/08/2024] [Indexed: 07/22/2024]
Abstract
Evolution of Buchnera-aphid host symbioses is often studied among species at macroevolutionary scales. Investigations within species offer a different perspective about how eco-evolutionary processes shape patterns of genetic variation at microevolutionary scales. Our study leverages new and publicly available whole-genome sequencing data to study Buchnera-aphid host evolution in Myzus persicae, the peach potato aphid, a globally invasive and polyphagous pest. Across 43 different asexual, clonally reproducing isofemale strains, we examined patterns of genomic covariation between Buchnera and their aphid host and considered the distribution of mutations in protein-coding regions of the Buchnera genome. We found Buchnera polymorphisms within aphid strains, suggesting the presence of genetically different Buchnera strains within the same clonal lineage. Genetic distance between pairs of Buchnera samples was positively correlated to genetic distance between their aphid hosts, indicating shared evolutionary histories. However, there was no segregation of genetic variation for both M. persicae and Buchnera with plant host (Brassicaceae and non-tobacco Solanaceae) and no associations between genetic and geographic distance at global or regional spatial scales. Abundance patterns of non-synonymous mutations were similar to synonymous mutations in the Buchnera genome, and both mutation classes had similar site frequency spectra. We hypothesize that a predominance of neutral processes results in the Buchnera of M. persicae to simply 'drift' with the evolutionary trajectory of their aphid hosts. Our study presents a unique microevolutionary characterization of Buchnera-aphid host genomic covariation across multiple aphid clones. This provides a new perspective on the eco-evolutionary processes generating and maintaining polymorphisms in a major pest aphid species and its obligate primary endosymbiont.
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Affiliation(s)
- Joshua A Thia
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Dongwu Zhan
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Katie Robinson
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, New South Wales, Australia
| | - Paul A Umina
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
- Cesar Australia Pty Ltd, Melbourne, Victoria, Australia
| | - Ary A Hoffmann
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Qiong Yang
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
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Mahmoud FM, Pritsch K, Siani R, Benning S, Radl V, Kublik S, Bunk B, Spröer C, Schloter M. Comparative genomic analysis of strain Priestia megaterium B1 reveals conserved potential for adaptation to endophytism and plant growth promotion. Microbiol Spectr 2024; 12:e0042224. [PMID: 38916310 PMCID: PMC11302069 DOI: 10.1128/spectrum.00422-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 05/17/2024] [Indexed: 06/26/2024] Open
Abstract
In our study, we aimed to explore the genomic and phenotypic traits of Priestia megaterium strain B1, which was isolated from root material of healthy apple plants, to adapt to the endophytic lifestyle and promote plant growth. We identified putative genes encoding proteins involved in chemotaxis, flagella biosynthesis, biofilm formation, secretory systems, detoxification, transporters, and transcription regulation. Furthermore, B1 exhibited both swarming and swimming motilities, along with biofilm formation. Both genomic and physiological analyses revealed the potential of B1 to promote plant growth through the production of indole-3-acetic acid and siderophores, as well as the solubilization of phosphate and zinc. To deduce potential genomic features associated with endophytism across members of P. megaterium strains, we conducted a comparative genomic analysis involving 27 and 31 genomes of strains recovered from plant and soil habitats, respectively, in addition to our strain B1. Our results indicated a closed pan genome and comparable genome size of strains from both habitats, suggesting a facultative host association and adaptive lifestyle to both habitats. Additionally, we performed a sparse Partial Least Squares Discriminant Analysis to infer the most discriminative functional features of the two habitats based on Pfam annotation. Despite the distinctive clustering of both groups, functional enrichment analysis revealed no significant enrichment of any Pfam domain in both habitats. Furthermore, when assessing genetic elements related to adaptation to endophytism in each individual strain, we observed their widespread presence among strains from both habitats. Moreover, all members displayed potential genetic elements for promoting plant growth.IMPORTANCEBoth genomic and phenotypic analyses yielded valuable insights into the capacity of P. megaterium B1 to adapt to the plant niche and enhance its growth. The comparative genomic analysis revealed that P. megaterium members, whether derived from soil or plant sources, possess the essential genetic machinery for interacting with plants and enhancing their growth. The conservation of these traits across various strains of this species extends its potential application as a bio-stimulant in diverse environments. This significance also applies to strain B1, particularly regarding its application to enhance the growth of plants facing apple replant disease conditions.
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Affiliation(s)
- Fatma M. Mahmoud
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
- Botany and Microbiology Department, Faculty of Science, Suez Canal University, Ismailia, Egypt
| | - Karin Pritsch
- Research Unit for Environmental Simulations, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Roberto Siani
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Sarah Benning
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Viviane Radl
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
- Chair for Environmental Microbiology, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
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Pogoreutz C, Ziegler M. Frenemies on the reef? Resolving the coral-Endozoicomonas association. Trends Microbiol 2024; 32:422-434. [PMID: 38216372 DOI: 10.1016/j.tim.2023.11.006] [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: 10/20/2023] [Revised: 11/09/2023] [Accepted: 11/13/2023] [Indexed: 01/14/2024]
Abstract
Stony corals are poster child holobionts due to their intimate association with diverse microorganisms from all domains of life. We are only beginning to understand the diverse functions of most of these microbial associates, including potential main contributors to holobiont health and resilience. Among these, bacteria of the elusive genus Endozoicomonas are widely perceived as beneficial symbionts based on their genomic potential and their high prevalence and ubiquitous presence in coral tissues. Simultaneously, evidence of pathogenic and parasitic Endozoicomonas lineages in other marine animals is emerging. Synthesizing the current knowledge on the association of Endozoicomonas with marine holobionts, we challenge the perception of a purely mutualistic coral-Endozoicomonas relationship and propose directions to elucidate its role along the symbiotic spectrum.
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Affiliation(s)
- Claudia Pogoreutz
- EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy, 66860 Perpignan Cedex, France.
| | - Maren Ziegler
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32 (IFZ), 35392, Giessen, Germany.
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Arai H, Watada M, Kageyama D. Two male-killing Wolbachia from Drosophila birauraia that are closely related but distinct in genome structure. ROYAL SOCIETY OPEN SCIENCE 2024; 11:231502. [PMID: 38204789 PMCID: PMC10776216 DOI: 10.1098/rsos.231502] [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: 10/03/2023] [Accepted: 12/11/2023] [Indexed: 01/12/2024]
Abstract
Insects harbour diverse maternally inherited bacteria and viruses, some of which have evolved to kill the male progeny of their hosts (male killing: MK). The fly species Drosophila biauraria carries a maternally transmitted MK-inducing partiti-like virus, but it was unknown if it carries other MK-inducing endosymbionts. Here, we identified two male-killing Wolbachia strains (wBiau1 and wBiau2) from D. biauraria and compared their genomes to elucidate their evolutionary processes. The two strains were genetically closely related but had exceptionally different genome structures with considerable rearrangements compared with combinations of other Wolbachia strains. Despite substantial changes in the genome structure, the two Wolbachia strains did not experience gene losses that would disrupt the male-killing expression or persistence in the host population. The two Wolbachia-infected matrilines carried distinct mitochondrial haplotypes, suggesting that wBiau1 and wBiau2 have invaded D. biauraria independently and undergone considerable genome changes owing to unknown selective pressures in evolutionary history. This study demonstrated the presence of three male-killers from two distinct origins in one fly species and highlighted the diverse and rapid genome evolution of MK Wolbachia in the host.
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Affiliation(s)
- Hiroshi Arai
- National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki 305-0851, Japan
| | - Masayoshi Watada
- Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime 780-8857, Japan
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo 192-0397, Japan
| | - Daisuke Kageyama
- National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki 305-0851, Japan
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Ferrarini MG, Vallier A, Vincent-Monégat C, Dell'Aglio E, Gillet B, Hughes S, Hurtado O, Condemine G, Zaidman-Rémy A, Rebollo R, Parisot N, Heddi A. Coordination of host and endosymbiont gene expression governs endosymbiont growth and elimination in the cereal weevil Sitophilus spp. MICROBIOME 2023; 11:274. [PMID: 38087390 PMCID: PMC10717185 DOI: 10.1186/s40168-023-01714-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 10/30/2023] [Indexed: 12/18/2023]
Abstract
BACKGROUND Insects living in nutritionally poor environments often establish long-term relationships with intracellular bacteria that supplement their diets and improve their adaptive and invasive powers. Even though these symbiotic associations have been extensively studied on physiological, ecological, and evolutionary levels, few studies have focused on the molecular dialogue between host and endosymbionts to identify genes and pathways involved in endosymbiosis control and dynamics throughout host development. RESULTS We simultaneously analyzed host and endosymbiont gene expression during the life cycle of the cereal weevil Sitophilus oryzae, from larval stages to adults, with a particular emphasis on emerging adults where the endosymbiont Sodalis pierantonius experiences a contrasted growth-climax-elimination dynamics. We unraveled a constant arms race in which different biological functions are intertwined and coregulated across both partners. These include immunity, metabolism, metal control, apoptosis, and bacterial stress response. CONCLUSIONS The study of these tightly regulated functions, which are at the center of symbiotic regulations, provides evidence on how hosts and bacteria finely tune their gene expression and respond to different physiological challenges constrained by insect development in a nutritionally limited ecological niche. Video Abstract.
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Affiliation(s)
- Mariana Galvão Ferrarini
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621, Villeurbanne, France
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Agnès Vallier
- Univ Lyon, INRAE, INSA Lyon, BF2I, UMR 203, 69621, Villeurbanne, France
| | | | - Elisa Dell'Aglio
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621, Villeurbanne, France
| | - Benjamin Gillet
- Institut de Génomique Fonctionnelle de Lyon (IGFL), CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université de Lyon, Lyon, France
| | - Sandrine Hughes
- Institut de Génomique Fonctionnelle de Lyon (IGFL), CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université de Lyon, Lyon, France
| | - Ophélie Hurtado
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621, Villeurbanne, France
| | - Guy Condemine
- Univ Lyon, Université Lyon 1, INSA de Lyon, CNRS UMR 5240 Microbiologie Adaptation et Pathogénie, Villeurbanne, France
| | - Anna Zaidman-Rémy
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621, Villeurbanne, France
- Institut universitaire de France (IUF), Paris, France
| | - Rita Rebollo
- Univ Lyon, INRAE, INSA Lyon, BF2I, UMR 203, 69621, Villeurbanne, France
| | - Nicolas Parisot
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621, Villeurbanne, France.
| | - Abdelaziz Heddi
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621, Villeurbanne, France.
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Jackrel SL, White JD, Perez-Coronel E, Koch RY. Selection for oligotrophy among bacteria inhabiting host microbiomes. mBio 2023; 14:e0141523. [PMID: 37646528 PMCID: PMC10653850 DOI: 10.1128/mbio.01415-23] [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: 06/02/2023] [Accepted: 07/04/2023] [Indexed: 09/01/2023] Open
Abstract
IMPORTANCE Understanding how natural selection has historically shaped the traits of microbial populations comprising host microbiomes would help predict how the functions of these microbes may continue to evolve over space and time. Numerous host-associated microbes have been found to adapt to their host, sometimes becoming obligate symbionts, whereas free-living microbes are best known to adapt to their surrounding environment. Our study assessed the selective pressures of both the host environment and the surrounding external environment in shaping the functional potential of host-associated bacteria. Despite residing within the resource-rich microbiome of their hosts, we demonstrate that host-associated heterotrophic bacteria show evidence of trait selection that matches the nutrient availability of their broader surrounding environment. These findings illustrate the complex mix of selective pressures that likely shape the present-day function of bacteria found inhabiting host microbiomes. Our study lends insight into the shifts in function that may occur as environments fluctuate over time.
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Affiliation(s)
- Sara L. Jackrel
- Department of Ecology, Behavior and Evolution, University of California San Diego, La Jolla, California, USA
| | - Jeffrey D. White
- Department of Biology, Framingham State University, Framingham, Massachusetts, USA
| | - Elisabet Perez-Coronel
- Department of Ecology, Behavior and Evolution, University of California San Diego, La Jolla, California, USA
| | - Ryan Y. Koch
- Department of Ecology, Behavior and Evolution, University of California San Diego, La Jolla, California, USA
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Coluzzi C, Guillemet M, Mazzamurro F, Touchon M, Godfroid M, Achaz G, Glaser P, Rocha EPC. Chance Favors the Prepared Genomes: Horizontal Transfer Shapes the Emergence of Antibiotic Resistance Mutations in Core Genes. Mol Biol Evol 2023; 40:msad217. [PMID: 37788575 PMCID: PMC10575684 DOI: 10.1093/molbev/msad217] [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: 07/04/2023] [Revised: 09/08/2023] [Accepted: 09/19/2023] [Indexed: 10/05/2023] Open
Abstract
Bacterial lineages acquire novel traits at diverse rates in part because the genetic background impacts the successful acquisition of novel genes by horizontal transfer. Yet, how horizontal transfer affects the subsequent evolution of core genes remains poorly understood. Here, we studied the evolution of resistance to quinolones in Escherichia coli accounting for population structure. We found 60 groups of genes whose gain or loss induced an increase in the probability of subsequently becoming resistant to quinolones by point mutations in the gyrase and topoisomerase genes. These groups include functions known to be associated with direct mitigation of the effect of quinolones, with metal uptake, cell growth inhibition, biofilm formation, and sugar metabolism. Many of them are encoded in phages or plasmids. Although some of the chronologies may reflect epidemiological trends, many of these groups encoded functions providing latent phenotypes of antibiotic low-level resistance, tolerance, or persistence under quinolone treatment. The mutations providing resistance were frequent and accumulated very quickly. Their emergence was found to increase the rate of acquisition of other antibiotic resistances setting the path for multidrug resistance. Hence, our findings show that horizontal gene transfer shapes the subsequent emergence of adaptive mutations in core genes. In turn, these mutations further affect the subsequent evolution of resistance by horizontal gene transfer. Given the substantial gene flow within bacterial genomes, interactions between horizontal transfer and point mutations in core genes may be a key to the success of adaptation processes.
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Affiliation(s)
- Charles Coluzzi
- Institut Pasteur, Université Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Martin Guillemet
- Institut Pasteur, Université Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Fanny Mazzamurro
- Institut Pasteur, Université Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, Paris, France
- Collège Doctoral, Sorbonne Université, Paris, France
| | - Marie Touchon
- Institut Pasteur, Université Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Maxime Godfroid
- SMILE Group, Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Guillaume Achaz
- SMILE Group, Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Philippe Glaser
- Institut Pasteur, Université de Paris Cité, CNRS, UMR6047, Unité EERA, Paris, France
| | - Eduardo P C Rocha
- Institut Pasteur, Université Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, Paris, France
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Rodríguez-Gijón A, Buck M, Andersson AF, Izabel-Shen D, Nascimento FJA, Garcia SL. Linking prokaryotic genome size variation to metabolic potential and environment. ISME COMMUNICATIONS 2023; 3:25. [PMID: 36973336 PMCID: PMC10042847 DOI: 10.1038/s43705-023-00231-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 03/02/2023] [Accepted: 03/14/2023] [Indexed: 03/29/2023]
Abstract
While theories and models have appeared to explain genome size as a result of evolutionary processes, little work has shown that genome sizes carry ecological signatures. Our work delves into the ecological implications of microbial genome size variation in benthic and pelagic habitats across environmental gradients of the brackish Baltic Sea. While depth is significantly associated with genome size in benthic and pelagic brackish metagenomes, salinity is only correlated to genome size in benthic metagenomes. Overall, we confirm that prokaryotic genome sizes in Baltic sediments (3.47 Mbp) are significantly bigger than in the water column (2.96 Mbp). While benthic genomes have a higher number of functions than pelagic genomes, the smallest genomes coded for a higher number of module steps per Mbp for most of the functions irrespective of their environment. Some examples of this functions are amino acid metabolism and central carbohydrate metabolism. However, we observed that nitrogen metabolism was almost absent in pelagic genomes and was mostly present in benthic genomes. Finally, we also show that Bacteria inhabiting Baltic sediments and water column not only differ in taxonomy, but also in their metabolic potential, such as the Wood-Ljungdahl pathway or the presence of different hydrogenases. Our work shows how microbial genome size is linked to abiotic factors in the environment, metabolic potential and taxonomic identity of Bacteria and Archaea within aquatic ecosystems.
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Affiliation(s)
- Alejandro Rodríguez-Gijón
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, 106 91, Sweden.
- Science for Life Laboratory, Stockholm, Sweden.
| | - Moritz Buck
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anders F Andersson
- Science for Life Laboratory, Stockholm, Sweden
- Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Dandan Izabel-Shen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, 106 91, Sweden
| | - Francisco J A Nascimento
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, 106 91, Sweden
- Baltic Sea Centre, Stockholm University, Stockholm, Sweden
| | - Sarahi L Garcia
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, 106 91, Sweden.
- Science for Life Laboratory, Stockholm, Sweden.
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Weevil Carbohydrate Intake Triggers Endosymbiont Proliferation: A Trade-Off between Host Benefit and Endosymbiont Burden. mBio 2023; 14:e0333322. [PMID: 36779765 PMCID: PMC10127669 DOI: 10.1128/mbio.03333-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023] Open
Abstract
Nutritional symbioses between insects and intracellular bacteria (endosymbionts) are a major force of adaptation, allowing animals to colonize nutrient-poor ecological niches. Many beetles feeding on tyrosine-poor substrates rely on a surplus of aromatic amino acids produced by bacterial endosymbionts. This surplus of aromatic amino acids is crucial for the biosynthesis of a thick exoskeleton, the cuticle, which is made of a matrix of chitin with proteins and pigments built from tyrosine-derived molecules, providing an important defensive barrier against biotic and abiotic stress. Other endosymbiont-related advantages for beetles include faster development and improved fecundity. The association between Sitophilus oryzae and the Sodalis pierantonius endosymbiont represents a unique case study among beetles: endosymbionts undergo an exponential proliferation in young adults concomitant with the cuticle tanning, and then they are fully eliminated. While endosymbiont clearance, as well as total endosymbiont titer, are host-controlled processes, the mechanism triggering endosymbiont exponential proliferation remains poorly understood. Here, we show that endosymbiont exponential proliferation relies on host carbohydrate intake, unlike the total endosymbiont titer or the endosymbiont clearance, which are under host genetic control. Remarkably, insect fecundity was preserved, and the cuticle tanning was achieved, even when endosymbiont exponential proliferation was experimentally blocked, except in the context of a severely unbalanced diet. Moreover, a high endosymbiont titer coupled with nutrient shortage dramatically impacted host survival, revealing possible environment-dependent disadvantages for the host, likely due to the high energy cost of exponentially proliferating endosymbionts. IMPORTANCE Beetles thriving on tyrosine-poor diet sources often develop mutualistic associations with endosymbionts able to synthesize aromatic amino acids. This surplus of aromatic amino acids is used to reinforce the insect's protective cuticle. An exceptional feature of the Sitophilus oryzae/Sodalis pierantonius interaction is the exponential increase in endosymbiotic titer observed in young adult insects, in concomitance with cuticle biosynthesis. Here, we show that host carbohydrate intake triggers endosymbiont exponential proliferation, even in conditions that lead to the detriment of the host survival. In addition, when hosts thrive on a balanced diet, endosymbiont proliferation is dispensable for several host fitness traits. The endosymbiont exponential proliferation is therefore dependent on the nutritional status of the host, and its consequences on host cuticle biosynthesis and survival depend on food quality and availability.
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10
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Li Q, Cheng Y, Fan J, Chen J. Metabolic relay gene of aphid and primary symbiont as RNAi target loci for aphid control. FRONTIERS IN PLANT SCIENCE 2023; 13:1092638. [PMID: 36743566 PMCID: PMC9890070 DOI: 10.3389/fpls.2022.1092638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/23/2022] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Aphids form a stable and mutually beneficial relationship with their primary symbiont Buchnera aphidicola, which play an important role in providing the missing nutrients to the host aphid. Based on the genome sequence of wheat aphid Siotobion miscanthi and its primary symbiont Buchnera that we obtained in our previously study, we identified a metabolic relay gene, ilvA, involved in the isoleucine synthesis pathway between aphids and Buchnera. METHOD In this study, we identified the location and sequence structure of ilvA gene in aphid genome, the expression level in different instars and tissues of aphids, and the effect of reducing ilvA expression on the growth and development of aphids by bioinformatics analysis, quantitative PCR, RNAi and bioassay experiments. RESULT Our study showed that ilvA was expressed at the highest level in the 2nd instar of the aphid, while the expression of this gene was significantly higher in the aphid bacteriocytes than in other tissues. Notably, this gene is localized on the aphid sex chromosome and remains highly conserved and collinearity across different aphid genomes. Knocking down the expression of ilvA reduced the aphid body weight and production. However, the indices of mortality decreased slightly, but were not significantly different, compared to the control. DISCUSSION The results show that the relay genes between aphids and their symbionts in the metabolism of essential nutrients have potential roles in the growth and development of aphids, meanwhile, providing target loci and new ideas for RNAi-based aphid green control strategies.
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Affiliation(s)
- Qian Li
- College of Bioscience and Resource Environment/Key Laboratory of Urban Agriculture (North China), Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Beijing University of Agriculture, Beijing, China
- The State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yu Cheng
- The State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jia Fan
- The State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Julian Chen
- The State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Ministry of Agricultural and Rural Affairs -Center of Applied Biological International (MARA-CABI) Joint Laboratory for Bio-Safety, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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11
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Li T, Wei Y, Zhao C, Li S, Gao S, Zhang Y, Wu Y, Lu C. Facultative symbionts are potential agents of symbiont-mediated RNAi in aphids. Front Microbiol 2022; 13:1020461. [PMID: 36504780 PMCID: PMC9727308 DOI: 10.3389/fmicb.2022.1020461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 11/07/2022] [Indexed: 11/24/2022] Open
Abstract
Aphids are major crop pests, and they can be controlled through the application of the promising RNA interference (RNAi) techniques. However, chemical synthesis yield of dsRNA for RNAi is low and costly. Another sustainable aphid pest control strategy takes advantage of symbiont-mediated RNAi (SMR), which can generate dsRNA by engineered microbes. Aphid host the obligate endosymbiont Buchnera aphidicola and various facultative symbionts that not only have a wide host range but are also vertically and horizontally transmitted. Thus, we described the potential of facultative symbionts in aphid pest control by SMR. We summarized the community and host range of these facultative symbionts, and then reviewed their probable horizontal transmitted routes and ecological functions. Moreover, recent advances in the cultivation and genetic engineering of aphid facultative symbionts were discussed. In addition, current legislation of dsRNA-based pest control strategies and their safety assessments were reviewed.
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Affiliation(s)
- Tong Li
- Institute of Plant Protection, Henan Key Laboratory of Crop Pest Control/Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Yongjun Wei
- School of Pharmaceutical Sciences, Laboratory of Synthetic Biology, Zhengzhou University, Zhengzhou, China
| | - Chenchen Zhao
- Henan International Laboratory for Green Pest Control /College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Shaojian Li
- Institute of Plant Protection, Henan Key Laboratory of Crop Pest Control/Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Suxia Gao
- Institute of Plant Protection, Henan Key Laboratory of Crop Pest Control/Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Yuanchen Zhang
- College of Biological and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Yuqing Wu
- Institute of Plant Protection, Henan Key Laboratory of Crop Pest Control/Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Chuantao Lu
- Institute of Plant Protection, Henan Key Laboratory of Crop Pest Control/Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Academy of Agricultural Sciences, Zhengzhou, China,Chuantao Lu
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12
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Garza DR, von Meijenfeldt FAB, van Dijk B, Boleij A, Huynen MA, Dutilh BE. Nutrition or nature: using elementary flux modes to disentangle the complex forces shaping prokaryote pan-genomes. BMC Ecol Evol 2022; 22:101. [PMID: 35974327 PMCID: PMC9382767 DOI: 10.1186/s12862-022-02052-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 07/22/2022] [Indexed: 11/15/2022] Open
Abstract
Background Microbial pan-genomes are shaped by a complex combination of stochastic and deterministic forces. Even closely related genomes exhibit extensive variation in their gene content. Understanding what drives this variation requires exploring the interactions of gene products with each other and with the organism’s external environment. However, to date, conceptual models of pan-genome dynamics often represent genes as independent units and provide limited information about their mechanistic interactions. Results We simulated the stochastic process of gene-loss using the pooled genome-scale metabolic reaction networks of 46 taxonomically diverse bacterial and archaeal families as proxies for their pan-genomes. The frequency by which reactions are retained in functional networks when stochastic gene loss is simulated in diverse environments allowed us to disentangle the metabolic reactions whose presence depends on the metabolite composition of the external environment (constrained by “nutrition”) from those that are independent of the environment (constrained by “nature”). By comparing the frequency of reactions from the first group with their observed frequencies in bacterial and archaeal families, we predicted the metabolic niches that shaped the genomic composition of these lineages. Moreover, we found that the lineages that were shaped by a more diverse metabolic niche also occur in more diverse biomes as assessed by global environmental sequencing datasets. Conclusion We introduce a computational framework for analyzing and interpreting pan-reactomes that provides novel insights into the ecological and evolutionary drivers of pan-genome dynamics. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-02052-3.
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13
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The C-Terminal Repeat Units of SpaA Mediate Adhesion of Erysipelothrix rhusiopathiae to Host Cells and Regulate Its Virulence. BIOLOGY 2022; 11:biology11071010. [PMID: 36101391 PMCID: PMC9311908 DOI: 10.3390/biology11071010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/22/2022] [Accepted: 06/27/2022] [Indexed: 11/17/2022]
Abstract
Simple Summary Erysipelothrix rhusiopathiae is an important zoonotic pathogen, which poses a serious harm to the pig industry. We aimed to evaluate the genomic differences between virulent and avirulent strains to study the pathogenic mechanism of Erysipelothrix rhusiopathiae. The results showed that the spaA gene of avirulent strain lacked 120bp, encoding repeat units at the C-terminal of SpaA, the virulence of the virulent strain with this 120 bp deletion was attenuated, and the mutant strain decreased adhesion to porcine iliac artery endothelial cells. Abstract Erysipelothrix rhusiopathiae is a causative agent of erysipelas in animals and erysipeloid in humans. However, current information regarding E. rhusiopathiae pathogenesis remains limited. Previously, we identified two E. rhusiopathiae strains, SE38 and G4T10, which were virulent and avirulent in pigs, respectively. Here, to further study the pathogenic mechanism of E. rhusiopathiae, we sequenced and assembled the genomes of strains SE38 and G4T10, and performed a comparative genomic analysis to identify differences or mutations in virulence-associated genes. Next, we comparatively analyzed 25 E. rhusiopathiae virulence-associated genes in SE38 and G4T10. Compared with that of SE38, the spaA gene of the G4T10 strain lacked 120 bp, encoding repeat units at the C-terminal of SpaA. To examine whether these deletions or splits influence E. rhusiopathiae virulence, these 120 bp were successfully deleted from the spaA gene in strain SE38 by homologous recombination. The mutant strain ΔspaA displayed attenuated virulence in mice and decreased adhesion to porcine iliac artery endothelial cells, which was also observed using the corresponding mutant protein SpaA’. Our results demonstrate that SpaA-mediated adhesion between E. rhusiopathiae and host cells is dependent on its C-terminal repeat units.
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14
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Martinez-Gutierrez CA, Aylward FO. Genome size distributions in bacteria and archaea are strongly linked to evolutionary history at broad phylogenetic scales. PLoS Genet 2022; 18:e1010220. [PMID: 35605022 PMCID: PMC9166353 DOI: 10.1371/journal.pgen.1010220] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 06/03/2022] [Accepted: 04/26/2022] [Indexed: 12/30/2022] Open
Abstract
The evolutionary forces that determine genome size in bacteria and archaea have been the subject of intense debate over the last few decades. Although the preferential loss of genes observed in prokaryotes is explained through the deletional bias, factors promoting and preventing the fixation of such gene losses often remain unclear. Importantly, statistical analyses on this topic typically do not consider the potential bias introduced by the shared ancestry of many lineages, which is critical when using species as data points because of the potential dependence on residuals. In this study, we investigated the genome size distributions across a broad diversity of bacteria and archaea to evaluate if this trait is phylogenetically conserved at broad phylogenetic scales. After model fit, Pagel's lambda indicated a strong phylogenetic signal in genome size data, suggesting that the diversification of this trait is influenced by shared evolutionary histories. We used a phylogenetic generalized least-squares analysis (PGLS) to test whether phylogeny influences the predictability of genome size from dN/dS ratios and 16S copy number, two variables that have been previously linked to genome size. These results confirm that failure to account for evolutionary history can lead to biased interpretations of genome size predictors. Overall, our results indicate that although bacteria and archaea can rapidly gain and lose genetic material through gene transfers and deletions, respectively, phylogenetic signal for genome size distributions can still be recovered at broad phylogenetic scales that should be taken into account when inferring the drivers of genome size evolution.
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Affiliation(s)
| | - Frank O. Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, Virginia, United States of America
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15
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Uthanumallian K, Iha C, Repetti SI, Chan CX, Bhattacharya D, Duchene S, Verbruggen H. Tightly Constrained Genome Reduction and Relaxation of Purifying Selection during Secondary Plastid Endosymbiosis. Mol Biol Evol 2022; 39:msab295. [PMID: 34613411 PMCID: PMC8763093 DOI: 10.1093/molbev/msab295] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Endosymbiosis, the establishment of a former free-living prokaryotic or eukaryotic cell as an organelle inside a host cell, can dramatically alter the genomic architecture of the endosymbiont. Plastids or chloroplasts, the light-harvesting organelle of photosynthetic eukaryotes, are excellent models to study this phenomenon because plastid origin has occurred multiple times in evolution. Here, we investigate the genomic signature of molecular processes acting through secondary plastid endosymbiosis-the origination of a new plastid from a free-living eukaryotic alga. We used phylogenetic comparative methods to study gene loss and changes in selective regimes on plastid genomes, focusing on green algae that have given rise to three independent lineages with secondary plastids (euglenophytes, chlorarachniophytes, and Lepidodinium). Our results show an overall increase in gene loss associated with secondary endosymbiosis, but this loss is tightly constrained by the retention of genes essential for plastid function. The data show that secondary plastids have experienced temporary relaxation of purifying selection during secondary endosymbiosis. However, this process is tightly constrained, with selection relaxed only relative to the background in primary plastids. Purifying selection remains strong in absolute terms even during the endosymbiosis events. Selection intensity rebounds to pre-endosymbiosis levels following endosymbiosis events, demonstrating the changes in selection efficiency during different origin phases of secondary plastids. Independent endosymbiosis events in the euglenophytes, chlorarachniophytes, and Lepidodinium differ in their degree of relaxation of selection, highlighting the different evolutionary contexts of these events. This study reveals the selection-drift interplay during secondary endosymbiosis and evolutionary parallels during organellogenesis.
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Affiliation(s)
| | - Cintia Iha
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
| | - Sonja I Repetti
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
| | - Cheong Xin Chan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | | | - Sebastian Duchene
- Deptartment of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
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16
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Szabó G, Schulz F, Manzano-Marín A, Toenshoff ER, Horn M. Evolutionarily recent dual obligatory symbiosis among adelgids indicates a transition between fungus- and insect-associated lifestyles. THE ISME JOURNAL 2022; 16:247-256. [PMID: 34294881 PMCID: PMC8692619 DOI: 10.1038/s41396-021-01056-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 06/28/2021] [Accepted: 07/01/2021] [Indexed: 02/07/2023]
Abstract
Adelgids (Insecta: Hemiptera: Adelgidae) form a small group of insects but harbor a surprisingly diverse set of bacteriocyte-associated endosymbionts, which suggest multiple replacement and acquisition of symbionts over evolutionary time. Specific pairs of symbionts have been associated with adelgid lineages specialized on different secondary host conifers. Using a metagenomic approach, we investigated the symbiosis of the Adelges laricis/Adelges tardus species complex containing betaproteobacterial ("Candidatus Vallotia tarda") and gammaproteobacterial ("Candidatus Profftia tarda") symbionts. Genomic characteristics and metabolic pathway reconstructions revealed that Vallotia and Profftia are evolutionary young endosymbionts, which complement each other's role in essential amino acid production. Phylogenomic analyses and a high level of genomic synteny indicate an origin of the betaproteobacterial symbiont from endosymbionts of Rhizopus fungi. This evolutionary transition was accompanied with substantial loss of functions related to transcription regulation, secondary metabolite production, bacterial defense mechanisms, host infection, and manipulation. The transition from fungus to insect endosymbionts extends our current framework about evolutionary trajectories of host-associated microbes.
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Affiliation(s)
- Gitta Szabó
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
- Department of Internal Medicine and Oncology, Semmelweis University, Budapest, Hungary.
| | - Frederik Schulz
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- US Department of Energy (DOE) Joint Genome Institute, Berkeley, CA, USA
| | - Alejandro Manzano-Marín
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Elena Rebecca Toenshoff
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Matthias Horn
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
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17
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Wittmeyer KT, Oppenheim SJ, Hopper KR. Assemblies of the genomes of parasitic wasps using meta-assembly and scaffolding with genetic linkage. G3 (BETHESDA, MD.) 2021; 12:6423991. [PMID: 34751385 PMCID: PMC8727961 DOI: 10.1093/g3journal/jkab386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/25/2021] [Indexed: 01/09/2023]
Abstract
Safe, effective biological-control introductions against invasive pests depend on narrowly host-specific natural enemies with the ability to adapt to a changing environment. As part of a project on the genetic architectures of these traits, we assembled and annotated the genomes of two aphid parasitoids, Aphelinus atriplicis and Aphelinus certus. We report here several assemblies of A. atriplicis made with Illumina and PacBio data, which we combined into a meta-assembly. We scaffolded the meta-assembly with markers from a genetic map of hybrids between A. atriplicis and A. certus. We used this genetic-linkage scaffolded (GLS) assembly of A. atriplicis to scaffold a de novo assembly of A. certus. The de novo assemblies of A. atriplicis differed in contiguity, and the meta-assembly of these assemblies was more contiguous than the best de novo assembly. Scaffolding with genetic-linkage data allowed chromosomal-level assembly of the A. atriplicis genome and scaffolding a de novo assembly of A. certus with this GLS assembly, greatly increased the contiguity of the A. certus assembly to the point where it was also at the chromosomal-level. However, completeness of the A. atriplicis assembly, as measured by percent complete, single-copy BUSCO hymenopteran genes, varied little among de novo assemblies and was not increased by meta-assembly or genetic scaffolding. Furthermore, the greater contiguity of the meta-assembly and GLS assembly had little or no effect on the numbers of genes identified, the proportions with homologs or functional annotations. Increased contiguity of the A. certus assembly provided modest improvement in assembly completeness, as measured by percent complete, single-copy BUSCO hymenopteran genes. The total genic sequence increased, and while the number of genes declined, gene length increased, which together suggest greater accuracy of gene models. More contiguous assemblies provide uses other than gene annotation, for example, identifying the genes associated with quantitative trait loci and understanding of chromosomal rearrangements associated with speciation.
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Affiliation(s)
- Kameron T Wittmeyer
- USDA-ARS, Beneficial Insect Introductions Research Unit, Newark, DE 19713, USA
| | | | - Keith R Hopper
- USDA-ARS, Beneficial Insect Introductions Research Unit, Newark, DE 19713, USA,Corresponding author: USDA-ARS, Beneficial Insect Introductions Research Unit, 501 South Chapel Street, Newark, DE 19713, USA.
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18
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Keepers KG, Pogoda CS, Lendemer JC, Kane NC, Manzitto-Tripp EA. Author response to Tagirdzhanova et al. (2021): "Lichen fungi do not depend on alga for ATP production: A comment on Pogoda et al. (2018)". Mol Ecol 2021; 30:4160-4161. [PMID: 34251071 DOI: 10.1111/mec.16053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 06/29/2021] [Indexed: 11/30/2022]
Affiliation(s)
- Kyle G Keepers
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Cloe S Pogoda
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - James C Lendemer
- Institute of Systematic Botany, The New York Botanical Garden, New York City, New York, USA
| | - Nolan C Kane
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Erin A Manzitto-Tripp
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA.,Museum of Natural History, University of Colorado, Boulder, Colorado, USA
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19
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Gauthier J, Boulain H, van Vugt JJFA, Baudry L, Persyn E, Aury JM, Noel B, Bretaudeau A, Legeai F, Warris S, Chebbi MA, Dubreuil G, Duvic B, Kremer N, Gayral P, Musset K, Josse T, Bigot D, Bressac C, Moreau S, Periquet G, Harry M, Montagné N, Boulogne I, Sabeti-Azad M, Maïbèche M, Chertemps T, Hilliou F, Siaussat D, Amselem J, Luyten I, Capdevielle-Dulac C, Labadie K, Merlin BL, Barbe V, de Boer JG, Marbouty M, Cônsoli FL, Dupas S, Hua-Van A, Le Goff G, Bézier A, Jacquin-Joly E, Whitfield JB, Vet LEM, Smid HM, Kaiser L, Koszul R, Huguet E, Herniou EA, Drezen JM. Chromosomal scale assembly of parasitic wasp genome reveals symbiotic virus colonization. Commun Biol 2021; 4:104. [PMID: 33483589 PMCID: PMC7822920 DOI: 10.1038/s42003-020-01623-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 12/10/2020] [Indexed: 02/06/2023] Open
Abstract
Endogenous viruses form an important proportion of eukaryote genomes and a source of novel functions. How large DNA viruses integrated into a genome evolve when they confer a benefit to their host, however, remains unknown. Bracoviruses are essential for the parasitism success of parasitoid wasps, into whose genomes they integrated ~103 million years ago. Here we show, from the assembly of a parasitoid wasp genome at a chromosomal scale, that bracovirus genes colonized all ten chromosomes of Cotesia congregata. Most form clusters of genes involved in particle production or parasitism success. Genomic comparison with another wasp, Microplitis demolitor, revealed that these clusters were already established ~53 mya and thus belong to remarkably stable genomic structures, the architectures of which are evolutionary constrained. Transcriptomic analyses highlight temporal synchronization of viral gene expression without resulting in immune gene induction, suggesting that no conflicts remain between ancient symbiotic partners when benefits to them converge.
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Affiliation(s)
- Jérémy Gauthier
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France ,grid.466902.f0000 0001 2248 6951Geneva Natural History Museum, 1208 Geneva, Switzerland
| | - Hélène Boulain
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France ,grid.418656.80000 0001 1551 0562EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Joke J. F. A. van Vugt
- grid.418375.c0000 0001 1013 0288Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Lyam Baudry
- Institut Pasteur, Unité Régulation Spatiale des Génomes, UMR 3525, CNRS, Paris, 75015 France ,grid.462844.80000 0001 2308 1657Sorbonne Université, Collège Doctoral, 75005 Paris, France
| | - Emma Persyn
- grid.462350.6Sorbonne Université, INRAE, CNRS, IRD, UPEC, Univ. de Paris, Institute of Ecology and Environmental Science of Paris (iEES-Paris), 75005 Paris, France
| | - Jean-Marc Aury
- grid.8390.20000 0001 2180 5818Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Benjamin Noel
- grid.8390.20000 0001 2180 5818Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Anthony Bretaudeau
- grid.410368.80000 0001 2191 9284IGEPP, INRAE, Institut Agro, Univ Rennes, 35000 Rennes, France ,grid.420225.30000 0001 2298 7270Univ Rennes, Inria, CNRS, IRISA, 35000 Rennes, France
| | - Fabrice Legeai
- grid.410368.80000 0001 2191 9284IGEPP, INRAE, Institut Agro, Univ Rennes, 35000 Rennes, France ,grid.420225.30000 0001 2298 7270Univ Rennes, Inria, CNRS, IRISA, 35000 Rennes, France
| | - Sven Warris
- grid.4818.50000 0001 0791 5666Applied Bioinformatics, Wageningen University & Research, Wageningen, The Netherlands
| | - Mohamed A. Chebbi
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Géraldine Dubreuil
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Bernard Duvic
- grid.503158.aUniversité Montpellier, INRAE, DGIMI, 34095 Montpellier, France
| | - Natacha Kremer
- grid.462854.90000 0004 0386 3493Laboratoire de Biométrie et Biologie Evolutive Université de Lyon, Université Claude Bernard Lyon 1, CNRS, UMR 5558, 43 bd du 11 novembre 1918, bat. G. Mendel, 69622 Villeurbanne Cedex, France
| | - Philippe Gayral
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Karine Musset
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Thibaut Josse
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Diane Bigot
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Christophe Bressac
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Sébastien Moreau
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Georges Periquet
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Myriam Harry
- grid.460789.40000 0004 4910 6535Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
| | - Nicolas Montagné
- grid.462350.6Sorbonne Université, INRAE, CNRS, IRD, UPEC, Univ. de Paris, Institute of Ecology and Environmental Science of Paris (iEES-Paris), 75005 Paris, France
| | - Isabelle Boulogne
- grid.462350.6Sorbonne Université, INRAE, CNRS, IRD, UPEC, Univ. de Paris, Institute of Ecology and Environmental Science of Paris (iEES-Paris), 75005 Paris, France
| | - Mahnaz Sabeti-Azad
- grid.462350.6Sorbonne Université, INRAE, CNRS, IRD, UPEC, Univ. de Paris, Institute of Ecology and Environmental Science of Paris (iEES-Paris), 75005 Paris, France
| | - Martine Maïbèche
- grid.462350.6Sorbonne Université, INRAE, CNRS, IRD, UPEC, Univ. de Paris, Institute of Ecology and Environmental Science of Paris (iEES-Paris), 75005 Paris, France
| | - Thomas Chertemps
- grid.462350.6Sorbonne Université, INRAE, CNRS, IRD, UPEC, Univ. de Paris, Institute of Ecology and Environmental Science of Paris (iEES-Paris), 75005 Paris, France
| | - Frédérique Hilliou
- grid.435437.20000 0004 0385 8766Université Côte d’Azur, INRAE, CNRS, ISA, 06903 Sophia-Antipolis, France
| | - David Siaussat
- grid.462350.6Sorbonne Université, INRAE, CNRS, IRD, UPEC, Univ. de Paris, Institute of Ecology and Environmental Science of Paris (iEES-Paris), 75005 Paris, France
| | - Joëlle Amselem
- grid.507621.7Université Paris-Saclay, INRAE, URGI, 78026 Versailles, France
| | - Isabelle Luyten
- grid.507621.7Université Paris-Saclay, INRAE, URGI, 78026 Versailles, France
| | - Claire Capdevielle-Dulac
- grid.460789.40000 0004 4910 6535Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
| | - Karine Labadie
- grid.8390.20000 0001 2180 5818Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Bruna Laís Merlin
- grid.11899.380000 0004 1937 0722Insect Interactions Laboratory, Department of Entomology and Acarology, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo 13418-900 Brazil
| | - Valérie Barbe
- grid.8390.20000 0001 2180 5818Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Jetske G. de Boer
- grid.418375.c0000 0001 1013 0288Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands ,grid.4818.50000 0001 0791 5666Laboratory of Entomology, Wageningen University, P.O. Box 16, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands ,grid.4830.f0000 0004 0407 1981Evolutionary Genetics, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Martial Marbouty
- Institut Pasteur, Unité Régulation Spatiale des Génomes, UMR 3525, CNRS, Paris, 75015 France
| | - Fernando Luis Cônsoli
- grid.11899.380000 0004 1937 0722Insect Interactions Laboratory, Department of Entomology and Acarology, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo 13418-900 Brazil
| | - Stéphane Dupas
- grid.460789.40000 0004 4910 6535Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
| | - Aurélie Hua-Van
- grid.460789.40000 0004 4910 6535Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
| | - Gaelle Le Goff
- grid.435437.20000 0004 0385 8766Université Côte d’Azur, INRAE, CNRS, ISA, 06903 Sophia-Antipolis, France
| | - Annie Bézier
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Emmanuelle Jacquin-Joly
- grid.462350.6Sorbonne Université, INRAE, CNRS, IRD, UPEC, Univ. de Paris, Institute of Ecology and Environmental Science of Paris (iEES-Paris), 75005 Paris, France
| | - James B. Whitfield
- Department of Entomology, 320 Morrill Hall, 505 South Goodwin Avenue, University of Illinois, Urbana, IL 61801 USA
| | - Louise E. M. Vet
- grid.418375.c0000 0001 1013 0288Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands ,grid.4818.50000 0001 0791 5666Laboratory of Entomology, Wageningen University, P.O. Box 16, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Hans M. Smid
- grid.4818.50000 0001 0791 5666Laboratory of Entomology, Wageningen University, P.O. Box 16, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Laure Kaiser
- grid.460789.40000 0004 4910 6535Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
| | - Romain Koszul
- Institut Pasteur, Unité Régulation Spatiale des Génomes, UMR 3525, CNRS, Paris, 75015 France
| | - Elisabeth Huguet
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Elisabeth A. Herniou
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Jean-Michel Drezen
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
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20
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Lobb B, Tremblay BJM, Moreno-Hagelsieb G, Doxey AC. An assessment of genome annotation coverage across the bacterial tree of life. Microb Genom 2020; 6. [PMID: 32124724 PMCID: PMC7200070 DOI: 10.1099/mgen.0.000341] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Although gene-finding in bacterial genomes is relatively straightforward, the automated assignment of gene function is still challenging, resulting in a vast quantity of hypothetical sequences of unknown function. But how prevalent are hypothetical sequences across bacteria, what proportion of genes in different bacterial genomes remain unannotated, and what factors affect annotation completeness? To address these questions, we surveyed over 27 000 bacterial genomes from the Genome Taxonomy Database, and measured genome annotation completeness as a function of annotation method, taxonomy, genome size, 'research bias' and publication date. Our analysis revealed that 52 and 79 % of the average bacterial proteome could be functionally annotated based on protein and domain-based homology searches, respectively. Annotation coverage using protein homology search varied significantly from as low as 14 % in some species to as high as 98 % in others. We found that taxonomy is a major factor influencing annotation completeness, with distinct trends observed across the microbial tree (e.g. the lowest level of completeness was found in the Patescibacteria lineage). Most lineages showed a significant association between genome size and annotation incompleteness, likely reflecting a greater degree of uncharacterized sequences in 'accessory' proteomes than in 'core' proteomes. Finally, research bias, as measured by publication volume, was also an important factor influencing genome annotation completeness, with early model organisms showing high completeness levels relative to other genomes in their own taxonomic lineages. Our work highlights the disparity in annotation coverage across the bacterial tree of life and emphasizes a need for more experimental characterization of accessory proteomes as well as understudied lineages.
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Affiliation(s)
- Briallen Lobb
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
| | | | - Gabriel Moreno-Hagelsieb
- Department of Biology, Wilfrid Laurier University, 75 University Avenue West, Waterloo, ON, Canada
| | - Andrew C Doxey
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
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21
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Masson F, Lemaitre B. Growing Ungrowable Bacteria: Overview and Perspectives on Insect Symbiont Culturability. Microbiol Mol Biol Rev 2020; 84:e00089-20. [PMID: 33177190 PMCID: PMC7667007 DOI: 10.1128/mmbr.00089-20] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Insects are often involved in endosymbiosis, that is, the housing of symbiotic microbes within their tissues or within their cells. Endosymbionts are a major driving force in insects' evolution, because they dramatically affect their host physiology and allow them to adapt to new niches, for example, by complementing their diet or by protecting them against pathogens. Endosymbiotic bacteria are, however, fastidious and therefore difficult to manipulate outside of their hosts, especially intracellular species. The coevolution between hosts and endosymbionts leads to alterations in the genomes of endosymbionts, limiting their ability to cope with changing environments. Consequently, few insect endosymbionts are culturable in vitro and genetically tractable, making functional genetics studies impracticable on most endosymbiotic bacteria. However, recently, major progress has been made in manipulating several intracellular endosymbiont species in vitro, leading to astonishing discoveries on their physiology and the way they interact with their host. This review establishes a comprehensive picture of the in vitro tractability of insect endosymbiotic bacteria and addresses the reason why most species are not culturable. By compiling and discussing the latest developments in the design of custom media and genetic manipulation protocols, it aims at providing new leads to expand the range of tractable endosymbionts and foster genetic research on these models.
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Affiliation(s)
- Florent Masson
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Bruno Lemaitre
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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22
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Koskella B, Bergelson J. The study of host-microbiome (co)evolution across levels of selection. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190604. [PMID: 32772660 PMCID: PMC7435161 DOI: 10.1098/rstb.2019.0604] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/01/2020] [Indexed: 02/07/2023] Open
Abstract
Microorganismal diversity can be explained in large part by selection imposed from both the abiotic and biotic environments, including-in the case of host-associated microbiomes-interactions with eukaryotes. As such, the diversity of host-associated microbiomes can be usefully studied across a variety of scales: within a single host over time, among host genotypes within a population, between populations and among host species. A plethora of recent studies across these scales and across diverse systems are: (i) exemplifying the importance of the host genetics in shaping microbiome composition; (ii) uncovering the role of the microbiome in shaping key host phenotypes; and (iii) highlighting the dynamic nature of the microbiome. They have also raised a critical question: do these complex associations fit within our existing understanding of evolution and coevolution, or do these often intimate and seemingly cross-generational interactions follow novel evolutionary rules from those previously identified? Herein, we describe the known importance of (co)evolution in host-microbiome systems, placing the existing data within extant frameworks that have been developed over decades of study, and ask whether there are unique properties of host-microbiome systems that require a paradigm shift. By examining when and how selection can act on the host and its microbiome as a unit (termed, the holobiont), we find that the existing conceptual framework, which focuses on individuals, as well as interactions among individuals and groups, is generally well suited for understanding (co)evolutionary change in these intimate assemblages. This article is part of the theme issue 'The role of the microbiome in host evolution'.
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Affiliation(s)
- Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
| | - Joy Bergelson
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
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23
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Kashkouli M, Castelli M, Floriano AM, Bandi C, Epis S, Fathipour Y, Mehrabadi M, Sassera D. Characterization of a novel Pantoea symbiont allows inference of a pattern of convergent genome reduction in bacteria associated with Pentatomidae. Environ Microbiol 2020; 23:36-50. [PMID: 32686279 DOI: 10.1111/1462-2920.15169] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 07/15/2020] [Indexed: 11/29/2022]
Abstract
Phytophagous stink bugs typically harbor nutritional symbiotic bacteria in their midgut, to integrate their unbalanced diet. In the Pentatomidae, most symbionts are affiliated to the genus Pantoea, and are polyphyletic. This suggests a scenario of an ancestral establishment of symbiosis, followed by multiple symbiont replacement events by akin environmental bacteria in different host lineages. In this study, a novel Pantoeaspecies ('CandidatusPantoea persica') was characterized from the gut of the pentatomid Acrosternum arabicum, and shown to be highly abundant in a specific portion of the gut and necessary for the host development. The genome of the symbiont (2.9 Mb), while presenting putative host-supportive metabolic pathways, including those for amino acids and vitamin synthesis, showed a high level of pseudogenization, indicating ongoing genome reduction. Comparative analyses with other free-living and symbiotic Pantoea highlighted a convergent pattern of genome reduction in symbionts of pentatomids, putatively following the typical phases modelized in obligate nutritional symbionts of insects. Additionally, this system has distinctive traits, as hosts are closely related, and symbionts originated multiple independent times from closely related free-living bacteria, displaying convergent and independent conspicuous genome reduction. Due to such peculiarities, this may become an ideal model to study genome evolutionary processes in insect symbionts.
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Affiliation(s)
- Marzieh Kashkouli
- Department of Entomology, Faculty of Agriculture, Tarbiat Modares University, Tehran, 14115-336, Iran
| | - Michele Castelli
- Department of Biosciences and Pediatric Clinical Research Center, University of Milan, Milan, 20133, Italy.,Department of Biology and Biotechnology, University of Pavia, 27100, Italy
| | - Anna M Floriano
- Department of Biology and Biotechnology, University of Pavia, 27100, Italy
| | - Claudio Bandi
- Department of Biosciences and Pediatric Clinical Research Center, University of Milan, Milan, 20133, Italy
| | - Sara Epis
- Department of Biosciences and Pediatric Clinical Research Center, University of Milan, Milan, 20133, Italy
| | - Yaghoub Fathipour
- Department of Entomology, Faculty of Agriculture, Tarbiat Modares University, Tehran, 14115-336, Iran
| | - Mohammad Mehrabadi
- Department of Entomology, Faculty of Agriculture, Tarbiat Modares University, Tehran, 14115-336, Iran
| | - Davide Sassera
- Department of Biology and Biotechnology, University of Pavia, 27100, Italy
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24
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Medina Munoz M, Spencer N, Enomoto S, Dale C, Rio RVM. Quorum sensing sets the stage for the establishment and vertical transmission of Sodalis praecaptivus in tsetse flies. PLoS Genet 2020; 16:e1008992. [PMID: 32797092 PMCID: PMC7449468 DOI: 10.1371/journal.pgen.1008992] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 08/26/2020] [Accepted: 07/14/2020] [Indexed: 12/19/2022] Open
Abstract
Bacterial virulence factors facilitate host colonization and set the stage for the evolution of parasitic and mutualistic interactions. The Sodalis-allied clade of bacteria exhibit striking diversity in the range of both plant and animal feeding insects they inhabit, suggesting the appropriation of universal molecular mechanisms that facilitate establishment. Here, we report on the infection of the tsetse fly by free-living Sodalis praecaptivus, a close relative of many Sodalis-allied symbionts. Key genes involved in quorum sensing, including the homoserine lactone synthase (ypeI) and response regulators (yenR and ypeR) are integral for the benign colonization of S. praecaptivus. Mutants lacking ypeI, yenR and ypeR compromised tsetse survival as a consequence of their inability to repress virulence. Genes under quorum sensing, including homologs of the binary insecticidal toxin PirAB and a putative symbiosis-promoting factor CpmAJ, demonstrated negative and positive impacts, respectively, on tsetse survival. Taken together with results obtained from experiments involving weevils, this work shows that quorum sensing virulence suppression plays an integral role in facilitating the establishment of Sodalis-allied symbionts in diverse insect hosts. This knowledge contributes to the understanding of the early evolutionary steps involved in the formation of insect-bacterial symbiosis. Further, despite having no established history of interaction with tsetse, S. praecaptivus can infect reproductive tissues, enabling vertical transmission through adenotrophic viviparity within a single host generation. This creates an option for the use of S. praecaptivus in the biocontrol of insect disease vectors via paratransgenesis.
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Affiliation(s)
- Miguel Medina Munoz
- Department of Biology, Eberly College of Arts and Sciences, West Virginia University, Morgantown, WV, United States of America
| | - Noah Spencer
- Department of Biology, Eberly College of Arts and Sciences, West Virginia University, Morgantown, WV, United States of America
| | - Shinichiro Enomoto
- Department of Biology, University of Utah, Salt Lake City, UT, United States of America
| | - Colin Dale
- Department of Biology, University of Utah, Salt Lake City, UT, United States of America
| | - Rita V. M. Rio
- Department of Biology, Eberly College of Arts and Sciences, West Virginia University, Morgantown, WV, United States of America
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25
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Abstract
Accurate DNA repair and replication are critical for genomic stability and cancer prevention. RAD51 and its gene family are key regulators of DNA fidelity through diverse roles in double-strand break repair, replication stress, and meiosis. RAD51 is an ATPase that forms a nucleoprotein filament on single-stranded DNA. RAD51 has the function of finding and invading homologous DNA sequences to enable accurate and timely DNA repair. Its paralogs, which arose from ancient gene duplications of RAD51, have evolved to regulate and promote RAD51 function. Underscoring its importance, misregulation of RAD51, and its paralogs, is associated with diseases such as cancer and Fanconi anemia. In this review, we focus on the mammalian RAD51 structure and function and highlight the use of model systems to enable mechanistic understanding of RAD51 cellular roles. We also discuss how misregulation of the RAD51 gene family members contributes to disease and consider new approaches to pharmacologically inhibit RAD51.
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Affiliation(s)
- Braulio Bonilla
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA;
| | - Sarah R Hengel
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA;
| | - McKenzie K Grundy
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA;
| | - Kara A Bernstein
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA;
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26
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Groussin M, Mazel F, Alm EJ. Co-evolution and Co-speciation of Host-Gut Bacteria Systems. Cell Host Microbe 2020; 28:12-22. [DOI: 10.1016/j.chom.2020.06.013] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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27
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Goodhead I, Blow F, Brownridge P, Hughes M, Kenny J, Krishna R, McLean L, Pongchaikul P, Beynon R, Darby AC. Large-scale and significant expression from pseudogenes in Sodalis glossinidius - a facultative bacterial endosymbiont. Microb Genom 2020; 6:e000285. [PMID: 31922467 PMCID: PMC7067036 DOI: 10.1099/mgen.0.000285] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 07/10/2019] [Indexed: 01/30/2023] Open
Abstract
The majority of bacterial genomes have high coding efficiencies, but there are some genomes of intracellular bacteria that have low gene density. The genome of the endosymbiont Sodalis glossinidius contains almost 50 % pseudogenes containing mutations that putatively silence them at the genomic level. We have applied multiple 'omic' strategies, combining Illumina and Pacific Biosciences Single-Molecule Real-Time DNA sequencing and annotation, stranded RNA sequencing and proteome analysis to better understand the transcriptional and translational landscape of Sodalis pseudogenes, and potential mechanisms for their control. Between 53 and 74 % of the Sodalis transcriptome remains active in cell-free culture. The mean sense transcription from coding domain sequences (CDSs) is four times greater than that from pseudogenes. Comparative genomic analysis of six Illumina-sequenced Sodalis isolates from different host Glossina species shows pseudogenes make up ~40 % of the 2729 genes in the core genome, suggesting that they are stable and/or that Sodalis is a recent introduction across the genus Glossina as a facultative symbiont. These data shed further light on the importance of transcriptional and translational control in deciphering host-microbe interactions. The combination of genomics, transcriptomics and proteomics gives a multidimensional perspective for studying prokaryotic genomes with a view to elucidating evolutionary adaptation to novel environmental niches.
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Affiliation(s)
- Ian Goodhead
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
- School of Science, Engineering and Environment, Peel Building, University of Salford, M5 4WT, UK
| | - Frances Blow
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
- Department of Entomology, Cornell University, Ithaca 14853, NY, USA
| | - Philip Brownridge
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Margaret Hughes
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - John Kenny
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Ritesh Krishna
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
- IBM Research UK, STFC Daresbury Laboratory, Warrington, WA4 4AD, UK
| | - Lynn McLean
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Pisut Pongchaikul
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Rob Beynon
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Alistair C. Darby
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
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28
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Evolutionary dynamics of the chromatophore genome in three photosynthetic Paulinella species. Sci Rep 2019; 9:2560. [PMID: 30796245 PMCID: PMC6384880 DOI: 10.1038/s41598-019-38621-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 01/04/2019] [Indexed: 11/21/2022] Open
Abstract
The thecate amoeba Paulinella is a valuable model for understanding plastid organellogenesis because this lineage has independently gained plastids (termed chromatophores) of alpha-cyanobacterial provenance. Plastid primary endosymbiosis in Paulinella occurred relatively recently (90–140 million years ago, Mya), whereas the origin of the canonical Archaeplastida plastid occurred >1,500 Mya. Therefore, these two events provide independent perspectives on plastid formation on vastly different timescales. Here we generated the complete chromatophore genome sequence from P. longichromatophora (979,356 bp, GC-content = 38.8%, 915 predicted genes) and P. micropora NZ27 (977,190 bp, GC-content = 39.9%, 911 predicted genes) and compared these data to that from existing chromatophore genomes. Our analysis suggests that when a basal split occurred among photosynthetic Paulinella species ca. 60 Mya, only 35% of the ancestral orthologous gene families from the cyanobacterial endosymbiont remained in chromatophore DNA. Following major gene losses during the early stages of endosymbiosis, this process slowed down significantly, resulting in a conserved gene content across extant taxa. Chromatophore genes faced relaxed selection when compared to homologs in free-living alpha-cyanobacteria, likely reflecting the homogeneous intracellular environment of the Paulinella host. Comparison of nucleotide substitution and insertion/deletion events among different P. micropora strains demonstrates that increases in AT-content and genome reduction are ongoing and dynamic processes in chromatophore evolution.
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29
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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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30
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Esser D, Lange J, Marinos G, Sieber M, Best L, Prasse D, Bathia J, Rühlemann MC, Boersch K, Jaspers C, Sommer F. Functions of the Microbiota for the Physiology of Animal Metaorganisms. J Innate Immun 2018; 11:393-404. [PMID: 30566939 PMCID: PMC6738199 DOI: 10.1159/000495115] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 10/30/2018] [Accepted: 10/30/2018] [Indexed: 12/11/2022] Open
Abstract
Animals are usually regarded as independent entities within their respective environments. However, within an organism, eukaryotes and prokaryotes interact dynamically to form the so-called metaorganism or holobiont, where each partner fulfils its versatile and crucial role. This review focuses on the interplay between microorganisms and multicellular eukaryotes in the context of host physiology, in particular aging and mucus-associated crosstalk. In addition to the interactions between bacteria and the host, we highlight the importance of viruses and nonmodel organisms. Moreover, we discuss current culturing and computational methodologies that allow a deeper understanding of underlying mechanisms controlling the physiology of metaorganisms.
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Affiliation(s)
- Daniela Esser
- Institute of Experimental Medicine, Christian Albrecht University Kiel, Kiel, Germany
| | - Janina Lange
- Zoological Institute, Christian Albrecht University Kiel, Kiel, Germany
| | - Georgios Marinos
- Institute of Experimental Medicine, Christian Albrecht University Kiel, Kiel, Germany
| | - Michael Sieber
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Lena Best
- Institute of Experimental Medicine, Christian Albrecht University Kiel, Kiel, Germany
| | - Daniela Prasse
- Institute of General Microbiology, Christian Albrecht University Kiel, Kiel, Germany
| | - Jay Bathia
- Zoological Institute, Christian Albrecht University Kiel, Kiel, Germany
| | - Malte C Rühlemann
- Institute of Clinical Molecular Biology, Christian Albrecht University Kiel, Kiel, Germany
| | - Kathrin Boersch
- Institute of Clinical Molecular Biology, Christian Albrecht University Kiel, Kiel, Germany
| | - Cornelia Jaspers
- Evolutionary Ecology of Marine Fishes, GEOMAR - Helmholtz Center for Ocean Research, Kiel, Germany
- National Institute of Aquatic Resources, Technical University of Denmark, Lyngby, Denmark
| | - Felix Sommer
- Institute of Clinical Molecular Biology, Christian Albrecht University Kiel, Kiel, Germany,
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31
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Leobold M, Bézier A, Pichon A, Herniou EA, Volkoff AN, Drezen JM. The Domestication of a Large DNA Virus by the Wasp Venturia canescens Involves Targeted Genome Reduction through Pseudogenization. Genome Biol Evol 2018; 10:1745-1764. [PMID: 29931159 PMCID: PMC6054256 DOI: 10.1093/gbe/evy127] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2018] [Indexed: 12/13/2022] Open
Abstract
Polydnaviruses (PDVs) are compelling examples of viral domestication, in which wasps express a large set of genes originating from a chromosomally integrated virus to produce particles necessary for their reproductive success. Parasitoid wasps generally use PDVs as a virulence gene delivery system allowing the protection of their progeny in the body of parasitized host. However, in the wasp Venturia canescens an independent viral domestication process led to an alternative strategy as the wasp incorporates virulence proteins in viral liposomes named virus-like particles (VLPs), instead of DNA molecules. Proteomic analysis of purified VLPs and transcriptome sequencing revealed the loss of some viral functions. In particular, the genes coding for capsid components are no longer expressed, which explains why VLPs do not incorporate DNA. Here a thorough examination of V. canescens genome revealed the presence of the pseudogenes corresponding to most of the genes involved in lost functions. This strongly suggests that an accumulation of mutations that leads to gene specific pseudogenization precedes the loss of viral genes observed during virus domestication. No evidence was found for block loss of collinear genes, although extensive gene order reshuffling of the viral genome was identified from comparisons between endogenous and exogenous viruses. These results provide the first insights on the early stages of large DNA virus domestication implicating massive genome reduction through gene-specific pseudogenization, a process which differs from the large deletions described for bacterial endosymbionts.
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Affiliation(s)
- Matthieu Leobold
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261, CNRS - Université de Tours, UFR des Sciences et Techniques, Parc de Grandmont, Tours, France
| | - Annie Bézier
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261, CNRS - Université de Tours, UFR des Sciences et Techniques, Parc de Grandmont, Tours, France
| | - Apolline Pichon
- Diversity, Genomes and Interactions Microorganisms-Insect, UMR INRA 1333, Université de Montpellier 2, Montpellier, France
| | - Elisabeth A Herniou
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261, CNRS - Université de Tours, UFR des Sciences et Techniques, Parc de Grandmont, Tours, France
| | - Anne-Nathalie Volkoff
- Diversity, Genomes and Interactions Microorganisms-Insect, UMR INRA 1333, Université de Montpellier 2, Montpellier, France
| | - Jean-Michel Drezen
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261, CNRS - Université de Tours, UFR des Sciences et Techniques, Parc de Grandmont, Tours, France
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32
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Alleman A, Hertweck KL, Kambhampati S. Random Genetic Drift and Selective Pressures Shaping the Blattabacterium Genome. Sci Rep 2018; 8:13427. [PMID: 30194350 PMCID: PMC6128925 DOI: 10.1038/s41598-018-31796-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 08/21/2018] [Indexed: 01/30/2023] Open
Abstract
Estimates suggest that at least half of all extant insect genera harbor obligate bacterial mutualists. Whereas an endosymbiotic relationship imparts many benefits upon host and symbiont alike, the intracellular lifestyle has profound effects on the bacterial genome. The obligate endosymbiont genome is a product of opposing forces: genes important to host survival are maintained through physiological constraint, contrasted by the fixation of deleterious mutations and genome erosion through random genetic drift. The obligate cockroach endosymbiont, Blattabacterium - providing nutritional augmentation to its host in the form of amino acid synthesis - displays radical genome alterations when compared to its most recent free-living relative Flavobacterium. To date, eight Blattabacterium genomes have been published, affording an unparalleled opportunity to examine the direction and magnitude of selective forces acting upon this group of symbionts. Here, we find that the Blattabacterium genome is experiencing a 10-fold increase in selection rate compared to Flavobacteria. Additionally, the proportion of selection events is largely negative in direction, with only a handful of loci exhibiting signatures of positive selection. These findings suggest that the Blattabacterium genome will continue to erode, potentially resulting in an endosymbiont with an even further reduced genome, as seen in other insect groups such as Hemiptera.
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Affiliation(s)
- Austin Alleman
- Department of Biology, University of Texas at Tyler, 3900 University Blvd., Tyler, Texas, 75799, United States.
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Johannes von Müller Weg 6, Mainz, 55128, Germany.
| | - Kate L Hertweck
- Department of Biology, University of Texas at Tyler, 3900 University Blvd., Tyler, Texas, 75799, United States
| | - Srini Kambhampati
- Department of Biology, University of Texas at Tyler, 3900 University Blvd., Tyler, Texas, 75799, United States
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Abstract
Obligate nutritional endosymbioses are arguably the most intimate of all interspecific associations. While many insect nutritional endosymbioses are well studied, a full picture of how two disparate organisms, a bacterial endosymbiont and a eukaryotic host, are integrated is still lacking. The mTOR pathway is known to integrate nutritional conditions with cell growth and survival in eukaryotes. Characterization and localization of amino acid transporters in aphids suggest the mTOR pathway as a point of integration between an aphid host and its amino acid-provisioning endosymbiont Buchnera aphidicola. The mTOR pathway is unannotated in aphids and unstudied in any nutritional endosymbiosis. We annotated mTOR pathway genes in two aphid species, Acyrthosiphon pisum and Myzus persicae, using both BLASTp searches and Hidden Markov Models. Using previously collected RNAseq data we constructed new reference transcriptomes for bacteriocyte, gut, and whole insect tissue for three lines of M. persicae. Annotation of the mTOR pathway identified homologs of all known invertebrate mTOR genes in both aphid species with some duplications. Differential expression analysis showed that genes specific to the amino acid-sensitive mTOR Complex 1 were more highly expressed in bacteriocytes than genes specific to the amino acid-insensitive mTOR Complex 2. Almost all mTOR genes involved in sensing amino acids showed higher expression in bacteriocytes than in whole insect tissue. When compared to gut, the putative glutamine/arginine sensing transporter ACYPI000333, an ortholog of SLC38A9, showed 6.5 times higher expression in bacteriocytes. Our results suggest that the mTOR pathway may be functionally important in mediating integration of Buchnera into aphid growth and reproduction.
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34
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Pawlowska TE, Gaspar ML, Lastovetsky OA, Mondo SJ, Real-Ramirez I, Shakya E, Bonfante P. Biology of Fungi and Their Bacterial Endosymbionts. ANNUAL REVIEW OF PHYTOPATHOLOGY 2018; 56:289-309. [PMID: 30149793 DOI: 10.1146/annurev-phyto-080417-045914] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Heritable symbioses, in which endosymbiotic bacteria (EB) are transmitted vertically between host generations, are an important source of evolutionary novelties. A primary example of such symbioses is the eukaryotic cell with its EB-derived organelles. Recent discoveries suggest that endosymbiosis-related innovations can be also found in associations formed by early divergent fungi in the phylum Mucoromycota with heritable EB from two classes, Betaproteobacteria and Mollicutes. These symbioses exemplify novel types of host-symbiont interactions. Studies of these partnerships fuel theoretical models describing mechanisms that stabilize heritable symbioses, control the rate of molecular evolution, and enable the establishment of mutualisms. Lastly, by altering host phenotypes and metabolism, these associations represent an important instrument for probing the basic biology of the Mucoromycota hosts, which remain one of the least explored filamentous fungi.
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Affiliation(s)
- Teresa E Pawlowska
- School of Integrative Plant Science, Plant Pathology and Plant Microbe-Biology, Cornell University, Ithaca, New York 14853, USA;
| | - Maria L Gaspar
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Olga A Lastovetsky
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
| | - Stephen J Mondo
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | | | - Evaniya Shakya
- School of Integrative Plant Science, Plant Pathology and Plant Microbe-Biology, Cornell University, Ithaca, New York 14853, USA;
| | - Paola Bonfante
- Department of Life Sciences & Systems Biology, University of Torino, 10125 Torino, Italy
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35
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Balikó G, Vernyik V, Karcagi I, Györfy Z, Draskovits G, Fehér T, Pósfai G. Rational Efforts to Streamline the Escherichia coliGenome. Synth Biol (Oxf) 2018. [DOI: 10.1002/9783527688104.ch4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Gabriella Balikó
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
| | - Viktor Vernyik
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
| | - Ildikó Karcagi
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
| | - Zsuzsanna Györfy
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
| | - Gábor Draskovits
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
| | - Tamás Fehér
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
| | - György Pósfai
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
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36
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Pogoda CS, Keepers KG, Lendemer JC, Kane NC, Tripp EA. Reductions in complexity of mitochondrial genomes in lichen-forming fungi shed light on genome architecture of obligate symbioses. Mol Ecol 2018; 27:1155-1169. [DOI: 10.1111/mec.14519] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 12/21/2017] [Accepted: 01/19/2018] [Indexed: 01/28/2023]
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37
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Michalik A, Schulz F, Michalik K, Wascher F, Horn M, Szklarzewicz T. Coexistence of novel gammaproteobacterial and Arsenophonus symbionts in the scale insect Greenisca brachypodii (Hemiptera, Coccomorpha: Eriococcidae). Environ Microbiol 2018; 20:1148-1157. [PMID: 29393559 DOI: 10.1111/1462-2920.14057] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 01/25/2018] [Indexed: 11/30/2022]
Abstract
Scale insects are commonly associated with obligate, intracellular microorganisms which play important roles in complementing their hosts with essential nutrients. Here we characterized the symbiotic system of Greenisca brachypodii, a member of the family Eriococcidae. Histological and ultrastructural analyses have indicated that G. brachypodii is stably associated with coccoid and rod-shaped bacteria. Phylogenetic analyses have revealed that the coccoid bacteria represent a sister group to the secondary symbiont of the mealybug Melanococcus albizziae, whereas the rod-shaped symbionts are close relatives of Arsenophonus symbionts in insects - to our knowledge, this is the first report of the presence of Arsenophonus bacterium in scale insects. As a comparison of 16S and 23S rRNA genes sequences of the G. brachypodii coccoid symbiont with other gammaprotebacterial sequences showed only low similarity (∼90%), we propose the name 'Candidatus Kotejella greeniscae' for its tentative classification. Both symbionts are transovarially transmitted from one generation to the next. The infection takes place in the neck region of the ovariole. The bacteria migrate between follicular cells, as well as through the cytoplasm of those cells to the perivitelline space, where they form a characteristic 'symbiont ball'. Our findings provide evidence for a polyphyletic origin of symbionts of Eriococcidae.
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Affiliation(s)
- Anna Michalik
- Department of Developmental Biology and Morphology of Invertebrates, Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9, 30-387 Kraków, Poland
| | - Frederik Schulz
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Althanstr. 14, A-1090 Vienna, Austria
| | - Katarzyna Michalik
- Department of Developmental Biology and Morphology of Invertebrates, Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9, 30-387 Kraków, Poland
| | - Florian Wascher
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Althanstr. 14, A-1090 Vienna, Austria
| | - Matthias Horn
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Althanstr. 14, A-1090 Vienna, Austria
| | - Teresa Szklarzewicz
- Department of Developmental Biology and Morphology of Invertebrates, Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9, 30-387 Kraków, Poland
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38
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Repar J, Warnecke T. Non-Random Inversion Landscapes in Prokaryotic Genomes Are Shaped by Heterogeneous Selection Pressures. Mol Biol Evol 2018; 34:1902-1911. [PMID: 28407093 PMCID: PMC5850607 DOI: 10.1093/molbev/msx127] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Inversions are a major contributor to structural genome evolution in prokaryotes. Here, using a novel alignment-based method, we systematically compare 1,651 bacterial and 98 archaeal genomes to show that inversion landscapes are frequently biased toward (symmetric) inversions around the origin–terminus axis. However, symmetric inversion bias is not a universal feature of prokaryotic genome evolution but varies considerably across clades. At the extremes, inversion landscapes in Bacillus–Clostridium and Actinobacteria are dominated by symmetric inversions, while there is little or no systematic bias favoring symmetric rearrangements in archaea with a single origin of replication. Within clades, we find strong but clade-specific relationships between symmetric inversion bias and different features of adaptive genome architecture, including the distance of essential genes to the origin of replication and the preferential localization of genes on the leading strand. We suggest that heterogeneous selection pressures have converged to produce similar patterns of structural genome evolution across prokaryotes.
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Affiliation(s)
- Jelena Repar
- Molecular Systems Group, MRC London Institute of Medical Sciences (LMS), London, United Kingdom.,Institute of Clinical Sciences, Molecular Systems Group, Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Tobias Warnecke
- Molecular Systems Group, MRC London Institute of Medical Sciences (LMS), London, United Kingdom.,Institute of Clinical Sciences, Molecular Systems Group, Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, United Kingdom
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39
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Thairu MW, Cheng S, Hansen AK. A sRNA in a reduced mutualistic symbiont genome regulates its own gene expression. Mol Ecol 2017; 27:1766-1776. [PMID: 29134727 DOI: 10.1111/mec.14424] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 10/29/2017] [Accepted: 10/31/2017] [Indexed: 01/10/2023]
Abstract
Similar to other nutritional endosymbionts that are obligate for host survival, the mutualistic aphid endosymbiont, Buchnera, has a highly reduced genome with few regulatory elements. Until recently, it was thought that aphid hosts were primarily responsible for regulating their symbiotic relationship. However, we recently revealed that Buchnera displays differential protein regulation, but not mRNA expression. We also identified a number of conserved small RNAs (sRNAs) that are expressed among Buchnera taxa. In this study, we investigate whether differential protein regulation in Buchnera is the result of post-transcriptional gene regulation via sRNAs. We characterize the sRNA profile of two Buchnera life stages: (i) when Buchnera is transitioning from an extracellular proliferating state in aphid embryos and (ii) when Buchnera is in an intracellular nonproliferating state in aphid bacteriocytes (specialized symbiont cells). Overall, we identified 90 differentially expressed sRNAs, 97% of which were upregulated in aphid embryos. Of these sRNAs, the majority were predicted to be involved in the regulation of various metabolic processes, including arginine biosynthesis. Using a heterologous dual expression vector, we reveal for the first time that a Buchnera antisense sRNA can post-transcriptionally interact with its cognate Buchnera coding sequence, carB, a gene involved in arginine biosynthesis. These results corroborate our in vivo RNAseq and proteomic data, where the candidate antisense sRNA carB and the protein CarB are significantly upregulated in aphid embryos. Overall, we demonstrate that Buchnera may regulate gene expression independently from its host by utilizing sRNAs.
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Affiliation(s)
- Margaret W Thairu
- Department of Entomology, University of Illinois, Urbana-Champaign, Urbana, IL, USA.,Department of Entomology, University of California Riverside, Riverside, CA, USA
| | - Siyuan Cheng
- Department of Entomology, University of Illinois, Urbana-Champaign, Urbana, IL, USA.,Program in Biological and Biomedical Sciences, Yale University, New Haven, CT, USA
| | - Allison K Hansen
- Department of Entomology, University of Illinois, Urbana-Champaign, Urbana, IL, USA.,Department of Entomology, University of California Riverside, Riverside, CA, USA
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40
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Wernegreen JJ. Ancient bacterial endosymbionts of insects: Genomes as sources of insight and springboards for inquiry. Exp Cell Res 2017; 358:427-432. [DOI: 10.1016/j.yexcr.2017.04.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 04/24/2017] [Accepted: 04/25/2017] [Indexed: 01/20/2023]
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41
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Repeated replacement of an intrabacterial symbiont in the tripartite nested mealybug symbiosis. Proc Natl Acad Sci U S A 2016; 113:E5416-24. [PMID: 27573819 DOI: 10.1073/pnas.1603910113] [Citation(s) in RCA: 147] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Stable endosymbiosis of a bacterium into a host cell promotes cellular and genomic complexity. The mealybug Planococcus citri has two bacterial endosymbionts with an unusual nested arrangement: the γ-proteobacterium Moranella endobia lives in the cytoplasm of the β-proteobacterium Tremblaya princeps These two bacteria, along with genes horizontally transferred from other bacteria to the P. citri genome, encode gene sets that form an interdependent metabolic patchwork. Here, we test the stability of this three-way symbiosis by sequencing host and symbiont genomes for five diverse mealybug species and find marked fluidity over evolutionary time. Although Tremblaya is the result of a single infection in the ancestor of mealybugs, the γ-proteobacterial symbionts result from multiple replacements of inferred different ages from related but distinct bacterial lineages. Our data show that symbiont replacement can happen even in the most intricate symbiotic arrangements and that preexisting horizontally transferred genes can remain stable on genomes in the face of extensive symbiont turnover.
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42
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O'Malley MA, Wideman JG, Ruiz-Trillo I. Losing Complexity: The Role of Simplification in Macroevolution. Trends Ecol Evol 2016; 31:608-621. [PMID: 27212432 DOI: 10.1016/j.tree.2016.04.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 04/18/2016] [Accepted: 04/19/2016] [Indexed: 10/21/2022]
Abstract
Macroevolutionary patterns can be produced by combinations of diverse and even oppositional dynamics. A growing body of data indicates that secondary simplifications of molecular and cellular structures are common. Some major diversifications in eukaryotes have occurred because of loss and minimalisation; numerous episodes in prokaryote evolution have likewise been driven by the reduction of structure. After examining a range of examples of secondary simplification and its consequences across the tree of life, we address how macroevolutionary explanations might incorporate simplification as well as complexification, and adaptive as well as nonadaptive dynamics.
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Affiliation(s)
- Maureen A O'Malley
- UMR5164, University of Bordeaux, 146 Rue Léo Saignat, Bordeaux 33076, France.
| | | | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Spain; Departament de Genètica, Universitat de Barcelona, 08028 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats, Pg Lluis Companys 23, 08010 Barcelona, Spain
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43
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Mondo SJ, Salvioli A, Bonfante P, Morton JB, Pawlowska TE. Nondegenerative Evolution in Ancient Heritable Bacterial Endosymbionts of Fungi. Mol Biol Evol 2016; 33:2216-31. [DOI: 10.1093/molbev/msw086] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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44
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Matelska D, Kurkowska M, Purta E, Bujnicki JM, Dunin-Horkawicz S. Loss of Conserved Noncoding RNAs in Genomes of Bacterial Endosymbionts. Genome Biol Evol 2016; 8:426-38. [PMID: 26782934 PMCID: PMC4779614 DOI: 10.1093/gbe/evw007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The genomes of intracellular symbiotic or pathogenic bacteria, such as of Buchnera, Mycoplasma, and Rickettsia, are typically smaller compared with their free-living counterparts. Here we showed that noncoding RNA (ncRNA) families, which are conserved in free-living bacteria, frequently could not be detected by computational methods in the small genomes. Statistical tests demonstrated that their absence is not an artifact of low GC content or small deletions in these small genomes, and thus it was indicative of an independent loss of ncRNAs in different endosymbiotic lineages. By analyzing the synteny (conservation of gene order) between the reduced and nonreduced genomes, we revealed instances of protein-coding genes that were preserved in the reduced genomes but lost cis-regulatory elements. We found that the loss of cis-regulatory ncRNA sequences, which regulate the expression of cognate protein-coding genes, is characterized by the reduction of secondary structure formation propensity, GC content, and length of the corresponding genomic regions.
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Affiliation(s)
- Dorota Matelska
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Malgorzata Kurkowska
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Elzbieta Purta
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, Poland Laboratory of Structural Bioinformatics, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Stanislaw Dunin-Horkawicz
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, Poland
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45
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Cassone BJ, Redinbaugh MG, Dorrance AE, Michel AP. Shifts in Buchnera aphidicola density in soybean aphids (Aphis glycines) feeding on virus-infected soybean. INSECT MOLECULAR BIOLOGY 2015; 24:422-31. [PMID: 25845267 DOI: 10.1111/imb.12170] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 01/21/2015] [Accepted: 01/26/2015] [Indexed: 06/04/2023]
Abstract
Vertically transmitted bacterial symbionts are common in arthropods. Aphids undergo an obligate symbiosis with Buchnera aphidicola, which provides essential amino acids to its host and contributes directly to nymph growth and reproduction. We previously found that newly adult Aphis glycines feeding on soybean infected with the beetle-transmitted Bean pod mottle virus (BPMV) had significantly reduced fecundity. We hypothesized that the reduced fecundity was attributable to detrimental impacts of the virus on the aphid microbiome, namely Buchnera. To test this, mRNA sequencing and quantitative real-time PCR were used to assay Buchnera transcript abundance and titre in A. glycines feeding on Soybean mosaic virus-infected, BPMV-infected, and healthy soybean for up to 14 days. Our results indicated that Buchnera density was lower and ultimately suppressed in aphids feeding on virus-infected soybean. While the decreased Buchnera titre may be associated with reduced aphid fecundity, additional mechanisms are probably involved. The present report begins to describe how interactions among insects, plants, and plant pathogens influence endosymbiont population dynamics.
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Affiliation(s)
- Bryan J Cassone
- Center for Applied Plant Sciences, The Ohio State University, OARDC, Wooster, OH, 44691, USA
- Department of Plant Pathology, The Ohio State University, OARDC, Wooster, OH, 44691, USA
| | - Margaret G Redinbaugh
- Department of Plant Pathology, The Ohio State University, OARDC, Wooster, OH, 44691, USA
- USDA, ARS Corn, Soybean and Wheat Quality Research Unit, Wooster, OH, 44691, USA
| | - Anne E Dorrance
- Department of Plant Pathology, The Ohio State University, OARDC, Wooster, OH, 44691, USA
| | - Andrew P Michel
- Department of Entomology, the Ohio State University, OARDC, Wooster, OH, 44691, USA
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46
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Wernegreen JJ. Endosymbiont evolution: predictions from theory and surprises from genomes. Ann N Y Acad Sci 2015; 1360:16-35. [PMID: 25866055 DOI: 10.1111/nyas.12740] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 01/27/2015] [Accepted: 02/11/2015] [Indexed: 10/23/2022]
Abstract
Genome data have created new opportunities to untangle evolutionary processes shaping microbial variation. Among bacteria, long-term mutualists of insects represent the smallest and (typically) most AT-rich genomes. Evolutionary theory provides a context to predict how an endosymbiotic lifestyle may alter fundamental evolutionary processes--mutation, selection, genetic drift, and recombination--and thus contribute to extreme genomic outcomes. These predictions can then be explored by comparing evolutionary rates, genome size and stability, and base compositional biases across endosymbiotic and free-living bacteria. Recent surprises from such comparisons include genome reduction among uncultured, free-living species. Some studies suggest that selection generally drives this streamlining, while drift drives genome reduction in endosymbionts; however, this remains an hypothesis requiring additional data. Unexpected evidence of selection acting on endosymbiont GC content hints that even weak selection may be effective in some long-term mutualists. Moving forward, intraspecific analysis offers a promising approach to distinguish underlying mechanisms, by testing the null hypothesis of neutrality and by quantifying mutational spectra. Such analyses may clarify whether endosymbionts and free-living bacteria occupy distinct evolutionary trajectories or, alternatively, represent varied outcomes of similar underlying forces.
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Affiliation(s)
- Jennifer J Wernegreen
- Nicholas School of the Environment and Center for Genomic and Computational Biology, Duke University, Durham, North Carolina
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47
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Abdul Rahman N, Parks DH, Willner DL, Engelbrektson AL, Goffredi SK, Warnecke F, Scheffrahn RH, Hugenholtz P. A molecular survey of Australian and North American termite genera indicates that vertical inheritance is the primary force shaping termite gut microbiomes. MICROBIOME 2015; 3:5. [PMID: 25830022 PMCID: PMC4379614 DOI: 10.1186/s40168-015-0067-8] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Accepted: 01/02/2015] [Indexed: 05/25/2023]
Abstract
BACKGROUND Termites and their microbial gut symbionts are major recyclers of lignocellulosic biomass. This important symbiosis is obligate but relatively open and more complex in comparison to other well-known insect symbioses such as the strict vertical transmission of Buchnera in aphids. The relative roles of vertical inheritance and environmental factors such as diet in shaping the termite gut microbiome are not well understood. RESULTS The gut microbiomes of 66 specimens representing seven higher and nine lower termite genera collected in Australia and North America were profiled by small subunit (SSU) rRNA amplicon pyrosequencing. These represent the first reported culture-independent gut microbiome data for three higher termite genera: Tenuirostritermes, Drepanotermes, and Gnathamitermes; and two lower termite genera: Marginitermes and Porotermes. Consistent with previous studies, bacteria comprise the largest fraction of termite gut symbionts, of which 11 phylotypes (6 Treponema, 1 Desulfarculus-like, 1 Desulfovibrio, 1 Anaerovorax-like, 1 Sporobacter-like, and 1 Pirellula-like) were widespread occurring in ≥50% of collected specimens. Archaea are generally considered to comprise only a minority of the termite gut microbiota (<3%); however, archaeal relative abundance was substantially higher and variable in a number of specimens including Macrognathotermes, Coptotermes, Schedorhinotermes, Porotermes, and Mastotermes (representing up to 54% of amplicon reads). A ciliate related to Clevelandella was detected in low abundance in Gnathamitermes indicating that protists were either reacquired after protists loss in higher termites or persisted in low numbers across this transition. Phylogenetic analyses of the bacterial communities indicate that vertical inheritance is the primary force shaping termite gut microbiota. The effect of diet is secondary and appears to influence the relative abundance, but not membership, of the gut communities. CONCLUSIONS Vertical inheritance is the primary force shaping the termite gut microbiome indicating that species are successfully and faithfully passed from one generation to the next via trophallaxis or coprophagy. Changes in relative abundance can occur on shorter time scales and appear to be an adaptive mechanism for dietary fluctuations.
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Affiliation(s)
- Nurdyana Abdul Rahman
- />Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Queensland Australia
| | - Donovan H Parks
- />Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Queensland Australia
| | - Dana L Willner
- />Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Queensland Australia
- />Current address: Department of Statistics, University of Illinois Urbana-Champaign, Champaign, IL USA
| | - Anna L Engelbrektson
- />DOE Joint Genome Institute, Walnut Creek, CA USA
- />Current address: Energy Biosciences Institute, University of California, Berkeley, CA USA
| | | | - Falk Warnecke
- />DOE Joint Genome Institute, Walnut Creek, CA USA
- />Jena School for Microbial Communication (JSMC) and Microbial Ecology Group, Friedrich Schiller University Jena, Jena, Germany
| | - Rudolf H Scheffrahn
- />Fort Lauderdale Research and Education Center, University of Florida, Davie, FL USA
| | - Philip Hugenholtz
- />Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Queensland Australia
- />DOE Joint Genome Institute, Walnut Creek, CA USA
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48
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Goodhead I, Darby AC. Taking the pseudo out of pseudogenes. Curr Opin Microbiol 2014; 23:102-9. [PMID: 25461580 DOI: 10.1016/j.mib.2014.11.012] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 11/11/2014] [Accepted: 11/12/2014] [Indexed: 12/23/2022]
Abstract
Pseudogenes are defined as fragments of once-functional genes that have been silenced by one or more nonsense, frameshift or missense mutations. Despite continuing increases in the speed of sequencing and annotating bacterial genomes, the identification and categorisation of pseudogenes remains problematic. Even when identified, pseudogenes are considered to be rare and tend to be ignored. On the contrary, pseudogenes are surprisingly prevalent and can persist for long evolutionary time periods, representing a record of once-functional genetic characteristics. Most importantly, pseudogenes provide an insight into prokaryotic evolutionary history as a record of phenotypic traits that have been lost. Focusing on the intracellular and symbiotic bacteria in which pseudogenes predominate, this review discusses the importance of identifying pseudogenes to fully understand the abilities of bacteria, and to understand prokaryotes within their evolutionary context.
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Affiliation(s)
- Ian Goodhead
- Functional and Comparative Genomics, School of Biological Sciences, University of Liverpool, Crown St., Liverpool L69 7ZB, UK
| | - Alistair C Darby
- Functional and Comparative Genomics, School of Biological Sciences, University of Liverpool, Crown St., Liverpool L69 7ZB, UK
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49
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Hansen AK, Degnan PH. Widespread expression of conserved small RNAs in small symbiont genomes. THE ISME JOURNAL 2014; 8:2490-502. [PMID: 25012903 PMCID: PMC4260695 DOI: 10.1038/ismej.2014.121] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Revised: 06/02/2014] [Accepted: 06/05/2014] [Indexed: 12/17/2022]
Abstract
Genome architecture of a microbe markedly changes when it transitions from a free-living lifestyle to an obligate symbiotic association within eukaryotic cells. These symbiont genomes experience numerous rearrangements and massive gene loss, which is expected to radically alter gene regulatory networks compared with those of free-living relatives. As such, it remains unclear whether and how these small symbiont genomes regulate gene expression. Here, using a label-free mass-spec quantification approach we found that differential protein regulation occurs in Buchnera, a model symbiont with a reduced genome, when it transitions between two distinct life stages. However, differential mRNA expression could not be detected between Buchnera life stages, despite the presence of a small number of putative transcriptional regulators. Instead a comparative analysis of small RNA expression profiles among five divergent Buchnera lineages, spanning a variety of Buchnera life stages, reveals 140 novel intergenic and antisense small RNAs and 517 untranslated regions that were significantly expressed, some of which have been conserved for ∼65 million years. In addition, the majority of these small RNAs exhibit both sequence covariation and thermodynamic stability, indicators of a potential structural RNA role. Together, these data suggest that gene regulation at the post-transcriptional level may be important in Buchnera. This is the first study to empirically identify Buchnera small RNAs, and we propose that these novel small RNAs may facilitate post-transcriptional regulation through translational inhibition/activation, and/or transcript stability. Ultimately, post-transcriptional regulation may shape metabolic complementation between Buchnera and its aphid host, thus impacting the animal's ecology and evolution.
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Affiliation(s)
- Allison K Hansen
- Department of Entomology, School of Integrative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Ecology and Evolutionary Biology, Microbial Diversity Institute, Yale University, New Haven, CT, USA
| | - Patrick H Degnan
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Microbial Pathogenesis, Microbial Diversity Institute, Yale University, New Haven, CT, USA
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50
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Nuñez PA, Romero H, Farber MD, Rocha EPC. Natural selection for operons depends on genome size. Genome Biol Evol 2014; 5:2242-54. [PMID: 24201372 PMCID: PMC3845653 DOI: 10.1093/gbe/evt174] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In prokaryotes, genome size is associated with metabolic versatility, regulatory complexity, effective population size, and horizontal transfer rates. We therefore analyzed the covariation of genome size and operon conservation to assess the evolutionary models of operon formation and maintenance. In agreement with previous results, intraoperonic pairs of essential and of highly expressed genes are more conserved. Interestingly, intraoperonic pairs of genes are also more conserved when they encode proteins at similar cell concentrations, suggesting a role of cotranscription in diminishing the cost of waste and shortfall in gene expression. Larger genomes have fewer and smaller operons that are also less conserved. Importantly, lower conservation in larger genomes was observed for all classes of operons in terms of gene expression, essentiality, and balanced protein concentration. We reached very similar conclusions in independent analyses of three major bacterial clades (α- and β-Proteobacteria and Firmicutes). Operon conservation is inversely correlated to the abundance of transcription factors in the genome when controlled for genome size. This suggests a negative association between the complexity of genetic networks and operon conservation. These results show that genome size and/or its proxies are key determinants of the intensity of natural selection for operon organization. Our data fit better the evolutionary models based on the advantage of coregulation than those based on genetic linkage or stochastic gene expression. We suggest that larger genomes with highly complex genetic networks and many transcription factors endure weaker selection for operons than smaller genomes with fewer alternative tools for genetic regulation.
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Affiliation(s)
- Pablo A Nuñez
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (CICVyA-INTA), Buenos Aires, Argentina
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