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Silva FJ, Domínguez-Santos R, Latorre A, García-Ferris C. Comparative Transcriptomics of Fat Bodies between Symbiotic and Quasi-Aposymbiotic Adult Females of Blattella germanica with Emphasis on the Metabolic Integration with Its Endosymbiont Blattabacterium and Its Immune System. Int J Mol Sci 2024; 25:4228. [PMID: 38673813 PMCID: PMC11050582 DOI: 10.3390/ijms25084228] [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: 02/21/2024] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024] Open
Abstract
We explored the metabolic integration of Blattella germanica and its obligate endosymbiont Blattabacterium cuenoti by the transcriptomic analysis of the fat body of quasi-aposymbiotic cockroaches, where the endosymbionts were almost entirely removed with rifampicin. Fat bodies from quasi-aposymbiotic insects displayed large differences in gene expression compared to controls. In quasi-aposymbionts, the metabolism of phenylalanine and tyrosine involved in cuticle sclerotization and pigmentation increased drastically to compensate for the deficiency in the biosynthesis of these amino acids by the endosymbionts. On the other hand, the uricolytic pathway and the biosynthesis of uric acid were severely decreased, probably because the reduced population of endosymbionts was unable to metabolize urea to ammonia. Metabolite transporters that could be involved in the endosymbiosis process were identified. Immune system and antimicrobial peptide (AMP) gene expression was also reduced in quasi-aposymbionts, genes encoding peptidoglycan-recognition proteins, which may provide clues for the maintenance of the symbiotic relationship, as well as three AMP genes whose involvement in the symbiotic relationship will require additional analysis. Finally, a search for AMP-like factors that could be involved in controlling the endosymbiont identified two orphan genes encoding proteins smaller than 200 amino acids underexpressed in quasi-aposymbionts, suggesting a role in the host-endosymbiont relationship.
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Affiliation(s)
- Francisco J. Silva
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia and Spanish Research Council, 46980 Paterna, Spain; (R.D.-S.); (A.L.)
- Genomics and Health Area, Foundation for the Promotion of Sanitary and Biomedical Research of the Valencia Region, 46020 Valencia, Spain
| | - Rebeca Domínguez-Santos
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia and Spanish Research Council, 46980 Paterna, Spain; (R.D.-S.); (A.L.)
- Genomics and Health Area, Foundation for the Promotion of Sanitary and Biomedical Research of the Valencia Region, 46020 Valencia, Spain
| | - Amparo Latorre
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia and Spanish Research Council, 46980 Paterna, Spain; (R.D.-S.); (A.L.)
- Genomics and Health Area, Foundation for the Promotion of Sanitary and Biomedical Research of the Valencia Region, 46020 Valencia, Spain
| | - Carlos García-Ferris
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia and Spanish Research Council, 46980 Paterna, Spain; (R.D.-S.); (A.L.)
- Genomics and Health Area, Foundation for the Promotion of Sanitary and Biomedical Research of the Valencia Region, 46020 Valencia, Spain
- Department of Biochemistry and Molecular Biology, University of Valencia, 46100 Burjassot, Spain
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2
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Valadez-Cano C, Olivares-Hernández R, Espino-Vázquez AN, Partida-Martínez LP. Genome-Scale Model of Rhizopus microsporus: Metabolic integration of a fungal holobiont with its bacterial and viral endosymbionts. Environ Microbiol 2024; 26:e16551. [PMID: 38072824 DOI: 10.1111/1462-2920.16551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 11/24/2023] [Indexed: 01/30/2024]
Abstract
Rhizopus microsporus often lives in association with bacterial and viral symbionts that alter its biology. This fungal model represents an example of the complex interactions established among diverse organisms in functional holobionts. We constructed a Genome-Scale Model (GSM) of the fungal-bacterial-viral holobiont (iHol). We employed a constraint-based method to calculate the metabolic fluxes to decipher the metabolic interactions of the symbionts with their host. Our computational analyses of iHol simulate the holobiont's growth and the production of the toxin rhizoxin. Analyses of the calculated fluxes between R. microsporus in symbiotic (iHol) versus asymbiotic conditions suggest that changes in the lipid and nucleotide metabolism of the host are necessary for the functionality of the holobiont. Glycerol plays a pivotal role in the fungal-bacterial metabolic interaction, as its production does not compromise fungal growth, and Mycetohabitans bacteria can efficiently consume it. Narnavirus RmNV-20S and RmNV-23S affected the nucleotide metabolism without impacting the fungal-bacterial symbiosis. Our analyses highlighted the metabolic stability of Mycetohabitans throughout its co-evolution with the fungal host. We also predicted changes in reactions of the bacterial metabolism required for the active production of rhizoxin. This iHol is the first GSM of a fungal holobiont.
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Affiliation(s)
- Cecilio Valadez-Cano
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato, Mexico
| | - Roberto Olivares-Hernández
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Ciudad de México, Mexico
| | - Astrid N Espino-Vázquez
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato, Mexico
| | - Laila P Partida-Martínez
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato, Mexico
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3
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Martin Říhová J, Gupta S, Darby AC, Nováková E, Hypša V. Arsenophonus symbiosis with louse flies: multiple origins, coevolutionary dynamics, and metabolic significance. mSystems 2023; 8:e0070623. [PMID: 37750682 PMCID: PMC10654098 DOI: 10.1128/msystems.00706-23] [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: 07/13/2023] [Accepted: 07/17/2023] [Indexed: 09/27/2023] Open
Abstract
IMPORTANCE Insects that live exclusively on vertebrate blood utilize symbiotic bacteria as a source of essential compounds, e.g., B vitamins. In louse flies, the most frequent symbiont originated in genus Arsenophonus, known from a wide range of insects. Here, we analyze genomic traits, phylogenetic origins, and metabolic capacities of 11 Arsenophonus strains associated with louse flies. We show that in louse flies, Arsenophonus established symbiosis in at least four independent events, reaching different stages of symbiogenesis. This allowed for comparative genomic analysis, including convergence of metabolic capacities. The significance of the results is twofold. First, based on a comparison of independently originated Arsenophonus symbioses, it determines the importance of individual B vitamins for the insect host. This expands our theoretical insight into insect-bacteria symbiosis. The second outcome is of methodological significance. We show that the comparative approach reveals artifacts that would be difficult to identify based on a single-genome analysis.
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Affiliation(s)
- Jana Martin Říhová
- Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Shruti Gupta
- Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Alistair C. Darby
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Eva Nováková
- Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
- Institute of Parasitology, Biology Centre, ASCR, v.v.i., České Budějovice, Czechia
| | - Václav Hypša
- Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
- Institute of Parasitology, Biology Centre, ASCR, v.v.i., České Budějovice, Czechia
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4
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Cazzaniga M, Domínguez-Santos R, Marín-Miret J, Gil R, Latorre A, García-Ferris C. Exploring Gut Microbial Dynamics and Symbiotic Interaction in Blattella germanica Using Rifampicin. BIOLOGY 2023; 12:955. [PMID: 37508385 PMCID: PMC10376618 DOI: 10.3390/biology12070955] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/26/2023] [Accepted: 06/30/2023] [Indexed: 07/30/2023]
Abstract
Blattella germanica harbours two cohabiting symbiotic systems: an obligate endosymbiont, Blattabacterium, located inside bacteriocytes and vertically transmitted, which is key in nitrogen metabolism, and abundant and complex gut microbiota acquired horizontally (mainly by coprophagy) that must play an important role in host physiology. In this work, we use rifampicin treatment to deepen the knowledge on the relationship between the host and the two systems. First, we analysed changes in microbiota composition in response to the presence and removal of the antibiotic with and without faeces in one generation. We found that, independently of faeces supply, rifampicin-sensitive bacteria are strongly affected at four days of treatment, and most taxa recover after treatment, although some did not reach control levels. Second, we tried to generate an aposymbiotic population, but individuals that reached the second generation were severely affected and no third generation was possible. Finally, we established a mixed population with quasi-aposymbiotic and control nymphs sharing an environment in a blind experiment. The analysis of the two symbiotic systems in each individual after reaching the adult stage revealed that endosymbiont's load does not affect the composition of the hindgut microbiota, suggesting that there is no interaction between the two symbiotic systems in Blattella germanica.
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Affiliation(s)
- Monica Cazzaniga
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia and Spanish Research Council, 46980 Paterna, Spain
| | - Rebeca Domínguez-Santos
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia and Spanish Research Council, 46980 Paterna, Spain
| | - Jesús Marín-Miret
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia and Spanish Research Council, 46980 Paterna, Spain
| | - Rosario Gil
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia and Spanish Research Council, 46980 Paterna, Spain
- Genomic and Health Area, Foundation for the Promotion of Sanitary and Biomedical Research of the Valencia Region, 46020 Valencia, Spain
| | - Amparo Latorre
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia and Spanish Research Council, 46980 Paterna, Spain
- Genomic and Health Area, Foundation for the Promotion of Sanitary and Biomedical Research of the Valencia Region, 46020 Valencia, Spain
| | - Carlos García-Ferris
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia and Spanish Research Council, 46980 Paterna, Spain
- Genomic and Health Area, Foundation for the Promotion of Sanitary and Biomedical Research of the Valencia Region, 46020 Valencia, Spain
- Department of Biochemistry and Molecular Biology, University of Valencia, 46100 Burjassot, Spain
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5
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Coevolution of Metabolic Pathways in Blattodea and Their Blattabacterium Endosymbionts, and Comparisons with Other Insect-Bacteria Symbioses. Microbiol Spectr 2022; 10:e0277922. [PMID: 36094208 PMCID: PMC9603385 DOI: 10.1128/spectrum.02779-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Many insects harbor bacterial endosymbionts that supply essential nutrients and enable their hosts to thrive on a nutritionally unbalanced diet. Comparisons of the genomes of endosymbionts and their insect hosts have revealed multiple cases of mutually-dependent metabolic pathways that require enzymes encoded in 2 genomes. Complementation of metabolic reactions at the pathway level has been described for hosts feeding on unbalanced diets, such as plant sap. However, the level of collaboration between symbionts and hosts that feed on more variable diets is largely unknown. In this study, we investigated amino acid and vitamin/cofactor biosynthetic pathways in Blattodea, which comprises cockroaches and termites, and their obligate endosymbiont Blattabacterium cuenoti (hereafter Blattabacterium). In contrast to other obligate symbiotic systems, we found no clear evidence of "collaborative pathways" for amino acid biosynthesis in the genomes of these taxa, with the exception of collaborative arginine biosynthesis in 2 taxa, Cryptocercus punctulatus and Mastotermes darwiniensis. Nevertheless, we found that several gaps specific to Blattabacterium in the folate biosynthetic pathway are likely to be complemented by their host. Comparisons with other insects revealed that, with the exception of the arginine biosynthetic pathway, collaborative pathways for essential amino acids are only observed in phloem-sap feeders. These results suggest that the host diet is an important driving factor of metabolic pathway evolution in obligate symbiotic systems. IMPORTANCE The long-term coevolution between insects and their obligate endosymbionts is accompanied by increasing levels of genome integration, sometimes to the point that metabolic pathways require enzymes encoded in two genomes, which we refer to as "collaborative pathways". To date, collaborative pathways have only been reported from sap-feeding insects. Here, we examined metabolic interactions between cockroaches, a group of detritivorous insects, and their obligate endosymbiont, Blattabacterium, and only found evidence of collaborative pathways for arginine biosynthesis. The rarity of collaborative pathways in cockroaches and Blattabacterium contrasts with their prevalence in insect hosts feeding on phloem-sap. Our results suggest that host diet is a factor affecting metabolic integration in obligate symbiotic systems.
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6
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Identification of the Gene Repertoire of the IMD Pathway and Expression of Antimicrobial Peptide Genes in Several Tissues and Hemolymph of the Cockroach Blattella germanica. Int J Mol Sci 2022; 23:ijms23158444. [PMID: 35955579 PMCID: PMC9369362 DOI: 10.3390/ijms23158444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/26/2022] [Accepted: 07/28/2022] [Indexed: 02/05/2023] Open
Abstract
Antimicrobial peptide (AMP) genes, triggered by Toll and IMD pathways, are essential components of the innate immune system in the German cockroach Blattella germanica. Besides their role in killing pathogenic bacteria, AMPs could be involved in controlling its symbiotic systems (endosymbiont and microbiota). We found that the IMD pathway was active in the adult female transcriptomes of six tissues (salivary glands, foregut, midgut, hindgut, Malpighian tubules and fat body) and hemolymph. Total expression of AMP genes was high in hemolymph and salivary glands and much lower in the other sample types. The expression of specific AMP genes was very heterogeneous among sample types. Two genes, defensin_g10 and drosomycin_g5, displayed relevant expression in the seven sample types, although higher in hemolymph. Other genes only displayed high expression in one tissue. Almost no expression of attacin-like and blattellicin genes was observed in any sample type, although some of them were among the genes with the highest expression in adult female whole bodies. The expression of AMP genes in salivary glands could help control pathogens ingested with food and even determine gut microbiota composition. The low expression levels in midgut and hindgut are probably related to the presence of beneficial microbiota. Furthermore, a reduction in the expression of AMP genes in fat body could be the way to prevent damage to the population of the endosymbiont Blattabacterium cuenoti within bacteriocytes.
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7
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Of Cockroaches and Symbionts: Recent Advances in the Characterization of the Relationship between Blattella germanica and Its Dual Symbiotic System. Life (Basel) 2022; 12:life12020290. [PMID: 35207577 PMCID: PMC8878154 DOI: 10.3390/life12020290] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 12/17/2022] Open
Abstract
Mutualistic stable symbioses are widespread in all groups of eukaryotes, especially in insects, where symbionts have played an essential role in their evolution. Many insects live in obligate relationship with different ecto- and endosymbiotic bacteria, which are needed to maintain their hosts’ fitness in their natural environment, to the point of even relying on them for survival. The case of cockroaches (Blattodea) is paradigmatic, as both symbiotic systems coexist in the same organism in two separated compartments: an intracellular endosymbiont (Blattabacterium) inside bacteriocytes located in the fat body, and a rich and complex microbiota in the hindgut. The German cockroach Blattella germanica is a good model for the study of symbiotic interactions, as it can be maintained in the laboratory in controlled populations, allowing the perturbations of the two symbiotic systems in order to study the communication and integration of the tripartite organization of the host–endosymbiont–microbiota, and to evaluate the role of symbiotic antimicrobial peptides (AMPs) in host control over their symbionts. The importance of cockroaches as reservoirs and transmission vectors of antibiotic resistance sequences, and their putative interest to search for AMPs to deal with the problem, is also discussed.
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8
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Hall RJ, Thorpe S, Thomas GH, Wood AJ. Simulating the evolutionary trajectories of metabolic pathways for insect symbionts in the genus Sodalis. Microb Genom 2020; 6:mgen000378. [PMID: 32543366 PMCID: PMC7478623 DOI: 10.1099/mgen.0.000378] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 04/27/2020] [Indexed: 01/13/2023] Open
Abstract
Insect-bacterial symbioses are ubiquitous, but there is still much to uncover about how these relationships establish, persist and evolve. The tsetse endosymbiont Sodalis glossinidius displays intriguing metabolic adaptations to its microenvironment, but the process by which this relationship evolved remains to be elucidated. The recent chance discovery of the free-living species of the genus Sodalis, Sodalis praecaptivus, provides a serendipitous starting point from which to investigate the evolution of this symbiosis. Here, we present a flux balance model for S. praecaptivus and empirically verify its predictions. Metabolic modelling is used in combination with a multi-objective evolutionary algorithm to explore the trajectories that S. glossinidius may have undertaken from this starting point after becoming internalized. The order in which key genes are lost is shown to influence the evolved populations, providing possible targets for future in vitro genetic manipulation. This method provides a detailed perspective on possible evolutionary trajectories for S. glossinidius in this fundamental process of evolutionary and ecological change.
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Affiliation(s)
- Rebecca J. Hall
- Department of Biology, University of York, York, YO10 5NG, UK
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2TQ, UK
| | - Stephen Thorpe
- Department of Biology, University of York, York, YO10 5NG, UK
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
| | - Gavin H. Thomas
- Department of Biology, University of York, York, YO10 5NG, UK
| | - A. Jamie Wood
- Department of Biology, University of York, York, YO10 5NG, UK
- Department of Mathematics, University of York, York, YO10 5DD, UK
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9
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Röhl A, Riou T, Bockmayr A. Computing irreversible minimal cut sets in genome-scale metabolic networks via flux cone projection. Bioinformatics 2020; 35:2618-2625. [PMID: 30590390 DOI: 10.1093/bioinformatics/bty1027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 12/06/2018] [Accepted: 12/14/2018] [Indexed: 12/19/2022] Open
Abstract
MOTIVATION Minimal cut sets (MCSs) for metabolic networks are sets of reactions which, if they are removed from the network, prevent a target reaction from carrying flux. To compute MCSs different methods exist, which may fail to find sufficiently many MCSs for larger genome-scale networks. RESULTS Here we introduce irreversible minimal cut sets (iMCSs). These are MCSs that consist of irreversible reactions only. The advantage of iMCSs is that they can be computed by projecting the flux cone of the metabolic network on the set of irreversible reactions, which usually leads to a smaller cone. Using oriented matroid theory, we show how the projected cone can be computed efficiently and how this can be applied to find iMCSs even in large genome-scale networks. AVAILABILITY AND IMPLEMENTATION Software is freely available at https://sourceforge.net/projects/irreversibleminimalcutsets/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Annika Röhl
- Department of Mathematics and Computer Science, FB Mathematik und Informatik, Freie Universität Berlin, Berlin, Germany
| | - Tanguy Riou
- Department FRANCE, Ecole Centrale de Nantes, Nantes, France
| | - Alexander Bockmayr
- Department of Mathematics and Computer Science, FB Mathematik und Informatik, Freie Universität Berlin, Berlin, Germany
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10
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Husnik F, Hypsa V, Darby A. Insect-Symbiont Gene Expression in the Midgut Bacteriocytes of a Blood-Sucking Parasite. Genome Biol Evol 2020; 12:429-442. [PMID: 32068830 PMCID: PMC7197495 DOI: 10.1093/gbe/evaa032] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2020] [Indexed: 12/18/2022] Open
Abstract
Animals interact with a diverse array of both beneficial and detrimental microorganisms. In insects, these symbioses in many cases allow feeding on nutritionally unbalanced diets. It is, however, still not clear how are obligate symbioses maintained at the cellular level for up to several hundred million years. Exact mechanisms driving host-symbiont interactions are only understood for a handful of model species and data on blood-feeding hosts with intracellular bacteria are particularly scarce. Here, we analyzed interactions between an obligately blood-sucking parasite of sheep, the louse fly Melophagus ovinus, and its obligate endosymbiont, Arsenophonus melophagi. We assembled a reference transcriptome for the insect host and used dual RNA-Seq with five biological replicates to compare expression in the midgut cells specialized for housing symbiotic bacteria (bacteriocytes) to the rest of the gut (foregut-hindgut). We found strong evidence for the importance of zinc in the system likely caused by symbionts using zinc-dependent proteases when acquiring amino acids, and for different immunity mechanisms controlling the symbionts than in closely related tsetse flies. Our results show that cellular and nutritional interactions between this blood-sucking insect and its symbionts are less intimate than what was previously found in most plant-sap sucking insects. This finding is likely interconnected to several features observed in symbionts in blood-sucking arthropods, particularly their midgut intracellular localization, intracytoplasmic presence, less severe genome reduction, and relatively recent associations caused by frequent evolutionary losses and replacements.
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Affiliation(s)
- Filip Husnik
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Vaclav Hypsa
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Alistair Darby
- Institute of Integrative Biology, University of Liverpool, United Kingdom
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11
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Röhl A, Bockmayr A. Finding MEMo: minimum sets of elementary flux modes. J Math Biol 2019; 79:1749-1777. [PMID: 31388689 DOI: 10.1007/s00285-019-01409-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 07/15/2019] [Indexed: 10/26/2022]
Abstract
Metabolic network reconstructions are widely used in computational systems biology for in silico studies of cellular metabolism. A common approach to analyse these models are elementary flux modes (EFMs), which correspond to minimal functional units in the network. Already for medium-sized networks, it is often impossible to compute the set of all EFMs, due to their huge number. From a practical point of view, this might also not be necessary because a subset of EFMs may already be sufficient to answer relevant biological questions. In this article, we study MEMos or minimum sets of EFMs that can generate all possible steady-state behaviours of a metabolic network. The number of EFMs in a MEMo may be by several orders of magnitude smaller than the total number of EFMs. Using MEMos, we can compute generating sets of EFMs in metabolic networks where the whole set of EFMs is too large to be enumerated.
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Affiliation(s)
- Annika Röhl
- Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 6, 14195, Berlin, Germany.
| | - Alexander Bockmayr
- Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 6, 14195, Berlin, Germany
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12
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Gerstl MP, Müller S, Regensburger G, Zanghellini J. Flux tope analysis: studying the coordination of reaction directions in metabolic networks. Bioinformatics 2019; 35:266-273. [PMID: 30649351 PMCID: PMC6330010 DOI: 10.1093/bioinformatics/bty550] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 05/30/2018] [Accepted: 06/29/2018] [Indexed: 01/06/2023] Open
Abstract
Motivation Elementary flux mode (EFM) analysis allows an unbiased description of metabolic networks in terms of minimal pathways (involving a minimal set of reactions). To date, the enumeration of EFMs is impracticable in genome-scale metabolic models. In a complementary approach, we introduce the concept of a flux tope (FT), involving a maximal set of reactions (with fixed directions), which allows one to study the coordination of reaction directions in metabolic networks and opens a new way for EFM enumeration. Results A FT is a (nontrivial) subset of the flux cone specified by fixing the directions of all reversible reactions. In a consistent metabolic network (without unused reactions), every FT contains a 'maximal pathway', carrying flux in all reactions. This decomposition of the flux cone into FTs allows the enumeration of EFMs (of individual FTs) without increasing the problem dimension by reaction splitting. To develop a mathematical framework for FT analysis, we build on the concepts of sign vectors and hyperplane arrangements. Thereby, we observe that FT analysis can be applied also to flux optimization problems involving additional (inhomogeneous) linear constraints. For the enumeration of FTs, we adapt the reverse search algorithm and provide an efficient implementation. We demonstrate that (biomass-optimal) FTs can be enumerated in genome-scale metabolic models of B.cuenoti and E.coli, and we use FTs to enumerate EFMs in models of M.genitalium and B.cuenoti. Availability and implementation The source code is freely available at https://github.com/mpgerstl/FTA. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Matthias P Gerstl
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria, EU
- Austrian Centre of Industrial Biotechnology, Vienna, Austria, EU
| | - Stefan Müller
- Faculty of Mathematics, University of Vienna, Vienna, Austria, EU
| | - Georg Regensburger
- Institute for Algebra, Johannes Kepler University Linz, Linz, Austria, EU
| | - Jürgen Zanghellini
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria, EU
- Austrian Centre of Industrial Biotechnology, Vienna, Austria, EU
- Austrian Biotech University of Applied Sciences, Tulln, Austria, EU
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13
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Hall RJ, Flanagan LA, Bottery MJ, Springthorpe V, Thorpe S, Darby AC, Wood AJ, Thomas GH. A Tale of Three Species: Adaptation of Sodalis glossinidius to Tsetse Biology, Wigglesworthia Metabolism, and Host Diet. mBio 2019; 10:e02106-18. [PMID: 30602581 PMCID: PMC6315101 DOI: 10.1128/mbio.02106-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 11/20/2018] [Indexed: 12/22/2022] Open
Abstract
The tsetse fly is the insect vector for the Trypanosoma brucei parasite, the causative agent of human African trypanosomiasis. The colonization and spread of the trypanosome correlate positively with the presence of a secondary symbiotic bacterium, Sodalis glossinidius The metabolic requirements and interactions of the bacterium with its host are poorly understood, and herein we describe a metabolic model of S. glossinidius metabolism. The model enabled the design and experimental verification of a defined medium that supports S. glossinidius growth ex vivo This has been used subsequently to analyze in vitro aspects of S. glossinidius metabolism, revealing multiple unique adaptations of the symbiont to its environment. Continued dependence on a sugar, and the importance of the chitin monomer N-acetyl-d-glucosamine as a carbon and energy source, suggests adaptation to host-derived molecules. Adaptation to the amino acid-rich blood diet is revealed by a strong dependence on l-glutamate as a source of carbon and nitrogen and by the ability to rescue a predicted l-arginine auxotrophy. Finally, the selective loss of thiamine biosynthesis, a vitamin provided to the host by the primary symbiont Wigglesworthia glossinidia, reveals an intersymbiont dependence. The reductive evolution of S. glossinidius to exploit environmentally derived metabolites has resulted in multiple weaknesses in the metabolic network. These weaknesses may become targets for reagents that inhibit S. glossinidius growth and aid the reduction of trypanosomal transmission.IMPORTANCE Human African trypanosomiasis is caused by the Trypanosoma brucei parasite. The tsetse fly vector is of interest for its potential to prevent disease spread, as it is essential for T. brucei life cycle progression and transmission. The tsetse's mutualistic endosymbiont Sodalis glossinidius has a link to trypanosome establishment, providing a disease control target. Here, we describe a new, experimentally verified model of S. glossinidius metabolism. This model has enabled the development of a defined growth medium that was used successfully to test aspects of S. glossinidius metabolism. We present S. glossinidius as uniquely adapted to life in the tsetse, through its reliance on the blood diet and host-derived sugars. Additionally, S. glossinidius has adapted to the tsetse's obligate symbiont Wigglesworthia glossinidia by scavenging a vitamin it produces for the insect. This work highlights the use of metabolic modeling to design defined growth media for symbiotic bacteria and may provide novel inhibitory targets to block trypanosome transmission.
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Affiliation(s)
- Rebecca J Hall
- Department of Biology, University of York, York, United Kingdom
| | | | | | | | - Stephen Thorpe
- Department of Biology, University of York, York, United Kingdom
| | - Alistair C Darby
- University of Liverpool, Institute of Integrative Biology, Liverpool, United Kingdom
| | - A Jamie Wood
- Department of Biology, University of York, York, United Kingdom
- Department of Mathematics, University of York, York, United Kingdom
| | - Gavin H Thomas
- Department of Biology, University of York, York, United Kingdom
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14
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Vicente CSL, Mondal SI, Akter A, Ozawa S, Kikuchi T, Hasegawa K. Genome analysis of new Blattabacterium spp., obligatory endosymbionts of Periplaneta fuliginosa and P. japonica. PLoS One 2018; 13:e0200512. [PMID: 29990378 PMCID: PMC6039017 DOI: 10.1371/journal.pone.0200512] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 06/27/2018] [Indexed: 11/18/2022] Open
Abstract
The successful adaptation of cockroaches is, in part, dependent of the activity of their obligatory endosymbionts, Blattabacterium spp., which are involved in uric acid degradation, nitrogen assimilation and nutrient provisioning. Their strategic localization, within bacteriocytes in the proximities of uric acid storage cells (urocytes), highlights their importance in the recycling of nitrogen from urea and ammonia, end-products not secreted by their host insects. In this study, we present the complete genome sequence of two new Blattabacterium spp. from Periplaneta fuliginosa (BPfu) and P. japonica (BPja), and detailed comparison with other Blattabacterium strains from different cockroach species. The genomes of BPfu and BPja show a high degree of stability as showed with for other Blattabacterium representatives, only presenting a 19-kb fragment inversion between BPja and BPfu. In fact, the phylogenomics showed BPja as an ancestor species of BPfu, BPLAN (P. americana) and BBor (Blatta orientalis), in congruence with their host cockroach phylogeny. Their functional profile is similar and closest to the omnivorous strain BBge (Blattella germanica). Interesting, BPja possesses the complete set of enzymes involved sulfate assimilatory pathway only found in BBge and BMda (Mastotermes darwiniensis). The newly sequenced genomes of BPja and BPfu emphasise the remarkable stability of Blattabacterium genomes supported by their long-term coevolution and obligatory lifestyle in their host insect.
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Affiliation(s)
- Cláudia S. L. Vicente
- NemaLab/ICAAM—Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Departamento de Biologia, Universidade de Évora, Núcleo da Mitra, Évora, Portugal
- Department of Environmental Biology, College of Bioscience & Biotechnology, Chubu University,Matsumoto, Kasugai, Aichi, Japan
| | - Shakhinur Islam Mondal
- Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
- Genetic Engineering and Biotechnology Department, Shahjalal University of Science and Technology, Kumargaon, Sylhet, Bangladesh
| | - Arzuba Akter
- Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
- Biochemistry and Molecular Biology Department, Shahjalal University of Science and Technology, Kumargaon, Sylhet, Bangladesh
| | - Sota Ozawa
- Department of Environmental Biology, College of Bioscience & Biotechnology, Chubu University,Matsumoto, Kasugai, Aichi, Japan
| | - Tasei Kikuchi
- Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Koichi Hasegawa
- Department of Environmental Biology, College of Bioscience & Biotechnology, Chubu University,Matsumoto, Kasugai, Aichi, Japan
- * E-mail:
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15
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Rosas T, García-Ferris C, Domínguez-Santos R, Llop P, Latorre A, Moya A. Rifampicin treatment of Blattella germanica evidences a fecal transmission route of their gut microbiota. FEMS Microbiol Ecol 2018; 94:4794938. [DOI: 10.1093/femsec/fiy002] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 01/08/2018] [Indexed: 02/04/2023] Open
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16
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Ponce-de-Leon M, Tamarit D, Calle-Espinosa J, Mori M, Latorre A, Montero F, Pereto J. Determinism and Contingency Shape Metabolic Complementation in an Endosymbiotic Consortium. Front Microbiol 2017; 8:2290. [PMID: 29213256 PMCID: PMC5702781 DOI: 10.3389/fmicb.2017.02290] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 11/06/2017] [Indexed: 01/06/2023] Open
Abstract
Bacterial endosymbionts and their insect hosts establish an intimate metabolic relationship. Bacteria offer a variety of essential nutrients to their hosts, whereas insect cells provide the necessary sources of matter and energy to their tiny metabolic allies. These nutritional complementations sustain themselves on a diversity of metabolite exchanges between the cell host and the reduced yet highly specialized bacterial metabolism—which, for instance, overproduces a small set of essential amino acids and vitamins. A well-known case of metabolic complementation is provided by the cedar aphid Cinara cedri that harbors two co-primary endosymbionts, Buchnera aphidicola BCc and Ca. Serratia symbiotica SCc, and in which some metabolic pathways are partitioned between different partners. Here we present a genome-scale metabolic network (GEM) for the bacterial consortium from the cedar aphid iBSCc. The analysis of this GEM allows us the confirmation of cases of metabolic complementation previously described by genome analysis (i.e., tryptophan and biotin biosynthesis) and the redefinition of an event of metabolic pathway sharing between the two endosymbionts, namely the biosynthesis of tetrahydrofolate. In silico knock-out experiments with iBSCc showed that the consortium metabolism is a highly integrated yet fragile network. We also have explored the evolutionary pathways leading to the emergence of metabolic complementation between reduced metabolisms starting from individual, complete networks. Our results suggest that, during the establishment of metabolic complementation in endosymbionts, adaptive evolution is significant in the case of tryptophan biosynthesis, whereas vitamin production pathways seem to adopt suboptimal solutions.
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Affiliation(s)
- Miguel Ponce-de-Leon
- Departamento de Bioquímica y Biología Molecular I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Daniel Tamarit
- Science for Life Laboratory, Department of Molecular Evolution, Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Jorge Calle-Espinosa
- Departamento de Bioquímica y Biología Molecular I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Matteo Mori
- Department of Physics, University of California, San Diego, La Jolla, CA, United States
| | - Amparo Latorre
- Departament de Genètica, Universitat de València, València, Spain.,Institute for Integrative Systems Biology, Universitat de València-CSIC, València, Spain
| | - Francisco Montero
- Departamento de Bioquímica y Biología Molecular I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Juli Pereto
- Institute for Integrative Systems Biology, Universitat de València-CSIC, València, Spain.,Departament de Bioquímica i Biologia Molecular, Universitat de València, València, Spain
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17
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Valadez-Cano C, Olivares-Hernández R, Resendis-Antonio O, DeLuna A, Delaye L. Natural selection drove metabolic specialization of the chromatophore in Paulinella chromatophora. BMC Evol Biol 2017; 17:99. [PMID: 28410570 PMCID: PMC5392233 DOI: 10.1186/s12862-017-0947-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 03/28/2017] [Indexed: 11/17/2022] Open
Abstract
Background Genome degradation of host-restricted mutualistic endosymbionts has been attributed to inactivating mutations and genetic drift while genes coding for host-relevant functions are conserved by purifying selection. Unlike their free-living relatives, the metabolism of mutualistic endosymbionts and endosymbiont-originated organelles is specialized in the production of metabolites which are released to the host. This specialization suggests that natural selection crafted these metabolic adaptations. In this work, we analyzed the evolution of the metabolism of the chromatophore of Paulinella chromatophora by in silico modeling. We asked whether genome reduction is driven by metabolic engineering strategies resulted from the interaction with the host. As its widely known, the loss of enzyme coding genes leads to metabolic network restructuring sometimes improving the production rates. In this case, the production rate of reduced-carbon in the metabolism of the chromatophore. Results We reconstructed the metabolic networks of the chromatophore of P. chromatophora CCAC 0185 and a close free-living relative, the cyanobacterium Synechococcus sp. WH 5701. We found that the evolution of free-living to host-restricted lifestyle rendered a fragile metabolic network where >80% of genes in the chromatophore are essential for metabolic functionality. Despite the lack of experimental information, the metabolic reconstruction of the chromatophore suggests that the host provides several metabolites to the endosymbiont. By using these metabolites as intracellular conditions, in silico simulations of genome evolution by gene lose recover with 77% accuracy the actual metabolic gene content of the chromatophore. Also, the metabolic model of the chromatophore allowed us to predict by flux balance analysis a maximum rate of reduced-carbon released by the endosymbiont to the host. By inspecting the central metabolism of the chromatophore and the free-living cyanobacteria we found that by improvements in the gluconeogenic pathway the metabolism of the endosymbiont uses more efficiently the carbon source for reduced-carbon production. In addition, our in silico simulations of the evolutionary process leading to the reduced metabolic network of the chromatophore showed that the predicted rate of released reduced-carbon is obtained in less than 5% of the times under a process guided by random gene deletion and genetic drift. We interpret previous findings as evidence that natural selection at holobiont level shaped the rate at which reduced-carbon is exported to the host. Finally, our model also predicts that the ABC phosphate transporter (pstSACB) which is conserved in the genome of the chromatophore of P. chromatophora strain CCAC 0185 is a necessary component to release reduced-carbon molecules to the host. Conclusion Our evolutionary analysis suggests that in the case of Paulinella chromatophora natural selection at the holobiont level played a prominent role in shaping the metabolic specialization of the chromatophore. We propose that natural selection acted as a “metabolic engineer” by favoring metabolic restructurings that led to an increased release of reduced-carbon to the host. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0947-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cecilio Valadez-Cano
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Km. 9.6 Libramiento Norte Carr. Irapuato-León, 36821, Guanajuato, Irapuato, Mexico
| | - Roberto Olivares-Hernández
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Cuajimalpa, Av. Vasco de Quiroga 4871, Santa Fe, Del. Cuajimalpa, C.P. 05348, Ciudad de Mexico, México, Mexico
| | - Osbaldo Resendis-Antonio
- Human Systems Biology Laboratory, Coordinación de la Investigación Científica-Red de Apoyo a la Investigación (RAI), UNAM, México City, Mexico.,Instituto Nacional de Medicina Genómica (INMEGEN), 14610, México City, Mexico
| | - Alexander DeLuna
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Guanajuato, Irapuato, Mexico
| | - Luis Delaye
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Km. 9.6 Libramiento Norte Carr. Irapuato-León, 36821, Guanajuato, Irapuato, Mexico.
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18
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Chance and necessity in the genome evolution of endosymbiotic bacteria of insects. ISME JOURNAL 2017; 11:1291-1304. [PMID: 28323281 PMCID: PMC5437351 DOI: 10.1038/ismej.2017.18] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 01/03/2017] [Accepted: 01/18/2017] [Indexed: 02/07/2023]
Abstract
An open question in evolutionary biology is how does the selection–drift balance determine the fates of biological interactions. We searched for signatures of selection and drift in genomes of five endosymbiotic bacterial groups known to evolve under strong genetic drift. Although most genes in endosymbiotic bacteria showed evidence of relaxed purifying selection, many genes in these bacteria exhibited stronger selective constraints than their orthologs in free-living bacterial relatives. Remarkably, most of these highly constrained genes had no role in the host–symbiont interactions but were involved in either buffering the deleterious consequences of drift or other host-unrelated functions, suggesting that they have either acquired new roles or their role became more central in endosymbiotic bacteria. Experimental evolution of Escherichia coli under strong genetic drift revealed remarkable similarities in the mutational spectrum, genome reduction patterns and gene losses to endosymbiotic bacteria of insects. Interestingly, the transcriptome of the experimentally evolved lines showed a generalized deregulation of the genome that affected genes encoding proteins involved in mutational buffering, regulation and amino acid biosynthesis, patterns identical to those found in endosymbiotic bacteria. Our results indicate that drift has shaped endosymbiotic associations through a change in the functional landscape of bacterial genes and that the host had only a small role in such a shift.
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19
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Zanghellini J, Gerstl MP, Hanscho M, Nair G, Regensburger G, Müller S, Jungreuthmayer C. Toward Genome-Scale Metabolic Pathway Analysis. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Jürgen Zanghellini
- Department of Biotechnology; University of Natural Resources and Life Sciences; Vienna, Muthgasse 18 A1190 Vienna Austria EU
- Austrian Centre of Industrial Biotechnology (ACIB); Muthgasse 11 A1190 Vienna Austria EU
| | - Matthias P. Gerstl
- Austrian Centre of Industrial Biotechnology (ACIB); Muthgasse 11 A1190 Vienna Austria EU
| | - Michael Hanscho
- Austrian Centre of Industrial Biotechnology (ACIB); Muthgasse 11 A1190 Vienna Austria EU
| | - Govind Nair
- Department of Biotechnology; University of Natural Resources and Life Sciences; Vienna, Muthgasse 18 A1190 Vienna Austria EU
- Austrian Centre of Industrial Biotechnology (ACIB); Muthgasse 11 A1190 Vienna Austria EU
| | - Georg Regensburger
- Institute for Algebra; Johannes Kepler University Linz; Altenberger Straβe 69 A-4040 Linz Austria EU
| | - Stefan Müller
- Johann Radon Institute for Computational and Applied Mathematics; Austrian Academy of Sciences; Altenberger Straβe 69 A-4040 Linz Austria EU
| | - Christian Jungreuthmayer
- Austrian Centre of Industrial Biotechnology (ACIB); Muthgasse 11 A1190 Vienna Austria EU
- TGM - Technologisches Gewerbemuseum; Wexstraβe 19-23 A1200 Vienna Austria EU
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20
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Calle-Espinosa J, Ponce-de-Leon M, Santos-Garcia D, Silva FJ, Montero F, Peretó J. Nature lessons: The whitefly bacterial endosymbiont is a minimal amino acid factory with unusual energetics. J Theor Biol 2016; 407:303-317. [PMID: 27473768 DOI: 10.1016/j.jtbi.2016.07.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 07/08/2016] [Accepted: 07/18/2016] [Indexed: 11/16/2022]
Abstract
Reductive genome evolution is a universal phenomenon observed in endosymbiotic bacteria in insects. As the genome reduces its size and irreversibly losses coding genes, the functionalities of the cell system, including the energetics processes, are more restricted. Several energetic pathways can also be lost. How do these reduced metabolic networks sustain the energy needs of the system? Among the bacteria with reduced genomes Candidatus Portiera aleyrodidarum, obligate endosymbiont of whiteflies, represents an extreme case since lacks several key mechanisms for ATP generation. Thus, to analyze the cell energetics in this system, a genome-scale metabolic model of this endosymbiont was constructed, and its energy production capabilities dissected using stoichiometric analysis. Our results suggest that energy generation is coupled to the synthesis of essential amino acids and carotenoids, crucial metabolites in the symbiotic association. A deeper insight showed that ATP production via carotenoid synthesis is also connected with amino acid production. This unusual association of energy production with anabolism suggests that, although minimized, endosymbiont metabolic networks maintain a remarkable biosynthetic potential.
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Affiliation(s)
- Jorge Calle-Espinosa
- Departamento de Bioquímica y Biología Molecular I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Ciudad Universitaria, Madrid 28045, Spain
| | - Miguel Ponce-de-Leon
- Departamento de Bioquímica y Biología Molecular I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Ciudad Universitaria, Madrid 28045, Spain
| | | | - Francisco J Silva
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, C/José Beltrán 2, Paterna 46980, Spain; Departament de Genètica, Universitat de València, Spain
| | - Francisco Montero
- Departamento de Bioquímica y Biología Molecular I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Ciudad Universitaria, Madrid 28045, Spain.
| | - Juli Peretó
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, C/José Beltrán 2, Paterna 46980, Spain; Departament de Bioquímica i Biologia Molecular, Universitat de València, Spain.
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21
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Latorre A, Manzano-Marín A. Dissecting genome reduction and trait loss in insect endosymbionts. Ann N Y Acad Sci 2016; 1389:52-75. [DOI: 10.1111/nyas.13222] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Revised: 08/02/2016] [Accepted: 08/08/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Amparo Latorre
- Institut Cavanilles de Biodiversitat I Biologia Evolutiva; Universitat de Valencia; C/Catedrático José Beltrán Paterna Valencia Spain
- Área de Genómica y Salud de la Fundación para el fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO)-Salud Pública; València Spain
| | - Alejandro Manzano-Marín
- Institut Cavanilles de Biodiversitat I Biologia Evolutiva; Universitat de Valencia; C/Catedrático José Beltrán Paterna Valencia Spain
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22
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23
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Gerstl MP, Klamt S, Jungreuthmayer C, Zanghellini J. Exact quantification of cellular robustness in genome-scale metabolic networks. Bioinformatics 2015; 32:730-7. [PMID: 26543173 PMCID: PMC4795620 DOI: 10.1093/bioinformatics/btv649] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 10/28/2015] [Indexed: 11/25/2022] Open
Abstract
Motivation: Robustness, the ability of biological networks to uphold their functionality in spite of perturbations, is a key characteristic of all living systems. Although several theoretical approaches have been developed to formalize robustness, it still eludes an exact quantification. Here, we present a rigorous and quantitative approach for the structural robustness of metabolic networks by measuring their ability to tolerate random reaction (or gene) knockouts. Results: In analogy to reliability theory, based on an explicit consideration of all possible knockout sets, we exactly quantify the probability of failure for a given network function (e.g. growth). This measure can be computed if the network’s minimal cut sets (MSCs) are known. We show that even in genome-scale metabolic networks the probability of (network) failure can be reliably estimated from MSCs with lowest cardinalities. We demonstrate the applicability of our theory by analyzing the structural robustness of multiple Enterobacteriaceae and Blattibacteriaceae and show a dramatically low structural robustness for the latter. We find that structural robustness develops from the ability to proliferate in multiple growth environments consistent with experimentally found knowledge. Conclusion: The probability of (network) failure provides thus a reliable and easily computable measure of structural robustness and redundancy in (genome-scale) metabolic networks. Availability and implementation: Source code is available under the GNU General Public License at https://github.com/mpgerstl/networkRobustnessToolbox. Contact:juergen.zanghellini@boku.ac.at Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Matthias P Gerstl
- Austrian Centre of Industrial Biotechnology, Vienna, Austria, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria, and
| | - Steffen Klamt
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Christian Jungreuthmayer
- Austrian Centre of Industrial Biotechnology, Vienna, Austria, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria, and
| | - Jürgen Zanghellini
- Austrian Centre of Industrial Biotechnology, Vienna, Austria, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria, and
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24
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Gil R, Peretó J. Small genomes and the difficulty to define minimal translation and metabolic machineries. Front Ecol Evol 2015. [DOI: 10.3389/fevo.2015.00123] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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25
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Mullins DE. Physiology of environmental adaptations and resource acquisition in cockroaches. ANNUAL REVIEW OF ENTOMOLOGY 2015; 60:473-492. [PMID: 25564743 DOI: 10.1146/annurev-ento-011613-162036] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Cockroaches are a group of insects that evolved early in geological time. Because of their antiquity, they for the most part display generalized behavior and physiology and accordingly have frequently been used as model insects to examine physiological and biochemical mechanisms involved with water balance, nutrition, reproduction, genetics, and insecticide resistance. As a result, a considerable amount of information on these topics is available. However, there is much more to be learned by employing new protocols, microchemical analytical techniques, and molecular biology tools to explore many unanswered questions.
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Affiliation(s)
- Donald E Mullins
- Department of Entomology, Virginia Tech, Blacksburg, Virginia 24061;
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26
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Santos-Garcia D, Latorre A, Moya A, Gibbs G, Hartung V, Dettner K, Kuechler SM, Silva FJ. Small but powerful, the primary endosymbiont of moss bugs, Candidatus Evansia muelleri, holds a reduced genome with large biosynthetic capabilities. Genome Biol Evol 2014; 6:1875-93. [PMID: 25115011 PMCID: PMC4122945 DOI: 10.1093/gbe/evu149] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Moss bugs (Coleorrhyncha: Peloridiidae) are members of the order Hemiptera, and like many hemipterans, they have symbiotic associations with intracellular bacteria to fulfill nutritional requirements resulting from their unbalanced diet. The primary endosymbiont of the moss bugs, Candidatus Evansia muelleri, is phylogenetically related to Candidatus Carsonella ruddii and Candidatus Portiera aleyrodidarum, primary endosymbionts of psyllids and whiteflies, respectively. In this work, we report the genome of Candidatus Evansia muelleri Xc1 from Xenophyes cascus, which is the only obligate endosymbiont present in the association. This endosymbiont possesses an extremely reduced genome similar to Carsonella and Portiera. It has crossed the borderline to be considered as an autonomous cell, requiring the support of the insect host for some housekeeping cell functions. Interestingly, in spite of its small genome size, Evansia maintains enriched amino acid (complete or partial pathways for ten essential and six nonessential amino acids) and sulfur metabolisms, probably related to the poor diet of the insect, based on bryophytes, which contains very low levels of nitrogenous and sulfur compounds. Several facts, including the congruence of host (moss bugs, whiteflies, and psyllids) and endosymbiont phylogenies and the retention of the same ribosomal RNA operon during genome reduction in Evansia, Portiera, and Carsonella, suggest the existence of an ancient endosymbiotic Halomonadaceae clade associated with Hemiptera. Three possible scenarios for the origin of these three primary endosymbiont genera are proposed and discussed.
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Affiliation(s)
- Diego Santos-Garcia
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain
| | - Amparo Latorre
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain
- Unidad Mixta de Investigación en Genómica y Salud (FISABIO-Salud Pública and Universitat de València), Spain
| | - Andrés Moya
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain
- Unidad Mixta de Investigación en Genómica y Salud (FISABIO-Salud Pública and Universitat de València), Spain
| | - George Gibbs
- School of Biological Science, Victoria University, Wellington, New Zealand
| | - Viktor Hartung
- Museum für Naturkunde, Leibniz-Institute for Research on Evolution and Biodiversity, Berlin, Germany
| | - Konrad Dettner
- Department of Animal Ecology II, University of Bayreuth, Germany
| | - Stefan Martin Kuechler
- Department of Animal Ecology II, University of Bayreuth, Germany
- *Corresponding author: E-mail: ;
| | - Francisco J. Silva
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain
- Unidad Mixta de Investigación en Genómica y Salud (FISABIO-Salud Pública and Universitat de València), Spain
- *Corresponding author: E-mail: ;
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Patiño-Navarrete R, Piulachs MD, Belles X, Moya A, Latorre A, Peretó J. The cockroach Blattella germanica obtains nitrogen from uric acid through a metabolic pathway shared with its bacterial endosymbiont. Biol Lett 2014; 10:rsbl.2014.0407. [PMID: 25079497 PMCID: PMC4126632 DOI: 10.1098/rsbl.2014.0407] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Uric acid stored in the fat body of cockroaches is a nitrogen reservoir mobilized in times of scarcity. The discovery of urease in Blattabacterium cuenoti, the primary endosymbiont of cockroaches, suggests that the endosymbiont may participate in cockroach nitrogen economy. However, bacterial urease may only be one piece in the entire nitrogen recycling process from insect uric acid. Thus, in addition to the uricolytic pathway to urea, there must be glutamine synthetase assimilating the released ammonia by the urease reaction to enable the stored nitrogen to be metabolically usable. None of the Blattabacterium genomes sequenced to date possess genes encoding for those enzymes. To test the host's contribution to the process, we have sequenced and analysed Blattella germanica transcriptomes from the fat body. We identified transcripts corresponding to all genes necessary for the synthesis of uric acid and its catabolism to urea, as well as for the synthesis of glutamine, asparagine, proline and glycine, i.e. the amino acids required by the endosymbiont. We also explored the changes in gene expression with different dietary protein levels. It appears that the ability to use uric acid as a nitrogen reservoir emerged in cockroaches after its age-old symbiotic association with bacteria.
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Affiliation(s)
- Rafael Patiño-Navarrete
- InstitutCavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, C/Catedràtic José Beltrán n° 2, Paterna 46980, Spain
| | - Maria-Dolors Piulachs
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas and Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta n° 37-49, Barcelona 08003, Spain
| | - Xavier Belles
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas and Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta n° 37-49, Barcelona 08003, Spain
| | - Andrés Moya
- InstitutCavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, C/Catedràtic José Beltrán n° 2, Paterna 46980, Spain
| | - Amparo Latorre
- InstitutCavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, C/Catedràtic José Beltrán n° 2, Paterna 46980, Spain
| | - Juli Peretó
- InstitutCavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, C/Catedràtic José Beltrán n° 2, Paterna 46980, Spain Departament de Bioquímica i Biologia Molecular, Universitat de València, Burjassot 46100, Spain
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Ponce-de-León M, Montero F, Peretó J. Solving gap metabolites and blocked reactions in genome-scale models: application to the metabolic network of Blattabacterium cuenoti. BMC SYSTEMS BIOLOGY 2013; 7:114. [PMID: 24176055 PMCID: PMC3819652 DOI: 10.1186/1752-0509-7-114] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 10/23/2013] [Indexed: 11/20/2022]
Abstract
Background Metabolic reconstruction is the computational-based process that aims to elucidate the network of metabolites interconnected through reactions catalyzed by activities assigned to one or more genes. Reconstructed models may contain inconsistencies that appear as gap metabolites and blocked reactions. Although automatic methods for solving this problem have been previously developed, there are many situations where manual curation is still needed. Results We introduce a general definition of gap metabolite that allows its detection in a straightforward manner. Moreover, a method for the detection of Unconnected Modules, defined as isolated sets of blocked reactions connected through gap metabolites, is proposed. The method has been successfully applied to the curation of iCG238, the genome-scale metabolic model for the bacterium Blattabacterium cuenoti, obligate endosymbiont of cockroaches. Conclusion We found the proposed approach to be a valuable tool for the curation of genome-scale metabolic models. The outcome of its application to the genome-scale model B. cuenoti iCG238 is a more accurate model version named as B. cuenoti iMP240.
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Affiliation(s)
| | - Francisco Montero
- Departamento de Bioquímica y Biología Molecular I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Ciudad Universitaria, Madrid 28045, Spain.
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Patiño-Navarrete R, Moya A, Latorre A, Peretó J. Comparative genomics of Blattabacterium cuenoti: the frozen legacy of an ancient endosymbiont genome. Genome Biol Evol 2013; 5:351-61. [PMID: 23355305 PMCID: PMC3590773 DOI: 10.1093/gbe/evt011] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Many insect species have established long-term symbiotic relationships with intracellular bacteria. Symbiosis with bacteria has provided insects with novel ecological capabilities, which have allowed them colonize previously unexplored niches. Despite its importance to the understanding of the emergence of biological complexity, the evolution of symbiotic relationships remains hitherto a mystery in evolutionary biology. In this study, we contribute to the investigation of the evolutionary leaps enabled by mutualistic symbioses by sequencing the genome of Blattabacterium cuenoti, primary endosymbiont of the omnivorous cockroach Blatta orientalis, and one of the most ancient symbiotic associations. We perform comparative analyses between the Blattabacterium cuenoti genome and that of previously sequenced endosymbionts, namely those from the omnivorous hosts the Blattella germanica (Blattelidae) and Periplaneta americana (Blattidae), and the endosymbionts harbored by two wood-feeding hosts, the subsocial cockroach Cryptocercus punctulatus (Cryptocercidae) and the termite Mastotermes darwiniensis (Termitidae). Our study shows a remarkable evolutionary stasis of this symbiotic system throughout the evolutionary history of cockroaches and the deepest branching termite M. darwiniensis, in terms of not only chromosome architecture but also gene content, as revealed by the striking conservation of the Blattabacterium core genome. Importantly, the architecture of central metabolic network inferred from the endosymbiont genomes was established very early in Blattabacterium evolutionary history and could be an outcome of the essential role played by this endosymbiont in the host's nitrogen economy.
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Affiliation(s)
- Rafael Patiño-Navarrete
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, València, Spain
| | - Andrés Moya
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, València, Spain
- Departament de Genètica, Universitat de València, València, Spain
- Centre for Public Health Research (CSISP), València, Spain
| | - Amparo Latorre
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, València, Spain
- Departament de Genètica, Universitat de València, València, Spain
- Centre for Public Health Research (CSISP), València, Spain
- *Corresponding authors: E-mail: ;
| | - Juli Peretó
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, València, Spain
- Departament de Bioquímica i Biologia Molecular, Universitat de València, València, Spain
- *Corresponding authors: E-mail: ;
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Sabree ZL, Huang CY, Okusu A, Moran NA, Normark BB. The nutrient supplying capabilities of Uzinura, an endosymbiont of armoured scale insects. Environ Microbiol 2013; 15:1988-99. [PMID: 23279075 DOI: 10.1111/1462-2920.12058] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Accepted: 11/22/2012] [Indexed: 11/28/2022]
Abstract
An emerging common physiological feature of plant sap-feeding insects is the presence of bacterial endosymbionts capable of providing essential nutrients to their host. These microbial partners are inviable outside of specialized host tissues, and therefore a cultivation-independent approach, namely high-throughput next-generation genome sequencing, can be used to characterize their gene content and metabolic potential. To this end, we sequenced the first complete genome of the obligate endosymbiont, Candidatus 'Uzinura diaspidicola', of armoured scale insects. At 263 431 bp, Uzinura has an extremely reduced genome that is composed largely of genes encoding enzymes involved in translation and amino acid biosynthesis. The tiny size of the Uzinura genome parallels that observed in some other insect endosymbionts. Despite this extreme genome reduction, the absence of a known obligate partner bacterial symbiont suggests that Uzinura alone can supply sufficient nutrients to its host.
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Affiliation(s)
- Zakee L Sabree
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.
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Abstract
Omics, including genomics, proteomics, and metabolomics, enable us to explain symbioses in terms of the underlying molecules and their interactions. The central task is to transform molecular catalogs of genes, metabolites, etc., into a dynamic understanding of symbiosis function. We review four exemplars of omics studies that achieve this goal, through defined biological questions relating to metabolic integration and regulation of animal-microbial symbioses, the genetic autonomy of bacterial symbionts, and symbiotic protection of animal hosts from pathogens. As omic datasets become increasingly complex, computationally sophisticated downstream analyses are essential to reveal interactions not evident from visual inspection of the data. We discuss two approaches, phylogenomics and transcriptional clustering, that can divide the primary output of omics studies-long lists of factors-into manageable subsets, and we describe how they have been applied to analyze large datasets and generate testable hypotheses.
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Affiliation(s)
- J Chaston
- Department of Entomology, Comstock Hall, Cornell University, Ithaca, New York 14853, USA
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