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Alsharif SM, Waznah MS, Ismaeil M, El-Sayed WS. 16S rDNA-based diversity analysis of bacterial communities associated with soft corals of the Red Sea, Al Rayyis, White Head, KSA. JOURNAL OF TAIBAH UNIVERSITY FOR SCIENCE 2023. [DOI: 10.1080/16583655.2022.2156762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Affiliation(s)
- Sultan M. Alsharif
- Department of Biology, College of Science, Taibah University, Al-Madinah, Kingdom of Saudi Arabia
| | - Moayad S. Waznah
- Department of Biology, College of Science, Taibah University, Al-Madinah, Kingdom of Saudi Arabia
| | - Mohamed Ismaeil
- Microbiology Department, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Wael S. El-Sayed
- Microbiology Department, Faculty of Science, Ain Shams University, Cairo, Egypt
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Li S, Wang J, Tian X, Toufeeq S, Huang W. Immunometabolic regulation during the presence of microorganisms and parasitoids in insects. Front Immunol 2023; 14:905467. [PMID: 37818375 PMCID: PMC10560992 DOI: 10.3389/fimmu.2023.905467] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 09/04/2023] [Indexed: 10/12/2023] Open
Abstract
Multicellular organisms live in environments containing diverse nutrients and a wide variety of microbial communities. On the one hand, the immune response of organisms can protect from the intrusion of exogenous microorganisms. On the other hand, the dynamic coordination of anabolism and catabolism of organisms is a necessary factor for growth and reproduction. Since the production of an immune response is an energy-intensive process, the activation of immune cells is accompanied by metabolic transformations that enable the rapid production of ATP and new biomolecules. In insects, the coordination of immunity and metabolism is the basis for insects to cope with environmental challenges and ensure normal growth, development and reproduction. During the activation of insect immune tissues by pathogenic microorganisms, not only the utilization of organic resources can be enhanced, but also the activated immune cells can usurp the nutrients of non-immune tissues by generating signals. At the same time, insects also have symbiotic bacteria in their body, which can affect insect physiology through immune-metabolic regulation. This paper reviews the research progress of insect immune-metabolism regulation from the perspective of insect tissues, such as fat body, gut and hemocytes. The effects of microorganisms (pathogenic bacteria/non-pathogenic bacteria) and parasitoids on immune-metabolism were elaborated here, which provide guidance to uncover immunometabolism mechanisms in insects and mammals. This work also provides insights to utilize immune-metabolism for the formulation of pest control strategies.
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Affiliation(s)
- Shirong Li
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- College of Life Sciences, Yan’an University, Yan’an, Shaanxi, China
| | - Jing Wang
- College of Life Sciences, Shangrao Normal University, Shangrao, China
| | - Xing Tian
- College of Life Sciences, Yan’an University, Yan’an, Shaanxi, China
| | - Shahzad Toufeeq
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Wuren Huang
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
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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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Militello G, Bich L, Moreno A. Functional Integration and Individuality in Prokaryotic Collective Organisations. Acta Biotheor 2021; 69:391-415. [PMID: 32816285 DOI: 10.1007/s10441-020-09390-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 08/11/2020] [Indexed: 11/25/2022]
Abstract
Both physiological and evolutionary criteria of biological individuality are underpinned by the idea that an individual is a functionally integrated whole. However, a precise account of functional integration has not been provided so far, and current notions are not developed in the details, especially in the case of composite systems. To address this issue, this paper focuses on the organisational dimension of two representative associations of prokaryotes: biofilms and the endosymbiosis between prokaryotes. Some critical voices have been raised against the thesis that biofilms are biological individuals. Nevertheless, it has not been investigated which structural and functional obstacles may prevent them from being fully integrated physiological or evolutionary units. By contrast, the endosymbiotic association of different species of prokaryotes has the potential for achieving a different type of physiological integration based on a common boundary and interlocked functions. This type of association had made it possible, under specific conditions, to evolve endosymbionts into fully integrated organelles. This paper therefore has three aims: first, to analyse the organisational conditions and the physiological mechanisms that enable integration in prokaryotic associations; second, to discuss the organisational differences between biofilms and prokaryotic endosymbiosis and the types of integration they achieve; finally, to provide a more precise account of functional integration based on these case studies.
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Affiliation(s)
- Guglielmo Militello
- IAS-Research Centre for Life, Mind and Society, Department of Logic and Philosophy of Science, University of the Basque Country (UPV/EHU), Avenida de Tolosa 70, 20018, Donostia-San Sebastian, Spain
| | - Leonardo Bich
- IAS-Research Centre for Life, Mind and Society, Department of Logic and Philosophy of Science, University of the Basque Country (UPV/EHU), Avenida de Tolosa 70, 20018, Donostia-San Sebastian, Spain.
| | - Alvaro Moreno
- IAS-Research Centre for Life, Mind and Society, Department of Logic and Philosophy of Science, University of the Basque Country (UPV/EHU), Avenida de Tolosa 70, 20018, Donostia-San Sebastian, Spain
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5
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Incipient genome erosion and metabolic streamlining for antibiotic production in a defensive symbiont. Proc Natl Acad Sci U S A 2021; 118:2023047118. [PMID: 33883280 PMCID: PMC8092579 DOI: 10.1073/pnas.2023047118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genome reduction is commonly observed in bacteria of several phyla engaging in obligate nutritional symbioses with insects. In Actinobacteria, however, little is known about the process of genome evolution, despite their importance as prolific producers of antibiotics and their increasingly recognized role as defensive partners of insects and other organisms. Here, we show that “Streptomyces philanthi,” a defensive symbiont of digger wasps, has a G+C-enriched genome in the early stages of erosion, with inactivating mutations in a large proportion of genes, causing dependency on its hosts for certain nutrients, which was validated in axenic symbiont cultures. Additionally, overexpressed catabolic and biosynthetic pathways of the bacteria inside the host indicate host–symbiont metabolic integration for streamlining and control of antibiotic production. Genome erosion is a frequently observed result of relaxed selection in insect nutritional symbionts, but it has rarely been studied in defensive mutualisms. Solitary beewolf wasps harbor an actinobacterial symbiont of the genus Streptomyces that provides protection to the developing offspring against pathogenic microorganisms. Here, we characterized the genomic architecture and functional gene content of this culturable symbiont using genomics, transcriptomics, and proteomics in combination with in vitro assays. Despite retaining a large linear chromosome (7.3 Mb), the wasp symbiont accumulated frameshift mutations in more than a third of its protein-coding genes, indicative of incipient genome erosion. Although many of the frameshifted genes were still expressed, the encoded proteins were not detected, indicating post-transcriptional regulation. Most pseudogenization events affected accessory genes, regulators, and transporters, but “Streptomyces philanthi” also experienced mutations in central metabolic pathways, resulting in auxotrophies for biotin, proline, and arginine that were confirmed experimentally in axenic culture. In contrast to the strong A+T bias in the genomes of most obligate symbionts, we observed a significant G+C enrichment in regions likely experiencing reduced selection. Differential expression analyses revealed that—compared to in vitro symbiont cultures—“S. philanthi” in beewolf antennae showed overexpression of genes for antibiotic biosynthesis, the uptake of host-provided nutrients and the metabolism of building blocks required for antibiotic production. Our results show unusual traits in the early stage of genome erosion in a defensive symbiont and suggest tight integration of host–symbiont metabolic pathways that effectively grants the host control over the antimicrobial activity of its bacterial partner.
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Nardi T, Olivieri E, Kariuki E, Sassera D, Castelli M. Sequence of a Coxiella Endosymbiont of the Tick Amblyomma nuttalli Suggests a Pattern of Convergent Genome Reduction in the Coxiella Genus. Genome Biol Evol 2021; 13:evaa253. [PMID: 33275132 PMCID: PMC7851586 DOI: 10.1093/gbe/evaa253] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2020] [Indexed: 12/20/2022] Open
Abstract
Ticks require bacterial symbionts for the provision of necessary compounds that are absent in their hematophagous diet. Such symbionts are frequently vertically transmitted and, most commonly, belong to the Coxiella genus, which also includes the human pathogen Coxiella burnetii. This genus can be divided in four main clades, presenting partial but incomplete cocladogenesis with the tick hosts. Here, we report the genome sequence of a novel Coxiella, endosymbiont of the African tick Amblyomma nuttalli, and the ensuing comparative analyses. Its size (∼1 Mb) is intermediate between symbionts of Rhipicephalus species and other Amblyomma species. Phylogenetic analyses show that the novel sequence is the first genome of the B clade, the only one for which no genomes were previously available. Accordingly, it allows to draw an enhanced scenario of the evolution of the genus, one of parallel genome reduction of different endosymbiont lineages, which are now at different stages of reduction from a more versatile ancestor. Gene content comparison allows to infer that the ancestor could be reminiscent of C. burnetii. Interestingly, the convergent loss of mismatch repair could have been a major driver of such reductive evolution. Predicted metabolic profiles are rather homogenous among Coxiella endosymbionts, in particular vitamin biosynthesis, consistently with a host-supportive role. Concurrently, similarities among Coxiella endosymbionts according to host genus and despite phylogenetic unrelatedness hint at possible host-dependent effects.
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Affiliation(s)
- Tiago Nardi
- Department of Biology and Biotechnology, University of Pavia, Italy
| | | | - Edward Kariuki
- Veterinary and Capture Service Department, Kenya Wildlife Service, Kenya
| | - Davide Sassera
- Department of Biology and Biotechnology, University of Pavia, Italy
| | - Michele Castelli
- Department of Biology and Biotechnology, University of Pavia, Italy
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Sutormin DA, Galivondzhyan AK, Polkhovskiy AV, Kamalyan SO, Severinov KV, Dubiley SA. Diversity and Functions of Type II Topoisomerases. Acta Naturae 2021; 13:59-75. [PMID: 33959387 PMCID: PMC8084294 DOI: 10.32607/actanaturae.11058] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/09/2020] [Indexed: 11/29/2022] Open
Abstract
The DNA double helix provides a simple and elegant way to store and copy genetic information. However, the processes requiring the DNA helix strands separation, such as transcription and replication, induce a topological side-effect - supercoiling of the molecule. Topoisomerases comprise a specific group of enzymes that disentangle the topological challenges associated with DNA supercoiling. They relax DNA supercoils and resolve catenanes and knots. Here, we review the catalytic cycles, evolution, diversity, and functional roles of type II topoisomerases in organisms from all domains of life, as well as viruses and other mobile genetic elements.
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Affiliation(s)
- D. A. Sutormin
- Institute of Gene Biology RAS, Moscow, 119334 Russia
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
| | - A. K. Galivondzhyan
- Lomonosov Moscow State University, Moscow, 119991 Russia
- Institute of Molecular Genetics RAS, Moscow, 123182 Russia
| | - A. V. Polkhovskiy
- Institute of Gene Biology RAS, Moscow, 119334 Russia
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
| | - S. O. Kamalyan
- Institute of Gene Biology RAS, Moscow, 119334 Russia
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
| | - K. V. Severinov
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
- Centre for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology RAS, Moscow, 119334 Russia
- Waksman Institute for Microbiology, Piscataway, New Jersey, 08854 USA
| | - S. A. Dubiley
- Institute of Gene Biology RAS, Moscow, 119334 Russia
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
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Nasir A, Romero-Severson E, Claverie JM. Investigating the Concept and Origin of Viruses. Trends Microbiol 2020; 28:959-967. [PMID: 33158732 PMCID: PMC7609044 DOI: 10.1016/j.tim.2020.08.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/25/2020] [Accepted: 08/27/2020] [Indexed: 12/21/2022]
Abstract
The ongoing COVID-19 pandemic has piqued public interest in the properties, evolution, and emergence of viruses. Here, we discuss how these basic questions have surprisingly remained disputed despite being increasingly within the reach of scientific analysis. We review recent data-driven efforts that shed light into the origin and evolution of viruses and explain factors that resist the widespread acceptance of new views and insights. We propose a new definition of viruses that is not restricted to the presence or absence of any genetic or physical feature, detail a scenario for how viruses likely originated from ancient cells, and explain technical and conceptual biases that limit our understanding of virus evolution. We note that the philosophical aspects of virus evolution also impact the way we might prepare for future outbreaks.
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Affiliation(s)
- Arshan Nasir
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, NM, USA.
| | - Ethan Romero-Severson
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Jean-Michel Claverie
- Aix Marseille University, CNRS, IGS, Structural and Genomic Information Laboratory (UMR7256), Mediterranean Institute of Microbiology (FR3479), Marseille, France
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Gupta A, Nair S. Dynamics of Insect-Microbiome Interaction Influence Host and Microbial Symbiont. Front Microbiol 2020; 11:1357. [PMID: 32676060 PMCID: PMC7333248 DOI: 10.3389/fmicb.2020.01357] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/27/2020] [Indexed: 12/21/2022] Open
Abstract
Insects share an intimate relationship with their gut microflora and this symbiotic association has developed into an essential evolutionary outcome intended for their survival through extreme environmental conditions. While it has been clearly established that insects, with very few exceptions, associate with several microbes during their life cycle, information regarding several aspects of these associations is yet to be fully unraveled. Acquisition of bacteria by insects marks the onset of microbial symbiosis, which is followed by the adaptation of these bacterial species to the gut environment for prolonged sustenance and successful transmission across generations. Although several insect-microbiome associations have been reported and each with their distinctive features, diversifications and specializations, it is still unclear as to what led to these diversifications. Recent studies have indicated the involvement of various evolutionary processes operating within an insect body that govern the transition of a free-living microbe to an obligate or facultative symbiont and eventually leading to the establishment and diversification of these symbiotic relationships. Data from various studies, summarized in this review, indicate that the symbiotic partners, i.e., the bacteria and the insect undergo several genetic, biochemical and physiological changes that have profound influence on their life cycle and biology. An interesting outcome of the insect-microbe interaction is the compliance of the microbial partner to its eventual genome reduction. Endosymbionts possess a smaller genome as compared to their free-living forms, and thus raising the question what is leading to reductive evolution in the microbial partner. This review attempts to highlight the fate of microbes within an insect body and its implications for both the bacteria and its insect host. While discussion on each specific association would be too voluminous and outside the scope of this review, we present an overview of some recent studies that contribute to a better understanding of the evolutionary trajectory and dynamics of the insect-microbe association and speculate that, in the future, a better understanding of the nature of this interaction could pave the path to a sustainable and environmentally safe way for controlling economically important pests of crop plants.
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Affiliation(s)
| | - Suresh Nair
- Plant-Insect Interaction Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
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Cavalier-Smith T, Chao EEY. Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria). PROTOPLASMA 2020. [PMID: 31900730 DOI: 10.1007/s00709-019-01442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.
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Affiliation(s)
| | - Ema E-Yung Chao
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
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Cavalier-Smith T, Chao EEY. Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria). PROTOPLASMA 2020; 257:621-753. [PMID: 31900730 PMCID: PMC7203096 DOI: 10.1007/s00709-019-01442-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 09/19/2019] [Indexed: 05/02/2023]
Abstract
Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.
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Affiliation(s)
| | - Ema E-Yung Chao
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
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12
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Abstract
Most scale insects, like many other plant sap-sucking hemipterans, harbor obligate symbionts of bacterial or fungal origin, which synthesize and provide the host with substances missing in their restricted diet. Histological, ultrastructural, and molecular analyses have revealed that scale insects differ in the type of symbionts, the localization of symbionts in the host body, and the mode of transmission of symbionts from one generation to the next. Symbiotic microorganisms may be distributed in the cells of the fat body, midgut epithelium, inside the cells of other symbionts, or the specialized cells of a mesodermal origin, termed bacteriocytes. In most scale insects, their symbiotic associates are inherited transovarially, wherein the mode of transmission may have a different course-the symbionts may invade larval ovaries containing undifferentiated germ cells or ovaries of adult females containing vitellogenic or choriogenic oocytes.
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Cicada Endosymbionts Have tRNAs That Are Correctly Processed Despite Having Genomes That Do Not Encode All of the tRNA Processing Machinery. mBio 2019; 10:mBio.01950-18. [PMID: 31213566 PMCID: PMC6581868 DOI: 10.1128/mbio.01950-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The smallest bacterial genomes, in the range of about 0.1 to 0.5 million base pairs, are commonly found in the nutritional endosymbionts of insects. These tiny genomes are missing genes that encode proteins and RNAs required for the translation of mRNAs, one of the most highly conserved and important cellular processes. In this study, we found that the bacterial endosymbionts of cicadas have genomes which encode incomplete tRNA sets and lack genes required for tRNA processing. Nevertheless, we found that endosymbiont tRNAs are correctly processed at their 5′ and 3′ ends and, surprisingly, that mostly exist as tRNA halves. We hypothesize that the cicada host must supply its symbionts with these missing tRNA processing activities. Gene loss and genome reduction are defining characteristics of endosymbiotic bacteria. The most highly reduced endosymbiont genomes have lost numerous essential genes related to core cellular processes such as replication, transcription, and translation. Computational gene predictions performed for the genomes of the two bacterial symbionts of the cicada Diceroprocta semicincta, “Candidatus Hodgkinia cicadicola” (Alphaproteobacteria) and “Ca. Sulcia muelleri” (Bacteroidetes), have found only 26 and 16 tRNA genes and 15 and 10 aminoacyl tRNA synthetase genes, respectively. Furthermore, the original “Ca. Hodgkinia cicadicola” genome annotation was missing several essential genes involved in tRNA processing, such as those encoding RNase P and CCA tRNA nucleotidyltransferase as well as several RNA editing enzymes required for tRNA maturation. How these cicada endosymbionts perform basic translation-related processes remains unknown. Here, by sequencing eukaryotic mRNAs and total small RNAs, we show that the limited tRNA set predicted by computational annotation of “Ca. Sulcia muelleri” and “Ca. Hodgkinia cicadicola” is likely correct. Furthermore, we show that despite the absence of genes encoding tRNA processing activities in the symbiont genomes, symbiont tRNAs have correctly processed 5′ and 3′ ends and seem to undergo nucleotide modification. Surprisingly, we found that most “Ca. Hodgkinia cicadicola” and “Ca. Sulcia muelleri” tRNAs exist as tRNA halves. We hypothesize that “Ca. Sulcia muelleri” and “Ca. Hodgkinia cicadicola” tRNAs function in bacterial translation but require host-encoded enzymes to do so.
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Legendre M, Alempic JM, Philippe N, Lartigue A, Jeudy S, Poirot O, Ta NT, Nin S, Couté Y, Abergel C, Claverie JM. Pandoravirus Celtis Illustrates the Microevolution Processes at Work in the Giant Pandoraviridae Genomes. Front Microbiol 2019; 10:430. [PMID: 30906288 PMCID: PMC6418002 DOI: 10.3389/fmicb.2019.00430] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 02/19/2019] [Indexed: 12/22/2022] Open
Abstract
With genomes of up to 2.7 Mb propagated in μm-long oblong particles and initially predicted to encode more than 2000 proteins, members of the Pandoraviridae family display the most extreme features of the known viral world. The mere existence of such giant viruses raises fundamental questions about their origin and the processes governing their evolution. A previous analysis of six newly available isolates, independently confirmed by a study including three others, established that the Pandoraviridae pan-genome is open, meaning that each new strain exhibits protein-coding genes not previously identified in other family members. With an average increment of about 60 proteins, the gene repertoire shows no sign of reaching a limit and remains largely coding for proteins without recognizable homologs in other viruses or cells (ORFans). To explain these results, we proposed that most new protein-coding genes were created de novo, from pre-existing non-coding regions of the G+C rich pandoravirus genomes. The comparison of the gene content of a new isolate, pandoravirus celtis, closely related (96% identical genome) to the previously described p. quercus is now used to test this hypothesis by studying genomic changes in a microevolution range. Our results confirm that the differences between these two similar gene contents mostly consist of protein-coding genes without known homologs, with statistical signatures close to that of intergenic regions. These newborn proteins are under slight negative selection, perhaps to maintain stable folds and prevent protein aggregation pending the eventual emergence of fitness-increasing functions. Our study also unraveled several insertion events mediated by a transposase of the hAT family, 3 copies of which are found in p. celtis and are presumably active. Members of the Pandoraviridae are presently the first viruses known to encode this type of transposase.
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Affiliation(s)
- Matthieu Legendre
- Aix Marseille Univ, CNRS, IGS, Structural and Genomic Information Laboratory (UMR7256), Mediterranean Institute of Microbiology (FR3479), Marseille, France
| | - Jean-Marie Alempic
- Aix Marseille Univ, CNRS, IGS, Structural and Genomic Information Laboratory (UMR7256), Mediterranean Institute of Microbiology (FR3479), Marseille, France
| | - Nadège Philippe
- Aix Marseille Univ, CNRS, IGS, Structural and Genomic Information Laboratory (UMR7256), Mediterranean Institute of Microbiology (FR3479), Marseille, France
| | - Audrey Lartigue
- Aix Marseille Univ, CNRS, IGS, Structural and Genomic Information Laboratory (UMR7256), Mediterranean Institute of Microbiology (FR3479), Marseille, France
| | - Sandra Jeudy
- Aix Marseille Univ, CNRS, IGS, Structural and Genomic Information Laboratory (UMR7256), Mediterranean Institute of Microbiology (FR3479), Marseille, France
| | - Olivier Poirot
- Aix Marseille Univ, CNRS, IGS, Structural and Genomic Information Laboratory (UMR7256), Mediterranean Institute of Microbiology (FR3479), Marseille, France
| | - Ngan Thi Ta
- Aix Marseille Univ, CNRS, IGS, Structural and Genomic Information Laboratory (UMR7256), Mediterranean Institute of Microbiology (FR3479), Marseille, France
| | - Sébastien Nin
- Aix Marseille Univ, CNRS, IGS, Structural and Genomic Information Laboratory (UMR7256), Mediterranean Institute of Microbiology (FR3479), Marseille, France
| | - Yohann Couté
- Inserm, BIG-BGE, CEA, Université Grenoble Alpes, Grenoble, France
| | - Chantal Abergel
- Aix Marseille Univ, CNRS, IGS, Structural and Genomic Information Laboratory (UMR7256), Mediterranean Institute of Microbiology (FR3479), Marseille, France
| | - Jean-Michel Claverie
- Aix Marseille Univ, CNRS, IGS, Structural and Genomic Information Laboratory (UMR7256), Mediterranean Institute of Microbiology (FR3479), Marseille, France
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15
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Bohlin J, Pettersson JHO. Evolution of Genomic Base Composition: From Single Cell Microbes to Multicellular Animals. Comput Struct Biotechnol J 2019; 17:362-370. [PMID: 30949307 PMCID: PMC6429543 DOI: 10.1016/j.csbj.2019.03.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 02/28/2019] [Accepted: 03/01/2019] [Indexed: 01/07/2023] Open
Abstract
Whole genome sequencing (WGS) of thousands of microbial genomes has provided considerable insight into evolutionary mechanisms in the microbial world. While substantially fewer eukaryotic genomes are available for analyses the number is rapidly increasing. This mini-review summarizes broadly evolutionary dynamics of base composition in the different domains of life from the perspective of prokaryotes. Common and different evolutionary mechanisms influencing genomic base composition in eukaryotes and prokaryotes are discussed. The conclusion from the data currently available suggests that while there are similarities there are also striking differences in how genomic base composition has evolved within prokaryotes and eukaryotes. For instance, homologous recombination appears to increase GC content locally in eukaryotes due to a non-selective process termed GC-biased gene conversion (gBGC). For prokaryotes on the other hand, increase in genomic GC content seems to be driven by the environment and selection. We find that similar phenomena observed for some organisms in each respective domain may be caused by very different mechanisms: while gBGC and recombination rates appear to explain the negative correlation between GC3 (GC content based on the third codon nucleotides) and genome size in some eukaryotes uptake of AT rich DNA sequences is the main reason for a similar negative correlation observed in prokaryotes. We provide further examples that indicate that base composition in prokaryotes and eukaryotes have evolved under very different constraints.
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Affiliation(s)
- Jon Bohlin
- Norwegian Institute of Public Health, Division of Infection Control and Environmental Health, Department of Infectious Disease Epidemiology and Modelling, Lovisenberggata 8, 0456 Oslo, Norway.,Centre for Fertility and Health, Norwegian Institute of Public Health, PO-Box 222 Skøyen, N-0213 Oslo, Norway.,Norwegian University of Life Sciences, Faculty of Veterinary Sciences, Production Animal Clinical Sciences, Ullevålsveien 72, 0454 Oslo, Norway
| | - John H-O Pettersson
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School the University of Sydney, New South Wales 2006, Australia.,Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Public Health Agency of Sweden, Nobels vg 18, SE-171 82 Solna, Sweden
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16
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Gil R, Latorre A. Unity Makes Strength: A Review on Mutualistic Symbiosis in Representative Insect Clades. Life (Basel) 2019; 9:E21. [PMID: 30823538 PMCID: PMC6463088 DOI: 10.3390/life9010021] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/11/2019] [Accepted: 02/19/2019] [Indexed: 12/14/2022] Open
Abstract
Settled on the foundations laid by zoologists and embryologists more than a century ago, the study of symbiosis between prokaryotes and eukaryotes is an expanding field. In this review, we present several models of insect⁻bacteria symbioses that allow for the detangling of most known features of this distinctive way of living, using a combination of very diverse screening approaches, including molecular, microscopic, and genomic techniques. With the increasing the amount of endosymbiotic bacteria genomes available, it has been possible to develop evolutionary models explaining the changes undergone by these bacteria in their adaptation to the intracellular host environment. The establishment of a given symbiotic system can be a root cause of substantial changes in the partners' way of life. Furthermore, symbiont replacement and/or the establishment of bacterial consortia are two ways in which the host can exploit its interaction with environmental bacteria for endosymbiotic reinvigoration. The detailed study of diverse and complex symbiotic systems has revealed a great variety of possible final genomic products, frequently below the limit considered compatible with cellular life, and sometimes with unanticipated genomic and population characteristics, raising new questions that need to be addressed in the near future through a wider exploration of new models and empirical observations.
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Affiliation(s)
- Rosario Gil
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València/CSIC. Calle Catedrático Agustín Escardino, 9, 46980 Paterna (Valencia), Spain.
- Departament de Genètica, Universitat de València. Calle Dr. Moliner, 50, 46100 Burjassot (València), Spain.
- Área de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO). Avenida de Cataluña 21, 46020 València, Spain.
| | - Amparo Latorre
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València/CSIC. Calle Catedrático Agustín Escardino, 9, 46980 Paterna (Valencia), Spain.
- Departament de Genètica, Universitat de València. Calle Dr. Moliner, 50, 46100 Burjassot (València), Spain.
- Área de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO). Avenida de Cataluña 21, 46020 València, Spain.
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17
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Claverie JM, Abergel C, Legendre M. [Giant viruses that create their own genes]. Med Sci (Paris) 2019; 34:1087-1091. [PMID: 30623766 DOI: 10.1051/medsci/2018300] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Since 2003 and the discovery of Mimivirus, the saga of giant viruses continues with the isolation of new amoeba viruses, which are now divided into seven distinct families, the origin (s) of which are still mysterious and controversial. Thanks to the isolation of 3 new members of the Pandoraviridae family, whose micrometric particles and genomes of more than 2 megabases encroach on the cellular world, we carried out a stringent re-analysis of their gene contents, using a combination of transcriptomic, proteomic and bioinformatic approaches. We concluded that the only scenario capable of accounting for the distribution and the huge proportion of orphan genes ("ORFans") that characterize Pandoraviruses is that they were created de novo within the intergenic regions. This process, perhaps shared among other large DNA viruses, challenges the central paradigm of molecular evolution according to which all genes / proteins have an ancestry history.
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Affiliation(s)
- Jean-Michel Claverie
- Aix-Marseille université et CNRS, Information génomique et structurale (IGS), UMR7256, Institut de microbiologie de la Méditerranée-IMM-FR 3479, parc scientifique de Luminy, 163, avenue de Luminy, case 934, 13288 Marseille Cedex 09, France
| | - Chantal Abergel
- Aix-Marseille université et CNRS, Information génomique et structurale (IGS), UMR7256, Institut de microbiologie de la Méditerranée-IMM-FR 3479, parc scientifique de Luminy, 163, avenue de Luminy, case 934, 13288 Marseille Cedex 09, France
| | - Matthieu Legendre
- Aix-Marseille université et CNRS, Information génomique et structurale (IGS), UMR7256, Institut de microbiologie de la Méditerranée-IMM-FR 3479, parc scientifique de Luminy, 163, avenue de Luminy, case 934, 13288 Marseille Cedex 09, France
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18
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Caetano-Anollés G, Nasir A, Kim KM, Caetano-Anollés D. Rooting Phylogenies and the Tree of Life While Minimizing Ad Hoc and Auxiliary Assumptions. Evol Bioinform Online 2018; 14:1176934318805101. [PMID: 30364468 PMCID: PMC6196624 DOI: 10.1177/1176934318805101] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 09/05/2018] [Indexed: 12/25/2022] Open
Abstract
Phylogenetic methods unearth evolutionary history when supported by three starting points of reason: (1) the continuity axiom begs the existence of a "model" of evolutionary change, (2) the singularity axiom defines the historical ground plan (phylogeny) in which biological entities (taxa) evolve, and (3) the memory axiom demands identification of biological attributes (characters) with historical information. Axiom consequences are interlinked, making the retrodiction enterprise an endeavor of reciprocal fulfillment. In particular, establishing direction of evolutionary change (character polarization) roots phylogenies and enables testing the existence of historical memory (homology). Unfortunately, rooting phylogenies, especially the "tree of life," generally follow narratives instead of integrating empirical and theoretical knowledge of retrodictive exploration. This stems mostly from a focus on molecular sequence analysis and uncertainties about rooting methods. Here, we review available rooting criteria, highlighting the need to minimize both ad hoc and auxiliary assumptions, especially argumentative ad hocness. We show that while the outgroup comparison method has been widely adopted, the generality criterion of nesting and additive phylogenetic change embodied in Weston rule offers the most powerful rooting approach. We also propose a change of focus, from phylogenies that describe the evolution of biological systems to those that describe the evolution of parts of those systems. This weakens violation of character independence, helps formalize the generality criterion of rooting, and provides new ways to study the problem of evolution.
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Affiliation(s)
- Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Arshan Nasir
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Kyung Mo Kim
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, Republic of Korea
| | - Derek Caetano-Anollés
- Department of Evolutionary Genetics, Max-Planck-Institut für Evolutionsbiologie, Plön, Germany
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19
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Senra MVX, Sung W, Ackerman M, Miller SF, Lynch M, Soares CAG. An Unbiased Genome-Wide View of the Mutation Rate and Spectrum of the Endosymbiotic Bacterium Teredinibacter turnerae. Genome Biol Evol 2018; 10:723-730. [PMID: 29415256 PMCID: PMC5833318 DOI: 10.1093/gbe/evy027] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2018] [Indexed: 12/14/2022] Open
Abstract
Mutations contribute to genetic variation in all living systems. Thus, precise estimates of mutation rates and spectra across a diversity of organisms are required for a full comprehension of evolution. Here, a mutation-accumulation (MA) assay was carried out on the endosymbiotic bacterium Teredinibacter turnerae. After ∼3,025 generations, base-pair substitutions (BPSs) and insertion–deletion (indel) events were characterized by whole-genome sequencing analysis of 47 independent MA lines, yielding a BPS rate of 1.14 × 10−9 per site per generation and indel rate of 1.55 × 10−10 events per site per generation, which are among the highest within free-living and facultative intracellular bacteria. As in other endosymbionts, a significant bias of BPSs toward A/T and an excess of deletion mutations over insertion mutations are observed for these MA lines. However, even with a deletion bias, the genome remains relatively large (∼5.2 Mb) for an endosymbiotic bacterium. The estimate of the effective population size (Ne) in T. turnerae is quite high and comparable to free-living bacteria (∼4.5 × 107), suggesting that the heavy bottlenecking associated with many endosymbiotic relationships is not prevalent during the life of this endosymbiont. The efficiency of selection scales with increasing Ne and such strong selection may have been operating against the deletion bias, preventing genome erosion. The observed mutation rate in this endosymbiont is of the same order of magnitude of those with similar Ne, consistent with the idea that population size is a primary determinant of mutation-rate evolution within endosymbionts, and that not all endosymbionts have low Ne.
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Affiliation(s)
- Marcus V X Senra
- Departamento de Zoologia, Universidade Federal de Juiz de Fora, Brazil
| | - Way Sung
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte
| | - Matthew Ackerman
- Biodesign Center for Mechanisms of Evolution, Arizona State University
| | - Samuel F Miller
- Biodesign Center for Mechanisms of Evolution, Arizona State University
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University
| | - Carlos Augusto G Soares
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Brazil
- Corresponding author: E-mail:
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20
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Bennett GM, Mao M. Comparative genomics of a quadripartite symbiosis in a planthopper host reveals the origins and rearranged nutritional responsibilities of anciently diverged bacterial lineages. Environ Microbiol 2018; 20:4461-4472. [PMID: 30047196 DOI: 10.1111/1462-2920.14367] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 06/15/2018] [Accepted: 07/23/2018] [Indexed: 11/28/2022]
Abstract
Insects in the Auchenorrhyncha (Hemiptera: Suborder) established nutritional symbioses with bacteria approximately 300 million years ago (MYA). The suborder split early during its diversification (~ 250 MYA) into the Fulgoroidea (planthoppers) and Cicadomorpha (leafhoppers and cicadas). The two lineages share some symbionts, including Sulcia and possibly a Betaproteobacteria that collaboratively provide their hosts with 10 essential amino acids (EAA). Some hosts harbour three bacteria, as is common among planthoppers. However, genomic studies are currently restricted to the dual-bacterial symbioses found in Cicadomorpha, leaving the origins and functions of these more complex symbioses unclear. To address these questions, we sequenced the genomes and performed phylogenomic analyses of 'Candidatus Sulcia muelleri' (Bacteroidetes), 'Ca. Vidania fulgoroideae' (Betaproteobacteria) and 'Ca. Purcelliella pentastirinorum' (Gammaproteobacteria) from a planthopper (Cixiidae: Oliarus). In contrast to the Cicadomorpha, nutritional synthesis responsibilities are rearranged between the cixiid symbionts. Although Sulcia has a highly conserved genome across the Auchenorrhyncha, in the cixiids it is greatly reduced and provides only three EAAs. Vidania contributes the remaining seven EAAs. Phylogenomic results suggest that it represents an ancient symbiont lineage paired with Sulcia throughout the Auchenorrhyncha. Finally, Purcelliella was recently acquired from plant-insect associated bacteria (Pantoea-Erwinia) to provide B vitamins and metabolic support to its degenerate partners.
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Affiliation(s)
- Gordon M Bennett
- Life and Environmental Sciences Unit, University of California, Merced, CA, 95343, USA.,Department of Plant and Environmental Protections Sciences, University of Hawaii at Mānoa, Honolulu, HI, 96822, USA
| | - Meng Mao
- Life and Environmental Sciences Unit, University of California, Merced, CA, 95343, USA.,Department of Plant and Environmental Protections Sciences, University of Hawaii at Mānoa, Honolulu, HI, 96822, USA
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21
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Zhang HH, Zhou QZ, Wang PL, Xiong XM, Luchetti A, Raoult D, Levasseur A, Santini S, Abergel C, Legendre M, Drezen JM, Béliveau C, Cusson M, Jiang SH, Bao HO, Sun C, Bureau TE, Cheng PF, Han MJ, Zhang Z, Zhang XG, Dai FY. Unexpected invasion of miniature inverted-repeat transposable elements in viral genomes. Mob DNA 2018; 9:19. [PMID: 29946369 PMCID: PMC6004678 DOI: 10.1186/s13100-018-0125-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 06/12/2018] [Indexed: 12/31/2022] Open
Abstract
Background Transposable elements (TEs) are common and often present with high copy numbers in cellular genomes. Unlike in cellular organisms, TEs were previously thought to be either rare or absent in viruses. Almost all reported TEs display only one or two copies per viral genome. In addition, the discovery of pandoraviruses with genomes up to 2.5-Mb emphasizes the need for biologists to rethink the fundamental nature of the relationship between viruses and cellular life. Results Herein, we performed the first comprehensive analysis of miniature inverted-repeat transposable elements (MITEs) in the 5170 viral genomes for which sequences are currently available. Four hundred and fifty one copies of ten miniature inverted-repeat transposable elements (MITEs) were found and each MITE had reached relatively large copy numbers (some up to 90) in viruses. Eight MITEs belonging to two DNA superfamilies (hobo/Activator/Tam3 and Chapaev-Mirage-CACTA) were for the first time identified in viruses, further expanding the organismal range of these two superfamilies. TEs may play important roles in shaping the evolution of pandoravirus genomes, which were here found to be very rich in MITEs. We also show that putative autonomous partners of seven MITEs are present in the genomes of viral hosts, suggesting that viruses may borrow the transpositional machinery of their cellular hosts' autonomous elements to spread MITEs and colonize their own genomes. The presence of seven similar MITEs in viral hosts, suggesting horizontal transfers (HTs) as the major mechanism for MITEs propagation. Conclusions Our discovery highlights that TEs contribute to shape genome evolution of pandoraviruses. We concluded that as for cellular organisms, TEs are part of the pandoraviruses' diverse mobilome.
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Affiliation(s)
- Hua-Hao Zhang
- 1College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China.,2State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
| | - Qiu-Zhong Zhou
- 3School of Life Sciences, Chongqing University, Chongqing, 400044 China
| | - Ping-Lan Wang
- 1College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Xiao-Min Xiong
- 4Clinical Medical College, Jiujiang University, Jiujiang, China
| | - Andrea Luchetti
- 5Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| | - Didier Raoult
- 6Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Aix-Marseille University, UM63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, AP-HM, 19-21 Boulevard Jean Moulin, 13385 Marseille, France
| | - Anthony Levasseur
- 6Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Aix-Marseille University, UM63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, AP-HM, 19-21 Boulevard Jean Moulin, 13385 Marseille, France
| | - Sebastien Santini
- Aix-Marseille University, Centre National de la Recherche Scientifique, Information Génomique and Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479), 13288 Marseille Cedex 9, France
| | - Chantal Abergel
- Aix-Marseille University, Centre National de la Recherche Scientifique, Information Génomique and Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479), 13288 Marseille Cedex 9, France
| | - Matthieu Legendre
- Aix-Marseille University, Centre National de la Recherche Scientifique, Information Génomique and Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479), 13288 Marseille Cedex 9, France
| | - Jean-Michel Drezen
- 8Institut de Recherche sur la Biologie de l'Insecte, CNRS UMR 7261, Université François-Rabelais de Tours, UFR Sciences et Techniques, 37200 Tours, France
| | - Catherine Béliveau
- 9Laurentian Forestry Centre, Canadian Forest Service, Natural Resources Canada, Quebec, Canada
| | - Michel Cusson
- 9Laurentian Forestry Centre, Canadian Forest Service, Natural Resources Canada, Quebec, Canada
| | - Shen-Hua Jiang
- 1College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Hai-Ou Bao
- 1College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Cheng Sun
- 10Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Thomas E Bureau
- 11Department of Biology, McGill University, Montréal, Quebec, Canada
| | - Peng-Fei Cheng
- 12Poyang Lake Eco-economy Research Center, Jiujiang University, Jiujiang, China
| | - Min-Jin Han
- 2State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
| | - Ze Zhang
- 3School of Life Sciences, Chongqing University, Chongqing, 400044 China
| | - Xiao-Gu Zhang
- 1College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Fang-Yin Dai
- 2State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
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22
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Gil R, Vargas-Chavez C, López-Madrigal S, Santos-García D, Latorre A, Moya A. Tremblaya phenacola PPER: an evolutionary beta-gammaproteobacterium collage. THE ISME JOURNAL 2018; 12:124-135. [PMID: 28914880 PMCID: PMC5739004 DOI: 10.1038/ismej.2017.144] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 05/31/2017] [Accepted: 07/28/2017] [Indexed: 02/07/2023]
Abstract
Many insects rely on bacterial endosymbionts to obtain nutrients that are scarce in their highly specialized diets. The most surprising example corresponds to the endosymbiotic system found in mealybugs from subfamily Pseudococcinae in which two bacteria, the betaproteobacterium 'Candidatus Tremblaya princeps' and a gammaproteobacterium, maintain a nested endosymbiotic consortium. In the sister subfamily Phenacoccinae, however, a single beta-endosymbiont, 'Candidatus Tremblaya phenacola', has been described. In a previous study, we detected a trpB gene of gammaproteobacterial origin in 'Ca. Tremblaya phenacola' from two Phenacoccus species, apparently indicating an unusual case of horizontal gene transfer (HGT) in a bacterial endosymbiont. What we found by sequencing the genome of 'Ca. Tremblaya phenacola' PPER, single endosymbiont of Phenacoccus peruvianus, goes beyond a HGT phenomenon. It rather represents a genome fusion between a beta and a gammaproteobacterium, followed by massive rearrangements and loss of redundant genes, leading to an unprecedented evolutionary collage. Mediated by the presence of several repeated sequences, there are many possible genome arrangements, and different subgenomic sequences might coexist within the same population.
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Affiliation(s)
- Rosario Gil
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, Valencia, Spain
- Evolutionary Systems Biology of Symbionts Research Program, Institute for Integrative Systems Biology, Universitat de València/CSIC, Paterna (Valencia), Spain
- Institute for Integrative Systems Biology, Universitat de València/CSIC, C/Catedrático José Beltrán 2, 46980 Paterna (Valencia), Spain. E-mail:
| | - Carlos Vargas-Chavez
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, Valencia, Spain
- Evolutionary Systems Biology of Symbionts Research Program, Institute for Integrative Systems Biology, Universitat de València/CSIC, Paterna (Valencia), Spain
| | - Sergio López-Madrigal
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, Valencia, Spain
| | - Diego Santos-García
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, Valencia, Spain
| | - Amparo Latorre
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, Valencia, Spain
- Evolutionary Systems Biology of Symbionts Research Program, Institute for Integrative Systems Biology, Universitat de València/CSIC, Paterna (Valencia), Spain
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana, Valencia, Spain
| | - Andrés Moya
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, Valencia, Spain
- Evolutionary Systems Biology of Symbionts Research Program, Institute for Integrative Systems Biology, Universitat de València/CSIC, Paterna (Valencia), Spain
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana, Valencia, Spain
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23
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Lazcano A, Peretó J. On the origin of mitosing cells: A historical appraisal of Lynn Margulis endosymbiotic theory. J Theor Biol 2017; 434:80-87. [DOI: 10.1016/j.jtbi.2017.06.036] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 06/25/2017] [Accepted: 06/27/2017] [Indexed: 01/17/2023]
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24
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López-Madrigal S, Gil R. Et tu, Brute? Not Even Intracellular Mutualistic Symbionts Escape Horizontal Gene Transfer. Genes (Basel) 2017; 8:genes8100247. [PMID: 28961177 PMCID: PMC5664097 DOI: 10.3390/genes8100247] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 09/14/2017] [Accepted: 09/22/2017] [Indexed: 01/21/2023] Open
Abstract
Many insect species maintain mutualistic relationships with endosymbiotic bacteria. In contrast to their free-living relatives, horizontal gene transfer (HGT) has traditionally been considered rare in long-term endosymbionts. Nevertheless, meta-omics exploration of certain symbiotic models has unveiled an increasing number of bacteria-bacteria and bacteria-host genetic transfers. The abundance and function of transferred loci suggest that HGT might play a major role in the evolution of the corresponding consortia, enhancing their adaptive value or buffering detrimental effects derived from the reductive evolution of endosymbionts’ genomes. Here, we comprehensively review the HGT cases recorded to date in insect-bacteria mutualistic consortia, and discuss their impact on the evolutionary success of these associations.
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Affiliation(s)
- Sergio López-Madrigal
- Biologie Fonctionnelle Insectes et Interactions, UMR203 BF2I, INRA, INSA-Lyon, Université de Lyon, 69100 Villeurbanne, France.
| | - Rosario Gil
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València/CSIC, 46980 Paterna (València), Spain.
- Departament de Genètica, Universitat de València, Dr. Moliner, 50, 46100 Burjassot (València), Spain.
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25
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Vera-Ponce de León A, Ormeño-Orrillo E, Ramírez-Puebla ST, Rosenblueth M, Degli Esposti M, Martínez-Romero J, Martínez-Romero E. Candidatus Dactylopiibacterium carminicum, a Nitrogen-Fixing Symbiont of Dactylopius Cochineal Insects (Hemiptera: Coccoidea: Dactylopiidae). Genome Biol Evol 2017; 9:2237-2250. [PMID: 30605507 PMCID: PMC5604089 DOI: 10.1093/gbe/evx156] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2017] [Indexed: 12/18/2022] Open
Abstract
The domesticated carmine cochineal Dactylopius coccus (scale insect) has commercial value and has been used for more than 500 years for natural red pigment production. Besides the domesticated cochineal, other wild Dactylopius species such as Dactylopius opuntiae are found in the Americas, all feeding on nutrient poor sap from native cacti. To compensate nutritional deficiencies, many insects harbor symbiotic bacteria which provide essential amino acids or vitamins to their hosts. Here, we characterized a symbiont from the carmine cochineal insects, Candidatus Dactylopiibacterium carminicum (betaproteobacterium, Rhodocyclaceae family) and found it in D. coccus and in D. opuntiae ovaries by fluorescent in situ hybridization, suggesting maternal inheritance. Bacterial genomes recovered from metagenomic data derived from whole insects or tissues both from D. coccus and from D. opuntiae were around 3.6 Mb in size. Phylogenomics showed that dactylopiibacteria constituted a closely related clade neighbor to nitrogen fixing bacteria from soil or from various plants including rice and other grass endophytes. Metabolic capabilities were inferred from genomic analyses, showing a complete operon for nitrogen fixation, biosynthesis of amino acids and vitamins and putative traits of anaerobic or microoxic metabolism as well as genes for plant interaction. Dactylopiibacterium nif gene expression and acetylene reduction activity detecting nitrogen fixation were evidenced in D. coccus hemolymph and ovaries, in congruence with the endosymbiont fluorescent in situ hybridization location. Dactylopiibacterium symbionts may compensate for the nitrogen deficiency in the cochineal diet. In addition, this symbiont may provide essential amino acids, recycle uric acid, and increase the cochineal life span.
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Affiliation(s)
- Arturo Vera-Ponce de León
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad
Nacional Autónoma de México, Cuernavaca, Mexico
| | - Ernesto Ormeño-Orrillo
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad
Nacional Autónoma de México, Cuernavaca, Mexico
- Laboratorio de Ecología Microbiana y Biotecnología, Departamento de
Biología, Facultad de Ciencias, Universidad Nacional Agraria La Molina, Lima, Peru
| | - Shamayim T Ramírez-Puebla
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad
Nacional Autónoma de México, Cuernavaca, Mexico
| | - Mónica Rosenblueth
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad
Nacional Autónoma de México, Cuernavaca, Mexico
| | - Mauro Degli Esposti
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad
Nacional Autónoma de México, Cuernavaca, Mexico
| | - Julio Martínez-Romero
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad
Nacional Autónoma de México, Cuernavaca, Mexico
| | - Esperanza Martínez-Romero
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad
Nacional Autónoma de México, Cuernavaca, Mexico
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26
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Nasir A, Kim KM, Caetano-Anollés G. Phylogenetic Tracings of Proteome Size Support the Gradual Accretion of Protein Structural Domains and the Early Origin of Viruses from Primordial Cells. Front Microbiol 2017; 8:1178. [PMID: 28690608 PMCID: PMC5481351 DOI: 10.3389/fmicb.2017.01178] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 06/09/2017] [Indexed: 01/05/2023] Open
Abstract
Untangling the origin and evolution of viruses remains a challenging proposition. We recently studied the global distribution of protein domain structures in thousands of completely sequenced viral and cellular proteomes with comparative genomics, phylogenomics, and multidimensional scaling methods. A tree of life describing the evolution of proteomes revealed viruses emerging from the base of the tree as a fourth supergroup of life. A tree of domains indicated an early origin of modern viral lineages from ancient cells that co-existed with the cellular ancestors. However, it was recently argued that the rooting of our trees and the basal placement of viruses was artifactually induced by small genome (proteome) size. Here we show that these claims arise from misunderstanding and misinterpretations of cladistic methodology. Trees are reconstructed unrooted, and thus, their topologies cannot be distorted a posteriori by the rooting methodology. Tracing proteome size in trees and multidimensional views of evolutionary relationships as well as tests of leaf stability and exclusion/inclusion of taxa demonstrated that the smallest proteomes were neither attracted toward the root nor caused any topological distortions of the trees. Simulations confirmed that taxa clustering patterns were independent of proteome size and were determined by the presence of known evolutionary relatives in data matrices, highlighting the need for broader taxon sampling in phylogeny reconstruction. Instead, phylogenetic tracings of proteome size revealed a slowdown in innovation of the structural domain vocabulary and four regimes of allometric scaling that reflected a Heaps law. These regimes explained increasing economies of scale in the evolutionary growth and accretion of kernel proteome repertoires of viruses and cellular organisms that resemble growth of human languages with limited vocabulary sizes. Results reconcile dynamic and static views of domain frequency distributions that are consistent with the axiom of spatiotemporal continuity that is tenet of evolutionary thinking.
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Affiliation(s)
- Arshan Nasir
- Department of Biosciences, COMSATS Institute of Information TechnologyIslamabad, Pakistan
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-ChampaignUrbana, IL, United States
| | - Kyung Mo Kim
- Division of Polar Life Sciences, Korea Polar Research InstituteIncheon, South Korea
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-ChampaignUrbana, IL, United States
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27
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Salvioli di Fossalunga A, Lipuma J, Venice F, Dupont L, Bonfante P. The endobacterium of an arbuscular mycorrhizal fungus modulates the expression of its toxin-antitoxin systems during the life cycle of its host. ISME JOURNAL 2017; 11:2394-2398. [PMID: 28548657 DOI: 10.1038/ismej.2017.84] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 04/11/2017] [Accepted: 04/19/2017] [Indexed: 02/06/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) are widespread root symbionts that perform important ecological services, such as improving plant nutrient and water acquisition. Some AMF from the Gigasporaceae family host a population of endobacteria, Candidatus Glomeribacter gigasporarum (Cagg). The analysis of the Cagg genome identified six putative toxin-antitoxin modules (TAs), consisting of pairs of stable toxins and unstable antitoxins that affect diverse physiological functions. Sequence analysis suggested that these TA modules were acquired by horizontal transfer. Gene expression patterns of two TAs (yoeB/yefM and chpB/chpS) changed during the fungal life cycle, with the expression during the pre-symbiotic phase higher than during the symbiosis with the plant host. The heterologous expression in Escherichia coli demonstrated the functionality only for the YoeB-YefM pair. On the basis of these observations, we speculate that TA modules might help Cagg adapt to its intracellular habitat, coordinating its proliferation with the physiological state of the AMF host.
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Affiliation(s)
| | - Justine Lipuma
- Institut Sophia Agrobiotech (ISA), INRA UMR 1355, CNRS UMR 7254, Université de Nice Sophia Antipolis, Sophia Antipolis, France
| | - Francesco Venice
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | - Laurence Dupont
- Institut Sophia Agrobiotech (ISA), INRA UMR 1355, CNRS UMR 7254, Université de Nice Sophia Antipolis, Sophia Antipolis, France
| | - Paola Bonfante
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
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28
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Silveira CB, Gregoracci GB, Coutinho FH, Silva GGZ, Haggerty JM, de Oliveira LS, Cabral AS, Rezende CE, Thompson CC, Francini-Filho RB, Edwards RA, Dinsdale EA, Thompson FL. Bacterial Community Associated with the Reef Coral Mussismilia braziliensis's Momentum Boundary Layer over a Diel Cycle. Front Microbiol 2017; 8:784. [PMID: 28588555 PMCID: PMC5438984 DOI: 10.3389/fmicb.2017.00784] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 04/18/2017] [Indexed: 11/13/2022] Open
Abstract
Corals display circadian physiological cycles, changing from autotrophy during the day to heterotrophy during the night. Such physiological transition offers distinct environments to the microbial community associated with corals: an oxygen-rich environment during daylight hours and an oxygen-depleted environment during the night. Most studies of coral reef microbes have been performed on samples taken during the day, representing a bias in the understanding of the composition and function of these communities. We hypothesized that coral circadian physiology alters the composition and function of microbial communities in reef boundary layers. Here, we analyzed microbial communities associated with the momentum boundary layer (MBL) of the Brazilian endemic reef coral Mussismilia braziliensis during a diurnal cycle, and compared them to the water column. We determined microbial abundance and nutrient concentration in samples taken within a few centimeters of the coral's surface every 6 h for 48 h, and sequenced microbial metagenomes from a subset of the samples. We found that dominant taxa and functions in the coral MBL community were stable over the time scale of our sampling, with no significant shifts between night and day samples. Interestingly, the two water column metagenomes sampled 1 m above the corals were also very similar to the MBL metagenomes. When all samples were analyzed together, nutrient concentration significantly explained 40% of the taxonomic dissimilarity among dominant genera in the community. Functional profiles were highly homogenous and not significantly predicted by any environmental variables measured. Our data indicated that water flow may overrule the effects of coral physiology in the MBL bacterial community, at the scale of centimeters, and suggested that sampling resolution at the scale of millimeters may be necessary to address diurnal variation in community composition.
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Affiliation(s)
- Cynthia B Silveira
- Instituto de Biologia, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil.,Department of Biology, San Diego State UniversitySan Diego, CA, USA
| | | | - Felipe H Coutinho
- Instituto de Biologia, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil.,Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical CentreNijmegen, Netherlands
| | - Genivaldo G Z Silva
- Department of Computational Science, San Diego State UniversitySan Diego, CA, USA
| | - John M Haggerty
- Department of Biology, San Diego State UniversitySan Diego, CA, USA
| | - Louisi S de Oliveira
- Instituto de Biologia, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil
| | - Anderson S Cabral
- Instituto de Biologia, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil
| | - Carlos E Rezende
- Laboratório de Ciências Ambientais, Universidade Estadual do Norte FluminenseCampos dos Goytacazes, Brazil
| | - Cristiane C Thompson
- Instituto de Biologia, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil
| | | | - Robert A Edwards
- Department of Computational Science, San Diego State UniversitySan Diego, CA, USA
| | - Elizabeth A Dinsdale
- Instituto de Biologia, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil
| | - Fabiano L Thompson
- Instituto de Biologia, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil.,Laboratório de Sistemas Avançados de Gestão da Produção, COPPE, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil
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29
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Speijer D. Alternating terminal electron-acceptors at the basis of symbiogenesis: How oxygen ignited eukaryotic evolution. Bioessays 2017; 39. [DOI: 10.1002/bies.201600174] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Dave Speijer
- Department of Medical Biochemistry; Academic Medical Centre (AMC); University of Amsterdam; Amsterdam The Netherlands
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30
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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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31
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Claverie JM, Abergel C. Giant viruses: The difficult breaking of multiple epistemological barriers. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2016; 59:89-99. [PMID: 26972873 DOI: 10.1016/j.shpsc.2016.02.015] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 02/27/2016] [Indexed: 06/05/2023]
Abstract
The discovery of the first "giant virus", Mimivirus, in 2003 could solely have been that of an exceptional freak, a blind alley of evolution as occasionally encountered in biology, albeit without conceptual significance. On the contrary, once broken this epistemological barrier, additional unrelated families of giant viruses such as the Pandoraviruses, the Pithoviruses and most recently Mollivirus, were quickly unraveled, suggesting that an entire chapter of microbiology had been ignored since Pasteur and Ivanovski. In this article, we examine to what extent the giant viruses challenge previous definitions of viruses, the diversity of forms they could take, and how they might have evolved from extinct ancestral cellular lineages. Inspired by the epistemology of Gaston Bachelard, we will also suggest the reasons for which giant viruses laid hidden in plain sight for more than a century. Finally, we propose a new definition for "viruses" that paradoxically emphasize the fact that they do not encode a single universally shared macromolecule or biochemical function.
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Affiliation(s)
- Jean-Michel Claverie
- Structural and Genomic Information Laboratory, UMR 7256 (IMM FR 3479) CNRS Aix-Marseille Université, Luminy Campus, Marseille, France; Assistance Publique des Hôpitaux de Marseille, La Timone, 13005, Marseille, France.
| | - Chantal Abergel
- Structural and Genomic Information Laboratory, UMR 7256 (IMM FR 3479) CNRS Aix-Marseille Université, Luminy Campus, Marseille, France
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32
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Parkinson JF, Gobin B, Hughes WOH. Heritability of symbiont density reveals distinct regulatory mechanisms in a tripartite symbiosis. Ecol Evol 2016; 6:2053-60. [PMID: 27099709 PMCID: PMC4831439 DOI: 10.1002/ece3.2005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 01/10/2016] [Accepted: 01/18/2016] [Indexed: 01/08/2023] Open
Abstract
Beneficial eukaryotic–bacterial partnerships are integral to animal and plant evolution. Understanding the density regulation mechanisms behind bacterial symbiosis is essential to elucidating the functional balance between hosts and symbionts. Citrus mealybugs, Planococcus citri (Risso), present an excellent model system for investigating the mechanisms of symbiont density regulation. They contain two obligate nutritional symbionts, Moranella endobia, which resides inside Tremblaya princeps, which has been maternally transmitted for 100–200 million years. We investigate whether host genotype may influence symbiont density by crossing mealybugs from two inbred laboratory‐reared populations that differ substantially in their symbiont density to create hybrids. The density of the M. endobia symbiont in the hybrid hosts matched that of the maternal parent population, in keeping with density being determined either by the symbiont or the maternal genotype. However, the density of the T. princeps symbiont was influenced by the paternal host genotype. The greater dependency of T. princeps on its host may be due to its highly reduced genome. The decoupling of T. princeps and M. endobia densities, in spite of their intimate association, suggests that distinct regulatory mechanisms can be at work in symbiotic partnerships, even when they are obligate and mutualistic.
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Affiliation(s)
| | - Bruno Gobin
- PCS-Ornamental Plant Research Schaessestraat 18 Destelbergen 9070 Belgium
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33
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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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34
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"Wigglesworthia morsitans" Folate (Vitamin B9) Biosynthesis Contributes to Tsetse Host Fitness. Appl Environ Microbiol 2015; 81:5375-86. [PMID: 26025907 DOI: 10.1128/aem.00553-15] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 05/26/2015] [Indexed: 01/31/2023] Open
Abstract
Closely related ancient endosymbionts may retain minor genomic distinctions through evolutionary time, yet the biological relevance of these small pockets of unique loci remains unknown. The tsetse fly (Diptera: Glossinidae), the sole vector of lethal African trypanosomes (Trypanosoma spp.), maintains an ancient and obligate mutualism with species belonging to the gammaproteobacterium Wigglesworthia. Extensive concordant evolution with associated Wigglesworthia species has occurred through tsetse species radiation. Accordingly, the retention of unique symbiont loci between Wigglesworthia genomes may prove instrumental toward host species-specific biological traits. Genome distinctions between "Wigglesworthia morsitans" (harbored within Glossina morsitans bacteriomes) and the basal species Wigglesworthia glossinidia (harbored within Glossina brevipalpis bacteriomes) include the retention of chorismate and downstream folate (vitamin B9) biosynthesis capabilities, contributing to distinct symbiont metabolomes. Here, we demonstrate that these W. morsitans pathways remain functionally intact, with folate likely being systemically disseminated through a synchronously expressed tsetse folate transporter within bacteriomes. The folate produced by W. morsitans is demonstrated to be pivotal for G. morsitans sexual maturation and reproduction. Modest differences between ancient symbiont genomes may still play key roles in the evolution of their host species, particularly if loci are involved in shaping host physiology and ecology. Enhanced knowledge of the Wigglesworthia-tsetse mutualism may also provide novel and specific avenues for vector control.
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35
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Abstract
The concept of the minimal cell has fascinated scientists for a long time, from both fundamental and applied points of view. This broad concept encompasses extreme reductions of genomes, the last universal common ancestor (LUCA), the creation of semiartificial cells, and the design of protocells and chassis cells. Here we review these different areas of research and identify common and complementary aspects of each one. We focus on systems biology, a discipline that is greatly facilitating the classical top-down and bottom-up approaches toward minimal cells. In addition, we also review the so-called middle-out approach and its contributions to the field with mathematical and computational models. Owing to the advances in genomics technologies, much of the work in this area has been centered on minimal genomes, or rather minimal gene sets, required to sustain life. Nevertheless, a fundamental expansion has been taking place in the last few years wherein the minimal gene set is viewed as a backbone of a more complex system. Complementing genomics, progress is being made in understanding the system-wide properties at the levels of the transcriptome, proteome, and metabolome. Network modeling approaches are enabling the integration of these different omics data sets toward an understanding of the complex molecular pathways connecting genotype to phenotype. We review key concepts central to the mapping and modeling of this complexity, which is at the heart of research on minimal cells. Finally, we discuss the distinction between minimizing the number of cellular components and minimizing cellular complexity, toward an improved understanding and utilization of minimal and simpler cells.
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36
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Rollat-Farnier PA, Santos-Garcia D, Rao Q, Sagot MF, Silva FJ, Henri H, Zchori-Fein E, Latorre A, Moya A, Barbe V, Liu SS, Wang XW, Vavre F, Mouton L. Two host clades, two bacterial arsenals: evolution through gene losses in facultative endosymbionts. Genome Biol Evol 2015; 7:839-55. [PMID: 25714744 PMCID: PMC5322557 DOI: 10.1093/gbe/evv030] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [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
Bacterial endosymbiosis is an important evolutionary process in insects, which can harbor both obligate and facultative symbionts. The evolution of these symbionts is driven by evolutionary convergence, and they exhibit among the tiniest genomes in prokaryotes. The large host spectrum of facultative symbionts and the high diversity of strategies they use to infect new hosts probably impact the evolution of their genome and explain why they undergo less severe genomic erosion than obligate symbionts. Candidatus Hamiltonella defensa is suitable for the investigation of the genomic evolution of facultative symbionts because the bacteria are engaged in specific relationships in two clades of insects. In aphids, H. defensa is found in several species with an intermediate prevalence and confers protection against parasitoids. In whiteflies, H. defensa is almost fixed in some species of Bemisia tabaci, which suggests an important role of and a transition toward obligate symbiosis. In this study, comparisons of the genome of H. defensa present in two B. tabaci species (Middle East Asia Minor 1 and Mediterranean) and in the aphid Acyrthosiphon pisum revealed that they belong to two distinct clades and underwent specific gene losses. In aphids, it contains highly virulent factors that could allow protection and horizontal transfers. In whiteflies, the genome lost these factors and seems to have a limited ability to acquire genes. However it contains genes that could be involved in the production of essential nutrients, which is consistent with a primordial role for this symbiont. In conclusion, although both lineages of H. defensa have mutualistic interactions with their hosts, their genomes follow distinct evolutionary trajectories that reflect their phenotype and could have important consequences on their evolvability.
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Affiliation(s)
- Pierre-Antoine Rollat-Farnier
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université de Lyon, Université Lyon1, Villeurbanne, France BAMBOO Research Team, INRIA Grenoble, Rhône-Alpes, France
| | - Diego Santos-Garcia
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain
| | - Qiong Rao
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China School of Agriculture and Food Science, Zhejiang Agriculture and Forestry University, Lin'an, Hangzhou, China
| | - Marie-France Sagot
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université de Lyon, Université Lyon1, Villeurbanne, France BAMBOO Research Team, INRIA Grenoble, Rhône-Alpes, France
| | - Francisco J Silva
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública) y el Instituto Cavanilles de Biodiversitad y Biología Evolutiva (Universitat de València), Valencia, Spain
| | - Hélène Henri
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université de Lyon, Université Lyon1, Villeurbanne, France
| | - Einat Zchori-Fein
- Department of Entomology, NeweYa'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Amparo Latorre
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública) y el Instituto Cavanilles de Biodiversitad y Biología Evolutiva (Universitat de València), Valencia, Spain
| | - Andrés Moya
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública) y el Instituto Cavanilles de Biodiversitad y Biología Evolutiva (Universitat de València), Valencia, Spain
| | - Valérie Barbe
- CEA/DSV/IG/Genoscope, 2 rue Gaston Cremieux, Evry, France
| | - Shu-Sheng Liu
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Xiao-Wei Wang
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Fabrice Vavre
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université de Lyon, Université Lyon1, Villeurbanne, France BAMBOO Research Team, INRIA Grenoble, Rhône-Alpes, France
| | - Laurence Mouton
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université de Lyon, Université Lyon1, Villeurbanne, France
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Ma W, Feng Y. Protocells: at the interface of life and non-life. Life (Basel) 2015; 5:447-58. [PMID: 25809963 PMCID: PMC4390862 DOI: 10.3390/life5010447] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Accepted: 02/02/2015] [Indexed: 02/07/2023] Open
Abstract
The cellular form, manifesting as a membrane-bounded system (comprising various functional molecules), is essential to life. The ultimate reason for this is that, typically, one functional molecule can only adopt one “correct” structure to perform one special function (e.g., an enzyme), and thus molecular cooperation is inevitable. While this is particularly true for advanced life with complex functions, it should have already been true for life at its outset with only limited functions, which entailed some sort of primitive cellular form—“protocells”. At the very beginning, the protocells may have even been unable to intervene in the growth of their own membrane, which can be called “pseudo-protocells”. Then, the ability to synthesize membrane components (amphiphiles) may have emerged under selective pressure, leading to “true-protocells”. The emergence of a “chromosome” (with genes linked together)—thus avoiding “gene-loss” during the protocell division, was another key event in the evolution of protocells. Such “unitary-protocells”, containing a central genetic molecule, may have appeared as a milestone—in principle, since then life could evolve endlessly, “gaining” more and more functions by introducing new genes. To synthesize in laboratory these different types of protocells, which stand at the interface between life and non-life, would greatly enhance our understanding on the essence of life.
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Affiliation(s)
- Wentao Ma
- College of Life Sciences, Wuhan University, Wuhan 430072, China.
| | - Yu Feng
- College of Life Sciences, Wuhan University, Wuhan 430072, China.
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López-Madrigal S, Latorre A, Moya A, Gil R. The link between independent acquisition of intracellular gamma-endosymbionts and concerted evolution in Tremblaya princeps. Front Microbiol 2015; 6:642. [PMID: 26161080 PMCID: PMC4479817 DOI: 10.3389/fmicb.2015.00642] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 06/12/2015] [Indexed: 02/05/2023] Open
Abstract
Many insect species establish mutualistic symbiosis with intracellular bacteria that complement their unbalanced diets. The betaproteobacterium "Candidatus Tremblaya" maintains an ancient symbiosis with mealybugs (Hemiptera: Pseudococcidae), which are classified in subfamilies Phenacoccinae and Pseudococcinae. Most Phenacoccinae mealybugs have "Candidatus Tremblaya phenacola" as their unique endosymbiont, while most Pseudococcinae mealybugs show a nested symbiosis (a bacterial symbiont placed inside another one) where every "Candidatus Tremblaya princeps" cell harbors several cells of a gammaproteobacterium. Genomic characterization of the endosymbiotic consortium from Planococcus citri, composed by "Ca. Tremblaya princeps" and "Candidatus Moranella endobia," unveiled several atypical features of the former's genome, including the concerted evolution of paralogous loci. Its comparison with the genome of "Ca. Tremblaya phenacola" PAVE, single endosymbiont of Phenacoccus avenae, suggests that the atypical reductive evolution of "Ca. Tremblaya princeps" could be linked to the acquisition of "Ca. Moranella endobia," which possess an almost complete set of genes encoding proteins involved in homologous recombination. In order to test this hypothesis, we performed comparative genomics between "Ca. Tremblaya phenacola" and "Ca. Tremblaya princeps" and searched for the co-occurrence of concerted evolution and homologous recombination genes in endosymbiotic consortia from four unexplored mealybug species, Dysmicoccus boninsis, Planococcus ficus, Pseudococcus longispinus, and Pseudococcus viburni. Our results support a link between concerted evolution and nested endosymbiosis.
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Affiliation(s)
- Sergio López-Madrigal
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de ValènciaValència, Spain
| | - Amparo Latorre
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de ValènciaValència, Spain
- Área de Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO) – Salud PúblicaValència, Spain
| | - Andrés Moya
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de ValènciaValència, Spain
- Área de Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO) – Salud PúblicaValència, Spain
| | - Rosario Gil
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de ValènciaValència, Spain
- *Correspondence: Rosario Gil, Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, C/Catedrático José Beltrán 2, 46980 Paterna, Valencia, Spain
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Abstract
Pulsed field gel electrophoresis (PFGE) is a quick and reliable procedure to resolve DNA molecules larger than 30 kb by applying an electric field that periodically changes direction. This technique can be used to estimate genome size of a microorganism, to reveal if a genome is circular or linear, to indicate the presence of megaplasmids, and to show if a strain contains only one or more chromosomes.
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Affiliation(s)
- Rosa Alduina
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Via delle Scienze, Ed. 16, Palermo, 90128, Italy,
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Abstract
UNLABELLED Obligate symbioses with bacteria allow insects to feed on otherwise unsuitable diets. Some symbionts have extremely reduced genomes and have lost many genes considered to be essential in other bacteria. To understand how symbiont genome degeneration proceeds, we compared the genomes of symbionts in two leafhopper species, Homalodisca vitripennis (glassy-winged sharpshooter [GWSS]) and Graphocephala atropunctata (blue-green sharpshooter [BGSS]) (Hemiptera: Cicadellidae). Each host species is associated with the anciently acquired "Candidatus Sulcia muelleri" (Bacteroidetes) and the more recently acquired "Candidatus Baumannia cicadellinicola" (Gammaproteobacteria). BGSS "Ca. Baumannia" retains 89 genes that are absent from GWSS "Ca. Baumannia"; these underlie central cellular functions, including cell envelope biogenesis, cellular replication, and stress response. In contrast, "Ca. Sulcia" strains differ by only a few genes. Although GWSS "Ca. Baumannia" cells are spherical or pleomorphic (a convergent trait of obligate symbionts), electron microscopy reveals that BGSS "Ca. Baumannia" maintains a rod shape, possibly due to its retention of genes involved in cell envelope biogenesis and integrity. Phylogenomic results suggest that "Ca. Baumannia" is derived from the clade consisting of Sodalis and relatives, a group that has evolved symbiotic associations with numerous insect hosts. Finally, the rates of synonymous and nonsynonymous substitutions are higher in "Ca. Baumannia" than in "Ca. Sulcia," which may be due to a lower mutation rate in the latter. Taken together, our results suggest that the two "Ca. Baumannia" genomes represent different stages of genome reduction in which many essential functions are being lost and likely compensated by hosts. "Ca. Sulcia" exhibits much greater genome stability and slower sequence evolution, although the mechanisms underlying these differences are poorly understood. IMPORTANCE In obligate animal-bacterial symbioses, bacteria experience extreme patterns of genome evolution, including massive gene loss and rapid evolution. However, little is known about this process, particularly in systems with complementary bacterial partners. To understand whether genome evolution impacts symbiont types equally and whether lineages follow the same evolutionary path, we sequenced the genomes of two coresident symbiotic bacteria from a plant sap-feeding insect and compared them to the symbionts from a related host species. We found that the older symbiont has a highly reduced genome with low rates of mutation and gene loss. In contrast, the younger symbiont has a larger genome that exhibits higher mutation rates and varies dramatically in the retention of genes related to cell wall biogenesis, cellular replication, and stress response. We conclude that while symbiotic bacteria evolve toward tiny genomes, this process is shaped by different selection intensities that may reflect the different ages and metabolic roles of symbiont types.
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Reyes-Prieto M, Latorre A, Moya A. Scanty microbes, the 'symbionelle' concept. Environ Microbiol 2014; 16:335-8. [PMID: 23968559 DOI: 10.1111/1462-2920.12220] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 07/11/2013] [Accepted: 07/18/2013] [Indexed: 02/05/2023]
Affiliation(s)
- Mariana Reyes-Prieto
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Calle Catedrático Agustín Escardino 9, 46980, Paterna, València, Spain
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López-Madrigal S, Beltrà A, Resurrección S, Soto A, Latorre A, Moya A, Gil R. Molecular evidence for ongoing complementarity and horizontal gene transfer in endosymbiotic systems of mealybugs. Front Microbiol 2014; 5:449. [PMID: 25206351 PMCID: PMC4144094 DOI: 10.3389/fmicb.2014.00449] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 08/06/2014] [Indexed: 02/05/2023] Open
Abstract
Intracellular bacterial supply of essential amino acids is common among sap-feeding insects, thus complementing the scarcity of nitrogenous compounds in plant phloem. This is also the role of the two mealybug endosymbiotic systems whose genomes have been sequenced. In the nested endosymbiotic system from Planococcus citri (Pseudococcinae), "Candidatus Tremblaya princeps" and "Candidatus Moranella endobia" cooperate to synthesize essential amino acids, while in Phenacoccus avenae (Phenacoccinae) this function is performed by its single endosymbiont "Candidatus Tremblaya phenacola." However, little is known regarding the evolution of essential amino acid supplementation strategies in other mealybug systems. To address this knowledge gap, we screened for the presence of six selected loci involved in essential amino acid biosynthesis in five additional mealybug species. We found evidence of ongoing complementarity among endosymbionts from insects of subfamily Pseudococcinae, as well as horizontal gene transfer affecting endosymbionts from insects of family Phenacoccinae, providing a more comprehensive picture of the evolutionary history of these endosymbiotic systems. Additionally, we report two diagnostic motifs to help identify invasive mealybug species.
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Affiliation(s)
- Sergio López-Madrigal
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de ValenciaValencia, Spain
| | - Aleixandre Beltrà
- Instituto Agroforestal Mediterráneo, Universitat Politecnica de ValenciaValencia, Spain
| | - Serena Resurrección
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de ValenciaValencia, Spain
| | - Antonia Soto
- Instituto Agroforestal Mediterráneo, Universitat Politecnica de ValenciaValencia, Spain
| | - Amparo Latorre
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de ValenciaValencia, Spain
- Área de Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO)–Salud PúblicaValencia, Spain
| | - Andrés Moya
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de ValenciaValencia, Spain
- Área de Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO)–Salud PúblicaValencia, Spain
| | - Rosario Gil
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de ValenciaValencia, Spain
- *Correspondence: Rosario Gil, Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, C/Catedrático José Beltrán 2, 46980 Valencia, Spain e-mail:
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Porcar M, Latorre A, Moya A. What Symbionts Teach us about Modularity. Front Bioeng Biotechnol 2013; 1:14. [PMID: 25023877 PMCID: PMC4090905 DOI: 10.3389/fbioe.2013.00014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 10/22/2013] [Indexed: 11/13/2022] Open
Abstract
The main goal of Synthetic Biology (SB) is to apply engineering principles to biotechnology in order to make life easier to engineer. These engineering principles include modularity: decoupling of complex systems into smaller, orthogonal sub-systems that can be used in a range of different applications. The successful use of modules in engineering is expected to be reproduced in synthetic biological systems. But the difficulties experienced up to date with SB approaches question the short-term feasibility of designing life. Considering the “engineerable” nature of life, here we discuss the existence of modularity in natural living systems, particularly in symbiotic interactions, and compare the behavior of such systems, with those of engineered modules. We conclude that not only is modularity present but it is also common among living structures, and that symbioses are a new example of module-like sub-systems having high similarity with modularly designed ones. However, we also detect and stress fundamental differences between man-made and biological modules. Both similarities and differences should be taken into account in order to adapt SB design to biological laws.
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Affiliation(s)
- Manuel Porcar
- Cavanilles Institute of Biodiversity and Evolutionary Biology, Universitat de València , València , Spain ; Fundació General de la Universitat de València , València , Spain
| | - Amparo Latorre
- Cavanilles Institute of Biodiversity and Evolutionary Biology, Universitat de València , València , Spain ; Unidad Mixta de Investigación en Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana - Salud Pública , València , Spain
| | - Andrés Moya
- Cavanilles Institute of Biodiversity and Evolutionary Biology, Universitat de València , València , Spain ; Unidad Mixta de Investigación en Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana - Salud Pública , València , Spain
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Alves JMP, Serrano MG, Maia da Silva F, Voegtly LJ, Matveyev AV, Teixeira MMG, Camargo EP, Buck GA. Genome evolution and phylogenomic analysis of Candidatus Kinetoplastibacterium, the betaproteobacterial endosymbionts of Strigomonas and Angomonas. Genome Biol Evol 2013; 5:338-50. [PMID: 23345457 PMCID: PMC3590767 DOI: 10.1093/gbe/evt012] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
It has been long known that insect-infecting trypanosomatid flagellates from the genera Angomonas and Strigomonas harbor bacterial endosymbionts (Candidatus Kinetoplastibacterium or TPE [trypanosomatid proteobacterial endosymbiont]) that supplement the host metabolism. Based on previous analyses of other bacterial endosymbiont genomes from other lineages, a stereotypical path of genome evolution in such bacteria over the duration of their association with the eukaryotic host has been characterized. In this work, we sequence and analyze the genomes of five TPEs, perform their metabolic reconstruction, do an extensive phylogenomic analyses with all available Betaproteobacteria, and compare the TPEs with their nearest betaproteobacterial relatives. We also identify a number of housekeeping and central metabolism genes that seem to have undergone positive selection. Our genome structure analyses show total synteny among the five TPEs despite millions of years of divergence, and that this lineage follows the common path of genome evolution observed in other endosymbionts of diverse ancestries. As previously suggested by cell biology and biochemistry experiments, Ca. Kinetoplastibacterium spp. preferentially maintain those genes necessary for the biosynthesis of compounds needed by their hosts. We have also shown that metabolic and informational genes related to the cooperation with the host are overrepresented amongst genes shown to be under positive selection. Finally, our phylogenomic analysis shows that, while being in the Alcaligenaceae family of Betaproteobacteria, the closest relatives of these endosymbionts are not in the genus Bordetella as previously reported, but more likely in the Taylorella genus.
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Affiliation(s)
- João M P Alves
- Department of Microbiology and Immunology and the Center for the Study of Biological Complexity, Virginia Commonwealth University, VA, USA.
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Husnik F, Nikoh N, Koga R, Ross L, Duncan RP, Fujie M, Tanaka M, Satoh N, Bachtrog D, Wilson ACC, von Dohlen CD, Fukatsu T, McCutcheon JP. Horizontal gene transfer from diverse bacteria to an insect genome enables a tripartite nested mealybug symbiosis. Cell 2013; 153:1567-78. [PMID: 23791183 DOI: 10.1016/j.cell.2013.05.040] [Citation(s) in RCA: 288] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 05/01/2013] [Accepted: 05/22/2013] [Indexed: 01/16/2023]
Abstract
The smallest reported bacterial genome belongs to Tremblaya princeps, a symbiont of Planococcus citri mealybugs (PCIT). Tremblaya PCIT not only has a 139 kb genome, but possesses its own bacterial endosymbiont, Moranella endobia. Genome and transcriptome sequencing, including genome sequencing from a Tremblaya lineage lacking intracellular bacteria, reveals that the extreme genomic degeneracy of Tremblaya PCIT likely resulted from acquiring Moranella as an endosymbiont. In addition, at least 22 expressed horizontally transferred genes from multiple diverse bacteria to the mealybug genome likely complement missing symbiont genes. However, none of these horizontally transferred genes are from Tremblaya, showing that genome reduction in this symbiont has not been enabled by gene transfer to the host nucleus. Our results thus indicate that the functioning of this three-way symbiosis is dependent on genes from at least six lineages of organisms and reveal a path to intimate endosymbiosis distinct from that followed by organelles.
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Affiliation(s)
- Filip Husnik
- Faculty of Science, University of South Bohemia and Institute of Parasitology, Biology Centre ASCR, České Budějovice 370 05, Czech Republic
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López-Madrigal S, Latorre A, Porcar M, Moya A, Gil R. Mealybugs nested endosymbiosis: going into the 'matryoshka' system in Planococcus citri in depth. BMC Microbiol 2013; 13:74. [PMID: 23548081 PMCID: PMC3620526 DOI: 10.1186/1471-2180-13-74] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 03/25/2013] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND In all branches of life there are plenty of symbiotic associations. Insects are particularly well suited to establishing intracellular symbiosis with bacteria, providing them with metabolic capabilities they lack. Essential primary endosymbionts can coexist with facultative secondary symbionts which can, eventually, establish metabolic complementation with the primary endosymbiont, becoming a co-primary. Usually, both endosymbionts maintain their cellular identity. An exception is the endosymbiosis found in mealybugs of the subfamily Pseudoccinae, such as Planococcus citri, with Moranella endobia located inside Tremblaya princeps. RESULTS We report the genome sequencing of M. endobia str. PCVAL and the comparative genomic analyses of the genomes of strains PCVAL and PCIT of both consortium partners. A comprehensive analysis of their functional capabilities and interactions reveals their functional coupling, with many cases of metabolic and informational complementation. Using comparative genomics, we confirm that both genomes have undergone a reductive evolution, although with some unusual genomic features as a consequence of coevolving in an exceptional compartmentalized organization. CONCLUSIONS M. endobia seems to be responsible for the biosynthesis of most cellular components and energy provision, and controls most informational processes for the consortium, while T. princeps appears to be a mere factory for amino acid synthesis, and translating proteins, using the precursors provided by M. endobia. In this scenario, we propose that both entities should be considered part of a composite organism whose compartmentalized scheme (somehow) resembles a eukaryotic cell.
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Affiliation(s)
- Sergio López-Madrigal
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Apartado Postal 22085, València, 46071, Spain
| | - Amparo Latorre
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Apartado Postal 22085, València, 46071, Spain
- Área de Genómica y Salud, Centro Superior de Investigación en Salud Pública (CSISP), Avenida de Cataluña 21, Valencia, 46020, Spain
| | - Manuel Porcar
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Apartado Postal 22085, València, 46071, Spain
- Fundació General de la Universitat de València, Apartado Postal 22085, València, 46071, Spain
| | - Andrés Moya
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Apartado Postal 22085, València, 46071, Spain
- Área de Genómica y Salud, Centro Superior de Investigación en Salud Pública (CSISP), Avenida de Cataluña 21, Valencia, 46020, Spain
| | - Rosario Gil
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Apartado Postal 22085, València, 46071, Spain
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Login FH, Heddi A. Insect immune system maintains long-term resident bacteria through a local response. JOURNAL OF INSECT PHYSIOLOGY 2013; 59:232-239. [PMID: 22771302 DOI: 10.1016/j.jinsphys.2012.06.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 06/23/2012] [Accepted: 06/27/2012] [Indexed: 05/27/2023]
Abstract
Long-term associations between bacteria and animals are widely represented in nature and play an important role in animal adaptation and evolution. In insects thriving on nutritionally unbalanced diets, intracellular symbiotic bacteria (endosymbionts) complement the host nutrients with amino acids and vitamins and interfere with host physiology and reproduction. Endosymbionts permanently infect host cells, called bacteriocytes, which express an adapted local immune response that permits symbiont maintenance and control. Among the immune players in bacteriocytes, the coleoptericin A (ColA) antimicrobial peptide of the cereal weevil, Sitophilus zeamais, was recently found to specifically trigger endosymbionts and to inhibit their cytokinesis, thereby limiting bacterial cell division and dispersion throughout the insect tissues. This review focuses on the biological and evolutionary features of Sitophilus symbiosis, and discusses the possible interactions of ColA with weevil endosymbiont proteins and pathways.
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Affiliation(s)
- Frédéric H Login
- INSA-Lyon, UMR203 BF2I, INRA, Biologie Fonctionnelle Insectes et Interactions, Bat. Louis-Pasteur 20 ave. Albert Einstein, F-69621 Villeurbanne, France
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Comparison of the genome sequences of "Candidatus Portiera aleyrodidarum" primary endosymbionts of the whitefly Bemisia tabaci B and Q biotypes. Appl Environ Microbiol 2013; 79:1757-9. [PMID: 23315735 DOI: 10.1128/aem.02976-12] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
"Candidatus Portiera aleyrodidarum" is the primary endosymbiont of whiteflies. We report two complete genome sequences of this bacterium from the worldwide invasive B and Q biotypes of the whitefly Bemisia tabaci. Differences in the two genome sequences may add insights into the complex differences in the biology of both biotypes.
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50
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Vogel KJ, Moran NA. Functional and evolutionary analysis of the genome of an obligate fungal symbiont. Genome Biol Evol 2013; 5:891-904. [PMID: 23563967 PMCID: PMC3673620 DOI: 10.1093/gbe/evt054] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2013] [Indexed: 01/21/2023] Open
Abstract
Nutritional symbionts of insects include some of the most bizarre genomes studied to date, with extremely reduced size, biased base composition, and limited metabolic abilities. A monophyletic group of aphids within the subfamily Cerataphidinae have lost the bacterial symbiont common to all other Aphididae (Buchnera aphidicola), which have been replaced by a eukaryotic one, the yeast-like symbiont (YLS). As symbionts are expected to experience reduced effective population size (Ne) and largely clonal life cycles, we used this system as a model to test the hypothesis that chronically high levels of genetic drift will result in an increase in size of a eukaryotic genome. We sequenced the genome of the YLS of the aphid Cerataphis brasiliensis and observed elevated rates of protein sequence evolution and intron proliferation in YLS orthologs relative to those of its closest-sequenced relative, consistent with predictions. A moderate amount of repetitive DNA was found along with evidence of directed mutation to prevent proliferation of repetitive elements. Despite increased intron numbers, the overall genome structure appears not to have undergone massive expansion and is around 25 Mb in size. Compared with Buchnera, the YLS appears to have a much broader metabolic repertoire, though many gene families have been reduced in the YLS relative to related fungi. The patterns observed in the YLS genome suggest that its symbiotic lifestyle is permissive to intron proliferation and accelerated sequence evolution, though other factors appear to limit its overall genome expansion.
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Affiliation(s)
- Kevin J Vogel
- Department of Ecology and Evolutionary Biology, University of Arizona, USA.
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