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Liang Y, Dikow RB, Su X, Wen J, Ren Z. Comparative genomics of the primary endosymbiont Buchnera aphidicola in aphid hosts and their coevolutionary relationships. BMC Biol 2024; 22:137. [PMID: 38902723 PMCID: PMC11188193 DOI: 10.1186/s12915-024-01934-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 05/28/2024] [Indexed: 06/22/2024] Open
Abstract
BACKGROUND Coevolution between modern aphids and their primary obligate, bacterial endosymbiont, Buchnera aphidicola, has been previously reported at different classification levels based on molecular phylogenetic analyses. However, the Buchnera genome remains poorly understood within the Rhus gall aphids. RESULTS We assembled the complete genome of the endosymbiont Buchnera in 16 aphid samples, representing 13 species in all six genera of Rhus gall aphids by shotgun genome skimming method. We compared the newly assembled genomes with those from GenBank to comprehensively investigate patterns of coevolution between the bacteria Buchnera and their aphid hosts. Buchnera genomes were mostly collinear, and the pan-genome contained 684 genes, in which the core genome contained 256 genes with some lineages having large numbers of tandem gene duplications. There has been substantial gene-loss in each Buchnera lineage. We also reconstructed the phylogeny for Buchnera and their host aphids, respectively, using 72 complete genomes of Buchnera, along with the complete mitochondrial genomes and three nuclear genes of 31 corresponding host aphid accessions. The cophylogenetic test demonstrated significant coevolution between these two partner groups at individual, species, generic, and tribal levels. CONCLUSIONS Buchnera exhibits very high levels of genomic sequence divergence but relative stability in gene order. The relationship between the symbionts Buchnera and its aphid hosts shows a significant coevolutionary pattern and supports complexity of the obligate symbiotic relationship.
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Affiliation(s)
- Yukang Liang
- School of Life Science and Shanxi Key Laboratory of Nucleic Acid Biopesticides, Shanxi University, 92 Wucheng Rd, Taiyuan Shanxi, 030006, China
| | - Rebecca B Dikow
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, 600 Maryland Avenue SW, Washington, DC, 20024, USA
| | - Xu Su
- School of Geography and Life Science, Qinghai Normal University, 38 Wusixi Road, Xining, 810008, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, MRC-166, Washington, DC, 20013-7012, USA.
| | - Zhumei Ren
- School of Life Science and Shanxi Key Laboratory of Nucleic Acid Biopesticides, Shanxi University, 92 Wucheng Rd, Taiyuan Shanxi, 030006, China.
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Popkes M, Valenzano DR. Microbiota-host interactions shape ageing dynamics. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190596. [PMID: 32772667 PMCID: PMC7435156 DOI: 10.1098/rstb.2019.0596] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2020] [Indexed: 12/12/2022] Open
Abstract
Occupying the interface between host and environment, host-associated microbes play fundamental roles in nutrient absorption, essential metabolite synthesis, development of the immune system, defence against pathogens and pathogenesis. Microbiota composition and function is rather stable during adulthood, while it dramatically changes during early development, frailty and disease. Ageing is associated with progressive decrease of homeostasis, often resulting in disruption of the physiological balance between host and commensal microbes, ultimately leading to dysbiosis and host demise. Generally, high microbial diversity is associated with health and a youthful state, while low individual microbial diversity and larger inter-individual microbial diversity is associated with ageing and disease states. Different species are equipped with species-specific commensal, symbiotic and pathogenic microbial communities. How and whether the specific host-microbiota consortia co-evolved with host physiology to ensure homeostasis and promote individual fitness remains an open question. In this essay, we propose that the evolution of vertebrate-specific immune adaptations may have enabled the establishment of highly diverse, species-specific commensal microbial communities. We discuss how the maintenance of intact immune surveillance mechanisms, which allow discrimination between commensal and pathogenic bacteria, fail during ageing and lead to the onset of known ageing-related diseases. We discuss how host-microbiota interactions are key to maintaining homeostasis despite external perturbations, but also how they affect a range of host-specific ageing-related phenotypes. This article is part of the theme issue 'The role of the microbiome in host evolution'.
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Affiliation(s)
- Miriam Popkes
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Dario Riccardo Valenzano
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- CECAD, University of Cologne, Cologne, Germany
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3
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Chong RA, Park H, Moran NA. Genome Evolution of the Obligate Endosymbiont Buchnera aphidicola. Mol Biol Evol 2020; 36:1481-1489. [PMID: 30989224 DOI: 10.1093/molbev/msz082] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
An evolutionary consequence of uniparentally transmitted symbiosis is degradation of symbiont genomes. We use the system of aphids and their maternally inherited obligate endosymbiont, Buchnera aphidicola, to explore the evolutionary process of genome degradation. We compared complete genome sequences for 39 Buchnera strains, including 23 newly sequenced symbiont genomes from diverse aphid hosts. We reconstructed the genome of the most recent shared Buchnera ancestor, which contained 616 protein-coding genes, and 39 RNA genes. The extent of subsequent gene loss varied across lineages, resulting in modern genomes ranging from 412 to 646 kb and containing 354-587 protein-coding genes. Loss events were highly nonrandom across loci. Genes involved in replication, transcription, translation, and amino acid biosynthesis are largely retained, whereas genes underlying ornithine biosynthesis, stress responses, and transcriptional regulation were lost repeatedly. Aside from losses, gene order is almost completely stable. The main exceptions involve movement between plasmid and chromosome locations of genes underlying tryptophan and leucine biosynthesis and supporting nutrition of aphid hosts. This set of complete genomes enabled tests for signatures of positive diversifying selection. Of 371 Buchnera genes tested, 29 genes show strong support for ongoing positive selection. These include genes encoding outer membrane porins that are expected to be involved in direct interactions with hosts. Collectively, these results indicate that extensive genome reduction occurred in the ancestral Buchnera prior to aphid diversification and that reduction has continued since, with losses greater in some lineages and for some loci.
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Affiliation(s)
- Rebecca A Chong
- Department of Integrative Biology, University of Texas at Austin, Austin, TX
- Department of Biology, University of Hawaii at Mānoa, Honolulu, HI
| | - Hyunjin Park
- Department of Integrative Biology, University of Texas at Austin, Austin, TX
| | - Nancy A Moran
- Department of Integrative Biology, University of Texas at Austin, Austin, TX
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4
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Zhang Z, Jiao S, Li X, Li M. Bacterial and fungal gut communities of Agrilus mali at different developmental stages and fed different diets. Sci Rep 2018; 8:15634. [PMID: 30353073 PMCID: PMC6199299 DOI: 10.1038/s41598-018-34127-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 10/03/2018] [Indexed: 11/17/2022] Open
Abstract
Agrilus mali (Coleoptera: Buprestidae) is an invasive wood borer pest that has caused considerable damage to the Xinjiang wild fruit forest. In this study, we investigated the bacterial and fungal intestinal microbial communities of A. mali during different developmental stages, including larvae, pupae and newly eclosed adults or fed different diets (leaves of Malus halliana and Malus pumila) using Illumina MiSeq high-throughput sequencing technology. The results showed that microbial alpha diversity first increased and then decreased during the developmental stages, with the most dominant bacteria and fungi exhibiting the dynamic patterns "Decrease", "Increase" and "Fluctuation". With respect to the different diets, the bacterial communities were similar between the newly eclosed adults and adults fed M. pumila leaves, while the structure of the fungal communities showed great differences between newly eclosed adults and adults fed different diets. Through a co-correlation network analysis, we observed complex microbial interactions among bacterial and fungal taxa that were associated with potential diverse functions and intricate biological processes in the intestinal microbiota of A. mali. Overall, the results of this study demonstrated that the invasive insect A. mali harbours diverse, dynamic, and presumably multifunctional microbial communities, an understanding of which could improve our ability to develop more effective management approaches to control A. mali.
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Affiliation(s)
- Zhengqing Zhang
- Laboratory of Forestry Pests Biological Control, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Shuo Jiao
- College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
| | - Xiaohui Li
- Laboratory of Forestry Pests Biological Control, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Menglou Li
- Laboratory of Forestry Pests Biological Control, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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5
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Boyd BM, Allen JM, Nguyen NP, Vachaspati P, Quicksall ZS, Warnow T, Mugisha L, Johnson KP, Reed DL. Primates, Lice and Bacteria: Speciation and Genome Evolution in the Symbionts of Hominid Lice. Mol Biol Evol 2017; 34:1743-1757. [PMID: 28419279 PMCID: PMC5455983 DOI: 10.1093/molbev/msx117] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Insects with restricted diets rely on symbiotic bacteria to provide essential metabolites missing in their diet. The blood-sucking lice are obligate, host-specific parasites of mammals and are themselves host to symbiotic bacteria. In human lice, these bacterial symbionts supply the lice with B-vitamins. Here, we sequenced the genomes of symbiotic and heritable bacterial of human, chimpanzee, gorilla, and monkey lice and used phylogenomics to investigate their evolutionary relationships. We find that these symbionts have a phylogenetic history reflecting the louse phylogeny, a finding contrary to previous reports of symbiont replacement. Examination of the highly reduced symbiont genomes (0.53–0.57 Mb) reveals much of the genomes are dedicated to vitamin synthesis. This is unchanged in the smallest symbiont genome and one that appears to have been reorganized. Specifically, symbionts from human lice, chimpanzee lice, and gorilla lice carry a small plasmid that encodes synthesis of vitamin B5, a vitamin critical to the bacteria-louse symbiosis. This plasmid is absent in an old world monkey louse symbiont, where this pathway is on its primary chromosome. This suggests the unique genomic configuration brought about by the plasmid is not essential for symbiosis, but once obtained, it has persisted for up to 25 My. We also find evidence that human, chimpanzee, and gorilla louse endosymbionts have lost a pathway for synthesis of vitamin B1, whereas the monkey louse symbiont has retained this pathway. It is unclear whether these changes are adaptive, but they may point to evolutionary responses of louse symbionts to shifts in primate biology.
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Affiliation(s)
- Bret M Boyd
- Department of Entomology, University of Georgia Athens, Athens, GA.,Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL
| | - Julie M Allen
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL.,Florida Museum of Natural History, University of Florida, Gainesville, FL
| | - Nam-Phuong Nguyen
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA
| | - Pranjal Vachaspati
- Department of Computer Science and Department of Bioengineering, University of Illinois Urbana-Champaign, Champaign, IL
| | | | - Tandy Warnow
- Department of Computer Science and Department of Bioengineering, University of Illinois Urbana-Champaign, Champaign, IL
| | - Lawrence Mugisha
- Conservation & Ecosystem Health Alliance (CEHA), Kampala, Uganda.,College of Veterinary Medicine, Animal Resources & Biosecurity (COVAB), Makerere University, Kampala, Uganda
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL
| | - David L Reed
- Florida Museum of Natural History, University of Florida, Gainesville, FL
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6
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Wade RN, Karley AJ, Johnson SN, Hartley SE. Impact of predicted precipitation scenarios on multitrophic interactions. Funct Ecol 2017. [DOI: 10.1111/1365-2435.12858] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Ruth N. Wade
- University of York Wentworth Way YorkYO10 5DD UK
- The James Hutton Institute Invergowrie DundeeDD2 5DA UK
| | | | - Scott N. Johnson
- Hawkesbury Institute for the Environment Western Sydney University Locked Bag 1797 Penrith NSW2751 Australia
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7
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Mori M, Ponce-de-León M, Peretó J, Montero F. Metabolic Complementation in Bacterial Communities: Necessary Conditions and Optimality. Front Microbiol 2016; 7:1553. [PMID: 27774085 PMCID: PMC5054487 DOI: 10.3389/fmicb.2016.01553] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 09/16/2016] [Indexed: 11/13/2022] Open
Abstract
Bacterial communities may display metabolic complementation, in which different members of the association partially contribute to the same biosynthetic pathway. In this way, the end product of the pathway is synthesized by the community as a whole. However, the emergence and the benefits of such complementation are poorly understood. Herein, we present a simple model to analyze the metabolic interactions among bacteria, including the host in the case of endosymbiotic bacteria. The model considers two cell populations, with both cell types encoding for the same linear biosynthetic pathway. We have found that, for metabolic complementation to emerge as an optimal strategy, both product inhibition and large permeabilities are needed. In the light of these results, we then consider the patterns found in the case of tryptophan biosynthesis in the endosymbiont consortium hosted by the aphid Cinara cedri. Using in-silico computed physicochemical properties of metabolites of this and other biosynthetic pathways, we verified that the splitting point of the pathway corresponds to the most permeable intermediate.
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Affiliation(s)
- Matteo Mori
- Departamento de Bioquímica y Biología Molecular I, Facultad de Ciencias Químicas, Universidad Complutense de MadridMadrid, Spain; Department of Physics, University of California, San DiegoLa Jolla, CA, USA
| | - Miguel Ponce-de-León
- Departamento de Bioquímica y Biología Molecular I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid Madrid, Spain
| | - Juli Peretó
- Department of Biochemistry and Molecular Biology and Institute for Integrative Systems Biology, Universitat de València-CSIC Valencia, Spain
| | - Francisco Montero
- Departamento de Bioquímica y Biología Molecular I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid Madrid, Spain
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8
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Manzano-Marín A, Simon JC, Latorre A. Reinventing the Wheel and Making It Round Again: Evolutionary Convergence in Buchnera-Serratia Symbiotic Consortia between the Distantly Related Lachninae Aphids Tuberolachnus salignus and Cinara cedri. Genome Biol Evol 2016; 8:1440-58. [PMID: 27190007 PMCID: PMC4898801 DOI: 10.1093/gbe/evw085] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2016] [Indexed: 12/23/2022] Open
Abstract
Virtually all aphids (Aphididae) harbor Buchnera aphidicola as an obligate endosymbiont to compensate nutritional deficiencies arising from their phloem diet. Many species within the Lachninae subfamily seem to be consistently associated also with Serratia symbiotica We have previously shown that both Cinara (Cinara) cedri and Cinara (Cupressobium) tujafilina (Lachninae: Eulachnini tribe) have indeed established co-obligate associations with both Buchnera and S. symbiotica However, while Buchnera genomes of both Cinara species are similar, genome degradation differs greatly between the two S. symbiotica strains. To gain insight into the essentiality and degree of integration of S. symbiotica within the Lachninae, we sequenced the genome of both Buchnera and S. symbiotica endosymbionts from the distantly related aphid Tuberolachnus salignus (Lachninae: Tuberolachnini tribe). We found a striking level of similarity between the endosymbiotic system of this aphid and that of C. cedri In both aphid hosts, S. symbiotica possesses a highly reduced genome and is found exclusively intracellularly inside bacteriocytes. Interestingly, T. salignus' endosymbionts present the same tryptophan biosynthetic metabolic complementation as C. cedri's, which is not present in C. tujafilina's. Moreover, we corroborate the riboflavin-biosynthetic-role take-over/rescue by S. symbiotica in T. salignus, and therefore, provide further evidence for the previously proposed establishment of a secondary co-obligate endosymbiont in the common ancestor of the Lachninae aphids. Finally, we propose that the putative convergent split of the tryptophan biosynthetic role between Buchnera and S. symbiotica could be behind the establishment of S. symbiotica as an obligate intracellular symbiont and the triggering of further genome degradation.
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Affiliation(s)
| | - Jean-Christophe Simon
- UMR1349 Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA), Rennes, France
| | - Amparo Latorre
- Institut Cavanilles de Biodiversitat I Biologia Evolutiva, Universitat de Valencia 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
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9
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Cassone BJ, Wenger JA, Michel AP. Whole Genome Sequence of the Soybean Aphid Endosymbiont Buchnera aphidicola and Genetic Differentiation among Biotype-Specific Strains. J Genomics 2015; 3:85-94. [PMID: 26516375 PMCID: PMC4618293 DOI: 10.7150/jgen.12975] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Endosymbiosis with microorganisms is common in insects, with more than 10% of species requiring the metabolic capabilities of intracellular bacteria for their nutrient acquisition. Aphids harbor an obligate mutualism with the vertically transferred endosymbiont, Buchnera aphidicola, which produces key nutrients lacking in the aphid's phloem-based diet that are necessary for normal development and reproduction. It is thought that, in some groups of insects, bacterial symbionts may play key roles in biotype evolution against host-plant resistance. The genome of Buchnera has been sequenced in several aphid strains but little genomic data is currently available for the soybean aphid (Aphis glycines), one of the most important pests of soybean in North America. In this study, DNA sequencing was used to assemble and annotate the genome sequence of the Buchnera A. glycines strain and to reconstruct phylogenetic relationships among different strains. In addition, we identified several fixed Buchnera SNPs between Aphis glycines biotypes that were avirulent or virulent to a soybean aphid resistance gene (Rag1). The results of this study describe the genetic and evolutionary relationships of the Buchnera A. glycines strain, and begin to define the roles of an aphid symbiont in host-plant resistance.
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Affiliation(s)
- Bryan J. Cassone
- 1. Department of Biology, Brandon University, Brandon, MB R7A 6A9, Canada
| | - Jacob A. Wenger
- 2. Department of Entomology, The Ohio State University, OARDC, Wooster, OH 44691, USA
| | - Andrew P. Michel
- 2. Department of Entomology, The Ohio State University, OARDC, Wooster, OH 44691, USA
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10
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Paoletti MG, Mazzon L, Martinez-Sañudo I, Simonato M, Beggio M, Dreon AL, Pamio A, Brilli M, Dorigo L, Engel AS, Tondello A, Baldan B, Concheri G, Squartini A. A unique midgut-associated bacterial community hosted by the cave beetle Cansiliella servadeii (Coleoptera: Leptodirini) reveals parallel phylogenetic divergences from universal gut-specific ancestors. BMC Microbiol 2013; 13:129. [PMID: 23758657 PMCID: PMC3695770 DOI: 10.1186/1471-2180-13-129] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Accepted: 05/28/2013] [Indexed: 11/10/2022] Open
Abstract
Background Cansiliella servadeii (Coleoptera) is an endemic troglobite living in deep carbonate caves in North-Eastern Italy. The beetle constantly moves and browses in its preferred habitat (consisting in flowing water and moonmilk, a soft speleothem colonized by microorganisms) self-preens to convey material from elytra, legs, and antennae towards the mouth. We investigated its inner and outer microbiota using microscopy and DNA-based approaches. Results Abundant microbial cell masses were observed on the external appendages. Cansiliella’s midgut is fully colonized by live microbes and culture-independent analyses yielded nearly 30 different 16S phylotypes that have no overlap with the community composition of the moonmilk. Many of the lineages, dominated by Gram positive groups, share very low similarity to database sequences. However for most cases, notwithstanding their very limited relatedness with existing records, phylotypes could be assigned to bacterial clades that had been retrieved from insect or other animals’ digestive traits. Conclusions Results suggest a history of remote separation from a common ancestor that harboured a set of gut-specific bacteria whose functions are supposedly critical for host physiology. The phylogenetic and coevolutionary implications of the parallel occurrences of these prokaryotic guilds appear to apply throughout a broad spectrum of animal diversity. Their persistence and conservation underlies a possibly critical role of precise bacterial assemblages in animal-bacteria interactions.
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Affiliation(s)
- Maurizio G Paoletti
- Dipartimento di Biologia, Università di Padova, via U. Bassi 58/B, 35131 Padova, Italy
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11
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Bhatia V, Uniyal PL, Bhattacharya R. Aphid resistance in Brassica crops: challenges, biotechnological progress and emerging possibilities. Biotechnol Adv 2011; 29:879-88. [PMID: 21802504 DOI: 10.1016/j.biotechadv.2011.07.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Revised: 07/07/2011] [Accepted: 07/12/2011] [Indexed: 10/18/2022]
Abstract
Aphids, (Hemiptera: Aphidoidea) a nefarious insect pest of Brassicaceae members including major vegetable and oilseed crops have coevolved with their host plant and emerged as most economically important insect pest of crop Brassicas. Their atypical feeding mechanism and unusual reproductive biology made them intractable to control below economic threshold level of damage to the crops. To a large extent aphid infestation is controlled by spraying agrochemicals of systemic mode of action and rarely by biological control. Use of systemic insecticides is highly cost intensive as well poses bigger threat of their incorporation in dietary chain. Breeding for genetic resistance against aphids has not been possible owing to the non-availability of resistance source within the crossable germplasms and lack of knowledge of the genetics of the trait. Genetic engineering with insect resistant transgenes seems to be the only potential avenue to address this difficult-to-accomplish breeding objective. Some success had been achieved in terms of developing aphid resistant cultivars through genetic engineering however, commercial utilization of such crops are still awaited. Thus protection of crops against aphids necessarily requires more research to identify either more effective insecticidal transgenes or biological phenomenon that can usher to new mechanism of resistance. The present review is an attempt to highlight the current status and possible avenues to develop aphid resistance in Brassicaceae crops.
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Affiliation(s)
- Varnika Bhatia
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute Campus, New Delhi, India
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12
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Genomic revelations of a mutualism: the pea aphid and its obligate bacterial symbiont. Cell Mol Life Sci 2011; 68:1297-309. [PMID: 21390549 PMCID: PMC3064905 DOI: 10.1007/s00018-011-0645-2] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Revised: 02/15/2011] [Accepted: 02/15/2011] [Indexed: 11/22/2022]
Abstract
The symbiosis of the pea aphid Acyrthosphion pisum with the bacterium Buchnera aphidicola APS represents the best-studied insect obligate symbiosis. Here we present a refined picture of this symbiosis by linking pre-genomic observations to new genomic data that includes the complete genomes of the eukaryotic and prokaryotic symbiotic partners. In doing so, we address four issues central to understanding the patterns and processes operating at the A. pisum/Buchnera APS interface. These four issues include: (1) lateral gene transfer, (2) host immunity, (3) symbiotic metabolism, and (4) regulation.
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Combination of molecular data support the existence of three main lineages in the phylogeny of aphids (Hemiptera: Aphididae) and the basal position of the subfamily Lachninae. Mol Phylogenet Evol 2010; 55:305-317. [DOI: 10.1016/j.ympev.2009.12.005] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2009] [Revised: 11/16/2009] [Accepted: 12/03/2009] [Indexed: 12/31/2022]
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14
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Huang CY, Lee CY, Wu HC, Kuo MH, Lai CY. Interactions of chaperonin with a weakly active anthranilate synthase from the aphid endosymbiont Buchnera aphidicola. MICROBIAL ECOLOGY 2008; 56:696-703. [PMID: 18478288 DOI: 10.1007/s00248-008-9389-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2007] [Revised: 01/30/2008] [Accepted: 03/10/2008] [Indexed: 05/26/2023]
Abstract
The endosymbiotic bacterium Buchnera provides its aphid host with essential amino acids. Buchnera is typical of intracellular symbiotic and parasitic microorganisms in having a small effective population size, which is believed to accelerate genetic drift and reduce the stability of gene products. It is hypothesized that Buchnera mitigates protein instability with an increased production of the chaperonins GroESL. In this paper, we report the expression and functional analysis of trpE, a plasmid-borne fast-evolving gene encoding the tryptophan biosynthesis enzyme anthranilate synthase. We overcame the problem of low enzyme stability by using an anthranilate synthase-deficient mutant of E. coli as the expression host and the method of genetic complementation for detection of the enzyme activity. We showed that the Buchnera anthranilate synthase was only weakly active at the temperature of 26 degrees C but became inactive at the higher temperatures of 32 degrees C and 37 degrees C and that the coexpression with chaperonin genes groESL of E. coli enhanced the function of the Buchnera enzyme. These findings are consistent with the proposed role of groESL in the Buchnera-aphid symbiosis.
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Affiliation(s)
- Chia-Ying Huang
- Department of Biology, National Changhua University of Education, 1 Jin Der Road, Changhua 50007, Taiwan, Republic of China
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15
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Mazzon L, Piscedda A, Simonato M, Martinez-Sanudo I, Squartini A, Girolami V. Presence of specific symbiotic bacteria in flies of the subfamily Tephritinae (Diptera Tephritidae) and their phylogenetic relationships: proposal of 'Candidatus Stammerula tephritidis'. Int J Syst Evol Microbiol 2008; 58:1277-87. [DOI: 10.1099/ijs.0.65287-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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DOHLEN CAROLDVON, MORAN NANCYA. Molecular data support a rapid radiation of aphids in the Cretaceous and multiple origins of host alternation. Biol J Linn Soc Lond 2008. [DOI: 10.1111/j.1095-8312.2000.tb01286.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Douglas A. Parallels and contrasts between symbiotic bacteria and bacterial-derived organelles: evidence from Buchnera, the bacterial symbiont of aphids. FEMS Microbiol Ecol 2006. [DOI: 10.1111/j.1574-6941.1997.tb00418.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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18
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Latorre A, Gil R, Silva FJ, Moya A. Chromosomal stasis versus plasmid plasticity in aphid endosymbiont Buchnera aphidicola. Heredity (Edinb) 2005; 95:339-47. [PMID: 16118664 DOI: 10.1038/sj.hdy.6800716] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The study of three genomes of the aphid endosymbiont Buchnera aphidicola has revealed an extraordinary stasis: conservation of gene order and genetic composition of the chromosome, while the chromosome size and number of genes has reduced. The reduction in genome size appears to be ongoing since some lineages we now know to have even smaller chromosomes than the first B. aphidicola analysed. The current sequencing by our group of one of these smaller genomes with an estimated size of 450 kb, and its comparison with the other three available genomes provide insights into the nature of processes involved in shrinkage. We discuss whether B. aphidicola might be driven to extinction and be replaced by secondary aphid endosymbionts. In some lineages, genes encoding key enzymes in the pathways leading to tryptophan and leucine biosynthesis (trpEG and leuABCD, respectively) are located on plasmids, rather than the main chromosome. In contrast to the stasis of the main chromosome, plasmid genes have frequently been transferred to the main chromosome and undergone other gene rearrangements. We propose a two-step scenario to explain these contrasting modes of evolution. Essential genes may have escaped regulation by moving to plasmids in a moving B. aphidicola ancestor. B. aphidicola became polyploidy at a given stage of its evolution and plasmid genes have been transferred to the main chromosome through several independent events.
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Affiliation(s)
- A Latorre
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Apartado de Correos 2085, 46071 Valencia, Spain.
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19
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Abstract
In many animal groups, mutualistic bacterial symbionts play a central role in host ecology, by provisioning rare nutrients and thus enabling specialization on restricted diets. Among such symbionts, genomic studies are most advanced for Buchnera, the obligate symbiont of aphids, which feed on phloem sap. The contents of the highly reduced Buchnera genomes have verified its role in aphid nutrition. Comparisons of Buchnera gene sets indicate ongoing, irreversible gene losses that are expected to affect aphid nutritional needs. Furthermore, almost all regulatory genes have been eliminated, raising the question of whether and how gene expression responds to environmental change. Microarray studies on genome-wide expression indicate that Buchnera has evolved some constitutive changes in gene expression: homologues of heat stress genes have elevated transcript levels in Buchnera (relative to other bacteria) even in the absence of stress. Additionally, the microarray results indicate that responses to heat stress and to amino acid availability are both few and modest. Observed responses are consistent with control by the few ancestral regulators retained in the genome. Initial studies on the role of host genes in mediating the symbiosis reveal distinctive expression patterns in host cells harbouring Buchnera. In the near future, a complete genome of pea aphid will accelerate progress in understanding the functional integration of aphid and Buchnera genomes. Although information for other insect symbioses is relatively limited, studies on symbionts of carpenter ants and tsetse flies indicate many similarities to Buchnera.
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Affiliation(s)
- Nancy A Moran
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA.
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20
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Moran NA, Dunbar HE, Wilcox JL. Regulation of transcription in a reduced bacterial genome: nutrient-provisioning genes of the obligate symbiont Buchnera aphidicola. J Bacteriol 2005; 187:4229-37. [PMID: 15937185 PMCID: PMC1151715 DOI: 10.1128/jb.187.12.4229-4237.2005] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Buchnera aphidicola, the obligate symbiont of aphids, has an extremely reduced genome, of which about 10% is devoted to the biosynthesis of essential amino acids needed by its hosts. Most regulatory genes for these pathways are absent, raising the question of whether and how transcription of these genes responds to the major shifts in dietary amino acid content encountered by aphids. Using full-genome microarrays for B. aphidicola of the host Schizaphis graminum, we examined transcriptome responses to changes in dietary amino acid content and then verified behavior of individual transcripts using quantitative reverse transcriptase PCR. The only gene showing a consistent and substantial (>twofold) response was metE, which underlies methionine biosynthesis and which is the only amino acid biosynthetic gene retaining its ancestral regulator (metR). In another aphid host, Acyrthosiphon pisum, B. aphidicola has no functional metR and shows no response in metE transcript levels to changes in amino acid concentrations. Thus, the only substantial transcriptional response involves the one gene for which an ancestral regulator is retained. This result parallels that from a previous study on heat stress, in which only the few genes retaining the global heat shock promoter showed responses in transcript abundance. The irreversible losses of transcriptional regulators constrain ability to alter gene expression in the context of environmental fluctuations affecting the symbiotic partners.
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Affiliation(s)
- Nancy A Moran
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA.
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21
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BIRKLE LM, MINTO LB, WALTERS KFA, DOUGLAS AE. Microbial genotype and insect fitness in an aphid-bacterial symbiosis. Funct Ecol 2004. [DOI: 10.1111/j.0269-8463.2004.00871.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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22
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Sabater-Muñoz B, van Ham RCHJ, Moya A, Silva FJ, Latorre A. Evolution of the leucine gene cluster in Buchnera aphidicola: insights from chromosomal versions of the cluster. J Bacteriol 2004; 186:2646-54. [PMID: 15090505 PMCID: PMC387811 DOI: 10.1128/jb.186.9.2646-2654.2004] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
In Buchnera aphidicola strains associated with the aphid subfamilies Thelaxinae, Lachninae, Pterocommatinae, and Aphidinae, the four leucine genes (leuA, -B, -C, and -D) are located on a plasmid. However, these genes are located on the main chromosome in B. aphidicola strains associated with the subfamilies Pemphiginae and Chaitophorinae. The sequence of the chromosomal fragment containing the leucine cluster and flanking genes has different positions in the chromosome in B. aphidicola strains associated with three tribes of the subfamily Pemphiginae and one tribe of the subfamily Chaitophorinae. Due to the extreme gene order conservation of the B. aphidicola genomes, the variability in the position of the leucine cluster in the chromosome may be interpreted as resulting from independent insertions from an ancestral plasmid-borne leucine gene. These findings do not support a chromosomal origin for the leucine genes in the ancestral B. aphidicola and do support a back transfer evolutionary scenario from a plasmid to the main chromosome.
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Affiliation(s)
- Beatriz Sabater-Muñoz
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, 46071 Valencia, Spain
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23
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Ortiz-Rivas B, Moya A, Martínez-Torres D. Molecular systematics of aphids (Homoptera: Aphididae): new insights from the long-wavelength opsin gene. Mol Phylogenet Evol 2004; 30:24-37. [PMID: 15022755 DOI: 10.1016/s1055-7903(03)00155-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Viviparous aphids (Aphididae) constitute a monophyletic group within the Homoptera with more than 4000 extant species worldwide but higher diversity in temperate regions. Several aspects of their biology account for attention paid to this group of insects. Their plant-sap-sucking way of feeding with many species transmitting viruses to crop plants has important implications on crop management strategies. Cyclical parthenogenesis associated in many groups to host alternation and elaborate polyphenisms is of special interests for evolutionists. Finally, the ancient association of most aphid species with intracellular endosymbiotic bacteria (Buchnera sp.) has also received much attention from evolutionists interested in mechanisms involved in the symbiotic process. Knowing the phylogenetic relationships among major aphid taxa is of special interest to evolutionists interested in the above issues. However, until recently, molecular approaches to aphid phylogeny were absent and discussions on the evolution of aphid life-cycles and on evolutionary aspects of their symbiotic association with Buchnera were framed by morphology-based phylogenies. Recently, two reports using molecular approaches attempted to address the yet unresolved phylogeny of Aphididae with limited although somehow different conclusions. In the present report we study the utility of the long-wave opsin gene in resolving phylogenetic relationships among seven subfamilies within the Aphididae. Our results corroborate some previously proposed relationships and suggest a revision of some others. In particular, our data support grouping the analysed aphid species into three main clades, being the subfamily Lachninae one of them, which contradicts its generally accepted sistership relationship with the subfamily Aphidinae. Moreover, our data also suggest a basal position of Lachninae which has implications on current discussions about the ancestrality of conifer-feeding in modern aphids.
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Affiliation(s)
- Benjamín Ortiz-Rivas
- Institut Cavanilles de Biodiversitat i Biología Evolutiva, Universitat de València, Apartado de Correos 22085, 46071 València, Spain
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Russell JA, Latorre A, Sabater-Muñoz B, Moya A, Moran NA. Side-stepping secondary symbionts: widespread horizontal transfer across and beyond the Aphidoidea. Mol Ecol 2003; 12:1061-75. [PMID: 12753224 DOI: 10.1046/j.1365-294x.2003.01780.x] [Citation(s) in RCA: 222] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
To elucidate the co-evolutionary relationships between phloem-feeding insects and their secondary, or facultative, bacterial symbionts, we explore the distributions of three such microbes--provisionally named the R-type (or PASS, or S-sym), T-type (or PABS), and U-type--across a number of aphid and psyllid hosts through the use of diagnostic molecular screening techniques and DNA sequencing. Although typically maternally transmitted, phylogenetic and pairwise divergence analyses reveal that these bacteria have been independently acquired by a variety of unrelated insect hosts, indicating that horizontal transfer has helped to shape their distributions. Based on the high genetic similarity between symbionts in different hosts, we argue that transfer events have occurred recently on an evolutionary timescale. In several instances, however, closely related symbionts associate with related hosts, suggesting that horizontal transfer between distant relatives may be rarer than transmission between close relatives. Our findings on the prevalence of these symbionts within many aphid taxa, along with published observations concerning their effects on host fitness, imply a significant role of facultative symbiosis in aphid ecology and evolution.
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Affiliation(s)
- J A Russell
- University of Arizona, Department of Ecology and Evolutionary Biology, Biological Sciences West, Tucson, Arizona 85721, USA.
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25
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Sabater-Muñoz B, Gómez-Valero L, van Ham RCHJ, Silva FJ, Latorre A. Molecular characterization of the leucine cluster in Buchnera sp. strain PSY, a primary endosymbiont of the aphid Pemphigus spyrothecae. Appl Environ Microbiol 2002; 68:2572-5. [PMID: 11976137 PMCID: PMC127582 DOI: 10.1128/aem.68.5.2572-2575.2002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Buchnera strains from most aphid subfamilies studied to date have been found to carry the leucine gene cluster (leuA, -B, -C, and -D) on a plasmid, an organization unique among bacteria. Here, however, we demonstrate a classical chromosomal location of the cluster in Buchnera sp. strain PSY from the aphid Pemphigus spyrothecae (subfamily Pemphiginae). The genes that flank leuABCD in Buchnera sp. strain PSY appear to be adjacent in the genome of Buchnera sp. strain APS, a strain carrying a leucine plasmid. We propose that the presence of a leucine plasmid predates the diversification of symbiotic Buchnera and that the chromosomal location observed in Buchnera sp. strain PSY arose by a transfer of the leucine genes from a plasmid to the chromosome.
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Affiliation(s)
- Beatriz Sabater-Muñoz
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, València 46071, Spain
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26
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Martinez-Torres D, Buades C, Latorre A, Moya A. Molecular systematics of aphids and their primary endosymbionts. Mol Phylogenet Evol 2001; 20:437-49. [PMID: 11527469 DOI: 10.1006/mpev.2001.0983] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Aphids constitute a monophyletic group within the order Homoptera (i.e., superfamily Aphidoidea). The Aphidoidea originated in the Jurassic about 150 my ago from some aphidiform ancestor whose origin can be traced back to about 250 my ago. They exhibit a mutualistic association with intracellular bacteria (Buchnera sp.) related to Escherichia coli. Buchnera is usually considered the aphids' primary endosymbiont. The association is obligate for both partners. The 16S rDNA-based phylogeny of Buchnera from four aphid families showed complete concordance with the morphology-based phylogeny of their aphid hosts, which pointed to a single original infection in a common ancestor of aphids some 100-250 my ago followed by cospeciation of aphids and Buchnera. This study concentrated on the molecular phylogeny of both the aphids and their primary endosymbionts of five aphid families including for the first time representatives of the family Lachnidae. We discuss results based on two Buchnera genes (16S rDNA and the beta subunit of the F-ATPase complex) and on one host mitochondrial gene (the subunit 6 of the F-ATPase complex). Although our data do not allow definitive evolutionary relationships to be established among the different aphid families, some traditionally accepted groupings are put into question from both bacterial and insect data. In particular, the Lachnidae and the Aphididae, which from morphological data are considered recently evolved sister groups, do not seem to be as closely related as is usually accepted. Finally, we discuss our results in the light of the proposed parallel evolution of aphids and their endosymbionts.
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Affiliation(s)
- D Martinez-Torres
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, València, Apartado de Correos 2085, 46071, Spain
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27
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Wernegreen JJ, Richardson AO, Moran NA. Parallel acceleration of evolutionary rates in symbiont genes underlying host nutrition. Mol Phylogenet Evol 2001; 19:479-85. [PMID: 11399154 DOI: 10.1006/mpev.2001.0929] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The overproduction of essential amino acids by Buchnera aphidicola, the primary bacterial mutualist of aphids, is considered an adaptation for increased production of nutrients that are lacking in aphids' diet of plant sap. Given their shared role in host nutrition, amino acid biosynthetic genes of Buchnera are expected to experience parallel changes in selection that depend on host diet quality, growth rate, and population structure. This study evaluates the hypothesis of parallel selection across biosynthetic pathways by testing for correlated changes in evolutionary rates at biosynthetic genes of Buchnera. Previous studies show fast evolutionary rates at tryptophan biosynthetic genes among Buchnera associated with the aphid genus Uroleucon and suggest reduced purifying selection on symbiont nutritional functions in this aphid group. Here, we test for parallel rate acceleration at other amino acid biosynthetic genes of Buchnera-Uroleucon, including those for leucine (leuABC) and isoleucine/valine biosynthesis (ilvC). Ratios of nonsynonymous to synonymous substitutions (d(N)/d(S)) were estimated using codon-based maximum-likelihood methods that account for the extreme AT compositional bias of Buchnera sequences. A significant elevation in d(N)/d(S) at biosynthetic loci but not at two housekeeping genes sampled (dnaN and tuf) suggests reduced host-level selection on biosynthetic capabilities of Buchnera-Uroleucon. In addition, the discovery of trpEG pseudogenes in Buchnera-U. obscurum further supports reduced selection on amino acid biosynthesis.
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Affiliation(s)
- J J Wernegreen
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, The Marine Biological Laboratory, 7 MBL Street, Woods Hole, Massachusetts 02543, USA.
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28
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Abstract
Endosymbiotic bacteria closely related to mammalian pathogens are widespread in invertebrates. Mutualistic and parasitic bacteria-host interactions on the various evolutionary levels apparently involve similar factors, indicating that relevant genetic information developed early in evolution. The detailed characterization of symbiotic interactions of bacteria with non-mammalian hosts should provide profound insights into the basic mechanisms of bacteria-host interactions and their evolution.
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Affiliation(s)
- W Goebel
- Dept of Microbiology, Biocentre, University of Würzburg, Am Hubland, D-97074, Würzburg, Germany
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29
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Wernegreen JJ, Moran NA. Vertical transmission of biosynthetic plasmids in aphid endosymbionts (Buchnera). J Bacteriol 2001; 183:785-90. [PMID: 11133977 PMCID: PMC94939 DOI: 10.1128/jb.183.2.785-790.2001] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2000] [Accepted: 10/16/2000] [Indexed: 11/20/2022] Open
Abstract
This study tested for horizontal transfer of plasmids among Buchnera aphidicola strains associated with ecologically and phylogenetically related aphid hosts (Uroleucon species). Phylogenetic congruence of Buchnera plasmid (trpEG and leuABC) and chromosomal (dnaN and trpB) genes supports strictly vertical long-term transmission of plasmids, which persist due to their contributions to host nutrition rather than capacity for infectious transfer. Synonymous divergences indicate elevated mutation on plasmids relative to chromosomal genes.
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Affiliation(s)
- J J Wernegreen
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA.
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30
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King ND, Hojnacki D, O'Brian MR. The Bradyrhizobium japonicum proline biosynthesis gene proC is essential for symbiosis. Appl Environ Microbiol 2000; 66:5469-71. [PMID: 11097929 PMCID: PMC92483 DOI: 10.1128/aem.66.12.5469-5471.2000] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2000] [Accepted: 09/15/2000] [Indexed: 11/20/2022] Open
Abstract
Plant host-derived proline is proposed to serve as an energy source for rhizobia in the rhizosphere and in symbiotic root nodules. The Bradyrhizobium japonicum proC gene was isolated, and a proC mutant strain that behaved as a strict proline auxotroph in culture was constructed. The proC strain elicited undeveloped nodules on soybeans that lacked nitrogen fixation activity and plant hemoglobin. We conclude that the proC gene is essential for symbiosis and suggest that the mutant does not obtain an exogenous supply of proline in association with soybeans sufficient to satisfy its auxotrophy.
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Affiliation(s)
- N D King
- Department of Biochemistry and Center for Microbial Pathogenesis, State University of New York at Buffalo, Buffalo, New York 14214, USA
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31
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Abstract
We describe polymerase chain reaction (PCR) primers for gut analysis of aphid predators. The primers amplify aphid mitochondrial COII fragments ranging in size from 77 to 386 bp. Using these primers, we were able to distinguish six species of US Great Plains cereal aphids, including two congeners, Rhopalosiphum maidis (Fitch) and R. padi (L.), and to detect them in extracts of coccinellid and chrysopid predators. We devised a protocol for deriving half-lives of detectability for the DNA of a single aphid consumed by predators maintained under simulated field dietary and temperature conditions. Using this protocol and primers that amplify a 198-bp fragment, we determined statistically different half-lives of detectability for a single R. maidis of 3.95 h in Chrysoperla plorabunda (Fitch) and 8. 78 h in Hippodamia convergens Guerin. The detectability half-life for a 339-bp R. maidis fragment was statistically longer in C. plorabunda but not in H. convergens. The sensitivity of the assay for the 198-bp fragment is 10-7 aphid equivalents. For species-specific predator gut analysis, PCR is superior to monoclonal antibody technology, giving comparable detectability half-lives with lower expense, much shorter development times, and greater certainty of a successful outcome.
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Affiliation(s)
- Y Chen
- Department of Entomology and Plant Pathology andDepartment of Statistics, Oklahoma State University, Stillwater, Oklahoma 74078 USA
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32
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Van Ham RC, Gonzalez-Candelas F, Silva FJ, Sabater B, Moya A, Latorre A. Postsymbiotic plasmid acquisition and evolution of the repA1-replicon in Buchnera aphidicola. Proc Natl Acad Sci U S A 2000; 97:10855-60. [PMID: 10984505 PMCID: PMC27113 DOI: 10.1073/pnas.180310197] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/1999] [Accepted: 07/05/2000] [Indexed: 02/07/2023] Open
Abstract
Buchnera aphidicola is an obligate, strictly vertically transmitted, bacterial symbiont of aphids. It supplies its host with essential amino acids, nutrients required by aphids but deficient in their diet of plant phloem sap. Several lineages of Buchnera show adaptation to their nutritional role in the form of plasmid-mediated amplification of key-genes involved in the biosynthesis of tryptophan (trpEG) and leucine (leuABCD). Phylogenetic analyses of these plasmid-encoded functions have thus far suggested the absence of horizontal plasmid exchange among lineages of Buchnera. Here, we describe three new Buchnera plasmids, obtained from species of the aphid host families Lachnidae and Pemphigidae. All three plasmids belong to the repA1 family of Buchnera plasmids, which is characterized by the presence of a repA1-replicon responsible for replication initiation. A comprehensive analysis of this family of plasmids unexpectedly revealed significantly incongruent phylogenies for different plasmid and chromosomally encoded loci. We infer from these incongruencies a case of horizontal plasmid transfer in Buchnera. This process may have been mediated by secondary endosymbionts, which occasionally undergo horizontal transmission in aphids.
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Affiliation(s)
- R C Van Ham
- Centro de Astrobiologia, Instituto Nacional de Técnica Aeroespacial, Edificio S-18, Carretera de Torrejón a Ajalvir, 28850 Torrejón de Ardoz, Spain
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33
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Wernegreen JJ, Moran NA. Decay of mutualistic potential in aphid endosymbionts through silencing of biosynthetic loci: Buchnera of Diuraphis. Proc Biol Sci 2000; 267:1423-31. [PMID: 10983826 PMCID: PMC1690690 DOI: 10.1098/rspb.2000.1159] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Buchnera, the primary bacterial endosymbiont of aphids, is known to provision essential amino acids lacking in the hosts' diet of plant sap. The recent discovery of silenced copies of genes for tryptophan biosynthesis (trpEG) in certain Buchnera lineages suggests a decay in symbiotic functions in some aphid species. However, neither the distribution of pseudogenes among lineages nor the impact of this gene silencing on amino-acid availability in hosts has been assessed. In Buchnera of the aphid Diuraphis noxia, tandem repeats of these pseudogenes have persisted in diverse lineages, and thpEG pseudogenes have originated at least twice within this aphid genus. Measures of amino-acid concentrations in Diuraphis species have shown that the presence of the pseudogene is associated with a decreased availability of tryptophan, indicating that gene silencing decreases nutrient provisioning by symbionts. In Buchnera of Diuraphis, rates of nonsynonymous substitutions are elevated in functional trpE copies, supporting the hypothesis that pseudogene origin and persistence reflect a reduced selection for symbiont biosynthetic contributions. The parallel evolution of trpEG pseudogenes in Buchnera of Diuraphis and certain other aphid hosts suggests that either selection at the host level is not effective or that fitness in these aphids is not limited by tryptophan availability.
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Affiliation(s)
- J J Wernegreen
- Department of Ecology and Evolutionary Biology, Center for Insect Science, University of Arizona, Tucson 85721, USA.
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34
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Clark MA, Moran NA, Baumann P, Wernegreen JJ. Cospeciation between bacterial endosymbionts (Buchnera) and a recent radiation of aphids (Uroleucon) and pitfalls of testing for phylogenetic congruence. Evolution 2000; 54:517-25. [PMID: 10937228 DOI: 10.1111/j.0014-3820.2000.tb00054.x] [Citation(s) in RCA: 173] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Previous studies of phylogenetic congruence between aphids and their symbiotic bacteria (Buchnera) supported long-term vertical transmission of symbionts. However, those studies were based on distantly related aphids and would not have revealed horizontal transfer of symbionts among closely related hosts. Aphid species of the genus Uroleucon are closely related phylogenetically and overlap in geographic ranges, habitats, and parasitoids. To examine support for congruence of phylogenies of Buchnera and Uroleucon, sequences from four mitochondrial, one nuclear, and one endosymbiont gene (trpB) were obtained. Congruence of phylogenies based on pooled aphid genes with phylogenies based on trpB was highly significant: Most nodes resolved by trpB corresponded to nodes resolved by the pooled aphid genes. Furthermore, no nodes were both inconsistent between the trees and strongly supported in both trees. Two kinds of analyses testing the null hypothesis of perfect congruence between pairwise combinations of datasets and tree topologies were performed: the Kishino-Hasegawa test and the likelihood-ratio test. Both tests indicated significant disagreement among most pairwise combinations of mitochondrial, nuclear, and symbiont datasets. Because rampant recombination among mitochondrial genomes of different aphid species is unlikely, inaccurate assumptions in the evolutionary models underlying these tests appear to be causing the hypothesis of a shared history to be incorrectly rejected. Moreover, trpB was more consistent with the aphid genes as a set than any single aphid gene was with the others, suggesting that the symbionts show the same phylogeny as the aphids. Overall, analyses support the interpretation that symbionts and aphids have undergone strict cospeciation, with no horizontal transmission of symbionts even among closely related, ecologically similar aphid hosts.
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Affiliation(s)
- M A Clark
- Microbiology Section, University of California, Davis 95616-8665, USA
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35
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Sandström J, Telang A, Moran NA. Nutritional enhancement of host plants by aphids - a comparison of three aphid species on grasses. JOURNAL OF INSECT PHYSIOLOGY 2000; 46:33-40. [PMID: 12770256 DOI: 10.1016/s0022-1910(99)00098-0] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Three aphid species were compared with respect to ability of enhancing the nutritional quality of their host plants. Rhopalosiphum padi, which does not induce macroscopic changes in its host plants, was compared with Schizaphis graminum and Diuraphis noxia, both of which induce distinctive types of chlorotic lesions. Phloem sap samples were collected from severed stylets of feeding aphids and from exudates of cut leaves of plants uninfested or infested with each aphid species. Samples were analyzed for concentrations of individual amino acids.Compared to R. padi, S. graminum ingested phloem sap with a two-fold higher concentration of amino acids and a much higher proportion of essential amino acids. Similar differences between these two aphid species were observed on both wheat and barley. For each aphid species, the absolute concentrations of amino acids and the relative proportions of essential amino acids were similar between the two host plants. Effects of D. noxia were similar to those of S. graminum, though less dramatic. Exudates from leaves infested with each aphid species showed relative concentrations of individual amino acids that were similar to those in the corresponding stylet exudates. Based on comparison of stylet exudates and cut leaf exudates from infested and uninfested plants, R. padi seems to have little effect on amino acid composition of phloem. Changes in the phloem induced by both S. graminum and D. noxia appear to be systemic, affecting at least the whole leaf they are feeding on. The changes observed for D. noxia and for S. graminum are likely to be nutritionally advantageous for the aphids and are expected to affect the aphids' dependence on nutritional supplementation by intracellular symbionts (Buchnera).
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Affiliation(s)
- J Sandström
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
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Caterino MS, Cho S, Sperling FA. The current state of insect molecular systematics: a thriving Tower of Babel. ANNUAL REVIEW OF ENTOMOLOGY 2000; 45:1-54. [PMID: 10761569 DOI: 10.1146/annurev.ento.45.1.1] [Citation(s) in RCA: 210] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Insect molecular systematics has undergone remarkable recent growth. Advances in methods of data generation and analysis have led to the accumulation of large amounts of DNA sequence data from most major insect groups. In addition to reviewing theoretical and methodological advances, we have compiled information on the taxa and regions sequenced from all available phylogenetic studies of insects. It is evident that investigators have not usually coordinated their efforts. The genes and regions that have been sequenced differ substantially among studies and the whole of our efforts is thus little greater than the sum of its parts. The cytochrome oxidase I, 16S, 18S, and elongation factor-1 alpha genes have been widely used and are informative across a broad range of divergences in insects. We advocate their use as standards for insect phylogenetics. Insect molecular systematics has complemented and enhanced the value of morphological and ecological data, making substantial contributions to evolutionary biology in the process. A more coordinated approach focused on gathering homologous sequence data will greatly facilitate such efforts.
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Affiliation(s)
- M S Caterino
- Department of Environmental Science, Policy and Management, University of California, Berkeley 94720-3112, USA
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Clark MA, Moran NA, Baumann P, Wernegreen JJ. COSPECIATION BETWEEN BACTERIAL ENDOSYMBIONTS (BUCHNERA) AND A RECENT RADIATION OF APHIDS (UROLEUCON) AND PITFALLS OF TESTING FOR PHYLOGENETIC CONGRUENCE. Evolution 2000. [DOI: 10.1554/0014-3820(2000)054[0517:cbbeba]2.0.co;2] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Abstract
Attempts to calibrate bacterial evolution have relied on the assumption that rates of molecular sequence divergence in bacteria are similar to those of higher eukaryotes, or to those of the few bacterial taxa for which ancestors can be reliably dated from ecological or geological evidence. Despite similarities in the substitution rates estimated for some lineages, comparisons of the relative rates of evolution at different classes of nucleotide sites indicate no basis for their universal application to all bacteria. However, there is evidence that bacteria have a constant genome-wide mutation rate on an evolutionary time scale but that this rate differs dramatically from the rate estimated by experimental methods.
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Affiliation(s)
- H Ochman
- Department of Ecology, University of Arizona, Tucson, AZ 85721, USA.
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Martínez-Torres D, Moya A, Latorre A. Plasmid-encoded anthranilate synthase (TrpEG) in Buchnera aphidicola from aphids of the family pemphigidae. Appl Environ Microbiol 1999; 65:117-25. [PMID: 9872768 PMCID: PMC90991 DOI: 10.1128/aem.65.1.117-125.1999] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Buchnera aphidicola is an obligate intracellular symbiont of aphids. One of its proposed functions is the synthesis of essential amino acids, nutrients required by aphids but deficient in their diet of plant phloem sap. The genetic organization of the tryptophan pathway in Buchnera from proliferous aphids of the family Aphididae has previously been shown to reflect a capacity to overproduce this essential amino acid (C.-Y. Lai, L. Baumann, and P. Baumann, Proc. Natl. Acad. Sci. USA 91:3819-3823, 1994). This involved amplification of the genes for the first enzyme in the pathway, anthranilate synthase (TrpEG), on a low-copy-number plasmid. Here we report on the finding and molecular characterization of TrpEG-encoding plasmids in Buchnera from aphids of the distantly related family Pemphigidae. Buchnera from Tetraneura caerulescens contained a 3.0-kb plasmid (pBTc2) that carried a single copy of trpEG and resembled trpEG plasmids of Buchnera from the Aphididae. The second plasmid (pBPs2), isolated from Buchnera of Pemphigus spyrothecae, contained a different replicon. It consisted of a putative origin of replication containing iterons and an open reading frame, designated repAC, which showed a high similarity to the gene encoding the replication initiation protein RepA of the RepA/C replicon from the broad-host-range IncA/C group of plasmids. The plasmid population was heterogeneous with respect to the number of tandem repeats of a 1.8-kb unit carrying repAC1, trpG, and remnants of trpE. The two principal forms consisted of either five or six copies of this repeat and a single-copy region carrying repAC2, the putative origin of replication, and trpE. The unexpected finding of elements of the RepA/C replicon in previously characterized trpEG plasmids from Buchnera of the Aphididae suggests that a replacement of replicons has occurred during the evolution of these plasmids, which may point to a common ancestry for all Buchnera trpEG amplifications.
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Silva FJ, van Ham RC, Sabater B, Latorre A. Structure and evolution of the leucine plasmids carried by the endosymbiont (Buchnera aphidicola) from aphids of the family Aphididae. FEMS Microbiol Lett 1998; 168:43-9. [PMID: 9812361 DOI: 10.1111/j.1574-6968.1998.tb13253.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
In all examined species of the family Aphididae, the bacterial endosymbiont Buchnera aphidicola carries a plasmid encoding the genes leuABCD (involved in leucine biosynthesis) along with repA1, repA2 and ORF1. The gene organisation of the leucine plasmids was conserved, except in Buchnera isolated from Pterocomma populeum, where ORF1 was located in a different position. An inverted repeat (LIR1) located between repA2 and leuA is found in all of the Buchnera leucine plasmids examined. The predicted secondary structure of the LIR1 transcript conforms to a long hairpin loop, suggesting an involvement in transcription termination or messenger stability. Phylogenetic reconstruction based on repA2 sequences suggests that horizontal transfer of Buchnera leucine plasmids has not occurred.
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Affiliation(s)
- F J Silva
- Institut Universitari Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain.
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Moreno E. Genome evolution within the alpha Proteobacteria: why do some bacteria not possess plasmids and others exhibit more than one different chromosome? FEMS Microbiol Rev 1998; 22:255-75. [PMID: 9862123 DOI: 10.1111/j.1574-6976.1998.tb00370.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Animal intracellular Proteobacteria of the alpha subclass without plasmids and containing one or more chromosomes are phylogenetically entwined with opportunistic, plant-associated, chemoautotrophic and photosynthetic alpha Proteobacteria possessing one or more chromosomes and plasmids. Local variations in open environments, such as soil, water, manure, gut systems and the external surfaces of plants and animals, may have selected alpha Proteobacteria with extensive metabolic alternatives, broad genetic diversity, and more flexible and larger genomes with ability for horizontal gene flux. On the contrary, the constant and isolated animal cellular milieu selected heterotrophic alpha Proteobacteria with smaller genomes without plasmids and reduced genetic diversity as compared to their plant-associated and phototrophic relatives. The characteristics and genome sizes in the extant species suggest that a second chromosome could have evolved from megaplasmids which acquired housekeeping genes. Consequently, the genomes of the animal cell-associated Proteobacteria evolved through reductions of the larger genomes of chemoautotrophic ancestors and became rich in adenosine and thymidine, as compared to the genomes of their ancestors. Genome organisation and phylogenetic ancestor-descendent relationships between extant bacteria of closely related genera and within the same monophyletic genus and species suggest that some strains have undergone transition from two chromosomes to a single replicon. It is proposed that as long as the essential information is correctly expressed, the presence of one or more chromosomes within the same genus or species is the result of contingency. Genetic drift in clonal bacteria, such as animal cell-associated alpha Proteobacteria, would depend almost exclusively on mutation and internal genetic rearrangement processes. Alternatively, genomic variations in reticulate bacteria, such as many intestinal and plant cell-associated Proteobacteria, will depend not only on these processes, but also on their genetic interactions with other bacterial strains. Common pathogenic domains necessary for the invasion and survival in association with cells have been preserved in the chromosomes of the animal and plant-associated alpha Proteobacteria. These pathogenic domains have been maintained by vertical inherence, extensively ameliorated to match the chromosome G + C content and evolved within chromosomes of alpha Proteobacteria.
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Affiliation(s)
- E Moreno
- Programa de Investigación en Enfermedades Tropicales (PIET), Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica.
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Rouhbakhsh D, Clark MA, Baumann L, Moran NA, Baumann P. Evolution of the tryptophan biosynthetic pathway in Buchnera (aphid endosymbionts): studies of plasmid-associated trpEG within the genus Uroleucon. Mol Phylogenet Evol 1997; 8:167-76. [PMID: 9299222 DOI: 10.1006/mpev.1997.0419] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Aphids obtain tryptophan from prokaryotic endosymbionts assigned to the genus Buchnera. The rate-limiting enzyme in tryptophan biosynthes, anthranilate synthase, is encoded by the genes trpE and trpG. In Buchnera within the family Aphididae, trpEG is plasmid-borne, apparently as an adaptation to overproduce tryptophan for hosts. To explore the evolution of these plasmids, sequences for trpEG, the upstream region containing the plasmid origin of replication, and chromosomal trpB were obtained for Buchnera of three species in the aphid genus Uroleucon and analyzed together with sequences for six other aphid species. Phylogenies based on trpB and trpEG agree with each other and with previous views of aphid phylogeny. Synonymous substitutions are about twice as high for plasmid-borne genes as for chromosomal genes in the same lineages, suggesting higher mutation rates for genes on plasmids. Nonsynonymous rates for trpEG are accelerated within Buchnera of Uroleucon, indicating a change in selection intensity within this genus. Accelerated evolution within Uroleucon also seems to characterize the upstream region containing the putative origin of replication.
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Affiliation(s)
- D Rouhbakhsh
- Microbiology Section, University of California, Davis, California, 95616-8665, USA
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Baumann P, Moran NA, Baumann L. The Evolution and Genetics of Aphid Endosymbionts. Bioscience 1997. [DOI: 10.2307/1313002] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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