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multiple origins of endosymbiosis within the enterobacteriaceae (gamma-proteobacteria): convergence of complex phylogenetic approaches.abstract: background: the bacterial family enterobacteriaceae gave rise to a variety of symbiotic forms, from the loosely associated commensals, often designated as secondary (s) symbionts, to obligate mutualists, called primary (p) symbionts. determination of the evolutionary processes behind this phenomenon has long been hampered by the unreliability of phylogenetic reconstructions within this group of bacteria. the main reasons have been the absence of sufficient data, the highly derived nat ...201122201529
reduced selective constraint in endosymbionts: elevation in radical amino acid replacements occurs genome-wide.as predicted by the nearly neutral model of evolution, numerous studies have shown that reduced n(e) accelerates the accumulation of slightly deleterious changes under genetic drift. while such studies have mostly focused on eukaryotes, bacteria also offer excellent models to explore the effects of n(e). most notably, the genomes of host-dependent bacteria with small n(e) show signatures of genetic drift, including elevated k(a)/k(s). here, i explore the utility of an alternative measure of sele ...201122194947
acyrthosiphon pisum aqp2: a multifunctional insect aquaglyceroporin.annotation of the recently sequenced genome of the pea aphid (acyrthosiphon pisum) identified a gene apaqp2 (acypi009194, gene id: 100168499) with homology to the major intrinsic protein/aquaporin superfamily of membrane channel proteins. phylogenetic analysis suggests that apaqp2 is a member of an insect-specific clade of this superfamily. homology model structures of apaqp2 showed a novel array of amino acids comprising the substrate selectivity-determining "aromatic/arginine" region of the pu ...201122166843
purifying selection, sequence composition and context-specific indel mutations shape intraspecific variation in a bacterial endosymbiont.comparative genomics of closely related bacterial strains can clarify mutational processes and selective forces that impact genetic variation. among primary bacterial endosymbionts of insects, such analyses have revealed ongoing genome reduction, raising questions about the ultimate evolutionary fate of these partnerships. here, we explored genomic variation within blochmannia vafer, an obligate mutualist of the ant camponotus vafer. polymorphism analysis of the illumina dataset used previously ...201122117087
Serratia symbiotica from the aphid Cinara cedri: a missing link from facultative to obligate insect endosymbiont.The genome sequencing of Buchnera aphidicola BCc from the aphid Cinara cedri, which is the smallest known Buchnera genome, revealed that this bacterium had lost its symbiotic role, as it was not able to synthesize tryptophan and riboflavin. Moreover, the biosynthesis of tryptophan is shared with the endosymbiont Serratia symbiotica SCc, which coexists with B. aphidicola in this aphid. The whole-genome sequencing of S. symbiotica SCc reveals an endosymbiont in a stage of genome reduction that is ...201122102823
dynamics of genome evolution in facultative symbionts of aphids.aphids are sap-feeding insects that host a range of bacterial endosymbionts including the obligate, nutritional mutualist buchnera plus several bacteria that are not required for host survival. among the latter, 'candidatus regiella insecticola' and 'candidatus hamiltonella defensa' are found in pea aphids and other hosts and have been shown to protect aphids from natural enemies. we have sequenced almost the entire genome of r. insecticola (2.07 mbp) and compared it with the recently published ...201021966902
Sequence conservation and functional constraint on intergenic spacers in reduced genomes of the obligate symbiont Buchnera.Analyses of genome reduction in obligate bacterial symbionts typically focus on the removal and retention of protein-coding regions, which are subject to ongoing inactivation and deletion. However, these same forces operate on intergenic spacers (IGSs) and affect their contents, maintenance, and rates of evolution. IGSs comprise both non-coding, non-functional regions, including decaying pseudogenes at varying stages of recognizability, as well as functional elements, such as genes for sRNAs and ...201121912528
host preference between symbiotic and aposymbiotic aphis fabae, by the aphid parasitoid, lysiphlebus ambiguus.few empirical studies have directly explored the association between buchnera aphidicola (enterobacteriales: enterobacteriaceae), the primary endosymbiont of aphids, and the life history strategies of aphid parasitoids. a series of paired-choice experiments were conducted to explore the preference of the parasitoid lysiphlebus ambiguus halliday (hymenoptera: aphididae) for symbiotic and aposymbiotic aphis fabae scopoli (hemiptera: aphididae) and the suitability of these hosts for parasitoid deve ...201121870967
facultative symbiont infections affect aphid reproduction.some bacterial symbionts alter their hosts reproduction through various mechanisms that enhance their transmission in the host population. in addition to its obligatory symbiont buchnera aphidicola, the pea aphid acyrthosiphon pisum harbors several facultative symbionts influencing several aspects of host ecology. aphids reproduce by cyclical parthenogenesis whereby clonal and sexual reproduction alternate within the annual life cycle. many species, including the pea aphid, also show variation i ...201121818272
multimodal dynamic response of the buchnera aphidicola pleu plasmid to variations in leucine demand of its host, the pea aphid acyrthosiphon pisum.aphids, important agricultural pests, can grow and reproduce thanks to their intimate symbiosis with the ?-proteobacterium buchnera aphidicola that furnishes them with essential amino acids lacking in their phloem sap diet. to study how b. aphidicola, with its reduced genome containing very few transcriptional regulators, responds to variations in the metabolic requirements of its host, we concentrated on the leucine metabolic pathway. we show that leucine is a limiting factor for aphid growth a ...201121797941
cellular tropism, population dynamics, host range and taxonomic status of an aphid secondary symbiont, smls (sitobion miscanthi l type symbiont).smls (sitobion miscanthi l type symbiont) is a newly reported aphid secondary symbiont. phylogenetic evidence from molecular markers indicates that smls belongs to the rickettsiaceae and has a sibling relationship with orientia tsutsugamushi. a comparative analysis of coxa nucleotide sequences further supports recognition of smls as a new genus in the rickettsiaceae. in situ hybridization reveals that smls is housed in both sheath cells and secondary bacteriocytes and it is also detected in aphi ...201121789197
reductive evolution of bacterial genome in insect gut environment.obligate endocellular symbiotic bacteria of insects and other organisms generally exhibit drastic genome reduction. recently, it was shown that symbiotic gut bacteria of some stinkbugs also have remarkably reduced genomes. here, we report the complete genome sequence of such a gut bacterium ishikawaella capsulata of the plataspid stinkbug megacopta punctatissima. gene repertoire and evolutionary patterns, including at richness and elevated evolutionary rate, of the 745,590 bp genome were strikin ...201121737395
the power of paired genomes.species interactions are fundamental to ecology. classic studies of competition, predation, parasitism and mutualism between macroscopic organisms have provided a foundation for the discipline, but many of the most important and intimate ecological interactions are microscopic in scale. these microscopic interactions include those occurring between eukaryotic hosts and their microbial symbionts. such symbioses, ubiquitous in nature, provide experimental challenges because the partners often cann ...201121692233
biomarker discovery from the top down: protein biomarkers for efficient virus transmission by insects (homoptera: aphididae) discovered by coupling genetics and 2-d dige.yellow dwarf viruses cause the most economically important virus diseases of cereal crops worldwide and are vectored by aphids. the identification of vector proteins mediating virus transmission is critical to develop sustainable virus management practices and to understand viral strategies for circulative movement in all insect vectors. previously, we applied 2-d dige to an aphid filial generation 2 population to identify proteins correlated with the transmission phenotype that were stably inhe ...201121648087
genome expansion and differential expression of amino acid transporters at the aphid/buchnera symbiotic interface.in insects some of the most ecologically important symbioses are nutritional symbioses that provide hosts with novel traits and thereby facilitate exploitation of otherwise inaccessible niches. one such symbiosis is the ancient obligate intracellular symbiosis of aphids with the γ-proteobacteria, buchnera aphidicola. while the nutritional basis of the aphid/buchnera symbiosis is well understood, the processes and structures that mediate the intimate interactions of symbiotic partners remain unch ...201121613235
the genome of buchnera aphidicola from the aphid cinara tujafilina provides new clues about the evolutionary history of metabolic losses in bacterial endosymbionts.the symbiotic association between aphids (homoptera) and buchnera aphidicola (γ-proteobacteria) started about 100-200 million years ago. as a consequence of this relationship, the bacterial genome has undergone a prominent size reduction. the downsize genome process starts when the bacterium enters the host, and will probably end with its extinction and replacement by another healthier bacterium, or with the establishment of metabolic complementation between two or more bacteria. nowadays, sever ...201121571878
tools-4-metatool (t4m): online suite of web-tools to process stoichiometric network analysis data from metatool.tools-4-metatool (t4m) is a suite of web-tools, implemented in perl, which analyses, parses, and manipulates files related to metatool. its main goal is to assist the work with metatool. t4m has two major sets of tools: analysis and compare. analysis visualizes the results of metatool (convex basis, elementary flux modes, and enzyme subsets) and facilitates the study of metabolic networks. it is composed of five tools: mdigraph, metamatrix, cbgraph, emgraph, and sortem. compare was developed to ...201121554926
symbiont infection affects aphid defensive behaviours.aphids harbour both an obligate bacterial symbiont, buchnera aphidicola, and a wide range of facultative ones. facultative symbionts can modify morphological, developmental and physiological host traits that favour their spread within aphid populations. we experimentally investigated the idea that symbionts may also modify aphid behavioural traits to enhance their transmission. aphids exhibit many behavioural defences against enemies. despite their benefits, these behaviours have some associated ...201121490007
metabolic modeling of endosymbiont genome reduction on a temporal scale.a fundamental challenge in systems biology is whether a cell-scale metabolic model can predict patterns of genome evolution by realistically accounting for associated biochemical constraints. here, we study the order in which genes are lost in an in silico evolutionary process, leading from the metabolic network of escherichia coli to that of the endosymbiont buchnera aphidicola. we examine how this order correlates with the order by which the genes were actually lost, as estimated from a phylog ...201121451589
large-scale label-free quantitative proteomics of the pea aphid-buchnera symbiosis.many insects are nutritionally dependent on symbiotic microorganisms that have tiny genomes and are housed in specialized host cells called bacteriocytes. the obligate symbiosis between the pea aphid acyrthosiphon pisum and the ?-proteobacterium buchnera aphidicola (only 584 predicted proteins) is particularly amenable for molecular analysis because the genomes of both partners have been sequenced. to better define the symbiotic relationship between this aphid and buchnera, we used large-scale, ...201121421797
genetic and metabolic determinants of nutritional phenotype in an insect-bacterial symbiosis.the pervasive influence of resident microorganisms on the phenotype of their hosts is exemplified by the intracellular bacterium buchnera aphidicola, which provides its aphid partner with essential amino acids (eaas). we investigated variation in the dietary requirement for eaas among four pea aphid (acyrthosiphon pisum) clones. buchnera-derived nitrogen contributed to the synthesis of all eaas for which aphid clones required a dietary supply, and to none of the eaas for which all four clones ha ...201121392141
genomic revelations of a mutualism: the pea aphid and its obligate bacterial symbiont.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 issue ...201121390549
new insights on the evolutionary history of aphids and their primary endosymbiont buchnera aphidicola.since the establishment of the symbiosis between the ancestor of modern aphids and their primary endosymbiont, buchnera aphidicola, insects and bacteria have coevolved. due to this parallel evolution, the analysis of bacterial genomic features constitutes a useful tool to understand their evolutionary history. here we report, based on data from b. aphidicola, the molecular evolutionary analysis, the phylogenetic relationships among lineages and a comparison of sequence evolutionary rates of symb ...201121350635
interactions between a luteovirus and the groel chaperonin protein of the symbiotic bacterium buchnera aphidicola of aphids.luteoviruses and poleroviruses are important plant viruses transmitted exclusively by aphids in a circulative manner via the aphid haemolymph. a chaperonin protein, groel, synthesized in aphids by a symbiotic bacterium, buchnera aphidicola, is hypothesized to bind to virus particles in the haemolymph, thereby promoting transmission. to investigate this hypothesis, the groel-binding site for barley yellow dwarf virus (bydv) was determined in vitro, and the abundance of groel protein in different ...201121346031
origin and examination of a leafhopper facultative endosymbiont.eukaryotes engage in intimate interactions with microbes that range in age and type of association. although many conspicuous examples of ancient insect associates are studied (e.g., buchnera aphidicola), fewer examples of younger associations are known. here, we further characterize a recently evolved bacterial endosymbiont of the leafhopper euscelidius variegatus (hemiptera, cicadellidae), called bev. we found that bev, continuously maintained in e. variegatus hosts at uc berkeley since 1984, ...201121336565
kick-starting the ratchet: the fate of mutators in an asexual population.muller's ratchet operates in asexual populations without intergenomic recombination. in this case, deleterious mutations will accumulate and population fitness will decline over time, possibly endangering the survival of the species. mutator mutations, i.e., mutations that lead to an increased mutation rate, will play a special role for the behavior of the ratchet. first, they are part of the ratchet and can come to dominance through accumulation in the ratchet. second, the fitness-loss rate of ...201121288878
aphid genome expression reveals host-symbiont cooperation in the production of amino acids.the evolution of intimate symbiosis requires the coordination of gene expression and content between the distinct partner genomes; this coordination allows the fusion of capabilities of each organism into a single integrated metabolism. in aphids, the 10 essential amino acids are scarce in the phloem sap diet and are supplied by the obligate bacterial endosymbiont (buchnera), which lives inside specialized cells called bacteriocytes. although buchnera's genome encodes most genes for essential am ...201121282658
genetics coupled to quantitative intact proteomics links heritable aphid and endosymbiont protein expression to circulative polerovirus transmission.yellow dwarf viruses in the family luteoviridae, which are the causal agents of yellow dwarf disease in cereal crops, are each transmitted most efficiently by different species of aphids in a circulative manner that requires the virus to interact with a multitude of aphid proteins. aphid proteins differentially expressed in f2 schizaphis graminum genotypes segregating for the ability to transmit cereal yellow dwarf virus-rpv (cydv-rpv) were identified using two-dimensional difference gel electro ...201021159868
structure and dynamics of the operon map of buchnera aphidicola sp. strain aps.gene expression regulation is still poorly documented in bacteria with highly reduced genomes. understanding the evolution and mechanisms underlying the regulation of gene transcription in buchnera aphidicola, the primary endosymbiont of aphids, is expected both to enhance our understanding of this nutritionally based association and to provide an intriguing case-study of the evolution of gene expression regulation in a reduced bacterial genome.201021108805
the evolution of mutualism.like altruism, mutualism, cooperation between species, evolves only by enhancing all participants' inclusive fitness. mutualism evolves most readily between members of different kingdoms, which pool complementary abilities for mutual benefit: some of these mutualisms represent major evolutionary innovations. mutualism cannot persist if cheating annihilates its benefits. in long-term mutualisms, symbioses, at least one party associates with the other nearly all its life. usually, a larger host ha ...201020942825
evolutionary relationships among primary endosymbionts of the mealybug subfamily phenacoccinae (hemiptera: coccoidea: pseudococcidae).mealybugs (coccoidea: pseudococcidae) are sap-sucking plant parasites that harbor bacterial endosymbionts within specialized organs. previous studies have identified two subfamilies, pseudococcinae and phenacoccinae, within mealybugs and determined the primary endosymbionts (p-endosymbionts) of the pseudococcinae to be betaproteobacteria ("candidatus tremblaya princeps") containing gammaproteobacteria secondary symbionts. here, the p-endosymbionts of phenacoccine mealybugs are characterized base ...201020851962
how the insect immune system interacts with an obligate symbiotic bacterium.the animal immune system provides defence against microbial infection, and the evolution of certain animal-microbial symbioses is predicted to involve adaptive changes in the host immune system to accommodate the microbial partner. for example, the reduced humoral immune system in the pea aphid acyrthosiphon pisum, including an apparently non-functional immune deficiency (imd) signalling pathway and absence of peptidoglycan recognition proteins (pgrps), has been suggested to be an adaptation for ...201120719775
sources of variation in dietary requirements in an obligate nutritional symbiosis.the nutritional symbiosis between aphids and their obligate symbiont, buchnera aphidicola, is often characterized as a highly functional partnership in which the symbiont provides the host with essential nutrients. despite this, some aphid lineages exhibit dietary requirements for nutrients typically synthesized by buchnera, suggesting that some aspect of the symbiosis is disrupted. to examine this phenomenon in the pea aphid, acyrthosiphon pisum, populations were assayed using defined artificia ...201120667882
combining next-generation sequencing strategies for rapid molecular resource development from an invasive aphid species, aphis glycines.aphids are one of the most important insect taxa in terms of ecology, evolutionary biology, genetics and genomics, and interactions with endosymbionts. additionally, many aphids are serious pest species of agricultural and horticultural plants. recent genetic and genomic research has expanded molecular resources for many aphid species, including the whole genome sequencing of the pea aphid, acrythosiphon pisum. however, the invasive soybean aphid, aphis glycines, lacks in any significant molecul ...201020614011
dynamics of a recurrent buchnera mutation that affects thermal tolerance of pea aphid hosts.mutations in maternally transmitted symbionts can affect host fitness. in this study we investigate a mutation in an obligate bacterial symbiont (buchnera), which has dramatic effects on the heat tolerance of pea aphid hosts (acyrthosiphon pisum). the heat-sensitive allele arises through a single base deletion in a homopolymer within the promoter of ibpa, which encodes a universal small heat-shock protein. in laboratory cultures reared under cool conditions (20°), the rate of fixation (1.4 × 10( ...201020610410
limited endosymbiont variation in diuraphis noxia (hemiptera: aphididae) biotypes from the united states and south africa.symbiosis allows an insect access to imbalanced food sources on which other organisms cannot survive. a bacterial endosymbiont, buchnera aphidicola, gives aphids the ability to feed on phloem depleted of certain essential amino acids by producing those required. pseudogenes and lower plasmid copy numbers of essential amino acid genes in b. aphidicola, endosymbiont of the russian wheat aphid, diuraphis noxia (kurdjumov) (hemiptera: aphididae), suggest that this symbiotic relationship is degenerat ...201020568636
genomic insight into the amino acid relations of the pea aphid, acyrthosiphon pisum, with its symbiotic bacterium buchnera aphidicola.the pea aphid genome includes 66 genes contributing to amino acid biosynthesis and 93 genes to amino acid degradation. in several respects, the pea aphid gene inventory complements that of its symbiotic bacterium, buchnera aphidicola (buchnera aps). unlike other insects with completely sequenced genomes, the pea aphid lacks the capacity to synthesize arginine, which is produced by buchnera aps. however, consistent with other insects, it has genes coding for individual reactions in essential amin ...201020482655
genomic evidence for complementary purine metabolism in the pea aphid, acyrthosiphon pisum, and its symbiotic bacterium buchnera aphidicola.the purine salvage pathway recycles purines to nucleotides, promoting efficient utilization of purine nucleotides. exceptionally among animals with completely sequenced genomes, the pea aphid lacks key purine recycling genes that code for purine nucleoside phosphorylase and adenosine deaminase, indicating that the aphid can neither metabolize nucleosides to the corresponding purines, nor adenosine to inosine. purine metabolism genes in the symbiotic bacterium buchnera complement aphid genes, and ...201020482654
structural calibration of the rates of amino acid evolution in a search for darwin in drifting biological systems.in the last two decades, many reports of proteins under positive selection have brought the neutral theory into question. however, the methods used to detect selection have ignored the evolvability of amino acids within proteins, which is fundamental to distinguishing positive selection from the relaxed constraints caused by genetic drift. disentangling these two counterbalancing forces is essential to test the neutral theory. here, we calibrate rates of amino acid divergence by using structural ...201020466746
the pea aphid genome sequence brings theories of insect defense into question.the genome sequence of the pea aphid is the first for a basal hemimetabolous insect and provides insights into developmental plasticity, symbiosis and insect immunity.201020236492
bacterial genes in the aphid genome: absence of functional gene transfer from buchnera to its host.genome reduction is typical of obligate symbionts. in cellular organelles, this reduction partly reflects transfer of ancestral bacterial genes to the host genome, but little is known about gene transfer in other obligate symbioses. aphids harbor anciently acquired obligate mutualists, buchnera aphidicola (gammaproteobacteria), which have highly reduced genomes (420-650 kb), raising the possibility of gene transfer from ancestral buchnera to the aphid genome. in addition, aphids often harbor oth ...201020195500
genome sequence of the pea aphid acyrthosiphon pisum.aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. here we present the 464 mb draft genome assembly of the pea aphid acyrthosiphon pisum. this first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. pea aphids are host-plant specialists, they can reprodu ...201020186266
insecticidal activity of recombinant avidin produced in yeast.an expression construct encoding chicken (gallus gallus) avidin was assembled from amplified fragments of genomic dna. recombinant, functional avidin was produced in pichia pastoris, with yields of up to 80 mg/l of culture supernatant. the recombinant avidin had similar insecticidal activity to egg white avidin when assayed against larvae of a lepidopteran crop pest, cabbage moth (mamestra brassicae), causing >90% reduction in growth and 100% mortality when fed in optimised diets at levels of 1. ...201020132821
[co-metabolic activity of aphid acyrthosiphon pisum and symbiotic bacterium buchnera aphidicola str. aps]. 200920088388
symbiosis as a source of selectable epigenetic variation: taking the heat for the big guy.evolutionary developmental biology is based on the principle that evolution arises from hereditable changes in development. most of this new work has centred on changes in the regulatory components of the genome. however, recent studies (many of them documented in this volume) have shown that development also includes interactions between the organism and its environment. one area of interest concerns the importance of symbionts for the production of the normal range of phenotypes. many, if not ...201020083641
wolbachia as a bacteriocyte-associated nutritional mutualist.many insects are dependent on bacterial symbionts that provide essential nutrients (ex. aphid-buchnera and tsetse-wiglesworthia associations), wherein the symbionts are harbored in specific cells called bacteriocytes that constitute a symbiotic organ bacteriome. facultative and parasitic bacterial symbionts like wolbachia have been regarded as evolutionarily distinct from such obligate nutritional mutualists. however, we discovered that, in the bedbug cimex lectularius, wolbachia resides in a ba ...201020080750
when bacteria lose a single dna base, aphids suffer. 200720076671
tritrophic interactions among macrosiphum euphorbiae aphids, their host plants and endosymbionts: investigation by a proteomic approach.the mi-1.2 gene in tomato confers resistance against certain clones of the potato aphid (macrosiphum euphorbiae). this study used 2d-dige coupled with protein identification by maldi-tof-ms to compare the proteome patterns of avirulent and semivirulent potato aphids and their bacterial endosymbionts on resistant (mi-1.2+) and susceptible (mi-1.2-) tomato lines. avirulent aphids had low survival on resistant plants, whereas the semivirulent clone could colonize these plants. eighty-two protein sp ...201019962988
systemic analysis of the symbiotic function of buchnera aphidicola, the primary endosymbiont of the pea aphid acyrthosiphon pisum.buchnera aphidicola is the primary obligate intracellular symbiont of most aphid species. b. aphidicola and aphids have been evolving in parallel since their association started, about 150 myr ago. both partners have lost their autonomy, and aphid diversification has been confined to smaller ecological niches by this co-evolution. b. aphidicola has undergone major genomic and biochemical changes as a result of adapting to intracellular life. several genomes of b. aphidicola from different aphid ...200919909925
effects of facultative symbionts and heat stress on the metabolome of pea aphids.we examined metabolite pools of pea aphids with different facultative symbiont infections, and characterized their effects on aphid metabolism in baseline and heat stress conditions. the bacterial symbiont serratia symbiotica protects aphid hosts from the detrimental results of heat stress and shields the obligate symbiont buchnera from effects of heat. we investigated whether broad effects on metabolism might correlate with this protection. both facultative symbiont infection and heat treatment ...201019907504
integrated metabonomic-proteomic analysis of an insect-bacterial symbiotic system.the health of animals, including humans, is dependent on their resident microbiota, but the complexity of the microbial communities makes these associations difficult to study in most animals. exceptionally, the microbiology of the pea aphid acyrthosiphon pisum is dominated by a single bacterium buchnera aphidicola (b. aphidicola). a (1)h nmr-based metabonomic strategy was applied to investigate metabolic profiles of aphids fed on a low essential amino acid diet and treated by antibiotic to elim ...201019860485
dynamics of genome evolution in facultative symbionts of aphids.summary aphids are sap-feeding insects that host a range of bacterial endosymbionts including the obligate, nutritional mutualist buchnera plus several bacteria that are not required for host survival. among the latter, 'candidatus regiella insecticola' and 'candidatus hamiltonella defensa' are found in pea aphids and other hosts and have been shown to protect aphids from natural enemies. we have sequenced almost the entire genome of r. insecticola (2.07 mbp) and compared it with the recently pu ...200919840097
post-pleistocene radiation of the pea aphid complex revealed by rapidly evolving endosymbionts.adaptation to different resources has the potential to cause rapid species diversification, but few studies have been able to quantify the time scale of recent adaptive radiations. the pea aphid, acyrthosiphon pisum, a model of speciation for host-specialized parasites, consists of several biotypes (races or species) living on distinct legume hosts. to document this radiation, we used rapidly evolving sequences from buchnera, the maternally transmitted bacterial endosymbiont of aphids. analyses ...200919805299
two species of symbiotic bacteria present in the soybean aphid (hemiptera: aphididae).aphids, which feed solely on plant phloem sap, have developed symbiotic associations with bacteria that provide them with the amino acids that are lacking in phloem. three soybean aphid (aphis glycines mat samura) populations were screened for the presence of buchnera aphidicola and three common species of secondary aphid symbionts (serratia symbiotica, hamiltonella defensa, and regiella insecticola). diagnostic polymerase chain reaction and subsequent dna sequencing showed the presence of two s ...200919791603
impact of host developmental age on the transcriptome of the symbiotic bacterium buchnera aphidicola in the pea aphid (acyrthosiphon pisum).of the 617 genes from buchnera aphidicola, the obligate bacterial symbiont of the pea aphid, 23% were differentially expressed in embryos compared to adults. genes involved in flagellar apparatus and riboflavin synthesis exhibited particularly robust upregulation in embryos, suggesting functional differences between the symbiosis in the adult and embryo insect.200919783752
facultative symbionts in aphids and the horizontal transfer of ecologically important traits.aphids engage in symbiotic associations with a diverse assemblage of heritable bacteria. in addition to their obligate nutrient-provisioning symbiont, buchnera aphidicola, aphids may also carry one or more facultative symbionts. unlike obligate symbionts, facultative symbionts are not generally required for survival or reproduction and can invade novel hosts, based on both phylogenetic analyses and transfection experiments. facultative symbionts are mutualistic in the context of various ecologic ...201019728837
microbial comparative pan-genomics using binomial mixture models.the size of the core- and pan-genome of bacterial species is a topic of increasing interest due to the growing number of sequenced prokaryote genomes, many from the same species. attempts to estimate these quantities have been made, using regression methods or mixture models. we extend the latter approach by using statistical ideas developed for capture-recapture problems in ecology and epidemiology.200919691844
morph-dependent expression and subcellular localization of host serine carboxypeptidase in bacteriocytes of the pea aphid associated with degradation of the endosymbiotic bacterium buchnera.pea aphids form a mutualistic association with the endosymbiotic bacterium buchnera, which is harbored in specialized host cells called bacteriocytes. the adult aphids display dimorphism in which there are winged and wingless morphs. we previously reported that the buchnera density in bacteriocytes of the winged morph (alate) decreases around final ecdysis, whereas that in the wingless morph (aptera) does not decrease; the decrease in density in alatae is accompanied by activation of the host ly ...200919583501
evolution and diversity of facultative symbionts from the aphid subfamily lachninae.many aphids harbor a variety of endosymbiotic bacteria. the functions of these symbionts can range from an obligate nutritional role to a facultative role in protecting their hosts against environmental stresses. one such symbiont is "candidatus serratia symbiotica," which is involved in defense against heat and potentially also in aphid nutrition. lachnid aphids have been the focus of several recent studies investigating the transition of this symbiont from a facultative symbiont to an obligate ...200919542349
deciphering the connectivity structure of biological networks using mixnet.as biological networks often show complex topological features, mathematical methods are required to extract meaningful information. clustering methods are useful in this setting, as they allow the summary of the network's topology into a small number of relevant classes. different strategies are possible for clustering, and in this article we focus on a model-based strategy that aims at clustering nodes based on their connectivity profiles.200919534742
the biology of genomes, 5-9 may 2009, cold spring harbor, new york. the bug and the bacterium: interdependent genomes. 200919498142
the slow:fast substitution ratio reveals changing patterns of natural selection in gamma-proteobacterial genomes.different microbial species are thought to occupy distinct ecological niches, subjecting each species to unique selective constraints, which may leave a recognizable signal in their genomes. thus, it may be possible to extract insight into the genetic basis of ecological differences among lineages by identifying unusual patterns of substitutions in orthologous gene or protein sequences. we used the ratio of substitutions in slow- versus fast-evolving sites (nucleotides in dna, or amino acids in ...200919458656
hamiltonella defensa, genome evolution of protective bacterial endosymbiont from pathogenic ancestors.eukaryotes engage in a multitude of beneficial and deleterious interactions with bacteria. hamiltonella defensa, an endosymbiont of aphids and other sap-feeding insects, protects its aphid host from attack by parasitoid wasps. thus h. defensa is only conditionally beneficial to hosts, unlike ancient nutritional symbionts, such as buchnera, that are obligate. similar to pathogenic bacteria, h. defensa is able to invade naive hosts and circumvent host immune responses. we have sequenced the genome ...200919451630
biosynthetic potentials from species-specific metabolic networks.studies of genome-scale metabolic networks allow for qualitative and quantitative descriptions of an organism's capability to convert nutrients into products. the set of synthesizable products strongly depends on the provided nutrients as well as on the structure of the metabolic network. here, we apply the method of network expansion and the concept of scopes, describing the synthesizing capacities of an organism when certain nutrients are provided. we analyze the biosynthetic properties of fou ...200819425129
patterns and rates of nucleotide substitution, insertion and deletion in the endosymbiont of ants blochmannia floridanus.genome reduction is a general process that has been studied in numerous symbiotic bacteria associated with insects. we investigated the last stages of genome degradation in blochmannia floridanus, a mutualistic bacterial endosymbiont of the ant camponotus floridanus. we determined the tempo (rates of insertion and deletion) and mode (size and number of insertion-deletion events) of the process in the last 200,000 years by analysing a total of 16 intergenic regions in several strains of this endo ...200819378410
selection for chaperone-like mediated genetic robustness at low mutation rate: impact of drift, epistasis and complexity.genetic robustness is defined as the constancy of a phenotype in the face of deleterious mutations. overexpression of chaperones, to assist the folding of proteins carrying deleterious mutations, is so far one of the most accepted molecular mechanisms enhancing genetic robustness. most theories on the evolution of robustness have focused on the implications of high mutation rate. here we show that genetic drift, which is modulated by population size, organism complexity, and epistasis, can be a ...200919307609
aphids acquired symbiotic genes via lateral gene transfer.aphids possess bacteriocytes, which are cells specifically differentiated to harbour the obligate mutualist buchnera aphidicola (gamma-proteobacteria). buchnera has lost many of the genes that appear to be essential for bacterial life. from the bacteriocyte of the pea aphid acyrthosiphon pisum, we previously identified two clusters of expressed sequence tags that display similarity only to bacterial genes. southern blot analysis demonstrated that they are encoded in the aphid genome. in this stu ...200919284544
species response to environmental change: impacts of food web interactions and evolution.how environmental change affects species abundances depends on both the food web within which species interact and their potential to evolve. using field experiments, we investigated both ecological and evolutionary responses of pea aphids (acyrthosiphon pisum), a common agricultural pest, to increased frequency of episodic heat shocks. one predator species ameliorated the decrease in aphid population growth with increasing heat shocks, whereas a second predator did not, with this contrast cause ...200919265021
a fragile metabolic network adapted for cooperation in the symbiotic bacterium buchnera aphidicola.in silico analyses provide valuable insight into the biology of obligately intracellular pathogens and symbionts with small genomes. there is a particular opportunity to apply systems-level tools developed for the model bacterium escherichia coli to study the evolution and function of symbiotic bacteria which are metabolically specialised to overproduce specific nutrients for their host and, remarkably, have a gene complement that is a subset of the e. coli genome.200919232131
age- and morph-dependent activation of the lysosomal system and buchnera degradation in aphid endosymbiosis.endosymbiosis in aphids is maintained through a mutualistic association between the host and a symbiotic bacterium, buchnera, which is harbored in specialized host cells called bacteriocytes. here, we examined the changes in the buchnera density in bacteriocytes in relation to the development and polyphenism of the host aphid. buchnera density in the winged morph aphids, alatae, decreased drastically around the final ecdysis, whereas in the wingless morph aphids, apterae, buchnera density decrea ...200919183557
the dynamics and time scale of ongoing genomic erosion in symbiotic bacteria.among cellular organisms, symbiotic bacteria provide the extreme examples of genome degradation and reduction. however, only isolated snapshots of eroding symbiont genomes have previously been available. we documented the dynamics of symbiont genome evolution by sequencing seven strains of buchnera aphidicola from pea aphid hosts. we estimated a spontaneous mutation rate of at least 4 x 10(-9) substitutions per site per replication, which is more than 10 times as high as the rates previously est ...200919150844
host-symbiont co-speciation and reductive genome evolution in gut symbiotic bacteria of acanthosomatid stinkbugs.host-symbiont co-speciation and reductive genome evolution have been commonly observed among obligate endocellular insect symbionts, while such examples have rarely been identified among extracellular ones, the only case reported being from gut symbiotic bacteria of stinkbugs of the family plataspidae. considering that gut symbiotic communities are vulnerable to invasion of foreign microbes, gut symbiotic associations have been thought to be evolutionarily not stable. stinkbugs of the family aca ...200919146674
symbiotic bacteria enable insect to use a nutritionally inadequate diet.animals generally require a dietary supply of various nutrients (vitamins, essential amino acids, etc.) because their biosynthetic capabilities are limited. the capacity of aphids to use plant phloem sap, with low essential amino acid content, has been attributed to their symbiotic bacteria, buchnera aphidicola, which can synthesize these nutrients; but this has not been demonstrated empirically. we demonstrate here that phloem sap obtained from the severed stylets of pea aphids acyrthosiphon pi ...200919129128
selection for translational robustness in buchnera aphidicola, endosymbiotic bacteria of aphids.its strong intergenerational bottlenecks and effectively asexual reproduction have led buchnera aphidicola, the endocellular symbiotic bacterium of aphids, to spectacular evolutionary and genomic changes in comparison with its free-living bacterial cousins. these changes summarize into high fixation rates of mildly deleterious destabilizing mutations. this predicts a sharp decline of its fitness and the consequent early demise of this endosymbiotic bacterium. its survival for hundreds of million ...200919126868
bacterial flagellar diversity and evolution: seek simplicity and distrust it?flagella are the chief organelles of motility in bacteria. in recent years, several new findings have illuminated the evolution of bacterial flagella, including cut-down versions of the organelle in buchnera, a dispensable atpase and structural evidence for homology between flig (a component of the flagellar motor) and mgte (a magnesium transporter). however, a fresh examination of the phylogenetic distribution of flagellar genes warns against a simplistic model of early flagellar evolution.200919081724
the microbial flora of aphis gossypii: patterns across host plants and geographical space.the cotton aphid, aphis gossypii, has a worldwide distribution and causes damage to numerous economically important crops. the bacterial symbionts associated with cotton aphids, sampled mainly from malvaceous and cucurbitaceous plants within japan and australia, were characterised using molecular profiling approaches. the goal was to document the aphid symbionts present and determine if patterns of microbial diversity are consistent with the existence of host plant related cryptic species in a. ...200919026656
endosymbiont gene functions impaired and rescued by polymerase infidelity at poly(a) tracts.among host-dependent bacteria that have evolved by extreme reductive genome evolution, long-term bacterial endosymbionts of insects have the smallest (160-790 kb) and most a + t-rich (>70%) bacterial genomes known to date. these genomes are riddled with poly(a) tracts, and 5-50% of genes contain tracts of 10 as or more. here, we demonstrate transcriptional slippage at poly(a) tracts within genes of buchnera aphidicola associated with aphids and blochmannia pennsylvanicus associated with ants. se ...200818815381
fine-scale cospeciation between brachycaudus and buchnera aphidicola: bacterial genome helps define species and evolutionary relationships in aphids.aphids harbour an obligatory symbiont, buchnera aphidicola, providing essential amino acids not supplied by their diet. these bacteria are transmitted vertically and phylogenic analyses suggest that they have 'cospeciated' with their hosts. we investigated this cospeciation phenomenon at a fine taxonomic level, within the aphid genus brachycaudus. we used dna-based methods of species delimitation in both organisms, to avoid biases in the definition of aphid and buchnera species and to infer asso ...200918782748
the insecticidal activity of recombinant garlic lectins towards aphids.the heterodimeric and homodimeric garlic lectins asai and asaii were produced as recombinant proteins in the yeast pichia pastoris. the proteins were purified as functional dimeric lectins, but underwent post-translational proteolysis. recombinant asaii was a single homogenous polypeptide which had undergone c-terminal processing similar to that occurring in planta. the recombinant asai was glycosylated and subject to variable and heterogenous proteolysis. both lectins showed insecticidal effect ...200818707000
complete rpob gene sequencing as a suitable supplement to dna-dna hybridization for bacterial species and genus delineation.dna-dna hybridization (ddh), the gold standard for bacterial species delineation, is a laborious method and the alternative, average nucleotide identity (ani), a genomic sequence-derived parameter, is not applicable to non-sequenced species. a universal cut-off value to delineate bacterial species does not exist, yet a ddh value <70 % and ani <95+/-0.5 % have proved useful in selected examples. we herein compare published values for ddh and ani with sequence similarity of rpob gene sequences ret ...200818676461
the evolution of the flagellar assembly pathway in endosymbiotic bacterial genomes.genome shrinkage is a common feature of most intracellular pathogens and symbionts. reduction of genome sizes is among the best-characterized evolutionary ways of intracellular organisms to save and avoid maintaining expensive redundant biological processes. endosymbiotic bacteria of insects are examples of biological economy taken to completion because their genomes are dramatically reduced. these bacteria are nonmotile, and their biochemical processes are intimately related to those of their h ...200818635679
featured organism: reductive evolution in bacteria: buchnera sp., rickettsia prowazekii and mycobacterium leprae.obligate intracellular bacteria commonly have much reduced genome sizes compared to their nearest free-living relatives. one reason for this is reductive evolution: the loss of genes rendered non-essential due to the intracellular habitat. this can occur because of the presence of orthologous genes in the host, combined with the ability of the bacteria to import the protein or metabolite products of the host genes. in this article we take a look at three such bacteria whose genomes have been ful ...200118628941
the striking case of tryptophan provision in the cedar aphid cinara cedri.buchnera aphidicola bcc has lost its symbiotic role as the tryptophan supplier to the aphid cinara cedri. we report the presence of a plasmid in this endosymbiont that contains the trpeg genes. the remaining genes for the pathway (trpdcba) are located on the chromosome of the secondary endosymbiont "candidatus serratia symbiotica." thus, we propose that a symbiotic consortium is necessary to provide tryptophan.200818586942
evolution of the secondary symbiont "candidatus serratia symbiotica" in aphid species of the subfamily lachninae.buchnera aphidicola bcc, the primary endosymbiont of the aphid cinara cedri (subfamily lachninae), is losing its symbiotic capacity and might be replaced by the coresident "candidatus serratia symbiotica." phylogenetic and morphological analyses within the subfamily lachninae indicate two different "ca. serratia symbiotica" lineages and support the longtime coevolution of both symbionts in c. cedri.200818502932
an effect of 16s rrna intercistronic variability on coevolutionary analysis in symbiotic bacteria: molecular phylogeny of arsenophonus triatominarum.the genes of ribosomal rna are the most popular and frequently used markers for bacterial phylogeny and reconstruction of insect-symbiont coevolution. in primary symbionts, such as buchnera and wigglesworthia, genome economization leads to the establishment of a single copy of these sequences. in phylogenetic studies, they provide sufficient information and yield phylogenetic trees congruent with host evolution. in contrast, other symbiotic lineages (e.g., the genus arsenophonus) carry a higher ...200818485654
interactions of chaperonin with a weakly active anthranilate synthase from the aphid endosymbiont buchnera aphidicola.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 ...200818478288
impact of bias discrepancy and amino acid usage on estimates of the effective number of codons used in a gene, and a test for selection on codon usage.the effective number of codons (nc) used in a gene is one of the most commonly used measures of synonymous codon usage bias, owing much of its popularity to the fact that it is species independent and that simulation studies have shown that it is less dependent of gene length than other measures. in this paper i provide a clear and practically meaningful definition of bias discrepancy (bd; when the degree of codon bias varies within a degeneracy class). moreover i evaluate the impact of bd and a ...200818248919
transmission of symbiotic bacteria buchnera to parthenogenetic embryos in the aphid acyrthosiphon pisum (hemiptera: aphidoidea).all phloem-feeding aphids have an absolute requirement for their primary bacterial symbionts buchnera sp. the bacteria are transmitted vertically to either embryos in the viviparous morph or to eggs in the oviparous morph, with the implication that the symbiont population regularly passes through a genetic 'bottleneck', i.e. only a small proportion of the maternal symbiont population is transmitted to offspring. in this paper, we visualise this process in viviparous aphids using a specific immun ...200318089009
how do endosymbionts become organelles? understanding early events in plastid evolution.what factors drove the transformation of the cyanobacterial progenitor of plastids (e.g. chloroplasts) from endosymbiont to bona fide organelle? this question lies at the heart of organelle genesis because, whereas intracellular endosymbionts are widespread in both unicellular and multicellular eukaryotes (e.g. rhizobial bacteria, chlorella cells in ciliates, buchnera in aphids), only two canonical eukaryotic organelles of endosymbiotic origin are recognized, the plastids of algae and plants and ...200718027391
the role of mutational dynamics in genome shrinkage.genome shrinkage occurs after whole genome duplications (wgds) and in the evolution of parasitic or symbiotic species. the dynamics of this process, whether it occurs by single gene deletions or also by larger deletions are however unknown. in yeast, genome shrinkage has occurred after a wgd. using a computational model of genome evolution, we show that in a random genome single gene deletions cannot explain the observed pattern of gene loss in yeast. the distribution of genes deleted per event ...200717768305
temporal fragmentation of speciation in bacteria.because bacterial recombination involves the occasional transfer of small dna fragments between strains, different sets of niche-specific genes may be maintained in populations that freely recombine at other loci. therefore, genetic isolation may be established at different times for different chromosomal regions during speciation as recombination at niche-specific genes is curtailed. to test this model, we separated sequence divergence into rate and time components, revealing that different reg ...200717717188
antibiotics, primary symbionts and wing polyphenism in three aphid species.the possible role of the primary buchnera symbionts in wing polyphenism is examined in three aphid species. presumptive winged aphids were fed on antibiotic-treated beans to destroy these symbionts. as previously reported, this leads to inhibited growth and low/zero fecundity. when such treatment is applied to the short-day-induced gynoparae (the winged autumn migrant) of the black bean aphid, aphis fabae, it also causes many insects to develop as wingless or winged/wingless intermediate adult f ...200717628287
conservation of the links between gene transcription and chromosomal organization in the highly reduced genome of buchnera aphidicola.genomic studies on bacteria have clearly shown the existence of chromosomal organization as regards, for example, to gene localization, order and orientation. moreover, transcriptomic analyses have demonstrated that, in free-living bacteria, gene transcription levels and chromosomal organization are mutually influenced. we have explored the possible conservation of relationships between mrna abundances and chromosomal organization in the highly reduced genome of buchnera aphidicola, the primary ...200717547756
genetic evidence from mitochondrial, nuclear, and endosymbiont markers for the evolution of host plant associated species in the aphid genus hyalopterus (hemiptera: aphididae).over the past several decades biologists' fascination with plant-herbivore interactions has generated intensive research into the implications of these interactions for insect diversification. the study of closely related phytophagous insect species or populations from an evolutionary perspective can help illuminate ecological and selective forces that drive these interactions. here we present such an analysis for aphids in the genus hyalopterus (hemiptera: aphididae), a cosmopolitan group that ...200717542845
modular organization in the reductive evolution of protein-protein interaction networks.the variation in the sizes of the genomes of distinct life forms remains somewhat puzzling. the organization of proteins into domains and the different mechanisms that regulate gene expression are two factors that potentially increase the capacity of genomes to create more complex systems. high-throughput protein interaction data now make it possible to examine the additional complexity generated by the way that protein interactions are organized.200717532860
optimization and clinical validation of a pathogen detection microarray.dna microarrays used as 'genomic sensors' have great potential in clinical diagnostics. biases inherent in random pcr-amplification, cross-hybridization effects, and inadequate microarray analysis, however, limit detection sensitivity and specificity. here, we have studied the relationships between viral amplification efficiency, hybridization signal, and target-probe annealing specificity using a customized microarray platform. novel features of this platform include the development of a robust ...200717531104
plasmids derived from gifsy-1/gifsy-2, lambdoid prophages contributing to the virulence of salmonella enterica serovar typhimurium: implications for the evolution of replication initiation proteins of lambdoid phages and enterobacteria.gifsy-1 and gifsy-2 are lambdoid prophages which contribute to the virulence of salmonella enterica serovar typhimurium. the nucleotide sequence of the replication region of both prophages is identical, and similar in organization to the replication region of bacteriophage lambda. to investigate the replication of the gifsy phages and the relationship between gifsy and host chromosome replication, a plasmid which contained all the genes and regulatory sequences required for autonomous replicatio ...200717526845
proteomic profiling of aphid macrosiphum euphorbiae responses to host-plant-mediated stress induced by defoliation and water deficit.abiotic and biotic host-plant stress, such as desiccation and herbivory, may strongly affect sap-sucking insects such as aphids via changes in plant chemicals of insect nutritional or plant defensive value. here, we examined (i) water deprivation and (ii) defoliation by the beetle leptinotarsa decemlineata as stresses indirectly affecting the aphid macrosiphum euphorbiae via its host plant solanum tuberosum. for plant-induced stress, aphids were reared on healthy vs. continuously stressed potato ...200717466324
aphid thermal tolerance is governed by a point mutation in bacterial symbionts.symbiosis is a ubiquitous phenomenon generating biological complexity, affecting adaptation, and expanding ecological capabilities. however, symbionts, which can be subject to genetic limitations such as clonality and genomic degradation, also impose constraints on hosts. a model of obligate symbiosis is that between aphids and the bacterium buchnera aphidicola, which supplies essential nutrients. we report a mutation in buchnera of the aphid acyrthosiphon pisum that recurs in laboratory lines a ...200717425405
selective elimination of aphid endosymbionts: effects of antibiotic dose and host genotype, and fitness consequences.multiple endosymbionts commonly coexist in the same host insects. in order to gain an understanding of the biological roles of the individual symbionts in such complex systems, experimental techniques for enabling the selective removal of a specific symbiont from the host are of great importance. by using the pea aphid-buchnera-serratia endosymbiotic system as a model, the efficacy, generality, and fitness consequences of selective elimination techniques at various antibiotic doses and under a v ...200717313660
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