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bacterial endosymbiosis in a chordate host: long-term co-evolution and conservation of secondary metabolism.intracellular symbiosis is known to be widespread in insects, but there are few described examples in other types of host. these symbionts carry out useful activities such as synthesizing nutrients and conferring resistance against adverse events such as parasitism. such symbionts persist through host speciation events, being passed down through vertical transmission. due to various evolutionary forces, symbionts go through a process of genome reduction, eventually resulting in tiny genomes wher ...201324324632
aphid amino acid transporter regulates glutamine supply to intracellular bacterial symbionts.endosymbiotic associations have played a major role in evolution. however, the molecular basis for the biochemical interdependence of these associations remains poorly understood. the aphid-buchnera endosymbiosis provides a powerful system to elucidate how these symbioses are regulated. in aphids, the supply of essential amino acids depends on an ancient nutritional symbiotic association with the gamma-proteobacterium buchnera aphidicola. buchnera cells are densely packed in specialized aphid ba ...201324367072
aphid amino acid transporter regulates glutamine supply to intracellular bacterial symbionts.endosymbiotic associations have played a major role in evolution. however, the molecular basis for the biochemical interdependence of these associations remains poorly understood. the aphid-buchnera endosymbiosis provides a powerful system to elucidate how these symbioses are regulated. in aphids, the supply of essential amino acids depends on an ancient nutritional symbiotic association with the gamma-proteobacterium buchnera aphidicola. buchnera cells are densely packed in specialized aphid ba ...201324367072
testing the reproducibility of multiple displacement amplification on genomes of clonal endosymbiont populations.the multiple displacement amplification method has revolutionized genomic studies of uncultured bacteria, where the extraction of pure dna in sufficient quantity for next-generation sequencing is challenging. however, the method is problematic in that it amplifies the target dna unevenly, induces the formation of chimeric reads and also amplifies contaminating dna. here, we have tested the reproducibility of the multiple displacement amplification method using serial dilutions of extracted genom ...201324312412
development of reference transcriptomes for the major field insect pests of cowpea: a toolbox for insect pest management approaches in west africa.cowpea is a widely cultivated and major nutritional source of protein for many people that live in west africa. annual yields and longevity of grain storage is greatly reduced by feeding damage caused by a complex of insect pests that include the pod sucking bugs, anoplocnemis curvipes fabricius (hemiptera: coreidae) and clavigralla tomentosicollis stål (hemiptera: coreidae); as well as phloem-feeding cowpea aphids, aphis craccivora koch (hemiptera: aphididae) and flower thrips, megalurothrips s ...201324278221
natural selection for operons depends on genome size.in prokaryotes, genome size is associated with metabolic versatility, regulatory complexity, effective population size, and horizontal transfer rates. we therefore analyzed the covariation of genome size and operon conservation to assess the evolutionary models of operon formation and maintenance. in agreement with previous results, intraoperonic pairs of essential and of highly expressed genes are more conserved. interestingly, intraoperonic pairs of genes are also more conserved when they enco ...201324201372
what symbionts teach us about modularity.the main goal of synthetic biology (sb) is to apply engineering principles to biotechnology in order to make life easier to engineer. these engineering principles include modularity: decoupling of complex systems into smaller, orthogonal sub-systems that can be used in a range of different applications. the successful use of modules in engineering is expected to be reproduced in synthetic biological systems. but the difficulties experienced up to date with sb approaches question the short-term f ...201325023877
solving gap metabolites and blocked reactions in genome-scale models: application to the metabolic network of blattabacterium cuenoti.metabolic reconstruction is the computational-based process that aims to elucidate the network of metabolites interconnected through reactions catalyzed by activities assigned to one or more genes. reconstructed models may contain inconsistencies that appear as gap metabolites and blocked reactions. although automatic methods for solving this problem have been previously developed, there are many situations where manual curation is still needed.201324176055
how does tremblaya princeps get essential proteins from its nested partner moranella endobia in the mealybug planoccocus citri?many insects maintain intracellular mutualistic symbiosis with a wide range of bacteria which are considered essential for their survival (primary or p-endosymbiont) and typically suffer drastic genome degradation. progressive loss of p-endosymbiont metabolic capabilities could lead to the recruitment of co-existent facultative endosymbiont (secondary or s-endosymbiont), thus adding more complexity to the symbiotic system. planococcus citri, among other mealybug species, harbors an unconventiona ...201324204799
a review of bacteria-animal lateral gene transfer may inform our understanding of diseases like cancer.lateral gene transfer (lgt) from bacteria to animals occurs more frequently than was appreciated prior to the advent of genome sequencing. in 2007, lgt from bacterial wolbachia endosymbionts was detected in ~33% of the sequenced arthropod genomes using a bioinformatic approach. today, wolbachia/host lgt is thought to be widespread and many other cases of bacteria-animal lgt have been described. in insects, lgt may be more frequently associated with endosymbionts that colonize germ cells and germ ...201324146634
in silico experimental evolution: a tool to test evolutionary scenarios.comparative genomics has revealed that some species have exceptional genomes, compared to their closest relatives. for instance, some species have undergone a strong reduction of their genome with a drastic reduction of their genic repertoire. deciphering the causes of these atypical trajectories can be very difficult because of the many phenomena that are intertwined during their evolution (e.g. changes of population size, environment structure and dynamics, selection strength, mutation rates.. ...201324564457
effects of heat shock on resistance to parasitoids and on life history traits in an aphid/endosymbiont system.temperature variation is an important factor determining the outcomes of interspecific interactions, including those involving hosts and parasites. this can apply to variation in average temperature or to relatively short but intense bouts of extreme temperature. we investigated the effect of heat shock on the ability of aphids (aphis fabae) harbouring protective facultative endosymbionts (hamiltonella defensa) to resist parasitism by hymenopteran parasitoids (lysiphlebus fabarum). furthermore, ...201324143175
seasonally variable intestinal metagenomes of the red palm weevil (rhynchophorus ferrugineus).the intestinal microbes residing in the red palm weevil (rpw, rhynchophorus ferrugineus) larva consume tender interior fibrous tissues of date palm trunks. the understanding of such microbiota at molecular level provides vital clues for the biological control of this devastating pest. using pyrosequencing and shotgun strategy, we first study taxonomic profiles of the microbiota sampled at different months (march, july and november), and then confirm the impact of high-temperature stress on the m ...201324102776
unpredicted impacts of insect endosymbionts on interactions between soil organisms, plants and aphids.ecologically significant symbiotic associations are frequently studied in isolation, but such studies of two-way interactions cannot always predict the responses of organisms in a community setting. to explore this issue, we adopt a community approach to examine the role of plant-microbial and insect-microbial symbioses in modulating a plant-herbivore interaction. potato plants were grown under glass in controlled conditions and subjected to feeding from the potato aphid macrosiphum euphorbiae. ...201323926148
shared metabolic pathways in a coevolved insect-bacterial symbiosis.the symbiotic bacterium buchnera aphidicola lacks key genes in the biosynthesis of five essential amino acids (eaas), and yet its animal hosts (aphids) depend on the symbiosis for the synthesis of these eaas (isoleucine, leucine, methionine, phenylalanine, and valine). we tested the hypothesis, derived from genome annotation, that the missing buchnera reactions are mediated by host enzymes, with the exchange of metabolic intermediates between the partners. the specialized host cells bearing buch ...201323892755
interwoven biology of the tsetse holobiont.microbial symbionts can be instrumental to the evolutionary success of their hosts. here, we discuss medically significant tsetse flies (diptera: glossinidae), a group comprised of over 30 species, and their use as a valuable model system to study the evolution of the holobiont (i.e., the host and associated microbes). we first describe the tsetse microbiota, which, despite its simplicity, harbors a diverse range of associations. the maternally transmitted microbes consistently include two gamma ...201323836873
role of symbiotic bacteria in the growth and development of the sunn pest, eurygaster integriceps.the sunn pest, eurygaster integriceps puton (hemiptera: scutelleridae), is the most important pest of wheat and barley in wide areas of the world. different aspects of the insect's life history have been studied, but to date nothing is known about their microbial symbionts. here, the contribution of symbiotic bacteria to the fitness of the bug was investigated by combining two different approaches to manipulate the host's microbial community: the supplementation of antibiotics into the insects' ...201324205987
recognizing short coding sequences of prokaryotic genome using a novel iteratively adaptive sparse partial least squares algorithm.significant efforts have been made to address the problem of identifying short genes in prokaryotic genomes. however, most known methods are not effective in detecting short genes. because of the limited information contained in short dna sequences, it is very difficult to accurately distinguish between protein coding and non-coding sequences in prokaryotic genomes. we have developed a new iteratively adaptive sparse partial least squares (iaspls) algorithm as the classifier to improve the accur ...201324067167
proteomic investigation of aphid honeydew reveals an unexpected diversity of proteins.aphids feed on the phloem sap of plants, and are the most common honeydew-producing insects. while aphid honeydew is primarily considered to comprise sugars and amino acids, its protein diversity has yet to be documented. here, we report on the investigation of the honeydew proteome from the pea aphid acyrthosiphon pisum. using a two-dimensional differential in-gel electrophoresis (2d-dige) approach, more than 140 spots were isolated, demonstrating that aphid honeydew also represents a diverse s ...201324086359
is ecological speciation a major trend in aphids? insights from a molecular phylogeny of the conifer-feeding genus cinara.in the past decade ecological speciation has been recognized as having an important role in the diversification of plant-feeding insects. aphids are host-specialised phytophagous insects that mate on their host plants and, as such, they are prone to experience reproductive isolation linked with host plant association that could ultimately lead to species formation. the generality of such a scenario remains to be tested through macroevolutionary studies. to explore the prevalence of host-driven s ...201324044736
detection of a novel intracellular microbiome hosted in arbuscular mycorrhizal fungi.arbuscular mycorrhizal fungi (amf) are important members of the plant microbiome. they are obligate biotrophs that colonize the roots of most land plants and enhance host nutrient acquisition. many amf themselves harbor endobacteria in their hyphae and spores. two types of endobacteria are known in glomeromycota: rod-shaped gram-negative candidatus glomeribacter gigasporarum, cagg, limited in distribution to members of the gigasporaceae family, and coccoid mollicutes-related endobacteria, mre, w ...201324008325
detection of a novel intracellular microbiome hosted in arbuscular mycorrhizal fungi.arbuscular mycorrhizal fungi (amf) are important members of the plant microbiome. they are obligate biotrophs that colonize the roots of most land plants and enhance host nutrient acquisition. many amf themselves harbor endobacteria in their hyphae and spores. two types of endobacteria are known in glomeromycota: rod-shaped gram-negative candidatus glomeribacter gigasporarum, cagg, limited in distribution to members of the gigasporaceae family, and coccoid mollicutes-related endobacteria, mre, w ...201324008325
applying horizontal gene transfer phenomena to enhance non-viral gene therapy.horizontal gene transfer (hgt) is widespread amongst prokaryotes, but eukaryotes tend to be far less promiscuous with their genetic information. however, several examples of hgt from pathogens into eukaryotic cells have been discovered and mimicked to improve non-viral gene delivery techniques. for example, several viral proteins and dna sequences have been used to significantly increase cytoplasmic and nuclear gene delivery. plant genetic engineering is routinely performed with the pathogenic b ...201323994344
how phloem-feeding insects face the challenge of phloem-located defenses.due to the high content of nutrient, sieve tubes are a primary target for pests, e.g., most phytophagous hemipteran. to protect the integrity of the sieve tubes as well as their content, plants possess diverse chemical and physical defense mechanisms. the latter mechanisms are important because they can potentially interfere with the food source accession of phloem-feeding insects. physical defense mechanisms are based on callose as well as on proteins and often plug the sieve tube. insects that ...201324009620
characterization of the bacterial community associated with larvae and adults of anoplophora chinensis collected in italy by culture and culture-independent methods.the wood-boring beetle anoplophora chinensis forster, native to china, has recently spread to north america and europe causing serious damage to ornamental and forest trees. the gut microbial community associated with these xylophagous beetles is of interest for potential biotechnological applications in lignocellulose degradation and development of pest-control measures. in this study the gut bacterial community of larvae and adults of a. chinensis, collected from different host trees in north ...201324069601
mom knows best: the universality of maternal microbial transmission.the sterile womb paradigm is an enduring premise in biology that human infants are born sterile. recent studies suggest that infants incorporate an initial microbiome before birth and receive copious supplementation of maternal microbes through birth and breastfeeding. moreover, evidence for microbial maternal transmission is increasingly widespread across animals. this collective knowledge compels a paradigm shift—one in which maternal transmission of microbes advances from a taxonomically spec ...201323976878
adaptive evolution of a generalist parasitoid: implications for the effectiveness of biological control agents.the use of alternative hosts imposes divergent selection pressures on parasitoid populations. in response to selective pressures, these populations may follow different evolutionary trajectories. divergent natural selection could promote local host adaptation in populations, translating into direct benefits for biological control, thereby increasing their effectiveness on the target host. alternatively, adaptive phenotypic plasticity could be favored over local adaptation in temporal and spatial ...201324062806
implementing an evolutionary framework for understanding genetic relationships of phenotypically defined insect biotypes in the invasive soybean aphid (aphis glycines).adaptive evolution of pest insects in response to the introduction of resistant cultivars is well documented and commonly results in virulent (i.e., capable of feeding upon resistant cultivars) insect populations being labeled as distinct biotypes. phenotypically defined, biotypes frequently remain evolutionarily indistinct, resulting in ineffective application of virulence control measures and shorter durability of resistant cultivars. here, we utilize an evolutionary framework to discern the g ...201324187586
comparative genomics of bifidobacterium animalis subsp. lactis reveals a strict monophyletic bifidobacterial taxon.strains of bifidobacterium animalis subsp. lactis are extensively exploited by the food industry as health-promoting bacteria, although the genetic variability of members belonging to this taxon has so far not received much scientific attention. in this article, we describe the complete genetic makeup of the b. animalis subsp. lactis bl12 genome and discuss the genetic relatedness of this strain with other sequenced strains belonging to this taxon. moreover, a detailed comparative genomic analys ...201323645200
genome reduction as the dominant mode of evolution.a common belief is that evolution generally proceeds towards greater complexity at both the organismal and the genomic level, numerous examples of reductive evolution of parasites and symbionts notwithstanding. however, recent evolutionary reconstructions challenge this notion. two notable examples are the reconstruction of the complex archaeal ancestor and the intron-rich ancestor of eukaryotes. in both cases, evolution in most of the lineages was apparently dominated by extensive loss of genes ...201323801028
microbial brokers of insect-plant interactions revisited.recent advances in sequencing methods have transformed the field of microbial ecology, making it possible to determine the composition and functional capabilities of uncultured microorganisms. these technologies have been instrumental in the recognition that resident microorganisms can have profound effects on the phenotype and fitness of their animal hosts by modulating the animal signaling networks that regulate growth, development, behavior, etc. against this backdrop, this review assesses th ...201323793897
simple topological properties predict functional misannotations in a metabolic network.misannotation in sequence databases is an important obstacle for automated tools for gene function annotation, which rely extensively on comparison with sequences with known function. to improve current annotations and prevent future propagation of errors, sequence-independent tools are, therefore, needed to assist in the identification of misannotated gene products. in the case of enzymatic functions, each functional assignment implies the existence of a reaction within the organism's metabolic ...201323812979
genome dynamics in legionella: the basis of versatility and adaptation to intracellular replication.legionella pneumophila is a bacterial pathogen present in aquatic environments that can cause a severe pneumonia called legionnaires' disease. soon after its recognition, it was shown that legionella replicates inside amoeba, suggesting that bacteria replicating in environmental protozoa are able to exploit conserved signaling pathways in human phagocytic cells. comparative, evolutionary, and functional genomics suggests that the legionella-amoeba interaction has shaped this pathogen more than p ...201323732852
phylogenetic analysis of symbionts in feather-feeding lice of the genus columbicola: evidence for repeated symbiont replacements.many groups of insects have obligate bacterial symbionts that are vertically transmitted. such associations are typically characterized by the presence of a monophyletic group of bacteria living in a well-defined host clade. in addition the phylogeny of the symbiotic bacteria is typically congruent with that of the host, signifying co-speciation. here we show that bacteria living in a single genus of feather lice, columbicola (insecta: phthiraptera), present an exception to this typical pattern.201323725492
environment exploration and colonization behavior of the pea aphid associated with the expression of the foraging gene.aphids respond to specific environmental cues by producing alternative morphs, a phenomenon called polyphenism, but also by modulating their individual behavior even within the same morph. this complex plasticity allows a rapid adaptation of individuals to fluctuating environmental conditions, but the underlying genetic and molecular mechanisms remain largely unknown. the foraging gene is known to be associated with behavior in various species and has been shown to mediate the behavioral shift i ...201323734236
diversity and function of bacterial microbiota in the mosquito holobiont.mosquitoes (diptera: culicidae) have been shown to host diverse bacterial communities that vary depending on the sex of the mosquito, the developmental stage, and ecological factors. some studies have suggested a potential role of microbiota in the nutritional, developmental and reproductive biology of mosquitoes. here, we present a review of the diversity and functions of mosquito-associated bacteria across multiple variation factors, emphasizing recent findings. mosquito microbiota is consider ...201323688194
the endosymbiont arsenophonus is widespread in soybean aphid, aphis glycines, but does not provide protection from parasitoids or a fungal pathogen.aphids commonly harbor bacterial facultative symbionts that have a variety of effects upon their aphid hosts, including defense against hymenopteran parasitoids and fungal pathogens. the soybean aphid, aphis glycines matsumura (hemiptera: aphididae), is infected with the symbiont arsenophonus sp., which has an unknown role in its aphid host. our research goals were to document the infection frequency and diversity of the symbiont in field-collected soybean aphids, and to determine whether arseno ...201323614027
a cross-taxon analysis of insect-associated bacterial diversity.although it is well known that plants and animals harbor microbial symbionts that can influence host traits, the factors regulating the structure of these microbial communities often remain largely undetermined. this is particularly true for insect-associated microbial communities, as few cross-taxon comparisons have been conducted to date. to address this knowledge gap and determine how host phylogeny and ecology affect insect-associated microbial communities, we collected 137 insect specimens ...201323613815
tyrosine pathway regulation is host-mediated in the pea aphid symbiosis during late embryonic and early larval development.nutritional symbioses play a central role in insects' adaptation to specialized diets and in their evolutionary success. the obligatory symbiosis between the pea aphid, acyrthosiphon pisum, and the bacterium, buchnera aphidicola, is no exception as it enables this important agricultural pest insect to develop on a diet exclusively based on plant phloem sap. the symbiotic bacteria provide the host with essential amino acids lacking in its diet but necessary for the rapid embryonic growth seen in ...201323575215
symbiont-mediated functions in insect hosts.the bacterial endosymbionts occur in a diverse array of insect species and are usually rely within the vertical transmission from mothers to offspring. in addition to primary symbionts, plant sap-sucking insects may also harbor several diverse secondary symbionts. bacterial symbionts play a prominent role in insect nutritional ecology by aiding in digestion of food or supplementing nutrients that insect hosts can't obtain sufficient amounts from a restricted diet of plant phloem. currently, seve ...201323710278
functional and evolutionary analysis of the genome of an obligate fungal symbiont.nutritional symbionts of insects include some of the most bizarre genomes studied to date, with extremely reduced size, biased base composition, and limited metabolic abilities. a monophyletic group of aphids within the subfamily cerataphidinae have lost the bacterial symbiont common to all other aphididae (buchnera aphidicola), which have been replaced by a eukaryotic one, the yeast-like symbiont (yls). as symbionts are expected to experience reduced effective population size (ne) and largely c ...201323563967
comparative genomics of wolbachia and the bacterial species concept.the importance of host-specialization to speciation processes in obligate host-associated bacteria is well known, as is also the ability of recombination to generate cohesion in bacterial populations. however, whether divergent strains of highly recombining intracellular bacteria, such as wolbachia, can maintain their genetic distinctness when infecting the same host is not known. we first developed a protocol for the genome sequencing of uncultivable endosymbionts. using this method, we have se ...201323593012
mealybugs nested endosymbiosis: going into the 'matryoshka' system in planococcus citri in depth.in all branches of life there are plenty of symbiotic associations. insects are particularly well suited to establishing intracellular symbiosis with bacteria, providing them with metabolic capabilities they lack. essential primary endosymbionts can coexist with facultative secondary symbionts which can, eventually, establish metabolic complementation with the primary endosymbiont, becoming a co-primary. usually, both endosymbionts maintain their cellular identity. an exception is the endosymbio ...201323548081
the evolution of genomic instability in the obligate endosymbionts of whiteflies.many insects depend on ancient associations with intracellular bacteria to perform essential metabolic functions. these endosymbionts exhibit striking examples of convergence in genome architecture, including a high degree of structural stability that is not typical of their free-living counterparts. however, the recently sequenced genome of the obligate whitefly endosymbiont portiera revealed features that distinguish it from other ancient insect associates, such as a low gene density and the p ...201323542079
bacterial communities associated with the surfaces of fresh fruits and vegetables.fresh fruits and vegetables can harbor large and diverse populations of bacteria. however, most of the work on produce-associated bacteria has focused on a relatively small number of pathogenic bacteria and, as a result, we know far less about the overall diversity and composition of those bacterial communities found on produce and how the structure of these communities varies across produce types. moreover, we lack a comprehensive view of the potential effects of differing farming practices on ...201323544058
genomic comparison between salmonella gallinarum and pullorum: differential pseudogene formation under common host restriction.salmonella serovars enteritidis and gallinarum are closely related, but their host ranges are very different: the former is host-promiscuous and the latter can infect poultry only. comparison of their genomic sequences reveals that gallinarum has undergone much more extensive degradation than enteritidis. this phenomenon has also been observed in other host restricted salmonella serovars, such as typhi and paratyphi a. the serovar gallinarum can be further split into two biovars: gallinarum and ...201323555032
endosymbiotic bacteria in insects: guardians of the immune system?insects have evolved obligate, mutualistic interactions with bacteria without further transmission to other eukaryotic organisms. such long-term obligate partnerships between insects and bacteria have a profound effect on various physiological functions of the host. here we provide an overview of the effects of endosymbiotic bacteria on the insect immune system as well as on the immune response of insects to pathogenic infections. potential mechanisms through which endosymbionts can affect the a ...201323508299
bacterial dna sifted from the trichoplax adhaerens (animalia: placozoa) genome project reveals a putative rickettsial endosymbiont.eukaryotic genome sequencing projects often yield bacterial dna sequences, data typically considered as microbial contamination. however, these sequences may also indicate either symbiont genes or lateral gene transfer (lgt) to host genomes. these bacterial sequences can provide clues about eukaryote-microbe interactions. here, we used the genome of the primitive animal trichoplax adhaerens (metazoa: placozoa), which is known to harbor an uncharacterized gram-negative endosymbiont, to search for ...201323475938
comparison of the genome sequences of "candidatus portiera aleyrodidarum" primary endosymbionts of the whitefly bemisia tabaci b and q biotypes."candidatus portiera aleyrodidarum" is the primary endosymbiont of whiteflies. we report two complete genome sequences of this bacterium from the worldwide invasive b and q biotypes of the whitefly bemisia tabaci. differences in the two genome sequences may add insights into the complex differences in the biology of both biotypes.201323315735
localization, concentration, and transmission efficiency of banana bunchy top virus in four asexual lineages of pentalonia aphids.banana bunchy top virus (bbtv) is the most destructive pathogenic virus of banana plants worldwide. the virus is transmitted in a circulative non-propagative manner by the banana aphid, pentalonia nigronervosa coquerel. in this work, we examined the localization, accumulation, and transmission efficiency of bbtv in four laboratory-established lineages of pentalonia aphids derived from four different host plants: taro (colocasia esculenta), heliconia (heliconia spp.), red ginger (alpinia purpurat ...201323435241
genomic analysis of the regulatory elements and links with intrinsic dna structural properties in the shrunken genome of buchnera.buchnera aphidicola is an obligate symbiotic bacterium, associated with most of the aphididae, whose genome has drastically shrunk during intracellular evolution. gene regulation in buchnera has been a matter of controversy in recent years as the combination of genomic information with the experimental results has been contradictory, refuting or arguing in favour of a functional and responsive transcription regulation in buchnera.the goal of this study was to describe the gene transcription regu ...201323375088
comparative genomics of blattabacterium cuenoti: the frozen legacy of an ancient endosymbiont genome.many insect species have established long-term symbiotic relationships with intracellular bacteria. symbiosis with bacteria has provided insects with novel ecological capabilities, which have allowed them colonize previously unexplored niches. despite its importance to the understanding of the emergence of biological complexity, the evolution of symbiotic relationships remains hitherto a mystery in evolutionary biology. in this study, we contribute to the investigation of the evolutionary leaps ...201323355305
phage loss and the breakdown of a defensive symbiosis in aphids.terrestrial arthropods are often infected with heritable bacterial symbionts, which may themselves be infected by bacteriophages. however, what role, if any, bacteriophages play in the regulation and maintenance of insect-bacteria symbioses is largely unknown. infection of the aphid acyrthosiphon pisum by the bacterial symbiont hamiltonella defensa confers protection against parasitoid wasps, but only when h. defensa is itself infected by the phage a. pisum secondary endosymbiont (apse). here, w ...201323193123
detection of genomic idiosyncrasies using fuzzy phylogenetic profiles.phylogenetic profiles express the presence or absence of genes and their homologs across a number of reference genomes. they have emerged as an elegant representation framework for comparative genomics and have been used for the genome-wide inference and discovery of functionally linked genes or metabolic pathways. as the number of reference genomes grows, there is an acute need for faster and more accurate methods for phylogenetic profile analysis with increased performance in speed and quality ...201323341912
relationship between water soluble carbohydrate content, aphid endosymbionts and clonal performance of sitobion avenae on cocksfoot cultivars.aphids feed on plant phloem sap, rich in sugars but poor in essential amino acids. however, sugars cause osmotic regulation problems for aphids, which they overcome by hydrolysing the sugars in their gut and polymerising the hydrolysis products into oligosaccharides, excreted with honeydew. aphids harbour primary bacterial endosymbionts, which supply them with essential amino acids necessary for survival. they also harbour secondary (facultative) endosymbionts (sfs), some of which have a positiv ...201323342134
transcriptome of dickeya dadantii infecting acyrthosiphon pisum reveals a strong defense against antimicrobial peptides.the plant pathogenic bacterium dickeya dadantii has recently been shown to be able to kill the aphid acyrthosiphon pisum. while the factors required to cause plant disease are now well characterized, those required for insect pathogeny remain mostly unknown. to identify these factors, we analyzed the transcriptome of the bacteria isolated from infected aphids. more than 150 genes were upregulated and 300 downregulated more than 5-fold at 3 days post infection. no homologue to known toxin genes c ...201323342088
aphids evolved novel secreted proteins for symbiosis with bacterial endosymbiont.aphids evolved novel cells, called bacteriocytes, that differentiate specifically to harbour the obligatory mutualistic endosymbiotic bacteria buchnera aphidicola. the genome of the host aphid acyrthosiphon pisum contains many orphan genes that display no similarity with genes found in other sequenced organisms, prompting us to hypothesize that some of these orphan genes are related to lineage-specific traits, such as symbiosis. we conducted deep sequencing of bacteriocytes mrna followed by whol ...201323173201
surveying the microbiome of ants: comparing 454 pyrosequencing with traditional methods to uncover bacterial diversity.we are only beginning to understand the depth and breadth of microbial associations across the eukaryotic tree of life. reliably assessing bacterial diversity is a key challenge, and next-generation sequencing approaches are facilitating this endeavor. in this study, we used 16s rrna amplicon pyrosequencing to survey microbial diversity in ants. we compared 454 libraries with sanger-sequenced clone libraries as well as cultivation of live bacteria. pyrosequencing yielded 95,656 bacterial 16s rrn ...201323124239
statistics for approximate gene clusters.genes occurring co-localized in multiple genomes can be strong indicators for either functional constraints on the genome organization or remnant ancestral gene order. the computational detection of these patterns, which are usually referred to as gene clusters, has become increasingly sensitive over the past decade. the most powerful approaches allow for various types of imperfect cluster conservation: cluster locations may be internally rearranged. the individual cluster locations may contain ...201324564620
the embedding problem for markov models of nucleotide substitution.continuous-time markov processes are often used to model the complex natural phenomenon of sequence evolution. to make the process of sequence evolution tractable, simplifying assumptions are often made about the sequence properties and the underlying process. the validity of one such assumption, time-homogeneity, has never been explored. violations of this assumption can be found by identifying non-embeddability. a process is non-embeddable if it can not be embedded in a continuous time-homogen ...201323935949
identification of novel adhesins of m. tuberculosis h37rv using integrated approach of multiple computational algorithms and experimental analysis.pathogenic bacteria interacting with eukaryotic host express adhesins on their surface. these adhesins aid in bacterial attachment to the host cell receptors during colonization. a few adhesins such as heparin binding hemagglutinin adhesin (hbha), apa, malate synthase of m. tuberculosis have been identified using specific experimental interaction models based on the biological knowledge of the pathogen. in the present work, we carried out computational screening for adhesins of m. tuberculosis. ...201323922800
comparative analysis of genome sequences from four strains of the buchnera aphidicola mp endosymbion of the green peach aphid, myzus persicae.myzus persicae, the green peach aphid, is a polyphagous herbivore that feeds from hundreds of species of mostly dicot crop plants. like other phloem-feeding aphids, m. persicae rely on the endosymbiotic bacterium, buchnera aphidicola (buchnera mp), for biosynthesis of essential amino acids and other nutrients that are not sufficiently abundant in their phloem sap diet. tobacco-specialized m. persicae are typically red and somewhat distinct from other lineages of this species. to determine whethe ...201324365332
lack of evidence for an interaction between buchnera groel and banana bunchy top virus (nanoviridae).circulative plant viruses such as luteovirids and geminiviruses have been shown to bind to groel proteins produced by endosymbiotic bacteria harboured within hemipteran vectors. these interactions seem to prevent the degradation of the viral particles in the aphid's haemocoel. similarly to luteovirids and geminiviruses, banana bunchy top virus (bbtv), a member of the nanoviridae family, is transmitted in a persistent, circulative manner and can be detected in the haemolymph of the aphid vector, ...201323816604
reconstructing the phylogeny of aphids (hemiptera: aphididae) using dna of the obligate symbiont buchnera aphidicola.reliable phylogenetic reconstruction, as a framework for evolutionary inference, may be difficult to achieve in some groups of organisms. particularly for lineages that experienced rapid diversification, lack of sufficient information may lead to inconsistent and unstable results and a low degree of resolution. coincidentally, such rapidly diversifying taxa are often among the biologically most interesting groups. aphids provide such an example. due to rapid adaptive diversification, they featur ...201323542003
diversity of proteobacterial endosymbionts in hemlock woolly adelgid (adelges tsugae) (hemiptera: adelgidae) from its native and introduced range.knowledge of intraspecific variation in symbioses may aid in understanding the ecology of widespread insects in different parts of their range. we investigated bacterial symbionts of adelges tsugae, a pest of hemlocks in eastern north america introduced from asia. amplification, cloning, and sequencing of bacterial 16s rdna, in situ hybridizations, and electron microscopy revealed that a. tsugae harbours up to five bacterial phylotypes, according to population. three gammaproteobacteria species ...201323452267
gene family assignment-free comparative genomics.the comparison of relative gene orders between two genomes offers deep insights into functional correlations of genes and the evolutionary relationships between the corresponding organisms. methods for gene order analyses often require prior knowledge of homologies between all genes of the genomic dataset. since such information is hard to obtain, it is common to predict homologous groups based on sequence similarity. these hypothetical groups of homologous genes are called gene families.201223281826
vesiculation from pseudomonas aeruginosa under sos.bacterial infections can be aggravated by antibiotic treatment that induces sos response and vesiculation. this leads to a hypothesis concerning association of sos with vesiculation. to test it, we conducted multiple analyses of outer membrane vesicles (omvs) produced from the pseudomonas aeruginosa wild type in which sos is induced by ciprofloxacin and from the lexa noncleavable (lexan) strain in which sos is repressed. the levels of omv proteins, lipids, and cytotoxicity increased for both the ...201222448133
insights from genomic comparisons of genetically monomorphic bacterial pathogens.some of the most deadly bacterial diseases, including leprosy, anthrax and plague, are caused by bacterial lineages with extremely low levels of genetic diversity, the so-called 'genetically monomorphic bacteria'. it has only become possible to analyse the population genetics of such bacteria since the recent advent of high-throughput comparative genomics. the genomes of genetically monomorphic lineages contain very few polymorphic sites, which often reflect unambiguous clonal genealogies. some ...201222312053
dna replication and strand asymmetry in prokaryotic and mitochondrial genomes.different patterns of strand asymmetry have been documented in a variety of prokaryotic genomes as well as mitochondrial genomes. because different replication mechanisms often lead to different patterns of strand asymmetry, much can be learned of replication mechanisms by examining strand asymmetry. here i summarize the diverse patterns of strand asymmetry among different taxonomic groups to suggest that (1) the single-origin replication may not be universal among bacterial species as the endos ...201222942672
meta-analysis of general bacterial subclades in whole-genome phylogenies using tree topology profiling.in the last two decades, a large number of whole-genome phylogenies have been inferred to reconstruct the tree of life (tol). underlying data models range from gene or functionality content in species to phylogenetic gene family trees and multiple sequence alignments of concatenated protein sequences. diversity in data models together with the use of different tree reconstruction techniques, disruptive biological effects and the steadily increasing number of genomes have led to a huge diversity ...201222915837
composition and seasonal variation of rhipicephalus turanicus and rhipicephalus sanguineus bacterial communities.a 16s rrna gene approach, including 454 pyrosequencing and quantitative pcr (qpcr), was used to describe the bacterial community in rhipicephalus turanicus and to evaluate the dynamics of key bacterial tenants of adult ticks during the active questing season. the bacterial community structure of rh. turanicus was characterized by high dominance of coxiella and rickettsia and extremely low taxonomic diversity. parallel diagnostic pcr further revealed a novel coxiella species which was present and ...201222467507
comparing the similarity of different groups of bacteria to the human proteome.numerous aspects of the relationship between bacteria and human have been investigated. one aspect that has recently received attention is sequence overlap at the proteomic level. however, there has not yet been a study that comprehensively characterizes the level of sequence overlap between bacteria and human, especially as it relates to bacterial characteristics like pathogenicity, g-c content, and proteome size. in this study, we began by performing a general characterization of the range of ...201222558081
microbial lifestyle and genome signatures.microbes are known for their unique ability to adapt to varying lifestyle and environment, even to the extreme or adverse ones. the genomic architecture of a microbe may bear the signatures not only of its phylogenetic position, but also of the kind of lifestyle to which it is adapted. the present review aims to provide an account of the specific genome signatures observed in microbes acclimatized to distinct lifestyles or ecological niches. niche-specific signatures identified at different leve ...201223024607
decoding in candidatus riesia pediculicola, close to a minimal trna modification set?a comparative genomic analysis of the recently sequenced human body louse unicellular endosymbiont candidatus riesia pediculicola with a reduced genome (582 kb), revealed that it is the only known organism that might have lost all post-transcriptional base and ribose modifications of the trna body, retaining only modifications of the anticodon-stem-loop essential for mrna decoding. such a minimal trna modification set was not observed in other insect symbionts or in parasitic unicellular bacteri ...201223308034
selection-driven extinction dynamics for group ii introns in enterobacteriales.transposable elements (tes) are one of the major driving forces of genome evolution, raising the question of the long-term dynamics underlying their evolutionary success. some tes were proposed to evolve under a pattern of periodic extinctions-recolonizations, in which elements recurrently invade and quickly proliferate within their host genomes, then start to disappear until total extinction. depending on the model, te extinction is assumed to be driven by purifying selection against colonized ...201223251705
translation in giant viruses: a unique mixture of bacterial and eukaryotic termination schemes.mimivirus and megavirus are the best characterized representatives of an expanding new family of giant viruses infecting acanthamoeba. their most distinctive features, megabase-sized genomes carried in particles of size comparable to that of small bacteria, fill the gap between the viral and cellular worlds. these giant viruses are also uniquely equipped with genes coding for central components of the translation apparatus. the presence of those genes, thought to be hallmarks of cellular organis ...201223271980
hamap in 2013, new developments in the protein family classification and annotation system.hamap (high-quality automated and manual annotation of proteins-available at http://hamap.expasy.org/) is a system for the classification and annotation of protein sequences. it consists of a collection of manually curated family profiles for protein classification, and associated annotation rules that specify annotations that apply to family members. hamap was originally developed to support the manual curation of uniprotkb/swiss-prot records describing microbial proteins. here we describe new ...201223193261
hamap in 2013, new developments in the protein family classification and annotation system.hamap (high-quality automated and manual annotation of proteins-available at http://hamap.expasy.org/) is a system for the classification and annotation of protein sequences. it consists of a collection of manually curated family profiles for protein classification, and associated annotation rules that specify annotations that apply to family members. hamap was originally developed to support the manual curation of uniprotkb/swiss-prot records describing microbial proteins. here we describe new ...201223193261
rather than by direct acquisition via lateral gene transfer, ghf5 cellulases were passed on from early pratylenchidae to root-knot and cyst nematodes.plant parasitic nematodes are unusual metazoans as they are equipped with genes that allow for symbiont-independent degradation of plant cell walls. among the cell wall-degrading enzymes, glycoside hydrolase family 5 (ghf5) cellulases are relatively well characterized, especially for high impact parasites such as root-knot and cyst nematodes. interestingly, ancestors of extant nematodes most likely acquired these ghf5 cellulases from a prokaryote donor by one or multiple lateral gene transfer ev ...201223171084
bioinformatic approaches for functional annotation and pathway inference in metagenomics data.metagenomic approaches are increasingly recognized as a baseline for understanding the ecology and evolution of microbial ecosystems. the development of methods for pathway inference from metagenomics data is of paramount importance to link a phenotype to a cascade of events stemming from a series of connected sets of genes or proteins. biochemical and regulatory pathways have until recently been thought and modelled within one cell type, one organism, one species. this vision is being dramatica ...201223175748
expression of small rna in aphis gossypii and its potential role in the resistance interaction with melon.the regulatory role of small rnas (srnas) in various biological processes is an active area of investigation; however, there has been limited information available on the role of srnas in plant-insect interactions. this study was designed to identify srnas in cotton-melon aphid (aphis gossypii) during the vat-mediated resistance interaction with melon (cucumis melo).201223173035
a novel human-infection-derived bacterium provides insights into the evolutionary origins of mutualistic insect-bacterial symbioses.despite extensive study, little is known about the origins of the mutualistic bacterial endosymbionts that inhabit approximately 10% of the world's insects. in this study, we characterized a novel opportunistic human pathogen, designated "strain hs," and found that it is a close relative of the insect endosymbiont sodalis glossinidius. our results indicate that ancestral relatives of strain hs have served as progenitors for the independent descent of sodalis-allied endosymbionts found in several ...201223166503
knowing your friends: invertebrate innate immunity fosters beneficial bacterial symbioses.the innate immune system is present in all animals and is a crucial first line of defence against pathogens. however, animals also harbour large numbers of beneficial microorganisms that can be housed in the digestive tract, in specialized organs or on tissue surfaces. although invertebrates lack conventional antibody-based immunity, they are capable of eliminating pathogens and, perhaps more importantly, discriminating them from other microorganisms. this review examines the interactions betwee ...201223147708
water stress and aphid feeding differentially influence metabolite composition in arabidopsis thaliana (l.).little is known about how drought stress influences plant secondary metabolite accumulation and how this affects plant defense against different aphids. we therefore cultivated arabidopsis thaliana (l.) plants under well-watered, drought, and water-logged conditions. two aphid species were selected for this study: the generalist myzus persicae (sulzer) and the crucifer specialist brevicoryne brassicae (l.). metabolite concentrations in the phloem sap, which influence aphid growth, changed partic ...201223144921
long chain n-acyl homoserine lactone production by enterobacter sp. isolated from human tongue surfaces.we report the isolation of n-acyl homoserine lactone-producing enterobacter sp. isolate t1-1 from the posterior dorsal surfaces of the tongue of a healthy individual. spent supernatants extract from enterobacter sp. isolate t1-1 activated the biosensor agrobacterium tumefaciens ntl4(pzlr4), suggesting production of long chain ahls by these isolates. high resolution mass spectrometry analysis of these extracts confirmed that enterobacter sp. isolate t1-1 produced a long chain n-acyl homoserine la ...201223202161
comparative genomics of serratia spp.: two paths towards endosymbiotic life.symbiosis is a widespread phenomenon in nature, in which insects show a great number of these associations. buchnera aphidicola, the obligate endosymbiont of aphids, coexists in some species with another intracellular bacterium, serratia symbiotica. of particular interest is the case of the cedar aphid cinara cedri, where b. aphidicola bcc and s. symbiotica scc need each other to fulfil their symbiotic role with the insect. moreover, various features seem to indicate that s. symbiotica scc is cl ...201223077583
factors behind junk dna in bacteria.although bacterial genomes have been traditionally viewed as being very compact, with relatively low amounts of repetitive and non-coding dna, this view has dramatically changed in recent years. the increase of available complete bacterial genomes has revealed that many species present abundant repetitive dna (i.e., insertion sequences, prophages or paralogous genes) and that many of these sequences are not functional but can have evolutionary consequences as concerns the adaptation to specializ ...201224705080
whole genome sequencing of mutation accumulation lines reveals a low mutation rate in the social amoeba dictyostelium discoideum.spontaneous mutations play a central role in evolution. despite their importance, mutation rates are some of the most elusive parameters to measure in evolutionary biology. the combination of mutation accumulation (ma) experiments and whole-genome sequencing now makes it possible to estimate mutation rates by directly observing new mutations at the molecular level across the whole genome. we performed an ma experiment with the social amoeba dictyostelium discoideum and sequenced the genomes of t ...201223056439
drift-barrier hypothesis and mutation-rate evolution.mutation dictates the tempo and mode of evolution, and like all traits, the mutation rate is subject to evolutionary modification. here, we report refined estimates of the mutation rate for a prokaryote with an exceptionally small genome and for a unicellular eukaryote with a large genome. combined with prior results, these estimates provide the basis for a potentially unifying explanation for the wide range in mutation rates that exists among organisms. natural selection appears to reduce the m ...201223077252
multiscale modeling of metabolism and macromolecular synthesis in e. coli and its application to the evolution of codon usage.biological systems are inherently hierarchal and multiscale in time and space. a major challenge of systems biology is to describe biological systems as a computational model, which can be used to derive novel hypothesis and drive experiments leading to new knowledge. the constraint-based reconstruction and analysis approach has been successfully applied to metabolism and to the macromolecular synthesis machinery assembly. here, we present the first integrated stoichiometric multiscale model of ...201223029152
pyrosequencing-based analysis of the microbiome associated with the horn fly, haematobia irritans.the horn fly, haematobia irritans, is one of the most economically important pests of cattle. insecticides have been a major element of horn fly management programs. growing concerns with insecticide resistance, insecticide residues on farm products, and non-availability of new generation insecticides, are serious issues for the livestock industry. alternative horn fly control methods offer the promise to decrease the use of insecticides and reduce the amount of insecticide residues on livestock ...201223028533
deep sequencing of the transcriptomes of soybean aphid and associated endosymbionts.the soybean aphid has significantly impacted soybean production in the u.s. transcriptomic analyses were conducted for further insight into leads for potential novel management strategies.201222984624
ibdsite: a galaxy-interacting, integrative database for supporting inflammatory bowel disease high throughput data analysis.inflammatory bowel diseases (ibd) refer to a group of inflammatory conditions concerning colon and small intestine, which cause socially uncomfortable symptoms and often are associated with an increased risk of colon cancer. ibd are complex disorders, which rely on genetic susceptibility, environmental factors, deregulation of the immune system, and host relationship with commensal microbiota. the complexity of these pathologies makes difficult to clearly understand the mechanisms of their onset ...201223095257
identification and biochemical evidence of a medium-chain-length polyhydroxyalkanoate depolymerase in the bdellovibrio bacteriovorus predatory hydrolytic arsenal.the obligate predator bdellovibrio bacteriovorus hd100 shows a large set of proteases and other hydrolases as part of its hydrolytic arsenal needed for its predatory life cycle. we present genetic and biochemical evidence that open reading frame (orf) bd3709 of b. bacteriovorus hd100 encodes a novel medium-chain-length polyhydroxyalkanoate (mcl-pha) depolymerase (phaz(bd)). the primary structure of phaz(bd) suggests that this enzyme belongs to the α/β-hydrolase fold family and has a typical seri ...201222706067
exploration of the core metabolism of symbiotic bacteria.a large number of genome-scale metabolic networks is now available for many organisms, mostly bacteria. previous works on minimal gene sets, when analysing host-dependent bacteria, found small common sets of metabolic genes. when such analyses are restricted to bacteria with similar lifestyles, larger portions of metabolism are expected to be shared and their composition is worth investigating. here we report a comparative analysis of the small molecule metabolism of symbiotic bacteria, explorin ...201222938206
multipartite control of the dna translocase, mfd.atp-dependent nucleic acid helicases and translocases play essential roles in many aspects of dna and rna biology. in order to ensure that these proteins act only in specific contexts, their activity is often regulated by intramolecular contacts and interaction with partner proteins. we have studied the bacterial mfd protein, which is an atp-dependent dna translocase that relocates or displaces transcription ecs in a variety of cellular contexts. when bound to rnap, mfd exhibits robust atpase an ...201222904071
arsenophonus groel interacts with clcuv and is localized in midgut and salivary gland of whitefly b. tabaci.cotton leaf curl virus (clcuv) (gemininiviridae: begomovirus) is the causative agent of leaf curl disease in cotton plants (gossypium hirsutum). clcuv is exclusively transmitted by the whitefly species b. tabaci (gennadius) (hemiptera: alerodidae). b. tabaci contains several biotypes which harbor dissimilar bacterial endo-symbiotic community. it is reported that these bacterial endosymbionts produce a 63 kda chaperon groel protein which binds to geminivirus particles and protects them from rapid ...201222900008
making the most of "omics" for symbiosis research.omics, including genomics, proteomics, and metabolomics, enable us to explain symbioses in terms of the underlying molecules and their interactions. the central task is to transform molecular catalogs of genes, metabolites, etc., into a dynamic understanding of symbiosis function. we review four exemplars of omics studies that achieve this goal, through defined biological questions relating to metabolic integration and regulation of animal-microbial symbioses, the genetic autonomy of bacterial s ...201222983030
the cellular immune response of the pea aphid to foreign intrusion and symbiotic challenge.recent studies suggest that the pea aphid (acyrthosiphon pisum) has low immune defenses. however, its immune components are largely undescribed, and notably, extensive characterization of circulating cells has been missing. here, we report characterization of five cell categories in hemolymph of adults of the ll01 pea aphid clone, devoid of secondary symbionts (ss): prohemocytes, plasmatocytes, granulocytes, spherulocytes and wax cells. circulating lipid-filed wax cells are rare; they otherwise ...201222848726
endosymbiont tolerance and control within insect hosts.bacterial endosymbioses are very common in insects and can range from obligate to facultative as well as from mutualistic to pathogenic associations. several recent studies provide new insight into how endosymbionts manage to establish chronic infections of their hosts without being eliminated by the host immune system. endosymbiont tolerance may be achieved either by specific bacterial adaptations or by host measurements shielding bacteria from innate defense mechanisms. nevertheless, insect ho ...201226466544
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