| 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 ... | 2008 | 19425129 |
| go4genome: a prokaryotic phylogeny based on genome organization. | determining the phylogeny of closely related prokaryotes may fail in an analysis of rrna or a small set of sequences. whole-genome phylogeny utilizes the maximally available sample space. for a precise determination of genome similarity, two aspects have to be considered when developing an algorithm of whole-genome phylogeny: (1) gene order conservation is a more precise signal than gene content; and (2) when using sequence similarity, failures in identifying orthologues or the in situ replaceme ... | 2009 | 19436929 |
| edgar: a software framework for the comparative analysis of prokaryotic genomes. | the introduction of next generation sequencing approaches has caused a rapid increase in the number of completely sequenced genomes. as one result of this development, it is now feasible to analyze large groups of related genomes in a comparative approach. a main task in comparative genomics is the identification of orthologous genes in different genomes and the classification of genes as core genes or singletons. | 2009 | 19457249 |
| comparative genomics of the inca/c multidrug resistance plasmid family. | multidrug resistance (mdr) plasmids belonging to the inca/c plasmid family are widely distributed among salmonella and other enterobacterial isolates from agricultural sources and have, at least once, also been identified in a drug-resistant yersinia pestis isolate (ip275) from madagascar. here, we present the complete plasmid sequences of the inca/c reference plasmid pra1 (143,963 bp), isolated in 1971 from the fish pathogen aeromonas hydrophila, and of the cryptic inca/c plasmid prax (49,763 b ... | 2009 | 19482926 |
| fine-structured multi-scaling long-range correlations in completely sequenced genomes--features, origin, and classification. | the sequential organization of genomes, i.e. the relations between distant base pairs and regions within sequences, and its connection to the three-dimensional organization of genomes is still a largely unresolved problem. long-range power-law correlations were found using correlation analysis on almost the entire observable scale of 132 completely sequenced chromosomes of 0.5 x 10(6) to 3.0 x 10(7) bp from archaea, bacteria, arabidopsis thaliana, saccharomyces cerevisiae, schizosaccharomyces po ... | 2009 | 19533117 |
| 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. | 2009 | 19534742 |
| 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 ... | 2009 | 19542349 |
| bioinformatic comparison of bacterial secretomes. | the rapid increasing number of completed bacterial genomes provides a good opportunity to compare their proteomes. this study was undertaken to specifically compare and contrast their secretomes-the fraction of the proteome with predicted n-terminal signal sequences, both type i and type ii. a total of 176 theoretical bacterial proteomes were examined using the exprot program. compared with the gram-positives, the gram-negative bacteria were found, on average, to contain a larger number of poten ... | 2009 | 19591790 |
| significant bias against the aca triplet in the tmrna sequence of escherichia coli k-12. | the toxin mazf in escherichia coli cleaves single-stranded rnas specifically at aca sequences. mazf overexpression virtually eliminates all cellular mrnas to completely block protein synthesis. however, protein synthesis can continue on an mrna that is devoid of aca triplets. the finding that ribosomal rnas remain intact in the face of complete translation arrest suggested a purpose for such preservation. we therefore examined the sequences of all transcribed rnas to determine if there was any s ... | 2009 | 19633073 |
| comparative sequence analysis of mycobacterium leprae and the new leprosy-causing mycobacterium lepromatosis. | mycobacterium lepromatosis is a newly discovered leprosy-causing organism. preliminary phylogenetic analysis of its 16s rrna gene and a few other gene segments revealed significant divergence from mycobacterium leprae, a well-known cause of leprosy, that justifies the status of m. lepromatosis as a new species. in this study we analyzed the sequences of 20 genes and pseudogenes (22,814 nucleotides). overall, the level of matching of these sequences with m. leprae sequences was 90.9%, which subst ... | 2009 | 19633074 |
| whole-genome analyses reveal genetic instability of acetobacter pasteurianus. | acetobacter species have been used for brewing traditional vinegar and are known to have genetic instability. to clarify the mutability, acetobacter pasteurianus nbrc 3283, which forms a multi-phenotype cell complex, was subjected to genome dna sequencing. the genome analysis revealed that there are more than 280 transposons and five genes with hyper-mutable tandem repeats as common features in the genome consisting of a 2.9-mb chromosome and six plasmids. there were three single nucleotide muta ... | 2009 | 19638423 |
| 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. | 2009 | 19691844 |
| implications of high level pseudogene transcription in mycobacterium leprae. | the mycobacterium leprae genome has less than 50% coding capacity and 1,133 pseudogenes. preliminary evidence suggests that some pseudogenes are expressed. therefore, defining pseudogene transcriptional and translational potentials of this genome should increase our understanding of their impact on m. leprae physiology. | 2009 | 19706172 |
| convergent evolution of metabolic roles in bacterial co-symbionts of insects. | a strictly host-dependent lifestyle has profound evolutionary consequences for bacterial genomes. most prominent is a sometimes-dramatic amount of gene loss and genome reduction. recently, highly reduced genomes from the co-resident intracellular symbionts of sharpshooters were shown to exhibit a striking level of metabolic interdependence. one symbiont, called sulcia muelleri (bacteroidetes), can produce eight of the 10 essential amino acids, despite having a genome of only 245 kb. the other, b ... | 2009 | 19706397 |
| 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 ... | 2010 | 19728837 |
| prevalence of cardinium bacteria in planthoppers and spider mites and taxonomic revision of "candidatus cardinium hertigii" based on detection of a new cardinium group from biting midges. | cardinium bacteria, members of the phylum cytophaga-flavobacterium-bacteroides (cfb), are intracellular bacteria in arthropods that are capable of inducing reproductive abnormalities in their hosts, which include parasitic wasps, mites, and spiders. a high frequency of cardinium infection was detected in planthoppers (27 out of 57 species were infected). a high frequency of cardinium infection was also found in spider mites (9 out of 22 species were infected). frequencies of double infection by ... | 2009 | 19734338 |
| the olive fly endosymbiont, "candidatus erwinia dacicola," switches from an intracellular existence to an extracellular existence during host insect development. | as polyphagous, holometabolous insects, tephritid fruit flies (diptera: tephritidae) provide a unique habitat for endosymbiotic bacteria, especially those microbes associated with the digestive system. here we examine the endosymbiont of the olive fly [bactrocera oleae (rossi) (diptera: tephritidae)], a tephritid of great economic importance. "candidatus erwinia dacicola" was found in the digestive systems of all life stages of wild olive flies from the southwestern united states. pcr and micros ... | 2009 | 19767463 |
| a strain of the bacterial symbiont regiella insecticola protects aphids against parasitoids. | aphids commonly harbour facultative bacterial endosymbionts and may benefit from their presence through increased resistance to parasitoids. this has been demonstrated for hamiltonella defensa and serratia symbiotica, while a third common endosymbiont, regiella insecticola, did not provide such protection. however, this symbiont was recently detected in a highly resistant clone of the peach-potato aphid, myzus persicae, from australia. to test if resistance was indeed conferred by the endosymbio ... | 2010 | 19776066 |
| a strain of the bacterial symbiont regiella insecticola protects aphids against parasitoids. | aphids commonly harbour facultative bacterial endosymbionts and may benefit from their presence through increased resistance to parasitoids. this has been demonstrated for hamiltonella defensa and serratia symbiotica, while a third common endosymbiont, regiella insecticola, did not provide such protection. however, this symbiont was recently detected in a highly resistant clone of the peach-potato aphid, myzus persicae, from australia. to test if resistance was indeed conferred by the endosymbio ... | 2010 | 19776066 |
| 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. | 2009 | 19783752 |
| 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 ... | 2009 | 19791603 |
| 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 ... | 2009 | 19805299 |
| 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 ... | 2010 | 19860485 |
| nitrogen recycling and nutritional provisioning by blattabacterium, the cockroach endosymbiont. | nitrogen acquisition and assimilation is a primary concern of insects feeding on diets largely composed of plant material. reclaiming nitrogen from waste products provides a rich reserve for this limited resource, provided that recycling mechanisms are in place. cockroaches, unlike most terrestrial insects, excrete waste nitrogen within their fat bodies as uric acids, postulated to be a supplement when dietary nitrogen is limited. the fat bodies of most cockroaches are inhabited by blattabacteri ... | 2009 | 19880743 |
| short-term signatures of evolutionary change in the salmonella enterica serovar typhimurium 14028 genome. | salmonella enterica serovar typhimurium is a gram-negative pathogen that causes gastroenteritis in humans and a typhoid-like disease in mice and is often used as a model for the disease promoted by the human-adapted s. enterica serovar typhi. despite its health importance, the only s. typhimurium strain for which the complete genomic sequence has been determined is the avirulent lt2 strain, which is extensively used in genetic and physiologic studies. here, we report the complete genomic sequenc ... | 2010 | 19897643 |
| short-term signatures of evolutionary change in the salmonella enterica serovar typhimurium 14028 genome. | salmonella enterica serovar typhimurium is a gram-negative pathogen that causes gastroenteritis in humans and a typhoid-like disease in mice and is often used as a model for the disease promoted by the human-adapted s. enterica serovar typhi. despite its health importance, the only s. typhimurium strain for which the complete genomic sequence has been determined is the avirulent lt2 strain, which is extensively used in genetic and physiologic studies. here, we report the complete genomic sequenc ... | 2010 | 19897643 |
| 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 ... | 2009 | 19909925 |
| evolutionary convergence and nitrogen metabolism in blattabacterium strain bge, primary endosymbiont of the cockroach blattella germanica. | bacterial endosymbionts of insects play a central role in upgrading the diet of their hosts. in certain cases, such as aphids and tsetse flies, endosymbionts complement the metabolic capacity of hosts living on nutrient-deficient diets, while the bacteria harbored by omnivorous carpenter ants are involved in nitrogen recycling. in this study, we describe the genome sequence and inferred metabolism of blattabacterium strain bge, the primary flavobacteria endosymbiont of the omnivorous german cock ... | 2009 | 19911043 |
| sense and sensibility: flagellum-mediated gene regulation. | the flagellum, a rotary engine required for motility in many bacteria, plays key roles in gene expression. it has been known for some time that flagellar substructures serve as checkpoints that coordinate flagellar gene expression with assembly. less well understood, however, are other more global effects on gene expression. for instance, the flagellum acts as a 'wetness' sensor in salmonella typhimurium, and as a mechanosensor in other bacteria. additionally, it has been implicated in a variety ... | 2010 | 19942438 |
| sense and sensibility: flagellum-mediated gene regulation. | the flagellum, a rotary engine required for motility in many bacteria, plays key roles in gene expression. it has been known for some time that flagellar substructures serve as checkpoints that coordinate flagellar gene expression with assembly. less well understood, however, are other more global effects on gene expression. for instance, the flagellum acts as a 'wetness' sensor in salmonella typhimurium, and as a mechanosensor in other bacteria. additionally, it has been implicated in a variety ... | 2010 | 19942438 |
| an evaluation of minimal cellular functions to sustain a bacterial cell. | both computational and experimental approaches have been used to determine the minimal gene set required to sustain a bacterial cell. such studies have provided clues to the minimal cellular-function set needed for life. we evaluate a minimal cellular-function set directly, instead of a geneset. | 2009 | 19943949 |
| cohesion group approach for evolutionary analysis of aspartokinase, an enzyme that feeds a branched network of many biochemical pathways. | aspartokinase (ask) exists within a variable network that supports the synthesis of 9 amino acids and a number of other important metabolites. lysine, isoleucine, aromatic amino acids, and dipicolinate may arise from the ask network or from alternative pathways. ask proteins were subjected to cohesion group analysis, a methodology that sorts a given protein assemblage into groups in which evolutionary continuity is assured. two subhomology divisions, ask(alpha) and ask(beta), have been recognize ... | 2009 | 19946135 |
| examination of genome homogeneity in prokaryotes using genomic signatures. | dna word frequencies, normalized for genomic at content, are remarkably stable within prokaryotic genomes and are therefore said to reflect a "genomic signature." the genomic signatures can be used to phylogenetically classify organisms from arbitrary sampled dna. genomic signatures can also be used to search for horizontally transferred dna or dna regions subjected to special selection forces. thus, the stability of the genomic signature can be used as a measure of genomic homogeneity. the fact ... | 2009 | 19956556 |
| 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 ... | 2010 | 19962988 |
| the complete genome sequence of xanthomonas albilineans provides new insights into the reductive genome evolution of the xylem-limited xanthomonadaceae. | the xanthomonadaceae family contains two xylem-limited plant pathogenic bacterial species, xanthomonas albilineans and xylella fastidiosa. x. fastidiosa was the first completely sequenced plant pathogen. it is insect-vectored, has a reduced genome and does not possess hrp genes which encode a type iii secretion system found in most plant pathogenic bacteria. x. fastidiosa was excluded from the xanthomonas group based on phylogenetic analyses with rrna sequences. | 2009 | 20017926 |
| modal codon usage: assessing the typical codon usage of a genome. | most genomes are heterogeneous in codon usage, so a codon usage study should start by defining the codon usage that is typical to the genome. although this is commonly taken to be the genomewide average, we propose that the mode-the codon usage that matches the most genes-provides a more useful approximation of the typical codon usage of a genome. we provide a method for estimating the modal codon usage, which utilizes a continuous approximation to the number of matching genes and a simplex opti ... | 2010 | 20018979 |
| modal codon usage: assessing the typical codon usage of a genome. | most genomes are heterogeneous in codon usage, so a codon usage study should start by defining the codon usage that is typical to the genome. although this is commonly taken to be the genomewide average, we propose that the mode-the codon usage that matches the most genes-provides a more useful approximation of the typical codon usage of a genome. we provide a method for estimating the modal codon usage, which utilizes a continuous approximation to the number of matching genes and a simplex opti ... | 2010 | 20018979 |
| indirect effects of temperature on stink bug fitness, via maintenance of gut-associated symbionts. | impacts of climate change on organisms are already apparent, with effects ranging from the individual to ecosystem scales. for organisms engaged in mutualisms, climate may affect population performance directly or indirectly through mediated effects on their mutualists. we tested this hypothesis for two stink bugs, acrosternum hilare and murgantia histrionica, and their gut-associated symbionts. we reared these species at two constant temperatures, 25 and 30 degrees c, and monitored population d ... | 2010 | 20023083 |
| indirect effects of temperature on stink bug fitness, via maintenance of gut-associated symbionts. | impacts of climate change on organisms are already apparent, with effects ranging from the individual to ecosystem scales. for organisms engaged in mutualisms, climate may affect population performance directly or indirectly through mediated effects on their mutualists. we tested this hypothesis for two stink bugs, acrosternum hilare and murgantia histrionica, and their gut-associated symbionts. we reared these species at two constant temperatures, 25 and 30 degrees c, and monitored population d ... | 2010 | 20023083 |
| the bacterial essence of tiny symbiont genomes. | bacterial genomes vary in size over two orders of magnitude. the mycoplasma genitalium genome has historically defined the extreme small end of this spectrum, and has therefore heavily informed theoretical and experimental work aimed at determining the minimal gene content necessary to support cellular life. recent genomic data from insect symbionts have revealed bacterial genomes that are incredibly small-two to four times smaller than m. genitalium-and these tiny genomes have raised questions ... | 2010 | 20044299 |
| conserved symbiotic plasmid dna sequences in the multireplicon pangenomic structure of rhizobium etli. | strains of the same bacterial species often show considerable genomic variation. to examine the extent of such variation in rhizobium etli, the complete genome sequence of r. etli ciat652 and the partial genomic sequences of six additional r. etli strains having different geographical origins were determined. the sequences were compared with each other and with the previously reported genome sequence of r. etli cfn42. dna sequences common to all strains constituted the greater part of these geno ... | 2010 | 20048063 |
| predicting the pathway involved in post-translational modification of elongation factor p in a subset of bacterial species. | background: the bacterial elongation factor p (ef-p) is strictly conserved in bacteria and essential for protein synthesis. it is homologous to the eukaryotic translation initiation factor 5a (eif5a). a highly conserved eif5a lysine is modified into an unusual amino acid derived from spermidine, hypusine. hypusine is absolutely required for eif5a's role in translation in saccharomyces cerevisiae. the homologous lysine of ef-p is also modified to a spermidine derivative in escherichia coli. howev ... | 2010 | 20070887 |
| when bacteria lose a single dna base, aphids suffer. | | 2007 | 20076671 |
| 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 ... | 2010 | 20080750 |
| 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 ... | 2010 | 20080750 |
| 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 ... | 2010 | 20083641 |
| [co-metabolic activity of aphid acyrthosiphon pisum and symbiotic bacterium buchnera aphidicola str. aps]. | | 2009 | 20088388 |
| the systemic imprint of growth and its uses in ecological (meta)genomics. | microbial minimal generation times range from a few minutes to several weeks. they are evolutionarily determined by variables such as environment stability, nutrient availability, and community diversity. selection for fast growth adaptively imprints genomes, resulting in gene amplification, adapted chromosomal organization, and biased codon usage. we found that these growth-related traits in 214 species of bacteria and archaea are highly correlated, suggesting they all result from growth optimi ... | 2010 | 20090831 |
| homopolymeric tracts represent a general regulatory mechanism in prokaryotes. | while, traditionally, regulation of gene expression can be grouped into transcriptional, translational, and post-translational mechanisms, some mechanisms of rapid genetic variation can also contribute to regulation of gene expression, e.g., phase variation. | 2010 | 20144225 |
| significant deviations in the configurations of homologous tandem repeats in prokaryotic genomes. | we explored the possibilities of whole-genome duplication (wgd) in prokaryotic species, where we performed statistical analyses of the configurations of the central angles between homologous tandem repeats (trs) on the circular chromosomes. at first, we detected trs on their chromosomes and identified equivalent tandem repeat pairs (etrps); here, an etrp is defined as a pair of tandem repeats sequentially similar to each other. then we carried out statistical analyses of the central angle distri ... | 2009 | 20172489 |
| significant deviations in the configurations of homologous tandem repeats in prokaryotic genomes. | we explored the possibilities of whole-genome duplication (wgd) in prokaryotic species, where we performed statistical analyses of the configurations of the central angles between homologous tandem repeats (trs) on the circular chromosomes. at first, we detected trs on their chromosomes and identified equivalent tandem repeat pairs (etrps); here, an etrp is defined as a pair of tandem repeats sequentially similar to each other. then we carried out statistical analyses of the central angle distri ... | 2009 | 20172489 |
| 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 ... | 2010 | 20186266 |
| 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 ... | 2010 | 20195500 |
| 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. | 2010 | 20236492 |
| onion thrips, thrips tabaci, have gut bacteria that are closely related to the symbionts of the western flower thrips, frankliniella occidentalis. | it has been shown that many insects have enterobacteriaceae bacteria in their gut system. the western flower thrips, frankliniella occidentalis pergande [thysanoptera: thripidae], has a symbiotic relation with erwinia species gut bacteria. to determine if other thripidae species have similar bacterial symbionts, the onion thrips, thrips tabaci, was studied because, like f. occidentalis, it is phytophagous. contrary to f. occidentalis, t. tabaci is endemic in europe and biotypes have been describ ... | 2008 | 20298113 |
| a metaproteomic analysis of the human salivary microbiota by three-dimensional peptide fractionation and tandem mass spectrometry. | metagenomics uses gene expression patterns to understand the taxonomy and metabolic activities of microbial communities. metaproteomics applies the same approach to community proteomes. previously, we used a novel three-dimensional peptide separation method to identify over 2000 salivary proteins. this study used those data to carry out the first metaproteomic analysis of the human salivary microbiota. the metagenomic software megan generated a phylogenetic tree, which was checked against the hu ... | 2010 | 20331792 |
| multiple interaction domains in ftsl, a protein component of the widely conserved bacterial ftslbq cell division complex. | a bioinformatic analysis of nearly 400 genomes indicates that the overwhelming majority of bacteria possess homologs of the escherichia coli proteins ftsl, ftsb, and ftsq, three proteins essential for cell division in that bacterium. these three bitopic membrane proteins form a subcomplex in vivo, independent of the other cell division proteins. here we analyze the domains of e. coli ftsl that are involved in the interaction with other cell division proteins and important for the assembly of the ... | 2010 | 20363951 |
| primary gut symbiont and secondary, sodalis-allied symbiont of the scutellerid stinkbug cantao ocellatus. | symbiotic associations with midgut bacteria have been commonly found in diverse phytophagous heteropteran groups, where microbiological characterization of the symbiotic bacteria has been restricted to the stinkbug families acanthosomatidae, plataspidae, pentatomidae, alydidae, and pyrrhocoridae. here we investigated the midgut bacterial symbiont of cantao ocellatus, a stinkbug of the family scutelleridae. a specific gammaproteobacterium was consistently identified from the insects of different ... | 2010 | 20400564 |
| chromosome stability and gene loss in cockroach endosymbionts. | insect endosymbiont genomes reflect massive gene loss. two blattabacterium genomes display colinearity and similar gene contents, despite high orthologous gene divergence, reflecting over 140 million years of independent evolution in separate cockroach lineages. we speculate that distant homologs may replace the functions of some eliminated genes through broadened substrate specificity. | 2010 | 20418442 |
| fluorescence in situ hybridization method using a peptide nucleic acid probe for identification of salmonella spp. in a broad spectrum of samples. | a fluorescence in situ hybridization (fish) method for the rapid detection of salmonella spp. using a novel peptide nucleic acid (pna) probe was developed. the probe theoretical specificity and sensitivity were both 100%. the pna-fish method was optimized, and laboratory testing on representative strains from the salmonella genus subspecies and several related bacterial species confirmed the predicted theoretical values of specificity and sensitivity. the pna-fish method has been successfully ad ... | 2010 | 20453122 |
| 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 ... | 2010 | 20482654 |
| 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 ... | 2010 | 20482655 |
| regulation of high-affinity iron acquisition homologues in the tsetse fly symbiont sodalis glossinidius. | sodalis glossinidius is a facultative intracellular bacterium that is a secondary symbiont of the tsetse fly (diptera: glossinidae). since studies with other facultative intracellular bacteria have shown that high-affinity iron acquisition genes are upregulated in vivo, we investigated the regulation of several sodalis genes that encode putative iron acquisition systems. these genes, sg1538 (hemt) and sg1516 (sita), are homologous to genes encoding periplasmic heme and iron/manganese transporter ... | 2010 | 20494987 |
| 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 ... | 2010 | 20568636 |
| 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( ... | 2010 | 20610410 |
| 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 ... | 2010 | 20614011 |
| host-microbial symbiosis in the vertebrate gastrointestinal tract and the lactobacillus reuteri paradigm. | vertebrates engage in symbiotic associations with vast and complex microbial communities that colonize their gastrointestinal tracts. recent advances have provided mechanistic insight into the important contributions of the gut microbiome to vertebrate biology, but questions remain about the evolutionary processes that have shaped symbiotic interactions in the gut and the consequences that arise for both the microbes and the host. here we discuss the biological principles that underlie microbial ... | 2011 | 20615995 |
| host-microbial symbiosis in the vertebrate gastrointestinal tract and the lactobacillus reuteri paradigm. | vertebrates engage in symbiotic associations with vast and complex microbial communities that colonize their gastrointestinal tracts. recent advances have provided mechanistic insight into the important contributions of the gut microbiome to vertebrate biology, but questions remain about the evolutionary processes that have shaped symbiotic interactions in the gut and the consequences that arise for both the microbes and the host. here we discuss the biological principles that underlie microbial ... | 2011 | 20615995 |
| mobile genetic element proliferation and gene inactivation impact over the genome structure and metabolic capabilities of sodalis glossinidius, the secondary endosymbiont of tsetse flies. | genome reduction is a common evolutionary process in symbiotic and pathogenic bacteria. this process has been extensively characterized in bacterial endosymbionts of insects, where primary mutualistic bacteria represent the most extreme cases of genome reduction consequence of a massive process of gene inactivation and loss during their evolution from free-living ancestors. sodalis glossinidius, the secondary endosymbiont of tsetse flies, contains one of the few complete genomes of bacteria at t ... | 2010 | 20649993 |
| chaperonin-dependent accelerated substitution rates in prokaryotes. | many proteins require the assistance of molecular chaperones in order to fold efficiently. chaperones are known to mask the effects of mutations that induce misfolding because they can compensate for the deficiency in spontaneous folding. one of the best studied chaperones is the eubacterial groel/groes system. in escherichia coli, three classes of proteins have been distinguished based on their degree of dependency on groel for folding: 1) those that do not require groel, 2) those that require ... | 2010 | 20660111 |
| 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 ... | 2011 | 20667882 |
| 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 ... | 2011 | 20667882 |
| characterizing the native codon usages of a genome: an axis projection approach. | codon usage can provide insights into the nature of the genes in a genome. genes that are "native" to a genome (have not been recently acquired by horizontal transfer) range in codon usage from a low-bias "typical" usage to a more biased "high-expression" usage characteristic of genes encoding abundant proteins. genes that differ from these native codon usages are candidates for foreign genes that have been recently acquired by horizontal gene transfer. in this study, we present a method for cha ... | 2011 | 20679093 |
| characterizing the native codon usages of a genome: an axis projection approach. | codon usage can provide insights into the nature of the genes in a genome. genes that are "native" to a genome (have not been recently acquired by horizontal transfer) range in codon usage from a low-bias "typical" usage to a more biased "high-expression" usage characteristic of genes encoding abundant proteins. genes that differ from these native codon usages are candidates for foreign genes that have been recently acquired by horizontal gene transfer. in this study, we present a method for cha ... | 2011 | 20679093 |
| genomic comparisons of brucella spp. and closely related bacteria using base compositional and proteome based methods. | classification of bacteria within the genus brucella has been difficult due in part to considerable genomic homogeneity between the different species and biovars, in spite of clear differences in phenotypes. therefore, many different methods have been used to assess brucella taxonomy. in the current work, we examine 32 sequenced genomes from genus brucella representing the six classical species, as well as more recently described species, using bioinformatical methods. comparisons were made at t ... | 2010 | 20707916 |
| aphid reproductive investment in response to mortality risks. | aphids are striking in their prodigious reproductive capacity and reliance on microbial endosymbionts, which provision their hosts with necessary amino acids and provide protection against parasites and heat stress. perhaps as a result of this bacterial dependence, aphids have limited immune function that may leave them vulnerable to bacterial pathogens. an alternative, non-immunological response that may be available to infected aphids is to increase reproduction, thereby ameliorating fitness l ... | 2010 | 20716370 |
| 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 ... | 2011 | 20719775 |
| 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 ... | 2011 | 20719775 |
| overoxidation of 2-cys peroxiredoxin in prokaryotes: cyanobacterial 2-cys peroxiredoxins sensitive to oxidative stress. | in eukaryotic organisms, hydrogen peroxide has a dual effect; it is potentially toxic for the cell but also has an important signaling activity. according to the previously proposed floodgate hypothesis, the signaling activity of hydrogen peroxide in eukaryotes requires a transient increase in its concentration, which is due to the inactivation by overoxidation of 2-cys peroxiredoxin (2-cys prx). sensitivity to overoxidation depends on the structural gglg and yf motifs present in eukaryotic 2-cy ... | 2010 | 20736168 |
| fitness and freezing: vector biology and human health. | microbes transmitted to mammals by arthropods contend with many factors that could impede survival. to survive, host fitness with infection must outweigh costs. in this issue of the jci, neelakanta et al. demonstrate that ticks infected with anaplasma phagocytophilum show enhanced fitness against freezing injury owing to induced expression of tick "antifreeze glycoprotein." this allows a. phagocytophilum to successfully propagate and survive to cause disease in nonnatural hosts, such as humans. ... | 2010 | 20739748 |
| genomic insights into bifidobacteria. | since the discovery in 1899 of bifidobacteria as numerically dominant microbes in the feces of breast-fed infants, there have been numerous studies addressing their role in modulating gut microflora as well as their other potential health benefits. because of this, they are frequently incorporated into foods as probiotic cultures. an understanding of their full interactions with intestinal microbes and the host is needed to scientifically validate any health benefits they may afford. recently, t ... | 2010 | 20805404 |
| reconstruction and flux-balance analysis of the plasmodium falciparum metabolic network. | genome-scale metabolic reconstructions can serve as important tools for hypothesis generation and high-throughput data integration. here, we present a metabolic network reconstruction and flux-balance analysis (fba) of plasmodium falciparum, the primary agent of malaria. the compartmentalized metabolic network accounts for 1001 reactions and 616 metabolites. enzyme-gene associations were established for 366 genes and 75% of all enzymatic reactions. compared with other microbes, the p. falciparum ... | 2010 | 20823846 |
| economical evolution: microbes reduce the synthetic cost of extracellular proteins. | protein evolution is not simply a race toward improved function. because organisms compete for limited resources, fitness is also affected by the relative economy of an organism's proteome. indeed, many abundant proteins contain relatively high percentages of amino acids that are metabolically less taxing for the cell to make, thus reducing cellular cost. however, not all abundant proteins are economical, and many economical proteins are not particularly abundant. here we examined protein compos ... | 2010 | 20824102 |
| 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 ... | 2010 | 20851962 |
| interspecific symbiont transfection confers a novel ecological trait to the recipient insect. | in japan, pea aphids acyrthosiphon pisum mainly feed on vetch and clover, and many aphid clones produce more progeny on vetch than on clover. in this context, particular genotypes of the facultative symbiont regiella insecticola enhance reproduction of infected pea aphids specifically on clover, thereby broadening the suitable food plant range of the insect. a species that is sympatric to a. pisum, vetch aphids megoura crassicauda, are commonly found on vetch but not on clover. laboratory rearin ... | 2010 | 20880856 |
| interspecific symbiont transfection confers a novel ecological trait to the recipient insect. | in japan, pea aphids acyrthosiphon pisum mainly feed on vetch and clover, and many aphid clones produce more progeny on vetch than on clover. in this context, particular genotypes of the facultative symbiont regiella insecticola enhance reproduction of infected pea aphids specifically on clover, thereby broadening the suitable food plant range of the insect. a species that is sympatric to a. pisum, vetch aphids megoura crassicauda, are commonly found on vetch but not on clover. laboratory rearin ... | 2010 | 20880856 |
| in silico prediction of human pathogenicity in the γ-proteobacteria. | although the majority of bacteria are innocuous or even beneficial for their host, others are highly infectious pathogens that can cause widespread and deadly diseases. when investigating the relationships between bacteria and other living organisms, it is therefore essential to be able to separate pathogenic organisms from non-pathogenic ones. using traditional experimental methods for this purpose can be very costly and time-consuming, and also uncertain since animal models are not always good ... | 2010 | 21048922 |
| 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. | 2010 | 21108805 |
| unprecedented loss of ammonia assimilation capability in a urease-encoding bacterial mutualist. | blochmannia are obligately intracellular bacterial mutualists of ants of the tribe camponotini. blochmannia perform key nutritional functions for the host, including synthesis of several essential amino acids. we used illumina technology to sequence the genome of blochmannia associated with camponotus vafer. | 2010 | 21126349 |
| 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 ... | 2010 | 21159868 |
| 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 ... | 2010 | 21159868 |
| the phylogeny of sodalis-like symbionts as reconstructed using surface-encoding loci. | phylogenetic analyses of 16s rrna support close relationships between the gammaproteobacteria sodalis glossinidius, a tsetse (diptera: glossinidae) symbiont, and bacteria infecting diverse insect orders. to further examine the evolutionary relationships of these sodalis-like symbionts, phylogenetic trees were constructed for a subset of putative surface-encoding genes (i.e. ompa, spr, slyb, rcsf, ycfm, and ompc). the ompa and ompc loci were used toward examining the intra- and interspecific dive ... | 2011 | 21251054 |
| strong strand composition bias in the genome of ehrlichia canis revealed by multiple methods. | genes located on the two replicating strands are found to have two separate base/codon usages in ehrlichia canis genome. although strand-specific codon usage is not the first observation, for the first time we have applied multiple methods to the analysis of strand composition bias. by combining multiple methods, comprehensive and interesting results are obtained. among three types of correspondence analysis (coa), absolute codon usages between genes on the two replicating strands are more disti ... | 2010 | 21253460 |
| massive genomic decay in serratia symbiotica, a recently evolved symbiont of aphids. | all vertically transmitted bacterial symbionts undergo a process of genome reduction over time, resulting in tiny, gene-dense genomes. comparison of genomes of ancient bacterial symbionts gives only limited information about the early stages in the transition from a free-living to symbiotic lifestyle because many changes become obscured over time. here, we present the genome sequence for the recently evolved aphid symbiont serratia symbiotica. the s. symbiotica genome exhibits several of the hal ... | 2011 | 21266540 |
| 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 ... | 2011 | 21282658 |
| 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 ... | 2011 | 21288878 |
| 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, ... | 2011 | 21336565 |
| the roles of no in microbial symbioses. | because of its unique chemical properties, nitric oxide (no) is a pluripotent signalling and effector molecule that is implicated in a variety of biological roles. although no is known to function in host innate immunity against pathogen invasion, its possible roles in microbial symbioses with animal and plant hosts remain relatively less well defined. in this review, we discuss the mechanisms by which bacteria sense and/or detoxify no. we then focus specifically on its roles in microbial symbio ... | 2011 | 21338463 |
| 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 ... | 2011 | 21346031 |
| the genome sequence of the leaf-cutter ant atta cephalotes reveals insights into its obligate symbiotic lifestyle. | leaf-cutter ants are one of the most important herbivorous insects in the neotropics, harvesting vast quantities of fresh leaf material. the ants use leaves to cultivate a fungus that serves as the colony's primary food source. this obligate ant-fungus mutualism is one of the few occurrences of farming by non-humans and likely facilitated the formation of their massive colonies. mature leaf-cutter ant colonies contain millions of workers ranging in size from small garden tenders to large soldier ... | 2011 | 21347285 |