Publications

new gammaproteobacteria associated with blood-feeding leeches and a broad phylogenetic analysis of leech endosymbionts.	many monophagous animals have coevolutionary relationships with bacteria that provide unavailable nutrients to the host. frequently, these microbial partners are vertically inherited and reside in specialized structures or tissues. here we report three new lineages of bacterial symbionts of blood-feeding leeches, one from the giant amazonian leech, haementeria ghilianii, and two others from placobdelloides species. these hosts each possess a different mycetome or esophageal organ morphology wher ...	2005	16151107
towards a genome-based taxonomy for prokaryotes.	the ranks higher than the species in the prokaryotic taxonomy are primarily designated based on phylogenetic analysis of the 16s rrna gene sequences, but no definite standards exist for the absolute relatedness (measured by 16s rrna or other means) between the ranks. accordingly, it remains unknown how comparable the ranks are between different organisms. to gain insights into this question, we studied the relationship between shared gene content and genetic relatedness for 175 fully sequenced s ...	2005	16159757
diversity in domain architectures of ser/thr kinases and their homologues in prokaryotes.	ser/thr/tyr kinases (styks) commonly found in eukaryotes have been recently reported in many bacterial species. recent studies elucidating their cellular functions have established their roles in bacterial growth and development. however functions of a large number of bacterial styks still remain elusive. the organisation of domains in a large dataset of bacterial styks has been investigated here in order to recognise variety in domain combinations which determine functions of bacterial styks.	2005	16171520
mathematical design of prokaryotic clone-based microarrays.	clone-based microarrays, on which each spot represents a random genomic fragment, are a good alternative to open reading frame-based microarrays, especially for microorganisms for which the complete genome sequence is not available. since the generation of a genomic dna library is a random process, it is beforehand uncertain which genes are represented. nevertheless, the genome coverage of such an array, which depends on different variables like the insert size and the number of clones in the li ...	2005	16191193
the players in a mutualistic symbiosis: insects, bacteria, viruses, and virulence genes.	aphids maintain mutualistic symbioses involving consortia of coinherited organisms. all possess a primary endosymbiont, buchnera, which compensates for dietary deficiencies; many also contain secondary symbionts, such as hamiltonella defensa, which confers defense against natural enemies. genome sequences of uncultivable secondary symbionts have been refractory to analysis due to the difficulties of isolating adequate dna samples. by amplifying dna from hemolymph of infected pea aphids, we obtai ...	2005	16195380
genetic analysis identifies a function for the quec (ybax) gene product at an initial step in the queuosine biosynthetic pathway in escherichia coli.	queuosine (q), one of the most complex modifications occurring at the wobble position of trnas with gun anticodons, is implicated in a number of biological activities, including accuracy of decoding, virulence, and cellular differentiation. despite these important implications, its biosynthetic pathway has remained unresolved. earlier, we observed that a naturally occurring strain of escherichia coli b105 lacked q modification in the trnas. in the present study, we developed a genetic screen to ...	2005	16199558
the subsystems approach to genome annotation and its use in the project to annotate 1000 genomes.	the release of the 1000th complete microbial genome will occur in the next two to three years. in anticipation of this milestone, the fellowship for interpretation of genomes (fig) launched the project to annotate 1000 genomes. the project is built around the principle that the key to improved accuracy in high-throughput annotation technology is to have experts annotate single subsystems over the complete collection of genomes, rather than having an annotation expert attempt to annotate all of t ...	2005	16214803
intra- and interspecific comparisons of bacterial diversity and community structure support coevolution of gut microbiota and termite host.	we investigated the bacterial gut microbiota from 32 colonies of wood-feeding termites, comprising four microcerotermes species (termitidae) and four reticulitermes species (rhinotermitidae), using terminal restriction fragment length polymorphism analysis and clonal analysis of 16s rrna. the obtained molecular community profiles were compared statistically between individuals, colonies, locations, and species of termites. both analyses revealed that the bacterial community structure was remarka ...	2005	16269686
paenibacillus polymyxa invades plant roots and forms biofilms.	paenibacillus polymyxa is a plant growth-promoting rhizobacterium with a broad host range, but so far the use of this organism as a biocontrol agent has not been very efficient. in previous work we showed that this bacterium protects arabidopsis thaliana against pathogens and abiotic stress (s. timmusk and e. g. h. wagner, mol. plant-microbe interact. 12:951-959, 1999; s. timmusk, p. van west, n. a. r. gow, and e. g. h. wagner, p. 1-28, in mechanism of action of the plant growth promoting bacter ...	2005	16269771
exploration of phylogenetic data using a global sequence analysis method.	molecular phylogenetic methods are based on alignments of nucleic or peptidic sequences. the tremendous increase in molecular data permits phylogenetic analyses of very long sequences and of many species, but also requires methods to help manage large datasets.	2005	16280081
preferential attachment in the evolution of metabolic networks.	many biological networks show some characteristics of scale-free networks. scale-free networks can evolve through preferential attachment where new nodes are preferentially attached to well connected nodes. in networks which have evolved through preferential attachment older nodes should have a higher average connectivity than younger nodes. here we have investigated preferential attachment in the context of metabolic networks.	2005	16281983
profile of nancy a. moran.		2005	16286644
abstracts from the xiii international entomophagous insects workshop, july 27-31, 2003, tucson, arizona, usa.		2003	16292358
extracting single genomes from heterogenous dna samples: a test case with carsonella ruddii, the bacterial symbiont of psyllids (insecta).	analysis of many bacterial genomes is impeded by the inability to separate individual species from complex mixtures of cells or to propagate cells in pure culture. this problem is an obstacle to the study of many bacterial symbionts that live intracellularly in insects and other animals. to recover bacterial dna from complex samples, we devised a method that facilitates the cloning of dna fragments of distinctive g+c contents in order to generate shotgun dna libraries enriched in inserts having ...	2005	16299593
a relative-entropy algorithm for genomic fingerprinting captures host-phage similarities.	the degeneracy of codons allows a multitude of possible sequences to code for the same protein. hidden within the particular choice of sequence for each organism are over 100 previously undiscovered biologically significant, short oligonucleotides (length, 2 to 7 nucleotides). we present an information-theoretic algorithm that finds these novel signals. applying this algorithm to the 209 sequenced bacterial genomes in the ncbi database, we determine a set of oligonucleotides for each bacterium w ...	2005	16321941
site-2 protease regulated intramembrane proteolysis: sequence homologs suggest an ancient signaling cascade.	site-2 proteases (s2ps) form a large family of membrane-embedded metalloproteases that participate in cellular signaling pathways through sequential cleavage of membrane-tethered substrates. using sequence similarity searches, we extend the s2p family to include remote homologs that help define a conserved structural core consisting of three predicted transmembrane helices with traditional metalloprotease functional motifs and a previously unrecognized motif (gxxxn/s/g). s2p relatives were ident ...	2006	16322567
horizontal transfer of bacterial symbionts: heritability and fitness effects in a novel aphid host.	members of several bacterial lineages are known only as symbionts of insects and move among hosts through maternal transmission. such vertical transfer promotes strong fidelity within these associations, favoring the evolution of microbially mediated effects that improve host fitness. however, phylogenetic evidence indicates occasional horizontal transfer among different insect species, suggesting that some microbial symbionts retain a generalized ability to infect multiple hosts. here we examin ...	2005	16332777
symbiosis and insect diversification: an ancient symbiont of sap-feeding insects from the bacterial phylum bacteroidetes.	several insect groups have obligate, vertically transmitted bacterial symbionts that provision hosts with nutrients that are limiting in the diet. some of these bacteria have been shown to descend from ancient infections. here we show that the large group of related insects including cicadas, leafhoppers, treehoppers, spittlebugs, and planthoppers host a distinct clade of bacterial symbionts. this newly described symbiont lineage belongs to the phylum bacteroidetes. analyses of 16s rrna genes in ...	2005	16332876
comparative genomic analyses of the bacterial phosphotransferase system.	we report analyses of 202 fully sequenced genomes for homologues of known protein constituents of the bacterial phosphoenolpyruvate-dependent phosphotransferase system (pts). these included 174 bacterial, 19 archaeal, and 9 eukaryotic genomes. homologues of pts proteins were not identified in archaea or eukaryotes, showing that the horizontal transfer of genes encoding pts proteins has not occurred between the three domains of life. of the 174 bacterial genomes (136 bacterial species) analyzed, ...	2005	16339738
growth kinetics of the endosymbiont buchnera aphidicola in the aphid schizaphis graminum.	the aphid schizaphis graminum is dependent on its prokaryotic endosymbiont, buchnera aphidicola. as a means of determining b. aphidicola numbers during the growth cycle of the aphid we have used the quantitative pcr to measure the number of copies of rrs (the gene coding for 16s rrna, which is present as one copy in the b. aphidicola genome). in addition we have measured the aphid wet weight and the dna and protein content. the results indicate an approximately parallel (23- to 31-fold) increase ...	1994	16349393
occurrence of nitric oxide synthase in megoura viciae buckton (homoptera, aphididae): an histochemical and immunohistochemical localisation.	nitric oxide (no) is known to be involved in many physiological reactions of insects. we analysed nos localisation in aphids of the species megoura viciae by means of histochemical reaction for the nadph-diaphorase activity and immunohistochemical methods for unos, nnos and inos. the obtained data provided a complex and peculiar pattern of nos distribution in cells and tissue of m. viciae. the histochemical reaction for nadph-diaphorase was an indicative, but not exact marker of nos localisation ...	2005	16377581
asap: a resource for annotating, curating, comparing, and disseminating genomic data.	asap is a comprehensive web-based system for community genome annotation and analysis. asap is being used for a large-scale effort to augment and curate annotations for genomes of enterobacterial pathogens and for additional genome sequences. new tools, such as the genome alignment program mauve, have been incorporated into asap in order to improve display and analysis of related genomes. recent improvements to the database and challenges for future development of the system are discussed. asap ...	2006	16381899
asap: a resource for annotating, curating, comparing, and disseminating genomic data.	asap is a comprehensive web-based system for community genome annotation and analysis. asap is being used for a large-scale effort to augment and curate annotations for genomes of enterobacterial pathogens and for additional genome sequences. new tools, such as the genome alignment program mauve, have been incorporated into asap in order to improve display and analysis of related genomes. recent improvements to the database and challenges for future development of the system are discussed. asap ...	2006	16381899
plasmids in the aphid endosymbiont buchnera aphidicola with the smallest genomes. a puzzling evolutionary story.	buchnera aphidicola, the primary endosymbiont of aphids, has undergone important genomic and biochemical changes as an adaptation to intracellular life. the most important structural changes include a drastic genome reduction and the amplification of genes encoding key enzymes for the biosynthesis of amino acids by their translocation to plasmids. molecular characterization through different aphid subfamilies has revealed that the genes involved in leucine and tryptophan biosynthesis show a vari ...	2006	16413149
strong asymmetric mutation bias in endosymbiont genomes coincide with loss of genes for replication restart pathways.	a large majority of bacterial genomes show strand asymmetry, such that g and t preferentially accumulate on the leading strand. the mechanisms are unknown, but cytosine deaminations are thought to play an important role. here, we have examined dna strand asymmetry in three strains of the aphid endosymbiont buchnera aphidicola. these are phylogenetically related, have similar genomic gc contents, and conserved gene order structures, yet b. aphidicola (bp) shows a fourfold higher replication-induc ...	2006	16476690
algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation.	comparison of metabolic networks is typically performed based on the organisms' enzyme contents. this approach disregards functional replacements as well as orthologies that are misannotated. direct comparison of the structure of metabolic networks can circumvent these problems.	2006	16478540
compositional discordance between prokaryotic plasmids and host chromosomes.	most plasmids depend on the host replication machinery and possess partitioning genes. these properties confine plasmids to a limited range of hosts, yielding a close and presumably stable relationship between plasmid and host. hence, it is anticipated that due to amelioration the dinucleotide composition of plasmids is similar to that of the genome of their hosts. however, plasmids are also thought to play a major role in horizontal gene transfer and thus are frequently exchanged between hosts, ...	2006	16480495
a comprehensive software suite for the analysis of cdnas.	we have developed a comprehensive software suite for bioinformatics research of cdnas; it is aimed at rapid characterization of the features of genes and the proteins they code. methods implemented include the detection of translation initiation and termination signals, statistical analysis of codon usage, comparative study of amino acid composition, comparative modeling of the structures of product proteins, prediction of alternative splice forms, and metabolic pathway reconstruction.	2005	16487083
paths of lateral gene transfer of lysyl-aminoacyl-trna synthetases with a unique evolutionary transition stage of prokaryotes coding for class i and ii varieties by the same organisms.	while the premise that lateral gene transfer (lgt) is a dominant evolutionary force is still in considerable dispute, the case for widespread lgt in the family of aminoacyl-trna synthetases (aars) is no longer contentious. aarss are ancient enzymes, guarding the fidelity of the genetic code. they are clustered in two structurally unrelated classes. only lysine aminoacyl-trna synthetase (lysrs) is found both as a class 1 and a class 2 enzyme (lysrs1-2). remarkably, in several extant prokaryotes b ...	2006	16529662
a dual-genome microarray for the pea aphid, acyrthosiphon pisum, and its obligate bacterial symbiont, buchnera aphidicola.	the best studied insect-symbiont system is that of aphids and their primary bacterial endosymbiont buchnera aphidicola. buchnera inhabits specialized host cells called bacteriocytes, provides nutrients to the aphid and has co-speciated with its aphid hosts for the past 150 million years. we have used a single microarray to examine gene expression in the pea aphid, acyrthosiphon pisum, and its resident buchnera. very little is known of gene expression in aphids, few studies have examined gene exp ...	2006	16536873
costs and benefits of symbiont infection in aphids: variation among symbionts and across temperatures.	symbiosis is prevalent throughout the tree of life and has had a significant impact on the ecology and evolution of many bacteria and eukaryotes. the benevolence of symbiotic interactions often varies with the environment, and such variation is expected to play an important role in shaping the prevalence and distributions of symbiosis throughout nature. in this study, we examine how the fitness of aphids is influenced by infection with one of three maternally transmitted bacteria, 'candidatus se ...	2006	16537132
costs and benefits of symbiont infection in aphids: variation among symbionts and across temperatures.	symbiosis is prevalent throughout the tree of life and has had a significant impact on the ecology and evolution of many bacteria and eukaryotes. the benevolence of symbiotic interactions often varies with the environment, and such variation is expected to play an important role in shaping the prevalence and distributions of symbiosis throughout nature. in this study, we examine how the fitness of aphids is influenced by infection with one of three maternally transmitted bacteria, 'candidatus se ...	2006	16537132
large-scale gene discovery in the pea aphid acyrthosiphon pisum (hemiptera).	aphids are the leading pests in agricultural crops. a large-scale sequencing of 40,904 ests from the pea aphid acyrthosiphon pisum was carried out to define a catalog of 12,082 unique transcripts. a strong at bias was found, indicating a compositional shift between drosophila melanogaster and a. pisum. an in silico profiling analysis characterized 135 transcripts specific to pea-aphid tissues (relating to bacteriocytes and parthenogenetic embryos). this project is the first to address the geneti ...	2006	16542494
structural proteomics of minimal organisms: conservation of protein fold usage and evolutionary implications.	determining the complete repertoire of protein structures for all soluble, globular proteins in a single organism has been one of the major goals of several structural genomics projects in recent years.	2006	16566839
chance and necessity in the evolution of minimal metabolic networks.	it is possible to infer aspects of an organism's lifestyle from its gene content. can the reverse also be done? here we consider this issue by modelling evolution of the reduced genomes of endosymbiotic bacteria. the diversity of gene content in these bacteria may reflect both variation in selective forces and contingency-dependent loss of alternative pathways. using an in silico representation of the metabolic network of escherichia coli, we examine the role of contingency by repeatedly simulat ...	2006	16572170
a database of bacterial lipoproteins (dolop) with functional assignments to predicted lipoproteins.	lipid modification of the n-terminal cys residue (n-acyl-s-diacylglyceryl-cys) has been found to be an essential, ubiquitous, and unique bacterial posttranslational modification. such a modification allows anchoring of even highly hydrophilic proteins to the membrane which carry out a variety of functions important for bacteria, including pathogenesis. hence, being able to identify such proteins is of great value. to this end, we have created a comprehensive database of bacterial lipoproteins, c ...	2006	16585737
phylogenomic analysis of the giy-yig nuclease superfamily.	the giy-yig domain was initially identified in homing endonucleases and later in other selfish mobile genetic elements (including restriction enzymes and non-ltr retrotransposons) and in enzymes involved in dna repair and recombination. however, to date no systematic search for novel members of the giy-yig superfamily or comparative analysis of these enzymes has been reported.	2006	16646971
identification and localization of a rickettsia sp. in bemisia tabaci (homoptera: aleyrodidae).	whiteflies (homoptera: aleyrodidae) are sap-sucking insects that harbor "candidatus portiera aleyrodidarum," an obligatory symbiotic bacterium which is housed in a special organ called the bacteriome. these insects are also home for a diverse facultative microbial community which may include hamiltonella, arsenophonus, fritchea, wolbachia, and cardinium spp. in this study, the bacteria associated with a b biotype of the sweet potato whitefly bemisia tabaci were characterized using molecular fing ...	2006	16672513
phylophenetic properties of metabolic pathway topologies as revealed by global analysis.	as phenotypic features derived from heritable characters, the topologies of metabolic pathways contain both phylogenetic and phenetic components. in the post-genomic era, it is possible to measure the "phylophenetic" contents of different pathways topologies from a global perspective.	2006	16684350
outer membrane protein genes and their small non-coding rna regulator genes in photorhabdus luminescens.	three major outer membrane protein genes of escherichia coli, ompf, ompc, and ompa respond to stress factors. transcripts from these genes are regulated by the small non-coding rnas micf, micc, and mica, respectively. here we examine photorhabdus luminescens, an organism that has a different habitat from e. coli for outer membrane protein genes and their regulatory rna genes.	2006	16716220
costs and benefits of a superinfection of facultative symbionts in aphids.	symbiotic associations between animals and inherited micro-organisms are widespread in nature. in many cases, hosts may be superinfected with multiple inherited symbionts. acyrthosiphon pisum (the pea aphid) may harbour more than one facultative symbiont (called secondary symbionts) in addition to the obligate primary symbiont, buchnera aphidicola. previously we demonstrated that, in a controlled genetic background, a. pisum infected with either serratia symbiotica or hamiltonella defensa (calle ...	2006	16720402
metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters.	mutualistic intracellular symbiosis between bacteria and insects is a widespread phenomenon that has contributed to the global success of insects. the symbionts, by provisioning nutrients lacking from diets, allow various insects to occupy or dominate ecological niches that might otherwise be unavailable. one such insect is the glassy-winged sharpshooter (homalodisca coagulata), which feeds on xylem fluid, a diet exceptionally poor in organic nutrients. phylogenetic studies based on rrna have sh ...	2006	16729848
comparative rates of evolution in endosymbiotic nuclear genomes.	the nucleomorphs associated with secondary plastids of cryptomonads and chlorarachniophytes are the sole examples of organelles with eukaryotic nuclear genomes. although not as widespread as their prokaryotic equivalents in mitochondria and plastids, nucleomorph genomes share similarities in terms of reduction and compaction. they also differ in several aspects, not least in that they encode proteins that target to the plastid, and so function in a different compartment from that in which they a ...	2006	16772046
comparative genomics and evolution of the hsp90 family of genes across all kingdoms of organisms.	hsp90 proteins are essential molecular chaperones involved in signal transduction, cell cycle control, stress management, and folding, degradation, and transport of proteins. hsp90 proteins have been found in a variety of organisms suggesting that they are ancient and conserved. in this study we investigate the nuclear genomes of 32 species across all kingdoms of organisms, and all sequences available in genbank, and address the diversity, evolution, gene structure, conservation and nomenclature ...	2006	16780600
who ate whom? adaptive helicobacter genomic changes that accompanied a host jump from early humans to large felines.	helicobacter pylori infection of humans is so old that its population genetic structure reflects that of ancient human migrations. a closely related species, helicobacter acinonychis, is specific for large felines, including cheetahs, lions, and tigers, whereas hosts more closely related to humans harbor more distantly related helicobacter species. this observation suggests a jump between host species. but who ate whom and when did it happen? in order to resolve this question, we determined the ...	2006	16789826
global transcriptome analysis of tropheryma whipplei in response to temperature stresses.	tropheryma whipplei, the agent responsible for whipple disease, is a poorly known pathogen suspected to have an environmental origin. the availability of the sequence of the 0.92-mb genome of this organism made a global gene expression analysis in response to thermal stresses feasible, which resulted in unique transcription profiles. a few genes were differentially transcribed after 15 min of exposure at 43 degrees c. the effects observed included up-regulation of the dnak regulon, which is comp ...	2006	16816195
tempo and mode of early gene loss in endosymbiotic bacteria from insects.	understanding evolutionary processes that drive genome reduction requires determining the tempo (rate) and the mode (size and types of deletions) of gene losses. in this study, we analysed five endosymbiotic genome sequences of the gamma-proteobacteria (three different buchnera aphidicola strains, wigglesworthia glossinidia, blochmannia floridanus) to test if gene loss could be driven by the selective importance of genes. we used a parsimony method to reconstruct a minimal ancestral genome of in ...	2006	16848891
genome blast distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences.	phylogenetic methods which do not rely on multiple sequence alignments are important tools in inferring trees directly from completely sequenced genomes. here, we extend the recently described genome blast distance phylogeny (gbdp) strategy to compute phylogenetic trees from all completely sequenced plastid genomes currently available and from a selection of mitochondrial genomes representing the major eukaryotic lineages. blastn, tblastx, or combinations of both are used to locate high-scoring ...	2006	16854218
analysis of nanoarchaeum equitans genome and proteome composition: indications for hyperthermophilic and parasitic adaptation.	nanoarchaeum equitans, the only known hyperthermophilic archaeon exhibiting parasitic life style, has raised some new questions about the evolution of the archaea and provided a model of choice to study the genome landmarks correlated with thermo-parasitic adaptation. in this context, we have analyzed the genome and proteome composition of n. equitans and compared the same with those of other mesophiles, hyperthermophiles and obligatory host-associated organisms.	2006	16869956
activity of rhodobacter sphaeroides rpohii, a second member of the heat shock sigma factor family.	we have identified a second rpoh homolog, rpoh(ii), in the alpha-proteobacterium rhodobacter sphaeroides. primary amino acid sequence comparisons demonstrate that r. sphaeroides rpoh(ii) belongs to a phylogenetically distinct group with rpoh orthologs from alpha-proteobacteria that contain two rpoh genes. like its previously identified paralog, rpoh(i), rpoh(ii) is able to complement the temperature-sensitive phenotype of an escherichia coli sigma(32) (rpoh) mutant. in addition, we show that rec ...	2006	16885439
the emerging diversity of rickettsia.	the best-known members of the bacterial genus rickettsia are associates of blood-feeding arthropods that are pathogenic when transmitted to vertebrates. these species include the agents of acute human disease such as typhus and rocky mountain spotted fever. however, many other rickettsia have been uncovered in recent surveys of bacteria associated with arthropods and other invertebrates; the hosts of these bacteria have no relationship with vertebrates. it is therefore perhaps more appropriate t ...	2006	16901827
sexual acquisition of beneficial symbionts in aphids.	a noted cost of mating is the risk of acquiring sexually transmitted infections that are detrimental to the recipient. but many microbial associates of eukaryotes are mutualistic, raising the possibility that sexual contact provides the opportunity to acquire symbionts that are beneficial. in aphids, facultative bacterial symbionts, which benefit hosts by conferring resistance to natural enemies or to heat, are transmitted maternally with high fidelity and are maintained stably throughout hundre ...	2006	16908834
evolution of vitamin b2 biosynthesis: 6,7-dimethyl-8-ribityllumazine synthases of brucella.	the penultimate step in the biosynthesis of riboflavin (vitamin b2) involves the condensation of 3,4-dihydroxy-2-butanone 4-phosphate with 5-amino-6-ribitylamino-2,4(1h,3h)-pyrimidinedione, which is catalyzed by 6,7-dimethyl-8-ribityllumazine synthase (lumazine synthase). pathogenic brucella species adapted to an intracellular lifestyle have two genes involved in riboflavin synthesis, ribh1 and ribh2, which are located on different chromosomes. the ribh2 gene was shown previously to specify a lu ...	2006	16923880
genome rearrangements, deletions, and amplifications in the natural population of bartonella henselae.	cats are the natural host for bartonella henselae, an opportunistic human pathogen and the agent of cat scratch disease. here, we have analyzed the natural variation in gene content and genome structure of 38 bartonella henselae strains isolated from cats and humans by comparative genome hybridizations to microarrays and probe hybridizations to pulsed-field gel electrophoresis (pfge) blots. the variation in gene content was modest and confined to the prophage and the genomic islands, whereas the ...	2006	16936024
data mining for proteins characteristic of clades.	a synapomorphy is a phylogenetic character that provides evidence of shared descent. ideally a synapomorphy is ubiquitous within the clade of related organisms and nonexistent outside the clade, implying that it arose after divergence from other extant species and before the last common ancestor of the clade. with the recent proliferation of genetic sequence data, molecular synapomorphies have assumed great importance, yet there is no convenient means to search for them over entire genomes. we h ...	2006	16936320
hundreds of flagellar basal bodies cover the cell surface of the endosymbiotic bacterium buchnera aphidicola sp. strain aps.	buchnera aphidicola is the endosymbiotic bacterium of the pea aphid. due to its small genome size, buchnera lacks many essential genes for autogenous life but obtains nutrients from the host. although the buchnera cell is nonmotile, it retains clusters of flagellar genes that lack the late genes necessary for motility, including the flagellin gene. in this study, we show that the flagellar genes are actually transcribed and translated and that the buchnera cell surface is covered with hundreds o ...	2006	16952945
relevance of the endosymbiosis of blochmannia floridanus and carpenter ants at different stages of the life cycle of the host.	expression of several genes possibly involved in the symbiotic relationship between the obligate intracellular endosymbiont blochmannia floridanus and its ant host camponotus floridanus was investigated at different developmental stages of the host by real-time quantitative pcr. these included a set of genes related to nitrogen metabolism (urec, uref, glna, and speb) as well as genes involved in the synthesis of the aromatic amino acid tyrosine (tyra, aspc, and hisc). the overall transcriptional ...	2006	16957225
codon usage bias and trna over-expression in buchnera aphidicola after aromatic amino acid nutritional stress on its host acyrthosiphon pisum.	codon usage bias and relative abundances of trna isoacceptors were analysed in the obligate intracellular symbiotic bacterium, buchnera aphidicola from the aphid acyrthosiphon pisum, using a dedicated 35mer oligonucleotide microarray. buchnera is archetypal of organisms living with minimal metabolic requirements and presents a reduced genome with high-evolutionary rate. codonusage in buchnera has been overcome by the high mutational bias towards at bases. however, several lines of evidence for c ...	2006	16963497
genome reduction in leptospira borgpetersenii reflects limited transmission potential.	leptospirosis is one of the most common zoonotic diseases in the world, resulting in high morbidity and mortality in humans and affecting global livestock production. most infections are caused by either leptospira borgpetersenii or leptospira interrogans, bacteria that vary in their distribution in nature and rely on different modes of transmission. we report the complete genomic sequences of two strains of l. borgpetersenii serovar hardjo that have distinct phenotypes and virulence. these two ...	2006	16973745
experimental and computational assessment of conditionally essential genes in escherichia coli.	genome-wide gene essentiality data sets are becoming available for escherichia coli, but these data sets have yet to be analyzed in the context of a genome scale model. here, we present an integrative model-driven analysis of the keio e. coli mutant collection screened in this study on glycerol-supplemented minimal medium. out of 3,888 single-deletion mutants tested, 119 mutants were unable to grow on glycerol minimal medium. these conditionally essential genes were then evaluated using a genome ...	2006	17012394
ftsz from divergent foreign bacteria can function for cell division in escherichia coli.	ftszs from mycoplasma pulmonis (mpuftsz) and bacillus subtilis (bsftsz) are only 46% and 53% identical in amino acid sequence to ftsz from escherichia coli (ecftsz). in the present study we show that mpuftsz and bsftsz can function for cell division in e. coli provided we make two modifications. first, we replaced their c-terminal tails with that from e. coli, giving the foreign ftsz the binding site for e. coli ftsa and zipa. second, we selected for mutations in the e. coli genome that facilita ...	2006	17015652
evolution of sensory complexity recorded in a myxobacterial genome.	myxobacteria are single-celled, but social, eubacterial predators. upon starvation they build multicellular fruiting bodies using a developmental program that progressively changes the pattern of cell movement and the repertoire of genes expressed. development terminates with spore differentiation and is coordinated by both diffusible and cell-bound signals. the growth and development of myxococcus xanthus is regulated by the integration of multiple signals from outside the cells with physiologi ...	2006	17015832
metagene: prokaryotic gene finding from environmental genome shotgun sequences.	exhaustive gene identification is a fundamental goal in all metagenomics projects. however, most metagenomic sequences are unassembled anonymous fragments, and conventional gene-finding methods cannot be applied. we have developed a prokaryotic gene-finding program, metagene, which utilizes di-codon frequencies estimated by the gc content of a given sequence with other various measures. metagene can predict a whole range of prokaryotic genes based on the anonymous genomic sequences of a few hund ...	2006	17028096
strict host-symbiont cospeciation and reductive genome evolution in insect gut bacteria.	host-symbiont cospeciation and reductive genome evolution have been identified in obligate endocellular insect symbionts, but no such example has been identified from extracellular ones. here we first report such a case in stinkbugs of the family plataspidae, wherein a specific gut bacterium is vertically transmitted via "symbiont capsule." in all of the plataspid species, females produced symbiont capsules upon oviposition and their gut exhibited specialized traits for capsule production. phylo ...	2006	17032065
a small microbial genome: the end of a long symbiotic relationship?	intracellular bacteria are characterized by genome reduction. the 422,434-base pair genome of buchnera aphidicola bcc, primary endosymbiont of the aphid cinara cedri, is approximately 200 kilobases smaller than the previously sequenced b. aphidicola genomes. b. aphidicola bcc has lost most metabolic functions, including the ability to synthesize the essential amino acid tryptophan and riboflavin. in addition, most retained genes are evolving rapidly. possibly, b. aphidicola bcc is losing its sym ...	2006	17038625
the reach of the genome signature in prokaryotes.	with the increased availability of sequenced genomes there have been several initiatives to infer evolutionary relationships by whole genome characteristics. one of these studies suggested good congruence between genome synteny, shared gene content, 16s ribosomal dna identity, codon usage and the genome signature in prokaryotes. here we rigorously test the phylogenetic signal of the genome signature, which consists of the genome-specific relative frequencies of dinucleotides, on 334 sequenced pr ...	2006	17040564
molecular evolution of the h-ns protein: interaction with hha-like proteins is restricted to enterobacteriaceae.	we show here that chromosomal hha-like genes are restricted to the enterobacteriaceae. the h-ns n-terminal domain of members of this family includes an unaltered seven-amino-acid sequence located between helixes 1 and 2, termed the hha signature, that contains key residues for h-ns-hha interaction.	2007	17041043
molecular evolution of the h-ns protein: interaction with hha-like proteins is restricted to enterobacteriaceae.	we show here that chromosomal hha-like genes are restricted to the enterobacteriaceae. the h-ns n-terminal domain of members of this family includes an unaltered seven-amino-acid sequence located between helixes 1 and 2, termed the hha signature, that contains key residues for h-ns-hha interaction.	2007	17041043
different levels of transcriptional regulation due to trophic constraints in the reduced genome of buchnera aphidicola aps.	symbiotic associations involving intracellular microorganisms and animals are widespread, especially for species feeding on poor or unbalanced diets. buchnera aphidicola, the obligate intracellular bacterium associated with most aphid species, provides its hosts with essential amino acids (eaas), nutrients in short supply in the plant phloem sap. the buchnera genome has undergone severe reductions during intracellular evolution. genes for eaa biosynthesis are conserved, but most of the transcrip ...	2006	17041159
towards the identification of essential genes using targeted genome sequencing and comparative analysis.	the identification of genes essential for survival is of theoretical importance in the understanding of the minimal requirements for cellular life, and of practical importance in the identification of potential drug targets in novel pathogens. with the great time and expense required for experimental studies aimed at constructing a catalog of essential genes in a given organism, a computational approach which could identify essential genes with high accuracy would be of great value.	2006	17052348
novel design and controls for focused dna microarrays: applications in quality assurance/control and normalization for the health canada toxarray.	microarray normalizations typically apply methods that assume absence of global transcript shifts, or absence of changes in internal control features such as housekeeping genes. these normalization approaches are not appropriate for focused arrays with small sets of genes where a large portion may be expected to change. furthermore, many microarrays lack control features that can be used for quality assurance (qa). here, we describe a novel external control series integrated with a design featur ...	2006	17052352
the bacterial species dilemma and the genomic-phylogenetic species concept.	the number of species of bacteria and archaea (ca 5000) is surprisingly small considering their early evolution, genetic diversity and residence in all ecosystems. the bacterial species definition accounts in part for the small number of named species. the primary procedures required to identify new species of bacteria and archaea are dna-dna hybridization and phenotypic characterization. recently, 16s rrna gene sequencing and phylogenetic analysis have been applied to bacterial taxonomy. althou ...	2006	17062409
leaner and meaner genomes in escherichia coli.	a 'better' escherichia coli k-12 genome has recently been engineered in which about 15% of the genome has been removed by planned deletions. comparison with related bacterial genomes that have undergone a natural reduction in size suggests that there is plenty of scope for yet more deletions.	2006	17076878
selection acts on dna secondary structures to decrease transcriptional mutagenesis.	single-stranded dna is more subject to mutation than double stranded. during transcription, dna is transiently single stranded and therefore subject to higher mutagenesis. however, if local intra-strand secondary structures are formed, some bases will be paired and therefore less sensitive to mutation than unpaired bases. using complete genome sequences of escherichia coli, we show that local intra-strand secondary structures can, as a consequence, be used to define an index of transcription-dri ...	2006	17083275
selection for unequal densities of sigma70 promoter-like signals in different regions of large bacterial genomes.	the evolutionary processes operating in the dna regions that participate in the regulation of gene expression are poorly understood. in escherichia coli, we have established a sequence pattern that distinguishes regulatory from nonregulatory regions. the density of promoter-like sequences, that could be recognizable by rna polymerase and may function as potential promoters, is high within regulatory regions, in contrast to coding regions and regions located between convergently transcribed genes ...	2006	17096598
genome reduction of the aphid endosymbiont buchnera aphidicola in a recent evolutionary time scale.	genome reduction, a typical feature of symbiotic bacteria, was analyzed in the last stages of evolution of buchnera aphidicola, the primary aphid endosymbiont, in two neutrally evolving regions: the pseudogene cmk and an intergenic region. these two regions were examined in endosymbionts from several lineages of their aphid host rhopalosiphum padi, and different species of the same genus, whose divergence times ranged from 0.62 to 19.51 million years. estimates of nucleotide substitution rates w ...	2007	17098378
dynamics of reductive genome evolution in mitochondria and obligate intracellular microbes.	reductive evolution in mitochondria and obligate intracellular microbes has led to a significant reduction in their genome size and guanine plus cytosine content (gc). we show that genome shrinkage during reductive evolution in prokaryotes follows an exponential decay pattern and provide a method to predict the extent of this decay on an evolutionary timescale. we validated predictions by comparison with estimated extents of genome reduction known to have occurred in mitochondria and buchnera ap ...	2007	17108184
operon prediction for sequenced bacterial genomes without experimental information.	various computational approaches have been proposed for operon prediction, but most algorithms rely on experimental or functional data that are only available for a small subset of sequenced genomes. in this study, we explored the possibility of using phylogenetic information to aid in operon prediction, and we constructed a bayesian hidden markov model that incorporates comparative genomic data with traditional predictors, such as intergenic distances. the prediction algorithm performs as well ...	2007	17122389
operon prediction for sequenced bacterial genomes without experimental information.	various computational approaches have been proposed for operon prediction, but most algorithms rely on experimental or functional data that are only available for a small subset of sequenced genomes. in this study, we explored the possibility of using phylogenetic information to aid in operon prediction, and we constructed a bayesian hidden markov model that incorporates comparative genomic data with traditional predictors, such as intergenic distances. the prediction algorithm performs as well ...	2007	17122389
coverage of whole proteome by structural genomics observed through protein homology modeling database.	we have been developing famsbase, a protein homology-modeling database of whole orfs predicted from genome sequences. the latest update of famsbase ( http://daisy.nagahama-i-bio.ac.jp/famsbase/ ), which is based on the protein three-dimensional (3d) structures released by november 2003, contains modeled 3d structures for 368,724 open reading frames (orfs) derived from genomes of 276 species, namely 17 archaebacterial, 130 eubacterial, 18 eukaryotic and 111 phage genomes. those 276 genomes are pr ...	2006	17146617
role of host nutrition in symbiont regulation: impact of dietary nitrogen on proliferation of obligate and facultative bacterial endosymbionts of the pea aphid acyrthosiphon pisum.	the impact of host nutrition on symbiont regulation in the pea aphid acyrthosiphon pisum was investigated. the population density of the obligate symbiont buchnera aphidicola positively correlated with dietary nitrogen levels. in contrast, the population density of the facultative symbiont serratia symbiotica increased in aphids reared on low-nitrogen diets, indicating distinct regulatory mechanisms in the same insect host.	2007	17158610
role of host nutrition in symbiont regulation: impact of dietary nitrogen on proliferation of obligate and facultative bacterial endosymbionts of the pea aphid acyrthosiphon pisum.	the impact of host nutrition on symbiont regulation in the pea aphid acyrthosiphon pisum was investigated. the population density of the obligate symbiont buchnera aphidicola positively correlated with dietary nitrogen levels. in contrast, the population density of the facultative symbiont serratia symbiotica increased in aphids reared on low-nitrogen diets, indicating distinct regulatory mechanisms in the same insect host.	2007	17158610
high precision multi-genome scale reannotation of enzyme function by eficaz.	the functional annotation of most genes in newly sequenced genomes is inferred from similarity to previously characterized sequences, an annotation strategy that often leads to erroneous assignments. we have performed a reannotation of 245 genomes using an updated version of eficaz, a highly precise method for enzyme function prediction.	2006	17166279
gismo--gene identification using a support vector machine for orf classification.	we present the novel prokaryotic gene finder gismo, which combines searches for protein family domains with composition-based classification based on a support vector machine. gismo is highly accurate; exhibiting high sensitivity and specificity in gene identification. we found that it performs well for complete prokaryotic chromosomes, irrespective of their gc content, and also for plasmids as short as 10 kb, short genes and for genes with atypical sequence composition. using gismo, we found se ...	2006	17175534
gismo--gene identification using a support vector machine for orf classification.	we present the novel prokaryotic gene finder gismo, which combines searches for protein family domains with composition-based classification based on a support vector machine. gismo is highly accurate; exhibiting high sensitivity and specificity in gene identification. we found that it performs well for complete prokaryotic chromosomes, irrespective of their gc content, and also for plasmids as short as 10 kb, short genes and for genes with atypical sequence composition. using gismo, we found se ...	2006	17175534
how repetitive are genomes?	genome sequences vary strongly in their repetitiveness and the causes for this are still debated. here we propose a novel measure of genome repetitiveness, the index of repetitiveness, ir, which can be computed in time proportional to the length of the sequences analyzed. we apply it to 336 genomes from all three domains of life.	2006	17187668
a possible heterodimeric prophage-like element in the genome of the insect endosymbiont sodalis glossinidius.	extrachromosomal element psog3 (52,162 nucleotides) in the genome of sodalis glossinidius contains redundant phage-related gene pairs, indicating that it may have been formed by the fusion of two ancestral phage genomes followed by gene degradation. we suggest that psog3 is a prophage that has undergone genome degeneration accompanying host adaptation to symbiosis.	2007	17209029
reductive genome evolution from the mother of rickettsia.	the rickettsia genus is a group of obligate intracellular alpha-proteobacteria representing a paradigm of reductive evolution. here, we investigate the evolutionary processes that shaped the genomes of the genus. the reconstruction of ancestral genomes indicates that their last common ancestor contained more genes, but already possessed most traits associated with cellular parasitism. the differences in gene repertoires across modern rickettsia are mainly the result of differential gene losses f ...	2007	17238289
the role of the s1 domain in exoribonucleolytic activity: substrate specificity and multimerization.	rnase ii is a 3'-5' exoribonuclease that processively hydrolyzes single-stranded rna generating 5' mononucleotides. this enzyme contains a catalytic core that is surrounded by three rna-binding domains. at its c terminus, there is a typical s1 domain that has been shown to be critical for rna binding. the s1 domain is also present in the other major 3'-5' exoribonucleases from escherichia coli: rnase r and polynucleotide phosphorylase (pnpase). in this report, we examined the involvement of the ...	2007	17242308
phylogenetic signal and functional categories in proteobacteria genomes.	a comprehensive evolutionary analysis of bacterial genomes implies to identify the hallmark of vertical and non-vertical signals and to discriminate them from the presence of mere phylogenetic noise. in this report we have addressed the impact of factors like the universal distribution of the genes, their essentiality or their functional role in the cell on the inference of vertical signal through phylogenomic methods.	2007	17288580
purifying selection in mitochondria, free-living and obligate intracellular proteobacteria.	the effectiveness of elimination of slightly deleterious mutations depends mainly on drift and recombination frequency. here we analyze the influence of these two factors on the strength of the purifying selection in mitochondrial and proteobacterial orthologous genes taking into account the differences in the organism lifestyles.	2007	17295908
genome analysis of dna repair genes in the alpha proteobacterium caulobacter crescentus.	the integrity of dna molecules is fundamental for maintaining life. the dna repair proteins protect organisms against genetic damage, by removal of dna lesions or helping to tolerate them. dna repair genes are best known from the gamma-proteobacterium escherichia coli, which is the most understood bacterial model. however, genome sequencing raises questions regarding uniformity and ubiquity of these dna repair genes and pathways, reinforcing the need for identifying genes and proteins, which may ...	2007	17352799
stripped-down dna repair in a highly reduced parasite.	encephalitozoon cuniculi is a member of a distinctive group of single-celled parasitic eukaryotes called microsporidia, which are closely related to fungi. some of these organisms, including e. cuniculi, also have uniquely small genomes that are within the prokaryotic range. thus, e. cuniculi has undergone a massive genome reduction which has resulted in a loss of genes from diverse biological pathways, including those that act in dna repair.dna repair is essential to any living cell. a loss of ...	2007	17374165
the power of phylogenetic approaches to detect horizontally transferred genes.	horizontal gene transfer plays an important role in evolution because it sometimes allows recipient lineages to adapt to new ecological niches. high genes transfer frequencies were inferred for prokaryotic and early eukaryotic evolution. does horizontal gene transfer also impact phylogenetic reconstruction of the evolutionary history of genomes and organisms? the answer to this question depends at least in part on the actual gene transfer frequencies and on the ability to weed out transferred ge ...	2007	17376230
transcriptional regulatory network discovery via multiple method integration: application to e. coli k12.	transcriptional regulatory network (trn) discovery from one method (e.g. microarray analysis, gene ontology, phylogenic similarity) does not seem feasible due to lack of sufficient information, resulting in the construction of spurious or incomplete trns. we develop a methodology, trnd, that integrates a preliminary trn, microarray data, gene ontology and phylogenic similarity to accurately discover trns and apply the method to e. coli k12. the approach can easily be extended to include other me ...	2007	17397539
aphid thermal tolerance is governed by a point mutation in bacterial symbionts.	symbiosis is a ubiquitous phenomenon generating biological complexity, affecting adaptation, and expanding ecological capabilities. however, symbionts, which can be subject to genetic limitations such as clonality and genomic degradation, also impose constraints on hosts. a model of obligate symbiosis is that between aphids and the bacterium buchnera aphidicola, which supplies essential nutrients. we report a mutation in buchnera of the aphid acyrthosiphon pisum that recurs in laboratory lines a ...	2007	17425405
branchclust: a phylogenetic algorithm for selecting gene families.	automated methods for assembling families of orthologous genes include those based on sequence similarity scores and those based on phylogenetic approaches. the first are easy to automate but usually they do not distinguish between paralogs and orthologs or have restriction on the number of taxa. phylogenetic methods often are based on reconciliation of a gene tree with a known rooted species tree; a limitation of this approach, especially in case of prokaryotes, is that the species tree is ofte ...	2007	17425803
on the origin and evolution of biosynthetic pathways: integrating microarray data with structure and organization of the common pathway genes.	the lysine, threonine, and methionine biosynthetic pathways share the three initial enzymatic steps, which are referred to as the common pathway (cp). in escherichia coli three different aspartokinases (aki, akii, akiii, the products of thra, metl and lysc, respectively) can perform the first step of the cp. moreover, two of them (aki and akii) are bifunctional, carrying also homoserine dehydrogenasic activity (hom product). the second step of the cp is catalyzed by a single aspartate semialdehy ...	2007	17430556
a global gene evolution analysis on vibrionaceae family using phylogenetic profile.	vibrionaceae represent a significant portion of the cultivable heterotrophic sea bacteria; they strongly affect nutrient cycling and some species are devastating pathogens. in this work we propose an improved phylogenetic profile analysis on 14 vibrionaceae genomes, to study the evolution of this family on the basis of gene content. the phylogenetic profile is based on the observation that genes involved in the same process (e.g. metabolic pathway or structural complex) tend to be concurrently p ...	2007	17430568
proteomic profiling of aphid macrosiphum euphorbiae responses to host-plant-mediated stress induced by defoliation and water deficit.	abiotic and biotic host-plant stress, such as desiccation and herbivory, may strongly affect sap-sucking insects such as aphids via changes in plant chemicals of insect nutritional or plant defensive value. here, we examined (i) water deprivation and (ii) defoliation by the beetle leptinotarsa decemlineata as stresses indirectly affecting the aphid macrosiphum euphorbiae via its host plant solanum tuberosum. for plant-induced stress, aphids were reared on healthy vs. continuously stressed potato ...	2007	17466324