Publications

accelerated evolution associated with genome reduction in a free-living prokaryote.	three complete genomes of prochlorococcus species, the smallest and most abundant photosynthetic organism in the ocean, have recently been published. comparative genome analyses reveal that genome shrinkage has occurred within this genus, associated with a sharp reduction in g+c content. as all examples of genome reduction characterized so far have been restricted to endosymbionts or pathogens, with a host-dependent lifestyle, the observed genome reduction in prochlorococcus is the first documen ...	2005	15693943
pseudomonas aeruginosa mutl protein functions in escherichia coli.	escherichia coli muts, mutl and muth proteins act sequentially in the mmrs (mismatch repair system). muth directs the repair system to the newly synthesized strand due to its transient lack of dam (dna-adenine methylase) methylation. although pseudomonas aeruginosa does not have the corresponding e. coli muth and dam homologues, and consequently the mmrs seems to work differently, we show that the mutl gene from p. aeruginosa is capable of complementing a mutl-deficient strain of e. coli. mutl f ...	2005	15709980
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
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
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
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
profile of nancy a. moran.		2005	16286644
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
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
genomes on the shrink.		2005	16105941
deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement.	when organismal phylogenies based on sequences of single marker genes are poorly resolved, a logical approach is to add more markers, on the assumption that weak but congruent phylogenetic signal will be reinforced in such multigene trees. such approaches are valid only when the several markers indeed have identical phylogenies, an issue which many multigene methods (such as the use of concatenated gene sequences or the assembly of supertrees) do not directly address. indeed, even when the true ...	2005	15819979
evolutionary origins of genomic repertoires in bacteria.	explaining the diversity of gene repertoires has been a major problem in modern evolutionary biology. in eukaryotes, this diversity is believed to result mainly from gene duplication and loss, but in prokaryotes, lateral gene transfer (lgt) can also contribute substantially to genome contents. to determine the histories of gene inventories, we conducted an exhaustive analysis of gene phylogenies for all gene families in a widely sampled group, the gamma-proteobacteria. we show that, although the ...	2005	15799709
a nomenclature for all signal recognition particle rnas.	the signal recognition particle (srp) is a cytosolic ribonucleoprotein complex that guides secretory proteins to biological membranes in all organisms. the srp rna is at the center of the structure and function of the srp. the comparison of the growing number of srp rna sequences provides a rich source for gaining valuable insight into the composition, assembly, and phylogeny of the srp. in order to assist in the continuation of these studies, we propose an srp rna nomenclature applicable to the ...	2005	15611297
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
protein length in eukaryotic and prokaryotic proteomes.	we analyzed length differences of eukaryotic, bacterial and archaeal proteins in relation to function, conservation and environmental factors. comparing eukaryotes and prokaryotes, we found that the greater length of eukaryotic proteins is pervasive over all functional categories and involves the vast majority of protein families. the magnitude of these differences suggests that the evolution of eukaryotic proteins was influenced by processes of fusion of single-function proteins into extended m ...	2005	15951512
identification of genomic features using microsyntenies of domains: domain teams.	the detection, across several genomes, of local conservation of gene content and proximity considerably helps the prediction of features of interest, such as gene fusions or physical and functional interactions. here, we want to process realistic models of chromosomes, in which genes (or genomic segments of several genes) can be duplicated within a chromosome, or be absent from some other chromosome(s). our approach adopts the technique of temporarily forgetting genes and working directly with p ...	2005	15899966
systematic association of genes to phenotypes by genome and literature mining.	one of the major challenges of functional genomics is to unravel the connection between genotype and phenotype. so far no global analysis has attempted to explore those connections in the light of the large phenotypic variability seen in nature. here, we use an unsupervised, systematic approach for associating genes and phenotypic characteristics that combines literature mining with comparative genome analysis. we first mine the medline literature database for terms that reflect phenotypic simil ...	2005	15799710
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
genomes are covered with ubiquitous 11 bp periodic patterns, the "class a flexible patterns".	the genomes of prokaryotes and lower eukaryotes display a very strong 11 bp periodic bias in the distribution of their nucleotides. this bias is present throughout a given genome, both in coding and non-coding sequences. until now this bias remained of unknown origin.	2005	16120222
the tyra family of aromatic-pathway dehydrogenases in phylogenetic context.	the tyra protein family includes members that catalyze two dehydrogenase reactions in distinct pathways leading to l-tyrosine and a third reaction that is not part of tyrosine biosynthesis. family members share a catalytic core region of about 30 kda, where inhibitors operate competitively by acting as substrate mimics. this protein family typifies many that are challenging for bioinformatic analysis because of relatively modest sequence conservation and small size.	2005	15888209
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
modular organization in the reductive evolution of protein-protein interaction networks.	the variation in the sizes of the genomes of distinct life forms remains somewhat puzzling. the organization of proteins into domains and the different mechanisms that regulate gene expression are two factors that potentially increase the capacity of genomes to create more complex systems. high-throughput protein interaction data now make it possible to examine the additional complexity generated by the way that protein interactions are organized.	2007	17532860
genetic evidence from mitochondrial, nuclear, and endosymbiont markers for the evolution of host plant associated species in the aphid genus hyalopterus (hemiptera: aphididae).	over the past several decades biologists' fascination with plant-herbivore interactions has generated intensive research into the implications of these interactions for insect diversification. the study of closely related phytophagous insect species or populations from an evolutionary perspective can help illuminate ecological and selective forces that drive these interactions. here we present such an analysis for aphids in the genus hyalopterus (hemiptera: aphididae), a cosmopolitan group that ...	2007	17542845
conservation of the links between gene transcription and chromosomal organization in the highly reduced genome of buchnera aphidicola.	genomic studies on bacteria have clearly shown the existence of chromosomal organization as regards, for example, to gene localization, order and orientation. moreover, transcriptomic analyses have demonstrated that, in free-living bacteria, gene transcription levels and chromosomal organization are mutually influenced. we have explored the possible conservation of relationships between mrna abundances and chromosomal organization in the highly reduced genome of buchnera aphidicola, the primary ...	2007	17547756
obligate symbiont involved in pest status of host insect.	the origin of specific insect genotypes that enable efficient use of agricultural plants is an important subject not only in applied fields like pest control and management but also in basic disciplines like evolutionary biology. conventionally, it has been presupposed that such pest-related ecological traits are attributed to genes encoded in the insect genomes. here, however, we report that pest status of an insect is principally determined by symbiont genotype rather than by insect genotype. ...	2007	17567556
reconstructing the ancestor of mycobacterium leprae: the dynamics of gene loss and genome reduction.	we have reconstructed the gene content and order of the last common ancestor of the human pathogens mycobacterium leprae and mycobacterium tuberculosis. during the reductive evolution of m. leprae, 1537 of 2977 ancestral genes were lost, among which we found 177 previously unnoticed pseudogenes. we find evidence that a massive gene inactivation took place very recently in the m. leprae lineage, leading to the loss of hundreds of ancestral genes. a large proportion of their nucleotide content ( a ...	2007	17623808
gene promoter scan methodology for identifying and classifying coregulated promoters.	a critical challenge of the postgenomic era is to understand how genes are differentially regulated. genetic and genomic approaches have been used successfully to assign genes to distinct regulatory networks in both prokaryotes and eukaryotes. however, little is known about what determines the differential expression of genes within a particular network, even when it involves a single transcription factor. the fact that coregulated genes may be differentially expressed suggests that subtle diffe ...	2007	17628149
rasta-bacteria: a web-based tool for identifying toxin-antitoxin loci in prokaryotes.	toxin/antitoxin (ta) systems, viewed as essential regulators of growth arrest and programmed cell death, are widespread among prokaryotes, but remain sparsely annotated. we present rasta-bacteria, an automated method allowing quick and reliable identification of ta loci in sequenced prokaryotic genomes, whether they are annotated open reading frames or not. the tool successfully confirmed all reported ta systems, and spotted new putative loci upon screening of sequenced genomes. rasta-bacteria i ...	2007	17678530
bacterial endosymbiont of the slender pigeon louse, columbicola columbae, allied to endosymbionts of grain weevils and tsetse flies.	the current study focuses on a symbiotic bacterium found in the slender pigeon louse, columbicola columbae (insecta: phthiraptera). molecular phylogenetic analyses indicated that the symbiont belongs to the gamma subdivision of the class proteobacteria and is allied to sodalis glossinidius, the secondary symbiont of tsetse flies (glossina spp.) and also to the primary symbiont of grain weevils (sitophilus spp.). relative-rate tests revealed that the symbiont of c. columbae exhibits accelerated m ...	2007	17766458
the role of mutational dynamics in genome shrinkage.	genome shrinkage occurs after whole genome duplications (wgds) and in the evolution of parasitic or symbiotic species. the dynamics of this process, whether it occurs by single gene deletions or also by larger deletions are however unknown. in yeast, genome shrinkage has occurred after a wgd. using a computational model of genome evolution, we show that in a random genome single gene deletions cannot explain the observed pattern of gene loss in yeast. the distribution of genes deleted per event ...	2007	17768305
the frontier between cell and organelle: genome analysis of candidatus carsonella ruddii.	bacterial symbioses are widespread among insects. the early establishment of such symbiotic associations has probably been one of the key factors for the evolutionary success of insects, since it may have allowed access to novel ecological niches and to new imbalanced food resources, such as plant sap or blood. several genomes of bacterial endosymbionts of different insect species have been recently sequenced, and their biology has been extensively studied. recently, the complete genome sequence ...	2007	17908294
analysis of gene order data supports vertical inheritance of the leukotoxin operon and genome rearrangements in the 5' flanking region in genus mannheimia.	the mannheimia subclades belong to the same bacterial genus, but have taken divergent paths toward their distinct lifestyles. for example, m. haemolytica + m. glucosida are potential pathogens of the respiratory tract in the mammalian suborder ruminantia, whereas m. ruminalis, the supposed sister group, lives as a commensal in the ovine rumen. we have tested the hypothesis that vertical inheritance of the leukotoxin (lktcabd) operon has occurred from the last common ancestor of genus mannheimia ...	2007	17915007
lateral gene transfer between obligate intracellular bacteria: evidence from the rickettsia massiliae genome.	rickettsia massiliae is a tick-borne obligate intracellular alpha-proteobacteria causing spotted fever in humans. here, we present the sequence of its genome, comprising a 1.3-mb circular chromosome and a 15.3-kb plasmid. the chromosome exhibits long-range colinearity with the other spotted fever group rickettsia genomes, except for a large fragment specific to r. massiliae that contains 14 tra genes presumably involved in pilus formation and conjugal dna transfer. we demonstrate that the tra re ...	2007	17916642
nutritional upgrading for omnivorous carpenter ants by the endosymbiont blochmannia.	carpenter ants (genus camponotus) are considered to be omnivores. nonetheless, the genome sequence of blochmannia floridanus, the obligate intracellular endosymbiont of camponotus floridanus, suggests a function in nutritional upgrading of host resources by the bacterium. thus, the strongly reduced genome of the endosymbiont retains genes for all subunits of a functional urease, as well as those for biosynthetic pathways for all but one (arginine) of the amino acids essential to the host.	2007	17971224